Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1490
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: 36357
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:4729 original size:39 final size:40
Alignment explanation
Indices: 4637--4845 Score: 290
Period size: 40 Copynumber: 5.3 Consensus size: 40
4627 ATGATAACGA
4637 CTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGG
1 CTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGG
4677 CTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCC-GG
1 CTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGG
4716 CTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGG
1 CTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGG
**
4756 --AAGTCCCGAAGGCATTTGTGCGAACTACTATATCCGGG
1 CTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGG
*
4794 CTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT-C-GG
1 CTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGG
* *
4832 TTAAATCCCGAAGG
1 CTAAGTCCCGAAGG
4846 TACTTGGTTT
Statistics
Matches: 158, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
38 50 0.32
39 40 0.25
40 68 0.43
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGG
Found at i:5424 original size:40 final size:40
Alignment explanation
Indices: 5291--5518 Score: 358
Period size: 40 Copynumber: 5.8 Consensus size: 40
5281 GATGATAACG
*
5291 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTT-ACTAATTCC
5332 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAATT-C
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
5370 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
5410 GGGCTAAGTCCCGAAGGCATTTGTGCGA-TTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
**
5449 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
*
5489 GGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT
5519 AGCTATATCC
Statistics
Matches: 178, Mismatches: 5, Indels: 9
0.93 0.03 0.05
Matches are distributed among these distances:
38 32 0.18
39 51 0.29
40 67 0.38
41 28 0.16
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:5452 original size:79 final size:79
Alignment explanation
Indices: 5291--5544 Score: 388
Period size: 79 Copynumber: 3.2 Consensus size: 79
5281 GATGATAACG
*
5291 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTT-ACTAATTCCGGGCTAAGTCCCGAAGGCATTTGT
*
5356 GCGAGTACTA-ATTC
65 GCGAGTACTATATCC
5370 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
*
5435 CGATTACTATATCC
66 CGAGTACTATATCC
** *
5449 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGA
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGT
5513 GCGAGTAGCTATATCC
65 GCGAGTA-CTATATCC
* *
5529 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
5545 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
78 44 0.27
79 111 0.68
80 8 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
CGAGTACTATATCC
Found at i:5502 original size:119 final size:119
Alignment explanation
Indices: 5291--5518 Score: 372
Period size: 119 Copynumber: 1.9 Consensus size: 119
5281 GATGATAACG
5291 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGT
1 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGT
* * *
5356 GCGAGTACTAATTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
66 GCGACTACTAATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTAATTCC
*
5410 GGGCTAAGTCCCGAAGGCATTTGTGCGA-TT-ACT-ATATCCGGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTG
5472 TGCGAACTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
65 TGCG-ACTACTA-ATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
5519 AGCTATATCC
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
116 2 0.02
117 33 0.32
118 8 0.08
119 59 0.58
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (119 bp):
GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGT
GCGACTACTAATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTAATTCC
Found at i:5525 original size:40 final size:38
Alignment explanation
Indices: 5291--5544 Score: 348
Period size: 40 Copynumber: 6.4 Consensus size: 38
5281 GATGATAACG
*
5291 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-T-ACTAA-TCC
*
5332 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAATTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAATCC
5370 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAA-TCC
*
5410 GGGCTAAGTCCCGAAGGCATTTGTGCGATTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTA-ATCC
*
5449 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTA-ATCC
*
5489 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTA-ATCC
* *
5529 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
5545 TACTTGGTTT
Statistics
Matches: 199, Mismatches: 9, Indels: 12
0.90 0.04 0.05
Matches are distributed among these distances:
38 31 0.16
39 63 0.32
40 77 0.39
41 28 0.14
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (38 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAATCC
Found at i:13484 original size:40 final size:40
Alignment explanation
Indices: 13352--13579 Score: 365
Period size: 40 Copynumber: 5.8 Consensus size: 40
13342 GATGATAACG
*
13352 GGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
13391 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT-C
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
13430 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
13470 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
**
13510 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
* *
13550 GGGCTAAGTCCCAAAGGCATTTGAGCGAGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT
13580 AGCTATATCC
Statistics
Matches: 179, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
39 69 0.39
40 110 0.61
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:13586 original size:40 final size:39
Alignment explanation
Indices: 13352--13605 Score: 361
Period size: 40 Copynumber: 6.4 Consensus size: 39
13342 GATGATAACG
*
13352 GGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA-TCC
*
13391 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCC
13430 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA-TCC
13470 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATCC
**
13510 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATCC
* *
13550 GGGCTAAGTCCCAAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTA-ATCC
* *
13590 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
13606 TACTTGGTTT
Statistics
Matches: 200, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
39 81 0.41
40 118 0.59
41 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCC
Found at i:18114 original size:21 final size:22
Alignment explanation
Indices: 18080--18120 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
18070 AAGGAAAATT
18080 ATATAAATCAAATT-ACATACA
1 ATATAAATCAAATTAACATACA
18101 ATATAAATTC-AATTAACATA
1 ATATAAA-TCAAATTAACATA
18121 ATTGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAAATCAAATTAACATACA
Found at i:22602 original size:68 final size:66
Alignment explanation
Indices: 22530--22700 Score: 177
Period size: 66 Copynumber: 2.6 Consensus size: 66
22520 CATCATGTGT
* * * *
22530 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
22593 TGTAG
62 TGTAG
** * *
22598 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGTGAAGGACACCATGTA
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
22663 G
66 G
* * * *
22664 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
22701 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
64 24 0.27
65 18 0.20
66 34 0.38
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:22635 original size:64 final size:64
Alignment explanation
Indices: 22554--22736 Score: 210
Period size: 66 Copynumber: 2.8 Consensus size: 64
22544 AGACATTATG
* * *
22554 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
22618 ATGTAGCTAGGTCGCATGCGTGGTTCCAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATA
1 ATGTAGCTAGGTCGCATGGGTGGTACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGATA
22683 A
64 A
* * *
22684 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
22737 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
65 21 0.21
66 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:26999 original size:68 final size:66
Alignment explanation
Indices: 26927--27098 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
26917 CATCATGTGT
* * * *
26927 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
26990 TGTAG
62 TGTAG
** * *
26995 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
27060 AG
65 AG
* * * *
27062 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
27099 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:27032 original size:64 final size:64
Alignment explanation
Indices: 26951--27134 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
26941 AGACATTATG
* * *
26951 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
27015 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
27080 AA
63 AA
* * *
27082 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
27135 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:30850 original size:5 final size:5
Alignment explanation
Indices: 30840--30876 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
30830 GATGCCAACT
30840 ATAAA ATAAA ATAAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA A
30877 ATTTGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Done.