Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2296
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: 14811
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:1052 original size:16 final size:15
Alignment explanation
Indices: 1033--1073 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1023 GAAAGAGAGG
1033 AAAAGAAAGAAGGAAA
1 AAAAGAAAGAA-GAAA
*
1049 AAAAGGAAGAAGAAA
1 AAAAGAAAGAAGAAA
1064 AAAAGGAAAG
1 AAAA-GAAAG
1074 GTTTTCGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAGAAA
Found at i:1063 original size:15 final size:16
Alignment explanation
Indices: 1033--1071 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1023 GAAAGAGAGG
*
1033 AAAAGAAAGAAGGAAA
1 AAAAGGAAGAAGGAAA
1049 AAAAGGAAGAA-GAAA
1 AAAAGGAAGAAGGAAA
1064 AAAAGGAA
1 AAAAGGAA
1072 AGGTTTTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAAGGAAGAAGGAAA
Found at i:5674 original size:16 final size:14
Alignment explanation
Indices: 5644--5685 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 14
5634 GGAAACTAGA
5644 AAAGAAAAAA-AAG
1 AAAGAAAAAAGAAG
*
5657 AAAG-AAAGAG-AG
1 AAAGAAAAAAGAAG
5669 AAAGAAAAAAGAAG
1 AAAGAAAAAAGAAG
5683 AAA
1 AAA
5686 ATAAGAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 10 0.42
13 9 0.38
14 5 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAGAAG
Found at i:5691 original size:11 final size:10
Alignment explanation
Indices: 5643--5693 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
5633 GGGAAACTAG
5643 AAAAGAA-AA
1 AAAAGAAGAA
5652 AAAAGAAAGAA
1 AAAAG-AAGAA
*
5663 AGAGAGAAAGAA
1 A-AAAG-AAGAA
5675 AAAAGAAGAA
1 AAAAGAAGAA
5685 AATAAGAAG
1 AA-AAGAAG
5694 GTTCTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 5 0.14
10 9 0.25
11 12 0.33
12 10 0.28
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
AAAAGAAGAA
Found at i:7072 original size:80 final size:75
Alignment explanation
Indices: 6931--7074 Score: 173
Period size: 80 Copynumber: 1.9 Consensus size: 75
6921 TCTATTAATT
*
6931 GTATTTAGGTATATTACCTTAAAAAATCCTTAGGATATTTGAGAACTTTCCATGTCGAAACATGG
1 GTATTTAGGTATATTACCTTAAAAAATCCTTAGGATATTTGAGAACTTTCCATGTCAAAACATGG
6996 TTTGTTAGGG
66 TTTGTTAGGG
* * * * *
7006 GTATTTAGGTAATATTACGGTTAAAATCAAGTCTTTAGGATCATTTGTGAGCTTT-CATGTTAAA
1 GTATTTAGGT-ATATTAC-CTTAAAA--AA-TCCTTAGGAT-ATTTGAGAACTTTCCATGTCAAA
7070 ACATG
60 ACATG
7075 TCCATTAGAG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
75 10 0.18
76 7 0.12
77 6 0.11
79 2 0.04
80 21 0.37
81 11 0.19
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38
Consensus pattern (75 bp):
GTATTTAGGTATATTACCTTAAAAAATCCTTAGGATATTTGAGAACTTTCCATGTCAAAACATGG
TTTGTTAGGG
Found at i:10277 original size:52 final size:52
Alignment explanation
Indices: 10192--10372 Score: 310
Period size: 52 Copynumber: 3.5 Consensus size: 52
10182 CCGAAATATG
**
10192 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
10244 AACTTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
10296 AAATTTGCCCTGCATGTATCGATACAGTTTATAGTGTATCGATACATCT-GGC
1 AAATTTG-CCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
10348 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
10373 AAGATCAGTG
Statistics
Matches: 123, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
51 18 0.15
52 65 0.53
53 40 0.33
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:10386 original size:53 final size:52
Alignment explanation
Indices: 10192--10394 Score: 279
Period size: 52 Copynumber: 3.9 Consensus size: 52
10182 CCGAAATATG
10192 AAATTTGCCTGCATGTATCGATAC--ATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAGATT--ATAGTGTATCGATACATCTGGGC
* **
10244 AACTTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAGATTATAGTGTATCGATACATCTGGGC
*
10296 AAATTTGCCCTGCATGTATCGATACAGTTTATAGTGTATCGATACATCT-GGC
1 AAATTTG-CCTGCATGTATCGATACAGATTATAGTGTATCGATACATCTGGGC
*
10348 AAATTTGCCTGCATGTATCGATACAAAGATCAGT-GTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATAC--AGATTA-TAGTGTATCGATACA
10395 ATGTATCGAT
Statistics
Matches: 139, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
51 17 0.12
52 62 0.45
53 57 0.41
54 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAGATTATAGTGTATCGATACATCTGGGC
Found at i:10401 original size:13 final size:13
Alignment explanation
Indices: 10383--10407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10373 AAGATCAGTG
10383 TGTATCGATACAA
1 TGTATCGATACAA
10396 TGTATCGATACA
1 TGTATCGATACA
10408 TTTAAGTGAT
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:11408 original size:55 final size:52
Alignment explanation
Indices: 11331--11534 Score: 176
Period size: 43 Copynumber: 4.1 Consensus size: 52
11321 TGATAAAGAC
* * * * * * *
11331 GCCAATATGTTGATTCACGGCCAACGATATGGGGCTTAAAGCTGAGAAAAAGGAT
1 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-G-AAAAGG-T
* * * *
11386 GTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGT
11438 GCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---AAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGT
* * * *
11481 GCCAATGTGCTGATTCAAGGTCGGCTACATTGGAC-TAAAGATGGAAAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGT
11532 GCC
1 GCC
11535 CACCGATTTG
Statistics
Matches: 122, Mismatches: 19, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
43 38 0.31
46 1 0.01
48 1 0.01
51 10 0.08
52 32 0.26
53 6 0.05
54 1 0.01
55 33 0.27
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (52 bp):
GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGT
Found at i:11457 original size:52 final size:51
Alignment explanation
Indices: 11378--11534 Score: 186
Period size: 43 Copynumber: 3.2 Consensus size: 51
11368 AAAGCTGAGA
* *
11378 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-TAAAGATGG
* *
11431 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACT-----T--
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTAAAGATGG
* *
11475 -AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTAAAGATGG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTAAAGATGG
11525 AAAAGGTGCC
1 AAAAGGTGCC
11535 CACCGATTTG
Statistics
Matches: 88, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
43 38 0.43
46 1 0.01
48 1 0.01
51 10 0.11
52 32 0.36
53 6 0.07
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (51 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTAAAGATGG
Found at i:11624 original size:29 final size:29
Alignment explanation
Indices: 11556--11997 Score: 300
Period size: 29 Copynumber: 15.1 Consensus size: 29
11546 GGGCTTCGAA
* *
11556 AAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
*
11584 -AAGGTTGCCACTGACTTGTGGGCTTTTT
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
11612 AAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
**
11641 AAAAATATGCCACTTGACTTGTGGGCTTTTG
1 AAAGGT-TGCCAC-TGACTTGTGGGCTTTTG
* *
11672 AACAGGGTGCCACTAACTTGTGGGCTTTT-
1 AA-AGGTTGCCACTGACTTGTGGGCTTTTG
11701 AAAGGTTGCCACTGACTTGT-GGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
**
11729 AAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTG
* *
11759 AAAAGGGTGCCACTAACTTGTGGGC---TG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTG
* * * **
11786 AAAAGAG-TGCTA-TAGAGTTGTGAGCTTACAAAAG
1 -AAAG-GTTGCCACT-GACTTGTGGGCTT----TTG
* * * *
11820 AAAAAGAG-TGCCACGGAGTTGTGGAC-TTGG
1 --AAAG-GTTGCCACTGACTTGTGGGCTTTTG
* * * **
11850 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
* *
11879 AAAAGGGTGCCACTGATTTGTGGGC-TTTG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTG
*
11908 -AAGGTTGCCACTGACTTGTGGGCTTTCG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
***
11936 AAAAAAAATGCCACTGACTTGTGGGC-TTTG
1 --AAAGGTTGCCACTGACTTGTGGGCTTTTG
*** *
11966 AAAAAAATGCCACTGACTTGTGGACTTTTG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTG
11996 AA
1 AA
11998 GGGTGATGAA
Statistics
Matches: 338, Mismatches: 48, Indels: 55
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.00
27 69 0.20
28 45 0.13
29 78 0.23
30 74 0.22
31 48 0.14
32 1 0.00
34 2 0.01
35 20 0.06
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTG
Found at i:11753 original size:118 final size:116
Alignment explanation
Indices: 11558--11784 Score: 330
Period size: 118 Copynumber: 1.9 Consensus size: 116
11548 GCTTCGAAAA
* * * * **
11558 AGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTTAAAGGTTGCCA
1 AGGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATTGCCA
* *
11623 CTGACTTGTGGGCTTTTGAAAAATATGCCACTTGACTTGTGGGCTTTTGAAC
66 CTGACTTGTGGGCTTTTGAAAAAGATGCCAC-TAACTTGTGGGCTTTTGAAC
11675 AGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGT-GGCTTTTGAAAAATATGC
1 AGGGTGCCACTAACTTGTGGGC-TTTAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAT-TGC
* *
11739 CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
64 CACTGACTTGTGGGCTTTTGAAAAAGATGCCACTAACTTGTGGGCT
11785 GAAAAGAGTG
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
117 43 0.44
118 55 0.56
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (116 bp):
AGGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATTGCCA
CTGACTTGTGGGCTTTTGAAAAAGATGCCACTAACTTGTGGGCTTTTGAAC
Found at i:11768 original size:87 final size:88
Alignment explanation
Indices: 11562--11784 Score: 364
Period size: 87 Copynumber: 2.6 Consensus size: 88
11552 CGAAAAAGGG
* * *
11562 TGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTTTAAAGGTTGCCAC
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGC-TTTTAAAGGTTGCCAC
11624 TGACTTGTGGGCTTTTGAAAAATA
65 TGACTTGTGGGCTTTTGAAAAATA
*
11648 TGCCACTTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCAC
1 TGCCAC-TGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCAC
11713 TGACTTGT-GGCTTTTGAAAAATA
65 TGACTTGTGGGCTTTTGAAAAATA
11736 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
11785 GAAAAGAGTG
Statistics
Matches: 128, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
86 6 0.05
87 53 0.41
88 25 0.20
89 24 0.19
90 20 0.16
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (88 bp):
TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACT
GACTTGTGGGCTTTTGAAAAATA
Found at i:11996 original size:30 final size:30
Alignment explanation
Indices: 11524--11997 Score: 349
Period size: 30 Copynumber: 16.1 Consensus size: 30
11514 ACTAAAGATG
* * *
11524 GAAAAGG-TGCCCACCGATTTGTGGGC-TTC
1 GAAAAGGATG-CCACTGACTTGTGGGCTTTT
* *
11553 GAAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 G-AAAAGGATGCCACTGACTTGTGGGCTTTT
*
11583 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
11611 -TAAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
11640 GAAAAATATGCCACTTGACTTGTGGGCTTTT
1 GAAAAGGATGCCAC-TGACTTGTGGGCTTTT
* * *
11671 GAACAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
*
11701 --AAAGGTTGCCACTGACTTGT-GGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
11728 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
11758 GAAAAGGGTGCCACTAACTTGTGGGC---T
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * * **
11785 GAAAA-GAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GAAAAGGA-TGCCACT-GACTTGTGGGCTT----TT
* * * * *
11819 GAAAAAGAGTGCCACGGAGTTGTGGAC-TTG
1 GAAAAGGA-TGCCACTGACTTGTGGGCTTTT
* **
11849 GAAAA-GATGCCACCGACTTGTGGGCTTCG
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
11878 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
11907 G--AAGGTTGCCACTGACTTGTGGGCTTTC
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
11935 GAAAAAAAATGCCACTGACTTGTGGGC-TTT
1 G-AAAAGGATGCCACTGACTTGTGGGCTTTT
** *
11965 GAAAAAAATGCCACTGACTTGTGGACTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
11995 GAA
1 GAA
11998 GGGTGATGAA
Statistics
Matches: 365, Mismatches: 52, Indels: 55
0.77 0.11 0.12
Matches are distributed among these distances:
26 2 0.01
27 67 0.18
28 38 0.10
29 80 0.22
30 108 0.30
31 48 0.13
34 6 0.02
35 16 0.04
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (30 bp):
GAAAAGGATGCCACTGACTTGTGGGCTTTT
Found at i:13441 original size:1 final size:1
Alignment explanation
Indices: 13437--13622 Score: 273
Period size: 1 Copynumber: 186.0 Consensus size: 1
13427 CCGGACCCCC
* * * * * *
13437 TTTTTTTTTGTTTGTTTTTTTATTGTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** **
13502 TTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTGG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13567 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13623 GGAGGACGCC
Statistics
Matches: 167, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 167 1.00
ACGTcount: A:0.01, C:0.00, G:0.05, T:0.94
Consensus pattern (1 bp):
T
Done.