Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399993.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3219.0, 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: 7482
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.27
Warning! 2258 characters in sequence are not A, C, G, or T
Found at i:1413 original size:173 final size:171
Alignment explanation
Indices: 728--2114 Score: 755
Period size: 171 Copynumber: 8.1 Consensus size: 171
718 NNNNNNNNNN
* * * * * *
728 GTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTTAATGGTTTTATAATCTTATAATTGATTT
1 GTCACCCATGCCTTCAAAAGTCGTATTACTCGCTTTAAATGATTTTATAATCTCATAATTGATTT
* * * * * *
793 TAGGTTGAA-TTGTTTTACATTTTTTGTTAGAACAGATTATAATTGAATGTTTTCCTTCGA-AAA
66 TAGGTTGAATTTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGAATGTCTACC-TCGAGAAA
* **********
856 CGTGAAGAAAAAGATATTCATTGACNNNNNNNNNNTATTTATA
130 CGTGAAGAAAAAGATATCCATTGAC-AGAAAAATCCATTTATA
* ** * * * ** * *
899 GTCACCCATTCCTTCAAAAACCTTACTATTTACTTTAAATGGTTTTATAACCTCATAATTGATTT
1 GTCACCCATGCCTTCAAAAGTCGTATTACTCGCTTTAAATGATTTTATAATCTCATAATTGATTT
* * * * * * * * *
964 TAGATTGAA-GTTTTTTACATTTTTAGTTAGAACATATTATAATTGAATGTCTGCCTTGGGAAAC
66 TAGGTTGAATTTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGAATGTCTACCTCGAGAAAC
* * * * * *
1028 ATGAA-AAGAAAGGTATTCATTGGCAAGAAAAGTCCATTTATNN
131 GTGAAGAA-AAAGATATCCATTGAC-AGAAAAATCCATTTAT-A
******** * * * * * * *
1071 NNNNNNNNT-CCTT-AAAAATCCTTATTACTCACTTCAAATGGTTTTATAATCTCATAACTGGTT
1 GTCACCCATGCCTTCAAAAGT-CGTATTACTCGCTTTAAATGATTTTATAATCTCATAATTGATT
* * ** * * * * * *
1134 TTAGATTGAA-TTTGTTTACATTTTTTATTAGAATAGTTTATAATTGAATGTTTGCC-CTAGTAA
65 TTAGGTTGAATTTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGAATGTCTACCTCGAG-AA
* * * ** *
1197 ATGTGAAGAGAAAGGTATTTATTGGTA-AGAAAAATCTATTTATA
129 ACGTGAAGAAAAAGATATCCATT-G-ACAGAAAAATCCATTTATA
* * * * *
1241 GCCACCTATTCCTTCAAAAGTCGTATTACTCGCTTTAAAT-AGTTTTATAATATCAAAATTGATT
1 GTCACCCATGCCTTCAAAAGTCGTATTACTCGCTTTAAATGA-TTTTATAATCTCATAATTGATT
* * * * * * *
1305 TTAGGTTCAATTTTTTTTTACATTTTTGGTTAAGATAGATTATAATTGAATGTTTATCTCAAAAA
65 TTAGGTTGAA-TTTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGAATGTCTACCTCGAGAA
* *
1370 ACGTGAAGAAAAAGAAATCCATTGACAGGAAAAGTCCATTTATA
129 ACGTGAAGAAAAAGATATCCATTGACA-GAAAAATCCATTTATA
* *********** * *
1414 GTCACCCATGTCTTCGNNNNNNNNNNTACTCGCTTTAAATGATTTTATAACCTCTTAATTGATTT
1 GTCACCCATGCCTTCAAAAGTCGTATTACTCGCTTTAAATGATTTTATAATCTCATAATTGATTT
** * * ** *
1479 TAAATTGAA-TTTTTTTACATTTTTGATTAAAACAGATTATAATTGAATACCTACCTGGAGAAAC
66 TAGGTTGAATTTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGAATGTCTACCTCGAGAAAC
* * * *
1543 ATGAAGAAAAAGATATCCATTGACACGAAAAGTTCATTTACA
131 GTGAAGAAAAAGATATCCATTGACA-GAAAAATCCATTTATA
* * * * *
1585 GTCTCCCACGCCTCCAAAAGTCTTATTACTCGCCTTAAATGATTTTATAATCTCATAATTGATTT
1 GTCACCCATGCCTTCAAAAGTCGTATTACTCGCTTTAAATGATTTTATAATCTCATAATTGATTT
* * * * * *
1650 TAGGTTGAATATTTTTT--ATTTTTAGTTAAAAAAGATAATAATTAAATGTCTGCCTTGAGAAAC
66 TAGGTTGAATTTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGAATGTCTACCTCGAGAAAC
* * * * * *
1713 GT-AAAAAAATAGATATTCATAGATAAAAAAACCCATTTATA
131 GTGAAGAAAA-AGATATCCATTGACAGAAAAATCCATTTATA
* *
1754 GTCACCCATGCCTTTAAAAATCGTATTACTCGCTTTAAAT-AGTTTTATAATCTCATAATTGATT
1 GTCACCCATGCCTTCAAAAGTCGTATTACTCGCTTTAAATGA-TTTTATAATCTCATAATTGATT
* * ** * * * ** * * * * * * *
1818 TCAAGCCGAA-TTGTTTTGCACTTTTAATTAAAACACATAATAACTGAATGTTTGCCT-AAGGAA
65 TTAGGTTGAATTTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGAATGTCTACCTCGA-GAA
* * ** * * *
1881 ACCTAAAGAAAAAGCCATTCATTGACAAGAAAAGTCTATTTATA
129 ACGTGAAGAAAAAGATATCCATTGAC-AGAAAAATCCATTTATA
* * * * * * * * * * * *
1925 ATCACTCATGCCTTCAAAAGCCTTATT-TTGTGCCTAAAATGTTTTTAAAATCTCGTAATTAATT
1 GTCACCCATGCCTTCAAAAGTCGTATTACT-CGCTTTAAATGATTTTATAATCTCATAATTGATT
** * * * * * *
1989 TTAACTTGAATTTTTTCT-CATTTTTGGTTAAAATAA-ATAATAATTGAATGTTTGCCTTGGGAA
65 TTAGGTTGAATTTTTTTTACATTTTTGGTTAAAA-AAGATTATAATTGAATGTCTACCTCGAGAA
* * * * * *
2052 ACATGAAGAAAAA-AAATTCATTGGCAAGAAAAGTCCATGTATA
129 ACGTGAAGAAAAAGATATCCATTGAC-AGAAAAATCCATTTATA
* *
2095 GTCACCCATACCTTCGAAAG
1 GTCACCCATGCCTTCAAAAG
2115 CCTTATNNNN
Statistics
Matches: 936, Mismatches: 250, Indels: 61
0.75 0.20 0.05
Matches are distributed among these distances:
168 6 0.01
169 79 0.08
170 150 0.16
171 555 0.59
172 22 0.02
173 121 0.13
174 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.37
Consensus pattern (171 bp):
GTCACCCATGCCTTCAAAAGTCGTATTACTCGCTTTAAATGATTTTATAATCTCATAATTGATTT
TAGGTTGAATTTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGAATGTCTACCTCGAGAAAC
GTGAAGAAAAAGATATCCATTGACAGAAAAATCCATTTATA
Found at i:1805 original size:169 final size:170
Alignment explanation
Indices: 1440--1818 Score: 426
Period size: 169 Copynumber: 2.2 Consensus size: 170
1430 NNNNNNNNNN
* *
1440 TACTCGCTTTAAATGATTTTATAACCTCTTAATTGATTTTAAATTGAATTTTTTTACATTTTTGA
1 TACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAATTGAATTTTTTTA-ATTTTTGA
* * * * * *
1505 TTAAAACAGATTATAATTGAATACCTACCTGGAGAAACATGAAGAAAAAGATATCCATTGACACG
65 TTAAAAAAGATAATAATTAAATACCTACCTGGAGAAACATGAAAAAAAAGATATCCATAGACACA
*** * * *
1570 AAAAGTTCATTTACAGTCTCCCACGCCTCCAAAAGTCTTAT
130 AAAAACCCATTTACAGTCACCCACGCCTCCAAAAATCGTAT
* **
1611 TACTCGCCTTAAATGATTTTATAATCTCATAATTGATTTTAGGTTGAATATTTTTT-ATTTTT-A
1 TACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAATTGAAT-TTTTTTAATTTTTGA
** * * * * *
1674 GTTAAAAAAGATAATAATTAAATGTCTGCCTTGAGAAACGT-AAAAAAATAGATATTCATAGATA
65 -TTAAAAAAGATAATAATTAAATACCTACCTGGAGAAACATGAAAAAAA-AGATATCCATAGACA
* * **
1738 -AAAAAACCCATTTATAGTCACCCATGCCTTTAAAAATCGTAT
128 CAAAAAACCCATTTACAGTCACCCACGCCTCCAAAAATCGTAT
1780 TACTCGCTTTAAAT-AGTTTTATAATCTCATAATTGATTT
1 TACTCGCTTTAAATGA-TTTTATAATCTCATAATTGATTT
1819 CAAGCCGAAT
Statistics
Matches: 175, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
168 1 0.01
169 74 0.42
170 50 0.29
171 44 0.25
172 6 0.03
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (170 bp):
TACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAATTGAATTTTTTTAATTTTTGAT
TAAAAAAGATAATAATTAAATACCTACCTGGAGAAACATGAAAAAAAAGATATCCATAGACACAA
AAAACCCATTTACAGTCACCCACGCCTCCAAAAATCGTAT
Found at i:1850 original size:340 final size:341
Alignment explanation
Indices: 1440--2053 Score: 729
Period size: 340 Copynumber: 1.8 Consensus size: 341
1430 NNNNNNNNNN
* * ** * * *
1440 TACTCGCTTTAAATGATTTTATAACCTCTTAATTGATTTTAAATTGAATTTTTTTACATTTTTGA
1 TACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTCAAACCGAATTGTTTTACACTTTTAA
* * * * * * *
1505 TTAAAACAGATTATAATTGAATACCTACCT-GGAGAAACATGAAGAAAAAGATATCCATTGACAC
66 TTAAAACACATAATAACTGAATACCTACCTAAG-GAAACATAAAGAAAAAGACATCCATTGACAA
* * * *
1569 GAAAAGT-TCATTTACAGTCTCCCACGCCTCCAAAAGTCTTATTACT-CGCCTTAAATGATTTTA
130 GAAAAGTCT-ATTTACAATCACCCACGCCTCCAAAAGCCTTATT-CTGCGCCTAAAATGATTTTA
* * **
1632 TAATCTCATAATTGATTTTAGGTTGAATATTTTT-T-ATTTTTAGTTAAAA-AAGATAATAATTA
193 AAATCTCATAATTAATTTTAACTTGAAT-TTTTTCTCATTTTTAGTTAAAATAA-ATAATAATTA
1694 AATGTCTGCCTTGAGAAACGTAAAAAAATAGATATTCATAGATAAAAAAACCCATTTATAGTCAC
256 AATGTCTGCCTTGAGAAACGTAAAAAAATAGATATTCATAGATAAAAAAACCCATTTATAGTCAC
1759 CCATGCCTTTAAAAATCGTAT
321 CCATGCCTTTAAAAATCGTAT
* * *
1780 TACTCGCTTTAAAT-AGTTTTATAATCTCATAATTGATTTCAAGCCGAATTGTTTTGCACTTTTA
1 TACTCGCTTTAAATGA-TTTTATAACCTCATAATTGATTTCAAACCGAATTGTTTTACACTTTTA
*** * * * *
1844 ATTAAAACACATAATAACTGAATGTTTGCCTAAGGAAACCTAAAGAAAAAGCCATTCATTGACAA
65 ATTAAAACACATAATAACTGAATACCTACCTAAGGAAACATAAAGAAAAAGACATCCATTGACAA
* * * * * * *
1909 GAAAAGTCTATTTATAATCACTCATGCCTTCAAAAGCCTTATTTTGTGCCTAAAATGTTTTTAAA
130 GAAAAGTCTATTTACAATCACCCACGCCTCCAAAAGCCTTATTCTGCGCCTAAAATGATTTTAAA
* * *
1974 ATCTCGTAATTAATTTTAACTTGAATTTTTTCTCATTTTTGGTTAAAATAAATAATAATTGAATG
195 ATCTCATAATTAATTTTAACTTGAATTTTTTCTCATTTTTAGTTAAAATAAATAATAATTAAATG
* *
2039 TTTGCCTTGGGAAAC
260 TCTGCCTTGAGAAAC
2054 ATGAAGAAAA
Statistics
Matches: 223, Mismatches: 44, Indels: 13
0.80 0.16 0.05
Matches are distributed among these distances:
339 7 0.03
340 173 0.78
341 41 0.18
342 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (341 bp):
TACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTCAAACCGAATTGTTTTACACTTTTAA
TTAAAACACATAATAACTGAATACCTACCTAAGGAAACATAAAGAAAAAGACATCCATTGACAAG
AAAAGTCTATTTACAATCACCCACGCCTCCAAAAGCCTTATTCTGCGCCTAAAATGATTTTAAAA
TCTCATAATTAATTTTAACTTGAATTTTTTCTCATTTTTAGTTAAAATAAATAATAATTAAATGT
CTGCCTTGAGAAACGTAAAAAAATAGATATTCATAGATAAAAAAACCCATTTATAGTCACCCATG
CCTTTAAAAATCGTAT
Found at i:2575 original size:173 final size:171
Alignment explanation
Indices: 2278--2590 Score: 443
Period size: 173 Copynumber: 1.8 Consensus size: 171
2268 NNNNNNNNNN
** *
2278 AAATGATTTTATAATCTCATAATTGATTTTATGTTGAATTTTTTTATATGTTTTATTAAAACAGA
1 AAATGATTTTATAATCTCATAATTGATTTTAAATTGAATTTTTTTACATGTTTTATTAAAACAGA
* * *
2343 TTATAATTGAATATGTACATCAGGAAACATGAAGCAAAAGATATCCATTGGTAAGAAAAGTCCAT
66 TTATAATTGAATATCTACATCAGGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCAT
2408 TTATAGTCACCCATGACTTTAAAAACCTTATTAGTCGCTTT
131 TTATAGTCACCCATGACTTTAAAAACCTTATTAGTCGCTTT
* *
2449 AAAT-ATTTTAATAATCTCATAGTTGATTTTGAAATTGAATTTTTTTTACAT-TTTTGGTTAAAA
1 AAATGATTTT-ATAATCTCATAATTGATTTT-AAATTGAA-TTTTTTTACATGTTTT-ATTAAAA
* * * * *
2512 CAGA-TACTTATTGAATGTCTGCCTCAGGAAACATGAAGAAAAAGGTATCCATTGGCAAGAAAAG
62 CAGATTA-TAATTGAATATCTACATCAGGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAG
2576 TCCATTTATAGTCAC
126 TCCATTTATAGTCAC
2591 TCANNNNNNN
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
170 5 0.04
171 23 0.19
172 12 0.10
173 84 0.68
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (171 bp):
AAATGATTTTATAATCTCATAATTGATTTTAAATTGAATTTTTTTACATGTTTTATTAAAACAGA
TTATAATTGAATATCTACATCAGGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCAT
TTATAGTCACCCATGACTTTAAAAACCTTATTAGTCGCTTT
Found at i:3738 original size:171 final size:171
Alignment explanation
Indices: 3448--3814 Score: 563
Period size: 171 Copynumber: 2.1 Consensus size: 171
3438 NNNNNNNNNN
* * *
3448 CAAAAGCCTTATTACTCGCTTTAAATGCTTTTATAATCTTATAATTGATTTTAAATTGAATTTTT
1 CAAAAGCCTTATTACTCGCTTTAAATACTTTTATAATCTTATAATTGATTTTAAACTAAATTTTT
** * *
3513 TTACGTTTTTGGTTAAAACAGAAAATTATTGAATGTCTGCCTCAGGAAACATGAAGAAAAAGATA
66 TTACGTTTTCAGTTAAAACAGAAAATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAGATA
* * * *
3578 TCTCTTGGCAAGAAAAGTCCATTTATATTCACCCATGACTT
131 TCTATCGGCAACAAAAGTCCATTTATAGTCACCCATGACTT
* * * *
3619 CAAAGGCCTTATTACTCACTTTAAATATTTTTATAATCTTATAATTTATTTTAAACTAAATTTTT
1 CAAAAGCCTTATTACTCGCTTTAAATACTTTTATAATCTTATAATTGATTTTAAACTAAATTTTT
* *
3684 TTACGTTTTCAGTTAAAACAGATAATAATTGAATGTTTACCTCAGGAAACATGAAGAAAAAGATA
66 TTACGTTTTCAGTTAAAACAGAAAATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAGATA
* *
3749 TTTATCGGTAACAAAAGTCCATTTATAGTCACCCATGACTT
131 TCTATCGGCAACAAAAGTCCATTTATAGTCACCCATGACTT
3790 CAAAAGCCTTATTACTCGCTTTAAA
1 CAAAAGCCTTATTACTCGCTTTAAA
3815 NNNNNNNNNN
Statistics
Matches: 175, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
171 175 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (171 bp):
CAAAAGCCTTATTACTCGCTTTAAATACTTTTATAATCTTATAATTGATTTTAAACTAAATTTTT
TTACGTTTTCAGTTAAAACAGAAAATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAGATA
TCTATCGGCAACAAAAGTCCATTTATAGTCACCCATGACTT
Found at i:4865 original size:140 final size:140
Alignment explanation
Indices: 4581--4867 Score: 314
Period size: 140 Copynumber: 2.0 Consensus size: 140
4571 TATCTATTGG
* * * * *
4581 CAAGAAAAGTCCATGTCTAGTCACCCATGCCTTCGAAATCCTTATTACTCGCTTTAAATAGTTTT
1 CAAGAAAAGTCCATGTATAGTCACCCATGACTTCGAAAGCCTTATTACTCACTTTAAATAGTTTA
* ** * * * * *
4646 ATAATCCTATAATTGATTTTGTACTGAATGTTTTTATGTTTTTTATTAGAATAGATTATAATTGC
66 ATAATCCTATAATTGACTTTAAACTGAATGTTTTTATGTTTTCTATTAAAACAGATAATAATTGA
*
4711 ATGTCTACCT
131 ATGTCTACCC
* *
4721 CAAGAAAAGTTCATTTATAGTCACCCATGACTTC-ACAAGCCTTATTACTCACTTTAAAT-GTAT
1 CAAGAAAAGTCCATGTATAGTCACCCATGACTTCGA-AAGCCTTATTACTCACTTTAAATAGT-T
* *
4784 TAATAAT-CTCATAATTGACTTTAAATTGAAT-TCTTTTATG-TTTCTAGTTAAAACAGATAATT
64 TAATAATCCT-ATAATTGACTTTAAACTGAATGT-TTTTATGTTTTCTA-TTAAAACAGATAATA
* *
4846 ATTGAATGTTTGCCC
126 ATTGAATGTCTACCC
4861 CAAGAAA
1 CAAGAAA
4868 CATGAAGAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
139 11 0.09
140 111 0.91
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (140 bp):
CAAGAAAAGTCCATGTATAGTCACCCATGACTTCGAAAGCCTTATTACTCACTTTAAATAGTTTA
ATAATCCTATAATTGACTTTAAACTGAATGTTTTTATGTTTTCTATTAAAACAGATAATAATTGA
ATGTCTACCC
Found at i:5007 original size:171 final size:170
Alignment explanation
Indices: 4722--5120 Score: 476
Period size: 171 Copynumber: 2.3 Consensus size: 170
4712 TGTCTACCTC
* * *
4722 AAGAAAAGTTCATTTATAGTCACCCATGACTTCACAAGCCTTATTACTCACTTTAAATGTATTAA
1 AAGAAAAGTCCATTTATAGTCACCCATGACTTCA-AAGCCTTATTACTCGCTTTAAATATATTAA
** *
4787 TAATCTCATAATTGACTTTAAATTGAATTCTTTTATGTTTCTAGTTAAAACAGATAATTATTGAA
65 TAATCTCATAATTGACTTTAAATTGAATTCTTTTACATTTCTAGTTAAAACAGATAATAATTGAA
* * * **
4852 TGTTTGCCCCAA-GAAACATGAAGAAAAAGATACCCATTGGT
130 TATCTG-CCAAAGGAAACATGAAGAAAAAGATACCCATCAGT
* ** * *
4893 AAGAAAAATCCATTTATAGTCATTCATGACTTCAAAGGCCTTATTACTCGCTTTAAATATTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATGACTTCAAA-GCCTTATTACTCGCTTTAAATATATTAA
* *** * * * *
4958 TAATCTCTTAATTTTTTTTCAATTGAATTTTTTTACATTTTTAGTTAAAATAGATAATAATTGAA
65 TAATCTCATAATTGACTTTAAATTGAATTCTTTTACATTTCTAGTTAAAACAGATAATAATTGAA
**
5023 TATCTGCCAAAGGAAACATGAAGAAAAAGATATTCATCAGT
130 TATCTGCCAAAGGAAACATGAAGAAAAAGATACCCATCAGT
* * * * *
5064 AACAAAAGCCCATTTATAGTTACCCATGCCTTTGAAAGCCTTATTACTCGCTTTAAA
1 AAGAAAAGTCCATTTATAGTCACCCATGAC-TTCAAAGCCTTATTACTCGCTTTAAA
5121 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
170 6 0.03
171 180 0.94
172 5 0.03
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (170 bp):
AAGAAAAGTCCATTTATAGTCACCCATGACTTCAAAGCCTTATTACTCGCTTTAAATATATTAAT
AATCTCATAATTGACTTTAAATTGAATTCTTTTACATTTCTAGTTAAAACAGATAATAATTGAAT
ATCTGCCAAAGGAAACATGAAGAAAAAGATACCCATCAGT
Found at i:5012 original size:311 final size:310
Alignment explanation
Indices: 4415--5020 Score: 684
Period size: 311 Copynumber: 2.0 Consensus size: 310
4405 CATTGGTAAA
* ** * * *
4415 AAAAGTCCATTTATAATCACCCATGTCTTCAAAAGCCTTATTTTGTGACTAAAATGTTTTTAAAT
1 AAAAGTCCATTTATAATCACCCATGACTTCAAAAGCCTTATTTACTCACTAAAATGTATTAAAAT
* * * * * * *
4480 CTCGTAATTGATTTTAACTTGAGTTTTTATACATTTTTTGTTAAAACTAATAACAATTGACTGTT
66 CTCATAATTGACTTTAAATTGAATTTTTATACATTTCTAGTTAAAACTAATAACAATTGAATGTT
* * ** * * * *
4545 TGCCCTAGGAAATGTGAAGAAAAAAATATCTATTGGCAAGAAAAGTCCATGTCTAGTCACCCATG
131 TGCCCCAAGAAACATGAAGAAAAAAATACCCATTGGCAAGAAAAATCCATGTATAGTCACCCATG
* * **
4610 CCTTCGAAATCCTTATTACTCGCTTTAAATAGTTTTATAATCCTATAATTGATTTTGTACTGAAT
196 ACTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCCTATAATTGATTTTCAACTGAAT
** * *
4675 GTTTTTATGTTTTTTATTAGAATAGATTATAATTGCATGTCTACCTCAAG
261 GTTTTTATCATTTTTATTAAAATAGATAATAATTGCATGTCTACCTCAAG
* * * *
4725 AAAAGTTCATTTATAGTCACCCATGACTTCACAAGCCTTA-TTACTCACTTTAAATGTATTAATA
1 AAAAGTCCATTTATAATCACCCATGACTTCAAAAGCCTTATTTACTCAC-TAAAATGTATTAA-A
** **
4789 ATCTCATAATTGACTTTAAATTGAATTCTTT-TATGTTTCTAGTTAAAAC-AGATAATTATTGAA
64 ATCTCATAATTGACTTTAAATTGAATT-TTTATACATTTCTAGTTAAAACTA-ATAACAATTGAA
* * * **
4852 TGTTTGCCCCAAGAAACATGAAGAAAAAGATACCCATTGGTAAGAAAAATCCATTTATAGTCATT
127 TGTTTGCCCCAAGAAACATGAAGAAAAAAATACCCATTGGCAAGAAAAATCCATGTATAGTCACC
* **
4917 CATGACTTC-AAAGGCCTTATTACTCGCTTTAAATATTTTTATAATCTCT-TAATTTTTTTTCAA
192 CATGACTTCGAAA-GCCTTATTACTCGCTTTAAATAGTTTTATAATC-CTATAATTGATTTTCAA
* *
4980 TTGAATTTTTTTA-CATTTTTAGTTAAAATAGATAATAATTG
255 CTGAATGTTTTTATCATTTTTA-TTAAAATAGATAATAATTG
5021 AATATCTGCC
Statistics
Matches: 242, Mismatches: 47, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
309 5 0.02
310 56 0.23
311 176 0.73
312 5 0.02
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (310 bp):
AAAAGTCCATTTATAATCACCCATGACTTCAAAAGCCTTATTTACTCACTAAAATGTATTAAAAT
CTCATAATTGACTTTAAATTGAATTTTTATACATTTCTAGTTAAAACTAATAACAATTGAATGTT
TGCCCCAAGAAACATGAAGAAAAAAATACCCATTGGCAAGAAAAATCCATGTATAGTCACCCATG
ACTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCCTATAATTGATTTTCAACTGAAT
GTTTTTATCATTTTTATTAAAATAGATAATAATTGCATGTCTACCTCAAG
Found at i:7209 original size:171 final size:169
Alignment explanation
Indices: 6895--7482 Score: 558
Period size: 171 Copynumber: 3.4 Consensus size: 169
6885 TTGTCTTGGA
* * * * *
6895 AAACATGAAGAAAAAGATATACATTGACAAGAAAAGTCCATGTCTATTCACCCACGCCTTCGAAA
1 AAACATGAAGAAAAAGATATACATTGACAAGAAAAGTCCATTTATATTCACCCATGACTTCAAAA
* * * *
6960 TCTTTATTACTCGCTTTAAATTGTTCTATAATC-CTATAATTGA-TTTTATGTTGAATTTTTTTA
66 GCCTTATTACTCGCTTTAAA-TGTTTTATAATCTC-ATAATTGATTTTTA-ATTGAA-TTTTTT-
** * ********** *
7023 TATTTTTTA-TTAAAATAGATTATAANNNNNNNNNNACCTCAGG
126 TACGTTTTAGTTAAAATAGATAATAATTGAATGTCTACCTCAAG
* * * *
7066 AAACATGAAGAAAAAGATATGCATTGCCAAGAAAGGTCCATTTATAGTCACCCATGACTTCAAAA
1 AAACATGAAGAAAAAGATATACATTGACAAGAAAAGTCCATTTATATTCACCCATGACTTCAAAA
*
7131 GCCTTATTACTCGCTTCAAATGCTTTTATAATCTCATAATTGATTTTTAATTGAATTTTTTTACG
66 GCCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAATTGATTTTTAATTGAATTTTTTTACG
* * * *
7196 TCTTTGGTTAAAATAGAAAATTATTGAATGTCTGCCTCAAG
130 T-TTTAGTTAAAATAGATAATAATTGAATGTCTACCTCAAG
* * * *
7237 AAACATGAAGAAAAAGATGTCCATTGACAAGAAAAGTCCATTTATATTCACCTATGACTTCAAAG
1 AAACATGAAGAAAAAGATATACATTGACAAGAAAAGTCCATTTATATTCACCCATGACTTCAAAA
* * *
7302 GCCTTATTACTCACTTTAAATGTTTTTATAATCTCATAACTT-ATTTTAAATT-AAATTTTTTAC
66 GCCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAA-TTGATTTTTAATTGAATTTTTTTAC
* * *
7365 GTTTTCAGTTAAAACAGATAATAATTGAATGT-TCGCCTTAAG
129 GTTTT-AGTTAAAATAGATAATAATTGAATGTCT-ACCTCAAG
** * ** * * * * **
7407 AAACATGAAGAAAAAGATATTTATCGGTAATAAAAGCCCATTTATAGTCACCCATGCCTTTGAAA
1 AAACATGAAGAAAAAGATATACATTGACAAGAAAAGTCCATTTATATTCACCCATGACTTCAAAA
7472 GCCTTATTACT
66 GCCTTATTACT
Statistics
Matches: 346, Mismatches: 63, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
169 7 0.02
170 114 0.33
171 217 0.63
172 8 0.02
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.35
Consensus pattern (169 bp):
AAACATGAAGAAAAAGATATACATTGACAAGAAAAGTCCATTTATATTCACCCATGACTTCAAAA
GCCTTATTACTCGCTTTAAATGTTTTATAATCTCATAATTGATTTTTAATTGAATTTTTTTACGT
TTTAGTTAAAATAGATAATAATTGAATGTCTACCTCAAG
Done.