Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold824
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: 28920
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:2760 original size:32 final size:32
Alignment explanation
Indices: 2724--2854 Score: 208
Period size: 32 Copynumber: 4.1 Consensus size: 32
2714 TTTCATTATT
* * *
2724 CATCACTATTCATCACTGTTCATGTATTGATA
1 CATCACTGTTCATCATTGTTCATGTATCGATA
*
2756 CATCACTGTTCATCATTGTTCATATATCGATA
1 CATCACTGTTCATCATTGTTCATGTATCGATA
2788 CATCACTGTTCATCATTGTTCATGTATCGATA
1 CATCACTGTTCATCATTGTTCATGTATCGATA
* *
2820 CATCACTGTTCATCATTATTCATCTATCGATA
1 CATCACTGTTCATCATTGTTCATGTATCGATA
2852 CAT
1 CAT
2855 TATGAATAGT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 92 1.00
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.40
Consensus pattern (32 bp):
CATCACTGTTCATCATTGTTCATGTATCGATA
Found at i:2775 original size:10 final size:10
Alignment explanation
Indices: 2716--2843 Score: 60
Period size: 10 Copynumber: 12.2 Consensus size: 10
2706 AATCTCATTT
*
2716 TCATTATTCA
1 TCATTGTTCA
* *
2726 TCACTATTCA
1 TCATTGTTCA
*
2736 TCACTGTTCA
1 TCATTGTTCA
* *
2746 TGTATTGATACA
1 T-CATTG-TTCA
*
2758 TCACTGTTCA
1 TCATTGTTCA
2768 TCATTGTTCA
1 TCATTGTTCA
*
2778 T-ATATCGATACA
1 TCAT-T-G-TTCA
*
2790 TCACTGTTCA
1 TCATTGTTCA
2800 TCATTGTTCA
1 TCATTGTTCA
* * *
2810 TGTATCGATACA
1 T-CATTG-TTCA
*
2822 TCACTGTTCA
1 TCATTGTTCA
*
2832 TCATTATTCA
1 TCATTGTTCA
2842 TC
1 TC
2844 TATCGATACA
Statistics
Matches: 88, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
9 2 0.02
10 59 0.67
11 13 0.15
12 13 0.15
13 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.42
Consensus pattern (10 bp):
TCATTGTTCA
Found at i:3370 original size:37 final size:33
Alignment explanation
Indices: 3295--3358 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
3285 CAAGTAATTG
*
3295 AGAGGTTCTATCTTAGCC-TTGAAAGATAGTGT
1 AGAGGTTCTATCTTAGCCTTTGAAAGAGAGTGT
3327 AGAGGTTCTATCTTAGCCTTTGTAAAAGAGAG
1 AGAGGTTCTATCTTAGCCTTTG--AAAGAGAG
3359 GGGTGTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 18 0.64
33 3 0.11
35 7 0.25
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (33 bp):
AGAGGTTCTATCTTAGCCTTTGAAAGAGAGTGT
Found at i:3724 original size:19 final size:21
Alignment explanation
Indices: 3693--3747 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 21
3683 TATAAACAGT
3693 AAATGTATCGATACATAAGTG
1 AAATGTATCGATACATAAGTG
* *
3714 -AATGT-TCGATACATGATTG
1 AAATGTATCGATACATAAGTG
3733 AAATGTATCGATACA
1 AAATGTATCGATACA
3748 AAACCACCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 12 0.40
20 10 0.33
21 8 0.27
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (21 bp):
AAATGTATCGATACATAAGTG
Found at i:3821 original size:19 final size:20
Alignment explanation
Indices: 3777--3824 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
3767 CAGGGAAGTG
** *
3777 TATCGATACATTACTGTTTG
1 TATCGATACATTACTCATTA
3797 TATCGATACATTA-TCATTA
1 TATCGATACATTACTCATTA
3816 TATCGATAC
1 TATCGATAC
3825 TGAAAGCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (20 bp):
TATCGATACATTACTCATTA
Found at i:4293 original size:32 final size:30
Alignment explanation
Indices: 4257--4315 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
4247 GAAATCAAAT
4257 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
4289 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
4316 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:5300 original size:20 final size:20
Alignment explanation
Indices: 5277--5349 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5267 ACAACTCAAA
5277 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
5297 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
5318 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
5338 GTATCGATACAT
1 GTATCGATACAT
5350 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:5328 original size:41 final size:42
Alignment explanation
Indices: 5277--5371 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
5267 ACAACTCAAA
*
5277 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
5318 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
5360 GTATCGATACAT
1 GTATCGATACAT
5372 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:5428 original size:13 final size:13
Alignment explanation
Indices: 5410--5435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5400 TACAGCAAGT
5410 ATGTATCGATACA
1 ATGTATCGATACA
5423 ATGTATCGATACA
1 ATGTATCGATACA
5436 CAAAATTGTA
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5449 original size:31 final size:32
Alignment explanation
Indices: 5392--5453 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
5382 TAGCCAAACT
*
5392 TGTATCGATACAGCAAGTATGTATCGATACAA
1 TGTATCGATACAGCAAATATGTATCGATACAA
5424 TGTATCGATACA-CAAA-ATTGTATCGATACA
1 TGTATCGATACAGCAAATA-TGTATCGATACA
5454 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 1 0.04
31 15 0.54
32 12 0.43
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAGCAAATATGTATCGATACAA
Found at i:11252 original size:13 final size:13
Alignment explanation
Indices: 11234--11259 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11224 ACAATTTTTG
11234 TGTATCGATACAT
1 TGTATCGATACAT
11247 TGTATCGATACAT
1 TGTATCGATACAT
11260 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11256 original size:32 final size:32
Alignment explanation
Indices: 11215--11277 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
11205 TACAAGCCAA
**
11215 TGTATCGATACAATTTTTG-TGTATCGATACAT
1 TGTATCGATAC-ATACTTGCTGTATCGATACAT
11247 TGTATCGATACATACTTGCTGTATCGATACA
1 TGTATCGATACATACTTGCTGTATCGATACA
11278 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATACTTGCTGTATCGATACAT
Found at i:11345 original size:20 final size:20
Alignment explanation
Indices: 11320--11392 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
11310 ATCTTTTTTT
11320 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
11340 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
11361 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
11381 ATGTATCGATAC
1 ATGTATCGATAC
11393 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:11371 original size:41 final size:42
Alignment explanation
Indices: 11298--11392 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
11288 CTGCCAAGAA
*
11298 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
11340 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
11381 ATGTATCGATAC
1 ATGTATCGATAC
11393 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:12950 original size:21 final size:21
Alignment explanation
Indices: 12924--12979 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
12914 AGGGTGGTTT
12924 TGTATCGATACATTTCAATCA
1 TGTATCGATACATTTCAATCA
* * *
12945 TGTATCGAAACA-TTCACTTA
1 TGTATCGATACATTTCAATCA
12965 TGTATCGATACATTT
1 TGTATCGATACATTT
12980 ACTGTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCAATCA
Found at i:13863 original size:32 final size:32
Alignment explanation
Indices: 13822--13952 Score: 208
Period size: 32 Copynumber: 4.1 Consensus size: 32
13812 ACTATTCATA
* *
13822 ATGTATCGATAGATGAATAATGATGAACAGTG
1 ATGTATCGATACATGAACAATGATGAACAGTG
13854 ATGTATCGATACATGAACAATGATGAACAGTG
1 ATGTATCGATACATGAACAATGATGAACAGTG
*
13886 ATGTATCGATATATGAACAATGATGAACAGTG
1 ATGTATCGATACATGAACAATGATGAACAGTG
* * *
13918 ATGTATCAATACATGAACAGTGATGAATAGTG
1 ATGTATCGATACATGAACAATGATGAACAGTG
13950 ATG
1 ATG
13953 AATAATGAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 92 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (32 bp):
ATGTATCGATACATGAACAATGATGAACAGTG
Found at i:13881 original size:10 final size:10
Alignment explanation
Indices: 13833--13960 Score: 60
Period size: 10 Copynumber: 12.2 Consensus size: 10
13823 TGTATCGATA
*
13833 GATGAATAAT
1 GATGAACAAT
*
13843 GATGAACAGT
1 GATGAACAAT
* *
13853 GATGTATCGAT
1 GATG-AACAAT
*
13864 ACATGAACAAT
1 -GATGAACAAT
*
13875 GATGAACAGT
1 GATGAACAAT
*
13885 GATGTATCGATAT
1 GATG-AAC-A-AT
13898 -ATGAACAAT
1 GATGAACAAT
*
13907 GATGAACAGT
1 GATGAACAAT
*
13917 GATGTATCAAT
1 GATG-AACAAT
* *
13928 ACATGAACAGT
1 -GATGAACAAT
* *
13939 GATGAATAGT
1 GATGAACAAT
*
13949 GATGAATAAT
1 GATGAACAAT
13959 GA
1 GA
13961 AAATGAGATT
Statistics
Matches: 88, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
9 2 0.02
10 56 0.64
11 19 0.22
12 10 0.11
13 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.27
Consensus pattern (10 bp):
GATGAACAAT
Found at i:17196 original size:21 final size:21
Alignment explanation
Indices: 17172--17230 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
17162 ATTTTGCAAC
17172 TCATTTCTTTTCTTTTCTAAT
1 TCATTTCTTTTCTTTTCTAAT
**
17193 TCA-TTCATTTTCTCCTCTAAT
1 TCATTTC-TTTTCTTTTCTAAT
**
17214 TCATTTAATTTCTTTTC
1 TCATTTCTTTTCTTTTC
17231 AAGAATATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.10
21 25 0.83
22 2 0.07
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (21 bp):
TCATTTCTTTTCTTTTCTAAT
Found at i:19351 original size:32 final size:32
Alignment explanation
Indices: 19310--19375 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
19300 ACTATTCATA
*
19310 ATGTATCGATACATGAACAGTGATGAACAGTG
1 ATGTATCGATACATGAACAATGATGAACAGTG
* * *
19342 ATGTATCGATAGATGAATAATGATGAATAGTG
1 ATGTATCGATACATGAACAATGATGAACAGTG
19374 AT
1 AT
19376 AAACAGTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACATGAACAATGATGAACAGTG
Found at i:20691 original size:18 final size:18
Alignment explanation
Indices: 20651--20687 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20641 GATGGTCTAG
20651 AATTTTTATATTTTAGAA
1 AATTTTTATATTTTAGAA
*
20669 AATTTTTGTATTTT-GAA
1 AATTTTTATATTTTAGAA
20686 AA
1 AA
20688 ATTTCCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
AATTTTTATATTTTAGAA
Found at i:25794 original size:29 final size:28
Alignment explanation
Indices: 25734--25791 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
25724 AATTTTTATT
* *
25734 TTAT-TTTTTATATTTTTAAAAAATATA
1 TTATATTTTTATATTTTGAAAAAAAATA
25761 TTATATTTTTATCATTTTGAAAATAAAATA
1 TTATATTTTTAT-ATTTTGAAAA-AAAATA
25791 T
1 T
25792 ATAACATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.15
28 7 0.27
29 9 0.35
30 6 0.23
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTATATTTTTATATTTTGAAAAAAAATA
Found at i:26869 original size:21 final size:21
Alignment explanation
Indices: 26843--26886 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
26833 TTTCCCCTTG
*
26843 TTTTTTATTTTTTCCTTGTTT
1 TTTTTTATTTTTTCCTTGCTT
*
26864 TTTTTTGTTTTTTCCTTGCTT
1 TTTTTTATTTTTTCCTTGCTT
26885 TT
1 TT
26887 CATGTGTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTTATTTTTTCCTTGCTT
Found at i:28890 original size:23 final size:23
Alignment explanation
Indices: 28860--28906 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28850 ACCGGATTTT
28860 TGGTGAGGCATATTGCACTAGCA
1 TGGTGAGGCATATTGCACTAGCA
28883 TGGTGAGGCATATTGCACTAGCA
1 TGGTGAGGCATATTGCACTAGCA
28906 T
1 T
28907 CATCGCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (23 bp):
TGGTGAGGCATATTGCACTAGCA
Done.