Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012611.1 Corchorus olitorius cultivar O-4 contig12644, 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: 79180
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:792 original size:30 final size:30
Alignment explanation
Indices: 756--812 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
746 CATCTTCAAG
756 TCCATGATAAGTCCTT-GGCGCATCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
786 TCCATGATAAGCCTTGGGCGCATCATT
1 TCCATGATAAGCCTTGGGCGCATCATT
813 AGCCCATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:1827 original size:28 final size:27
Alignment explanation
Indices: 1756--1827 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1746 GGTCATCCAT
*
1756 GGGCATTTTGGTCATTTGTGCACCAAA
1 GGGCATTTTGGTCATTTGTACACCAAA
* **
1783 GGGCATTTTGGTCATTTGTACATTCAGG
1 GGGCATTTTGGTCATTTGTACA-CCAAA
*
1811 GGGCATTTTGGTAATTT
1 GGGCATTTTGGTCATTT
1828 TAAGTCCACT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTGTACACCAAA
Found at i:1966 original size:17 final size:17
Alignment explanation
Indices: 1944--1976 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1934 ATCGATTCAT
*
1944 TCACGTGTACGTTTTAG
1 TCACGTGCACGTTTTAG
1961 TCACGTGCACGTTTTA
1 TCACGTGCACGTTTTA
1977 ATTAGGTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (17 bp):
TCACGTGCACGTTTTAG
Found at i:2809 original size:14 final size:14
Alignment explanation
Indices: 2790--2820 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2780 GGGTACAATT
2790 CAGTAAGGATCAAA
1 CAGTAAGGATCAAA
2804 CAGTAAGGATCAAA
1 CAGTAAGGATCAAA
2818 CAG
1 CAG
2821 AAGCAGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (14 bp):
CAGTAAGGATCAAA
Found at i:15309 original size:11 final size:11
Alignment explanation
Indices: 15270--15311 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
15260 CAATGACAGC
15270 CAAAATCCGTCA
1 CAAAA-CCGTCA
*
15282 CAAAACC-TCT
1 CAAAACCGTCA
*
15292 GAAAACCGTCA
1 CAAAACCGTCA
15303 CAAAACCGT
1 CAAAACCGT
15312 ATTTGTGACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 12 0.48
12 5 0.20
ACGTcount: A:0.43, C:0.33, G:0.10, T:0.14
Consensus pattern (11 bp):
CAAAACCGTCA
Found at i:16023 original size:53 final size:53
Alignment explanation
Indices: 15952--16060 Score: 184
Period size: 53 Copynumber: 2.1 Consensus size: 53
15942 GGTACTATAA
*
15952 ACAAAAGATTTTGGTGAAACATTGTTCCATTCACCA-AGTACTATAAACTAGAT
1 ACAAAAGACTTTGGTGAAACATTGTTCCATTCACCACA-TACTATAAACTAGAT
*
16005 ACAAAAGACTTTGGTGAAACATTGTTCCATTCACCACATACTATAAACTATAT
1 ACAAAAGACTTTGGTGAAACATTGTTCCATTCACCACATACTATAAACTAGAT
16058 ACA
1 ACA
16061 GAAACATTGT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 52 0.98
54 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.29
Consensus pattern (53 bp):
ACAAAAGACTTTGGTGAAACATTGTTCCATTCACCACATACTATAAACTAGAT
Found at i:16779 original size:11 final size:11
Alignment explanation
Indices: 16759--16799 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
16749 ATCTTACAAA
16759 TTACAGCAGTT
1 TTACAGCAGTT
*
16770 TTACACCAGTT
1 TTACAGCAGTT
16781 TTACAGCAGTT
1 TTACAGCAGTT
*
16792 TTTCAGCA
1 TTACAGCA
16800 ATTTGTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (11 bp):
TTACAGCAGTT
Found at i:18049 original size:21 final size:21
Alignment explanation
Indices: 18025--18075 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
18015 TCATCATCCA
18025 TCTCCATCTCATGGTCTTCAT
1 TCTCCATCTCATGGTCTTCAT
18046 TCTCCATCTCATGGTCTTCAT
1 TCTCCATCTCATGGTCTTCAT
*
18067 CCTCCATCT
1 TCTCCATCT
18076 ACTTGATGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.14, C:0.37, G:0.08, T:0.41
Consensus pattern (21 bp):
TCTCCATCTCATGGTCTTCAT
Found at i:18576 original size:30 final size:30
Alignment explanation
Indices: 18486--18577 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
18476 AAAAAAGGAA
* * *
18486 CAACAACCTCAAAATATATCACCAAAAGTAC
1 CAACAGCCTCAAAATACATCA-CAAAAGTTC
* * *
18517 CAGCAGCCTCAAAATAGATCACAAAAAGTTT
1 CAACAGCCTCAAAATACATCAC-AAAAGTTC
18548 CAACAGCCAT-AAAATACATCACAAAAGTTC
1 CAACAGCC-TCAAAATACATCACAAAAGTTC
18578 TAAAAGTGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 8 0.16
31 42 0.82
32 1 0.02
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.17
Consensus pattern (30 bp):
CAACAGCCTCAAAATACATCACAAAAGTTC
Found at i:19562 original size:30 final size:30
Alignment explanation
Indices: 19526--19603 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
19516 CCAAGGAAAA
*
19526 AAAATGGCGCATATTTTTTTATTGAGAATT
1 AAAATGGCGCCTATTTTTTTATTGAGAATT
19556 AAAATGGCGCCTATTTTTTTATTGAGAATT
1 AAAATGGCGCCTATTTTTTTATTGAGAATT
19586 AAAATGGCGCCTATTTTT
1 AAAATGGCGCCTATTTTT
19604 CCCACACGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (30 bp):
AAAATGGCGCCTATTTTTTTATTGAGAATT
Found at i:21494 original size:15 final size:15
Alignment explanation
Indices: 21474--21503 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21464 TAGAACTAGG
*
21474 TGTAGAAGTTGTAGT
1 TGTAGAAGTAGTAGT
21489 TGTAGAAGTAGTAGT
1 TGTAGAAGTAGTAGT
21504 CCTAGCTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (15 bp):
TGTAGAAGTAGTAGT
Found at i:22813 original size:61 final size:61
Alignment explanation
Indices: 22742--23016 Score: 451
Period size: 61 Copynumber: 4.5 Consensus size: 61
22732 TGAAAAAACT
* *
22742 TTGAAAACTTTGAAAAACTTGAATTGAATACTTTGAAAATTTGATGGGATCTTTCCCTAAA
1 TTGAACACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
*
22803 TTGAACACTTTGAAAAAAACTTGAATTGAATACTTTGGAAAACTTGATGGGATTTTTCCCTAAA
1 TTGAACACTTTG--AAAAACTTGAATTGAATACTTT-GAAAACTTGATGGGATCTTTCCCTAAA
*
22867 TTGAACACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTATA
1 TTGAACACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
* *
22928 TTGAACACTTTGAAAAACTTGAATTGAATACTTAGAAAACTTGATGAGATCTTTCCCTAAA
1 TTGAACACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
* *
22989 TTGAAAACTTTGAAAGACTTGAATTGAA
1 TTGAACACTTTGAAAAACTTGAATTGAA
23017 ATTCGTTTTG
Statistics
Matches: 201, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
61 120 0.60
62 22 0.11
63 22 0.11
64 37 0.18
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (61 bp):
TTGAACACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
Found at i:22899 original size:23 final size:22
Alignment explanation
Indices: 22865--22910 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
22855 TTTTTCCCTA
22865 AATTGAACACTTTGAAAAACTTG
1 AATTGAACACTTTG-AAAACTTG
*
22888 AATTGAATACTTTGAAAACTTG
1 AATTGAACACTTTGAAAACTTG
22910 A
1 A
22911 TGGGATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
AATTGAACACTTTGAAAACTTG
Found at i:22960 original size:23 final size:22
Alignment explanation
Indices: 22927--22971 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
22917 CTTTCCCTAT
*
22927 ATTGAACACTTTGAAAAACTTGA
1 ATTGAACACTTAG-AAAACTTGA
*
22950 ATTGAATACTTAGAAAACTTGA
1 ATTGAACACTTAGAAAACTTGA
22972 TGAGATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (22 bp):
ATTGAACACTTAGAAAACTTGA
Found at i:23027 original size:125 final size:124
Alignment explanation
Indices: 22742--23016 Score: 464
Period size: 125 Copynumber: 2.2 Consensus size: 124
22732 TGAAAAAACT
*
22742 TTGAAAACTTTGAAAAACTTGAATTGAATACTTTGAAAATTTGATGGGATCTTTCCCTAAATTGA
1 TTGAAAACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAATTGA
* * *
22807 ACACTTTGAAAAAAACTTGAATTGAATACTTTGGAAAACTTGATGGGATTTTTCCCTAAA
66 ACACTTTG-AAAAAACTTGAATTGAATACTTTAGAAAACTTGATGAGATCTTTCCCTAAA
* *
22867 TTGAACACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTATATTGA
1 TTGAAAACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAATTGA
22932 ACACTTTG-AAAAACTTGAATTGAATAC-TTAGAAAACTTGATGAGATCTTTCCCTAAA
66 ACACTTTGAAAAAACTTGAATTGAATACTTTAGAAAACTTGATGAGATCTTTCCCTAAA
*
22989 TTGAAAACTTTGAAAGACTTGAATTGAA
1 TTGAAAACTTTGAAAAACTTGAATTGAA
23017 ATTCGTTTTG
Statistics
Matches: 142, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
122 53 0.37
123 19 0.13
125 70 0.49
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (124 bp):
TTGAAAACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAATTGA
ACACTTTGAAAAAACTTGAATTGAATACTTTAGAAAACTTGATGAGATCTTTCCCTAAA
Found at i:29678 original size:29 final size:30
Alignment explanation
Indices: 29646--29703 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
29636 GTAAAAATGC
* *
29646 ATGAAATGTCATG-ATAAAATGCAAAACAT
1 ATGAAATCTCAAGAATAAAATGCAAAACAT
*
29675 ATGAAATCTTAAGAATAAAATGCAAAACA
1 ATGAAATCTCAAGAATAAAATGCAAAACA
29704 CATAGCATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.22
Consensus pattern (30 bp):
ATGAAATCTCAAGAATAAAATGCAAAACAT
Found at i:36369 original size:22 final size:22
Alignment explanation
Indices: 36343--36386 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
36333 TTTGGTTGGA
36343 CCCAATCTGCTTTGGGCCTCAT
1 CCCAATCTGCTTTGGGCCTCAT
36365 CCCAATCTGCTTTGGGCCTCAT
1 CCCAATCTGCTTTGGGCCTCAT
36387 AGTCACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.18, T:0.32
Consensus pattern (22 bp):
CCCAATCTGCTTTGGGCCTCAT
Found at i:40695 original size:15 final size:18
Alignment explanation
Indices: 40659--40694 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40649 AAAAGAAATG
40659 AAATAGGCTTTTAATAAA
1 AAATAGGCTTTTAATAAA
40677 AAAT-GGCTTTTAA-AAA
1 AAATAGGCTTTTAATAAA
40693 AA
1 AA
40695 TCAAGGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (18 bp):
AAATAGGCTTTTAATAAA
Found at i:41984 original size:178 final size:178
Alignment explanation
Indices: 41685--42040 Score: 658
Period size: 178 Copynumber: 2.0 Consensus size: 178
41675 CCTCTAATCA
*
41685 CTCTTGATGATCTCACACAATCTACCTTTTTCCACTCCTTTTAGCTTCAATAGGCCTAATAAGAA
1 CTCTTGATGATCTCACACAATCTACATTTTTCCACTCCTTTTAGCTTCAATAGGCCTAATAAGAA
* * *
41750 CAACTTGTAAGGATCAATTCTCTCTTCTCGTGACCTACTTGAGGAACAAACAATTAGTGGCAAAA
66 CAACTTGTAAGGATCAATTCGCTCTTCTCATGACCTACTTGAGGAACAAACAATTAGTAGCAAAA
41815 ACTTTATGTGAAACAAAGATAAGTGATCTAGAATAACCAAACCAAACT
131 ACTTTATGTGAAACAAAGATAAGTGATCTAGAATAACCAAACCAAACT
*
41863 CTCTTGATGATCTCACACAATCTACATTTTTCCACTCCTTTTAGCTTTAATAGGCCTAATAAGAA
1 CTCTTGATGATCTCACACAATCTACATTTTTCCACTCCTTTTAGCTTCAATAGGCCTAATAAGAA
41928 CAACTTGTAAGGATCAATTCGCTCTTCTCATGACCTACTTGAGGAACAAACAATTAGTAGCAAAA
66 CAACTTGTAAGGATCAATTCGCTCTTCTCATGACCTACTTGAGGAACAAACAATTAGTAGCAAAA
*
41993 ACTTTATGTGAAACAAAGATAAGTGATCTAGAATAATCAAACCAAACT
131 ACTTTATGTGAAACAAAGATAAGTGATCTAGAATAACCAAACCAAACT
42041 TGAAGTCTCC
Statistics
Matches: 172, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
178 172 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (178 bp):
CTCTTGATGATCTCACACAATCTACATTTTTCCACTCCTTTTAGCTTCAATAGGCCTAATAAGAA
CAACTTGTAAGGATCAATTCGCTCTTCTCATGACCTACTTGAGGAACAAACAATTAGTAGCAAAA
ACTTTATGTGAAACAAAGATAAGTGATCTAGAATAACCAAACCAAACT
Found at i:43538 original size:18 final size:18
Alignment explanation
Indices: 43515--43552 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
43505 GCACAACACG
*
43515 CGCCGTTAGATCTGTCCA
1 CGCCGTTAGATCGGTCCA
43533 CGCCGTTAGATCGGTCCA
1 CGCCGTTAGATCGGTCCA
43551 CG
1 CG
43553 TGGATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.24
Consensus pattern (18 bp):
CGCCGTTAGATCGGTCCA
Found at i:46037 original size:21 final size:21
Alignment explanation
Indices: 46011--46126 Score: 164
Period size: 21 Copynumber: 5.5 Consensus size: 21
46001 AGATGCTAGG
46011 AGCTCATTGGAGCAA-GTTCCA
1 AGCTCATTGGAG-AAGGTTCCA
*
46032 AGCTCATTGGAGCAA-GTTTCA
1 AGCTCATTGGAG-AAGGTTCCA
46053 AGCTCATTGGAGAAGGTTCCA
1 AGCTCATTGGAGAAGGTTCCA
* *
46074 AGCTCTTTGGAGAAGGTTACA
1 AGCTCATTGGAGAAGGTTCCA
*
46095 AGCTCATTGGAGAAGGTTTCA
1 AGCTCATTGGAGAAGGTTCCA
46116 AGCTCATTGGA
1 AGCTCATTGGA
46127 ATTGCCTAAG
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
20 2 0.02
21 86 0.98
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
AGCTCATTGGAGAAGGTTCCA
Found at i:47032 original size:25 final size:24
Alignment explanation
Indices: 46996--47042 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
46986 TACTTCTATT
46996 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
47019 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
47043 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:48693 original size:33 final size:33
Alignment explanation
Indices: 48592--48696 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
48582 TTGCAAAAAG
* * * *
48592 TGTTTTAGATGTTGTTAGTGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
** * * *
48625 TAATTTAAGTGTTGTTTGTAATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
48658 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC
48691 TGTTTT
1 TGTTTT
48697 GGATGCTAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
32 3 0.05
33 55 0.95
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
Found at i:50560 original size:21 final size:21
Alignment explanation
Indices: 50534--50712 Score: 263
Period size: 21 Copynumber: 8.5 Consensus size: 21
50524 AGATGCTAGG
50534 AGCTCATTGGAGCAA-GTTCCA
1 AGCTCATTGGAG-AAGGTTCCA
50555 AGCTCATTGGAGCAA-GTTCCA
1 AGCTCATTGGAG-AAGGTTCCA
50576 AGCTCATTGGAGAAGGTTCCA
1 AGCTCATTGGAGAAGGTTCCA
*
50597 AGCTCATTGGAGAATGTTCCA
1 AGCTCATTGGAGAAGGTTCCA
*
50618 AGCTCATAGGAGAAGGTTCCA
1 AGCTCATTGGAGAAGGTTCCA
*
50639 AGCTCATTGGAGAATGTTCCA
1 AGCTCATTGGAGAAGGTTCCA
* * *
50660 AGCTCTTTGGAGGAGGTTACA
1 AGCTCATTGGAGAAGGTTCCA
*
50681 AGCTCATTGGAGAAGGTTTCA
1 AGCTCATTGGAGAAGGTTCCA
50702 AGCTCATTGGA
1 AGCTCATTGGA
50713 ATTGCCTAAG
Statistics
Matches: 145, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
20 2 0.01
21 143 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (21 bp):
AGCTCATTGGAGAAGGTTCCA
Found at i:54820 original size:21 final size:21
Alignment explanation
Indices: 54796--54838 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54786 GGCGCCCACA
* *
54796 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
54817 TGGTTTGCCTGATCACCCATG
1 TGGTTTGCCTGAACACCCATG
54838 T
1 T
54839 AGGCAGTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:59131 original size:33 final size:32
Alignment explanation
Indices: 59094--59183 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 32
59084 AGAATTTGTT
59094 TCATCACAAACAACACCTAAAACAGATTTAGTG
1 TCATCACAAACAACA-CTAAAACAGATTTAGTG
** * *
59127 TCATCACAAACAACACTCAAATTAGGTTTATTG
1 TCATCACAAACAACACT-AAAACAGATTTAGTG
*
59160 TCATCACTAACAACATCTAAAACA
1 TCATCACAAACAACA-CTAAAACA
59184 CTCTTTGCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 2 0.04
33 44 0.92
34 2 0.04
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.24
Consensus pattern (32 bp):
TCATCACAAACAACACTAAAACAGATTTAGTG
Found at i:59132 original size:66 final size:66
Alignment explanation
Indices: 59046--59183 Score: 156
Period size: 66 Copynumber: 2.1 Consensus size: 66
59036 GTGATCAACC
* ** * *
59046 AAAACAGATTTGTTTTCATCACAATTAGCA-TCCAAATTAGAATTTGTT-TCATCACAAACAACA
1 AAAACAGATTTGTTGTCATCACAAACAACACT-CAAATTAG-ATTTATTGTCATCACAAACAACA
59109 CCT
64 CCT
* * *
59112 AAAACAGATTTAG-TGTCATCACAAACAACACTCAAATTAGGTTTATTGTCATCACTAACAACAT
1 AAAACAGATTT-GTTGTCATCACAAACAACACTCAAATTAGATTTATTGTCATCACAAACAACAC
59176 CT
65 CT
59178 AAAACA
1 AAAACA
59184 CTCTTTGCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
65 5 0.08
66 54 0.89
67 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (66 bp):
AAAACAGATTTGTTGTCATCACAAACAACACTCAAATTAGATTTATTGTCATCACAAACAACACC
T
Found at i:60606 original size:16 final size:15
Alignment explanation
Indices: 60568--60609 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
60558 ACATAGGTTG
*
60568 ACAGAAAACAATTAA
1 ACAGAAAACAACTAA
60583 ACAGAAAACAACTAA
1 ACAGAAAACAACTAA
60598 ACTAGAAAACAA
1 AC-AGAAAACAA
60610 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAACTAA
Found at i:62622 original size:25 final size:24
Alignment explanation
Indices: 62585--62631 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
62575 CTAGAAAATT
62585 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
62611 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
62632 AATAGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:62641 original size:28 final size:26
Alignment explanation
Indices: 62585--62641 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
62575 CTAGAAAATT
* *
62585 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGATAGATGAGATGAA
62611 TGAAAAACTTGATGATAGATGA-ATAGAA
1 TGAAAAACTT--TGATAGATGAGAT-GAA
62639 TGA
1 TGA
62642 TAGATTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 10 0.38
27 2 0.08
28 14 0.54
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (26 bp):
TGAAAAACTTTGATAGATGAGATGAA
Found at i:63490 original size:21 final size:21
Alignment explanation
Indices: 63464--63505 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
63454 GCATCTTAGG
63464 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
63485 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
63506 TTCTTTGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:68405 original size:26 final size:26
Alignment explanation
Indices: 68337--68418 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 26
68327 TTTCTTAAGC
68337 AAATCCAAAAGAAGATTTTGGGAAATA
1 AAATCCAAAAGAAGATTTT-GGAAATA
*
68364 AGATTATTCCAGAAGAAGATTTTGGAAACT-
1 A-A--A-TCCAAAAGAAGATTTTGGAAA-TA
68394 AAATCCAAAAGAAGATTTTGGAAAT
1 AAATCCAAAAGAAGATTTTGGAAAT
68419 TGATAAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
25 1 0.02
26 20 0.42
27 2 0.04
28 1 0.02
29 1 0.02
30 7 0.15
31 16 0.33
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.26
Consensus pattern (26 bp):
AAATCCAAAAGAAGATTTTGGAAATA
Found at i:70527 original size:178 final size:178
Alignment explanation
Indices: 70258--70595 Score: 486
Period size: 178 Copynumber: 1.9 Consensus size: 178
70248 CCGATTAAGC
* *
70258 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAATTTTCCTGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * * *
70323 CATTTAATGTTTCAAGTATCAAAAATGTTTTCGAAA-AATTTGTTGTTTCGGTTAAC-GAGAATA
66 AATTTAATGTTTCAAGTATAAAAAATG-CTTCGAAAGAATTAGTTGTTTCAGTTAACAGA-AATA
*
70386 GATGGTCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGA
129 GATGGTCCACTTAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGA
* * * *
70436 TGATTCAAGTGTCTCTTCAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTTGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
*
70501 AATTTAATG-TTCAAGGTATAAAAAATGCTTCTAAAGAATTAGTTGTTTCAGTTAACAGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCGAAAGAATTAGTTGTTTCAGTTAACAGAAATAG
*
70565 ATGGTCTACTTAATATTACATAATTTGTGCT
130 ATGGTCCACTTAATATTACATAATTTGTGCT
70596 TCTTGTGGAA
Statistics
Matches: 142, Mismatches: 14, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
177 14 0.10
178 126 0.89
179 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCGAAAGAATTAGTTGTTTCAGTTAACAGAAATAGA
TGGTCCACTTAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGA
Found at i:74040 original size:37 final size:37
Alignment explanation
Indices: 73990--74062 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
73980 TGAAACAGAA
73990 TTTTTCAGCAAAGCTCTAAATAACTCCAATTTACTTG
1 TTTTTCAGCAAAGCTCTAAATAACTCCAATTTACTTG
74027 TTTTTCAGCAAAGCTCTAAATAACTCCAATTTACTT
1 TTTTTCAGCAAAGCTCTAAATAACTCCAATTTACTT
74063 CCTTTTGGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (37 bp):
TTTTTCAGCAAAGCTCTAAATAACTCCAATTTACTTG
Found at i:74242 original size:24 final size:24
Alignment explanation
Indices: 74215--74263 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
74205 AAATACCAAG
74215 GACTCCGTCAAGATCTTTACATGT
1 GACTCCGTCAAGATCTTTACATGT
*
74239 GACTCCGTCTAGATCTTTACATGT
1 GACTCCGTCAAGATCTTTACATGT
74263 G
1 G
74264 GAATTTCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (24 bp):
GACTCCGTCAAGATCTTTACATGT
Found at i:75833 original size:42 final size:42
Alignment explanation
Indices: 75776--75859 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
75766 AATTTATTTG
*
75776 TTAATTAGATTCTTTCAGATTTCATTAAAAGATTATAAAGAA
1 TTAATTAGATTCTTTCAGATTTCATTAAAAGATTACAAAGAA
75818 TTAATTAGATTCTTTCAGATTTCATTAAAAGATTACAAAGAA
1 TTAATTAGATTCTTTCAGATTTCATTAAAAGATTACAAAGAA
75860 GAAGAATTAG
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:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (42 bp):
TTAATTAGATTCTTTCAGATTTCATTAAAAGATTACAAAGAA
Found at i:76624 original size:11 final size:11
Alignment explanation
Indices: 76608--76641 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
76598 TTATTTACAT
76608 TATTTAGAGTA
1 TATTTAGAGTA
*
76619 TATTTAGATTA
1 TATTTAGAGTA
*
76630 TATTTTGAGTA
1 TATTTAGAGTA
76641 T
1 T
76642 TTATATTGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (11 bp):
TATTTAGAGTA
Done.