Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3565
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: 40364
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Found at i:7117 original size:26 final size:26
Alignment explanation
Indices: 7087--7138 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
7077 CACCAATGAA
*
7087 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
7113 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
7139 CTTTTCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:7192 original size:103 final size:102
Alignment explanation
Indices: 6953--7319 Score: 594
Period size: 103 Copynumber: 3.6 Consensus size: 102
6943 TAGCCGTTAT
* *
6953 TGGTGGAT-CCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
*
7017 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
7055 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
*
7120 ATCAGCACATAGCAACCCCCTTTTCATGTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
7157 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
7222 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
7261 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
7320 TTTATATACA
Statistics
Matches: 250, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
102 78 0.31
103 134 0.54
104 37 0.15
105 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:7219 original size:26 final size:26
Alignment explanation
Indices: 7190--7241 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
7180 ACCAATGAAA
*
7190 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
7216 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
7242 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:7688 original size:29 final size:30
Alignment explanation
Indices: 7655--7711 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
7645 CCACCCAACT
7655 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* ** *
7684 TTTTGCATAATTACTCTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
7712 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:9558 original size:32 final size:32
Alignment explanation
Indices: 9522--9611 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
9512 ATTTTTACCC
* *
9522 ATGGCTGTGTGCCAATTATATTACCGTCACTG
1 ATGGCTATGTGCCAATTATATTACCGTCACCG
* * *
9554 ATGGCTATGTGCCAGACT-TATTACAGTTACCG
1 ATGGCTATGTGCCA-ATTATATTACCGTCACCG
* * * *
9586 ATGCCTTTGTGTCAATTATAATACCG
1 ATGGCTATGTGCCAATTATATTACCG
9612 CTACTGAAGG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
31 2 0.04
32 41 0.91
33 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34
Consensus pattern (32 bp):
ATGGCTATGTGCCAATTATATTACCGTCACCG
Found at i:11529 original size:16 final size:16
Alignment explanation
Indices: 11508--11540 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11498 CAGCAAATCT
*
11508 CGAAATGTCGAAAAGC
1 CGAAATGCCGAAAAGC
11524 CGAAATGCCGAAAAGC
1 CGAAATGCCGAAAAGC
11540 C
1 C
11541 AAAAGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.09
Consensus pattern (16 bp):
CGAAATGCCGAAAAGC
Found at i:11867 original size:28 final size:29
Alignment explanation
Indices: 11755--11879 Score: 180
Period size: 29 Copynumber: 4.3 Consensus size: 29
11745 GAAAGCATGT
11755 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
11784 ATAAGAATGTGATTTAGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
11813 ATACGAATGTGATTTGGGCCTAATGGGGC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
11842 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
11870 ATATGCATGT
1 ATATGAATGT
11880 ATGTAGACCT
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 22 0.26
29 63 0.74
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:14131 original size:27 final size:26
Alignment explanation
Indices: 14101--14189 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 26
14091 ATGGAGGAAA
*
14101 TGTTCTGATGGCTAC-GCCACAAATATC
1 TGTTCTGGTGGCT-CTGCCAC-AATATC
*
14128 TGTTTCTGGTGGCTCTACCACAATATC
1 TG-TTCTGGTGGCTCTGCCACAATATC
* *
14155 TGTATCTGGTGACTCTGTCACAATATC
1 TGT-TCTGGTGGCTCTGCCACAATATC
14182 TGTTCTGG
1 TGTTCTGG
14190 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
26 6 0.11
27 34 0.63
28 14 0.26
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (26 bp):
TGTTCTGGTGGCTCTGCCACAATATC
Found at i:16506 original size:57 final size:57
Alignment explanation
Indices: 16416--16532 Score: 189
Period size: 57 Copynumber: 2.1 Consensus size: 57
16406 TGGTAAGGTA
* * * *
16416 CATCTGGGCGAGTGTAGGACACGTTCTGGTGCTTGTTTTCGGTGCGGATCTATGGAG
1 CATCTGGGCGAGTGTAGGAAACATTCTGCTGCTTGTTTTCGGTGCCGATCTATGGAG
*
16473 CATCTGGGCGAGTGTAGGAAACATTCTGCTGCTTTTTTTCGGTGCCGATCTATGGAG
1 CATCTGGGCGAGTGTAGGAAACATTCTGCTGCTTGTTTTCGGTGCCGATCTATGGAG
16530 CAT
1 CAT
16533 AAAGTCAAGG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.32
Consensus pattern (57 bp):
CATCTGGGCGAGTGTAGGAAACATTCTGCTGCTTGTTTTCGGTGCCGATCTATGGAG
Found at i:22712 original size:27 final size:27
Alignment explanation
Indices: 22682--22743 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
22672 ATTTACTAAA
*
22682 ATACCCCTAAGTATG-AAAATTACCATT
1 ATACCCCTAAG-ATGCAAAATGACCATT
* *
22709 ATACCCCT-AGGTGCAAAATGACCGTT
1 ATACCCCTAAGATGCAAAATGACCATT
22735 ATACCCCTA
1 ATACCCCTA
22744 GGGTTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 20 0.67
27 8 0.27
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.26
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATGACCATT
Found at i:22915 original size:27 final size:26
Alignment explanation
Indices: 22862--22934 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
22852 GGTGGCTATG
* *
22862 CCACAAATATCTGTTTCTAGTGGCTCTA
1 CCAC-AATATCTG-TTCTGGTGACTCTA
*
22890 CCACAATATCTGTATCTGGTGACTCTG
1 CCACAATATCTGT-TCTGGTGACTCTA
* *
22917 TCACACTATCTGTTCTGG
1 CCACAATATCTGTTCTGG
22935 CGGCCGTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 6 0.15
27 29 0.74
28 4 0.10
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (26 bp):
CCACAATATCTGTTCTGGTGACTCTA
Found at i:25768 original size:27 final size:26
Alignment explanation
Indices: 25724--25775 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
25714 CTCGCTGCAA
*
25724 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
25751 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
25776 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:27871 original size:17 final size:18
Alignment explanation
Indices: 27849--27882 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27839 TGAAGCATAT
27849 AGAAAGA-CAGAATCGTG
1 AGAAAGATCAGAATCGTG
*
27866 AGAAAGATCGGAATCGT
1 AGAAAGATCAGAATCGT
27883 TTTAGGAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.12, G:0.29, T:0.15
Consensus pattern (18 bp):
AGAAAGATCAGAATCGTG
Found at i:32229 original size:2 final size:2
Alignment explanation
Indices: 32222--32255 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
32212 GCTTCGCCAC
*
32222 AT AT AT AT AT AG 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
32256 TTGTTCTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34999 original size:68 final size:67
Alignment explanation
Indices: 34927--35076 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
34917 CATCATGTGT
* * * *
34927 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
34989 ATGTAG
62 ATGTAG
** * *
34995 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
35060 AG
66 AG
35062 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
35077 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:35032 original size:64 final size:64
Alignment explanation
Indices: 34951--35134 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
34941 AGACATTATG
* *
34951 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
35015 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
35080 AA
63 AA
** * * *
35082 ACTG--GCTAGGTTACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
35135 CGAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 21 0.22
65 8 0.08
66 15 0.15
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:36956 original size:28 final size:28
Alignment explanation
Indices: 36924--37051 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
36914 ATAGTAAGTC
*
36924 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
36952 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
36981 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
37009 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
37038 CGCACACTTAGTGC
1 CGCACACTTAGTGC
37052 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:37014 original size:57 final size:57
Alignment explanation
Indices: 36923--37051 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
36913 TATAGTAAGT
*
36923 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
36980 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
37037 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
37052 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Done.