Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4782.1
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: 44497
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:2414 original size:19 final size:18
Alignment explanation
Indices: 2378--2421 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2368 GTTACCAAAA
2378 TATAAATTTTAGAATTTT
1 TATAAATTTTAGAATTTT
*
2396 TATAAATATTTAG-GTTTT
1 TATAAAT-TTTAGAATTTT
*
2414 TAAAAATT
1 TATAAATT
2422 ATTTTAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATAAATTTTAGAATTTT
Found at i:3050 original size:213 final size:212
Alignment explanation
Indices: 2679--3098 Score: 777
Period size: 213 Copynumber: 2.0 Consensus size: 212
2669 CAAAGAGATC
2679 TTAACTCTTATTTGTTATTTGAGTTATTCAAATTATAAAGTTCAACTCGACTAGAACTTGAAACT
1 TTAACTCTTATTTGTTATTTGAGTTATTCAAATTATAAAGTTCAACTCGACTAGAACTTGAAACT
**
2744 TAAATTAATTATTCGAGTTAACTCGAAAAAATTAAATAATTTGAATAACTCGATTAAATTAACTC
66 TAAATTAATTATTCGAGTTAACTCGAAAAAATTAAATAATTAAAATAACTCGATTAAATTAACTC
*
2809 AAAATAATAATAATAAAACAATTTTTCAAATTAAATTAAATTTTACTCACCTTTAAACTTCTCCG
131 AAAATAATAATAATAAAACAAATTTTCAAATTAAA-TAAATTTTACTCACCTTTAAACTTCTCCG
2874 ATCTGCGGTATAAGGATA
195 ATCTGCGGTATAAGGATA
*
2892 TTAACTCTTATTTGTTATTTGAGTTATTCGAATTATAAAGTTCAACTCGACTAGAACTTGAAACT
1 TTAACTCTTATTTGTTATTTGAGTTATTCAAATTATAAAGTTCAACTCGACTAGAACTTGAAACT
*
2957 TAAATTAATTATTCGAGTTGACTCGAAAAAATTAAATAATTAAAATAACTCGATTAAATTAACTC
66 TAAATTAATTATTCGAGTTAACTCGAAAAAATTAAATAATTAAAATAACTCGATTAAATTAACTC
*
3022 AAAATAATAATAATAAAACAAATTTTCAAGTTAAATAAATTTTACTCACCTTTAAACTTCTCCGA
131 AAAATAATAATAATAAAACAAATTTTCAAATTAAATAAATTTTACTCACCTTTAAACTTCTCCGA
3087 TCTGCGGTATAA
196 TCTGCGGTATAA
3099 TATCTCTAAG
Statistics
Matches: 201, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
212 42 0.21
213 159 0.79
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (212 bp):
TTAACTCTTATTTGTTATTTGAGTTATTCAAATTATAAAGTTCAACTCGACTAGAACTTGAAACT
TAAATTAATTATTCGAGTTAACTCGAAAAAATTAAATAATTAAAATAACTCGATTAAATTAACTC
AAAATAATAATAATAAAACAAATTTTCAAATTAAATAAATTTTACTCACCTTTAAACTTCTCCGA
TCTGCGGTATAAGGATA
Found at i:3529 original size:19 final size:18
Alignment explanation
Indices: 3507--3546 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
3497 AATAAAACAC
*
3507 TAAAAATTTATTTTAAAAA
1 TAAAAAGTT-TTTTAAAAA
3526 TAAAAAAGTTTTTTAAAAA
1 T-AAAAAGTTTTTTAAAAA
3545 TA
1 TA
3547 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 1 0.05
19 11 0.58
20 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAAAAGTTTTTTAAAAA
Found at i:17420 original size:727 final size:718
Alignment explanation
Indices: 16006--18282 Score: 3119
Period size: 744 Copynumber: 3.1 Consensus size: 718
15996 CTTGTCTCAA
* **
16006 AAACAAGGTGAATGGATGTTCATGATTTGTATTCTTAATAACTTGTAATGACGATTGTGATGCAC
1 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTTGTAATGGTGATTGTGATGCAC
* * *
16071 ATTCAATATGAACAACAAACTTACAAGGAGAACAACCATAAACAAATCCTCTTCGCCGTGGTACT
66 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAACAAATCCTCTTCGCCTTGTTACT
* *
16136 TGGCATACCTTGCAAGAGAGTCGTTTGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGTC
131 TGGCATATCTTGCAAGAGAGTCGTTCGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGG-C
* *
16201 A-CATGATTGAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCACAATCAGGAG
195 ACCATGATTCAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCACAGTCAGGAG
* *
16265 AAAAGTGTGTACACA-TTGCTAATGGTTCCCAACATCCAAAGCACTTACTAACATCTTTGAGTTT
260 AAAAGTGTGTATA-ATTTGCTAATGGTTCCCAACATCCAAAGCACTTA-T--TATC----A----
* * *
16329 TTTATCACCATTTTCAGTGGAAATCAATGGATCATGAAGGGCAACATGCTCAAGCTCTTTCAAAT
313 TCT-TCA--A-GTTCA-T-----TC-A---ATCTTGAAGGGCAACATGCTCAAGCTCTTTCAAAT
* * * * * * **
16394 TATTCTCAGCAATATTAAGTGTAAACAAAGCACATTTAATATGAAATTCCAATTCACAACTAGAG
364 TATTCTCAGCAATATTAAATGTAAACAAAGCACATTAAATACGAAAGTCAAAATGGC-A--AGAG
* ** * *** * * * * * *
16459 CAGTGATAAACAGACTTGTCACCAAATTCATGGCAGAAACTGCAAAAGTA-CGCTCCAGATAAAT
426 CAGTGATAAACAAACTCATTACCGCCTTTATCGCAAAAATTGCAAATGTACCG-TCCAGATGAAT
* * * *
16523 GAGGTG-ACTTTTGCATAAGAAGAAGAGGATGGTTGA-GATGAAAAGGGTGATTAAGCTCCAAAG
490 AAGGTGCA-TTTTGCAGAAGAAGAAGAGGAT-GATGAGGATGAAAAGGATGATTAAGCTCCAAAG
16586 GTGCCTCGGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGTAAAAACATGTAGCA
553 GTGCCTCGGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGTAAAAACATGTAGCA
16651 GACACCTTATCCCCACACCTGGAGCAATCAGTTACACCGCTTTGATTGTCGATCAGCTGCTCTTG
618 GACACCTTATCCCCACACCTGGAGCAATCAGTTACACCGCTTTGATTGTCGATCAGCTGCTCTTG
16716 ATTCAACATAAGAAACAGGGGATGTTGGTGCTCATT
683 ATTCAACATAAGAAACAGGGGATGTTGGTGCTCATT
*
16752 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGGTGATTGTGATGCAC
1 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTTGTAATGGTGATTGTGATGCAC
*
16817 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAAAAAATCCACTTTCCGTACTTCGC
66 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCAT-AAACAA---A---TCC-T-CTTCGC
* * * *
16882 CTTGTTACTCGACATATCTTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGCTT
122 CTTGTTACTTGGCATATCTTGCAAGAGAGTCGTTCGCTATTAAATTGTAGAACAAGAGGATGCTT
16947 GCGATGGCACCCATGATTCAGTTTGAAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCA
187 GCGATGGCA-CCATGATTCAGTTTG-AAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCA
* *** *
17012 CAGTCAGGAGAAAAGTGTGTATAATTTGTTAATGGTTCCTGGCACCCAAAGCACTTATTATCATC
250 CAGTCAGGAGAAAAGTGTGTATAATTTGCTAATGGTTCCCAACATCCAAAGCACTTATTATCATC
17077 TTCAAGTTC-TTC-ATCTTGAAGGGCAACATGCTCAAGCTCTTTCAAATTATTCTCAGCAATATT
315 TTCAAGTTCATTCAATCTTGAAGGGCAACATGCTCAAGCTCTTTCAAATTATTCTCAGCAATATT
17140 AAATGTAAACAAAGCACATTAAATACGAAAGTCAAAATGGCAAGAGCAGTGATAAACAAACTCAT
380 AAATGTAAACAAAGCACATTAAATACGAAAGTCAAAATGGCAAGAGCAGTGATAAACAAACTCAT
17205 TACCGCCTTTATCGCAAAAATTGCAAATGTACCGTCCAGATGAATAAGGTGCATTTTGCAGAAGA
445 TACCGCCTTTATCGCAAAAATTGCAAATGTACCGTCCAGATGAATAAGGTGCATTTTGCAGAAGA
17270 AGAAGAGGATGATGAGGATGAAAAGGATGATTAAGCTCCAAAGGTGCCTCGGCACATACCTTGTG
510 AGAAGAGGATGATGAGGATGAAAAGGATGATTAAGCTCCAAAGGTGCCTCGGCACATACCTTGTG
17335 AAGATAAAACCCACAGTGCTCCGCACAGTAAAAACATGTAGCAGACACCTTATCCCCACACCTGG
575 AAGATAAAACCCACAGTGCTCCGCACAGTAAAAACATGTAGCAGACACCTTATCCCCACACCTGG
17400 AGCAATCAGTTACACCGCTTTGATTGTCGATCAGCTGCTCTTGATTCAACATAAGAAACAGGGGA
640 AGCAATCAGTTACACCGCTTTGATTGTCGATCAGCTGCTCTTGATTCAACATAAGAAACAGGGGA
17465 TGTTGGTGCTCATT
705 TGTTGGTGCTCATT
*
17479 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTTGTAATGGTGATTGTGATGCGC
1 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTTGTAATGGTGATTGTGATGCAC
17544 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAACAAATCCTCTTCGCCTTGTTACT
66 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAACAAATCCTCTTCGCCTTGTTACT
** *
17609 TGGCATATCTTGCAAGAGAGTCGTTCGCTATTAAATTGTAGAGTAAGAGGATGCTTGTGATGGCA
131 TGGCATATCTTGCAAGAGAGTCGTTCGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGCA
* * * * *
17674 CTTATGATTTAGTTTGAAAGGAAGCTTAGCGCATTTTTCATGTAAATTAAATCTACAGTCAGGAG
196 C-CATGATTCAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCACAGTCAGGAG
* * * *
17739 AAAAGTGTGCATACTTTGCTAATGGTTCCCAACATCCAAAGCACTTACTAACATCTTCAAGTTCT
260 AAAAGTGTGTATAATTTGCTAATGGTTCCCAACATCCAAAGCACTTATTATCATCTTCAAG----
* *
17804 TCATCACCATTGCTAGTGGAAATCAAAGGAAGTTGAAGGGCAAAATGGTCAAGCTCTTTCAAATT
321 T--T---CATT-C-------AATC--------TTGAAGGGCAACATGCTCAAGCTCTTTCAAATT
17869 ATTCTCAGCAATATTAAATGTAAACAAAGCACATTAAATACGAAAGTCAAAATGGCAAGAGCAGT
365 ATTCTCAGCAATATTAAATGTAAACAAAGCACATTAAATACGAAAGTCAAAATGGCAAGAGCAGT
17934 GATAAACAAACTCATTACCGCCTTTATCGCAAAAATTGCAAATGTACCGTCCAGATGAATAAGGT
430 GATAAACAAACTCATTACCGCCTTTATCGCAAAAATTGCAAATGTACCGTCCAGATGAATAAGGT
* *
17999 GCATTTTGCAGAAGAAGAAGAGGATGATGAGGATGAAAAGGATGTTTAAGCTCCAAAGGTGCGTC
495 GCATTTTGCAGAAGAAGAAGAGGATGATGAGGATGAAAAGGATGATTAAGCTCCAAAGGTGCCTC
* * * * *
18064 GGCACATGCCTTGTGAAGATAAAACCCACAGTGCTCCACACAGCAAAAACATGGAGCAGACGCCT
560 GGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGTAAAAACATGTAGCAGACACCT
* * * * * * * *
18129 TCTCCCCGCAGCTCGAGCAATCAGTTACACCCCTTTGATTATCCATCAGCTGCTCTTGAGTCAAC
625 TATCCCCACACCTGGAGCAATCAGTTACACCGCTTTGATTGTCGATCAGCTGCTCTTGATTCAAC
* *
18194 ATAAGAAACAGGGGATGTTGGTGCCCGTT
690 ATAAGAAACAGGGGATGTTGGTGCTCATT
*
18223 AAACAAGGTAAATGGATGTTCATGATTTGTACTCTTAATAACTTGTAATGGTGATTGTGA
1 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTTGTAATGGTGATTGTGA
18283 AATTTTAGAA
Statistics
Matches: 1393, Mismatches: 94, Indels: 90
0.88 0.06 0.06
Matches are distributed among these distances:
717 99 0.07
718 85 0.06
719 1 0.00
720 3 0.00
721 1 0.00
723 2 0.00
726 10 0.01
727 374 0.27
728 4 0.00
729 1 0.00
730 83 0.06
735 2 0.00
736 3 0.00
740 1 0.00
742 3 0.00
743 1 0.00
744 427 0.31
745 3 0.00
746 101 0.07
747 5 0.00
750 2 0.00
753 3 0.00
754 6 0.00
755 71 0.05
756 15 0.01
757 87 0.06
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (718 bp):
AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTTGTAATGGTGATTGTGATGCAC
ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAACAAATCCTCTTCGCCTTGTTACT
TGGCATATCTTGCAAGAGAGTCGTTCGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGCA
CCATGATTCAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCACAGTCAGGAGA
AAAGTGTGTATAATTTGCTAATGGTTCCCAACATCCAAAGCACTTATTATCATCTTCAAGTTCAT
TCAATCTTGAAGGGCAACATGCTCAAGCTCTTTCAAATTATTCTCAGCAATATTAAATGTAAACA
AAGCACATTAAATACGAAAGTCAAAATGGCAAGAGCAGTGATAAACAAACTCATTACCGCCTTTA
TCGCAAAAATTGCAAATGTACCGTCCAGATGAATAAGGTGCATTTTGCAGAAGAAGAAGAGGATG
ATGAGGATGAAAAGGATGATTAAGCTCCAAAGGTGCCTCGGCACATACCTTGTGAAGATAAAACC
CACAGTGCTCCGCACAGTAAAAACATGTAGCAGACACCTTATCCCCACACCTGGAGCAATCAGTT
ACACCGCTTTGATTGTCGATCAGCTGCTCTTGATTCAACATAAGAAACAGGGGATGTTGGTGCTC
ATT
Found at i:40335 original size:3 final size:3
Alignment explanation
Indices: 40329--40358 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
40319 AAAAAACGAC
40329 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40359 CTAAATTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.