Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold425
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: 49850
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10356 original size:9 final size:9
Alignment explanation
Indices: 10342--10376 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
10332 AGAAGTGAGC
10342 AAAAAAAGA
1 AAAAAAAGA
*
10351 AAAAAAAGT
1 AAAAAAAGA
10360 AAAAAAAGA
1 AAAAAAAGA
10369 ACAAAAAA
1 A-AAAAAA
10377 AAGTGAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.86, C:0.03, G:0.09, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:10385 original size:22 final size:21
Alignment explanation
Indices: 10327--10385 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
10317 GAAATTCAAA
* *
10327 AAAAAAGAAGTGAGCAAAAAAAG
1 AAAAAA-AAGTGA-AAAAAAAAC
10350 AAAAAAAAGT-AAAAAAAGAAC
1 AAAAAAAAGTGAAAAAAA-AAC
10371 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
10386 GTCTTGTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 5 0.16
21 13 0.41
22 8 0.25
23 6 0.19
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGTGAAAAAAAAAC
Found at i:13234 original size:20 final size:21
Alignment explanation
Indices: 13204--13252 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
13194 TTAGCTCGTT
*
13204 TCAAGCTCACTCGAGCTCAAG
1 TCAAGCTCACTCAAGCTCAAG
*
13225 TCAA-CTCACTCAAGCTCAAT
1 TCAAGCTCACTCAAGCTCAAG
13245 TC-AGCTCA
1 TCAAGCTCA
13253 ATTTTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.22
Consensus pattern (21 bp):
TCAAGCTCACTCAAGCTCAAG
Found at i:20479 original size:56 final size:55
Alignment explanation
Indices: 20390--20555 Score: 242
Period size: 56 Copynumber: 3.0 Consensus size: 55
20380 TCTTACATGT
* * *
20390 AATCACATATCAATGCCAACGTATTAAACGTGGTTTTACTCGCACACATATATCAG
1 AATCACATATCGATG-CAACGTATTAAATGTGGTCTTACTCGCACACATATATCAG
* * * *
20446 AGTCACATATCGATGCGAACGTATTAAATGTGGTCTTGCTCGCACACATATACCGG
1 AATCACATATCGATGC-AACGTATTAAATGTGGTCTTACTCGCACACATATATCAG
*
20502 AATCACATATCGATGCCACGTATTAAATGTGGTCTTACTCGCACACATATATCA
1 AATCACATATCGATGCAACGTATTAAATGTGGTCTTACTCGCACACATATATCA
20556 ATGCCATGGT
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
55 35 0.36
56 62 0.64
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (55 bp):
AATCACATATCGATGCAACGTATTAAATGTGGTCTTACTCGCACACATATATCAG
Found at i:24512 original size:21 final size:20
Alignment explanation
Indices: 24464--24521 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
24454 TCAGTTTCCA
*
24464 TCAGCTCGCTTGAGCTCGAT
1 TCAGCTCGTTTGAGCTCGAT
24484 TCAGCTCGTTTGAGCTCGAAT
1 TCAGCTCGTTTGAGCTCG-AT
* *
24505 TTAGCTCGTTTCAGCTC
1 TCAGCTCGTTTGAGCTC
24522 ATTTCTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.16, C:0.28, G:0.22, T:0.34
Consensus pattern (20 bp):
TCAGCTCGTTTGAGCTCGAT
Found at i:24520 original size:10 final size:10
Alignment explanation
Indices: 24464--24526 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
24454 TCAGTTTCCA
*
24464 TCAGCTCGCT
1 TCAGCTCGTT
* *
24474 TGAGCTCGAT
1 TCAGCTCGTT
24484 TCAGCTCGTT
1 TCAGCTCGTT
*
24494 TGAGCTCGAATT
1 TCAGCTCG--TT
24506 T-AGCTCGTT
1 TCAGCTCGTT
*
24515 TCAGCTCATT
1 TCAGCTCGTT
24525 TC
1 TC
24527 TTCTTCATCT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 3 0.07
10 32 0.73
11 6 0.14
12 3 0.07
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.37
Consensus pattern (10 bp):
TCAGCTCGTT
Found at i:28917 original size:12 final size:11
Alignment explanation
Indices: 28897--28939 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
28887 TGAATGTGAA
28897 AAAAG-AAAAG
1 AAAAGAAAAAG
28907 AAAATGAAAAAG
1 AAAA-GAAAAAG
28919 AAAAGAAAAA-
1 AAAAGAAAAAG
28929 AATAAGAAAAA
1 AA-AAGAAAAA
28940 AAATGCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.20
11 15 0.50
12 9 0.30
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:28922 original size:22 final size:21
Alignment explanation
Indices: 28897--28985 Score: 67
Period size: 22 Copynumber: 4.2 Consensus size: 21
28887 TGAATGTGAA
28897 AAAAGAAAAGAAAATGAAAAAG
1 AAAAGAAAA-AAAATGAAAAAG
*
28919 AAAAGAAAAAAATAAGAAAAA-
1 AAAAGAAAAAAA-ATGAAAAAG
* * * *
28940 AAATGCAAAAATA-GCAAAAG
1 AAAAGAAAAAAAATGAAAAAG
*
28960 AAAA-AAAACAAAGTGAGAAAAG
1 AAAAGAAAA-AAAATGA-AAAAG
28982 AAAA
1 AAAA
28986 AGAAGAGCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
19 8 0.15
20 6 0.12
21 13 0.25
22 25 0.48
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (21 bp):
AAAAGAAAAAAAATGAAAAAG
Found at i:31984 original size:21 final size:20
Alignment explanation
Indices: 31936--31993 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
31926 TCAGTTTCCA
* *
31936 TCAGCTCGCTTGAGCTTGAT
1 TCAGCTCGTTTGAGCTCGAT
31956 TCAGCTCGTTTGAGCTCGAAT
1 TCAGCTCGTTTGAGCTCG-AT
* *
31977 TTAGCTCGTTTCAGCTC
1 TCAGCTCGTTTGAGCTC
31994 ATTTCTTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.36
Consensus pattern (20 bp):
TCAGCTCGTTTGAGCTCGAT
Found at i:33269 original size:21 final size:21
Alignment explanation
Indices: 33243--33305 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
33233 TTGGTATTTG
33243 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
33264 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
33285 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
33306 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36268 original size:22 final size:22
Alignment explanation
Indices: 36242--36304 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
36232 AAATAAGTTG
*
36242 GGCACATAGCCATAATCAGGTT
1 GGCACAAAGCCATAATCAGGTT
* *
36264 GGCACAGAGCCAT-ATGTAGGTT
1 GGCACAAAGCCATAAT-CAGGTT
*
36286 GGCGCAAAGCCATAATCAG
1 GGCACAAAGCCATAATCAG
36305 AATAATTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (22 bp):
GGCACAAAGCCATAATCAGGTT
Found at i:36534 original size:41 final size:41
Alignment explanation
Indices: 36447--36563 Score: 180
Period size: 41 Copynumber: 2.8 Consensus size: 41
36437 AAAAGCCACC
* *
36447 GGTGGATCCACGGTCGTCAAGCAACCATAACGATCCTTAATT
1 GGTGGATCCACGGTCGTCAAGCAACCAT-GCGATCCTCAATT
*
36489 GGTGGATCCACGGTTGTCAAGCAACCATGCGATCCTCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
* *
36530 GGTGGATCCACGATCGTCAATCAACCATGCGATC
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATC
36564 TCTAATTTCC
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 42 0.61
42 27 0.39
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (41 bp):
GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
Found at i:36858 original size:27 final size:27
Alignment explanation
Indices: 36825--37228 Score: 302
Period size: 27 Copynumber: 15.0 Consensus size: 27
36815 TTTGTAAATC
* *
36825 TACAAACCAAGGGTATTTTGATAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
* * *
36852 TGCAAA-CTAATGGTATTGCT-GTAATTT
1 TACAAATC-AAGGGTATT-TTGGTAATTT
**
36879 TTGAAAGTCAAGGGTATTTCT-GTAATTT
1 TACAAA-TCAAGGGTATTT-TGGTAATTT
** *
36907 TGTAAATCAAGGGTATTTCT-ATAATTT
1 TACAAATCAAGGGTATTT-TGGTAATTT
* *
36934 TCCAAATCAAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
*
36961 TCCAAATCAAGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
** *
36988 TACAAATTGAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
* * ** *
37015 TATAAGTTGAGGGTATTTTGATAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
** * * * *
37042 TACAGGTCGAGAGTATTTCGTTAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
* *
37069 CACAAAT-TAGGAGTATTTTGGTAATTT
1 TACAAATCAAGG-GTATTTTGGTAATTT
* *
37096 TACAAA-CCAGAGGTATTTTGATAATTT
1 TACAAATCAAG-GGTATTTTGGTAATTT
37123 TACAAA-CTAAGGGTATTTTGGTAATTT
1 TACAAATC-AAGGGTATTTTGGTAATTT
* *
37150 TACTAATCGAGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
* * ***
37177 TATAAACCAAGGGTA-TTCAATAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
** * *
37203 TGTAAACCAAGGGTATTTTAGTAATT
1 TACAAATCAAGGGTATTTTGGTAATT
37229 CTACCCTACA
Statistics
Matches: 311, Mismatches: 54, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
26 25 0.08
27 260 0.84
28 25 0.08
29 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTTGGTAATTT
Found at i:36892 original size:55 final size:53
Alignment explanation
Indices: 36827--36977 Score: 169
Period size: 55 Copynumber: 2.8 Consensus size: 53
36817 TGTAAATCTA
* * * *
36827 CAAACCAAGGGTATTTTGATAATTTTGCAAA-CTAATGGTATTGCTGTAATTTTT
1 CAAATCAAGGGTATTTTG-TAATTTTGCAAATC-AAGGGTATTGCTATAATTTTC
* * *
36881 GAAAGTCAAGGGTATTTCTGTAATTTTGTAAATCAAGGGTATTTCTATAATTTTC
1 CAAA-TCAAGGGTATTT-TGTAATTTTGCAAATCAAGGGTATTGCTATAATTTTC
* *
36936 CAAATCAAGGGTATTTCGGTAATTTTCCAAATCAAGGGTATT
1 CAAATCAAGGGTATTT-TGTAATTTTGCAAATCAAGGGTATT
36978 TTGGTAATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
54 38 0.46
55 42 0.51
56 3 0.04
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (53 bp):
CAAATCAAGGGTATTTTGTAATTTTGCAAATCAAGGGTATTGCTATAATTTTC
Found at i:37241 original size:26 final size:26
Alignment explanation
Indices: 37212--37280 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 26
37202 TTGTAAACCA
37212 AGGGTATTTTAGTAATTCTACCCTAC
1 AGGGTATTTTAGTAATTCTACCCTAC
* * **
37238 AGGGGCATTTTAGTCATTCTATGCTAC
1 A-GGGTATTTTAGTAATTCTACCCTAC
37265 AGGGTATTTTAGTAAT
1 AGGGTATTTTAGTAAT
37281 ACTAGTGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 14 0.39
27 22 0.61
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.39
Consensus pattern (26 bp):
AGGGTATTTTAGTAATTCTACCCTAC
Found at i:37248 original size:80 final size:80
Alignment explanation
Indices: 37083--37232 Score: 187
Period size: 80 Copynumber: 1.9 Consensus size: 80
37073 AATTAGGAGT
** * *
37083 ATTTTGGTAATTTTACAAACCAGAGGTATTTTGATAATTTTACAAACTAAGGGTATTTTGGTAAT
1 ATTTTGGTAATTTTACAAACCAGAGGTATTTCAATAATTTTACAAACCAAGGGTATTTTAGTAAT
* *
37148 TTTACTAATCGAGGGT
66 TCTACTAA-CGAGGGC
* **
37164 ATTTTGGTAATTTTATAAACCA-AGGGTA-TTCAATAATTTTGTAAACCAAGGGTATTTTAGTAA
1 ATTTTGGTAATTTTACAAACCAGA-GGTATTTCAATAATTTTACAAACCAAGGGTATTTTAGTAA
37227 TTCTAC
65 TTCTAC
37233 CCTACAGGGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 35 0.58
81 25 0.42
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (80 bp):
ATTTTGGTAATTTTACAAACCAGAGGTATTTCAATAATTTTACAAACCAAGGGTATTTTAGTAAT
TCTACTAACGAGGGC
Found at i:47747 original size:13 final size:12
Alignment explanation
Indices: 47717--47750 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47707 AATGTGAAAC
*
47717 AAAAAGAAATTG
1 AAAAAGAAGTTG
47729 AAAAAGAAGTTG
1 AAAAAGAAGTTG
47741 AAGAAAGAAG
1 AA-AAAGAAG
47751 AGAAATGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Done.