Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03615.F1
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: 5912
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:4378 original size:839 final size:839
Alignment explanation
Indices: 2727--4403 Score: 2942
Period size: 839 Copynumber: 2.0 Consensus size: 839
2717 CTTTGATTTT
* * * *
2727 TGCATTGGCATAAGAAGAGAAAGTTGGTATGAAAAGAGGCACCTTGAAATTTGTCCAATCTCAAG
1 TGCATTAGCACAAGAAGAGAAAGTTGGTACGAAAAGAGGCACCTTGAAACTTGTCCAATCTCAAG
* *
2792 ATCTTTGAGAATCGGTAAGTCTGTAGATGCATGCAAGCAACTATTTGAAGATGTAGAATCTCTTG
66 ATCTTTGAGAATCGATAAGTCTGAAGATGCATGCAAGCAACTATTTGAAGATGTAGAATCTCTTG
* *
2857 AATTGGGTGATGTGAAGGGTCACCCAAACCTTATTCCGAGCTTGGACTTGGGATTTAGTAAGTTG
131 AATTGGATGATGTGAAGGGTCACCCAAAACTTATTCCGAGCTTGGACTTGGGATTTAGTAAGTTG
* *
2922 ACTTCTCTAGATCTTCGATGGTGCAACTCTATGCAATGCCTAATTGATGCATCAAAGCAACAGGT
196 ACTTCTCTAGATCTTCGATGGTACAACTCTAAGCAATGCCTAATTGATGCATCAAAGCAACAGGT
2987 GCCAATCACTGCATTCTCTAATTTGAGAAAGTTATCATTAAGTTGTATGTTTGATTTGGAAGAGA
261 GCCAATCACTGCATTCTCTAATTTGAGAAAGTTATCATTAAGTTGTATGTTTGATTTGGAAGAGA
* *
3052 TGTGCAATGTTCCCCAGCCGCAAGGTTTTTTACAAAAGCTTGAAGAGGTTAAAGTTGAAGGTTGT
326 TGTGCAATGTTCCCCAGCCGCAAGGTTTTTTACAAAAGCTTGAAGAGGTTAAAGTTGAAAGCTGT
* * * *
3117 TATAATATGCAAGTTTTATTCCCGATTGTTGAATTTAGGGGCATAGAACAGGAAGGGCCCAGTCG
391 TATAATATGCAAGTTTTATTCCCGATTGTTGAATTGAGGAGCATAGAACAAGAAGGGCACAGTCG
*
3182 TCATTTAAGCCTCCAAAGTCTGAAGATTGTTGAAATAGAGGGATGCGTTAATTTGAAATATATCT
456 TCATTTAAGCCTCCAAAGTCTGAAGATTGTTGAAATAGAGGGATGCGATAATTTGAAATATATCT
3247 TCCCAATGTCAGTTGCTAATAGCCTTGGGCAATTGCATACTTTGAAGATAAAGAGTTGCTCACAA
521 TCCCAATGTCAGTTGCTAATAGCCTTGGGCAATTGCATACTTTGAAGATAAAGAGTTGCTCACAA
*
3312 TTGGAAGATATAATCCAAGACAGACCATTGGCATACAAATGTCTACTCCAAAGTCTAAGGGATGT
586 TTGGAAGATATAATCCAAGACAGACCAGTGGCATACAAATGTCTACTCCAAAGTCTAAGGGATGT
*
3377 ATGTGTGTCTCATTGCAATAACTTGACATCTCTTTTCCTTATTGTTCTATGGTCAAAGATTGGGA
651 ATGTGTATCTCATTGCAATAACTTGACATCTCTTTTCCTTATTGTTCTATGGTCAAAGATTGGGA
* * **
3442 AATTTGATTATACTTTTCATTTCAGGTTTCGTTGATTGATTTGCCTCAATTGAAAGGAAGGGATG
716 AATTTGATTATACTTTTCATTTCAGGTTTCATTGATTGACTTGCCTCAATTGAAAAAAAGGGATG
* *
3507 TGAACGACATTATGTTCACACAATCATCTTTGCAGAAGTTAAAAGTGCACAATTGTCCA
781 TGAAAGACATTATGCTCACACAATCATCTTTGCAGAAGTTAAAAGTGCACAATTGTCCA
* *
3566 TGCATTAGCACAAGAAGAGAAAGTTGGTACGAAAAGAGGGACCTTGAAACTTGTTCAATCTCAAG
1 TGCATTAGCACAAGAAGAGAAAGTTGGTACGAAAAGAGGCACCTTGAAACTTGTCCAATCTCAAG
3631 ATCTTTGAGAATCGATAAGTCTGAAGATGCATGCAAGCAACTATTTGAAGATGTAGAATCTCTTG
66 ATCTTTGAGAATCGATAAGTCTGAAGATGCATGCAAGCAACTATTTGAAGATGTAGAATCTCTTG
*
3696 AATTGGATGATGTGGAGGGTCACCCAAAACTTATTCCGAGCTTGGACTTGGGATTTAGTAAGTTG
131 AATTGGATGATGTGAAGGGTCACCCAAAACTTATTCCGAGCTTGGACTTGGGATTTAGTAAGTTG
* * * *
3761 ACTTCTCTAGATCTTGGTTGTTACCACTCTAAGCAATGCCTAATTGATGCATCAAAGCAACAGGT
196 ACTTCTCTAGATCTTCGATGGTACAACTCTAAGCAATGCCTAATTGATGCATCAAAGCAACAGGT
*
3826 GCCAATCACTGCATTCTCTAATTTGAGAAAGTTATCCTTAAG-TGATATGTTTGATTTGGAAGAG
261 GCCAATCACTGCATTCTCTAATTTGAGAAAGTTATCATTAAGTTG-TATGTTTGATTTGGAAGAG
*
3890 ATGTGCAATGTTCCCCAGCTGCAAGGTTTTTTACAAAAGCTTGAAGAGGTTAAAGTTGAAAGCTG
325 ATGTGCAATGTTCCCCAGCCGCAAGGTTTTTTACAAAAGCTTGAAGAGGTTAAAGTTGAAAGCTG
*
3955 TTATAATATGCAAGTTTTATTCCCGATTGTTGAATTGAGGAGCATAGAACAAGAAGGGCACATTC
390 TTATAATATGCAAGTTTTATTCCCGATTGTTGAATTGAGGAGCATAGAACAAGAAGGGCACAGTC
4020 GTCATTTAAGCCTCCAAAGTCTGAAGATTGTTGAAATAGAGGGATGCGATAATTTGAAATATATC
455 GTCATTTAAGCCTCCAAAGTCTGAAGATTGTTGAAATAGAGGGATGCGATAATTTGAAATATATC
*
4085 TTCCCAATGTCAGTTGCTAATAGCCTTGGGCAATTGCATACTTTGAAGATAAAGAGTTGCTCGCA
520 TTCCCAATGTCAGTTGCTAATAGCCTTGGGCAATTGCATACTTTGAAGATAAAGAGTTGCTCACA
*
4150 ATTGGAAGATATAATCCAAGACCGACCAGTGGCATACAAATGTCTACTCCAAAGTCTAAGGGATG
585 ATTGGAAGATATAATCCAAGACAGACCAGTGGCATACAAATGTCTACTCCAAAGTCTAAGGGATG
*
4215 TATGTGTATCTCATTGCAATAACTTGACATCTGTTTTCCTTATTGTTCTATGGTCAAAGATTGGG
650 TATGTGTATCTCATTGCAATAACTTGACATCTCTTTTCCTTATTGTTCTATGGTCAAAGATTGGG
*
4280 AAATTTGATTATGCTTTTCATTTCAGGTTTCATTGATTGACTTGCCTCAATTGAAAAAAAGGGAT
715 AAATTTGATTATACTTTTCATTTCAGGTTTCATTGATTGACTTGCCTCAATTGAAAAAAAGGGAT
* * * * *
4345 GTGAAAGGCATTTTGCTGACACAGTCGTCTTTGCAGAAGTTAAAAGTGCACAATTGTCC
780 GTGAAAGACATTATGCTCACACAATCATCTTTGCAGAAGTTAAAAGTGCACAATTGTCC
4404 TCAATTGACA
Statistics
Matches: 793, Mismatches: 44, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
838 2 0.00
839 791 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (839 bp):
TGCATTAGCACAAGAAGAGAAAGTTGGTACGAAAAGAGGCACCTTGAAACTTGTCCAATCTCAAG
ATCTTTGAGAATCGATAAGTCTGAAGATGCATGCAAGCAACTATTTGAAGATGTAGAATCTCTTG
AATTGGATGATGTGAAGGGTCACCCAAAACTTATTCCGAGCTTGGACTTGGGATTTAGTAAGTTG
ACTTCTCTAGATCTTCGATGGTACAACTCTAAGCAATGCCTAATTGATGCATCAAAGCAACAGGT
GCCAATCACTGCATTCTCTAATTTGAGAAAGTTATCATTAAGTTGTATGTTTGATTTGGAAGAGA
TGTGCAATGTTCCCCAGCCGCAAGGTTTTTTACAAAAGCTTGAAGAGGTTAAAGTTGAAAGCTGT
TATAATATGCAAGTTTTATTCCCGATTGTTGAATTGAGGAGCATAGAACAAGAAGGGCACAGTCG
TCATTTAAGCCTCCAAAGTCTGAAGATTGTTGAAATAGAGGGATGCGATAATTTGAAATATATCT
TCCCAATGTCAGTTGCTAATAGCCTTGGGCAATTGCATACTTTGAAGATAAAGAGTTGCTCACAA
TTGGAAGATATAATCCAAGACAGACCAGTGGCATACAAATGTCTACTCCAAAGTCTAAGGGATGT
ATGTGTATCTCATTGCAATAACTTGACATCTCTTTTCCTTATTGTTCTATGGTCAAAGATTGGGA
AATTTGATTATACTTTTCATTTCAGGTTTCATTGATTGACTTGCCTCAATTGAAAAAAAGGGATG
TGAAAGACATTATGCTCACACAATCATCTTTGCAGAAGTTAAAAGTGCACAATTGTCCA
Found at i:4937 original size:162 final size:162
Alignment explanation
Indices: 4670--5001 Score: 513
Period size: 162 Copynumber: 2.0 Consensus size: 162
4660 TTACAAATTC
* * * *
4670 TGAAGATAAAGAGGTGCTTTGGAATGGAAGAAATAATTCAAAACTCACCAGTATCAACCATAAGC
1 TGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAAACTCACAAGTATCAACCATAAAC
* *
4735 TTCCAATGTCTAAGGGAAGTACAAGTTACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
66 TTCCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
4800 TGTTGCTAATAATCTTGGG-AGATTGCAAACCT
131 TGTTGCTAATAATCTTGGGCA-ATTGCAAACCT
* * **
4832 TGAAGATAGAGAGATGCTTTGGAATGGCAGAAATAATCCAAGTCTCACAAGTATCAACCATAAAC
1 TGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAAACTCACAAGTATCAACCATAAAC
* * *
4897 TTTCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTTCCGATGTG
66 TTCCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
* *
4962 TGTTGCTAATAGTCTTGGGCAATTGCAAACTT
131 TGTTGCTAATAATCTTGGGCAATTGCAAACCT
4994 TGAAGATA
1 TGAAGATA
5002 TGGAGTTGTT
Statistics
Matches: 154, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
162 153 0.99
163 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (162 bp):
TGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAAACTCACAAGTATCAACCATAAAC
TTCCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
TGTTGCTAATAATCTTGGGCAATTGCAAACCT
Done.