Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1440
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: 15619
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Found at i:487 original size:24 final size:24
Alignment explanation
Indices: 446--508 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
436 CATATTTAGA
* * * *
446 TAATTTTATATCTATTTACACATT
1 TAATTTTATATTTATTTAAAAAAT
*
470 TAATTTTATATTTTTTTAAAAAAT
1 TAATTTTATATTTATTTAAAAAAT
494 TAATTTTGATATTTA
1 TAATTTT-ATATTTA
509 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 26 0.81
25 6 0.19
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (24 bp):
TAATTTTATATTTATTTAAAAAAT
Found at i:927 original size:30 final size:30
Alignment explanation
Indices: 891--962 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
881 TTATTATATT
*
891 TTTATATTTAAATAAAATTTTAATATTTAA
1 TTTATATATAAATAAAATTTTAATATTTAA
* * *
921 TTTATATATAAATAAGATTTTATTTTTTAA
1 TTTATATATAAATAAAATTTTAATATTTAA
951 TTTA-ATA-AAATA
1 TTTATATATAAATA
963 TTTAAAAAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.13
29 3 0.08
30 30 0.79
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTATATATAAATAAAATTTTAATATTTAA
Found at i:1013 original size:29 final size:28
Alignment explanation
Indices: 981--1064 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
971 GCTATAAAAG
*
981 TATTTAT-TTTTAATAAGTTTTTATATTTT
1 TATTTATATTTAAATAA-TTTTT-TATTTT
1010 TA-TTATATTTAAATAATTTTTTATTTT
1 TATTTATATTTAAATAATTTTTTATTTT
*
1037 TAATTTATATTTAAATAA-ATTTTATTTT
1 T-ATTTATATTTAAATAATTTTTTATTTT
1065 AAATTAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.14
28 19 0.38
29 24 0.48
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
TATTTATATTTAAATAATTTTTTATTTT
Found at i:1020 original size:28 final size:29
Alignment explanation
Indices: 982--1069 Score: 103
Period size: 28 Copynumber: 3.1 Consensus size: 29
972 CTATAAAAGT
*
982 ATTTAT-TTTTAATAAGTTTTTATATTTTT-
1 ATTTATATTTAAATAA-TTTTT-TATTTTTA
1011 A-TTATATTTAAATAATTTTTTATTTTTA
1 ATTTATATTTAAATAATTTTTTATTTTTA
* *
1039 ATTTATATTTAAATAA-ATTTTATTTTAA
1 ATTTATATTTAAATAATTTTTTATTTTTA
1067 ATT
1 ATT
1070 AAAAATTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.13
28 23 0.43
29 23 0.43
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (29 bp):
ATTTATATTTAAATAATTTTTTATTTTTA
Found at i:1072 original size:17 final size:17
Alignment explanation
Indices: 1012--1068 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 17
1002 TATATTTTTA
1012 TTATATTTAAAT-AATT
1 TTATATTTAAATAAATT
* *
1028 TTTTATTT---TTAA-T
1 TTATATTTAAATAAATT
1041 TTATATTTAAATAAATT
1 TTATATTTAAATAAATT
1058 TTAT-TTTAAAT
1 TTATATTTAAAT
1069 TAAAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 9 0.27
14 2 0.06
16 17 0.52
17 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTAAATAAATT
Found at i:1078 original size:28 final size:29
Alignment explanation
Indices: 1018--1080 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
1008 TTTATTATAT
* * * * *
1018 TTAAATAATTTTTTATTTTTAATTTATAT
1 TTAAATAATATTTTATTTTAAATTAAAAA
1047 TTAAATAA-ATTTTATTTTAAATTAAAAA
1 TTAAATAATATTTTATTTTAAATTAAAAA
1075 TTAAAT
1 TTAAAT
1081 TTATGTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATAATATTTTATTTTAAATTAAAAA
Found at i:1098 original size:23 final size:24
Alignment explanation
Indices: 1043--1099 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
1033 TTTTTAATTT
*
1043 ATATTTAAA-TAAATTTTATTTTA
1 ATATTTAAATTAAATTTTATGTTA
*
1066 A-ATTAAAAATTAAA-TTTATGTTA
1 ATATT-TAAATTAAATTTTATGTTA
1089 ATATTTAAATT
1 ATATTTAAATT
1100 TTATTTGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.11
23 18 0.64
24 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATTTAAATTAAATTTTATGTTA
Found at i:1268 original size:12 final size:12
Alignment explanation
Indices: 1251--1295 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
1241 ATACATGTGA
*
1251 AAATAAATTAAT
1 AAATAAAATAAT
1263 AAATAAAAT-AT
1 AAATAAAATAAT
*
1274 -AA-AAAATATT
1 AAATAAAATAAT
1284 AAATAAAATAAT
1 AAATAAAATAAT
1296 TCATAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
9 5 0.19
10 3 0.11
11 4 0.15
12 15 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:2844 original size:2 final size:2
Alignment explanation
Indices: 2832--2863 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2822 TTCTTCCTGC
*
2832 AT AT GT 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
2864 CTTCATTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3514 original size:6 final size:7
Alignment explanation
Indices: 3505--3530 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3495 ATGTTTTTTG
3505 TTTTTAT
1 TTTTTAT
3512 TTTTTAT
1 TTTTTAT
3519 TTTTTAT
1 TTTTTAT
3526 TTTTT
1 TTTTT
3531 TGTTGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:6664 original size:2 final size:2
Alignment explanation
Indices: 6657--6684 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6647 ATTCGTAAAA
6657 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
6685 TTCTCCACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6715 original size:36 final size:36
Alignment explanation
Indices: 6668--6740 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
6658 TATATATATA
6668 TATATATATATATATATTTCTCCACTACAACATTGT
1 TATATATATATATATATTTCTCCACTACAACATTGT
6704 TATATATATATATATATTTCTCCACTACAACATTGT
1 TATATATATATATATATTTCTCCACTACAACATTGT
6740 T
1 T
6741 GACATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (36 bp):
TATATATATATATATATTTCTCCACTACAACATTGT
Found at i:8302 original size:42 final size:43
Alignment explanation
Indices: 8256--8360 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 43
8246 TTTATATAAT
*
8256 TATAAAATAATTAATTAAATAATTT-AA-ATT-TTTAAATAAATA
1 TATAAAATAATTTATTAAA-AATTTAAATATTATTTAAA-AAATA
* *
8298 TATAAAATAATATCTATTAAAATTTTAAATATTATTTAAAATATA
1 TATAAAATAAT-T-TATTAAAAATTTAAATATTATTTAAAAAATA
*
8343 TAAAAAATAATTTATTAA
1 TATAAAATAATTTATTAA
8361 TACACTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
42 11 0.20
43 11 0.20
44 9 0.17
45 17 0.31
46 6 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (43 bp):
TATAAAATAATTTATTAAAAATTTAAATATTATTTAAAAAATA
Found at i:9487 original size:19 final size:19
Alignment explanation
Indices: 9460--9555 Score: 59
Period size: 19 Copynumber: 4.8 Consensus size: 19
9450 CTTTCGAGGG
*
9460 ATTTCTTTTTTCTTTTTCT
1 ATTTTTTTTTTCTTTTTCT
**
9479 ATTTTTTTTTAATTTTTCT
1 ATTTTTTTTTTCTTTTTCT
* * *
9498 TTTTTTTAATTATTATTTTT-A
1 ATTTTTT--TT-TTCTTTTTCT
**
9519 ATTTCTTTCCTTCTTTTTCTT
1 ATTT-TTTTTTTCTTTTTC-T
*
9540 CTTTTTTTTTTCTTTT
1 ATTTTTTTTTTCTTTT
9556 AATTTTGTTA
Statistics
Matches: 57, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
19 29 0.51
20 10 0.18
21 8 0.14
22 10 0.18
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTTTTTTTCTTTTTCT
Found at i:9516 original size:16 final size:16
Alignment explanation
Indices: 9481--9517 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
9471 CTTTTTCTAT
* *
9481 TTTTTTTTAATTTTTC
1 TTTTTTTTAATTATTA
9497 TTTTTTTTAATTATTA
1 TTTTTTTTAATTATTA
9513 TTTTT
1 TTTTT
9518 AATTTCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTAATTATTA
Found at i:11607 original size:2 final size:2
Alignment explanation
Indices: 11600--11636 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11590 TTTCTGTTTC
11600 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
11637 CGTATATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:12636 original size:7 final size:7
Alignment explanation
Indices: 12612--12652 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
12602 GGTGGTTCTC
12612 AAAAAA-
1 AAAAAAT
*
12618 AAAAAACC
1 AAAAAA-T
12626 AAAAAAT
1 AAAAAAT
12633 AAAAAAT
1 AAAAAAT
12640 -AAAAAT
1 AAAAAAT
12646 AAAAAAT
1 AAAAAAT
12653 TTGCAGGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
6 12 0.39
7 13 0.42
8 6 0.19
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:12652 original size:13 final size:13
Alignment explanation
Indices: 12627--12652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12617 AAAAAAACCA
12627 AAAAATAAAAAAT
1 AAAAATAAAAAAT
12640 AAAAATAAAAAAT
1 AAAAATAAAAAAT
12653 TTGCAGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:14364 original size:22 final size:22
Alignment explanation
Indices: 14326--14376 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
14316 TTTTAAAAAA
* * *
14326 TAAT-ATTTTTATTTATTTTTT
1 TAATAATTTGTATATATTTTAT
14347 TAATAATTTGTATATATTTTAT
1 TAATAATTTGTATATATTTTAT
14369 TAA-AATTT
1 TAATAATTT
14377 TAAATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TAATAATTTGTATATATTTTAT
Found at i:14383 original size:20 final size:22
Alignment explanation
Indices: 14339--14383 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
14329 TATTTTTATT
* *
14339 TATTTTTTTAATAATTTGTATA
1 TATTTTATTAATAATTTGTAAA
14361 TATTTTATTAA-AATTT-TAAA
1 TATTTTATTAATAATTTGTAAA
14381 TAT
1 TAT
14384 AAATAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTTTATTAATAATTTGTAAA
Done.