Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold10336.1
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: 3746
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:361 original size:16 final size:16
Alignment explanation
Indices: 334--378 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
324 GTAATTGAAT
334 AATTATCTTGAAATGTA
1 AATTA-CTTGAAATGTA
351 AATTACTTGAAATGTA
1 AATTACTTGAAATGTA
367 AATTACTTGAAA
1 AATTACTTGAAA
379 GGTCATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (16 bp):
AATTACTTGAAATGTA
Found at i:709 original size:15 final size:15
Alignment explanation
Indices: 689--717 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
679 AAGTGACTTG
689 TTTTCTTTACAATAA
1 TTTTCTTTACAATAA
704 TTTTCTTTACAATA
1 TTTTCTTTACAATA
718 TTTCAAAACG
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:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTCTTTACAATAA
Found at i:787 original size:27 final size:26
Alignment explanation
Indices: 749--802 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
739 TTTTAATGAT
*
749 TTTCAGACAAATATATTACCCAAAAA
1 TTTCAGACAAATATATCACCCAAAAA
* *
775 TTTCTAGATAAATATATCACCCGAAAA
1 TTTC-AGACAAATATATCACCCAAAAA
802 T
1 T
803 CGAAAATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (26 bp):
TTTCAGACAAATATATCACCCAAAAA
Found at i:966 original size:24 final size:24
Alignment explanation
Indices: 907--970 Score: 96
Period size: 23 Copynumber: 2.7 Consensus size: 24
897 TAATTCAAAT
907 TTCAAATCGAAAATTTCCTATGCA
1 TTCAAATCGAAAATTTCCTATGCA
*
931 TTC-AATCGAAAATTTCC-AGTTCA
1 TTCAAATCGAAAATTTCCTA-TGCA
954 TTCAAATCGAAAATTTC
1 TTCAAATCGAAAATTTC
971 AAATCGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 1 0.03
23 20 0.54
24 16 0.43
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (24 bp):
TTCAAATCGAAAATTTCCTATGCA
Found at i:973 original size:14 final size:14
Alignment explanation
Indices: 954--983 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
944 TTCCAGTTCA
954 TTCAAATCGAAAAT
1 TTCAAATCGAAAAT
968 TTCAAATCGAAAAT
1 TTCAAATCGAAAAT
982 TT
1 TT
984 TCAGTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (14 bp):
TTCAAATCGAAAAT
Found at i:1274 original size:45 final size:45
Alignment explanation
Indices: 1214--1301 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
1204 TATTGTATTC
* *
1214 AAATCGAAATTTTCCACTCCATTCAAATCGATAATTTCAAATCAA
1 AAATCGAAAATTTCCACTACATTCAAATCGATAATTTCAAATCAA
* **
1259 AAATCGAAAATTTCCAGTACATTCATTTCGATAATTTCAAATC
1 AAATCGAAAATTTCCACTACATTCAAATCGATAATTTCAAATC
1302 GAAATTTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (45 bp):
AAATCGAAAATTTCCACTACATTCAAATCGATAATTTCAAATCAA
Found at i:1301 original size:38 final size:38
Alignment explanation
Indices: 1259--1348 Score: 108
Period size: 38 Copynumber: 2.4 Consensus size: 38
1249 TTCAAATCAA
* **
1259 AAATCGAAAATTTCCAGTACATTCATTTCGATAATTTC
1 AAATCGAAAATTTCCACTACATTCAAATCGATAATTTC
* * *
1297 AAATCGAAATTTTTCACTGCATTCAAATCGATAATTTC
1 AAATCGAAAATTTCCACTACATTCAAATCGATAATTTC
* *
1335 AAATTGATAATTTC
1 AAATCGAAAATTTC
1349 AAATCGAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (38 bp):
AAATCGAAAATTTCCACTACATTCAAATCGATAATTTC
Found at i:1337 original size:14 final size:14
Alignment explanation
Indices: 1318--1362 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
1308 TTTCACTGCA
1318 TTCAAATCGATAAT
1 TTCAAATCGATAAT
*
1332 TTCAAATTGATAAT
1 TTCAAATCGATAAT
*
1346 TTCAAATCGAAAAT
1 TTCAAATCGATAAT
1360 TTC
1 TTC
1363 TAGAGAAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (14 bp):
TTCAAATCGATAAT
Done.