Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2378
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: 15190
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Found at i:2901 original size:37 final size:37
Alignment explanation
Indices: 2851--2929 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
2841 TTATTACGAA
* *
2851 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
2888 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
2925 GTCTT
1 GTCTT
2930 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:3124 original size:47 final size:47
Alignment explanation
Indices: 3046--3487 Score: 733
Period size: 47 Copynumber: 9.4 Consensus size: 47
3036 CCCTTCGGGA
* * * * * * *
3046 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
3093 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
3140 CTTACCACATATATTACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATA-TACACTTTCACATTCATCACATCGGCCATTAGGC
*
3188 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3235 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3281 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3328 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3375 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3422 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3469 CTTATCACATATATACACT
1 CTTATCACATATATACACT
3488 GTCTTGGCTG
Statistics
Matches: 371, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 45 0.12
47 281 0.76
48 45 0.12
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:3341 original size:140 final size:141
Alignment explanation
Indices: 3046--3487 Score: 742
Period size: 140 Copynumber: 3.1 Consensus size: 141
3036 CCCTTCGGGA
* * * * * * * * * *
3046 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
3111 TTTCACATTCATCACATCGGCCATTAGGCCTTACCACATATATTACACTTTCACATTCATCACAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA-TACACTTTCACATTCATCACAT
*
3176 CGGCCATTTGGC
130 CGGCCATTAGGC
3188 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
3253 TTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
3317 GGCCATTAGGC
131 GGCCATTAGGC
*
3328 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
3393 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
3458 GGCTATTAGGC
131 GGCCATTAGGC
3469 CTTATCACATATATACACT
1 CTTATCACATATATACACT
3488 GTCTTGGCTG
Statistics
Matches: 285, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
140 117 0.41
141 93 0.33
142 75 0.26
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:11092 original size:14 final size:14
Alignment explanation
Indices: 11073--11101 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11063 CCAATAGTTG
11073 AGTAATGCTCAAAC
1 AGTAATGCTCAAAC
11087 AGTAATGCTCAAAC
1 AGTAATGCTCAAAC
11101 A
1 A
11102 TTAGTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
AGTAATGCTCAAAC
Found at i:12076 original size:2 final size:2
Alignment explanation
Indices: 12071--12100 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12061 GATATATATA
12071 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12101 AATGAATTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:14976 original size:52 final size:48
Alignment explanation
Indices: 14900--15029 Score: 138
Period size: 52 Copynumber: 2.6 Consensus size: 48
14890 ATTGTTAGAA
* *
14900 CACATGTAGTACTATGTGTAGGCTACTATGTGTTTA-AGATAGTTTTAGGT
1 CACATGTAGTACTAAGTGTAGGCTACTATGTG-TAACAGATAG--TTAGGT
* *
14950 CACATGTGTAGTACTAAGTGTAGGCTATTACGTGTAACAGATAGTTAGGT
1 CACA--TGTAGTACTAAGTGTAGGCTACTATGTGTAACAGATAGTTAGGT
** *
15000 TGCATGT-GTACTAAGTGCAGGCTACTATGT
1 CACATGTAGTACTAAGTGTAGGCTACTATGT
15030 ACCAGATAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
47 20 0.29
48 3 0.04
50 12 0.18
51 2 0.03
52 31 0.46
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (48 bp):
CACATGTAGTACTAAGTGTAGGCTACTATGTGTAACAGATAGTTAGGT
Done.