Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1025
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: 38812
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:5608 original size:27 final size:27
Alignment explanation
Indices: 5578--5754 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5568 ATATTAAGTC
* * *
5578 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
5605 CGCACACTTAGTGC-ACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
5632 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
5659 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
5686 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
5713 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
5740 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5755 GTACAATTTA
Statistics
Matches: 131, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
26 7 0.05
27 116 0.89
28 8 0.06
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:5672 original size:81 final size:81
Alignment explanation
Indices: 5578--5754 Score: 230
Period size: 81 Copynumber: 2.2 Consensus size: 81
5568 ATATTAAGTC
* *
5578 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCA-CATAATCAAACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCATCATAATC-AACTCGCACACTTA
* *
5642 GTGCTACATAGTCAACT
65 GTGCAACATAGTCAAAT
** ** * * **
5659 CGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAG
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCATCATAATCAACTCGCACACTTAG
5724 TGCAACATAGTCAAAT
66 TGCAACATAGTCAAAT
5740 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5755 GTACAATTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 76 0.93
82 6 0.07
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (81 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCATCATAATCAACTCGCACACTTAG
TGCAACATAGTCAAAT
Found at i:23483 original size:42 final size:42
Alignment explanation
Indices: 23419--23503 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
23409 TGTGTGACTT
*
23419 GGCCCTGTGACTTCAATTTGTTGATGATGTCATAAACAGAGA
1 GGCCCTGTGACTTCAATTTGTTGATGACGTCATAAACAGAGA
* * *
23461 GGCCTTGTGACTTCAATTTGTTGATTACGTCATAAATAGAGA
1 GGCCCTGTGACTTCAATTTGTTGATGACGTCATAAACAGAGA
23503 G
1 G
23504 TTACAAGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
GGCCCTGTGACTTCAATTTGTTGATGACGTCATAAACAGAGA
Found at i:25744 original size:54 final size:55
Alignment explanation
Indices: 25659--25768 Score: 186
Period size: 54 Copynumber: 2.0 Consensus size: 55
25649 ATGTTAGCTC
* * *
25659 AGAATTGTATAAGAAAAGGCTATGAAGCTTATCAAGCTTGTGTGCTGAATACAAA
1 AGAATTGTATAAGAAAAGACTATGAAACTTATCAAGCTTATGTGCTGAATACAAA
25714 AGAA-TGTATAAGAAAAGACTATGAAACTTATCAAGCTTATGTGCTGAATACAAA
1 AGAATTGTATAAGAAAAGACTATGAAACTTATCAAGCTTATGTGCTGAATACAAA
25768 A
1 A
25769 AAGTCTGAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 48 0.92
55 4 0.08
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (55 bp):
AGAATTGTATAAGAAAAGACTATGAAACTTATCAAGCTTATGTGCTGAATACAAA
Found at i:28734 original size:41 final size:40
Alignment explanation
Indices: 28681--28845 Score: 131
Period size: 41 Copynumber: 4.0 Consensus size: 40
28671 AGTTCGACTC
*
28681 TTAG-CACCGGCTCAAAAGCCCTTCGAGACCAAGCTCAGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCAGA
* * * * *
28720 TTAGACTACTGGCTCGAAGGCCCTTCG-GAACTAAG-TCCGG
1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAG-ACCAAGCTCAGA
* * * * * *
28760 TTATGACACTGGCTCTAAAAAGCCTTTCAAAACTAAGTTCGGTTA
1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCAG--A
28805 TTAG-CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCAGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCAGA
28844 TT
1 TT
28846 TAAACCTCGA
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
39 7 0.07
40 16 0.16
41 44 0.45
42 14 0.14
43 12 0.12
44 1 0.01
45 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCAGA
Found at i:37086 original size:41 final size:40
Alignment explanation
Indices: 37033--37196 Score: 167
Period size: 41 Copynumber: 4.0 Consensus size: 40
37023 AGTCCGACTC
*
37033 TTAG-CACCGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
* * *
37072 TTAGACTACTGGCTCGAAGGCCCTTCGA-ACTAAG-TCCGG-
1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAGACCAAGCT-CGGA
* * *
37111 TTATGACACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTA
1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCGG--A
37156 TTAG-CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
37195 TT
1 TT
37197 TAAACCCCGA
Statistics
Matches: 105, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
39 19 0.18
40 12 0.11
41 51 0.49
42 9 0.09
43 10 0.10
44 1 0.01
45 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
Done.