Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold823
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: 32234
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Found at i:886 original size:51 final size:50
Alignment explanation
Indices: 791--887 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
781 AGATAACAAC
* * * *
791 TTAAGATAGAGAAAAGGATTATAAATATAGATATTTGAATTTTAAATATA
1 TTAAGATAGAAAAAAGGATTATAAATATAGAGATTTAAAATTTAAATATA
*
841 TTAAGATAGAAAAAAATGATTATAAATATTA-AGATTTAAAATTTAAA
1 TTAAGATAG-AAAAAAGGATTATAAATA-TAGAGATTTAAAATTTAAA
888 CATACTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
50 9 0.22
51 29 0.73
52 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (50 bp):
TTAAGATAGAAAAAAGGATTATAAATATAGAGATTTAAAATTTAAATATA
Found at i:10381 original size:241 final size:242
Alignment explanation
Indices: 9932--10390 Score: 703
Period size: 241 Copynumber: 1.9 Consensus size: 242
9922 GAAGAAAATC
9932 AATAACTGCTCAAAATCATGAAAATAGGAACTTCAGATATTTCAAGCCCCTTCTCAAATCATTGA
1 AATAACTGCTCAAAATCATGAAAATAGGAACTTCAGATATTTCAAGCCCCTTCTCAAATCATTGA
*
9997 ACACACATTAGGAGAAAGTTCGTTCTACAGATACGTAAACTTACAGGAAAATTAAAATATATAGC
66 ACACACATTAGGAGAAAGGTCGTTCTACAGATACGTAAACTTACAGGAAAATTAAAATATATAGC
*
10062 AATAAAAAACAAAAATAATGATATCTAAAGATAGGAAAAAAGAAAATTAATAATAATAAAAAAAG
131 AATAAAAAACAAAAATAATGATATCAAAAGATAGGAAAAAAGAAAATTAATAATAATAAAAAAAG
**
10127 AGGCCCCCAGTTTACAAGTGGATATTGTATAGGATGGATTGGAAGAA
196 AGGCCAACAGTTTACAAGTGGATATTGTATAGGATGGATTGGAAGAA
* * * **
10174 AATAGCTGCTC-AAATCATGAAAGTGGGAACTTTGGATATTTCAAGCCCCTTCTCAAATCATTGA
1 AATAACTGCTCAAAATCATGAAAATAGGAACTTCAGATATTTCAAGCCCCTTCTCAAATCATTGA
* * * * *
10238 ACGCACATTAGGAGAAAGGTGGTTCTACAGATATGTAAATTTACAGGAAAAATTAAGATATATAG
66 ACACACATTAGGAGAAAGGTCGTTCTACAGATACGTAAACTTACAGG-AAAATTAAAATATATAG
*
10303 CAATCAAAAGA-AAAAATAATGATATCAAAAGATAGG-AAAAA-AAAATTAATAATAATAATAAA
130 CAAT-AAAAAACAAAAATAATGATATCAAAAGATAGGAAAAAAGAAAATTAATAATAATAA-AAA
*
10365 AA-AGGGGCAACAGTTTACAAGTGGAT
193 AAGA-GGCCAACAGTTTACAAGTGGAT
10391 GATATATAAG
Statistics
Matches: 197, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
240 18 0.09
241 120 0.61
242 54 0.27
243 5 0.03
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.24
Consensus pattern (242 bp):
AATAACTGCTCAAAATCATGAAAATAGGAACTTCAGATATTTCAAGCCCCTTCTCAAATCATTGA
ACACACATTAGGAGAAAGGTCGTTCTACAGATACGTAAACTTACAGGAAAATTAAAATATATAGC
AATAAAAAACAAAAATAATGATATCAAAAGATAGGAAAAAAGAAAATTAATAATAATAAAAAAAG
AGGCCAACAGTTTACAAGTGGATATTGTATAGGATGGATTGGAAGAA
Found at i:22974 original size:84 final size:84
Alignment explanation
Indices: 22832--22999 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
22822 AAATATTATT
22832 TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACATGAAATTAGCA
1 TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACATGAAATTAGCA
22897 TGTTTACCGAGCACCTGAG
66 TGTTTACCGAGCACCTGAG
*
22916 TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACGTGAAATTAGCA
1 TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACATGAAATTAGCA
22981 TGTTTACCGAGCACCTGAG
66 TGTTTACCGAGCACCTGAG
23000 ACTATGTATT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (84 bp):
TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACATGAAATTAGCA
TGTTTACCGAGCACCTGAG
Found at i:26731 original size:19 final size:19
Alignment explanation
Indices: 26677--26741 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
26667 TTTTTTTAAT
*
26677 AAAAAAATCAGAAA-AGAATT
1 AAAAAAATCA-AAATA-AATA
*
26697 AAAAATAT-AAATATAAATA
1 AAAAAAATCAAA-ATAAATA
26716 AAAAAAATCAAAATAAA-A
1 AAAAAAATCAAAATAAATA
26734 AAACAAAA
1 AAA-AAAA
26742 AAAGTAACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.16
19 21 0.55
20 11 0.29
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAAAAATCAAAATAAATA
Found at i:29949 original size:28 final size:28
Alignment explanation
Indices: 29905--29965 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
29895 ACTATTAATT
29905 TTTAAATAAAATTTTAAAATATGATTAA
1 TTTAAATAAAATTTTAAAATATGATTAA
* *
29933 TTTAAAT-AAATTATTAAAATATTATTAT
1 TTTAAATAAAATT-TTAAAATATGATTAA
29961 TTTAA
1 TTTAA
29966 TTAACGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TTTAAATAAAATTTTAAAATATGATTAA
Found at i:30031 original size:32 final size:31
Alignment explanation
Indices: 29964--30032 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
29954 TTATTATTTT
* * * *
29964 AATTAACGAAAAATCACTAAATTGATTAATG
1 AATTCACGAAAAATCACTAAAATAATTAATA
*
29995 AATTCACGTAAAAATCACTAAAATAATTAGTA
1 AATTCACG-AAAAATCACTAAAATAATTAATA
30027 AATTCA
1 AATTCA
30033 TATAAAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (31 bp):
AATTCACGAAAAATCACTAAAATAATTAATA
Found at i:30039 original size:32 final size:32
Alignment explanation
Indices: 29972--30039 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
29962 TTAATTAACG
* * * *
29972 AAAAATCACTAAATTGATTAATGAATTCACGT
1 AAAAATCACTAAAATAATTAATAAATTCACAT
* *
30004 AAAAATCACTAAAATAATTAGTAAATTCATAT
1 AAAAATCACTAAAATAATTAATAAATTCACAT
30036 AAAA
1 AAAA
30040 CTTCTCTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.29
Consensus pattern (32 bp):
AAAAATCACTAAAATAATTAATAAATTCACAT
Found at i:30138 original size:12 final size:12
Alignment explanation
Indices: 30121--30163 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
30111 AATTTATTAA
30121 TATTATTAAAGT
1 TATTATTAAAGT
*
30133 TATTATTATATTAGA
1 TATTATTA-A--AGT
30148 TATTATTAAAGT
1 TATTATTAAAGT
30160 TATT
1 TATT
30164 GTTATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 14 0.54
13 1 0.04
14 1 0.04
15 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
TATTATTAAAGT
Found at i:30150 original size:27 final size:27
Alignment explanation
Indices: 30106--30174 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
30096 TTATAATATT
30106 TTATTAATT-TATTA-ATATTATTAAAG
1 TTATT-ATTATATTAGATATTATTAAAG
30132 TTATTATTATATTAGATATTATTAAAG
1 TTATTATTATATTAGATATTATTAAAG
*
30159 TTATTGTTATTATTAG
1 TTATTATTA-TATTAG
30175 TTTAATAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 3 0.08
26 10 0.26
27 20 0.51
28 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (27 bp):
TTATTATTATATTAGATATTATTAAAG
Found at i:30192 original size:35 final size:32
Alignment explanation
Indices: 30091--30220 Score: 121
Period size: 32 Copynumber: 4.2 Consensus size: 32
30081 TATCAACTGT
* * *
30091 TATTATTATAA-TATT-TTATTAATTTATTAA
1 TATTATTAAAATTATTATTATTAGTTTAATAA
* *
30121 TATTATTAAAGTTATTATTA-TA--TT-A-GA
1 TATTATTAAAATTATTATTATTAGTTTAATAA
*
30148 TATTATTAAAGTTATTGTTATTATTAGTTTAATAA
1 TATTATTAAA---ATTATTATTATTAGTTTAATAA
*
30183 TATTATTAAAATTATTATTATTTGTTTAATAA
1 TATTATTAAAATTATTATTATTAGTTTAATAA
30215 TATTAT
1 TATTAT
30221 AATCTTTAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
27 11 0.14
29 2 0.02
30 17 0.21
31 8 0.10
32 29 0.36
33 2 0.02
34 1 0.01
35 11 0.14
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (32 bp):
TATTATTAAAATTATTATTATTAGTTTAATAA
Done.