Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2029
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: 9857
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Found at i:2295 original size:1 final size:1
Alignment explanation
Indices: 2289--2411 Score: 102
Period size: 1 Copynumber: 123.0 Consensus size: 1
2279 GGCGTCCTCC
* * ** ** * * *
2289 AAAAAAAAAAAAAAACAAAACAAAAAAACGAAAAAAATGAAAAAACAAAAAAAAAAAAACAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
2354 AAAAAAAACAAAAAAAAAAAACAAAAACAATAAAAAAAACAAACAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2412 GGGGGTCCGG
Statistics
Matches: 92, Mismatches: 30, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 92 1.00
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:2357 original size:41 final size:41
Alignment explanation
Indices: 2291--2411 Score: 138
Period size: 45 Copynumber: 2.8 Consensus size: 41
2281 CGTCCTCCAA
*
2291 AAAAAAAAAAAAACAAAACAAAAA-AACGAAAAAAATGAAAAAAC
1 AAAAAAAAAAAAAC-AAACAAAAACAA--AAAAAAA-AAAAAAAC
2335 AAAAAAAAAAAAACAAACAAAAA-AAAACAAAAAAAAAAAAC
1 AAAAAAAAAAAAACAAACAAAAACAAAA-AAAAAAAAAAAAC
2376 AAAAACAATAAAAAAAACAAACAAAAACAAAAAAAA
1 --AAA-AA-AAAAAAAACAAACAAAAACAAAAAAAA
2412 GGGGGTCCGG
Statistics
Matches: 70, Mismatches: 1, Indels: 11
0.85 0.01 0.13
Matches are distributed among these distances:
41 9 0.13
42 5 0.07
43 14 0.20
44 16 0.23
45 22 0.31
46 4 0.06
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.02
Consensus pattern (41 bp):
AAAAAAAAAAAAACAAACAAAAACAAAAAAAAAAAAAAAAC
Found at i:2359 original size:45 final size:42
Alignment explanation
Indices: 2291--2411 Score: 158
Period size: 41 Copynumber: 2.9 Consensus size: 42
2281 CGTCCTCCAA
*
2291 AAAAAAAAAAAAACAAA-ACAAAAAAACGAAAAAAATGAAAAAAC
1 AAAAAAAAAAAAACAAACAAAAAAAAAC-AAAAAAA--AAAAAAC
2335 AAAAAAAAAAAAACAAACAAAAAAAAAC-AAAAAAAAAAAAC
1 AAAAAAAAAAAAACAAACAAAAAAAAACAAAAAAAAAAAAAC
* *
2376 AAAAACAATAAAAA-AAACAAACAAAAACAAAAAAAA
1 AAAAA-AAAAAAAACAAACAAAAAAAAACAAAAAAAA
2412 GGGGGTCCGG
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
41 25 0.35
42 14 0.20
43 6 0.08
44 17 0.24
45 9 0.13
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.02
Consensus pattern (42 bp):
AAAAAAAAAAAAACAAACAAAAAAAAACAAAAAAAAAAAAAC
Found at i:2390 original size:58 final size:61
Alignment explanation
Indices: 2295--2408 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 61
2285 CTCCAAAAAA
* *
2295 AAAAAAAAACAAAACAAAAAAACGAAAAAAAT-GAAAAAACAAA-AAAAA-AAAAACAAAC
1 AAAAAAAAACAAAAAAAAAAAACGAAAAAAATAAAAAAAACAAACAAAAACAAAAACAAAC
2353 AAAAAAAAACAAAAAAAAAAAAC-AAAAACAATAAAAAAAACAAACAAAAACAAAAA
1 AAAAAAAAACAAAAAAAAAAAACGAAAAA-AATAAAAAAAACAAACAAAAACAAAAA
2409 AAAGGGGGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
57 5 0.10
58 25 0.50
59 10 0.20
60 5 0.10
61 5 0.10
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.02
Consensus pattern (61 bp):
AAAAAAAAACAAAAAAAAAAAACGAAAAAAATAAAAAAAACAAACAAAAACAAAAACAAAC
Found at i:2403 original size:22 final size:21
Alignment explanation
Indices: 2288--2411 Score: 119
Period size: 22 Copynumber: 5.7 Consensus size: 21
2278 CGGCGTCCTC
2288 CAAAAA-AAAAAAAAAACAAAA
1 CAAAAACAAAAAAAAAAC-AAA
**
2309 CAAAAA-AACGAAAAAAATGAAA
1 CAAAAACAA--AAAAAAAACAAA
*
2331 -AAACAAAAAAAAAAAAACAAA
1 CAAA-AACAAAAAAAAAACAAA
* *
2352 CAAAAAAAAACAAAAAAAAAAAA
1 C-AAAAACAA-AAAAAAAACAAA
2375 CAAAAACAATAAAAAAAACAAA
1 CAAAAACAA-AAAAAAAACAAA
2397 CAAAAACAAAAAAAA
1 CAAAAACAAAAAAAA
2412 GGGGGTCCGG
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
21 27 0.31
22 37 0.42
23 24 0.27
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (21 bp):
CAAAAACAAAAAAAAAACAAA
Found at i:3904 original size:30 final size:28
Alignment explanation
Indices: 3849--4323 Score: 289
Period size: 30 Copynumber: 16.0 Consensus size: 28
3839 ATCACCTTCA
* *
3849 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CTTTTTC
*
3878 AAAGCCCACAAGTCAGTGGCATTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTTTTTC
*
3906 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGC-ACTTTTTC
* *
3934 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA--CTTTTTC
* * *
3964 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-CTTTTTC
* * *
3993 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA--CTTTTTC
* * * *
4023 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA--CTTTTTC
** * *
4058 TTTTCAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCA-CTTTTTC
*
4090 AAAAGCCCACAAGTCCAGTGGCATATTTTTC
1 -AAAGCCCACAAGT-CAGTGGCA-CTTTTTC
* *
4121 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGC-ACTTTTTC
* *
4150 AAAGCCCACAAGTTGAGTGGCACCTTTTC
1 AAAGCCCACAAG-TCAGTGGCACTTTTTC
*
4179 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCA-CTTTTTC
* *
4209 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGC-ACTTTTTC
*
4238 AAAGCCCACAAGTCAAGTGGCAAC--CTTC
1 AAAGCCCACAAGTC-AGTGGC-ACTTTTTC
* *
4266 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA--CTTTTTC
* * *
4296 GAAGCCCACAAGTCGGTGGCACCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTTTTTC
4324 CATCTTTAAG
Statistics
Matches: 363, Mismatches: 57, Indels: 53
0.77 0.12 0.11
Matches are distributed among these distances:
26 2 0.01
27 25 0.07
28 60 0.17
29 97 0.27
30 104 0.29
31 28 0.08
32 7 0.02
33 16 0.04
35 24 0.07
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACTTTTTC
Found at i:3949 original size:27 final size:27
Alignment explanation
Indices: 3842--3984 Score: 115
Period size: 29 Copynumber: 5.0 Consensus size: 27
3832 GACATTCATC
*
3842 ACCTTCAAAAGTCCACAAGTCAGTGGCA
1 ACCTTC-AAAGCCCACAAGTCAGTGGCA
***
3870 TTTTTTTCAAAGCCCACAAGTCAGTGGCA
1 --ACCTTCAAAGCCCACAAGTCAGTGGCA
***
3899 TTTTTTCAAAAGCCCACAAGTCAGTGGCA
1 -ACCTTC-AAAGCCCACAAGTCAGTGGCA
*
3928 ACCTTCAAAGCCCACAAATCAGTGGCA
1 ACCTTCAAAGCCCACAAGTCAGTGGCA
* * *
3955 CCCTTTTCCGAAGCCCACAAGTCGGTGGCA
1 ACC--TT-CAAAGCCCACAAGTCAGTGGCA
3985 TCTTTTCCAA
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.23
28 10 0.10
29 43 0.44
30 22 0.23
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22
Consensus pattern (27 bp):
ACCTTCAAAGCCCACAAGTCAGTGGCA
Found at i:4195 original size:58 final size:60
Alignment explanation
Indices: 3845--4321 Score: 310
Period size: 58 Copynumber: 8.0 Consensus size: 60
3835 ATTCATCACC
* *** ***
3845 TTCAAAAGTCCACAAG-TCAGTGGCATTTTTTTC-AAAGCCCACAAGTCAGTGGCATTTT
1 TTCAAAAGCCCACAAGTTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* * *
3903 TTCAAAAGCCCACAAG-TCAGTGGCAACC--TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
** * * * * * *
3960 TTCCGAAGCCCACAAG-TCGGTGGCA-TCTTTTCCAAAGTCCACAACTCCGTGGC-ACTCTTT
1 TTCAAAAGCCCACAAGTTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-C--T
** * * * * *** * *
4020 TTCTTTTGTAAGCTCACAA-CTCTA-TAGCACTCTTTTTCTTTTCAGCCCACAAGTTAGTGGCAC
1 TTC----AAAAGCCCACAAGTTC-AGTGGCAC-CCTTTTC--AAAAGCCCACAAGTCAGTGGCAA
4083 CCTT
58 CC-T
* ***
4087 TTCAAAAGCCCACAAGTCCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* **
4147 TT-AAAAGCCCACAAGTTGAGTGGCA-CCTTTTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCT
*
4206 TTCAAAAGCCCACAAG-TCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAAGTGGCAACC-
1 TTCAAAAGCCCACAAGTTCAGTGGCACCCTTTTCAAAAGCCCACAAGTC-AGTGGCAACCT
* ** *
4263 TTC-AAAGCCCACAA-ATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGC-ACCT
1 TTCAAAAGCCCACAAGTTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
4320 TT
1 TT
4322 TCCATCTTTA
Statistics
Matches: 335, Mismatches: 57, Indels: 55
0.75 0.13 0.12
Matches are distributed among these distances:
56 49 0.15
57 36 0.11
58 84 0.25
59 61 0.18
60 23 0.07
61 20 0.06
63 16 0.05
64 20 0.06
66 5 0.01
67 5 0.01
68 15 0.04
69 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (60 bp):
TTCAAAAGCCCACAAGTTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:4226 original size:88 final size:87
Alignment explanation
Indices: 4063--4321 Score: 373
Period size: 88 Copynumber: 3.0 Consensus size: 87
4053 TTTTCTTTTC
4063 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCCAGTGGCATATTTTTCAAAAGCC
1 AGCCCACAAGTTAGTGGCA-CCTTTTCAAAAGCCCACAAGT-CAGTGGCATATTTTTCAAAAGCC
4128 CACAAGTCAGTGGCAACCTTTAAA
64 CACAAGTCAGTGGCAACCTTTAAA
4152 AGCCCACAAGTTGAGTGGCACCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTT-AGTGGCACCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
4217 ACAAGTCAGTGGCAACCTTTAAA
65 ACAAGTCAGTGGCAACCTTTAAA
* * *** **
4240 AGCCCACAAGTCAAGTGGCAACC--TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCC
1 AGCCCACAAGT-TAGTGGC-ACCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCC
*
4302 CACAAGTCGGTGGC-ACCTTT
64 CACAAGTCAGTGGCAACCTTT
4322 TCCATCTTTA
Statistics
Matches: 159, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
85 6 0.04
86 43 0.27
87 3 0.02
88 64 0.40
89 36 0.23
90 7 0.04
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (87 bp):
AGCCCACAAGTTAGTGGCACCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCA
CAAGTCAGTGGCAACCTTTAAA
Found at i:4388 original size:43 final size:43
Alignment explanation
Indices: 4327--4416 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
4317 CCTTTTCCAT
*
4327 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
* *
4370 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
4413 CTTT
1 CTTT
4417 TCCATCTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:5300 original size:13 final size:13
Alignment explanation
Indices: 5282--5306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5272 CATAAAGTGT
5282 TGTATCGATACAA
1 TGTATCGATACAA
5295 TGTATCGATACA
1 TGTATCGATACA
5307 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5322 original size:32 final size:33
Alignment explanation
Indices: 5262--5327 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
5252 TTTCAACGAT
5262 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
** *
5295 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
5327 T
1 T
5328 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:5386 original size:13 final size:13
Alignment explanation
Indices: 5368--5392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5358 ATCACTTAAA
5368 TGTATCGATACAT
1 TGTATCGATACAT
5381 TGTATCGATACA
1 TGTATCGATACA
5393 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5483 original size:51 final size:51
Alignment explanation
Indices: 5403--5527 Score: 189
Period size: 51 Copynumber: 2.5 Consensus size: 51
5393 CTGATCTTTG
* *
5403 TATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAATA
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTAT-AAATA
** *
5455 TATCGATA-ATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAATA
5505 TATCGATACATGCAGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
5528 TCATATTTCG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 10 0.15
51 49 0.73
52 8 0.12
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (51 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAATA
Done.