Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1293
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: 27666
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1681 original size:32 final size:31
Alignment explanation
Indices: 1639--1746 Score: 94
Period size: 32 Copynumber: 3.4 Consensus size: 31
1629 ATACAGCTTT
*
1639 AAGCCTTCAGTAGCGGTATTATAATTGGCACA
1 AAGCCATCAGTAGCGGTA-TATAATTGGCACA
* *
1671 AAGCCATCAGTAACTGTA-ATAAGTTTGGCACA
1 AAGCCATCAGTAGCGGTATATAA--TTGGCACA
* *
1703 TAGCCATCAGT-GACGGTAATATAATCGGCACA
1 AAGCCATCAGTAG-CGGT-ATATAATTGGCACA
* *
1735 CAGCCATGAGTA
1 AAGCCATCAGTA
1747 AATATGATCG
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
30 4 0.07
32 52 0.85
33 1 0.02
34 4 0.07
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (31 bp):
AAGCCATCAGTAGCGGTATATAATTGGCACA
Found at i:1756 original size:27 final size:27
Alignment explanation
Indices: 1720--1822 Score: 82
Period size: 27 Copynumber: 3.8 Consensus size: 27
1710 CAGTGACGGT
* *
1720 AATATAATCGGCACACAGCCATGAGTA
1 AATATGATCGGCACAAAGCCATGAGTA
* * * * *
1747 AATATGATCGACACAGAGTCATCAATA
1 AATATGATCGGCACAAAGCCATGAGTA
* *
1774 AATATGATAGGCACATAGCCACTG-GTA
1 AATATGATCGGCACAAAGCCA-TGAGTA
* **
1801 AATACGATTTGCACAAAGCCAT
1 AATATGATCGGCACAAAGCCAT
1823 AATCAGCATA
Statistics
Matches: 59, Mismatches: 16, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
26 1 0.02
27 57 0.97
28 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (27 bp):
AATATGATCGGCACAAAGCCATGAGTA
Found at i:2361 original size:81 final size:81
Alignment explanation
Indices: 2259--2527 Score: 266
Period size: 81 Copynumber: 3.3 Consensus size: 81
2249 TTACACTACA
* * *
2259 AGGGTATTTCAGTAATATTACAAATCAGGGGTATTTGGGTAATTTTATAAACTAGGGGTATTTTA
1 AGGGTATTTCAGTAATTTTACAAATCAGGGGTATTTCGATAATTTTATAAACTAGGGGTATTTTA
*
2324 GTAATTTTATAATCTG
66 GTAATTTTAAAATCTG
* * * * *
2340 AGGGTATTTCACTAATTTTACAAA-CCGAGGGTATTTTGATAATTTTATAATCTAAGGGTATTTT
1 AGGGTATTTCAGTAATTTTACAAATCAG-GGGTATTTCGATAATTTTATAAACTAGGGGTATTTT
2404 AGTAATTTTACAAA-CTG
65 AGTAATTTTA-AAATCTG
* * * * *
2421 GGGGTATTT-TGATAATTTTAC-AATCTAAGGGTATTTCGATAATTTTACAAA-TCGAGGGTA-T
1 AGGGTATTTCAG-TAATTTTACAAATC-AGGGGTATTTCGATAATTTTATAAACTAG-GGGTATT
*
2482 TTCGATAATTTTACAAATC-G
63 TTAG-TAATTTTA-AAATCTG
* *
2502 -GGGTAATTCGGTAATTTTACAAATCA
1 AGGGTATTTCAGTAATTTTACAAATCA
2528 AGGTCTTAAA
Statistics
Matches: 157, Mismatches: 21, Indels: 21
0.79 0.11 0.11
Matches are distributed among these distances:
80 26 0.17
81 128 0.82
82 3 0.02
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (81 bp):
AGGGTATTTCAGTAATTTTACAAATCAGGGGTATTTCGATAATTTTATAAACTAGGGGTATTTTA
GTAATTTTAAAATCTG
Found at i:2497 original size:27 final size:27
Alignment explanation
Indices: 2233--2526 Score: 225
Period size: 27 Copynumber: 10.9 Consensus size: 27
2223 TACCCTACAG
* * *
2233 GGGTATTTCAATAATTTTAC-ACTACAA
1 GGGTATTTCGATAATTTTACAAAT-CGA
*
2260 GGGTATTTC-AGTAATATTACAAATC-A
1 GGGTATTTCGA-TAATTTTACAAATCGA
* * * *
2286 GGGGTATTTGGGTAATTTTATAAA-CTA
1 -GGGTATTTCGATAATTTTACAAATCGA
* *
2313 GGGGTATTT-TAGTAATTTTA-TAATCTGA
1 -GGGTATTTCGA-TAATTTTACAAATC-GA
*
2341 GGGTATTTC-ACTAATTTTACAAACCGA
1 GGGTATTTCGA-TAATTTTACAAATCGA
* * *
2368 GGGTATTTTGATAATTTTA-TAATCTAA
1 GGGTATTTCGATAATTTTACAAATC-GA
* *
2395 GGGTATTT-TAGTAATTTTACAAA-CTGG
1 GGGTATTTCGA-TAATTTTACAAATC-GA
* *
2422 GGGTATTTTGATAATTTTAC-AATCTAA
1 GGGTATTTCGATAATTTTACAAATC-GA
2449 GGGTATTTCGATAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
2476 GGGTATTTCGATAATTTTACAAATCG-
1 GGGTATTTCGATAATTTTACAAATCGA
* *
2502 GGGTAATTCGGTAATTTTACAAATC
1 GGGTATTTCGATAATTTTACAAATC
2527 AAGGTCTTAA
Statistics
Matches: 222, Mismatches: 28, Indels: 35
0.78 0.10 0.12
Matches are distributed among these distances:
26 34 0.15
27 174 0.78
28 14 0.06
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAATCGA
Found at i:6782 original size:15 final size:16
Alignment explanation
Indices: 6746--6775 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6736 ACATATCATT
6746 TATTTCATTATATCAA
1 TATTTCATTATATCAA
6762 TATTTCA-TATATCA
1 TATTTCATTATATCA
6776 TAGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTCATTATATCAA
Found at i:9682 original size:39 final size:40
Alignment explanation
Indices: 9519--9659 Score: 216
Period size: 39 Copynumber: 3.6 Consensus size: 40
9509 GGATGATAAC
* * *
9519 CGGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACTA-ATT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT
9558 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT
* *
9597 CCGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT
9636 CGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
9660 AGCAAGTAGT
Statistics
Matches: 94, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
38 27 0.29
39 53 0.56
40 14 0.15
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT
Found at i:17539 original size:40 final size:40
Alignment explanation
Indices: 17482--17664 Score: 291
Period size: 40 Copynumber: 4.6 Consensus size: 40
17472 CGGATGATAA
* *
17482 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
17522 CCGGGCTAAGTCTCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
17562 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
17602 CC-GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
17640 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
17665 AGCAAGTAGT
Statistics
Matches: 133, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
38 29 0.22
39 16 0.12
40 87 0.65
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:17647 original size:78 final size:80
Alignment explanation
Indices: 17478--17664 Score: 308
Period size: 78 Copynumber: 2.4 Consensus size: 80
17468 TATTCGGATG
*
17478 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCTCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCTCGAAGGCA
*
17543 TTTGTGTGAGTTACT
66 TTTGTGCGAGTTACT
* *
17558 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC-GGCTAAGTC-CGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCTAAGTCTCGAAGGC
17620 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACT
17636 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
17665 AGCAAGTAGT
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
78 50 0.50
79 11 0.11
80 40 0.40
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCTCGAAGGCA
TTTGTGCGAGTTACT
Found at i:17679 original size:78 final size:77
Alignment explanation
Indices: 17478--17696 Score: 287
Period size: 78 Copynumber: 2.8 Consensus size: 77
17468 TATTCGGATG
* *
17478 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCTCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ATTATA-TCC-GGCTAAGTC-CGAAGGC
*
17542 ATTTGTGTGAGTTACT
62 ATTTGTGCGAGTTACT
* * *
17558 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCGAAGGCATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TATTATATCCGGCTAAGTCCGAAGGCATT
17623 TGTGCGAGTTACT
65 TGTGCGAGTTACT
* * *
17636 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATATTCGGCTAAATCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-TTATATCCGGCTAAGT-CCGAAG
17697 ATGCTTGGGT
Statistics
Matches: 126, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
77 2 0.02
78 67 0.53
79 15 0.12
80 40 0.32
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (77 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTATTATATCCGGCTAAGTCCGAAGGCATTT
GTGCGAGTTACT
Found at i:17964 original size:22 final size:21
Alignment explanation
Indices: 17923--17965 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
17913 GAATGTGCAT
17923 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
17945 ATATGAATGTTATACC-TTAGC
1 ATATGAA-GTTAT-CCATTAGC
17966 GAAACTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 12 0.63
23 5 0.26
24 2 0.11
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:19923 original size:30 final size:29
Alignment explanation
Indices: 19889--19948 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
19879 TCCTTAACTC
*
19889 AAACTTTAGCAAAATTACAATTTTGCCCCT
1 AAACTTTAGCAAAATTAC-ACTTTGCCCCT
* * *
19919 AAACTTTTGCATATTTACACTTTGCCCCT
1 AAACTTTAGCAAAATTACACTTTGCCCCT
19948 A
1 A
19949 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (29 bp):
AAACTTTAGCAAAATTACACTTTGCCCCT
Found at i:25300 original size:45 final size:44
Alignment explanation
Indices: 25237--25339 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 44
25227 AAGACATGGA
*
25237 ACATGCATTGGCCTCGAGACGTAAGTCAGTGTAAGA-CA-GTCTGGG
1 ACATGCATCGG-CTCGAGACGT--GTCAGTGTAAGACCATGTCTGGG
*
25282 ACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCTGGG
1 ACATGCATCGGCT-CGAGACGTGTCAGTGTAAGACCATGTCTGGG
25327 ACATGGCATCGGC
1 ACAT-GCATCGGC
25340 ACAGATATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
43 12 0.23
44 4 0.08
45 28 0.54
46 8 0.15
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.22
Consensus pattern (44 bp):
ACATGCATCGGCTCGAGACGTGTCAGTGTAAGACCATGTCTGGG
Done.