Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007287.1 Corchorus capsularis cultivar CVL-1 contig07308, 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: 19115
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:171 original size:22 final size:21
Alignment explanation
Indices: 141--199 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
131 AATTCTTGCT
* *
141 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
163 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
182 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
200 ACACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:186 original size:11 final size:11
Alignment explanation
Indices: 169--200 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
159 ATTGTCTTCA
169 AATCTTCAAAT
1 AATCTTCAAAT
*
180 TATCTTCAAAT
1 AATCTTCAAAT
191 AATCTTCAAA
1 AATCTTCAAA
201 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:200 original size:22 final size:22
Alignment explanation
Indices: 141--200 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
131 AATTCTTGCT
* *
141 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
163 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
182 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
201 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:6087 original size:49 final size:49
Alignment explanation
Indices: 6023--6301 Score: 380
Period size: 49 Copynumber: 5.7 Consensus size: 49
6013 AAACATTAAC
* * *
6023 GCCTTCCGTCCGGGAAGGGCGTTTTTTGGAAAAAGCAGGTAAAAA-AGGT
1 GCCTTCCGTCCGGGAAGGGCG-TTTTGGGAAAAAGCAAGTAAAAATAAGT
* * *
6072 GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAGGTAAAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGT
* * * * *
6121 GCCTTCCGTTCGGGAAGGGTGTTTTGGGAAATAGCATGTAAAAAGAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGT
* *
6170 GACTTCCGTCCGGGAAGGGCGTTTTGGTGGAAAAAGTAAGTAAAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTT-G-GGAAAAAGCAAGTAAAAATAAGT
*
6221 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGTAAGTAAAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGT
* *
6270 GCCTTCCGTCCGGGAAGCGCATTTTGGGAAAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAA
6302 CGAGAACGAA
Statistics
Matches: 208, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
48 21 0.10
49 142 0.68
50 2 0.01
51 43 0.21
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (49 bp):
GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGT
Found at i:6237 original size:100 final size:98
Alignment explanation
Indices: 6023--6301 Score: 373
Period size: 100 Copynumber: 2.8 Consensus size: 98
6013 AAACATTAAC
* * * *
6023 GCCTTCCGTCCGGGAAGGGCGTTTTTTGGAAAAAGCAGGTAAAAAAGGTGCCTTCCGTCTGGGAA
1 GCCTTCCGTCCGGGAAGGGCG-TTTTGGGAAAAAGCAAGTAAAAAAAGTGCCTTCCGTCCGGGAA
* *
6088 GGGCGTTTT-GGGAAATAGCAGGTAAAAATAAGT
65 GGGCGTTTTGGGGAAAAAGCAAGTAAAAATAAGT
* * * * *
6121 GCCTTCCGTTCGGGAAGGGTGTTTTGGGAAATAGCATGTAAAAAGAAGTGACTTCCGTCCGGGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAA-AAGTGCCTTCCGTCCGGGAA
*
6186 GGGCGTTTTGGTGGAAAAAGTAAGTAAAAATAAGT
65 GGGCGTTTTGG-GGAAAAAGCAAGTAAAAATAAGT
*
6221 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGTAAGTAAAAATAAGTGCCTTCCGTCCGGGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAA-AAGTGCCTTCCGTCCGGGAA
* *
6286 GCGCATTTT-GGGAAAA
65 GGGCGTTTTGGGGAAAA
6302 CGAGAACGAA
Statistics
Matches: 158, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
97 20 0.13
98 51 0.32
99 2 0.01
100 85 0.54
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (98 bp):
GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAAAGTGCCTTCCGTCCGGGAAG
GGCGTTTTGGGGAAAAAGCAAGTAAAAATAAGT
Found at i:6262 original size:149 final size:147
Alignment explanation
Indices: 6025--6300 Score: 426
Period size: 149 Copynumber: 1.9 Consensus size: 147
6015 ACATTAACGC
* * * *
6025 CTTCCGTCCGGGAAGGGCGTTTTTTGGAAAAAGCAGGTAAAAAAGGTGCCTTCCGTCTGGGAAGG
1 CTTCCGTCCGGGAAGGGCGTTTTGTGGAAAAAGCAAGTAAAAAAAGTGCCTTCCGTCCGGGAAGG
* * * * **
6090 GCGTTTTGGGAAATAGCAGGTAAAAATAAGTGCCTTCCGTTCGGGAAGGGTGTTTTGGGAAATAG
66 GCGTTTTGGGAAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGCGCATTTTGGGAAATAG
6155 CATGTAAAAAGAAGTGA
131 CATGTAAAAAGAAGTGA
*
6172 CTTCCGTCCGGGAAGGGCGTTTTGGTGGAAAAAGTAAGTAAAAATAAGTGCCTTCCGTCCGGGAA
1 CTTCCGTCCGGGAAGGGCGTTTT-GTGGAAAAAGCAAGTAAAAA-AAGTGCCTTCCGTCCGGGAA
*
6237 GGGCGTTTTGGGAAAAAGTAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGCGCATTTTGGGAAA
64 GGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGCGCATTTTGGGAAA
6301 ACGAGAACGA
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
147 23 0.20
148 17 0.15
149 75 0.65
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (147 bp):
CTTCCGTCCGGGAAGGGCGTTTTGTGGAAAAAGCAAGTAAAAAAAGTGCCTTCCGTCCGGGAAGG
GCGTTTTGGGAAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGCGCATTTTGGGAAATAG
CATGTAAAAAGAAGTGA
Found at i:9780 original size:33 final size:33
Alignment explanation
Indices: 9733--9828 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 33
9723 TTATTGATGC
*
9733 TGAAATTA-AAAGACCAGTCTGTGGTCGA-CAT
1 TGAAATTAGAAAGACCAGTCTGTGGTCGAGAAT
* *
9764 TGAAATTGAGAAAGACCTGTCTGAGGTCGAGAAT
1 TGAAATT-AGAAAGACCAGTCTGTGGTCGAGAAT
9798 TGAAGATCTCAGAAAGAGACCAGTCTGTGGT
1 TGAA-AT-T-AG-AA-AGACCAGTCTGTGGT
9829 TGCTTTTGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
31 7 0.13
32 1 0.02
33 18 0.35
34 6 0.12
35 2 0.04
36 3 0.06
37 2 0.04
38 13 0.25
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (33 bp):
TGAAATTAGAAAGACCAGTCTGTGGTCGAGAAT
Found at i:9920 original size:47 final size:47
Alignment explanation
Indices: 9869--9975 Score: 126
Period size: 47 Copynumber: 2.3 Consensus size: 47
9859 GTTGAAGAAA
* * *
9869 ACCAACTGTGGTCACTAAATTGTAGAC-TCGCATGGAAGCGTGAAAAG
1 ACCAACTGTGGTCACCAAATTGTA-ACTTCGCATAGAAGCGAGAAAAG
* * *
9916 ACCAATTGTGGTCACCAAATTGTAACTTTGCATAGAAGTGAGAAAAG
1 ACCAACTGTGGTCACCAAATTGTAACTTCGCATAGAAGCGAGAAAAG
* *
9963 ACCGACTTTGGTC
1 ACCAACTGTGGTC
9976 GAAAATATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 2 0.04
47 48 0.96
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (47 bp):
ACCAACTGTGGTCACCAAATTGTAACTTCGCATAGAAGCGAGAAAAG
Found at i:10126 original size:15 final size:15
Alignment explanation
Indices: 10106--10209 Score: 55
Period size: 15 Copynumber: 6.4 Consensus size: 15
10096 AAATTCTGAG
*
10106 AAGTTGCAAATTGAA
1 AAGTTGGAAATTGAA
* *
10121 AAGTTGTTGAAGTGTTGTA
1 AAGTTG--GAA--ATTGAA
*
10140 AAGTTGTAAATTGAA
1 AAGTTGGAAATTGAA
***
10155 AAGTTGTTCATTGAA
1 AAGTTGGAAATTGAA
*
10170 AAGTTGTTGAAATGCTGTA
1 AAGTTG--GAAAT--TGAA
*
10189 AAGTTGAAAATTGAA
1 AAGTTGGAAATTGAA
10204 AAGTTG
1 AAGTTG
10210 TTGAAATGCT
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
15 38 0.57
17 10 0.15
19 19 0.28
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (15 bp):
AAGTTGGAAATTGAA
Found at i:10177 original size:49 final size:48
Alignment explanation
Indices: 10033--10210 Score: 203
Period size: 51 Copynumber: 3.6 Consensus size: 48
10023 CGAAGGATTA
* * *
10033 CTGTAAAATTGTAAATTCCGAAGAGTTGTAAATTGAAAAGTTGCTGTAATG
1 CTGTAAAGTTGTAAATT--GAAAAGTTGTAAATTGAAAAGTTGTTG-AATG
* * *
10084 CTGTAAACTTGTAAATTCTGAGAAGTTGCAAATTGAAAAGTTGTTGAAGTG
1 CTGTAAAGTTGTAAA-T-TGAAAAGTTGTAAATTGAAAAGTTGTTGAA-TG
* **
10135 TTGTAAAGTTGTAAATTGAAAAGTTGTTCATTGAAAAGTTGTTGAAATG
1 CTGTAAAGTTGTAAATTGAAAAGTTGTAAATTGAAAAGTTGTTG-AATG
*
10184 CTGTAAAGTTGAAAATTGAAAAGTTGT
1 CTGTAAAGTTGTAAATTGAAAAGTTGT
10211 TGAAATGCTC
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
49 51 0.46
50 5 0.05
51 52 0.47
52 1 0.01
53 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (48 bp):
CTGTAAAGTTGTAAATTGAAAAGTTGTAAATTGAAAAGTTGTTGAATG
Found at i:10211 original size:49 final size:49
Alignment explanation
Indices: 10033--10211 Score: 187
Period size: 49 Copynumber: 3.6 Consensus size: 49
10023 CGAAGGATTA
* * * * * *
10033 CTGTAAAATTGTAAATTCCGAAGAGTTGTAAATTGAAAAGTTGCTGTAATG
1 CTGTAAAGTTGAAAATT--GAAAAGTTGTTAATTGAAAAGTTGTTGAAATG
* * * ** *
10084 CTGTAAACTTGTAAATTCTGAGAAGTTGCAAATTGAAAAGTTGTTGAAGTG
1 CTGTAAAGTTG-AAAAT-TGAAAAGTTGTTAATTGAAAAGTTGTTGAAATG
* * *
10135 TTGTAAAGTTGTAAATTGAAAAGTTGTTCATTGAAAAGTTGTTGAAATG
1 CTGTAAAGTTGAAAATTGAAAAGTTGTTAATTGAAAAGTTGTTGAAATG
10184 CTGTAAAGTTGAAAATTGAAAAGTTGTT
1 CTGTAAAGTTGAAAATTGAAAAGTTGTT
10212 GAAATGCTCC
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
49 54 0.51
50 3 0.03
51 45 0.42
52 3 0.03
53 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (49 bp):
CTGTAAAGTTGAAAATTGAAAAGTTGTTAATTGAAAAGTTGTTGAAATG
Found at i:10299 original size:39 final size:38
Alignment explanation
Indices: 10245--10520 Score: 271
Period size: 39 Copynumber: 7.3 Consensus size: 38
10235 CGAAAACTGC
*
10245 TGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTTGT
1 TGAAAGATGACCTGTTTCCAGTCGAACTTGATAA-TTGT
* * ** * *
10284 TGAAAGATGACCTGTTTCCAATCAAACTAAACAAGTGT
1 TGAAAGATGACCTGTTTCCAGTCGAACTTGATAATTGT
* *
10322 TGAAAGACGACCTGTTTCCAGTCGTAA---GATAATTGC
1 TGAAAGATGACCTGTTTCCAGTCG-AACTTGATAATTGT
*
10358 TGAAAGATGACCTGTTTCCAGTC-AACTTTGATAACTTAT
1 TGAAAGATGACCTGTTTCCAGTCGAAC-TTGATAA-TTGT
* * * *
10397 TGAAAGATGACCTGTTTCCAGTCAAACTTAATAAGTGC
1 TGAAAGATGACCTGTTTCCAGTCGAACTTGATAATTGT
* *
10435 TGAAAGACGACCTGTTTCCAGTCGTAA---GATAATTGC
1 TGAAAGATGACCTGTTTCCAGTCG-AACTTGATAATTGT
*
10471 TGAAAGATGACCTGTTTCCAGTC-AACTTTGATAACTTAT
1 TGAAAGATGACCTGTTTCCAGTCGAAC-TTGATAA-TTGT
10510 TGAAAAGATGA
1 TG-AAAGATGA
10521 TCTCTGATAA
Statistics
Matches: 195, Mismatches: 28, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
34 4 0.02
36 56 0.29
38 57 0.29
39 67 0.34
40 11 0.06
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (38 bp):
TGAAAGATGACCTGTTTCCAGTCGAACTTGATAATTGT
Found at i:10440 original size:113 final size:113
Alignment explanation
Indices: 10242--10520 Score: 479
Period size: 113 Copynumber: 2.5 Consensus size: 113
10232 AACCGAAAAC
* *
10242 TGCTGAAAGATGACCTGTTTCCAGTCGA-TCTTGATAACTTGTTGAAAGATGACCTGTTTCCAAT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATAACTTATTGAAAGATGACCTGTTTCCAAT
*
10306 CAAACTAAACAAGTGTTGAAAGACGACCTGTTTCCAGTCGTAAGATAAT
65 CAAACTAAACAAGTGCTGAAAGACGACCTGTTTCCAGTCGTAAGATAAT
*
10355 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTATTGAAAGATGACCTGTTTCCAGTC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTATTGAAAGATGACCTGTTTCCAATC
* *
10420 AAACTTAATAAGTGCTGAAAGACGACCTGTTTCCAGTCGTAAGATAAT
66 AAACTAAACAAGTGCTGAAAGACGACCTGTTTCCAGTCGTAAGATAAT
10468 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTATTGAAAAGATGA
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTATTG-AAAGATGA
10521 TCTCTGATAA
Statistics
Matches: 158, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
113 149 0.94
114 9 0.06
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (113 bp):
TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTATTGAAAGATGACCTGTTTCCAATC
AAACTAAACAAGTGCTGAAAGACGACCTGTTTCCAGTCGTAAGATAAT
Found at i:10495 original size:74 final size:75
Alignment explanation
Indices: 10242--10504 Score: 268
Period size: 74 Copynumber: 3.5 Consensus size: 75
10232 AACCGAAAAC
* * * *
10242 TGCTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTTGTTGAAAGATGACCTGTTTCCAATC
1 TGCTGAAAGATGACCTGTTTCCAGTCAAACTTGATAA-TTGCTGAAAGATGACCTGTTTCCAGTC
* *
10307 AAACTAA-ACAAG
65 --ACTAAGATAAT
* * *
10319 TGTTGAAAGACGACCTGTTTCCAGTCGTAA---GATAATTGCTGAAAGATGACCTGTTTCCAGTC
1 TGCTGAAAGATGACCTGTTTCCAGTC-AAACTTGATAATTGCTGAAAGATGACCTGTTTCCAGTC
**
10381 AACTTTGATAACT
65 -ACTAAGATAA-T
** * * *
10394 TATTGAAAGATGACCTGTTTCCAGTCAAACTTAATAAGTGCTGAAAGACGACCTGTTTCCAGTC-
1 TGCTGAAAGATGACCTGTTTCCAGTCAAACTTGATAATTGCTGAAAGATGACCTGTTTCCAGTCA
*
10458 GTAAGATAAT
66 CTAAGATAAT
10468 TGCTGAAAGATGACCTGTTTCCAGTC-AACTTTGATAA
1 TGCTGAAAGATGACCTGTTTCCAGTCAAAC-TTGATAA
10505 CTTATTGAAA
Statistics
Matches: 157, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
73 7 0.04
74 61 0.39
75 35 0.22
77 53 0.34
78 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (75 bp):
TGCTGAAAGATGACCTGTTTCCAGTCAAACTTGATAATTGCTGAAAGATGACCTGTTTCCAGTCA
CTAAGATAAT
Found at i:10716 original size:132 final size:135
Alignment explanation
Indices: 10396--10769 Score: 508
Period size: 136 Copynumber: 2.8 Consensus size: 135
10386 TGATAACTTA
* * * *
10396 TTGAAAGATGACCTGTTTCCAGTCAAAC-TTAATAAGTGCTGAAAGACGACCTGTTTCCAGTCGT
1 TTGAAAGATGACCTGTTTCCAGTC-AACTTTGATTACTGTTGAAAGACGACCTGTTTCCAGTCGT
* *
10460 AAGATAATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTATTGAAAAGATGATCTC
65 AATATAATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAC-TATTGAAAAGAGGATCTC
10525 TGATAAC
129 TGATAAC
* * *
10532 TTGAAAGATGACCTGTTTCAAGTCAACTTTGATTATTGTTGAAAGACGACCTGTTTCCAATCGTA
1 TTGAAAGATGACCTGTTTCCAGTCAACTTTGATTACTGTTGAAAGACGACCTGTTTCCAGTCGTA
* * * * *
10597 ATATAATTGCTGAAAGATGACATGTTTCTAGTCAACTTTGGTAA-T-TTG-GAAGAGGATCTTTG
66 ATATAATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTATTGAAAAGAGGATCTCTG
10659 ATAAC
131 ATAAC
*
10664 TTGAAAGATGACCTGTTTCCAGTCAACTTTGATTACTGTTGAAAGATGACCTGTTTCCAGTC--A
1 TTGAAAGATGACCTGTTTCCAGTCAACTTTGATTACTGTTGAAAGACGACCTGTTTCCAGTCGTA
*
10727 ACTTTGATTATTGCTGAAAGATGACCTGTTTCCAGTCAACTTT
66 A---T-ATAATTGCTGAAAGATGACCTGTTTCCAGTCAACTTT
10770 TCGATTATTG
Statistics
Matches: 213, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
130 2 0.01
132 74 0.35
133 4 0.02
134 35 0.16
135 3 0.01
136 95 0.45
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (135 bp):
TTGAAAGATGACCTGTTTCCAGTCAACTTTGATTACTGTTGAAAGACGACCTGTTTCCAGTCGTA
ATATAATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTATTGAAAAGAGGATCTCTG
ATAAC
Found at i:10792 original size:40 final size:38
Alignment explanation
Indices: 10665--10798 Score: 223
Period size: 38 Copynumber: 3.5 Consensus size: 38
10655 TTTGATAACT
* *
10665 TGAAAGATGACCTGTTTCCAGTCAACTTTGATTACTGT
1 TGAAAGATGACCTGTTTCCAGTCAACTTTGATTATTGC
10703 TGAAAGATGACCTGTTTCCAGTCAACTTTGATTATTGC
1 TGAAAGATGACCTGTTTCCAGTCAACTTTGATTATTGC
10741 TGAAAGATGACCTGTTTCCAGTCAACTTTTCGATTATTGC
1 TGAAAGATGACCTGTTTCCAGTCAAC-TTT-GATTATTGC
*
10781 TGAAAGGTGACCTGTTTC
1 TGAAAGATGACCTGTTTC
10799 TTGAAGATGG
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
38 62 0.68
39 3 0.03
40 26 0.29
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (38 bp):
TGAAAGATGACCTGTTTCCAGTCAACTTTGATTATTGC
Found at i:12531 original size:14 final size:13
Alignment explanation
Indices: 12481--12530 Score: 64
Period size: 14 Copynumber: 3.7 Consensus size: 13
12471 GCACGAAACC
12481 TTTTGAAAACTCAT
1 TTTTGAAAAC-CAT
* *
12495 TTTCGAAAACCTT
1 TTTTGAAAACCAT
12508 TTTCTGAAAACCAT
1 TTT-TGAAAACCAT
12522 TTTTGAAAA
1 TTTTGAAAA
12531 ATGTGTCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTTGAAAACCAT
Found at i:13925 original size:8 final size:8
Alignment explanation
Indices: 13912--13945 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
13902 ACCTTCTTGA
13912 AAAAATTC
1 AAAAATTC
13920 AAAAATTC
1 AAAAATTC
*
13928 AGAAACTTC
1 A-AAAATTC
13937 AAAAATTC
1 AAAAATTC
13945 A
1 A
13946 TATCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Done.