Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401395.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4524.0, 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: 7096
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.31
Warning! 1018 characters in sequence are not A, C, G, or T
Found at i:370 original size:142 final size:141
Alignment explanation
Indices: 110--372 Score: 343
Period size: 142 Copynumber: 1.9 Consensus size: 141
100 ATAATCTGTT
* *
110 TTAACTAAAAAAGTAAAAAAATTAAACTTAAATCCAATTATGATATTATAAACCACTTAAAGCGA
1 TTAACTAAAAAAGTAAAAAAATTAAACTTAAATCCAATTATGAGATTATAAACAACTTAAAGCGA
* * * * *
175 GCAATAAGGCTTTTGCAGGAATAAGTGACTGTAAATGGACTTTTCTTCCCAATGAATGTCTTTTT
66 GAAATAAGGCTTTTGAAGAAATAAGTGACTATAAATGAACTTTTCTTCCCAATGAATGTCTTTTT
240 CTTCATATTTC
131 CTTCATATTTC
* * * * *
251 TTAACTAAAAATGTAGAAAAATTCAACTTAAAAT-CAGTTATGAGATTATAATACAATTTAAAGC
1 TTAACTAAAAAAGTAAAAAAATTAAACTT-AAATCCAATTATGAGATTATAA-ACAACTTAAAGC
* *
315 GAGAAATAAGGCTTTTGAAGAAAT-GGTTGACTATAAATGAACTCTTT-TTCTCAATGAA
64 GAGAAATAAGGCTTTTGAAGAAATAAG-TGACTATAAATGAACT-TTTCTTCCCAATGAA
373 ATAGTTTTTC
Statistics
Matches: 104, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
141 42 0.40
142 59 0.57
143 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (141 bp):
TTAACTAAAAAAGTAAAAAAATTAAACTTAAATCCAATTATGAGATTATAAACAACTTAAAGCGA
GAAATAAGGCTTTTGAAGAAATAAGTGACTATAAATGAACTTTTCTTCCCAATGAATGTCTTTTT
CTTCATATTTC
Found at i:692 original size:170 final size:169
Alignment explanation
Indices: 251--1145 Score: 837
Period size: 170 Copynumber: 5.3 Consensus size: 169
241 TTCATATTTC
* * * * * * *
251 TTAACTAAAAATGTAGAAAAATTCAACTTAAAATCAGTTATGAGATTATAATACAATTTAAAGCG
1 TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGTG
* * * *
316 AGAAATAAGGCTTTTG-AAGAAATGGTTGACTATAAAT-GAACTCTTT-TTCTCAATGAAATAG-
66 AGTAATAAGACTTTTGAAAG-AATGGGTGACTATAAATAG-ACT-TTTCTTC-CAATG--ATTGC
* * *
377 TTTTTCTACATGTTTCTCGAGGTGGGCATTCAATTATAGTCTGTT
125 TTTTTCTACATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
** * * **
422 TTAATGAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
1 TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGTG
* * * *
487 AGTGATAAGATTTTTGAAA-AATGGGTGATTATAAATGGACTTTTCTTACCAATGATTGCTTTTA
66 AGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTT-CCAATGATTGCTTTT-
* **
551 TCTACATATTTCTCAAGGTAGACATAT-AATTATAGTCTACT
129 TCTACATGTTTCTCAAGGTAGACAT-TCAATTATAGTCTGTT
* * *
592 TTAACCAATAATATGAAAAAATT-AACTTAAAATCAATTATGAGGTTATAAAATAATTTAAAGTG
1 TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGTG
* * * *
656 TGTAAGAAGACTTTTGAAAGAATGGGTGGCTATAAATAGACTTTTATTCTCAATGATTGGCTTTT
66 AGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTC-CAATGATT-GCTTTT
* ** * * *
721 TGTACACATTTTTCAAGGTAAGA-ATTCGATTAGAGTCTGTT
129 TCTACATGTTTCTCAAGGT-AGACATTCAATTATAGTCTGTT
* * *
762 TTAACAAAAAATTTTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGC
1 TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-TAATTTAAAG-
* ** * * * * *
826 T-AGTAACAA-ACCTTTTGAGGGAAGGGGTGACCATAAATAGAGTTTTCTTGCCAATGAATGTTT
64 TGAGTAATAAGA-CTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTT-CCAATGATTGCTT
*
889 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
127 TTTCTACATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
* * * * * ***
932 TTAACTAAAAATGTAAAAAAATTCAATTTTAAATCAATTATGAGATTATAAAATAA-ATACCTTT
1 TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTA--AAG
* * ** * **
996 TTA-TAATAAGGCTTTTGAAAGAAAAGGTGACTATAAATAGACTTTTTTTGCCAATGAATACCTT
64 TGAGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTT-CCAATG-ATTGCTT
* * * *
1060 TTTCTTCATGTTTCTTAAGGTAGACGTTCAATTATAGTCTGCT
127 TTTCTACATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
* ** *
1103 TTAGCCAAAAAT-GCAAAAAATTGAACTTAAAATCAATTATGAG
1 TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
1146 CCTTTTGATG
Statistics
Matches: 600, Mismatches: 100, Indels: 49
0.80 0.13 0.07
Matches are distributed among these distances:
168 3 0.00
169 67 0.11
170 310 0.52
171 215 0.36
172 5 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (169 bp):
TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGTG
AGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCCAATGATTGCTTTTTC
TACATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
Found at i:1208 original size:140 final size:141
Alignment explanation
Indices: 1022--1275 Score: 350
Period size: 140 Copynumber: 1.8 Consensus size: 141
1012 GAAAGAAAAG
* * * * *
1022 GTGACTATAAATAGACTTTTTTTGCCAATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACGT
1 GTGACTATAAATAGACTTTTCTTACCAATGAATACCTTTTTCTTCATATTTCTCAAGGTAGACAT
* * *
1087 TCAATTATAG-TCTGCTTTAGCCAAAAAT-GCAAAAAATTGAACTTAAAATCAATTATGAGCCTT
66 TCAATTATAGAT-TGCTTTAACCAAAAATAGAAAAAAATTCAACTTAAAATCAATTATGAGCCTT
1150 TTGATGGAATGA
130 TTGATGGAATGA
* * *
1162 GTGACTATAAATGGACTTTTCTTACTAATGAATACCTTTTTGTTCATATTTCTCAAGGTAGACAT
1 GTGACTATAAATAGACTTTTCTTACCAATGAATACCTTTTTCTTCATATTTCTCAAGGTAGACAT
* * * *
1227 TTAATTTTAGATTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAA
66 TCAATTATAGATTGCTTTAACCAAAAATAGAAAAAAATTCAACTTAAAA
1276 GCAGCTATAA
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
140 79 0.81
141 18 0.19
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (141 bp):
GTGACTATAAATAGACTTTTCTTACCAATGAATACCTTTTTCTTCATATTTCTCAAGGTAGACAT
TCAATTATAGATTGCTTTAACCAAAAATAGAAAAAAATTCAACTTAAAATCAATTATGAGCCTTT
TGATGGAATGA
Found at i:2439 original size:341 final size:338
Alignment explanation
Indices: 1249--2492 Score: 889
Period size: 342 Copynumber: 3.6 Consensus size: 338
1239 TGTTTTAACC
* ** * ** ** *
1249 AAAAATATAAAAAAATTCAACTTAAAAG-CAGCTATAAGATTATAAAATAATTTAAAGTAAGTAA
1 AAAAATGTAAAAAAA-TCAACTT-AAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGCAA
* * * * * ** * * *
1313 TAAGGCTTTTGAAGGAAT-GGTTGACTATAAATAGACTT-TTATTCTCAATGAATGGCTTTTT-T
64 TAAGACTTTTAAAAGAATAGG-TGACTATAAATGGAATTCTCCTGC-CAAGGAATGACTTTTTCT
* * * * ** *
1375 ACATGTTTC-CTGAGGCAAGCATTCAATTATAGTTTGTTTTAATGAAAATTATAAAAAAATCAAG
127 TCACGTTTCTC-GAGGTAAGCATTCAATTATAGTCTGTTTTAACAAAAAATAT-AAAAAATCAAG
* * * * **
1439 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAAGAATGGGT
190 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAACGATT
* * * * * * ** ** *
1504 GACTATAAATAA-ACTTTTTT-TACCAATAAATGCCTTTCTCTTCATGTT--TCTTGA-TGTGAA
255 GACAACAAA-AAGACTTTTTTCT--CAATGAATGGCTTTTTCTACACATTCCTCAAGACAG-G-A
* **
1564 CATTCAATTATAATCTA-TTTTAACA
315 C-TTCAATTATAATC-AGGTTTAATG
* * * * * *
1589 AAAAAAGTAAAAAAAAATTAAACTTAAAATCAATTTTGAGATTATAAAACCA-TTAAACTCGAGT
1 AAAAATGT--AAAAAAA-TCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAA-GCGAGC
* * * * * * * ** *
1653 AATAAGGCTTTTGAAGGAATAGGAGACTACAAATAG-ATTTTTTTACC--GGTTAAT-ACTTTTT
62 AATAAGACTTTTAAAAGAATAGGTGACTATAAATGGAATTCTCCTGCCAAGG--AATGAC-TTTT
* * * * *
1714 TCATT-ACGTTTCTCAAGTTAGGCATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAATAGT
124 TC-TTCACGTTTCTCGAGGTAAGCATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAA-A-T
* * *
1778 CAA-TCTGAAAGCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
186 CAAGT-TAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
* * * *
1842 TGATTGACAATAAAAAGACTTTTTTCTCAATGAATGGCTTTTTCTACACATTTCTCAAGACCGGA
250 CGATTGACAACAAAAAGACTTTTTTCTCAATGAATGGCTTTTTCTACACATTCCTCAAGACAGGA
* *
1907 CTTCAATTATAGTCAGTTTTAATG
315 CTTCAATTATAATCAGGTTTAATG
* *
1931 AAAAATGTTAAAAAATCAACTTAAAGTCAATTATGAGATTATAAAATCATTTAAAGCGAGCAATA
1 AAAAATGTAAAAAAATCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATA
* ** * * * * * *
1996 AGGCTTTTGCAGGAATAGGTGACTATAAATGGACTTCTCTTGCCAATGAATGTCTTTTTCTTCAT
66 AGACTTTTAAAAGAATAGGTGACTATAAATGGAATTCTCCTGCCAAGGAATGACTTTTTCTTCAC
*
2061 GTTTCTCGAGGTAGGCATTCAATTATAGTCTGTTTTAACAAAAAATATAGAAAAATCCAAGTTAA
131 GTTTCTCGAGGTAAGCATTCAATTATAGTCTGTTTTAACAAAAAATATA-AAAAAT-CAAGTTAA
** * * *
2126 AATTTATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAACGGTTGACT
194 AATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAACGATTGACA
** *********
2191 ACAAATGGACTTTTCTTCTCAATGAATGGCTTTTTNNNNNNNNNNCCT-AAGACAGG-CATTCAA
259 ACAAAAAGACTTTT-TTCTCAATGAATGGCTTTTT-CTACACATTCCTCAAGACAGGAC-TTCAA
*
2254 TTATAATCCGGTTTAATG
321 TTATAATCAGGTTTAATG
********** **
2272 AAAAATGTAAAAAAATTCAACTTAANNNNNNNNNNGAGATTATAAAACCATTTAAAGCGATTAAT
1 AAAAATGTAAAAAAA-TCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGCAAT
* * * *
2337 AAGATTTTTAAAAGAATAGGTG-CTATAGATGGAATTTTCCT-CTCAAGGAATGAGTTTTT-TTA
65 AAGACTTTTAAAAGAATAGGTGACTATAAATGGAATTCTCCTGC-CAAGGAATGACTTTTTCTT-
* * *
2399 CACGTTT-TCTGAGGTAAGCATTCAATTATAATCTGTTTTAACTAAAAATATAAAACAATTCTAG
128 CACGTTTCTC-GAGGTAAGCATTCAATTATAGTCTGTTTTAACAAAAAATATAAAA-AA-TCAAG
2463 TTAAAATCAATTATGAGATTATAAAACAAT
190 TTAAAATCAATTATGAGATTATAAAACAAT
2493 NNNNNNNNNN
Statistics
Matches: 731, Mismatches: 134, Indels: 77
0.78 0.14 0.08
Matches are distributed among these distances:
339 70 0.10
340 163 0.22
341 198 0.27
342 211 0.29
343 82 0.11
344 6 0.01
345 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.34
Consensus pattern (338 bp):
AAAAATGTAAAAAAATCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATA
AGACTTTTAAAAGAATAGGTGACTATAAATGGAATTCTCCTGCCAAGGAATGACTTTTTCTTCAC
GTTTCTCGAGGTAAGCATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAATCAAGTTAAAA
TCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAACGATTGACAAC
AAAAAGACTTTTTTCTCAATGAATGGCTTTTTCTACACATTCCTCAAGACAGGACTTCAATTATA
ATCAGGTTTAATG
Found at i:2488 original size:170 final size:168
Alignment explanation
Indices: 1147--2632 Score: 934
Period size: 170 Copynumber: 8.7 Consensus size: 168
1137 AATTATGAGC
* * ** *
1147 CTTTTGATGGAAT-GAGTGACTATAAATGGACTTTTCTTACT-AATGAATACCTTTTTGTT-CAT
1 CTTTTGAAGGAATAG-GTGACTATAAATAGACTTTTCTT-CTCAATGAAT-GGTTTTT-TTACAC
* * * * *
1209 ATTTCTCAAGGT-AGACATTTAATTTTAGAT-TGTTTTAACCAAAAATATAAAAAAATTCAACTT
62 GTTTCT-GAGGTAAG-CATTCAATTATAG-TCTGTTTTAACTAAAAATAT-AAAAAATTCAACTT
* ** * ** **
1272 AAAAGCAGCTATAAGATTATAAAATAATTTAAAGTAAGTAATAAGG
123 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
* * *
1318 CTTTTGAAGGAAT-GGTTGACTATAAATAGACTTTTATTCTCAATGAATGGCTTTTTTACATGTT
1 CTTTTGAAGGAATAGG-TGACTATAAATAGACTTTTCTTCTCAATGAATGGTTTTTTTACACGTT
* * * * *
1382 TCCTGAGGCAAGCATTCAATTATAGTTTGTTTTAA-TGAAAATTATAAAAAAATCAAGTTAAAAT
65 T-CTGAGGTAAGCATTCAATTATAGTCTGTTTTAACT-AAAAATATAAAAAATTCAACTTAAAAT
1446 CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
128 CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
* * * * * * * * *
1487 CTTTTAAAAGAATGGGTGACTATAAATAAACTTTTTTTAC-CAATAAATGCCTTTCTCTT-CATG
1 CTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTT-CTCAATGAATG-GTTT-TTTTACACG
* * * * * *
1550 TTTCTTGATGTGAA-CATTCAATTATAATCTATTTTAACAAAAAAAGTAAAAAAAAATTAAACTT
63 TTTC-TGAGGT-AAGCATTCAATTATAGTCTGTTTTAAC-TAAAAA-T-ATAAAAAATTCAACTT
* *
1614 AAAATCAATTTTGAGATTATAAAACCA-TTAAACTCGAGTAATAAGG
123 AAAATCAATTATGAGATTATAAAACCATTTAAA-GCGAGTAATAAGG
* * * ** * ** * *
1660 CTTTTGAAGGAATAGGAGACTACAAATAGA-TTTTTTTAC-CGGTTAATACTTTTTTCATTACGT
1 CTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTT-CTCAATGAATGGTTTTTTTA-CACGT
* * * * * * *
1723 TTCTCAAGTTAGGCATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAATAGTCAA-TCTGAA
64 TTCT-GAGGTAAGCATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAA-ATTCAACT-TAAA
* **
1787 AGCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGG
126 ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
* * * * *
1830 CTTTTGAAGGAAT-GATTGACAATAAAAAGACTTTT-TTCTCAATGAATGGCTTTTTCTACACAT
1 CTTTTGAAGGAATAG-GTGACTATAAATAGACTTTTCTTCTCAATGAATGG-TTTTTTTACACGT
* * * * * *
1893 TTCTCAAG-ACCGGACTTCAATTATAGTCAGTTTTAA-TGAAAAATGTTAAAAAA-TCAACTTAA
64 TTCTGAGGTA-AGCA-TTCAATTATAGTCTGTTTTAACT-AAAAAT-ATAAAAAATTCAACTTAA
* * *
1955 AGTCAATTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGG
125 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
* * * * *
1999 CTTTTGCAGGAATAGGTGACTATAAATGGACTTCTCTTGC-CAATGAAT-GTCTTTTTCTTCATG
1 CTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTT-CTCAATGAATGGT-TTTTT-TACACG
* * * *
2062 TTTCTCGAGGTAGGCATTCAATTATAGTCTGTTTTAACAAAAAATATAGAAAAATCCAAGTTAAA
63 TTTCT-GAGGTAAGCATTCAATTATAGTCTGTTTTAACTAAAAATATA-AAAAATTCAACTTAAA
** * *
2127 ATTTATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGG
126 ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
* * * *******
2170 CTTTTGAAGGAA-CGGTTGACTACAAATGGACTTTTCTTCTCAATGAATGGCTTTTTNNNNNNNN
1 CTTTTGAAGGAATAGG-TGACTATAAATAGACTTTTCTTCTCAATGAATGG-TTTTT-TTACACG
*** * ** * * * * * *
2234 NNCCTAAGACAGGCATTCAATTATAATCCGGTTTAA-TGAAAAATGTAAAAAAATTCAACTTAAN
63 TTTCTGAGGTAAGCATTCAATTATAGTCTGTTTTAACT-AAAAATAT-AAAAAATTCAACTTAAA
********* * *
2298 NNNNNNNNNGAGATTATAAAACCATTTAAAGCGATTAATAAGA
126 ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
* * * * * * * *
2341 TTTTTAAAAGAATAGGTG-CTATAGATGGAATTTTCCTCTCAAGGAATGAGTTTTTTTACACGTT
1 CTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTCTCAATGAATG-GTTTTTTTACACG-T
* * *
2405 TTCTGAGGTAAGCATTCAATTATAATCTGTTTTAACTAAAAATATAAAACAATTCTAGTTAAAAT
64 TTCTGAGGTAAGCATTCAATTATAGTCTGTTTTAACTAAAAATATAAAA-AATTCAACTTAAAAT
* **********
2470 CAATTATGAGATTATAAAACAATNNNNNNNNNNTAATAAGG
128 CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
* * * * * * ** * *
2511 CTTTTGAAGGAATTGATGACTGTAAATGGACTTTTCTTCCCAACGAATAACTTTTTCTACATGTT
1 CTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTCTCAATGAAT-GGTTTTTTTACACGTT
* * * *
2576 TCGTAAGGCAAACATTCAATTATAGTCTGTTTTAA-TGAAAAATGTAAAAAAATTCAA
65 TC-TGAGGTAAGCATTCAATTATAGTCTGTTTTAACT-AAAAATAT-AAAAAATTCAA
2633 NNNNNNNNNN
Statistics
Matches: 1017, Mismatches: 237, Indels: 122
0.74 0.17 0.09
Matches are distributed among these distances:
168 2 0.00
169 188 0.18
170 352 0.35
171 335 0.33
172 65 0.06
173 75 0.07
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.35
Consensus pattern (168 bp):
CTTTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTCTCAATGAATGGTTTTTTTACACGTTT
CTGAGGTAAGCATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAAATTCAACTTAAAATCAA
TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
Found at i:5237 original size:170 final size:171
Alignment explanation
Indices: 4953--5303 Score: 420
Period size: 170 Copynumber: 2.1 Consensus size: 171
4943 NNNNNNNNNN
* * * *
4953 AATCTCATAATTGATTTTAAGTTGAATTTTTTTAAATTTTTGGTTAAAATAGATTGTAATCGAAT
1 AATCTCATAATTGATTTTAAGTTCAATTTTTTCAAATTATTGGTTAAAATAGATTATAATCGAAT
* * * *
5018 GCCTACCCTAAAAAATGTATAGAAAAAGCCATTCATGGAGAATAAAAGTCCATTTCTAGTCACCC
66 GCCTACCCTAAAAAATGTATAGAAAAAGCCATTCATGGACAAGAAAAGTCCATATATAGTCACCC
* * *
5083 ATTCCTCCAAAAGCCTCATTACTCGCTTTAAATTGTTTTTT
131 ATTCCTCCAAAAACCTCATTACTCGCTTTAAATGGTTTTAT
** * * * *
5124 AATCTCATAATTGATTTTAAG-TCAATTTTTTCGTATTATTGGTTAAAGTATATTATAATTGTAT
1 AATCTCATAATTGATTTTAAGTTCAATTTTTTCAAATTATTGGTTAAAATAGATTATAATCGAAT
* * * * * *
5188 GTCTACCTTGAGAAATGTGTAGATAAAAG-CATTCATTGG-CAAGAAAAGTCCATATATAGTCGC
66 GCCTACCCTAAAAAATGTATAGA-AAAAGCCATTCA-TGGACAAGAAAAGTCCATATATAGTCAC
* * * *
5251 CCATTCTTTCAAAAATCTTATTACTCGCTTTAAATGGTTTTAT
129 CCATTCCTCCAAAAACCTCATTACTCGCTTTAAATGGTTTTAT
5294 AATCTCATAA
1 AATCTCATAA
5304 NNNNNNNNNN
Statistics
Matches: 151, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
170 122 0.81
171 29 0.19
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (171 bp):
AATCTCATAATTGATTTTAAGTTCAATTTTTTCAAATTATTGGTTAAAATAGATTATAATCGAAT
GCCTACCCTAAAAAATGTATAGAAAAAGCCATTCATGGACAAGAAAAGTCCATATATAGTCACCC
ATTCCTCCAAAAACCTCATTACTCGCTTTAAATGGTTTTAT
Found at i:6595 original size:172 final size:161
Alignment explanation
Indices: 6382--6725 Score: 340
Period size: 172 Copynumber: 2.1 Consensus size: 161
6372 NNNNNNNNNT
* * *
6382 AAAA-TCAA-TTATGAGATTATAAAACCATTTAAAGTGAGTAATAAACCTTTTGA-TGGAATGGG
1 AAAATTCAACTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTT-ACAGGAATAGG
* * * * *
6444 TGACTATAAAAGGA-GTTTTCTTGCCAATGAATGCT-TTTTTC-TCTACGTTTCCCGAGGTAAAT
65 TGACTATAAAAGGACCTTTT-TTGCCAAT-AATGATCGTTTTCTTC-ACATTTCCCAAGGTAAAT
* *
6506 ATTCAATTATAGTCTATTTTTAACCAAAAATGTAAA
127 ATTCAATTATAGTCTA-TTCTAACAAAAAATGTAAA
**
6542 AAAATTCAACTTNNNNNNNNNNATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAC
1 AAAATTCAACTT----------ATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTTAC
** * * *
6607 AGGAATAGGTGACTATAAGTGGACCTTTTTTGTCAATAATTATCGTTTTCTTCACATTTCTCAAG
56 AGGAATAGGTGACTATAAAAGGACCTTTTTTGCCAATAATGATCGTTTTCTTCACATTTCCCAAG
* *
6672 GTAGATATTCAATTATAGTCTATTCTAACAAAAAATGTAGA
121 GTAAATATTCAATTATAGTCTATTCTAACAAAAAATGTAAA
6713 AAAATTCAACTTA
1 AAAATTCAACTTA
6726 AAATCAATTA
Statistics
Matches: 149, Mismatches: 19, Indels: 31
0.75 0.10 0.16
Matches are distributed among these distances:
160 4 0.03
161 5 0.03
162 2 0.01
171 33 0.22
172 99 0.66
173 6 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (161 bp):
AAAATTCAACTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTTACAGGAATAGGT
GACTATAAAAGGACCTTTTTTGCCAATAATGATCGTTTTCTTCACATTTCCCAAGGTAAATATTC
AATTATAGTCTATTCTAACAAAAAATGTAAA
Found at i:6759 original size:171 final size:171
Alignment explanation
Indices: 6209--7096 Score: 631
Period size: 171 Copynumber: 5.2 Consensus size: 171
6199 NNNNNNNNNN
* *
6209 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATGAGGCTTTTGGAAGAATAGGT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGT
* * * * * *
6274 GACTAGAAATGGACTTTTATT-CTCCATGAATGGCT-TTTTCTACACATTTTTTAGGGTAGACAT
66 GACTATAAATGGACTTTT-TTGC-CAATGAAT-GATGTTTTCTACACATTTCTCAAGGTAGACAT
** * * *************
6337 TTGATTACAGTCTA-TTTTAACTAAAAAT-TNNNNNNNNNNNNNN
128 TCAATTATAGTCTACTTTTAACAAAAAATGT-AAAAAAATTCAAC
* * * ** ** *
6380 NTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAACCTTTTGATGGAATGGGT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGT
* * * * * * * * *
6445 GACTATAAAAGGAGTTTTCTTGCCAATGAATGCTTTTTTCT-CTACGTTTCCCGAGGTAAATATT
66 GACTATAAATGGACTTTT-TTGCCAATGAATGATGTTTTCTAC-ACATTTCTCAAGGTAGACATT
* *
6509 CAATTATAGTCTATTTTTAACCAAAAATGTAAAAAAATTCAAC
129 CAATTATAGTCTACTTTTAACAAAAAATGTAAAAAAATTCAAC
********** * *
6552 TTNNNNNNNNNNATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-ACAGGAATAGG
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGA-AAGAATAGG
* * * * *
6616 TGACTATAAGTGGACCTTTTTTGTCAAT-AATTATCGTTTTCTTCACATTTCTCAAGGTAGATAT
65 TGACTATAAATGGA-CTTTTTTGCCAATGAATGAT-GTTTTCTACACATTTCTCAAGGTAGACAT
* *
6680 TCAATTATAGTCTA-TTCTAACAAAAAATGTAGAAAAATTCAAC
128 TCAATTATAGTCTACTTTTAACAAAAAATGTAAAAAAATTCAAC
* * * *
6723 TTAAAATCAATTATGAGATTATAGAACAATTTAAAGCGAGAAATAAGGCTTTTGAAAAAAT-GAT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAG-G
* * **
6787 TGACTATAAATGGACTTTGTTT-CTCAATGAATGGTTTTTTCTACACATTTCTTGAGGTA-AGCA
65 TGACTATAAATGGACTTT-TTTGC-CAATGAATGATGTTTTCTACACATTTCTCAAGGTAGA-CA
** ** *****
6850 TTCAATTATAGT-TTGTTTTAATGAAAAATGTAAAAAAATNNNNN
127 TTCAATTATAGTCTACTTTTAACAAAAAATGTAAAAAAATTCAAC
***** * * * **
6894 NNNNNATCAATTATGAGATTATAAAACTATGTAAAGTGAGTAATAAGATTTTTGAAAGAATAGGT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGT
* * ** * *
6959 GACTATAAATGGACTTTTTTTGCCAATGAATGCT-TTATCTACATGTTTCTCAAGCTAGACATAC
66 GACTATAAATGGAC-TTTTTTGCCAATGAATGATGTTTTCTACACATTTCTCAAGGTAGACATTC
* *
7023 AATTATAATCTAC-TTTAACCAATAAAATG--AAAAAATT-GAC
130 AATTATAGTCTACTTTTAA-CAA-AAAATGTAAAAAAATTCAAC
7063 TTAAAATCAATTATGAGATTATAAAACAATTTAA
1 TTAAAATCAATTATGAGATTATAAAACAATTTAA
Statistics
Matches: 551, Mismatches: 143, Indels: 48
0.74 0.19 0.06
Matches are distributed among these distances:
169 27 0.05
170 52 0.09
171 335 0.61
172 131 0.24
173 6 0.01
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.34
Consensus pattern (171 bp):
TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGT
GACTATAAATGGACTTTTTTGCCAATGAATGATGTTTTCTACACATTTCTCAAGGTAGACATTCA
ATTATAGTCTACTTTTAACAAAAAATGTAAAAAAATTCAAC
Done.