Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1855
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: 154734
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:136635 original size:187 final size:186
Alignment explanation
Indices: 136346--136698 Score: 462
Period size: 187 Copynumber: 1.9 Consensus size: 186
136336 GTAAAAGCAA
* * * * **
136346 GGTTGGAGTATCCCTCGGAGATAGTGGGGTTGGAGTATCCCAAAAATGAAAAATTTGGTGTTTTG
1 GGTTGGAGTATCCCTCAGAGATAGTGGAGTTAGAGTATCCCAAAAATGAAAAATTTAGCATTTTG
* *
136411 GAAGTAAAATCGAGGTTGGAGTATCTCTTCAGAGATGGTGGGATTGGAGTATCCCTAGAGATGAA
66 AAAGTAAAATCGAGGTTGGAGTATCTCTTCAGAGATGGTGGGATTGGAGTATCCCTAAAGATGAA
* *
136476 AAGTT-TGATGTTTTAGAAGT-AAAAACGGGGTTAAAGTATCCCCCGAAGATGCTGG
131 AAATTCAG-TGTTTTAGAAGTGAAAAACGGGGTTAAAGTATCCCCCGAAGATGCTGG
* * * *
136531 GGTTGGAGTATCTCCTTAGAGATGGTGGAGTTAGAGTATCCCCAGAGATGAAAAATTTAGCATTT
1 GGTTGGAGTATC-CCTCAGAGATAGTGGAGTTAGAGTAT-CCCAAAAATGAAAAATTTAGCATTT
* * *
136596 TGAAAGTAGAAAT-GGGGTTGGAGTATC-CTCTCGGAGATGGTGGGGTTGGAGTATCCCTAAAGA
64 TGAAAGTA-AAATCGAGGTTGGAGTATCTCT-TCAGAGATGGTGGGATTGGAGTATCCCTAAAGA
**
136659 TGAAAAATTCAGTGTTTTAGAAGTGAAAATGGGGGTTAAA
127 TGAAAAATTCAGTGTTTTAGAAGTGAAAAACGGGGTTAAA
136699 ACCTTTTGAT
Statistics
Matches: 143, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
185 12 0.08
186 23 0.16
187 90 0.63
188 18 0.13
ACGTcount: A:0.30, C:0.10, G:0.31, T:0.28
Consensus pattern (186 bp):
GGTTGGAGTATCCCTCAGAGATAGTGGAGTTAGAGTATCCCAAAAATGAAAAATTTAGCATTTTG
AAAGTAAAATCGAGGTTGGAGTATCTCTTCAGAGATGGTGGGATTGGAGTATCCCTAAAGATGAA
AAATTCAGTGTTTTAGAAGTGAAAAACGGGGTTAAAGTATCCCCCGAAGATGCTGG
Found at i:139251 original size:20 final size:20
Alignment explanation
Indices: 139228--139269 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
139218 CAATTCAAGC
*
139228 ATGTATTAATACATTCACTT
1 ATGTATCAATACATTCACTT
* *
139248 ATGTATCGATACATTGACTT
1 ATGTATCAATACATTCACTT
139268 AT
1 AT
139270 TCTGTCGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (20 bp):
ATGTATCAATACATTCACTT
Found at i:139279 original size:21 final size:20
Alignment explanation
Indices: 139236--139281 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
139226 GCATGTATTA
*
139236 ATACATTCACTTATGTATCG
1 ATACATTCACTTATCTATCG
* *
139256 ATACATTGACTTATTCTGTCG
1 ATACATTCACTTA-TCTATCG
139277 ATACA
1 ATACA
139282 AATTGTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (20 bp):
ATACATTCACTTATCTATCG
Found at i:139932 original size:30 final size:30
Alignment explanation
Indices: 139890--139964 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
139880 TGAGCTGAGT
*
139890 TAGCTAGTGTCTAGCTCCCTTGT-GCTAAGC
1 TAGCTGGTGTCTAGCT-CCTTGTAGCTAAGC
* * * * *
139920 TTGTTGGTGTCTAACTCTTTTTAGCTAAGC
1 TAGCTGGTGTCTAGCTCCTTGTAGCTAAGC
139950 TAGCTGGTGTCTAGC
1 TAGCTGGTGTCTAGC
139965 AACCATGAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (30 bp):
TAGCTGGTGTCTAGCTCCTTGTAGCTAAGC
Found at i:144311 original size:50 final size:51
Alignment explanation
Indices: 144206--144332 Score: 184
Period size: 50 Copynumber: 2.5 Consensus size: 51
144196 AGATGTATTG
* * *
144206 ATACATTAAAAAATATATTGATACATCTAGGTAAAAAGACAGAATGTATCG
1 ATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCA
* * * *
144257 ATACATTGAAGAATGTATCGATACATCTGGGT-AGAAGACAGAATGTATCA
1 ATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCA
144307 ATACATTAAAAAATGTATCGATACAT
1 ATACATTAAAAAATGTATCGATACAT
144333 TTCGTTAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 40 0.60
51 27 0.40
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.28
Consensus pattern (51 bp):
ATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCA
Found at i:145933 original size:20 final size:20
Alignment explanation
Indices: 145910--145947 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
145900 TTATGTATTG
145910 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
145930 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
145948 AATAGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:146003 original size:21 final size:20
Alignment explanation
Indices: 145977--146032 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
145967 CTGCCAGTTT
**
145977 CATGTATCGATACAATTTGGC
1 CATGTATCGATACAA-TTGAA
*
145998 CATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
146017 CATGTATCGATACAAT
1 CATGTATCGATACAAT
146033 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.53
21 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:146036 original size:13 final size:13
Alignment explanation
Indices: 146018--146044 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
146008 TATAATGAAC
146018 ATGTATCGATACA
1 ATGTATCGATACA
146031 ATGTATCGATACA
1 ATGTATCGATACA
146044 A
1 A
146045 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:146059 original size:33 final size:32
Alignment explanation
Indices: 145999--146063 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
145989 CAATTTGGCC
* *
145999 ATGTATCGATATAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
146031 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
146064 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:146637 original size:36 final size:36
Alignment explanation
Indices: 146588--146662 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
146578 TCGTCGTTTT
*
146588 TCTCCCCTTAAAAATA-TTCTCCCCCTTAAACGATTA
1 TCTCCCC-TAAAAAAAGTTCTCCCCCTTAAACGATTA
* *
146624 TCTCCTCTAAAAAAAGTTCTCCCCCTTAAATGATTA
1 TCTCCCCTAAAAAAAGTTCTCCCCCTTAAACGATTA
146660 TCT
1 TCT
146663 TCTCCCCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 7 0.20
36 28 0.80
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.35
Consensus pattern (36 bp):
TCTCCCCTAAAAAAAGTTCTCCCCCTTAAACGATTA
Found at i:148539 original size:13 final size:13
Alignment explanation
Indices: 148521--148549 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
148511 AAATAGTACC
148521 CAATGTATCGATA
1 CAATGTATCGATA
148534 CAATGTATCGATA
1 CAATGTATCGATA
148547 CAA
1 CAA
148550 GGAATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:151757 original size:39 final size:39
Alignment explanation
Indices: 151681--151771 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 39
151671 TTTTCTTTCT
151681 CCCTTAATTAAAGTAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTCGTA-ATTCTCC
*
151721 CCCTTAA-T-AAGATAATTTTAGCAAATTTACGT-ATTCTCC
1 CCCTTAATTAAAG-TAATTTTAACAAA-TT-CGTAATTCTCC
* *
151760 CCTTTTATTAAA
1 CCCTTAATTAAA
151772 AAATCTCCCC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
38 3 0.07
39 25 0.58
40 10 0.23
41 5 0.12
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (39 bp):
CCCTTAATTAAAGTAATTTTAACAAATTCGTAATTCTCC
Found at i:153166 original size:20 final size:21
Alignment explanation
Indices: 153126--153168 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
153116 GGCTAGTATG
* *
153126 GGGACTGCCCGGTTGCGACCT
1 GGGACTGCCCGGTCGCAACCT
153147 GGGACTG-CCGGTCGCAACCT
1 GGGACTGCCCGGTCGCAACCT
153167 GG
1 GG
153169 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.12, C:0.33, G:0.40, T:0.16
Consensus pattern (21 bp):
GGGACTGCCCGGTCGCAACCT
Done.