Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_035317
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: 349058
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:26606 original size:12 final size:12
Alignment explanation
Indices: 26589--26613 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26579 AGACCACTCG
26589 ACTATACTATAA
1 ACTATACTATAA
26601 ACTATACTATAA
1 ACTATACTATAA
26613 A
1 A
26614 GGAGAGGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ACTATACTATAA
Left flanking sequence: Indices 26089 -- 26588
ACCAGTGTGGAAAACTTATCTGTGCCCCAGAACAATTCAAGCTTAGCTAGCTTTTGAAATAGCTG
AAGCTAACTGGAGTTAGAGCCTTGCCTGAGAAAATCTCTCTCAACTACCCGTCCGACTCCGACCT
CTTAATAGTCCCCGATGCTGCTTTTCCATGCCATCATATGTGCATACGCATACTGACCTACTATA
CCGCTCCCTCGGCTCTAGACTAAAGCATCACTTCATTTCCACCTTATTGAAGATCTGGTGGTATT
TCGTCATTTGAATCTTGTTCATCTTTCTTTCTAGAATGAGGCTCACGGATGAGATAATACAACCC
AAGCGGGCGGCGGACAAGAGGATGGAAAATGTCGAGATTTCTTAGTTAGCAATAGCACTGTATTA
TTTATGATTACTTAAGTAAAGGGGCCCGGTGACGGGTTGTTTATCTAAATTCCCAACCCCTCGGC
CTCACTTTGGAGTCAGCTACTTCGTCACTGAAGAAAGACCACTCG
Right flanking sequence: Indices 26614 -- 27113
GGAGAGGAGTTTGGAGGGCCGGTGGTGGGGCAGAGCTTTAGCCTCCTGAAGTCCGCTGAAGCGGT
CAAACTAAGCCTGAAGTTCCTCTTGTTCCACATCGCCTCAAAGCGAAACCTGATTTTCTTCTCGA
TAATCATCCGCCCCGCACTCTGAAAATCAACGGATGGAAGTCACTGCTTTACCATAATAATAAAT
AGAGTCGATGGTGAAGCTATAAAGTGCTTGGGGAAAGAGCCGCTGAGATTTTGATATAATAGTAT
GCAAAAAAAGGCTCGTCCTAATGCATATATATTTAGCGGCCTCCGGGGGGAAACTACCTTTGTCG
ATCTTTTTTTTCGAGAGCTGAGCTGAGAAAGGGAAAGAGAGGGGTCGATCTTCCTCCGACCTATT
AGATCCTTTACATCAAAATACGGTCAAGCGACCTTCTCCTAAAATCAAGCAACCCCTCTCGACTC
ACCTCTCTCTCTAGATTTCTCGGGGTTGAAAAAGATGCCCTGGAT
Found at i:31759 original size:154 final size:154
Alignment explanation
Indices: 31479--31786 Score: 616
Period size: 154 Copynumber: 2.0 Consensus size: 154
31469 AGAGCTTGGG
31479 AAGCTCGGACCCGGTCGACGAATTGATAAGTTACCCAATAACTAGCTTTTACAACACTCCCCCCC
1 AAGCTCGGACCCGGTCGACGAATTGATAAGTTACCCAATAACTAGCTTTTACAACACTCCCCCCC
31544 AACTCAATTTCGCGATAAGGGGTAAGAAAGTTGTCTTTTTATCGGACTGGGGGTCTTTCTCTACA
66 AACTCAATTTCGCGATAAGGGGTAAGAAAGTTGTCTTTTTATCGGACTGGGGGTCTTTCTCTACA
31609 GCAGTTGGTATCGGCAGCTATCTC
131 GCAGTTGGTATCGGCAGCTATCTC
31633 AAGCTCGGACCCGGTCGACGAATTGATAAGTTACCCAATAACTAGCTTTTACAACACTCCCCCCC
1 AAGCTCGGACCCGGTCGACGAATTGATAAGTTACCCAATAACTAGCTTTTACAACACTCCCCCCC
31698 AACTCAATTTCGCGATAAGGGGTAAGAAAGTTGTCTTTTTATCGGACTGGGGGTCTTTCTCTACA
66 AACTCAATTTCGCGATAAGGGGTAAGAAAGTTGTCTTTTTATCGGACTGGGGGTCTTTCTCTACA
31763 GCAGTTGGTATCGGCAGCTATCTC
131 GCAGTTGGTATCGGCAGCTATCTC
31787 TCGAGCACAG
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 154 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (154 bp):
AAGCTCGGACCCGGTCGACGAATTGATAAGTTACCCAATAACTAGCTTTTACAACACTCCCCCCC
AACTCAATTTCGCGATAAGGGGTAAGAAAGTTGTCTTTTTATCGGACTGGGGGTCTTTCTCTACA
GCAGTTGGTATCGGCAGCTATCTC
Left flanking sequence: Indices 30979 -- 31478
TGCCATCGGACGTGAAAGAGGCAGTCTCACGATCGGGCATGAGTGTCCGGAAGTTTGAATTCTAT
ACTCCCGCGGGTCGGAAAGCGGCGAGGGAAGGAGGGGGACACTGGGCGGGATCTTTCAACAGCGA
ATTCCCCATACAGATAGAGGCACCGGTGAAAAAGATAGTCCGAAGGCTTCGGGATCGAGGTCTCA
TTAGCCGAAAAAGACCCTGGCCAATTCACGTGGCCTGCTTGACGAACGTCAGCGACGGAGACATC
GTAAATTGGTCCGCGGGCATCGCTATCAGTCCTCTGTCCTACTACAGGTGCTGCGACAACCTTTA
CCAAGTCCGAACGATTGTCGACCACCAGATCCGCTGGTCTGCCCTCTTCACCCTAGCCCACAAGC
ACAAATCCTCGGCGCGGAATATAATCCCAAAGTACTCCAAAGACTCAAATATAGTCAATCAAGAA
GGTGGTCAGACCCTTGCAGAGTTCCCAAACAGCATAGAGCTTGGG
Right flanking sequence: Indices 31787 -- 32286
TCGAGCACAGGTTGAGTCCTATATATTTCTTTTTCCAAAGCTTCATCTCCCTCGCAGTTCTACAG
GTCCTCCATGCGAGGACGGACAGGTTGGTTCGAGGACTAATGTCAGTCAAAACTAAGGAAAGGGG
GGGTCCTGATTCCGGGACGGAGCCGTATGACGCGAGAGTGTCACGTACGGTTCCTTTGAGAAGGG
TGTGATACCACCACCTATCAGGCCCGACGAACGGTCCACGGAGCTGCATCCCTACTCACCTGGTC
CATGCACATCGCTCTCTCCAGGAGGTTGGCCGCCCATCCTAGATCTTCCCATTTCCAATAAGATC
CCGGGCTCGATCCGGTTTAGTATCAAGGTTCTTCTCTTTCTTTTCCTATATATATGGGTCCGCGC
AGCATTTCCACGATATCGTTATGATCAATTAATGGGACTTGGTCGGAAAGTGTTATTGCCTCTAT
CATTAGCTCGGGTAGTCGCCGTTTCTGGTGTTTCAGTCACCTTTC
Found at i:82562 original size:13 final size:13
Alignment explanation
Indices: 82544--82569 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82534 GAGCCGCAGG
82544 TTATATAGAGCAT
1 TTATATAGAGCAT
82557 TTATATAGAGCAT
1 TTATATAGAGCAT
82570 ACAGAATACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TTATATAGAGCAT
Left flanking sequence: Indices 82044 -- 82543
TCTTGTTTAACCTTGAATGCAATTTATGGATTCTACAGCAATAGTCCCTCGGACTCGGAAAGTAA
TAACGAAAATGGCTGACCCAATAGCAGATTCCGCAGCTGCCACTGTTGGAACTAATGAAGCAAAT
GATTGACCCATCATATCATCCAAAGAAACGGAAAATACCAAAAAGTTCGAATTCACTGCTAATAA
CATTGATTCAATTGGCATTGACATAATAGGAATATTTCGTCTATTTAGGAGGATTCCCCGAATAC
CTAAAATAGAGATGATCATCGAAAATGTCAAATATTTCTGGGGATCCGTTTCGGGAACGTGGAAT
GTCAGTCAGAGAATTTCAAATGAGATATTGGATTCTTCTTTCTTTTTGGGTGTTGTGAAGCAGTG
GCAAAAAATAGAAAAAAGCTGCAAATAAATAGGCAGACGTCTCTCTAAAGCTCTCCCAAGATGAA
CGGGAAACTATACCAGAGGGGGACTATACTCATCCGAGCCGCAGG
Right flanking sequence: Indices 82570 -- 83069
ACAGAATACGAGAATTTCCACCTTGTTTTCCGACTCGTCGGACGGTCCCATCAACTTGGGGCTCA
CATCTCTCCCTCTTCTTCTAGGTCCCGCTGGCTCTCCCTCACATATACAAGCTTCAACTACAGCC
TATTAAAACGCAAACTGGATTTGAAATCACACTGCTTATATACCTGGTATTGAACTCCATCTTTA
GTCCCCTTTTTTCATTTCTTTTTCCAACTACGCGAGAAACTTCTTCTGTGTGAGTTGGAGGAGGA
AACGGGCCACCATCCCGGATCAGATCGGCTTACCCTACATCGACGTGCTTCCCCTTTCTCTAATA
ATGACATTTGACGATGCCTTCGCTTGCGGAGGTGCCTCCCTCCCCAAAAGTCCATATCCCCCCGC
TTTATATCAAGCTCAAACGGATGCTTGATATGCCTTTAATATCATTCGAGGGCTAAGGCCGAGTT
CTGAGGGAAAGGTAGAAAACGCAAACTGGGATGATGGCACGGACT
Found at i:145221 original size:18 final size:18
Alignment explanation
Indices: 145198--145235 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
145188 CATTTTTTGC
145198 ATTATTTTACTATCCGTA
1 ATTATTTTACTATCCGTA
145216 ATTATTTTACTATCCGTA
1 ATTATTTTACTATCCGTA
145234 AT
1 AT
145236 AGTACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTATTTTACTATCCGTA
Left flanking sequence: Indices 144698 -- 145197
AGAGGATAGCGAGTTACAAATTCTGTCTCGGTAGGACATGTATTTCTATTACTATTAAATTAATA
AATGGCGGGGTTACCATTATCCCTTTTTTGTAGTGATGAATCTTGTATGCGTTCCTAAGAAAATA
AATTTGTCCATTTCATTTTTCGAGGTATCAAAGGGGCATGGAAACACATAGAATAGAACTCTTGA
ATGGAAATGGAAAAGAGATGTAGCTCCAGTTCCGTCGGAAATGGTAAGATCTTTGGCGCAAGAAG
AAGGGGGTGATCCGTATCATCTTGACTTGGTTCTGCTTCCTCTCCCTTTGATTTGAACAATACCG
GGTCGGGTTCTTCTCCTACCAGTATCGAATAGAACATGCTGAACAAAATCTTCTTCATGTAAAAC
CTGCTCGATTTAGATCGGAAAAATCGTACGAATTTGATGAATGTGCTATGGCTCGAATCCGTAGT
CAATCCTATTTCGGGAGCAGTTGACAATTGAATCCCATTTTTTGC
Right flanking sequence: Indices 145236 -- 145735
AGTACGAAAAGAAGGCCCGGCTCCAAGTTGTTCAGGACAGGAATAGTGGCGTTGAGTTTCTCGAC
CCTTTGCTTTAGGATTAGTCAGTTCTATTTATAGGGGGAAGGGATATAACTCAGCGGTAGAGTGC
CACCTTGACGTGGTGGAAGTCATCAGTTCGAGCCTGATTATCCCTAAACCCAATGTGAGTTTTTC
TATTTGATTTTGTTTGACTTGCCCCCCGCCGTGATCAAACGAGAATGGATAAGAGGCTCGTGGGA
TTGACGTGATAGGGTAGGGATGGCTATATTGCTGGGAGCGAACTCCAGGCTAATATGAAGCGCAT
AGATACAAGTTATGCCTTGGAATGAAAGACAATTGAGAATCAGCTTTGTCCACAAACAAGGAAGC
TATAAGTAATGCAACTATGAATCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGC
ATGCTTAACACATTCAAGTAGGACGGGAAGTGGCCCTGAAGTTTG
Found at i:164156 original size:172 final size:172
Alignment explanation
Indices: 163870--164213 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
163860 CAGCAACACA
163870 AAACGAGGGTTTCGCTCGTTATAGGACTTGACCAAACATCTCACGACACGAGCTGACGACAGCCA
1 AAACGAGGGTTTCGCTCGTTATAGGACTTGACCAAACATCTCACGACACGAGCTGACGACAGCCA
163935 TGCAGCACCTGTATGAAAGGCACATCCCGGGGAGGACTGATAGCTTTTCTTGTTCATATGTCAAG
66 TGCAGCACCTGTATGAAAGGCACATCCCGGGGAGGACTGATAGCTTTTCTTGTTCATATGTCAAG
164000 GGCTGGTAAGGTTTTGCGCGTTGTATCGAATTAAAGCACATG
131 GGCTGGTAAGGTTTTGCGCGTTGTATCGAATTAAAGCACATG
164042 AAACGAGGGTTTCGCTCGTTATAGGACTTGACCAAACATCTCACGACACGAGCTGACGACAGCCA
1 AAACGAGGGTTTCGCTCGTTATAGGACTTGACCAAACATCTCACGACACGAGCTGACGACAGCCA
164107 TGCAGCACCTGTATGAAAGGCACATCCCGGGGAGGACTGATAGCTTTTCTTGTTCATATGTCAAG
66 TGCAGCACCTGTATGAAAGGCACATCCCGGGGAGGACTGATAGCTTTTCTTGTTCATATGTCAAG
164172 GGCTGGTAAGGTTTTGCGCGTTGTATCGAATTAAAGCACATG
131 GGCTGGTAAGGTTTTGCGCGTTGTATCGAATTAAAGCACATG
164214 CTCCACCGCT
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (172 bp):
AAACGAGGGTTTCGCTCGTTATAGGACTTGACCAAACATCTCACGACACGAGCTGACGACAGCCA
TGCAGCACCTGTATGAAAGGCACATCCCGGGGAGGACTGATAGCTTTTCTTGTTCATATGTCAAG
GGCTGGTAAGGTTTTGCGCGTTGTATCGAATTAAAGCACATG
Left flanking sequence: Indices 163370 -- 163869
AACAATCCGAACTGAGGCAATCTTTCCGGATTCGCTCCGCCTTACAGCCTTGCTTCCCATTGTCA
TTGCCATTGTAGCACGTGTGTGGCCCAGCCCATAAGGGCCATGCGGACTTGACGTCATCCCCACC
TTCCTCCAGTATCTCACTGGCAGTCCCTCGTGAGTGCGGCACGCACCTTGTCGATTTCTTTCGGA
GCGGGACGTAGTACTATACTATTAAGCTAGCTTTCGACAAAAGAAAAAAACCACAGCTTTTATCG
AGAATAGTCCACACCACCGGGTGGCTCGACTGAGTGCCGAGCACACTAAACAAACCGCCGCCAAC
TCGACGTCGTCGCCGGAAAAAGCTATCAATTAGTACACTGAGCTCACTTCCCCGTCTGACGTCCC
CTAGGTAGGTCTCAGTGGTGAACGAGGGTTGGTGTGGCGGGCCCTGCCTGAAAGTAGAGGTGGGC
TCGGGGGTGCGCGGGGGATCCTTAGGCACATGTCTCAGCAACACA
Right flanking sequence: Indices 164214 -- 164713
CTCCACCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCGGTCTTGCGACTGTACTCCCCAG
GCGGAGTCTTGAACGCGTTAGCTGGGCCCCTGATCCGCGTGGACCAAGGGCGAAGACTCATCGTT
TACGGCATGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCATGCTTTCGCACCTCAGCGTCGG
TAGGGACCCAGAGAGCTGCCTTCGCTTTTGGCCTTCCTTCGTGGATCTAAGGATTTCACCCCTAC
ACACGAAATTCCACTCTCCTCTGTCTCACTCGACGTTCATTGGTTTCGAGAGCATTCCGCCTATT
TTTGGCGACTTTCACTTGCACAAGACCTGATGAACCGCCTACGTGCCCTTGACGCCTAGTCATTC
CGAAGAACACTTGCCCCCCCCGTCTTACCGCGGCTGCTGGCACGGAGTTAGCCGGGGCTTCTTCC
TCGAGTCCTGTCATGATCGCGCACTCGACGAAAGAGCTTGACAAG
Found at i:180210 original size:15 final size:15
Alignment explanation
Indices: 180190--180219 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
180180 TGCATACTAT
180190 TATATAGAAATCTCA
1 TATATAGAAATCTCA
*
180205 TATATATAAATCTCA
1 TATATAGAAATCTCA
180220 GCGGAGGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (15 bp):
TATATAGAAATCTCA
Left flanking sequence: Indices 179690 -- 180189
ATTTTCACCACTTCTTAAGATCGTTAAAGTAGGAGGCTGGGAAAGCTTTCTCGCCTGCTTGACTA
GACGGACTAGAATTGCATGGGCTTCAGACTGCTCCTACAATGGAAATAGGTTTTCTTAGCACGTC
AGACTAGAGGAGCTTAATTAATATAACTAGATCACTGGGCACTGAAACTCTTAGAATATGGGATG
GGCCTATTGATACTTGGCCTTTGGCTACGATGCGCTGGATTTAGGAACTGCACTTCTACAAATAT
CAAGAAGGGGCATTGGCCGAAAAGGTGGAAGGCTAGGCCTATTTAAGATAGTGCCATGTTTCAAA
TCGACAACTATAGGCCCAAAAAACTGGCTCAGCTGGATAGTATTAGCTTTAGTTATATCGCGGAC
GGGTGGAGCTGCTAGATATAGCTTACTGGACACTTTCAGAGATCAGATTAGGCACTATTTATTAC
TAAGAGTCCAAAAAAGGAGGAGACTTCTTCGATTTTGCATACTAT
Right flanking sequence: Indices 180220 -- 180719
GCGGAGGTCCCCGACCTAAACCAGGCTCTTCTATTGATCGGTTGAGTGGTCTGCCTCAGTGTCCA
CAGGCCCGATCCTTCCTCCACACATGAGGATAGGGTCGAACTAGGCGAGGCTTTCAGAGTCAAGA
AATTCAGGCTGCTAATTATAGCTTTGCTAAGCTGAGGATAGACCTGGATACTCTATTATCCGGGA
GCGCGAGACCTCTTTAGTATTCTCTTATTGTATGGATGGCCAGTCGATTGTTCTCCCTAAAAGAA
GCTTGTAGGCCTCCTTGTTTTTAGAGTACCCATGGGCTTGTAGATTGCTGAGTCATCACGGCGAG
GAAATCCTGACTTCAGGATCGTATCAAAGAGTTCGAAACCCAGTTTCAGAGTCAAGCCGAACCTA
TAAGCTCTGATACCAATCTGAGGCAGAGAGATCCATCTTCTAGAGTTCGACGAATCAGACCCTCT
CATCCGCGAAGCTGGGGTGGGATATATGCGCAAATCCCCTCATGG
Found at i:275439 original size:15 final size:15
Alignment explanation
Indices: 275419--275457 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
275409 ACATTCTAGT
*
275419 ACAGGAAATATCTTA
1 ACAGGAAATATCCTA
* *
275434 ACAGGAGATATCCTC
1 ACAGGAAATATCCTA
275449 ACAGGAAAT
1 ACAGGAAAT
275458 GCCATCCAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (15 bp):
ACAGGAAATATCCTA
Left flanking sequence: Indices 274919 -- 275418
TGACCACTCGAGACCACCTAGAAAGGATTAGCAAGGGCTATCTCTAGGCTTTCTGCTATTCCTAG
CTTTATCCCGCTGTAGCCTACTTTCTTGCCTTAGCTCTATCTCCTGCGATTATTTCTCAAAAAGA
AGCCACTTTCACTCCTGCTTGCTCATTTGAAAGAAAAGAAGTTGAAAGCTCACTTTCTCACTTTG
TGGAAATAATATATGCTTGATCACAATCCTTTTTTTTAGGCTGCTGAAAATCATACTTTTTCTTA
ATCAAGGAAATAATTCATAATCACCGGAAACTAGCTTGCTTACTGACTGAAGTCAGCTTTAGATG
ACTCACTTGTTTTTGAGTTTGCTTATAATCAGGAAGTCTGACCTTAGGACTAGGACTGTCCAGCA
AAGACTATATAATATAGTGTTGATGATCTGGATAGTAATGTTGTTGGGCCGTTGACCTAATAAAT
ATGTTAACAATAAAACAAGATAAGGGCTAATTGTCACATTCTAGT
Right flanking sequence: Indices 275458 -- 275957
GCCATCCAAGGTAGGACCGCTATCTGGTAGTGCTTTCCTTTAGATAGTTAGCTCGTTACTAAAGG
GCGTGCTGCCTATCCCTAATCTATTACTTACTTAATTGACTTGATAGCTTTCCCGAAAAGATCGG
ATTTGCGCTAATGCAGATTCGCGAAGAACGGATTCGATAGCGCCGTCTTCTTCCTTCACACAAGG
CCATGCCTTTAATACGACAGGACCAATGGCAACTGATGAAACAAGAGAAAAAGCTATCGAACCAG
ACACTATACACTATACCTGGTGATTAGTCTTCTTTCAGGGCAGCTCGGGACTCGAGGGTGGGGGT
CAGGGTCTTTGCTTTTTGCTATTGTTGAATCGACCATTCACTCCTAGGTAGCTGTGAATGAGAAT
GGTAAGCGAAGATGAGATTGAACTCTTTCGAGATGCGAAGAATCATATCCCTAAGCAAGGCGCGT
AGCGACTGCGATCTTATCCTCTTATCCAAGGTCAGGAATCAGATA
Found at i:308791 original size:17 final size:18
Alignment explanation
Indices: 308768--308810 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
308758 GAAGCTCTAT
308768 GAAAGCGGCGA-GAAAG-
1 GAAAGCGGCGATGAAAGA
308784 GAAAAGCGG-GATGAAAGA
1 G-AAAGCGGCGATGAAAGA
308802 GAAAGCGGC
1 GAAAGCGGC
308811 TCTCTCTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.44, C:0.12, G:0.42, T:0.02
Consensus pattern (18 bp):
GAAAGCGGCGATGAAAGA
Left flanking sequence: Indices 308268 -- 308767
GTCTTTGATGATGATCCAAGCTGCTATTGCCATTTCATCGAGTGCCAGCTCAGTTGAAAGATATC
TATAGGGGCTAGTCCTATCTAATCATAAATCTCACAAGCAAACCCATCTTCTTTTTTCTCGACTT
TTAAGCGCTGAAGAAAGAAATAACCAGAATTTGCTAGAACTATTTCTGTGAAGTTTTCAATCCTT
TAACCCCTTTCCTGCATTAGGAAAGCTAGGGATATGGATCTTACGAAAACGACGTTCTCAATCAG
GTAAGCGGTGAACAAGAAGTGCCTTTTTCAAGTAATTGAGTAAGTGCATGATCCTATCCTCTCTC
ATCTCAGATGTGTTTTGGCCTCGACAGTTTTCTAAACACGTTGGAAGCCTTATATTATAGTATAG
TATAGTCTAGTTTGGCGAGTAATTTCGTCCCTCACTTCAAAAGTGCTCAAGGAGAAGTCAGTTAA
AACTGTTTATGGTGACTTAAGGCAAGCTAACTGTCGAAGCTCTAT
Right flanking sequence: Indices 308811 -- 309310
TCTCTCTATCTCCTCAACGCGAAAGTCAAAGATTTTTGACACAACATAACTCGACAGGCGCAGTC
AGCGGCGGTATTTATTACTAAGAGTCCAAAAAAGGAGCTCTTTAAGCACTTGAGAACTTCAACTC
AATCCAAAATAGCTGTGGAAGCTGAGGTTTCAGATGCTGTTGCAACTAAACCAGAGGATCAGAAT
TTAGTAGAGGGAATAGGATCGACGTTCTATGGATTATAGAAAAACCGAGTTATTCTCTTCCAAAA
ATGAGACTGAACTATCAAAATGAATAGTAACCATAGTCACTAAGGGAGTCAGCTCTTCCTCCTAC
GCTTCGCTGCGCTCTGCTCCCACCTCGCTACTTTCACCCTATAGCTCCGTCCCCGCCCTTGCCAG
GTGTCGACTCGTATTGAACTCAGCATTGGCTTAAAGAAATTTCCCTAAGCCTACAGACCTGAGTG
ATTTATATCTATATCTCCTTCTTTCGCCATCATCTTAGTTTTCGA
Found at i:312156 original size:16 final size:16
Alignment explanation
Indices: 312137--312168 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
312127 GAAATTATAC
*
312137 CATTTCTAAATCAAAT
1 CATTTATAAATCAAAT
312153 CATTTATAAATCAAAT
1 CATTTATAAATCAAAT
312169 AAATAACATA
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:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (16 bp):
CATTTATAAATCAAAT
Left flanking sequence: Indices 311637 -- 312136
CTTCTGACCAGACAAGAGATCTGTAATTGTCAGTAAAGTTGTTTCTTTATTTGTTTCTGATTTTT
TCTTAATTTGATTGATTTTTTTATTTCTTAATTATTTATTCAAATCCAAAAATGCTTATTTTATA
CATAGGTTGTCCGTTCAGCATTGTATAAAAAAGGGCAAAGTGTCCTCCTTTTTTTGTAGGAAACG
GTTCAAATGATTTTATCCATATGAGTGTTCTATATCGGATAAATTACCAACTATTCATTTTCTTT
TTTATTTATTGAAATTGGAAACCGTTTTTGTACTAACATAGTGGTAGAAAGAATACCCTGTTGTG
CCTGGACTTCAAACTGTTTAGCTTTAACCATGTTCATGGTCCCAAATTATTGGTTGATAGAGAAT
CAAAGTGAATTTACCAATAAATCACGAAATGCTATGGTTCTTACATATGATTTATTAATTTATTC
ATAAGTAATTCGTCGGGATCTGCACCTTTCTTTTCGAAATTATAC
Right flanking sequence: Indices 312169 -- 312668
AAATAACATATAACATCAAAAATCAAGCGCAGTTGGTTGGATCCAACCTATTCTTGAAATACACA
ACTCGCACACACTCCCTTTCCAAAATAAATCAACACACCAAGCACTACGCTTAGATTTATTGGAT
TTGTTGCTAAAATATCGGTATTAAACCCAAAACTCCCGGCGGATGGCCAATGGCCCAAGGAAACG
AAAGAATCGGTTACATTTTTCATATGTTCTCCTTTTATAGATAGGACTAACAAAAAATAGAGTTC
TTTTTGTATCACTTCGACCTCTTTTTTTGATTGACTTCTTATTTATTTTATTATTTTTAAGTTTC
GACCAATCAATATAATATAAGTATCTTATTGGGTTAGGTCGCGGGTCTTACGTCAATTGTCAAAT
ACCTTATTTGTATTTGTTGCAATCTTTGCTAAAAAGAAAAAGGATTTCCTTTAATTGTACTAAGA
ACGGGAAGGAAGAAAGCGAGCGGATCCGCTAATTCCTCATCCTCA
Found at i:338084 original size:22 final size:22
Alignment explanation
Indices: 338056--338101 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
338046 GCTGTCTGCG
338056 CGAGTCACCTTCTTCTAAGCTC
1 CGAGTCACCTTCTTCTAAGCTC
338078 CGAGTCACCTTCTTCTAAGCTC
1 CGAGTCACCTTCTTCTAAGCTC
338100 CG
1 CG
338102 CTGGACGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.37, G:0.15, T:0.30
Consensus pattern (22 bp):
CGAGTCACCTTCTTCTAAGCTC
Left flanking sequence: Indices 337556 -- 338055
GGTCCGGGGGTGCCACTGTCCCGGGAGAGTCTCAGGAGCCCACCTGCCCTTCATACTCTTTTCTA
CTGATCCCACTCAATCTTTTACACCGATGTTTCTCTCGAATAAATAACCAAATATAACACGTCGA
GGAGAAAAGACTGCTAAATCTTTCCAGAAGGAGGGAAGGCGCTCCCTAAGCTACAACTCACAGCC
TGCTGAAAAAGGCGAGGCTCCGCGCGCCCCCACACCTCCTCTCCCCCGCTTGCTGTGAACCCGTC
GAGGGGCTTCATTGATTAGTAAACGTCACGGTGCTGGTGACGGTCGGGACCGTGGTCGTCCGTCT
CCGGTTTGCCGGCCGATAAGATCACTGAGATTGACCAGCCAGCTGGGCCCACTCCTTATTTCTTT
TAGCAAATCGAGAAAGTCAACCACCTTTCTGGATTTTCCTCTATCTCCAGCTATAATTCACTTCG
TTCCAATCCATATATAATATCTAAAATCAAGCTCAGCTGTCTGCG
Right flanking sequence: Indices 338102 -- 338601
CTGGACGACACGGCATTCTCGTTCGAACAAAGAGGGGCCGGCCGTACTTGTGATGGTTCCCCAGG
ATCCAATAAACCCACTTAGGTCTACGTTGCCACGATCTTCTTCCCTGTCAGCGGGCGGGCTGCTT
TTCCAAAGGGATATCAAGACTATTAAGCACAGGGGGCAAACTTTTTCTAGGAAATAAGCAAGTCA
ACTACCTTTTTTTTGGTTGGACGCATATTCTGTCCGGCCCCACTTCTTTGTTTTCGATCGGAGCA
TCAAGCAGCGCAACCCGGTTCTACTTGACTAAGCCCCATGCTCGTCCAAGGAGGGAGTTTGCTTT
ACCCTCCGACCCTGTTTTTTGGCTATAAACTGACTTTCGAATGAAGAATGAAGAGTGCCCTGCCC
CTCTTTTTTCTTCCCAGGTATGAAGTGTCTGGTTTGATAGAACCAGGAGTCGTCGGATGTCGGAA
GTTGGTAAAGACCCACCCCTTGTTTCAGTCAGAATGAGTCCCCGG
Done.