Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2716
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: 5015
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Found at i:3954 original size:159 final size:159
Alignment explanation
Indices: 2370--4427 Score: 630
Period size: 158 Copynumber: 13.1 Consensus size: 159
2360 AGTTCATCCT
** * * * * * * *
2370 TTAAATAAGACAAATATCAATTCTCCTAACAATCCCCATTCTTTTCATGATTGGGAACGAAAAAC
1 TTAAATAAGACAAGCATCGATTCTCGTAACAGTCTCCATTCTTTTCAAGATTGGGAACTATAAAC
* * * **
2435 ACATTTCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCATAAGAAAAGCTTTTCTTTCCA
66 ACATTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTTCCA
** * * * *
2500 CTGTTTTTGATAGAATCGAAGTTTGTCAC
131 CCATTTTTGATAAAATCAAAGTTTGCCTC
* * * * * * * * * *
2529 TTAAATAAGACAAACAT-GA--ATAGTCACACTAATCCCCATTATTTTCAGGATTAGGCACCAT-
1 TTAAATAAGACAAGCATCGATTCTCGT-A-AC-AGTCTCCATTCTTTTCAAGATTGGGAACTATA
* ** * *
2590 AA-ACATTCTCTTCTCATTAGGATACGCGATATTGATGTTTTGGTTAT-GCAAGAAAGGCATTTT
63 AACACATTC-CCT-TCATTAGGATACATGATATTGATGCTTTGGTT-TCGCAAGAAAAGC-TTTT
* *
2653 C---CCACCAATTTTTG-TAAAGTCTAAGTTCCTGCCTC
124 CTTTCCACC-ATTTTTGATAAAATCAAAGTT--TGCCTC
* * * * * ** * * *
2688 --AAATGAGGCAA-CATGGATTCTAGTATCTAGTAATGATCTTTATTCATTTT-GAGATTAGGCA
1 TTAAATAAGACAAGCATCGATTCTCGTA---A--CA-G-TCTCCATTC-TTTTCAAGATTGGGAA
** * * * * * ** * *
2749 CTATAAGTATATTGTCCTT-ATTAGG-TAAATGATATTAATGATTTTCTTT-TCATAG-AAA-TT
58 CTATAAACACATT-CCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCA-AGAAAAGCT
* **
2809 TTTCTTTGC-CC-TATTTTCCTAAAATCAAAGTTCAT-CC-C
121 TTTCTTTCCACCAT-TTTTGATAAAATCAAAGTT--TGCCTC
* * * ** *
2847 TT-AATAAGACAAGCATCGATCCTCGTAATAGTCTAC-GCCATTTTCAAGATTGGGAACCCA-AA
1 TTAAATAAGACAAGCATCGATTCTCGTAACAGTCTCCATTC-TTTTCAAGATTGGGAA-CTATAA
* * * * * *
2909 ACATATTCCCTTCATCAAGATACATGACATTGATGCTTTGGTGTCACAAGAAAAGCTTTTCTTTC
64 ACACATTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTTC
*** * * *
2974 CACTGGTTTT-ATAGAATCAAAGTTTGTCTT
129 CACCATTTTTGATAAAATCAAAGTTTGCCTC
* * * * * * * * *
3004 TTAAAT--GACAGGAACAT-GAATACTCAT-ACTAATC-CTATTCTTTTCAGGATTAGGCACCAT
1 TTAAATAAGACA--AGCATCG-ATTCTCGTAAC-AGTCTCCATTCTTTTCAAGATTGGGAACTAT
* * ** * * * * *
3064 AAATATAGTTTTC-TCTTTAGGATACACGATATTGATGATTTGGTTCCTCAAGAAAAGC-TTT-T
62 AAACACA-TTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCT
* * * *
3126 TTCCTACCAATTTTTG-CAAAGTCTAAGTTCTTACCTC
126 TTCC-ACC-ATTTTTGATAAAATCAAAG-T-TTGCCTC
* * * * * * * * * *
3163 --AAATGAGGCAAACATAGATTCTAGTAA-TGATCTTCATTCATTTT-GAGATTAGGCACTA-AA
1 TTAAATAAGACAAGCATCGATTCTCGTAACAG-TCTCCATTC-TTTTCAAGATTGGGAACTATAA
* * * * * ** * * * *
3223 AGCACATTCTCATCTTTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCTTT
64 A-CACATTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTT
** * * **
3288 GCC-TTATTTTT-CTAAAATCAATGTTCACAC-C
128 -CCACCATTTTTGATAAAATCAAAGTTTGC-CTC
* * *
3319 TTAAATAAGACAAGCATCAATTCTCATAACAGACTCCATT-TTTTC-AGATTGGGAACCTA-AAA
1 TTAAATAAGACAAGCATCGATTCTCGTAACAGTCTCCATTCTTTTCAAGATTGGGAA-CTATAAA
* * * * * *
3381 CACATT-CCTGTCATTAAGATACATGACATTGATGCTTTAGTGTCGCAAGCAAAGCTTTTCTCTC
65 CACATTCCCT-TCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTTC
* * *
3445 CACCATTTTTGATAGAATCAAAGTTTGTCTT
129 CACCATTTTTGATAAAATCAAAGTTTGCCTC
* * * ** * * ** * * * * *
3476 TTAAATAAAACAAACTTTAATACTCATAGTAATC-CTCATGCTTTTCAAGATTAGGCACCATAAA
1 TTAAATAAGACAAGCATCGATTCTCGTAACAGTCTC-CATTCTTTTCAAGATTGGGAACTATAAA
* * * ** * * * *
3540 CATAGT-CTTCTCATTAGGATACGCG-TATTGATGTTTTGGTTTCACAAGAAAGGCCTTT-TTTC
65 CACATTCCCT-TCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTTC
* * *
3602 CTCCAATTTTG-TAAAATCTAAGTTAATGCCTC
129 CACCATTTTTGATAAAATCAAAGTT--TGCCTC
* * * * ** * *
3634 --AAATAAGAC-AGACAT-GAATTCTAGTAA-TGATCTTCATTAGTTTT-GTGATTAGGCACTAT
1 TTAAATAAGACAAG-CATCG-ATTCTCGTAACAG-TCTCCATT-CTTTTCAAGATTGGGAACTAT
* *** * * ** * ** *
3693 AAAGA-ACTTATTTTCATTAGGATAAATGATATTGATGATTTTCTTTTGCGTGAAAATCTTTTCT
62 AAACACA-TTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCT
* *** * * *
3757 TTGCC-CTATTTTCCTTAAAATCAAAGTATACCCC
126 TT-CCACCATTTTTGATAAAATCAAAGTTTGCCTC
* * * *
3791 TTAAATTAGACAGGCATCGATTCTTGTAACAGTCTCCATTCTTTTCAAGATTGGGAACTAGAAAC
1 TTAAATAAGACAAGCATCGATTCTCGTAACAGTCTCCATTCTTTTCAAGATTGGGAACTATAAAC
* * *
3856 ACATTCCCTTCATTAGGATACACGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCA
66 ACATTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTTCCA
*
3921 CCATTTTTGATAGAATCAAAGTTTGCCTC
131 CCATTTTTGATAAAATCAAAGTTTGCCTC
*** * ** * *
3950 TTAAATAAGACAAG--TC-AAAAT-G----A-TCCCCATTCTTTTCGTGATTAGGCAGC-ATAAA
1 TTAAATAAGACAAGCATCGATTCTCGTAACAGTCTCCATTCTTTTCAAGATT-GGGAACTATAAA
** * ** * * * *
4005 CGTAGTCTTTTGATAAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAGGC-TTTCTTCCC
65 CACATTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTTCC
* *
4069 ACCCATTTTTG-TAAACTCTAAGTTCATGCCTC
130 A-CCATTTTTGATAAAATCAAAGTT--TGCCTC
* * * * * ** * * * * *
4101 --AAATGAGCCAAACATGGATTCTAGT-ATTGATCTTCATTCATTTTC-TGACTAGGCACTATAA
1 TTAAATAAGACAAGCATCGATTCTCGTAACAG-TCTCCATTC-TTTTCAAGATTGGGAACTATAA
* * * ** * * *
4162 ACACATTCTCTTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTG
64 ACACATTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTT-
* *** *
4227 CC-CTATTTTCCTTAAAATCAAAG-TT-CATTCC
128 CCACCATTTTTGATAAAATCAAAGTTTGC-CT-C
* * * *
4258 TTAGA-AAGACAAGCATTGATTCTCGTAACAATCTCCATTCTTTTCAAGATTGGGAA-TCAAAAA
1 TTAAATAAGACAAGCATCGATTCTCGTAACAGTCTCCATTCTTTTCAAGATTGGGAACT-ATAAA
* * * * * * * **
4321 GACATCCCCTTCGTTAGGATACACG-TCATAGATGCTTTAGTGTCGCAAGAAAATATTTTCTTTC
65 CACATTCCCTTCATTAGGATACATGAT-ATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTTC
* *
4385 CACC-GTTTTGATAGAATCAAAGTTTGCCTC
129 CACCATTTTTGATAAAATCAAAGTTTGCCTC
4415 TTAAATAAGACAA
1 TTAAATAAGACAA
4428 ACATGAGTAG
Statistics
Matches: 1361, Mismatches: 404, Indels: 269
0.67 0.20 0.13
Matches are distributed among these distances:
149 28 0.02
150 74 0.05
151 12 0.01
152 2 0.00
153 11 0.01
154 22 0.02
155 35 0.03
156 159 0.12
157 269 0.20
158 340 0.25
159 291 0.21
160 30 0.02
161 34 0.02
162 19 0.01
163 23 0.02
164 6 0.00
165 6 0.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (159 bp):
TTAAATAAGACAAGCATCGATTCTCGTAACAGTCTCCATTCTTTTCAAGATTGGGAACTATAAAC
ACATTCCCTTCATTAGGATACATGATATTGATGCTTTGGTTTCGCAAGAAAAGCTTTTCTTTCCA
CCATTTTTGATAAAATCAAAGTTTGCCTC
Done.