Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold710
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: 25100
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:536 original size:16 final size:15
Alignment explanation
Indices: 510--545 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
500 AACAGTATTT
*
510 TAAAAAAATAATAAA
1 TAAAAAAATAAAAAA
525 TAAAATAAATAAAAAA
1 TAAAA-AAATAAAAAA
541 TAAAA
1 TAAAA
546 CAATGGAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:1364 original size:22 final size:23
Alignment explanation
Indices: 1315--1364 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1305 AAAATTATAT
*
1315 ATATTAAAATTTAAATATTAAAT
1 ATATTAAAATTTAAATATTAAAA
* **
1338 TTATTAAAA-TTATTTATTAAAA
1 ATATTAAAATTTAAATATTAAAA
1360 ATATT
1 ATATT
1365 TATATAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTAAAATTTAAATATTAAAA
Found at i:1372 original size:14 final size:13
Alignment explanation
Indices: 1336--1372 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1326 TAAATATTAA
*
1336 ATTTATTAAAATT
1 ATTTATTAAAAAT
1349 ATTTATTAAAAAT
1 ATTTATTAAAAAT
1362 ATTTATATAAA
1 ATTTAT-TAAA
1373 TTAATAGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTATTAAAAAT
Found at i:1579 original size:2 final size:2
Alignment explanation
Indices: 1572--1605 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1562 ACATGAAGTG
1572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1606 TATGTTTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2150 original size:2 final size:2
Alignment explanation
Indices: 2143--2186 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
2133 AAGCTTTCTT
* *
2143 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA GA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2183 TA TA
1 TA TA
2187 AAGAAAGCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3533 original size:24 final size:26
Alignment explanation
Indices: 3478--3534 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
3468 TTATTTACTT
* *
3478 TTATTTTATTTTTATATAAATATTTA
1 TTATTTTATATTTATATAAATATCTA
**
3504 AAATTTTA-ATTT-TATAAATATCTA
1 TTATTTTATATTTATATAAATATCTA
3528 TTATTTT
1 TTATTTT
3535 TACCATATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 16 0.64
25 3 0.12
26 6 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTATATTTATATAAATATCTA
Found at i:3985 original size:22 final size:23
Alignment explanation
Indices: 3960--4026 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 23
3950 AATTTGAATC
*
3960 ATTTTAA-ATTTAAATTAATTAA
1 ATTTTAATATTTAAATTAATAAA
3982 A-TTTAATATTTAAATTAATAAA
1 ATTTTAATATTTAAATTAATAAA
* *
4004 ATTTGAATTAATTAAATATAATA
1 ATTTTAA-TATTTAAAT-TAATA
4027 TTTAGATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 5 0.13
22 16 0.42
23 4 0.11
24 8 0.21
25 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTTTAATATTTAAATTAATAAA
Found at i:4006 original size:37 final size:37
Alignment explanation
Indices: 3964--4046 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 37
3954 TGAATCATTT
*
3964 TAAATTTAAATTAATTAAATTTAATATTTA-AATTAA
1 TAAATTTAAATTAATTAAATATAATATTTAGAATTAA
* *
4000 TAAAATTTGAATTAATTAAATATAATATTTAGATTTAA
1 T-AAATTTAAATTAATTAAATATAATATTTAGAATTAA
4038 TAAATTTAA
1 TAAATTTAA
4047 TTATTTTGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 1 0.02
37 34 0.83
38 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (37 bp):
TAAATTTAAATTAATTAAATATAATATTTAGAATTAA
Found at i:4029 original size:22 final size:22
Alignment explanation
Indices: 3999--4052 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
3989 ATTTAAATTA
*
3999 ATAAAATTT-GAATTAATTAAAT
1 ATAATATTTAGAATTAA-TAAAT
*
4021 ATAATATTTAGATTTAATAAAT
1 ATAATATTTAGAATTAATAAAT
*
4043 TTAATTATTT
1 ATAA-TATTT
4053 TGAGTTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
ATAATATTTAGAATTAATAAAT
Found at i:5193 original size:23 final size:24
Alignment explanation
Indices: 5167--5217 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
5157 AAAATAAAAA
5167 ATTATAA-ATTATAAATATTAAAT
1 ATTATAATATTATAAATATTAAAT
* **
5190 ATTA-AATTTTATATTTATTAAAT
1 ATTATAATATTATAAATATTAAAT
5213 ATTAT
1 ATTAT
5218 TTCTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTATAATATTATAAATATTAAAT
Found at i:9101 original size:19 final size:19
Alignment explanation
Indices: 9061--9102 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
9051 ATTAATGTAA
*
9061 AAATAATATTTAAATATTT
1 AAATAATATTTAAATATAT
*
9080 AAATATTATTATAAATA-AT
1 AAATAATATT-TAAATATAT
9099 AAAT
1 AAAT
9103 TAAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATATTTAAATATAT
Found at i:13214 original size:2 final size:2
Alignment explanation
Indices: 13207--13247 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
13197 AATTCTTGCA
*
13207 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
13248 AAGAATGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14200 original size:14 final size:14
Alignment explanation
Indices: 14145--14243 Score: 78
Period size: 14 Copynumber: 7.1 Consensus size: 14
14135 TGTTAGGTAA
14145 CTGTGTCAAAAGTAC
1 CTGTGTC-AAAGTAC
* *
14160 CTGTG-CTAAAATGC
1 CTGTGTC-AAAGTAC
* *
14174 CTATATC-AAGTAC
1 CTGTGTCAAAGTAC
*
14187 CTATGTCAAAGTAC
1 CTGTGTCAAAGTAC
* **
14201 TTGTGTCAAAGTGT
1 CTGTGTCAAAGTAC
*
14215 CTGTG-CCAAGTAC
1 CTGTGTCAAAGTAC
14228 CTGTGTCAAAGTAC
1 CTGTGTCAAAGTAC
14242 CT
1 CT
14244 ACGCCAGGCA
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
13 20 0.31
14 38 0.59
15 6 0.09
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (14 bp):
CTGTGTCAAAGTAC
Found at i:14209 original size:27 final size:27
Alignment explanation
Indices: 14145--14244 Score: 76
Period size: 27 Copynumber: 3.6 Consensus size: 27
14135 TGTTAGGTAA
* * *
14145 CTGTGTCAAAAGTACCTGTGCTAAAATGC
1 CTGTGTC-AAAGTACCTATGC-AAAGTAC
* *
14174 CTATATC-AAGTACCTATGTCAAAGTAC
1 CTGTGTCAAAGTACCTATG-CAAAGTAC
* ** * *
14201 TTGTGTCAAAGTGTCTGTGCCAAGTAC
1 CTGTGTCAAAGTACCTATGCAAAGTAC
14228 CTGTGTCAAAGTACCTA
1 CTGTGTCAAAGTACCTA
14245 CGCCAGGCAC
Statistics
Matches: 53, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
27 39 0.74
28 9 0.17
29 5 0.09
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (27 bp):
CTGTGTCAAAGTACCTATGCAAAGTAC
Found at i:14249 original size:27 final size:27
Alignment explanation
Indices: 14181--14277 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 27
14171 TGCCTATATC
*
14181 AAGTACCTATGTCAAAGTACTTGTGTCA
1 AAGTACCTATG-CCAAGTACTTGTGTCA
** * *
14209 AAGTGTCTGTGCCAAGTACCTGTGTCA
1 AAGTACCTATGCCAAGTACTTGTGTCA
* * * *
14236 AAGTACCTACGCCAGGCACTTGTGCCA
1 AAGTACCTATGCCAAGTACTTGTGTCA
*
14263 AAGTACCTGTGCCAA
1 AAGTACCTATGCCAA
14278 AGAGTATTAT
Statistics
Matches: 53, Mismatches: 16, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
27 45 0.85
28 8 0.15
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (27 bp):
AAGTACCTATGCCAAGTACTTGTGTCA
Found at i:14275 original size:14 final size:14
Alignment explanation
Indices: 14181--14279 Score: 76
Period size: 14 Copynumber: 7.2 Consensus size: 14
14171 TGCCTATATC
* *
14181 AAGTACCTATGTCA
1 AAGTACCTGTGCCA
* *
14195 AAGTACTTGTGTCA
1 AAGTACCTGTGCCA
**
14209 AAGTGTCTGTGCC-
1 AAGTACCTGTGCCA
*
14222 AAGTACCTGTGTCA
1 AAGTACCTGTGCCA
**
14236 AAGTACCTACGCC-
1 AAGTACCTGTGCCA
* * *
14249 AGGCACTTGTGCCA
1 AAGTACCTGTGCCA
14263 AAGTACCTGTGCCA
1 AAGTACCTGTGCCA
14277 AAG
1 AAG
14280 AGTATTATGG
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
13 18 0.29
14 45 0.71
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (14 bp):
AAGTACCTGTGCCA
Found at i:14854 original size:14 final size:14
Alignment explanation
Indices: 14837--14875 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
14827 CCCACGAGGC
14837 ATTATCCGTAAGGT
1 ATTATCCGTAAGGT
14851 ATTATTCACTGTAAGGT
1 ATTA-TC-C-GTAAGGT
14868 ATTATCCG
1 ATTATCCG
14876 CGAGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.23
15 3 0.14
16 3 0.14
17 11 0.50
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (14 bp):
ATTATCCGTAAGGT
Found at i:24044 original size:210 final size:207
Alignment explanation
Indices: 23619--24242 Score: 976
Period size: 210 Copynumber: 3.0 Consensus size: 207
23609 AAAATATTTT
* * * *
23619 AGATTCAAATTACTTTGATTTAAATTATTATTTAATTAA-TAAAATATAATTTTATTTAAATTTT
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAA-ATATTTTTATTTAAATTTT
* *
23683 ATT--AAAA-AT-AAAATTAATATAAAGATATAATTTTAATATTTAATAAATTTTAAACAATAAA
65 ATTAAAAAATATAAAAATTTATATAAAAATATAATTTTAATATTTAATAAATTTTAAACAATAAA
* *
23744 ATAAGTTTTCAAAATCAACAAACATTTTG-TATATACATTTTTTTTATATAAGAACCTAACCAAA
130 ATAAGTTTTCAAAATCAACAAACATTTTGATAAATACATTTTTTTTATATAGGAACCTAACCAAA
*
23808 TATAAATATAACT
195 TATAAATATAACC
23821 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAATATTTTTATTTAAATTTTA
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAATATTTTTATTTAAATTTTA
*
23886 TTAAAAAATATAAAAATTTATATAAAAATATAATTTTAATATTTTAATAAATTTTAAATAATAAA
66 TTAAAAAATATAAAAATTTATATAAAAATATAATTTTAATA-TTTAATAAATTTTAAACAATAAA
23951 ATAAGTTTTCAAAATCAACAAAACATTTTGAATAAATACATTTTTTTTATATAGGAACCTAACCA
130 ATAAGTTTTCAAAATCAAC-AAACATTTTG-ATAAATACATTTTTTTTATATAGGAACCTAACCA
24016 AATATAAATATAACC
193 AATATAAATATAACC
* *
24031 AGATTCTAATTAATCTGATTTAAAGTATTATTTAATTAATAAAAAATATTTTTATTTAAATTTTA
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAATATTTTTATTTAAATTTTA
*
24096 TTAAAAAACATATAAAAATTAATATAAAAAAATATAATTTTAATATTTAATAAATTTTAAACAAT
66 TT-AAAAA-ATATAAAAATT--TATATAAAAATATAATTTTAATATTTAATAAATTTTAAACAAT
* *
24161 AAAATAAGTTTTCAAAATCAACAAACA-TTTGAGTAAATACA-TTTTTTTCTGTAGGAACCTAAC
127 AAAATAAGTTTTCAAAATCAACAAACATTTTGA-TAAATACATTTTTTTTATATAGGAACCTAAC
24224 CAAATATAAATATAACC
191 CAAATATAAATATAACC
24241 AG
1 AG
24243 TAATGCTACC
Statistics
Matches: 392, Mismatches: 16, Indels: 20
0.92 0.04 0.05
Matches are distributed among these distances:
202 57 0.15
203 5 0.01
204 4 0.01
205 2 0.01
206 27 0.07
207 41 0.10
208 10 0.03
210 150 0.38
211 17 0.04
212 16 0.04
213 41 0.10
214 22 0.06
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (207 bp):
AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAATATTTTTATTTAAATTTTA
TTAAAAAATATAAAAATTTATATAAAAATATAATTTTAATATTTAATAAATTTTAAACAATAAAA
TAAGTTTTCAAAATCAACAAACATTTTGATAAATACATTTTTTTTATATAGGAACCTAACCAAAT
ATAAATATAACC
Found at i:24138 original size:21 final size:23
Alignment explanation
Indices: 24087--24141 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
24077 TATTTTTATT
24087 TAAATTTT-AT-TAAAAAACATA
1 TAAATTTTAATATAAAAAACATA
**
24108 TAAAAATTAATATAAAAAA-ATA
1 TAAATTTTAATATAAAAAACATA
24130 T-AATTTTAATAT
1 TAAATTTTAATAT
24142 TTAATAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 15 0.54
22 6 0.21
23 7 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATTTTAATATAAAAAACATA
Found at i:24661 original size:25 final size:22
Alignment explanation
Indices: 24633--24693 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 22
24623 ATTAAATTTG
24633 ATAATATTAAAAATAATTAACATAT
1 ATAATA-TAAAAATAATTAA-A-AT
24658 ATAATA-ATAAAA-AATTAAAAT
1 ATAATATA-AAAATAATTAAAAT
*
24679 ATAATATAAGAATAA
1 ATAATATAAAAATAA
24694 ATAATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 11 0.34
22 4 0.12
23 7 0.22
24 4 0.12
25 6 0.19
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAATATAAAAATAATTAAAAT
Found at i:24677 original size:33 final size:33
Alignment explanation
Indices: 24638--24701 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
24628 ATTTGATAAT
24638 ATTAAAA-ATAAT-TAACATATATAATAATAAAAA
1 ATTAAAATATAATATAACA-ATA-AATAATAAAAA
*
24671 ATTAAAATATAATATAAGAATAAATAATAAA
1 ATTAAAATATAATATAACAATAAATAATAAA
24702 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 16 0.57
34 8 0.29
35 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (33 bp):
ATTAAAATATAATATAACAATAAATAATAAAAA
Found at i:24680 original size:23 final size:25
Alignment explanation
Indices: 24633--24698 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
24623 ATTAAATTTG
* *
24633 ATAATATTAAAAATAATTAACATAT
1 ATAATAATAAAAATAATTAAAATAT
24658 ATAATAAT-AAAA-AATTAAAATAT
1 ATAATAATAAAAATAATTAAAATAT
*
24681 A-ATATAAGAATAAATAAT
1 ATA-ATAATAA-AAATAAT
24699 AAATATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 1 0.03
23 15 0.44
24 5 0.15
25 10 0.29
26 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAATAATAAAAATAATTAAAATAT
Done.