Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397580.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_569.0, 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: 6126
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:639 original size:151 final size:151
Alignment explanation
Indices: 361--664 Score: 360
Period size: 151 Copynumber: 2.0 Consensus size: 151
351 GTTTACAAAC
* * * * * *
361 CATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTCGAGTGACTATAAATGCACTTTTCGTATCAAT
1 CATTTAAACCAAGTAATAAGGATTTCGAAGCCACGAGTAACTATAAATGCACTTTTCGTAACAAT
* *
426 GGATGACTTTTACTTCACGTTCCCCAAGGCAGACATTCAATTATAACCTTTTCTAACAAAAAATG
66 GAATGACTTTTACTTCACGTTCCCCAAGGCAGACATTCAATTATAACCTTTTCTAACAAAAAATA
*
491 TGAAAA-AATTCAACTTAAAAT
131 T-AAAAGAATTCAACCTAAAAT
* * *
512 CATTTAAACCAAGTAATAAGGATTTTGAAGCCACGAGTAACTATAAGTGGACTTTTC-TAGACAA
1 CATTTAAACCAAGTAATAAGGATTTCGAAGCCACGAGTAACTATAAATGCACTTTTCGTA-ACAA
* * * * * * * * * **
576 TGAATGGCTTTTTCTTTATGTTTCTCGAGGCAGACATTCAATTATAATCTTTTTTAATTAAAAAT
65 TGAATGACTTTTACTTCACGTTCCCCAAGGCAGACATTCAATTATAACCTTTTCTAACAAAAAAT
*
641 ATAAAAGAATTTAACCTAAAAT
130 ATAAAAGAATTCAACCTAAAAT
663 CA
1 CA
665 ATTATAAGAT
Statistics
Matches: 127, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
150 6 0.05
151 121 0.95
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (151 bp):
CATTTAAACCAAGTAATAAGGATTTCGAAGCCACGAGTAACTATAAATGCACTTTTCGTAACAAT
GAATGACTTTTACTTCACGTTCCCCAAGGCAGACATTCAATTATAACCTTTTCTAACAAAAAATA
TAAAAGAATTCAACCTAAAAT
Found at i:791 original size:171 final size:171
Alignment explanation
Indices: 551--6126 Score: 2310
Period size: 171 Copynumber: 32.8 Consensus size: 171
541 GCCACGAGTA
* * * * *
551 ACTATAAGTGGACTTTTC-TAGACAATGAATGGCTTTTTCTTTATGTTTCTCGAGGCAGACATTC
1 ACTATAAATGGACTTTTCTTA-TCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTC
** * * * *
615 AATTATAATCTTTTTTAATTAAAAATATAAAAGAATTTAACCTAAAATCAATTATAAGATTATAA
65 AATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * **
680 AATCATTTAACGTGCGTAATAAGACTTTTGAAAGAATGAATG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * *
722 ACTATAAATGGACTTTTCTTATCAATGAATGTCTCTTTT-TTCACGTTTCTTGAGGTAGACATTC
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCT-TTTTCTTCACGTTTCTCGAGGCAGACATTC
********** * *
786 AATTATAATNNNNNNNNNNCAAAAATGTAAAA-ATATTCAACTTAAAATAAATTATGAGAGTATA
65 AATTATAATCTTTTTTAACCAAAAATGTAAAAGA-ATTCAACTTAAAATCAATTATGAGATTATA
********** *
850 AAACCATTTAAAGTGAGTAANNNNNNNNNNG-AAGAAATCGGTG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAG-AATGGGTG
* * * * * * *
893 ACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCACGTTTCCCAAGGTAGATATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * *
958 ACTATAAT-TTGTTTT-ACCAAAAACGTAAAAAAAAGTTCAACTTAAAATCAATTATGAGATTAT
66 ATTATAATCTT-TTTTAACCAAAAATGT-AAAAGAA-TTCAACTTAAAATCAATTATGAGATTAT
* * ********** * *
1021 AAAACTATTTAAAATGANNNNNNNNNNTTTTGAAGGAATGCGTG
128 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * *
1065 ACTATAAATGGACTTTTCTTATCAATGACTGTCTTTTTCTTTACATTTCTCGAGGTAAACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * *
1130 ATTATAATATGTGTTAATCAAAAATGT-AAAGAAATTTAACTTAAAATCAATTATGAGGTTATAA
66 ATTATAATCTTTTTTAACCAAAAATGTAAAAG-AATTCAACTTAAAATCAATTATGAGATTATAA
********** * * * *
1194 NNNNNNNNNNAGCGAGTAATAAGGCTTTCGAAGGTATGGGTG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * ** *
1236 AATATAAGTAGACTTTT-TTAGTCAATGAATGGGTTTTTCTTCACG-TTCCCTGAGGCAGACATT
1 ACTATAAATGGACTTTTCTTA-TCAATGAATGCCTTTTTCTTCACGTTTCTC-GAGGCAGACATT
* * * * * **
1299 TAATTATAATCTCTTTTAACTAAAAATATAAAAGAATTCAACCTAAAATTGATTATGAGATTATA
64 CAATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATA
**
1364 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATAAGTG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * *
1407 ATTATAAATGGACTTTTATTGTCAATGAATGCCTCTTTT-TTCATGTTTCTCGAGACAGACATTC
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCT-TTTTCTTCACGTTTCTCGAGGCAGACATTC
* ** ** * * * *
1471 AATTATAATCTATTTTAACTGAAAATGTAAAACTATTCAACTCAAAATCAATTATAAAATAATAA
65 AATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAA
** * *
1536 AACCATTGCAAGTGAGTAATAAGGCTTTTGAAGGAATGGGCG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
** * * * * *
1578 ACTATAAACAGACTTTTCTTGTTAATGAATGCCTTTTTATTCATGTTTCTTGAGGCAGACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * ***********
1643 ATTATAGTTTTTTTTAAGCAAAAATGTAAAAAAATTTAACTTAAAATTNNNNNNNNNNTTATAAA
66 ATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
1708 ACTATTTAAAGTGAGTAATAAGGCTTTTGAAAAAATGGATC
131 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * * * * * * *
1749 ACAATAAATAGACTTTTCGT-GCTAATGACTACCTTTTTCTTCACATTTCTCAATGTAAACATTC
1 ACTATAAATGGACTTTTCTTATC-AATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTC
* * * * * * * *
1813 AATTGTAATATTTGTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAATATGAGGTGATAA
65 AATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAA
* *
1878 AACCATTAAAAGTGAGTAATAAGGC--TTGCATAGACATGGGTG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTG-AAAGA-ATGGGTG
* * * * * * * * * * *
1920 ACTATAAGTGAACTTTTCTAATCAATAAATGGCTTTTTCATCAC-ATTCCCTGAGGTAAACACTC
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTC-GAGGCAGACATTC
* * * * *****
1984 AATTATAATATGTTTTAACC-AAAAGGTAAAAGAATTCAACATAAAATCAATTATGAGATNNNNN
65 AATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAA
***** * * *
2048 NNNNNTTTAAAATGAGTAATAAGACTTTTGAAAGGATGGGTG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * * * *
2090 ACTATAAACGGACTTTTCTTGTCAATGAATG-CTTTTTTTTTATGTTTATCGAGGCAAACATTCG
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * *
2154 ATTATAAT-TTGTTTTAACGAAAGA-GTAAAAAAATT-ATACATAAAATCAATTATAAGATTATA
66 ATTATAATCTT-TTTTAACCAAAAATGTAAAAGAATTCA-ACTTAAAATCAATTATGAGATTATA
* *
2216 AAACCATTTAAAGTGAGTAATAAGACTTTT-AAAGGGATGGGTG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAA-GAATGGGTG
* * * * * * *
2259 ACTATAAATTGTCTTTTCTTACCAATGGATG--TTTTT-TT-ATGTTTCTCGAGGCAAACATTCG
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * *
2320 ATTATAATCTATTTTAATCAACAATGTAAAA-ATATTCAAATCAAAATCAATTATGTGATTATAA
66 ATTATAATCTTTTTTAACCAAAAATGTAAAAGA-ATTCAACTTAAAATCAATTATGAGATTATAA
* * * * * *
2384 AACTATTTAAAGCGAGTAATAAGGCTTTT-AAACACTTGAGTAA
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGA-ATGGGT-G
* * * * * * * * * * * *
2427 AC-ATAAATGCACTTTTC--ACGCTAATGGATGACTTTTGCTTTATGTTTCTCAAGGTAAACGTA
1 ACTATAAATGGACTTTTCTTA-TC-AATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATT
* * * * * *********
2489 CAATCATAATATATTTTAATCAAAAATGTAAAAAAATTCAACTNNNNNNNNNNTT-TGAGATTAT
64 CAATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACT-TAAAATCAATTATGAGATTAT
* * * *
2553 AAAACTATTTAAAGTGAGTTATAAGGGTTTT-AAAGGGATGGGTG
128 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAA-GAATGGGTG
* * ** * * * * * *
2597 ATTATAAGTGGACTTTTCTTGCCAATGAATG-CTTTTTTTTTATGTTTCTCAAGACAGACATTCG
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * * * *
2661 ATTATAAT-TTGTTTTATCAAAAAATGTTAAAA-TATTCAAATTAATATTAATT-TTATTATTAT
66 ATTATAATCTT-TTTTAACCAAAAATG-TAAAAGAATTCAACTTAAAATCAATTATGA-GATTAT
* * * * ** *
2723 AAAACTATTTAAAGCGAGTAATAACGCTTTTGAAGGCTTGAGTG
128 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* *** * * * * *
2767 AATATAAACACACTTTTC--ACTCCAATGGATGCCTTTTGCTTCATGTTTCCCAAGGCAGACATT
1 ACTATAAATGGACTTTTCTTA-T-CAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATT
* * * ** ** *
2830 CAATCATAATATATTTTAATAAAAAATGTAAAA-AA-AAAACTTAAAATGAATTATGAGATTATA
64 CAATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATA
** *
2893 AAATTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * ** * * * *
2936 ATTGTAAATGAACTTTTCTTGCCAAT-AATGACTTTTTC-TC-TGTTT-TCTGAAGGTAGA-AAT
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTC-G-AGGCAGACATT
* * *
2996 CAA-TAT-AGC-CTTTTAACTC-AAAATGTAAAACAATTCCAACTTAAAATCAATTAT-AGAATT
64 CAATTATAATCTTTTTTAAC-CAAAAATGTAAAAGAATT-CAACTTAAAATCAATTATGAG-ATT
* * * * * ** *
3056 AGTAAAACTATTTAAAGTAAGAAATAAGGCTTCTGAAGGCTTGAGTG
126 A-TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* ** * * * * * *
3103 ACTATAAATGAACTTTTCACACCAATTG-ATGGCTTTTGT-TTCACGTTTCCCAAGGAAAACATT
1 ACTATAAATGGACTTTTCTTATCAA-TGAATGCCTTTT-TCTTCACGTTTCTCGAGGCAGACATT
** ** * **********
3166 CAATTATCGTGATTTTTAACCAAAAATGTAAAAAAATTCAACTTANNNNNNNNNNTGAGATTATA
64 CAATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATA
* * * *
3231 AAACTATTTAACGTGAGTAATAAAGTTTTTGAAAGAATGGGTG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * * ** * *
3274 ACTGTAAATGAACTTTTCTTACCAATAAATACCTTTTTTTTCACGTTTCTTAAGGTAGACGTTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * * *******
3339 ATTGTAAT-TTGTTCT-ATCATAAATATAAAAAAAATTCAACTTAAAATCAATTATGANNNNNNN
66 ATTATAATCTT-TTTTAACCAAAAATGT-AAAAGAATTCAACTTAAAATCAATTATGAGATTATA
*** * * *
3402 NNNCCATTTAAAGTGAGTAATAAGGGTTTT-AAAGGGATGGATG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAA-GAATGGGTG
* * * * * * * *
3445 ACT-T-TATAGACTTTTCTTACCAATGAATGCCTTTTT-TTCACATTTTTGGAGGTAGACATTCG
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * *
3507 ATTATAA-CTTGATTTAACAAAAAATGTAAAA-ATATTCAAATTAAAATCAATTATGTGATTATA
66 ATTATAATCTT-TTTTAACCAAAAATGTAAAAGA-ATTCAACTTAAAATCAATTATGAGATTATA
********** * * * ** *
3570 NNNNNNNNNNAAGCGAGTAATAAGACTTTTGAAGGCTTGAGTG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * * * * * * * * *
3613 ATTATAAACGCA-TTTT-TCACTCCAAT-AGATGACTTTTCCTTTATGTTTCCCAATGTAAACAA
1 ACTATAAATGGACTTTTCTTA-T-CAATGA-ATGCCTTTTTCTTCACGTTTCTCGAGGCAGAC-A
* *** * * * * * *
3675 TT-AATCATAATAGATTTTAATCAAAACTATAAAAAAATTTAACTTAAAATCAATTATGAGATGA
62 TTCAATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTA
* * * * * * *
3739 TAAAACCTTTTAAAGCGAGTAACAAGGCTTTTGAAGGTATCGGTA
127 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * ** * * * * *
3784 ACTATAAATGAACTTTTTTTAGGAATGAATACCTTTTTCTTTACGTTACGCAAGGCAGACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * * ******
3849 ATTATAATCTGTTCTAACAAAAAATATAAAAAAATTCAACCTAAAATCAATTATGAGATNNNNNN
66 ATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAA
**** * * * *
3914 NNNNTTTAAAGCGAGTAATAAGGCTTTTGAAAAAATGAGAG
131 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * ** * ** * * * * * * *
3955 ACTATAAATAGATTTTTCTTGCCAATAAATATCATTTTCTTCATGTTTTTTGAGGTAAACATTCG
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * * *
4020 ATTATAATATGTTCTAACCAAAAATATAAAA-ATATTGAACTTAAAATCAATTTTGATATTATAA
66 ATTATAATCTTTTTTAACCAAAAATGTAAAAGA-ATTCAACTTAAAATCAATTATGAGATTATAA
********** *
4084 AACCATTTAAAGNNNNNNNNNNGGCTTTTGAAGGAATGGGTG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * *
4126 ACAATAAATGGACTTTTCTTA-CCATGAATGCCTTTTTCTTAATGTTTCTTGAGGCAAACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * * * * ********
4190 ATTTTAGTCTGTTTTAACCAAATATGCAAAGAAAAATCAACTTAAAATCAGTTATGANNNNNNNN
66 ATTATAATCTTTTTTAACCAAAAATGTAAA-AGAATTCAACTTAAAATCAATTATGAGATTATAA
** * * * * *
4255 NNCTATTTAAAGCGAGTAATAATGCTTTTGAAGGAATAGGTG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
** * * * * * *
4297 GTTATAAATGGACTTTTCTT-GCTAATAAATACCTTTTTCTTCACATTT-TCCTAGGCAAACATT
1 ACTATAAATGGACTTTTCTTATC-AATGAATGCCTTTTTCTTCACGTTTCT-CGAGGCAGACATT
* * * * * * *****
4360 TAATTATAAT-TTGTTCTAACCAAAAATATAAAAAAATTCAACTTAAAATAAATTTTGAGNNNNN
64 CAATTATAATCTT-TTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTAT
***** *
4424 NNNNNCATTTAAAGTGAGTAATAAGGGTTTT-AAAGGAATGGGTG
128 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAA-GAATGGGTG
* * * * * * *
4468 GCTATAATTGGAC--TTCATACCAATGAATGCCTTTTTCTTCACATTTCTCAAGGCAAACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * *
4531 ATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
66 ATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
4596 ACTATTTACAGTGAGTAATAAGGTTTTTGAAGGAA----TG
131 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * ** ** ** *
4633 ---AT---T-GACTTTT-TATACCAATAAAAT-CCTTTTTGTTC-ACATTTCCCCGAGCAGGCAC
1 ACTATAAATGGACTTTTCT-TATCAAT-GAATGCC--TTT-TTCTTCACGT-TTCTCG-AGGCAG
* * * * **** * ** * * *
4688 TCAATT-ATAATCTGATC-TAACCAA--AAATATAAAAATATTCAACTTAAAAC-T--AAT-TAT
59 AC-ATTCA-ATTATAATCTTTTTTAACCAAAAATGTAAA-A--GAA-TT-CAACTTAAAATCAAT
* * * * * *
4745 GA-GATTA-T--AAAACCATTTAAA-TTA-TACAATAAGGCTTTTGAAAAAATAGATG
117 TATGA-GATTATAAAACCATTTAAAGTGAGT--AATAAGGCTTTTGAAAGAATGGGTG
* ** ** * * ** * * *
4797 ACTATAAATAGACTTTTCTTGCCAATGAAAACTTTTTTTTTCATATTTCTCAAGGTAAACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
********* * **
4862 ATTATAAT-TTGTTTTAACCNNNNNNNNNNAAA-AATTTAACTTAAAATCAATTATGCTATTATA
66 ATTATAATCTT-TTTTAACC-AAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATA
* * * *
4925 AAGCCTTTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* ** * * * * * *
4968 AATATAAATAAACTTTTCTT-CCTAATGAATGGCTTTTTGTACATGTTTC-CTGAGACAGACATT
1 ACTATAAATGGACTTTTCTTATC-AATGAATGCCTTTTTCTTCACGTTTCTC-GAGGCAGACATT
* * * * * * * *
5031 CAATTATAATCTGTTTTAGCTAAAAATGTAGAAA-AACTCAACTTAAATTTAACTGTGAGATTAT
64 CAATTATAATCTTTTTTAACCAAAAATGTA-AAAGAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
5095 AAAACTATTTAAAGTAAGTAATAATGC-TTTGAAGGAATGGATG
128 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * * ** * *
5138 ACCATAAATGGACTTTTCTTACCAATCATTGCCATTTTCTTCGCGTTTCTTTAGGTAAACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * * ** * *
5203 GTTATAATCTGTGTTAACTAAAAAT-AAAAAAAATTCAAAATAAAATCAATTATGAGGTGATAAA
66 ATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * *
5267 ACCATTGAAAGTGAGTAACAAGGCTTTTGAATGAATTGGTT
131 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* **** * * * * *
5308 ACTATAAACGGACTTTTCCGGCCAATGAATACTTTTTTATTCACGTTTC-CTGAGGTAAACATTC
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTC-GAGGCAGACATTC
* * * * * * * **********
5372 AATTATTATCTGTTCTAACTAAAAATATAAAACAATTCAACTTAAAATCAATTTTNNNNNNNNNN
65 AATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAA
* * **
5437 AACCATTTAAAGTGAGTAATAAGGCTTTAGAAGGAATAAGTG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * * * *
5479 GCTATAAATGGACTTTTCTTGTCAATAAATGCCTTTTTCTTCATGTTTCTTGAGACGGACATTAA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * * * * * * *****
5544 ATTATAGTATGCTTTCAA-GAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGATNNNNN
66 ATTATAATCT-TTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAA
***** * * * *
5608 NNNNNTTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGAGTG
130 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * ** * * * * * *
5650 ACTATAATTGGACTTTACTTGCCAATGACTACCTTTCTCTTTAGGTTTCTTGAGGCAGACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * ******
5715 ATTAT-AGCTTGTTTTAA-GAAAAA-GTAAAAAAAATTCAACTTAAAATCAATTATGAGNNNNNN
66 ATTATAATCTT-TTTTAACCAAAAATGT-AAAAGAATTCAACTTAAAATCAATTATGAGATTATA
**** * * *
5777 NNNNCATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGGATG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * * * * * *
5820 ACTCTAAATAGACTTTTCTTGTAAATAAATGACTTTTTCTTTACGGTTC-CTGAGGCAGATATTT
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTC-GAGGCAGACATTC
* * * * **
5884 AATTGTAATC-TGTTTCACCAAAAATGTAAAAAAATTCAACCGAAAATCAAATT-TGAGATTATA
65 AATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATC-AATTATGAGATTATA
* ********** * *
5947 AAACCATATAAAGTGAGTAANNNNNNNNNNGAAGGAATGGGAG
129 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
** * * * * ** * * *
5990 ACTATAAATGGACTTTTCTTGCCAATGATTGCCTATCTCTTTAAATTTATCTAGGGAGACATTCA
1 ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* * * *
6055 ATTATAGTCTGTTTTAAGCAAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGTTTATAAA
66 ATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAA
6119 ACCATTTA
131 ACCATTTA
Statistics
Matches: 4014, Mismatches: 1205, Indels: 373
0.72 0.22 0.07
Matches are distributed among these distances:
158 4 0.00
159 3 0.00
160 38 0.01
161 3 0.00
162 19 0.00
163 26 0.01
164 20 0.00
165 21 0.01
166 85 0.02
167 169 0.04
168 127 0.03
169 432 0.11
170 793 0.20
171 2003 0.50
172 232 0.06
173 39 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
ACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGCAGACATTCA
ATTATAATCTTTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAA
ACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
Found at i:2805 original size:341 final size:339
Alignment explanation
Indices: 2194--2972 Score: 949
Period size: 341 Copynumber: 2.3 Consensus size: 339
2184 AAATTATACA
* * * *
2194 TAAAATCAATTATAAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTAAAGGGATGGGTG
1 TAAAATGAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGGATGGGTG
* * * * * * *
2259 ACTATAAATTGTCTTTTCTTACCAATGGATG---TTTTTTTATGTTTCTCGAGGCAAACATTCGA
66 ATTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTTTTATGTTTCTCAAGACAAACATTCGA
* *
2321 TTATAATCTATTTTAATCAACAATGTAAAAATATTCAAATCAAAATCAATTATGTGATTATAAAA
131 TTATAATCTATTTTAATCAAAAATGTAAAAATATTCAAATCAAAATCAATTATATGATTATAAAA
* ** *
2386 CTATTTAAAGCGAGTAATAAGGCTTTTAAACACTTGAGTAAACATAAATGCACTTTTCACGCTAA
196 CTATTTAAAGCGAGTAATAACGCTTTTAAACACTTGAGTAAACATAAACACACTTTTCACGCCAA
* * * * *
2451 TGGATGACTTTTGCTTTATGTTTCTCAAGGTAAACGTACAATCATAATATATTTTAATCAAAAAT
261 TGGATGACTTTTGCTTCATGTTTCCCAAGGCAAACATACAATCATAATATATTTTAATAAAAAAT
*
2516 GTAAAAAAATTCAACT
326 GTAAAAAAA--AAACT
********* * *
2532 NNNNNNNNNNTT-TGAGATTATAAAACTATTTAAAGTGAGTTATAAGGGTTTTAAAGGGATGGGT
1 -TAAAATGAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGGATGGGT
* *
2596 GATTATAAGTGGACTTTTCTTGCCAATGAATGCTTTTTTTTTATGTTTCTCAAGACAGACATTCG
65 GATTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTTTTATGTTTCTCAAGACAAACATTCG
* * * * * * * *
2661 ATTATAATTTGTTTT-ATCAAAAAATGTTAAAATATTCAAATTAATATTAATTTTATTATTATAA
130 ATTATAATCTATTTTAATC-AAAAATGTAAAAATATTCAAATCAAAATCAATTATATGATTATAA
* ** * * *
2725 AACTATTTAAAGCGAGTAATAACGCTTTTGAAGGCTTGAGTGAATATAAACACACTTTTCACTCC
194 AACTATTTAAAGCGAGTAATAACGCTTTTAAACACTTGAGTAAACATAAACACACTTTTCACGCC
* * *
2790 AATGGATGCCTTTTGCTTCATGTTTCCCAAGGCAGACATTCAATCATAATATATTTTAATAAAAA
259 AATGGATGACTTTTGCTTCATGTTTCCCAAGGCAAACATACAATCATAATATATTTTAATAAAAA
2855 ATGTAAAAAAAAAACT
324 ATGTAAAAAAAAAACT
* * *
2871 TAAAATGAATTATGAGATTATAAAATTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
1 TAAAATGAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGGATGGGTG
* *
2936 ATTGTAAATGAACTTTTCTTGCCAAT-AATGACTTTTT
66 ATTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTT
2973 CTCTGTTTTC
Statistics
Matches: 365, Mismatches: 69, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
338 79 0.22
339 83 0.23
340 3 0.01
341 200 0.55
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (339 bp):
TAAAATGAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGGATGGGTG
ATTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTTTTATGTTTCTCAAGACAAACATTCGA
TTATAATCTATTTTAATCAAAAATGTAAAAATATTCAAATCAAAATCAATTATATGATTATAAAA
CTATTTAAAGCGAGTAATAACGCTTTTAAACACTTGAGTAAACATAAACACACTTTTCACGCCAA
TGGATGACTTTTGCTTCATGTTTCCCAAGGCAAACATACAATCATAATATATTTTAATAAAAAAT
GTAAAAAAAAAACT
Found at i:4527 original size:169 final size:160
Alignment explanation
Indices: 4259--4595 Score: 347
Period size: 169 Copynumber: 2.0 Consensus size: 160
4249 NNNNNNNNCT
* * * * * *
4259 ATTTAAAGCGAGTAATAATGCTTTTGAAGGAATAGGTGGTTATAAATGGACTTTTCTTGCTAATA
1 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGGCTATAAATGGAC-TTTCATACCAATA
* * *
4324 AATACCTTTTTCTTCACATTTTCCTAGGCAAACATTTAATTATAATTTGTTCTAACCAAAAATAT
65 AATACCTTTTTCTTCACATTTTCCAAGGCAAACATTCAATTATAATCTGTTCTAACCAAAAATAT
*
4389 AAAAAAATTCAACTTAAAATAAATTTTGAGNNNNNNNNNNC
130 AAAAAAATTCAACTTAAAATAAATTATGAG----------C
* * * * *
4430 ATTTAAAGTGAGTAATAAGGGTTTTAAAGGAATGGGTGGCTATAATTGGAC-TTCATACCAATGA
1 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGGCTATAAATGGACTTTCATACCAATAA
* * * * *
4494 ATGCCTTTTTCTTCACA-TTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAACTAAAAATGT
66 ATACCTTTTTCTTCACATTTTC-CAAGGCAAACATTCAATTATAATCTGTTCTAACCAAAAATAT
*
4558 AAAAAAATTCAACTTAAAATCAATTATGAG-
130 AAAAAAATTCAACTTAAAATAAATTATGAGC
4588 ATTATAAA
1 ATT-TAAA
4596 ACTATTTACA
Statistics
Matches: 143, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
158 3 0.02
159 4 0.03
168 4 0.03
169 88 0.62
171 44 0.31
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.35
Consensus pattern (160 bp):
ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGGCTATAAATGGACTTTCATACCAATAA
ATACCTTTTTCTTCACATTTTCCAAGGCAAACATTCAATTATAATCTGTTCTAACCAAAAATATA
AAAAAATTCAACTTAAAATAAATTATGAGC
Found at i:5876 original size:170 final size:162
Alignment explanation
Indices: 5440--5933 Score: 397
Period size: 170 Copynumber: 2.9 Consensus size: 162
5430 NNNNNNNAAC
* * *
5440 CATTTAAAGTGAGTAATAAGGCTTTAGAAGGAATAAGTGGCTATAAATGGACTTTTCTTGTCAAT
1 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGTCAAT
* * * * *
5505 AAATGCCTTTTTCTTCATGTTTCTTGAGACGGACATTAAATTATAGTATGCTTTCAAGAAAAATA
66 AAATGACTTTTTCTTTA-GGTTCTTGAGGCAGACATTAAATTATAGTATGCTTTCAAGAAAAATA
5570 TAAAAAAATTCAACTTAAAATCAATTATAAGAT
130 TAAAAAAATTCAACTTAAAATCAATTATAAGAT
** * * * *
5603 NNNNNNNNNNTTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGAGTGACTATAATTGGACTTTAC
1 --------CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTC
* * * * * *
5668 TTGCCAATGACT-ACCTTTCTCTTTAGGTTTCTTGAGGCAGACATTCAATTATAGCT-TG-TTTT
58 TTGTCAATAAATGA-CTTTTTCTTTAGG-TTCTTGAGGCAGACATTAAATTATAG-TATGCTTTC
* **
5730 AAGAAAAAGTA-AAAAAAATTCAACTTAAAATCAATTATGAGNNNNNNNNNN
120 AAGAAAAA-TATAAAAAAATTCAACTTAAAATCAATTATAAG--------AT
* * * *
5781 CATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATG-GATGACTCTAAATAGACTTTTCTTGTAAA
1 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAG-TGACTATAAATGGACTTTTCTTGTCAA
* * * * * * **
5845 TAAATGACTTTTTCTTTACGGTTCCTGAGGCAGATATTTAATTGTAATCTG-TTTCACCAAAAAT
65 TAAATGACTTTTTCTTTA-GGTTCTTGAGGCAGACATTAAATTATAGTATGCTTTCAAGAAAAAT
* **
5909 GTAAAAAAATTCAACCGAAAATCAA
129 ATAAAAAAATTCAACTTAAAATCAA
5934 ATTTGAGATT
Statistics
Matches: 258, Mismatches: 48, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
169 3 0.01
170 158 0.61
171 96 0.37
172 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.33
Consensus pattern (162 bp):
CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGTCAAT
AAATGACTTTTTCTTTAGGTTCTTGAGGCAGACATTAAATTATAGTATGCTTTCAAGAAAAATAT
AAAAAAATTCAACTTAAAATCAATTATAAGAT
Done.