Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399508.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2768.0, 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: 7015
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.30
Warning! 1256 characters in sequence are not A, C, G, or T
Found at i:967 original size:171 final size:169
Alignment explanation
Indices: 218--1923 Score: 892
Period size: 172 Copynumber: 10.0 Consensus size: 169
208 NNNNNNNNNN
* * * * **
218 GAGAATATAAAACCATTTAAAGCGAGTGATAAGCCTTTTGAAGGAAT-GAGTGACTATAAATAAA
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAG-GTGACTATAAATGGA
*** ** * * * *
282 CTTTT-TTGCCAATGAATTCCTTTTGGTTCATGTTTCTCT-AGATAGACATTAAATTATAGTTTG
65 CTTTTCTTGCCAATGAA-AGATTTTCTTTCATG-TTCT-TGAGGTAGACATTCAATTATAGTCTA
* * * * * **
345 TTTTAACCAAAAA-AGGAAAAACATTTATCTTAAAATCTGTTAT
127 TTTTAACTAAAAATA-TAAAAAAATTCAACTTAAAATCAATTAT
* * * * *
388 GAGATTATAAAATCATTTAAAGCGAGAAATAAGCCTTTCT-AAGGAATGGGTGACTATAAATGGA
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTT-TGAAGGAATAGGTGACTATAAATGG-
* * * * * * ** * *
452 ATTTTTCTTGACAATGTATA-TTTTTTTCTTCACGTTTCTCAAGGTACACGTTCAATTACT-GTC
64 ACTTTTCTTGCCAATG-AAAGATTTTCT-TTCATG-TTCTTGAGGTAGACATTCAATTA-TAGTC
* * * * * *
515 TGTTTTAACCAAAAGTGTAAAAAAATTTAACTTAAAATCAGTTAT
125 TATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTAT
* ** * * * * *
560 GAGATTATAAAACTATTTGGAGCGAGTAATAAGGTTTTTGAAGGAATTGGTAACTATAAATAGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
* * * * * * * * * *
625 TTTTTTTTGCCAATGAATGCCTTTT-TCTTCATGTTTCTTGAAGTAGATATTTAGTTATAATTTG
66 -TTTTCTTGCCAATGAAAG-ATTTTCT-TTCATG-TTCTTGAGGTAGACATTCAATTATAGTCTA
* * * *
689 TTTTAA-TCAAAAAAAGTAAAGAAATTGAACTTAAAATCAATTTT
127 TTTTAACT-AAAAATA-TAAAAAAATTCAACTTAAAATCAATTAT
********** * * * *
733 GAGATTATAAANNNNNNNNNNGTGAGTAATAAGGCTTTTAAAGGTAT-GGATGACTAT-AATGGA
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAGG-TGACTATAAATGGA
* * * *
796 CTTTTCTTGCCAATGAAAGAGTTTTGTTTCATGCTTCTTGAGGTAGACATTCAATCATTGTCTGT
65 CTTTTCTTGCCAATGAAAGA-TTTTCTTTCATG-TTCTTGAGGTAGACATTCAATTATAGTCTAT
* *
861 TTTAACTAAAAATATAAAAAAATTCAACTTTAAATCAGTTAT
128 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTAT
* * * * * * *
903 GAGATTATAAAACTATTTAAAGCAAATAACAAAGCTTTTTAAGAAATTGGTGACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
* * * *
968 TTTTCTT-CTTAATGAATAGATTTT-TCTACATGTT-TTCCAAGGTA-AGCATTCAACTATAGTC
66 TTTTCTTGC-CAATGAA-AGATTTTCT-TTCATGTTCTT--GAGGTAGA-CATTCAATTATAGTC
*********
1029 TATTTTAA-TGAAAAATATNNNNNNNNNNCAACTTAAAATCAATTAT
125 TATTTTAACT-AAAAATAT-AAAAAAATTCAACTTAAAATCAATTAT
* * * ** *
1075 GAGATTGTAAAACAATTTAAAACGAGTAATGAGGCTTTTGAAGGAATAGGTGACTATAAATGGAG
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
* * * * * *
1140 TTTTGTTGCAAATGAATAGCTTTTTCTAT-ATGTTTCATGAGGCA-ACAATTCAATTATAGTCTA
66 TTTTCTTGCCAATGAA-AG-ATTTTCTTTCATG-TTCTTGAGGTAGAC-ATTCAATTATAGTCTA
* *
1203 TTTTAA-TCAAAAATATGAAAGCAAATTCAACTT-AAATACAACTAT
127 TTTTAACT-AAAAATAT-AAA-AAAATTCAACTTAAAAT-CAATTAT
* * * * *
1248 GAGATTATAAAACTATTTAAAGAGAGTAATAAGCCTTTTGAAGGAATGGGGTGACTATAAATGGA
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAAT-AGGTGACTATAAATGGA
*** *
1313 CTTTTCTTGGCCCAATTGAATCCCTTTTCTTT-ATG----T---GTAGACATTCAATTATAGTTT
65 CTTTTCTT-G-CCAA-TGAA-AGATTTTCTTTCATGTTCTTGAGGTAGACATTCAATTATAGTCT
* * * * *
1370 GTTTTAACTAAAAATGTAAAAACATTCAACTTGAAATCAGTTAT
126 ATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTAT
* * * * * * * *
1414 GAGGTTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGATGGAATGGGCGACTACAAATAGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
******** * * * *
1479 TTTTCTTGCCAATGANNNNNNNNNNCTTCACAT-TTCTTGAGGTAGACATTTAATTATTGTCTCT
66 TTTTCTTGCCAATGA--AAGATTTTCTT-TCATGTTCTTGAGGTAGACATTCAATTATAGTCTAT
* *
1543 TTTAACTAAAATTGTAAAAAAATTCAACTTAAAATCAATTAT
128 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTAT
* * * * *
1585 GAGATTAT-AAACCATTTAAAGTGCGTAACATGGCTTTTGAAGGAATAAGTGACTATAAATGTAC
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
* ** * * *
1649 TTTTCTT-CTCAGT-AAATGACTTTATCTACACAT-TTCCT-AGGACAAACATTCAATTATAGTC
66 TTTTCTTGC-CAATGAAA-GA-TTT-TCT-TTCATGTTCTTGAGG-TAGACATTCAATTATAGTC
* * *
1710 TATTTTCA-TAAAAAATATGAACAAATTCAACTTAAAATCAATTAT
125 TATTTTAACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTAT
** * ********** * * *
1755 GAGATTATAAAATAATTTAAAGCAAGNNNNNNNNNNTTTAAAGGAATGGGTGAGTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
* ** * * * * * * * *
1820 TTTTTTTATCAATGAATGCTTTT-TCTTAACGTTTCTTAAGGTAGACAGTCAATTATAGTATGTT
66 TTTTCTTGCCAATGAAAGATTTTCT-TTCATG-TTCTTGAGGTAGACATTCAATTATAGTCTATT
* * *
1884 TTAACCAAAAATGTAAAAAAATTCAATTTAAAATCAATTA
129 TTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTA
1924 NNNNNNNNNN
Statistics
Matches: 1181, Mismatches: 285, Indels: 140
0.74 0.18 0.09
Matches are distributed among these distances:
162 3 0.00
163 7 0.01
164 1 0.00
165 24 0.02
166 57 0.05
167 7 0.01
168 32 0.03
169 12 0.01
170 302 0.26
171 253 0.21
172 311 0.26
173 129 0.11
174 24 0.02
175 1 0.00
176 13 0.01
177 5 0.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
GAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
TTTTCTTGCCAATGAAAGATTTTCTTTCATGTTCTTGAGGTAGACATTCAATTATAGTCTATTTT
AACTAAAAATATAAAAAAATTCAACTTAAAATCAATTAT
Found at i:1443 original size:166 final size:159
Alignment explanation
Indices: 1187--1776 Score: 463
Period size: 170 Copynumber: 3.5 Consensus size: 159
1177 TGAGGCAACA
* *
1187 ATTCAATTATAGTCTATTTTAA-TCAAAAATATGAAAGCAAATTCAACTTAAATACAACTATGAG
1 ATTCAATTATAGTCTATTTTAACT-AAAAATGT-AAA--AAATTCAACTTAAAT-CAATTATGAG
* * *
1251 ATTATAAAACTATTTAAAGAGAGTAATAAGCCTTTTGAAGGAATGGGGTGACTATAAATGGACTT
61 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGGTGACTATAAATGGACTT
* * *
1316 TTCTTGGCCCAATTGA-ATCCCTTTTCTTTATGTGTAGAC
125 TTCTT-G-CCAA-TGACATCACATTTCTTGA-G-GTAGAC
* * * *
1355 ATTCAATTATAGTTTGTTTTAACTAAAAATGTAAAAACATTCAACTTGAAATCAGTTATGAGGTT
1 ATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAA-ATTCAACTT-AAATCAATTATGAGATT
* * * *
1420 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGATGGAATGGGCGACTACAAATAGACTTTTCT
64 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
*
1485 TGCCAATGANNNNNNNNNNCTTCACATTTCTTGAGGTAGAC
129 TGCCAATGA----------CATCACATTTCTTGAGGTAGAC
* * * *
1526 ATTTAATTATTGTCTCTTTTAACTAAAATTGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
1 ATTCAATTATAGTCTATTTTAACTAAAAATGT-AAAAAATTCAACTT-AAATCAATTATGAGATT
* * * ** *
1591 AT-AAACCATTTAAAGTGCGTAACATGGCTTTTGAAGGAATAAGTGACTATAAATGTACTTTTCT
64 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
* * *
1655 T-CTCAGTAAATGACTTTATCTACACATTTCCT-AGGACAAAC
129 TGC-C----AATGAC---A--T-CACATTTCTTGAGG-TAGAC
* * *
1696 ATTCAATTATAGTCTATTTTCA-TAAAAAATATGAACAAATTCAACTTAAAATCAATTATGAGAT
1 ATTCAATTATAGTCTATTTTAACT-AAAAATGT-AAAAAATTCAACTT-AAATCAATTATGAGAT
**
1760 TATAAAATAATTTAAAG
63 TATAAAACCATTTAAAG
1777 CAAGNNNNNN
Statistics
Matches: 344, Mismatches: 49, Indels: 55
0.77 0.11 0.12
Matches are distributed among these distances:
162 3 0.01
163 4 0.01
164 2 0.01
165 24 0.07
166 56 0.16
167 7 0.02
168 27 0.08
169 7 0.02
170 123 0.36
171 70 0.20
172 6 0.02
173 10 0.03
174 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (159 bp):
ATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAATTCAACTTAAATCAATTATGAGATTAT
AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG
CCAATGACATCACATTTCTTGAGGTAGAC
Found at i:2426 original size:171 final size:169
Alignment explanation
Indices: 1952--2565 Score: 626
Period size: 171 Copynumber: 3.6 Consensus size: 169
1942 NNNNNNNNNN
* * * *
1952 CTATAAATGGACTTTTCTTGCCAATGAACACTTGTTTTTTCACGTTT-CTCAAGCTAGACATTCA
1 CTATAAATAGACTTTTCTTGCCAATAAAC-CTT-TTTTTTCATGTTTCCT-AAGGTAGACATTCA
* *
2016 ATTATTA-ACTGTTTTAA-CTAAAATGTAAAACAATTCAACCTT-AAATCAAG-TATGAGATTAT
63 ATTA-TAGTCTGTTTTAATCAAAAATGTAAAACAATTCAA-CTTAAAATC-AGTTATGAGATTAT
* * * *
2077 AACACCATTTAACGCGAGTAGTAAGACTTTTGAAGGAATGGGAGA
125 AACACCATTTAAAGCGAGTAATAAGTCTTTTGAAGGAATGGGTGA
* * * * * * *
2122 CTAAAAATAGACTTTTCTT-CTCAATAAA----TATCTACATATTTCAC-GAGGTA-AGCATTTA
1 CTATAAATAGACTTTTCTTGC-CAATAAACCTTTTTTTTCATGTTTC-CTAAGGTAGA-CATTCA
* * * *
2180 ATTATAGTCTGTTTTAATGAAAAATATAAAAAAAATTCAACTTAAATACCA-TTATGAGATTATA
63 ATTATAGTCTGTTTTAATCAAAAATGT-AAAACAATTCAACTTAAA-ATCAGTTATGAGATTATA
* * * *
2244 AAACTATTTAAAACGAGTAATAAGTCTTTTGAGGGAATGGGTGA
126 ACACCATTTAAAGCGAGTAATAAGTCTTTTGAAGGAATGGGTGA
* *
2288 CTATAAATAGACTTTTCTTGCAAACAAATCCTTTTTTCTTCATGTTTCCTAAGGTAGACATTCAA
1 CTATAAATAGACTTTTCTTGCCAATAAA-CCTTTTTT-TTCATGTTTCCTAAGGTAGACATTCAA
*
2353 TTATAGTCTGTTTTTATCAAAAATGTAAAACAATTCAACTTAAAATCAGTTATGAGATTATAACA
64 TTATAGTCTGTTTTAATCAAAAATGTAAAACAATTCAACTTAAAATCAGTTATGAGATTATAACA
** * *
2418 CCATTTAAAGTAAGTAACAAGAT-TTTTGAAGGAATGAGTGA
129 CCATTTAAAGCGAGTAATAAG-TCTTTTGAAGGAATGGGTGA
* * * * * *
2459 CTATAAATGGACTTTTCTTGCTAATGAATCCATTTTTTTTCATGTTTCTTGAGGTACACATTCAA
1 CTATAAATAGACTTTTCTTGCCAAT-AAACC-TTTTTTTTCATGTTTCCTAAGGTAGACATTCAA
* *
2524 TTATTGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTA
64 TTATAGTCTGTTTTAATCAAAAATGTAAAACAATTCAACTTA
2566 NNNNNNNNNN
Statistics
Matches: 364, Mismatches: 57, Indels: 45
0.78 0.12 0.10
Matches are distributed among these distances:
163 3 0.01
164 30 0.08
165 9 0.02
166 86 0.24
167 3 0.01
169 1 0.00
170 26 0.07
171 154 0.42
172 51 0.14
173 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (169 bp):
CTATAAATAGACTTTTCTTGCCAATAAACCTTTTTTTTCATGTTTCCTAAGGTAGACATTCAATT
ATAGTCTGTTTTAATCAAAAATGTAAAACAATTCAACTTAAAATCAGTTATGAGATTATAACACC
ATTTAAAGCGAGTAATAAGTCTTTTGAAGGAATGGGTGA
Found at i:2920 original size:170 final size:170
Alignment explanation
Indices: 2744--3051 Score: 393
Period size: 170 Copynumber: 1.8 Consensus size: 170
2734 NNNNNNNNNN
* *
2744 ATTTAAAGCGAGTAATAAGGA-TTTTGAAGAAATAGGAGACTATAAATGAACTTTTTTTGCCAAA
1 ATTTAAAGC-AGTAATAAGGACTTTTGAAGAAATAGGAGACTATAAATGAACTTTTCTTACCAAA
* * *
2808 GAATGCTTGTTTCTTTATGTTTCTCTAGATAGATATTCAATTATAGTCCATTTTAACCAAAATGC
65 GAATACTTGTTTCTTTACGTTTATCTAGATAGATATTCAATTATAGTCCATTTTAACCAAAATGC
2873 AAAAAAATTCAACTTAAAAACAATTATGAGATTATAAAACC
130 AAAAAAATTCAACTTAAAAACAATTATGAGATTATAAAACC
********** * * *
2914 ATTTAAAGCNNNNNNNNNNACTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTACCAATG
1 ATTTAAAGCAGTAATAAGGACTTTTGAAGAAATAGGAGACTATAAATGAACTTTTCTTACCAAAG
* * ** *
2979 AATACTTGTTTCTTTACGTTTATCTAGTTAGATATTCAATTATTGTCTGTTTTAACCAAAATGTA
66 AATACTTGTTTCTTTACGTTTATCTAGATAGATATTCAATTATAGTCCATTTTAACCAAAATGCA
3044 AAAAAATT
131 AAAAAATT
3052 TAANNNNNNN
Statistics
Matches: 114, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
169 1 0.01
170 113 0.99
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
ATTTAAAGCAGTAATAAGGACTTTTGAAGAAATAGGAGACTATAAATGAACTTTTCTTACCAAAG
AATACTTGTTTCTTTACGTTTATCTAGATAGATATTCAATTATAGTCCATTTTAACCAAAATGCA
AAAAAATTCAACTTAAAAACAATTATGAGATTATAAAACC
Found at i:4514 original size:171 final size:170
Alignment explanation
Indices: 4006--4519 Score: 471
Period size: 172 Copynumber: 3.0 Consensus size: 170
3996 NNNNNAAGCA
* * * * * *
4006 AGTAATAAGACTTTTGAAGGAATAAG-AGACTATAAATGGACTTTTCTT-CTCAATGAATGGT-T
1 AGTAATAAAACTTTTGAAGGAATAGGTA-ACGATAAATAGACTTTTCTTGC-CAATAAAT-CTCT
* * ** * * * *
4068 TTTTCTACATATTT-TACAAGGTAAGCATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAA
63 TTCTCTTCACCTTTCT-CAAGGTAAACATTAAATTATAGCCTATTTTAATGAAAAA--TAAAAAA
* * * *
4132 AAATTTAACTTAAATACAATTATGGGATTATAAAACCATTTAAAATG
125 AAATTAAACTTAAAT-CAGTTATGAGATTATAAAACCATTTAAAGTG
* * ** * * * *
4179 TGTGATAATCCTTTTGAAGGAATGGGTAACTATAAATGGACTTTTCTTGCCAATAAATCTCTTTT
1 AGTAATAAAACTTTTGAAGGAATAGGTAACGATAAATAGACTTTTCTTGCCAATAAATCTCTTTC
** * ** * ** *
4244 TCTTCATGTTTCTCAAGGTAAACATTTAATTATAGTTTGTTTTAACAAAAAAATATAAAAAAATT
66 TCTTCACCTTTCTCAAGGTAAACATTAAATTATAGCCTATTTTAA-TGAAAAATAAAAAAAAATT
*
4309 AAACTTAAAATTAGTTATGAGATTATAAAACCATTTAAAGTG
130 AAACTT-AAATCAGTTATGAGATTATAAAACCATTTAAAGTG
* * * * *
4351 AGTAATAAAACTTTTGAAGGAATAGGTGACGATAAATAGACTTTTTTTGTCGATGAATGC-CTTT
1 AGTAATAAAACTTTTGAAGGAATAGGTAACGATAAATAGACTTTTCTTGCCAATAAAT-CTCTTT
** * * *
4415 CTCTTCACCTTTCTTGAGGTACACATTAAATTATTGCCTATTTTAATGAAAAATACAAAAAAATT
65 CTCTTCACCTTTCTCAAGGTAAACATTAAATTATAGCCTATTTTAATGAAAAATAAAAAAAAATT
*
4480 CAACTTGAAATCAGTTATGAGATTATAAAACCATTTAAAG
130 AAACTT-AAATCAGTTATGAGATTATAAAACCATTTAAAG
4520 CGANNNNNNN
Statistics
Matches: 284, Mismatches: 50, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
171 53 0.19
172 129 0.45
173 94 0.33
174 8 0.03
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
AGTAATAAAACTTTTGAAGGAATAGGTAACGATAAATAGACTTTTCTTGCCAATAAATCTCTTTC
TCTTCACCTTTCTCAAGGTAAACATTAAATTATAGCCTATTTTAATGAAAAATAAAAAAAAATTA
AACTTAAATCAGTTATGAGATTATAAAACCATTTAAAGTG
Found at i:4593 original size:171 final size:171
Alignment explanation
Indices: 3355--5015 Score: 601
Period size: 171 Copynumber: 9.7 Consensus size: 171
3345 NNNNNNNNNN
* ** * * **
3355 ATAGACTTTTCTTGTCAATGAATGC-CTTTTTCTTCATGTTTCTCAAGGTAGACATTGAATTACA
1 ATAGACTTTTCTTGTCAATGAAT-CTCTTTTTCTTCACGTTTCTTGAGGTACACATTAAATTATT
** * * * * * * * **
3419 GTCTGTTTTAACTAAAAATGTAAAAACATTCAGCTCAAAATCAATTACGAGATTATAAAATTATT
65 GTCTGTTTTAAAAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGATTATAAAACCATT
* * **********
3484 TAAAGCAAGTAATAAGACTTTTGAAGGAANNNNNNNNNNTAA
130 TAAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
* ** * * * * * * * * *
3526 ATGGACTTTTCTTACCAATGAATCCCTTTTCCTACACGTGTCTAGAGGTAGACTTTCAATTATAG
1 ATAGACTTTTCTTGTCAATGAATCTCTTTTTCTTCACGTTTCTTGAGGTACACATTAAATTATTG
** * * * *
3591 TCTGTTTTAATCAAAAATATAAAAAACTTCAGCTTAAAATCAGTTATGATATTATAAAACCATTT
66 TCTGTTTTAAAAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGATTATAAAACCATTT
* * * * *
3656 AAAGCGAGTAA-CAAGCTTTTTTAAGAAATGGGTGAATATAA
131 AAAGCGAGTAATAAAAC-TTTTGAAGGAATGGGTGACTATAA
* * ** * * ** ** ** * *
3697 ATGGACTTTTCTTCTCAATGAATAACTTTTT-TTAACTATTTCTCAAGCAAGGCATTCAATTATA
1 ATAGACTTTTCTTGTCAATGAATCTCTTTTTCTTCAC-GTTTCTTGAGGTACACATTAAATTATT
* ** * * * * * *
3761 GTTTGTTTTAATGAAAATTGTAAAAAAATTCAACTTAAAATCAGTTATGAGTTTTTAAAACAATT
65 GTCTGTTTTAAAAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGATTATAAAACCATT
** * * * *
3826 TAAAGCGAGTAATAAGGCTTTTGATGAAAAGGGTGACTACAA
130 TAAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
* * * * * * * * * * *
3868 ATGGATTTTTTTTGCCCATGAATGC-CTTTTTCTTCATGTTTCTTGAAGTAAATATTCAATTATA
1 ATAGACTTTTCTTGTCAATGAAT-CTCTTTTTCTTCACGTTTCTTGAGGTACACATTAAATTATT
** * *******************************
3932 GTCTGTTTTAACCAAAAATGTAAAAAAATTCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
65 GTCTGTTTTAAAAAAAAATATAAAAAAATT-AA-ACTTAAAATCAGTTATGAGATTATAAAACCA
**** * * ** *
3997 NNNNAAGCAAGTAATAAGACTTTTGAAGGAATAAGAGACTATAA
128 TTTAAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
* * * * ** ** *
4041 ATGGACTTTTCTTCTCAATGAATGGT-TTTTTCTACATATTT-TACAAGGTA-AGCATTCAATTA
1 ATAGACTTTTCTTGTCAATGAAT-CTCTTTTTCTTCACGTTTCT-TGAGGTACA-CATTAAATTA
* ** * * * *
4103 TAGTCTGTTTTAATGAAAAATGTAAAAAAAAATTTAACTT-AAATACAATTATGGGATTATAAAA
63 TTGTCTGTTTTAA--AAAAAAATATAAAAAAATTAAACTTAAAAT-CAGTTATGAGATTATAAAA
** * * ** *
4167 CCATTTAAAATGTGTGATAATCCTTTTGAAGGAATGGGTAACTATAA
125 CCATTTAAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
* * * * ** * * *
4214 ATGGACTTTTCTTGCCAATAAATCTCTTTTTCTTCATGTTTCTCAAGGTAAACATTTAATTATAG
1 ATAGACTTTTCTTGTCAATGAATCTCTTTTTCTTCACGTTTCTTGAGGTACACATTAAATTATTG
* *
4279 TTTGTTTTAACAAAAAAATATAAAAAAATTAAACTTAAAATTAGTTATGAGATTATAAAACCATT
66 TCTGTTTTAA-AAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGATTATAAAACCATT
* * *
4344 TAAAGTGAGTAATAAAACTTTTGAAGGAATAGGTGACGATAA
130 TAAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
* * * *
4386 ATAGACTTTTTTTGTCGATGAATGC-CTTTCTCTTCACCTTTCTTGAGGTACACATTAAATTATT
1 ATAGACTTTTCTTGTCAATGAAT-CTCTTTTTCTTCACGTTTCTTGAGGTACACATTAAATTATT
* * ** * * *
4450 GCCTATTTTAATGAAAAATACAAAAAAATTCAACTTGAAATCAGTTATGAGATTATAAAACCATT
65 GTCTGTTTTAAAAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGATTATAAAACCATT
********** *
4515 TAAAGCGANNNNNNNNNNTTTTGAAGAAATGGGTGACTATAA
130 TAAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
* * * * *
4557 ATAGACTTTTCTTGTCAATGAATTTTTTTTTCTTCACGTTTCTTGAGATACACATTCAGTTATTG
1 ATAGACTTTTCTTGTCAATGAATCTCTTTTTCTTCACGTTTCTTGAGGTACACATTAAATTATTG
** * ********** * *
4622 TCTGTTTTAACCAAAAATGTAAAAAAATTNNNNNNNNNNTCAATTATGAGATTATAAAACTATTT
66 TCTGTTTTAAAAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGATTATAAAACCATTT
* * **** * *
4687 AAAGCAAGTATTATGGTTTTTGAAGAAATAGGTGACTATAA
131 AAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
* * * * * * * ** * * ***
4728 ATGGATTTTTCTTCTCAATTAATGATTTTTTTCTGCACGTTTCTCAAGGCA-AGCATTCAATNNN
1 ATAGACTTTTCTTGTCAATGAAT-CTCTTTTTCTTCACGTTTCTTGAGGTACA-CATTAAATTAT
******* ** * * * * * **
4792 NNNNNNNTTTAATGAAAAATAT-AAAAAATTTAATTTAAAATTAGTTATAAGATCATAAAAAAAT
64 TGTCTGTTTTAAAAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGATTATAAAACCAT
* * * * *
4856 TTAAAACAAGTAATAAAGCTTTTGAAGGAATGCGTGATTATAA
129 TTAAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
* * * * * ** ** * *
4899 ATGGACTTTTTTTGTCAATAAATGTCTTTTTCTTCACATTTCTCAAGAAAGACATTCAAA-TATA
1 ATAGACTTTTCTTGTCAATGAATCTCTTTTTCTTCACGTTTCTTGAGGTACACATT-AAATTATT
* * * * * * *
4963 GTCTGTTTTAATAAAAAACACAAAAATATTCAACTTCAAATCAATTATGAGAT
65 GTCTGTTTTAAAAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGAT
5016 NNNNNNNNNN
Statistics
Matches: 1085, Mismatches: 380, Indels: 50
0.72 0.25 0.03
Matches are distributed among these distances:
170 43 0.04
171 659 0.61
172 183 0.17
173 184 0.17
174 3 0.00
175 13 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.35
Consensus pattern (171 bp):
ATAGACTTTTCTTGTCAATGAATCTCTTTTTCTTCACGTTTCTTGAGGTACACATTAAATTATTG
TCTGTTTTAAAAAAAAATATAAAAAAATTAAACTTAAAATCAGTTATGAGATTATAAAACCATTT
AAAGCGAGTAATAAAACTTTTGAAGGAATGGGTGACTATAA
Found at i:6068 original size:172 final size:171
Alignment explanation
Indices: 5341--6087 Score: 648
Period size: 170 Copynumber: 4.4 Consensus size: 171
5331 NNNNNNNNNN
* * * *
5341 TTACCAATGAATGCTTTTCTCTTCATGTTTCTTGAGGTAAACATTCAATTATAGTCTATTTTAAC
1 TTACCAATAAATGCTTTTTTCTTCACGTTTCTT-AGGTAGACATTCAATTATAGTCTATTTTAAC
* * * * * *
5406 CAAAAATG-AAAAAAACATTGAACATAAAATCAATTTTGAGATAATAAAATCATTTCAAGCGAGT
65 CAAAAATGTAAAAAAA-ATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGT
* *
5470 AATAAGGCTTTTGAAGGAACGAGAGACTATAAATGGATTTTTC
129 AATAAGGCTTTTGAAGGAACGAGAGACTATAAATAGACTTTTC
* * * * * **********
5513 TTGCCAATGAATG-TTTTTTCTTTACGTTTCTCAAAGTAGACANNNNNNNNNNGTCTATTTTAAC
1 TTACCAATAAATGCTTTTTTCTTCACGTTTCT-TAGGTAGACATTCAATTATAGTCTATTTTAAC
* * * *
5577 CAAAAATGT-AAAAAACTTCATCTTAAAATCAATTATGAGATTATAAAGCCATTTAACA-TGAGT
65 CAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAA-AGTGAGT
* * * *
5640 AATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTA
129 AATAAGGCTTTTGAAGGAACGAGAGACTATAAATAGACTTTTC
* * * * * * * *
5683 TT-CTCAATTAATAGC-TTTTTCTACATGTTTTCATAGGCAGACATTCAATTGTAGTCTGTTTTC
1 TTAC-CAATAAAT-GCTTTTTTCTTCACG-TTTCTTAGGTAGACATTCAATTATAGTCTATTTTA
** * * * * ** * *
5746 ATGACAAA--TATAAAAAATTGAGCTTAAAAGCAATTATGAGATTATAAAATAATTTAAAGCGTG
63 ACCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAG
* *
5809 TAATAA-GCTTTTTGAAGGAACAAGTGACTATAAATAGACTTTTC
128 TAATAAGGC-TTTTGAAGGAACGAGAGACTATAAATAGACTTTTC
* * * * * * ** * *
5853 TTACCAATAAGTACCTTTTTCCTCATGTTCCTCTATATAGACATTTAATTATAATCTATTTTAAC
1 TTACCAATAAATGCTTTTTTCTTCACGTTTCT-TAGGTAGACATTCAATTATAGTCTATTTTAAC
* * * * *
5918 CAAAAAGGTAAAAAAAATTGAACTTAAAATTAATTTTTAGATTATAAAACCATTTAAAGTTAGTA
65 CAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * *
5983 ATAAGACTTTTGAAGGAATGAGTGACTATAAATAGAGTTTTC
130 ATAAGGCTTTTGAAGGAACGAGAGACTATAAATAGACTTTTC
* * *
6025 TTATCAATAAATGCTTTTTTCTTCACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTA
1 TTACCAATAAATGCTTTTTTCTTCACGTTTCTT-AGGTAGACATTCAATTATAGTCTATTTTA
6088 NNNNNNNNNN
Statistics
Matches: 442, Mismatches: 116, Indels: 34
0.75 0.20 0.06
Matches are distributed among these distances:
169 9 0.02
170 205 0.46
171 81 0.18
172 146 0.33
173 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
TTACCAATAAATGCTTTTTTCTTCACGTTTCTTAGGTAGACATTCAATTATAGTCTATTTTAACC
AAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAA
TAAGGCTTTTGAAGGAACGAGAGACTATAAATAGACTTTTC
Found at i:7013 original size:171 final size:171
Alignment explanation
Indices: 6708--7015 Score: 433
Period size: 171 Copynumber: 1.8 Consensus size: 171
6698 NNNNNNNNNN
* **
6708 TCACATTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAGCAAATTCAAC
1 TCACATTTCTTAAGGTAGAAATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
* * * *
6773 TTAAAATTACTTATGAGATAATAAAACCATTTAAAGCGAGTAATACGGTTTTTAAAGAAATGAGA
66 TCAAAATCACTTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGGTTTTGAAAGAAATGAGA
6838 GACTATAAATGGACTTTTCTTGTCAATGAATATCTTTTTCT
131 GACTATAAATGGACTTTTCTTGTCAATGAATATCTTTTTCT
* * *
6879 TCACGTTTCTTAAGGTAGATAATT-AATTATAGTCTGTTTTAGCCAAATATGTAAAAAAAATT-A
1 TCACATTTCTTAAGGTAGA-AATTCAATTATAGTCTGTTTTAACCAAAAATGT-AAAAAAATTCA
* * **
6942 ACTCAAAATCAGTTATGAGATTATAAAACTGTTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATG
64 ACTCAAAATCACTTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGG-TTTTGAAAGAAATG
*
7006 GGAGACTATA
128 AGAGACTATA
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
171 101 0.85
172 18 0.15
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (171 bp):
TCACATTTCTTAAGGTAGAAATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
TCAAAATCACTTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGGTTTTGAAAGAAATGAGA
GACTATAAATGGACTTTTCTTGTCAATGAATATCTTTTTCT
Done.