Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005077.1 Corchorus capsularis cultivar CVL-1 contig05095, 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: 6762
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Found at i:1034 original size:27 final size:27
Alignment explanation
Indices: 964--1038 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
954 GGACTTGAGG
* **
964 TGACCAAAATGCCCCTAAATGTGCAAA
1 TGACCAAAATGTCCCTGGATGTGCAAA
*
991 TGACCAAAATATCCCTGGATGTGCAAA
1 TGACCAAAATGTCCCTGGATGTGCAAA
1018 TGACCAAAATGTCCCTGGATG
1 TGACCAAAATGTCCCTGGATG
1039 ACCCTGATGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (27 bp):
TGACCAAAATGTCCCTGGATGTGCAAA
Found at i:1460 original size:18 final size:17
Alignment explanation
Indices: 1429--1462 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1419 TCTCGATTAG
1429 GATTTGAATCGAAACAA
1 GATTTGAATCGAAACAA
*
1446 GATTTAGAATTGAAACA
1 GATTT-GAATCGAAACA
1463 GGAAACCCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (17 bp):
GATTTGAATCGAAACAA
Found at i:1505 original size:51 final size:50
Alignment explanation
Indices: 1420--1529 Score: 168
Period size: 51 Copynumber: 2.2 Consensus size: 50
1410 GACTAGAGAT
* *
1420 CTCGATTAGGATTTGAATCGAAACAAGATTTAGAATTGAAACAGGAAACC
1 CTCGATTAGGATTTGAATCGAAACAAAATTTAGAATTGAAACAAGAAACC
*
1470 CTCGATTAGGATTTGGAAAT-GAAACAAAATTTAGAATTGAAACAAGAAACG
1 CTCGATTAGGATTT-G-AATCGAAACAAAATTTAGAATTGAAACAAGAAACC
1521 CTCGATTAG
1 CTCGATTAG
1530 AGACCTCGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
50 14 0.25
51 38 0.69
52 3 0.05
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.25
Consensus pattern (50 bp):
CTCGATTAGGATTTGAATCGAAACAAAATTTAGAATTGAAACAAGAAACC
Found at i:1545 original size:64 final size:64
Alignment explanation
Indices: 1469--1785 Score: 539
Period size: 64 Copynumber: 4.9 Consensus size: 64
1459 AACAGGAAAC
*
1469 CCTCGATTAGGATTTG-GAAATGAAACAAAATTTAGAATTGAAACAAGAAACGCTCGATTAGAGA
1 CCTCGATTAGGATTTGAG-AATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
*
1533 CCTCGATTAGGATTTG-GAAATGAAACAAAATTCAGAATTGAAACAAGAAACCCTCGATTAGAGA
1 CCTCGATTAGGATTTGAG-AATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
* *
1597 ACTCGATCAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
1 CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
*
1661 CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGACTAGAGA
1 CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
*
1725 CCTCGATTAGGATTTGAGAACGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTA
1 CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAG-AAACCCTCGATTA
1786 CGATTTGGAA
Statistics
Matches: 241, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
64 228 0.95
65 13 0.05
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (64 bp):
CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
Found at i:1638 original size:18 final size:18
Alignment explanation
Indices: 1608--1642 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1598 CTCGATCAGG
1608 ATTTGAGAATGAAACAAA
1 ATTTGAGAATGAAACAAA
1626 ATTT-AGAATTGAAACAA
1 ATTTGAGAA-TGAAACAA
1643 GAAACCCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (18 bp):
ATTTGAGAATGAAACAAA
Found at i:1702 original size:18 final size:18
Alignment explanation
Indices: 1672--1706 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1662 CTCGATTAGG
1672 ATTTGAGAATGAAACAAA
1 ATTTGAGAATGAAACAAA
1690 ATTT-AGAATTGAAACAA
1 ATTTGAGAA-TGAAACAA
1707 GAAACCCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (18 bp):
ATTTGAGAATGAAACAAA
Found at i:1791 original size:52 final size:52
Alignment explanation
Indices: 1725--2415 Score: 428
Period size: 52 Copynumber: 12.0 Consensus size: 52
1715 CGACTAGAGA
*
1725 CCTCGATTAGGATTTGAGAACGAAACAAAATTTAGAATTGAAACAAGAAAAC
1 CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAAC
* *
1777 CCTCGATTACGATTTG-GAAATGAAACAAAATTTACAATTGAAACAAGAAAAC
1 CCTCGATTAGGATTTGAG-AATGAAACAAAATTTAGAATTGAAACAAGAAAAC
* * *
1829 CCTCGATTAGAGACCTCTATTATGATTTGGAAATGAAACAAAATTTAGAATTGAAATAA-CAAAC
1 CCTCGATTAG-G------ATT-TGA----GAAT-GAAACAAAATTTAGAATTGAAACAAGAAAAC
*
1893 CCTCGATTAGGATTTG-GAAATGAAA-ATGAATTTAGAATTGAAACAAGAAACTCGACC
1 CCTCGATTAGGATTTGAG-AATGAAACA-AAATTTAGAATTGAAACAAGAAA----A-C
*
1950 AGAGACCTCGATTAGGATTTGAGAATGAAACAAAATTTTGAATTGAAACAAGAAAAC
1 -----CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAAC
* *
2007 CCTCGATTAGGTTTTG-GAAATGAAACAAAATTTAGAATTGAAACAACAAAAC
1 CCTCGATTAGGATTTGAG-AATGAAACAAAATTTAGAATTGAAACAAGAAAAC
*
2059 CCTCGATTAGGATTTTGA-AATGAAACAAAATTTAGAATTGAAATAAG-AAAC
1 CCTCGATTAGGA-TTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAAC
* **
2110 CCTCGATTAGGGACCTCGATTAGGATTTGGAAATGAAACTGAATTTAGAATTGAAACAAGAAACT
1 CCTCGATTA-GGA--T---TT--GA----GAAT-GAAACAAAATTTAGAATTGAAACAAGAAA--
2175 CGACC
51 --A-C
2180 ATAGACCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAAC
1 -----CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAAC
*
2237 CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAAC
1 CCTCGATTAG-GA--T---TT--GA----GAAT-GAAACAAAATTTAGAATTGAAACAAGAAAAC
* * *
2302 CCTCGATTCGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAATAAG-AAAC
1 CCTCGATT--AG-----GATT-TGA----GAAT-GAAACAAAATTTAGAATTGAAACAAGAAAAC
* **
2366 CCTCGATTAGGATTTG-GAAATGAAGCTGAATTTAGAATTGAAACAAGAAA
1 CCTCGATTAGGATTTGAG-AATGAAACAAAATTTAGAATTGAAACAAGAAA
2416 CTCGACCAGG
Statistics
Matches: 522, Mismatches: 38, Indels: 158
0.73 0.05 0.22
Matches are distributed among these distances:
50 1 0.00
51 60 0.11
52 162 0.31
53 8 0.02
55 1 0.00
56 6 0.01
57 10 0.02
58 6 0.01
59 3 0.01
60 4 0.01
62 73 0.14
63 8 0.02
64 54 0.10
65 101 0.19
66 1 0.00
67 4 0.01
69 4 0.01
70 1 0.00
71 2 0.00
72 1 0.00
74 3 0.01
75 9 0.02
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (52 bp):
CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAAC
Found at i:1866 original size:65 final size:64
Alignment explanation
Indices: 1777--1902 Score: 198
Period size: 65 Copynumber: 2.0 Consensus size: 64
1767 ACAAGAAAAC
1777 CCTCGATTACGATTTGGAAATGAAACAAAATTTACAATTGAAACAAGAAAACCCTCGATTAGAGA
1 CCTCGATTACGATTTGGAAATGAAACAAAATTTACAATTGAAACAA-AAAACCCTCGATTAGAGA
* * * * *
1842 CCTCTATTATGATTTGGAAATGAAACAAAATTTAGAATTGAAATAACAAACCCTCGATTAG
1 CCTCGATTACGATTTGGAAATGAAACAAAATTTACAATTGAAACAAAAAACCCTCGATTAG
1903 GATTTGGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 14 0.25
65 42 0.75
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (64 bp):
CCTCGATTACGATTTGGAAATGAAACAAAATTTACAATTGAAACAAAAAACCCTCGATTAGAGA
Found at i:2066 original size:230 final size:229
Alignment explanation
Indices: 1661--2471 Score: 1022
Period size: 230 Copynumber: 3.5 Consensus size: 229
1651 CGATTAGAGA
* *
1661 CCTCGATTAGGATTT-GAGAATGAAACA-AAATTTAGAATTGAAACAAGAAACCCTCGACTAGAG
1 CCTCGATTAGGATTTGGA-AATGAAA-ATGAATTTAGAATTGAAACAAGAAA--CTCGACCAGAG
* * *
1724 ACCTCGATTAGGATTTGAGAACGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTACGA
62 ACCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGGT
*
1789 TTTGGAAATGAAACAAAATTTACAATTGAAACAAGAAAACCCTCGATTAGAGACCTCTATTATGA
127 TTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAGACCTC-ATTATGA
*
1854 TTTGGAAATGAAACAAAATTTAGAATTGAAATAACAAAC
191 TTTGGAAATGAAACAAAATTTAGAATTGAAATAAGAAAC
1893 CCTCGATTAGGATTTGGAAATGAAAATGAATTTAGAATTGAAACAAGAAACTCGACCAGAGACCT
1 CCTCGATTAGGATTTGGAAATGAAAATGAATTTAGAATTGAAACAAGAAACTCGACCAGAGACCT
*
1958 CGATTAGGATTTGAGAATGAAACAAAATTTTGAATTGAAACAAGAAAACCCTCGATTAGGTTTTG
66 CGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGGTTTTG
*
2023 GAAATGAAACAAAATTTAGAATTGAAACAACAAAACCCTCGATTAG-G--------AT--TTT-G
131 GAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAGACCTCATTATGATTTGG
2076 AAATGAAACAAAATTTAGAATTGAAATAAGAAACCCTC
196 AAATGAAACAAAATTTAGAATTGAAATAAGAAA----C
*
2114 GATTAGGGACCTCGATTAGGATTTGGAAATGAAACTGAATTTAGAATTGAAACAAGAAACTCGAC
1 ---------CCTCGATTAGGATTTGGAAATGAAAATGAATTTAGAATTGAAACAAGAAACTCGAC
*
2179 CATAGACCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGAT
57 CAGAGACCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGAT
2244 TAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGAT
122 T--AG-----G--T----TTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGAT
* *
2309 TCGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAATAAGAAAC
174 TAGAGACCTC-ATTATGATTTGGAAATGAAACAAAATTTAGAATTGAAATAAGAAAC
** *
2366 CCTCGATTAGGATTTGGAAATGAAGCTGAATTTAGAATTGAAACAAGAAACTCGACCAGGGACCT
1 CCTCGATTAGGATTTGGAAATGAAAATGAATTTAGAATTGAAACAAGAAACTCGACCAGAGACCT
** * * * *
2431 AAAGTAGGATTTGAAAATGAATA-AAAACTTGGAATTGAAAC
66 CGATTAGGATTTGAGAATGAA-ACAAAATTTAGAATTGAAAC
2472 CCTAATAGTA
Statistics
Matches: 513, Mismatches: 24, Indels: 73
0.84 0.04 0.12
Matches are distributed among these distances:
217 33 0.06
218 3 0.01
220 2 0.00
221 1 0.00
229 1 0.00
230 238 0.46
231 1 0.00
232 46 0.09
233 2 0.00
237 1 0.00
239 1 0.00
243 143 0.28
244 2 0.00
252 1 0.00
253 1 0.00
255 3 0.01
256 34 0.07
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.24
Consensus pattern (229 bp):
CCTCGATTAGGATTTGGAAATGAAAATGAATTTAGAATTGAAACAAGAAACTCGACCAGAGACCT
CGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGGTTTTG
GAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAGACCTCATTATGATTTGG
AAATGAAACAAAATTTAGAATTGAAATAAGAAAC
Found at i:2226 original size:18 final size:18
Alignment explanation
Indices: 2196--2230 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2186 CTCGATTAGG
2196 ATTTGAGAATGAAACAAA
1 ATTTGAGAATGAAACAAA
2214 ATTT-AGAATTGAAACAA
1 ATTTGAGAA-TGAAACAA
2231 GAAAACCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (18 bp):
ATTTGAGAATGAAACAAA
Found at i:2272 original size:65 final size:64
Alignment explanation
Indices: 2059--2375 Score: 496
Period size: 65 Copynumber: 5.0 Consensus size: 64
2049 ACAACAAAAC
* * *
2059 CCTCGATTAGGATTTTGAAATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAGGGA
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
** ** *
2123 CCTCGATTAGGATTTGGAAATGAAACTGAATTTAGAATTGAAACAAGAAA--CTCGACCATAGA
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
2185 CCTCGATTAGGATTT-GAGAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAG
1 CCTCGATTAGGATTTGGA-AATGAAACAAAATTTAGAATTGAAACAAG-AAACCCTCGATTAGAG
2249 A
64 A
*
2250 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTCGAGA
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAG-AAACCCTCGATTAGAGA
*
2315 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAG
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAG
2376 GATTTGGAAA
Statistics
Matches: 232, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
61 2 0.01
62 50 0.22
63 3 0.01
64 59 0.25
65 116 0.50
66 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.25
Consensus pattern (64 bp):
CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
Found at i:2284 original size:127 final size:128
Alignment explanation
Indices: 2059--2375 Score: 500
Period size: 127 Copynumber: 2.5 Consensus size: 128
2049 ACAACAAAAC
*
2059 CCTCGATTAGGATTTTGA-AATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAGGGA
1 CCTCGATTAGGA-TTTGAGAATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAGAGA
** *
2123 CCTCGATTAGGATTTGGAAATGAAACTGAATTTAGAATTGAAACAAG-AAA-CTCGA-CCATAGA
65 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCTCGATCC-GAGA
*
2185 CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAGA
1 CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAATAAG-AAACCCTCGATTAGAGA
*
2250 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTCGAGA
65 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAA-CCTCGATCCGAGA
2315 CCTCGATTAGGATTTG-GAAATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAG
1 CCTCGATTAGGATTTGAG-AATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAG
2376 GATTTGGAAA
Statistics
Matches: 177, Mismatches: 7, Indels: 11
0.91 0.04 0.06
Matches are distributed among these distances:
125 5 0.03
126 40 0.23
127 61 0.34
128 3 0.02
129 15 0.08
130 52 0.29
131 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.25
Consensus pattern (128 bp):
CCTCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAGAGAC
CTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCTCGATCCGAGA
Found at i:2373 original size:51 final size:51
Alignment explanation
Indices: 2315--2416 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
2305 CGATTCGAGA
*
2315 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAATAAGAAAC
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
* **
2366 CCTCGATTAGGATTTGGAAATGAAGCTGAATTTAGAATTGAAACAAGAAAC
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
2417 TCGACCAGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (51 bp):
CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
Found at i:2411 original size:473 final size:464
Alignment explanation
Indices: 1533--2471 Score: 1379
Period size: 473 Copynumber: 2.0 Consensus size: 464
1523 CGATTAGAGA
*
1533 CCTCGATTAGGATTTGGAAATGAAACAAAATTCAGAATTGAAACAAGAAACCCTCGATTAGAGAA
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTCAGAATTGAAACAAAAAACCCTCGATTA-AG-A
1598 CTCGATCAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACC
64 ---GAT----ATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACC
*
1663 TCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGACTAGAGACCT
122 TCGATTAGGATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAA-CCTCGACCAGAGACCT
1728 CGATTAGGATTTGAGAACGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTACGATTTG
186 CGATTAGGATTTGAGAACGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTACGATTTG
* *
1793 GAAATGAAACAAAATTTACAATTGAAACAAGAAAACCCTCGATTAGAGACCTCTATTATGATTTG
251 GAAATGAAACAAAATTTACAATTGAAACAAGAAAACCCTCGATTAGAGACCTCGATTAGGATTTG
1858 GAAATGAAACAAAATTTAGAATTGAAATAACAAACCCTCGATTAGGATTTGGAAATGAAAATGAA
316 GAAATGAAACAAAATTTAGAATTGAAATAACAAACCCTCGATTAGGATTTGGAAATGAAAATGAA
** * * *
1923 TTTAGAATTGAAACAAGAAACTCGACCAGAGACCTCGATTAGGATTTGAGAATGAA-ACAAAATT
381 TTTAGAATTGAAACAAGAAACTCGACCAGAGACCTAAAGTAGGATTTGAAAATGAATA-AAAACT
*
1987 TTGAATTGAAACAAGAAAAC
445 TGGAATTGAAACAAGAAAAC
* *
2007 CCTCGATTAGGTTTTGGAAATGAAACAAAATTTAGAATTGAAACAACAAAACCCTCGATT-AG-G
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTCAGAATTGAAACAA-AAAACCCTCGATTAAGAG
* *
2070 AT-TTTGA-AATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAGGGACCTCGATTAG
65 ATATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAG
** *
2133 GATTTG-GAAATGAAACTGAATTTAGAATTGAAACAAGAAA-CTCGACCATAGACCTCGATTAGG
130 GATTTGAG-AATGAAACAAAATTTAGAATTGAAACAAGAAACCTCGACCAGAGACCTCGATTAGG
*
2196 ATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAGACCTCGATTAGG
194 ATTTGAGAACGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATT----A---C------G
* *
2261 ATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTCGAGACCTCGATTAGG
246 ATTTGGAAATGAAACAAAATTTACAATTGAAACAAGAAAACCCTCGATTAGAGACCTCGATTAGG
* *
2326 ATTTGGAAATGAAACAAAATTTAGAATTGAAATAAGAAACCCTCGATTAGGATTTGGAAATGAAG
311 ATTTGGAAATGAAACAAAATTTAGAATTGAAATAACAAACCCTCGATTAGGATTTGGAAATGAAA
* *
2391 CTGAATTTAGAATTGAAACAAGAAACTCGACCAGGGACCTAAAGTAGGATTTGAAAATGAATAAA
376 ATGAATTTAGAATTGAAACAAGAAACTCGACCAGAGACCTAAAGTAGGATTTGAAAATGAATAAA
2456 AACTTGGAATTGAAAC
441 AACTTGGAATTGAAAC
2472 CCTAATAGTA
Statistics
Matches: 425, Mismatches: 24, Indels: 33
0.88 0.05 0.07
Matches are distributed among these distances:
460 69 0.16
461 1 0.00
462 90 0.21
463 5 0.01
464 1 0.00
467 1 0.00
468 3 0.01
473 198 0.47
474 45 0.11
475 12 0.03
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (464 bp):
CCTCGATTAGGATTTGGAAATGAAACAAAATTCAGAATTGAAACAAAAAACCCTCGATTAAGAGA
TATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGG
ATTTGAGAATGAAACAAAATTTAGAATTGAAACAAGAAACCTCGACCAGAGACCTCGATTAGGAT
TTGAGAACGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTACGATTTGGAAATGAAAC
AAAATTTACAATTGAAACAAGAAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAAC
AAAATTTAGAATTGAAATAACAAACCCTCGATTAGGATTTGGAAATGAAAATGAATTTAGAATTG
AAACAAGAAACTCGACCAGAGACCTAAAGTAGGATTTGAAAATGAATAAAAACTTGGAATTGAAA
CAAGAAAAC
Found at i:2858 original size:113 final size:113
Alignment explanation
Indices: 2660--2895 Score: 454
Period size: 113 Copynumber: 2.1 Consensus size: 113
2650 TCCGATGACT
*
2660 CCCTTTTATGAAATATATGCCATTCATTAAGTAAATGCCCCACAAGGATCCTATTTTACTTCCAA
1 CCCTTTTGTGAAATATATGCCATTCATTAAGTAAATGCCCCACAAGGATCCTATTTTACTTCCAA
2725 TGTGGACTTCCCCAATTAATGAAATTAAGACTTATGTTCCGGCTTACC
66 TGTGGACTTCCCCAATTAATGAAATTAAGACTTATGTTCCGGCTTACC
*
2773 CCCTTTTGTGAAATATATGCCATTCATTGAGTAAATGCCCCACAAGGATCCTATTTTACTTCCAA
1 CCCTTTTGTGAAATATATGCCATTCATTAAGTAAATGCCCCACAAGGATCCTATTTTACTTCCAA
2838 TGTGGACTTCCCCAATTAATGAAATTAAGACTTATGTTCCGGCTTACC
66 TGTGGACTTCCCCAATTAATGAAATTAAGACTTATGTTCCGGCTTACC
2886 CCCTTTTGTG
1 CCCTTTTGTG
2896 GTTGAACACC
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 121 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (113 bp):
CCCTTTTGTGAAATATATGCCATTCATTAAGTAAATGCCCCACAAGGATCCTATTTTACTTCCAA
TGTGGACTTCCCCAATTAATGAAATTAAGACTTATGTTCCGGCTTACC
Done.