Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000250.1 Corchorus capsularis cultivar CVL-1 contig00250, 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, 783
Length: 1305
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Found at i:98 original size:41 final size:40
Alignment explanation
Indices: 5--409 Score: 348
Period size: 41 Copynumber: 9.8 Consensus size: 40
1 ATTC
*
5 CCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTT
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTT
* * *
45 CACAGTCTGTCCTTCCCCACCGGAAGGTGTTGTTTAGGTTT
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA-GTTT
* * *
86 CCCAGTTTGTCCTTCCCCACCGGAAGGTGCTATTTATGTTT
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA-GTTT
* ** * *
127 CCCAGTCTGCCCTT-CTTAGTCGGAAGGTGTTGTTTTGTTT
1 CCCAGTTTGCCCTTCCCCA-CCGGAAGGTGTTGTTTAGTTT
* * * *
167 TCCAGTTTTCCCTTCCCCAACGGAAGGTGTTGTCTAAGTCTATGCTT
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG--T---T-TA-GTTT
* * * *
214 CCCAGTTTGTCATTCCCCATCGGAAGGTGTTATTTAGTTT
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTT
* * *
254 TCCTGTTTTGCCCTTCCCCACCAGAAGGTGTTGTTTAGATTT
1 CCCAG-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAG-TTT
** * * **
296 CCCAGTTTGCCCTTCCATATCGGAAGGTGTTGTTCACATT
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTT
* **
336 CCC-GTTTTGCCCTTTCCTCACCGGAAGGTGTTGTTTACATT
1 CCCAG-TTTGCCC-TTCCCCACCGGAAGGTGTTGTTTAGTTT
* *
377 -CCTGTCTTGCCCTTCCTCACCGGAAGGTGTTGT
1 CCCAGT-TTGCCCTTCCCCACCGGAAGGTGTTGT
410 CTACTTTTCT
Statistics
Matches: 297, Mismatches: 52, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
39 1 0.00
40 103 0.35
41 153 0.52
42 8 0.03
45 2 0.01
46 1 0.00
47 29 0.10
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (40 bp):
CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTT
Found at i:266 original size:128 final size:129
Alignment explanation
Indices: 12--328 Score: 330
Period size: 128 Copynumber: 2.5 Consensus size: 129
2 TTCCCCATTT
* * * * * *
12 TGCCCTTCCCCACCGGAAGGTGTTGTTTAG-TTTCACAGTCTGTCCTTCCCCACCGGAAGGTGTT
1 TGCCCTTCCCCACCAGAAGGTGTTGTTTAGATTTCCCAGTTTGCCCTTCCACAACGGAAGGTGTT
* * *
76 G--T---T-TAGGTTTCCCAGTTTGTCCTTCCCCACCGGAAGGTGCTATTTATGTTTCCCAGTC
66 GTCTAAGTCTATGCTTCCCAGTTTGTCATTCCCCACCGGAAGGTGCTATTTATGTTTCCCAGTC
** * * * * * *
134 TGCCCTT-CTTAGTCGGAAGGTGTTGTTTTG-TTTTCCAGTTTTCCCTTCCCCAACGGAAGGTGT
1 TGCCCTTCCCCA-CCAGAAGGTGTTGTTTAGATTTCCCAGTTTGCCCTTCCACAACGGAAGGTGT
* * * *
197 TGTCTAAGTCTATGCTTCCCAGTTTGTCATTCCCCATCGGAAGGTGTTATTTA-GTTTTCCTGTT
65 TGTCTAAGTCTATGCTTCCCAGTTTGTCATTCCCCACCGGAAGGTGCTATTTATGTTTCCCAG-T
*
261 T
129 C
* *
262 TGCCCTTCCCCACCAGAAGGTGTTGTTTAGATTTCCCAGTTTGCCCTTCCATATCGGAAGGTGTT
1 TGCCCTTCCCCACCAGAAGGTGTTGTTTAGATTTCCCAGTTTGCCCTTCCACAACGGAAGGTGTT
327 GT
66 GT
329 TCACATTCCC
Statistics
Matches: 157, Mismatches: 28, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
121 2 0.01
122 52 0.33
124 1 0.01
127 8 0.05
128 61 0.39
129 33 0.21
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.38
Consensus pattern (129 bp):
TGCCCTTCCCCACCAGAAGGTGTTGTTTAGATTTCCCAGTTTGCCCTTCCACAACGGAAGGTGTT
GTCTAAGTCTATGCTTCCCAGTTTGTCATTCCCCACCGGAAGGTGCTATTTATGTTTCCCAGTC
Found at i:392 original size:210 final size:209
Alignment explanation
Indices: 17--412 Score: 469
Period size: 210 Copynumber: 1.9 Consensus size: 209
7 CATTTTGCCC
* * *
17 TTCCCCACCGGAAGGTGTTGTTTAGTTTCACAGTCTGTCCTTCCCCACCGGAAGGTGTTGTTTAG
1 TTCCCCACCGGAAGGTGTTATTTAGTTTCACAGTCTGCCCTTCCCCACCAGAAGGTGTTGTTTAG
* * * * ** * *
82 GTTTCCCAGTTTGTCCTTCCCCACCGGAAGGTGCTATTTATGTTTCCCAGTCTGCCCTTCTTAGT
66 ATTTCCCAGTTTGCCCTTCCACACCGGAAGGTGCTATTCATCATTCCCAGTCTGCCCTTCTCAGC
*** *
147 CGGAAGGTGTTGTTTTGTTTTCCAGTTTTCCCTTCCCCAACGGAAGGTGTTGTCTAAGTCTATGC
131 CGGAAGGTGTTGTTTTACATTCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTCTAAGTCTATGC
212 TTCCCAGTTTGTCA
196 TTCCCAGTTTGTCA
* * *
226 TTCCCCATCGGAAGGTGTTATTTAGTTTTC-CTGTTTTGCCCTTCCCCACCAGAAGGTGTTGTTT
1 TTCCCCACCGGAAGGTGTTATTTAG-TTTCACAG-TCTGCCCTTCCCCACCAGAAGGTGTTGTTT
* * * * *
290 AGATTTCCCAGTTTGCCCTTCCATATCGGAAGGTGTTGTTCA-CATTCCC-GTTTTGCCCTTTCC
64 AGATTTCCCAGTTTGCCCTTCCACACCGGAAGGTGCTATTCATCATTCCCAG-TCTGCCC-TT-C
* * *
353 TCA-CCGGAAGGTGTTG-TTTACATTCCTGTCTTGCCCTTCCTCACCGGAAGGTGTTGTCTA
126 TCAGCCGGAAGGTGTTGTTTTACATTCCAGT-TTGCCCTTCCCCAACGGAAGGTGTTGTCTA
413 CTTTTCTTGT
Statistics
Matches: 155, Mismatches: 26, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
208 1 0.01
209 45 0.29
210 106 0.68
211 3 0.02
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (209 bp):
TTCCCCACCGGAAGGTGTTATTTAGTTTCACAGTCTGCCCTTCCCCACCAGAAGGTGTTGTTTAG
ATTTCCCAGTTTGCCCTTCCACACCGGAAGGTGCTATTCATCATTCCCAGTCTGCCCTTCTCAGC
CGGAAGGTGTTGTTTTACATTCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTCTAAGTCTATGC
TTCCCAGTTTGTCA
Done.