Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014244.1 Corchorus capsularis cultivar CVL-1 contig14265, 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: 48151
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Found at i:818 original size:36 final size:36
Alignment explanation
Indices: 771--842 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
761 GATACGAATC
*
771 TAGTTTTGTTAGATTCAAATCCACCTTTGAGACCCG
1 TAGTTCTGTTAGATTCAAATCCACCTTTGAGACCCG
*
807 TAGTTCTGTTAGATTCAAATCCACGTTTGAGACCCG
1 TAGTTCTGTTAGATTCAAATCCACCTTTGAGACCCG
843 CCAAAGATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (36 bp):
TAGTTCTGTTAGATTCAAATCCACCTTTGAGACCCG
Found at i:9350 original size:30 final size:30
Alignment explanation
Indices: 9314--9376 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
9304 TGTCTTCAAG
9314 TCCATGATAAGTCCTT-GGCGCATCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
9344 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
9374 TCC
1 TCC
9377 CCCTTGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.19, C:0.35, G:0.17, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:12732 original size:60 final size:60
Alignment explanation
Indices: 12665--13273 Score: 1004
Period size: 60 Copynumber: 10.2 Consensus size: 60
12655 AAGCGTCTCA
*
12665 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTT
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
* * *
12725 AGGTATTAGTTGTCTACGGATTAGCCTACCTCAAGTGTTGACCACGGATTGGTCTCTTTC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
*
12785 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTAC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
*
12845 AAGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCT-TTTCC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTT-C
* * *
12905 AGGTATTAGTTGGCTATGGACTTGCCTACTTCAAGTGTTGATCACGGATTGGTCTCTTTC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
* *
12965 AGGAATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCTTTC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
*
13025 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCTTTC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
* * * *
13085 AGGTATTAGTTGGCCACGGACTGGCCTACTTCAAGTATTGACCACGGATTGATCTCTTTC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
* *
13145 AGGTATTAGTTGGCTACGGACTGGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
* * * *
13205 AGGTATTAGTTGGCTACGGACTGGCCTACTTCAAGTATTGATCACGGGTTGGTCTCTTTC
1 AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
13265 AGGTATTAG
1 AGGTATTAG
13274 GCTTAGTTTG
Statistics
Matches: 518, Mismatches: 29, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
59 2 0.00
60 513 0.99
61 3 0.01
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (60 bp):
AGGTATTAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTC
Found at i:12773 original size:28 final size:28
Alignment explanation
Indices: 12680--12894 Score: 103
Period size: 28 Copynumber: 7.2 Consensus size: 28
12670 TTAGTTGGCT
*
12680 ACGGACTAGCCTACTTCAAGTGTTGACC
1 ACGGATTAGCCTACTTCAAGTGTTGACC
* * * * * *
12708 ACGGATTGGTCT-CTTTTAGGTATTAGTTGTCT
1 ACGGATTAGCCTAC-TTCA---AGT-GTTGACC
*
12740 ACGGATTAGCCTACCTCAAGTGTTGACC
1 ACGGATTAGCCTACTTCAAGTGTTGACC
* * * * *
12768 ACGGATTGGTCT-CTTTCAGGTATTAGTTGGCT
1 ACGGATTAGCCTAC-TTCA---AGT-GTTGACC
*
12800 ACGGACTAGCCTACTTCAAGTGTTGACC
1 ACGGATTAGCCTACTTCAAGTGTTGACC
* * * *
12828 ACGGATTGGTCT-CTTACAAGTATTAGTTGGCT
1 ACGGATTAGCCTACTT-CAAG---T-GTTGACC
*
12860 ACGGACTAGCCTACTTCAAGTGTTGACC
1 ACGGATTAGCCTACTTCAAGTGTTGACC
12888 ACGGATT
1 ACGGATT
12895 GGTCTTTTCC
Statistics
Matches: 132, Mismatches: 37, Indels: 36
0.64 0.18 0.18
Matches are distributed among these distances:
27 5 0.04
28 59 0.45
29 5 0.04
31 5 0.04
32 53 0.40
33 5 0.04
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (28 bp):
ACGGATTAGCCTACTTCAAGTGTTGACC
Found at i:13025 original size:28 final size:28
Alignment explanation
Indices: 12994--13085 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 28
12984 ACTAGCCTAC
12994 TTCAAGTGTTGACCACGGGTTGGTCTCT
1 TTCAAGTGTTGACCACGGGTTGGTCTCT
* * * ** * *
13022 TTCAGGTATTAGTTGGCTACGGACTAGCCTAC-
1 TTCA---AGT-GTTGACCACGGGTTGGTCT-CT
13054 TTCAAGTGTTGACCACGGGTTGGTCTCT
1 TTCAAGTGTTGACCACGGGTTGGTCTCT
13082 TTCA
1 TTCA
13086 GGTATTAGTT
Statistics
Matches: 44, Mismatches: 14, Indels: 12
0.63 0.20 0.17
Matches are distributed among these distances:
27 1 0.02
28 21 0.48
29 2 0.05
31 2 0.05
32 17 0.39
33 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (28 bp):
TTCAAGTGTTGACCACGGGTTGGTCTCT
Found at i:13145 original size:28 final size:28
Alignment explanation
Indices: 13054--13271 Score: 100
Period size: 28 Copynumber: 7.4 Consensus size: 28
13044 ACTAGCCTAC
* *
13054 TTCAAGTGTTGACCACGGGTTGGTCTCT
1 TTCAAGTATTGACCACGGATTGGTCTCT
* * * *
13082 TTCAGGTATTAGTTGGCCACGGACTGGCCTAC-
1 TTCA---AGTA-TTGACCACGGATTGGTCT-CT
*
13114 TTCAAGTATTGACCACGGATTGATCTCT
1 TTCAAGTATTGACCACGGATTGGTCTCT
* * * * *
13142 TTCAGGTATTAGTTGGCTACGGACTGGCCTAC-
1 TTCA---AGTA-TTGACCACGGATTGGTCT-CT
13174 TTCAAGTATTGACCACGGATTGGTCTCT
1 TTCAAGTATTGACCACGGATTGGTCTCT
* * * * *
13202 TTCAGGTATTAGTTGGCTACGGACTGGCCTAC-
1 TTCA---AGTA-TTGACCACGGATTGGTCT-CT
* *
13234 TTCAAGTATTGATCACGGGTTGGTCTCT
1 TTCAAGTATTGACCACGGATTGGTCTCT
*
13262 TTCAGGTATT
1 TTCAAGTATT
13272 AGGCTTAGTT
Statistics
Matches: 137, Mismatches: 35, Indels: 36
0.66 0.17 0.17
Matches are distributed among these distances:
27 3 0.02
28 61 0.45
29 9 0.07
31 8 0.06
32 53 0.39
33 3 0.02
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (28 bp):
TTCAAGTATTGACCACGGATTGGTCTCT
Found at i:13734 original size:32 final size:32
Alignment explanation
Indices: 13693--13848 Score: 98
Period size: 32 Copynumber: 5.1 Consensus size: 32
13683 ATTGGTCTCT
*
13693 TTCAGGTATTAGTTGGCCACGGACTGGCCTAC
1 TTCAAGTATTAGTTGGCCACGGACTGGCCTAC
* * *
13725 TTCAAG---TA-TTGACCACGGATTGGTCT-C
1 TTCAAGTATTAGTTGGCCACGGACTGGCCTAC
* ** *
13752 TTTCAGGTATTAGTTGGCTGCGGACAGGCCTAC
1 -TTCAAGTATTAGTTGGCCACGGACTGGCCTAC
* ** *
13785 TTCAAG---T-GTTGACCACGGGTTGGTCT-C
1 TTCAAGTATTAGTTGGCCACGGACTGGCCTAC
* *
13812 TTTCAAGTATAAGTTGGCTACGGACTGGCCTAC
1 -TTCAAGTATTAGTTGGCCACGGACTGGCCTAC
13845 TTCA
1 TTCA
13849 GTGTCGACCA
Statistics
Matches: 87, Mismatches: 25, Indels: 24
0.64 0.18 0.18
Matches are distributed among these distances:
27 2 0.02
28 38 0.44
29 3 0.03
31 2 0.02
32 40 0.46
33 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (32 bp):
TTCAAGTATTAGTTGGCCACGGACTGGCCTAC
Found at i:13734 original size:60 final size:60
Alignment explanation
Indices: 13641--13872 Score: 340
Period size: 60 Copynumber: 3.9 Consensus size: 60
13631 AAACCAGGCC
* **
13641 TTAGTTGGCTACAGACTAACCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAGGTA
1 TTAGTTGGCTACGGACTGGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAGGTA
*
13701 TTAGTTGGCCACGGACTGGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAGGTA
1 TTAGTTGGCTACGGACTGGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAGGTA
* * * * *
13761 TTAGTTGGCTGCGGACAGGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCTTTCAAGTA
1 TTAGTTGGCTACGGACTGGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAGGTA
* * * *
13821 TAAGTTGGCTACGGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCTCTT
1 TTAGTTGGCTACGGACTGGCCTACTTCAAGTATTGACCACGGATTGGTCTCTT
13873 CCAAGCGTCA
Statistics
Matches: 156, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 22 0.14
60 134 0.86
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (60 bp):
TTAGTTGGCTACGGACTGGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAGGTA
Found at i:13756 original size:28 final size:28
Alignment explanation
Indices: 13665--13762 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
13655 ACTAACCTAC
13665 TTCAAGTATTGACCACGGATTGGTCTCT
1 TTCAAGTATTGACCACGGATTGGTCTCT
* * * *
13693 TTCAGGTATTAGTTGGCCACGGACTGGCCTAC-
1 TTCA---AGTA-TTGACCACGGATTGGTCT-CT
13725 TTCAAGTATTGACCACGGATTGGTCTCT
1 TTCAAGTATTGACCACGGATTGGTCTCT
*
13753 TTCAGGTATT
1 TTCAAGTATT
13763 AGTTGGCTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
27 1 0.02
28 28 0.51
29 3 0.05
31 3 0.05
32 19 0.35
33 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.35
Consensus pattern (28 bp):
TTCAAGTATTGACCACGGATTGGTCTCT
Found at i:13891 original size:59 final size:60
Alignment explanation
Indices: 13643--13909 Score: 320
Period size: 60 Copynumber: 4.5 Consensus size: 60
13633 ACCAGGCCTT
* ** * * *
13643 AGTTGGCTACAGACTAACCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAGGTATT
1 AGTTGGCTACGGACTGGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTCAAGTATA
* * * *
13703 AGTTGGCCACGGACTGGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAGGTATT
1 AGTTGGCTACGGACTGGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTCAAGTATA
* * *
13763 AGTTGGCTGCGGACAGGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCTTTCAAGTATA
1 AGTTGGCTACGGACTGGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTCAAGTATA
* * * ** *
13823 AGTTGGCTACGGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCTCTTCCAAGCGTC
1 AGTTGGCTACGGACTGGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTCAAGTATA
** * *
13882 AGTAAGCTACAGACTAGCCTACTTCAAG
1 AGTTGGCTACGGACTGGCCTACTTCAAG
13910 CATCGACCAC
Statistics
Matches: 182, Mismatches: 24, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
59 48 0.26
60 134 0.74
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (60 bp):
AGTTGGCTACGGACTGGCCTACTTCAAGTGTTGACCACGGATTGGTCTCTTTCAAGTATA
Found at i:18091 original size:16 final size:17
Alignment explanation
Indices: 18067--18100 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18057 GAAGACTAGC
*
18067 TGAGGTGGCA-AAGGAG
1 TGAGCTGGCACAAGGAG
18083 TGAGCTGGCACAAGGAG
1 TGAGCTGGCACAAGGAG
18100 T
1 T
18101 TTGATGAAGG
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:0.29, C:0.12, G:0.44, T:0.15
Consensus pattern (17 bp):
TGAGCTGGCACAAGGAG
Found at i:20126 original size:36 final size:36
Alignment explanation
Indices: 20095--20197 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
20085 CTTTTTTGTT
* * *
20095 TTTGTTTTTTTTATCTGATTTTTTTTTTTTTTCGCAA
1 TTTG-TTTTTTAATTTGATTTTTTTTTTTTTTTGCAA
* *
20132 TTTGATTTTTGATTTGATTTTTTTTTTTTTTTGCAA
1 TTTGTTTTTTAATTTGATTTTTTTTTTTTTTTGCAA
*
20168 TTTGATTTTTGAATTTGATTTTTTTTTTTT
1 TTTG-TTTTTTAATTTGATTTTTTTTTTTT
20198 GAGACCTTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 32 0.55
37 26 0.45
ACGTcount: A:0.13, C:0.04, G:0.10, T:0.74
Consensus pattern (36 bp):
TTTGTTTTTTAATTTGATTTTTTTTTTTTTTTGCAA
Found at i:20154 original size:37 final size:37
Alignment explanation
Indices: 20110--20197 Score: 160
Period size: 36 Copynumber: 2.4 Consensus size: 37
20100 TTTTTTTATC
*
20110 TGATTTTTTTTTTTTTTCGCAATTTGATTTTTG-ATT
1 TGATTTTTTTTTTTTTTTGCAATTTGATTTTTGAATT
20146 TGATTTTTTTTTTTTTTTGCAATTTGATTTTTGAATT
1 TGATTTTTTTTTTTTTTTGCAATTTGATTTTTGAATT
20183 TGATTTTTTTTTTTT
1 TGATTTTTTTTTTTT
20198 GAGACCTTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 32 0.64
37 18 0.36
ACGTcount: A:0.14, C:0.03, G:0.10, T:0.73
Consensus pattern (37 bp):
TGATTTTTTTTTTTTTTTGCAATTTGATTTTTGAATT
Found at i:20363 original size:47 final size:47
Alignment explanation
Indices: 20248--20392 Score: 227
Period size: 47 Copynumber: 3.0 Consensus size: 47
20238 AAAACCCGTT
* * *
20248 GACCAACTTTGGTCACTATATTGAAAACTCGCGTGGAAACGAGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGG-AA-GCGAGAAAA
*
20297 GACCATCTTTGGTCTCTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
*
20344 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGACAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
20391 GA
1 GA
20393 TTGTCTGAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
47 55 0.61
48 2 0.02
49 33 0.37
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (47 bp):
GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
Found at i:20773 original size:70 final size:69
Alignment explanation
Indices: 20510--21001 Score: 602
Period size: 69 Copynumber: 7.1 Consensus size: 69
20500 CCTTGACTTA
* * * *
20510 TGGAAAAGCCCATGTTGCTTGGATGGAACCAATGCTTGAACTGGCTCGTATGGAAACGAGTTTGG
1 TGGAAAAGCCCTTGTTGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTGG
*
20575 CTTT
66 CTTG
* * * *
20579 TGGAAAAGCCCATGTTGCTTGGATGGAACCAATGCTTAAACT-ATCTCGTATGGAAACGACTCTG
1 TGGAAAAGCCCTTGTTGCTTGGATGGAACCAAAGCTTAAACTGA-CTCGTATGGAAACGAGTTTG
*
20643 ACTTG
65 GCTTG
* *
20648 TGGAAAAG-CCTCTGTTGCTTGGATGGAACCAAGGC-TAAACTGACTCGTGTGGAAACGAGTTTG
1 TGGAAAAGCCCT-TGTTGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTG
20711 GCTTG
65 GCTTG
* * *
20716 TGGAAAAGCCCTTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTGGAAACGAGTTTG
1 TGGAAAAGCCCTTG-TTGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTG
20781 GCTTG
65 GCTTG
* * * *
20786 TGGAAAAGCCTTTGTTGCTTGGATGGAACCAAGGC-TAAACTGACTCGTATGGAAATGAGATTGG
1 TGGAAAAGCCCTTGTTGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTGG
20850 CTTG
66 CTTG
* * *
20854 TGGAAAAGCCCCTGAATT-TTTGGATGGAACCAAAGCTTAATCT-ACCTCGTATGGAAACGAGTT
1 TGGAAAAGCCCTTG--TTGCTTGGATGGAACCAAAGCTTAAACTGA-CTCGTATGGAAACGAGTT
20917 TGGCTTG
63 TGGCTTG
* * * * *
20924 TGGAAAAGCCCTTGAATGCTTGGGTGGAACCAAAGTTTGAGCT-ACCTCGTATGGAAACGAGTTT
1 TGGAAAAGCCCTTG-TTGCTTGGATGGAACCAAAGCTTAAACTGA-CTCGTATGGAAACGAGTTT
* *
20988 GACTTA
64 GGCTTG
20994 TGGAAAAG
1 TGGAAAAG
21002 TCGAAGCATT
Statistics
Matches: 374, Mismatches: 38, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
68 80 0.21
69 153 0.41
70 141 0.38
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (69 bp):
TGGAAAAGCCCTTGTTGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTGG
CTTG
Found at i:21596 original size:50 final size:50
Alignment explanation
Indices: 21521--21621 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
21511 TAAAATGCCC
* * * *
21521 TTTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTAT
1 TTTGAAAAGCAAATCTTGATATTGGACTCACAAATGAAATGAAATCCTAT
* * * *
21571 TTTGAAAATCGAATCTTGATATTGGACTCACAAGTGAAATGAAATCTTAT
1 TTTGAAAAGCAAATCTTGATATTGGACTCACAAATGAAATGAAATCCTAT
21621 T
1 T
21622 ATAAAACTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (50 bp):
TTTGAAAAGCAAATCTTGATATTGGACTCACAAATGAAATGAAATCCTAT
Found at i:21943 original size:6 final size:6
Alignment explanation
Indices: 21932--21963 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
21922 TTCATTCTCT
21932 TTTTTC TTTTTC TTTTTC -TTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT
21964 CTTTTTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:21950 original size:21 final size:20
Alignment explanation
Indices: 21929--21969 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
21919 TTCTTCATTC
*
21929 TCTTTT-TTCTTTTTCTTTT
1 TCTTTTCTTTTTTTTCTTTT
21948 TCTTTTCTTTTTCTTTCTTTT
1 TCTTTTCTTTTT-TTTCTTTT
21969 T
1 T
21970 TCATGCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TCTTTTCTTTTTTTTCTTTT
Found at i:21964 original size:10 final size:11
Alignment explanation
Indices: 21932--21969 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
21922 TTCATTCTCT
21932 TTTTTCTTTTTC
1 TTTTTC-TTTTC
21944 TTTTTCTTTTC
1 TTTTTCTTTTC
21955 TTTTTC-TTTC
1 TTTTTCTTTTC
21965 TTTTT
1 TTTTT
21970 TCATGCACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.35
11 11 0.42
12 6 0.23
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:21970 original size:17 final size:17
Alignment explanation
Indices: 21929--21971 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
21919 TTCTTCATTC
21929 TCTTTTTTCTTTTTCTT
1 TCTTTTTTCTTTTTCTT
21946 T-TTCTTTTCTTTTTCTT
1 TCTT-TTTTCTTTTTCTT
21963 TCTTTTTTC
1 TCTTTTTTC
21972 ATGCACTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TCTTTTTTCTTTTTCTT
Found at i:24919 original size:6 final size:6
Alignment explanation
Indices: 24908--24947 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
24898 CGTTTCACTT
*
24908 TTTTTC TTTTTC -TTTTC -TTTTC TTTTTA TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
24948 ATCAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:25461 original size:74 final size:75
Alignment explanation
Indices: 25358--25508 Score: 207
Period size: 74 Copynumber: 2.0 Consensus size: 75
25348 GGATTTTAAT
* * *
25358 CACCTTGAAATCATTGCTTTGACTAAAACTGATTTTGAAACAT-CTTTGGTTAAAA-CTCAACAT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATGCTTTGATTAAAACCT-AACAT
*
25421 TCTTTTGCTCA
65 TCCTTTGCTCA
* * * *
25432 CACCTCGAAACCATTGCTTTGATTGAAACTGATTTTGAAACCTGTTTTGATTAAAACCTAACATT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATGCTTTGATTAAAACCTAACATT
25497 CCTTTGCTCA
66 CCTTTGCTCA
25507 CA
1 CA
25509 GTCTAGATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 38 0.57
75 27 0.40
76 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.36
Consensus pattern (75 bp):
CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATGCTTTGATTAAAACCTAACATT
CCTTTGCTCA
Found at i:25648 original size:3 final size:3
Alignment explanation
Indices: 25642--25710 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
25632 TTTTATCCCT
25642 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25690 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
25711 CTATCATTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28149 original size:13 final size:13
Alignment explanation
Indices: 28123--28157 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
28113 TAATGCATCC
28123 AAAACATTTAATA
1 AAAACATTTAATA
28136 AAAATCATTT-ATA
1 AAAA-CATTTAATA
28149 AAAACATTT
1 AAAACATTT
28158 TGTTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAACATTTAATA
Found at i:32968 original size:21 final size:21
Alignment explanation
Indices: 32943--32993 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
32933 AAGGTTAGGC
32943 GGCCCCATAAGGTGGAACTTG
1 GGCCCCATAAGGTGGAACTTG
*
32964 GGCCCCGA-ATGGTGGAACTTG
1 GGCCCC-ATAAGGTGGAACTTG
*
32985 GGCTCCATA
1 GGCCCCATA
32994 TCTGGCACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (21 bp):
GGCCCCATAAGGTGGAACTTG
Found at i:39769 original size:13 final size:13
Alignment explanation
Indices: 39751--39777 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39741 ATAAGAGGAA
39751 GTAGGTGTGAGGT
1 GTAGGTGTGAGGT
39764 GTAGGTGTGAGGT
1 GTAGGTGTGAGGT
39777 G
1 G
39778 GAATTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.56, T:0.30
Consensus pattern (13 bp):
GTAGGTGTGAGGT
Found at i:41541 original size:31 final size:29
Alignment explanation
Indices: 41497--41568 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
41487 AAATTTGGTG
*
41497 AGGGACCCAATTGCTCAATTAA-CTCAACTTC
1 AGGGACCC-ATTGCTC-ACTAAGCTC-ACTTC
*
41528 AGGGACTCCATTGCTCACTAAGTTCACTTC
1 AGGGAC-CCATTGCTCACTAAGCTCACTTC
41558 AGGGACCCATT
1 AGGGACCCATT
41569 TGCACATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 5 0.14
30 15 0.41
31 15 0.41
32 2 0.05
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (29 bp):
AGGGACCCATTGCTCACTAAGCTCACTTC
Found at i:42628 original size:29 final size:31
Alignment explanation
Indices: 42590--42664 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
42580 CAGTTAACTC
* *
42590 CACTTCAGGGACTAAATTGCATAT-TT-TC-A
1 CACTTGAGGGACCAAATTGC-TATGTTCTCTA
* *
42619 CACTTGAGGGACCAATTTGCTATGTTCTCTC
1 CACTTGAGGGACCAAATTGCTATGTTCTCTA
42650 CACTTGAGGGACCAA
1 CACTTGAGGGACCAA
42665 TTTTGTACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 19 0.49
30 2 0.05
31 15 0.38
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (31 bp):
CACTTGAGGGACCAAATTGCTATGTTCTCTA
Found at i:46350 original size:16 final size:15
Alignment explanation
Indices: 46329--46363 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46319 TTTTATCCTC
46329 GGGTCACTCCAGTTTT
1 GGGTCA-TCCAGTTTT
*
46345 GGGTCATTCAGTTTT
1 GGGTCATCCAGTTTT
46360 GGGT
1 GGGT
46364 TTTTCGAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.11, C:0.17, G:0.31, T:0.40
Consensus pattern (15 bp):
GGGTCATCCAGTTTT
Done.