Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1979
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: 4356
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Found at i:1178 original size:17 final size:17
Alignment explanation
Indices: 1158--1249 Score: 54
Period size: 16 Copynumber: 5.5 Consensus size: 17
1148 TTAATCAATG
1158 TAAAATATGATGATATT
1 TAAAATATGATGATATT
1175 TAAAATAT-AT-AT-TT
1 TAAAATATGATGATATT
1189 AATAAAA-ATGAT-ATAATAT
1 --TAAAATATGATGAT-AT-T
* * *
1208 ATAAATTTTAATCGATA--
1 -TAAAATATGAT-GATATT
1225 TAAAATATGATGATATT
1 TAAAATATGATGATATT
1242 TAAAATAT
1 TAAAATAT
1250 ATATTTAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
14 2 0.03
15 8 0.14
16 19 0.33
17 16 0.28
18 6 0.10
19 4 0.07
20 1 0.02
21 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (17 bp):
TAAAATATGATGATATT
Found at i:1211 original size:67 final size:67
Alignment explanation
Indices: 1122--1279 Score: 244
Period size: 67 Copynumber: 2.3 Consensus size: 67
1112 TTTTATCTTT
* * *
1122 ATAAAAATAATACAGTATTATAAATTTTAATCAATGTAAAATATGATGATATTTAAAATATATAT
1 ATAAAAATAATATAATA-TATAAATTTTAATCAATATAAAATATGATGATATTTAAAATATATAT
1187 TTA
65 TTA
* *
1190 ATAAAAATGATATAATATATAAATTTTAATCGATATAAAATATGATGATATTTAAAATATATATT
1 ATAAAAATAATATAATATATAAATTTTAATCAATATAAAATATGATGATATTTAAAATATATATT
1255 TA
66 TA
*
1257 ATAAAAATAATATTTATATATAA
1 ATAAAAATAATA-TAATATATAA
1280 TTTGTATAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
67 59 0.72
68 23 0.28
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (67 bp):
ATAAAAATAATATAATATATAAATTTTAATCAATATAAAATATGATGATATTTAAAATATATATT
TA
Found at i:1301 original size:22 final size:22
Alignment explanation
Indices: 1263--1304 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1253 TTTAATAAAA
*
1263 ATAATATTTATATATAATTTGT
1 ATAATATTTATAAATAATTTGT
1285 ATAATA-TTATAAAATAATTT
1 ATAATATTTAT-AAATAATTT
1305 TGAATGATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAATATTTATAAATAATTTGT
Found at i:2706 original size:17 final size:19
Alignment explanation
Indices: 2681--2718 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
2671 TCGAGATAAG
2681 TATTAAATAT-AA-ATATT
1 TATTAAATATGAATATATT
*
2698 TATTTAATATGAATATATT
1 TATTAAATATGAATATATT
2717 TA
1 TA
2719 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 2 0.11
19 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATTAAATATGAATATATT
Found at i:2936 original size:11 final size:12
Alignment explanation
Indices: 2921--2957 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2911 AAGGAAGTGT
*
2921 AAAAATAAAATC
1 AAAAATAAAATA
2933 AAAAATAAAAT-
1 AAAAATAAAATA
2944 AAAAATAAAATA
1 AAAAATAAAATA
2956 AA
1 AA
2958 GCAAAATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:2938 original size:12 final size:11
Alignment explanation
Indices: 2920--2957 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
2910 AAAGGAAGTG
2920 TAAAAATAAAA
1 TAAAAATAAAA
2931 TCAAAAATAAAA
1 T-AAAAATAAAA
2943 TAAAAATAAAA
1 TAAAAATAAAA
2954 TAAA
1 TAAA
2958 GCAAAATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:3100 original size:19 final size:20
Alignment explanation
Indices: 3073--3113 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3063 TATAAAGTCC
3073 AACAATTTAACT-TAAAAAA
1 AACAATTTAACTGTAAAAAA
* *
3092 AACACTTTAATTGTAAAAAA
1 AACAATTTAACTGTAAAAAA
3112 AA
1 AA
3114 AAAAATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (20 bp):
AACAATTTAACTGTAAAAAA
Done.