Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g01356.P1
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: 23603
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:1278 original size:26 final size:28
Alignment explanation
Indices: 1249--1317 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 28
1239 AAGATGACTG
1249 TATAAAAAATT-TT-AATAAATAAAA-AA
1 TATAAAAAATTATTAAAT-AATAAAATAA
* *
1275 TATATAAAATTATTAAATATTAAAATAA
1 TATAAAAAATTATTAAATAATAAAATAA
*
1303 TATAAGAAAAATATT
1 TATAA-AAAATTATT
1318 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.29
27 8 0.23
28 9 0.26
29 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (28 bp):
TATAAAAAATTATTAAATAATAAAATAA
Found at i:1761 original size:21 final size:20
Alignment explanation
Indices: 1736--1774 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1726 AATATATAAT
*
1736 TTTAATTACCTAAACCCAAAA
1 TTTAACTACC-AAACCCAAAA
*
1757 TTTAACTACCCAACCCAA
1 TTTAACTACCAAACCCAA
1775 CCAACAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.26
Consensus pattern (20 bp):
TTTAACTACCAAACCCAAAA
Found at i:4060 original size:3 final size:3
Alignment explanation
Indices: 4054--4324 Score: 176
Period size: 3 Copynumber: 90.7 Consensus size: 3
4044 AATAATAATG
* * * **
4054 TTA TTA TTA TTT TTA CTA TTA TTGT TTA TTA TCG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * *
4100 CTA CTA TTA TTA TTA TTA TT- TTA TT- TTA CTA TTA TT- TATA TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT-A
* * * * * *
4144 TTA TTG TTA TTA TTA TTA CTA TCA TTA TTA TTT TTA CTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
4192 TTT TCTA TAA TTA TTA TT- TCTA TCA TTA TTA TTA TTA TT- TTG CTA
1 TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * * * *
4237 TTA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TTA -TC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
4284 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4325 TTTAAAACCA
Statistics
Matches: 216, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
2 9 0.04
3 198 0.92
4 9 0.04
ACGTcount: A:0.29, C:0.09, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:10770 original size:59 final size:59
Alignment explanation
Indices: 10634--10770 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 59
10624 AGTGTTAACT
*
10634 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTAACAGAGTATATTG
1 GGCCTT-GCCCATATCAGTATTAATCTGGGCCATAGCCCCTTACAGT-ACAGAGTATATTG
* *
10695 GGCCTAGCCCATATCAGTATTAATCTGGGCCGTAG-CCCTATACAAGT-C-GAGATATATTG
1 GGCCTTGCCCATATCAGTATTAATCTGGGCCATAGCCCCT-TAC-AGTACAGAG-TATATTG
10754 GGCCTTGCCCATATCAG
1 GGCCTTGCCCATATCAG
10771 CACAGTTGGG
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
58 3 0.04
59 28 0.41
60 30 0.43
61 8 0.12
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (59 bp):
GGCCTTGCCCATATCAGTATTAATCTGGGCCATAGCCCCTTACAGTACAGAGTATATTG
Found at i:13202 original size:15 final size:15
Alignment explanation
Indices: 13165--13193 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13155 TTTTTCTATC
13165 TAATAATAATAATTA
1 TAATAATAATAATTA
13180 TAATAATAATAATT
1 TAATAATAATAATT
13194 TTATAAATAT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:19114 original size:21 final size:20
Alignment explanation
Indices: 19089--19127 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
19079 ATTTATTTAT
*
19089 TTTAATTACCTAAACCCAAAA
1 TTTAACTACC-AAACCCAAAA
*
19110 TTTAACTACCCAACCCAA
1 TTTAACTACCAAACCCAA
19128 CCAACAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.26
Consensus pattern (20 bp):
TTTAACTACCAAACCCAAAA
Found at i:20864 original size:64 final size:64
Alignment explanation
Indices: 20785--20909 Score: 205
Period size: 64 Copynumber: 2.0 Consensus size: 64
20775 TTTTTTTGTG
* *
20785 CTCTTTTTGTTGATTTGCTCTACAGAAACTCAAGGAAAAAGCTGCATTCAGAAACCCAGATTCA
1 CTCTTTTTGTTGATTTACTCTACAGAAACTCAAGGAAAAACCTGCATTCAGAAACCCAGATTCA
* * *
20849 CTCTTTTTGTTGATTTACTCTACAGAAACTCAAGGACAAACCTGTATTCAGAAACCTAGAT
1 CTCTTTTTGTTGATTTACTCTACAGAAACTCAAGGAAAAACCTGCATTCAGAAACCCAGAT
20910 GAATTTTACT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (64 bp):
CTCTTTTTGTTGATTTACTCTACAGAAACTCAAGGAAAAACCTGCATTCAGAAACCCAGATTCA
Done.