Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017911.1 Corchorus olitorius cultivar O-4 contig17944, 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: 92783
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:5710 original size:2 final size:2
Alignment explanation
Indices: 5703--5743 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5693 TACATTACAA
5703 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5744 CATTTTCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:5810 original size:27 final size:27
Alignment explanation
Indices: 5780--5835 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5770 GAGCTAAATT
5780 TAAAATGGTTTTTTCATTTTGCATCTC
1 TAAAATGGTTTTTTCATTTTGCATCTC
5807 TAAAATGGTTTTTTCATTTTGCATCTC
1 TAAAATGGTTTTTTCATTTTGCATCTC
5834 TA
1 TA
5836 TGTTTACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (27 bp):
TAAAATGGTTTTTTCATTTTGCATCTC
Found at i:7104 original size:15 final size:15
Alignment explanation
Indices: 7081--7111 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7071 AGTTCATGTA
*
7081 CTTGTCATATTTGGT
1 CTTGCCATATTTGGT
7096 CTTGCCATATTTGGT
1 CTTGCCATATTTGGT
7111 C
1 C
7112 AATAAAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
CTTGCCATATTTGGT
Found at i:7149 original size:20 final size:20
Alignment explanation
Indices: 7126--7163 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7116 AAATCCAATT
7126 GTTAATCAACGGCCCCAACC
1 GTTAATCAACGGCCCCAACC
* *
7146 GTTAATTAATGGCCCCAA
1 GTTAATCAACGGCCCCAA
7164 ATCCCAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
GTTAATCAACGGCCCCAACC
Found at i:11612 original size:29 final size:31
Alignment explanation
Indices: 11580--11646 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
11570 ATGCAATTTG
11580 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
11609 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
11640 GGATATA
1 GGATATA
11647 GTCCGTTAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:11816 original size:31 final size:31
Alignment explanation
Indices: 11778--11855 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
11768 CTAACTGATT
**
11778 TATCCTTAATTGCTTGAAATCGAAAACGTCA
1 TATCCTTAATTGCTTGAAATAAAAAACGTCA
*
11809 TATCCTTAATTGCTTGAAATAAAAAACGTTA
1 TATCCTTAATTGCTTGAAATAAAAAACGTCA
11840 TATCCTTAATTGCTTG
1 TATCCTTAATTGCTTG
11856 TTTTGTAACG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (31 bp):
TATCCTTAATTGCTTGAAATAAAAAACGTCA
Found at i:11905 original size:31 final size:29
Alignment explanation
Indices: 11801--11911 Score: 89
Period size: 31 Copynumber: 3.7 Consensus size: 29
11791 TTGAAATCGA
* * *
11801 AAACGTCATATCCTTAATTGCTTGAAAT-AAA
1 AAACGTTATATCCTTAATTGCTTG---TGCAG
***
11832 AAACGTTATATCCTTAATTGCTTGTTTTG
1 AAACGTTATATCCTTAATTGCTTGTGCAG
*
11861 TAACGTTATATCCTTAATTGCTTGTGGCAG
1 AAACGTTATATCCTTAATTGCTTGT-GCAG
* *
11891 CAAACGTTAAATCCTAAATTG
1 -AAACGTTATATCCTTAATTG
11912 ATTATTTGAC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 1 0.02
29 24 0.36
30 1 0.02
31 40 0.61
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (29 bp):
AAACGTTATATCCTTAATTGCTTGTGCAG
Found at i:12938 original size:31 final size:30
Alignment explanation
Indices: 12887--13027 Score: 133
Period size: 31 Copynumber: 4.6 Consensus size: 30
12877 AGAGGATAAG
* * *
12887 CAAGTAATTTAGGATATAACGTTTTC-TGCCT
1 CAAGCAATTAAGGATATAACGTTTTCAT--TT
* * ***
12918 CAAGCAATTAAGGACATAACG-TTACAAAA
1 CAAGCAATTAAGGATATAACGTTTTCATTT
*
12947 CAAGCAATTAAGGATATAACGTTTTTTATTT
1 CAAGCAATTAAGGATATAACG-TTTTCATTT
* *
12978 CAAGCAATTAGGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTC-ATTT
13009 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
13028 TCAGTTAGGG
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
29 20 0.23
30 7 0.08
31 61 0.69
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (30 bp):
CAAGCAATTAAGGATATAACGTTTTCATTT
Found at i:13000 original size:60 final size:62
Alignment explanation
Indices: 12887--13027 Score: 151
Period size: 60 Copynumber: 2.3 Consensus size: 62
12877 AGAGGATAAG
* * *
12887 CAAGTAATTTAGGATATAACGTTTTCTGCCTCAAGCAATTAAGGACATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCTACCTCAAGCAATTAAGGACATAACGTTTACGAAAA
* ** * * * * ***
12947 CAAGCAATTAAGGATATAACGTTTTTTATTTCAAGCAATTAGGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCTACCTCAAGCAATTAAGGACATAACGTTTACGAAAA
13009 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
13028 TCAGTTAGGG
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
60 43 0.65
61 3 0.05
62 20 0.30
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (62 bp):
CAAGCAATTAAGGATATAACGTTTTCTACCTCAAGCAATTAAGGACATAACGTTTACGAAAA
Found at i:13231 original size:29 final size:31
Alignment explanation
Indices: 13157--13223 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
13147 CCTAACGGAC
13157 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
13188 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
13217 TATATCC
1 TATATCC
13224 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:17993 original size:18 final size:18
Alignment explanation
Indices: 17970--18005 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17960 GTTACTCATT
*
17970 AGGTACATTTAAAACTAA
1 AGGTACATTGAAAACTAA
17988 AGGTACATTGAAAACTAA
1 AGGTACATTGAAAACTAA
18006 GGATTACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (18 bp):
AGGTACATTGAAAACTAA
Found at i:24472 original size:19 final size:18
Alignment explanation
Indices: 24439--24474 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24429 TGGAAATAAT
24439 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
24457 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
24475 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:31274 original size:19 final size:18
Alignment explanation
Indices: 31241--31276 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31231 TGGAAATAAT
31241 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
31259 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
31277 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:33981 original size:29 final size:29
Alignment explanation
Indices: 33940--34084 Score: 179
Period size: 28 Copynumber: 5.1 Consensus size: 29
33930 TTACTTCTCA
* *
33940 TTTTGGTCGTTTTGCATGTCCAGGGGCAT
1 TTTTGGTCATTTTGCATATCCAGGGGCAT
* *
33969 TTTTGGTCATTTTACATGTCCAGGGGCA-
1 TTTTGGTCATTTTGCATATCCAGGGGCAT
*
33997 TTTTGGTCATTTTACATATCCAGGGGCA-
1 TTTTGGTCATTTTGCATATCCAGGGGCAT
* * *
34025 CTTTGGTCATTTTGCATTTCTAGGGGCAT
1 TTTTGGTCATTTTGCATATCCAGGGGCAT
* *
34054 TTTTGGTCA-TTTGCACATCCAGGGGGAT
1 TTTTGGTCATTTTGCATATCCAGGGGCAT
34082 TTT
1 TTT
34085 GGCCACTTCA
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 69 0.67
29 34 0.33
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (29 bp):
TTTTGGTCATTTTGCATATCCAGGGGCAT
Found at i:35256 original size:22 final size:22
Alignment explanation
Indices: 35190--35263 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
35180 TTCATACACA
*
35190 CAAGGTTCAAAGCTCAAACCAG
1 CAAGGTTCAAAGCTCAAATCAG
* *
35212 CAAAGGTCCAAGAACGTCCAAATCAG
1 C-AAGGTTCAA-AGC-T-CAAATCAG
35238 CAAGGTTCAAAGCTCAAATCAG
1 CAAGGTTCAAAGCTCAAATCAG
35260 CAAG
1 CAAG
35264 AGATGTCCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 13 0.30
23 9 0.21
24 4 0.09
25 9 0.21
26 8 0.19
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.14
Consensus pattern (22 bp):
CAAGGTTCAAAGCTCAAATCAG
Found at i:49576 original size:51 final size:51
Alignment explanation
Indices: 49454--49702 Score: 351
Period size: 51 Copynumber: 4.9 Consensus size: 51
49444 AGATATCCAG
* * * * *
49454 AAGAGTGAATTGGAAAACTGTTCAAAGGATAGGCGGAATACGGTCC-TTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
*
49504 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* *
49555 AAGATTTAATTCGG-AGACAGTTCAAAGGATAGGCGGAAGACGGTCC-TTTT
1 AAGATTGAATT-GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* **
49605 AAGATTGAATTGGAAAACAGTTCAAAGGATAAGCGGAAGACGACCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* *
49656 AAGATTGAATTGGATGACAGTTCAAAGGATAAGCAGAAGACGGTCCT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCT
49703 CATTATATAT
Statistics
Matches: 176, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
49 2 0.01
50 82 0.47
51 90 0.51
52 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (51 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
Found at i:49598 original size:101 final size:101
Alignment explanation
Indices: 49454--49702 Score: 374
Period size: 101 Copynumber: 2.5 Consensus size: 101
49444 AGATATCCAG
* ** * *
49454 AAGAGTGAATTGGAAAACTGTTCAAAGGATAGGCGGAATACGGTCCTTTTAAGATTGAATTGGAA
1 AAGATTGAATTGGATGACAGTTCAAAGGATAGGCGGAAGACGGTCCTTTTAAGATTGAATTGGAA
* **
49519 GACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTT
66 AACAGTTCAAAGGATAAGCAGAAGACGACCCTTTTT
*
49555 AAGATTTAATTCGGA-GACAGTTCAAAGGATAGGCGGAAGACGGTCCTTTTAAGATTGAATTGGA
1 AAGATTGAATT-GGATGACAGTTCAAAGGATAGGCGGAAGACGGTCCTTTTAAGATTGAATTGGA
*
49619 AAACAGTTCAAAGGATAAGCGGAAGACGACCCTTTTT
65 AAACAGTTCAAAGGATAAGCAGAAGACGACCCTTTTT
* *
49656 AAGATTGAATTGGATGACAGTTCAAAGGATAAGCAGAAGACGGTCCT
1 AAGATTGAATTGGATGACAGTTCAAAGGATAGGCGGAAGACGGTCCT
49703 CATTATATAT
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
100 3 0.02
101 128 0.96
102 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (101 bp):
AAGATTGAATTGGATGACAGTTCAAAGGATAGGCGGAAGACGGTCCTTTTAAGATTGAATTGGAA
AACAGTTCAAAGGATAAGCAGAAGACGACCCTTTTT
Found at i:56737 original size:26 final size:26
Alignment explanation
Indices: 56708--56763 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
56698 CTTACCCATA
* *
56708 TCTTTTTATTTTTTTTTCG-TTATTTT
1 TCTTTTTATTTATCTTT-GTTTATTTT
*
56734 TCTTTTTCTTTATCTTTGTTTATTTT
1 TCTTTTTATTTATCTTTGTTTATTTT
56760 TCTT
1 TCTT
56764 AGTCACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.79
Consensus pattern (26 bp):
TCTTTTTATTTATCTTTGTTTATTTT
Found at i:60569 original size:16 final size:17
Alignment explanation
Indices: 60536--60569 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
60526 ACCTTTTCCA
60536 TCAAATTCATCAAATTT
1 TCAAATTCATCAAATTT
*
60553 TCAAATT-ATCAAGTTT
1 TCAAATTCATCAAATTT
60569 T
1 T
60570 GGAGAAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (17 bp):
TCAAATTCATCAAATTT
Found at i:62788 original size:3 final size:3
Alignment explanation
Indices: 62775--62837 Score: 117
Period size: 3 Copynumber: 20.7 Consensus size: 3
62765 CTTTAATTAA
62775 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62821 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
62838 GGTTAGTAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62938 original size:26 final size:25
Alignment explanation
Indices: 62896--62944 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
62886 TGTCCCTCTG
*
62896 AAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGAGTTAGTAACCTC
*
62921 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAA-AAAAAGAGAGTTAGTAACC
62945 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.53, C:0.10, G:0.20, T:0.16
Consensus pattern (25 bp):
AAAAAAAAAGAGAGTTAGTAACCTC
Found at i:69529 original size:67 final size:66
Alignment explanation
Indices: 69456--70078 Score: 442
Period size: 67 Copynumber: 9.4 Consensus size: 66
69446 TTCTTTTTTC
69456 CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAGTATTTTCAAA
1 CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTC--A
69520 TTT
64 TTT
* * *
69523 CCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTC-TTTTGCATTTAAGTGTAGCATTTTCATT
1 CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCATT
69587 T
66 T
* * * * *
69588 CCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTTACATTCAAGTTTAGTATTTTGA
1 CC-AAAATACCCTTTCGGTCGAAGGGTCA-TTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCA
69652 TTT
64 TTT
* * * * * *
69655 CCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTT-TTCTTTTTGCATTCAAGTTTACTATTTTCG
1 CCA-AAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCA
69719 TTT
64 TTT
* * * * *
69722 CCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGCA-TTCAGTTTTAGT-TTTAC-
1 CCA-AAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAG-TTTAGTATTTTCA
69784 TTT
64 TTT
* * * * * * **
69787 CCAAAAATACCATTCCGGTCGAAGGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTAGT-CGTT
1 CC-AAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC---TTTTTGCATTTAAGTTTAGTATTTT
69851 C-TTT
62 CATTT
* * * * *
69855 CCAAAGAATACCCTTTCGGTCAAAGGGTCA-ATTCTGTCATTCTTG-AGTTTGAGTTTA--CTTT
1 CC-AA-AATACCCTTTCGGTCGAAGGGTCATTTTC-GTC-TTTTTGCA-TTTAAGTTTAGTATTT
*
69916 TGATTT
61 TCATTT
** * * * * *
69922 CCAAAAATACCCTTTTCGGT-GAAAGGGTCAGTTTTATTATTTTCGCATTTCAGTTTA-T-TCTA
1 CC-AAAATACCC-TTTCGGTCG-AAGGGTCA-TTTTCGTCTTTTTGCATTTAAGTTTAGTATTTT
69984 C-TTT
62 CATTT
* * * * * *
69988 CCAAAAATACCCTTTCGGT-GAAAGGGTCAGTTTCATCATTTTAGCATTTCAGTTTA-T-TCTAC
1 CC-AAAATACCCTTTCGGTCG-AAGGGTCATTTTCGTC-TTTTTGCATTTAAGTTTAGTATTTTC
70050 A-TT
63 ATTT
* *
70053 CCAAAAATGCCCTTTCGGTCAAAGGG
1 CC-AAAATACCCTTTCGGTCGAAGGG
70079 CGAGCTTTGT
Statistics
Matches: 461, Mismatches: 69, Indels: 54
0.79 0.12 0.09
Matches are distributed among these distances:
64 4 0.01
65 104 0.23
66 65 0.14
67 232 0.50
68 27 0.06
69 29 0.06
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (66 bp):
CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCATT
T
Found at i:69740 original size:134 final size:131
Alignment explanation
Indices: 69452--70078 Score: 494
Period size: 134 Copynumber: 4.7 Consensus size: 131
69442 TCAGTTCTTT
* * * * *
69452 TTTCCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTA-TATTTT
* * * * *
69516 CAAATTTCC-AAAATACCCTTTCGGTCGAAGGGTCA-TTTCCGTC-TTTTGCATTTAAGTGTAGC
65 --GATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTT-CTTCTTTTTGCATTCAAGTTTA-C
*
69578 ATTTTC
126 TTTTTC
69584 ATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTTACATTCAAGTTTAGTATT
1 -TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGT-TTCGTCTTTTTACATTCAAGTTTA-TATT
* * *
69648 TTGATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTTTCTTTTTGCATTCAAGTTTACTA
63 TTGATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCTTCTTTTTGCATTCAAGTTTACT-
69713 TTTTC
127 TTTTC
* * ** *
69718 GTTTCCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGCATTC-AGTTT-TAGTTT
1 -TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTATA-TTT
* * * * * * *
69781 T-ACTTTCCAAAAATACCATTCCGGTCGAAGGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTA
64 TGA-TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCTTC---TTTTTGCATTCAAGTTTA
* **
69845 GTCGTTC
125 CTTTTTC
* * * ** *
69852 TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCA-ATTCTGTCATTCTTGA-GTTTGAGTTTA-CT
1 TTTCCAAA-AATACCCTTTCGGTCAAAGGGTCAGTTTC-GTC-TT-TTTACATTCAAGTTTATAT
* * * *
69914 TTTGATTTCCAAAAATACCCTTTTCGGTGAAAGGGTCAGTTTTATTATTTTCGCATTTC-AGTTT
62 TTTGATTTCCAAAAATACCC-TTTCGGTCAAAGGGTCAG-TTTCTTCTTTTTGCA-TTCAAGTTT
* *
69978 A-TTCTAC
124 ACTTTTTC
* * * *
69985 TTTCCAAAAATACCCTTTCGGTGAAAGGGTCAGTTTCATCATTTTAGCATTTC-AGTTTAT-TCT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCTTTTTA-CA-TTCAAGTTTATATTT
** *
70048 ACA-TTCCAAAAATGCCCTTTCGGTCAAAGGG
64 TGATTTCCAAAAATACCCTTTCGGTCAAAGGG
70079 CGAGCTTTGT
Statistics
Matches: 398, Mismatches: 69, Indels: 57
0.76 0.13 0.11
Matches are distributed among these distances:
130 16 0.04
131 17 0.04
132 77 0.19
133 93 0.23
134 128 0.32
135 40 0.10
136 23 0.06
137 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (131 bp):
TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTATATTTTG
ATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCTTCTTTTTGCATTCAAGTTTACTTTTT
C
Found at i:69874 original size:201 final size:194
Alignment explanation
Indices: 69447--70078 Score: 590
Period size: 201 Copynumber: 3.2 Consensus size: 194
69437 GGTCATCAGT
* * * *
69447 TCTTTTTTCCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAGT
1 TCTTCTTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTT-GTCTTTTTGCATTTAAGTTTACT
* * * *
69511 ATTTTCAAATTTCCAAAATACCCTTTCGGTCGAAGGGTCA-TTTCCGTC-TTTTGCATTTAAGTG
65 ATTTTC--GTTTCCAAAATACCCTTTCGGTTGAAGGGTCAGTTT-CGTCTTTTTGCATTTCAGTT
* * * * *
69574 TAGCATTTT-CATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTTACATTCA
127 TAG--TTTTAC-TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGT-TTCATCATTTTGCATTTA
69637 AGTTTAG
188 AGTTTAG
* * * * * *
69644 TATTTTGATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTTTCTTTTTGCATTCAAGTTT
1 --TCTT-CTTTCCAAAAATACCCTTTCGGTCAAAGGGTC-ATTTTGTCTTTTTGCATTTAAGTTT
*
69709 ACTATTTTCGTTTCCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGCA-TTCAGT
62 ACTATTTTCGTTTCCA-AAATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGCATTTCAG-
* *
69773 TTTAGTTTTACTTTCCAAAAATACCATTCCGGTCGAAGGGTCAGTTTCATCAGGTTGTTGCATTT
125 TTTAGTTTTACTTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCATCA--TT-TTGCATTT
*
69838 AAGTCTAG
187 AAGTTTAG
* * *
69846 TCGTTCTTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAATTCTGTCATTCTTG-AGTTTGAGTT
1 TC-TTCTTTCCAAA-AATACCCTTTCGGTCAAAGGGTC-ATTTTGTC-TTTTTGCA-TTTAAGTT
**
69910 TAC--TTTT-GATTTCCAAAAATACCCTTTTCGG-TGAAAGGGTCAGTTTTAT-TATTTTCGCAT
61 TACTATTTTCG-TTTCC-AAAATACCC-TTTCGGTTG-AAGGGTCAGTTTCGTCT-TTTT-GCAT
*
69970 TTCAGTTTA-TTCTACTTTCCAAAAATACCCTTTCGGT-GAAAGGGTCAGTTTCATCATTTTAGC
120 TTCAGTTTAGTTTTACTTTCCAAAAATACCCTTTCGGTCG-AAGGGTCAGTTTCATCATTTT-GC
* *
70033 ATTTCAGTTTAT
183 ATTTAAGTTTAG
* * *
70045 TCTACATTCCAAAAATGCCCTTTCGGTCAAAGGG
1 TCTTCTTTCCAAAAATACCCTTTCGGTCAAAGGG
70079 CGAGCTTTGT
Statistics
Matches: 364, Mismatches: 44, Indels: 52
0.79 0.10 0.11
Matches are distributed among these distances:
197 20 0.05
198 13 0.04
199 62 0.17
200 90 0.25
201 140 0.38
202 34 0.09
203 5 0.01
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (194 bp):
TCTTCTTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTGTCTTTTTGCATTTAAGTTTACTA
TTTTCGTTTCCAAAATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGCATTTCAGTTTAGT
TTTACTTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCATCATTTTGCATTTAAGTTTAG
Found at i:74793 original size:9 final size:9
Alignment explanation
Indices: 74726--74801 Score: 54
Period size: 9 Copynumber: 8.8 Consensus size: 9
74716 CTCAACGATA
*
74726 TCTCCATGA
1 TCTCCATGC
*
74735 TCTTCATGC
1 TCTCCATGC
74744 ATCTCCATGC
1 -TCTCCATGC
*
74754 T-TCCTTGC
1 TCTCCATGC
* *
74762 ACTCCACGC
1 TCTCCATGC
74771 TCATCC-T--
1 TC-TCCATGC
74778 T-TCCATGC
1 TCTCCATGC
74786 TCTCCATGC
1 TCTCCATGC
74795 TCTCCAT
1 TCTCCAT
74802 TGTCATCTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
5 3 0.06
6 1 0.02
7 1 0.02
8 7 0.14
9 28 0.55
10 11 0.22
ACGTcount: A:0.14, C:0.41, G:0.09, T:0.36
Consensus pattern (9 bp):
TCTCCATGC
Found at i:75510 original size:12 final size:12
Alignment explanation
Indices: 75493--75517 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75483 TGTCATACTA
75493 TATCATTTGCAT
1 TATCATTTGCAT
75505 TATCATTTGCAT
1 TATCATTTGCAT
75517 T
1 T
75518 TTTTGCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TATCATTTGCAT
Found at i:79153 original size:36 final size:37
Alignment explanation
Indices: 79071--79186 Score: 173
Period size: 36 Copynumber: 3.2 Consensus size: 37
79061 TCAACTTAGT
* *
79071 TTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATAG
1 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCATAG
*
79108 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTTA-AG
1 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCATAG
*
79144 TTTTCAAATTGGGAAAGTTCCCACC-AGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCATAG
*
79180 TATTCAA
1 TTTTCAA
79187 TTTAGCTCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 7 0.10
36 35 0.48
37 31 0.42
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCATAG
Found at i:79173 original size:27 final size:27
Alignment explanation
Indices: 79142--79230 Score: 74
Period size: 27 Copynumber: 3.4 Consensus size: 27
79132 CAAGTTTTTA
79142 AGTTTTCAAATTGGGAAAGTTCCCACC
1 AGTTTTCAAATTGGGAAAGTTCCCACC
* **** * ** *
79169 AGTTTTCAAAGTATTCAATTTAGC-TC
1 AGTTTTCAAATTGGGAAAGTTCCCACC
*
79195 -TTTTTCAAATTGGGAAAGTTCCCACC
1 AGTTTTCAAATTGGGAAAGTTCCCACC
79221 AGTTTTCAAA
1 AGTTTTCAAA
79231 GTATTCACTT
Statistics
Matches: 40, Mismatches: 20, Indels: 4
0.62 0.31 0.06
Matches are distributed among these distances:
25 14 0.35
26 2 0.05
27 24 0.60
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (27 bp):
AGTTTTCAAATTGGGAAAGTTCCCACC
Found at i:79206 original size:52 final size:52
Alignment explanation
Indices: 79144--79383 Score: 372
Period size: 52 Copynumber: 4.6 Consensus size: 52
79134 AGTTTTTAAG
*
79144 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
* *
79196 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCACTTTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
* * * * *
79248 TTTTCAAGTCGGGAAAGTTCCCATCAGTTTTCAAAATATTTAATTTAACTCT
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
* **
79300 TTTTCAAATTGGGAAAGTTCCCATCATTTTTCAAAGTATTCAATTTAGCTGG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
79352 TTTTCAAATTGGGAAAGTTCCCATCAGGTTTT
1 TTTTCAAATTGGGAAAGTTCCCATCA-GTTTT
79384 AGTTTTCAAT
Statistics
Matches: 170, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 166 0.98
53 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (52 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
Found at i:86720 original size:5 final size:5
Alignment explanation
Indices: 86705--86736 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
86695 TTTTCTTCCC
86705 TTCTT TT-TT TTCTT TTCTT TTCTT TTCTT TTC
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTC
86737 CTTCAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:88391 original size:3 final size:3
Alignment explanation
Indices: 88383--88416 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
88373 GTCACCAACG
* *
88383 TTC TTC TTC TTC TTC TTC TTC GTC TTC TAC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
88417 GTTAAAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.32, G:0.03, T:0.62
Consensus pattern (3 bp):
TTC
Done.