Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399615.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2866.1, 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: 7370
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.29
Warning! 1596 characters in sequence are not A, C, G, or T
Found at i:760 original size:170 final size:170
Alignment explanation
Indices: 10--2122 Score: 1315
Period size: 171 Copynumber: 12.4 Consensus size: 170
1 CCATGGTCA
* * * * * * * * *
10 ACATTCAATTATAGTCTATATTCATGAGAAATATAAATAAATTCAACCTAAAATCAATTTTGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * * ***********
75 TTGTAAAATCATGTAAAGCGAGTAATAAGGCTTTTAAAGGNNNNNNNNNNTATAAATGGACTTTT
66 TTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTT
** * * *
140 CTTGTTAATGACTATCTTTTTCTTCATGTTTCTCAAGGTAG
131 CTTGCCAATGAATA-CTTTTTCTTCATATTTCCCAAGGTAG
* * * * * * *
181 ATATACAATTATTGTCTGTTTTAATAAAAAATATAAAATAATTCAAATTAAAATCAATTATGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
********** * * * * *
246 TTATAAAACNNNNNNNNNNGAGTAATAAGGCTTTTTAAGGAATGGGTGACTATAAATAGAATTTT
66 TTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTT
* * * ***
311 CTTGCGATTGAATCCCTTTTTCTTCATATTTCTTGAGGTAG
131 CTTGCCAATGAAT-ACTTTTTCTTCATATTTCCCAAGGTAG
* ************
352 ACATTCAATTATAGTCTGTTTTAACCANNNNNNNNNNNNNAATTCAACTTAAAATCAATTATGAG
1 ACATTCAATTATAGTCTGTTTTAATCA-AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * * *
417 ATTATAAAACTATTTAAAATGACTAATAAGGCTTTTGAAGGAATTGATGACCATAAATAGACTTT
65 ATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTT
* * * *
482 TCTTGCCATTGAATTTCTTTTTCTTCATGTTTCCTAAGGTAG
130 TCTTGCCAATGAA-TACTTTTTCTTCATATTTCCCAAGGTAG
* ** * * *
524 ACATTCAATTATAGTCTATTTTAATCAAAAACATAAAACAATTCAGCTTAAAATCAATTCTGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * ** *
589 TTATAAAACCATTTAAAACAAGTAATGAGTCTTTTGAAGAAATAGAAGGCTATAAATGGAC-TTT
66 TTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTT
* *
653 CTT-CCAAATGAATGCATTTTTCTCCATATTTCCCAAGGTAG
131 CTTGCC-AATGAATAC-TTTTTCTTCATATTTCCCAAGGTAG
* * * * * * *
694 ATATTCAATTATAGTATGTTGTAATGAGAAATATAAAAAAATTCAACTTAAAATCAATTTTGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * * * *
759 TTATAAAATCATTTACAGCGAGTAATAATGCTTTTAAAGAAATGGGTGACTATAAATGAACTTTT
66 TTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTT
* * * *
824 CTTGTCAATGACTATCTTTTTCTTCA-AGTTTCTCAAGATAG
131 CTTGCCAATGAATA-CTTTTTCTTCATA-TTTCCCAAGGTAG
* * * *
865 ACATAT-AATTATTGTCTGTTTTAATCAAAAATGTAAAATAATT-AGACTGAAAATCAATTATAA
1 ACAT-TCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCA-ACTTAAAATCAATTATGA
* ** * **
928 GATTATAAAACTATTTAAAACGAGTAATAAGAATTTTGAA-AGAGTAGGTGACTATAAA-AAACT
64 GATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGA-AATAGGTGACTATAAATGGACT
* * * *
991 TTTC-TGCACAATGAATAGTTTTTTCTACACATTT-CC-TGTGTCA-
128 TTTCTTGC-CAATGAATA-CTTTTTCTTCATATTTCCCAAG-GT-AG
* *
1034 AGCATTCAATTATAGTCTATTTTAATCAAAAATGTAAAAAAACTT-AACTTAAAATCAGTTATGA
1 A-CATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAA-TTCAACTTAAAATCAATTATGA
* * **********
1098 GATTACAAAACTATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTNNNNNNNNNNTT
64 GATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTT
* * *
1163 TTCTTACCAATAAATACCTTTTTCTTCATATTTCTCAAGGTAG
129 TTCTTGCCAATGAATA-CTTTTTCTTCATATTTCCCAAGGTAG
* *
1206 ACATTTAATTATAGTCTGTTTT-A--AAAAATGTATAAAAATTCAACTTAAAATCAATTATGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
********** * *
1268 TTATAAAACCANNNNNNNNNNGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGGACTTTT
66 TTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTT
* * * * *****
1333 CTTGCCATTGAATCCCTTTTTCGTCATGTTTGTTGTGGTAG
131 CTTGCCAATGAAT-ACTTTTTCTTCATATTTCCCAAGGTAG
* * *
1374 ACATTCAATTATAGTCTGTTTTAA-CTAAAAACGTAAAAAGATTCAACTTAAAATCAATTATGAA
1 ACATTCAATTATAGTCTGTTTTAATC-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
*********** *
1438 ATTATAAAACCATTTAAAGNNNNNNNNNNGGCTTTTGAAGAAAT-GAGAGACTATAAATGGACTT
65 ATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAG-GTGACTATAAATGGACTT
* * * * *
1502 TTCTT-CCAAATGAATATATTTTTCTTTATATTTCCTATGGTTG
129 TTCTTGCC-AATGAATA-CTTTTTCTTCATATTTCCCAAGGTAG
* * * * * * *
1545 ACATTCAATTATAGTCTATATTCA-CGAGAAATAG-AAAAAAATTCAACCTAAAATTAATTTTGA
1 ACATTCAATTATAGTCTGTTTTAATC-AAAAAT-GTAAAAAAATTCAACTTAAAATCAATTATGA
* * * * * * * *
1608 GATTATAAAACCATTTAAAGCAAGTCATAAAGTTTTTAAAGGAAT-GG-G----T--ATGGACAT
64 GATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTT
** * * *
1665 TTCTTATCAATGACTATCTTTTTCTTCATGTTTCTCAAGGTAG
129 TTCTTGCCAATGAATA-CTTTTTCTTCATATTTCCCAAGGTAG
* * * * ** * *
1708 ATATACAATTATTA-TTTGTTTTAATTAAAAAAATAAAATAATTCGACTTAAAATCAATTATGAG
1 ACATTCAATTA-TAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
********** * * * *
1772 ATTATANNNNNNNNNNAAATGAGTAATAAGGCTTTTGAAGGAAT-GGCTGACTGTAAATGAACTT
65 ATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGG-TGACTATAAATGGACTT
* * * * * *
1836 TTCTTTCCAATGAATAGTTTTTTTTACACAATTACCAA-GTCA-
129 TTCTTGCCAATGAATACTTTTTCTT-CATATTTCCCAAGGT-AG
* ***********
1878 AGCATTCAATTATAGTCTGTTTTAATAAAAAATGTAANNNNNNNNNNTTTAAAATCAATTATGAG
1 A-CATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * *
1943 ATTATAAAACTATTTAAAACAAGTAACAAGGCTTTTAAAGGAAT-GTGTGACTATAAATGGACTT
65 ATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAG-GTGACTATAAATGGACTT
* * * * * *
2007 TCCTTACCAATTAATACCTGTTTCTTCATGTTTCTCAAGGTAG
129 TTCTTGCCAATGAATA-CTTTTTCTTCATATTTCCCAAGGTAG
** * *
2050 ACATTCAATTATAGTCT-AATTAAACAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
2114 TTATAAAAC
66 TTATAAAAC
2123 NNNNNNNNNN
Statistics
Matches: 1476, Mismatches: 412, Indels: 109
0.74 0.21 0.05
Matches are distributed among these distances:
163 112 0.08
164 3 0.00
165 2 0.00
167 2 0.00
168 127 0.09
169 13 0.01
170 322 0.22
171 740 0.50
172 153 0.10
173 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.35
Consensus pattern (170 bp):
ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTT
CTTGCCAATGAATACTTTTTCTTCATATTTCCCAAGGTAG
Found at i:1016 original size:341 final size:339
Alignment explanation
Indices: 10--2122 Score: 1091
Period size: 341 Copynumber: 6.2 Consensus size: 339
1 CCATGGTCA
* * * * * * *
10 ACATTCAATTATAGTCTATATTCATGAGAAATATAAATAAATTCAACCTAAAATCAATTTTGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAGAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * *********** *
75 TTGTAAAA-TCATGTAAAGCGAGTAATAAGGCTTTTAAAGGNNNNNNNNNNTATAAATGGACTTT
66 TTATAAAACT-ATTTAAAACGAGTAATAAGGCTTTTAAAGAAATAGGTGACTATAAATGAACTTT
** * * * * *
139 TCTTGTTAATGACTATCTTTTTCTTCATGTTTCTCAAGGTAGATATACAATTATTGTCTGTTTTA
130 TCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTCAAGGTAGACATATAATTATAGTCTGTTTTA
* * **********
204 ATAAAAAATATAAAATAATTCAAATTAAAATCAATTATGAGATTATAAAACNNNNNNNNNNGAGT
195 ATCAAAAATATAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGT
* * * * * * **
269 AATAAGGCTTTTTAAGGAATGGGTGACTATAAATAGAA-TTTTCTTGCGATTGAATCCCTTTTTC
260 AATAAGACTTTTGAAAGAATAGGTGACTATAAATA-AACTTTTC-TGCCAATGAAT-GATTTTTC
* **
333 TTCATATTTCTTGAGGTAG
322 TACATATTTC-CCAGGTAG
* ************
352 ACATTCAATTATAGTCTGTTTTAACCANNNNNNNNNNNNNAATTCAACTTAAAATCAATTATGAG
1 ACATTCAATTATAGTCTGTTTTAATCA-GAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * *
417 ATTATAAAACTATTTAAAATGACTAATAAGGCTTTTGAAGGAATTGATGACCATAAAT-AGACTT
65 ATTATAAAACTATTTAAAACGAGTAATAAGGCTTTTAAAGAAATAGGTGACTATAAATGA-ACTT
* * * *
481 TTCTTGCCATTGAATTTCTTTTTCTTCATGTTTC-CTAAGGTAGACAT-TCAATTATAGTCTATT
129 TTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTC-AAGGTAGACATAT-AATTATAGTCTGTT
* * * * *
544 TTAATCAAAAACATAAAACAATTCAGCTTAAAATCAATTCTGAGATTATAAAACCATTTAAAACA
192 TTAATCAAAAATATAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACG
* * ** * ** *
609 AGTAATGAGTCTTTTG-AAGAAATAGAAGGCTATAAATGGAC-TTTCTTCCAAATGAATGCATTT
257 AGTAATAAGACTTTTGAAAG-AATAGGTGACTATAAATAAACTTTTCTGCC-AATGAATG-ATTT
*
672 TTCTCCATATTTCCCAAGGTAG
319 TTCTACATATTTCCC-AGGTAG
* * * * *
694 ATATTCAATTATAGTATGTTGTAATGAGAAATATAAAAAAATTCAACTTAAAATCAATTTTGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAGAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * *
759 TTATAAAA-TCATTTACAGCGAGTAATAATGCTTTTAAAGAAATGGGTGACTATAAATGAACTTT
66 TTATAAAACT-ATTTAAAACGAGTAATAAGGCTTTTAAAGAAATAGGTGACTATAAATGAACTTT
* * * *
823 TCTTGTCAATGACTATCTTTTTCTTCAAGTTTCTCAAGATAGACATATAATTATTGTCTGTTTTA
130 TCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTCAAGGTAGACATATAATTATAGTCTGTTTTA
* * * *
888 ATCAAAAATGTAAAATAATT-AGACTGAAAATCAATTATAAGATTATAAAACTATTTAAAACGAG
195 ATCAAAAATATAAAATAATTCA-ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACGAG
* * *
952 TAATAAGAATTTTGAAAGAGTAGGTGACTATAAA-AAACTTTTCTGCACAATGAATAGTTTTTTC
259 TAATAAGACTTTTGAAAGAATAGGTGACTATAAATAAACTTTTCTGC-CAATGAAT-GATTTTTC
* *
1016 TACACATTT-CCTGTGTCA-
322 TACATATTTCCCAG-GT-AG
* * * *
1034 AGCATTCAATTATAGTCTATTTTAATCAAAAATGTAAAAAAACTT-AACTTAAAATCAGTTATGA
1 A-CATTCAATTATAGTCTGTTTTAATCAGAAATATAAAAAAA-TTCAACTTAAAATCAATTATGA
* * **********
1098 GATTACAAAACTATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGTGACTNNNNNNNNNNTT
64 GATTATAAAACTATTTAAAACGAGTAATAAGGCTTTTAAAGAAATAGGTGACTATAAATGAACTT
* * * *
1163 TTCTTACCAATAAATACCTTTTTCTTCATA-TTTCTCAAGGTAGACATTTAATTATAGTCTGTTT
129 TTCTTGCCAATGAATATCTTTTTCTTCA-AGTTTCTCAAGGTAGACATATAATTATAGTCTGTTT
* *********
1227 T-A--AAAAATGTATAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCANNNNNNNNN
193 TAATCAAAAATATA-AAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACG
* * * * ** * **
1288 NGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGGACTTTTCTTGCCATTGAATCCCTTTT
257 AGTAATAAGACTTTTGAAAGAATAGGTGACTATAAATAAACTTTTC-TGCCAATGAAT-GATTTT
* ****
1353 TCGT-CATGTTTGTTGTGGTAG
320 TC-TACATATTT-CCCAGGTAG
* ** * *
1374 ACATTCAATTATAGTCTGTTTTAA-CTAAAAACGTAAAAAGATTCAACTTAAAATCAATTATGAA
1 ACATTCAATTATAGTCTGTTTTAATC-AGAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* *********** * * *
1438 ATTATAAAACCATTTAAAGNNNNNNNNNNGGCTTTTGAAGAAAT-GAGAGACTATAAATGGACTT
65 ATTATAAAACTATTTAAAACGAGTAATAAGGCTTTTAAAGAAATAG-GTGACTATAAATGAACTT
* * * * *
1502 TTCTT-CCAAATGAATATATTTTTCTTTATA-TTTC-CTATGGTTGACAT-TCAATTATAGTCTA
129 TTCTTGCC-AATGAATATCTTTTTCTTCA-AGTTTCTC-AAGGTAGACATAT-AATTATAGTCTG
* * * * * * * *
1563 TATTCA-CGAGAAATAGAAAAAAATTCAACCTAAAATTAATTTTGAGATTATAAAACCATTTAAA
190 TTTTAATC-AAAAATATAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * ** * **
1627 GCAAGTCATAA-AGTTTTTAAAGGAAT-GG-G----T--ATGGACATTTCTTATCAATGACTAT-
254 ACGAGTAATAAGACTTTTGAAA-GAATAGGTGACTATAAATAAACTTTTC-TGCCAATGA--ATG
* * * *
1682 CTTTTTCTTCATGTTTCTCAAGGTAG
315 ATTTTTCTACATATTTC-CCAGGTAG
* * * * * * * *
1708 ATATACAATTATTA-TTTGTTTTAATTAAAAAAATAAAATAATTCGACTTAAAATCAATTATGAG
1 ACATTCAATTA-TAGTCTGTTTTAATCAGAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
********** * * * *
1772 ATTATANNNNNNNNNNAAATGAGTAATAAGGCTTTTGAAGGAAT-GGCTGACTGTAAATGAACTT
65 ATTATAAAACTATTTAAAACGAGTAATAAGGCTTTTAAAGAAATAGG-TGACTATAAATGAACTT
* * *
1836 TTCTTTCCAATGAATAGT-TTTTT-TTACACAATTAC-CAA-GTCA-AGCAT-TCAATTATAGTC
129 TTCTTGCCAATGAATA-TCTTTTTCTT-CA-AGTTTCTCAAGGT-AGA-CATAT-AATTATAGTC
* * *********** *
1895 TGTTTTAATAAAAAATGTAANNNNNNNNNNTTTAAAATCAATTATGAGATTATAAAACTATTTAA
188 TGTTTTAATCAAAAATATAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * ** * * *
1960 AACAAGTAACAAGGCTTTT-AAAGGAAT-GTGTGACTATAAATGGACTTTCCTTACCAATTAAT-
253 AACGAGTAATAAGACTTTTGAAA-GAATAG-GTGACTATAAATAAACTTTTC-TGCCAATGAATG
* * * *
2022 ACCTGTTTCTTCATGTTTCTCAAGGTAG
315 A--TTTTTCTACATATTTC-CCAGGTAG
** * *
2050 ACATTCAATTATAGTCT-AATTAAACAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
1 ACATTCAATTATAGTCTGTTTTAATCAGAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
2114 TTATAAAAC
66 TTATAAAAC
2123 NNNNNNNNNN
Statistics
Matches: 1347, Mismatches: 354, Indels: 141
0.73 0.19 0.08
Matches are distributed among these distances:
333 7 0.01
334 219 0.16
335 14 0.01
336 4 0.00
338 79 0.06
339 172 0.13
340 22 0.02
341 445 0.33
342 193 0.14
343 191 0.14
344 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.35
Consensus pattern (339 bp):
ACATTCAATTATAGTCTGTTTTAATCAGAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAACTATTTAAAACGAGTAATAAGGCTTTTAAAGAAATAGGTGACTATAAATGAACTTTT
CTTGCCAATGAATATCTTTTTCTTCAAGTTTCTCAAGGTAGACATATAATTATAGTCTGTTTTAA
TCAAAAATATAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTA
ATAAGACTTTTGAAAGAATAGGTGACTATAAATAAACTTTTCTGCCAATGAATGATTTTTCTACA
TATTTCCCAGGTAG
Found at i:3149 original size:171 final size:171
Alignment explanation
Indices: 2751--4090 Score: 579
Period size: 171 Copynumber: 7.9 Consensus size: 171
2741 NNNNNNNNNN
* * * * * * * * ** **
2751 GGCTTTTAAAGAAATGGGTGACTATAAATGGACTTTTCTTGTCAATG-A-CTGTTTTTTTTTATG
1 GGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCATTGAATCCGTTTTTCTACACA
** * * * * *
2814 TTTCTTGAGGTAGACAAACAATTATTGTCTATTTTAA-TAAAAATGTAAAATAATT-AGACTTAA
66 TTTCTTGAGGTAGACATTCAATTATAGTTTGTTTTAACTAAAAATATAAAAAAATTCA-ACTTAA
* * * * * * *
2877 AATCAATTATGAGGTTACAAAACCATTTAAAGCGAGTAATAA
130 AATCAATTATGAGATTATAAAATCATTGAAGGTGACTAATAA
* * * * * ** *
2919 AGTTTTTGAAGGAATAGGTGACTGTAAATAAACTTTTCTTCCCAAAGAAT-AGTTTTTTCTACAC
1 GGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCATTGAATCCG-TTTTTCTACAC
* * *
2983 ATTTCCTGAGCG-AGGCATTCAATTATAGTTTGTTTT-ACTCAAAAATGTAAAAAAATTCAACTT
65 ATTTCTTGAG-GTAGACATTCAATTATAGTTTGTTTTAACT-AAAAATATAAAAAAATTCAACTT
* * **********
3046 AAAATCAATTATGAAATTACAAAATCATTNNNNNNNNNNAATAA
128 AAAATCAATTATGAGATTATAAAATCATTGAAGGTGACTAATAA
* * ** **
3090 GGCTTTTGAAGGAATGGGTGACTATAAATAGAGTTTTCTTGCCATTGAATCCGTTTTTCTTTATT
1 GGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCATTGAATCCGTTTTTCTACACA
* * * * * * *
3155 TTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACAAAAAATATAAAAAATTTTAATTTAAA
66 TTTCTTGAGGTAGACATTCAATTATAGTTTGTTTTAACTAAAAATATAAAAAAATTCAACTTAAA
3220 ATCAATTATGAGATTATAAAA-CTATTGAAGGTGACTAATAA
131 ATCAATTATGAGATTATAAAATC-ATTGAAGGTGACTAATAA
* * * * * * *
3261 GGCTTTTTAAGGAATTA-GTGACCAAAAATGGACTTTTCTTGCTATTGAATCCCTTTTTCTGCAC
1 GGCTTTTGAAGGAA-TAGGTGACTATAAATAGACTTTTCTTGCCATTGAATCCGTTTTTCTACAC
* * * *
3325 GTTTCTTGAGGTTGACATTCAATTATAGTCTT-TTTTAACTAAAAACATAAAAAAATACAACTTA
65 ATTTCTTGAGGTAGACATTCAATTATAGT-TTGTTTTAACTAAAAATATAAAAAAATTCAACTTA
* * * * **
3389 AAATAAATTATGAGATTATAAAATCATTTAAAGCGAGAAATAA
129 AAATCAATTATGAGATTATAAAATCATTGAAGGTGACTAATAA
* ** * * * *** * *
3432 GTCTTTTGAAAAAAT-GAGAGACTATAAATGGACTTTTCTT-CTAAATT-AATGTAATTTTTTTT
1 GGCTTTTGAAGGAATAG-GTGACTATAAATAGACTTTTCTTGC--CATTGAAT-CCGTTTTTCTA
** ** * * * ** * *
3494 CATGTTT-TCCAATGTAGACATTCAATTATAGTCTGTTTTCAGGAGAAATATAAAAAAATTTAAC
62 CACATTTCT-TGAGGTAGACATTCAATTATAGTTTGTTTTAACTAAAAATATAAAAAAATTCAAC
* ********** * * * *
3558 TTAAAATCAATTTTGAGANNNNNNNNNNATTTAAAGCGAGTAATAA
126 TTAAAATCAATTATGAGATTATAAAATCATTGAAGGTGACTAATAA
* * * ** **
3604 GGCTTTTAAAGAAATAGGTGAATATAAATAGACTTTTCTTATCATTGACTAT-C-TTTTTCTTTA
1 GGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCATTGA--ATCCGTTTTTCTACA
* ** * * * * *
3667 CGTTTCTCAAGGTAGATATACAATTATTGTCTGTTTTAA-TCAAAAATATAAAACAATT-AGACT
64 CATTTCTTGAGGTAGACATTCAATTATAGTTTGTTTTAACT-AAAAATATAAAAAAATTCA-ACT
* * * * * * *
3730 TACACTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
127 TAAAATCAATTATGAGATTATAAAATCATTGAAGGTGACTAATAA
* ********** * * * * *
3775 GGTTTTTGANNNNNNNNNNGACTGTAAAT-GAACTTTTCTTCCCAATGAAT-AGTTTTTTCTGCA
1 GGCTTTTGAAGGAATAGGTGACTATAAATAG-ACTTTTCTTGCCATTGAATCCG-TTTTTCTACA
* ** * ** * *********
3838 CATTTCCTGAGCCA-AGCATTCAGTTATAGCCTATTTTAA-TCAAAAATATAAAAANNNNNNNNN
64 CATTTCTTGAGGTAGA-CATTCAATTATAGTTTGTTTTAACT-AAAAATATAAAAAAATTCAACT
* * * * *
3901 NAAAATCAATTATGAGATTAT-AAAT-ATTTTAAAGCGAGTAATAA
127 TAAAATCAATTATGAGATTATAAAATCA-TTGAAGGTGACTAATAA
* * * * * ** ** * *
3945 GGCTTGTGAAGGAATTGGGGACCATAAATGGACTTTTCTTGTTATTGAATCCCATTTTCTTCACG
1 GGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCATTGAATCCGTTTTTCTACACA
* * * * ** *
4010 TTTCCTGAGGTAAACATTCAATTATAGTCTGTTTTAACCAAAAACGT-AAAAAATTCAATTTAAA
66 TTTCTTGAGGTAGACATTCAATTATAGTTTGTTTTAACTAAAAATATAAAAAAATTCAACTTAAA
4074 ATCAATTATGAGATTAT
131 ATCAATTATGAGATTAT
4091 NNNNNNNNNN
Statistics
Matches: 873, Mismatches: 260, Indels: 77
0.72 0.21 0.06
Matches are distributed among these distances:
168 36 0.04
169 30 0.03
170 136 0.16
171 538 0.62
172 130 0.15
173 1 0.00
174 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
GGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCATTGAATCCGTTTTTCTACACA
TTTCTTGAGGTAGACATTCAATTATAGTTTGTTTTAACTAAAAATATAAAAAAATTCAACTTAAA
ATCAATTATGAGATTATAAAATCATTGAAGGTGACTAATAA
Found at i:3348 original size:342 final size:329
Alignment explanation
Indices: 2751--3416 Score: 662
Period size: 342 Copynumber: 2.0 Consensus size: 329
2741 NNNNNNNNNN
* * * *
2751 GGCTTTTAAAGAAATGGGTGACTATAAATGGACTTTTCTTGTCAATGACTGTTTTTTTTTATGTT
1 GGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGACCGTTTTTCTTTATGTT
** * *
2816 TCTTGAGGTAGACAAACAATTATTGTCTATTTTAATAAAAATGTAAAATAATTAGACTTAAAATC
66 TCTTGAGGTAGACAAACAATTATAATCTATTTTAAAAAAAATATAAAATAATTAGACTTAAAATC
* * * ***
2881 AATTATGAGGTTACAAAACCATTTAAAGCGAGTAATAAAGTTTTTGAAGGAATAGGTGACTGTAA
131 AATTATGAGATTACAAAACCATTGAAAGCGACTAATAAAGTTTTTGAAGGAATAGGTGACCAAAA
** *
2946 ATAAACTTTTCTTCCCAAAGAATAGTTTTTTCTACACATTTCCTGAGCGAGGCATTCAATTATAG
196 ATAAACTTTTCTTCCCAAAGAATACCTTTTTCTACACATTTCCTGAGCGAGACATTCAATTATAG
** * *
3011 T-TTGTTTT-ACTCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTACAAAATCAT
261 TCTT-TTTTAACT-AAAAACATAAAAAAATACAACTTAAAATAAATTATGAAATTACAAAATCAT
3074 TNNNNNNNNNNAATAA
324 T----------AATAA
* * * * *
3090 GGCTTTTGAAGGAATGGGTGACTATAAATAGAGTTTTCTTGCCATTGAATCCGTTTTTCTTTATT
1 GGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATG-A-CCGTTTTTCTTTATG
*** * *
3155 TTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACAAAAAATATAAAA-AATTTTA-ATTTA
64 TTTCTTGAGGTAGACAAACAATTATAATCTATTTTAA-AAAAAATATAAAATAA--TTAGACTTA
* * * * *
3218 AAATCAATTATGAGATTATAAAACTATTGAAGGTGACTAATAAGGCTTTTT-AAGGAATTA-GTG
126 AAATCAATTATGAGATTACAAAACCATTGAAAGCGACTAATAAAG-TTTTTGAAGGAA-TAGGTG
** * * ** * * * * *
3281 ACCAAAAATGGACTTTTCTTGCTATTGAATCCCTTTTTCTGCACGTTTCTTGAG-GTTGACATTC
189 ACCAAAAATAAACTTTTCTTCCCAAAGAATACCTTTTTCTACACATTTCCTGAGCG-AGACATTC
* *
3345 AATTATAGTCTTTTTTAACTAAAAACATAAAAAAATACAACTTAAAATAAATTATGAGATTATAA
253 AATTATAGTCTTTTTTAACTAAAAACATAAAAAAATACAACTTAAAATAAATTATGAAATTACAA
3410 AATCATT
318 AATCATT
3417 TAAAGCGAGA
Statistics
Matches: 268, Mismatches: 49, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
339 41 0.15
340 1 0.00
341 46 0.17
342 165 0.62
343 15 0.06
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.37
Consensus pattern (329 bp):
GGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGACCGTTTTTCTTTATGTT
TCTTGAGGTAGACAAACAATTATAATCTATTTTAAAAAAAATATAAAATAATTAGACTTAAAATC
AATTATGAGATTACAAAACCATTGAAAGCGACTAATAAAGTTTTTGAAGGAATAGGTGACCAAAA
ATAAACTTTTCTTCCCAAAGAATACCTTTTTCTACACATTTCCTGAGCGAGACATTCAATTATAG
TCTTTTTTAACTAAAAACATAAAAAAATACAACTTAAAATAAATTATGAAATTACAAAATCATTA
ATAA
Found at i:4825 original size:171 final size:170
Alignment explanation
Indices: 4342--4837 Score: 462
Period size: 171 Copynumber: 2.9 Consensus size: 170
4332 NNNNNNNNNN
* * ** *
4342 TTTAACTTAAAATCACTTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-AAAGA
1 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGATTTTTGAAGGA
* * * **
4406 AATGAATGACTATACATGGACTTTTCTTGTCAATGACCATCTTTTTCTTCACGTTTCTCGAGGTA
66 ATTG-GTGACTATAAATGGACTTTTCTTGTCAATGACTGTCTTTTTCTTCACGTTTCTCGA-GTA
* * * * *
4471 GACATGCAATTATTA-TCTATTTTAATCAAAAATGTAAAATAA
129 GACATACAATTA-TAGTCTGTTTTAATAAAAAATATAAAAAAA
* * *
4513 -TTAGACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGTTTTTTGAAGG
1 TTTA-ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGATTTTTGAAGG
* * ********** ** * * * *
4577 AATAGGTGACTGTAANNNNNNNNNNCTTCCCAATAAATAGT-TTTTTCTAT-ACATTTCTTGAGT
65 AATTGGTGACTATAAATGGACTTTTCTTGTCAATGACT-GTCTTTTTCT-TCACGTTTCTCGAGT
*
4640 CAGACATTCAATTATAGTCTGTTTTAATAAAAAATATAAAAAAA
128 -AGACATACAATTATAGTCTGTTTTAATAAAAAATATAAAAAAA
* * ** *
4684 TTTAACTGAAAATCAATTATGAGATTATAAACCCATTTAAAATGAGTAATATGATTTTTGAAGGA
1 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGATTTTTGAAGGA
* * *
4749 ATTGGTGATTATAAATGGACTTTTCTTGTCAATGACTGTCTTTTTCTTCACGTTTCTCAACATAG
66 ATTGGTGACTATAAATGGACTTTTCTTGTCAATGACTGTCTTTTTCTTCACGTTTCTCGA-GTAG
* *
4814 ATATACAATTATTGTCTGTTTTAA
130 ACATACAATTATAGTCTGTTTTAA
4838 NNNNNNNNNN
Statistics
Matches: 248, Mismatches: 67, Indels: 20
0.74 0.20 0.06
Matches are distributed among these distances:
170 10 0.04
171 226 0.91
172 12 0.05
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.38
Consensus pattern (170 bp):
TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGATTTTTGAAGGA
ATTGGTGACTATAAATGGACTTTTCTTGTCAATGACTGTCTTTTTCTTCACGTTTCTCGAGTAGA
CATACAATTATAGTCTGTTTTAATAAAAAATATAAAAAAA
Found at i:5518 original size:171 final size:161
Alignment explanation
Indices: 5220--5688 Score: 388
Period size: 171 Copynumber: 2.8 Consensus size: 161
5210 TATGAGATTA
* * *
5220 TAAAAGTATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATTGACTTTTCTT
1 TAAAACTATTTAAAGCGAGTAAAAAGGCTTTTAAAGGAATAGGTGACTATAAATAGACTTTTCTT
* * * *
5285 ATCAATCAATGCATTTTTCTTTATGTTTCTTAAGGTAGACATTCAATTATAGTCTTTTTTAACCA
66 ACCAATCAATCCATTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTTTTTTAACCA
*
5350 AAAATGTAAAAA-AATTCATCTTAAAATCAAT
131 AAAATGTAAAAACAATT-AACTTAAAATCAAT
* * *
5381 TNNNNNNNNNNAAAACTATTTAAAGCTAGTAAAAAGGCTTTTGAAGGAATGGGTGACTATAAATA
1 T----------AAAACTATTTAAAGCGAGTAAAAAGGCTTTTAAAGGAATAGGTGACTATAAATA
* * * * * *
5446 GACTTTTCTTGCCATTGAATCCTTTTTTCTTCACGTTTGTTGAGGTAGACATTCAATTATAGT-T
56 GACTTTTCTTACCAATCAATCCATTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCT
* *
5510 TGTTTTAACTAAAAATGTAAAAACAATTAACTTAAAATTAGATATGAGAT
121 T-TTTTAACCAAAAATGTAAAAACAATTAACTT---A--A-A-ATCA-AT
* * * * * * * *
5560 TATAAAATCATTTAAAGCAACTAATAAGGTTTTTGAAA-GAATGGGTGACTTTAAATGGACTTTT
1 TA-AAACT-ATTTAAAGCGAGTAAAAAGGCTTTT-AAAGGAATAGGTGACTATAAATAGACTTTT
* * * * * * *
5624 CTTACTAATGAATCCCTTTTTCTTCACATTTCTTTTA-GTAAACATTCAATTATAGTCTATTTTA
63 CTTACCAATCAATCCATTTTTCTTCACGTTTC-TTAAGGTAGACATTCAATTATAGTCTTTTTTA
5688 A
127 A
5689 TAAAATCAAT
Statistics
Matches: 247, Mismatches: 36, Indels: 40
0.76 0.11 0.12
Matches are distributed among these distances:
161 1 0.00
169 1 0.00
170 6 0.02
171 220 0.89
172 10 0.04
174 1 0.00
176 1 0.00
177 1 0.00
178 3 0.01
179 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.38
Consensus pattern (161 bp):
TAAAACTATTTAAAGCGAGTAAAAAGGCTTTTAAAGGAATAGGTGACTATAAATAGACTTTTCTT
ACCAATCAATCCATTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTTTTTTAACCA
AAAATGTAAAAACAATTAACTTAAAATCAAT
Found at i:5988 original size:170 final size:170
Alignment explanation
Indices: 5689--6049 Score: 447
Period size: 170 Copynumber: 2.1 Consensus size: 170
5679 TCTATTTTAA
* ** *
5689 TAAAATCAATTATGAGATTATAAAACTAATTAAAGTAAGTAATAGTCCTTTTCAAGAAATGGGTG
1 TAAAATCAGTTATGAGATTATAAAACTAATTAAAGTAAGTAATAAACCTTTTCAAGAAATAGGTG
* * * * *
5754 AGAATAAATGGACTTTTCTTCACAATGAATGGCTTTTTCTACATGTTTCTTGAGGCAAGCATTCA
66 ACAATAAATGGACTTTTCTTCACAATGAATAGCTTTTTCTAAATGCTTCTTAAGGCAAGCATTCA
* ** * *
5819 ATTATTGTTTGTTTTAACAAAAATGTAAAAAAATTTGATT
131 ATTATAGCCTGTTTTAACAAAAATGTAAAAAAATTTAACT
* * * *
5859 TAAAATCAGTTATGAGAGTATAAAACTATTTAAAGCT-AGTAATAAAGCTTTTGAAGAAATAGGT
1 TAAAATCAGTTATGAGATTATAAAACTAATTAAAG-TAAGTAATAAACCTTTTCAAGAAATAGGT
* *** * * *
5923 GACTATAAATGGACTTTTCTTGTGAATGAATAGCTTTTTCTAAATGCTTGTTAAGGTAGGCATTC
65 GACAATAAATGGACTTTTCTTCACAATGAATAGCTTTTTCTAAATGCTTCTTAAGGCAAGCATTC
* * *
5988 AATTATAGCCTGTTTTAACCAAAATTTAAAATAATTTAACT
130 AATTATAGCCTGTTTTAACAAAAATGTAAAAAAATTTAACT
6029 TAAAATCAG-TATGAGATTATA
1 TAAAATCAGTTATGAGATTATA
6050 NNNNNNNNNN
Statistics
Matches: 161, Mismatches: 29, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
169 11 0.07
170 149 0.93
171 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (170 bp):
TAAAATCAGTTATGAGATTATAAAACTAATTAAAGTAAGTAATAAACCTTTTCAAGAAATAGGTG
ACAATAAATGGACTTTTCTTCACAATGAATAGCTTTTTCTAAATGCTTCTTAAGGCAAGCATTCA
ATTATAGCCTGTTTTAACAAAAATGTAAAAAAATTTAACT
Found at i:5989 original size:317 final size:318
Alignment explanation
Indices: 5418--6005 Score: 721
Period size: 317 Copynumber: 1.9 Consensus size: 318
5408 AGTAAAAAGG
* * * * *
5418 CTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCATTGAATCCTTTTTTCTTCACGTT
1 CTTTTCAAGAAATGGGTGACAATAAATAGACTTTTCTTGCCAATGAATCCTTTTTTCTACACGTT
* *
5483 TGTTGAGGTAGACATTCAATTATAGTTTGTTTTAACTAAAAATGTAAAAACAATTAACTTAAAAT
66 TCTTGAGGAAGACATTCAATTATAGTTTGTTTTAACTAAAAATGTAAAAACAATTAACTTAAAAT
* * * * * *
5548 TAGATATGAGATTATAAAATCATTTAAAGCAACTAATAAGGTTTTTGAAAGAATGGGTGACTTTA
131 CAGATATGAGAGTATAAAATCATTTAAAGCAACTAATAAAGCTTTTGAAAGAATAGGTGACTATA
* * *
5613 AATGGACTTTTCTTACTAATGAATCCCTTTTTCTTCACATTTCTTTTAGTAAACATTCAATTATA
196 AATGGACTTTTCTTACTAATGAATACCTTTTTCTTCACAATGCTTTTAGTAAACATTCAATTATA
*
5678 GTCTATTTTAATAAAATCAATTATGAGATTATAAAACTAATTAAAGTAAGTAATAGTC
261 GCCTATTTTAATAAAATCAATTATGAGATTATAAAACTAATTAAAGTAAGTAATAGTC
* * * *
5736 CTTTTCAAGAAATGGGTGAGAATAAATGGACTTTTCTT-CACAATGAATGGC-TTTTTCTACATG
1 CTTTTCAAGAAATGGGTGACAATAAATAGACTTTTCTTGC-CAATGAAT-CCTTTTTTCTACACG
* * *
5799 TTTCTTGAGGCAAG-CATTCAATTATTGTTTGTTTTAAC-AAAAATGTAAAAA-AATTTGATTTA
64 TTTCTTGAGG-AAGACATTCAATTATAGTTTGTTTTAACTAAAAATGTAAAAACAA-TTAACTTA
* * *
5861 AAATCAGTTATGAGAGTATAAAA-CTATTTAAAGCTAGTAATAAAGCTTTTG-AAGAAATAGGTG
127 AAATCAGATATGAGAGTATAAAATC-ATTTAAAGCAACTAATAAAGCTTTTGAAAG-AATAGGTG
* * **
5924 ACTATAAATGGACTTTTCTT-GTGAATGAATAGCTTTTTC-T-A-AATGCTTGTTAAGGTAGGCA
190 ACTATAAATGGACTTTTCTTACT-AATGAATACCTTTTTCTTCACAATGCTT-TT-A-GTAAACA
*
5985 TTCAATTATAGCCTGTTTTAA
251 TTCAATTATAGCCTATTTTAA
6006 CCAAAATTTA
Statistics
Matches: 228, Mismatches: 32, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
314 5 0.02
315 3 0.01
316 9 0.04
317 126 0.55
318 82 0.36
319 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (318 bp):
CTTTTCAAGAAATGGGTGACAATAAATAGACTTTTCTTGCCAATGAATCCTTTTTTCTACACGTT
TCTTGAGGAAGACATTCAATTATAGTTTGTTTTAACTAAAAATGTAAAAACAATTAACTTAAAAT
CAGATATGAGAGTATAAAATCATTTAAAGCAACTAATAAAGCTTTTGAAAGAATAGGTGACTATA
AATGGACTTTTCTTACTAATGAATACCTTTTTCTTCACAATGCTTTTAGTAAACATTCAATTATA
GCCTATTTTAATAAAATCAATTATGAGATTATAAAACTAATTAAAGTAAGTAATAGTC
Done.