Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6485.1
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: 11420
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Found at i:1260 original size:12 final size:12
Alignment explanation
Indices: 1243--1278 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1233 ATTCATTTGA
*
1243 CATTCATGCATT
1 CATTCATACATT
1255 CATTCATACATT
1 CATTCATACATT
1267 CATTCATACATT
1 CATTCATACATT
1279 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.42
Consensus pattern (12 bp):
CATTCATACATT
Found at i:9800 original size:14 final size:14
Alignment explanation
Indices: 9781--9809 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9771 TGCTGAGGTC
9781 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
9795 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
9809 T
1 T
9810 CGTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:9966 original size:14 final size:14
Alignment explanation
Indices: 9947--9975 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9937 TGCTGAGGTC
9947 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
9961 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
9975 T
1 T
9976 CGTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:9999 original size:166 final size:165
Alignment explanation
Indices: 9725--10464 Score: 851
Period size: 166 Copynumber: 4.5 Consensus size: 165
9715 TTCGTAAAAA
9725 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
*
9790 TCTGTTTTTCAATTTCTGTTCGTAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCT
66 TCTGTTTTTCAATTTCTGTTCGT-AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
9855 CAAGACACGCTGAGGTAATTTCAATTTCTGTTTGTC
130 CAGGACACGCTGAGGTAATTTCAATTTCTGTTTGTC
9891 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
9956 TCTGTTTTTCAATTTCTGTTCGTAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
66 TCTGTTTTTCAATTTCTGTTCGT-AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
10021 C-GGCTTACATGCTGAGGTCTTTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAA
130 CAGG---ACACGCTGAGG-----T-AA-------T-TTCAATTTCTGTTTGT--C
* * * *
10075 AAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTTAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGT-CTTTTCAA
*
10137 TTTCTG---------TT-T-TTC-----AAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCC
64 TTTCTGTTTTTCAATTTCTGTTCGTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * *
10186 TCGGGATATGCTGAGGTAATTTCAATTTCTGTTTGTC
129 TCAGGACACGCTGAGGTAATTTCAATTTCTGTTTGTC
* * *
10223 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATTCTGAGGTTTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
*
10288 TCTGTTCTTCAATTTCTGTTCGTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
66 TCTGTTTTTCAATTTCTGTTCGTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * *
10353 AGGACACGCTGAGGTATTTTTAAATTTCTGTTTTTC
131 AGGACACGCTGAGGTA-ATTTCAATTTCTGTTTGTC
* * * **
10389 AAAAAATCAACTCATATTGTGAAAGGTGAGTTGAGCCTCGAG---ACACGCTGAGGTAATTTCAA
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GCTCACATGCTGAGGTCTTTTCAA
*
10451 TTTCTGTTTGTCAA
64 TTTCTGTTTTTCAA
10465 AAATTAACCC
Statistics
Matches: 496, Mismatches: 34, Indels: 89
0.80 0.05 0.14
Matches are distributed among these distances:
147 2 0.00
148 36 0.07
149 13 0.03
150 25 0.05
151 1 0.00
158 4 0.01
159 2 0.00
160 3 0.01
164 10 0.02
165 80 0.16
166 184 0.37
167 38 0.08
168 11 0.02
172 3 0.01
173 2 0.00
174 4 0.01
181 1 0.00
182 26 0.05
183 12 0.02
184 37 0.07
185 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (165 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
TCTGTTTTTCAATTTCTGTTCGTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
AGGACACGCTGAGGTAATTTCAATTTCTGTTTGTC
Found at i:10031 original size:93 final size:90
Alignment explanation
Indices: 9873--10150 Score: 411
Period size: 93 Copynumber: 3.1 Consensus size: 90
9863 GCTGAGGTAA
* *
9873 TTTCAATTTCTGTTTGT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
1 TTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCT-AC
9936 ATGCTGAGGTCTTTTCAATTTCTGTT
65 ATGCTGAGGTCTTTTCAATTTCTGTT
9962 TTTCAATTTCTGTTCGTAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTT
1 TTTCAATTTCTGTTCGT--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-T
10027 ACATGCTGAGGTCTTTTCAATTTCTGTT
63 ACATGCTGAGGTCTTTTCAATTTCTGTT
* *
10055 CTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGG--AC
1 TTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTAC
* * *
10118 ACGCTGAGGTATTTTTAAATTTCTGTT
65 ATGCTGAGGT-CTTTTCAATTTCTGTT
10145 TTTCAA
1 TTTCAA
10151 AAAATCAACT
Statistics
Matches: 174, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
89 27 0.16
90 19 0.11
91 40 0.23
92 2 0.01
93 85 0.49
94 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (90 bp):
TTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTACA
TGCTGAGGTCTTTTCAATTTCTGTT
Found at i:10061 original size:14 final size:14
Alignment explanation
Indices: 10042--10069 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10032 CTGAGGTCTT
10042 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
10056 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
10070 GTAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (14 bp):
TTCAATTTCTGTTC
Found at i:10249 original size:73 final size:74
Alignment explanation
Indices: 10056--10502 Score: 321
Period size: 75 Copynumber: 5.8 Consensus size: 74
10046 ATTTCTGTTC
* * * *
10056 TTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACG
1 TTCAATTTCTGTTTGT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
*
10121 CTGAGGTATTT
64 CTGAGGTATAT
* * * * *
10132 TTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGATATGC
1 TTCAATTTCTGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
10197 TGAGGTA-AT
65 TGAGGTATAT
* * **
10206 TTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATT
1 TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACG
*
10271 CTGAGGT-TTT
64 CTGAGGTATAT
* ** * * * * *
10281 TTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAAAAAAATCA-ACT-C-ATATTGCGAGAGGTGA
1 TTCAATTTCTG---------TT-TG-TC-AAAAATCAACTCATATTGCGAGA--G-GTGAGTTGA
* *
10343 GTTGAGCCTCAGGACACGCTGAGGTATTT
51 G-----CCTCGGGACACGCTGAGGTATAT
* * * * *
10372 TTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGTGAAAGGTGAGTTGAGCCTCGAGACACGC
1 TTCAATTTCTGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
10437 TGAGGTA-AT
65 TGAGGTATAT
* * *
10446 TTCAATTTCTGTTTGTCAAAAATTAACCCATATTGCGAGAGGTGAGTTGAGTCTCGG
1 TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
10503 CTCACATGCT
Statistics
Matches: 290, Mismatches: 53, Indels: 59
0.72 0.13 0.15
Matches are distributed among these distances:
73 72 0.25
74 32 0.11
75 89 0.31
76 13 0.04
80 19 0.07
81 4 0.01
82 2 0.01
83 2 0.01
84 4 0.01
85 3 0.01
86 5 0.02
87 17 0.06
90 10 0.03
91 13 0.04
92 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (74 bp):
TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCT
GAGGTATAT
Found at i:10300 original size:14 final size:14
Alignment explanation
Indices: 10281--10308 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10271 CTGAGGTTTT
10281 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
10295 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
10309 GTAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (14 bp):
TTCAATTTCTGTTC
Found at i:10373 original size:92 final size:89
Alignment explanation
Indices: 10223--10390 Score: 230
Period size: 92 Copynumber: 1.8 Consensus size: 89
10213 TCTGTTTGTC
* ** *
10223 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATTCTGAGGTTTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACACGCTGAGG-TTTTTAAATT
10288 TCTGTTCTTCAATTTCTGTTCGTAAAA
63 TCTGTTCTTCAATTTCTGTTCGTAAAA
10315 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTATTTTTAAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCACACGCTGAGG--TTTTTAAATT
*
10379 TCTGTTTTTCAA
63 TCTGTTCTTCAA
10391 AAAATCAACT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
90 9 0.13
91 20 0.29
92 37 0.54
93 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (89 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCTGAGGTTTTTAAATTTCT
GTTCTTCAATTTCTGTTCGTAAAA
Found at i:10415 original size:240 final size:239
Alignment explanation
Indices: 9984--10547 Score: 988
Period size: 240 Copynumber: 2.4 Consensus size: 239
9974 TTCGTAAAAA
* * *
9984 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTTACATGCTGAGGTCTTTTCAATT
1 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTTTTTTCAATT
10049 TCTGTTCTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCA
66 TCTGTTCTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCA
10114 GGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAG
131 GGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAG
* * *
10179 TTGAGCCTCGGGATATGCTGAGGTAATTTCAATTTCTGTTTGTC
196 TTGAGCCTCGAGACACGCTGAGGTAATTTCAATTTCTGTTTGTC
*
10223 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATTCTGAGGTTTTTTCAATT
1 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTTTTTTCAATT
*
10288 TCTGTTCTTCAATTTCTGTTCGTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
66 TCTGTTCTTCAATTTCTGTTCGT-AAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTC
*
10353 AGGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGTGAAAGGTGA
130 AGGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAAAGGTGA
10418 GTTGAGCCTCGAGACACGCTGAGGTAATTTCAATTTCTGTTTGTC
195 GTTGAGCCTCGAGACACGCTGAGGTAATTTCAATTTCTGTTTGTC
* *
10463 AAAAATTAACCCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGCTGAGGTCTTTTT-AAT
1 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGT-TTTTTCAAT
10527 TTCTGCTT-TTCAATTTCTGTT
65 TTCTG-TTCTTCAATTTCTGTT
10548 TTTTCAATTT
Statistics
Matches: 310, Mismatches: 12, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
239 84 0.27
240 219 0.71
241 7 0.02
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (239 bp):
AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTTTTTTCAATT
TCTGTTCTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCA
GGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAG
TTGAGCCTCGAGACACGCTGAGGTAATTTCAATTTCTGTTTGTC
Found at i:10423 original size:75 final size:73
Alignment explanation
Indices: 10314--10539 Score: 292
Period size: 75 Copynumber: 3.0 Consensus size: 73
10304 TGTTCGTAAA
10314 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTT-AATT
10379 TCTGTTTTTC
64 TCTGTTTTTC
* * * *
10389 AAAAAATCAACTCATATTGTGAAAGGTGAGTTGAGCCTCGAGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GACACGCTGAGGTATTTTTAATTT
*
10454 CTGTTTGTC
65 CTGTTTTTC
* * * * *
10463 -AAAAATTAACCCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGCTGAGGTCTTTTTAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTATTTTTAAT
*
10527 TTCTGCTTTTC
63 TTCTGTTTTTC
10538 AA
1 AA
10540 TTTCTGTTTT
Statistics
Matches: 130, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
72 1 0.01
73 34 0.26
74 14 0.11
75 80 0.62
76 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (73 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTTAATTTC
TGTTTTTC
Found at i:10541 original size:14 final size:15
Alignment explanation
Indices: 10516--10557 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
10506 ACATGCTGAG
*
10516 GTCTTTTTAATTTCT
1 GTCTTTTCAATTTCT
10531 G-CTTTTCAATTTCT
1 GTCTTTTCAATTTCT
*
10545 GTTTTTTCAATTT
1 GTCTTTTCAATTT
10558 ATATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (15 bp):
GTCTTTTCAATTTCT
Found at i:10553 original size:15 final size:14
Alignment explanation
Indices: 10519--10568 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
10509 TGCTGAGGTC
10519 TTTTT-AATTTCTG
1 TTTTTCAATTTCTG
*
10532 CTTTTCAATTTCTG
1 TTTTTCAATTTCTG
* *
10546 TTTTTTCAATTTATA
1 -TTTTTCAATTTCTG
10561 TTTTTCAA
1 TTTTTCAA
10569 AAATCCACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
15 11 0.35
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.64
Consensus pattern (14 bp):
TTTTTCAATTTCTG
Found at i:11352 original size:30 final size:30
Alignment explanation
Indices: 11316--11420 Score: 174
Period size: 30 Copynumber: 3.5 Consensus size: 30
11306 ACTTTTCTCA
*
11316 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
11346 ACTAGCCACACCTTTTCCACCACCAACTCT
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
11376 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
11406 ACTAGCCACACCTTT
1 ACTAGCCACACCTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.25, C:0.47, G:0.04, T:0.25
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Done.