Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1101
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: 35611
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:3194 original size:101 final size:101
Alignment explanation
Indices: 3062--3243 Score: 265
Period size: 101 Copynumber: 1.8 Consensus size: 101
3052 CAGTTTTAGG
* * * * *
3062 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATTGATAGGTCGCATGTGTAGTAC
1 TCACGTATGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGATAAGTCACATGTGTAGTAC
3127 TAAGTGCAAGCTACTATGCATACCCGTTAACTTCGA
66 TAAGTGCAAGCTACTATGCATACCCGTTAACTTCGA
* ** *
3163 TCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGATAAGTCACGTGTGTAGTAC
1 TCACGTATGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGATAAGTCACATGTGTAGTAC
* *
3228 TAAGTGTAGGCTACTA
66 TAAGTGCAAGCTACTA
3244 CGTGTACCAG
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 70 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACGTATGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGATAAGTCACATGTGTAGTAC
TAAGTGCAAGCTACTATGCATACCCGTTAACTTCGA
Found at i:3301 original size:50 final size:50
Alignment explanation
Indices: 3058--3304 Score: 253
Period size: 50 Copynumber: 4.9 Consensus size: 50
3048 AAGACAGTTT
* *
3058 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATTGA
1 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA
* * * * ** * *
3108 TAGGTCGCATGTGTAGTACTAAGTGCAAGCTACTATGCATACCCG-TTAA
1 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA
* * * ** *
3157 CTTCGATCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGA
1 --TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA
* *
3209 TAAGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTGA
1 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA
* * * * * *
3259 TAGGTCGCATGTGTTGTACTAAGTGCAAGCTACTATGCGTACCAGA
1 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
3305 GAGCTTCGGT
Statistics
Matches: 155, Mismatches: 39, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
49 3 0.02
50 117 0.75
51 33 0.21
52 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA
Found at i:4119 original size:180 final size:180
Alignment explanation
Indices: 3861--4219 Score: 494
Period size: 180 Copynumber: 2.0 Consensus size: 180
3851 ATCCGAGATC
3861 TGTACCATGAGATAAATAATTTTTAGTGAAGAAAGATCAAAACTATGAGACAGTGAAATAGGGAT
1 TGTACCATGAGATAAATAATTTTTAGTGAAGAAAGATCAAAACTATGAGACAGTGAAATAGGGAT
* *
3926 ATTTATTATGAATAAACTGTACTAATTTACTAAACAAAAAATTCTTAAAATTTTATGGTAAGAAT
66 ATTTA-TATGAATAAACTGTACTAATTGACTAAACAAAAAATTCTAAAAATTTTATGGTAAGAAT
*
3991 ATATGTGAGTCTAGTTTCTT-GG-AAAATTAGC-AATTCTTAATTTGGAGTCG
130 ATATGTGAGTCTAGTTT-TTGGGAAAAATTAACGAA-TCTTAATTTGGAGTCG
* * * * * * * *
4041 TGTACCATGCGTTAAATAATTTTTAGTGAATAGAGGTCAGAACTGTTG-GATAGTGAAATAGAGT
1 TGTACCATGAGATAAATAATTTTTAGTGAAGAAAGATCAAAACT-ATGAGACAGTGAAATAG-G-
* * *
4105 GATATTTA-ATGAATAAACTTTACTAATTGGCTAAACCAAAAATTCTAAAAATTTTATGGTAAGA
63 GATATTTATATGAATAAACTGTACTAATTGACTAAACAAAAAATTCTAAAAATTTTATGGTAAGA
*
4169 ATATATGTGAGTCTAGTTTTTGGGAAAAATTAACGGATCTTAATTTGGAGT
128 ATATATGTGAGTCTAGTTTTTGGGAAAAATTAACGAATCTTAATTTGGAGT
4220 TCCGTAGCTC
Statistics
Matches: 158, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
179 2 0.01
180 122 0.77
181 25 0.16
182 9 0.06
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (180 bp):
TGTACCATGAGATAAATAATTTTTAGTGAAGAAAGATCAAAACTATGAGACAGTGAAATAGGGAT
ATTTATATGAATAAACTGTACTAATTGACTAAACAAAAAATTCTAAAAATTTTATGGTAAGAATA
TATGTGAGTCTAGTTTTTGGGAAAAATTAACGAATCTTAATTTGGAGTCG
Found at i:6764 original size:42 final size:42
Alignment explanation
Indices: 6711--6874 Score: 184
Period size: 42 Copynumber: 3.9 Consensus size: 42
6701 AGGGTTATTA
* * *
6711 AGACTATGTGTAAGACCATATCCAGGATATGGCATTAATATG
1 AGACTACGTGTAAGACCATATCTAGGATATGGCATTGATATG
* *
6753 AGACTACGTGTAAGACCATATCTGGGATATGGCATCGATATG
1 AGACTACGTGTAAGACCATATCTAGGATATGGCATTGATATG
* * * * * * *
6795 AGACTTCGTGTAAGACTATAGCTGGGCTATTGGCTTTGATACG
1 AGACTACGTGTAAGACCATATCTAGGATA-TGGCATTGATATG
* * *
6838 AGATTACATGTAATACCATATCTAGGATATGGCATTG
1 AGACTACGTGTAAGACCATATCTAGGATATGGCATTG
6875 GTACGGTACC
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 69 0.69
43 31 0.31
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (42 bp):
AGACTACGTGTAAGACCATATCTAGGATATGGCATTGATATG
Found at i:17867 original size:21 final size:20
Alignment explanation
Indices: 17843--17891 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
17833 TTCCTAGCAC
*
17843 ATTTATTCAAAAAATTTTATA
1 ATTT-TTCAAAAAATTTTACA
**
17864 ATTTTTCATCAAATTTTACA
1 ATTTTTCAAAAAATTTTACA
17884 ATTTTTCA
1 ATTTTTCA
17892 TTTTAGTCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTTCAAAAAATTTTACA
Found at i:17877 original size:20 final size:20
Alignment explanation
Indices: 17854--17892 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17844 TTTATTCAAA
*
17854 AAATTTTATAATTTTTCATC
1 AAATTTTACAATTTTTCATC
17874 AAATTTTACAATTTTTCAT
1 AAATTTTACAATTTTTCAT
17893 TTTAGTCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTTACAATTTTTCATC
Found at i:19629 original size:41 final size:41
Alignment explanation
Indices: 19502--19687 Score: 243
Period size: 41 Copynumber: 4.6 Consensus size: 41
19492 CTCGCACAAG
* * * * * * *
19502 GCCTTCGGGTCTTAACCCAGATATGGTCAC-TAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
*
19542 GCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
* *
19582 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGCTTAGCACAAAA
19623 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
*
19664 GCCTTCGGGACTTAGCCCAGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
19688 CATTCGAGTA
Statistics
Matches: 131, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 3 0.02
40 58 0.44
41 67 0.51
42 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
Found at i:27471 original size:39 final size:40
Alignment explanation
Indices: 27426--27633 Score: 116
Period size: 40 Copynumber: 5.2 Consensus size: 40
27416 CGGGGTTTAG
* * *
27426 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
27465 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
27505 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
27545 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
** * * * *
27586 CCGGATATAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
27627 CC-GATAT
1 CCGGATAT
27634 CATTCGAGTA
Statistics
Matches: 149, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 18 0.12
40 66 0.44
41 62 0.42
42 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:27576 original size:41 final size:41
Alignment explanation
Indices: 27449--27633 Score: 252
Period size: 40 Copynumber: 4.6 Consensus size: 41
27439 CTCGCACAAG
* * * * * *
27449 GCCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
*
27489 GCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
* *
27529 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGCTTAGCACAAAA
27570 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
27611 GCCTTCGGGACTTAGCCC-GATAT
1 GCCTTCGGGACTTAGCCCGGATAT
27634 CATTCGAGTA
Statistics
Matches: 132, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 64 0.48
41 62 0.47
42 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
Found at i:31465 original size:56 final size:56
Alignment explanation
Indices: 31379--31498 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
31369 ACAAGGGATG
31379 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
31435 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
31491 ATGGGCAA
1 ATGGGCAA
31499 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:32714 original size:39 final size:40
Alignment explanation
Indices: 32619--32840 Score: 274
Period size: 40 Copynumber: 5.6 Consensus size: 40
32609 TCGAATGATG
* * * *
32619 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
32659 T-CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
32698 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
32737 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
32777 TCCGGGTTACGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
32818 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
32841 GAACGAGTAG
Statistics
Matches: 160, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
39 56 0.35
40 102 0.64
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:32831 original size:80 final size:79
Alignment explanation
Indices: 32619--32840 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 79
32609 TCGAATGATG
* * * * * *
32619 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT-CGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
*
32681 TTGTGCGAGATACTAAT
63 TTGTGCGAGATACTAAA
*
32698 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
*
32763 TGCGAGTTACTAAA
66 TGCGAGATACTAAA
* * * *
32777 TCCGGGTTACGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
32841 GAACGAGTAG
Statistics
Matches: 124, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
78 18 0.15
79 58 0.47
80 46 0.37
81 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Done.