Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397895.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1200.0, 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: 7212
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.29
Warning! 1346 characters in sequence are not A, C, G, or T
Found at i:1156 original size:171 final size:170
Alignment explanation
Indices: 796--1744 Score: 837
Period size: 171 Copynumber: 5.6 Consensus size: 170
786 NNNNNNNNNN
* * * * * *
796 AGTAATAAGACTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTGTT
1 AGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTT
* * * * * *
861 TCTTCATGCTTCTCGAGCTAGACATTTAATTATAATCTATTTTAATC-AAAAATGTAAAAAAAAT
66 TCTTTATGTTTCTCAAGGTAGACATTCAATTATAATCTATTCTAA-CAAAAAATGT--AAAAAAT
* * * *
925 TGAACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGGG
128 TCAACTTAAAATCAATTATGAGATTACAAAACTATTTAAAGTG
* * * * *
968 AGTAATAGGGCTTTTGAAGGAATAAGTGTCTAGAAATAGACTTTTCTTGTCAATGAATGCCTTTT
1 AGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTT
* * * *
1033 TCTTTAGGTTTC-CTATGGTAGACATTCAATTATAATCTATTCTAACTAAAAAGGTCAAAAAATT
66 TCTTTATGTTTCTC-AAGGTAGACATTCAATTATAATCTATTCTAACAAAAAATGT-AAAAAATT
* * *
1097 TAACCTAAAATCAATTATGAGGTTACAAAACTATTTAAAGTG
129 CAACTTAAAATCAATTATGAGATTACAAAACTATTTAAAGTG
* ** * * *
1139 AGTAATAAGGTTTTTGAAAAAATAAGTGACTAT-AATAGAGTTTTCTTGCCAATGAATGCATTTT
1 AGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTT
* * * *
1203 TCTTCATGTTTCTGAAGGTAGACATTCAATTATAGTCTATT-TAAGC-AAAAATGTGCAAAGAAT
66 TCTTTATGTTTCTCAAGGTAGACATTCAATTATAATCTATTCTAA-CAAAAAATGT--AAAAAAT
* * * * *
1266 TCAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAATTG
128 TCAACTTAAAATCAATTATGAGATTACAAAACTATTTAAAGTG
* * * * *
1309 AGTAATAAGGCTCTTGAAGGAAT-GGATAACTATAAATAGGCATTTC-CGACCAATGAATGCCTT
1 AGTAATAAGGCTTTTGAAGGAATAGG-TGACTATAAATAGACTTTTCTTG-CCAATGAATGCCTT
* * * * * *
1372 CTTCTTTACGTTTCTCAAGGTAGAGACTCAATTATAGTCTGTTCTAACAAAAAATGTAAAAACAT
64 TTTCTTTATGTTTCTCAAGGTAGACATTCAATTATAATCTATTCTAACAAAAAATGTAAAAA-AT
* * * * **
1437 TCAACCTAAAATGAATTAAG-GCATTACAAAACTATTTGAAGCA
128 TCAACTTAAAATCAATTATGAG-ATTACAAAACTATTTAAAGTG
* * * * * *
1480 AGTAATAAGGCTTTTAAAGGTATGGGTAACTATAAAT-GAACTTTT-TTGTCAATGAAT-ACTTT
1 AGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAG-ACTTTTCTTGCCAATGAATGCCTTT
* * * * * * * *
1542 TTTTTTCATGTTTATCAAGGTAGACATTCAATTCTATTCTGTTTTTACAAAAAATATAAAAGAAT
65 TTCTTT-ATGTTTCTCAAGGTAGACATTCAATTATAATCTATTCTAACAAAAAATGTAAAA-AAT
* ** *
1607 TTAACTTAAAATCAATTATG-GCATTACAAAACTATTTTTTAGCG
128 TCAACTTAAAATCAATTATGAG-ATTACAAAACTA-TTTAAAGTG
* * * * * *
1651 AGTAACAAGGC-TTTGAAGGTATGGGTGATTGTAAATGGACTTTTCTTGCCAATGAATG-CTATT
1 AGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCT-TT
* * ** *
1714 TTATTCATGTTTCTTGAGGTAAACATTCAAT
65 TTCTTTATGTTTCTCAAGGTAGACATTCAAT
1745 CCTAGTCTGT
Statistics
Matches: 636, Mismatches: 119, Indels: 45
0.80 0.15 0.06
Matches are distributed among these distances:
169 19 0.03
170 250 0.39
171 252 0.40
172 115 0.18
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (170 bp):
AGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTT
TCTTTATGTTTCTCAAGGTAGACATTCAATTATAATCTATTCTAACAAAAAATGTAAAAAATTCA
ACTTAAAATCAATTATGAGATTACAAAACTATTTAAAGTG
Found at i:1753 original size:341 final size:339
Alignment explanation
Indices: 796--1755 Score: 940
Period size: 341 Copynumber: 2.8 Consensus size: 339
786 NNNNNNNNNN
* * * * *
796 AGTAATAAGACTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTGTT
1 AGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCATTTT
* * * * * *
861 TCTTCATGCTTCTCGAGCTAGACATTTAATTATAATCTATTTTAATCAAAAATGTAAAAAAAATT
66 TCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCT-TTTTAAGCAAAAATGTAAAAAGAATT
* * *
926 GAACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGGGAGTAATAGGGCTTTTGAAGGAAT
130 CAACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGCGAGTAATAAGGC-TTTGAAGGAAT
** * * * *
991 AAGTG-TCTAG-AAATAGACTTTTCTTGTCAATGAATGCCTTTTTCTTTAGGTTTCCTATGGTAG
194 GGGTGAT-T-GTAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTTA-GGTAG
* * * *
1054 ACATTCAATTATAATCTATTCTAACTAAAAAGGTCAAAAAATTTAACCTAAAATCAATTATGAGG
256 ACATTCAATTATAGTCTGTTCTAACAAAAAAGGTCAAAAAATTCAACCTAAAATCAATTA-GAGG
**
1119 TTACAAAACTATTTAAAGTG
320 TTACAAAACTATTTAAAGCA
* * ** *
1139 AGTAATAAGGTTTTTGAAA-AAATAAGTGACTAT-AAT-AGAGTTTTCTTGCCAATGAATGCATT
1 AGTAATAAGGCTTTT-AAAGGAATGGGTGACTATAAATGA-ACTTTTCTTGCCAATGAATGCATT
* * * **
1201 TTTCTTCATGTTTCTGAAGGTAGACATTCAATTATAGTCTATTTAAGCAAAAATGTGCAAAGAAT
64 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTTTTTAAGCAAAAATGTAAAAAGAAT
* * **
1266 TCAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAATTGAGTAATAAGGCTCTTGAAGGAA
129 TCAACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCT-TTGAAGGAA
* * * * * * * *
1331 TGGATAACTATAAATAGG-CATTTC-CGACCAATGAATGCCTTCTTCTTTACGTTTCTCAAGGTA
193 TGGGTGATTGTAAAT-GGACTTTTCTTG-CCAATGAATGCCTTTTTCTTTACGTTTCT-TAGGTA
* * * *
1394 GAGACTCAATTATAGTCTGTTCTAACAAAAAATGT-AAAAACATTCAACCTAAAATGAATTA-AG
255 GACATTCAATTATAGTCTGTTCTAACAAAAAAGGTCAAAAA-ATTCAACCTAAAATCAATTAGAG
*
1457 GCATTACAAAACTATTTGAAGCA
319 G--TTACAAAACTATTTAAAGCA
* * * * *
1480 AGTAATAAGGCTTTTAAAGGTATGGGTAACTATAAATGAACTTTT-TTGTCAATGAATACTTTTT
1 AGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCATTTT
* * * * * *
1544 TTTTCATGTTTATCAAGGTAGACATTCAATTCTATTCTGTTTTTA-CAAAAA-ATATAAAAGAAT
66 TCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCT-TTTTAAGCAAAAATGTA-AAAAGAAT
* * * ** * *
1607 TTAACTTAAAATCAATTATG-GCATTACAAAACTATTTTTTAGCGAGTAACAAGGCTTTGAAGGT
129 TCAACTTAAAATCAATTTTGAG-ATTATAAAACTA-TTTAAAGCGAGTAATAAGGCTTTGAAGGA
* * *
1671 ATGGGTGATTGTAAATGGACTTTTCTTGCCAATGAATG-CTATTTTATTCATGTTTCTTGAGGTA
192 ATGGGTGATTGTAAATGGACTTTTCTTGCCAATGAATGCCT-TTTTCTTTACGTTTCTT-AGGTA
* **
1735 AACATTCAATCCTAGTCTGTT
255 GACATTCAATTATAGTCTGTT
1756 NNNNNNNNNN
Statistics
Matches: 496, Mismatches: 99, Indels: 46
0.77 0.15 0.07
Matches are distributed among these distances:
339 3 0.01
340 16 0.03
341 361 0.73
342 88 0.18
343 25 0.05
344 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (339 bp):
AGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCATTTT
TCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTTTTTAAGCAAAAATGTAAAAAGAATTC
AACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGAAGGAATGG
GTGATTGTAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTTAGGTAGACATT
CAATTATAGTCTGTTCTAACAAAAAAGGTCAAAAAATTCAACCTAAAATCAATTAGAGGTTACAA
AACTATTTAAAGCA
Found at i:2442 original size:172 final size:171
Alignment explanation
Indices: 2134--2454 Score: 389
Period size: 172 Copynumber: 1.9 Consensus size: 171
2124 NNNNNNNNNN
* * *
2134 AAAGAATTCAAATTTAAATCAATTTTGACATTATAAAACTATTTAAAGTGACTAATAAGGCTTTA
1 AAAGAATTCAAATTGAAATCAATTTTGACATTATAAAACCATTTAAACTGACTAATAAGGCTTTA
* * * * **
2199 AAAGGAATGAGTGACTATAAATGGACTTTTCTTATCAACGATTTCCTTTTTGTACATGTTTCTTG
66 AAAGGAATGAGTAACTATAAATGGACATTTCCTATCAACGATGTCCTTTTTGTACA-GTTTCTCA
2264 AGGTAGAAATTATA-TTATAACCTGGTTTAACTAAAAACATAC
130 AGGTAGAAATT-TAGTTATAACCTGGTTTAACTAAAAACATAC
** * *
2306 AAAGAATTCAAATTGAAATCAATTTTGAGGTTATAAAACCATTTAAACTGAGTGATAAGGCTCTT
1 AAAGAATTCAAATTGAAATCAATTTTGACATTATAAAACCATTTAAACTGACTAATAAGGCT-TT
* * * * * *
2371 -GAAGGAATG-GATAACTATAAATGGGCATTTCCTGTCAATGAATGTCTTTTTCTTTACA-TTTC
65 AAAAGGAATGAG-TAACTATAAATGGACATTTCCTATCAACG-ATGTCCTTTT-TGTACAGTTTC
2433 TCAAGGTAGAAATTTAGTTATA
127 TCAAGGTAGAAATTTAGTTATA
2455 GTCTGTTCTA
Statistics
Matches: 125, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
171 3 0.02
172 107 0.86
173 10 0.08
174 5 0.04
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (171 bp):
AAAGAATTCAAATTGAAATCAATTTTGACATTATAAAACCATTTAAACTGACTAATAAGGCTTTA
AAAGGAATGAGTAACTATAAATGGACATTTCCTATCAACGATGTCCTTTTTGTACAGTTTCTCAA
GGTAGAAATTTAGTTATAACCTGGTTTAACTAAAAACATAC
Found at i:2838 original size:171 final size:170
Alignment explanation
Indices: 2149--3704 Score: 746
Period size: 171 Copynumber: 9.1 Consensus size: 170
2139 ATTCAAATTT
* * * * **
2149 AAATCAATTTTGACATTATAAAACTATTTAAAGTGACTAATAAGGCTTTAAAAGGAAT-GAGTGA
1 AAATCAATTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAG-GTGA
* ** * * * * * ** *
2213 CTATAAATGGACTTTTCTTATCAACGATTTCCTTTTTGTACATGTTTCTTGAGGTAGAAATT-AT
65 CTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCA-
** * ** * ** *
2277 ATTATAACCTGGTT-TAACTAAAAACATACAAAGAATTCAAATTG
129 ATTATAGTCT-ATTCTAAC-AAAAATGTA-AAAAAATTCAACCTA
* * * * * * * *
2321 AAATCAATTTTGAGGTTATAAAACCATTTAAACTGAGTGATAAGGCTCTTGAAGGAAT-GGATAA
1 AAATCAATTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGG-TGA
* * * * * * * ** * * *
2385 CTATAAATGGGCATTTCCTGTCAATGAATGTCTTTTTCTTTACATTTCTCAAGGTAGAAATTTAG
65 CTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
* *
2450 TTATAGTCTGTTCTAACAAAAAATGTAGAAAAATTCAACCTA
130 TTATAGTCTATTCTAAC-AAAAATGTAAAAAAATTCAACCTA
* *********************** * * *
2492 AAATGAATTATGNNNNNNNNNNNNNNNNNNNNNNAAGTAATAAGACTTTTAAAGGAATGGGTGAC
1 AAATCAATTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* ** * * * * *
2557 TATAAATGGACTTTTCTTGCCAACAAATGCCTGTTTCTTCATGCTTCTCGAGCTAGACATTTAAT
66 TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * * * ********** * *
2622 TATAATTTGTTTTAATCAAAAANNNNNNNNNNTTGAACTTA
131 TATAGTCTATTCTAA-CAAAAATGTAAAAAAATTCAACCTA
* * * *
2663 AAATCAATTTTGAGATTATAAAACTATTTAAAGGGAGTAAT-AGGACTTTTGAAGGAATAAGTGA
1 AAATCAATTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGG-CTTTTGAAGGAATAGGTGA
* * * * *
2727 CTATAAATAGACTTTTCTTCCCAATGAATGCCTTTTTCTTTAGGTTTCCCATGGTAGACATTCAA
65 CTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
* * * * *
2792 TTATAATCTATTCTAACTAAAAAGGTCAAAATATTTAACCTA
130 TTATAGTCTATTCTAAC-AAAAATGTAAAAAAATTCAACCTA
* * ** *
2834 AAATCAATTATGAGGTTACAAAACTATTTAAAGTGAGCAATAAGGCTTTTGAAAAAATAGGCGAC
1 AAATCAATTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* ** * *
2899 TATAAATAGAGTTTTCTTGCCAATGAATGTATTTTTCTTCACGTTTCTGAAGGTAGACATTCAAT
66 TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* ** *
2964 TATAGTCTATT-TAAGCAAAAATGTGCAAAAAATTCAAATTT
131 TATAGTCTATTCTAA-CAAAAATGT-AAAAAAATTCAACCTA
* * * ********** *
3005 AAATCAACTT-TGAGATTATAAAACTATTTAAATTGAGTAATAAGGCTCTTNNNNNNNNNNGTAA
1 AAATCAA-TTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGA
* * * * * * * *
3069 CTATAAATGGGCATTTCCTACCAATGAATGCCTTCTTCTTTATGTTTCTCAAGGTAGAGATTCAA
65 CTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
* *
3134 TCATAGTCTGTTCTAACAAAAAATGTAAAAAAATTCAACCTA
130 TTATAGTCTATTCTAAC-AAAAATGTAAAAAAATTCAACCTA
* * * * * * ** *
3176 AAATGAATTATGACATTACAAAACCATTTGAAGTAAGTAATAAGGCTTTTAAAGGTTTGGGTGAC
1 AAATCAATTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* * * *
3241 TATAAATGGACTTTTTTTGCCAATGAATACCTTTTT-TTCATGTTTCTCAAGGTAGACATTTAAT
66 TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * * * * * *
3305 TCTATTCTGTTTTTACCAAAAATGTAAAAAAATTTAACTTA
131 TATAGTCT-ATTCTAACAAAAATGTAAAAAAATTCAACCTA
** * * *
3346 AAATCAATTATG-GTATTACAAAACTATTTTTTAGCGAGTAATAAGGC-TTTGAAGGTATGGGTG
1 AAATCAATTATGAG-ATTACAAAACTA-TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTG
* * * *********** ** *
3409 ATTGTAAATGGACTTTTCTTGCCNNNNNNNNNNNTTTTCTTCATGTTTCTTGAGGTAAACATTCA
64 ACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
* * * * * **
3474 ATTCTAGTCTGTTTTAACTAAAAT-TATAAACATATTCAAGTTAA
129 ATTATAGTCTATTCTAACAAAAATGTA-AAA-AAATTCAACCT-A
* * * *** ** ** *
3518 AAAT-AATTATTAGTTTATAAAACTATTTAAACCAAGTAATAAGGCTTTCAAAGGCTTAAGTGAC
1 AAATCAATTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* * ** ** * ** * ** *
3582 TTTAAATAGACTTTTCGTATCAATGGTTGGC-TTCACTCCATG-TTCTCCAAGAAAGACATTCAT
66 TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCT-CAAGGTAGACATTCAA
* * * **
3645 TTATAGCCTTTTTTAACCAAAAATGTAAAAAAATTCAAATTA
130 TTATAGTCTATTCTAA-CAAAAATGTAAAAAAATTCAACCTA
*
3687 AAATCAATTTTGAGATTA
1 AAATCAATTATGAGATTA
3705 TNNNNNNNNN
Statistics
Matches: 1024, Mismatches: 333, Indels: 56
0.72 0.24 0.04
Matches are distributed among these distances:
169 11 0.01
170 207 0.20
171 661 0.65
172 144 0.14
173 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
AAATCAATTATGAGATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
TATAGTCTATTCTAACAAAAATGTAAAAAAATTCAACCTA
Found at i:5131 original size:171 final size:171
Alignment explanation
Indices: 4696--6982 Score: 1927
Period size: 172 Copynumber: 13.4 Consensus size: 171
4686 CAATTTTGAG
* * * * * *
4696 ATTATAATCTGTTCTAACC-AAAATATCAAAAAGTTCAACCTAAAATAAATTATGAGATTATGAA
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
4760 ACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTTACTATAAATGGA-TGTTTCTCGCT
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACT-TTTCTTGCC
* * * * *
4824 AATGACAAT--CTTTTTCTTCAGGTTTCCCATGGCAGACGTTCA
130 AATG--AATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* ** ** ** * *
4866 ATTATAATCTGTTCAAATAAAAAAAAATAAAAAAGCTCAA-TCGAAAATCAATTATGAGATTATG
1 ATTATAATCTGTTCTAA-CCAAAAATGTAAAAAAATTCAACT-TAAAATCAATTATGAGATTATA
* * * *** *
4930 AAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGGGATCTCTTGC
64 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC
* * *
4995 CAATGAATGCATCTTTCTTTACGTTTCTCAAGGTAGACATTCA
129 CAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
** * * * *
5038 ATTATTGTCTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATG-GCATTACAA
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG-ATTATAA
* * *
5102 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTTGCC
65 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
* * * *
5167 AATGAATGCTTTTTTCTTCATGTTTCTTAAAGTAGACATTCA
130 AATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * * * *
5209 ATTCTACTCTGTTTTATCCAATAATGTAAAAATAATTCAACTTAAAATCAATTATG-GTATTACA
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAG-ATTATA
** * *
5273 AAACCATTTAAAGCCAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGC
64 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC
* ** * * *
5338 CAATAAATATCTTTTTCTTCACATTTCTCGAGGTAAACATTCA
129 CAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* *
5381 ATTATAATCTGTTCTAACCAAAAACGTAAAAAAATTCAACTTAAAATCATTTATGAGATTATAAA
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * * * * **
5446 ATCATTTAACGTGAGTAAGAAAGCTTTTAAAGGATTGGGTAACTATAAAAAGACTTTTCTTGCCA
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCA
* * * * *
5511 GTGAATACCTTTTTCTACACGTTTCTCAAGGGAAACATTCA
131 ATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * * * *
5552 ATTATTATCTGTTCTAATCCAAAAACGTGAAAAAATTCAACCTAAAATCAATTATAAGAATATAA
1 ATTATAATCTGTTCTAA-CCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * *
5617 AACCATTGAAAGTGAGTAATAA-GCTTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTCGC
65 AACCATTTAAAGTGAGTAATAAGGC-TTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC
* * ** ** *
5681 CAATAAATGCTTTTTTCTTCATATTTCTCAAGCAAAACATTCA
129 CAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * ** * * * * *
5724 ATTATAATCTATTTTAATAAAAAATGTTAAAAATTTGAACTTAAAATCAATTTTGAAATTATAAA
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
5789 ACCATTTAAAGTGAGTAATAAGCCTTTTAAAAGAATGGGTGACTATAAAAGGACTTTTCTTGCCA
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCA
* * * *
5854 ATGAATACCTTTTTCTTCATGTTTC-CTAAGGCAGATATTCA
131 ATGAATGCCTTTTTCTTCACGTTTCTC-AAGGTAGACATTCA
* * * *
5895 ATCATTATCTGTTCTAACCAAAAATGTTAAAAAATTCAACCTAAAATCAATTATGAGATTATAAA
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
5960 ACCATTTAAAGTGAGTAGTAAGGCTTTTGAAAGAATGGGTGATTATAAATGGACTTTTCTTACCA
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCA
* * * *
6025 ATGAATACCTTTTTCTTCACATTTCCCAAGGT-GAATATTCA
131 ATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAG-ACATTCA
* * * * *
6066 ATGATAATCTGTTCTAACCAAAAATGTCAAAAAGTTTAACCTAAAATCAATTATGAGATTATAAA
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* *
6131 ACCATTTAAAGTGAATAATAAGGCTTTTGAAGGAATGGGTAACTATAAATGGA--TTTCTTGCCA
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCA
* * *
6194 ATGGATGCCTTTTTCTTCACATTTC-CTAAGGT-GAATATTCA
131 ATGAATGCCTTTTTCTTCACGTTTCTC-AAGGTAG-ACATTCA
* * ********** * * *
6235 ATGATAATCTATNNNNNNNNNNAATGTCAAAAAGTTCAACCTAAAATCAATTATGAGATTATAAA
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * *** *
6300 ACCATTCAAAATGAGTAATAAGGCTTTTAAAGGAATAGAAAAATATAAATGGACTTTTCTTGCCA
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCA
* ** ** *
6365 ATGAATACCTTTTTCTTCATATTTCTTGAGCTAGACATTCA
131 ATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
********** * * * * ** *
6406 ATTANNNNNNNNNNTAACTAATAATGTACAAAGAATTCAAATTTGAATCAATTTTGAGATTATAA
1 ATTATAATCTGTTCTAACCAAAAATGTA-AAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * **********
6471 AATCATTTAAAGGGAGTAATATGGCTTTTGAAGGAATGGGTGANNNNNNNNNNACTTTTCTTGCC
65 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
* * * * ** *
6536 AATGAATTCCTTTTTGTGCATGTTTCTTGAGGTAAACATT-A
130 AATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * * * * *
6577 TATTCT-ATCCTGTTTTAACCAAAGATGTACAAAGAATTTAAATTTAAATCAATT-TCGAGATTA
1 -ATTATAAT-CTGTTCTAACCAAAAATGTA-AAAAAATTCAACTTAAAATCAATTAT-GAGATTA
* * * * *
6640 TAAAACTATTTAAATTGAGTAATAAGGCTTTTAAAGGAATTGGTGATTATAAA-GAGACTTTTCT
62 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG-GACTTTTCT
* * * * ** * * *
6704 TGTCAATAAATGCCTTTTTCTTCATGTTTCTCGAGCCAAATAGTCA
126 TGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * * * *
6750 ATTATAATCTGTAT-TAA--AAATATATATATAATAATTTAAACTTAAATTCAATTTTGAGATTA
1 ATTATAATCTGT-TCTAACCAAA-A-ATGTA-AAAAAATTCAACTTAAAATCAATTATGAGATTA
* * * * * * *
6812 TAAAATCGTTCAAAGCGAGTAATAGGGCTTTTGAAGGAATGGTTGACTATAAATGGACTTATCTT
62 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT
** * * * * * * * * *
6877 GCCAATGGCTACGTTTTTTTTCAAGCTTCCCATGGCAGACGTTCA
127 GCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * * * * *
6922 ATTATAATCTATTCTAACC-GAAACGTCAAAAAGTTCAACCTAAAATCAATTATAAGATTAT
1 ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
6983 GANNNNNNNN
Statistics
Matches: 1725, Mismatches: 356, Indels: 72
0.80 0.17 0.03
Matches are distributed among these distances:
168 1 0.00
169 144 0.08
170 52 0.03
171 722 0.42
172 799 0.46
173 7 0.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.34
Consensus pattern (171 bp):
ATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCA
ATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
Found at i:5380 original size:343 final size:341
Alignment explanation
Indices: 4696--6982 Score: 1937
Period size: 343 Copynumber: 6.7 Consensus size: 341
4686 CAATTTTGAG
* * * * * * * * *
4696 ATTATAATCTGTTCTAAC-CAAAATATCAAAAAGTTCAACCTAAAATAAATTATGAGATTATGAA
1 ATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAA
* * * * *
4760 ACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTTACTATAAATGGA-TGTTTCTCGCT
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACT-TTTCTTGCC
* * ** * * * * ** **
4824 AATGACA-ATCTTTTTCTTCAGGTTTCCCATGGCAGACGTTCAATTATAATCTGTTCAAATAAAA
130 AATGA-ATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTCT-ATCTGTTTTAA-CCAA
** ** * * * * *
4888 AAAAATAAAAAAGCTCAATCGAAAATCAATTATGAGATTATGAAACTATTTAAAGCGAGTAATAA
192 AAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAA
* * *** * * * * * * *
4953 GGCTTTTGAAGGAATGGATGACTATAAATGGGGATCTCTTGCCAATGAATGCATCTTTCTTTACG
257 GGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATACCTTTTTCTTCACA
* *
5018 TTTCTCAAGGTAGACATTCA
322 TTTCTCAAGCTAAACATTCA
** *
5038 ATTATTGTCTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATG-GCATTACAA
1 ATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAG-ATTATAA
* *
5102 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTTGCC
65 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCC
* * * * *
5167 AATGAATGCTTTTTTCTTCATGTTTCTTAAAGTAGACATTCAATTCTACTCTGTTTTATCCAATA
130 AATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTCTA-TCTGTTTTAACCAAAA
* * **
5232 ATGTAAAAATAATTCAACTTAAAATCAATTATG-GTATTACAAAACCATTTAAAGCCAGTAATAA
194 ATGTAAAAA-AATTCAACCTAAAATCAATTATGAG-ATTATAAAACCATTTAAAGTGAGTAATAA
** * *
5296 GGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCACA
257 GGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATACCTTTTTCTTCACA
* *
5361 TTTCTCGAGGTAAACATTCA
322 TTTCTCAAGCTAAACATTCA
* * * * *
5381 ATTATAATCTGTTCTAACCAAAAACGTAAAAAAATTCAACTTAAAATCATTTATGAGATTATAAA
1 ATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAA
* * * * * * * *
5446 ATCATTTAACGTGAGTAAGAAAGCTTTTAAAGGATTGGGTAACTATAAAAAGACTTTTCTTGCCA
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCA
* * * * * * * *
5511 GTGAATACCTTTTTCTACACGTTTCTCAAGGGAAACATTCAATTATTATCTGTTCTAATCCAAAA
131 ATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATT-CTATCTGTTTTAA-CCAAAA
* * * * *
5576 ACGTGAAAAAATTCAACCTAAAATCAATTATAAGAATATAAAACCATTGAAAGTGAGTAATAA-G
194 ATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
* * * * *
5640 CTTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTCGCCAATAAATGCTTTTTTCTTCATAT
259 C-TTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATACCTTTTTCTTCACAT
*
5705 TTCTCAAGCAAAACATTCA
323 TTCTCAAGCTAAACATTCA
* * * * *
5724 ATTATAATCTATTTTAATAAAAAATGT-TAAAAATTTGAACTTAAAATCAATTTTGAAATTATAA
1 ATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTT-AACTTAAAATCAATTATGAGATTATAA
* * *
5788 AACCATTTAAAGTGAGTAATAAGCCTTTTAAAAGAATGGGTGACTATAAA-AGGACTTTTCTTGC
65 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATA-GACTTTTCTTGC
* * * *
5852 CAATGAATACCTTTTTCTTCATGTTTCCTAAGGCAGATATTCAA-TCATTATCTGTTCTAACCAA
129 CAATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTC--TATCTGTTTTAACCAA
* *
5916 AAATGTTAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAGTAA
192 AAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAA
* * *
5981 GGCTTTTGAAA-GAATGGGTGATTATAAATGGACTTTTCTTACCAATGAATACCTTTTTCTTCAC
257 GGCTTTT-AAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATACCTTTTTCTTCAC
* * * *
6045 ATTTCCCAAGGTGAATATTCA
321 ATTTCTCAAGCTAAACATTCA
* * * * * *
6066 ATGATAATCTGTTCTAACCAAAAATGTCAAAAAGTTTAACCTAAAATCAATTATGAGATTATAAA
1 ATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAA
* * *
6131 ACCATTTAAAGTGAATAATAAGGCTTTTGAAGGAATGGGTAACTATAAATGGA--TTTCTTGCCA
66 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCA
* * ** * * ** * **********
6194 ATGGATGCCTTTTTCTTCACATTTCCTAAGGT-GAATATTCAATGATAATCTATNNNNNNNNNNA
131 ATGAATACCTTTTTCTTCATGTTTCTTAAGGTAG-ACATTCAATTCT-ATCTGTTTTAACCAAAA
* * * *
6258 ATGTCAAAAAGTTCAACCTAAAATCAATTATGAGATTATAAAACCATTCAAAATGAGTAATAAGG
194 ATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
* *** * * *
6323 CTTTTAAAGGAATAGAAAAATATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATATT
259 CTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATACCTTTTTCTTCACATT
** *
6388 TCTTGAGCTAGACATTCA
324 TCTCAAGCTAAACATTCA
********** * * * * * ** *
6406 ATTANNNNNNNNNNTAACTAATAATGTACAAAGAATTCAAATTTGAATCAATTTTGAGATTATAA
1 ATTATAATCTGTTTTAACAAAAAATGTA-AAAAAATTTAACTTAAAATCAATTATGAGATTATAA
* * * **********
6471 AATCATTTAAAGGGAGTAATATGGCTTTTGAAGGAATGGGTGANNNNNNNNNNACTTTTCTTGCC
65 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCC
* * * * *
6536 AATGAATTCCTTTTTGTGCATGTTTCTTGAGGTAAACATT-ATATTCTATCCTGTTTTAACCAAA
130 AATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTCA-ATTCTAT-CTGTTTTAACCAAA
* * * ** * * *
6600 GATGTACAAAGAATTTAAATTTAAATCAATT-TCGAGATTATAAAACTATTTAAATTGAGTAATA
193 AATGTA-AAAAAATTCAACCTAAAATCAATTAT-GAGATTATAAAACCATTTAAAGTGAGTAATA
* * * *
6664 AGGCTTTTAAAGGAATTGGTGATTATAAA-GAGACTTTTCTTGTCAATAAATGCCTTTTTCTTCA
256 AGGCTTTTAAAGGAATGGGTGACTATAAATG-GACTTTTCTTGCCAATAAATACCTTTTTCTTCA
** * * * *
6728 TGTTTCTCGAGCCAAATAGTCA
320 CATTTCTCAAGCTAAACATTCA
* * * * * * *
6750 ATTATAATCTGTATTAA-AAATATATATATAATAATTTAAACTTAAATTCAATTTTGAGATTATA
1 ATTATAATCTGTTTTAACAAA-AAATGTAAAAAAATTT-AACTTAAAATCAATTATGAGATTATA
* * * * * * * *
6814 AAATCGTTCAAAGCGAGTAATAGGGCTTTTGAAGGAATGGTTGACTATAAATGGACTTATCTTGC
64 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGC
** * * * * ** * * * * * * *
6879 CAATGGCTACGTTTTTTTTCAAGCTTCCCATGGCAGACGTTCAATTATAATCTATTCTAACC-GA
129 CAATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTCT-ATCTGTTTTAACCAAA
* * * *
6943 AACGTCAAAAAGTTCAACCTAAAATCAATTATAAGATTAT
193 AATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTAT
6983 GANNNNNNNN
Statistics
Matches: 1542, Mismatches: 365, Indels: 76
0.78 0.18 0.04
Matches are distributed among these distances:
339 5 0.00
340 190 0.12
341 67 0.04
342 289 0.19
343 734 0.48
344 254 0.16
345 3 0.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.34
Consensus pattern (341 bp):
ATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAA
ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCA
ATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTCTATCTGTTTTAACCAAAAAT
GTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCT
TTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATACCTTTTTCTTCACATTTC
TCAAGCTAAACATTCA
Done.