Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2532
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: 42984
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4968 original size:39 final size:40
Alignment explanation
Indices: 4891--4997 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
4881 TAGCTCCTCG
* * *
4891 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
4931 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
**
4970 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
4998 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:4996 original size:79 final size:78
Alignment explanation
Indices: 4897--5116 Score: 221
Period size: 79 Copynumber: 2.8 Consensus size: 78
4887 CTCGTTCAAG
* ** * *
4897 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCATTCAATGCCTTCGGGACTTAACCCGGATTTT
1 TGCCTTCGGGACTTAGCCCGG-TATAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA-ATT
*
4962 AA-AACTCGCACGAA
64 AATAACTCGCACAAA
* * * *
4976 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTC-GGACTTAACCCGGAATT
1 TGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGGAATT
5040 AATAACTCGCACAAA
64 AATAACTCGCACAAA
* * * * *
5055 TACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CTTAGCCCGG-TATAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCGGA
5117 CAGCATTCAA
Statistics
Matches: 115, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
78 8 0.07
79 81 0.70
80 26 0.23
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (78 bp):
TGCCTTCGGGACTTAGCCCGGTATAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGAATTAA
TAACTCGCACAAA
Found at i:5037 original size:39 final size:40
Alignment explanation
Indices: 4934--5116 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
4924 TAACTCATTC
* * *
4934 AATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGTAACTCGCACA
*
4974 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
* *
5014 AAGGCCTTC-GGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
* ** * *
5053 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAGTAAC-TCGCACA
*
5094 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5117 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 43 0.36
40 67 0.55
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
Found at i:18345 original size:43 final size:43
Alignment explanation
Indices: 18297--18382 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
18287 ATCACATGTA
* * *
18297 TCGCATCCATTATGAACTTGGACCACTCAACAAGCTCGGATGC
1 TCGCATCCATAATGAAATCGGACCACTCAACAAGCTCGGATGC
* * * **
18340 TCGCATCTATAATGAAATCGGACCATTTAATGAGCTCGGATGC
1 TCGCATCCATAATGAAATCGGACCACTCAACAAGCTCGGATGC
18383 CACATATATC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (43 bp):
TCGCATCCATAATGAAATCGGACCACTCAACAAGCTCGGATGC
Found at i:19853 original size:20 final size:20
Alignment explanation
Indices: 19828--19866 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19818 TGTATTCTTA
* *
19828 AAATTTTAGAATTTTTCATC
1 AAATTTTACAACTTTTCATC
19848 AAATTTTACAACTTTTCAT
1 AAATTTTACAACTTTTCAT
19867 TTTAGTCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (20 bp):
AAATTTTACAACTTTTCATC
Found at i:20617 original size:17 final size:17
Alignment explanation
Indices: 20595--20630 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
20585 ATTAGGGCAA
20595 GTATGAAAAAATAAAAG
1 GTATGAAAAAATAAAAG
20612 GTATGAAAAAATAAAAG
1 GTATGAAAAAATAAAAG
20629 GT
1 GT
20631 TTCTATTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (17 bp):
GTATGAAAAAATAAAAG
Found at i:23069 original size:26 final size:26
Alignment explanation
Indices: 23040--23147 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
23030 TGGTACAAAT
23040 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
23066 TGATAATAGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
23092 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
23118 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
23144 TGAT
1 TGAT
23148 GGGCATTTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:32853 original size:46 final size:45
Alignment explanation
Indices: 32803--32974 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 45
32793 TGAGCATCCA
32803 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-CGAATGTCCG
* * **
32849 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATATAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATCGAA-T--G--TCCG
*
32896 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATTCGAACG-CCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA-TCGAATGTCC-G
* *
32942 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
32975 GTGGGTTACA
Statistics
Matches: 105, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 57 0.54
47 29 0.28
48 3 0.03
50 2 0.02
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATCGAATGTCCG
Found at i:32955 original size:93 final size:93
Alignment explanation
Indices: 32796--32967 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
32786 GGATGGTTGA
*
32796 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
32861 TGAGTCCGAGTTCGTGAGATATAACTAG
66 TGAGTCCGAGTTCGTGAGATATAACTAG
* * *
32889 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATTCGAACG-CCTGAGCTCGTTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
32953 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
32968 CTTATGGGTG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATATAACTAG
Found at i:39614 original size:88 final size:88
Alignment explanation
Indices: 39492--39654 Score: 249
Period size: 88 Copynumber: 1.8 Consensus size: 88
39482 AAGGTTGAGC
* *
39492 ATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCGAA-TCGTTGAG-TGAG
1 ATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-CGAACGCCGAACTCGTTGAGTTGAG
39555 TCCGAGTTCGTGAGATTAACTAGG
65 TCCGAGTTCGTGAGATTAACTAGG
* *
39579 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATCGAACGCCTAAGCTCGTTGAGTTGA
1 ATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATCGAACGCCGAA-CTCGTTGAGTTGA
39644 GTCCGAGTTCG
64 GTCCGAGTTCG
39655 CTTATGGGCG
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
87 12 0.18
88 34 0.50
89 8 0.12
90 14 0.21
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (88 bp):
ATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATCGAACGCCGAACTCGTTGAGTTGAGT
CCGAGTTCGTGAGATTAACTAGG
Found at i:39635 original size:45 final size:44
Alignment explanation
Indices: 39496--39661 Score: 173
Period size: 45 Copynumber: 3.8 Consensus size: 44
39486 TTGAGCATCC
* * *
39496 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCG
1 AACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGAT-CGAACGCCG
* *
39541 AA-TCGTTGAG-TGAGTCCGAGTTCG-TGA--GAT-TAACTAGGATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATCGAAC---G--CCG
*
39584 AACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATCGAACGCCT
1 AACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATCGAACGCCG
39628 AAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AA-CTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
39662 GCGGGTTACA
Statistics
Matches: 101, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
38 2 0.02
40 3 0.03
41 1 0.01
42 2 0.02
43 17 0.17
44 20 0.20
45 47 0.47
46 3 0.03
48 3 0.03
49 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (44 bp):
AACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATCGAACGCCG
Found at i:42893 original size:188 final size:183
Alignment explanation
Indices: 42281--42974 Score: 636
Period size: 188 Copynumber: 3.8 Consensus size: 183
42271 TCTTGTTATC
* * * *
42281 TCAG-GAGATAA-ACTTGGGGCTTAAATCT-GCACCATTGCCG-ATACATGGAAATAAGA-TTCG
1 TCAGAGAGATAAGGCTTGGGGCTTAAAT-TAACTCCATTGCCGAATACATGGAGATAAGATTTCG
* * *
42341 CTATCTTCGATCTGCTTCTA-TAACTATTT-GAGGAGATAAGAATCTTCAAATCTTCAGTC--GC
65 CCATCTTCGATCTGC-TCCACT-ACTGTTTAGAGGAGATAAG-ATCTTC-AATCTTCAGTCTGGC
* * * * *
42402 TTCCTTGCTACCTCTGGAAGAATAAGAACTCAA-CTTCAACCTGCT-TCTTGCTA-ACCG
126 TTCCTTGCTACCTCAGGAAGAATAAG-AC-CAATCTTCAACCTACTCTCCTGCTACCCCA
* * * *
42459 TCAGAGAGATAAGGCTTGGGGCTT--ATCT-GCTCCATTGTCGGATACATGGAGATAAG-GTT-G
1 TCAGAGAGATAAGGCTTGGGGCTTAAAT-TAACTCCATTGCCGAATACATGGAGATAAGATTTCG
*
42519 CCATCTTCGATCTGCTCCACTA-TGCTTAG-GGAGATAAGATCTTCAATCTTCAGTCCT-GCTTC
65 CCATCTTCGATCTGCTCCACTACTGTTTAGAGGAGATAAGATCTTCAATCTTCAGT-CTGGCTTC
* * * *
42581 CTTGCTACCTCAGGAAGAATAAGACCCATCTTCAACCTGCTCTCCTGCTACCGCG
129 CTTGCTACCTCAGGAAGAATAAGACCAATCTTCAACCTACTCTCCTGCTACCCCA
** **
42636 TCAGAGAGATAAGGCTTGGGGCTTAAATTTGCTCCATTTTCGAATACCATGGAGATAAGAAATTT
1 TCAGAGAGATAAGGCTTGGGGCTTAAATTAACTCCATTGCCGAATA-CATGGAGATAAG--A-TT
** *
42701 TCGCCATCTTTAATCTGCTCCTCTACTGTTTTAGAGGAGATAAGATCTTCAATCTTTCAGTCTGG
62 TCGCCATCTTCGATCTGCTCCACTACTG-TTTAGAGGAGATAAGATCTTCAATC-TTCAGTCTGG
* * *
42766 GTTCCTTGCTA-CTCAGGAAGTATTAAGGACTAATC-TCAACC-ACTCT-CTGCTTACCACCA
125 CTTCCTTGCTACCTCAGGAAG-AATAA-GACCAATCTTCAACCTACTCTCCTGC-TACC-CCA
* *
42825 TC-GAGA-ATAAGGCTTGGGGCTTAAATCTAAACTTCATTGCCGATACATACATAGAGATAAGAT
1 TCAGAGAGATAAGGCTTGGGGCTTAAAT-T-AACTCCATTGCCG--A-ATACATGGAGATAAGAT
42888 TTCGCCATCTTCGATCTGCTCCACTACTGTTTAGA-GAGATAAGATCTTC-ATCTTCAGTCT-GC
61 TTCGCCATCTTCGATCTGCTCCACTACTGTTTAGAGGAGATAAGATCTTCAATCTTCAGTCTGGC
*
42950 TTTTCTTGCTACCCTGCAGGAAGAA
126 -TTCCTTGCTA-CCT-CAGGAAGAA
42975 GTAAAGACTC
Statistics
Matches: 439, Mismatches: 39, Indels: 68
0.80 0.07 0.12
Matches are distributed among these distances:
174 12 0.03
175 21 0.05
176 46 0.10
177 31 0.07
178 35 0.08
179 39 0.09
180 22 0.05
183 1 0.00
184 19 0.04
185 23 0.05
186 19 0.04
187 41 0.09
188 70 0.16
189 39 0.09
190 6 0.01
191 12 0.03
192 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (183 bp):
TCAGAGAGATAAGGCTTGGGGCTTAAATTAACTCCATTGCCGAATACATGGAGATAAGATTTCGC
CATCTTCGATCTGCTCCACTACTGTTTAGAGGAGATAAGATCTTCAATCTTCAGTCTGGCTTCCT
TGCTACCTCAGGAAGAATAAGACCAATCTTCAACCTACTCTCCTGCTACCCCA
Done.