Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008291.1 Corchorus capsularis cultivar CVL-1 contig08312, 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: 60615
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:815 original size:51 final size:51
Alignment explanation
Indices: 677--904 Score: 273
Period size: 51 Copynumber: 4.5 Consensus size: 51
667 GATCACAGAA
* * *
677 TCAAACTCCTGCCCCGATTACTGCAACAAATGATGCTGGAATTTCCAATCC
1 TCAAACTCCTGCCCCGAGTACTGCACCAAATGATGCTGGAATTTCCAGTCC
* *
728 TTAAACTCCTG-CCTGAGTACTGCACCAAATGATGCTGGAATTTCCAGTCC
1 TCAAACTCCTGCCCCGAGTACTGCACCAAATGATGCTGGAATTTCCAGTCC
* * * *
778 TCAAACTCCTGCCCTGAGTACAGCACCAAATGATGCTGGCATTTCCCGTCC
1 TCAAACTCCTGCCCCGAGTACTGCACCAAATGATGCTGGAATTTCCAGTCC
* * * * * *
829 TCAAACTCTTGCCCCGAGTACTGCAGC-AA-GCCTCCCTGGCATTTCCCGTCC
1 TCAAACTCCTGCCCCGAGTACTGCACCAAATG-AT-GCTGGAATTTCCAGTCC
*
880 TCAAACTCCTTCCCCGAGTACTGCA
1 TCAAACTCCTGCCCCGAGTACTGCA
905 GCAAGCCTCC
Statistics
Matches: 157, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 48 0.31
51 108 0.69
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (51 bp):
TCAAACTCCTGCCCCGAGTACTGCACCAAATGATGCTGGAATTTCCAGTCC
Found at i:905 original size:51 final size:51
Alignment explanation
Indices: 813--955 Score: 234
Period size: 51 Copynumber: 2.8 Consensus size: 51
803 CCAAATGATG
813 CTGGCATTTCCCGTCCTCAAACT-CTTGCCCCGAGTACTGCAGCAAGCCTCC
1 CTGGCATTTCCCGTCCTCAAACTCCTT-CCCCGAGTACTGCAGCAAGCCTCC
864 CTGGCATTTCCCGTCCTCAAACTCCTTCCCCGAGTACTGCAGCAAGCCTCC
1 CTGGCATTTCCCGTCCTCAAACTCCTTCCCCGAGTACTGCAGCAAGCCTCC
* * * *
915 ATGGCATTTCCCATCCTCCAAGTCCTTCCCCGAGTACTGCA
1 CTGGCATTTCCCGTCCTCAAACTCCTTCCCCGAGTACTGCA
956 ACACCGTTTA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
51 84 0.97
52 3 0.03
ACGTcount: A:0.18, C:0.41, G:0.16, T:0.24
Consensus pattern (51 bp):
CTGGCATTTCCCGTCCTCAAACTCCTTCCCCGAGTACTGCAGCAAGCCTCC
Found at i:920 original size:102 final size:102
Alignment explanation
Indices: 677--955 Score: 264
Period size: 102 Copynumber: 2.7 Consensus size: 102
667 GATCACAGAA
* * * * * * * *
677 TCAAACTCCTGCCCCGATTACTGCAACAAATGATGCTGGAATTTCCAATCCTTAAACTCC-TGCC
1 TCAAACTCCTGCCCCGAGTACAGCACCAAATGATCCTGGCATTTCCCATCCTCAAACTCCTTCCC
* * * *
741 TGAGTACTGCACCAAATG-AT-GCTGGAATTTCCAGTCC
66 CGAGTACTGCAGC-AA-GCCTCCCTGGAATTTCCAGTCC
* * *
778 TCAAACTCCTGCCCTGAGTACAGCACCAAATGATGCTGGCATTTCCCGTCCTCAAACT-CTTGCC
1 TCAAACTCCTGCCCCGAGTACAGCACCAAATGATCCTGGCATTTCCCATCCTCAAACTCCTT-CC
* *
842 CCGAGTACTGCAGCAAGCCTCCCTGGCATTTCCCGTCC
65 CCGAGTACTGCAGCAAGCCTCCCTGGAATTTCCAGTCC
* * * * * *
880 TCAAACTCCTTCCCCGAGTACTGCAGC-AA-GCCTCCATGGCATTTCCCATCCTCCAAGTCCTTC
1 TCAAACTCCTGCCCCGAGTACAGCACCAAATG-ATCC-TGGCATTTCCCATCCTCAAACTCCTTC
943 CCCGAGTACTGCA
64 CCCGAGTACTGCA
956 ACACCGTTTA
Statistics
Matches: 147, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
100 3 0.02
101 58 0.39
102 83 0.56
103 3 0.02
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (102 bp):
TCAAACTCCTGCCCCGAGTACAGCACCAAATGATCCTGGCATTTCCCATCCTCAAACTCCTTCCC
CGAGTACTGCAGCAAGCCTCCCTGGAATTTCCAGTCC
Found at i:2512 original size:10 final size:10
Alignment explanation
Indices: 2497--2522 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2487 AGTTGCTGCC
2497 AAATTCCAGA
1 AAATTCCAGA
2507 AAATTCCAGA
1 AAATTCCAGA
2517 AAATTC
1 AAATTC
2523 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:3460 original size:6 final size:6
Alignment explanation
Indices: 3449--3480 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3439 ATTAATTTGC
3449 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
3481 GCTTTGCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:5882 original size:32 final size:32
Alignment explanation
Indices: 5846--5954 Score: 137
Period size: 32 Copynumber: 3.4 Consensus size: 32
5836 ATTTGCGGCT
*
5846 TCTTCTGAAGAAAACGCCGTGATATAGAGGCG
1 TCTTCTGAAGAAAACGCCGTGATATAGGGGCG
*
5878 TCTTCTGAAGAAAACGCCGTGATATAGGGGCA
1 TCTTCTGAAGAAAACGCCGTGATATAGGGGCG
* * * * *
5910 ACTTATGAAGCAAATGCGGTGATATAGGGGCG
1 TCTTCTGAAGAAAACGCCGTGATATAGGGGCG
* *
5942 CCTTCAGAAGAAA
1 TCTTCTGAAGAAA
5955 CGACGGCGTA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.21
Consensus pattern (32 bp):
TCTTCTGAAGAAAACGCCGTGATATAGGGGCG
Found at i:6122 original size:34 final size:34
Alignment explanation
Indices: 6084--6261 Score: 286
Period size: 34 Copynumber: 5.3 Consensus size: 34
6074 GTTTAAGGGG
6084 AAACGCCGCCATATGACGGCGTTTGTTTCAATAT
1 AAACGCCGCCATATGACGGCGTTTGTTTCAATAT
*
6118 AAACGTCGCCATATGACGGCGTTTGTTTCAATAT
1 AAACGCCGCCATATGACGGCGTTTGTTTCAATAT
*
6152 AAACGCCGCCACATGACGGCGTTTGTTTCAATAT
1 AAACGCCGCCATATGACGGCGTTTGTTTCAATAT
*
6186 AAACGTCGCCATATGACGGCGTTTGTTTCAATAT
1 AAACGCCGCCATATGACGGCGTTTGTTTCAATAT
* * *
6220 AAACGCCGCCACATGACGGCGTTTCTTT-AATAA
1 AAACGCCGCCATATGACGGCGTTTGTTTCAATAT
*
6253 AAATGCCGC
1 AAACGCCGC
6262 TACGCTTACT
Statistics
Matches: 134, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 12 0.09
34 122 0.91
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (34 bp):
AAACGCCGCCATATGACGGCGTTTGTTTCAATAT
Found at i:6788 original size:37 final size:37
Alignment explanation
Indices: 6744--6814 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
6734 CTTGATCAAC
* *
6744 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
6781 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
6815 ATGGCTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:6900 original size:60 final size:60
Alignment explanation
Indices: 6828--6990 Score: 281
Period size: 60 Copynumber: 2.7 Consensus size: 60
6818 GCTAATTGTT
** * * *
6828 CAAATAAGGGCCTAACGTTTGATAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
6888 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
6948 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
6991 TATCTCACGC
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
Found at i:6959 original size:29 final size:29
Alignment explanation
Indices: 6859--6959 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
6849 ATAAAATGCT
* * *
6859 CAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTGAATTTGGC
* * **
6888 CAAATAAGGG-CCTAACGTTTGCCAAAAT-GC
1 CAAATAAGGGCCCGATC-TTTG--AATTTGGC
6918 TCAAATAAGGGCCCGATCTTTGAATTTGGC
1 -CAAATAAGGGCCCGATCTTTGAATTTGGC
6948 CAAATAAGGGCC
1 CAAATAAGGGCC
6960 TAACGTTTGC
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.05
29 28 0.50
30 4 0.07
31 17 0.30
32 4 0.07
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTGAATTTGGC
Found at i:6968 original size:29 final size:30
Alignment explanation
Indices: 6827--6992 Score: 137
Period size: 31 Copynumber: 5.5 Consensus size: 30
6817 GGCTAATTGT
*
6827 TCAAATAAGGGCCTAACGTTTGATAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
* * * **
6858 TCAAATAAGGGTCTGATC-TTT-TAATTTGGC
1 TCAAATAAGGGCCT-AACGTTTGCAAAAT-GC
6888 -CAAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
* * **
6918 TCAAATAAGGGCCCGATC-TTTG-AATTTGGC
1 TCAAATAAGGG-CCTAACGTTTGCAAAAT-GC
6948 -CAAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
6978 TCAAATAAGGGCCTA
1 TCAAATAAGGGCCTA
6993 TCTCACGCGT
Statistics
Matches: 106, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 6 0.06
29 36 0.34
30 8 0.08
31 50 0.47
32 6 0.06
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (30 bp):
TCAAATAAGGGCCTAACGTTTGCAAAATGC
Found at i:7059 original size:31 final size:31
Alignment explanation
Indices: 7021--7093 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
7011 CTGACACCAA
7021 ACCCTTATTTGAGCATTTTCGATAACGTTAG
1 ACCCTTATTTGAGCATTTTCGATAACGTTAG
**
7052 ACCCTTATTTGAGCATTTTTTATAACGTTAG
1 ACCCTTATTTGAGCATTTTCGATAACGTTAG
7083 ACCCTTATTTG
1 ACCCTTATTTG
7094 GCCATATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (31 bp):
ACCCTTATTTGAGCATTTTCGATAACGTTAG
Found at i:7123 original size:60 final size:60
Alignment explanation
Indices: 7053--7219 Score: 214
Period size: 60 Copynumber: 2.8 Consensus size: 60
7043 TAACGTTAGA
** *
7053 CCCTTATTTGAGCATTTTTTATAACGTTAGACCCTTATTTGGCCATATTAAAAGACCGGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGACCCTTATTTGGCCATATTAAAAAACCGGG
* *
7113 CCCTTATTTGAGCATTTTCAATAACATTA-AGCCCTTATTTGGCCAAATTAAAAAACCGGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGA-CCCTTATTTGGCCATATTAAAAAACCGGG
* *
7173 CCCTTATTTGAACATTTTGGC-A-AACGTTAGGCCCTTATTTGAGCCAT
1 CCCTTATTTGAGCATTTT--CAATAACGTTAGACCCTTATTTG-GCCAT
7220 TATATCATAA
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
59 1 0.01
60 86 0.92
61 5 0.05
62 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCAATAACGTTAGACCCTTATTTGGCCATATTAAAAAACCGGG
Found at i:7150 original size:31 final size:31
Alignment explanation
Indices: 7021--7153 Score: 121
Period size: 31 Copynumber: 4.4 Consensus size: 31
7011 CTGACACCAA
* *
7021 ACCCTTATTTGAGCATTTTCGATAACGTTAG
1 ACCCTTATTTGAGCATTTTCAATAACATTAG
** *
7052 ACCCTTATTTGAGCATTTTTTATAACGTTAG
1 ACCCTTATTTGAGCATTTTCAATAACATTAG
* * ***
7083 ACCCTTATTTG-GCCATATT-AA-AAGACCGG
1 ACCCTTATTTGAG-CATTTTCAATAACATTAG
*
7112 GCCCTTATTTGAGCATTTTCAATAACATTA-
1 ACCCTTATTTGAGCATTTTCAATAACATTAG
7142 AGCCCTTATTTG
1 A-CCCTTATTTG
7154 GCCAAATTAA
Statistics
Matches: 81, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
29 18 0.22
30 5 0.06
31 58 0.72
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (31 bp):
ACCCTTATTTGAGCATTTTCAATAACATTAG
Found at i:7182 original size:29 final size:29
Alignment explanation
Indices: 7084--7182 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
7074 TAACGTTAGA
*
7084 CCCTTATTTGGCCATATTAAAAGACCGGG
1 CCCTTATTTGGCCATATTAAAAAACCGGG
* * ****
7113 CCCTTATTTGAG-CATTTTCAATAACATTAAG
1 CCCTTATTTG-GCCATATT-AA-AAAACCGGG
*
7144 CCCTTATTTGGCCAAATTAAAAAACCGGG
1 CCCTTATTTGGCCATATTAAAAAACCGGG
7173 CCCTTATTTG
1 CCCTTATTTG
7183 AACATTTTGG
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
29 29 0.55
30 6 0.11
31 18 0.34
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (29 bp):
CCCTTATTTGGCCATATTAAAAAACCGGG
Found at i:15137 original size:30 final size:30
Alignment explanation
Indices: 15059--15773 Score: 837
Period size: 30 Copynumber: 23.6 Consensus size: 30
15049 CATTGTGTAT
15059 ATGACAACTTCTGGTGTCAATTGCAAAAATC
1 ATGACAACTTCTGGTGTCAATTGC-AAAATC
15090 ATGACAA---CTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* **
15117 ATGACAACTTCTGGTATCAATTGCAAGGTC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* ** ** * *
15147 ATGATATTTTCAAGTTTCAATTGCGAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
15177 TTGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
15207 ATGATAACTTCTGGTGTCATTTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
15237 ATGACAACTTCTGGTGTCAATTTCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
15267 ATGACAACTTCTGGTGTCATTTGCAAAATG
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
15297 ATGATAACTTCTGGTGTCAATTTCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
15327 AAGACAACTTCTGGTGTCAATAGCAAAAATC
1 ATGACAACTTCTGGTGTCAATTGC-AAAATC
15358 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
15388 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
15418 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
15448 ATGACAACTTCTGGTGTCAATTGTAAAAATC
1 ATGACAACTTCTGGTGTCAATTG-CAAAATC
* * *
15479 ATGACAACTTCTGGTGTCAATTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* ** * *
15509 ATGACAACTTCTGGTGTCATTTATAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
15539 ATTGACAACTTCTAGTGTCAATTGTAAGATC
1 A-TGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
15570 ATGACAACTTCTGGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
15600 ATTGACAACTTCTGGTGTCAATTGTAAAATC
1 A-TGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
15631 ATGACAACTTCTGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
15661 ATGACAACTTCTGGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
15691 ATTGACAACTTCTGGTGCCAATTGTAACACC
1 A-TGACAACTTCTGGTGTCAATTGCAAAATC
* *
15722 ATTGACAACTTCTAGTGTCAA-TGGAGATTTAAT-
1 A-TGACAACTTCTGGTGTCAATTGCA-A---AATC
15755 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
15774 TTTGGAGACT
Statistics
Matches: 599, Mismatches: 73, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
27 13 0.02
28 14 0.02
30 392 0.65
31 161 0.27
32 17 0.03
33 1 0.00
34 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:15680 original size:91 final size:90
Alignment explanation
Indices: 15059--15777 Score: 831
Period size: 91 Copynumber: 7.9 Consensus size: 90
15049 CATTGTGTAT
*
15059 ATGACAACTTCTGGTGTCAATTGCAAAAATCATGACAA---CTGGTGTCAATTGCAAAATCATGA
1 ATGACAACTTCTGGTGTCAATTG-TAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGA
* * *
15121 CAACTTCTGGTATCAATTGCAAGGTC
65 CAACTTCTGGTGTCATTTGCAAGATC
* ** ** * ** * *
15147 ATGATATTTTCAAGTTTCAATTGCGAAATCTTGACAACTTCTGGTGTCAATTGCAAAATCATGAT
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
*
15212 AACTTCTGGTGTCATTTGCAAAATC
66 AACTTCTGGTGTCATTTGCAAGATC
* *
15237 ATGACAACTTCTGGTGTCAATT-TCAAAATCATGACAACTTCTGGTGTCATTTGCAAAATGATGA
1 ATGACAACTTCTGGTGTCAATTGT-AAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGA
* *
15301 TAACTTCTGGTGTCAATTT-CAAAATC
65 CAACTTCTGGTGTC-ATTTGCAAGATC
* * *
15327 AAGACAACTTCTGGTGTCAATAGCAAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGA
1 ATGACAACTTCTGGTGTCAATTG-TAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGA
* *
15392 CAACTTCTGGTGTCAATTGCAAAATC
65 CAACTTCTGGTGTCATTTGCAAGATC
* *
15418 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGTAAAAATCATGA
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTG-CAAAATCATGA
* * *
15483 CAACTTCTGGTGTCAATTGTAAGACC
65 CAACTTCTGGTGTCATTTGCAAGATC
* * * * * * *
15509 ATGACAACTTCTGGTGTCATTTATAAGATTATTGACAACTTCTAGTGTCAATTGTAAGATCATGA
1 ATGACAACTTCTGGTGTCAATTGTAAAATCA-TGACAACTTCTGGTGTCAATTGCAAAATCATGA
* *
15574 CAACTTCTGGTGTCATTTGTAAGATT
65 CAACTTCTGGTGTCATTTGCAAGATC
* * * *
15600 ATTGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCATTTGTAAGACCATGA
1 A-TGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGA
* *
15665 CAACTTCTGGTGTCATTTGTAAGATT
65 CAACTTCTGGTGTCATTTGCAAGATC
* * * * *
15691 ATTGACAACTTCTGGTGCCAATTGTAACACCATTGACAACTTCTAGTGTCAA-TGGAGATTTAAT
1 A-TGACAACTTCTGGTGTCAATTGTAAAATCA-TGACAACTTCTGGTGTCAATTGCA-A---AAT
15755 -ATGACAACTTCTGGTGTCATTTG
60 CATGACAACTTCTGGTGTCATTTG
15778 GAGACTTTGA
Statistics
Matches: 550, Mismatches: 65, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
87 11 0.02
88 17 0.03
90 170 0.31
91 263 0.48
92 65 0.12
94 23 0.04
95 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (90 bp):
ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
AACTTCTGGTGTCATTTGCAAGATC
Found at i:17658 original size:162 final size:161
Alignment explanation
Indices: 17409--17716 Score: 562
Period size: 162 Copynumber: 1.9 Consensus size: 161
17399 TCCTATTATA
* *
17409 TATTGTACATGAAGGTATAGTGGTACCAATTAGAGACATTCGGTGTATTTTGGATAGACGTTTGC
1 TATTATACATGAAGGTATAATGGTACCAATTAGAGACATTCGGTGTATTTTGGATAGACGTTTGC
*
17474 TTTCTCTGATCTTTAAAACCTTAATAAACTTTGCAAATTGGTTTCGACAATGTTTTTCTGAATTT
66 TTTCTCTGATCTTTAAAACCTTAATAAACTTTGCAAATTGGTTTCGACAAAGTTTTTCTGAATTT
17539 TCGAAACCCTAAGATTTAAGTGTTGGTACTCC
131 TCGAAA-CCTAAGATTTAAGTGTTGGTACTCC
17571 TATTATACATGAAGGTATAATGGTACCAATTAGAGACATTCGGTGTATTTTGGATAGACGTTTGC
1 TATTATACATGAAGGTATAATGGTACCAATTAGAGACATTCGGTGTATTTTGGATAGACGTTTGC
* *
17636 TTTCTCTGATTTTTAAAACCTTAATAAACTTTGCAAATTGGTTTTGACAAAGTTTTTCTGAATTT
66 TTTCTCTGATCTTTAAAACCTTAATAAACTTTGCAAATTGGTTTCGACAAAGTTTTTCTGAATTT
17701 TCGAAACCTAAGATTT
131 TCGAAACCTAAGATTT
17717 TCGCATATGA
Statistics
Matches: 141, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
161 10 0.07
162 131 0.93
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (161 bp):
TATTATACATGAAGGTATAATGGTACCAATTAGAGACATTCGGTGTATTTTGGATAGACGTTTGC
TTTCTCTGATCTTTAAAACCTTAATAAACTTTGCAAATTGGTTTCGACAAAGTTTTTCTGAATTT
TCGAAACCTAAGATTTAAGTGTTGGTACTCC
Found at i:25899 original size:8 final size:7
Alignment explanation
Indices: 25870--25928 Score: 66
Period size: 8 Copynumber: 7.9 Consensus size: 7
25860 TATCAGATTT
25870 TATATAA
1 TATATAA
25877 TATATATA
1 TATATA-A
25885 TATTATAA
1 TA-TATAA
25893 GTATATAGA
1 -TATATA-A
25902 TATATAA
1 TATATAA
25909 -ATATAA
1 TATATAA
25915 TATGATAA
1 TAT-ATAA
25923 TATATA
1 TATATA
25929 TTAAAATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.13
7 12 0.26
8 21 0.46
9 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:25929 original size:25 final size:23
Alignment explanation
Indices: 25871--25933 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 23
25861 ATCAGATTTT
*
25871 ATATAATATATATAT-ATTATAA
1 ATATAATATATATATAAATATAA
* *
25893 GTAT-ATAGATATATAAATATAA
1 ATATAATATATATATAAATATAA
25915 TATGATAATATATAT-TAAA
1 -AT-ATAATATATATATAAA
25934 ATTATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 9 0.28
22 9 0.28
23 1 0.03
24 6 0.19
25 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
ATATAATATATATATAAATATAA
Found at i:27103 original size:45 final size:44
Alignment explanation
Indices: 27039--27163 Score: 193
Period size: 41 Copynumber: 2.9 Consensus size: 44
27029 TCACTGATCA
27039 GTTTCAATTATGTTCTGTTTTACTCAATTTCTAATCTGTAAAATT
1 GTTTCAATTATGTTCTGTTTT-CTCAATTTCTAATCTGTAAAATT
*
27084 GTTTCAATTATGTTCTG-TTT-T-AATTTCTAATATGTAAAATT
1 GTTTCAATTATGTTCTGTTTTCTCAATTTCTAATCTGTAAAATT
*
27125 GTTTCAATTATGTTCTGTTTTGCTCAATTTATAATCTGT
1 GTTTCAATTATGTTCTGTTTT-CTCAATTTCTAATCTGT
27164 TTTTAATTAA
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
41 36 0.49
42 4 0.05
44 4 0.05
45 29 0.40
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (44 bp):
GTTTCAATTATGTTCTGTTTTCTCAATTTCTAATCTGTAAAATT
Found at i:27244 original size:21 final size:21
Alignment explanation
Indices: 27198--27255 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
27188 TGGTCTGTTA
27198 CTGTTTTGATCAATTTCTAAT
1 CTGTTTTGATCAATTTCTAAT
* * *
27219 ATGTTTTGATTAGTTTC-AATT
1 CTGTTTTGATCAATTTCTAA-T
* *
27240 CTGTTCTAATCAATTT
1 CTGTTTTGATCAATTT
27256 GGAATTGAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
CTGTTTTGATCAATTTCTAAT
Found at i:29986 original size:13 final size:13
Alignment explanation
Indices: 29968--29993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29958 TTCTGTCTTA
29968 CTGTTTTTGAGTT
1 CTGTTTTTGAGTT
29981 CTGTTTTTGAGTT
1 CTGTTTTTGAGTT
29994 GCTGCTGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (13 bp):
CTGTTTTTGAGTT
Found at i:38995 original size:21 final size:19
Alignment explanation
Indices: 38945--38996 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
38935 ATTAATCAAC
38945 ATTTGGTGTAATGATTCTT
1 ATTTGGTGTAATGATTCTT
* *
38964 -TTTAAGTGTAATGGTATCATT
1 ATTT-GGTGTAATGAT-TC-TT
38985 ATTTGGTGTAAT
1 ATTTGGTGTAAT
38997 AAAAAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 2 0.08
21 9 0.35
22 3 0.12
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.50
Consensus pattern (19 bp):
ATTTGGTGTAATGATTCTT
Found at i:40253 original size:24 final size:24
Alignment explanation
Indices: 40221--40342 Score: 127
Period size: 24 Copynumber: 5.1 Consensus size: 24
40211 TCGAAGCCTT
*
40221 CGCCGGGTGATATCAAAAATTTGA
1 CGCCGGGTGATAGCAAAAATTTGA
* * *
40245 CGCCGGGTGATGGCGAGAATTTGA
1 CGCCGGGTGATAGCAAAAATTTGA
* * *
40269 CACCGGATGATATCAAAAATTTGA
1 CGCCGGGTGATAGCAAAAATTTGA
* * *
40293 CGCCGGGTGATGGCGAGAATTTGA
1 CGCCGGGTGATAGCAAAAATTTGA
* * *
40317 CGCCGGGTGATGGCGAGAATTTGA
1 CGCCGGGTGATAGCAAAAATTTGA
40341 CG
1 CG
40343 GCTTCTGATC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (24 bp):
CGCCGGGTGATAGCAAAAATTTGA
Found at i:40299 original size:48 final size:48
Alignment explanation
Indices: 40223--40327 Score: 192
Period size: 48 Copynumber: 2.2 Consensus size: 48
40213 GAAGCCTTCG
40223 CCGGGTGATATCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACA
1 CCGGGTGATATCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACA
* *
40271 CCGGATGATATCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACG
1 CCGGGTGATATCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACA
40319 CCGGGTGAT
1 CCGGGTGAT
40328 GGCGAGAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (48 bp):
CCGGGTGATATCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACA
Found at i:40338 original size:48 final size:48
Alignment explanation
Indices: 40223--40342 Score: 168
Period size: 48 Copynumber: 2.5 Consensus size: 48
40213 GAAGCCTTCG
* *
40223 CCGGGTGATATCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACA
1 CCGGATGATAGCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACA
* *
40271 CCGGATGATATCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACG
1 CCGGATGATAGCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACA
* * * *
40319 CCGGGTGATGGCGAGAATTTGACG
1 CCGGATGATAGCAAAAATTTGACG
40343 GCTTCTGATC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.23
Consensus pattern (48 bp):
CCGGATGATAGCAAAAATTTGACGCCGGGTGATGGCGAGAATTTGACA
Found at i:40351 original size:24 final size:24
Alignment explanation
Indices: 40238--40342 Score: 129
Period size: 24 Copynumber: 4.4 Consensus size: 24
40228 TGATATCAAA
*
40238 AATTTGACGCCGGGTGATGGCGAG
1 AATTTGACGCCGGCTGATGGCGAG
* * ** * *
40262 AATTTGACACCGGATGATATCAAA
1 AATTTGACGCCGGCTGATGGCGAG
*
40286 AATTTGACGCCGGGTGATGGCGAG
1 AATTTGACGCCGGCTGATGGCGAG
*
40310 AATTTGACGCCGGGTGATGGCGAG
1 AATTTGACGCCGGCTGATGGCGAG
40334 AATTTGACG
1 AATTTGACG
40343 GCTTCTGATC
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (24 bp):
AATTTGACGCCGGCTGATGGCGAG
Found at i:41989 original size:165 final size:165
Alignment explanation
Indices: 41717--42203 Score: 974
Period size: 165 Copynumber: 3.0 Consensus size: 165
41707 CTACTATTAG
41717 TTGCATTCTTGTAGATTTGTTGTATGCCTTTTCACATTTCTATATTCGCTGGTTCAGAAAATTGG
1 TTGCATTCTTGTAGATTTGTTGTATGCCTTTTCACATTTCTATATTCGCTGGTTCAGAAAATTGG
41782 TTTTGCATTCTTGATTCATTCATGGAAGCAGAATATATTAAACTTAAACCAGTTCACACAACAGA
66 TTTTGCATTCTTGATTCATTCATGGAAGCAGAATATATTAAACTTAAACCAGTTCACACAACAGA
41847 CTGGGAATCCTATCCGTTTGTATGTTCACATGGTT
131 CTGGGAATCCTATCCGTTTGTATGTTCACATGGTT
41882 TTGCATTCTTGTAGATTTGTTGTATGCCTTTTCACATTTCTATATTCGCTGGTTCAGAAAATTGG
1 TTGCATTCTTGTAGATTTGTTGTATGCCTTTTCACATTTCTATATTCGCTGGTTCAGAAAATTGG
41947 TTTTGCATTCTTGATTCATTCATGGAAGCAGAATATATTAAACTTAAACCAGTTCACACAACAGA
66 TTTTGCATTCTTGATTCATTCATGGAAGCAGAATATATTAAACTTAAACCAGTTCACACAACAGA
42012 CTGGGAATCCTATCCGTTTGTATGTTCACATGGTT
131 CTGGGAATCCTATCCGTTTGTATGTTCACATGGTT
42047 TTGCATTCTTGTAGATTTGTTGTATGCCTTTTCACATTTCTATATTCGCTGGTTCAGAAAATTGG
1 TTGCATTCTTGTAGATTTGTTGTATGCCTTTTCACATTTCTATATTCGCTGGTTCAGAAAATTGG
42112 TTTTGCATTCTTGATTCATTCATGGAAGCAGAATATATTAAACTTAAACCAGTTCACACAACAGA
66 TTTTGCATTCTTGATTCATTCATGGAAGCAGAATATATTAAACTTAAACCAGTTCACACAACAGA
42177 CTGGGAATCCTATCCGTTTGTATGTTC
131 CTGGGAATCCTATCCGTTTGTATGTTC
42204 GACCCATCCT
Statistics
Matches: 322, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 322 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (165 bp):
TTGCATTCTTGTAGATTTGTTGTATGCCTTTTCACATTTCTATATTCGCTGGTTCAGAAAATTGG
TTTTGCATTCTTGATTCATTCATGGAAGCAGAATATATTAAACTTAAACCAGTTCACACAACAGA
CTGGGAATCCTATCCGTTTGTATGTTCACATGGTT
Found at i:50041 original size:6 final size:6
Alignment explanation
Indices: 50030--50055 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
50020 CAGTATATTA
50030 AGAAAG AGAAAG AGAAAG AGAAAG AG
1 AGAAAG AGAAAG AGAAAG AGAAAG AG
50056 TGGCAACGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:50104 original size:6 final size:6
Alignment explanation
Indices: 50085--50125 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
50075 CTCTCAAAGG
* *
50085 GGAAGA GGACGA GGAAGA GGAAGA GGAAGA TGAAGA GGAAG
1 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAG
50126 TGAAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.46, C:0.02, G:0.49, T:0.02
Consensus pattern (6 bp):
GGAAGA
Found at i:50269 original size:27 final size:29
Alignment explanation
Indices: 50226--50318 Score: 105
Period size: 32 Copynumber: 3.0 Consensus size: 29
50216 AGCCATATGA
*
50226 CCAGGTATAAAATATATTAATTTATGTTT
1 CCAGATATAAAATATATTAATTTATGTTT
50255 CCAGATATAAAATATTTTATTAATTTATGTTT
1 CCAGATATAAAATA---TATTAATTTATGTTT
* *
50287 CCAGGTATAAGATATTTTATTAATTTATGTTT
1 CCAGATATAA-A-A-TATATTAATTTATGTTT
50319 ATGTTTTTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
29 13 0.24
32 39 0.71
33 1 0.02
34 1 0.02
35 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (29 bp):
CCAGATATAAAATATATTAATTTATGTTT
Found at i:50281 original size:32 final size:32
Alignment explanation
Indices: 50240--50318 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
50230 GTATAAAATA
50240 TATTAATTTATGTTTCCAGATATAAAATATTT
1 TATTAATTTATGTTTCCAGATATAAAATATTT
* *
50272 TATTAATTTATGTTTCCAGGTATAAGATATTT
1 TATTAATTTATGTTTCCAGATATAAAATATTT
50304 TATTAATTTATGTTT
1 TATTAATTTATGTTT
50319 ATGTTTTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (32 bp):
TATTAATTTATGTTTCCAGATATAAAATATTT
Found at i:50643 original size:19 final size:19
Alignment explanation
Indices: 50621--50660 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
50611 TCATGTTCTT
50621 TTTCTATTTCCTCTATGAG
1 TTTCTATTTCCTCTATGAG
50640 TTTCTATTTCCTCTATGAG
1 TTTCTATTTCCTCTATGAG
50659 TT
1 TT
50661 AGTTGCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.55
Consensus pattern (19 bp):
TTTCTATTTCCTCTATGAG
Found at i:56837 original size:27 final size:28
Alignment explanation
Indices: 56782--56837 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
56772 TCTCGTTTTT
*
56782 AAAAGTTAAGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGCCAATTTATCCCAAAA
*
56810 AAAATTTAAGGGCCAATTTATCCCAAAA
1 AAAAGTTAAGGGCCAATTTATCCCAAAA
56838 TGGATAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (28 bp):
AAAAGTTAAGGGCCAATTTATCCCAAAA
Found at i:58115 original size:13 final size:13
Alignment explanation
Indices: 58094--58125 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
58084 TTTGCAATTG
*
58094 TCTTTTTTTAAAA
1 TCTTGTTTTAAAA
58107 TCTTGTTTTAAAA
1 TCTTGTTTTAAAA
58120 TCTTGT
1 TCTTGT
58126 CTTTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.59
Consensus pattern (13 bp):
TCTTGTTTTAAAA
Done.