Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_031846
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 103098
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Found at i:2401 original size:16 final size:16
Alignment explanation
Indices: 2380--2411 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2370 GTCGAGTTGG
2380 CTCAACTTGCGCTGCT
1 CTCAACTTGCGCTGCT
2396 CTCAACTTGCGCTGCT
1 CTCAACTTGCGCTGCT
2412 ATTGTTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.19, T:0.31
Consensus pattern (16 bp):
CTCAACTTGCGCTGCT
Left flanking sequence: Indices 1880 -- 2379
AATGTGCAACCACATAATAAGTATCATGTAAAGCGATGTCCAGCCCAGAATTGGCCAATACTATT
CCAGTGAGAGTAGAGTAGGTGCCCTTACTCGCGTGGGGCCAATTTTGGGTTTCCCTTGCGCTTTT
AGTGCACCTCTCTCGTAACCGTACATGATAGTTTTCCCATCATACGGCTTGCCCGCGCGTTTAAT
TCTCTCACGACTTGGCACGGGTTTCATAGCCTGTACCGACGTGTCGAAAGAGGCTGCGGTGCCTC
TCCGGTTTCCTTTTTTTCCCTCTGAGTTTATCTTTTCGATCGAAGAGAGAGAGCCCGAAGAAGTA
TTTTCCGTGGTCGGCTCTCTCGTGCTCGAGCTTGGCAAGTATAGCCAGAGAATAACGCGGCAGCA
AGGGCGCAATATATATTATATATTGCGCACCCCTTCAACAACTTTCTCAGTTTCATGAGTTTAGT
CTGGGCAGCATCTCGTTTATCTGTGAGATGTTCTTGTCGAGTTGG
Right flanking sequence: Indices 2412 -- 2911
ATTGTTGTGTCCTCTTTATTGGTCCGGATTTGTTGACTAGGCATTCGGTATCGTCCAGTATAGAT
CTGCCGCGTAGTCTTTTGAAAAGAGGCGTAGCGGGCCAAGCTTTTTGGTTGGGGTTTTCCCACAT
ACTTGTGTGCTCTTCTTGTCTTGGTTCAAACTTCTATAGGCTAAATAAATACAAGGGTCGAAGAC
TAAAACATTTGTATGCCAACTCGATCAGGTCTCCTTGAAATAGAAATCTGCAAGGGTTAAGGTTG
TTGTTAAGGCTGCTTTTGTCGTTGTTGAGAATGGAATGCAGTTCTTTCGCTATCAGGTTAATTAT
TCGCCTGACTAGTGAAGTCCTCACACGCCTGTGCGCCTGGCCCGCGTAGCAAGGGTATAGCAAAA
AGATTTTTCCAAACCTCATTTATCGAGGGCCTCCTCAGCAAAGTGAGGTGGTGGGTCACCTGCTG
TCCCGTGCTTGACAGAAATGGCGTCATCCGGTTAGGTGTTGGGAT
Found at i:17465 original size:17 final size:16
Alignment explanation
Indices: 17445--17480 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
17435 TTTTTTCTTT
*
17445 TTTTTTTTTTTTTCGAA
1 TTTTTTTATTTTTC-AA
17462 TTTTTTTATTTTTCAA
1 TTTTTTTATTTTTCAA
17478 TTT
1 TTT
17481 ATGGGAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTTTTATTTTTCAA
Left flanking sequence: Indices 16945 -- 17444
AGAAAAAGCTAGCAACATTTCGAATCCATACGGTGAAACCTTTGGCTTTTCTGTCATTTGTTATG
CGAAGGCCGAAGAATAGAAGCTTTCGGCCCTGCCAATGAATCATTTTTTTGTTTCAATTTTGAGT
TTTTTTATCTTGTATTCTTTTCTTCTTTAAAGCAAAATCCTAAAAACAAATAGAGCAGATGGTCC
AACTACAGAACTTTTTTTTTTTTCTTATGTTTATGGTTGTGCTTTGTGGTACGGCAGCACCCATA
CTATTTCAATGGTTGGTAAGTAGAGATGTTCCCACAGGTGCTCCTTTTTTTCATGGTACTATAAT
ACCTATTTTTACCTCTTTATTATTGCTTCTAGTTCATGTACATTCCAGGGGATTCATACGCTCTA
TGGAGAAAACAGAAAGGATAGTTTTGGTAAAAGCAAAATCCATTTTATTACTCAACATAATTGAA
AAAAGCTCCCCAAAAACTAGAGCTAGAAATGCATTTTTTTTCTTT
Right flanking sequence: Indices 17481 -- 17980
ATGGGAGATTTGTCATATTTAGAATCTTTCTGTAGTGTGCTTTGTTTTTTATTATTTTGTACATT
TTTTTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAACGTAGGCTTGGAATGGAAG
AAAAAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGTGCTTTGTTGGCCTGACAGA
AAAAAGAAACAAAGAAATAAAAAGAAAAAAAAATTTTCCTTTTTATTTCTTTCAAATAAATCAAA
AATATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTT
TGGCTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAAT
AGATTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGTCATGACTTTCGAAAAGT
TCCCATGACTATGAAAATTTCACATGGAGGAGTTTGCATCTTTAT
Found at i:17961 original size:19 final size:20
Alignment explanation
Indices: 17919--17961 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
17909 GGATGTTGGT
* *
17919 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
17939 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
17958 CATG
1 CATG
17962 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGACTATCGAAAAGTTCA
Left flanking sequence: Indices 17419 -- 17918
GAGCTAGAAATGCATTTTTTTTCTTTTTTTTTTTTTTTTCGAATTTTTTTATTTTTCAATTTATG
GGAGATTTGTCATATTTAGAATCTTTCTGTAGTGTGCTTTGTTTTTTATTATTTTGTACATTTTT
TTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAACGTAGGCTTGGAATGGAAGAAA
AAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGTGCTTTGTTGGCCTGACAGAAAA
AAGAAACAAAGAAATAAAAAGAAAAAAAAATTTTCCTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 17962 -- 18461
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCCAAATTAGTGCAAG
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCAA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAAAAAGGCCGCGGGTAACGCTAGTTGGCAAAA
TGGCGTTAAGCATTCCTAACAATACGGAAAAAGAGGTCGTGATGATATTCATCTACGTTCGTACT
GTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCTCATTAAGT
TCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAAC
Found at i:40329 original size:81 final size:81
Alignment explanation
Indices: 40194--40343 Score: 255
Period size: 81 Copynumber: 1.9 Consensus size: 81
40184 AAAATACTCG
* *
40194 CTATCGGATTTGAACCGATAACCCAGAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGACTTGAACCGATAACCCAGAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
40259 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* * *
40275 CTATCGGACTTGAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCAC
1 CTATCGGACTTGAACCGATAACCCAGAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
40340 CAAG
66 CAAG
40344 TGAGCTTAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGACTTGAACCGATAACCCAGAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 39694 -- 40193
CAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTGGAAATAACATC
AGTATTTCAACAACTTTTTGAGCTCATTTTTCACCCATATAATTCTTTATGTTTTTGTTTGAACA
AGCCAATTTATGCTTCACCCACTATACAAGAAAAGATGCAAGGAGGGTTACTTAGTCACCAGAGG
ATAACCACTTAGTAACTAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTAACAG
AACTGGGGCGCGTAGTTTATAGTAAAGCTTTTTTTTTTTAATATTTTGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTCCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 40344 -- 40843
TGAGCTTAAGGAAACGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCTAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCGTTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTCATCGATTTCTACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAATAAAA
TAATGCTTTTTTATAAAGAAATAATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATAGAATATAGTAGAAAATAATAAGTTGGCGAGGAAGTAAAAATATATA
TATATCTATAGATATATATATATTTTTTTTTATTTTGTGGATTAC
Found at i:103082 original size:10 final size:10
Alignment explanation
Indices: 103067--103092 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
103057 TCTTCTTATA
103067 AATAATCTTT
1 AATAATCTTT
103077 AATAATCTTT
1 AATAATCTTT
103087 AATAAT
1 AATAAT
103093 GCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (10 bp):
AATAATCTTT
Left flanking sequence: Indices 102567 -- 103066
ATCGGGGGGGGGGGAAGAGTTGTGCATCATAGGTACCTTCTTATTGCTGCGAAGGGCAATATGAA
AATAACCCCCCTATCCAACCTCATTCTGTTGCGCGAAATCCATCATTGGCTAAGCAATTATTTGG
TTATGCCATCTTAGGTTTCGCTTTAACAGAAGCTATTGCTTTGTTTGCCTTAATGATGGCCTTTT
TGATCTTATTTGTTTTTTAATTTTTTGGTGCTGGGATTTTTTGGGAAAAAAACTATATTTTGGCC
GCACCCTATTCGCAAAGCCAATAGGGCTGCGCCCAAAAAATCTAGATTTTTTAGCACCTTAGGGC
CGAACGATTAGTACGTTCGAGCCCTTCACCACTTGTTACCAAAAGCATAAGCGTAAAAAAACTGA
ACTGACAAAGATTTTAACCTTAAAGGCTCATTGGATAAAAAAAGAAGCAGGACAAATATATCTAT
ATATATATTTTTTTTTCTTTTTTAGCTGCTTCACTTCTTCTTATA
Right flanking sequence: Indices 103093 -- 103098
GCATAG
Done.