Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002540.1 Corchorus capsularis cultivar CVL-1 contig02548, 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, 936
Length: 1561
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:1146 original size:15 final size:15
Alignment explanation
Indices: 1126--1169 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
1116 TTAATTTCGA
1126 TATAGTACTATATAG
1 TATAGTACTATATAG
1141 TATAGTACTATATAG
1 TATAGTACTATATAG
1156 TATAGTACTATATA
1 TATAGTACTATATA
1170 ACTGCAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (15 bp):
TATAGTACTATATAG
Found at i:1329 original size:27 final size:30
Alignment explanation
Indices: 1300--1363 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
1290 TTATTTTTAT
1300 TCTATTTTCTATATTC-T-ATT-TATTTAT
1 TCTATTTTCTATATTCATAATTCTATTTAT
* *
1327 TCTATATTCTTTATTCTATAATTCTATTTAT
1 TCTATTTTCTATATTC-ATAATTCTATTTAT
1358 TCTATT
1 TCTATT
1364 ATATATAGTT
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:1334 original size:7 final size:7
Alignment explanation
Indices: 1297--1353 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
1287 AATTTATTTT
1297 TATTCTA
1 TATTCTA
*
1304 TTTTCTA
1 TATTCTA
1311 TATTCTA
1 TATTCTA
* *
1318 T-TTATT
1 TATTCTA
1324 TATTCTA
1 TATTCTA
*
1331 TATTCTT
1 TATTCTA
1338 TATTCTA
1 TATTCTA
1345 TAATTCTA
1 T-ATTCTA
1353 T
1 T
1354 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:1346 original size:14 final size:14
Alignment explanation
Indices: 1291--1362 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
1281 ATTCGAAATT
1291 TATT-TTTATTCTA
1 TATTCTTTATTCTA
* *
1304 TTTTCTATATTCTA
1 TATTCTTTATTCTA
*
1318 T-TTATTTATTCTA
1 TATTCTTTATTCTA
1331 TATTCTTTATTCTA
1 TATTCTTTATTCTA
1345 TAATTCTATTTATTCTA
1 T-ATTC--TTTATTCTA
1362 T
1 T
1363 TATATATAGT
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:1363 original size:22 final size:22
Alignment explanation
Indices: 1311--1368 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
1301 CTATTTTCTA
*
1311 TATTCTATTTATTTATTCTATAT
1 TATTCTATTTA-TAATTCTATAT
*
1334 TCTT-TATTCTATAATTCTAT-T
1 TATTCTATT-TATAATTCTATAT
1355 TATTCTATTATATA
1 TATTCTATT-TATA
1369 TAGTTAGAAT
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:1390 original size:23 final size:23
Alignment explanation
Indices: 1362--1409 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1352 ATTTATTCTA
1362 TTATATATAGTTAGAATATATTT
1 TTATATATAGTTAGAATATATTT
1385 TTATATATAGTTAGAATATATTT
1 TTATATATAGTTAGAATATATTT
1408 TT
1 TT
1410 GAGAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (23 bp):
TTATATATAGTTAGAATATATTT
Found at i:1416 original size:14 final size:14
Alignment explanation
Indices: 1397--1425 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1387 ATATATAGTT
1397 AGAATATATTTTTG
1 AGAATATATTTTTG
1411 AGAATATATTTTTG
1 AGAATATATTTTTG
1425 A
1 A
1426 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:1417 original size:25 final size:23
Alignment explanation
Indices: 1366--1418 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 23
1356 ATTCTATTAT
*
1366 ATATAGTTAGAATATATTTTTAT
1 ATATAGTTAGAATATATTTTTAA
1389 ATATAGTTAGAATATATTTTTGAGA
1 ATATAGTTAGAATATATTTTT-A-A
1414 ATATA
1 ATATA
1419 TTTTTGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 21 0.78
24 1 0.04
25 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (23 bp):
ATATAGTTAGAATATATTTTTAA
Found at i:1498 original size:12 final size:12
Alignment explanation
Indices: 1481--1517 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1471 AATAAAAATT
1481 TATGAAATTATG
1 TATGAAATTATG
1493 TATGAAATTATG
1 TATGAAATTATG
1505 TATGAAATTATG
1 TATGAAATTATG
1517 T
1 T
1518 TTATGAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (12 bp):
TATGAAATTATG
Found at i:1531 original size:13 final size:13
Alignment explanation
Indices: 1479--1537 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 13
1469 AGAATAAAAA
1479 TTTATGAAATTATG
1 TTTATG-AATTATG
1493 --TATGAAATTATG
1 TTTATG-AATTATG
1505 --TATGAAATTATG
1 TTTATG-AATTATG
*
1517 TTTATGAATTCTG
1 TTTATGAATTATG
1530 TTTATGAA
1 TTTATGAA
1538 AAGATCTATC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
12 24 0.57
13 14 0.33
14 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (13 bp):
TTTATGAATTATG
Done.