Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00227.F14
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: 4890
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Found at i:511 original size:145 final size:145
Alignment explanation
Indices: 308--650 Score: 404
Period size: 146 Copynumber: 2.4 Consensus size: 145
298 TTCAATTCCC
* * * * *
308 AGCTAGAATTTGCTGAAAATCATTTTTGTTTTTGGTTGTTCGTTTGAGCATTTGAGCTTTGGTGA
1 AGCTCGAATTTGCTGAAAATCATTGTT-TTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGA
* * * * * * *
373 GATTCTTGGCTTTGGGTTAGTGTGCTTTTCGATTTTATTTCAATTCCCTTTAGTATAATT-GCC-
65 GATTCTTGGCTCTGGGTT--TGTGCTTTTCAAATTTATTCCAATACCCTTTACTATAATTACCCT
436 TTGTTTTTTTGACTTCAT
128 TTGTTTTTTTGACTTCAT
*
454 AGCTCGAATTTGCTGAAAATCATTGCTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGAG
1 AGCTCGAATTTGCTGAAAATCATTGTTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGAG
* ** *
519 ATTCTTGGCTCTGGGTTTTTTTTTTTCAAATTTATTCCAATACCCTTTACTCTAATTACCCTTTT
66 ATTCTTGGCTCTGGGTTTGTGCTTTTCAAATTTATTCCAATACCCTTTACTATAATTACCC-TTT
* * *
584 TTTTTTTTTACTTCTT
130 GTTTTTTTGACTTCAT
* * * *
600 AGTTCG-ATTTCGTTGAAAATCATTGTTTTATTGGTTATTCGCTTGAGCATT
1 AGCTCGAATTT-GCTGAAAATCATTGTTTTATTGGTTGTTCGTTTGAGCATT
651 TGATCTTTCA
Statistics
Matches: 168, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
143 31 0.18
144 2 0.01
145 55 0.33
146 80 0.48
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (145 bp):
AGCTCGAATTTGCTGAAAATCATTGTTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGAG
ATTCTTGGCTCTGGGTTTGTGCTTTTCAAATTTATTCCAATACCCTTTACTATAATTACCCTTTG
TTTTTTTGACTTCAT
Found at i:649 original size:146 final size:144
Alignment explanation
Indices: 308--960 Score: 402
Period size: 146 Copynumber: 4.4 Consensus size: 144
298 TTCAATTCCC
* * * * *
308 AGCTAGAATTTGCTGAAAATCATTTTTGTTTTTGGTTGTTCGTTTGAGCATTTGAGCTTTGGTGA
1 AGCTCGAATTTGCTGAAAATCATTGTT-TTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGA
* * * * * * *
373 GATTCTTGGCTTTGGGTTAGTGTGCTTTTCGATTTTATTTCAATTCCCTTTAGTATAATTGCCTT
65 GATTCTTGGCTCTGGGTTA-TGTGCTTTTCAAATTTATTCCAATACCCTTTACTATAATTCCCTT
438 GTTTTTTTGACTTCAT
129 GTTTTTTTGACTTCAT
*
454 AGCTCGAATTTGCTGAAAATCATTGCTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGAG
1 AGCTCGAATTTGCTGAAAATCATTGTTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGAG
* ** *
519 ATTCTTGGCTCTGGGTT-TTTTTTTTTCAAATTTATTCCAATACCCTTTACTCTAATTACCCTTT
66 ATTCTTGGCTCTGGGTTATGTGCTTTTCAAATTTATTCCAATACCCTTTACTATAATT-CCC--T
* * *
583 TTTTTTTTTTACTTCTT
128 TGTTTTTTTGACTTCAT
* * * * * * ***
600 AGTTCG-ATTTCGTTGAAAATCATTGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCATG-
1 AGCTCGAATTT-GCTGAAAATCATTGTTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGA
* * * * * * *
663 GTGTTTTTGGCTCTGGGTTAGGTTTTTTTTTTCTTTTCAAATTTA-TCTCAATACTCTTTAGTCT
65 G-ATTCTTGGCTCTGGGTTA--------TGTGCTTTTCAAATTTATTC-CAATACCCTTTACTAT
* * * *
727 AAGTGCCTTGGTTTTTTTTTTTTTAAACTTCCT
120 AATTCCCTT-G------TTTTTTT-GACTTCAT
* * * * * ***
760 AGCTCGATTTTGCTGAAAATCATTGTTATATTGGTTGTTCGTTTGACCATTTGATCTTTCATG-G
1 AGCTCGAATTTGCTGAAAATCATTGTTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGAG
* * * ** * *
824 TGTTCTTGGCTCTGAGTTAGGTTTTTTTTTTTTTCAAATTTATTTCAATACCCTTTACTCTAATT
66 -ATTCTTGGCTCT--G---GG-TTATGTGCTTTTCAAATTTATTCCAATACCCTTTACTATAATT
* *
889 GCCTTG-TTTTTTAACTTCAT
124 CCCTTGTTTTTTTGACTTCAT
* * * * *
909 ATCTCTAATTTTGCTGAAAATC-TCCGTTTTATTGGTTATTCGCTTGAGCATT
1 AGCTCGAA-TTTGCTGAAAATCAT-TGTTTTATTGGTTGTTCGTTTGAGCATT
961 TGATCTTTCG
Statistics
Matches: 411, Mismatches: 63, Indels: 62
0.77 0.12 0.12
Matches are distributed among these distances:
143 31 0.08
144 2 0.00
145 56 0.14
146 102 0.25
149 13 0.03
150 42 0.10
152 2 0.00
154 4 0.01
155 33 0.08
157 1 0.00
158 38 0.09
159 8 0.02
160 71 0.17
161 3 0.01
162 1 0.00
165 2 0.00
166 2 0.00
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.51
Consensus pattern (144 bp):
AGCTCGAATTTGCTGAAAATCATTGTTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGAG
ATTCTTGGCTCTGGGTTATGTGCTTTTCAAATTTATTCCAATACCCTTTACTATAATTCCCTTGT
TTTTTTGACTTCAT
Found at i:981 original size:150 final size:147
Alignment explanation
Indices: 406--1050 Score: 606
Period size: 150 Copynumber: 4.3 Consensus size: 147
396 GCTTTTCGAT
* * *
406 TTTATTTCAATTCCCTTTAGTATAATTGCCTTGTTTTTTTGACTTCATAGCTCGAA-TTTGCTGA
1 TTTATTTCAATACCCTTTAGTCTAATTGCCTTG-TTTTTTAACTTCATAGCTC-AATTTTGCTGA
* * * * * *** *
470 AAATCATTGCTTTATTGGTTGTTCGTTTGAGCATTCGAGCTTGGGTGAG-ATTCTTGGCTCT-G-
64 AAATCATTGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCATG-GTGTTCTTGGCTCTGGT
532 -GG--TTTTTTTTTTTCAAA
128 TGGTTTTTTTTTTTTTCAAA
* * * * * * * * * *
549 TTTATTCCAATACCCTTTACTCTAATTACCCTTTTTTTTTTTTTACTTCTTAGTTCGATTTCGTT
1 TTTATTTCAATACCCTTTAGTCTAATT-GCC---TTGTTTTTTAACTTCATAGCTCAATTTTGCT
*
614 GAAAATCATTGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCATGGTGTTTTTGGCTCTGG
62 GAAAATCATTGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCATGGTGTTCTTGGCTCT-G
679 GTTAGGTTTTTTTTTTCTTTTCAAA
126 GTT-GG-TTTTTTTTT-TTTTCAAA
* * * * *
704 TTTATCTCAATACTCTTTAGTCTAAGTGCCTTGGTTTTTTTTTTTTTAAACTTCCTAGCTCGATT
1 TTTATTTCAATACCCTTTAGTCTAATTGCCTT-G-------TTTTTT-AACTTCATAGCTCAATT
* * * *
769 TTGCTGAAAATCATTGTTATATTGGTTGTTCGTTTGACCATTTGATCTTTCATGGTGTTCTTGGC
57 TTGCTGAAAATCATTGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCATGGTGTTCTTGGC
834 TCTGAGTTAGGTTTTTTTTTTTTTCAAA
122 TCTG-GTT-GGTTTTTTTTTTTTTCAAA
* *
862 TTTATTTCAATACCCTTTACTCTAATTGCCTTGTTTTTTAACTTCATATCTCTAATTTTGCTGAA
1 TTTATTTCAATACCCTTTAGTCTAATTGCCTTGTTTTTTAACTTCATAGCTC-AATTTTGCTGAA
* * *
927 AATC-TCCGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCGTGGTGTTCTTGACTCTGGTT
65 AATCAT-TGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCATGGTGTTCTTGGCTCTGGTT
** *
991 TTTTGTGTTTTTTTTTTCAAT
129 GGTT-T-TTTTTTTTTTCAAA
* *
1012 TTTATTTCGATA-CCTTTCAGTCTAATTGCCTCGTTTTTT
1 TTTATTTCAATACCCTTT-AGTCTAATTGCCTTGTTTTTT
1051 GTTACTTCCT
Statistics
Matches: 413, Mismatches: 59, Indels: 53
0.79 0.11 0.10
Matches are distributed among these distances:
143 23 0.06
144 2 0.00
145 2 0.00
146 71 0.17
147 2 0.00
148 3 0.01
149 21 0.05
150 112 0.27
151 4 0.01
154 9 0.02
155 30 0.07
157 1 0.00
158 36 0.09
159 16 0.04
160 81 0.20
ACGTcount: A:0.17, C:0.16, G:0.15, T:0.52
Consensus pattern (147 bp):
TTTATTTCAATACCCTTTAGTCTAATTGCCTTGTTTTTTAACTTCATAGCTCAATTTTGCTGAAA
ATCATTGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCATGGTGTTCTTGGCTCTGGTTGG
TTTTTTTTTTTTTCAAA
Found at i:1098 original size:150 final size:150
Alignment explanation
Indices: 624--1118 Score: 367
Period size: 150 Copynumber: 3.2 Consensus size: 150
614 GAAAATCATT
** * * *
624 GTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCATGGTGTTTTTGGCTCTGGGTTAGGTTTT
1 GTTTTATTCATTATTCGCTTGAGCATTTGATCTTTCATGGTGTTCTTGACTCTGAGTTAGG-TTT
* * * * *
689 TTTTTTCTTTTCAAATTTATCTCAATACTCTTTAGTCTAAGTGCCTTGGTTTTTTTTTTTTTAAA
65 TTTTTT-TTTTCAAATTTATTTCAATACCCTTTACTCTAATTGCC-TCG-------TTTTTT-AA
* * * * ** * * *
754 CTTCCTAGCTC-GATTTTGCTGAAAATCAT-T
120 CTTCATATCTCTAAATTCACTCAAAA-CCTCC
* ** * * * *
784 GTTATATTGGTTGTTCGTTTGACCATTTGATCTTTCATGGTGTTCTTGGCTCTGAGTTAGGTTTT
1 GTTTTATTCATTATTCGCTTGAGCATTTGATCTTTCATGGTGTTCTTGACTCTGAGTTAGGTTTT
*
849 TTTTTTTTTCAAATTTATTTCAATACCCTTTACTCTAATTGCCTTGTTTTTTAACTTCATATCTC
66 TTTTTTTTTCAAATTTATTTCAATACCCTTTACTCTAATTGCCTCGTTTTTTAACTTCATATCTC
* ** * *
914 TAATTTTGCTGAAAATCTCC
131 TAAATTCACTCAAAACCTCC
** * **
934 GTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCGTGGTGTTCTTGACTCTG-GTT-TTTTGT
1 GTTTTATTCATTATTCGCTTGAGCATTTGATCTTTCATGGTGTTCTTGACTCTGAGTTAGGTT-T
* * * * *
997 GTTTTTTTTTTCAATTTTATTTCGATA-CCTTTCAGTCTAATTGCCTCGTTTTTTGTTACTTCCT
65 -TTTTTTTTTTCAAATTTATTTCAATACCCTTT-ACTCTAATTGCCTCG-TTTTT-TAACTTCAT
**
1061 ATCTC-AAATTCACTCAAAACCTTT
126 ATCTCTAAATTCACTCAAAACCTCC
*
1085 GTTTT-TTCATTATTAGCTTGAGCA-TTGAATCTTT
1 GTTTTATTCATTATTCGCTTGAGCATTTG-ATCTTT
1119 AGTAATCTTC
Statistics
Matches: 286, Mismatches: 41, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
148 2 0.01
149 24 0.08
150 126 0.44
151 22 0.08
152 12 0.04
157 2 0.01
158 34 0.12
159 9 0.03
160 55 0.19
ACGTcount: A:0.17, C:0.16, G:0.15, T:0.52
Consensus pattern (150 bp):
GTTTTATTCATTATTCGCTTGAGCATTTGATCTTTCATGGTGTTCTTGACTCTGAGTTAGGTTTT
TTTTTTTTTCAAATTTATTTCAATACCCTTTACTCTAATTGCCTCGTTTTTTAACTTCATATCTC
TAAATTCACTCAAAACCTCC
Found at i:1152 original size:150 final size:150
Alignment explanation
Indices: 848--1152 Score: 316
Period size: 150 Copynumber: 2.0 Consensus size: 150
838 AGTTAGGTTT
*
848 TTTTTTTTTTCAAATTTATTTCAATACCCTTTACTCTAATTGCCTTGTTTTTTAACTTCATATCT
1 TTTTTTTTTTCAAATTTATTTCAATACCCTTTACTCTAATTGCCTCGTTTTTTAACTTCATATCT
* ** * * ** * * ** *
913 CTAATTTTGCTGAAAATCTCCGTTTTATTGGTTATTCGCTTGAGCATTTGATCTTTCGTGGTGTT
66 CTAAATTCACTCAAAACCTCCGTTTTATTCATTATTAGCTTGAGCATTTGATCTTTAGTAATCTT
* *
978 CTTGACTCTGGTTTTTTGTG
131 CTTGACTCTGGTGTTTTGTA
* * * * *
998 TTTTTTTTTTCAATTTTATTTCGATA-CCTTTCAGTCTAATTGCCTCGTTTTTTGTTACTTCCTA
1 TTTTTTTTTTCAAATTTATTTCAATACCCTTT-ACTCTAATTGCCTCG-TTTTT-TAACTTCATA
**
1062 TCTC-AAATTCACTCAAAACCTTTGTTTT-TTCATTATTAGCTTGAGCA-TTGAATCTTTAGTAA
63 TCTCTAAATTCACTCAAAACCTCCGTTTTATTCATTATTAGCTTGAGCATTTG-ATCTTTAGTAA
1124 TCTTCTT-AGCTCTGGGTGTTTT-TA
127 TCTTCTTGA-CTCT-GGTGTTTTGTA
1148 TTTTT
1 TTTTT
1153 AAATTCAATA
Statistics
Matches: 127, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
149 9 0.07
150 77 0.61
151 29 0.23
152 12 0.09
ACGTcount: A:0.18, C:0.17, G:0.12, T:0.53
Consensus pattern (150 bp):
TTTTTTTTTTCAAATTTATTTCAATACCCTTTACTCTAATTGCCTCGTTTTTTAACTTCATATCT
CTAAATTCACTCAAAACCTCCGTTTTATTCATTATTAGCTTGAGCATTTGATCTTTAGTAATCTT
CTTGACTCTGGTGTTTTGTA
Done.