Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1657
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: 18490
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Found at i:4800 original size:158 final size:156
Alignment explanation
Indices: 4611--5643 Score: 589
Period size: 157 Copynumber: 6.6 Consensus size: 156
4601 TACACATTCA
* * *
4611 TCTCATTTAAGGGATGAATTTTTATTCTAAGGAAAATGTTGGAAA-AAAAGCTTTTCTTGCAAAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAGAAAAGCTTTTCTTGCAAAA
* * *
4675 CCAAAGCATTAATATCATGTATCCAAATGAGAAAAATGTGCTTTTGCTGCCTAACCATGAATAGA
66 CCAAAGCATCAATATCATGTATCC-AATGAGAAAAA--TGCTTTTGCTGCCAAACCATGAAAAGA
* *
4740 CTAGAGATTACTACAAGAATCCATGTTTG
128 ATAGAGATTATTACAAGAATCCATGTTTG
* * * *
4769 TCTTATTTAAGGGATGAACTTTGATTCTAAGGAATATGGTGGAAA-AAGATGGTTTTC-TGCAAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAGAA-AAGCTTTTCTTGCAAA
* * * * *** ** * **
4832 AGCAAAGTATCAATATCGTGTATCCTAATAAGGGGAATGCATTTTTTTGCCCAATTATGAAAAGA
65 ACCAAAGCATCAATATCATGTATCC-AATGAGAAAAATGC-TTTTGCTGCCAAACCATGAAAAGA
* ** * *
4897 CTAGAGATTATTATGAGAAACCATATTTG
128 ATAGAGATTATTACAAGAATCCATGTTTG
* * * * * * * * * * **
4926 TCTCATTTGAGGCATGAA-TTT-ACATCTTAGAAAAATAGTGAAAACAAAATCATTTCTTGGGAA
1 TCTCATTTAAGGGATGAACTTTGA-TTCTAAGGAAAATGGTGGAAAGAAAAGCTTTTCTTGCAAA
** * * * ** *
4989 ATTAAAGCATCATTATCATGTATCCAATGACAAGAACACTTTTGCAGTGCCAAATCTAT-AAAAG
65 ACCAAAGCATCAATATCATGTATCCAATGAGAAAAATGCTTTTGC--TGCCAAA-CCATGAAAAG
* *
5053 AATGGAGATTATTACAAGAATCCATCTTTG
127 AATAGAGATTATTACAAGAATCCATGTTTG
* * * ** * **
5083 CCTCATTTAAGGGATTAACTATGATTCTAAGGAAAATAATGGAAAGAAAAGCCTTTTTTTGTGAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAGAAAAG-CTTTTCTTGCAAA
* * ** * * *
5148 ACCAAAGTATCAATA-C-TGTTTATCCCAATTAGGAAAACATTTTTTTTGTTGCCAAATCTTGAA
65 ACCAAAGCATCAATATCATG--TAT-CCAATGA-GAAAA-A-TGCTTTTGCTGCCAAACCATGAA
** * *
5211 AAGAATTCAGATTATTACATGAATCCATGTTTC
124 AAGAATAGAGATTATTACAAGAATCCATGTTTG
* * * * **
5244 TCTCATTTAAGTGATGAACTTTGATTATAAGGAAAATGGTAGAAAGAAAAGCTTTTTTTGTGAAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAGAAAAGCTTTTCTTGCAAAA
* * ** * * * * *
5309 CTAAAACATCAATATTGTATATCCTAATTG-GAGAACATG-TTTT-TTAGCCTAATCATGAAAA-
66 CCAAAGCATCAATATCATGTATCC-AA-TGAGA-AAAATGCTTTTGCT-GCCAAACCATGAAAAG
* *
5370 AATGGAGATT-TATATAAGAATCC-TGTTTG
127 AATAGAGATTAT-TACAAGAATCCATGTTTG
* * * * *
5399 TCTCATTT--GAGA-G-AC---AATTTTAA-GAAAATGGT-GAAA-AAAAGCTTTTCTTGGAAGA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAGAAAAGCTTTTCTTGCAAAA
* * * * *
5454 CCAAAGCATC-ATATTATGTATCCCAA-GAGAAAAAATG-TTTAG-GGCCTATCACA--AAAA-A
66 CCAAAGCATCAATATCATGTAT-CCAATGAG-AAAAATGCTTTTGCTGCCAAAC-CATGAAAAGA
* * *
5512 GTGGAGATTATTACAAGAATCTATGTTTG
128 ATAGAGATTATTACAAGAATCCATGTTTG
* * * * * * * *
5541 TCTCATTTGATGAACGAACTTTGACTCCAAGGAAAATGGTGAAAAGAAAAGTTTTTCTTGCAAAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAGAAAAGCTTTTCTTGCAAAA
* * *
5606 CCAAGGCATATCAGTATTATGTATCGCAATGAAGAAAA
66 CCAAAGC--ATCAATATCATGTATC-CAATG-AGAAAA
5644 TGTTTTTTCA
Statistics
Matches: 675, Mismatches: 152, Indels: 98
0.73 0.16 0.11
Matches are distributed among these distances:
141 22 0.03
142 21 0.03
143 11 0.02
144 13 0.02
145 26 0.04
146 6 0.01
147 9 0.01
148 6 0.01
149 4 0.01
150 9 0.01
151 5 0.01
152 23 0.03
153 3 0.00
154 4 0.01
155 32 0.05
156 58 0.09
157 153 0.23
158 103 0.15
159 37 0.05
160 39 0.06
161 84 0.12
162 2 0.00
163 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (156 bp):
TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAGAAAAGCTTTTCTTGCAAAA
CCAAAGCATCAATATCATGTATCCAATGAGAAAAATGCTTTTGCTGCCAAACCATGAAAAGAATA
GAGATTATTACAAGAATCCATGTTTG
Found at i:5215 original size:161 final size:157
Alignment explanation
Indices: 5036--5406 Score: 428
Period size: 161 Copynumber: 2.4 Consensus size: 157
5026 ACTTTTGCAG
* *
5036 TGCCAAATCTAT-AAAAGAATGGAGATTATTACAAGAATCCATCTTTGCCTCATTTAAGGGATTA
1 TGCCAAATCT-TGAAAAGAATGGAGATTATTACAAGAATCCATGTTTGCCTCATTTAAGGGATGA
* * **
5100 ACTATGATTCTAAGGAAAATAATGGAAAGAAAAGCCTTTTTTTGTGAAACCAAAGTATCAATACT
65 ACTATGATTATAAGGAAAATAATAGAAAGAAAAG-CTTTTTTTGTGAAACCAAAACATCAATACT
* *
5165 GTTTATCCCAATTAGGAAAACATTTTTTTTGT
129 GTATATCCCAATT-GGAAAACA-TGTTTTT-T
** * *
5197 TGCCAAATCTTGAAAAGAATTCAGATTATTACATGAATCCATGTTT-CTCTCATTTAAGTGATGA
1 TGCCAAATCTTGAAAAGAATGGAGATTATTACAAGAATCCATGTTTGC-CTCATTTAAGGGATGA
* ** * *
5261 ACTTTGATTATAAGGAAAATGGTAGAAAGAAAAGCTTTTTTTGTGAAACTAAAACATCAATATTG
65 ACTATGATTATAAGGAAAATAATAGAAAGAAAAGCTTTTTTTGTGAAACCAAAACATCAATACTG
* *
5326 TATATCCTAATTGGAGAACATGTTTTTT
130 TATATCCCAATTGGAAAACATGTTTTTT
* * * * *
5354 AGCCTAATCATGAAAA-AATGGAGATT-TATATAAGAATCC-TGTTTGTCTCATTT
1 TGCCAAATCTTGAAAAGAATGGAGATTAT-TACAAGAATCCATGTTTGCCTCATTT
5407 GAGAGACAAT
Statistics
Matches: 179, Mismatches: 27, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
155 13 0.07
156 17 0.09
157 14 0.08
158 6 0.03
159 7 0.04
160 39 0.22
161 83 0.46
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (157 bp):
TGCCAAATCTTGAAAAGAATGGAGATTATTACAAGAATCCATGTTTGCCTCATTTAAGGGATGAA
CTATGATTATAAGGAAAATAATAGAAAGAAAAGCTTTTTTTGTGAAACCAAAACATCAATACTGT
ATATCCCAATTGGAAAACATGTTTTTT
Found at i:15925 original size:18 final size:18
Alignment explanation
Indices: 15898--15988 Score: 64
Period size: 18 Copynumber: 4.9 Consensus size: 18
15888 CCTCCTCCTG
15898 TCATCCCTCCTCTCTCTA
1 TCATCCCTCCTCTCTCTA
* *
15916 TTATCTCTCCTGTCTCTCCTCTA
1 TCA--TC-CCT-CCTCT-CTCTA
*
15939 TCATCCCTCCTATCTCTA
1 TCATCCCTCCTCTCTCTA
*
15957 -CTATCTCT-C-CTC-CTA
1 TC-ATCCCTCCTCTCTCTA
15972 TCATCCCTCCTCTCTCT
1 TCATCCCTCCTCTCTCT
15989 TCTTTCTCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
15 8 0.15
16 4 0.07
17 5 0.09
18 14 0.25
19 3 0.05
20 5 0.09
21 5 0.09
22 4 0.07
23 7 0.13
ACGTcount: A:0.11, C:0.46, G:0.01, T:0.42
Consensus pattern (18 bp):
TCATCCCTCCTCTCTCTA
Found at i:15939 original size:23 final size:22
Alignment explanation
Indices: 15907--15973 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
15897 GTCATCCCTC
* * *
15907 CTCTCTCTATTATCTCTCCTGT
1 CTCTCTCTATCATCCCTCCTAT
15929 CTCTCCTCTATCATCCCTCCTAT
1 CTCT-CTCTATCATCCCTCCTAT
*
15952 CTCT-ACTATC-TCTCCTCCTAT
1 CTCTCTCTATCATC-CCTCCTAT
15973 C
1 C
15974 ATCCCTCCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 2 0.05
21 14 0.36
22 4 0.10
23 19 0.49
ACGTcount: A:0.12, C:0.43, G:0.01, T:0.43
Consensus pattern (22 bp):
CTCTCTCTATCATCCCTCCTAT
Found at i:15947 original size:41 final size:42
Alignment explanation
Indices: 15889--15967 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
15879 TTCTTCTCTC
* * *
15889 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
15931 CTCCT-CTATCATCCCTCCTATCTCTACTATCTCTCCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCT
15968 CCTATCATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 29 0.85
42 5 0.15
ACGTcount: A:0.10, C:0.46, G:0.03, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
Found at i:15978 original size:33 final size:32
Alignment explanation
Indices: 15917--15997 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 32
15907 CTCTCTCTAT
* *
15917 TATCTCTCCTGTCTCTCCTCTATCATCCCTCC
1 TATCTCTACTATCTCTCCTCTATCATCCCTCC
15949 TATCTCTACTATCTCTCCTCCTATCATCCCTCC
1 TATCTCTACTATCTCTCCT-CTATCATCCCTCC
* * *
15982 TCTCTCTTCTTTCTCT
1 TATCTCTACTATCTCT
15998 TTGAGGCTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 17 0.40
33 26 0.60
ACGTcount: A:0.10, C:0.44, G:0.01, T:0.44
Consensus pattern (32 bp):
TATCTCTACTATCTCTCCTCTATCATCCCTCC
Found at i:17798 original size:249 final size:252
Alignment explanation
Indices: 17352--17857 Score: 858
Period size: 249 Copynumber: 2.0 Consensus size: 252
17342 AAGCAAGTCA
*
17352 CAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
1 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
*
17417 TCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
66 TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
*
17482 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGACCTT
131 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
* * * *
17547 GAAATCCTT-CCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCAT
196 GAAA-CCTTCCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
17604 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
1 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
* * *
17669 TCC-AA-ATATGCAATTGACCAGCTTGGGCTCTTCTAGCTCC-AATTGGGTTTACTTTCAAATAG
66 TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
* * *
17731 GGCAGCAACCGTCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTT
131 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
17796 GAAACCTTCCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
196 GAAACCTTCCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
17853 CAACC
1 CAACC
17858 CTTCCTTCTT
Statistics
Matches: 240, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
248 4 0.02
249 135 0.56
250 32 0.13
251 2 0.01
252 67 0.28
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (252 bp):
CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
GAAACCTTCCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
Done.