Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g02230.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: 30965
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:1450 original size:25 final size:26
Alignment explanation
Indices: 1409--1460 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
1399 TTTACAGTTT
1409 TACCCCTAGGTGAAAATT-ACCGAAA
1 TACCCCTAGGTGAAAATTGACCGAAA
* *
1434 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGTG-AAAATTGACCGAAA
1460 T
1 T
1461 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 1 0.04
25 15 0.65
26 7 0.30
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGTGAAAATTGACCGAAA
Found at i:1949 original size:134 final size:137
Alignment explanation
Indices: 1708--1991 Score: 520
Period size: 134 Copynumber: 2.1 Consensus size: 137
1698 GAGTAGTCTC
1708 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1773 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCT-TGGCCCAGTA-C
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
1836 ACTGTTA
131 ACTGTTA
*
1843 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1907 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
1972 ACTGTTA
131 ACTGTTA
**
1979 CCTGAATGGGCTT
1 CCCAAATGGGCTT
1992 AGGCCCAATA
Statistics
Matches: 144, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
134 95 0.66
135 30 0.21
136 19 0.13
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:5733 original size:26 final size:26
Alignment explanation
Indices: 5696--5805 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5686 TGATACAAAT
* *
5696 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
5722 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5748 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
5774 TAATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5800 TGATAA
1 TGATAA
5806 GAATTTCATG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:7806 original size:136 final size:137
Alignment explanation
Indices: 7561--7846 Score: 520
Period size: 136 Copynumber: 2.1 Consensus size: 137
7551 GAGTAGTCTC
7561 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
7626 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
7691 ACTGTTA
131 ACTGTTA
*
7698 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
7762 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
7827 ACTGTTA
131 ACTGTTA
**
7834 CCTGAATGGGCTT
1 CCCAAATGGGCTT
7847 AGGCCCAATA
Statistics
Matches: 144, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
136 124 0.86
137 20 0.14
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:9691 original size:69 final size:71
Alignment explanation
Indices: 9576--9719 Score: 238
Period size: 69 Copynumber: 2.1 Consensus size: 71
9566 AAAAAGTTCT
*
9576 CTCTCTCTCTCAATCAATTTTCAGGAAATATATCTGCCCTTAAGAGCCTAACATTGCTTGAATCT
1 CTCTCTCTCTCAATCAATTCTCAGGAAATATATCTGCCCTTAAGAGCCTAACATTGCTTGAATCT
9641 TTGGAC
66 TTGGAC
* * *
9647 CTCTCT-TCT-AATCAGTTCTCTGGAAATATATCTGCCCTTCAGAGCCTAACATTGCTTGAATCT
1 CTCTCTCTCTCAATCAATTCTCAGGAAATATATCTGCCCTTAAGAGCCTAACATTGCTTGAATCT
9710 TTGGAC
66 TTGGAC
9716 CTCT
1 CTCT
9720 AACATTGCTT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 60 0.87
70 3 0.04
71 6 0.09
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.36
Consensus pattern (71 bp):
CTCTCTCTCTCAATCAATTCTCAGGAAATATATCTGCCCTTAAGAGCCTAACATTGCTTGAATCT
TTGGAC
Found at i:9727 original size:95 final size:95
Alignment explanation
Indices: 9623--9814 Score: 357
Period size: 95 Copynumber: 2.0 Consensus size: 95
9613 CCTTAAGAGC
*
9623 CTAACATTGCTTGAATCTTTGGACCTCTCTTCTAATCAGTTCTCTGGAAATATATCTGCCCTTCA
1 CTAACATTGCTTGAATCTTTGGACCTCTCTTCTAATCAGTTCTCTAGAAATATATCTGCCCTTCA
9688 GAGCCTAACATTGCTTGAATCTTTGGACCT
66 GAGCCTAACATTGCTTGAATCTTTGGACCT
*
9718 CTAACATTGCTTGAATCTTTGGACCTCTCTTCTAATCAGTTCTCTAGAAATATATCTGTCCTTCA
1 CTAACATTGCTTGAATCTTTGGACCTCTCTTCTAATCAGTTCTCTAGAAATATATCTGCCCTTCA
*
9783 GAGCCTAACATTGCTTGAATTTTTGGACCT
66 GAGCCTAACATTGCTTGAATCTTTGGACCT
9813 CT
1 CT
9815 CTTCTAACCA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (95 bp):
CTAACATTGCTTGAATCTTTGGACCTCTCTTCTAATCAGTTCTCTAGAAATATATCTGCCCTTCA
GAGCCTAACATTGCTTGAATCTTTGGACCT
Found at i:9728 original size:26 final size:26
Alignment explanation
Indices: 9692--9745 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
9682 CCTTCAGAGC
9692 CTAACATTGCTTGAATCTTTGGACCT
1 CTAACATTGCTTGAATCTTTGGACCT
9718 CTAACATTGCTTGAATCTTTGGACCT
1 CTAACATTGCTTGAATCTTTGGACCT
9744 CT
1 CT
9746 CTTCTAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (26 bp):
CTAACATTGCTTGAATCTTTGGACCT
Found at i:9860 original size:69 final size:69
Alignment explanation
Indices: 9717--9862 Score: 211
Period size: 69 Copynumber: 2.1 Consensus size: 69
9707 TCTTTGGACC
* * *
9717 TCTAACATTGCTTGAATCTTTGGACCTCTCTTCTAATCAGTTCTCTAGAAATATATCTGTCCTTC
1 TCTAACATTGCTTGAATCTTTGGACCTCTCTTCTAACCAGTTCTCTAGAAATATATCAGCCCTTC
*
9782 AGAG
66 AAAG
* * * * *
9786 CCTAACATTGCTTGAATTTTTGGACCTCTCTTCTAACCAGTTCTTTGGAAATATATCAGCCCTTG
1 TCTAACATTGCTTGAATCTTTGGACCTCTCTTCTAACCAGTTCTCTAGAAATATATCAGCCCTTC
9851 AAAG
66 AAAG
9855 TCTAACAT
1 TCTAACAT
9863 CCCTCCAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (69 bp):
TCTAACATTGCTTGAATCTTTGGACCTCTCTTCTAACCAGTTCTCTAGAAATATATCAGCCCTTC
AAAG
Found at i:9878 original size:69 final size:69
Alignment explanation
Indices: 9736--9878 Score: 169
Period size: 69 Copynumber: 2.1 Consensus size: 69
9726 GCTTGAATCT
* * * * ** **
9736 TTGGACCTCTCTTCTAATCAGTTCTCTAGAAATATATCTGTCCTTCAGAGCCTAACATTGCTTGA
1 TTGGACCTCTCTTCTAACCAGTTCTCTAGAAATATATCAGCCCTTCAAAGCCTAACATCCCTCCA
*
9801 ATTT
66 ATTA
* * * *
9805 TTGGACCTCTCTTCTAACCAGTTCTTTGGAAATATATCAGCCCTTGAAAGTCTAACATCCCTCCA
1 TTGGACCTCTCTTCTAACCAGTTCTCTAGAAATATATCAGCCCTTCAAAGCCTAACATCCCTCCA
9870 ATTA
66 ATTA
9874 TTGGA
1 TTGGA
9879 TATTTCAAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.36
Consensus pattern (69 bp):
TTGGACCTCTCTTCTAACCAGTTCTCTAGAAATATATCAGCCCTTCAAAGCCTAACATCCCTCCA
ATTA
Found at i:15362 original size:11 final size:10
Alignment explanation
Indices: 15330--15354 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15320 TGATGGCCAG
15330 AAAAAGACTA
1 AAAAAGACTA
15340 AAAAAGACTA
1 AAAAAGACTA
15350 AAAAA
1 AAAAA
15355 TACATAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAGACTA
Found at i:15490 original size:2 final size:2
Alignment explanation
Indices: 15483--15518 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
15473 TGCAACTAAA
* *
15483 AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15519 CAAAATCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:15657 original size:11 final size:11
Alignment explanation
Indices: 15641--15665 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15631 TTTTCAACAT
15641 GTTAAATCCAA
1 GTTAAATCCAA
15652 GTTAAATCCAA
1 GTTAAATCCAA
15663 GTT
1 GTT
15666 GTCAATGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (11 bp):
GTTAAATCCAA
Found at i:19231 original size:3 final size:3
Alignment explanation
Indices: 19223--19322 Score: 62
Period size: 3 Copynumber: 32.3 Consensus size: 3
19213 TGAATTTCTA
* * *
19223 TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TAT TAT GTACA TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TA-T TAT
* * * *
19271 TAT T-T ATAC TA- TACT TAA TAT TTT TAT TAT TAT TA- TATT TAC TAT
1 TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
19316 TAT TAT T
1 TAT TAT T
19323 TATAAATATT
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
2 5 0.07
3 59 0.79
4 11 0.15
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:19502 original size:3 final size:3
Alignment explanation
Indices: 19496--19562 Score: 82
Period size: 3 Copynumber: 21.7 Consensus size: 3
19486 TTATTACTGC
*
19496 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
*
19542 TA- TATT TAT ATAA TAT TAT TA
1 TAT TA-T TAT -TAT TAT TAT TA
19563 ATAGGTACTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 2 0.04
3 47 0.84
4 7 0.12
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:19828 original size:24 final size:22
Alignment explanation
Indices: 19801--19848 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19791 TAGTGTGTTT
19801 TATTATATGTATATATACTCTCAA
1 TATTATAT-T-TATATACTCTCAA
* *
19825 TATTATATTTTTATACTCTTAA
1 TATTATATTTATATACTCTCAA
19847 TA
1 TA
19849 CCATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 1 0.05
24 8 0.36
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTATATTTATATACTCTCAA
Found at i:19854 original size:22 final size:22
Alignment explanation
Indices: 19814--19855 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19804 TATATGTATA
**
19814 TATACTCTCAATATTATATTTT
1 TATACTCTCAATACCATATTTT
*
19836 TATACTCTTAATACCATATT
1 TATACTCTCAATACCATATT
19856 ATTCTTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (22 bp):
TATACTCTCAATACCATATTTT
Found at i:25350 original size:26 final size:26
Alignment explanation
Indices: 25314--25423 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
25304 TGATACAAAT
25314 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
25340 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
25366 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
25392 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
25418 TGATAA
1 TGATAA
25424 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:26893 original size:28 final size:26
Alignment explanation
Indices: 26851--26925 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
26841 AAAAGTAGCT
* * *
26851 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
*
26879 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
26905 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
26926 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.55
27 1 0.02
28 18 0.43
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:27070 original size:27 final size:27
Alignment explanation
Indices: 27029--27144 Score: 178
Period size: 27 Copynumber: 4.3 Consensus size: 27
27019 GAGGAAGCGT
*
27029 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
27056 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
27083 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
27110 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
27138 TCTGGTG
1 TCTGGTG
27145 ACCTGTCACA
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
27 74 0.91
28 7 0.09
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:27114 original size:54 final size:55
Alignment explanation
Indices: 27029--27167 Score: 194
Period size: 54 Copynumber: 2.6 Consensus size: 55
27019 GAGGAAGCGT
* * *
27029 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
27083 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
27138 TCTGGTGAC-CTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
27168 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
53 12 0.16
54 56 0.73
55 9 0.12
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
Done.