Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold707
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: 34792
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Found at i:68 original size:28 final size:29
Alignment explanation
Indices: 9--70 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1 CTAAGAAT
*
9 AAAATTATAAAAATATTAATAATTATTTA
1 AAAATTATAAAAATATTAATAATTATTCA
38 AAAATT-TAAAAA-ATTAAATAATT-TTACA
1 AAAATTATAAAAATATT-AATAATTATT-CA
66 AAAAT
1 AAAAT
71 AATTTCGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.17
28 19 0.63
29 6 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATTATAAAAATATTAATAATTATTCA
Found at i:9447 original size:30 final size:30
Alignment explanation
Indices: 9411--9471 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
9401 GATATACTCT
9411 TAGATGATGCAGTAGTATCAGAAAAAAAGG
1 TAGATGATGCAGTAGTATCAGAAAAAAAGG
* * *
9441 TAGATGATGCTGTGGTATCAGGAAAAAAGG
1 TAGATGATGCAGTAGTATCAGAAAAAAAGG
9471 T
1 T
9472 GGAAGAGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.23
Consensus pattern (30 bp):
TAGATGATGCAGTAGTATCAGAAAAAAAGG
Found at i:17740 original size:2 final size:2
Alignment explanation
Indices: 17733--17769 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
17723 TTATTTTATA
*
17733 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
17770 TTTCATGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:18021 original size:9 final size:10
Alignment explanation
Indices: 18003--18033 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
17993 TGTATTGTCC
18003 TTTTCTTTTT
1 TTTTCTTTTT
18013 TTTTCTTTTT
1 TTTTCTTTTT
*
18023 TTTTCCTTTT
1 TTTTCTTTTT
18033 T
1 T
18034 AAGGTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:19993 original size:78 final size:78
Alignment explanation
Indices: 19864--20013 Score: 246
Period size: 78 Copynumber: 1.9 Consensus size: 78
19854 GAGTCACATC
* *
19864 TCATGTAACTGTAGTGAATCAGGATTACATTTTCAAGTCAAATCCTATCCACCTTAGGTTACCAT
1 TCATGTAACTGTAGCGAATCAGGATTACATTTTCAAGTCAAATCCTATCCACCTTAAGTTACCAT
19929 AATGAATCATATA
66 AATGAATCATATA
* * *
19942 TCATGTAACTGTAGCGAATTAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCAT
1 TCATGTAACTGTAGCGAATCAGGATTACATTTTCAAGTCAAATCCTATCCACCTTAAGTTACCAT
*
20007 AGTGAAT
66 AATGAAT
20014 TAGGAATAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (78 bp):
TCATGTAACTGTAGCGAATCAGGATTACATTTTCAAGTCAAATCCTATCCACCTTAAGTTACCAT
AATGAATCATATA
Found at i:20044 original size:40 final size:40
Alignment explanation
Indices: 19980--20117 Score: 168
Period size: 40 Copynumber: 3.5 Consensus size: 40
19970 CTTTTCAGGT
* * *
19980 CAAATCCTATCCACCTTAAGTTACCATAGTGAATTAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* * *
20020 TAAATCTTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* ** **
20060 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
*
20100 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
20118 TATTCTCGAG
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
Found at i:24578 original size:52 final size:49
Alignment explanation
Indices: 24493--24859 Score: 440
Period size: 46 Copynumber: 7.6 Consensus size: 49
24483 TTTGAGTACT
* **
24493 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
24539 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
24591 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
24637 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
24683 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
24735 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
24787 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
24833 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
24860 GCTACACTTA
Statistics
Matches: 292, Mismatches: 15, Indels: 28
0.87 0.04 0.08
Matches are distributed among these distances:
46 155 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:24613 original size:98 final size:97
Alignment explanation
Indices: 24493--24859 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
24483 TTTGAGTACT
* *
24493 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
24558 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
24591 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
24651 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
24683 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
24748 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
24787 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
24852 GATAAGTG
65 GA-AAGTG
24860 GCTACACTTA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 145 0.60
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:24841 original size:196 final size:196
Alignment explanation
Indices: 24507--24859 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
24497 ATCAAGTGAT
* * *
24507 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
24572 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
24637 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
24702 G
196 G
* *
24703 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
24768 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
24833 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
24860 GCTACACTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:24867 original size:37 final size:37
Alignment explanation
Indices: 24823--25004 Score: 298
Period size: 37 Copynumber: 5.0 Consensus size: 37
24813 GATAGCTTTA
*
24823 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
24860 GCTACACTTATCTGATCAAGAAACAAAGTG-TAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
24896 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
24933 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
24970 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
25005 ATCATACGTA
Statistics
Matches: 137, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
35 11 0.08
36 40 0.29
37 86 0.63
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:24942 original size:73 final size:74
Alignment explanation
Indices: 24823--25004 Score: 307
Period size: 73 Copynumber: 2.5 Consensus size: 74
24813 GATAGCTTTA
24823 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAAG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAAG
24888 TG-TAAGTG
66 TGATAAGTG
* *
24896 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATGTGATCAAGAAACAAAG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAAG
*
24961 TGATAGGTG
66 TGATAAGTG
*
24970 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
25005 ATCATACGTA
Statistics
Matches: 103, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
72 12 0.12
73 69 0.67
74 22 0.21
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (74 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAAG
TGATAAGTG
Found at i:26320 original size:49 final size:49
Alignment explanation
Indices: 26259--26451 Score: 323
Period size: 49 Copynumber: 3.9 Consensus size: 49
26249 ATGTGAACAT
26259 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
26309 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
26358 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
26407 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
26452 AGAAAACGAA
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 133 0.97
50 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:28612 original size:21 final size:21
Alignment explanation
Indices: 28588--28627 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28578 TAGATATGTG
* *
28588 ATGACGTTATCTTTAAAATGC
1 ATGAAGTTATCTTGAAAATGC
*
28609 ATGAATTTATCTTGAAAAT
1 ATGAAGTTATCTTGAAAAT
28628 ATGTTGAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
ATGAAGTTATCTTGAAAATGC
Done.