Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold83
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: 1211110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 9456 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:1208432 original size:69 final size:66
Alignment explanation
Indices: 1208273--1208820 Score: 301
Period size: 60 Copynumber: 8.5 Consensus size: 66
1208263 CCGGAACCCA
*
1208273 TTTCAAAGCCCAGCACAAAGTCGGTGGCAA-CCATTTTCAAAGGCCCACACAATCGTTGGCAACC
1 TTTCAAAGCACA-CAC-AAGTCGGTGGCAACCCATTTTCAAAGGCCCACACAATCGTTGGCAACC
*
1208337 CTT
64 CTC
*
1208340 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTCTAAA-GCCCACGACAAGTCGGGTTGCGC
1 TTTCAAAGCACACACAAGTCGGTGGCAACCCATTTTC-AAAGGCCCAC-ACAA-TC--GTTG-GC
1208404 -A-CCTC
60 AACCCTC
* * * * * *
1208409 TTTCAAAG-ATACAACACGTCGGTGGCAAACCCA-TTTC-AACGCCTACATCAGTCGGTGGCAAA
1 TTTCAAAGCACAC-ACAAGTCGGTGGC-AACCCATTTTCAAAGGCCCACA-CAATCGTTGGC--A
*
1208471 ACCAT-
61 ACCCTC
* *
1208476 TTTCAAAGCCCACA-AAGTCGGTGGCAACCC---TTCAAA--ACCACACAAGTCAG-TGGCAACC
1 TTTCAAAGCACACACAAGTCGGTGGCAACCCATTTTCAAAGGCCCACACAA-TC-GTTGGCAACC
*
1208534 C-A
64 CTC
* * * *
1208536 TTTCAATGCCCACAC-AGTCGGTGGCAACCC-TTTTCAAA-GCACACACAAGTCGGT-G-AA-CC
1 TTTCAAAGCACACACAAGTCGGTGGCAACCCATTTTCAAAGGCCCACACAA-TCGTTGGCAACCC
*
1208595 -A
65 TC
* * * * * * *
1208596 TTTCCAATCCCACCACAAGTCGGTGGCAATTTCCATTTTTC-AACGCCCACACAGTAG-TGGCAA
1 TTTCAAAGCACA-CACAAGTCGGTGGCAA--CCCA-TTTTCAAAGGCCCACACAATCGTTGGCAA
1208659 CCCT-
62 CCCTC
* ** *
1208663 TTTCAAAGCCCCACACAAGTCGGTGGCAACCCCATTCCCAAA-G-CCACACAAGTCGGTGG--AC
1 TTTCAAAG-CACACACAAGTCGGTGGCAA-CCCATTTTCAAAGGCCCACACAA-TCGTTGGCAAC
*
1208724 CC-A
63 CCTC
*
1208727 TTTCAAAGC-CACAC-AGTCGGTGGCAAACCC--TTTCAAA-GCCCACACAAGTCGGTGGCAACC
1 TTTCAAAGCACACACAAGTCGGTGGC-AACCCATTTTCAAAGGCCCACACAA-TCGTTGGCAACC
1208787 CT-
64 CTC
* *
1208789 TTCCAAAGCCCACA-AAGTC-GTGGCAACCCATT
1 TTTCAAAGCACACACAAGTCGGTGGCAACCCATT
1208821 CAATAGCCCA
Statistics
Matches: 395, Mismatches: 36, Indels: 104
0.74 0.07 0.19
Matches are distributed among these distances:
59 6 0.02
60 60 0.15
61 25 0.06
62 54 0.14
63 25 0.06
64 26 0.07
65 32 0.08
66 50 0.13
67 58 0.15
68 19 0.05
69 27 0.07
70 11 0.03
71 2 0.01
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (66 bp):
TTTCAAAGCACACACAAGTCGGTGGCAACCCATTTTCAAAGGCCCACACAATCGTTGGCAACCCT
C
Found at i:1208773 original size:190 final size:189
Alignment explanation
Indices: 1208286--1208814 Score: 507
Period size: 190 Copynumber: 2.7 Consensus size: 189
1208276 CAAAGCCCAG
* * *
1208286 CACAAAGTCGGTGGCAACCATTTTCAAAGGCCCACACAA-TC-GTTGGCAACCCTTTTTCAAAGC
1 CACAAAGTCGGTGGCAACC--CTTCAAA--ACCACACAAGTCAG-TGG-AACCC-ATTTCAAAGC
* *
1208349 CCACACAAGTCGGTGGCAACCCATTTTCTAAAGCCCACGACAAGTCGGGTTGCGC-ACC-TCTTT
59 CCACAC-AGTCGGTGGCAACCC-TTTTC-AAAGCACAC-ACAAGTC-GG-TG-GCAACCAT-TTC
** ** * *
1208412 CAAAG-ATACAACACGTCGGTGGCAA-ACCCA--TTTCAACGCCTACATCAGTCGGTGGCAAAAC
116 CAAAGCCCACAA-A-GTC-GTGGCAATTTCCATTTTTCAACGCCCACATCAGTCAGTGGC-AAAC
1208473 CATTTTCAAAGCC
177 CATTTTCAAAGCC
*
1208486 CACAAAGTCGGTGGCAACCCTTCAAAACCACACAAGTCAGTGGCAACCCATTTCAATGCCCACAC
1 CACAAAGTCGGTGGCAACCCTTCAAAACCACACAAGTCAGTGG-AACCCATTTCAAAGCCCACAC
*
1208551 AGTCGGTGGCAACCCTTTTCAAAGCACACACAAGTCGGT-G-AACCATTTCC-AATCCCACCACA
65 AGTCGGTGGCAACCCTTTTCAAAGCACACACAAGTCGGTGGCAACCATTTCCAAAGCCCA-CA-A
*
1208613 AGTCGGTGGCAATTTCCATTTTTCAACGCCCACA-CAGT-AGTGGC-AACCCTTTTCAAAGCCC
128 AGTC-GTGGCAATTTCCATTTTTCAACGCCCACATCAGTCAGTGGCAAACCATTTTCAAAG-CC
* *
1208674 CACACAAGTCGGTGGCAACCCCATTCCCAAAGCCACACAAGTCGGTGG-ACCCATTTCAAAG-CC
1 CACA-AAGTCGGTGGCAA-CCC-TT--CAAAACCACACAAGTCAGTGGAACCCATTTCAAAGCCC
* *
1208737 ACACAGTCGGTGGCAAACCC-TTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTCCAAAGCCCA
61 ACACAGTCGGTGGC-AACCCTTTTCAAAGCACACACAAGTCGGTGGCAACCATTTCCAAAGCCCA
1208801 CAAAGTCGTGGCAA
125 CAAAGTCGTGGCAA
1208815 CCCATTCAAT
Statistics
Matches: 289, Mismatches: 20, Indels: 50
0.81 0.06 0.14
Matches are distributed among these distances:
187 15 0.05
188 25 0.09
189 25 0.09
190 54 0.19
191 40 0.14
192 18 0.06
193 33 0.11
194 5 0.02
195 15 0.05
196 22 0.08
197 11 0.04
198 7 0.02
200 19 0.07
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (189 bp):
CACAAAGTCGGTGGCAACCCTTCAAAACCACACAAGTCAGTGGAACCCATTTCAAAGCCCACACA
GTCGGTGGCAACCCTTTTCAAAGCACACACAAGTCGGTGGCAACCATTTCCAAAGCCCACAAAGT
CGTGGCAATTTCCATTTTTCAACGCCCACATCAGTCAGTGGCAAACCATTTTCAAAGCC
Found at i:1208841 original size:222 final size:223
Alignment explanation
Indices: 1208265--1208845 Score: 592
Period size: 222 Copynumber: 2.6 Consensus size: 223
1208255 ACACCCCTCC
* *
1208265 GGAACCCATTTCAAAGCCCAGCACAAAGTCGGTGGCAACCATTTTCAAAGGCCCACACAA-TCGT
1 GGAACCCATTTCAAAG-CCA-CAC-AAGTCGGTGGCAACC-CTTTCAAA-GCCCACACAAGTCGG
1208329 TGGCAACCCTTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTCTAA-AGCCCACGACAAG
61 TGGCAACCC-TTTTCAAAGCCCACACAAGTC-GTGGCAACCCA-TTTC-AATAGCCCAC-ACAAG
* * * *
1208393 TCGGGTTGCGC-ACCTCTTTCAAAGATACAACACGTCGGTGGCAAACCCATTTCAACGCCTACAT
121 TC-GG-TG-GCAACCTCTTTCAAAGACACAACACGTCAGTGGCAAACCCATTTCAAAGCCCACAT
**
1208457 CAGTCGGTGGCAAAACCATTTTCAAAGCCCACAAAGTCGGT
183 CAGTCGGTGGCAAAACCATTCCCAAAGCCCACAAAGTCGGT
* * *
1208498 GGCAACCC--TTCAAAACCACACAAGTCAGTGGCAACCCATTTCAATGCCCACAC-AGTCGGTGG
1 GG-AACCCATTTCAAAGCCACACAAGTCGGTGGCAACCC-TTTCAAAGCCCACACAAGTCGGTGG
*
1208560 CAACCCTTTTCAAAGCACACACAAGTCG-GTG-AA-CCATTTCCAAT--CCCACCACAAGTCGGT
64 CAACCCTTTTCAAAGCCCACACAAGTCGTG-GCAACCCATTT-CAATAGCCCA-CACAAGTCGGT
* * * *
1208620 GGCAATTTCCATTTTTCAACG-C-CCACACAGT-AGTGGC-AACCCTTTTCAAAGCCCCACA-CA
126 GGCAA---CC-TCTTTCAAAGACACAACAC-GTCAGTGGCAAACCCATTTCAAAG-CCCACATC-
**
1208680 AGTCGGTGGCAACCCCATTCCCAAAG-CCACACAAGTCGGT
184 AGTCGGTGGCAAAACCATTCCCAAAGCCCACA-AAGTCGGT
1208720 GG-ACCCATTTCAAAGCCACAC-AGTCGGTGGCAAACCCTTTCAAAGCCCACACAAGTCGGTGGC
1 GGAACCCATTTCAAAGCCACACAAGTCGGTGGC-AACCCTTTCAAAGCCCACACAAGTCGGTGGC
* *
1208783 AACCCTTTCCAAAGCCCACA-AAGTCGTGGCAACCCA-TTCAATAGCCCACACGAGTCGGTGGCA
65 AACCCTTTTCAAAGCCCACACAAGTCGTGGCAACCCATTTCAATAGCCCACACAAGTCGGTGGCA
1208846 CTTCTTTTCA
Statistics
Matches: 299, Mismatches: 24, Indels: 61
0.78 0.06 0.16
Matches are distributed among these distances:
219 2 0.01
220 7 0.02
221 54 0.18
222 122 0.41
223 17 0.06
224 12 0.04
225 3 0.01
226 2 0.01
227 21 0.07
228 20 0.07
229 20 0.07
230 3 0.01
231 3 0.01
232 6 0.02
233 2 0.01
234 5 0.02
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (223 bp):
GGAACCCATTTCAAAGCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTCGGTGGCA
ACCCTTTTCAAAGCCCACACAAGTCGTGGCAACCCATTTCAATAGCCCACACAAGTCGGTGGCAA
CCTCTTTCAAAGACACAACACGTCAGTGGCAAACCCATTTCAAAGCCCACATCAGTCGGTGGCAA
AACCATTCCCAAAGCCCACAAAGTCGGT
Found at i:1208876 original size:94 final size:93
Alignment explanation
Indices: 1208273--1208869 Score: 363
Period size: 94 Copynumber: 6.2 Consensus size: 93
1208263 CCGGAACCCA
* ** *
1208273 TTTCAAAGCCCAGCACAAAGTCGGTGGCAA--CCATTTTCAAAGGCCCACACAA-TCGTTGGCAA
1 TTTCAAAGCCC-CCAC-AAGTCGGTGGCAACCCCATTCCCAAA-G-CCACACAAGTCGGTGG--A
* *
1208335 CCCTTTTTCAAAGCCCACACAAGTCGGTGGCAACCCAT
60 CCC-ATTTCAAAG-CCACAC-AGTCGGTGGCAAACC-T
* * * ** *
1208373 TTTCTAAAGCCCACGACAAGTCGGGTTGCGC-ACCTC-TT-TCAAAGATACAACACGTCGGTGGC
1 TTTC-AAAGCCC-CCACAAGTC-GG-TG-GCAACCCCATTCCCAAAGCCAC-ACAAGTCGGTGG-
*
1208435 AAACCCATTTCAACGCCTACATCAGTCGGTGGCAAAACCAT
59 --ACCCATTTCAAAGCC-ACA-CAGTCGGTGGC-AAACC-T
* * *
1208476 TTTCAAAGCCCACA-AAGTCGGTGGCAA-CCC-TT--CAAAACCACACAAGTCAGTGGCAACCCA
1 TTTCAAAGCCCCCACAAGTCGGTGGCAACCCCATTCCCAAAGCCACACAAGTCGGTGG--ACCCA
* *
1208536 TTTCAATGCCCACACAGTCGGTGGCAACCCT
64 TTTCAAAG-CCACACAGTCGGTGGCAAACCT
* * * ** *
1208567 TTTCAAAGCACACACAAGTCGGT-G-AA--CCATTTCCAATCCCACCACAAGTCGGTGGCAATTT
1 TTTCAAAGCCCCCACAAGTCGGTGGCAACCCCATTCCCAAAGCCA-CACAAGTCGGTGG--A--C
* * *
1208628 CCATTTTTCAACGCCCACACAGT-AGTGGCAACCCT
61 CCA--TTTCAAAG-CCACACAGTCGGTGGCAAACCT
1208663 TTTCAAAGCCCCACACAAGTCGGTGGCAACCCCATTCCCAAAGCCACACAAGTCGGTGGACCCAT
1 TTTCAAAGCCCC-CACAAGTCGGTGGCAACCCCATTCCCAAAGCCACACAAGTCGGTGGACCCAT
*
1208728 TTCAAAGCCACACAGTCGGTGGCAAACCC
65 TTCAAAGCCACACAGTCGGTGGCAAACCT
* *
1208757 TTTCAAAGCCCACACAAGTCGGTGGCAA-CCC-TTTCCAAAGCC-CACAAAGTC-GTGGCAACCC
1 TTTCAAAGCCCCCACAAGTCGGTGGCAACCCCATTCCCAAAGCCACAC-AAGTCGGTGG--ACCC
***
1208818 A-TTCAATAGCCCACACGAGTCGGTGGCACTTCT
63 ATTTCAA-AG-CCACAC-AGTCGGTGGCAAACCT
* *
1208851 TTTCAAGGCCCCCAGAAGT
1 TTTCAAAGCCCCCACAAGT
1208870 TAGTGGCCCC
Statistics
Matches: 414, Mismatches: 48, Indels: 76
0.77 0.09 0.14
Matches are distributed among these distances:
89 2 0.00
90 11 0.03
91 35 0.08
92 28 0.07
93 57 0.14
94 71 0.17
95 15 0.04
96 30 0.07
97 34 0.08
98 5 0.01
99 4 0.01
100 29 0.07
101 31 0.07
102 41 0.10
103 20 0.05
104 1 0.00
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.19
Consensus pattern (93 bp):
TTTCAAAGCCCCCACAAGTCGGTGGCAACCCCATTCCCAAAGCCACACAAGTCGGTGGACCCATT
TCAAAGCCACACAGTCGGTGGCAAACCT
Found at i:1209079 original size:1 final size:1
Alignment explanation
Indices: 1209073--1209100 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1209063 ATGGCAATTG
1209073 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1209101 CTCTCATCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1210561 original size:21 final size:23
Alignment explanation
Indices: 1210534--1210582 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1210524 ACCATGATCT
1210534 TTTTTTA-TTA-TG-TTTCTGCA
1 TTTTTTATTTATTGCTTTCTGCA
1210554 TGTTTTTATTTATTGCTTTCTGCA
1 T-TTTTTATTTATTGCTTTCTGCA
1210578 TTTTT
1 TTTTT
1210583 AACTATGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 3 0.12
23 6 0.24
24 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.67
Consensus pattern (23 bp):
TTTTTTATTTATTGCTTTCTGCA
Found at i:1210583 original size:22 final size:20
Alignment explanation
Indices: 1210535--1210583 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
1210525 CCATGATCTT
1210535 TTTTTATTATGTTTCTGCATG
1 TTTTTATTATGTTTCTGCA-G
1210556 TTTTTATTTATTGCTTTCTGCA-
1 TTTTTA-TTA-TG-TTTCTGCAG
1210578 TTTTTA
1 TTTTTA
1210584 ACTATGGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.24
22 9 0.36
23 2 0.08
24 8 0.32
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.65
Consensus pattern (20 bp):
TTTTTATTATGTTTCTGCAG
Done.