Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1276
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: 33531
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:3764 original size:30 final size:30
Alignment explanation
Indices: 3728--3787 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3718 TTCCCGAGCC
3728 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
3758 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
3788 CGTATTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:4565 original size:50 final size:49
Alignment explanation
Indices: 4442--4679 Score: 257
Period size: 49 Copynumber: 4.8 Consensus size: 49
4432 TGAGGTCACG
* * *
4442 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTGGTCGAA
* * * * *
4491 TGTGTAGTACTAAGTGCAGGCTACTATGCGTATCTGATAACTTCGATC-AA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT-AGTT-GGTCGAA
* * *
4541 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTGAGGTC-ACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGT-TGGTCGA-A
* * *
4591 TGTGTAGTACTAAGTGCAGGCTACTACGTGT-TCCGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAT-CAGATAGTTGGTCGAA
* * *
4640 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAG
4680 CTTCGGCTAC
Statistics
Matches: 155, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
49 78 0.50
50 74 0.48
51 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTGGTCGAA
Found at i:4643 original size:99 final size:99
Alignment explanation
Indices: 4442--4677 Score: 316
Period size: 99 Copynumber: 2.4 Consensus size: 99
4432 TGAGGTCACG
* * *
4442 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTGGTCGCATGTGTAGTACTAAGTG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTAGGTCACATGTGTAGTACTAAGTG
* *
4507 CAGGCTACTATGCGTATCTGATAACTTCGATCAA
66 CAGGCTACTACGCGTATCGGATAACTTCGATCAA
* *
4541 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTGAGGTCACGTGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGT-AGGTCACATGTGTAGTACTAAGT
* * *
4606 GCAGGCTACTACGTGT-TCCGGATAA-TT-GGTCGTA
65 GCAGGCTACTACGCGTAT-CGGATAACTTCGATC-AA
* *
4640 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
4678 AGCTTCGGCT
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
98 3 0.02
99 78 0.64
100 40 0.33
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (99 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTAGGTCACATGTGTAGTACTAAGTG
CAGGCTACTACGCGTATCGGATAACTTCGATCAA
Found at i:8780 original size:14 final size:14
Alignment explanation
Indices: 8761--8787 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8751 ACTAAGCACT
8761 TGTTTTGGTATGTA
1 TGTTTTGGTATGTA
8775 TGTTTTGGTATGT
1 TGTTTTGGTATGT
8788 TTACGCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.30, T:0.59
Consensus pattern (14 bp):
TGTTTTGGTATGTA
Found at i:9235 original size:12 final size:12
Alignment explanation
Indices: 9218--9250 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
9208 TCAATAAGTT
9218 ACACGGCTTAGC
1 ACACGGCTTAGC
*
9230 ACACGGCCTAGC
1 ACACGGCTTAGC
9242 ACACGGCTT
1 ACACGGCTT
9251 GCGACACGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.15
Consensus pattern (12 bp):
ACACGGCTTAGC
Found at i:14666 original size:94 final size:93
Alignment explanation
Indices: 14509--14680 Score: 215
Period size: 94 Copynumber: 1.8 Consensus size: 93
14499 GACGAGGGCT
*
14509 AGTGTAAGACGTGTCTGGGACATGCATCAGCCGCATCATGATAGCTCGTGTAAGACCACGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCGCATCATGATAGCTCGTGTAAGACCACGTCTGG
*
14574 GGCATGGCATCGGCGTAGAGGTGAGTGCC
66 GACAT-GCATCGGCGTAGAGGTGAGTGCC
* * * * **
14603 AGTGTAAGACATG-CTTGGGACATGCATCGGCCTCGATGATGTTAGC-CAGTGTAAGA-CGTGTC
1 AGTGTAAGACATGTC-TGGGACATGCATCAGCCGC-ATCATGATAGCTC-GTGTAAGACCACGTC
14665 TGGGACATGCATCGGC
63 TGGGACATGCATCGGC
14681 TAAGTTTCGT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
93 9 0.13
94 41 0.61
95 17 0.25
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.23
Consensus pattern (93 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCGCATCATGATAGCTCGTGTAAGACCACGTCTGG
GACATGCATCGGCGTAGAGGTGAGTGCC
Found at i:16158 original size:93 final size:93
Alignment explanation
Indices: 15999--16169 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
15989 GCCCATAAGT
* ** *
15999 GAACTCGGACTCAACTCAATGAGCTCGGGTGATTGTCTCCATGAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGGACATTGTCTCCATAAGTGAACTCGGACTCAACTCAA
*
16064 CGATTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
16092 GAACTCGGACTCAACTCAACGAGTTC-GGACATT-TGCATCCATAAGTGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGCTCGGGACATTGT-C-TCCATAAGTGAACTCGGACTCAACTC
16155 AACGAGTTCGGATGC
64 AACGAGTTCGGATGC
16170 TCAACCATCC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
91 1 0.01
92 6 0.09
93 63 0.90
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGGACATTGTCTCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:16159 original size:46 final size:45
Alignment explanation
Indices: 15991--16166 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 45
15981 TGTAACCCGC
* * **
15991 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGTGATTGTC-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTG-CAT
* * *
16037 CCATGAGTGAACTCGGACTCAACTCAACGATTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTGCAT
* *
16087 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACA-TTGCAT
16130 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
16167 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 4 0.04
46 59 0.55
47 28 0.26
48 2 0.02
49 3 0.03
50 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
Found at i:16185 original size:46 final size:45
Alignment explanation
Indices: 16042--16185 Score: 127
Period size: 46 Copynumber: 3.1 Consensus size: 45
16032 TGTCTCCATG
*
16042 AGTGAACTCGGACTCAACTCAACGATTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * *
16089 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCT
16135 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
16181 AGTGA
1 AGTGA
16186 CATGTCACTT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
44 8 0.10
45 2 0.03
46 33 0.42
47 30 0.38
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:24824 original size:47 final size:46
Alignment explanation
Indices: 24751--25070 Score: 250
Period size: 47 Copynumber: 6.7 Consensus size: 46
24741 TCGGTATTGA
* * *
24751 GATGATGGCTAGTGTAAGATATGTCTGGGACATGCATCAGCCGCAT
1 GATGATAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCGCAT
* * * * *
24797 CATGATAGCCCGTGTAAGACCACGTCTGGGACATGGCATC-GGCGTA-
1 GATGATAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCGCAT
* *
24843 GAGGTGAGT-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAT
1 GA--TGA-TAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCGC-AT
* * * *
24892 GATGTTAGCCAGTGTAAGACGTGTCTGGAACATGCATCAGCCTCGAT
1 GATGATAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCGC-AT
* *
24939 GATGTTAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCACGTAT
1 GATGATAGCCAGTGTAAGACATGTCTGGGACATGCATCAGC-CGCAT
* * * * * * * *
24986 ACACGAGAGCTAGTATAAGACCATGTCTGGGACATGGCGTCGGCCTCAAT
1 -GATGATAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCGC-AT
* ** *
25036 GAAGATAGCCAGCATAAGACCATGTCTAGGACATG
1 GATGATAGCCAGTGTAAGA-CATGTCTGGGACATG
25071 GCAGTGGCAA
Statistics
Matches: 222, Mismatches: 38, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
46 22 0.10
47 111 0.50
48 35 0.16
49 46 0.21
50 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (46 bp):
GATGATAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCGCAT
Found at i:24878 original size:94 final size:94
Alignment explanation
Indices: 24717--25029 Score: 303
Period size: 94 Copynumber: 3.3 Consensus size: 94
24707 AGAGCCAATA
** * * * * *
24717 TAAGACCAAATCTGGGACATGGCATCGGTATTGAGATGA-TGGCTAGTGTAAGATATGTCTGGGA
1 TAAGACCATGTCTGGGACATGGCATCGGCATAGAG-TGAGTAGCCAGTGTAAGACATGTCTGGGA
*
24781 CATGCATCAGCCGCATCATGATAGCCCGTG
65 CATGCATCAGCCGCATCATGATAGCCAGTG
* *
24811 TAAGACCACGTCTGGGACATGGCATCGGCGTAGAGGTGAGT-GCCAGTGTAAGACATGTCTGGGA
1 TAAGACCATGTCTGGGACATGGCATCGGCATAGA-GTGAGTAGCCAGTGTAAGACATGTCTGGGA
* * * *
24875 CATGCATCGGCCTCGATGATGTTAGCCAGTG
65 CATGCATCAGCCGC-ATCATGATAGCCAGTG
* * * * *
24906 TAAGA-CGTGTCTGGAACAT-GCATCAGCCTCGA-TGATGTTAGCCAGTGTAAGACATGTCTGGG
1 TAAGACCATGTCTGGGACATGGCATCGGCATAGAGTGA-G-TAGCCAGTGTAAGACATGTCTGGG
* * * * *
24968 ACATGCATCAGCACGTATACACGAGAGCTAGTA
64 ACATGCATCAGC-CGCAT-CATGATAGCCAGTG
*
25001 TAAGACCATGTCTGGGACATGGCGTCGGC
1 TAAGACCATGTCTGGGACATGGCATCGGC
25030 CTCAATGAAG
Statistics
Matches: 178, Mismatches: 31, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
91 3 0.02
92 1 0.01
93 11 0.06
94 111 0.62
95 34 0.19
96 12 0.07
97 6 0.03
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (94 bp):
TAAGACCATGTCTGGGACATGGCATCGGCATAGAGTGAGTAGCCAGTGTAAGACATGTCTGGGAC
ATGCATCAGCCGCATCATGATAGCCAGTG
Found at i:30667 original size:39 final size:40
Alignment explanation
Indices: 30550--30772 Score: 248
Period size: 39 Copynumber: 5.7 Consensus size: 40
30540 GCTCCTCGTT
* *
30550 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * *
30590 CAAATGCCTTCGGGAATTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
30630 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
30669 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
30708 CAAATGCCTT-TGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
30749 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
30773 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.01
39 86 0.53
40 63 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:30727 original size:79 final size:80
Alignment explanation
Indices: 30550--30772 Score: 253
Period size: 79 Copynumber: 2.8 Consensus size: 80
30540 GCTCCTCGTT
* * * * * *
30550 CAAATGCCTTCGGGACATAGCCCGGTTATAGT-AATTCGCACAAATGCCTTCGGGAATTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATTGTCACTTCGCACAAATGCCTTCGGGACTTAGCCCG
*
30614 GATTTAGTAACTCGCA
65 GAATTAGTAACTCGCA
30630 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGT-A-TCTCGCACAAATGCCTTCGGG-CTTAGCCC
1 CAAATGCCTTCGGGCTTAGCCCGGATATT-GTCACT-TCGCACAAATGCCTTCGGGACTTAGCCC
*
30691 GGAATTAGTATCTCGCA
64 GGAATTAGTAACTCGCA
* * * *
30708 CAAATGCCTTTGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATTGTCACTTCGCACAAATGCCTTCGGGACTTAGCCCG
30771 GA
65 GA
30773 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 45 0.36
79 56 0.45
80 23 0.18
81 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATTGTCACTTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Done.