Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013446.1 Corchorus olitorius cultivar O-4 contig13479, 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: 3445
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Found at i:247 original size:22 final size:22
Alignment explanation
Indices: 171--385 Score: 111
Period size: 22 Copynumber: 9.7 Consensus size: 22
161 TGATAAGAAC
*
171 AAATTTTGATAACGTTC-TAAT-
1 AAATTTTGATAACCTTCAT-ATG
* * * *
192 TAATTTTGATAATC-ACACTATA
1 AAATTTTGATAACCTTCA-TATG
** *
214 AAATTTCAATAACCTTCGTATG
1 AAATTTTGATAACCTTCATATG
* * *
236 AAATTTTGATAATCTCCATAAG
1 AAATTTTGATAACCTTCATATG
* **
258 AGATTTTGATAACCTTTTTTTATG
1 AAATTTTGATAACC--TTCATATG
* *
282 AAATTTTGGTAACC-TCTGTATG
1 AAATTTTGATAACCTTC-ATATG
*
304 AAATTTTGATAA--TTACACTACG
1 AAATTTTGATAACCTT-CA-TATG
* *
326 AAGTTTTGATAACCTCCATATG
1 AAATTTTGATAACCTTCATATG
* *
348 AAATTTTGGTAACC-ACACTATG
1 AAATTTTGATAACCTTCA-TATG
*
370 AAATTTTAATAACCTT
1 AAATTTTGATAACCTT
386 ACTATGTGAT
Statistics
Matches: 141, Mismatches: 39, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
20 1 0.01
21 17 0.12
22 103 0.73
23 3 0.02
24 17 0.12
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTTCATATG
Found at i:333 original size:68 final size:66
Alignment explanation
Indices: 223--381 Score: 171
Period size: 68 Copynumber: 2.4 Consensus size: 66
213 AAAATTTCAA
* ***
223 TAACCT-TCGTATGAAATTTTGATAATCTCCATAAGAGATTTTGATAACCTTTTTTTATGAAATT
1 TAACCTCT-GTATGAAATTTTGATAATCTACATAAGAGATTTTGATAACC--TCCATATGAAATT
287 TTGG
63 TTGG
*
291 TAACCTCTGTATGAAATTTTGATAAT-TACACTACGA-AGTTTTGATAACCTCCATATGAAATTT
1 TAACCTCTGTATGAAATTTTGATAATCTACA-TAAGAGA-TTTTGATAACCTCCATATGAAATTT
354 TGG
64 TGG
* ** *
357 TAACCACACTATGAAATTTTAATAA
1 TAACCTCTGTATGAAATTTTGATAA
382 CCTTACTATG
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
66 35 0.44
67 4 0.05
68 39 0.49
69 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (66 bp):
TAACCTCTGTATGAAATTTTGATAATCTACATAAGAGATTTTGATAACCTCCATATGAAATTTTG
G
Found at i:339 original size:44 final size:44
Alignment explanation
Indices: 235--384 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 44
225 ACCTTCGTAT
* * * **** *
235 GAAATTTTGATAATCTCCATAAGAGATTTTGATAACCTTTTTTTAT
1 GAAATTTTGATAACCTCCATATGAAATTTTGATAACC--ACACTAC
* ** **
281 GAAATTTTGGTAACCTCTGTATGAAATTTTGATAATTACACTAC
1 GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
* * *
325 GAAGTTTTGATAACCTCCATATGAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
*
369 GAAATTTTAATAACCT
1 GAAATTTTGATAACCT
385 TACTATGTGA
Statistics
Matches: 81, Mismatches: 23, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
44 52 0.64
46 29 0.36
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (44 bp):
GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
Found at i:1829 original size:166 final size:165
Alignment explanation
Indices: 1638--2039 Score: 398
Period size: 170 Copynumber: 2.4 Consensus size: 165
1628 ACAAAATTTA
* *
1638 GAAGTTGAGGTTTTAGGCTTTGAAGAAAAATTTGTTTGGCAAGTCACTTTCCAATGAGCTCTATT
1 GAAGTTGAGGTTTTAGGCTTTGAAGAAAAATTTATTTGGCAAGTCACTTTCCAATAAGCTCTATT
* * *
1703 GACTCTGAAACATGACATATGAGCGATGGTTACACAAATAATGCA-TTCGGAATTAACATTTT-C
66 -ACTCTGAAACATAACATATGAGCGATGGTTACACAAAAAATGCACTT-GGAATGAACATTTTCC
* *
1766 TCAAGAATAACGTTCTGCGCACAAACACG-TAAAATCGT
129 T-AAGAACAACGTTCTGCGCACAAACACGCT-AAATCGG
* * ** * ** *
1804 GAAGTTTAAGTTTTAGGCTTTGAAGAAAGTTTTTTTTTTTTGGCAAACCCACTTTCCAATTAGCT
1 GAAGTTGAGGTTTTAGGCTTTGAAGAAA----AATTTATTTGGC-AAGTCACTTTCCAATAAGCT
* * * * *
1869 -TACTTACTCTGAAACATAACATTTGAGCGTTGGTTTCACAAAAAATGTACTTGGAATGAGCATT
61 CTA-TTACTCTGAAACATAACATATGAGCGATGGTTACACAAAAAATGCACTTGGAATGAACATT
* * * *
1933 TTCCTAAGAACAATGTTTTGCGCTCAAACATGCTAAATCGG
125 TTCCTAAGAACAACGTTCTGCGCACAAACACGCTAAATCGG
** ** * * *
1974 GAAGTTGAGGTTTTAGGCTTTTTAGAAAGCTTTATTTGACAAGTCCACTTTACAATAAACTCTAT
1 GAAGTTGAGGTTTTAGGCTTTGAAGAAAAATTTATTTGGCAAGT-CACTTTCCAATAAGCTCTAT
2039 T
65 T
2040 TAAATGTAAT
Statistics
Matches: 190, Mismatches: 35, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
165 2 0.01
166 49 0.26
167 2 0.01
170 113 0.59
171 24 0.13
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (165 bp):
GAAGTTGAGGTTTTAGGCTTTGAAGAAAAATTTATTTGGCAAGTCACTTTCCAATAAGCTCTATT
ACTCTGAAACATAACATATGAGCGATGGTTACACAAAAAATGCACTTGGAATGAACATTTTCCTA
AGAACAACGTTCTGCGCACAAACACGCTAAATCGG
Found at i:1935 original size:170 final size:171
Alignment explanation
Indices: 1682--1994 Score: 402
Period size: 170 Copynumber: 1.8 Consensus size: 171
1672 TTTGGCAAGT
* *
1682 CACTTTCCAATGAGCTCTATTGACTCTGAAACATGACATATGAGCGATGGTTACACAAATAATGC
1 CACTTTCCAATGAGCTCTATTGACTCTGAAACATAACATATGAGCGATGGTTACACAAAAAATGC
* * *
1747 ATTCGGAATTAACATTTT-CTCAAGAATAACGTTCTGCGCACAAACACG-TAAAATCGTGAAGTT
66 ATTCGGAATGAACATTTTCCT-AAGAACAACGTTCTGCGCACAAACACGCT-AAATCGGGAAGTT
*
1810 TAAGTTTTAGGCTTTGAAGAAAGTTTTTTTTTTTTGGCAAACC
129 GAAGTTTTAGGCTTTGAAGAAAGTTTTTTTTTTTTGGCAAACC
* * * *
1853 CACTTTCCAATTAGCT-TACTT-ACTCTGAAACATAACATTTGAGCGTTGGTTTCACAAAAAATG
1 CACTTTCCAATGAGCTCTA-TTGACTCTGAAACATAACATATGAGCGATGGTTACACAAAAAATG
* * * * * *
1916 TACTT-GGAATGAGCATTTTCCTAAGAACAATGTTTTGCGCTCAAACATGCTAAATCGGGAAGTT
65 CA-TTCGGAATGAACATTTTCCTAAGAACAACGTTCTGCGCACAAACACGCTAAATCGGGAAGTT
*
1980 GAGGTTTTAGGCTTT
129 GAAGTTTTAGGCTTT
1995 TTAGAAAGCT
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
170 99 0.82
171 22 0.18
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (171 bp):
CACTTTCCAATGAGCTCTATTGACTCTGAAACATAACATATGAGCGATGGTTACACAAAAAATGC
ATTCGGAATGAACATTTTCCTAAGAACAACGTTCTGCGCACAAACACGCTAAATCGGGAAGTTGA
AGTTTTAGGCTTTGAAGAAAGTTTTTTTTTTTTGGCAAACC
Found at i:2213 original size:22 final size:22
Alignment explanation
Indices: 2127--2248 Score: 99
Period size: 22 Copynumber: 5.6 Consensus size: 22
2117 CTCTAGTGTA
* *
2127 GAAATATT-GATAACCACATTTT
1 GAAAT-TTCGATAACCACACTAT
2149 GCAAATTT-GATAACCTA-A-TAT
1 G-AAATTTCGATAACC-ACACTAT
* *** *
2170 GAAATTTAGATAATTTCCCTAT
1 GAAATTTCGATAACCACACTAT
*
2192 GAAAATTCGATAACCACACTAT
1 GAAATTTCGATAACCACACTAT
* *
2214 GAAATTTGGGTAACCACACTAT
1 GAAATTTCGATAACCACACTAT
2236 GAAATTTCGATAA
1 GAAATTTCGATAA
2249 TCTCAGTGTG
Statistics
Matches: 79, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
20 6 0.08
21 8 0.10
22 60 0.76
23 5 0.06
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (22 bp):
GAAATTTCGATAACCACACTAT
Found at i:2261 original size:66 final size:64
Alignment explanation
Indices: 2121--2270 Score: 142
Period size: 66 Copynumber: 2.3 Consensus size: 64
2111 TTCATGCTCT
* * *
2121 AGTGTAGAAATATTGATAACCACATTTTGCAAATTTGATAACCTAATATGAAATTTAGATAATTT
1 AGTGT-GAAA-ATTGATAACCACACTATGCAAATTTGATAACCTAATATGAAATTTAGATAATCT
2186 C
64 C
** * * *
2187 CCTATGAAAATTCGATAACCACACTATG-AAATTTGGGTAACC-ACACTATGAAATTTCGATAAT
1 AGTGTGAAAATT-GATAACCACACTATGCAAATTT-GATAACCTA-A-TATGAAATTTAGATAAT
2250 CTC
62 CTC
*
2253 AGTGTGAAATTTTGATAA
1 AGTGTGAAA-ATTGATAA
2271 TCTGCCTATA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
64 10 0.15
65 24 0.36
66 31 0.46
67 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (64 bp):
AGTGTGAAAATTGATAACCACACTATGCAAATTTGATAACCTAATATGAAATTTAGATAATCTC
Found at i:2419 original size:22 final size:22
Alignment explanation
Indices: 2370--2524 Score: 59
Period size: 22 Copynumber: 6.7 Consensus size: 22
2360 GTAACCGCAT
* *
2370 TATGAAAATTTTGATAACCACACC
1 TATG-AAATTTCGATAACCTC-CC
2394 -ATGAAATTTCGATAACCTCCC
1 TATGAAATTTCGATAACCTCCC
* *
2415 TATGAGAATGAAACTGT-GATATCCTCTC
1 TATGA-AAT-----T-TCGATAACCTCCC
* *
2443 TATGTATTTTCGATAACCTCTCC
1 TATGAAATTTCGATAACCTC-CC
*
2466 -ATAAAATTTTC-ATAACCTCCC
1 TATGAAA-TTTCGATAACCTCCC
* * * *
2487 TATAAAATTTTGTTAACCTCTC
1 TATGAAATTTCGATAACCTCCC
*
2509 TA-GCAAATTTTGATAA
1 TATG-AAATTTCGATAA
2525 GCACAAATTT
Statistics
Matches: 101, Mismatches: 16, Indels: 30
0.69 0.11 0.20
Matches are distributed among these distances:
21 8 0.08
22 65 0.64
23 11 0.11
27 2 0.02
28 14 0.14
29 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.35
Consensus pattern (22 bp):
TATGAAATTTCGATAACCTCCC
Found at i:2576 original size:22 final size:22
Alignment explanation
Indices: 2551--2654 Score: 97
Period size: 22 Copynumber: 4.7 Consensus size: 22
2541 CCTCCCTCCC
* *
2551 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGATAACCTCTA
2573 TATGAAATTTTGATAA-CTAC-A
1 TATGAAATTTTGATAACCT-CTA
* *
2594 CTATGAAGTTTTGATAATCTCTA
1 -TATGAAATTTTGATAACCTCTA
* *
2617 TATGAAATTTTGGTAACCAC-A
1 TATGAAATTTTGATAACCTCTA
*
2638 CTACGAAATTTTGATAA
1 -TATGAAATTTTGATAA
2655 TCTTTCTATG
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
21 3 0.04
22 62 0.91
23 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTA
Found at i:2606 original size:44 final size:44
Alignment explanation
Indices: 2550--2654 Score: 147
Period size: 44 Copynumber: 2.4 Consensus size: 44
2540 ACCTCCCTCC
* * *
2550 CTATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACA
1 CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACCACA
* * *
2594 CTATGAAGTTTTGATAATCTCTATATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACCACA
*
2638 CTACGAAATTTTGATAA
1 CTATGAAATTTTGATAA
2655 TCTTTCTATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACCACA
Done.