Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5103.1
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: 33312
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:131 original size:66 final size:66
Alignment explanation
Indices: 25--157 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
15 TTCTAGACAA
25 TAAGTATCACATTCAAACATTTTGGTGACTCGGTTTAGCGGTCCCAAAACCACTTCCCGACTAGG
1 TAAGTATCACATTCAAACATTTTGGTGACTCGGTTTAGCGGTCCCAAAACCACTTCCCGACTAGG
90 G
66 G
*
91 TAAGTATCACATTCAAACATTTTGGTGACTCGGTTTAGCGGTCCCGAAACCACTTCCCGACTAGG
1 TAAGTATCACATTCAAACATTTTGGTGACTCGGTTTAGCGGTCCCAAAACCACTTCCCGACTAGG
156 G
66 G
157 T
1 T
158 CAACTTTGGG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (66 bp):
TAAGTATCACATTCAAACATTTTGGTGACTCGGTTTAGCGGTCCCAAAACCACTTCCCGACTAGG
G
Found at i:6802 original size:55 final size:53
Alignment explanation
Indices: 6660--6867 Score: 213
Period size: 55 Copynumber: 3.8 Consensus size: 53
6650 ATCCTTTTGA
* * *
6660 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * * *
6713 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATGG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G
* **
6767 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-G
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * * * *
6820 AAACCTCACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -AA-CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGGATCCTT
6868 AAACCCTAAT
Statistics
Matches: 128, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
52 2 0.02
53 45 0.35
54 7 0.05
55 72 0.56
56 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (53 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:6804 original size:108 final size:110
Alignment explanation
Indices: 6660--6860 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
6650 ATCCTTTTGA
* *
6660 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
6723 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATGGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATGGT
* *
6768 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
6833 TTCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
6861 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 8 0.09
110 27 0.32
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATGGT
Found at i:17084 original size:40 final size:40
Alignment explanation
Indices: 17034--18056 Score: 1836
Period size: 40 Copynumber: 25.6 Consensus size: 40
17024 TTGAATGCTG
* * * * * *
17034 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
** * * * *
17074 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
17114 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
17154 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17194 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17234 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17274 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17314 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17354 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17394 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17434 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17474 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17514 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17554 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17594 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17634 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17674 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17714 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17754 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17794 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17834 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17874 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17914 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
17954 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17994 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
18033 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
18057 TGAACGAGGA
Statistics
Matches: 960, Mismatches: 20, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
39 36 0.04
40 916 0.95
41 8 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:19838 original size:16 final size:15
Alignment explanation
Indices: 19812--19852 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
19802 GTGTTTGCTC
19812 TTTTTTCTTTTCTGG
1 TTTTTTCTTTTCTGG
19827 TTTTTTCATTTTCT-G
1 TTTTTTC-TTTTCTGG
*
19842 TTTATTCTTTT
1 TTTTTTCTTTT
19853 TATTATTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTTTTCTTTTCTGG
Found at i:21350 original size:7 final size:7
Alignment explanation
Indices: 21338--21372 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
21328 TCTAAAAAAA
21338 TTTCAAT
1 TTTCAAT
21345 TTTCAAT
1 TTTCAAT
21352 TTTCAAT
1 TTTCAAT
21359 TTTCAAT
1 TTTCAAT
21366 TTTCAAT
1 TTTCAAT
21373 GTTTTAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTCAAT
Found at i:27348 original size:143 final size:142
Alignment explanation
Indices: 27149--27860 Score: 621
Period size: 143 Copynumber: 4.9 Consensus size: 142
27139 CTAGCGAAAC
* * *
27149 AGACTAAAGACGGCA-AATCTTATTTCCCTAGCGTTGCAGTGGAATAGATTAAAGCTACAAATTA
1 AGACTAAAGACAG-AGAATCTTATTTCCCT-GCATTGCAGTGGAACAGATTAAAGCTACAAATTA
* *
27213 TGGCGAATCTTATCTTTCTTAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTACCTAA
64 TGGCGAATCTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTAA
27278 AGTTGCAGCGGAGT
129 AGTTGCAGCGGAGT
* *
27292 AGACTAAAGACAGCGAATCTTATTTCCCTGCCATTGTAGTGGAACAGATTAAAGCTACAAATTAT
1 AGACTAAAGACAGAGAATCTTATTTCCCTG-CATTGCAGTGGAACAGATTAAAGCTACAAATTAT
* * * * * *
27357 GGCTAATCTTATC-TTCTTGAAGTTGCAATGGAGCAGATTGAAGCCACTAGCCTTATCTCCTTGA
65 GGCGAATCTTATCTTTC-TGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTAA
* * *
27421 AGTTGCCGCGAAGC
129 AGTTGCAGCGGAGT
* * * * **
27435 AGATTGAAGACAGTGAATCTTATTTCCCTAGCATTGTAGCAGAACAGATTAAAGCTACAAATTGA
1 AGACTAAAGACAGAGAATCTTATTTCCCT-GCATTGCAGTGGAACAGATTAAAGCTACAAATT-A
* * * ** * * **** * *
27500 -AGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACTGTGAATCTTATTTCC
64 TGGCGA--A-TCTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAG-CCACCAACCTTATCTCC
*** * *
27564 CTGGCGTTACAGTGGAACTGATT
125 CTAAAGTTGCAGCGG-A--G--T
* * * * * * *
27587 AATGCAAC-AAATTATA-ATAGATCTTATCTT-CCTGAAGTTGCAGTGAAACTGATTAAAGCAAC
1 -A-G--ACTAAA-GACAGAGA-ATCTTAT-TTCCCTGCA-TTGCAGTGGAACAGATTAAAGCTAC
* * *
27649 AAATTATGAC-AGATCTTATCTTTCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATC
58 AAATTATGGCGA-ATCTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATC
* *
27713 TCCCTAAAGTTGTAGCAGAGT
122 TCCCTAAAGTTGCAGCGGAGT
*
27734 AGACTGAAGACAGAGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTACAAATTAT
1 AGACTAAAGACAGAGAATCTTATTTCCCT-GCATTGCAGTGGAACAGATTAAAGCTACAAATTAT
* * * *
27799 GGCGGATCTTATCCTTCTGAAGTCGCAGTGAAGCAGATTGAAGCCACCAATCC-TATCTCCCT
65 GGCGAATCTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAA-CCTTATCTCCCT
27861 GATATTTTAG
Statistics
Matches: 444, Mismatches: 95, Indels: 60
0.74 0.16 0.10
Matches are distributed among these distances:
142 6 0.01
143 273 0.61
144 10 0.02
145 2 0.00
146 30 0.07
147 20 0.05
148 1 0.00
149 1 0.00
150 1 0.00
151 1 0.00
152 18 0.04
153 32 0.07
154 2 0.00
155 7 0.02
156 38 0.09
157 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (142 bp):
AGACTAAAGACAGAGAATCTTATTTCCCTGCATTGCAGTGGAACAGATTAAAGCTACAAATTATG
GCGAATCTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTAAAG
TTGCAGCGGAGT
Found at i:27587 original size:102 final size:102
Alignment explanation
Indices: 27393--27599 Score: 279
Period size: 102 Copynumber: 2.0 Consensus size: 102
27383 AATGGAGCAG
* * * *
27393 ATTGAAGCCACTAGCCTTATCTCCTTGAAGTTGCCGCGAAGCAGATTGAAGACAGTGAATCTTAT
1 ATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGAAGCAGACTGAAGACAGTGAATCTTAT
** *
27458 TTCCCTAGCATTGTAGCAGAACAGATTAAAGCTACAA
66 TTCCCTAGCATTACAGCAGAACAGATTAAAGCAACAA
* *
27495 ATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACTGTGAATCTTAT
1 ATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGAAGCAGACTGAAGACAGTGAATCTTAT
* * ** * *
27560 TTCCCTGGCGTTACAGTGGAACTGATTAATGCAACAA
66 TTCCCTAGCATTACAGCAGAACAGATTAAAGCAACAA
27597 ATT
1 ATT
27600 ATAATAGATC
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (102 bp):
ATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGAAGCAGACTGAAGACAGTGAATCTTAT
TTCCCTAGCATTACAGCAGAACAGATTAAAGCAACAA
Found at i:27637 original size:54 final size:54
Alignment explanation
Indices: 27573--27685 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
27563 CCTGGCGTTA
* * * *
27573 CAGTGGAACTGATTAATGCAACAAATTATAATAGATCTTATCTTCCTGAAGTTG
1 CAGTGAAACTGATTAAAGCAACAAATTATAACAGATCTTATCTTCCTAAAGTTG
* *
27627 CAGTGAAACTGATTAAAGCAACAAATTATGACAGATCTTATCTTTCTAAAGTTG
1 CAGTGAAACTGATTAAAGCAACAAATTATAACAGATCTTATCTTCCTAAAGTTG
27681 CAGTG
1 CAGTG
27686 GAGCAGATTG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (54 bp):
CAGTGAAACTGATTAAAGCAACAAATTATAACAGATCTTATCTTCCTAAAGTTG
Found at i:28655 original size:16 final size:15
Alignment explanation
Indices: 28629--28669 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
28619 GTGTTTGCTC
28629 TTTTTTCTTTTCTGG
1 TTTTTTCTTTTCTGG
28644 TTTTTTCATTTTCT-G
1 TTTTTTC-TTTTCTGG
*
28659 TTTATTCTTTT
1 TTTTTTCTTTT
28670 TATTATTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTTTTCTTTTCTGG
Done.