Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1574
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: 41891
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3233 original size:46 final size:45
Alignment explanation
Indices: 3180--3354 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
3170 TATTTGGGCA
3180 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
3226 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
3273 TCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
3318 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3355 CGGGTTACAT
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 1 0.01
45 24 0.22
46 51 0.47
47 24 0.22
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:3334 original size:92 final size:93
Alignment explanation
Indices: 3176--3346 Score: 299
Period size: 92 Copynumber: 1.8 Consensus size: 93
3166 AGGATATTTG
* *
3176 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3241 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
3269 GGCATCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3333 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
3347 ACTTATGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 50 0.68
93 24 0.32
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:6262 original size:15 final size:15
Alignment explanation
Indices: 6242--6309 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 15
6232 GTATCTTGGG
6242 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
6257 TCTC-TTATTCTGGA
1 TTTCTTTATCCTGGA
* *
6271 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
6286 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
6301 TTTCTTTAT
1 TTTCTTTAT
6310 TCGGTTTTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.12, C:0.18, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:6284 original size:29 final size:30
Alignment explanation
Indices: 6233--6311 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
6223 CATAGTATCG
* *
6233 TATCTTGGGTTTCTTTATCCTGGATCTCT-
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* *
6262 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
6292 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
6312 GGTTTTCTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 23 0.53
30 18 0.42
31 1 0.02
ACGTcount: A:0.11, C:0.18, G:0.15, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:8744 original size:46 final size:45
Alignment explanation
Indices: 8691--8866 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
8681 TATTTGGGCA
8691 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
8737 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
8784 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
8830 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
8867 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:8804 original size:93 final size:93
Alignment explanation
Indices: 8687--8858 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
8677 AGGATATTTG
* *
8687 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
8752 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
8780 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
8845 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
8859 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:12652 original size:24 final size:24
Alignment explanation
Indices: 12620--12666 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
12610 CAAATCTGAG
12620 TTAGAAAAATATTTTAATATTATT
1 TTAGAAAAATATTTTAATATTATT
12644 TTAGAAAAATATTTTAATATTAT
1 TTAGAAAAATATTTTAATATTAT
12667 ATTCTATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TTAGAAAAATATTTTAATATTATT
Found at i:13974 original size:43 final size:43
Alignment explanation
Indices: 13818--13975 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 43
13808 ATATGTTATT
* *
13818 GTGTAAGACCATGTCTGGGATGTTGGCATCGACT-TATGATTTAC
1 GTGTAAGACCATGTCTGGGATATTGGCATCGA-TATTTGA-TTAC
* * * *
13862 GTGTAAAACCATGTCTGGGACATCGGCATCG-TATTTGATTTC
1 GTGTAAGACCATGTCTGGGATATTGGCATCGATATTTGATTAC
*
13904 GTGTAAGATCC-TGTCTGGGATAATGGCATCGATATTTGATTAC
1 GTGTAAGA-CCATGTCTGGGATATTGGCATCGATATTTGATTAC
* * * *
13947 ATGTAAGACCAGGTCTAGGATGTTGGCAT
1 GTGTAAGACCATGTCTGGGATATTGGCAT
13976 TGTACAAGCT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 30 0.32
43 37 0.39
44 27 0.29
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGATATTGGCATCGATATTTGATTAC
Found at i:21910 original size:54 final size:54
Alignment explanation
Indices: 21828--21935 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
21818 CATATGAGTA
21828 AGGTTCCATATGCTTCTACAGTTGGAAGCCTTATGTATGCGATGCTTTACGCAT
1 AGGTTCCATATGCTTCTACAGTTGGAAGCCTTATGTATGCGATGCTTTACGCAT
*
21882 AGGTTCCATATGCTTCTACAGTTGGAAGCCTTATGTATGTGATGCTTTACGCAT
1 AGGTTCCATATGCTTCTACAGTTGGAAGCCTTATGTATGCGATGCTTTACGCAT
21936 GTCTAGATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (54 bp):
AGGTTCCATATGCTTCTACAGTTGGAAGCCTTATGTATGCGATGCTTTACGCAT
Found at i:23010 original size:14 final size:14
Alignment explanation
Indices: 22991--23022 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
22981 CACATTTCAC
*
22991 TATTATGTCTTTTG
1 TATTATGTCTTTTA
23005 TATTATGTCTTTTA
1 TATTATGTCTTTTA
23019 TATT
1 TATT
23023 TTGCATGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.66
Consensus pattern (14 bp):
TATTATGTCTTTTA
Found at i:23144 original size:25 final size:25
Alignment explanation
Indices: 23110--23160 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
23100 TTGTAAAGAA
23110 TGTTTACATTCCAAGAAAGATGACT
1 TGTTTACATTCCAAGAAAGATGACT
23135 TGTTTACATTCCAAGAAAGATGACT
1 TGTTTACATTCCAAGAAAGATGACT
23160 T
1 T
23161 ACTTCAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (25 bp):
TGTTTACATTCCAAGAAAGATGACT
Found at i:24768 original size:29 final size:28
Alignment explanation
Indices: 24732--24792 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
24722 CATCTCATTC
24732 ATATGGCCCATCAGACCCAAATCACCTTT
1 ATATGGCCCATCAGACCCAAATCACC-TT
* * *
24761 ATATGGCCCGTTAGGCCCAAATCACCTT
1 ATATGGCCCATCAGACCCAAATCACCTT
24789 ATAT
1 ATAT
24793 TCATGCTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (28 bp):
ATATGGCCCATCAGACCCAAATCACCTT
Found at i:26305 original size:16 final size:16
Alignment explanation
Indices: 26281--26312 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26271 AAGTTTAGGA
*
26281 TTTCGGGATTTTTGAG
1 TTTCAGGATTTTTGAG
26297 TTTCAGGATTTTTGAG
1 TTTCAGGATTTTTGAG
26313 GAGTTACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
TTTCAGGATTTTTGAG
Found at i:30227 original size:30 final size:30
Alignment explanation
Indices: 30171--30227 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
30161 TACGAGCATT
* *
30171 GGGGCAAAAGTGCAAATATGTGAAAGTTTA
1 GGGGCAAAAGTGAAAATATGTAAAAGTTTA
*
30201 GGGGTCAAAA-TGAAAATTTGTAAAAGT
1 GGGG-CAAAAGTGAAAATATGTAAAAGT
30228 ATGATTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (30 bp):
GGGGCAAAAGTGAAAATATGTAAAAGTTTA
Found at i:32291 original size:40 final size:40
Alignment explanation
Indices: 32217--32517 Score: 455
Period size: 40 Copynumber: 7.6 Consensus size: 40
32207 AACCCAAGTA
* * * *
32217 CCTTCGGGATTTAG-CCGGAT-TTAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAA-TAGCACAAATG
* * *
32256 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
32296 CCTTC-GGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
32335 CCTTCGGGACTTAGCCCGGATATAATCAATAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
32375 CCTTCGGGACTTAGCCCGGATATAATCAATAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
32415 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
32455 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
32495 CCTTCGGGACTTAACCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
32518 CATTCGAATA
Statistics
Matches: 242, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
39 47 0.19
40 191 0.79
41 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
Found at i:35686 original size:27 final size:27
Alignment explanation
Indices: 35656--35811 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
35646 TGCTATTCAC
* *
35656 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * * *
35683 TCAAATCGCACCCTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
35710 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
35738 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
** *
35765 TCTTTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
35792 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
35812 TGTACAATTT
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 81 0.78
28 22 0.21
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:35727 original size:55 final size:55
Alignment explanation
Indices: 35661--35812 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 55
35651 TTCACTCAAC
* *
35661 TCGCACACTTAGTGCCACGTAATCAAATCGCACCCTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TTAGAT
* ** * ***
35716 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCTTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTAGAT
* *
35770 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
35813 GTACAATTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 40 0.50
55 40 0.50
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (55 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTAGAT
Done.