Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007855.1 Corchorus capsularis cultivar CVL-1 contig07876, 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: 4821
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:206 original size:4 final size:4
Alignment explanation
Indices: 197--234 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
187 CACTCCAAAA
* *
197 AAAT AAAT AAAT AAAT AAAT AAA- ATAT AAAA AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
235 AATAAAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 2 0.07
4 27 0.93
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:220 original size:23 final size:21
Alignment explanation
Indices: 195--241 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
185 CCCACTCCAA
*
195 AAAAATAAATAAATAAATAAAT
1 AAAAATAAA-AAATAAAAAAAT
*
217 AAAATATAAAAAA-ATAAAAAT
1 AAAA-ATAAAAAATAAAAAAAT
238 AAAA
1 AAAA
242 TGAAATGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAAATAAAAAATAAAAAAAT
Found at i:235 original size:8 final size:8
Alignment explanation
Indices: 193--236 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
183 TTCCCACTCC
193 AAAAAAAT
1 AAAAAAAT
*
201 AAATAAAT
1 AAAAAAAT
*
209 AAATAAAT
1 AAAAAAAT
*
217 -AAAATAT
1 AAAAAAAT
224 AAAAAAAT
1 AAAAAAAT
232 AAAAA
1 AAAAA
237 TAAAATGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 5 0.16
8 26 0.84
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAAAAT
Found at i:236 original size:16 final size:16
Alignment explanation
Indices: 193--238 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
183 TTCCCACTCC
193 AAAAAAATAAATAA-AT
1 AAAAAAATAAA-AATAT
*
209 AAATAAAT-AAAATAT
1 AAAAAAATAAAAATAT
224 AAAAAAATAAAAATA
1 AAAAAAATAAAAATA
239 AAATGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAAAATAAAAATAT
Found at i:242 original size:21 final size:23
Alignment explanation
Indices: 193--241 Score: 50
Period size: 23 Copynumber: 2.2 Consensus size: 23
183 TTCCCACTCC
193 AAAAAAATAAATAAAT-AAATA-
1 AAAAAAATAAATAAATAAAATAT
*
214 AATAAAATATAAAAAAATAAAA-AT
1 AA-AAAA-ATAAATAAATAAAATAT
238 AAAA
1 AAAA
242 TGAAATGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
21 2 0.09
22 4 0.17
23 12 0.52
24 5 0.22
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAAAATAAATAAATAAAATAT
Found at i:327 original size:14 final size:14
Alignment explanation
Indices: 310--396 Score: 77
Period size: 14 Copynumber: 5.9 Consensus size: 14
300 ATGGCTTTTT
310 TTTTTTCAAAAATG
1 TTTTTTCAAAAATG
*
324 TTTTTTCAAAAAAG
1 TTTTTTCAAAAATG
* *
338 TTTTTTAAAAAGAGGG
1 TTTTTTCAAAA-A-TG
354 TCATGATTTTCAAAAATG
1 T--T--TTTTCAAAAATG
*
372 TTTTGTCAAAAATG
1 TTTTTTCAAAAATG
386 -TTTTTCAAAAA
1 TTTTTTCAAAAA
397 AATAATTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
13 10 0.17
14 34 0.57
15 1 0.02
16 3 0.05
18 3 0.05
19 1 0.02
20 8 0.13
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (14 bp):
TTTTTTCAAAAATG
Found at i:1081 original size:16 final size:16
Alignment explanation
Indices: 1062--1093 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1052 AAAGAGGGGG
1062 ATGAAAAAATAAAAAT
1 ATGAAAAAATAAAAAT
*
1078 ATGAGAAAATAAAAAT
1 ATGAAAAAATAAAAAT
1094 GGAAAAGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (16 bp):
ATGAAAAAATAAAAAT
Found at i:1904 original size:23 final size:23
Alignment explanation
Indices: 1874--1928 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1864 TTATCATGCA
*
1874 TTTTGCATTGCATCATGAAACAT
1 TTTTGCATCGCATCATGAAACAT
1897 TTTTGCATCGCATCATGAAACAT
1 TTTTGCATCGCATCATGAAACAT
1920 TTTTGCATC
1 TTTTGCATC
1929 AAAGTATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (23 bp):
TTTTGCATCGCATCATGAAACAT
Found at i:2177 original size:24 final size:24
Alignment explanation
Indices: 2123--2220 Score: 90
Period size: 24 Copynumber: 4.0 Consensus size: 24
2113 TGATCCAACT
* * *
2123 CTTCCATTCTTCAATT-TTTCAATA
1 CTTCAATTCTTCAATTACTT-AATG
* * *
2147 CTCCAATTCTTCGATTACTTATTG
1 CTTCAATTCTTCAATTACTTAATG
* *
2171 CTTCAATTTTTCAATTACTCAATG
1 CTTCAATTCTTCAATTACTTAATG
2195 CTTCAATTCTTCAATTCACTTCAATG
1 CTTCAATTCTTCAATT-ACTT-AATG
2221 ACCCAGGGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
24 49 0.84
25 5 0.09
26 4 0.07
ACGTcount: A:0.26, C:0.24, G:0.04, T:0.46
Consensus pattern (24 bp):
CTTCAATTCTTCAATTACTTAATG
Found at i:2185 original size:8 final size:8
Alignment explanation
Indices: 2122--2211 Score: 69
Period size: 8 Copynumber: 11.2 Consensus size: 8
2112 ATGATCCAAC
*
2122 TCTTCCAT
1 TCTTCAAT
2130 TCTTCAAT
1 TCTTCAAT
*
2138 TTTTCAAT
1 TCTTCAAT
* *
2146 ACTCCAAT
1 TCTTCAAT
*
2154 TCTTCGAT
1 TCTTCAAT
2162 TACTT--AT
1 T-CTTCAAT
2169 TGCTTCAAT
1 T-CTTCAAT
*
2178 TTTTCAAT
1 TCTTCAAT
2186 TAC-TCAAT
1 T-CTTCAAT
*
2194 GCTTCAAT
1 TCTTCAAT
2202 TCTTCAAT
1 TCTTCAAT
2210 TC
1 TC
2212 ACTTCAATGA
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
7 7 0.11
8 51 0.80
9 6 0.09
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.48
Consensus pattern (8 bp):
TCTTCAAT
Found at i:2369 original size:22 final size:22
Alignment explanation
Indices: 2314--2499 Score: 150
Period size: 22 Copynumber: 8.5 Consensus size: 22
2304 TTCATTTCCT
* * *
2314 AATTATTCAATGCCTCAATTCC
1 AATTCTTCAATGCTTCAATTTC
*
2336 AAATT-TTTAATGCTTCAATTTC
1 -AATTCTTCAATGCTTCAATTTC
*
2358 AATTCTTCAATGTTTC--TTTC
1 AATTCTTCAATGCTTCAATTTC
*
2378 AATTCCTT-AATGATTCAATTTC
1 AATT-CTTCAATGCTTCAATTTC
* *
2400 AATAT-TTCAATTCTTCAAATTC
1 AAT-TCTTCAATGCTTCAATTTC
* * *
2422 AATTCATCAATGTTTCAGTTTC
1 AATTCTTCAATGCTTCAATTTC
* *
2444 AATAT-TCCAATGCTTCAACTTC
1 AAT-TCTTCAATGCTTCAATTTC
* * *
2466 AATTCTTCGATGTTTCAATTGC
1 AATTCTTCAATGCTTCAATTTC
2488 AATTCTTCAATG
1 AATTCTTCAATG
2500 TATAGCAAAA
Statistics
Matches: 129, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
20 15 0.12
21 11 0.09
22 97 0.75
23 6 0.05
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.45
Consensus pattern (22 bp):
AATTCTTCAATGCTTCAATTTC
Found at i:2410 original size:14 final size:14
Alignment explanation
Indices: 2391--2454 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
2381 TCCTTAATGA
2391 TTCAATTTCAATAT
1 TTCAATTTCAATAT
2405 TTCAATTCTTCAA-A-
1 TTCAA-T-TTCAATAT
*
2419 TTCAATTCATCAATGT
1 TTCAATT--TCAATAT
*
2435 TTCAGTTTCAATAT
1 TTCAATTTCAATAT
*
2449 TCCAAT
1 TTCAAT
2455 GCTTCAACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
12 1 0.03
13 1 0.03
14 24 0.62
15 2 0.05
16 11 0.28
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (14 bp):
TTCAATTTCAATAT
Done.