Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2526
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: 21054
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Found at i:3371 original size:27 final size:27
Alignment explanation
Indices: 3339--3390 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
3329 CCGCTGAATC
*
3339 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
3366 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
3391 TTCACATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.13
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:3493 original size:103 final size:103
Alignment explanation
Indices: 3305--3568 Score: 406
Period size: 104 Copynumber: 2.6 Consensus size: 103
3295 TAACCGTTAT
* **
3305 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCTCGGGGG
3370 AATCAGCACATAGCAACCCC-TTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCTTTTCACATTTCAAAGATA
*
3408 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCTCGGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCTCGGGGGA
*
3473 ATCAGCACATAGTAACCCCCTTTTCACATTTCAAAGATA
66 ATCAGCACATAGCAA-CCCCTTTTCACATTTCAAAGATA
** **
3512 TGGTGGATCA-CGCACAGAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCC
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCC
3569 CTTTATATAC
Statistics
Matches: 148, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 25 0.17
103 54 0.36
104 68 0.46
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCTCGGGGGA
ATCAGCACATAGCAACCCCTTTTCACATTTCAAAGATA
Found at i:5786 original size:26 final size:27
Alignment explanation
Indices: 5691--5798 Score: 102
Period size: 26 Copynumber: 4.1 Consensus size: 27
5681 ATAATATGAT
* *
5691 CACTAAGTGTGCGAAATTGA-CATGCT-G
1 CACTAAGTGTGCG-AGTTGATTATG-TAG
*
5718 CACTAAGTGTGCGAGTTGA-AATGTAG
1 CACTAAGTGTGCGAGTTGATTATGTAG
* *
5744 CA-T-AGTGTGCGATTTGATTACGTAG
1 CACTAAGTGTGCGAGTTGATTATGTAG
*
5769 CACTAAGT-TGCGAGTTGATTATATAG
1 CACTAAGTGTGCGAGTTGATTATGTAG
5795 CACT
1 CACT
5799 GGATGACGGA
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
24 13 0.19
25 9 0.13
26 31 0.45
27 16 0.23
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (27 bp):
CACTAAGTGTGCGAGTTGATTATGTAG
Found at i:7468 original size:26 final size:28
Alignment explanation
Indices: 7428--7479 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
7418 TCATGCTATA
* *
7428 TATCAACTCGCCACACTTAGT-CTACTG
1 TATCAAATCGCCACACTGAGTGCTACTG
7455 TATCAAATCG-CACACTGAGTGCTAC
1 TATCAAATCGCCACACTGAGTGCTAC
7480 ATAGTCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (28 bp):
TATCAAATCGCCACACTGAGTGCTACTG
Found at i:7579 original size:25 final size:21
Alignment explanation
Indices: 7545--7603 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 21
7535 TATATCATCT
7545 TCGCACACTTAGTAAAATAGTCAAA
1 TCGCACACTTAGT-AAAT-GTC--A
* *
7570 TCGCACACTTACTACATGTCA
1 TCGCACACTTAGTAAATGTCA
7591 TCGCACACTTAGT
1 TCGCACACTTAGT
7604 GTGTACAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
23 3 0.10
24 3 0.10
25 12 0.39
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
TCGCACACTTAGTAAATGTCA
Found at i:15332 original size:28 final size:28
Alignment explanation
Indices: 15265--15336 Score: 112
Period size: 27 Copynumber: 2.6 Consensus size: 28
15255 GCTATATAAC
*
15265 AACTCGCACACTTA-TGCTACGTAATCA
1 AACTCGCACACTTAGTGCTACATAATCA
*
15292 AA-TCGCACACTTAGTGCTACATAGTCA
1 AACTCGCACACTTAGTGCTACATAATCA
15319 AACTCGCACACTTAGTGC
1 AACTCGCACACTTAGTGC
15337 CGCATGGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.27
27 15 0.37
28 15 0.37
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (28 bp):
AACTCGCACACTTAGTGCTACATAATCA
Found at i:15427 original size:25 final size:26
Alignment explanation
Indices: 15268--15427 Score: 111
Period size: 26 Copynumber: 6.3 Consensus size: 26
15258 ATATAACAAC
* * *
15268 TCGCACACTTA-TGCTACGTAATCAAA
1 TCGCACACTTAGTGCAACATAGTC-AA
*
15294 TCGCACACTTAGTGCTACATAGTCAAA
1 TCGCACACTTAGTGCAACATAGTC-AA
** * *
15321 CTCGCACACTTAGTGCCGCATGGTCAT
1 -TCGCACACTTAGTGCAACATAGTCAA
* *
15348 TC-CACA--TAGTGCATCATA-TCATT
1 TCGCACACTTAGTGCAACATAGTCA-A
*
15371 TCGCACACTTAGTGCAACATATTCAA
1 TCGCACACTTAGTGCAACATAGTCAA
*
15397 TC-CACACTT-TTGCAACA-AGTCAAA
1 TCGCACACTTAGTGCAACATAGTC-AA
15421 TCGCACA
1 TCGCACA
15428 GTAGTGTACA
Statistics
Matches: 112, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
22 3 0.03
23 15 0.13
24 15 0.13
25 15 0.13
26 26 0.23
27 17 0.15
28 21 0.19
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
TCGCACACTTAGTGCAACATAGTCAA
Found at i:16867 original size:12 final size:12
Alignment explanation
Indices: 16850--16874 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16840 ACTTCACTAG
16850 CCAACATTGTTC
1 CCAACATTGTTC
16862 CCAACATTGTTC
1 CCAACATTGTTC
16874 C
1 C
16875 ACCATAGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.08, T:0.32
Consensus pattern (12 bp):
CCAACATTGTTC
Done.