Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012189.1 Corchorus capsularis cultivar CVL-1 contig12210, 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: 57444
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1023 original size:22 final size:22
Alignment explanation
Indices: 995--1096 Score: 93
Period size: 22 Copynumber: 4.7 Consensus size: 22
985 CACATTTGAT
* *
995 TGAAGTTTTGATAGTC-TCCCTA
1 TGAAGTTTTGATA-ACATCACTA
1017 TGAAGTTTTGATAACATCACTA
1 TGAAGTTTTGATAACATCACTA
* * *
1039 TGAAATTTTGATAACTTCCCTA
1 TGAAGTTTTGATAACATCACTA
* *
1061 T-AAATTTTGGTAACCA-CACTA
1 TGAAGTTTTGATAA-CATCACTA
*
1082 TGAAATTTTGATAAC
1 TGAAGTTTTGATAAC
1097 CTCGCCATGA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
21 18 0.26
22 50 0.74
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
TGAAGTTTTGATAACATCACTA
Found at i:1083 original size:43 final size:44
Alignment explanation
Indices: 1011--1109 Score: 132
Period size: 43 Copynumber: 2.3 Consensus size: 44
1001 TTTGATAGTC
*
1011 TCCCTATGAAGTTTTGATAACATCACTATGAAATTTTGATAACT
1 TCCCTATGAAATTTTGATAACATCACTATGAAATTTTGATAACT
* *
1055 TCCCTAT-AAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
1 TCCCTATGAAATTTTGATAA-CATCACTATGAAATTTTGATAACT
1098 TCGCC-ATGAAAT
1 TC-CCTATGAAAT
1110 GTTAGTAACT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
43 34 0.69
44 15 0.31
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (44 bp):
TCCCTATGAAATTTTGATAACATCACTATGAAATTTTGATAACT
Found at i:1097 original size:22 final size:22
Alignment explanation
Indices: 1014--1097 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
1004 GATAGTCTCC
*
1014 CTATGAAGTTTTGATAA-CATCA
1 CTATGAAATTTTGATAACCA-CA
** *
1036 CTATGAAATTTTGATAACTTCC
1 CTATGAAATTTTGATAACCACA
*
1058 CTAT-AAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
1079 CTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAACC
1098 TCGCCATGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
21 17 0.33
22 34 0.67
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:1106 original size:22 final size:22
Alignment explanation
Indices: 1016--1109 Score: 93
Period size: 22 Copynumber: 4.3 Consensus size: 22
1006 TAGTCTCCCT
* * *
1016 ATGAAGTTTTGATAACATCACT
1 ATGAAATTTTGATAACCTCACC
*
1038 ATGAAATTTTGATAACTTC-CC
1 ATGAAATTTTGATAACCTCACC
* * *
1059 TAT-AAATTTTGGTAACCACACT
1 -ATGAAATTTTGATAACCTCACC
*
1081 ATGAAATTTTGATAACCTCGCC
1 ATGAAATTTTGATAACCTCACC
1103 ATGAAAT
1 ATGAAAT
1110 GTTAGTAACT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 16 0.28
22 42 0.72
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCACC
Found at i:3011 original size:22 final size:22
Alignment explanation
Indices: 2986--3074 Score: 90
Period size: 22 Copynumber: 4.0 Consensus size: 22
2976 GATGATCTCA
*
2986 CTATAAAATTTTGATAGCCTCG
1 CTATAAAATTTTGATAACCTCG
*
3008 CTATGAAATTTTGATAAACCTC-
1 CTATAAAATTTTGAT-AACCTCG
* **
3030 CTAATAAAATTTTGATATCCTAT
1 CT-ATAAAATTTTGATAACCTCG
* *
3053 CCATAAAAGTTTGATAACCTCG
1 CTATAAAATTTTGATAACCTCG
3075 TTAAGAAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 36 0.67
23 18 0.33
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
CTATAAAATTTTGATAACCTCG
Found at i:3039 original size:23 final size:23
Alignment explanation
Indices: 2986--3046 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2976 GATGATCTCA
*
2986 CTATAAAATTTTGAT-AGCCTCG
1 CTATAAAATTTTGATAAACCTCG
*
3008 CTATGAAATTTTGATAAACCTC-
1 CTATAAAATTTTGATAAACCTCG
3030 CTAATAAAATTTTGATA
1 CT-ATAAAATTTTGATA
3047 TCCTATCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCG
Found at i:3066 original size:45 final size:44
Alignment explanation
Indices: 2988--3073 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
2978 TGATCTCACT
* * * *
2988 ATAAAATTTTGATAGCCTCGCTATGAAATTTTGATAAACCTCCTA
1 ATAAAATTTTGATAGCCTAGCCATAAAAGTTTGAT-AACCTCCTA
* *
3033 ATAAAATTTTGATATCCTATCCATAAAAGTTTGATAACCTC
1 ATAAAATTTTGATAGCCTAGCCATAAAAGTTTGATAACCTC
3074 GTTAAGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
44 6 0.17
45 29 0.83
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (44 bp):
ATAAAATTTTGATAGCCTAGCCATAAAAGTTTGATAACCTCCTA
Found at i:3084 original size:45 final size:45
Alignment explanation
Indices: 2990--3094 Score: 106
Period size: 45 Copynumber: 2.4 Consensus size: 45
2980 ATCTCACTAT
* * * * *
2990 AAAATTTTGATAGCCTCGCTATGAAATTTTGATAAACCTCCTAAT
1 AAAATTTTGATAGCCTAGCCATAAAAGTTTGATAAACCTCCTAAG
* * *
3035 AAAATTTTGATATCCTATCCATAAAAGTTTGAT-AACCTCGTTAAG
1 AAAATTTTGATAGCCTAGCCATAAAAGTTTGATAAACCTC-CTAAG
*
3080 AAAA-TTTGTTAGCCT
1 AAAATTTTGATAGCCT
3095 CTCTATCATG
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
44 15 0.31
45 34 0.69
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (45 bp):
AAAATTTTGATAGCCTAGCCATAAAAGTTTGATAAACCTCCTAAG
Found at i:3657 original size:43 final size:44
Alignment explanation
Indices: 3599--3702 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
3589 GTTAACTTCC
* * * * * * *
3599 CTATGAAATTTTGATAATATTCC-ATGGAATTGTGATAATTACA
1 CTATAAAATTTTGATAAGATCCCTACGAAATTCTGATAATGACA
* *
3642 CTATAAAATTGTGATAAGATCCCTACGAAATTCTGGTAATGACA
1 CTATAAAATTTTGATAAGATCCCTACGAAATTCTGATAATGACA
3686 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
3703 CAACACAATA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 19 0.38
44 31 0.62
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (44 bp):
CTATAAAATTTTGATAAGATCCCTACGAAATTCTGATAATGACA
Found at i:3717 original size:23 final size:22
Alignment explanation
Indices: 3533--3748 Score: 78
Period size: 22 Copynumber: 9.8 Consensus size: 22
3523 AGAATGCTCT
* *
3533 CTATAAAATTTTGACAATATAC-
1 CTATAAAATTTTGATAACA-ACA
* ** *
3555 CTATAAAATTTTAATAACCTCT
1 CTATAAAATTTTGATAACAACA
* * ** *
3577 TTATAAAATTTTGTTAACTTCC
1 CTATAAAATTTTGATAACAACA
* * *
3599 CTATGAAATTTTGATAATATTC-
1 CTATAAAATTTTGATAACA-ACA
** * **
3621 C-ATGGAATTGTGATAATTACA
1 CTATAAAATTTTGATAACAACA
* * * *
3642 CTATAAAATTGTGATAAGATCC
1 CTATAAAATTTTGATAACAACA
** * * **
3664 CTACGAAATTCTGGTAATGACA
1 CTATAAAATTTTGATAACAACA
3686 CTATAAAATTTTGATAACAACA
1 CTATAAAATTTTGATAACAACA
* * *
3708 CAATACAAATTTTGGTAACTACA
1 CTATA-AAATTTTGATAACAACA
**
3731 CTATGGAATTTTGATAAC
1 CTATAAAATTTTGATAAC
3749 CTTCTTATGA
Statistics
Matches: 143, Mismatches: 46, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
20 1 0.01
21 16 0.11
22 106 0.74
23 20 0.14
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (22 bp):
CTATAAAATTTTGATAACAACA
Found at i:3733 original size:45 final size:43
Alignment explanation
Indices: 3638--3792 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 43
3628 TTGTGATAAT
* * * *
3638 TACACTATAAAATTGTGATAAGATCCCTACGAAATTCTGGTAA
1 TACACTATAAAATTTTGATAACAACCATACGAAATTCTGGTAA
*
3681 TGACACTATAAAATTTTGATAACAACACAATAC-AAATTTTGGTAA
1 T-ACACTATAAAATTTTGATAACAAC-C-ATACGAAATTCTGGTAA
** *** * * *
3726 CTACACTATGGAATTTTGATAACCTTCTTATGAAATTTTGGTAA
1 -TACACTATAAAATTTTGATAACAACCATACGAAATTCTGGTAA
**
3770 TCACACTATGGAATTTTGATAAC
1 T-ACACTATAAAATTTTGATAAC
3793 TACACACACT
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
43 4 0.04
44 55 0.59
45 31 0.33
46 4 0.04
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (43 bp):
TACACTATAAAATTTTGATAACAACCATACGAAATTCTGGTAA
Found at i:3757 original size:22 final size:21
Alignment explanation
Indices: 3683--3797 Score: 79
Period size: 22 Copynumber: 5.2 Consensus size: 21
3673 TCTGGTAATG
**
3683 ACACTATAAAATTTTGATAAC
1 ACACTATGGAATTTTGATAAC
* ** *
3704 AACACAATACAAATTTTGGTAAC
1 -ACACTAT-GGAATTTTGATAAC
3727 TACACTATGGAATTTTGATAAC
1 -ACACTATGGAATTTTGATAAC
* * *
3749 -CTTCTTATGAAATTTTGGTAATC
1 AC-AC-TATGGAATTTTGATAA-C
3772 ACACTATGGAATTTTGATAAC
1 ACACTATGGAATTTTGATAAC
3793 TACAC
1 -ACAC
3798 ACACTATGAT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.01
21 2 0.03
22 49 0.67
23 20 0.27
24 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (21 bp):
ACACTATGGAATTTTGATAAC
Found at i:8115 original size:17 final size:16
Alignment explanation
Indices: 8093--8129 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
8083 TTAATTAAGA
*
8093 AAATTCATAGATATTAT
1 AAATTCATAAATA-TAT
8110 AAATTCATAAATATAT
1 AAATTCATAAATATAT
8126 AAAT
1 AAAT
8130 AATAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATTCATAAATATAT
Found at i:8966 original size:2 final size:2
Alignment explanation
Indices: 8959--8991 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8949 AGAGTAGCGA
8959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8992 GACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13268 original size:106 final size:104
Alignment explanation
Indices: 13072--13275 Score: 236
Period size: 106 Copynumber: 1.9 Consensus size: 104
13062 ATATTTTAAT
13072 AAATTGTTTATAATATTTTCTAAAACCCTATGAGATAGAGTATCAAAATTTAAAATTTACCCTTT
1 AAATTGTTTATAATATTTTCTAAAACCCTA-GAGATAGAGTATCAAAATTTAAAATTTACCCTTT
** *
13137 AAAAAATTATAACCTTTCTAGTTGGGGCTAAACCTTATTA
65 AAAAAATTATAAAATTTCTAGTTGGGACTAAACCTTATTA
* * * *
13177 AAATTGTTTATAATTTTTTTCTAAAACCCTA-AGATAATGGGTCTCAAAATTTAAGATTTACCC-
1 AAATTGTTTATAA-TATTTTCTAAAACCCTAGAGAT-A-GAGTATCAAAATTTAAAATTTACCCT
* *
13240 TT-AAAATTTGGGATAAAATTT-TATTTGGGACTAAAC
63 TTAAAAAATT---ATAAAATTTCTAGTTGGGACTAAAC
13276 TTGGTGAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
104 10 0.12
105 16 0.19
106 51 0.61
107 7 0.08
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (104 bp):
AAATTGTTTATAATATTTTCTAAAACCCTAGAGATAGAGTATCAAAATTTAAAATTTACCCTTTA
AAAAATTATAAAATTTCTAGTTGGGACTAAACCTTATTA
Found at i:18009 original size:2 final size:2
Alignment explanation
Indices: 18002--18034 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17992 GTAAAACTAG
18002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18035 GGTCTCAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18947 original size:133 final size:134
Alignment explanation
Indices: 18708--19075 Score: 361
Period size: 133 Copynumber: 2.6 Consensus size: 134
18698 TTTCATGAAT
** * *
18708 TTGATTGATTGCTCTTGGCTTGATATTCTTTCCCTATG-GCTTGATAAGCTTGTTATCAAAAGCT
1 TTGATTGATT-CTCTTGGCTTGATAAGCTTT-CCTATGATCTTAATAAGCTTGTTATCAAAAGCT
* * * *
18772 CTTTCCTTTACCAAATTGATTAATGAAGGTCTTAATAAGCTTGTTAGC-G-AAAGCTCTTTCCTT
64 CTTTCCTTTAGCAAATTGATTAATCAAGCTCTTAATAAGCTTG-AAGCTGTAAAGCTCTTTCCTT
18835 TAGCAAA
128 TAGCAAA
* *
18842 TTGATTGATTCCTCTTGCCTTGATAAGCTTTCCTA-GATCTTAATAAGCTTGTTATTAAAAGCTC
1 TTGATTGATT-CTCTTGGCTTGATAAGCTTTCCTATGATCTTAATAAGCTTGTTATCAAAAGCTC
* *
18906 TTTCCTTTAGCAAATTGATTAATTACAAGCT-TTGAT-TGCTTGAAGCTTGTTATTAAAAGCTCT
65 TTTCCTTTAGCAAATTGATTAA-T-CAAGCTCTTAATAAGCTTGAAGC-TG----T-AAAGCTCT
18969 TTCCTTTAGCAAA
122 TTCCTTTAGCAAA
* *
18982 TTGATTGAATTCTCTTGGCTTTATAAGATTTCCTAGATAGAATGATGGCTTAATAAGCTTGTTAT
1 TTGATTG-ATTCTCTTGGCTTGATAAGCTTTCC----T---ATGAT--CTTAATAAGCTTGTTAT
*
19047 CAAAAGTTCTTTCCTTTAGCAAATTGATT
56 CAAAAGCTCTTTCCTTTAGCAAATTGATT
19076 GATTGCTCTT
Statistics
Matches: 194, Mismatches: 18, Indels: 28
0.81 0.08 0.12
Matches are distributed among these distances:
132 4 0.02
133 54 0.28
134 33 0.17
135 4 0.02
140 47 0.24
141 3 0.02
144 1 0.01
147 1 0.01
148 3 0.02
150 44 0.23
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (134 bp):
TTGATTGATTCTCTTGGCTTGATAAGCTTTCCTATGATCTTAATAAGCTTGTTATCAAAAGCTCT
TTCCTTTAGCAAATTGATTAATCAAGCTCTTAATAAGCTTGAAGCTGTAAAGCTCTTTCCTTTAG
CAAA
Found at i:19008 original size:140 final size:134
Alignment explanation
Indices: 18708--19075 Score: 384
Period size: 140 Copynumber: 2.6 Consensus size: 134
18698 TTTCATGAAT
* ** * *
18708 TTGATTGATTGCTCTTGGCTTGATATTCTTTCCCTATG-GCTTGATAAGCTTGTTATCAAAAGCT
1 TTGATTGATTCCTCTTGGCTTGATAAGCTTT-CCTATGATCTTAATAAGCTTGTTATCAAAAGCT
* * * *
18772 CTTTCCTTTACCAAATTGATTAATGAAGGTCTTAATAAGCTTGTTAGCGAAAGCTCTTTCCTTTA
65 CTTTCCTTTAGCAAATTGATTAATCAAGCTCTTAATAAGCTTGTTAGCAAAAGCTCTTTCCTTTA
18837 GCAAA
130 GCAAA
* *
18842 TTGATTGATTCCTCTTGCCTTGATAAGCTTTCCTA-GATCTTAATAAGCTTGTTATTAAAAGCTC
1 TTGATTGATTCCTCTTGGCTTGATAAGCTTTCCTATGATCTTAATAAGCTTGTTATCAAAAGCTC
* **
18906 TTTCCTTTAGCAAATTGATTAATTACAAGCT-TTGATTGCTTGAAGCTTGTTATTAAAAGCTCTT
66 TTTCCTTTAGCAAATTGATTAA-T-CAAGCTCTT-A----AT-AAGCTTGTTAGCAAAAGCTCTT
18970 TCCTTTAGCAAA
123 TCCTTTAGCAAA
* *
18982 TTGATTGAATT-CTCTTGGCTTTATAAGATTTCCTAGATAGAATGATGGCTTAATAAGCTTGTTA
1 TTGATTG-ATTCCTCTTGGCTTGATAAGCTTTCC----T---ATGAT--CTTAATAAGCTTGTTA
*
19046 TCAAAAGTTCTTTCCTTTAGCAAATTGATT
56 TCAAAAGCTCTTTCCTTTAGCAAATTGATT
19076 GATTGCTCTT
Statistics
Matches: 195, Mismatches: 19, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
132 1 0.01
133 49 0.25
134 30 0.15
135 5 0.03
139 1 0.01
140 57 0.29
141 3 0.02
144 1 0.01
147 1 0.01
148 3 0.02
150 44 0.23
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (134 bp):
TTGATTGATTCCTCTTGGCTTGATAAGCTTTCCTATGATCTTAATAAGCTTGTTATCAAAAGCTC
TTTCCTTTAGCAAATTGATTAATCAAGCTCTTAATAAGCTTGTTAGCAAAAGCTCTTTCCTTTAG
CAAA
Found at i:23852 original size:2 final size:2
Alignment explanation
Indices: 23845--23883 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
23835 ATTCGTACTT
23845 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
23884 GATAAGTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24069 original size:31 final size:32
Alignment explanation
Indices: 24025--24086 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
24015 AAATAATAAC
24025 AATTATTTTTACGTTAAACATCTTATAATTAT
1 AATTATTTTTACGTTAAACATCTTATAATTAT
*
24057 AATTA-TTTTACGTTAAACATCTTATTATTA
1 AATTATTTTTACGTTAAACATCTTATAATTA
24087 CGTTAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (32 bp):
AATTATTTTTACGTTAAACATCTTATAATTAT
Found at i:27981 original size:94 final size:93
Alignment explanation
Indices: 27878--28048 Score: 297
Period size: 94 Copynumber: 1.8 Consensus size: 93
27868 AGTTAAATTA
*
27878 GTAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTT
1 GTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAAT-AAAAATAGAGTTTT
*
27943 TAGTTGAGTAAAACTATAAAAGTAAAATG
65 TAGTTGAATAAAACTATAAAAGTAAAATG
* *
27972 GTAAAATGGTAAAAATAAAATAGTTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 GTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
28037 AGTTGAATAAAA
66 AGTTGAATAAAA
28049 GTTTAAACAA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 26 0.36
94 47 0.64
ACGTcount: A:0.51, C:0.01, G:0.15, T:0.33
Consensus pattern (93 bp):
GTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTGAATAAAACTATAAAAGTAAAATG
Found at i:29897 original size:894 final size:895
Alignment explanation
Indices: 28223--29975 Score: 2996
Period size: 894 Copynumber: 1.9 Consensus size: 895
28213 ATTTCATCAA
28223 AAATGAATGCTATCAAATTTATAATACATAGTTACCAAAAAAGCTATATAGTTATGAAAAATGCT
1 AAATGAATGCTATCAAATTTATAATACATAGTTACCAAAAAAGCTATATAGTTATGAAAAATGCT
* *
28288 TGACACCAACAAATCCAATAATTAATGATAAGTAATTTTGGTAACAATTTAATCAATAAATGAGG
66 TGACACCAACAAATCCAATAATTAATGATAAGTAATTTTAGTAACAATTTAATCAATAAATGAGA
* * *
28353 TTATCAAATTTACAATACTTAAGTTACTTAAAAAGCTATAATAGTTATTAAAAAAAGTTTTATAT
131 CTATCAAATTTACAATACTTAAGTTACTTAAAAAGCTATAACAATTATTAAAAAAAGTTTTATAT
28418 GTATCAACAAATTTAAAACCATTCATATCATTTGTCAAATTATTCCGAAAAAACGACATTTGAGC
196 GTATCAACAAATTTAAAACCATTCATATCATTTGTCAAATTATTCCGAAAAAACGACATTTGAGC
*
28483 GTTGGTTTCAAAAAAAAGAAAAAGAGGCATTTGAAATGAGAGTTTTCTCAAGAACAATGTTTTGT
261 GTTGGTTT---AAAAAAGAAAAAGAGACATTTGAAATGAGAGTTTTCTCAAGAACAATGTTTTGT
*
28548 GTGAAAACAAAGAAAATCGTGAAGTTGATGATTTTGTCTTCTTTAAAAAAATTATTTGGTAAGTC
323 GTGAAAACAAAGAAAATCGTGAAGTTGATG----TGTCTTCTTAAAAAAAATTATTTGGTAAGTC
*
28613 TAGTTTCCAATAAGCTCTACTCAGTTCGAGACACAACATTTGAGAGTTGTATTTGTTCGCAAAAC
384 TAGTTTCCAATAAACTCTACTCAGTTCGAGACACAACATTTGAGAGTTGTATTTGTTCGCAAAAC
* *
28678 CATGAAGTTGAGGTTTTAGGTTTTTAAAAAACTCTTTGTTTGGCGAGTCAATTTTCCAATAAGTT
449 CATGAAGTTGAGGTTTTAGGTTTTTAAAAAAATCTTTGTTTGGCGAGTCAATTTTCCAATAAGCT
*
28743 CTACTGACTTCAATACATGACATTAGAGCGTTGGTTTCAAAAAAAAAAAAAGAAAGAAATTATTC
514 CTACTGACTTCAATACATGACATTAGAGCGTTGGTTTC--AAAAAAAAAAAGAAAGAAATCATTC
* *
28808 TGATCATTTTCAAATAAATAATGTTTTGTGTAAAAGCGCACAAAATTGTGAAGTTGAGGTTTTAG
577 TGATCATTTTCAAATAAATAATGTTTCGTGTAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAG
* *
28873 GCCTTGAAGAAAACTTTGTTTGGCAAGTCACTTTCTAATAAGCTCTACTAATTAAGTACGAAACA
642 GCCTTGAAGAAAACTTTGTTTGGCAAGTCACTTTCCAATAAGCTCTACTAATTAACTACGAAACA
28938 TGACATAGGAACGATAGTTACACAAATAATGCATTTGGAATTAACATTTTCTCAAGAACAACGTT
707 TGACATAGGAACGATAGTTACACAAATAATGCATTTGGAATTAACATTTTCTCAAGAACAACGTT
*
29003 CTGCGCACAAACACACAAAATCGTAAAGTTCAAGTTTTAAATTTGAATATTTTTTTTTTTGGCAA
772 CTGCGCACAAACACACAAAATCGTAAAGTTCAAGTTTTAAATTTGAATAATTTTTTTTTTGGCAA
29068 ACCCACTTTCCAATAACTAATTATAAGTATTTTGGTATACTAATGGTTACACTAATGAT
837 ACCCACTTTCCAATAACTAATTATAAGTATTTTGGTATACTAATGGTTACACTAATGAT
*
29127 AAATGGATGCTATCAAATTTATAATACATAGTTACCAAAAAAGCTATATAGTTATGAAAAATGCT
1 AAATGAATGCTATCAAATTTATAATACATAGTTACCAAAAAAGCTATATAGTTATGAAAAATGCT
29192 TGACACCAACAAATCCAATAATTAATGATAAGTAATTTTAGTAACAATTTAATCAATAAATGAGA
66 TGACACCAACAAATCCAATAATTAATGATAAGTAATTTTAGTAACAATTTAATCAATAAATGAGA
29257 CTATCAAATTTACAATACTTTAATTTAGTTACTTAAAAAGCTATAACAATTATTAAAAAAAGTTT
131 CTATCAAATTTACAATAC-TT-A---AGTTACTTAAAAAGCTATAACAATTATTAAAAAAAGTTT
*
29322 TATATGTATCAACAAATTTAAAATCATTCATATCATTTGTCAAATTATTCCGAAAAAACGACATT
191 TATATGTATCAACAAATTTAAAACCATTCATATCATTTGTCAAATTATTCCGAAAAAACGACATT
* * * * *
29387 TGAGTGTTGGTTT-AAAAA-AAAATGAGATATTTGAAATGAGCGTTTTCTTAAGAACAATGTTTT
256 TGAGCGTTGGTTTAAAAAAGAAAAAGAGACATTTGAAATGAGAGTTTTCTCAAGAACAATGTTTT
** *
29450 GTGTGAAAACGCAGAAAATCGTGAAGTTGATG-GTCTTCTTAAAAAAAATTATTTGGTAATTCTA
321 GTGTGAAAACAAAGAAAATCGTGAAGTTGATGTGTCTTCTTAAAAAAAATTATTTGGTAAGTCTA
* *
29514 GTTTCCAATAAACTCTACTCAGTTTGAGACACAACATTTGAGAGTTGTATTTGTTTGCAAAACCA
386 GTTTCCAATAAACTCTACTCAGTTCGAGACACAACATTTGAGAGTTGTATTTGTTCGCAAAACCA
29579 TGAAGTTGAGGTTTTAGGTTTTTAAAAAAATCTTTGTTTGGCGAGTCAA-TTTCCAATAAGCTCT
451 TGAAGTTGAGGTTTTAGGTTTTTAAAAAAATCTTTGTTTGGCGAGTCAATTTTCCAATAAGCTCT
*
29643 ACTGACTTCAATACATGACATTAGAGCGTTGGTTTC-AAAAAAAGAA-AAAGAAATCATTCTGAT
516 ACTGACTTCAATACATGACATTAGAGCGTTGGTTTCAAAAAAAAAAAGAAAGAAATCATTCTGAT
29706 CATTTTCAAATAAATAATGTTTCGTGTAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAGGCCT
581 CATTTTCAAATAAATAATGTTTCGTGTAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAGGCCT
* *
29771 TGCAGAAAACTTTGTTTGGCAAGTCACTTTCCAATAAGCTCTACTAATTAACTCCGAAACATGAC
646 TGAAGAAAACTTTGTTTGGCAAGTCACTTTCCAATAAGCTCTACTAATTAACTACGAAACATGAC
* * * *
29836 ATATGAACGATGGTTACACAAATAATGTATTTGGAATTAACATTTTCTCAAGAATAACGTTCTGC
711 ATAGGAACGATAGTTACACAAATAATGCATTTGGAATTAACATTTTCTCAAGAACAACGTTCTGC
* * *
29901 GCACAAACACACTAAATCGTAAAGTTCAAGTTTTAAGTTTGAATAATTTTTTTTTTGGTAAACCC
776 GCACAAACACACAAAATCGTAAAGTTCAAGTTTTAAATTTGAATAATTTTTTTTTTGGCAAACCC
29966 ACTTTCCAAT
841 ACTTTCCAAT
29976 TAGCTTACTC
Statistics
Matches: 806, Mismatches: 38, Indels: 20
0.93 0.04 0.02
Matches are distributed among these distances:
894 272 0.34
895 9 0.01
898 50 0.06
899 140 0.17
904 214 0.27
905 7 0.01
906 1 0.00
909 113 0.14
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (895 bp):
AAATGAATGCTATCAAATTTATAATACATAGTTACCAAAAAAGCTATATAGTTATGAAAAATGCT
TGACACCAACAAATCCAATAATTAATGATAAGTAATTTTAGTAACAATTTAATCAATAAATGAGA
CTATCAAATTTACAATACTTAAGTTACTTAAAAAGCTATAACAATTATTAAAAAAAGTTTTATAT
GTATCAACAAATTTAAAACCATTCATATCATTTGTCAAATTATTCCGAAAAAACGACATTTGAGC
GTTGGTTTAAAAAAGAAAAAGAGACATTTGAAATGAGAGTTTTCTCAAGAACAATGTTTTGTGTG
AAAACAAAGAAAATCGTGAAGTTGATGTGTCTTCTTAAAAAAAATTATTTGGTAAGTCTAGTTTC
CAATAAACTCTACTCAGTTCGAGACACAACATTTGAGAGTTGTATTTGTTCGCAAAACCATGAAG
TTGAGGTTTTAGGTTTTTAAAAAAATCTTTGTTTGGCGAGTCAATTTTCCAATAAGCTCTACTGA
CTTCAATACATGACATTAGAGCGTTGGTTTCAAAAAAAAAAAGAAAGAAATCATTCTGATCATTT
TCAAATAAATAATGTTTCGTGTAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAGGCCTTGAAG
AAAACTTTGTTTGGCAAGTCACTTTCCAATAAGCTCTACTAATTAACTACGAAACATGACATAGG
AACGATAGTTACACAAATAATGCATTTGGAATTAACATTTTCTCAAGAACAACGTTCTGCGCACA
AACACACAAAATCGTAAAGTTCAAGTTTTAAATTTGAATAATTTTTTTTTTGGCAAACCCACTTT
CCAATAACTAATTATAAGTATTTTGGTATACTAATGGTTACACTAATGAT
Found at i:30816 original size:22 final size:22
Alignment explanation
Indices: 30785--30884 Score: 94
Period size: 22 Copynumber: 4.6 Consensus size: 22
30775 CTCCAATGTA
* *
30785 GAAATATTGATAACCACATTTT
1 GAAATTTTGATAACCACATTAT
* *
30807 GAAATTTTGATAACCTCGTTAT
1 GAAATTTTGATAACCACATTAT
* *
30829 GAAA-ATTGATAACCACACTAT
1 GAAATTTTGATAACCACATTAT
* * * * *
30850 GAAATTTCGATAATCTCAATGT
1 GAAATTTTGATAACCACATTAT
30872 GAAATTTTGATAA
1 GAAATTTTGATAA
30885 TCTGCCTATA
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 17 0.27
22 45 0.73
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (22 bp):
GAAATTTTGATAACCACATTAT
Found at i:30875 original size:43 final size:44
Alignment explanation
Indices: 30778--30884 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 44
30768 TTTCATGCTC
* * *
30778 CAATGTAGAAATATTGATAACCACATTTTGAAATTTTGATAACCT
1 CAATGT-GAAATATTGATAACCACACTATGAAATTTCGATAACCT
** * *
30823 CGTTATGAAA-ATTGATAACCACACTATGAAATTTCGATAATCT
1 CAATGTGAAATATTGATAACCACACTATGAAATTTCGATAACCT
*
30866 CAATGTGAAATTTTGATAA
1 CAATGTGAAATATTGATAA
30885 TCTGCCTATA
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
43 36 0.72
44 11 0.22
45 3 0.06
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (44 bp):
CAATGTGAAATATTGATAACCACACTATGAAATTTCGATAACCT
Found at i:31084 original size:22 final size:21
Alignment explanation
Indices: 31054--31138 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 21
31044 AACCTCCCTC
*
31054 TCTATGAAATTTTGTTAACTT
1 TCTATGAAATTTTGGTAACTT
**
31075 TCGTATGAAATTTTATTAACTT
1 TC-TATGAAATTTTGGTAACTT
*
31097 TCCTAAGAAATTTTGGTAACCTAT
1 T-CTATGAAATTTTGGTAA-CT-T
31121 T-TATGAAATTTTGGTAAC
1 TCTATGAAATTTTGGTAAC
31139 CACACTATGG
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
21 3 0.05
22 47 0.85
23 3 0.05
24 2 0.04
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.46
Consensus pattern (21 bp):
TCTATGAAATTTTGGTAACTT
Found at i:31147 original size:22 final size:22
Alignment explanation
Indices: 31103--31155 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
31093 ACTTTCCTAA
**
31103 GAAATTTTGGTAACCTATTTAT
1 GAAATTTTGGTAACCTAACTAT
31125 GAAATTTTGGTAACC-ACACTAT
1 GAAATTTTGGTAACCTA-ACTAT
*
31147 GGAATTTTG
1 GAAATTTTG
31156 ATAATATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (22 bp):
GAAATTTTGGTAACCTAACTAT
Found at i:31969 original size:109 final size:109
Alignment explanation
Indices: 31773--32068 Score: 432
Period size: 109 Copynumber: 2.7 Consensus size: 109
31763 ACTATTATAG
* *
31773 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
31838 TCTTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
31887 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
31952 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
* * **
31996 CTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
32060 TTTTTACCA
63 TTTTTACCA
32069 TTTTAATTTA
Statistics
Matches: 170, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
108 1 0.01
109 123 0.72
110 8 0.05
111 17 0.10
114 21 0.12
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
Found at i:32154 original size:26 final size:26
Alignment explanation
Indices: 32118--32167 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
32108 TGATAGTTCA
32118 ATGTATTATGATTAAAATTTGTTAGG
1 ATGTATTATGATTAAAATTTGTTAGG
32144 ATGTATTATGATTAAAATTTGTTA
1 ATGTATTATGATTAAAATTTGTTA
32168 TTTTCCTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (26 bp):
ATGTATTATGATTAAAATTTGTTAGG
Found at i:40225 original size:13 final size:13
Alignment explanation
Indices: 40207--40233 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40197 TTGGGAGTGG
40207 ATTTGATGAAGTT
1 ATTTGATGAAGTT
40220 ATTTGATGAAGTT
1 ATTTGATGAAGTT
40233 A
1 A
40234 CTAATCTATT
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (13 bp):
ATTTGATGAAGTT
Done.