Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3397
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: 42000
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Found at i:5248 original size:26 final size:26
Alignment explanation
Indices: 5203--5274 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 26
5193 GAGGAAGTGC
*
5203 AAAAGGGC-TTTG-CCTCAGTTTAC-CG
1 AAAAGGGCTTTTGCCCT-AGTTT-CTCA
5228 AAAAGGGCTTTTGCCCTAGTTTCTCA
1 AAAAGGGCTTTTGCCCTAGTTTCTCA
5254 AAAAGGGCTTTTGCCCTAGTT
1 AAAAGGGCTTTTGCCCTAGTT
5275 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 9 0.21
26 31 0.72
27 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCTAGTTTCTCA
Found at i:5287 original size:25 final size:26
Alignment explanation
Indices: 5228--5287 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
5218 CAGTTTACCG
5228 AAAAG-GGCTTTTGCCCTAGTTTCTC
1 AAAAGAGGCTTTTGCCCTAGTTTCTC
5253 AAAA-AGGGCTTTTGCCCTAGTTAT-T-
1 AAAAGA-GGCTTTTGCCCTAGTT-TCTC
5278 AAAAGAGGCT
1 AAAAGAGGCT
5288 AGGCCTCCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
25 12 0.39
26 18 0.58
27 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (26 bp):
AAAAGAGGCTTTTGCCCTAGTTTCTC
Found at i:5544 original size:31 final size:31
Alignment explanation
Indices: 5492--5574 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
5482 TATTTTTAGT
*
5492 AAAGGCTTC-GCCCGGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
5522 AAAGGCTTCGGCCTAGTGATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
5553 AAAGGCTTAGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
5575 CTGAGATTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 14 0.30
31 33 0.70
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:13194 original size:25 final size:26
Alignment explanation
Indices: 13121--13192 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
13111 GAGGAAATGC
*
13121 AAAAGGGC-TTTGCCCTAGTTTACCG-
1 AAAAGGGCTTTTGCCCTAGTTTA-TGA
*
13146 AAAAGGGCTTTTACCCTAGTTTATGA
1 AAAAGGGCTTTTGCCCTAGTTTATGA
*
13172 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCTAGTT
13193 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 9 0.22
26 32 0.78
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCTAGTTTATGA
Found at i:13205 original size:25 final size:26
Alignment explanation
Indices: 13145--13205 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
13135 CTAGTTTACC
*
13145 GAAAAG-GGCTTTTACCCTAGTTTAT
1 GAAAAGAGGCTTTTACCCCAGTTTAT
*
13170 GAAAA-AGGGCTTTTGCCCCAG-TTAT
1 GAAAAGA-GGCTTTTACCCCAGTTTAT
*
13195 TAAAAGAGGCT
1 GAAAAGAGGCT
13206 AGGCCTCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (26 bp):
GAAAAGAGGCTTTTACCCCAGTTTAT
Found at i:19112 original size:94 final size:94
Alignment explanation
Indices: 18946--19305 Score: 287
Period size: 94 Copynumber: 3.8 Consensus size: 94
18936 TGATTTGTGC
* * * *
18946 GCTAGTGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGCGAGTCAGTGTAAGACCATGTC
1 GCTACTGTAAGACATGTCTGGGACATGCTTCAGCCACATTATGAGAGCCAGTGTAAGACCATGTC
19011 TGGGACATGGCATCAGCATCCAGACGAGG
66 TGGGACATGGCATCAGCATCCAGACGAGG
* *
19040 GCTACTGTAAGACATGTCTGGGGA-ATG-TATCAGCCATATTATGAGAGCCTGTGTAAGACCATG
1 GCTACTGTAAGACATGTCT-GGGACATGCT-TCAGCCACATTATGAGAGCCAGTGTAAGACCATG
* * * * *
19103 TTTGGGACATGGCATCGGCA-CAAAGATGAGT
64 TCTGGGACATGGCATCAGCATC-CAGACGAGG
* ** * * * *
19134 GCCAGAGTAAGACATGTCTGGGACATGCATCAGCCTCGACA-GA-GATAGCCAATGTAAGA-CAT
1 GCTACTGTAAGACATGTCTGGGACATGCTTCAG-C-C-ACATTATGAGAGCCAGTGTAAGACCAT
* * **
19196 GTCTGGGGCA-CGCATTGGC-T--AG--GAGTTG
63 GTCTGGGACATGGCATCAGCATCCAGACGAG--G
* * * *
19224 TGCTAGTGTAAGACATGTCTGCGACATGCATCAG-CACGTATATATGAGAGCCAGTGTAAGACGA
1 -GCTACTGTAAGACATGTCTGGGACATGCTTCAGCCAC--AT-TATGAGAGCCAGTGTAAGACCA
19288 TGTCTGGGACATGGCATC
62 TGTCTGGGACATGGCATC
19306 GGCAATATAT
Statistics
Matches: 212, Mismatches: 35, Indels: 38
0.74 0.12 0.13
Matches are distributed among these distances:
87 2 0.01
88 4 0.02
89 1 0.00
90 2 0.01
91 31 0.15
92 14 0.07
93 24 0.11
94 112 0.53
95 18 0.08
96 2 0.01
97 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (94 bp):
GCTACTGTAAGACATGTCTGGGACATGCTTCAGCCACATTATGAGAGCCAGTGTAAGACCATGTC
TGGGACATGGCATCAGCATCCAGACGAGG
Found at i:19158 original size:47 final size:46
Alignment explanation
Indices: 18949--19309 Score: 207
Period size: 47 Copynumber: 7.7 Consensus size: 46
18939 TTTGTGCGCT
* ** * *
18949 AGTGTAAGACATGTCTGGGACATGCTTCGGC-CACATTATGCGAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCACA-AAGATGAGAGCC
* * * * *
18995 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATC-CAGACGAGGGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-CAAAGATGAGAGCC
* * * **
19043 ACTGTAAGACATGTCTGGGGA-ATGTATCAGC-CATATTATGAGAGCC
1 AGTGTAAGACATGTCT-GGGACATGCATCGGCACA-AAGATGAGAGCC
* * *
19089 TGTGTAAGACCATGTTTGGGACATGGCATCGGCACAAAGATGAGTGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAAAGATGAGAGCC
* * * * *
19137 AGAGTAAGACATGTCTGGGACATGCATCAGCCTCGACAGA-GATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCAC-AAAGATGAGAGCC
* * * * * * * * *
19184 AATGTAAGACATGTCTGGGGCACGCATTGG--CTAGGA-GTTGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCACAAAGATG-AGAGCC
* * * *
19228 AGTGTAAGACATGTCTGCGACATGCATCAGCACGTATATATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCAC--AAAGATGAGAGCC
19276 AGTGTAAGACGATGTCTGGGACATGGCATCGGCA
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCA
19310 ATATATCCCA
Statistics
Matches: 232, Mismatches: 62, Indels: 38
0.70 0.19 0.11
Matches are distributed among these distances:
43 3 0.01
44 28 0.12
46 40 0.17
47 75 0.32
48 62 0.27
49 15 0.06
50 9 0.04
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCACAAAGATGAGAGCC
Found at i:30413 original size:137 final size:138
Alignment explanation
Indices: 30205--30485 Score: 465
Period size: 137 Copynumber: 2.0 Consensus size: 138
30195 AAGAACATAC
* ** *
30205 ATATAGTTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATC
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATGTATC
* *
30270 AATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
66 AATATAAACAATTATAATAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
*
30335 TGGAAGGA
131 TGGAAAGA
* *
30343 ATATAATTAATTTATGAATTTGATTCATAC-AAATATTAATTGTATATATTTTACCAAATGTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATGTATC
*
30407 AATATAAACAATTATAATAATTAATTTCGGTCAATATATAAAAGACATGGAAATTAATATTCTTT
66 AATATAAACAATTATAATAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
30472 TGGAAAGA
131 TGGAAAGA
30480 ATATAA
1 ATATAA
30486 GTCATTTTTC
Statistics
Matches: 133, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
137 105 0.79
138 28 0.21
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATGTATC
AATATAAACAATTATAATAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
TGGAAAGA
Found at i:33785 original size:25 final size:25
Alignment explanation
Indices: 33746--33836 Score: 101
Period size: 25 Copynumber: 3.6 Consensus size: 25
33736 ATTCCGACTC
*
33746 ACAGCTTGTGTGAGCATACCAATTT
1 ACAGCTCGTGTGAGCATACCAATTT
* * * *
33771 ATAGCTCGTGAGAGCATGCCAATCT
1 ACAGCTCGTGTGAGCATACCAATTT
** *
33796 ACAGCTCAAGTGAGCATACTAATTT
1 ACAGCTCGTGTGAGCATACCAATTT
*
33821 ACAGCTCGTATGAGCA
1 ACAGCTCGTGTGAGCA
33837 AACATGTGCA
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (25 bp):
ACAGCTCGTGTGAGCATACCAATTT
Found at i:36358 original size:29 final size:29
Alignment explanation
Indices: 36320--36398 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
36310 ATATCTCTGA
*
36320 AAGTAAGCCTTAGTGGTGATCTCTGTTAT
1 AAGTAAGCCTTTGTGGTGATCTCTGTTAT
* *
36349 AATTAAGCCTTTGTGGTGATCTGTGTTAT
1 AAGTAAGCCTTTGTGGTGATCTCTGTTAT
*
36378 CAGTAAGCCTTTGTGGTGATC
1 AAGTAAGCCTTTGTGGTGATC
36399 CCCGTCAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (29 bp):
AAGTAAGCCTTTGTGGTGATCTCTGTTAT
Done.