Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1178
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: 32103
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:3079 original size:27 final size:27
Alignment explanation
Indices: 3049--3226 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
3039 ATATTGAGCC
* * *
3049 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
3076 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
3103 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
3131 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
3158 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
3185 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
3212 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3227 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:3142 original size:55 final size:55
Alignment explanation
Indices: 3049--3226 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
3039 ATATTGAGCC
* * *
3049 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
3103 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
3158 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
3212 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3227 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:3188 original size:82 final size:81
Alignment explanation
Indices: 3070--3225 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
3060 TGCTATACAA
* * *
3070 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
3135 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
3152 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
3216 CACTTAGTGC
65 CACTTAGTGC
3226 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16114 original size:24 final size:24
Alignment explanation
Indices: 16082--16130 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
16072 TCCCTTATGA
*
16082 TGGTCTACGAGACTTAAAACATAC
1 TGGTCTACGAGACCTAAAACATAC
16106 TGGTCTACGAGACCTAAAACATAC
1 TGGTCTACGAGACCTAAAACATAC
16130 T
1 T
16131 TTTAAGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (24 bp):
TGGTCTACGAGACCTAAAACATAC
Found at i:21566 original size:27 final size:28
Alignment explanation
Indices: 21536--21711 Score: 132
Period size: 27 Copynumber: 6.5 Consensus size: 28
21526 ATATTAAGTC
* * *
21536 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCCACATAATCAAACT
21563 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCCACATAATCAAACT
* * ** *
21591 CGCACACTTAGTGTCGCATGGTC-AATT
1 CGCACACTTAGTGCCACATAATCAAACT
** **
21618 CGCACACTTAGTG-CATCATTTTC-ATTT
1 CGCACACTTAGTGCCA-CATAATCAAACT
* **
21645 CGCACACTTAGTGCAACATGGTCAAA-T
1 CGCACACTTAGTGCCACATAATCAAACT
* **
21672 CGCACACTTAGTGCTACATAGCCAAA-T
1 CGCACACTTAGTGCCACATAATCAAACT
21699 -GCACACTTAGTGC
1 CGCACACTTAGTGC
21712 TGTACAATTT
Statistics
Matches: 126, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.11
27 87 0.69
28 25 0.20
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCCACATAATCAAACT
Found at i:30924 original size:27 final size:27
Alignment explanation
Indices: 30858--31012 Score: 136
Period size: 27 Copynumber: 5.7 Consensus size: 27
30848 TAATTGTACA
* * *
30858 GCACTAAGTGTGCG-ATTGGCTATGTA
1 GCACTAAGTGTGCGAATTGACCATGTT
*
30884 GCA-TAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAATTGACCATGTT
* ** *
30910 GCACTAAGTGTGCGAAATGAAAATGAT
1 GCACTAAGTGTGCGAATTGACCATGTT
*
30937 GCACTAAGTGTGCGAATTGACCATG-C
1 GCACTAAGTGTGCGAATTGACCATGTT
* ** *
30963 GACACTAAAGTGTGCGAGTTTGATTATGTG
1 G-CACT-AAGTGTGCGA-ATTGACCATGTT
*
30993 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
31013 TTTATATAGC
Statistics
Matches: 105, Mismatches: 18, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
25 10 0.10
26 15 0.14
27 48 0.46
28 20 0.19
29 11 0.10
30 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACCATGTT
Found at i:31001 original size:28 final size:26
Alignment explanation
Indices: 30857--31034 Score: 128
Period size: 27 Copynumber: 6.6 Consensus size: 26
30847 GTAATTGTAC
*
30857 AGCACTAAGTGTGCGATTGGCTATGT
1 AGCACTAAGTGTGCGATTGACTATGT
*
30883 AGCA-TAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * **
30909 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
*
30935 ATGCACTAAGTGTGCGAATTGACCATG-
1 A-GCACTAAGTGTGCG-ATTGACTATGT
* *
30962 CGACACTAAAGTGTGCGAGTTTGATTATGT
1 AG-CACT-AAGTGTGCGA--TTGACTATGT
* * *
30992 GGCACTAAGTGTGCGAGTTGATTTATAT
1 AGCACTAAGTGTGCGA-TTGA-CTATGT
*
31020 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31035 GACTTAATAT
Statistics
Matches: 124, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
25 11 0.09
26 16 0.13
27 47 0.38
28 38 0.31
29 11 0.09
30 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Done.