Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2472
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: 14871
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2618 original size:23 final size:23
Alignment explanation
Indices: 2592--2649 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
2582 AAGTTGATAA
2592 AAAT-TCAATG-CTAATTGAAACTG
1 AAATATCAATGTCTAATT-AAAC-G
*
2615 AAATATGAATGTCTAATTAAACG
1 AAATATCAATGTCTAATTAAACG
*
2638 AAATATGAATGT
1 AAATATCAATGT
2650 TTCTTTTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 17 0.53
24 9 0.28
25 6 0.19
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.31
Consensus pattern (23 bp):
AAATATCAATGTCTAATTAAACG
Found at i:3108 original size:884 final size:881
Alignment explanation
Indices: 1703--3444 Score: 2074
Period size: 892 Copynumber: 2.0 Consensus size: 881
1693 TGTAGTAATG
* *
1703 AAAATCAATGCTAATTCAACTGAAATATTTGAATTGTTCTTAATTAAATTGAAATATGAATGTTT
1 AAAATCAATGCTAATTAAACTGAAATA-TTGAATTGTTCTTAATTAAATCGAAATATGAATGTTT
*
1768 TCTTTTATATGTAACGTTATTATAGTCCAATGTGGTATAACACTTTCTATAAATGCCCAATTATT
65 TCTTTTATATGTAACGATATTATAGTCCAATGTGGTATAACACTTTCTATAAATGCCCAATTATT
1833 TCCCTGCAAAATCTTGCTCGAAATTAATTTTACGAACCAAATTTAACTAGTAACACAGATTCGAG
130 TCCC-GCAAAATCTTGCTCGAAATTAATTTTACGAACCAAATTTAACTAGTAACACAGATTCGAG
*
1898 CGATATGCAAGCTTTAATGTTATATTCCGTACTAGTGGTTTTATTCTTAACTTGCGGCAGGCAGT
194 CGATATGCAAGCATTAATGTTATATTCCGTACTAGTGGTTTTATTCTTAACTTGCGG-AGGCAGT
* * * *
1963 AATGGCTACGAAGGAGAACGGCCGGATGTTAAGGAAAATAATTGTGAAACTAAAATGGTTGCCCT
258 AATGGCTACGAAGGAGAACGACCAGATATTAAGGAAAATAATTGTAAAACTAAAATGGTTGCCCT
* *
2028 GTGTTTATAGAAGCTTTCCTACGATAATTTCGAGAGAGGAAGTATTTTCACAAGTGTTGACGGCG
323 GTGTTTATAGAAGCTTTCCTACGATAATTTCGAGACAGGAAGTATTTTAACAAGTGTTGACGGCG
*
2093 AACTTGTTCTCGATCTATATGTGTTCGGGAAAAGTTGCCACTCAGCATTAGTAAAGAGGCTCTAG
388 AAC---TTCTCG----ATATGTGTTCGGGAAAAGTTGCCACTCAACATTAGTAAAGAGGCTCTAG
* *
2158 AAAATCCTCTATTTCAAAGACTTAAGCCCAGCGGCAATTATAGCGAAGAGGCATTCAGACATGG-
446 AAAATCCTCTATTTCAAAGACTAAAGCCCAGCGACAATTATAGCGAAGAGGCATTCAGACATGGA
*
2222 AATTG-CCTTGC-TTG-ATCGCATTCACCATCTTCCG-TCTGCT-TAAGGATAT-TGATTGCTTC
511 AATTGCCCTTGCATTGCATCG-ATTCACCATC-TCCGATCTGCTGGAA-GATATATGATTGCTT-
* *
2281 AGCTAAC-AAA-T-GGTTACAAAGACG-TAACGCCGGCCTAAATTGTTCTTTTGTTTTTATCTTG
572 AGCTAACAAAACTCGGTTAC-AAGACGTTAACG--GGCCAAAATTGTTCTTTTGTCTTTAT-TT-
* *
2342 TTGATATTG-TCC-GAAGCTTCATT-AAAGT-TGCA-TAAA-TTTAAGCCT-AGTTAA-AT-TAT
632 TTGATATTGTTCCTAAAGCGTCATTAAAAGTGT-CATTAAATTTTAAGCCTGAGTTAACATGTA-
*
2398 TATTTAATTCTAAAAAAAATTAAATGCTTCTACGAGAAG-CATTACTTAATTCACATTATGATTT
695 TATTTAATTCT-AAAAAAATTAAATGCTTCTA-GAGAAGCCATTACTTAA-T-ACACTATGA-TT
* * ** *
2462 TTTATACATGCCATTATTTTTTACTTTTATAGCATTGGAAAACTC-G-GATGCATTTCAAATCGA
755 TTTATACATG-CATTATTTTTAAC-TTTATAGCATTGG--AACTCAGAAAACCATCTCAAATCGA
2525 GCACTAGATATTGTTTCACATTGTTTAATTCACACAAATATATTATTTATAAACATTAAGTTGAT
816 GCACTAGATATTGTTTCACATTGTTTAATTCACACAAATATATTATTTATAAACATTAAGTTGAT
2590 A
881 A
2591 AAAATTCAATGCTAATTGAAACTGAAATA-TGAA-TG-TC-TAATTAAA-CGAAATATGAATG-T
1 AAAA-TCAATGCTAATT-AAACTGAAATATTGAATTGTTCTTAATTAAATCGAAATATGAATGTT
*
2650 TTCTTTTCT-TGTAACGATATTATAGTCCTCCAATGTGGCTATAACACTTTCCTATAAATG-CCA
64 TTCTTTTATATGTAACGATATTATAG---TCCAATGTGG-TATAACACTTT-CTATAAATGCCCA
* * * *
2713 GTTTTTTCCC-CAAAATCTTGTTCTGATATTAATTTTACGAACCAAATTTTAACTAGTAACATCA
124 ATTATTTCCCGCAAAATCTTGCTC-GAAATTAATTTTACGAACCAAA-TTTAACTAGTAACA-CA
* * * *
2777 GATTCGAATCTAGCGGTATGGCAAGCCATTCATGTTTTATTTCGTACTAGTGG-TTTATTCTTAA
186 GATTCG-----AGCGATAT-GCAAG-CATTAATGTTATATTCCGTACTAGTGGTTTTATTCTTAA
2841 CTTGC-G-GGCAGTAATGGCTAC-ATAGTCGAGAACGACCAGATTATTAAGGAAAATAATTGTCA
244 CTTGCGGAGGCAGTAATGGCTACGA-AG--GAGAACGACCAGA-TATTAAGGAAAATAATTGT-A
*
2903 AAACTAAAATGGGTTTGCCCCTGTGTTCT-TAGAAGCTTT-C-ACGAGTATTTTCGAGACAGG-A
304 AAACTAAAAT-GG-TTG-CCCTGTGTT-TATAGAAGCTTTCCTACGA-TAATTTCGAGACAGGAA
* * * * *
2964 -TATTTCTAACAAGTGTTGCCTGGTGAAC-T-T-G-T-TGTGTT-GGGACAAGTTTTCCGCTCAA
364 GTATTT-TAACAAGTGTTGAC-GGCGAACTTCTCGATATGTGTTCGGGAAAAG-TTGCCACTCAA
*
3022 CATTAGTAAAGAGGACTCTAGAAAAATCCTCTA-TTCAAAGACCTAAAGCGCAGCGAC-A-TATA
426 CATTAGTAAAGAGG-CTCTAG-AAAATCCTCTATTTCAAAGA-CTAAAGCCCAGCGACAATTATA
3084 GCGAAGA-GCATTCAAGACATGGAATAATTGCCCTTGCATTGCATCGATTCACCATCTCCGATCT
488 GCGAAGAGGCATTC-AGACATGG-A-AATTGCCCTTGCATTGCATCGATTCACCATCTCCGATCT
* *
3148 GCTGGAAGATATATGATTTCTTAGCTAACAAAAACTTCGGTTACAAGACGTTAATGGGCCAAAAT
550 GCTGGAAGATATATGATTGCTTAGCTAAC-AAAAC-TCGGTTACAAGACGTTAACGGGCCAAAAT
3213 TGTTCTTTTGTCTTTATTTTTGATATTGTTTCCTAAAGCGTCATTAAAAGTGTCATTAAATTTTA
613 TGTTCTTTTGTCTTTATTTTTGATATTG-TTCCTAAAGCGTCATTAAAAGTGTCATTAAATTTTA
* * * * **
3278 AGCCTGTGTTAACATGTATATTTAGTTCTAAGAAAATTAAATGGTTCTATTGAAGCCATTACTTA
677 AGCCTGAGTTAACATGTATATTTAATTCTAAAAAAATTAAATGCTTCTAGAGAAGCCATTACTTA
3343 ATACACTATGATTTTTATACATGCATTATTTTTAACTTTATAGCATTGGAACTCAGAAAACCATC
742 ATACACTATGATTTTTATACATGCATTATTTTTAACTTTATAGCATTGGAACTCAGAAAACCATC
3408 TCAAATCGAGCACTAGATATTGTTTCACATTGTTTAA
807 TCAAATCGAGCACTAGATATTGTTTCACATTGTTTAA
3445 AATTGGACAC
Statistics
Matches: 744, Mismatches: 48, Indels: 120
0.82 0.05 0.13
Matches are distributed among these distances:
882 15 0.02
883 22 0.03
884 71 0.10
885 55 0.07
886 61 0.08
887 24 0.03
888 18 0.02
889 44 0.06
890 56 0.08
891 7 0.01
892 101 0.14
893 67 0.09
894 67 0.09
895 32 0.04
896 37 0.05
897 52 0.07
898 13 0.02
899 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (881 bp):
AAAATCAATGCTAATTAAACTGAAATATTGAATTGTTCTTAATTAAATCGAAATATGAATGTTTT
CTTTTATATGTAACGATATTATAGTCCAATGTGGTATAACACTTTCTATAAATGCCCAATTATTT
CCCGCAAAATCTTGCTCGAAATTAATTTTACGAACCAAATTTAACTAGTAACACAGATTCGAGCG
ATATGCAAGCATTAATGTTATATTCCGTACTAGTGGTTTTATTCTTAACTTGCGGAGGCAGTAAT
GGCTACGAAGGAGAACGACCAGATATTAAGGAAAATAATTGTAAAACTAAAATGGTTGCCCTGTG
TTTATAGAAGCTTTCCTACGATAATTTCGAGACAGGAAGTATTTTAACAAGTGTTGACGGCGAAC
TTCTCGATATGTGTTCGGGAAAAGTTGCCACTCAACATTAGTAAAGAGGCTCTAGAAAATCCTCT
ATTTCAAAGACTAAAGCCCAGCGACAATTATAGCGAAGAGGCATTCAGACATGGAAATTGCCCTT
GCATTGCATCGATTCACCATCTCCGATCTGCTGGAAGATATATGATTGCTTAGCTAACAAAACTC
GGTTACAAGACGTTAACGGGCCAAAATTGTTCTTTTGTCTTTATTTTTGATATTGTTCCTAAAGC
GTCATTAAAAGTGTCATTAAATTTTAAGCCTGAGTTAACATGTATATTTAATTCTAAAAAAATTA
AATGCTTCTAGAGAAGCCATTACTTAATACACTATGATTTTTATACATGCATTATTTTTAACTTT
ATAGCATTGGAACTCAGAAAACCATCTCAAATCGAGCACTAGATATTGTTTCACATTGTTTAATT
CACACAAATATATTATTTATAAACATTAAGTTGATA
Found at i:8945 original size:25 final size:26
Alignment explanation
Indices: 8907--8957 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
8897 TAAATTAATG
8907 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
8933 CTAATTAAA-TGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
8958 TTCTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (26 bp):
CTAATTAAACTGAAATATTGAATGTT
Found at i:10958 original size:26 final size:26
Alignment explanation
Indices: 10929--10980 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10919 AAAATTAATG
10929 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
10955 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
10981 TTCTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
CTAATTAAACTGAAATATTGAATGTT
Found at i:13050 original size:26 final size:26
Alignment explanation
Indices: 13020--13071 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
13010 TAAATTAATG
13020 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
13046 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
13072 TTCTTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
CTAATTAAACTGAAATATTGAATGTT
Done.