Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400043.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3263.0, 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: 8415
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.27
Warning! 2248 characters in sequence are not A, C, G, or T
Found at i:670 original size:171 final size:168
Alignment explanation
Indices: 473--1258 Score: 698
Period size: 171 Copynumber: 4.6 Consensus size: 168
463 NNNNNNNNNN
* * * **
473 AATGTAAAAAAATTTAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAACTGGTAATAAG
1 AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACAAGTAATAAG
* * * *
538 CCTTTTGAAGGAATTGGTGACTATAAATGGACTTTTTTTCTATATAAATGGCTTGTTT-TAAACG
66 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCCA-ATAAATGG-TT-TTTCTACACG
* *
602 TTTTTCAAGACAGGCATTCAATTGTACCCTGTTTTAAGTAAA
128 TTTTTCAAGACAGGCATTCAATTGTAGCCTGTTTTAA-CAAA
* * * * *
644 AATGTAAAACAATTCAACTTAAAATCAATTATGACATTACAAAGA-AATTTAAAGCTAGTAATAC
1 AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA-ACAATTTAAAACAAGTAATA-
* * * * *
708 A-G-TGTTTGAAGGAATGAGTGACTATAAATGAACTTTTCTTGCCAAGAAATGAGTTTTTCTTCA
64 AGGCT-TTTGAAGGAATGGGTGACTATAAATGGACTTTT-TTTCCAATAAATG-GTTTTTCTACA
* * * * *
771 CGTTTCTGAATGAACA--CATTCAATTATTGTCT-TTTTCAACAAA
126 CGTTTTTCAA-G-ACAGGCATTCAATTGTAGCCTGTTTT-AACAAA
* * * *
814 AATGTAAAACAATTCAA-TTAAAATCAATTATGCGATTATAAAACAATTTAAAGCGAGTAATAAG
1 AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACAAGTAATAAG
* * * * * *
878 GCTTTTGAAGGAATGGGTGACTATAAACGGACTTCTCTTGCCAATGAAT-GTAGTTTTCTTCATG
66 GCTTTTGAAGGAATGGGTGACTATAAATGGACTT-TTTTTCCAATAAATGGT--TTTTCTACACG
* ** * * * * *
942 TTTCT-AGAGGTAGTCGTTCAATTATTGTCC-GTTTTATCAAA
128 TTTTTCA-AGACAGGCATTCAATTGTAG-CCTGTTTTAACAAA
* *
983 AAGTATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAACAAGTAATAA
1 AA-TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACAAGTAATAA
* * ** * * *
1048 GGCTTTTGAAAGAATAGGTGACTATAAATAAACTTTTCTTCTCAATGAATGGCTTTTTGTACACG
65 GGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTC-CAATAAATGG-TTTTTCTACACG
* * * *
1113 TTTCTT-GAGGCAGGCATTCAATTGTAGTCTATTTTAAACAAA
128 TTT-TTCAAGACAGGCATTCAATTGTAGCCTGTTTT-AACAAA
* * * * *
1155 AATGTAAAAAAATTTAACTAAAAATCAATTACGACATTACAAAACAATTT-AAACAAAGTAATAA
1 AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAAC-AAGTAATAA
* *
1219 GGCTCTTGAAGAAATGGGTGACTATAAATGGACTTTTTTT
65 GGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTT
1259 ATCGATGAAT
Statistics
Matches: 506, Mismatches: 80, Indels: 58
0.79 0.12 0.09
Matches are distributed among these distances:
167 3 0.01
168 4 0.01
169 113 0.22
170 56 0.11
171 309 0.61
172 17 0.03
173 4 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (168 bp):
AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACAAGTAATAAG
GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCCAATAAATGGTTTTTCTACACGTTT
TTCAAGACAGGCATTCAATTGTAGCCTGTTTTAACAAA
Found at i:900 original size:340 final size:340
Alignment explanation
Indices: 473--1258 Score: 841
Period size: 340 Copynumber: 2.3 Consensus size: 340
463 NNNNNNNNNN
** * *
473 AATGTAAAAAAATTTAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAACTG-GTAATAA
1 AATGTAAAAAAATTTAACTTAAAATCAATTATGCGATTATAAAACAATTT-AAACAGAGTAATAA
* * * * *
537 GCCTTTTGAAGGAATTGGTGACTATAAATGGACTTTTTTTCTATATAAATGGCTTGTTTTAAACG
65 GGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCCA-ATAAAT-G-TAGTTTTAAACA
* * *
602 TTTTTC-A-AGACAGGCATTCAATT-GTACCCTGTTTTAAGT-AAAAA-TGTAAAACAATTCAAC
127 TGTTTCTAGAGACAGGCATTCAATTAGTACCC-GTTTT-A-TCAAAAAGTATAAAAAAATTCAAC
* * *
662 TTAAAATCAATTATGACATTACAAAGA-AATTTAAAGCTAGTAATACAGTG-TTTGAAGGAAT-G
189 TTAAAATCAATTATGACATTACAAA-ATAATTTAAAACAAGTAATA-AG-GCTTTGAAAGAATAG
* * *
724 AGTGACTATAAATGAACTTTTCTTGC-CAA-GAAATGAG-TTTTTCTTCACGTTTC-TGAATGAA
251 -GTGACTATAAATAAACTTTTCTT-CTCAATG-AATG-GCTTTTTCTACACGTTTCTTG-AGGAA
* *
785 CACATTCAATTATTGTCT-TTTTCAACAAA
311 CACATTCAATTATAGTCTATTTTAAACAAA
* *
814 AATGTAAAACAATTCAA-TTAAAATCAATTATGCGATTATAAAACAATTTAAAGC-GAGTAATAA
1 AATGTAAAAAAATTTAACTTAAAATCAATTATGCGATTATAAAACAATTTAAA-CAGAGTAATAA
* * * * ***
877 GGCTTTTGAAGGAATGGGTGACTATAAACGGACTTCTCTTGCCAATGAATGTAGTTTTCTTCATG
65 GGCTTTTGAAGGAATGGGTGACTATAAATGGACTT-TTTTTCCAATAAATGTAGTTTTAAACATG
** * * * **
942 TTTCTAGAGGTAGTCGTTCAATTATTGTCCGTTTTATCAAAAAGTATAAAAAAATTCAACTTAAA
129 TTTCTAGAGACAGGCATTCAATTAGTACCCGTTTTATCAAAAAGTATAAAAAAATTCAACTTAAA
* *
1007 ATCAATTATGAGATTATAAAATAATTTAAAACAAGTAATAAGGCTTTTGAAAGAATAGGTGACTA
194 ATCAATTATGACATTACAAAATAATTTAAAACAAGTAATAAGGC-TTTGAAAGAATAGGTGACTA
* * ** *
1072 TAAATAAACTTTTCTTCTCAATGAATGGCTTTTTGTACACGTTTCTTGAGGCAGGCATTCAATTG
258 TAAATAAACTTTTCTTCTCAATGAATGGCTTTTTCTACACGTTTCTTGAGGAACACATTCAATTA
1137 TAGTCTATTTTAAACAAA
323 TAGTCTATTTTAAACAAA
* * * *
1155 AATGTAAAAAAATTTAACTAAAAATCAATTACGAC-ATTACAAAACAATTTAAACAAAGTAATAA
1 AATGTAAAAAAATTTAACTTAAAATCAATTATG-CGATTATAAAACAATTTAAACAGAGTAATAA
* *
1219 GGCTCTTGAAGAAATGGGTGACTATAAATGGACTTTTTTT
65 GGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTT
1259 ATCGATGAAT
Statistics
Matches: 372, Mismatches: 53, Indels: 40
0.80 0.11 0.09
Matches are distributed among these distances:
338 14 0.04
339 17 0.05
340 214 0.58
341 56 0.15
342 70 0.19
343 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (340 bp):
AATGTAAAAAAATTTAACTTAAAATCAATTATGCGATTATAAAACAATTTAAACAGAGTAATAAG
GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCCAATAAATGTAGTTTTAAACATGTT
TCTAGAGACAGGCATTCAATTAGTACCCGTTTTATCAAAAAGTATAAAAAAATTCAACTTAAAAT
CAATTATGACATTACAAAATAATTTAAAACAAGTAATAAGGCTTTGAAAGAATAGGTGACTATAA
ATAAACTTTTCTTCTCAATGAATGGCTTTTTCTACACGTTTCTTGAGGAACACATTCAATTATAG
TCTATTTTAAACAAA
Found at i:2005 original size:170 final size:168
Alignment explanation
Indices: 1608--2057 Score: 446
Period size: 170 Copynumber: 2.6 Consensus size: 168
1598 NNNNNNNNNN
* * * * *
1608 GGACTTTTCTTGCCAATGAATGCATTTTTCCTCATGTTTCACG-AGGTAGACATTCAATTATTAT
1 GGACTTTTCTTGCCAATGAATG-GTTTTTCTTAATGTTTC-TGAAGATAGACATTCAATTATTAT
* * * *
1672 TTGTTTTATCCATAAATGTAAAATAATTCAACTTAAAATCAATTATAAAATTATAAAATAATTTA
64 TTG-TTTA-ACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAAATTATAAAACAATTTA
* * * ** *
1737 AAGCGGGTAATAAGGCTTTTGCAGGAATGGGTGATTATAAAT
127 AAGCGAGTAATAAGGCATTTGAAGGAATCAGTGACTATAAAT
* * * * * *
1779 GAACTTTTCTT-CTATATGAATGGCTTTTT-TCACATGTTTTTTGAGGCAT-G-CATTCAATT-G
1 GGACTTTTCTTGCCA-ATGAATGG-TTTTTCTTA-ATG-TTTCTGAAG-ATAGACATTCAATTAT
* * * *
1839 TACTCTGTTTAAGCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAGCAAT
61 TA-TTTGTTTAA-CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAAATTATAAAACAAT
*
1904 TTAAAGTGAGTAATAAGGCATTTGAAGGAATCAGTGACTATAAAT
124 TTAAAGCGAGTAATAAGGCATTTGAAGGAATCAGTGACTATAAAT
*
1949 GGACTTTTCTTGCCAATGAATGTGTTTTTCTTAACGTTTCTGAAGATAGACATTCAATTATTATT
1 GGACTTTTCTTGCCAATGAATG-GTTTTTCTTAATGTTTCTGAAGATAGACATTCAATTATTA-T
* * *
2014 ATTTTTTAACTAAAAATATCAAAAAATTCAA-TTAAAATCAATTA
64 -TTGTTTAAC-AAAAATGTAAAAAAATTCAACTTAAAATCAATTA
2058 NNNNNNNNNN
Statistics
Matches: 225, Mismatches: 38, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
168 2 0.01
169 8 0.04
170 125 0.56
171 60 0.27
172 29 0.13
173 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (168 bp):
GGACTTTTCTTGCCAATGAATGGTTTTTCTTAATGTTTCTGAAGATAGACATTCAATTATTATTT
GTTTAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAAATTATAAAACAATTTAAAGC
GAGTAATAAGGCATTTGAAGGAATCAGTGACTATAAAT
Found at i:2691 original size:172 final size:170
Alignment explanation
Indices: 2148--2692 Score: 490
Period size: 172 Copynumber: 3.2 Consensus size: 170
2138 NNNNNNNNNN
* *
2148 AAGGTTTTTGAAGGAATGGGTGACTATAAATGGACTTTTATTACCAATGAATGC-TATTTTCTTC
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTATTATCAATGAATGCGT-TTTTCTTC
* * * * ** * *
2212 AAATTTCTCAAGGTAGACGTTCAATTATTGTCTGTTTTATTAAAAA-ATAAAAAAAGATCAACTT
65 AAGTTTCTTAAGGTAAACATTCAATTATTGTCTGTTTTACCAAAAATGTAAAAAAA-TTCAACTT
* *
2276 AAAATCT-ATTATGAGATTATAAAAGAATTTAAAGCGAGTAAT
129 AAAAT-TAATTATGAGATTATAAAACAATTTAAAGCGAATAAT
********** * * *
2318 AAGGCTTTTNNNNNNNNNNGTGACTATAAATGGACTTTTCTTCTCAATGAATG-GCTTTTTGTAT
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTATTATCAATGAATGCG-TTTTTCT-T
* * * ** * * * *
2382 -ACGTTTCTTGAGGCAAGTATTCAATTGTAGTCTGTTTTCAGCAAAAATGTAAAAAAATTCAATT
64 CAAGTTTCTTAAGGTAAACATTCAATTATTGTCTGTTTT-ACCAAAAATGTAAAAAAATTCAACT
* * * *
2446 TAAAATCAATTACGACATTATAAAACAATTTAAA-CAAAGTAAT
128 TAAAATTAATTATGAGATTATAAAACAATTTAAAGCGAA-TAAT
* * * * * * * * *
2489 AAGGCTCTTAAAGAAATAGGTGATTATAAATTGATTTTTTTTTATCGATGAATGCGTTTTTCTTC
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGA-CTTTTATTATCAATGAATGCGTTTTTCTTC
* * * *
2554 ATGTTTCTTTAGGTAAACATTCAATTATTGTCTTTTTTAACCAAAAATGTAAAAAAATTCACCTT
65 AAGTTTCTTAAGGTAAACATTCAATTATTGTCTGTTTT-ACCAAAAATGTAAAAAAATTCAACTT
*
2619 AAAATTAATTATGAGATTACAAAACAATTTAAAGCGAATAAT
129 AAAATTAATTATGAGATTATAAAACAATTTAAAGCGAATAAT
*
2661 AAGGCTTTTGAAGGAATGGGTAACTATAAATG
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATG
2693 NNNNNNNNNN
Statistics
Matches: 285, Mismatches: 79, Indels: 20
0.74 0.21 0.05
Matches are distributed among these distances:
170 73 0.26
171 68 0.24
172 140 0.49
173 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.36
Consensus pattern (170 bp):
AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTATTATCAATGAATGCGTTTTTCTTCA
AGTTTCTTAAGGTAAACATTCAATTATTGTCTGTTTTACCAAAAATGTAAAAAAATTCAACTTAA
AATTAATTATGAGATTATAAAACAATTTAAAGCGAATAAT
Found at i:3446 original size:171 final size:170
Alignment explanation
Indices: 3019--3843 Score: 680
Period size: 171 Copynumber: 4.8 Consensus size: 170
3009 NNNNNNNNNN
** * *
3019 AAGGCTTTTGAAGGAATCAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCGTTTTTCTTAA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCGTTTTTCTTCA
* * * * *
3084 TGTTTCTGAAGGTAGACATTCAATTATTATTAT-TTTTAACTAAAAATATAAAAAAATTCAA-TT
66 TGTTTCTCAA-GTACACATTCAATTA-TAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTT
* *
3147 AAAATCAATTATGAGATTATAAAACTATTGAAAGCGAGTAAT
129 AAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
************ * * * *
3189 AAGGCTTTTGNNNNNNNNNNNNACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTGTTCA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCGTTTTTCTTCA
* * * * * * *
3254 TGTTTCTCAAGATAGACATTCAATTATTGTTTGTTTTAACCAAAAATATAAAAGAATTTAACCTA
66 TGTTTCTCAAG-TACACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTA
* * *
3319 AAATCAATTATGATATTATACAACAATTTAAAGCAAGTAAT
130 AAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
* * * * * *
3360 AAGACTTTTGAAGGAATGGGCGACTATGAATAGACTTTTCTTGTCAACAAATGCGTTTTTCTTCA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCGTTTTTCTTCA
* * * * * *
3425 CGTTTTTTTAAGTACACATTCAATTATAGTCTCTTTTAACAAAAAATACAAAAGAATTCAACTTA
66 TG-TTTCTCAAGTACACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTA
* *
3490 AAATGAATTATGAGATTATAAAACAATTTAAAGCGTGTAAT
130 AAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
** * * *
3531 AAGGCTTTTGACCGAATGGGTGACTATAAATGGACTTTT-TTTCTCAATAAATG-GCTTTTTATA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATAAATGCG-TTTTTCTT
* * * *
3594 CATGTTTCTCGAG-ACAGGCATTCAATTATAGTCTGTTTAAATAAAAAATATAAAAAAATTTAAC
64 CATGTTTCTCAAGTACA--CATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAAC
* **********
3658 TTTAAATCAATTATGAGATTATAAAANNNNNNNNNNCGAGTAAT
127 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
* * * * * *
3702 AAGGCTTTTGAAGGAATGGGTGAATATAAATTGACTTTT-TTTCTAAATGGATTGC-TTTTTCTA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAAT-AAATGCGTTTTTCT-
* * * * ** * * *
3765 T-ATGTTTC-CTGAG-ACAAAAATTCAGTTATAGTTTGTTTTAATGAAAAATGTAAAACAATTTA
63 TCATGTTTCTC-AAGTAC--ACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCA
3827 ACTTAAAATCAATTATG
125 ACTTAAAATCAATTATG
3844 NNNNNNNNNN
Statistics
Matches: 524, Mismatches: 117, Indels: 27
0.78 0.18 0.04
Matches are distributed among these distances:
169 7 0.01
170 107 0.20
171 399 0.76
172 10 0.02
173 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCGTTTTTCTTCA
TGTTTCTCAAGTACACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAA
AATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
Found at i:3647 original size:342 final size:341
Alignment explanation
Indices: 3023--3680 Score: 800
Period size: 342 Copynumber: 1.9 Consensus size: 341
3013 NNNNNNAAGG
* * ** *
3023 CTTTTGAAGGAATCAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCGTTTTTCTTAATGTT
1 CTTTTGAAGGAATCAGCGACTATAAATAGACTTTTCTTGCCAACAAATGCGTTTTTCTTAACGTT
* * * *
3088 TCTGAAGGTAGACATTCAATTATTATTATTTTTAACTAAAAATATAAAAAAATTCAATTAAAATC
66 TCTGAAGGTACACATTCAATTATTAGTATTTTTAACAAAAAATACAAAAAAATTCAATTAAAATC
* ************
3153 AATTATGAGATTATAAAACTATTGAAAGCGAGTAATAAGGCTTTTGNNNNNNNNNNNNACTATAA
131 AATTATGAGATTATAAAACAATTGAAAGCGAGTAATAAGGCTTTTGACCGAATGGGTGACTATAA
* * * * *
3218 ATGGACTTTTCTTACCAATGAATGCCTTTTTGTTCATGTTTCTCAAGATAGACATTCAATTATTG
196 ATGGACTTTTCTTACCAATAAATGCCTTTTTATACATGTTTCTCAAGACAGACATTCAATTATAG
* * * * *
3283 TTTGTTTTAACCAAAAATATAAAAGAATTTAACCTAAAATCAATTATGATATTATACAACAATTT
261 TCTGTTTAAACAAAAAATATAAAAAAATTTAACCTAAAATCAATTATGAGATTATACAACAATTT
3348 AAAGCAAGTAATAAGA
326 AAAGCAAGTAATAAGA
** * * *
3364 CTTTTGAAGGAATGGGCGACTATGAATAGACTTTTCTTGTCAACAAATGCGTTTTTCTTCACGTT
1 CTTTTGAAGGAATCAGCGACTATAAATAGACTTTTCTTGCCAACAAATGCGTTTTTCTTAACG-T
* * * *
3429 TTTTTAA-GTACACATTCAATTA-TAGTCTCTTTTAACAAAAAATACAAAAGAATTCAACTTAAA
65 TTCTGAAGGTACACATTCAATTATTAGTAT-TTTTAACAAAAAATACAAAAAAATTCAA-TTAAA
* * *
3492 ATGAATTATGAGATTATAAAACAATTTAAAGCGTGTAATAAGGCTTTTGACCGAATGGGTGACTA
128 ATCAATTATGAGATTATAAAACAATTGAAAGCGAGTAATAAGGCTTTTGACCGAATGGGTGACTA
* * * *
3557 TAAATGGACTTTT-TTTCTCAATAAATGGCTTTTTATACATGTTTCTCGAGACAGGCATTCAATT
193 TAAATGGACTTTTCTTAC-CAATAAATGCCTTTTTATACATGTTTCTCAAGACAGACATTCAATT
* * *
3621 ATAGTCTGTTTAAATAAAAAATATAAAAAAATTTAACTTTAAATCAATTATGAGATTATA
257 ATAGTCTGTTTAAACAAAAAATATAAAAAAATTTAACCTAAAATCAATTATGAGATTATA
3681 AAANNNNNNN
Statistics
Matches: 262, Mismatches: 51, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
340 4 0.02
341 95 0.36
342 163 0.62
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (341 bp):
CTTTTGAAGGAATCAGCGACTATAAATAGACTTTTCTTGCCAACAAATGCGTTTTTCTTAACGTT
TCTGAAGGTACACATTCAATTATTAGTATTTTTAACAAAAAATACAAAAAAATTCAATTAAAATC
AATTATGAGATTATAAAACAATTGAAAGCGAGTAATAAGGCTTTTGACCGAATGGGTGACTATAA
ATGGACTTTTCTTACCAATAAATGCCTTTTTATACATGTTTCTCAAGACAGACATTCAATTATAG
TCTGTTTAAACAAAAAATATAAAAAAATTTAACCTAAAATCAATTATGAGATTATACAACAATTT
AAAGCAAGTAATAAGA
Found at i:4359 original size:171 final size:169
Alignment explanation
Indices: 4074--4511 Score: 542
Period size: 171 Copynumber: 2.6 Consensus size: 169
4064 NNNNNNNNNN
* * * * *
4074 ACTATAAATAGACTTTTTTTCTCAATGAATGGCTTTTTCTACACGTTTCTCGAGGCAAGTATTCA
1 ACTATAAATAGACTTTTCTTCTTAATGAATGGCTTTTTCTA-TCGTTTCTC-AAGCAAGCATTCA
** * *
4139 ATTATAGTCTGTTTTAATGAAAAAAGCAAAAAAATTCAACATAAAATCAATTATGAGATTATAAA
64 ATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACATAAAATCAATTATGAGATTATAAA
* * *
4204 ATCATTTATAGCGAA-TAATAAGGCTTTT-AACAGAATGGGTG
129 ATAATTTAAAG-GAAGTAATAAGACTTTTGAA-AGAATGGGTG
*
4245 ACTATAAATAGACTTTTCTTCTTAATGAATGGCTTTTTCTATGCGTTTCTCAAGCAAGCATTGAA
1 ACTATAAATAGACTTTTCTTCTTAATGAATGGCTTTTTCTAT-CGTTTCTCAAGCAAGCATTCAA
* * * * *
4310 TTACATTTTGTTTTAACCAAAAATGTAAAAAAATTCAAACTTAAAATCAATTATGAGATTATATA
65 TTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTC-AACATAAAATCAATTATGAGATTATAAA
*
4375 ATAATTTAAAGTAAGTAATAAGACTTTTGAAAGAATGGGTG
129 ATAATTTAAAGGAAGTAATAAGACTTTTGAAAGAATGGGTG
* * **
4416 ACTATAAATAGACTTTTCTTCCTAATGAAT-ACTTTTGTCT-TCATGTTTCTCAAGGTAGACATT
1 ACTATAAATAGACTTTTCTTCTTAATGAATGGCTTTT-TCTATC--GTTTCTCAAGCAAG-CATT
*
4479 CAATTATAGTCTGTTTTAACCGAAAATGTAAAA
62 CAATTATAGTCTGTTTTAACCAAAAATGTAAAA
4512 NNNNNNNNNN
Statistics
Matches: 231, Mismatches: 28, Indels: 15
0.84 0.10 0.05
Matches are distributed among these distances:
169 1 0.00
170 48 0.21
171 148 0.64
172 34 0.15
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (169 bp):
ACTATAAATAGACTTTTCTTCTTAATGAATGGCTTTTTCTATCGTTTCTCAAGCAAGCATTCAAT
TATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACATAAAATCAATTATGAGATTATAAAAT
AATTTAAAGGAAGTAATAAGACTTTTGAAAGAATGGGTG
Found at i:4852 original size:170 final size:171
Alignment explanation
Indices: 4565--5190 Score: 403
Period size: 170 Copynumber: 3.7 Consensus size: 171
4555 NNNNNNNGCG
* * * * *
4565 AGTAATAAGGCTTTTGAAGGAATGGGTGACCATAAATGGACTTTTCTTCTATATGAATGGCTTTT
1 AGTAATAACGCTTTTGAAGAAATGAGTGACCATAAATGGACTTTTCTTCCATATGAATGACTTTT
* * * *
4630 TCTACAAGTTTCTTGAGGCAGACATTCAATTATAGTCTGTTTTAAGCAAAAAT-ATAAAAAATTT
66 TCTACAAGTTTCTTGAAGCAGACATTCAATTATAGTCTATTTTAACCAAAAATGACAAAAAA-TT
*
4694 CAACTTAAAATTAATTATGACATTATAAAATAATTTAAACAA
130 CAACTTAAAATCAATTATGACATTATAAAATAATTTAAACAA
* * *
4736 AGTAATAACGCTTTTGAAGAAATGAGTGGCTATAAATAGG-CTTTTCTTGCCA-ATGAAT-ATTT
1 AGTAATAACGCTTTTGAAGAAATGAGTGACCATAAAT-GGACTTTTCTT-CCATATGAATGACTT
* * * * * *
4798 TTTCTTCACGTTTCTCT-AAGTAGGCATTCAATTATAGTTTATTTTAACCAAAAATGCCAAAAAA
64 TTTCTACAAGTTTCT-TGAAGCAGACATTCAATTATAGTCTATTTTAACCAAAAATGACAAAAAA
* * ********** ***
4862 TTCAACTTAAAATCAATTATAAGANNNNNNNNNNATTTAAAGTG
128 TTCAACTTAAAATCAATTATGACATTATAAAATAATTTAAACAA
* * * * * * * * *
4906 AGTAATAAGGTTTTTGAAGAACTGGGTGACTATAAATTGACTTTT-TTTCTTAATGAATGGCTTT
1 AGTAATAACGCTTTTGAAGAAATGAGTGACCATAAATGGACTTTTCTTCCAT-ATGAATGACTTT
* * * * **
4970 TTCTACACGTTT-TCTG-AGATAGGCATTCAATTATAGTCTGTTTTAATGAAAAATGTA-AAAAC
65 TTCTACAAGTTTCT-TGAAG-CAGACATTCAATTATAGTCTATTTTAACCAAAAATG-ACAAAA-
* * ************
5032 AATTCAACGTAAAATCAATTATGAGATTATAAAACNNNNNNNNNNG
126 AATTCAACTTAAAATCAATTATGACATTATAAAATAATTTAAACAA
* * * * * *
5078 AGTAATAAAGCTTTTGAAGGAATGTGCGACTATAAATGGACTTTTCTTAC-TAATGAAT-ACCTT
1 AGTAATAACGCTTTTGAAGAAATGAGTGACCATAAATGGACTTTTCTTCCAT-ATGAATGA-CTT
* * * *
5141 TTTCTTCACA-TTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCA
64 TTTCTACA-AGTTTCTTGAAGCAGACATTCAATTATAGTCTATTTTAACCA
5191 NNNNNNNNNN
Statistics
Matches: 353, Mismatches: 85, Indels: 33
0.75 0.18 0.07
Matches are distributed among these distances:
168 1 0.00
169 3 0.01
170 123 0.35
171 103 0.29
172 118 0.33
173 5 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
AGTAATAACGCTTTTGAAGAAATGAGTGACCATAAATGGACTTTTCTTCCATATGAATGACTTTT
TCTACAAGTTTCTTGAAGCAGACATTCAATTATAGTCTATTTTAACCAAAAATGACAAAAAATTC
AACTTAAAATCAATTATGACATTATAAAATAATTTAAACAA
Found at i:5606 original size:171 final size:169
Alignment explanation
Indices: 5404--5829 Score: 466
Period size: 173 Copynumber: 2.5 Consensus size: 169
5394 TCAAGCCAAG
** * * *
5404 CATTCAATTGCAGTTTGCTTTAAACAAAAATGTAAAAAAATTCAGCGTAAAATTAATTATGACAT
1 CATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCA-CTTAAAATTAATTATGACAT
* *
5469 TATAAAATAATTTAAAGAAAGTAATAAGGCTTTTGAAGAAATAG-GTG-TCTATAAATAGAACTT
65 TATAAAACAATTTAAAGAAAGTAATAAGGCTTTTGAAGAAAT-GTATGAT-TATAAATAG-ACTT
* *
5532 TT-TTTCCAATGAATACGC-TTTCCTTCACGTTTCTCTAA-GTAGA
127 TTCTTGCCAATGAA-A-GCTTTTCCTTCACGTTTCT-GAAGGTAGA
* *
5575 CTTTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAACAATTTCAACTTAAAATTAATTACGAC
1 CATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAA-AA-TTC-ACTTAAAATTAATTATGAC
* * ** *
5640 ATTATAAAGCAATTAAAAGCGAGTAATAAGGCTTTTGAAGGAATGTATGATTATAAATAGACTTT
63 ATTATAAAACAATTTAAAGAAAGTAATAAGGCTTTTGAAGAAATGTATGATTATAAATAGACTTT
* ** *
5705 TCTTGCTAATGAAAGCATTTTTTTTTCACGTTTCTGAAGGTGGA
128 TCTTGCCAATGAAAGC--TTTTCCTTCACGTTTCTGAAGGTAGA
* * * * * * *
5749 CATTCAATTATTGTCTGTTTTAACCAAAAATTTAAAATAATTCAATTAAAATCAATTATGAGATT
1 CATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCACTTAAAATTAATTATGACATT
5814 ATAAAACAATTTAAAG
66 ATAAAACAATTTAAAG
5830 CGAGNNNNNN
Statistics
Matches: 214, Mismatches: 31, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
171 67 0.31
172 13 0.06
173 81 0.38
174 53 0.25
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (169 bp):
CATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCACTTAAAATTAATTATGACATT
ATAAAACAATTTAAAGAAAGTAATAAGGCTTTTGAAGAAATGTATGATTATAAATAGACTTTTCT
TGCCAATGAAAGCTTTTCCTTCACGTTTCTGAAGGTAGA
Found at i:5677 original size:173 final size:169
Alignment explanation
Indices: 5319--5953 Score: 554
Period size: 171 Copynumber: 3.7 Consensus size: 169
5309 NNNNNNNNNN
* * * * * *
5319 TAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGCCTTTTCTTCTATATG-ATTGACTTTTT
1 TAATAAGGCTTTTGAAGGAAT-GGTGTCTATAAATAGACTTTTTTTCCA-ATGAATAG-CTTTTT
* * ** * *
5383 CTAT-ATGTTTCTC-AAGCCA-AGCATTCAATTGCAGTTTGCTTTAAACAAAAATGTAAAAAAAT
63 CT-TCACGTTTCTCTAAG-TAGA-CATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAAT
* * * **
5445 TCAGCGTAAAATTAATTATGACATTATAAAATAATTTAAAGAAAG
125 TCAACTTAAAATTAATTATGACATTATAAAACAATTTAAAGCGAG
* *
5490 TAATAAGGCTTTTGAAGAAATAGGTGTCTATAAATAGAACTTTTTTTCCAATGAATACGC-TTTC
1 TAATAAGGCTTTTGAAGGAAT-GGTGTCTATAAATAG-ACTTTTTTTCCAATGAATA-GCTTTTT
*
5554 CTTCACGTTTCTCTAAGTAGACTTTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAACAATTT
63 CTTCACGTTTCTCTAAGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAA-AA-TT
* * *
5619 CAACTTAAAATTAATTACGACATTATAAAGCAATTAAAAGCGAG
126 CAACTTAAAATTAATTATGACATTATAAAACAATTTAAAGCGAG
* * *
5663 TAATAAGGCTTTTGAAGGAATGTATGAT-TATAAATAGACTTTTCTTGCTAATGAA-AGCATTTT
1 TAATAAGGCTTTTGAAGGAATG-GTG-TCTATAAATAGACTTTT-TTTCCAATGAATAGC--TTT
* * * * * * *
5726 TTTTTCACGTTTCT-GAAGGTGGACATTCAATTATTGTCTGTTTTAACCAAAAATTTAAAATAAT
61 TTCTTCACGTTTCTCTAA-GTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAAT
* *
5790 TCAA-TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAG
125 TCAACTTAAAATTAATTATGACATTATAAAACAATTTAAAGCGAG
********** * * * *
5834 NNNNNNNNNNTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-CTATAGAATGGCTTTTTC
1 TAATAAGGCTTTTGAAGGAAT-GGTGTCTATAAATAGACTTTTTTTCCAAT-GAATAGCTTTTTC
* *
5898 TACATGTTTCTCTAAGTAGACATTCAATTATAGTCTT-TTTTAACCAAAAATGTAAA
64 TTCACGTTTCTCTAAGTAGACATTCAATTATAGT-TTGTTTTAACCAAAAATGTAAA
5954 NNNNNNNNNN
Statistics
Matches: 376, Mismatches: 67, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
169 51 0.14
170 8 0.02
171 150 0.40
172 32 0.09
173 83 0.22
174 52 0.14
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (169 bp):
TAATAAGGCTTTTGAAGGAATGGTGTCTATAAATAGACTTTTTTTCCAATGAATAGCTTTTTCTT
CACGTTTCTCTAAGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACT
TAAAATTAATTATGACATTATAAAACAATTTAAAGCGAG
Found at i:7582 original size:171 final size:164
Alignment explanation
Indices: 7258--7619 Score: 343
Period size: 171 Copynumber: 2.1 Consensus size: 164
7248 NNNNNNNNNN
*
7258 AAAACAAACTATAATTGAATGCTTGCCTTGGAAACCGTGTAGAAAAAGCCATTCAATGAGAAGAA
1 AAAACAAACTATAATTGAATACTTGCCTTGGAAACCGTGTAGAAAAAGCCATTCAATGAGAAGAA
* * * * ****
7323 AAGTCTATTTATAGTCACTCATTCCGTTAAAAGCTTTATTATTCGCTTTNNNNNNNNNNATAATC
66 AAGTCTATTTATAGTCACCCATTCCGTTAAAAACCTTATTACTCGCTTT------TTTTATAATC
* *
7388 TCATAATTGATTTTAACTTGAATTTTTTTACT-TTTTTCATT
125 TCATAATTGATTTTAACTTGAATTGTTTTA-TATTTTTCA-G
* * *
7429 AAAACAAACTATAATTGAATACTTTCCTTGAGAAA-TGTGTAGAAAAAGCCATTCATTGAGAAGA
1 AAAACAAACTATAATTGAATACTTGCCTTG-GAAACCGTGTAGAAAAAGCCATTCAATGAGAAGA
* * ****
7493 AAAGTTTATTTATAGTGACCCATTCC-TTCAAAAACCTTATTACTCGNNNNNNNNNNTTTTATAA
65 AAAGTCTATTTATAGTCACCCATTCCGTT-AAAAACCTTATTACTCG------CTTTTTTTATAA
* *
7557 TCTCATAATTGATTTTAAGTTGAATTGTTTTATATTTTTGAG
123 TCTCATAATTGATTTTAACTTGAATTGTTTTATATTTTTCAG
* *
7599 AAAACAGACAATAATTGAATA
1 AAAACAAACTATAATTGAATA
7620 TCTACCTTAA
Statistics
Matches: 158, Mismatches: 24, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
170 22 0.14
171 132 0.84
172 4 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.36
Consensus pattern (164 bp):
AAAACAAACTATAATTGAATACTTGCCTTGGAAACCGTGTAGAAAAAGCCATTCAATGAGAAGAA
AAGTCTATTTATAGTCACCCATTCCGTTAAAAACCTTATTACTCGCTTTTTTTATAATCTCATAA
TTGATTTTAACTTGAATTGTTTTATATTTTTCAG
Done.