Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002842.1 Corchorus olitorius cultivar O-4 contig02844, 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: 1716
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1075 original size:15 final size:15
Alignment explanation
Indices: 1055--1083 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1045 TTAATTTCGA
1055 TATAGTACTATATAG
1 TATAGTACTATATAG
1070 TATAGTACTATATA
1 TATAGTACTATATA
1084 ACTGCAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (15 bp):
TATAGTACTATATAG
Found at i:1249 original size:27 final size:30
Alignment explanation
Indices: 1220--1283 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
1210 TTATTTTTAT
1220 TCTATTTTCTATATTC-T-ATT-TATTTAT
1 TCTATTTTCTATATTCATAATTCTATTTAT
* *
1247 TCTATATTCTTTATTCTATAATTCTATTTAT
1 TCTATTTTCTATATTC-ATAATTCTATTTAT
1278 TCTATT
1 TCTATT
1284 ATATATAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 14 0.47
29 1 0.03
30 3 0.10
31 12 0.40
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.64
Consensus pattern (30 bp):
TCTATTTTCTATATTCATAATTCTATTTAT
Found at i:1254 original size:7 final size:7
Alignment explanation
Indices: 1217--1273 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
1207 AATTTATTTT
1217 TATTCTA
1 TATTCTA
*
1224 TTTTCTA
1 TATTCTA
1231 TATTCTA
1 TATTCTA
* *
1238 T-TTATT
1 TATTCTA
1244 TATTCTA
1 TATTCTA
*
1251 TATTCTT
1 TATTCTA
1258 TATTCTA
1 TATTCTA
1265 TAATTCTA
1 T-ATTCTA
1273 T
1 T
1274 TTATTCTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
6 4 0.10
7 29 0.73
8 7 0.17
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (7 bp):
TATTCTA
Found at i:1266 original size:14 final size:14
Alignment explanation
Indices: 1211--1282 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
1201 ATTCGAAATT
1211 TATT-TTTATTCTA
1 TATTCTTTATTCTA
* *
1224 TTTTCTATATTCTA
1 TATTCTTTATTCTA
*
1238 T-TTATTTATTCTA
1 TATTCTTTATTCTA
1251 TATTCTTTATTCTA
1 TATTCTTTATTCTA
1265 TAATTCTATTTATTCTA
1 T-ATTC--TTTATTCTA
1282 T
1 T
1283 TATATATAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
13 14 0.29
14 21 0.43
15 4 0.08
17 10 0.20
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTCTTTATTCTA
Found at i:1283 original size:22 final size:22
Alignment explanation
Indices: 1231--1288 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
1221 CTATTTTCTA
*
1231 TATTCTATTTATTTATTCTATAT
1 TATTCTATTTA-TAATTCTATAT
*
1254 TCTT-TATTCTATAATTCTAT-T
1 TATTCTATT-TATAATTCTATAT
1275 TATTCTATTATATA
1 TATTCTATT-TATA
1289 TAGAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.14
22 20 0.69
23 5 0.17
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTCTATTTATAATTCTATAT
Found at i:1309 original size:14 final size:14
Alignment explanation
Indices: 1290--1318 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1280 TATTATATAT
1290 AGAATATATTTTTG
1 AGAATATATTTTTG
1304 AGAATATATTTTTG
1 AGAATATATTTTTG
1318 A
1 A
1319 TTTTCTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (14 bp):
AGAATATATTTTTG
Found at i:1373 original size:12 final size:12
Alignment explanation
Indices: 1356--1380 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1346 ATAGAAAATT
1356 TATGAAATTATG
1 TATGAAATTATG
1368 TATGAAATTATG
1 TATGAAATTATG
1380 T
1 T
1381 TTATGAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TATGAAATTATG
Found at i:1394 original size:13 final size:13
Alignment explanation
Indices: 1354--1400 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
1344 AGATAGAAAA
1354 TTTATGAAATTATG
1 TTTATG-AATTATG
1368 --TATGAAATTATG
1 TTTATG-AATTATG
*
1380 TTTATGAATTCTG
1 TTTATGAATTATG
1393 TTTATGAA
1 TTTATGAA
1401 AAGATCTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.40
13 14 0.47
14 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (13 bp):
TTTATGAATTATG
Done.