Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold552
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: 80969
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.28
Warning! 14688 characters in sequence are not A, C, G, or T
Found at i:16726 original size:23 final size:23
Alignment explanation
Indices: 16691--16802 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
16681 CGGTTTTGGG
* *
16691 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
16714 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
16737 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACGAAATGGTAATGCGA
* *
16760 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
*
16783 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
16803 GTTCAAAAAG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:16753 original size:46 final size:46
Alignment explanation
Indices: 16691--16802 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
16681 CGGTTTTGGG
*
16691 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * *
16737 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
16783 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
16803 GTTCAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:28321 original size:28 final size:30
Alignment explanation
Indices: 28289--28344 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
28279 TTAGGACTTA
28289 TCTTTT-AATT-T-CTTGCTGTCAATTTTTT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTTT
28317 TCTTTTAAATTCTGCTTGTGTCAATTTT
1 TCTTTTAAATTCTGCTTGTGTCAATTTT
28345 ATTTAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.24
29 4 0.16
30 11 0.44
31 4 0.16
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (30 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTTT
Found at i:29214 original size:14 final size:13
Alignment explanation
Indices: 29193--29267 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 13
29183 AAAACAAGTG
29193 AGGAAAAAGAAAA
1 AGGAAAAAGAAAA
29206 AGGAGAAAAGAAAA
1 AGGA-AAAAGAAAA
* *
29220 A-TAAAAGTGAAAA
1 AGGAAAA-AGAAAA
*
29233 AGAAGAAAATGAAAA
1 AG--GAAAAAGAAAA
* *
29248 TGAAAAAAGCAAAA
1 AGGAAAAAG-AAAA
29262 AGGAAA
1 AGGAAA
29268 GCGAGAGAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
12 3 0.06
13 16 0.33
14 18 0.38
15 7 0.15
16 4 0.08
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.05
Consensus pattern (13 bp):
AGGAAAAAGAAAA
Found at i:29248 original size:27 final size:28
Alignment explanation
Indices: 29201--29253 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
29191 TGAGGAAAAA
*
29201 GAAAAAGGAGAAAAGAAAAAT-AAAAGT
1 GAAAAAGAAGAAAAGAAAAATGAAAAGT
29228 GAAAAAGAAGAAAATG-AAAATGAAAA
1 GAAAAAGAAGAAAA-GAAAAATGAAAA
29254 AAGCAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (28 bp):
GAAAAAGAAGAAAAGAAAAATGAAAAGT
Found at i:29262 original size:21 final size:20
Alignment explanation
Indices: 29211--29254 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
29201 GAAAAAGGAG
29211 AAAAGAAAAAT-AAAAGTGA
1 AAAAGAAAAATGAAAAGTGA
29230 AAAAGAAGAAAATGAAAA-TGA
1 AAAAG-A-AAAATGAAAAGTGA
29251 AAAA
1 AAAA
29255 AGCAAAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
20 1 0.05
21 12 0.55
22 4 0.18
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (20 bp):
AAAAGAAAAATGAAAAGTGA
Found at i:33315 original size:19 final size:20
Alignment explanation
Indices: 33291--33328 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
33281 TGAGCTGATT
33291 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
33310 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
33329 AGTCAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:35571 original size:13 final size:13
Alignment explanation
Indices: 35553--35577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35543 TGTGTGGCAT
35553 TTTGATACCAAAA
1 TTTGATACCAAAA
35566 TTTGATACCAAA
1 TTTGATACCAAA
35578 TGATAGAGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGATACCAAAA
Found at i:38560 original size:17 final size:18
Alignment explanation
Indices: 38526--38558 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38516 TCCTGATTTA
38526 GCTAAGTCCAAGTCAAAT
1 GCTAAGTCCAAGTCAAAT
38544 GCTAA-TCCAAG-CAAA
1 GCTAAGTCCAAGTCAAA
38559 ATATGAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (18 bp):
GCTAAGTCCAAGTCAAAT
Found at i:47772 original size:10 final size:10
Alignment explanation
Indices: 47725--47773 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
47715 GAACGAGATC
47725 ATTGAGCTAG
1 ATTGAGCTAG
*
47735 AATTGAGCTAA
1 -ATTGAGCTAG
*
47746 ATTGAGCTCG
1 ATTGAGCTAG
47756 ATTGAGCTAG
1 ATTGAGCTAG
*
47766 ATCGAGCT
1 ATTGAGCT
47774 TGAAAGGATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (10 bp):
ATTGAGCTAG
Found at i:51849 original size:170 final size:170
Alignment explanation
Indices: 51567--51899 Score: 594
Period size: 170 Copynumber: 2.0 Consensus size: 170
51557 TACAACTCGG
* *
51567 TGACCTCAAAATTGGCCTAAGCTTGAGGGCCCCAAGTGCAAAATGAAGCTTAATTTCATCTCAAT
1 TGACCTCAAAATTGGCCTAAGCTCGAGGGCCCCAAGTGCAAAATGAAGCTTAATTTCAGCTCAAT
*
51632 GAGCTCAATTCTAGCTCCTTAAAGCTCGTCTAGTTCAACCCAAGCTCATTTAGCTTAATTTCAAC
66 GAGCTCAATTCTAGCTCCTTAAAGCTCGTCTAGTTCAACCCAAGCTCATTTAGCTTAACTTCAAC
51697 CCATTTTTAATTTGCTGGAATAAATATTTAGTTGTTGGAA
131 CCATTTTTAATTTGCTGGAATAAATATTTAGTTGTTGGAA
*
51737 TGACCTCAAAATTGGCCTAAGCTCGAGGGCCCCAAGTGTAAAATGAAGCTTAATTTCAGCTCAAT
1 TGACCTCAAAATTGGCCTAAGCTCGAGGGCCCCAAGTGCAAAATGAAGCTTAATTTCAGCTCAAT
* *
51802 GAGCTCAATTCTAGCTTCTTCAAGCTCGTCTAGTTCAACCCAAGCTCATTTAGCTTAACTTCAAC
66 GAGCTCAATTCTAGCTCCTTAAAGCTCGTCTAGTTCAACCCAAGCTCATTTAGCTTAACTTCAAC
* *
51867 CCATTTTTAATTTGTTGGAATAAGTATTTAGTT
131 CCATTTTTAATTTGCTGGAATAAATATTTAGTT
51900 ACTGGAATAA
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
170 155 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (170 bp):
TGACCTCAAAATTGGCCTAAGCTCGAGGGCCCCAAGTGCAAAATGAAGCTTAATTTCAGCTCAAT
GAGCTCAATTCTAGCTCCTTAAAGCTCGTCTAGTTCAACCCAAGCTCATTTAGCTTAACTTCAAC
CCATTTTTAATTTGCTGGAATAAATATTTAGTTGTTGGAA
Found at i:51939 original size:19 final size:19
Alignment explanation
Indices: 51915--52027 Score: 108
Period size: 19 Copynumber: 6.1 Consensus size: 19
51905 AATAAATTAC
*
51915 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
51934 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
51953 TGCATCTTAGTTAAATAAGT
1 T-CATCTTAGTTAATTAAGT
** * * *
51973 TGC-T-GGAATAAATT-A-C
1 T-CATCTTAGTTAATTAAGT
51989 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
52008 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
52027 T
1 T
52028 GCTTAAATCA
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
15 1 0.01
16 2 0.03
17 7 0.09
18 6 0.08
19 39 0.52
20 20 0.27
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:60811 original size:20 final size:19
Alignment explanation
Indices: 60782--60819 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
60772 AGCTAATAAC
60782 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
60801 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
60820 CAAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:66502 original size:20 final size:20
Alignment explanation
Indices: 66477--66521 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
66467 TAAGTTCACA
66477 TAATTAAAAC-AAGACAC-AAT
1 TAATT-AAACTAAGAC-CTAAT
66497 TAATTAAACTAAGACCTAAT
1 TAATTAAACTAAGACCTAAT
66517 TAATT
1 TAATT
66522 CGGTTTGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
TAATTAAACTAAGACCTAAT
Found at i:72703 original size:10 final size:10
Alignment explanation
Indices: 72672--72742 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
72662 AGCTAATAAC
72672 GAGCTC-AAT
1 GAGCTCGAAT
*
72681 GAG-TTGAATT
1 GAGCTCGAA-T
72691 GAGCTCGAAT
1 GAGCTCGAAT
*
72701 GAGCT-GACTT
1 GAGCTCGA-AT
72711 GAGCTCGAAT
1 GAGCTCGAAT
72721 GAGCT--AATTT
1 GAGCTCGAA--T
72731 GAGCTCGAAT
1 GAGCTCGAAT
72741 GA
1 GA
72743 ACTAACAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
8 3 0.06
9 7 0.14
10 31 0.63
11 6 0.12
12 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (10 bp):
GAGCTCGAAT
Found at i:72703 original size:20 final size:20
Alignment explanation
Indices: 72672--72742 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
72662 AGCTAATAAC
*
72672 GAGCTC-AATGAGTTGAATT
1 GAGCTCGAATGAGCTGAATT
*
72691 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
72711 GAGCTCGAATGAGCT-AATTT
1 GAGCTCGAATGAGCTGAA-TT
72731 GAGCTCGAATGA
1 GAGCTCGAATGA
72743 ACTAACAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.15
20 40 0.85
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Done.