Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1286
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: 8890
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:659 original size:128 final size:127
Alignment explanation
Indices: 431--682 Score: 387
Period size: 128 Copynumber: 2.0 Consensus size: 127
421 ACGCATTGAT
* *
431 CATACCACTCAAGATTTTGACACAAAGCAAGGCATAAGCATTTTAAGAGCATGCGCATGGCTATT
1 CATACCACTCAAGATTTTGACACAAAGCAAGGCACAAACATTTTAAGAGCATGCGCATGGCTATT
* * * *
496 TTGACAAGAAAATTAGAAATTTGAACCTCATTTAATCAATATTCCAGACCTGAAAATTAAGAG
66 TTGACAACAAAATCAGAAATTTGAACCTCATTTAATAAAGA-TCCAGACCTGAAAATTAAGAG
* * * *
559 CATACCACTCAAGGTTTTGACACAAAGTAAGGCACAAACATTTTAGGAGCATGTGCATGGCTATT
1 CATACCACTCAAGATTTTGACACAAAGCAAGGCACAAACATTTTAAGAGCATGCGCATGGCTATT
**
624 TTGATTACAAAATCAGAAATTTGAACCTCATTTAATAAAGATCCAGACCTGAAAATTAA
66 TTGACAACAAAATCAGAAATTTGAACCTCATTTAATAAAGATCCAGACCTGAAAATTAA
683 ATTTATCCTA
Statistics
Matches: 112, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
127 18 0.16
128 94 0.84
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (127 bp):
CATACCACTCAAGATTTTGACACAAAGCAAGGCACAAACATTTTAAGAGCATGCGCATGGCTATT
TTGACAACAAAATCAGAAATTTGAACCTCATTTAATAAAGATCCAGACCTGAAAATTAAGAG
Found at i:1854 original size:20 final size:20
Alignment explanation
Indices: 1829--1901 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
1819 GTAAAAAGAT
1829 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
1849 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
1869 TGCATGGATCGATACATTGA
1 AGAATGTATCGATACATTGA
1889 A-AATGTATCGATA
1 AGAATGTATCGATA
1902 TATCTGGGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 10 0.22
20 35 0.78
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1857 original size:51 final size:50
Alignment explanation
Indices: 1781--1936 Score: 147
Period size: 51 Copynumber: 3.3 Consensus size: 50
1771 TTTTAACTAG
*
1781 ATGTATCGATACATT-ATTCAATGTATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGA--AAATGTATCGATACATCTGGGTAAAAAGATAGA
* *
1832 ATGTATCGATACATTGAAGAATGTATCGATACA--T---T-----CAT-GC
1 ATGTATCGATACATTGAA-AATGTATCGATACATCTGGGTAAAAAGATAGA
* *
1872 ATGGATCGATACATTGAAAATGTATCGATATATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAATGTATCGATACATCTGGGTAAAAAGATAGA
*
1922 ATGTATTGATACATT
1 ATGTATCGATACATT
1937 TGGGTAAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 27
0.70 0.08 0.23
Matches are distributed among these distances:
39 13 0.16
40 18 0.22
41 3 0.04
44 1 0.01
46 1 0.01
49 3 0.04
50 14 0.17
51 29 0.35
52 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAATGTATCGATACATCTGGGTAAAAAGATAGA
Found at i:2942 original size:28 final size:28
Alignment explanation
Indices: 2858--3294 Score: 416
Period size: 28 Copynumber: 14.9 Consensus size: 28
2848 TTAAAAAAAA
*
2858 GGTGCCACTAACTTGTGTGGGCTTTGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG
*
2889 AGTTGCCA-TCGACTTGTGTGGGCTTTGAAAG
1 -GGTGCCACT-GAC-T-TGTGGGCTTTGAAAG
*
2920 GGTGCCCCCT-ACTTGTGGGCTTTG-AAG
1 GGTG-CCACTGACTTGTGGGCTTTGAAAG
2947 GGTATGCCACTGACTTGTGGGCTTTGAAAG
1 GG--TGCCACTGACTTGTGGGCTTTGAAAG
*
2977 GGTATGCCGACTAACTTGTGGGCTTTGAAAG
1 GG--TGCC-ACTGACTTGTGGGCTTTGAAAG
* * *
3008 GGTGCTACTGACTTGTGGG-TTTTAGAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3035 GGTGCCACTGATTTTGTGTGGGCTTTGAAAG
1 GGTGCCACTGA--CT-TGTGGGCTTTGAAAG
3066 GGTATGCCACTGACTTGTGGGCTTTGAAAG
1 GG--TGCCACTGACTTGTGGGCTTTGAAAG
* * *
3096 GATGCCATTGATTTATGTGGGCTTTGAAAG
1 GGTGCCACTGA-CT-TGTGGGCTTTGAAAG
*
3126 GGTATGCCACTGACTAGTGGGCTTTGAAAG
1 GG--TGCCACTGACTTGTGGGCTTTGAAAG
*
3156 GGTGCCACTGACTTGTGAGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * **
3184 GATGCTATTGACTTGTGGTATTTTG-AAG
1 GGTGCCACTGACTTGTGG-GCTTTGAAAG
*
3212 AGATGCCACTGACTTGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3241 GATGCCACTGACTTGTGAGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3269 GATGCCACTAACTTGTGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
3295 GAGATGAACG
Statistics
Matches: 347, Mismatches: 37, Indels: 46
0.81 0.09 0.11
Matches are distributed among these distances:
27 21 0.06
28 131 0.38
29 45 0.13
30 70 0.20
31 40 0.12
32 31 0.09
33 9 0.03
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:2994 original size:60 final size:57
Alignment explanation
Indices: 2860--3300 Score: 398
Period size: 60 Copynumber: 7.5 Consensus size: 57
2850 AAAAAAAAGG
* *
2860 TGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCA-TCGACTTGTGTGGGCTTTGAAAGGG-
1 TGCCACTAAC-T-TGTGGGCTTTG--AAGGGATGCCACT-GAC-T-TGTGGGCTTTGAAAGGGA
*
2922 TGCCCCCT-ACTTGTGGGCTTTGAAGGGTATGCCACTGACTTGTGGGCTTTGAAAGGGTA
1 TG-CCACTAACTTGTGGGCTTTGAAGGG-ATGCCACTGACTTGTGGGCTTTGAAAGGG-A
* * *
2981 TGCCGACTAACTTGTGGGCTTTGAAAGGG-TGCTACTGACTTGTGGG-TTTTAGAGGG-
1 TGCC-ACTAACTTGTGGGCTTTG-AAGGGATGCCACTGACTTGTGGGCTTTGAAAGGGA
**
3037 TGCCACTGATTTTGTGTGGGCTTTGAAAGGGTATGCCACTGACTTGTGGGCTTTGAAA-GGA
1 TGCCACT-A-ACT-TGTGGGCTTTG-AAGGG-ATGCCACTGACTTGTGGGCTTTGAAAGGGA
* ** *
3098 TGCCATTGATTTATGTGGGCTTTGAAAGGGTATGCCACTGACTAGTGGGCTTTGAAAGGG-
1 TGCCACT-AACT-TGTGGGCTTTG-AAGGG-ATGCCACTGACTTGTGGGCTTTGAAAGGGA
* * * * * ** *
3158 TGCCACTGACTTGTGAGCTTTGAAAGGATGCTATTGACTTGTGGTATTTTG-AAGAGA
1 TGCCACTAACTTGTGGGCTTTGAAGGGATGCCACTGACTTGTGG-GCTTTGAAAGGGA
* * *
3215 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAA-GGA
1 TGCCACTAACTTGTGGGCTTTGAAGGGATGCCACTGACTTGTGGGCTTTGAAAGGGA
*
3271 TGCCACTAACTTGTGGGCTTTGAAGAGATG
1 TGCCACTAACTTGTGGGCTTTGAAGGGATG
3301 AACGTTCTAG
Statistics
Matches: 323, Mismatches: 37, Indels: 44
0.80 0.09 0.11
Matches are distributed among these distances:
55 3 0.01
56 56 0.17
57 68 0.21
58 42 0.13
59 29 0.09
60 96 0.30
61 21 0.07
62 4 0.01
63 4 0.01
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (57 bp):
TGCCACTAACTTGTGGGCTTTGAAGGGATGCCACTGACTTGTGGGCTTTGAAAGGGA
Found at i:3012 original size:88 final size:85
Alignment explanation
Indices: 2873--3300 Score: 463
Period size: 88 Copynumber: 4.9 Consensus size: 85
2863 CACTAACTTG
* * * *
2873 TGTGGGCTTTGAAAAGAGTTGCCA-TCGACTTGTGTGGGCTTTGAAAGGGTGCCCCCT-ACTTGT
1 TGTGGGCTTTG-AAAGGGATGCCACT-GAC-T-TGTGGGCTTTGAAAGGATG-CCACTGACTTGT
2936 GGGCTTTGAAGGGTATGCCACTGACT
61 GGGCTTTGAAGGG-ATGCCACTGACT
* * *
2962 TGTGGGCTTTGAAAGGGTATGCCGACTAACTTGTGGGCTTTGAAAGGGTGCTACTGACTTGTGGG
1 TGTGGGCTTTGAAAGGG-ATGCC-ACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGG
* *
3027 -TTTTAGAGGG-TGCCACTGATTTT
64 CTTTGA-AGGGATGCCACTGA--CT
* *
3050 GTGTGGGCTTTGAAAGGGTATGCCACTGACTTGTGGGCTTTGAAAGGATGCCATTGATTTATGTG
1 -TGTGGGCTTTGAAAGGG-ATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGA-CT-TGTG
3115 GGCTTTGAAAGGGTATGCCACTGACT
62 GGCTTTG-AAGGG-ATGCCACTGACT
* * * * **
3141 AGTGGGCTTTGAAAGGG-TGCCACTGACTTGTGAGCTTTGAAAGGATGCTATTGACTTGTGGTAT
1 TGTGGGCTTTGAAAGGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGG-GC
*
3205 TTTGAAGAGATGCCACTGACT
65 TTTGAAGGGATGCCACTGACT
* *
3226 TGTGGGCTTTGAAA-GGATGCCACTGACTTGTGAGCTTTGAAAGGATGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
*
3290 TTGAAGAGATG
66 TTGAAGGGATG
3301 AACGTTCTAG
Statistics
Matches: 296, Mismatches: 27, Indels: 37
0.82 0.08 0.10
Matches are distributed among these distances:
84 14 0.05
85 66 0.22
86 18 0.06
87 12 0.04
88 102 0.34
89 40 0.14
90 25 0.08
91 9 0.03
92 1 0.00
93 9 0.03
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (85 bp):
TGTGGGCTTTGAAAGGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
TTGAAGGGATGCCACTGACT
Found at i:4607 original size:12 final size:11
Alignment explanation
Indices: 4542--4607 Score: 64
Period size: 11 Copynumber: 5.7 Consensus size: 11
4532 CATCTGACCC
4542 TTTTTTTGTTTG
1 TTTTTTT-TTTG
4554 -TTTTTTTTTG
1 TTTTTTTTTTG
4564 TTTTTGGTTTTT-
1 TTTTT--TTTTTG
*
4576 TCTATTTTTTTG
1 T-TTTTTTTTTG
4588 TTTTTTTTCTTG
1 TTTTTTTT-TTG
4600 TTTTTTTT
1 TTTTTTTT
4608 GGTACGAAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
10 4 0.09
11 21 0.46
12 13 0.28
13 8 0.17
ACGTcount: A:0.02, C:0.03, G:0.11, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:7238 original size:13 final size:13
Alignment explanation
Indices: 7214--7248 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
7204 TAAATTTAAA
*
7214 AATTAATTTAATT
1 AATTAATATAATT
*
7227 AATTTATATAATT
1 AATTAATATAATT
7240 AATTAATAT
1 AATTAATAT
7249 TTAATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTAATATAATT
Found at i:7255 original size:18 final size:19
Alignment explanation
Indices: 7189--7255 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 19
7179 GTGTGACATG
7189 ATTTAATAA-TAA-TAATAA
1 ATTTAATAATTAATTAAT-A
*
7207 ATTTAAAAATTAATTTAATTA
1 ATTTAATAATTAA-TTAA-TA
7228 ATTTATATAATTAATTAAT-
1 ATTTA-ATAATTAATTAATA
7247 ATTTAATAA
1 ATTTAATAA
7256 ATTTTAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
18 12 0.29
19 8 0.19
20 1 0.02
21 13 0.31
22 8 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTAATAATTAATTAATA
Done.