Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ905371
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: 282934
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:28710 original size:24 final size:24
Alignment explanation
Indices: 28683--28730 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28673 AACTTGCAAA
*
28683 CATAACCAGGCAGTGAGGGATCTT
1 CATAACCAGGCAGTGAGGAATCTT
* *
28707 CATACCCAGGCGGTGAGGAATCTT
1 CATAACCAGGCAGTGAGGAATCTT
28731 AAGGGGAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (24 bp):
CATAACCAGGCAGTGAGGAATCTT
Left flanking sequence: Indices 28183 -- 28682
AAATCAGGTCTTGTAATATACTGCAGGGCTCCAACGATGCTTCTGTACAGAGATGGATTATGAAA
TGGAGTAGAAGAGACTGCAGCAGAGGACTGATTTTAAAGTTAATTGGAGAAGAGCAGGGCTTACA
ATTCAGCATAGCAGCTCTCTGGAGGAGATCCAACGCATATTTTTGCTGTGTTAAAAAAAGTCCAC
GATCATTCTTGTCTTGAGTACCTCAATGCCAAGAAAATAGTTCAAGTTCCCGAGGTTCTTTATAG
CAAACTGAGCACTTAATTCAGTGATTAGAGTGGAGATATAAGAGGTATCACTGCCAGTTATAATA
ATATCATCCACATAAACCGCAAGAATTGTAGTTCGCAAACTGTTAGTTTGAATAAATAACGAGGA
ATCACTACGGCTCATAAGAAAGCCTTTACTGATTAAAAAGCTATAAAACTTATCATACCAAGCGC
GTGATGCCTGTTTAAGACCATACAATGCTTTCTGCAACTTGCAAA
Right flanking sequence: Indices 28731 -- 29230
AAGGGGAGGGGTTGGTAGTGAAGGGAAGTCCAGGGCTGTGTCTGATCAGCTTACTGGGAGAATTC
CAGGCGAGGGAGTATTGGTAAGGTTATGGAGGAAAGAGGAAATAGGATTTTGGGCATCTCTCGTT
GCTTCGGATGTTTATGAGAAAGAAGCTTCTCACAGATATTGACTTTTAGATAGATACCAGCATAG
TATCTTAATTAGCAGTTTCTTGAACTTGGTTGCACTCGTAAAGCAGCTTAAGAGAGCAACGAAAG
ACGGAGCGGTGATATTTCCTGACTAGCAAGTGGAGGATCATTCCAGGCTCTAATTCAGTCTCTGA
TGGCGTAGCTGATGTGTCATGCTAGGAAGCTGAGCTAGGGCATTTCTTCTTTCGGTTTAAGTGTT
CTAAGAAGTGAAAACCCTCCTCTCCGCTTCTGGCAGCATAGAAGGAAGCTTGGGGGAAAGGTCTA
AGTGCAAGCATTGAGTCAAACTGATTCAGGTATAGCAATGTAGTT
Found at i:55605 original size:21 final size:21
Alignment explanation
Indices: 55546--55597 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
55536 GCCAATACCC
* * * *
55546 GCAATCAAGTCATACTCAACA
1 GCAATCAAGTTAAAATCACCA
55567 GCAATCAAGTTAAAATCACCA
1 GCAATCAAGTTAAAATCACCA
55588 GCAATCAAGT
1 GCAATCAAGT
55598 AAGCATCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (21 bp):
GCAATCAAGTTAAAATCACCA
Left flanking sequence: Indices 55046 -- 55545
AGGGTCCTCTTGGAAATCCTGCTCCTTCTACGGCTGCTAGTATCCTTGTTCTTCTACTCGCAGGC
AGGGCTGCTCTTGCTATTGTTGCTAGGATCCTCTTATCCTATTGGTTGCTAGTCCCGGGCTTCTA
GGACAAAGTGTAAAGAGAAGAGTTAGAGTTCTTCCTCTTTCTCCCCTATCACTTAAAGGGAGATG
GCCTAATTTCTATTCTATCTATGGATCGAGAATAATCGTCAGTTTGAGGCCTGTCTTTGAACATA
AGGCATGAGAATCCTTCTCAGCGGAGTCTCTGTGTGTTGAGATCGAGGGTAGTTTGATTCTGGGA
ACCGAGCCGGCTTCGGCCAACGAATGAAGTTCTTTAGTAGGTTATCCGGGCATAGTTGAGTTAGG
AGCGAGGGAGTTCCATTTACTAGCAATATCCTCTTATTCTCGGGAAAGGGCAGTTCCAGCTAGGG
CTAGAGGACAGTCACATTCCTATTAGTAGGTTGAGGCCAATACCC
Right flanking sequence: Indices 55598 -- 56097
AAGCATCAACTGCTTTACCGTATAACAGTTCCTTGAGCAGATGTGATTGCAAATCTTCTACTACC
AAAGAATCTCTATCCGTCTTCCTTCCAACTAGCACAGAGCCTATACGCACTGAGGAGAATTGCTA
TGACCTAGCAGACCTGCACTAGCAAGACCTCTTTGCATCCGTTAGAGTAAAACCCTTGGCTTGGC
GTTCTGCCCCTTTTCGGTATGGTCCTTTCATTCAGGCCTTTCCTTATGCACCGATGGTTTCATGA
TTCCTTGAAAAAAAAAATGTTTGCGAGCGTCAAAGCACCTAACCATACCTACTACACCATGCACT
CCGCCGGTAAGCAGCCCGGACATGAAAGAAAGTGCATTTGGAAGCATATGTGTGCCACTTTGGCA
CGAGATTTCAGCTCTACTTTGACTTTCATGGTTCCACTGTTCGTCGAGATCCCTTGAGTGCTACT
AAATGTAGAGAAAGACATTCATAGCTTGAACCTTCTGGTCACTTC
Found at i:111048 original size:17 final size:17
Alignment explanation
Indices: 111026--111070 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
111016 TGGGGAAGAA
*
111026 AGGAAATCTGTCTTTAT
1 AGGAAATCTGTATTTAT
* *
111043 AGGAAATTTATATTTAT
1 AGGAAATCTGTATTTAT
*
111060 AGGGAATCTGT
1 AGGAAATCTGT
111071 GCTTACTAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (17 bp):
AGGAAATCTGTATTTAT
Left flanking sequence: Indices 110526 -- 111025
CTCCCTGTCAGCTCCCTTCAACCATACATATATCTTAAATCTAGCTGGGTGCATGCAGACGTTTG
CGGACATCACCTATGGTGAATTTCCCGAAGCACATCTCGTTGGATGGATGTCGTTGCCGCGAAGT
GAGCTGGGCCACCTTCTGAGCGGAAGTGCCTTTGTAGCCTAGATCGTGCTCAGCTGGATAGGTTC
TTACTCTTACTTACGGATCGAAATAACAAAAGAAAGAACTAGAGCCCTGCTGTTCTAAAGCACAA
GTAAGGGCTTTTTTGTTCTACCAGAGAGAGTCTATTCTCACACTGAATCAATCATTCGAAGGGTC
GGGGAAGGAAGCGATGATCGGTCTATCCCATTAAGCGTAATCCCGTTAGCCAATGAAAGGACTAC
CTTTCTTGGACTGTGAGCGACGACACCAGATCAGAGCTAAGCGAGAAACGAGAAGCTGCGGTGAA
TCAATCAGTATTAGCTAAGGCAAGCATTCTAATTCTGGGGAAGAA
Right flanking sequence: Indices 111071 -- 111570
GCTTACTAAGCCTTTGTTTGAAGGACCGGTCTGAAAGTGCAAGACTAGCTGGACCCGGACTGACT
AATCGCTAAGAGCTCGTCCCGAGAGAACTCTCAGTACGGCATTCAGTAAGAAGTTAGCCAAGTTC
TGTTAGCCGTTACGTTAGGGTGACTCGAGAAAGTTTGAAAGGGAATTCCGATAGCCCTTAAGCTT
CAAGCTATCCGGCTTCAAGCCGTGAAGGAGGAATCCGAGTTACATCCTCTTAAAATAAGGAAGAT
CGTTCATCAGCGCTTTCAGTAACTAAGAGTCAATCAGGTGCGTAATCAAGCTCATCTCATTACTT
AGGATCTCACTCTCTCAATCTCCTATCTGGATTCTTTGCTTAGTCAGAGTTGAATCTTATAATAA
GGACAAGAAAGACTGGCATTCAGGTAAGGCATGATTCGGAAGATAGTGAATCTCTCCTTACTTGA
CTCTAGAAAGCTCTTTCTTTGCAAGTGGCAAGCAAGACTATGGTT
Found at i:122823 original size:25 final size:25
Alignment explanation
Indices: 122794--122844 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
122784 GAAAGCAGTG
122794 AATAACGA-ATTCGTAAAGCCGGTTC
1 AATAACGATA-TCGTAAAGCCGGTTC
122819 AATAACGATATCGTAAAGCCGGTTC
1 AATAACGATATCGTAAAGCCGGTTC
122844 A
1 A
122845 TTTCAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (25 bp):
AATAACGATATCGTAAAGCCGGTTC
Left flanking sequence: Indices 122294 -- 122793
TTCATTTCAGTTTCTTTATATCTTTCGTATTCTACTCGTAAAGTAGCTAACGATATCGTAAAGCG
AGGAGTCGGTTTCAGAGATTCGGAATTCGACACTGCTAACGAACTTGGTATCTAAGTCAAGCCGG
TTTGGAATTCGAGGTAGCGCTTTCTTTCTTTAGCAGTAGCACCAGTCATGAACCCTTATCACTCC
AACTCGTACTCATAGTTAAGCAGCGGCAAGACTAAGAAGGGCAAGAGCCAGAGCTTCTATTTACT
CAACTGCTGATTCAATTGCGACAAGAGCTGATTCGAGAGCATCAATGAATGTGCTTGCGTCCTCT
TCTTTATTATACCTCCCAATGGGAACTGTGCACAACCGATTCCTCCACCTCATCTCTCAAAAGAG
GGCATTCTAGAGCATTAGTGTATTGTAAGGAAATCGACACTGCTCACGAACATGTCCATAAAAGC
TAGCGGTGAGAGCTTTATATATCGTAAAGCGAGGAGAAAGCAGTG
Right flanking sequence: Indices 122845 -- 123344
TTTCAGTATAGAATGAGAGTAAGGGTTTCTATGTTCTTATAGTATTCTTATTCGGTTTCATATGA
AATGGCTAGCGGATTCTCTCAGACATTAGGCAGATCAAAGTCGTAACGTAATAAGAAGGCCGGTT
ATGAGAAGCAGGCATGTAACCCTGCATCACCTACTCGCTCAGGAAAGTCAGAAGGGAAGTCAGAA
GGTTAGAAAGTGATGGTAAGCTTTATATATCGTAAAGCGAGGATCAAGCTAGCGGTGAGTTGAAA
TCAATAGCATTAGACTTTGAAATCGACACTGCTAACGAACTTGGTATCTAAGTCAAGCCGGTTTG
GAATTCGATACTGAACTCGCTTTTGAAATCGACACTGCTTTCCCGCCGATTCCTAAGATTGCCGG
GGAGAGGGGCAAAGAAGCTCGACCAGAGGGAGCGTGGGTAAGAAGAAAGCATCAAAGCGAGGATT
CGGAAAGCATTAGAAATCGACACTGCTAACGAATTCGACTAGCGC
Found at i:189204 original size:20 final size:20
Alignment explanation
Indices: 189179--189219 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
189169 TGGCTAGCCC
189179 CTTCTTTCCTTATCTAATGA
1 CTTCTTTCCTTATCTAATGA
189199 CTTCTTTCCTTATCTAATGA
1 CTTCTTTCCTTATCTAATGA
189219 C
1 C
189220 ATAGATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.05, T:0.49
Consensus pattern (20 bp):
CTTCTTTCCTTATCTAATGA
Left flanking sequence: Indices 188679 -- 189178
TCGAACATAAGGCAGAAAGATCAGACTCAGTTCGAGATTCCTTACGAATTAGGGTAAATCAAGGA
CCCTTTCTTCCTAATCAAAAAGAAAGCCCTGTTCTAGCAAACTCTGTCTTAACAGATGATTCTTT
AGATTCGGATGGAGATGCTTTTGAGGGGCTTTATTTAGCTGTATGTTACGAAGCGTAGGGTCTTT
CAACAACTAGAGCGGTCCTCTCGGAAGGATGTTGACCCCGTCACCGATGCTCTTGGCTTTCGTGT
GTCACTGATTTAGCTTCCGATTGGGTCAGTGTGAAGCATTGGGTTTCTGCCTTAAGCTCGCCTGT
GACTGTCCTACTCTCCCAAGTCAGTTTCGAATCTGGATGACCTACTGTTTTGACTACGTTACAGC
TGGATCGGTTAGTTCTGGGATGATTGATGCCTTCCATACATCAGCATTCTAGAAGTACAGCTTTT
GTTGTGTGTGTTCTTTCCAACTGGAAAGACTTGGCTGGCTAGCCC
Right flanking sequence: Indices 189220 -- 189719
ATAGATAGAAAATTCTTGCCGGAGAGTGATAATTGAGTAACGATTGATTCAAGCCCGTCACAAGG
TGCCAGAGTAGACTTCTAAGCAAGATCGAGTATAGAGTGAGGAAAGCCTTAGTCTGAAAACACAA
GAAGTAGGTAGCCGTTATCAGTCCACCGAAAGTGGTCAATCAGGCTTCGCACCTTCCCTTACTAA
GCTTTCAGTCCTAATAGCGACTTCCTTGCCTTAATAAGCTCCCAGGAAAGCCTGCTTTAGAATAT
AAGAGTTTTTTCTTTCTGCCACTCAATCAGAAGTGTTATACTAATAGGTTGATGCTTTCGCTTAA
GCAAATGGTGCCTTTTGGTCCCGTCTCCTTTTGGGCCCATTGGTAGCATAGGAGAACCCGACGTA
ACTAGAGAGTAGTTGTCGGCAAATCAAGTCGACGATCTTTCCTTTTCCCGGAGCGCCTTCCTTGA
CGCGTCTGCGTCTGGTGCCTCGGAGCCTGCGGTATAGAGAACGGA
Done.