Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_045040
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: 631094
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Found at i:7352 original size:22 final size:21
Alignment explanation
Indices: 7306--7349 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
7296 CACCCGAGGG
*
7306 AAGGAGACTCCGGAGGAAAAA
1 AAGGAGACTCCCGAGGAAAAA
7327 AAGGAGACTCCCGAGGAAAAA
1 AAGGAGACTCCCGAGGAAAAA
7348 AA
1 AA
7350 AGGGGATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.16, G:0.30, T:0.05
Consensus pattern (21 bp):
AAGGAGACTCCCGAGGAAAAA
Left flanking sequence: Indices 6806 -- 7305
TCGAGAGCATTTTGATCAAGCTCTAGATGTGGATCATTATCTCTACATTTGGGACACCGAATATA
GAGAGATCCAATTTTTAGAAAAGAAGGGGTTGCTGCAGGACCGGCTCCATGAACTGATGCTTGGG
GAACGAAAGATCGATCGCATTATGGATCTTTCGCCCTATTCAGATGTGAGGAGGGAAGCCTATCA
CTTTGTTCAAGACAAAGTGGGACCGGTAAGCAGCCTAGAACACTCCTTTCAACGCGATATCATGG
AAGGCTCTCTAGGTTTGTTTATTCAACAACTGAATGAGGGTGGTAGGGAATCCGACTTTTACGGG
GAATTCTATCGTTATTTCACGGATGAAGAATTCCGCCGTGGAGCGGGCCTGCCCCTACCTTGAGA
AGCCCTCATATATATATATATCCTAAATAGAGAGGCCTTCTTCCATTTCCTATGGCTGGCGGGGT
TCAAAACTGGATGCGGTTTTCCCGCCTACTGCCCACACCCGAGGG
Right flanking sequence: Indices 7350 -- 7849
AGGGGATCCAAATATTCAAAGGTAGGTTCTTCCGAGAGTTCATCTTTTTTAATGGGATATAGTGC
GCTTTTTTTGGATTTGCTTGGGTAAAAATGGCCGGATGAACTACAAAAGGTCTGATACCTAACAT
TTCTTCTTGTTGAGTTGAAGTGGTAGGTTATGTAGGCGCTCGAAACTGCTTCTCACTAGACAAGA
TGGTACAGCAATGAGGGTTCGACCTATTCTATTTCCGGCAAAAAAGAAAAAAAAAAGTTGCAGAC
CTGCTTACATTATATATGTAATTTTTAGAGTGAAGTGAGCCCTGGGAGGGCGCACGAACGGAAGG
ATAAAACTGTCTTAATTAACCCCTTAGGAGAGTGCAGTGAACAAGCAAGGATACAGAATGAGATA
AGACAGTTACCGAACAATATACCTTATATGAAGTACTGTACTGAATGAGTACTAAGAGTGAGACA
GAAACCTATCAAGTTACCCACTTCCATCAGAAAATCAACGGTGTG
Found at i:31014 original size:21 final size:21
Alignment explanation
Indices: 30990--31030 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30980 CAAGGTCCAT
* *
30990 AGAATCTCTTCCTAAACCCTA
1 AGAATCTATTCCAAAACCCTA
31011 AGAATCTATTCCAAAACCCT
1 AGAATCTATTCCAAAACCCT
31031 GATCAGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.32, G:0.05, T:0.27
Consensus pattern (21 bp):
AGAATCTATTCCAAAACCCTA
Left flanking sequence: Indices 30490 -- 30989
ACTCCTCCGGTATGCATTCAAGAAGAATGAATCGAGGAGGATAGGTAACCTTACTTGGCTTACTA
TCTTGATCCCTTTCCTGATGTTGAGAATAAAGGATAGGATCAAGTCAGCCGAAAGATCATATGAT
TAGAATGGTGTTGATTCCTCATTGCTGGAGTAAAGAAAGCATTCTAAGGAGCAGGAGAAGTCAGA
ACTATCTACTTTCCCCTCCGTAACCCTGCTTCCTCTTCTCTTACTCTTCCTCAAAGGTAACTAAA
GAATAAACTAATAAGGCTGACGCTGGCCTTACGGAGGAAGTATAGGACTTAGAAGTTACAGGGGA
TCTAGTGTGCAGCCATGGAAACTCTCTTAACAGTTAAGATTTAGACTTTCCGGAAGTTTAAGAGT
TCTATTTAGAGTTACACTTCCGTCCATAAAGACTTCTATTTCATTAGTGTAGTTATATTTAGAGC
CGTAAAGAAGAAAAAAGAGAAAGACTTGGTTTTTCCAAGGTCCAT
Right flanking sequence: Indices 31031 -- 31530
GATCAGGGAACATACTATTGAATCAGCTATTTTAGAAGCTAAGAGATCCTATCCTCCCACCTTTT
CTCATCCCCTAAACCCTTATCTTCTCTTCAAATTATCTTCTCTGCAAACTCCCGTATCTTCTCAT
CAAATTCCCTCCCGTCTCTTTACCGTAACGAGGACGGAGTAAGTAGCAGCAGTTGAAGATCATCT
GATCCTTACGTAGGCTAAGACGTAGGCTAAGTCCCTTTAGATGGCCTAGACCCGTAATCAGTATC
TTCACTTCAGTAAGGGATTGACTTCAGATACTGCTTACGGGCCTACCTGATCTGTATCATGTCGG
GCAGTTGCCCTAAGATAACAACTAGTGGGAATCGAAGTCTGATCATTCAAAGGAAGGCATATAAG
ACTTGACTTTACATTCCTAGGATAGGGCAAATTCTCAATAGAGAAATGAAACTGTAAATCTTATA
AGATCAGTGACTATAGATCAGAAGCAGAGTAGAATAGTCCGTTCC
Found at i:31133 original size:16 final size:16
Alignment explanation
Indices: 31112--31143 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31102 CCCTAAACCC
*
31112 TTATCTTCTCTTCAAA
1 TTATCTTCTCTGCAAA
31128 TTATCTTCTCTGCAAA
1 TTATCTTCTCTGCAAA
31144 CTCCCGTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.25, G:0.03, T:0.47
Consensus pattern (16 bp):
TTATCTTCTCTGCAAA
Left flanking sequence: Indices 30612 -- 31111
CATATGATTAGAATGGTGTTGATTCCTCATTGCTGGAGTAAAGAAAGCATTCTAAGGAGCAGGAG
AAGTCAGAACTATCTACTTTCCCCTCCGTAACCCTGCTTCCTCTTCTCTTACTCTTCCTCAAAGG
TAACTAAAGAATAAACTAATAAGGCTGACGCTGGCCTTACGGAGGAAGTATAGGACTTAGAAGTT
ACAGGGGATCTAGTGTGCAGCCATGGAAACTCTCTTAACAGTTAAGATTTAGACTTTCCGGAAGT
TTAAGAGTTCTATTTAGAGTTACACTTCCGTCCATAAAGACTTCTATTTCATTAGTGTAGTTATA
TTTAGAGCCGTAAAGAAGAAAAAAGAGAAAGACTTGGTTTTTCCAAGGTCCATAGAATCTCTTCC
TAAACCCTAAGAATCTATTCCAAAACCCTGATCAGGGAACATACTATTGAATCAGCTATTTTAGA
AGCTAAGAGATCCTATCCTCCCACCTTTTCTCATCCCCTAAACCC
Right flanking sequence: Indices 31144 -- 31643
CTCCCGTATCTTCTCATCAAATTCCCTCCCGTCTCTTTACCGTAACGAGGACGGAGTAAGTAGCA
GCAGTTGAAGATCATCTGATCCTTACGTAGGCTAAGACGTAGGCTAAGTCCCTTTAGATGGCCTA
GACCCGTAATCAGTATCTTCACTTCAGTAAGGGATTGACTTCAGATACTGCTTACGGGCCTACCT
GATCTGTATCATGTCGGGCAGTTGCCCTAAGATAACAACTAGTGGGAATCGAAGTCTGATCATTC
AAAGGAAGGCATATAAGACTTGACTTTACATTCCTAGGATAGGGCAAATTCTCAATAGAGAAATG
AAACTGTAAATCTTATAAGATCAGTGACTATAGATCAGAAGCAGAGTAGAATAGTCCGTTCCGAG
GCTTGCAGATCCTACTGATCCTTTAGAAGCTAAAGTAGCTAACTTTAGGCTATTCGGTTTGACTT
ACGCTTTCATTACTTATGATTCTCTTCTTTGAAGTAGCTTTTTCT
Found at i:124970 original size:25 final size:24
Alignment explanation
Indices: 124932--124978 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
124922 CCGCTAGCTG
124932 TCACTCCTTGCCCTATTCGGTCGCT
1 TCACTCCTTGCCCT-TTCGGTCGCT
124957 TCACTCCTCT-CCCTTTCGGTCG
1 TCACTCCT-TGCCCTTTCGGTCG
124979 AGTTCTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 12 0.57
26 1 0.05
ACGTcount: A:0.06, C:0.43, G:0.15, T:0.36
Consensus pattern (24 bp):
TCACTCCTTGCCCTTTCGGTCGCT
Left flanking sequence: Indices 124432 -- 124931
TCCTCCGACCCGGAGTGGATTCTAGGGGAAGGGCAGAGCCTCACCTTGCAGTAGGAAGGTGTTCG
TTGCTGGGACGGGTTCAAACTGGACTGAAGGGAGGAGGAATTAAATAGTCCTCTCTTCCTGGGGA
TTCATCACTGGCTAGGGCTTTCGAATCAAAGCATGGGCATCTGCAACTAAGAGGGAGCAGTAGAT
CGTCGATTGAAGAGCCAGGTCAGTAAACTTCTATTGGGACTTCTATTGATTATTGATTCGACTAT
AGGGACTCCTAGCAACAAACTTGTATGACGGGGCCCCCATGGAGACGCAGGAGATGCAGGAGCCG
CCAGCCGGATCGACCAATAAATGATAGGCCAGAGGGATGGGCTCATTCGACTAATTAGTGATCCC
TGGCCCTACCTAACAAAGAGATGTCCCTAAACAAAAATAGGGGATTGGTTGATCGGAAAGCTCGG
GCAGGAGTAGGACATTCCATAAAAATCTTTCTGATCCGCTAGCTG
Right flanking sequence: Indices 124979 -- 125478
AGTTCTTACAAACCTCTCAAATCCTATTTTTTCATCGACAGGTAGGGTGAATTCTAAGGTTCCTT
ATTCTGGTTGTAAAGCGGAAGAAGAGGGAGAAAGAATGGGCACAGCCCCACCAGCAGCCCGCGTT
TTCGACCCGAAAGGAATTGAAAATGAAACAAGAATCTGTGTTCACTATCTATGGAGCGGAGTGAC
TATCCTTAATCTCCTCTTCCCTATCTCCCCCTTGCCTTTTTTTCTTGGCCATTTCTTTTTTTGTA
TTGTTTATTATGATTGATCTGTAGTTCAAGGGCACTCTTCCTAATCCGAGTTTAAGATGGAATAA
GACCCAGACGTAGAGTCCCGTCGGCCGGGAAGGGATTTATTCTATTGATTTTTTATTCCCTTCAG
TCCTTACCTTTAAATAAGGGATTCTTCTCTTTCCCCACGAGGGAAAGCCCTTCCCAGATGGAGTA
GTGCATCTCTGTCTTGAAAGCCCGCCCTACATATAGGAGTTCCTA
Found at i:174489 original size:15 final size:16
Alignment explanation
Indices: 174471--174503 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
174461 GAGTCAGCCA
174471 AAAAG-AAAGACCACC
1 AAAAGTAAAGACCACC
*
174486 AAAAGTAACGACCACC
1 AAAAGTAAAGACCACC
174502 AA
1 AA
174504 GATACGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.27, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAGTAAAGACCACC
Left flanking sequence: Indices 173971 -- 174470
GGGCTTAGGTCAACACTTATATAATAGCCAGTCATCAATTGGAAGCGGGCAAGATGGTGATGAAT
TGCAATTGGTCTAAACCTTCGACCAGCGACTTATTGCGACCCGCCCAGAATGCCAATACATACTA
AGACCTTATTCACATCAGGAGGAGCTACGGCAGCTCGAGGAGGAGCTAGGGCGGACCCAAGAAGC
CCAAGAACGGGATAGGGCCCGAGCCGTAGAGCGACAAAGACTTTGGCAGGACATATATAGAATCC
GCCAAAGAAGTCAGGTTTTCAAAATCGAAAAGGAAAGACTCAGATTCAGAATTAATGAAATTCAA
TATCAGCAAGACCGACGAAGAAGATTCGGTCGTGGGTAGAAACTTTGCTTGGGCCTTTCGTTTTC
GATTCCCATTAGCCGGGTAGCCTTAAAATTCGCTTAGTAGCTTAACTCTTTCTACTGGCGTGGCG
CTGCTGGATGCTTCTGATCAATAGAACAGGAAAAGGAGTCAGCCA
Right flanking sequence: Indices 174504 -- 175003
GATACGCATAGTGATTCGATCTTTTGATCACCCATTTTTTGAAAACCATTTTGGGGGGCTTCCGC
CTTACACACGGAAGATTGGATTGCCTGAATCACGAGTCTTATATACTGTGTTACGATCACCTCAT
ATTGATAAAAAGTCCAGAGAACAATTTGAAATGGAAATCAAGAAACAATTTCTGGTCATAAAAAC
AGAAACGCATGAATTGCGCAAGAAGTTCTTTCGGTTAAAACGCCGTGCGACTCGGAGGACATAAG
ACTTCTTGGTCAAGCCAAAAAGATTGCCGGCAGAATGCTCCTACCCCACCATGCCTGGCCCTTTA
CCTTACCTTAAGAAGAAATGGGGGGGTATGAAGCGTGGGAAAGAATGCAAGAAGTGTATGATACA
ACAGGTAACCTTAAGGAGTGGCGGCAAAGCTCTTGATTGATCAACGCGAGTGAACTGTGCTTAGA
CGCTTCGTAAAACCGCACCGATCTACGAGAGGAGCTGATGGATGA
Found at i:236204 original size:16 final size:17
Alignment explanation
Indices: 236172--236217 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
236162 CATCCCTTGG
236172 GGTTAGTTCATTCTCTT
1 GGTTAGTTCATTCTCTT
*
236189 GGTTAGTTGA-TCTCTT
1 GGTTAGTTCATTCTCTT
* *
236205 GCTTAGTTTATTC
1 GGTTAGTTCATTC
236218 CAATTACTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (17 bp):
GGTTAGTTCATTCTCTT
Left flanking sequence: Indices 235672 -- 236171
CTTTAAAGTAAAGCTGCTTCTTAGAGTTGGCTTTTGCAATTGCAATCTGTCTCTGGCTCCTCGCT
TTGAACTCAAATAAGACCTTCTTTTGGTCGAGTGACTTCAAACCTCTCCCAGCAAGAAAACGGAT
GCGCGAAAGCCTATCTATACTATAGTAGGGGGCTTTCGCTAACGCGCGCCCCTATCTCGTCAGCC
GTTGCTTGTTTAAGAAACCGGTTTTTTTCGGCACTCGGTTCCTTCGTCTTAAGTAAAGTTCAGTT
TACTTTTTCGATTCGGAACTCTTAGTCGGTGAGATCGATTTTTTGTTCGAGGTTCCAGAAAAAAG
AGAGGAAGCACCGCCCAATGGTGCTTTTACGAAAGTACGGTCACCGGTGGCTAATACCTTCTCGA
CACTATCGAACCTGAAATCCACTCTCAATCGCTCTTTTTAGTGGGGAGGAATTGTTTTTTTTCCT
GGGGCGGGACCATGCCTTGGATTTCAATCCGAGATCATCCCTTGG
Right flanking sequence: Indices 236218 -- 236717
CAATTACTGCCCCTCTTTTGCTTGATGAAAGACATCCTGGCAAAGGCTGTGTATATTAAAAAAGG
GGACTTTCATGGGTCCGATGGCTCTTTGACTGGTGTGCCTGAAAATGTGATGGATAAATGGGCTT
TTGAAACTCGATTTGTCGCAACAAAACAAGAGGTATTGTCTCCGCCTTTTCAAGTAGGGATCATC
TCTCAAGTGTTATGATCCTCCATTGCTGCTCGGTAGTGGCCTAAGGCTCAATGATTGATCTTCTG
CGCTAAGGCTAGCATCTCATCCCATCTTGAATCTTATTGCTTTGAGCTCTCTTCGGAAAAGTGTA
AAAGTGTAACCTGCTGCTCCTTGATTTCACATAAACAACTGAGTGCCTTCTGCTCCTTTTGGTCT
TCTCTTTCTGTGTCTATTGATCTCCTGCCCACTCACATTCTCTTTATCGAATCCTTCTAGGCAGA
TATGACTACTCCTGCTTGCTCTTGGCCTTGGCTGCTTAGAGACAT
Found at i:259086 original size:18 final size:18
Alignment explanation
Indices: 259065--259107 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
259055 CAACCTTGTT
259065 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
259083 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
259101 GACTATG
1 GACTATG
259108 GCAGGGCTTT
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:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 258565 -- 259064
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 259108 -- 259607
GCAGGGCTTTAGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTGA
AGATTTAAAAGGCGAGCACTGAAATGAGAAATTTCATTCGTGACGCTGAACGACACATTCTAAAA
CTAAAGCGCACACTAGAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCGGAGCCGGAGCCCGGCAT
GTTCGCCTGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTTTAGATAACAAAAAGTGTC
CCTTACCGGGGTCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTAGGGCGA
CCGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAG
GGGAAGAGGGCCCTCGGCCCGATCATCCAATTCACTCCAACAGACAGGCATGGTTCTGTAGTCAA
AGCAACTTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTC
Found at i:261480 original size:25 final size:24
Alignment explanation
Indices: 261438--261484 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
261428 TGTAAGAACT
261438 CGACCGAAAGGGAGAGGAGTGAAG
1 CGACCGAAAGGGAGAGGAGTGAAG
261462 CGACCGAATAGGGCA-AGGAGTGA
1 CGACCGAA-AGGG-AGAGGAGTGA
261485 GTGCGCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 12 0.57
26 1 0.05
ACGTcount: A:0.36, C:0.15, G:0.43, T:0.06
Consensus pattern (24 bp):
CGACCGAAAGGGAGAGGAGTGAAG
Left flanking sequence: Indices 260938 -- 261437
CTAACGGGGTCTCGGTTGATTTCCCTTCCTTTAGCTACTCAGATGTTTCAGTTCGCTAAGTTTTA
AAAGTCCAAAGAGCGCAGACTAGCCACGGAGCTTGGATACGGTTTCCCGATCGGAGATCCATGGA
TCACAGACGGTATCTCCCCATGGCCTTTCGCCTCTGAAAGCGTCCTTCCTTCTCAATGCCCGGGC
ATCCATCCAATGCATTCTTTTCTATCTTGTACCTTAACCTTAGTACACTGAACACCAACCCAATC
TCAAGGAAAAAAGAAAAACTACAAGCAACTAAAGAAGGGTGACGAAGCTTCTTTGCATCCCATAG
TGCTGTCGCACTAAGCGACTACCGTTCCAGAGTCGTACAACGAAGTGATTAGCATACCAGAGTGA
CGCAAGGCTCTAAGCTCGTACCTTATAGCTCTTTATGCTCTCTCCGCTCGCTCCTTTTCGTAGCG
TAGATCTTGATTCTCTTACGAGATTTTGAGAGGTTTGTAAGAACT
Right flanking sequence: Indices 261485 -- 261984
GTGCGCTTTCGAAAGTTTCGACTTTTCGCCCCAGACTCTTCTTTTATTTATTAAAAAAATAATCC
AGATATCTCCGAGAAACTACACTAAAGGGAACTGTTAAGTACAGACGATGCAACGAAATGATAGT
AACACCTGGGGCCTTCGAAATACCAAATTCCAGCTTAAGTCCAACAGGCCTACACTTTAACTAGG
AACAGAAAGGTCCGCGAAATAACCGCGTTGCTCGATCAGTGAAACCAGAGTGATGGTCTTCTGGG
ACGATACATTCGTAATGGATCCATCATATACGTTTTTTTAGATAGTTTTCATTTTGAGCGAGAGT
CTGAAACTAGGGGGATCCGGAGTTGCCGAAATCTATACTAGTTTGCCCAGTAATGTTGTGGCTGC
AATGCGTAGGCCGTCGTTCTCTGCTCTTTACTTTATATACGCAATTCAAAGTCGGAATTAGCTGG
TAGGAATAAGAGCAGTAGCTGAACTATCCCGCTTTTAGCCCGCCC
Found at i:332569 original size:15 final size:15
Alignment explanation
Indices: 332549--332578 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
332539 GCAGCAAGCC
332549 AGTAGTATTAGAATA
1 AGTAGTATTAGAATA
332564 AGTAGTATTAGAATA
1 AGTAGTATTAGAATA
332579 CCAGCCGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
AGTAGTATTAGAATA
Left flanking sequence: Indices 332049 -- 332548
TAGTTAAAGCATCCTCTATTGGAAATAGAAGAGTTAGAGCTTGAAGAGAAAGATCGGAGAAAAAG
AGCGTAACCTAAAACATCAAAGACTTGGGGGCCGAAAGCCCGGTCTTCCCTTCTCATCCAACACC
TGGTGATTCAATTCCTATTTATGCGCGGAGAGAGATTAAGACTGATATTTAGTTGATTTCCCCTC
ATTCATCTGATATTAGTAGGCCTGTAGACAAGCAAGCCTCCTCTTCCCTGGGAAGTTAGGGAGTG
AATTCTAGTCGTCTAGGGTGAAGTTAGCGGTAAGATCGTTAGGAATTTCTTTAGTAGATACTTGA
CTTTCCCGGAGTCAAGGCTGTAAGATTGAAAGTTAGAAGTTTAGGAAGTTTAGTTTGAAGACATG
AAGTCATTATATTGAGGATTTCTGTCATTCTAACCCAGAAGCAAGGAAAGAAGAAAACAAAGATG
AGGCAATTTAACCTCCAGCTTCTGATCTTGTAGAGGCAGCAAGCC
Right flanking sequence: Indices 332579 -- 333078
CCAGCCGTACTGGAGAAAGATCAGGAGAAAAAAGTCATTCTATTGTTAGGAAATCCCCTGCTTCA
ACAGAAAAGGTAGGAAATGCAGTTGCAAGCCGGGGATGAAATACCATATAAATAAGGTAAGATTC
TCCATTAGCAGCTCTAGAGGGAAAGCCTTAGAAAGAAGTAACGGAAGTTAGAAAGACTAAAGTCT
ATCATTTCCCGTCCAGCTTCTGATCTTGTAGGCCGGGAAGCCAGTAAGATATCTTTATCTTTTGC
TTGCAATCAAGTCAGCCTAACAGAACTGTAACTTGCAAGCAAGGGAAGACTGTAACGAAGAAGAA
AGCAAATAACCCTCGGCTCTTTAGTTCCTAATACCGATTTAAGAGCCCGGAAGAATTCCCAGTTT
TCCGGATATCAGGAATTCCTGATTTACAGATTTAGGGACTAGAGAGAACAACAAGCCTAACTAAA
AACAACCAATCCCATTTGATTTGGCACTTCACTTCCTTTCGAAAA
Found at i:433291 original size:33 final size:33
Alignment explanation
Indices: 433249--433332 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
433239 TCCTTCGCCC
433249 GCCTCCCTTTCCCTACCAAAGCCCGCCTGCCTT
1 GCCTCCCTTTCCCTACCAAAGCCCGCCTGCCTT
*
433282 GCCTCCCTTTCCCTACCAAAGTCCGCCTGCCTT
1 GCCTCCCTTTCCCTACCAAAGCCCGCCTGCCTT
*
433315 GCCCCCCTTTCCCCTACC
1 GCCTCCCTTT-CCCTACC
433333 CCGCGGCCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 41 0.85
34 7 0.15
ACGTcount: A:0.11, C:0.54, G:0.11, T:0.25
Consensus pattern (33 bp):
GCCTCCCTTTCCCTACCAAAGCCCGCCTGCCTT
Left flanking sequence: Indices 432749 -- 433248
TGACAGGCACTCCAGGACCCGCCAACGCTCATGAAAACCCGGGTCGGTCCTCCATTCATCTGACC
GGAGGTGTGGATAACGAGGCCACCTTCACAACCTTCTCCCTTCTGTCCTTATGTTGTAGTAAGGT
AGGGCGGTTCGCTTGAGTTGCTCAACCGCCCCTTAGCCCGGTGCTCATGACGCGCTACGGAACCT
CCACCGTGCCGGGGGACCAAGCAGGGCATAGCTAGCGGCATAGGAGCCGACTCGGCGTCAGCGGC
TTCGTGCCGCACTGGAGTGATCCAATATGTGGTTCCGCACGTTCCACCACTTCTCCGTTCATTTC
CAATACTGATCGTGAAACACCATGAGCAGCAGGATGTTGAGGTCCGGAATTCGAAGTGAAATTTT
TTATTTGCCCGTTCCTAGTCGTCATGGGAAAAAAGGAAGAAATAAGAAAGAGATTATTCCCTGAG
AGCTTGTCCAGTACTACCAGTACCATAAATGCATCTCCTTCGCCC
Right flanking sequence: Indices 433333 -- 433832
CCGCGGCCTAACTAAAGAGCTTCTCGATTGAAACGAACCCAAGGCAAGGCATACAACGAAAGAGA
TATCGTAACGTCTGATGGCATTTAAGACTCGTTGATAGAAACGAGTATCCCTCGTGCCCAACGTA
TCAATTTCTGAGAGGTATCGCTGGTACGTCCCAAGAGAATAAGGGCTCCCTCGCGGGTAAAAAAC
CACCCCCCGTATATGATGGCGATTTTCGACGATCCTAATCGGATCAAAGCCATCATATACCAAAG
CCGCTTCGACCCGACGCTCGATAAGAACTTGCACCCCAACTATCCTTTGAAGGGTCCCTTCTGTT
ATTTGTTGACCCAGCGTGTTGATAGATAGTCGAGGGTATAGTTCTGAGCGCCTTTGATCATCTGG
TATTAAGGGTTGCCCCAATTCGGGAATAATTGGGGGGGATGGTTCTAGGTCATCCGCAGGAGCTT
CTATAGCCGCCCCTGGGAGTTCGACAGTCGGTGGTGTCGGCGGAC
Found at i:547874 original size:18 final size:18
Alignment explanation
Indices: 547853--547895 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
547843 CAACCTTGTT
547853 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
547871 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
547889 GACTATG
1 GACTATG
547896 GCAGGGCTTT
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:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 547353 -- 547852
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 547896 -- 548395
GCAGGGCTTTAGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTGA
AGATTTAAAAGGCGAGCACTGAAATGAGAAATTTCATTCGTGACGCTGAACGACACATTCTAAAA
CTAAAGCGCACACTAGAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCGGAGCCGGAGCCCGGCAT
GTTCGCCTGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTTTAGATAACAAAAAGTGTC
CCTTACCGGGGTCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTAGGGCGA
CCGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAG
GGGAAGAGGGCCCTCGGCCCGATCATCCAATTCACTCCAACAGACAGGCATGGTTCTGTAGTCAA
AGCAACTTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTC
Found at i:550268 original size:25 final size:24
Alignment explanation
Indices: 550226--550272 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
550216 TGTAAGAACT
550226 CGACCGAAAGGGAGAGGAGTGAAG
1 CGACCGAAAGGGAGAGGAGTGAAG
550250 CGACCGAATAGGGCA-AGGAGTGA
1 CGACCGAA-AGGG-AGAGGAGTGA
550273 GTGCGCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 12 0.57
26 1 0.05
ACGTcount: A:0.36, C:0.15, G:0.43, T:0.06
Consensus pattern (24 bp):
CGACCGAAAGGGAGAGGAGTGAAG
Left flanking sequence: Indices 549726 -- 550225
CTAACGGGGTCTCGGTTGATTTCCCTTCCTTTAGCTACTCAGATGTTTCAGTTCGCTAAGTTTTA
AAAGTCCAAAGAGCGCAGACTAGCCACGGAGCTTGGATACGGTTTCCCGATCGGAGATCCATGGA
TCACAGACGGTATCTCCCCATGGCCTTTCGCCTCTGAAAGCGTCCTTCCTTCTCAATGCCCGGGC
ATCCATCCAATGCATTCTTTTCTATCTTGTACCTTAACCTTAGTACACTGAACACCAACCCAATC
TCAAGGAAAAAAGAAAAACTACAAGCAACTAAAGAAGGGTGACGAAGCTTCTTTGCATCCCATAG
TGCTGTCGCACTAAGCGACTACCGTTCCAGAGTCGTACAACGAAGTGATTAGCATACCAGAGTGA
CGCAAGGCTCTAAGCTCGTACCTTATAGCTCTTTATGCTCTCTCCGCTCGCTCCTTTTCGTAGCG
TAGATCTTGATTCTCTTACGAGATTTTGAGAGGTTTGTAAGAACT
Right flanking sequence: Indices 550273 -- 550772
GTGCGCTTTCGAAAGTTTCGACTTTTCGCCCCAGACTCTTCTTTTATTTATTAAAAAAATAATCC
AGATATCTCCGAGAAACTACACTAAAGGGAACTGTTAAGTACAGACGATGCAACGAAATGATAGT
AACACCTGGGGCCTTCGAAATACCAAATTCCAGCTTAAGTCCAACAGGCCTACACTTTAACTAGG
AACAGAAAGGTCCGCGAAATAACCGCGTTGCTCGATCAGTGAAACCAGAGTGATGGTCTTCTGGG
ACGATACATTCGTAATGGATCCATCATATACGTTTTTTTAGATAGTTTTCATTTTGAGCGAGAGT
CTGAAACTAGGGGGATCCGGAGTTGCCGAAATCTATACTAGTTTGCCCAGTAATGTTGTGGCTGC
AATGCGTAGGCCGTCGTTCTCTGCTCTTTACTTTATATACGCAATTCAAAGTCGGAATTAGCTGG
TAGGAATAAGAGCAGTAGCTGAACTATCCCGCTTTTAGCCCGCCC
Found at i:587379 original size:15 final size:15
Alignment explanation
Indices: 587359--587390 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
587349 CGGGCTTTCA
587359 TAAATCAGTATCTCT
1 TAAATCAGTATCTCT
*
587374 TAAATCAGTATTTCT
1 TAAATCAGTATCTCT
587389 TA
1 TA
587391 TGAATAGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (15 bp):
TAAATCAGTATCTCT
Left flanking sequence: Indices 586859 -- 587358
CTTTGCCATCTGCTTTTTTGGCTTCTTGACGGCCCGTGCCTCTCCGCTTTTTGAGTCTTCTCGGA
CGTGACAGATCCAAGATGAAATCTGATCGGGGCTTTCTCCTTTTCTTTCATGATTGAGCCGATAA
GAGCAGAGAATGAGAAAGTCAACCGAATTAAAATAAAAAGGAATTTCCTTTGAAATTCTGTCGAA
GCCGATAGGGATAGGAAGGTGCAATGCGGACCTTTTATAAGTTCAAAGGTAAGAATATTAAGAAG
TCATGTGACCATGCAGGCGGGCCTGGACTCTTTTCTTTCTCCTCCGGCGAATGATTTCACTTTTC
TGGCCCTCAACCAAAGACTAAAAACTCACCCAAGCCTTTGGGTAAGGCTAAGTAGGGTAGGAAAC
TCTTTCTTGCGGATTTCACAGTTCACGTGTCCCCGCATTTAAGTCTGAAACGGGTGCTAGCTTGA
AAACCGCCACAGTTAGCTGTCGGTTGAGGCCTCACCGGGCTTTCA
Right flanking sequence: Indices 587391 -- 587890
TGAATAGTAGGGCACTGAGGGAGAACTTATCGACGACAAAAAAGACGAGGTTTCTGTTGGAGGGT
CCCTGCCGCCCCGAGTCAAATGGAATTTAAAATACTTTTTTTATAAACAAGGTGGCATCTCGAAA
GTGCCGCTAGGCGGTTTAATCATGGAACGTCCAAAAAGCCTGGTAAAATGCGAACATTATTATTC
TAAAAAGATGCCCTAGAACATACATGTTATTGAATTGAGTGAGAGGTCCCTTTCTTTCCTACTAC
TGAACCCGGAAATTGCGTAGATTGCTTTGCTTGGAATTCCCTAAGTAACCCAATCCCTGTCATTT
CACACGGAAAATGGTATGTTTGAGCGTTTGAAGTGGACGAACAATCAGCGTACGTAATCGAGTTT
CATGCCATCATGTCTTTCTGCCCAGCAGCGCTGGAAACCGCTTTCATGCGTCTTGGTTGTTGGTA
GAGGCCTGAAAAGATTCTATTTGAAATAGTTTCAAAGGCTTGAAG
Done.