Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_041177
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: 362069
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8616 original size:27 final size:27
Alignment explanation
Indices: 8586--8638 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
8576 AACGAGGCAC
* **
8586 AACCACATGGAGCTCCTGATCTTCCAG
1 AACCACATGGAGATCAGGATCTTCCAG
8613 AACCACATGGAGATCAGGATCTTCCA
1 AACCACATGGAGATCAGGATCTTCCA
8639 CAGGATGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (27 bp):
AACCACATGGAGATCAGGATCTTCCAG
Left flanking sequence: Indices 8086 -- 8585
TACATCACCATAGTGGATGGATAAAGAAAGTCTATTCCGTTCCAATTGAACCGAACTGGTTTTAC
ATTTGAATTTCTCTTAATTCTACGTTCCTGAAATGGATCCTATTCTTTTCTTTTTTATTGTCCGC
TGTCTATGCTGGTGCCTTGGGGTCTATGTTTCGTGGGTCCATTGGACCCGGCTCTTCCATGGGCT
CCCGGGATTTTGGAAATTCGTTATTGCGGAAAGTCTGGGGGGGATCCTTTTTGGCGCCACCAATT
CGGCGGATATTTTCTTCGGAGACGGGTTTGAGGGGGGTCACTTTCCAATGGAAAGGAATGAAGGG
GAGGGAACCTCAGGCACAAATCCTGTTCTTCCGTGGAGATATTCTTCTCCCGTACCTTCCATCTC
GTCCCAGGGAAGCGAGTGGATCGAAGAATGTTACGGGAACCAGGGGGAGGCTTCTTCTTCCCGAC
CTAACCTGGCACCACCTCAGGCACACCCCGTAACAAACGAGGCAC
Right flanking sequence: Indices 8639 -- 9138
CAGGATGAACTAGTAGATCTGGTCGAGAGAGGTGAACGAGAACAGCAGCTAAGGGATAAACTATC
AAGATATTATTATGATAATGATATGAACATCCTTGATCCTCGCTTCGAGCGCAAGTTGCAAACCC
ATGTTTGTTTCGAAATAGAACTAGAAGCATTGAAGGCTATACGCCAGATAGTATAAATAGATACC
GGGATCAATTCCGTGAGTTATTCTTTTATAATAACAATTTCCAAGGAAAGCGTATAAAAATATCT
GATCTTAATAACTATATAAGAGAAATGAGAGATATGTCAAAACACTTTTTTGATAGTAAACCATG
GGAAAGAATTCTGAATGCACGTGAAAATAAAGAAATTTTCCTATACAAACCAGATGAATCATTAT
ATCATGTATATGAAAATGAATATAGATAATCTAATTAATATGATAAAAAAGAAAAGACTTAAATA
ACATTATGAAAAAAATGATGATATTAATTAGGCCAGGGGATGGTT
Found at i:24623 original size:24 final size:24
Alignment explanation
Indices: 24591--24639 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
24581 CAACGGATTC
* *
24591 CTCACCCTCAGGAGCCCGAAGTAA
1 CTCACCCTCAGCAGCCCCAAGTAA
* *
24615 CTCATCCTCATCAGCCCCAAGTAA
1 CTCACCCTCAGCAGCCCCAAGTAA
24639 C
1 C
24640 GAATCCGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.41, G:0.14, T:0.16
Consensus pattern (24 bp):
CTCACCCTCAGCAGCCCCAAGTAA
Left flanking sequence: Indices 24091 -- 24590
TGCTGATAGTACTACTAGCTCTTGACTTAAAGGGCAGTAAGTAGCTCACCAATTTCGGGTGTACG
CGTCCCGTAGTCTAACAGGTATTCATGTCTTCTATAGCAGTATGGTATATGTAACGTTGTTGGTT
CCAGGTTGCTTAGGACTGTCAGGTTGCTAGTCTTTCGATGGTTCCCAACCCCTTTTCTCAAAAAT
CCCATTTCCTTCCATGATATTATATGGGAAATTTTTTTGTAGTATCCGTTGAGTCATTCGCAGAA
GCAGCTCTTTCAAAAGCACCCAAATCTGATGAAGGAACTGTGGAATCCGCGGTTTCTTTCATTCG
CTGAAAAACAACGCACCGAAAAAAAAAAATCCTATGGATCATAGCACAGGCATCATCCTAAGAAG
CTCCGCCTAGGGCTGCTCTTTCCTTCTCAATCTGAATCGGCTGAAGAGTCATTTTTCCCTGAAGC
CGAGACCGAACTAACATATCTAATTTATCCCGAAACAACGGATTC
Right flanking sequence: Indices 24640 -- 25139
GAATCCGAATGCCTATCTCCAGCCGAATTCATTTCATAAGACTTATCGGAAGAAGCAATTGGATA
AGAATCATACGCTGAATGAGCAGACGAATCGACCGAGGAAAGAGATGCTTACACACTAGAACAGA
ACCTAACTCCACTTCTTTTTTTCTTTCTCCTGCTGCTATCCTCTCAACAGGTCAGTCAATATCAG
TAGTGGAAGAAGCAGAGTAGTCCCCTGGTCATCAGTTAGTAGTTGAATAATCCCAGTAGTGGTCC
TCTTGCCTAGCGGAGTCAGCCCTTAATGGACAATGATAGGCAGACCAAAGATTGCACATCGCAGT
CTAAGCTTTGCGCACCGGCACAGCAGAATTTGAATCCGCTGGCTCAGATGAGTGGCTCTTGGCTT
ACTTCCTTGAGAAGGGCTTTCTGTAACTAAGAAATGATAATTGTTGACCCATATGTCAGGCTCAG
AAAGAGGATGAAACTGACAATTTCACACTTAGAGATTGAGCTCGT
Found at i:37919 original size:18 final size:18
Alignment explanation
Indices: 37879--37921 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
37869 ACCGCCCTGC
37879 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
37898 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
37915 CATAGTC
1 CATAGTC
37922 AACAAGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 37379 -- 37878
TGCTTTGACTACAGAACCATGCCTGTCTGTTGGAGCGAATTGGATGATCGGGCCGAGGGCTGCCC
CCTCTCCCCCTCACTCTCCTTTCCCTAATATGAACCTTGAGTCATCAAAGCCTTTCTGACTCGGC
CTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAAAGGTAGTTTACTTGCTTACTTGTTAGAGTA
AGGCGAAACTCTCGTCGTAGTTTGTTTGGCGACCTAAGGGGCGGACACTTTTTGTTATCTAAAGG
CGAAGACTCTGAAGTGGGCGAACACTCGGCCCAGCGGGCGAACATGCCGGGCTCCGGCTCCGCGC
ACCTGCTGACACCTTTCGAAGCACTTTCTAGTGTGCGCTTTAGTTTTAGAATGTGTCGTTCAGCG
TCACGAGTCTACTTTCTCATTTCAGTGCTCGCCTTTTTGAATCTTCAGTAGGGGCCTTTAGTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 37922 -- 38421
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCCCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:54860 original size:18 final size:18
Alignment explanation
Indices: 54837--54875 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
54827 AGGGTTTTCT
54837 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
54855 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
54873 TAT
1 TAT
54876 CGACCGCGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Left flanking sequence: Indices 54337 -- 54836
GTCTCGAACAGTGATTCGGTTGATGATAAAGAAAGAGAATTCTTGGTTCAGTTCTCCACCTTAAC
GACAGAAAAAAGGATTGATCAAATTCTATTGAGTCTGACTCAGAGTGATCATTTATAAAAGAATG
ACTCTGGTTATCAAATGATTGAACAACCGGGAGCAATTGACTTACGATACTTAGTTGACATTCAT
AAAAAGTATCATATGAATTATGAGTTCAATACATCCTGTTTAGCAGAAAGACGGATATTCCTTGC
TCATTATCAGACAATCACTTATTCACAAACCTCCTGTGGGTCTAATAGTTTTCATTTCCCATCTC
ATGGAAAACCTTTTTCGCTCCGCTTAGCCCTATCCCTCTCTAGGGGTATTTTAGTGATAGGTTCT
ATAGGAACTGGACGATCCTATTTGGTCAAATACCTAGCGACAAACTCCTATGTTCCTTTCATTAC
AGTATTTCTGAACAAGTTCCTGGATAACAAGCCTAAGGGTTTTCT
Right flanking sequence: Indices 54876 -- 55375
CGACCGCGACCTTGATACGGAGCTGGAGCTTCTAACTATGATGAATGCGCTAACTATGGATATGA
TGCCGGAAATAGACCGGTTTTATATCACCCTTCAATTCGAATTAGCAAAAGCAATGTCTCCTTGC
ATAATATGGATTCCAAACATTCATGATCTGGATGTGAATGAGTCGAATTACTTATCCCTCGGTCT
ATTAGTGAACTATCTCTCCAGGGATTGTGAAAGATGTTCCACTAGAAATATTCTTGTTATTGCTT
CGACTCATATTCCCCAAAAAGTGGATCCCGCTCTAATAGCTCCGAATAAATTAAATAAATGCATT
AAGATACGAAGGCTTCTTATTCCACAACAACGAAAGCACTTTTTCACTCTTTCATATACTAGGGG
ATTTCACTTGGAAAAGAAAATGTTCCATACTAATGGATTCGGGTCCATAACCATGGGTTCCAATG
TACGAGATCTTGTAGCACTTACCAATGAGGCCCTATCGATTAGTA
Found at i:113434 original size:16 final size:18
Alignment explanation
Indices: 113396--113437 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
113386 AGCCTACGGT
113396 CTATATGGAAGTAGTGCCC
1 CTATATGGAAGTAG-GCCC
113415 CTATATGGAAGTA-G-CC
1 CTATATGGAAGTAGGCCC
113431 CTATATG
1 CTATATG
113438 ATGGATGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.39
17 1 0.04
19 13 0.57
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (18 bp):
CTATATGGAAGTAGGCCC
Left flanking sequence: Indices 112896 -- 113395
GATCGATGAAAAAAAAAGATAGCTATCTAGATCCATGGATAGAGATCAAGTTGGTAGTACTCGAT
TGAGCCTCTTAGATGCGTCTATGCCAAAGTCAACACAATTATTGAAGAAAACGGGTGGAAGTGGC
CTTTCTCTTCAAGAGTAGGATATCCTCGGGGTTGGCGTATGTGGTTCCGGTCTTTCGTTGATAAA
GTCGTAGGCAAACCTCACCTACAGAGTGTGGAGCCTAAGTGAAGATTTTCAAAGAAGTATAAGTA
AGGGTGCGGAGGAAGATAGTGGTGAGTCTCGTCGATCGGATTAATGAATGATTACGATAGCTCTT
ATTCCCGTATTCCCGATCCCCGGTACGAAGAAGAAATGCATTCATTCGGTCTTTCCCTAGCCTTA
CAACCTAGGCCAACAAGAGGCTGCTTACTTGACTCGCTCTGCGCAAGGGTCCAGGCGCGAGGAGA
ACTCAAGAGATAAGTTCATACCCCTAATGAAACAAAGCCTACGGT
Right flanking sequence: Indices 113438 -- 113937
ATGGATGGCCTAGAAGAAGAGTTCCGAAAGGAATTGACCAGTAGCATATGCGGAAGGCTCAGACT
CTGACTTCAATGGTGGCCCCCTAAAAAATCATATTTCAAAACTTACATGCGGCCTTGGTCTAAGT
GCCGAATCATAAGTGCAATCCGAAGCAAAATGAAGAAGTAAAGGAATTTTGTGTCCATCCAAGGG
CGTGCTTTTGATTGAATGCAGTGTGGTTGGCATCGTAGAGGGCGTACGCTTAATCACTAAGCTCA
GGACCAGTCGACCTGTGCTCCCTCTCCGTCCTTTTGTATGTGAAAGTATGTACCCACCCCCCTGT
GACAATGAGACTGGTGAAATCCCTACCTACCTAATAGCTAAAAATAAGTAAGCCCTCTTAGGCGA
GCTAGTAGTAGTGAGTAGCGAATAGTACAAAAACCTACCCTTCTCGAAATAGAGGAGCCTACAGC
TCAACCTGCTCTCGACCGTGACAGGAGTGTTCCGCACCTGAGAGG
Found at i:137023 original size:19 final size:19
Alignment explanation
Indices: 137001--137041 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
136991 TCATACCGAA
* *
137001 TAAGAGGTGCGTAGCCTTT
1 TAAGAGGAGCCTAGCCTTT
137020 TAAGAGGAGCCTAGCCTTT
1 TAAGAGGAGCCTAGCCTTT
137039 TAA
1 TAA
137042 CAGAAAGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (19 bp):
TAAGAGGAGCCTAGCCTTT
Left flanking sequence: Indices 136501 -- 137000
CCTACTTTTTTTTCTAAGGTGAATGCCTAAGGAGGCGGCTCTCTTGTGAAATGAAAGAAGGAATC
TTTTTCTTATAGCTAGCTTGAACTTCTGCTTTGTCTCTTTCGGTGTATAAGATGCACCTATCCGG
GGTTCTGTTCAAAGTGCGGTAGATCAACATAGGTGTACCCTTCGTAAATTCGTTAACCAGTAGCG
GTTGCGCTTTCCGTTCTTTTGGCAAAAACCATTAGAATAGCGGTTTTTTCCGTAAATTCCTTGTT
TGGTACAGTAGTGGTTTCCTGAATGAACCTATCTTCGTTTCCCCTGTATCAGCAGGGGCTTATGA
GTGCCAGGTAACATAAGTGCGTTATCTCTTTATCTCAGATCCCAGAATCTGATATGATATTCACC
CTTGCCTATACGGTGGATGCCTTTCAGCTCCTATAACTTCACATTGGGCTGCAGTTCTGCCTTTC
CTTAGAATCAATGTCTTAGAGTAATCAAAGAAACTTCATACCGAA
Right flanking sequence: Indices 137042 -- 137541
CAGAAAGCAGTCTAGTAAATCGACTAGGAGGAGAAATCCACAAAAAAAAAAGCTTAAGATGGCAA
GGTACTTAGCAGGGCGTGCAAAGAAGGATAGAGTAAGAACCAAAGCAAGGACTGATTATACCGCT
CCTGACCCCATGGCACCTATGGGGAGGAAGTCGCAGACTTAAGACAACCCCCTTCCCGTTAAGGT
GGGCATCCATATCACGTGCCGTCCTATGCTAAAGACAGCACTCTGTTGGTTGTGACACAAGAGGT
GTAGTAATAAACTTTATTGGCATCTCCAAACAGTTGGATTGGAAGTTGTTCCTTACCTTACAAGA
CCAGTACCTTGAATTTTAGTCGGAAGCTGGATTTCGTACAGTTACGAAAGTAGTGCACGTCGGCG
CCGGACTCACTGGAGAGGGAGTCGCGGGTTAAACCGTGATAACCTTTGTGGTTACTTTGGTCTAA
ACAGCCTTAGTAACTACGTCCTTTAAGCCTAGTAGGCGGTGCACC
Found at i:138658 original size:30 final size:30
Alignment explanation
Indices: 138616--138682 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
138606 TCAACTGGAA
138616 GACTAG-AACGGAAG-G-GAAGAAGGCAAACT
1 GACTAGAAACGGAAGTGCGAA-AA-GCAAACT
138645 GACTAGAAACGGAAGTGCTGAAAAGCAAACT
1 GACTAGAAACGGAAGTGC-GAAAAGCAAACT
138676 GACTAGA
1 GACTAGA
138683 CTGGAATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 6 0.18
30 8 0.24
31 15 0.44
32 2 0.06
33 3 0.09
ACGTcount: A:0.45, C:0.15, G:0.30, T:0.10
Consensus pattern (30 bp):
GACTAGAAACGGAAGTGCGAAAAGCAAACT
Left flanking sequence: Indices 138116 -- 138615
ATGCGTGGCGCTAAAGAGGAAGACGTCACTTACTGTACTACTATCGGCTTTTTTCCGTAGGTTGA
AGAACAAGAAAGCTATTCTCCGGTCTAGGAGTTCAAACAACTTCTAATCGTATTCTAAGATTCTA
GGTTCTTTTTTGAAACTTTCTACTAGTTCTAAGCTTGCAGCTCAACTCAAGAGCAAGGTAAGGAC
AGGTGGCATAGCGCAGTCCTCACCGATGTGGTGTCCAGTCACAACCTAAATAAGAAAAATCTTTT
CCTTTTACTATAGATTTTGAACCTCGCAAGACGAGAGTCGGCTCGAGGATAAAAATCCTTTCCTC
AAGCTGACCCAGCCTGAAGGAAGTTTAATCCTAAAGAACAAAATGCACTGAGTCCTAGGCTTTCT
AAAAATGAAATCCATTTTGATGGCACACCGAGGCTTCCCTGTCTTCCTGTGGTAGTTTCTAAGGA
GAGAAAAAAAGCCAAAGTCGATAAAGCATACATAGTCAACTGGAA
Right flanking sequence: Indices 138683 -- 139182
CTGGAATGCAGACTGACCAGACAGAACAGTTACACAGACATACTATATGGGCCTGATATACAGAC
TGAAAGCTTGGACAGTTGAAGGGTCAAATAGGTCTTCGGGAGCGGCTTGGGGGGAGGGGGCTTTC
CCATCCCGCAACCTCCTATGGACTCTAAGGGGTGGGATTTCGGGGTAGAAGGTTCATGGTAGGTA
GTTCCAATGCGGCGATAAACATCCTTCTAGTATGTAGCGAGATCCGTCCTCCAACCAAGGGATCG
ATATACAAATCATAACTAAGGCTAGCCCGCTGGTAGTAGAAGGAAGCAAAGATTCAGGCTTGAGT
TCGAGATCGAGACCAAGAAGTAGGGATAGAGGCAAAGGCTTCCCTTCGCTCACGTCCGAACCTGG
ATCGATATCCAGTTCCACCAGCGGCAGAGACTGTTGGATAGGTACCCCCAGCAGTTGCTTCAGCT
AACCAATTGGAATAGGTACAACTGGTAAAGCTACAGCCGCTCCTG
Found at i:158997 original size:13 final size:13
Alignment explanation
Indices: 158968--158999 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
158958 TTTCCCTCTC
158968 TTTTCTTTTTTGA
1 TTTTCTTTTTTGA
158981 -TTTCTTTTTTGA
1 TTTTCTTTTTTGA
158993 TTTTCTT
1 TTTTCTT
159000 CCTTTCCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTTTGA
Left flanking sequence: Indices 158468 -- 158967
GAATCTACAACGCACTAGAACGCCCTTGTTGACGATCCTTTACTCCGACAGCATCTAGGGTTCCT
CGAACAATGTGATATCTCACACCGGGTAAATCCTTAACCCTTCCCCCTCTTACTAAGACTACAGA
ATGTTCTTGTAAATTATGGCCAATACCAGGTATATAAGCAGTGATTTCAAATCCAGAGGTTAAGC
GTACTCTGGCAACTTTACGTAAGGCAGAGTTTGGTTTTTTGGGGGTGATAGTGGAAAAGTTGACA
GATAAGTCCCCCTTACTGCCACTCTACAGAACCGTACATGAGATTTTCATCTCATACGGCTCCTC
GTTCAATTCTTTTGAAGTCATTGGATCCTTTTCCTCGTTCGAGAACCTCTTCCCTTCTTCCACTC
CGTTCCGAAGAGTAACTAGGACCAATTCAGTCACGTTTTCATTCATTTGGAATCTGGGCTCTTCT
ACTTCTTTATTTACTTTACTTATTTTTTGATTACTTTTCCCTCTC
Right flanking sequence: Indices 159000 -- 159499
CCTTTCCATCATTCCTTAAGTGCCATAGGTTTGATCCTGTAGAATCTGACTCATTTTCTCATTGA
GCGAAAGGTACGAAATAAATCTGATTTCTTTTTCGATCAAAAGTACTATGTGAAATCTTCGGTTT
TTTCCTCTTTCTCTATCCCTATCCGTAGGTACAGCGTTTGAATCAATAGAGAACCTTTTCTTCTG
TATCTGTATAAATCGATATTATTACATTCCAATTCCTTCCCGATACCTCCCAAGGAAAATCCCGA
ATCGGATCCCAAATTGACGGGTTAGTGTGAGCTTATCCATGCGGTTATGCACTATTCGAATAGGA
ATCCATTTTCTGAAAGATCCTGGCTTTCGTGCTTTGGTGGGTCTCCGAGATCCTTTCGATGACCT
ATGTTGTGTTGAAGGGATATCTATATGATCCGATATGATTCGATCGATTGCGTAAAGCCCGCGGT
AGCAACGGAACCGGGGAAAGTATACAGAAAAGACAGTTCTTTTCT
Found at i:171571 original size:14 final size:13
Alignment explanation
Indices: 171544--171568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171534 TTCTTCCCAC
171544 TAAACGAATCCCG
1 TAAACGAATCCCG
171557 TAAACGAATCCC
1 TAAACGAATCCC
171569 CGTGCTTGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (13 bp):
TAAACGAATCCCG
Left flanking sequence: Indices 171044 -- 171543
CCTCTTTTTCTACATATGCGGTGGCGGGCGGAGCACTCTATATGACCGGCTAGGGTTACCAGAGA
AGAGGGGACAACTTCTTTCTCCCTTGCCTTGCTTTTTCTGATTGAAAGTAGCAAGCCACTCTACT
ACTGGTACAGAGGCCAGATAGAAGGTTGCTTTTGTCTTGTAAGCAACCATGCCTATATAAGAAAT
TTTGCTTACCAAAGTCAAGTGGTCTTACTAAAAATAAGCAACCAGTTCCAAGTGACATGGCTTTA
TTCCTTTCCAGAGAAGGTTGCTCATCCAGCCCAGCGGATCCATTGTTTATGCGGCAGTGCCTAAT
ATGAGTTTGCTCCTGCCCCAGACAGCTTCGAGGTTCCCATCGATCGATTACAGAGGTTTCAACCA
CTGAACTTGCTTATGTTCCCCTTTGACCGAGTGCTATTTCTATAAAAAAGATTGAGTAGGAAAAA
CTGGAATTGGCTTCAATCGAGATTGCCTCGGCTTCTTCTTCCCAC
Right flanking sequence: Indices 171569 -- 172068
CGTGCTTGAGTAGAAGTGGCTTCCTATCTTCGCCCTCTAGCGTTCAATCTCCACTTTCATTTTCC
CGTCTTTTTTGCTTGAAAAGGATTTCTCCCCATAAACGGACATAAGAATCGAAAAAGTTTCATTT
TCCCCGTGAAAGTCAATTTCCTTTAATAAGTGACATCGAAATGTGCCAGTGTTTCATTTTCCCCG
TATTTTTTATTAAACCCTCTTCTTACCATTAGCACAGCTTCGAAAATCGTTCTCTTTTATTCGCC
TATACCTATATGTGACAAATGAATAAAAAATAAAATGGAGAACTCGATCGAAGGGAAGGCTTGAG
TTCAGAGACGAAGATAAGGCTTGGTGGCTTGCTTGCTAGTTTAGCTTTCCCTCTTTTTAATCTAT
ATCAGATCCTCCATTACTTCTTCGCCAATACCTTTTAGCTTTCCTTTAGCTGCTACTTTTCGCCC
AATCAGAGTAGTCAGTGTGCCTGCGTAGTCCTTCTTTGACGAAAT
Found at i:175849 original size:15 final size:16
Alignment explanation
Indices: 175829--175859 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
175819 AGCTAACTGA
175829 ACGAAAA-ATGATAAG
1 ACGAAAAGATGATAAG
175844 ACGAAAAGATGATAAG
1 ACGAAAAGATGATAAG
175860 GCTGATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.06, G:0.23, T:0.13
Consensus pattern (16 bp):
ACGAAAAGATGATAAG
Left flanking sequence: Indices 175329 -- 175828
CAAGGGTGGTAAGACCAGCAGTTGACCCGCTTTCTATTAACTTATCTGATCCAGTGTCATATCCA
GTTGACCGGGTCGAACTATCAGAAGTGGAGAAGGCAAGAAGAGCACCAAAAAAAGGGGCGGAGAT
CTCACCTGCGGCAGAGGTAGCAGCATCTAAGCCAGTATCTGGGCAAGTTGGCTTCATCGACTCAG
CAATTGAAGTGGTTGATCTTGAACCAATTTGTTCATCAGTTGCCCCATTAATTACCCGGTAAACT
CTCCTGGATCAATAGCATTGGATCGGGAATGTGGCCATTTCACTATTTTACATTGATCCACAGCA
GATAGAGGATCCGAAAGGAGAAGACTAAGCCTTTCTATTTTTAGACTGTTCACATTTCACCGGCC
AGGTTCGAGACTCTCTTCCCTTTCCTTTATAACTAGACTAAAGTAAAGATACTTGTTGAGTTGAG
GAAGCATCTGATTTCTAACTACGAGTCTGTTTTCAAGCTAACTGA
Right flanking sequence: Indices 175860 -- 176359
GCTGATTTACTTGTGAAACTCTATCTTCAGTCTTTGTCGAGCCGCCAAACGGCTGTCGAACAGAA
TTGTAGAGTCCATAGTCTCTCTTCCTGAGTCTAAAGAGAAAGAACGCCTCATTAACAACAAAGTC
TAAGAGGTTTCTCAATCTTATAAGACCCTAATCTTTAGGTATATTCCTAAGATTGCATCTATCCC
CTTGTGTCAGGGAATAAGGTGGATGCCCTCCTGGAAGGCAGGTGAATCTGCGTGTAAGGAAGCGG
GGATCTTTTCCCTTCTCCCTTTTGAGCTCAACTGGGCTATGTATAATTACAGTGACTTTAGAGTC
ACCCGGAAATCTAAAGCGCAAATTGCGCCTTTTCCAATTTTCCGGTTCCCATGTTGGTCTCACCA
CGTTAGATATCCCTACGATGCTTAAACAAATCAGATGATCTCTGATTGGTCGTTGAGAGAGTCAG
ATTCATTCCTCAGAGATATGAGTACTGATTCTGATGTTCTCGCTT
Found at i:192802 original size:15 final size:15
Alignment explanation
Indices: 192782--192815 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
192772 ATCTATTGTA
*
192782 TGAAGAGAGTAGGAG
1 TGAAGAGAGGAGGAG
*
192797 TGAAGAGCGGAGGAG
1 TGAAGAGAGGAGGAG
192812 TGAA
1 TGAA
192816 AGGCAGTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.47, T:0.12
Consensus pattern (15 bp):
TGAAGAGAGGAGGAG
Left flanking sequence: Indices 192282 -- 192781
GCTTGCCCTTAGGGTTATAACACGATAGGGGGTGAAAGTCAGAGAAGAGCTAGTAAATGGGATTA
GTTACCAGGCACTATCAAAAAAGAAGTAGAAGTCTACGTAGCGTAGTGAGTGCTTCCCAGGTGGG
GATCGTGAACCTATCTATTTCCCTGCTAGTGCACTAATGGAAGGCCCGTAGGGAAAGAAGGCGGA
TAGCTAGCCTTAGTCTTCCTGTTGCTAGGCGCAAGGGGAAGCTAATCTTTATTACCTGTAGTGTT
TAAACCTTCCTTTCTCTATTCTAGTGTTATAAGGACAAGTTAGCTTCAGATAGCTAGATGTAGCC
ACTGGACTTTTTTGATGTATTACCCTGAATCATGTAGCTCCTAATCGAATAGTGCTTCTAGACGA
AGAGCGGAAGAGAGAGCAAGAGCTGCAACCTATTCTGCTATTATGCATTGCAGCTGCCTCTGTCT
GCTCTTTCTTAGCTTTCTTCTTGGCGCTCCGTAGAATCTATTGTA
Right flanking sequence: Indices 192816 -- 193315
AGGCAGTCGAATCCCTTCCTCTAGAGAGGAGTTCCCCTTTCCTACTACTTTCGATTTTATGCCTG
TCCTTATGAGTCTTGAGTCTTCTTTCTTTGTCTTAAGCATTGGTTTGTAGGTTTAGAGCACGCTA
GGCTCTATTAATTAGAATGGATTATATCGATCAGTTCGGGATAGGGGCATGCAGTATAGAATCTC
TCTTTCTTTCCTCTAGGACCCTCCTTATGAGCGAAGGGATCCCTGCTAGAGGTACTCGCGTAACT
TCTTTTTGAGGATTCTCAGTTGCCTTTGTTCGGTTATAGAAGACAATGAAATATCTGGTATTTAG
GGAATAGAGTAGGATAAGAAGGAATGTATAGGATAGAACGGAATTGAATTATTGAATAAAGAAGA
ATGGGCTTATTGCATCAAAAGGAAGGAATGGATCCATACCGCCTATTCCTTAGAGTTAAGCCAAT
ATGGGCAAGAGGATGGGAGGATAATAGTACATGACAGAAGGCGGT
Found at i:275436 original size:39 final size:39
Alignment explanation
Indices: 275382--275460 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
275372 CGATTTTCTA
*
275382 TTCACTCATGATCTGGCCTGGTCGACCCGATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
275421 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
275460 T
1 T
275461 GAAGGATGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.32
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
Left flanking sequence: Indices 274882 -- 275381
GCCCACACCTGTGTAGAGTAGATCGTTCAACACCTGCGGCACAAACCCATTTTTGACCTATTGGT
CCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCAACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGAATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCAAGCAACCAGACTTAACATAAATGTAGTCACTGGAGCC
ATTCTAAAAAGGGAGAAATTAGCACTACTTGGTGAAATAGGTTCTTTTAGAATCAATTTAAAACC
ATCTGCTAGAGGTTGTAACAATCCGAATGATCCCACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCAGCTGGAACAGCTATGTACGTTTTCGATTTTCTA
Right flanking sequence: Indices 275461 -- 275960
GAAGGATGGGACCTTTTCTCGAAAAACTCCGGATCCAGAGAAGAGTTGAAGATGGTGCAACATCG
AATCCTGTTACGTTACTTCGAATGGAATCTTAGCCCGCCTCACTTGCTTTCTTTACTGCATAAGG
GCATAAGCGAAGTCAAGAGATTTCCTTCTAACTAGTGGCTGAGAGTAAGCAAGCTACCTTCATTC
AACAGATTTGTGGTTGAGTCAATAACATGCTCTGGGTCGGGAATCTTTGCTCTTCTCTTTTGCAT
TTCCGCTGCCTGCGTTCTTCTTCGTGTCCGTCCGTATCGCAAAGCTGGTCGACGCCAGCTGTAAT
GGTTGAAAATAGGGGGCCAACCAAGACCCCTAATAAATTTGTTCGATAAAGCAAACGATTCGTTC
CGACAACTTCGGACCAGATTAATTTGAATTAGCCGATCTTACAAAATCGATCGGGCGGGCTGGTT
GGGAAGGGGTGATTAGCGGAGAAAAGAATCGCTGAGAGATAGATT
Done.