Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold925
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: 17904
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:4107 original size:50 final size:50
Alignment explanation
Indices: 4032--4291 Score: 418
Period size: 50 Copynumber: 5.2 Consensus size: 50
4022 AGTTGTTGTC
*
4032 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
4082 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
4132 ATTGTTGACAAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGAC-AATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
4183 ATTGTTAACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
4233 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
4283 ATTGTTGAC
1 ATTGTTGAC
4292 TCTAAGTATA
Statistics
Matches: 196, Mismatches: 8, Indels: 12
0.91 0.04 0.06
Matches are distributed among these distances:
49 1 0.01
50 146 0.74
51 49 0.25
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:4221 original size:101 final size:100
Alignment explanation
Indices: 4032--4288 Score: 462
Period size: 101 Copynumber: 2.6 Consensus size: 100
4022 AGTTGTTGTC
* *
4032 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTAACGATTC
4096 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
65 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
4132 ATTGTTGACAAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTAACGATTC
1 ATTGTTGAC-AATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTAACGATTC
4197 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
65 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
4233 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTT
4289 GACTCTAAGT
Statistics
Matches: 151, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
100 55 0.36
101 94 0.62
102 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (100 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTAACGATTCT
TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:8760 original size:50 final size:50
Alignment explanation
Indices: 8685--8994 Score: 518
Period size: 50 Copynumber: 6.2 Consensus size: 50
8675 AGTTGTTGTC
*
8685 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAG-AGAGAGGTGGCCATA
1 ATTGTTGACGATTC-TTCACCAACCTTTGACAATAGAAG-GAGGTGGCCATA
8735 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
8785 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
* *
8835 ATTGTTGACAAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGAC-GATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
8886 ATTGTTAACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
8936 ATTGTTGACAATTCTTCACCAACCTTTGACAATAG-AGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAG-GAGGTGGCCATA
8986 ATTGTTGAC
1 ATTGTTGAC
8995 TCTAAGTATA
Statistics
Matches: 248, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
49 2 0.01
50 195 0.79
51 51 0.21
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:8897 original size:101 final size:100
Alignment explanation
Indices: 8699--8991 Score: 525
Period size: 101 Copynumber: 2.9 Consensus size: 100
8689 TTGACTATCA
*
8699 TTCACCAACCTTTGACAATAG-AGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTG
1 TTCACCAACCTTTGACAATAGAAG-GAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTG
* *
8763 ACAATAGAAGGAGGTGGCCATAATTGTTGACGATTC
65 ACAATAGAGGGAGGTGGCCATAATTGTTAACGATTC
8799 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAAATTCTTCACCAACCTTTG
1 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGAC-AATTCTTCACCAACCTTTG
8864 ACAATAGAGGGAGGTGGCCATAATTGTTAACGATTC
65 ACAATAGAGGGAGGTGGCCATAATTGTTAACGATTC
8900 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGA
1 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGA
*
8965 CAATAGAGAGAGGTGGCCATAATTGTT
66 CAATAGAGGGAGGTGGCCATAATTGTT
8992 GACTCTAAGT
Statistics
Matches: 187, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
100 88 0.47
101 99 0.53
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (100 bp):
TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGA
CAATAGAGGGAGGTGGCCATAATTGTTAACGATTC
Found at i:8978 original size:151 final size:151
Alignment explanation
Indices: 8699--8994 Score: 549
Period size: 151 Copynumber: 2.0 Consensus size: 151
8689 TTGACTATCA
*
8699 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTGA
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTAACGATTCTTCACCAACCTTTGA
*
8764 CAATAGAAGGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTG
66 CAATAGAAGGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTG
8829 GCCATAATTGTTGACAAATTC
131 GCCATAATTGTTGACAAATTC
*
8850 TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTAACGATTCTTCACCAACCTTTGA
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTAACGATTCTTCACCAACCTTTGA
8915 CAATAGAAGGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGACAATAG-AGAGAGGT
66 CAATAGAAGGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAG-GAGGT
8979 GGCCATAATTGTTGAC
130 GGCCATAATTGTTGAC
8995 TCTAAGTATA
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
150 2 0.01
151 139 0.99
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (151 bp):
TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTAACGATTCTTCACCAACCTTTGA
CAATAGAAGGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTG
GCCATAATTGTTGACAAATTC
Found at i:10619 original size:2 final size:2
Alignment explanation
Indices: 10612--10647 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10602 TCAAAACCCA
10612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10648 GGAAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11315 original size:18 final size:18
Alignment explanation
Indices: 11257--11316 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
11247 TAATATAAAT
11257 ATAAATAATTTTATTTTA
1 ATAAATAATTTTATTTTA
**
11275 AT-AA-AATTTTATAATAAA
1 ATAAATAATTTTAT--TTTA
11293 TATAAATAATTTTATTTTA
1 -ATAAATAATTTTATTTTA
11312 ATAAA
1 ATAAA
11317 ATCGCATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
18 9 0.27
19 4 0.12
20 2 0.06
21 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAAATAATTTTATTTTA
Found at i:11611 original size:18 final size:18
Alignment explanation
Indices: 11562--11616 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
11552 ATAGTTTTAG
*
11562 TATAGTATATCTAATATTTA
1 TATA-TATAT-TAATATATA
11582 TATATGAT-TTAATATATA
1 TATAT-ATATTAATATATA
11600 TATATATATTAA-ATATA
1 TATATATATTAATATATA
11617 AAATGTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.22
18 17 0.53
19 2 0.06
20 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (18 bp):
TATATATATTAATATATA
Found at i:12640 original size:32 final size:32
Alignment explanation
Indices: 12604--12666 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
12594 AAATTATTTT
*
12604 AATTTGTTTATAAATATA-AAT-TTCATATATAA
1 AATTT-TTTA-AAATATAGAATATACATATATAA
*
12636 AATTTTTTAATATATAGAATATACATATATA
1 AATTTTTTAAAATATAGAATATACATATATA
12667 CTTATAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.22
31 7 0.26
32 14 0.52
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (32 bp):
AATTTTTTAAAATATAGAATATACATATATAA
Found at i:12698 original size:19 final size:19
Alignment explanation
Indices: 12676--12727 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
12666 ACTTATAAAG
*
12676 TATATATAATATTAGTTTA
1 TATATATAATATTAGTATA
*
12695 TATATATAATTTTAGTATA
1 TATATATAATATTAGTATA
12714 TATATACTAATATT
1 TATATA-TAATATT
12728 TATTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
TATATATAATATTAGTATA
Found at i:13592 original size:17 final size:17
Alignment explanation
Indices: 13572--13605 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13562 TATAAATTTA
* *
13572 ATTTTTATTTTTAAATT
1 ATTTTTAATTTAAAATT
13589 ATTTTTAATTTAAAATT
1 ATTTTTAATTTAAAATT
13606 TTGATTCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTAATTTAAAATT
Found at i:15587 original size:21 final size:23
Alignment explanation
Indices: 15553--15595 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
15543 TAAATTTAAG
15553 ATATAATTATAAAAATATTACGA
1 ATATAATTATAAAAATATTACGA
*
15576 ATATAA-TA-AAAATTATTACG
1 ATATAATTATAAAAATATTACG
15596 GTAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (23 bp):
ATATAATTATAAAAATATTACGA
Done.