Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold456
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: 41635
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:3238 original size:26 final size:27
Alignment explanation
Indices: 3158--3239 Score: 105
Period size: 26 Copynumber: 3.1 Consensus size: 27
3148 GCAATGGCAC
*
3158 CACTAAGTGTGCGAGTTTGACTATGTAG
1 CACTAAGTGTGCGAG-TTGATTATGTAG
* *
3186 CAC-AAGTGTGCGATTTGATTACGTAG
1 CACTAAGTGTGCGAGTTGATTATGTAG
*
3212 CACTAA-TGTGCGAGTTGATTATATAG
1 CACTAAGTGTGCGAGTTGATTATGTAG
3238 CA
1 CA
3240 ACTTGTAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 32 0.68
27 12 0.26
28 3 0.06
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (27 bp):
CACTAAGTGTGCGAGTTGATTATGTAG
Found at i:11249 original size:27 final size:27
Alignment explanation
Indices: 11218--11395 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
11208 TAAATTGTAC
11218 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
11245 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
11271 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
11299 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
11327 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
11354 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
11381 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
11396 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:11332 original size:82 final size:81
Alignment explanation
Indices: 11219--11374 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
11209 AAATTGTACA
* *
11219 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
11283 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
11300 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
11365 TGCGAGTTGA
65 TGCGAATTGA
11375 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:11386 original size:82 final size:81
Alignment explanation
Indices: 11215--11395 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
11205 GATTAAATTG
* *
11215 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
11280 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
11296 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
11360 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
11378 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
11396 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:20134 original size:53 final size:54
Alignment explanation
Indices: 20046--20261 Score: 258
Period size: 55 Copynumber: 4.0 Consensus size: 54
20036 TATGTGGTAT
* * * *
20046 CCTTTTGAAACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* *
20100 CCTTATG-AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTG
* * * *
20153 CCTTATAGAAACTTATCAATGCCACGTCTTGACATGGTCTTACATGATATCCTTG
1 CCTTAT-GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* * *
20208 CCTTA-GAAACCTTATCCATTGCAATGCCTTGGCATGGTCTTACATGGTATCCTT
1 CCTTATGAAA-CTTA-CCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
20262 AAACCCTAAT
Statistics
Matches: 137, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
52 2 0.01
53 48 0.35
54 11 0.08
55 74 0.54
56 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
Found at i:20191 original size:108 final size:110
Alignment explanation
Indices: 20052--20254 Score: 313
Period size: 108 Copynumber: 1.9 Consensus size: 110
20042 GTATCCTTTT
* * *
20052 GAAACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTTA-C
1 GAAACTTACCAATGCCACGTCTCGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTTATC
*
20114 CAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
65 CAATGCAATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
* *
20160 GAAACTTATCAATGCCACGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTATCC
1 GAAACTTACCAATGCCACGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTATCC
*
20225 ATTGCAATGCCTTGGCATGGTCTTACATGG
66 AATGCAATGCCTTGGCATGGTCTTACATGG
20255 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 50 0.59
109 4 0.05
110 30 0.35
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (110 bp):
GAAACTTACCAATGCCACGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTATCC
AATGCAATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
Found at i:21678 original size:43 final size:43
Alignment explanation
Indices: 21631--21725 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
21621 CCAGATATGA
* * *
21631 TCTTACATGTAATTTCATATCGATGCCAATAGCCCAGCTATAG
1 TCTTACACGAAATCTCATATCGATGCCAATAGCCCAGCTATAG
* *
21674 TCTTACACGAAATCTCATATCGATGCCAATAGCCTAGCTATGG
1 TCTTACACGAAATCTCATATCGATGCCAATAGCCCAGCTATAG
21717 TCTTACACG
1 TCTTACACG
21726 TATTATAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (43 bp):
TCTTACACGAAATCTCATATCGATGCCAATAGCCCAGCTATAG
Found at i:24012 original size:47 final size:44
Alignment explanation
Indices: 23940--24063 Score: 151
Period size: 47 Copynumber: 2.7 Consensus size: 44
23930 TTATTTGTGT
**
23940 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATT-ATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG---CATTAACAAGA
*
23986 GCTAGTGTAAGACCATGTCTGAGACATGTCATCGGCATTGAAACAAGA
1 GCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCATT--AACAAGA
24034 GCTAGTGTAAGACATGTCTGGGACATGCAT
1 GCTAGTGTAAGACATGTCTGGGACATGCAT
24064 TGGCTACGAG
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
45 4 0.06
46 15 0.22
47 28 0.41
48 22 0.32
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTAACAAGA
Found at i:24139 original size:140 final size:147
Alignment explanation
Indices: 23945--24258 Score: 350
Period size: 140 Copynumber: 2.2 Consensus size: 147
23935 TGTGTGCTAG
23945 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTCT-G
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTCTAG
* * *
24007 AGACATGTCATCGGCATTGA-A-ACAAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATTGG-
66 -GACATGGCATCAGCATGGATATACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGC
24067 CTACGAGAT-G-T-GTCAA
130 CT-CGAGATCGATAGTCAA
* * *
24083 TGTAAGACCATGTCTGGGGCATGGCATCGG-CAC-TTAT-AGAGGTGTCAGTTTAAGACCATGTC
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGA-G-CT-AGTGTAAGACCATGTC
*** * *
24145 TAGGACATGGCATCAGCATGGATATGTGAGAGTTAGTGTAAGACCATGTCTGGGACATGGCGTTG
63 TAGGACATGGCATCAGCATGGATATACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTG
** *
24210 GCCTCGATTTCGATAGTCAC
128 GCCTCGAGATCGATAGTCAA
*
24230 TGTAAGACCATGTCTAGGACATGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATCG
24259 ACTTGATGGA
Statistics
Matches: 146, Mismatches: 16, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
137 3 0.02
138 12 0.08
139 17 0.12
140 39 0.27
141 2 0.01
142 14 0.10
143 14 0.10
144 10 0.07
145 3 0.02
146 1 0.01
147 31 0.21
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (147 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTCTAG
GACATGGCATCAGCATGGATATACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCC
TCGAGATCGATAGTCAA
Found at i:24193 original size:50 final size:49
Alignment explanation
Indices: 24133--24257 Score: 144
Period size: 49 Copynumber: 2.5 Consensus size: 49
24123 GGTGTCAGTT
* * *
24133 TAAGACCATGTCTAGGACATGGCATCAGCATGGATATGT-GAGAGTTAGTG
1 TAAGACCATGTCTAGGACATGGCATCAGCATCGAT-T-TCGAGAGTCACTG
* * ** * *
24183 TAAGACCATGTCTGGGACATGGCGTTGGCCTCGATTTCGATAGTCACTG
1 TAAGACCATGTCTAGGACATGGCATCAGCATCGATTTCGAGAGTCACTG
24232 TAAGACCATGTCTAGGACATGGCATC
1 TAAGACCATGTCTAGGACATGGCATC
24258 GACTTGATGG
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
48 1 0.02
49 32 0.52
50 29 0.47
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (49 bp):
TAAGACCATGTCTAGGACATGGCATCAGCATCGATTTCGAGAGTCACTG
Found at i:29291 original size:28 final size:28
Alignment explanation
Indices: 29226--29324 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
29216 CATGAGATTG
* * *
29226 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
29255 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
29283 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
29311 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
29325 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:36386 original size:28 final size:28
Alignment explanation
Indices: 36321--36419 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
36311 CATGAGATTG
* * *
36321 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
36350 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
36378 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
36406 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
36420 GCCTTATCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:40891 original size:45 final size:48
Alignment explanation
Indices: 40748--41108 Score: 259
Period size: 47 Copynumber: 7.7 Consensus size: 48
40738 TTTGTGTGCT
*** *
40748 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATG-AGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGA-GATGTAGAGCC
* * ** * *
40794 AGTGTAAGACCATGTTTGAGACATGGCATCAACATTGAGACG-AGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGATGTAGAGCC
40842 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTTGAGATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGTAGAGCC
* * *
40887 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-T-ACGA--AAGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGA-GATGTAGAGCC
* * ** * **
40930 AGTGTAATACCATGTCTGGGACATGGCATCAGCACGGATATGTGAGAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGATGT-AGAGCC
* * ** * * *
40980 AGTGTAAGACCATGTCTGGGACATGACATCGGCCTCGATTTCTATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CTTGAGATGTAGAGCC
* * * *
41029 AGTGTAAGACCATGT-TGAAGACATGGCATCGACTT--GATGGATGAGCT
1 AGTGTAAGACCATGTCTG-GGACATGGCATCGGCTTGAGATGTA-GAGCC
41076 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
41109 ATTACACCAT
Statistics
Matches: 249, Mismatches: 48, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
42 1 0.00
43 11 0.04
44 17 0.07
45 48 0.19
46 18 0.07
47 55 0.22
48 29 0.12
49 31 0.12
50 38 0.15
51 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGTAGAGCC
Found at i:40998 original size:139 final size:138
Alignment explanation
Indices: 40748--41105 Score: 355
Period size: 139 Copynumber: 2.5 Consensus size: 138
40738 TTTGTGTGCT
*
40748 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTTTGA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACA-TA-GAGAGCCAGTGTAAGACCATGTCTGA
**
40813 GACATGGCATCAACATTGAGACGAGAGCTAGTGTAAGACATGTCTGGGACATG-CATCGGCTTGA
64 GACATGGCATCAACACGGAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGACATCGGCTTGA
40877 GATGTAAGCC
129 GATGTAAGCC
* * * * *
40887 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-A-AGTGTCAGTGTAATACCATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATAGAGAGCCAGTGTAAGACCATGTCTGAG
* * * *
40950 ACATGGCATCAGCACGGATATGTGAGAGTTAGTGTAAGACCATGTCTGGGACATGACATCGGCCT
65 ACATGGCATCAACACGGAGA--CGAGAGCTAGTGTAAGA-CATGTCTGGGACATGACATCGG-CT
* ** * *
41015 CGATTTCTATAGTC
126 TGAGATGTA-AGCC
* * *** * *
41029 AGTGTAAGACCATGT-TGAAGACATGGCATCGACTTGATGGATGAGCTAGTGTAAGACCATGTCT
1 AGTGTAAGA-CATGTCTG-GGACAT-GCATCGGCCACATAGA-GAGCCAGTGTAAGACCATGTCT
*
41093 GGGACATGGCATC
62 GAGACATGGCATC
41106 GGCATTACAC
Statistics
Matches: 180, Mismatches: 26, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
136 37 0.21
138 16 0.09
139 48 0.27
140 7 0.04
141 7 0.04
142 14 0.08
143 11 0.06
144 8 0.04
145 1 0.01
146 31 0.17
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (138 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATAGAGAGCCAGTGTAAGACCATGTCTGAGA
CATGGCATCAACACGGAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGACATCGGCTTGAGA
TGTAAGCC
Done.