Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399089.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2365.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10356
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.25
Warning! 3129 characters in sequence are not A, C, G, or T
Found at i:1202 original size:170 final size:170
Alignment explanation
Indices: 918--1230 Score: 401
Period size: 170 Copynumber: 1.8 Consensus size: 170
908 NNNNNNNNNN
* * *
918 AACAGATAATAATTGAACGTCTGCCACGGGAAACCTAAAGAAAAAGGTAGTCGTTGGCAAGAAAA
1 AACAGATAATAATTGAACGTCTGCCACGGAAAACCTAAAGAAAAACGTAGTCATTGGCAAGAAAA
* ** * *
983 GTCCATTTATAATAACTCAATCCTTCAAAGGCTTTATTACTCCCTTTAAATGGTTTCATAATCTC
66 GTCCATTTATAATAACTCAATCCTTCAAAAGCCCTATTACTCACTTTAAACGGTTTCATAATCTC
*
1048 ATAATAGATTTTAGGTTGAACTTTTTGATGTTTTGGTTAG
131 AAAATAGATTTTAGGTTGAACTTTTTGATGTTTTGGTTAG
* * *
1088 AACAGATAATAATTGAACGTCTGCCATGGAAAACTTGAAGAAAAACGTAGTCATTGGCAAGAAAA
1 AACAGATAATAATTGAACGTCTGCCACGGAAAACCTAAAGAAAAACGTAGTCATTGGCAAGAAAA
* ********** *
1153 GTCCATTTATAGTNNNNNNNNNNTTCAAAAGCCCTATTACTCACTTTAAACGGTTTTATAATCTC
66 GTCCATTTATAATAACTCAATCCTTCAAAAGCCCTATTACTCACTTTAAACGGTTTCATAATCTC
*
1218 AAAATTGATTTTA
131 AAAATAGATTTTA
1231 AGTTCAAATT
Statistics
Matches: 118, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
170 118 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.31
Consensus pattern (170 bp):
AACAGATAATAATTGAACGTCTGCCACGGAAAACCTAAAGAAAAACGTAGTCATTGGCAAGAAAA
GTCCATTTATAATAACTCAATCCTTCAAAAGCCCTATTACTCACTTTAAACGGTTTCATAATCTC
AAAATAGATTTTAGGTTGAACTTTTTGATGTTTTGGTTAG
Found at i:1423 original size:172 final size:172
Alignment explanation
Indices: 1181--1504 Score: 384
Period size: 172 Copynumber: 1.9 Consensus size: 172
1171 NNNNNTTCAA
* * * *
1181 AAGCCCTATTACTCACTTTAAACGGTTTTATAATCTCAAAATTGATTTTAAGTTCAAATTATTAT
1 AAGCCCTAGTACTCACTTTAAACGGCTTTATAATCTCAAAATTGATTTTAAATTCAAATTATCAT
* * * *
1246 ACATTTTTTATTAAAACA-GATTATAAT-TGAATATCTATCTCAACAAATATGAAGAAAAAGGTA
66 ACATTTTTGATTAAAACAGGA-TATAATAT-AATATCTACCTCAACAAACATGAAGAAAAAGGAA
* **
1309 TTTATTGGTGAGAAAAGTCCATTTATAACCACCCATTCTTTTAG
129 TTCATTGGCAAGAAAAGTCCATTTATAACCACCCATTCTTTTAG
* * ** * *
1353 AAGCCTTAGTACTCACTTTAAATGGCTTTATAATCTCAAAATTGA-TTTAAATTTGAATTCCTCG
1 AAGCCCTAGTACTCACTTTAAACGGCTTTATAATCTCAAAATTGATTTTAAATTCAAATT-ATCA
* * * * * * *
1417 TACATTTTTGGTTAAAATAGGATATAATATAATGTTTACCTCGAGAAACATGTAGAAAAAGGAAT
65 TACATTTTTGATTAAAACAGGATATAATATAATATCTACCTCAACAAACATGAAGAAAAAGGAAT
1482 TCATTGGCAAGAAAAGTCCATTT
130 TCATTGGCAAGAAAAGTCCATTT
1505 TTGGTTAAAA
Statistics
Matches: 125, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
171 11 0.09
172 111 0.89
173 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (172 bp):
AAGCCCTAGTACTCACTTTAAACGGCTTTATAATCTCAAAATTGATTTTAAATTCAAATTATCAT
ACATTTTTGATTAAAACAGGATATAATATAATATCTACCTCAACAAACATGAAGAAAAAGGAATT
CATTGGCAAGAAAAGTCCATTTATAACCACCCATTCTTTTAG
Found at i:7597 original size:171 final size:171
Alignment explanation
Indices: 7322--8456 Score: 1188
Period size: 171 Copynumber: 6.6 Consensus size: 171
7312 TTGAGAATAT
* * * **
7322 AAAACCATTTAAAGTGATTAATTAGGCTTTTGAA-GTACCAGGTGACTATAAATAGAAC-TTTCT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTA-TGGGTGACTATAAATAG-ACTTTTCT
* * * * *
7385 TGCCAATGAATGCATTTTTCTTTATGTTTCTCAAGGTAGACATTCAATTATAGTTTGTTTGAACA
64 TGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACA
*
7450 AAAA-GTATAAAATAATTCAACTTAAAATCAATTATGGCATTAC
129 AAAATGTA-AAAATAATTCAACTTTAAATCAATTATGGCATTAC
* *
7493 AAAACCATTTAAAGCGAGTAGTAAGGCTTTTGAAGGTATGGGTGACTATAAATTGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTTG
* * * * * ** * *
7558 CCAATGAATACTTTTTCCTTCATGTTTCTGAAAGTAGACAATCAATCCTAGTCTACTCTAACCAA
66 CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAA-CAA
* * * * * *
7623 AAATGTACAAATAATTCAAATTTAAATCAATTTTAAGAATT-T
130 AAATGTAAAAATAATTCAACTTTAAATCAATTAT-GGCATTAC
* * * ** * *
7665 TAATCCATTTAAA-CTGAGTAATAAGGCTTTTGAAGGAATAAGTGACTATAAATTGTC-TTTCTT
1 AAAACCATTTAAAGC-GAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTT
* * * * **
7728 GGCAAAGAATGCCTTTTTCTTTACATTTCTTC-AGGTAGACATTCAATTATAGTCTA-TTTAACT
65 GCCAATGAATGCTTTTTTCTTCATGTTTC-TCAAGGTAGACATTCAATTATAGTCTATTTTAAC-
*
7791 AAAAATGTAAAAATAATTCAACTTGAAATCAATTATGGCATTAC
128 AAAAATGTAAAAATAATTCAACTTTAAATCAATTATGGCATTAC
* * ** *
7835 AAAACCATTTAAAGCGAGAAATAAAGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTTG
* * *
7900 CCAATGAATGCTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTGTTTTAACTAA
66 CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAAC-AA
* * * * * *
7965 AAATGTACAAAGAATTCAAATTTAACTCAATT-TCGCATTTAT
130 AAATGTAAAAATAATTCAACTTTAAATCAATTATGGCA-TTAC
* * *
8007 AAAACCATTTAAAGCGAGAAACAAGGCTTTAT-AAGGAATGGGTGACTATAAATAGACTTTTCTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTT-TGAAGGTATGGGTGACTATAAATAGACTTTTCTT
* ** * * *
8071 GCCAATAAATAATTTTTTCTTCATGTTTCTCATGGTAGACATTCAACTT-TAATCTATTTTAACC
65 GCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA-TTATAGTCTATTTTAACA
* * * * *
8135 AAAATGTACAAAA-AATTTAAGTTTGAATCAATTTTGAG-ATTAT
129 AAAATGTA-AAAATAATTCAACTTTAAATCAATTATG-GCATTAC
* * * * * * *
8178 AAAACCTTTTAAA-CTGAGTAATAAGGCTCTTGAAGGAATGAG-CATCTATAAATGGACATTTCT
1 AAAACCATTTAAAGC-GAGTAATAAGGCTTTTGAAGGTATGGGTGA-CTATAAATAGACTTTTCT
* * * *
8241 TGCCAATGACTG-TCTTTTTCTTTATGTTTCACAAGGTAGACATTCAATTATAGTCTATTTTAAT
64 TGCCAATGAATGCT-TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAAC
* * *
8305 AGAAAATGTAAAAA-AATTCAACTTAAAATTAATTATGGTATTAC
128 A-AAAATGTAAAAATAATTCAACTTTAAATCAATTATGGCATTAC
* *
8349 AAAACCATTTAATGCGACTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTTG
* * *
8414 ACAATAAATGCTTTTTTCTTCATATTTCTCAAGGTAGACATTC
66 CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTC
8457 NNNNNNNNNN
Statistics
Matches: 795, Mismatches: 140, Indels: 58
0.80 0.14 0.06
Matches are distributed among these distances:
169 5 0.01
170 91 0.11
171 441 0.55
172 248 0.31
173 10 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (171 bp):
AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTTG
CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACAAA
AATGTAAAAATAATTCAACTTTAAATCAATTATGGCATTAC
Found at i:8326 original size:514 final size:513
Alignment explanation
Indices: 7362--8456 Score: 1438
Period size: 514 Copynumber: 2.1 Consensus size: 513
7352 TGAAGTACCA
* * *
7362 GGTGACTATAAATAGAAC-TTTCTTGCCAATGAATGCATTTTTCTTTATGTTTCTCAAGGTAGAC
1 GGTGACTATAAAT-GGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGAC
* * * *
7426 ATTCAATTATAGTTTGTTTGAACAAAAAGTATAAAATAATTCAACTTAAAATCAATTATGGCATT
65 ATTCAATTATAGTCTGTTTGAACAAAAAGTATAAAAGAATTCAAATTAAAATCAATTATCGCATT
* ** * *
7491 ACAAAACCATTTAAAGCGAGTAGTAAGGCTTTTGAAGGTATGGGTGACTATAAATTGACTTTTCT
130 ACAAAACCATTTAAAGCGAGAAACAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCT
* * * *
7556 TGCCAATGAATACTTTTTCCTTCATGTTTCTGAAAGTAGACAATCAATCCTAGTCTACTCTAACC
195 TGCCAATAAATAATTTTTCCTTCATGTTTCTCAAAGTAGACAATCAATCCTAATCTACTCTAACC
* * *
7621 AAAAATGTACAAATAATTCAAATTTAAATCAATTTTAAGAATTTTAATCCATTTAAACTGAGTAA
260 AAAAATGTACAAAAAATTCAAATTTAAATCAATTTTAAGAATTTAAAACCATTTAAACTGAGTAA
* * * * *
7686 TAAGGCTTTTGAAGGAATAAGTGACTATAAATTGTCTTTCTTGGCAAAGAATGCCTTTTTCTTTA
325 TAAGGCTCTTGAAGGAATAAGTCACTATAAATGGACTTTCTTGCCAAAGAATGCCTTTTTCTTTA
* *
7751 CATTTCTTCAGGTAGACATTCAATTATAGTCTATTTAACTAAAAATGTAAAAATAATTCAACTTG
390 CATTTCTACAGGTAGACATTCAATTATAGTCTATTTAACTAAAAATGTAAAAATAATTCAACTTA
*
7816 AAATCAATTATGGCATTACAAAACCATTTAAAGCGAGAAATAAAGCTTTCAAAGGTATG
455 AAATCAATTATGGCATTACAAAACCATTTAAAGCGACAAATAAAGCTTTCAAAGGTATG
*
7875 GGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAGGGTAGACA
1 GGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACA
* * * * *
7940 TTCAATTCTAGTCTGTTTTAACTAAAAATGTA-CAAAGAATTCAAATTTAACTCAATT-TCGCAT
66 TTCAATTATAGTCTGTTTGAAC-AAAAA-GTATAAAAGAATTCAAATTAAAATCAATTATCGCA-
*
8003 TTATAAAACCATTTAAAGCGAGAAACAAGGCTTTAT-AAGGAATGGGTGACTATAAATAGACTTT
128 TTACAAAACCATTTAAAGCGAGAAACAAGGCTTT-TGAAGGAATGGGTGACTATAAATAGACTTT
* ** * * * *
8067 TCTTGCCAATAAATAATTTTTTCTTCATGTTTCTCATGGTAGACATTCAA-CTTTAATCTATTTT
192 TCTTGCCAATAAATAATTTTTCCTTCATGTTTCTCAAAGTAGACAATCAATC-CTAATCTACTCT
* * * * *
8131 AACC-AAAATGTACAAAAAATTTAAGTTTGAATCAATTTTGAG-ATTATAAAACCTTTTAAACTG
256 AACCAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTAAGAATT-TAAAACCATTTAAACTG
* * * *
8194 AGTAATAAGGCTCTTGAAGGAATGAG-CATCTATAAATGGACATTTCTTGCCAATGACTGTCTTT
320 AGTAATAAGGCTCTTGAAGGAATAAGTCA-CTATAAATGGAC-TTTCTTGCCAAAGAATGCCTTT
**
8258 TTCTTTATGTTTC-ACAAGGTAGACATTCAATTATAGTCTATTTTAA-TAGAAAATGTAAAAA-A
383 TTCTTTACATTTCTAC-AGGTAGACATTCAATTATAGTCTA-TTTAACTA-AAAATGTAAAAATA
* * * * * **
8320 ATTCAACTTAAAATTAATTATGGTATTACAAAACCATTTAATGCGACTAATAAGGCTTTTGAAGG
445 ATTCAACTTAAAATCAATTATGGCATTACAAAACCATTTAAAGCGACAAATAAAGCTTTCAAAGG
8385 TATG
510 TATG
* * * *
8389 GGTGACTATAAATAGACTTTTCTTGACAATAAATGCTTTTTTCTTCATATTTCTCAAGGTAGACA
1 GGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACA
8454 TTC
66 TTC
8457 NNNNNNNNNN
Statistics
Matches: 506, Mismatches: 64, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
512 7 0.01
513 163 0.32
514 315 0.62
515 21 0.04
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (513 bp):
GGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACA
TTCAATTATAGTCTGTTTGAACAAAAAGTATAAAAGAATTCAAATTAAAATCAATTATCGCATTA
CAAAACCATTTAAAGCGAGAAACAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT
GCCAATAAATAATTTTTCCTTCATGTTTCTCAAAGTAGACAATCAATCCTAATCTACTCTAACCA
AAAATGTACAAAAAATTCAAATTTAAATCAATTTTAAGAATTTAAAACCATTTAAACTGAGTAAT
AAGGCTCTTGAAGGAATAAGTCACTATAAATGGACTTTCTTGCCAAAGAATGCCTTTTTCTTTAC
ATTTCTACAGGTAGACATTCAATTATAGTCTATTTAACTAAAAATGTAAAAATAATTCAACTTAA
AATCAATTATGGCATTACAAAACCATTTAAAGCGACAAATAAAGCTTTCAAAGGTATG
Found at i:9356 original size:172 final size:171
Alignment explanation
Indices: 8975--10356 Score: 1283
Period size: 172 Copynumber: 8.1 Consensus size: 171
8965 NNNNNNCTTC
* * * * *
8975 ATGTTTCTCGAGCTAGACGTTCAATTATAATATGTTTTAACCAGAAAA-GT-AAAAGAATTCAAC
1 ATGTTTCTCAAG-TAGACATTCAATTATAGTATGTTTTAACCA-AAAATGTGAAAAGATTTCAAA
* * * * ** *
9038 TTGAAATCAATTTTGAGAATATAAAACTATTTAAAGTGACTAATTAGGCTTTTGAACCAATGTGT
64 TTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
********** * * * *
9103 GACTATANNNNNNNNNNTCTTGCCAATGAGTACTTTTTTCTTC
129 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
* * * * * * * *
9146 ATATTTTTCAAGGTAGGCATTCAATTCTACTCTGTTTTAACCATAAATGTGCAAAGATTTCAAAT
1 ATGTTTCTCAA-GTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTGAAAAGATTTCAAAT
* * * * * * *
9211 TTAAATCAATTTTCATATTACAAAACCATTTAAAGGGAGTAATAAGGCTTTTAAAGGAATGGGTG
65 TAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * ** *
9276 ACTATAAATCGAGTTCTCTTACCTATGAATGCTTACTTATTT
130 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
* * * * * * *
9318 ATGTTTCTCACGCTAGACATTTAATTATAATATGTTTTAACTAGAAAA-GTAAAAAAATTTCAAC
1 ATGTTTCTCAAG-TAGACATTCAATTATAGTATGTTTTAACCA-AAAATGTGAAAAGATTTCAAA
* * * * * * *
9382 TTAAAATCAATTTTGAGAATATAAAACCATTTAAAGTGATTAATTAGGCTTTTGTAGTAATAGGT
64 TTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
* *
9447 GACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTC
129 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
* * * * *
9490 ATCTTTCTTAAGGTAGACATTCAATTCTAGTATGTTTTAACCAAAAATGTGTAAGGATTTCAAAT
1 ATGTTTCTCAA-GTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTGAAAAGATTTCAAAT
* * * * * * *
9555 TCAAATCAATTTTGAGATTTTAAAACCATTTAAAGTAAGTAATAAGACCTTTAAAGGAATGGGTG
65 TAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * *
9620 GCTATAAATGGACTTCTCTTGCCAATGAATGCTTTCTACTTT
130 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
* ** * * * *
9662 ATGTTTCTCGAGCTAGATGTTCAATTATAATATGTTTTAA-CAAGACAA-GTAAAAAAATTTGAA
1 ATGTTTCTCAAG-TAGACATTCAATTATAGTATGTTTTAACCAA-A-AATGTGAAAAGATTTCAA
* * * *
9725 CTTAAAATCAATTTTGAGATGATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATGGG
63 ATTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGG
* * * * *
9790 TGACTATAAATAGACTTTTCTTCCCAATGAATACTTTTTCCTTG
128 TGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
* * * * *
9834 ATGTTTATCAAAGTAGACATTCAATTCA-AGTCTGTTTTAACC-AAAATGTGTAGAGAATTCAAA
1 ATGTTTCTC-AAGTAGACATTCAATT-ATAGTATGTTTTAACCAAAAATGTGAAAAGATTTCAAA
* * *
9897 TTGAAATCAATTTTGAGATTAT-AAACTATTTAAAGTGAGTAATAAGCCTCTTGAAGGAATGGGT
64 TTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
* * * *
9961 GACTATAAATGGACTTTTCTTACAAATGAATCCCTTTTTCCTT
129 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
* * * * * * * * *
10004 ATGTTTCTTGAAGTAGACATTTACTTATAGTCTATTTCAACCAAAAATTTAAAAAAATTT--AAT
1 ATGTTTC-TCAAGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTGAAAAGATTTCAAAT
* * * *
10067 TCAAAATCAATTATG-GAATTAAAAAACTATTTAAAGCGGGTAATAAGGCTTTTGAAGGAATGGG
65 T-AAAATCAATTTTGAG-ATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGG
*
10131 TGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTC
128 TGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
* * * * **
10175 ATGTTTCTCAAGGTAGACATTCAATTCTTGTCTGTTTCAACCAAAAATGTGTTAAGATTTCAAAT
1 ATGTTTCTCAA-GTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTGAAAAGATTTCAAAT
* * * * * * *
10240 TTAAATCAATTTTGATATTATAAAATTATTTAAAGTGAGTAATAAGTCTTTTTAAGGAATAGTTG
65 TAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * **
10305 ACTATAAATGGAGTTCTCTTACCTATGAATGCTTACTTCTTT
130 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
10347 ATGTTTCTCA
1 ATGTTTCTCA
Statistics
Matches: 970, Mismatches: 217, Indels: 47
0.79 0.18 0.04
Matches are distributed among these distances:
169 6 0.01
170 128 0.13
171 207 0.21
172 615 0.63
173 14 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (171 bp):
ATGTTTCTCAAGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTGAAAAGATTTCAAATT
AAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
CTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTT
Found at i:9610 original size:344 final size:342
Alignment explanation
Indices: 8975--10356 Score: 1620
Period size: 344 Copynumber: 4.0 Consensus size: 342
8965 NNNNNNCTTC
* *
8975 ATGTTTCTCGAGCTAGACGTTCAATTATAATATGTTTTAACCAGAAAAGTAAAAGAA-TTCAACT
1 ATGTTTCTC-AGCTAGACATTCAATTATAATATGTTTTAACCAGAAAAGTAAAAAAATTTCAACT
* * * * *
9039 TGAAATCAATTTTGAGAATATAAAACTATTTAAAGTGACTAATTAGGCTTTTGAACCAATGTGTG
65 TAAAATCAATTTTGAGAATATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATGGGTG
********** * * * *
9104 ACTATANNNNNNNNNNTCTTGCCAATGAGTACTTTTTTCTTCATATTTTTCAAGGTAGGCATTCA
130 ACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
* * * * * * *
9169 ATTCTACTCTGTTTTAACCATAAATGTGCAAAGATTTCAAATTTAAATCAATTTTCATATTACAA
195 ATTCTAGTCTGTTTTAACCAAAAATGTGTAAGGATTTCAAATTTAAATCAATTTTGAGATTATAA
* * * *
9234 AACCATTTAAAGGGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATCGAGTTCTCTTACC
260 AACCATTTAAAGTGAGTAATAA-GCCTTTAAAGGAATGGGTGACTATAAATGGACTTCTCTTACC
*
9299 TATGAATGCTTACTTATTT
324 AATGAATGCTTACTTATTT
* *
9318 ATGTTTCTCACGCTAGACATTTAATTATAATATGTTTTAACTAGAAAAGTAAAAAAATTTCAACT
1 ATGTTTCTCA-GCTAGACATTCAATTATAATATGTTTTAACCAGAAAAGTAAAAAAATTTCAACT
* * * * *
9383 TAAAATCAATTTTGAGAATATAAAACCATTTAAAGTGATTAATTAGGCTTTTGTAGTAATAGGTG
65 TAAAATCAATTTTGAGAATATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATGGGTG
* * *
9448 ACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATCTTTCTTAAGGTAGACATTCA
130 ACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
* * *
9513 ATTCTAGTATGTTTTAACCAAAAATGTGTAAGGATTTCAAATTCAAATCAATTTTGAGATTTTAA
195 ATTCTAGTCTGTTTTAACCAAAAATGTGTAAGGATTTCAAATTTAAATCAATTTTGAGATTATAA
* * *
9578 AACCATTTAAAGTAAGTAATAAGACCTTTAAAGGAATGGGTGGCTATAAATGGACTTCTCTTGCC
260 AACCATTTAAAGTGAGTAATAAG-CCTTTAAAGGAATGGGTGACTATAAATGGACTTCTCTTACC
*
9643 AATGAATGCTTTC-TACTTT
324 AATGAATGCTTACTTA-TTT
** * * *
9662 ATGTTTCTCGAGCTAGATGTTCAATTATAATATGTTTTAACAAGACAAGTAAAAAAATTTGAACT
1 ATGTTTCTC-AGCTAGACATTCAATTATAATATGTTTTAACCAGAAAAGTAAAAAAATTTCAACT
9727 TAAAATCAATTTTGAG-ATGATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATGGGT
65 TAAAATCAATTTTGAGAAT-ATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATGGGT
* * * * * *
9791 GACTATAAATAGACTTTTCTTCCCAATGAATACTTTTTCCTTGATGTTTATCAAAGTAGACATTC
129 GACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTC
* * *
9856 AATTCAAGTCTGTTTTAACC-AAAATGTGT-AGAGAATTCAAATTGAAATCAATTTTGAGATTAT
194 AATTCTAGTCTGTTTTAACCAAAAATGTGTAAG-GATTTCAAATTTAAATCAATTTTGAGATTAT
* * *
9919 -AAACTATTTAAAGTGAGTAATAAGCCTCTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTA
258 AAAACCATTTAAAGTGAGTAATAAGCCT-TTAAAGGAATGGGTGACTATAAATGGACTTCTCTTA
* * * **
9983 CAAATGAATCCCTT-TTTCCTT
322 CCAATGAAT-GCTTACTTATTT
* * * * * * * *
10004 ATGTTTCTTGAAG-TAGACATTTACTTATAGTCTATTTCAACCA-AAAATTTAAAAAAATTT-AA
1 ATGTTTC-T-CAGCTAGACATTCAATTATAATATGTTTTAACCAGAAAA-GTAAAAAAATTTCAA
* * * ** *
10066 -TTCAAAATCAATTATG-GAATTAAAAAACTATTTAAAGCGGGTAATAAGGCTTTTGAAGGAATG
63 CTT-AAAATCAATTTTGAGAA-TATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATG
* *
10129 GGTGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACA
126 GGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACA
* * *
10194 TTCAATTCTTGTCTGTTTCAACCAAAAATGTGTTAA-GATTTCAAATTTAAATCAATTTTGATAT
191 TTCAATTCTAGTCTGTTTTAACCAAAAATGTG-TAAGGATTTCAAATTTAAATCAATTTTGAGAT
** * * * * *
10258 TATAAAATTATTTAAAGTGAGTAATAAGTCTTTTTAAGGAATAGTTGACTATAAATGGAGTTCTC
255 TATAAAACCATTTAAAGTGAGTAATAAG-CCTTTAAAGGAATGGGTGACTATAAATGGACTTCTC
* *
10323 TTACCTATGAATGCTTACTTCTTT
319 TTACCAATGAATGCTTACTTATTT
10347 ATGTTTCTCA
1 ATGTTTCTCA
Statistics
Matches: 890, Mismatches: 127, Indels: 46
0.84 0.12 0.04
Matches are distributed among these distances:
340 3 0.00
341 137 0.15
342 147 0.17
343 174 0.20
344 428 0.48
345 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (342 bp):
ATGTTTCTCAGCTAGACATTCAATTATAATATGTTTTAACCAGAAAAGTAAAAAAATTTCAACTT
AAAATCAATTTTGAGAATATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATGGGTGA
CTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
TTCTAGTCTGTTTTAACCAAAAATGTGTAAGGATTTCAAATTTAAATCAATTTTGAGATTATAAA
ACCATTTAAAGTGAGTAATAAGCCTTTAAAGGAATGGGTGACTATAAATGGACTTCTCTTACCAA
TGAATGCTTACTTATTT
Found at i:10299 original size:685 final size:687
Alignment explanation
Indices: 8975--10355 Score: 1783
Period size: 685 Copynumber: 2.0 Consensus size: 687
8965 NNNNNNCTTC
* *
8975 ATGTTTCTCGAGCTAGACGTTCAATTATAATATGTTTTAACCAGAAAAGTAAAAGAATTCAACTT
1 ATGTTTCTCGAGCTAGACGTTCAATTATAATATGTTTTAACAAGAAAAGTAAAAAAATTCAACTT
* * *
9040 GAAATCAATTTTGAGAATATAAAACTATTTAAAGTGACTAATTAGGCTTTTGAACCAATGTGTGA
66 AAAATCAATTTTGAGAATATAAAACTATTTAAAGTGACTAATAAGGCTTTTGAACCAATGGGTGA
********** * * * * * *
9105 CTATANNNNNNNNNNTCTTGCCAATGAGTACTTTTTTCTTCATATTTTTCAAGGTAGGCATTCAA
131 CTATAAATAGACTTTTCTTCCCAATGAATACTTTTTCCTTCATATTTATCAAAGTAGACATTCAA
* * * *
9170 TTCTACTCTGTTTTAACCATAAATGTGCAAAGATTTCAAATTTAAATCAATTTTCATATTACAAA
196 TTCAACTCTGTTTTAACCATAAATGTGCAAAGAATTCAAATTGAAATCAATTTTCAGATTACAAA
* * * **
9235 ACCATTTAAAGGGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATCGAGTTCTCTTACCT
261 ACCATTTAAAGGGAGTAATAAGCCTCTTAAAGGAATGGGTGACTATAAATCGACTTCTCTTACAA
* * * * * *
9300 ATGAATGCTTACTTATTTATGTTTCTCACGCTAGACATTTAATTATAATATGTTTTAACTAGAAA
326 ATGAATCCTTACTTACTTATGTTTCTCAAGCTAGACATTTAATTATAATATATTTCAACCAGAAA
* * * * *
9365 AGTAAAAAAATTTCAACTTAAAATCAATTTTGAGAATATAAAACCATTTAAAGTGATTAATTAGG
391 AGTAAAAAAATTTCAACTTAAAATCAATTATGAGAATAAAAAACCATTTAAAGCGAGTAATAAGG
* * *
9430 CTTTTGTAGTAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATCTT
456 CTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATCTT
* *
9495 TCTTAAGGTAGACATTCAATTCTAGTATGTTTTAACCAAAAATGTGTAAGGATTTCAAATTCAAA
521 TCTCAAGGTAGACATTCAATTCTAGTATGTTTCAACCAAAAATGTGTAAGGATTTCAAATTCAAA
* * *
9560 TCAATTTTGAGATTTTAAAACCATTTAAAGTAAGTAATAAGACCTTTAAAGGAATGGGTGGCTAT
586 TCAATTTTGAGATTATAAAACCATTTAAAGTAAGTAATAAGACCTTTAAAGGAATAGGTGACTAT
* *
9625 AAATGGACTTCTCTTGCCAATGAATGCTTTCTACTTT
651 AAATGGACTTCTCTTACCAATGAATGCTTACTACTTT
* * *
9662 ATGTTTCTCGAGCTAGATGTTCAATTATAATATGTTTTAACAAGACAAGTAAAAAAATTTGAACT
1 ATGTTTCTCGAGCTAGACGTTCAATTATAATATGTTTTAACAAGAAAAGTAAAAAAA-TTCAACT
* *
9727 TAAAATCAATTTTGAG-ATGATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATGGGT
65 TAAAATCAATTTTGAGAAT-ATAAAACTATTTAAAGTGACTAATAAGGCTTTTGAACCAATGGGT
* *
9791 GACTATAAATAGACTTTTCTTCCCAATGAATACTTTTTCCTTGATGTTTATCAAAGTAGACATTC
129 GACTATAAATAGACTTTTCTTCCCAATGAATACTTTTTCCTTCATATTTATCAAAGTAGACATTC
* * * * *
9856 AATTCAAGTCTGTTTTAACCA-AAATGTGTAGAGAATTCAAATTGAAATCAATTTTGAGATTA-T
194 AATTCAACTCTGTTTTAACCATAAATGTGCAAAGAATTCAAATTGAAATCAATTTTCAGATTACA
* * * * *
9919 AAACTATTTAAAGTGAGTAATAAGCCTCTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTAC
259 AAACCATTTAAAGGGAGTAATAAGCCTCTTAAAGGAATGGGTGACTATAAATCGACTTCTCTTAC
* * * * * *
9984 AAATGAATCCCTT-TTTCCTTATGTTTCTTGAAG-TAGACATTTACTTATAGTCTATTTCAACCA
324 AAATGAAT-CCTTACTTACTTATGTTTC-TCAAGCTAGACATTTAATTATAATATATTTCAACCA
* * *
10047 -AAAATTTAAAAAAATTT-AA-TTCAAAATCAATTATG-GAATTAAAAAACTATTTAAAGCGGGT
387 GAAAA-GTAAAAAAATTTCAACTT-AAAATCAATTATGAGAA-TAAAAAACCATTTAAAGCGAGT
*
10108 AATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCT
449 AATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCT
* * *
10173 TCATGTTTCTCAAGGTAGACATTCAATTCTTGTCTGTTTCAACCAAAAATGTGTTAA-GATTTCA
514 TCATCTTTCTCAAGGTAGACATTCAATTCTAGTATGTTTCAACCAAAAATGTG-TAAGGATTTCA
* * ** * * * *
10237 AATTTAAATCAATTTTGATATTATAAAATTATTTAAAGTGAGTAATAAGTCTTTTTAAGGAATAG
578 AATTCAAATCAATTTTGAGATTATAAAACCATTTAAAGTAAGTAATAAGACCTTTAAAGGAATAG
* * * *
10302 TTGACTATAAATGGAGTTCTCTTACCTATGAATGCTTACTTCTTT
643 GTGACTATAAATGGACTTCTCTTACCAATGAATGCTTACTACTTT
10347 ATGTTTCTC
1 ATGTTTCTC
10356 A
Statistics
Matches: 593, Mismatches: 93, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
684 5 0.01
685 252 0.42
686 112 0.19
687 96 0.16
688 128 0.22
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (687 bp):
ATGTTTCTCGAGCTAGACGTTCAATTATAATATGTTTTAACAAGAAAAGTAAAAAAATTCAACTT
AAAATCAATTTTGAGAATATAAAACTATTTAAAGTGACTAATAAGGCTTTTGAACCAATGGGTGA
CTATAAATAGACTTTTCTTCCCAATGAATACTTTTTCCTTCATATTTATCAAAGTAGACATTCAA
TTCAACTCTGTTTTAACCATAAATGTGCAAAGAATTCAAATTGAAATCAATTTTCAGATTACAAA
ACCATTTAAAGGGAGTAATAAGCCTCTTAAAGGAATGGGTGACTATAAATCGACTTCTCTTACAA
ATGAATCCTTACTTACTTATGTTTCTCAAGCTAGACATTTAATTATAATATATTTCAACCAGAAA
AGTAAAAAAATTTCAACTTAAAATCAATTATGAGAATAAAAAACCATTTAAAGCGAGTAATAAGG
CTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATCTT
TCTCAAGGTAGACATTCAATTCTAGTATGTTTCAACCAAAAATGTGTAAGGATTTCAAATTCAAA
TCAATTTTGAGATTATAAAACCATTTAAAGTAAGTAATAAGACCTTTAAAGGAATAGGTGACTAT
AAATGGACTTCTCTTACCAATGAATGCTTACTACTTT
Done.