Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7431.1
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: 6947
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Found at i:998 original size:16 final size:14
Alignment explanation
Indices: 979--1031 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 14
969 TTAACTTGAT
979 TTTTTTTTTGGTCACC
1 TTTTTTTTT-GTCA-C
995 TTTTTTTTTGCTCGA-
1 TTTTTTTTTG-TC-AC
1010 TTTTTTTTT-TCAC
1 TTTTTTTTTGTCAC
1023 TTTTTTTTT
1 TTTTTTTTT
1032 TTATTTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.03
13 11 0.32
15 10 0.29
16 11 0.32
17 1 0.03
ACGTcount: A:0.06, C:0.13, G:0.08, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTGTCAC
Found at i:1198 original size:13 final size:13
Alignment explanation
Indices: 1180--1256 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 13
1170 TACTTGCGGA
*
1180 TTTTTTTTTCACT
1 TTTTTTTTTCAAT
*
1193 TTTTTTTTTGAATAT
1 TTTTTTTTT-CA-AT
1208 TTTTTTTTCAATCAAT
1 TTTTTTTT---TCAAT
1224 TTTTTTTTTCGAAT
1 TTTTTTTTTC-AAT
*
1238 TTTTTTTTT-GAT
1 TTTTTTTTTCAAT
1250 TTTTTTT
1 TTTTTTT
1257 GTTACTCCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
12 9 0.17
13 11 0.20
14 13 0.24
15 9 0.17
16 10 0.19
17 1 0.02
18 1 0.02
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:1199 original size:14 final size:15
Alignment explanation
Indices: 1180--1246 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 15
1170 TACTTGCGGA
*
1180 TTTTTTTTTC--ACT
1 TTTTTTTTTCAAATT
* *
1193 TTTTTTTTT-GAATA
1 TTTTTTTTTCAAATT
*
1207 TTTTTTTTTCAATCAAT
1 TTTTTTTTTCAA--ATT
*
1224 TTTTTTTTTCGAATT
1 TTTTTTTTTCAAATT
1239 TTTTTTTT
1 TTTTTTTT
1247 GATTTTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
13 9 0.21
14 10 0.24
15 11 0.26
17 12 0.29
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTCAAATT
Found at i:1277 original size:178 final size:171
Alignment explanation
Indices: 1011--1361 Score: 546
Period size: 178 Copynumber: 2.0 Consensus size: 171
1001 TTTGCTCGAT
1011 TTTTTTTTTCACTTTTTTTTTTTATTTGTTTCAATCAATTTTTTTTTCGAATTTTTTTGATTTTT
1 TTTTTTTTTCACTTTTTTTTTTTATTTGTTTCAATCAATTTTTTTTTCGAATTTTTTTGATTTTT
1076 TTTGTTACTCCAATACAATAGTAAGATAAATACAAGGG-AAAAAAA-TTAAATTACAACTCAAA-
66 TTTGTTACTCCAATACAATAGTAAGATAAATACAAGGGAAAAAAAATTTAAATTACAACTCAAAT
1138 TTTTTTTTGATTTTTTTTTCACGTTTCGAACCTACTTGCGGA
131 TTTTTTTTGA-TTTTTTTTCACGTTTCGAACCTACTTGCGGA
*
1180 TTTTTTTTTCACTTTTTTTTTTGAATATTTTTTTTTCAATCAATTTTTTTTTTCGAATTTTTTTT
1 TTTTTTTTTCACTTTTTTTTTT---TA--TTTGTTTCAATCAA-TTTTTTTTTCGAA---TTTTT
*
1245 TTGATTTTTTTTGTTACTCCAATACAATAGTAAGCTAAATACAAGGGAAAAAAAATTTAAATTAC
57 TTGATTTTTTTTGTTACTCCAATACAATAGTAAGATAAATACAAGGGAAAAAAAATTTAAATTAC
1310 AACTCAAACTTTTTTTTTTTGATTTTTTTTCACGTTTCGAACCTACTTGCGG
122 AACTCAAA---TTTTTTTTTGATTTTTTTTCACGTTTCGAACCTACTTGCGG
1362 CCTTATTACG
Statistics
Matches: 165, Mismatches: 2, Indels: 16
0.90 0.01 0.09
Matches are distributed among these distances:
169 22 0.13
172 2 0.01
174 13 0.08
175 13 0.08
178 51 0.31
179 7 0.04
180 17 0.10
183 30 0.18
184 10 0.06
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (171 bp):
TTTTTTTTTCACTTTTTTTTTTTATTTGTTTCAATCAATTTTTTTTTCGAATTTTTTTGATTTTT
TTTGTTACTCCAATACAATAGTAAGATAAATACAAGGGAAAAAAAATTTAAATTACAACTCAAAT
TTTTTTTTGATTTTTTTTCACGTTTCGAACCTACTTGCGGA
Found at i:2705 original size:10 final size:10
Alignment explanation
Indices: 2692--2729 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2682 TTGTAGCTAA
2692 ATTGAGCTCG
1 ATTGAGCTCG
2702 ATTGAGCT-G
1 ATTGAGCTCG
2711 ACTTGAGCTCG
1 A-TTGAGCTCG
*
2722 AGTGAGCT
1 ATTGAGCT
2730 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:2709 original size:20 final size:20
Alignment explanation
Indices: 2669--2729 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
2659 ACCAATAAAA
2669 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
2689 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
2709 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
2729 T
1 T
2730 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:2730 original size:20 final size:20
Alignment explanation
Indices: 2693--2730 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2683 TGTAGCTAAA
*
2693 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
2713 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
2731 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Done.