Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03615.F3
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: 5728
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Found at i:4194 original size:747 final size:747
Alignment explanation
Indices: 2727--4219 Score: 2601
Period size: 747 Copynumber: 2.0 Consensus size: 747
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 TTCGTTGATTGATTTGCCTCAATTGAAAGGAAGGGATGTGAACGACATTATGTTCACACAATCAT
651 TTCATTGATTGACTTGCCTCAATTGAAAAAAAGGGATGTGAAAGACATTATGCTCACACAATCAT
3442 CTTTGCAGAAGTTAAAAGTGCACAATTGTCCA
716 CTTTGCAGAAGTTAAAAGTGCACAATTGTCCA
* *
3474 TGCATTAGCACAAGAAGAGAAAGTTGGTACGAAAAGAGGGACCTTGAAACTTGTTCAATCTCAAG
1 TGCATTAGCACAAGAAGAGAAAGTTGGTACGAAAAGAGGCACCTTGAAACTTGTCCAATCTCAAG
3539 ATCTTTGAGAATCGATAAGTCTGAAGATGCATGCAAGCAACTATTTGAAGATGTAGAATCTCTTG
66 ATCTTTGAGAATCGATAAGTCTGAAGATGCATGCAAGCAACTATTTGAAGATGTAGAATCTCTTG
*
3604 AATTGGATGATGTGGAGGGTCACCCAAAACTTATTCCGAGCTTGGACTTGGGATTTAGTAAGTTG
131 AATTGGATGATGTGAAGGGTCACCCAAAACTTATTCCGAGCTTGGACTTGGGATTTAGTAAGTTG
* * * *
3669 ACTTCTCTAGATCTTGGTTGTTACCACTCTAAGCAATGCCTAATTGATGCATCAAAGCAACAGGT
196 ACTTCTCTAGATCTTCGATGGTACAACTCTAAGCAATGCCTAATTGATGCATCAAAGCAACAGGT
*
3734 GCCAATCACTGCATTCTCTAATTTGAGAAAGTTATCCTTAAG-TGATATGTTTGATTTGGAAGAG
261 GCCAATCACTGCATTCTCTAATTTGAGAAAGTTATCATTAAGTTG-TATGTTTGATTTGGAAGAG
*
3798 ATGTGCAATGTTCCCCAGCTGCAAGGTTTTTTACAAAAGCTTGAAGAGGTTAAAGTTGAAAGCTG
325 ATGTGCAATGTTCCCCAGCCGCAAGGTTTTTTACAAAAGCTTGAAGAGGTTAAAGTTGAAAGCTG
*
3863 TTATAATATGCAAGTTTTATTCCCGATTGTTGAATTGAGGAGCATAGAACAAGAAGGGCACATTC
390 TTATAATATGCAAGTTTTATTCCCGATTGTTGAATTGAGGAGCATAGAACAAGAAGGGCACAGTC
3928 GTCATTTAAGCCTCCAAAGTCTGAAGATTGTTGAAATAGAGGGATGCGATAATTTGAAATATATC
455 GTCATTTAAGCCTCCAAAGTCTGAAGATTGTTGAAATAGAGGGATGCGATAATTTGAAATATATC
*
3993 TTCCCAATGTCAGTTGCTAATAGCCTTGGGCAATTGCATACTTTGAAGATAAAGAGTTGCTCGCA
520 TTCCCAATGTCAGTTGCTAATAGCCTTGGGCAATTGCATACTTTGAAGATAAAGAGTTGCTCACA
*
4058 ATTGGAAGATATAATCCAAGACCGACCAGTGGCATACAAATGTCTACTCCAAAGTCTAAGGGATG
585 ATTGGAAGATATAATCCAAGACAGACCAGTGGCATACAAATGTCTACTCCAAAGTCTAAGGGATG
* * * * *
4123 TTTCATTGATTGACTTGCCTCAATTGAAAAAAAGGGATGTGAAAGGCATTTTGCTGACACAGTCG
650 TTTCATTGATTGACTTGCCTCAATTGAAAAAAAGGGATGTGAAAGACATTATGCTCACACAATCA
4188 TCTTTGCAGAAGTTAAAAGTGCACAATTGTCC
715 TCTTTGCAGAAGTTAAAAGTGCACAATTGTCC
4220 TCAATTGACA
Statistics
Matches: 704, Mismatches: 41, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
746 2 0.00
747 702 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (747 bp):
TGCATTAGCACAAGAAGAGAAAGTTGGTACGAAAAGAGGCACCTTGAAACTTGTCCAATCTCAAG
ATCTTTGAGAATCGATAAGTCTGAAGATGCATGCAAGCAACTATTTGAAGATGTAGAATCTCTTG
AATTGGATGATGTGAAGGGTCACCCAAAACTTATTCCGAGCTTGGACTTGGGATTTAGTAAGTTG
ACTTCTCTAGATCTTCGATGGTACAACTCTAAGCAATGCCTAATTGATGCATCAAAGCAACAGGT
GCCAATCACTGCATTCTCTAATTTGAGAAAGTTATCATTAAGTTGTATGTTTGATTTGGAAGAGA
TGTGCAATGTTCCCCAGCCGCAAGGTTTTTTACAAAAGCTTGAAGAGGTTAAAGTTGAAAGCTGT
TATAATATGCAAGTTTTATTCCCGATTGTTGAATTGAGGAGCATAGAACAAGAAGGGCACAGTCG
TCATTTAAGCCTCCAAAGTCTGAAGATTGTTGAAATAGAGGGATGCGATAATTTGAAATATATCT
TCCCAATGTCAGTTGCTAATAGCCTTGGGCAATTGCATACTTTGAAGATAAAGAGTTGCTCACAA
TTGGAAGATATAATCCAAGACAGACCAGTGGCATACAAATGTCTACTCCAAAGTCTAAGGGATGT
TTCATTGATTGACTTGCCTCAATTGAAAAAAAGGGATGTGAAAGACATTATGCTCACACAATCAT
CTTTGCAGAAGTTAAAAGTGCACAATTGTCCA
Found at i:4753 original size:162 final size:162
Alignment explanation
Indices: 4486--4817 Score: 513
Period size: 162 Copynumber: 2.0 Consensus size: 162
4476 TTACAAATTC
* * * *
4486 TGAAGATAAAGAGGTGCTTTGGAATGGAAGAAATAATTCAAAACTCACCAGTATCAACCATAAGC
1 TGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAAACTCACAAGTATCAACCATAAAC
* *
4551 TTCCAATGTCTAAGGGAAGTACAAGTTACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
66 TTCCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
4616 TGTTGCTAATAATCTTGGG-AGATTGCAAACCT
131 TGTTGCTAATAATCTTGGGCA-ATTGCAAACCT
* * **
4648 TGAAGATAGAGAGATGCTTTGGAATGGCAGAAATAATCCAAGTCTCACAAGTATCAACCATAAAC
1 TGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAAACTCACAAGTATCAACCATAAAC
* * *
4713 TTTCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTTCCGATGTG
66 TTCCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
* *
4778 TGTTGCTAATAGTCTTGGGCAATTGCAAACTT
131 TGTTGCTAATAATCTTGGGCAATTGCAAACCT
4810 TGAAGATA
1 TGAAGATA
4818 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.