Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01059.P4
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: 18505
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:5299 original size:91 final size:95
Alignment explanation
Indices: 5145--5593 Score: 455
Period size: 91 Copynumber: 4.8 Consensus size: 95
5135 GATAAATTAT
* * * * **
5145 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCG-TGTTGATGCATGTCCCA
1 CGATGCCATGTCCCAGACATCGTCTTACACTGGCTATC-TCTAT-CGAGGCCGATGCATGTCCCA
5209 GACATGTCTTACAT-TAGCACAACTCT-TAGC
64 GACATGTCTTACATCTAGCACAACTCTCTAGC
* *
5239 CGATG-CGTGTCCCAGACA-CATCTTACACTGGCTATCTCTATCGAGGCCGATGCATGTCCCAGA
1 CGATGCCATGTCCCAGACATCGTCTTACACTGGCTATCTCTATCGAGGCCGATGCATGTCCCAGA
* * *
5302 CATGTCTTAC-TCTGGCAC-TCATCTCTGTGC
66 CATGTCTTACATCTAGCACAAC-TCTCT-AGC
* * * * * * *
5332 CGATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATATATGCG-TGCTGATGCATGTCCCA
1 CGATGCCATGTCCCAGACATCGTCTTACACTGGCTATC-TCTAT-CGAGGCCGATGCATGTCCCA
5396 GACATGTCTTACA-CTAGCACAACTCT-TAGC
64 GACATGTCTTACATCTAGCACAACTCTCTAGC
* * *
5426 CGATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATCTCTGTCGAGGCTGATGCATGTCCCAGA
1 CGATGCCATGTCCCAGACATCGTCTTACACTGGCTATCTCTATCGAGGCCGATGCATGTCCCAGA
* *
5489 CATGTCTTAC-TCTGGCAC-TCATCTCTATGC
66 CATGTCTTACATCTAGCACAAC-TCTCTA-GC
* * *
5519 CGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATAAT-GTGGCCGAAGCATGTCCCA
1 CGATGCCATGTCCCAGACATCGTCTTACACTGGCTATCTC-T-ATCGAGGCCGATGCATGTCCCA
5581 GACATGTCTTACA
64 GACATGTCTTACA
5594 CTGGCGCATA
Statistics
Matches: 295, Mismatches: 39, Indels: 41
0.79 0.10 0.11
Matches are distributed among these distances:
90 7 0.02
91 78 0.26
92 33 0.11
93 41 0.14
94 64 0.22
95 29 0.10
96 40 0.14
97 3 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (95 bp):
CGATGCCATGTCCCAGACATCGTCTTACACTGGCTATCTCTATCGAGGCCGATGCATGTCCCAGA
CATGTCTTACATCTAGCACAACTCTCTAGC
Found at i:5300 original size:47 final size:46
Alignment explanation
Indices: 5145--5598 Score: 326
Period size: 47 Copynumber: 9.7 Consensus size: 46
5135 GATAAATTAT
* * *
5145 CGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCATATATGCGTGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCATCTC-TAT-CGAG-GC
* * * *
5195 TGATGCATGTCCCAGACATGTCTTACATTAGCACAACTCT-T--A-GC
1 CGATGCATGTCCCAGACATGTCTTACACT-G-GCATCTCTATCGAGGC
* **
5239 CGATGCGTGTCCCAGACACATCTTACACTGGCTATCTCTATCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-ATCTCTATCGAGGC
* * *
5286 CGATGCATGTCCCAGACATGTCTTACTCTGGCA-CTCATCTCTG-TGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCATCTC-TATC-GAGGC
* * * *
5332 CGATGCCATGTCTCAGACATGGTCTTACACTAGC-TCTCATATATGCGTGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCATCTC-TAT-CGAG-GC
* * *
5382 TGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCT-T--A-GC
1 CGATGCATGTCCCAGACATGTCTTACACT-G-GCATCTCTATCGAGGC
* * *
5426 CGATGCGTGTCCCAGACACGTCTTACACTGGCTATCTCTGTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-ATCTCTATCGAGGC
* * * * *
5473 TGATGCATGTCCCAGACATGTCTTACTCTGGCA-CTCATCTCTATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCATCTC-TATCGAGGC
*
5519 CGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCATCTC-T-ATCGAGGC
*
5567 CGAAGCATGTCCCAGACATGTCTTACACTGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC
5599 GCATAAATCA
Statistics
Matches: 325, Mismatches: 50, Indels: 62
0.74 0.11 0.14
Matches are distributed among these distances:
42 2 0.01
43 12 0.04
44 55 0.17
45 6 0.02
46 37 0.11
47 102 0.31
48 60 0.18
49 31 0.10
50 14 0.04
51 6 0.02
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCATCTCTATCGAGGC
Found at i:5437 original size:140 final size:136
Alignment explanation
Indices: 5196--5598 Score: 322
Period size: 140 Copynumber: 2.9 Consensus size: 136
5186 TATGCGTGTT
* * * *
5196 GATGCATGTCCCAGACATGTCTTACATTAGCAC-AACTCT-TA-GCCGATG-CGTGTCCCAGACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCA-TATATATGCCGATGCCATGTCCCAGACA
** * * * * *
5257 -CATCTTACACTGGC-TATCTCTATCGAGGCCGATGCATGTCCCAGACATGTCTTACTCTGGCAC
65 TGGTCTTACACTAGCACAACTCT-T--A-GCCGATGCATGTCCCAGACACGTCTTACACTGG--C
5320 TCATCTCTGT-GCC
124 T-ATCTCTGTGGCC
* * * *
5333 GATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATATATGCGTGCTGATG-CATGTCCCAG
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCATATAT--ATGCCGATGCCATGTCCCAG
*
5397 ACAT-GTCTTACACTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACGTCTTACACTGGCTAT
62 ACATGGTCTTACACTAGCACAACTCTTAGCCGATGCATGTCCCAGACACGTCTTACACTGGCTAT
*
5461 CTCTGTCGAGGCT
127 CTCTGT---GGCC
* * * *
5474 GATGCATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATATATATGCCGATGCCATGTCCCAGACAT
* * * * * * *
5539 GGTCTTACACTGGCTCTCATAAT-GTGGCCGAAGCATGTCCCAGACATGTCTTACACTGGC
66 GGTCTTACACTAG--CACA-ACTCTTAGCCGATGCATGTCCCAGACACGTCTTACACTGGC
5599 GCATAAATCA
Statistics
Matches: 216, Mismatches: 32, Indels: 32
0.77 0.11 0.11
Matches are distributed among these distances:
137 19 0.09
138 29 0.13
139 44 0.20
140 45 0.21
141 42 0.19
142 2 0.01
143 30 0.14
144 5 0.02
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (136 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACTCATATATATGCCGATGCCATGTCCCAGACAT
GGTCTTACACTAGCACAACTCTTAGCCGATGCATGTCCCAGACACGTCTTACACTGGCTATCTCT
GTGGCC
Found at i:5460 original size:187 final size:187
Alignment explanation
Indices: 5145--5595 Score: 789
Period size: 187 Copynumber: 2.4 Consensus size: 187
5135 GATAAATTAT
*
5145 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCGTGTTGATGCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCGTGCTGATGCATGTCCCAG
*
5210 ACATGTCTTACATTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACATCTTACACTGGCTATC
66 ACATGTCTTACACTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACATCTTACACTGGCTATC
*
5275 TCTATCGAGGCCGATGCATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTGTGC
131 TCTATCGAGGCCGATGCATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTATGC
* *
5332 CGATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATATATGCGTGCTGATGCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCGTGCTGATGCATGTCCCAG
*
5397 ACATGTCTTACACTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACGTCTTACACTGGCTATC
66 ACATGTCTTACACTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACATCTTACACTGGCTATC
* *
5462 TCTGTCGAGGCTGATGCATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTATGC
131 TCTATCGAGGCCGATGCATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTATGC
* * *
5519 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTG-GCCGAAGCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCGTGCTGATGCATGTCCCAG
5582 ACATGTCTTACACT
66 ACATGTCTTACACT
5596 GGCGCATAAA
Statistics
Matches: 251, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
185 29 0.12
186 4 0.02
187 218 0.87
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (187 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCGTGCTGATGCATGTCCCAG
ACATGTCTTACACTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACATCTTACACTGGCTATC
TCTATCGAGGCCGATGCATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTATGC
Found at i:10588 original size:276 final size:276
Alignment explanation
Indices: 10095--10646 Score: 1104
Period size: 276 Copynumber: 2.0 Consensus size: 276
10085 TTAGTGGACT
10095 CTACTAGCATGTTTATACGAGGTATTAATTCTATACATATGTAAGAGTGGGTAGATCCTGGGTCA
1 CTACTAGCATGTTTATACGAGGTATTAATTCTATACATATGTAAGAGTGGGTAGATCCTGGGTCA
10160 ATTAAAGCGACAACAGTTATATCGTGAATAGAAAAGGTACCCGTGATCACGTCTGGAAACTCTAC
66 ATTAAAGCGACAACAGTTATATCGTGAATAGAAAAGGTACCCGTGATCACGTCTGGAAACTCTAC
10225 CTCTTCTCGGGCTCTATAGCATAGGTCATCGCTGGCACTTTGCCTTCGACCTCATCGCGGCATCT
131 CTCTTCTCGGGCTCTATAGCATAGGTCATCGCTGGCACTTTGCCTTCGACCTCATCGCGGCATCT
10290 CTCGGTGTACCTCTACTACTAGTCCCACTCCCAGAGTTCCTTTGAGGCCTACCCCTCAAGGGAGC
196 CTCGGTGTACCTCTACTACTAGTCCCACTCCCAGAGTTCCTTTGAGGCCTACCCCTCAAGGGAGC
10355 ACTGCTTGCTTTCACA
261 ACTGCTTGCTTTCACA
10371 CTACTAGCATGTTTATACGAGGTATTAATTCTATACATATGTAAGAGTGGGTAGATCCTGGGTCA
1 CTACTAGCATGTTTATACGAGGTATTAATTCTATACATATGTAAGAGTGGGTAGATCCTGGGTCA
10436 ATTAAAGCGACAACAGTTATATCGTGAATAGAAAAGGTACCCGTGATCACGTCTGGAAACTCTAC
66 ATTAAAGCGACAACAGTTATATCGTGAATAGAAAAGGTACCCGTGATCACGTCTGGAAACTCTAC
10501 CTCTTCTCGGGCTCTATAGCATAGGTCATCGCTGGCACTTTGCCTTCGACCTCATCGCGGCATCT
131 CTCTTCTCGGGCTCTATAGCATAGGTCATCGCTGGCACTTTGCCTTCGACCTCATCGCGGCATCT
10566 CTCGGTGTACCTCTACTACTAGTCCCACTCCCAGAGTTCCTTTGAGGCCTACCCCTCAAGGGAGC
196 CTCGGTGTACCTCTACTACTAGTCCCACTCCCAGAGTTCCTTTGAGGCCTACCCCTCAAGGGAGC
10631 ACTGCTTGCTTTCACA
261 ACTGCTTGCTTTCACA
10647 TCTTGTTTTC
Statistics
Matches: 276, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
276 276 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (276 bp):
CTACTAGCATGTTTATACGAGGTATTAATTCTATACATATGTAAGAGTGGGTAGATCCTGGGTCA
ATTAAAGCGACAACAGTTATATCGTGAATAGAAAAGGTACCCGTGATCACGTCTGGAAACTCTAC
CTCTTCTCGGGCTCTATAGCATAGGTCATCGCTGGCACTTTGCCTTCGACCTCATCGCGGCATCT
CTCGGTGTACCTCTACTACTAGTCCCACTCCCAGAGTTCCTTTGAGGCCTACCCCTCAAGGGAGC
ACTGCTTGCTTTCACA
Found at i:14662 original size:48 final size:46
Alignment explanation
Indices: 14586--14701 Score: 135
Period size: 47 Copynumber: 2.5 Consensus size: 46
14576 CTGATACATG
* * * *
14586 TCCCAGACATGTCTTACTCTGGCACTCAT-CTCTGTGCCGATGCCATA
1 TCCCAGACATGTCTTACACTGGCACTCATAATGTG-GCCGAAG-CATA
* * *
14633 TCCCAGACATGGTCTTACACTGTCTCTCATAATGTGGCCGAAGCATG
1 TCCCAGACAT-GTCTTACACTGGCACTCATAATGTGGCCGAAGCATA
14680 TCCCAGACATGTCTTACACTGG
1 TCCCAGACATGTCTTACACTGG
14702 TGCACAAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
46 11 0.19
47 23 0.39
48 22 0.37
49 3 0.05
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (46 bp):
TCCCAGACATGTCTTACACTGGCACTCATAATGTGGCCGAAGCATA
Found at i:14688 original size:94 final size:91
Alignment explanation
Indices: 14432--14701 Score: 262
Period size: 94 Copynumber: 2.9 Consensus size: 91
14422 ATGGGATAAA
* * * *
14432 TTGCCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATATATGCGTGCTGATGCATGTC
1 TTGCCGATGCCATGTCCCAGACATGGTCTTACACTGTCTCTCATA-ATGAG-GCTGAAGCATGTC
* *
14497 CTAGACATGTCTTACACTAGCACAACTC
64 CCAGACATGTCTTACACTGGCACAACTC
* * * * * *
14525 TTAGCCAATG-CGTGTCCTAGACA-CGTCTTACACTGGCTATCTC-T-GTCGAGGCTGATA-CAT
1 TT-GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-TCTCTCATAAT-GAGGCTGA-AGCAT
* *
14585 GTCCCAGACATGTCTTACTCTGGCACTCATCTC
61 GTCCCAGACATGTCTTACACTGGCA--CAACTC
* * *
14618 TGTGCCGATGCCATATCCCAGACATGGTCTTACACTGTCTCTCATAATGTGGCCGAAGCATGTCC
1 T-TGCCGATGCCATGTCCCAGACATGGTCTTACACTGTCTCTCATAATGAGGCTGAAGCATGTCC
14683 CAGACATGTCTTACACTGG
65 CAGACATGTCTTACACTGG
14702 TGCACAAATC
Statistics
Matches: 140, Mismatches: 24, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
91 31 0.22
92 12 0.09
93 32 0.23
94 54 0.39
95 11 0.08
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (91 bp):
TTGCCGATGCCATGTCCCAGACATGGTCTTACACTGTCTCTCATAATGAGGCTGAAGCATGTCCC
AGACATGTCTTACACTGGCACAACTC
Done.