Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold807
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: 11642
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Found at i:2597 original size:52 final size:52
Alignment explanation
Indices: 2516--2636 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2506 GAAAAGTTTA
*
2516 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
2568 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
2620 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
2637 AAAAATCAGT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:2664 original size:13 final size:13
Alignment explanation
Indices: 2646--2670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2636 AAAAAATCAG
2646 TGTATCGATACAA
1 TGTATCGATACAA
2659 TGTATCGATACA
1 TGTATCGATACA
2671 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2750 original size:13 final size:13
Alignment explanation
Indices: 2732--2756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2722 ACAAAAAAAA
2732 TGTATCGATACAT
1 TGTATCGATACAT
2745 TGTATCGATACA
1 TGTATCGATACA
2757 CAACATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3907 original size:42 final size:46
Alignment explanation
Indices: 3705--3963 Score: 251
Period size: 49 Copynumber: 5.4 Consensus size: 46
3695 AAAATGATGT
* * *
3705 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG-T-----AGGTGC
*
3757 CGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG-T--AGGTGC
* * * * *
3806 C--TGTACTGAGTCAAGGCCAGCTACATTGGATTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG-T--AGGTGC
3853 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTT-AA-T-GGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGTAGGTGC
*
3895 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA---GTAGGTGC
3944 CAATATGCTGATTCAAGGCC
1 CAATATGCTGATTCAAGGCC
3964 TGTCACACTA
Statistics
Matches: 180, Mismatches: 18, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
42 31 0.17
43 7 0.04
44 2 0.01
45 1 0.01
47 43 0.24
48 7 0.04
49 52 0.29
52 37 0.21
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (46 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGTAGGTGC
Found at i:4321 original size:360 final size:363
Alignment explanation
Indices: 3581--4323 Score: 1397
Period size: 363 Copynumber: 2.1 Consensus size: 363
3571 AAAAGGATGT
*
3581 CAATGTGCTGATTCAAGGCCTGTCACACTAGACTTAAGTGTGATGAGGATGGAGTGTGATAAAAG
1 CAATATGCTGATTCAAGGCCTGTCACACTAGACTTAAGTGTGATGAGGATGGAGTGTGATAAAAG
3646 GACCAATACGTTGATTCACGGCCAACGATATTGGATTTAAAGATGATGAAAAATGATGTCAATGT
66 GACCAATACGTTGATTCACGGCCAACGATATTGGATTTAAAGATGATGAAAAATGATGTCAATGT
3711 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGC
131 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGC
*
3776 CAGCTATATTGGACTTAAAGATGAAGGTGCCTGTACTGAGTCAAGGCCAGCTACATTGGATTTAA
196 CAGCGATATTGGACTTAAAGATGAAGGTGCCTGTACTGAGTCAAGGCCAGCTACATTGGATTTAA
3841 AGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATGGACTTAATGGTGCCAATGTGCTGA
261 AGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATGGACTTAATGGTGCCAATGTGCTGA
3906 TTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGC
326 TTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGC
3944 CAATATGCTGATTCAAGGCCTGTCACACTAGACTTAAGTGTGATGAGGATGGAGTGTGATAAAAG
1 CAATATGCTGATTCAAGGCCTGTCACACTAGACTTAAGTGTGATGAGGATGGAGTGTGATAAAAG
*
4009 GACCAATACGTTGATTCACGGCCAACGATATTGGATTTAAAGATGATGAAAAATGATGTTAATGT
66 GACCAATACGTTGATTCACGGCCAACGATATTGGATTTAAAGATGATGAAAAATGATGTCAATGT
4074 G-TGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAA-GTGCCGATATGCTGATTCAAGGC
131 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGC
*
4137 CAGCGATATTGGACTTAAAGAT-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGATTT
196 CAGCGATATTGGACTTAAAGATGAAGGTGCC--TGTACTGAGTCAAGGCCAGCTACATTGGATTT
4201 AAAGAT-AAGG-GCCAATATGCTGATTCAAGGCCAGCTATATGGACTTAATGGTGCCAATGTGCT
259 AAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATGGACTTAATGGTGCCAATGTGCT
4264 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGC
324 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGC
4304 CAATATGCTGATTCAAGGCC
1 CAATATGCTGATTCAAGGCC
4324 AGCTATATTG
Statistics
Matches: 374, Mismatches: 4, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
360 121 0.32
361 48 0.13
362 76 0.20
363 129 0.34
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (363 bp):
CAATATGCTGATTCAAGGCCTGTCACACTAGACTTAAGTGTGATGAGGATGGAGTGTGATAAAAG
GACCAATACGTTGATTCACGGCCAACGATATTGGATTTAAAGATGATGAAAAATGATGTCAATGT
GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGC
CAGCGATATTGGACTTAAAGATGAAGGTGCCTGTACTGAGTCAAGGCCAGCTACATTGGATTTAA
AGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATGGACTTAATGGTGCCAATGTGCTGA
TTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGC
Found at i:4322 original size:49 final size:49
Alignment explanation
Indices: 4250--4394 Score: 218
Period size: 49 Copynumber: 2.9 Consensus size: 49
4240 TGGACTTAAT
* **
4250 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGTA
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAAA
*
4299 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAAA
* *
4348 GGTGCCAATATGTGTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 GGTGCCAATATG-CTGATTCAAGGCCAGCTATATTGGACTTA-AAGG
4395 GTTGCCACCG
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 57 0.66
50 27 0.31
51 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (49 bp):
GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAAA
Found at i:4341 original size:138 final size:140
Alignment explanation
Indices: 4114--4381 Score: 416
Period size: 138 Copynumber: 1.9 Consensus size: 140
4104 AGATGGAAAA
* *
4114 GTGCCGATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAGGTGCCAATGTGCTGAGT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAGGTGCCAATATGCTGAGT
*
4179 CAAGGCCAGCTACATTGGATTTAAAGAT-AAGG-GCCAATATG-CTGATTCAAGGCCAGCTATAT
66 CAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGTCTGATTCAAGGCCAGCTATAT
4241 GGACTTAATG
131 GGACTTAATG
* * * * *
4251 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-AAGGTGCCAATATGCTGAG
* *
4316 TCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGTGTGATTCAAGGCCAGCTATA
65 TCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGTCTGATTCAAGGCCAGCTATA
4381 T
130 T
4382 TGGGCTTAGA
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
137 41 0.35
138 43 0.37
139 4 0.03
140 9 0.08
141 20 0.17
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (140 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAGGTGCCAATATGCTGAGT
CAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGTCTGATTCAAGGCCAGCTATAT
GGACTTAATG
Found at i:4416 original size:30 final size:30
Alignment explanation
Indices: 4382--4470 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
4372 CCAGCTATAT
*
4382 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
*
4412 TGGGCTTTGGAAAAGGG-TGCCACTGA-TT-TG
1 TGGGC-TT--AGAAGGGTTGCCACTGACTTGTG
*
4442 TGGGCTTTGAA-GGTTGCCACTGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
4471 GGCTTTCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 2 0.04
27 11 0.22
28 2 0.04
29 4 0.08
30 12 0.24
31 4 0.08
32 8 0.16
33 6 0.12
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (30 bp):
TGGGCTTAGAAGGGTTGCCACTGACTTGTG
Found at i:4462 original size:27 final size:27
Alignment explanation
Indices: 4382--4476 Score: 100
Period size: 27 Copynumber: 3.3 Consensus size: 27
4372 CCAGCTATAT
* *
4382 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAA-GGTTGCCACTGA-TT-TG
*
4412 TGGGCTTTGGAAAAGGGTGCCACTGATTTG
1 TGGGCTTT-G--AAGGTTGCCACTGATTTG
*
4442 TGGGCTTTGAAGGTTGCCACTGACTTG
1 TGGGCTTTGAAGGTTGCCACTGATTTG
4469 TGGGCTTT
1 TGGGCTTT
4477 CGAAAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
27 24 0.42
29 1 0.02
30 17 0.30
31 3 0.05
32 10 0.18
33 2 0.04
ACGTcount: A:0.16, C:0.17, G:0.36, T:0.32
Consensus pattern (27 bp):
TGGGCTTTGAAGGTTGCCACTGATTTG
Found at i:4490 original size:57 final size:60
Alignment explanation
Indices: 4382--4509 Score: 163
Period size: 57 Copynumber: 2.2 Consensus size: 60
4372 CCAGCTATAT
* * *** * *
4382 TGGGCTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTG
1 TGGGCTTTGAAGGGTTGCCACCGACTTGTGTGGGCTTTCGAAAAAAATGCCACCGACTTG
*
4442 TGGGCTTTGAA-GGTTGCCACTGAC-T-TGTGGGCTTTCGAAAAAAATGCCACCGACTTG
1 TGGGCTTTGAAGGGTTGCCACCGACTTGTGTGGGCTTTCGAAAAAAATGCCACCGACTTG
4499 TGGGCTTTGAA
1 TGGGCTTTGAA
4510 AAAAATGCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 37 0.62
58 1 0.02
59 12 0.20
60 10 0.17
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (60 bp):
TGGGCTTTGAAGGGTTGCCACCGACTTGTGTGGGCTTTCGAAAAAAATGCCACCGACTTG
Found at i:4497 original size:30 final size:29
Alignment explanation
Indices: 4410--4535 Score: 139
Period size: 30 Copynumber: 4.3 Consensus size: 29
4400 CACCGACTTG
*** *
4410 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT-GAAAAAAATGCCACTGACT
***
4440 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAAATGCCACTGACT
*
4467 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTT-GAAAAAAATGCCACTGACT
4497 TGTGGGCTTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTGAAAAAAATGCCACTGACT
*
4526 TGTGGACTTT
1 TGTGGGCTTT
4536 TGAAGGGTGA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
27 24 0.28
28 1 0.01
29 28 0.33
30 32 0.38
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAAAATGCCACTGACT
Found at i:4538 original size:30 final size:30
Alignment explanation
Indices: 4456--4539 Score: 134
Period size: 29 Copynumber: 2.8 Consensus size: 30
4446 CTTTGAAGGT
*
4456 TGCCACTGACTTGTGGGCTTTCGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTTGAAAAAAA
*
4486 TGCCACCGACTTGTGGGC-TTTGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTTGAAAAAAA
*
4515 TGCCACTGACTTGTGGACTTTTGAA
1 TGCCACTGACTTGTGGGCTTTTGAA
4540 GGGTGATGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 26 0.53
30 23 0.47
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (30 bp):
TGCCACTGACTTGTGGGCTTTTGAAAAAAA
Found at i:5977 original size:1 final size:1
Alignment explanation
Indices: 5973--6078 Score: 140
Period size: 1 Copynumber: 106.0 Consensus size: 1
5963 CCGGACCCCC
* * * * * *
5973 TTTTTGTTTTTTGTTTTTTTTTTTTGTTGTTTTTTTTTTTTTTTTGTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
**
6038 TTTTTTTTTTTTTTTTTTTTTTTTCGTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6079 GGAGGACGCC
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 90 1.00
ACGTcount: A:0.00, C:0.01, G:0.07, T:0.92
Consensus pattern (1 bp):
T
Done.