Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold9633.1
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: 4311
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Found at i:1473 original size:171 final size:168
Alignment explanation
Indices: 1213--1538 Score: 517
Period size: 171 Copynumber: 1.9 Consensus size: 168
1203 TTTTTCCCGC
*
1213 CGCCGGGAAATCGCTAACTACAAAAGGAAATAATTTTCCCAAGGGAACACTGTTGTACGTCCATT
1 CGCCGGGAAATCGCTAACTACAAAAGGAAATAATTTTCCCAAGGGAAAACTGTTGTACGTCCATT
* * * * *
1278 TGGTTTGGGGGCTGAAATCTACTCACGGGCATCCTTGGAGTCCGAACACATGAAAAAACCATCAT
66 CGGTTTGGGGGCTGAAATCTACTCACGAGCATCCTCGGAGTCCGAACACA-CAAAAAAACATCAT
**
1343 GTCACCGCGGATAATTTCGGAAAATTCCATATTTTTAAGT
130 GTCACCGCGGA-AATCCCGGAAAATTCCATATTTTTAAGT
* * * *
1383 CGCCGGGAAATCGCTAACTACAACGAGGAAATTATTTTTCCAATGGAAAACTGTTGTACGTCCAT
1 CGCCGGGAAATCGCTAACTACAA-AAGGAAATAATTTTCCCAAGGGAAAACTGTTGTACGTCCAT
1448 TCGGTTTGGGGGCTGAAATCTACTCACGAGCATCCTCGGAGTCCGAACACACAAAAAAACATCAT
65 TCGGTTTGGGGGCTGAAATCTACTCACGAGCATCCTCGGAGTCCGAACACACAAAAAAACATCAT
1513 GTCACCGCGGAAATCCCGGAAAATTC
130 GTCACCGCGGAAATCCCGGAAAATTC
1539 TCTATTCTTT
Statistics
Matches: 143, Mismatches: 12, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
169 13 0.09
170 46 0.32
171 84 0.59
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (168 bp):
CGCCGGGAAATCGCTAACTACAAAAGGAAATAATTTTCCCAAGGGAAAACTGTTGTACGTCCATT
CGGTTTGGGGGCTGAAATCTACTCACGAGCATCCTCGGAGTCCGAACACACAAAAAAACATCATG
TCACCGCGGAAATCCCGGAAAATTCCATATTTTTAAGT
Found at i:3791 original size:171 final size:172
Alignment explanation
Indices: 3406--4303 Score: 760
Period size: 171 Copynumber: 5.3 Consensus size: 172
3396 AAGGCAATTC
* * * * * * **
3406 GGCACCATTGCTC-AAGATTTCCCCCTTGGATTCTCTCTATATTTTCCGAAGATCATCC-TGGGA
1 GGCAACATTGCTCGAA-ATTTCTCCCTTGGATTTTCTCGAAATTTTCCGAGGATGGTCCTTGGGA
* * * * * **
3469 GTCCATA-CTGAATATAAAATGTGTCAAATCGGATTAACAAATGAAATTGATCAAACG--TCAGC
65 GGCCAAAGGT-AATATAAAATGTGTCAAATCGGATGAACAAATGAAATTGATGAAACGAAAGAGC
* * *
3531 CTGCTCCGAATTTACGCGACTCT-ACTCGTACGAATGACGGATGT
129 CTGCTCCGAATTTACGCGACT-TGACGCGAATGAATGACGGATGT
* ** * * * *
3575 GGCAACAATGCAGGAAATTTCCCCCTTGGAATTTT-TCGGAATTTTCCTAAGATGGT-CTTGGGA
1 GGCAACATTGCTCGAAATTTCTCCCTTGG-ATTTTCTCGAAATTTTCCGAGGATGGTCCTTGGGA
* * * * * ** *
3638 GGCCAAAGTTGATAAAAAATGAGTCAAATCGGATGAACAAATGAAATTGACGAAACGACCGATCC
65 GGCCAAAGGTAATATAAAATGTGTCAAATCGGATGAACAAATGAAATTGATGAAACGAAAGAGCC
* * ** *
3703 TGCTCCGAATTTACGCGACTGGACTCGTTTGAATGATGGATGT
130 TGCTCCGAATTTACGCGACTTGACGCGAATGAATGACGGATGT
* * * * *
3746 GGCAACATTGCTCGAGATGTCTCACTTCGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGG-G
1 GGCAACATTGCTCGAAATTTCTCCCTTGGATTTTCTCGAAATTTTCCGAGGATGGTCCTTGGGAG
* * * * ** * *
3810 TCCATAA-TTAATACAAAATGTGTCAAATCCGATGAACAAATGAAAAAGATGTAACGGAAGAGCC
66 GCCA-AAGGTAATATAAAATGTGTCAAATCGGATGAACAAATGAAATTGATGAAACGAAAGAGCC
* *
3874 TGCTCCGGATTTACGCGACTTGACGCGAATGAATGACGGATGC
130 TGCTCCGAATTTACGCGACTTGACGCGAATGAATGACGGATGT
* * ** *
3917 GGCAACATTGCAT-GAAATTTCACCCTTGGAATTTCTCGAAATTTTCTTATGG-TGGTCC-CGGG
1 GGCAACATTGC-TCGAAATTTCTCCCTTGGATTTTCTCGAAATTTTCCGA-GGATGGTCCTTGGG
** * * * *
3979 AGGCCGTAGGAAATATAAAATGTGTCAAATCCGATGAACAAATGAAATCGATGTAACGAAAGAGC
64 AGGCCAAAGGTAATATAAAATGTGTCAAATCGGATGAACAAATGAAATTGATGAAACGAAAGAGC
* * * **
4044 CTGCTCCGAAGTTACGCGACTTTACGC-ATTG-ATAGATAGATGT
129 CTGCTCCGAATTTACGCGACTTGACGCGAATGAAT-GACGGATGT
* *
4087 GACAACATTGCTCGAGATTTCAT-CCTTGGATTTTCTCGAAATTTTCCGAGGATGGTCCTT-GGA
1 GGCAACATTGCTCGAAATTTC-TCCCTTGGATTTTCTCGAAATTTTCCGAGGATGGTCCTTGGGA
* ** * *
4150 GGTCATCGGTGATATAAAACGTGTCAAATCGGATGAACAAATGAAATCT-ATGAAACGAAAGAGC
65 GGCCAAAGGTAATATAAAATGTGTCAAATCGGATGAACAAATGAAAT-TGATGAAACGAAAGAGC
* * * *
4214 CTGCTTCGAAGTTACGCGACTTTACGCGTAA-G-AT-AGGTAGATGT
129 CTGCTCCGAATTTACGCGACTTGACGCG-AATGAATGACG--GATGT
* ** *
4258 GACAACATTGCTCGGGATTTCAT-CCTTGGATTTACTCGAAATTTTC
1 GGCAACATTGCTCGAAATTTC-TCCCTTGGATTTTCTCGAAATTTTC
4304 TTAAGATG
Statistics
Matches: 598, Mismatches: 107, Indels: 46
0.80 0.14 0.06
Matches are distributed among these distances:
168 1 0.00
169 94 0.16
170 154 0.26
171 337 0.56
172 12 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (172 bp):
GGCAACATTGCTCGAAATTTCTCCCTTGGATTTTCTCGAAATTTTCCGAGGATGGTCCTTGGGAG
GCCAAAGGTAATATAAAATGTGTCAAATCGGATGAACAAATGAAATTGATGAAACGAAAGAGCCT
GCTCCGAATTTACGCGACTTGACGCGAATGAATGACGGATGT
Found at i:3962 original size:342 final size:339
Alignment explanation
Indices: 3406--4241 Score: 935
Period size: 342 Copynumber: 2.5 Consensus size: 339
3396 AAGGCAATTC
* * * * * * **
3406 GGCACCATTGCTCAAGATTTCCCCCTTGGATTCTCTCTATATTTTCCGAAGATCATCC-TGGGAG
1 GGCAACATTGCTCGAGATTT-CTCCTTGGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGG-G
* * * * * **
3470 TCCATACTGAATATAAAATGTGTCAAATCGGATTAACAAATGAAATTGATCAAAC-G-TCAGCCT
64 TCCATAATTAATATAAAATGTGTCAAATCGGATGAACAAATGAAATAGATGAAACGGAAGAGCCT
* * * *
3533 GCTCCGAATTTACGCGACTCTACTCGTACGAATGACGGATGTGGCAACAATGCAGGAAATTTCCC
129 GCTCCGAATTTACGCGACT-TACGCGAACGAATGACGGATGCGGCAACAATGCAGGAAATTTCAC
* * ** ***
3598 CCTTGGAATTTTTCGGAATTTTCCTAAGATGGTCTTGGGAGGCCAAAGTTGATAAAAAATGAGTC
193 CCTTGGAATTTCTCGAAATTTTCCTAAGATGGTCCCGGGAGGCCAAAGGAAATAAAAAATGAGTC
* * ** * * *
3663 AAATCGGATGAACAAATGAAATTGACGAAACGACCGATCCTGCTCCGAATTTACGCGACTGGACT
258 AAATCCGATGAACAAATGAAATCGACGAAACGAAAGAGCCTGCTCCGAAGTTACGCGACTGGACG
* *
3728 CGTTTGA-ATGATGGATGT
323 C-ATTGATA-GATAGATGT
* *
3746 GGCAACATTGCTCGAGATGTCTCACTTCGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGGGT
1 GGCAACATTGCTCGAGATTTCTC-CTTGGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGGGT
* * * *
3811 CCATAATTAATACAAAATGTGTCAAATCCGATGAACAAATGAAAAAGATGTAACGGAAGAGCCTG
65 CCATAATTAATATAAAATGTGTCAAATCGGATGAACAAATGAAATAGATGAAACGGAAGAGCCTG
* * * *
3876 CTCCGGATTTACGCGACTTGACGCGAATGAATGACGGATGCGGCAACATTGCATGAAATTTCACC
130 CTCCGAATTTACGCGACTT-ACGCGAACGAATGACGGATGCGGCAACAATGCAGGAAATTTCACC
* * * ** * *
3941 CTTGGAATTTCTCGAAATTTTCTTATGGTGGTCCCGGGAGGCCGTAGGAAATATAAAATGTGTCA
194 CTTGGAATTTCTCGAAATTTTCCTAAGATGGTCCCGGGAGGCCAAAGGAAATAAAAAATGAGTCA
* * **
4006 AATCCGATGAACAAATGAAATCGATGTAACGAAAGAGCCTGCTCCGAAGTTACGCGACTTTACGC
259 AATCCGATGAACAAATGAAATCGACGAAACGAAAGAGCCTGCTCCGAAGTTACGCGACTGGACGC
4071 ATTGATAGATAGATGT
324 ATTGATAGATAGATGT
* *
4087 GACAACATTGCTCGAGATTTCATCCTTGGATTTTCTCGAAATTTTCCGAGGATGGTCCTTGGAGG
1 GGCAACATTGCTCGAGATTTC-TCCTTGGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGG-GG
*** * * ** *
4152 T-CATCGGTGATATAAAACGTGTCAAATCGGATGAACAAATGAAATCTATGAAACGAAAGAGCCT
64 TCCATAATTAATATAAAATGTGTCAAATCGGATGAACAAATGAAATAGATGAAACGGAAGAGCCT
* *
4216 GCTTCGAAGTTACGCGACTTTACGCG
129 GCTCCGAATTTACGCGAC-TTACGCG
4242 TAAGATAGGT
Statistics
Matches: 412, Mismatches: 75, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
339 2 0.00
340 92 0.22
341 144 0.35
342 174 0.42
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (339 bp):
GGCAACATTGCTCGAGATTTCTCCTTGGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGGGTC
CATAATTAATATAAAATGTGTCAAATCGGATGAACAAATGAAATAGATGAAACGGAAGAGCCTGC
TCCGAATTTACGCGACTTACGCGAACGAATGACGGATGCGGCAACAATGCAGGAAATTTCACCCT
TGGAATTTCTCGAAATTTTCCTAAGATGGTCCCGGGAGGCCAAAGGAAATAAAAAATGAGTCAAA
TCCGATGAACAAATGAAATCGACGAAACGAAAGAGCCTGCTCCGAAGTTACGCGACTGGACGCAT
TGATAGATAGATGT
Found at i:4266 original size:341 final size:337
Alignment explanation
Indices: 3411--4311 Score: 931
Period size: 341 Copynumber: 2.6 Consensus size: 337
3401 AATTCGGCAC
* * * * * ** *
3411 CATTGCTCAAGATTTCCCCCTTGGATTCTCTCTATATTTTCCGAAGATCATCCTGGGA-GTCCAT
1 CATTGCTCGAGATTT-CTCCTTGGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGAGGTCCAT
* * **
3475 ACTGAATATAAAATGTGTCAAATCGGATTAACAAATGAAATTGATCAAACG-TCAGCCTGCTCCG
65 -CTG-ATATAAAATGTGTCAAATCGGATGAACAAATGAAATT-ATGAAACGAAGAGCCTGCTCCG
* * * * * *
3539 AATTTACGCGACTCTACTCGTACGAATGACGGATGTGGCAACAATGCAGGAAATTTCCCCCTTGG
127 AATTTACGCGACTTTACGCGTAAGAATGAC-GATGTGGCAACATTGCATGAAATTTCACCCTTGG
* * * ** *** *
3604 AATTTTTCGGAATTTTCCTAAGATGGTCTTGGGAGGCCAAAGTTGATAAAAAATGAGTCAAATCG
191 AATTTCTCGAAATTTTCTTAAGATGGTCCCGGGAGGCCAAAGGAAATAAAAAATGAGTCAAATCC
* ** * * * *
3669 GATGAACAAATGAAATTGACGAAACGACCGATCCTGCTCCGAATTTACGCGACTGGACTCGTTTG
256 GATGAACAAATGAAATCGACGAAACGAAAGAGCCTGCTCCGAAGTTACGCGACTGGACGCGATTG
* *
3734 AATGATGGATGTGGCAA
321 AATGATAGATGTGACAA
* *
3751 CATTGCTCGAGATGTCTCACTTCGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGG-GGTCCAT
1 CATTGCTCGAGATTTCTC-CTTGGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGAGGTCCAT
* * * * ** *
3815 AATTAATACAAAATGTGTCAAATCCGATGAACAAATGAAAAAGATGTAACGGAAGAGCCTGCTCC
65 --CTGATATAAAATGTGTCAAATCGGATGAACAAATG-AAATTATGAAAC-GAAGAGCCTGCTCC
* * *
3880 GGATTTACGCGACTTGACGCG-AATGAATGACGGATGCGGCAACATTGCATGAAATTTCACCCTT
126 GAATTTACGCGACTTTACGCGTAA-GAATGAC-GATGTGGCAACATTGCATGAAATTTCACCCTT
* * ** * *
3944 GGAATTTCTCGAAATTTTCTTATGGTGGTCCCGGGAGGCCGTAGGAAATATAAAATGTGTCAAAT
189 GGAATTTCTCGAAATTTTCTTAAGATGGTCCCGGGAGGCCAAAGGAAATAAAAAATGAGTCAAAT
* * **
4009 CCGATGAACAAATGAAATCGATGTAACGAAAGAGCCTGCTCCGAAGTTACGCGACTTTACGC-AT
254 CCGATGAACAAATGAAATCGACGAAACGAAAGAGCCTGCTCCGAAGTTACGCGACTGGACGCGAT
4073 TG-ATAGATAGATGTGACAA
319 TGAAT-GATAGATGTGACAA
*
4092 CATTGCTCGAGATTTCATCCTTGGATTTTCTCGAAATTTTCCGAGGATGGTCCTTGGAGGT-CAT
1 CATTGCTCGAGATTTC-TCCTTGGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGAGGTCCAT
* *
4156 CGGTGATATAAAACGTGTCAAATCGGATGAACAAATGAAATCTATGAAACGAAAGAGCCTGCTTC
65 C--TGATATAAAATGTGTCAAATCGGATGAACAAATGAAAT-TATGAAACG-AAGAGCCTGCTCC
* * * ** *
4221 GAAGTTACGCGACTTTACGCGTAAGATAGGTA-GATGTGACAACATTGC-TCGGGATTTCATCCT
126 GAATTTACGCGACTTTACGCGTAAGA-ATG-ACGATGTGGCAACATTGCAT-GAAATTTCACCCT
4284 TGG-ATTTACTCGAAATTTTCTTAAGATG
188 TGGAATTT-CTCGAAATTTTCTTAAGATG
Statistics
Matches: 461, Mismatches: 81, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
339 2 0.00
340 95 0.21
341 189 0.41
342 174 0.38
343 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (337 bp):
CATTGCTCGAGATTTCTCCTTGGATTTTCTCTAAATTTTCCGAGGATGGTCCTTGGAGGTCCATC
TGATATAAAATGTGTCAAATCGGATGAACAAATGAAATTATGAAACGAAGAGCCTGCTCCGAATT
TACGCGACTTTACGCGTAAGAATGACGATGTGGCAACATTGCATGAAATTTCACCCTTGGAATTT
CTCGAAATTTTCTTAAGATGGTCCCGGGAGGCCAAAGGAAATAAAAAATGAGTCAAATCCGATGA
ACAAATGAAATCGACGAAACGAAAGAGCCTGCTCCGAAGTTACGCGACTGGACGCGATTGAATGA
TAGATGTGACAA
Done.