Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g02497.F1
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: 4087
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Found at i:1284 original size:45 final size:45
Alignment explanation
Indices: 1227--1499 Score: 410
Period size: 45 Copynumber: 6.2 Consensus size: 45
1217 AGCTTTCCTC
* * *
1227 TCTT-CTTCTCATCCTCTATTCTCTTCTTCTCTTTTTCTTTTCGT
1 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
* *
1271 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCATTGCTTTTCGT
1 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
* * * * *
1316 TCTTGGTTCTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGT
1 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
* *
1361 TCTTGGTTCTTATCCTC-TTT-TC-TCTTGTCCTTTTCTTTTCGT
1 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
1403 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
1 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
1448 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
1 TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
1493 TCTTGCT
1 TCTTGCT
1500 CCTCTAATTT
Statistics
Matches: 210, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
42 33 0.16
43 5 0.02
44 9 0.04
45 163 0.78
ACGTcount: A:0.04, C:0.30, G:0.07, T:0.59
Consensus pattern (45 bp):
TCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGT
Found at i:1444 original size:132 final size:135
Alignment explanation
Indices: 1232--1497 Score: 421
Period size: 132 Copynumber: 2.0 Consensus size: 135
1222 TCCTCTCTTC
*
1232 TTCTCATCCTCTATTCTCTTCTTCTCTTTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTT
1 TTCTCATCCTCTATTCTCTTCTTCTCCTTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTT
*
1297 CTTGTCCATTGCTTTTCGTTCTTGGTTCTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTT
66 CTTGTCCATTGCTTTTCGTTCTTGCTTCTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTT
1362 CTTGG
131 CTTGG
* *
1367 TTCTTATCCTCT-TT-TC-TCTTGTCCTTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTT
1 TTCTCATCCTCTATTCTCTTCTTCTCCTTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTT
* * * * * *
1429 CTTGTCCTTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGTT
66 CTTGTCCATTGCTTTTCGTTCTTGCTTCTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTT
1494 CTTG
131 CTTG
1498 CTCCTCTAAT
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
132 106 0.88
133 2 0.02
134 2 0.02
135 11 0.09
ACGTcount: A:0.04, C:0.30, G:0.08, T:0.59
Consensus pattern (135 bp):
TTCTCATCCTCTATTCTCTTCTTCTCCTTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTT
CTTGTCCATTGCTTTTCGTTCTTGCTTCTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTT
CTTGG
Found at i:1552 original size:132 final size:131
Alignment explanation
Indices: 1259--1536 Score: 362
Period size: 132 Copynumber: 2.1 Consensus size: 131
1249 CTTCTTCTCT
* *
1259 TTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCATTGCTTTTCGTTCTTGGTT
1 TTTTCTCTTCGTTCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCATTGCTTTTCGTTCTTGCTT
* * * *
1324 CTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTTCTTGGTTCTTATCCTCTTTTCTCTTGT
66 CTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTTCTTGCTTCTAATCCTCTCTTCTCTTAT
1389 CC
131 -C
* * *
1391 TTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGTTCTTGCTT
1 TTTTCTCTTCGTTCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCATTGCTTTTCGTTCTTGCTT
* * * * *
1456 CTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGTTCTTGCTCCTCTAAT-TTCTGCTTCTGC
66 CTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTTCTTGCT--TCTAATCCTCT-CTTCT-C
1520 TTAT-
127 TTATC
1524 TTTTCGTCTTCGT
1 TTTTC-TCTTCGT
1537 CTTCGTTTCG
Statistics
Matches: 128, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
132 101 0.79
133 8 0.06
134 15 0.12
135 4 0.03
ACGTcount: A:0.04, C:0.29, G:0.09, T:0.59
Consensus pattern (131 bp):
TTTTCTCTTCGTTCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCATTGCTTTTCGTTCTTGCTT
CTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTTCTTGCTTCTAATCCTCTCTTCTCTTAT
C
Found at i:1562 original size:132 final size:131
Alignment explanation
Indices: 1259--1569 Score: 328
Period size: 132 Copynumber: 2.4 Consensus size: 131
1249 CTTCTTCTCT
* ** * *
1259 TTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCATTGCTTTTCGTTCTTGGTT
1 TTTTCTCTTCGTTCTTGCTTCTCATCCTCTTGCCTCTTCTTGTCCTTTGCTTTTCGTTCTTGCTT
* * * *
1324 CTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTTCTTGGTTCTTATCCTCTTTTCTCTTGT
66 CTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTTCTTGCTTCTAATCCTCTCTTCTCTTAT
1389 CC
131 -C
* ** *
1391 TTTTCTTTTCGTTCTTGCTTCTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGTTCTTGCTT
1 TTTTCTCTTCGTTCTTGCTTCTCATCCTCTTGCCTCTTCTTGTCCTTTGCTTTTCGTTCTTGCTT
* * * * *
1456 CTCATCCTCTTTTCTCTTCTTGTCCTTTTCTTTTCGTTCTTGCTCCTCTAAT-TTCTGCTTCTGC
66 CTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTTCTTGCT--TCTAATCCTCT-CTTCT-C
1520 TTAT-
127 TTATC
* *
1524 TTTTCGTCTTCG-TCTT-CGTT-TCGTCCTC-TGCCTGCTTCTTATCCTT
1 TTTTC-TCTTCGTTCTTGC-TTCTCATCCTCTTGCCT-CTTCTTGTCCTT
1570 CCCTTGCTGT
Statistics
Matches: 155, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
131 3 0.02
132 120 0.77
133 14 0.09
134 14 0.09
135 4 0.03
ACGTcount: A:0.04, C:0.30, G:0.09, T:0.58
Consensus pattern (131 bp):
TTTTCTCTTCGTTCTTGCTTCTCATCCTCTTGCCTCTTCTTGTCCTTTGCTTTTCGTTCTTGCTT
CTCATCCTCGTTTATCTTCTTCTCCATTTCTTTTCGTTCTTGCTTCTAATCCTCTCTTCTCTTAT
C
Found at i:1602 original size:6 final size:6
Alignment explanation
Indices: 1576--1651 Score: 80
Period size: 6 Copynumber: 12.7 Consensus size: 6
1566 CCTTCCCTTG
* * * * * * *
1576 CTGTGC CTGTGG TTGTTC CTGTGC CTGTGG TTGTGC CTGTGG TTGTGC
1 CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC
*
1624 CTGTGC CTGTGC CTGTTC CTGTGC CTGT
1 CTGTGC CTGTGC CTGTGC CTGTGC CTGT
1652 TCACGTGCCT
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.00, C:0.25, G:0.34, T:0.41
Consensus pattern (6 bp):
CTGTGC
Found at i:2486 original size:27 final size:27
Alignment explanation
Indices: 2448--2502 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2438 TCAGATGTCT
2448 CGTCCTTGGACTTTGGATCCCCAGCAG
1 CGTCCTTGGACTTTGGATCCCCAGCAG
2475 CGTCCTTGGACTTTGGATCCCCAGCAG
1 CGTCCTTGGACTTTGGATCCCCAGCAG
2502 C
1 C
2503 CGTATCAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (27 bp):
CGTCCTTGGACTTTGGATCCCCAGCAG
Done.