Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1168
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: 223387
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
File 2 of 2
Found at i:181958 original size:14 final size:14
Alignment explanation
Indices: 181911--181958 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
181901 GTACGAATGG
*
181911 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
181925 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
181939 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
181953 ATTGGT
1 AATGGT
181959 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:184225 original size:30 final size:31
Alignment explanation
Indices: 184191--184287 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
184181 AGCTCACTCC
*
184191 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
184221 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
184251 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
184281 TAGCTCA
1 TAGCTCA
184288 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:186020 original size:12 final size:12
Alignment explanation
Indices: 186003--186055 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 12
185993 TATATAAGTC
186003 AAAAAAATTCGA
1 AAAAAAATTCGA
186015 AAAAAAATTC-A
1 AAAAAAATTCGA
*
186026 AAAAAAATTTGA
1 AAAAAAATTCGA
186038 AAAAAAA-TCTGA
1 AAAAAAATTC-GA
186050 AAAAAA
1 AAAAAA
186056 GTGTTTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 11 0.30
12 26 0.70
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:186029 original size:23 final size:24
Alignment explanation
Indices: 186003--186055 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
185993 TATATAAGTC
186003 AAAAAAATTCGAAAAAAAAT-TCA
1 AAAAAAATTCGAAAAAAAATCTCA
* *
186026 AAAAAAATTTGAAAAAAAATCTGA
1 AAAAAAATTCGAAAAAAAATCTCA
186050 AAAAAA
1 AAAAAA
186056 GTGTTTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (24 bp):
AAAAAAATTCGAAAAAAAATCTCA
Found at i:187113 original size:5 final size:6
Alignment explanation
Indices: 187092--187143 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
187082 AAAGCCTTTG
* * **
187092 AAAAGCA AAAAGA AAAAGA AAAAGA AAATGA GATTGA AAAAGA GAAAAGA
1 AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA
187142 AA
1 AA
187144 TTTGAGAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
6 27 0.71
7 11 0.29
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAAGA
Found at i:187130 original size:24 final size:24
Alignment explanation
Indices: 187103--187180 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
187093 AAAGCAAAAA
187103 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAGATT
* *
187127 GAAAAAGAGAAAAGAAATTTGAGAGT
1 GAAAAAGA-AAAAGAAA-ATGAGATT
* * * * *
187153 AAAAAAGAAGATGAAAAAGAAATT
1 GAAAAAGAAAAAGAAAATGAGATT
187177 GAAA
1 GAAA
187181 CAAAAGAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
24 15 0.36
25 14 0.33
26 13 0.31
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAGATT
Found at i:187149 original size:26 final size:24
Alignment explanation
Indices: 187103--187161 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
187093 AAAGCAAAAA
*
187103 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAGAGT
*
187127 GAAAAAGAGAAAAGAAATTTGAGAGT
1 GAAAAAGA-AAAAGAAA-ATGAGAGT
*
187153 AAAAAAGAA
1 GAAAAAGAA
187162 GATGAAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.27
25 9 0.30
26 13 0.43
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAGAGT
Found at i:189328 original size:30 final size:31
Alignment explanation
Indices: 189294--189389 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 31
189284 GCTCACTCCT
*
189294 AGCTC-ACTTTCAACTCACGAGCTAAACCTC
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTC
* * * * *
189324 AGCTCAAC-TTCAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTC
* *
189354 AGCTCAACTTT-AGCTCACGAGCTAAAGCTT
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTC
189384 AGCTCA
1 AGCTCA
189390 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (31 bp):
AGCTCAACTTTCAGCTCACGAGCTAAACCTC
Found at i:193474 original size:82 final size:79
Alignment explanation
Indices: 193354--193508 Score: 238
Period size: 82 Copynumber: 1.9 Consensus size: 79
193344 AATTTTTTTA
*
193354 ATATACTTTTTTTATAACTACTAAAATGATAATTACAATATAAAACTTGAATTTCACGAAGTAAA
1 ATATACTTTTTTTATAACTACTAAAATGATAAATACAATATAAAACTTGAATTTCACGAAG-AAA
193419 TTTTTTTTTGTATAT
65 TTTTTTTTTGTATAT
* * * *
193434 ATATATTTTTGTTTATAAACTACTAAAATGGTAAATACAATATAATACTTGAATTTCACGAAGCA
1 ATATACTTTT-TTTAT-AACTACTAAAATGATAAATACAATATAAAACTTGAATTTCACGAAGAA
193499 ATTTTTTTTT
64 ATTTTTTTTT
193509 CTTTTTTTAC
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 9 0.13
81 16 0.24
82 43 0.63
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (79 bp):
ATATACTTTTTTTATAACTACTAAAATGATAAATACAATATAAAACTTGAATTTCACGAAGAAAT
TTTTTTTTGTATAT
Found at i:194162 original size:14 final size:14
Alignment explanation
Indices: 194115--194162 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
194105 GTACGAATGG
194115 AATGGTAGGAACAA
1 AATGGTAGGAACAA
*
194129 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
194143 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
194157 ATTGGT
1 AATGGT
194163 CGGTTTAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.29, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:194810 original size:20 final size:20
Alignment explanation
Indices: 194785--194839 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
194775 TGTGGTTCAA
*
194785 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
194805 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
194825 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
194840 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:198548 original size:17 final size:18
Alignment explanation
Indices: 198528--198566 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
198518 TGCACACACA
198528 AATTAATTCAG-CACATT
1 AATTAATTCAGACACATT
*
198545 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
198563 AATT
1 AATT
198567 TTCGGTTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:199544 original size:27 final size:27
Alignment explanation
Indices: 199512--199574 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
199502 TTGTGTCGTT
*
199512 AATACCCCTAGT-TTGTAAAATTACCGA
1 AATACCCCTA-TAGTGTAAAATTACCGA
* *
199539 AATACCCTTATAGTGTAAAATTATCGA
1 AATACCCCTATAGTGTAAAATTACCGA
199566 AATACCCCT
1 AATACCCCT
199575 GTAGGGTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (27 bp):
AATACCCCTATAGTGTAAAATTACCGA
Found at i:201970 original size:30 final size:31
Alignment explanation
Indices: 201936--202032 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 31
201926 TAAACTAAAA
201936 TGAGCT-AAGCTTTAGCTCCTGAGCTAAAGT
1 TGAGCTAAAGCTTTAGCTCCTGAGCTAAAGT
* * * * * * *
201966 TGAGCTGAGGC-TAAACTCCTAAACTGAAGT
1 TGAGCTAAAGCTTTAGCTCCTGAGCTAAAGT
* *
201996 TGAGCTAAAG-TTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAAGCTTTAGCTCCTGAGCT-AAAGT
202026 TGAGCTA
1 TGAGCTA
202033 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
30 43 0.88
31 6 0.12
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (31 bp):
TGAGCTAAAGCTTTAGCTCCTGAGCTAAAGT
Found at i:202806 original size:30 final size:30
Alignment explanation
Indices: 202772--202868 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
202762 TAAACTAAAA
202772 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
202802 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
202832 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
202862 TGAGCTA
1 TGAGCTA
202869 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:204153 original size:23 final size:22
Alignment explanation
Indices: 204101--204154 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
204091 TCCACGTCTT
*
204101 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
204123 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
204146 TTTCTTTTC
1 TTTCTTTTC
204155 CACTCTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 13 0.48
24 6 0.22
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:204864 original size:22 final size:21
Alignment explanation
Indices: 204811--204873 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
204801 TTGGTATTTG
*
204811 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
204832 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
* *
204853 GGTATTTGGTATGAATTGGTA
1 GG-AATTGGTATGAAATGGTA
204874 ACGGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 22 0.58
22 16 0.42
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (21 bp):
GGAATTGGTATGAAATGGTAT
Found at i:204871 original size:10 final size:10
Alignment explanation
Indices: 204812--204873 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
204802 TGGTATTTGG
*
204812 GAATTGGTAC
1 GAATTGGTAT
*
204822 GAAATGGTAT
1 GAATTGGTAT
204832 GGAATTGGTAT
1 -GAATTGGTAT
*
204843 GAAATGGTAT
1 GAATTGGTAT
*
204853 GGTATTTGGTAT
1 -G-AATTGGTAT
204865 GAATTGGTA
1 GAATTGGTA
204874 ACGGTTCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 24 0.57
11 11 0.26
12 7 0.17
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (10 bp):
GAATTGGTAT
Found at i:210761 original size:17 final size:18
Alignment explanation
Indices: 210722--210763 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
210712 AAGAAGAAAA
210722 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
210739 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
210756 TCAAAAGA
1 ACAAAAGA
210764 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Done.