Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398472.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1769.0, 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: 8256
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.31
Warning! 1100 characters in sequence are not A, C, G, or T
Found at i:538 original size:173 final size:168
Alignment explanation
Indices: 1--1014 Score: 656
Period size: 171 Copynumber: 5.9 Consensus size: 168
* *
1 GACATTTAATTATAATTTATTTTAA-TAAGCAATATAAAAAAATTTAACTTAAAATCAGTTATGA
1 GACATTCAATTATAATTTATTTTAACTAA-AAATATAAAAAAA-TTAACTTAAAATCA-TTATGA
* * * * * * **
65 GAGTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTCGGGTGACTATAAATAAACTT
63 GATTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCGAAGGCTTGAG-GACTATAAATGGACTT
* * * *
130 TGCTTGCCAATGAATGGCTTTTTCTTCATGTTTCCTGAAGCA
127 TTCTTGCCAATGAATGGCTTTTTCTTCATGTTTTCTAAAGTA
* * **
172 AACATTCAATTATAATTTTTTTTAACTAAAAACGTAAAAAAATTAACTTAAAATCAATTATGAGA
1 GACATTCAATTATAATTTATTTTAACTAAAAATATAAAAAAATTAACTTAAAATC-ATTATGAGA
* * * ******** *
237 TTATAAAGCCATTTAAAGCATGTAATAAGGCTTTCGAAGG-TGTG-GNNNNNNNNNNATGGGCTT
65 TTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCGAAGGCT-TGAG--GACTATAAATGGACTT
* **
300 TTCTTGCCAATGAATGACTTTTTCTTCATGTTTTCTAGGGTCA
127 TTCTTGCCAATGAATGGCTTTTTCTTCATGTTTTCTAAAGT-A
* * * *
343 -ACATTCAAATATTATCTATTTTAACTAAAAATATAAAAAAATCTACCTTAAAATCGATTATGAG
1 GACATTCAATTATAATTTATTTTAACTAAAAATATAAAAAAAT-TAACTTAAAATC-ATTATGAG
* * *
407 ATTTATAAAACCATTTAAAGTAAGTACTAGGGCTTTCAAAGGCTTGAAGGACTATAAATGGACTT
64 A-TTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCGAAGGCTTG-AGGACTATAAATGGAC-T
* * * ** *
472 TTTCTTACCAATGGATGGCTTTTACTTCACATTTTCTAAAATA
126 TTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTTCTAAAGTA
* ********** *
515 GACATTCAATTATAATATATTTTAACTAAAAATA-AAAAAANNNNNNNNNNAATCAATTATAAGA
1 GACATTCAATTATAATTTATTTTAACTAAAAATATAAAAAAATTAACTTAAAATC-ATTATGAGA
* * * * * * *
579 TTATAAAATCGTTTAAAGCT-AGTAATAAGGCTTTCAAAGGCATGAAAGACTATAAATGAATTTT
65 TTATAAAACCATTTAAAG-TAAGTAATAAGGCTTTCGAAGGCTTG-AGGACTATAAATGGACTTT
** * * * * * *
643 TCTTGTTAATAAATGACTTTTTCTTCAAGTTTCCCAAGGTA
128 TCTTGCCAATGAATGGCTTTTTCTTCATGTTTTCTAAAGTA
* * * *********
684 GACATTCAATTATAATCTAATTTAACCAAAAATATAAAAAAATTAAACTTNNNNNNNNNNATGAG
1 GACATTCAATTATAATTTATTTTAACTAAAAATATAAAAAAATT-AACTT-AAAATCATTATGAG
* * * * * *
749 ATTATAAAACCATTTAAAGCATGTAATTAGGCTTTCGAAGGCATGTGCGAATATAAATGGACTTT
64 ATTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCGAAGGCTTGAG-GACTATAAATGGACTTT
* * * *
814 TCTTGTCAATGAATGGCTTTTTCTTCATGTTTTCGAAGGAA
128 TCTTGCCAATGAATGGCTTTTTCTTCATGTTTTCTAAAGTA
* * * * * * ********* * *
855 AACATTCAAATATTATCTCTTTTAACCAAAAATATAANNNNNNNNNNCTGAAAATAAATTATGAG
1 GACATTCAATTATAATTTATTTTAACTAAAAATATAA-AAAAATTAACTTAAAAT-CATTATGAG
* * * * * * *
920 ATTATAAAACTATTTAAAGTGAGGAATAAGGCTTTTGAAGGCTTGAATGACTATAAATGCACTTC
64 ATTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCGAAGGCTTG-AGGACTATAAATGGACTTT
* * * *
985 ACTTGCAAATTG-GTGGCTTTTGCTTCATGT
128 TCTTGCCAA-TGAATGGCTTTTTCTTCATGT
1015 NNNNNNNNNN
Statistics
Matches: 641, Mismatches: 180, Indels: 44
0.74 0.21 0.05
Matches are distributed among these distances:
169 64 0.10
170 187 0.29
171 269 0.42
172 55 0.09
173 65 0.10
174 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (168 bp):
GACATTCAATTATAATTTATTTTAACTAAAAATATAAAAAAATTAACTTAAAATCATTATGAGAT
TATAAAACCATTTAAAGTAAGTAATAAGGCTTTCGAAGGCTTGAGGACTATAAATGGACTTTTCT
TGCCAATGAATGGCTTTTTCTTCATGTTTTCTAAAGTA
Found at i:636 original size:170 final size:161
Alignment explanation
Indices: 392--725 Score: 316
Period size: 169 Copynumber: 2.0 Consensus size: 161
382 AATCTACCTT
* * * * * *
392 AAAATCGATTATGAGATTTATAAAACCATTTAAAGTAAGTACTAGGGCTTTCAAAGGCTTGAAGG
1 AAAATCAATTATAAGATTTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCAAAGGCATGAAAG
* ** * * *
457 ACTATAAATGGACTTTTTCTTACCAATGGATGGCTTTTACTTCACA-TTTTCTAAAATAGACATT
66 ACTATAAAT-GAATTTTTCTTACCAATAAATGACTTTTACTTCA-AGTTTCCCAAAATAGACATT
* *
521 CAATTATAATATATTTTAACTAAAAATA-AAAA
129 CAATTATAATATAATTTAACCAAAAATATAAAA
* *
553 AANNNNNNNNNNAATCAATTATAAGA-TTATAAAATCGTTTAAAGCT-AGTAATAAGGCTTTCAA
1 AA----------AATCAATTATAAGATTTATAAAACCATTTAAAG-TAAGTAATAAGGCTTTCAA
*** * *
616 AGGCATGAAAGACTATAAATGAATTTTTCTTGTTAATAAATGACTTTTTCTTCAAGTTTCCCAAG
55 AGGCATGAAAGACTATAAATGAATTTTTCTTACCAATAAATGACTTTTACTTCAAGTTTCCCAAA
* *
681 GTAGACATTCAATTATAATCTAATTTAACCAAAAATATAAAA
120 ATAGACATTCAATTATAATATAATTTAACCAAAAATATAAAA
723 AAA
1 AAA
726 TTAAACTTNN
Statistics
Matches: 137, Mismatches: 23, Indels: 27
0.73 0.12 0.14
Matches are distributed among these distances:
160 1 0.01
161 2 0.01
168 1 0.01
169 65 0.47
170 55 0.40
171 13 0.09
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.33
Consensus pattern (161 bp):
AAAATCAATTATAAGATTTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCAAAGGCATGAAAG
ACTATAAATGAATTTTTCTTACCAATAAATGACTTTTACTTCAAGTTTCCCAAAATAGACATTCA
ATTATAATATAATTTAACCAAAAATATAAAA
Found at i:1618 original size:176 final size:175
Alignment explanation
Indices: 1264--1637 Score: 475
Period size: 176 Copynumber: 2.1 Consensus size: 175
1254 NNAAGGCTTT
* * * * * *
1264 AGTGACTATGAATGAACTTTTCTTG-CTAATGGATGGCTTTTGTTTCACGTTTTTTGAAGCAAAT
1 AGTGACTATAAATGGACTTTTCTCGAC-AATGGATGGCTTTTGCTTCACGTTTTCTGAAGCAAAC
* *
1328 ATTCAATTTAATTATAATATATTTTAATAGAAAGATAAAAAAATTCAAACTAAAATCAATTATGA
65 ATTCAATTCAATTATAATATATTTTAATAAAAAGATAAAAAAATTCAAACTAAAATCAATTATGA
* * * ** *
1393 TATTATAAAACCTTTTAAAGTGAGTAATAAGGTTCTCAAAGGCTTG
130 GATTATAAAACCATTTAAAGCGAGTAATAAAATTCTCAAAGACTTG
* * * *
1439 AGTGACTATAAATTGATTTTTCTCGACAATGGGTGGCTTTTGCTTCATC-TTTTCTGAAGCAGAC
1 AGTGACTATAAATGGACTTTTCTCGACAATGGATGGCTTTTGCTTCA-CGTTTTCTGAAGCAAAC
* * * *
1503 ATTCAATTCAATTATAATATATTTTAATAAAAAATATAAAAAAATT-TAACTTACAATCTATTAT
65 ATTCAATTCAATTATAATATATTTTAAT-AAAAAGATAAAAAAATTCAAAC-TAAAATCAATTAT
* *
1567 GAGATTATAAAACCATTTAAAGCGAGTAATAAAATTTTCGAAGACTTG
128 GAGATTATAAAACCATTTAAAGCGAGTAATAAAATTCTCAAAGACTTG
1615 AGTGACTATAAATGGACTTTTCT
1 AGTGACTATAAATGGACTTTTCT
1638 TTCTGATAGA
Statistics
Matches: 169, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
175 80 0.47
176 89 0.53
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (175 bp):
AGTGACTATAAATGGACTTTTCTCGACAATGGATGGCTTTTGCTTCACGTTTTCTGAAGCAAACA
TTCAATTCAATTATAATATATTTTAATAAAAAGATAAAAAAATTCAAACTAAAATCAATTATGAG
ATTATAAAACCATTTAAAGCGAGTAATAAAATTCTCAAAGACTTG
Found at i:1670 original size:176 final size:176
Alignment explanation
Indices: 1312--1800 Score: 494
Period size: 176 Copynumber: 2.8 Consensus size: 176
1302 TTTGTTTCAC
* * * * *
1312 GTTTTTTGAAGCAAATATTCAATTTAATTATAATATATTTTAAT-AGAAAGATAAAAAAATTCAA
1 GTTTTCTGAAGCAAACATTCAATTCAATTATAATATATTTTAATAAGAAATATAAAAAAATTCTA
* * * * * *
1376 AC-TAAAATCAATTATGATATTATAAAACCTTTTAAAGTGAGTAATAAGGTTCTCAAAGGCTTGA
66 ACTTAAAATCAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAGATTTTCGAA-GCTTGA
* * * * * * * *
1440 GTGACTATAAATTGATTTTTCTCGACAATGGGTGGCTTTTGCTTCAT
130 GTGACTATAAATGGACTTTTCTCGACAATAGATGACTTGTACCTCAT
* * *
1487 CTTTTCTGAAGCAGACATTCAATTCAATTATAATATATTTTAATAAAAAATATAAAAAAATT-TA
1 GTTTTCTGAAGCAAACATTCAATTCAATTATAATATATTTTAATAAGAAATATAAAAAAATTCTA
* * * *
1551 ACTTACAATCTATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAATTTTCGAAGACTTGA
66 ACTTAAAATCAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAGATTTTCGAAG-CTTGA
** *
1616 GTGACTATAAATGGACTTTTCT-TTCTGATAGATGACTTGTACCTCAT
130 GTGACTATAAATGGACTTTTCTCGAC-AATAGATGACTTGTACCTCAT
* * * * * * * *
1663 GTTTTCTG-AG-ATAGA-T--ATTCAATTATAATCTATTTTCACAAGCAATATAATATAATTCT-
1 GTTTTCTGAAGCAAACATTCAATTCAATTATAATATATTTTAATAAGAAATATAAAAAAATTCTA
* * * *
1722 ACTTAAAATCAATTATGACATTATGAAATCATTTAAAGCGAGTAATAAGACTTTCGAACGCTTGT
66 ACTTAAAATCAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAGATTTTCGAA-GCTTGA
*
1787 CTGACTATAAATGG
130 GTGACTATAAATGG
1801 NNNNNNNNNN
Statistics
Matches: 261, Mismatches: 47, Indels: 16
0.81 0.15 0.05
Matches are distributed among these distances:
171 102 0.39
172 2 0.01
173 1 0.00
174 3 0.01
175 46 0.18
176 107 0.41
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (176 bp):
GTTTTCTGAAGCAAACATTCAATTCAATTATAATATATTTTAATAAGAAATATAAAAAAATTCTA
ACTTAAAATCAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAGATTTTCGAAGCTTGAG
TGACTATAAATGGACTTTTCTCGACAATAGATGACTTGTACCTCAT
Found at i:2622 original size:171 final size:171
Alignment explanation
Indices: 2326--2709 Score: 492
Period size: 171 Copynumber: 2.2 Consensus size: 171
2316 NNNNNNNNNN
* * * ** *
2326 AATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGGTTTTTGAAGGCTTTAGGGACT
1 AATCAATTATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTATAGGGACT
* *
2391 ATAAATGGACATTTCTCACCAATAGATGGCTTTTGCTTCATGTTTTCCAAAGTAGACATTCAATT
66 ATAAATGGACATTTCTCACCAATAGATAGCTTTTGCTTCATATTTTCCAAAGTAGACATTCAATT
*
2456 ATAATATACTTTAATAAAAAATGTAAAGA-AATTCAACTTAA
131 ATAATATACTTTAATAAAAAATGTAAA-ACAATTCAACCTAA
* **
2497 AATCAATTACTG-CATTATAAAACTATTTAAAGCAAGTAATAAGGCTTTCAAAGG-TATAGGTGA
1 AATCAATTA-TGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTATAGG-GA
* * *
2560 CTATAAATGGACTTTTCT-ATCCAAT-GAATAGCTTTTGCTTCATATTTT-CTAAGATGGACATT
64 CTATAAATGGACATTTCTCA-CCAATAG-ATAGCTTTTGCTTCATATTTTCCAAAG-TAGACATT
* *
2622 CAATTATAATATATTTTAGTAAAAAATGTAAAACAATTCAACCTAA
126 CAATTATAATATACTTTAATAAAAAATGTAAAACAATTCAACCTAA
* * *
2668 AACCAATTGTGATATTATAAAACCATTTAAAGTGAGTAATAA
1 AATCAATTATGACATTATAAAACCATTTAAAGTGAGTAATAA
2710 TTCTTNNNNN
Statistics
Matches: 183, Mismatches: 23, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
170 14 0.08
171 167 0.91
172 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (171 bp):
AATCAATTATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTATAGGGACT
ATAAATGGACATTTCTCACCAATAGATAGCTTTTGCTTCATATTTTCCAAAGTAGACATTCAATT
ATAATATACTTTAATAAAAAATGTAAAACAATTCAACCTAA
Found at i:3575 original size:170 final size:171
Alignment explanation
Indices: 2813--4555 Score: 1249
Period size: 170 Copynumber: 10.2 Consensus size: 171
2803 NNNNNNNNNN
* * *
2813 CATTCAATTATAATCTATTTTAACCAACAGTATAAAAAAA-TCAACTTAAAATCAATTATGAGAT
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
* *
2877 TATGAAAA-CATTTAAAACAAGTAATAAGGCTTTAGAAGGCATTGA-TGACTATAAATGGACTTT
66 TAT-AAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGC-TTGAGTGACTATAAATGGACTTT
* * **
2940 TCTTGCCAATGAAT-AGCTTTTTCTTCA-CCTTTCCTGAA-GCAGA
129 TCTTGCCAATGGATGA-CTTTTGCTTCATGTTTTCC--AAGGCAGA
* * * * * * * **********
2983 CATTCAACTGTAATATGTATTAACCATAAATATAAACAAATCCANNNNNNNNNNAATTATGAGAT
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
** ** * * * *
3048 TATAAAATTATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTAACTAATTATAAATGGAC-TTTC
66 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTTTC
* * * * *
3112 GTACCAATGG--GCAGCTTTTGCTTTACG-TTTCTTAAGGCAGA
131 TTGCCAATGGATG-A-CTTTTGCTTCATGTTTTC-CAAGGCAGA
* * * *
3153 CATTCAATTATAATCTATTTTAACCAACAATATTAAAAAATT-AAATTAAAATCAATTATGAGAT
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
********** * * * *
3217 TATAANNNNNNNNNNAGCAAGTAATTAGGCTTTCGAAGG-TATGCA-CGACAATAAATGGACTTT
66 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCT-TG-AGTGACTATAAATGGACTTT
* * * * * * *
3280 TCTTACCAATGAATGGCTTTT-TTTGCTTATTTCCCATA-GCAGA
129 TCTTGCCAATGGATGACTTTTGCTT-CATGTTTTCCA-AGGCAGA
* * *** * *
3323 CACTCAAATATAAT-TAGTTTTAATTGAAAATGT-AAATAATTCAACTTAAAATCAATTATGAGA
1 CATTCAATTATAATATA-TTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
********** * * *
3386 TNNNNNNNNNNTTTAAAGCGAGTAATAAGGCTTTTAAACGCTAT-AGTGACTATAAATGGACTTT
65 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCT-TGAGTGACTATAAATGGACTTT
* * *
3450 TCTTACCAATGGATGACTTTTGCTTCACGTTTTCCAAGGCACA
129 TCTTGCCAATGGATGACTTTTGCTTCATGTTTTCCAAGGCAGA
* * * * *
3493 CATTCAGTTATAATATATTTTAA-TAAAAATGTAAAAAAATTCAACTCAAAATCAATTATGATAT
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * * *
3557 TATAAAACCATATAAAGCGAGTAATAATGCTTTTGAAGGCATGAAG-GACTATAAATGAACTTTT
66 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTG-AGTGACTATAAATGGACTTTT
* * * * * * *
3621 CTTTCCGATGGATGGAC-TTTGGTTCAT-ATTTCCTGAGGGAAA
130 CTTGCCAATGGAT-GACTTTTGCTTCATGTTTTCC-AAGGCAGA
* ** ** * * *
3663 CATTCAATTATAATTTATTTTAAGTAGCAATATAAAAGAATTTGAA-TAAAAATCAATTATGAGA
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAA-AAATTCAACTTAAAATCAATTATGAGA
* * * *
3727 -TAGTAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGTTTGGGTGACTATAAATGGATTTT
65 TTA-TAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTT
** * * **
3791 TCTTGCCAATAAAT-ATCTTTTTCTTCATGTTTCCCAAGATAGA
129 TCTTGCCAATGGATGA-CTTTTGCTTCATGTTTTCCAAGGCAGA
* * * * * * *
3834 CAATT-AATTACAATTTGTTTTAGCC-AAAATACAAAAAAACTT-AATTTAAAATCGATTATGAG
1 C-ATTCAATTATAATATATTTTAACCAAAAATATAAAAAAA-TTCAACTTAAAATCAATTATGAG
* * * * * *
3896 ATTATAAAACCACTTAAAGCTAGCAATAAGGCTTTCGAAGGCTTGAGTGACTATGAATAGACTTT
64 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTT
* * * * * *
3961 TCTTGCCAATGGATGGCTTTTGCTTTATATTTT-TAGAAGTAGA
129 TCTTGCCAATGGATGACTTTTGCTTCATGTTTTCCA-AGGCAGA
* * *
4004 CATTCAATTATAATATATTTTAATC-AAAA-ATAAAACAATTCAACTTAAAATCAATCATGAGAT
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
** * * * * *
4067 GGTAAAACCATTTAAA-AAAGTAATAAGACTTTCGAAGGCAT-AGATGACTATAAATAGACTTTT
66 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAG-TGACTATAAATGGACTTTT
* * * * * *
4130 CTTGCCAATGAAT-AGCTTTTTCTTCATGTTTCCCTAGACAAA
130 CTTGCCAATGGATGA-CTTTTGCTTCATGTTTTCCAAGGCAGA
* * * * * * *
4172 CATTTAAATATTATCTGTTTTAACCAAAAATGTAAAAAAA-TCTAACTTAAAATTAATTATGAGA
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATTC-AACTTAAAATCAATTATGAGA
* * ** *
4236 TTGTAAAACCATTTAAGGCGTGTAATAAGG-TTTTCAAAGAG-TTGAGTGACTATAAATGGACTT
65 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTT-GAAG-GCTTGAGTGACTATAAATGGACTT
* * * *
4299 TTCCTACCAATGGACGACTTTTGCTTCATG-TTTCCTAAGGTAGA
128 TTCTTGCCAATGGATGACTTTTGCTTCATGTTTTCC-AAGGCAGA
* ** * * * * *
4343 CATTTAAACATAATTTGTTTTAACCATAAATATAAAAACATTTAACTTAAAATCAATTATGAGAT
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
* *
4408 TATAAAACTATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATGGACTTTTC
66 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTTTC
* * *
4473 TTGCTAATGGATGACTTTTGCTTCATGTTTCCCAAGGCATA
131 TTGCCAATGGATGACTTTTGCTTCATGTTTTCCAAGGCAGA
* * * *
4514 CATTCAGTTAGAATATATTTTAACCACAAATGTAAAAAAATT
1 CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATT
4556 TTAACTTTCG
Statistics
Matches: 1211, Mismatches: 303, Indels: 117
0.74 0.19 0.07
Matches are distributed among these distances:
167 2 0.00
168 88 0.07
169 132 0.11
170 552 0.46
171 411 0.34
172 26 0.02
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.34
Consensus pattern (171 bp):
CATTCAATTATAATATATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTTTC
TTGCCAATGGATGACTTTTGCTTCATGTTTTCCAAGGCAGA
Found at i:4893 original size:170 final size:169
Alignment explanation
Indices: 4580--5439 Score: 778
Period size: 170 Copynumber: 5.1 Consensus size: 169
4570 AAAACCATTC
* * * * ** * * *
4580 ATGGATTTTTCTTTCTAATTGATGGCTTTTGCTTCATGTTT-TTTAAGGGAGACATTCAATTATA
1 ATGGACTTTTCTTACCAATGGATGGCTTTTGCTTCACATTTCCTGAA-GCAGACATTCAATTATA
* * *
4644 ATCTATTTTAACCAA-CAATATAAATGAATTCAACTTAAAATCAATTATGAGATTGTAAAACTAT
65 ATAT-TTTTAA-CAATAAATATAAA-AAATTCAACTTAAAATCAATTATGAGATTGTAAAACTAT
* *
4708 TTAAAGCAAGTAATAAGACTTTCGAAGGTATGGGTGACTATAA
127 TTAAAGCGAGTAATAAGACTTTCGAAGGCATGGGTGACTATAA
* * * ** *
4751 ATGGACTTTTCTTACCAATGAAT-GTTTTTTCTTCATGTTTCCT-ATAGCAGACATTCAAATATA
1 ATGGACTTTTCTTACCAATGGATGGCTTTTGCTTCACATTTCCTGA-AGCAGACATTCAATTATA
* * * *
4814 ATATGTTTTAACTATAAATATACAAAAATTCAGCTTAACATCAATTATGAGATTGTAAAACCATT
65 ATAT-TTTTAACAATAAATATA-AAAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATT
* ** * ** *
4879 TAAAGCGAGTAATAAGTCTTTTAAAGGCTTTAGTGACCATAA
128 TAAAGCGAGTAATAAGACTTTCGAAGGCATGGGTGACTATAA
* ** * *
4921 ATGGACTTTTCTTACAAATGGATGGCTTTTGCTTCATGTTT-CTCAAAGCAGACATTCAAATATA
1 ATGGACTTTTCTTACCAATGGATGGCTTTTGCTTCACATTTCCT-GAAGCAGACATTCAATTATA
* * * *
4985 ATCTGTTTTAACAATGAATATAAAAAACTTTAACTGAAAATCAATTATGAGATTGTAAAACTATT
65 ATAT-TTTTAACAATAAATATAAAAAA-TTCAACTTAAAATCAATTATGAGATTGTAAAACTATT
* * * *
5050 TAAAGTGAGTAACAAGGC-TTCGAAGGAATGGGTGACTATAA
128 TAAAGCGAGTAATAAGACTTTCGAAGGCATGGGTGACTATAA
* ** * * * * * *
5091 ATGGACTTTTTTTGTCAATGGATGGCTTCTACTTCACATTTTCTGAGGCCGATATTCAATTATAA
1 ATGGACTTTTCTTACCAATGGATGGCTTTTGCTTCACATTTCCTGAAGCAGACATTCAATTATAA
* * *
5156 TA----T-ACTAA-AAATATAATAAAATACAACTTAAAATCAATTATGAGATTATAAAACCATTT
66 TATTTTTAAC-AATAAATATAA-AAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATTT
* * * *
5215 AAAGCAAGTAATAATGA-TTTCGAAGGCATGAGTGAATACAA
129 AAAGCGAGTAATAA-GACTTTCGAAGGCATGGGTGACTATAA
* * * *
5256 ATGGACTTTTCTCT-TCAATGGATGGCTTTTGCTTTACATTTCCTGAGGTAGACATTCAATTATA
1 ATGGACTTTTCT-TACCAATGGATGGCTTTTGCTTCACATTTCCTGAAGCAGACATTCAATTATA
* * * * * * * *
5320 ATCTATTTTTACCAACTAGATA-AAAAACTTCAACCTAAATTCAATTATAAGATTATAAAATTAT
65 A--TATTTTTAACAA-TAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTAT
* ** *
5384 TTAAAGCGAGTAACAAGGGTTTGGAAGGCATGGGTGACTATAA
127 TTAAAGCGAGTAATAAGACTTTCGAAGGCATGGGTGACTATAA
5427 ATGGACTTTTCTT
1 ATGGACTTTTCTT
5440 GTTGATGGTG
Statistics
Matches: 564, Mismatches: 101, Indels: 49
0.79 0.14 0.07
Matches are distributed among these distances:
164 53 0.09
165 82 0.15
166 1 0.00
167 2 0.00
169 2 0.00
170 211 0.37
171 205 0.36
172 4 0.01
173 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (169 bp):
ATGGACTTTTCTTACCAATGGATGGCTTTTGCTTCACATTTCCTGAAGCAGACATTCAATTATAA
TATTTTTAACAATAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATTTAA
AGCGAGTAATAAGACTTTCGAAGGCATGGGTGACTATAA
Found at i:5011 original size:459 final size:459
Alignment explanation
Indices: 4184--5019 Score: 1133
Period size: 459 Copynumber: 1.8 Consensus size: 459
4174 TTTAAATATT
* * *
4184 ATCTGTTTTAACCAAAAATGTAAAAAAATCTAACTTAAAATTAATTATGAGATTGTAAAACCATT
1 ATCTATTTTAACCAAAAATATAAAAAAATCTAACTTAAAATCAATTATGAGATTGTAAAACCATT
* ** ** *
4249 TAAGGCGTGTAATAAGGTTTTCAAAGAGTTGAGTGACTATAAATGGACTTTTCCTACCAATGGAC
66 TAAAGCAAGTAATAAGACTTTCAAAGAGTTGAGTGACTATAAATGGACTTTTCCTACCAATGAAC
* * *
4314 GACTTTTGCTTCATGTTTCCTAAGGTAGACATTTAAACATAATTTGTTTTAACCATAAATATAAA
131 GACTTTTGCTTCATGTTTCCTAAGGCAGACATTCAAACATAATATGTTTTAACCATAAATATAAA
* * *
4379 AACATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGCTTTCGA
196 AACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAA
* * * *
4444 AGGCTTGAGTGACTATAAATGGACTTTTCTTGCTAATGGATGACTTTTGCTTCATGTTTCCCAAG
261 AGGCTTGAGTGACCATAAATGGACTTTTCTTACAAATGGATGACTTTTGCTTCATGTTTCCCAAA
* ** * * *
4509 GCATACATTCAGTTAGAATATATTTTAACCACAAATGTAAAAAAATTTTAACTTTCGAAGTAAAA
326 GCAGACATTCAAATAGAATATATTTTAACAACAAATAT-AAAAAACTTTAACTTTCGAAGTAAAA
4574 CCATTCATGGATTTTTCTTTCTAATTGATGGCTTTTGCTTCATGTTTTTTAAGGGAGACATTCAA
390 CCATTCATGGATTTTTCTTTCTAATTGATGGCTTTTGCTTCATGTTTTTTAAGGGAGACATTCAA
4639 TTATA
455 TTATA
* ** *
4644 ATCTATTTTAACCAACAATATAAATGAAT-TCAACTTAAAATCAATTATGAGATTGTAAAACTAT
1 ATCTATTTTAACCAAAAATATAAAAAAATCT-AACTTAAAATCAATTATGAGATTGTAAAACCAT
* * *
4708 TTAAAGCAAGTAATAAGACTTTCGAAG-GTATGGGTGACTATAAATGGACTTTTCTTACCAATGA
65 TTAAAGCAAGTAATAAGACTTTCAAAGAGT-TGAGTGACTATAAATGGACTTTTCCTACCAATGA
* * * * *
4772 ATG-TTTTTTCTTCATGTTTCCTATA-GCAGACATTCAAATATAATATGTTTTAACTATAAATAT
129 ACGACTTTTGCTTCATGTTTCCTA-AGGCAGACATTCAAACATAATATGTTTTAACCATAAATAT
* * * * *
4835 ACAAAA-ATTCAGCTTAACATCAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGTCTT
193 A-AAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTT
* * * *
4899 TTAAAGGCTTTAGTGACCATAAATGGACTTTTCTTACAAATGGATGGCTTTTGCTTCATGTTTCT
257 TCAAAGGCTTGAGTGACCATAAATGGACTTTTCTTACAAATGGATGACTTTTGCTTCATGTTTCC
* * * **
4964 CAAAGCAGACATTCAAATATAATCTGTTTTAACAATGAATATAAAAAACTTTAACT
322 CAAAGCAGACATTCAAATAGAATATATTTTAACAACAAATATAAAAAACTTTAACT
5020 GAAAATCAAT
Statistics
Matches: 321, Mismatches: 51, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
458 13 0.04
459 194 0.60
460 114 0.36
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (459 bp):
ATCTATTTTAACCAAAAATATAAAAAAATCTAACTTAAAATCAATTATGAGATTGTAAAACCATT
TAAAGCAAGTAATAAGACTTTCAAAGAGTTGAGTGACTATAAATGGACTTTTCCTACCAATGAAC
GACTTTTGCTTCATGTTTCCTAAGGCAGACATTCAAACATAATATGTTTTAACCATAAATATAAA
AACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAA
AGGCTTGAGTGACCATAAATGGACTTTTCTTACAAATGGATGACTTTTGCTTCATGTTTCCCAAA
GCAGACATTCAAATAGAATATATTTTAACAACAAATATAAAAAACTTTAACTTTCGAAGTAAAAC
CATTCATGGATTTTTCTTTCTAATTGATGGCTTTTGCTTCATGTTTTTTAAGGGAGACATTCAAT
TATA
Found at i:5042 original size:171 final size:167
Alignment explanation
Indices: 4580--5439 Score: 842
Period size: 171 Copynumber: 5.1 Consensus size: 167
4570 AAAACCATTC
* * * *
4580 ATGGATTTTTCTTTCTAATTGATGGCTTTTGCTTCATGTTTTTTAAGGGAGACATTCAATTATAA
1 ATGGACTTTTCTTTC-AATGGATGGCTTTTGCTTCATG-TTTCTAAGGCAGACATTCAATTATAA
* *
4645 TCTATTTTAACCAACAATATAAATGAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATTT
64 TCTATTTTAA-CAATAATATAAA-AAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATTT
* * *
4710 AAAGCAAGTAATAAGACTTTCGAAGGTATGGGTGACTATAA
127 AAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAA
* * * * *
4751 ATGGACTTTTCTTACCAATGAAT-GTTTTTTCTTCATGTTTCCTATA-GCAGACATTCAAATATA
1 ATGGACTTTTCTT-TCAATGGATGGCTTTTGCTTCATGTTT-CTA-AGGCAGACATTCAATTATA
* * * * * *
4814 ATATGTTTTAACTATAAATATACAAAAATTCAGCTTAACATCAATTATGAGATTGTAAAACCATT
63 ATCTATTTTAACAAT-AATATA-AAAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATT
* ** * ** *
4879 TAAAGCGAGTAATAAGTCTTTTAAAGGCTTTAGTGACCATAA
126 TAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAA
* * *
4921 ATGGACTTTTCTTACAAATGGATGGCTTTTGCTTCATGTTTCTCAAAGCAGACATTCAAATATAA
1 ATGGACTTTTCTTTC-AATGGATGGCTTTTGCTTCATGTTTCT-AAGGCAGACATTCAATTATAA
* * *
4986 TCTGTTTTAACAATGAATATAAAAAACTTTAACTGAAAATCAATTATGAGATTGTAAAACTATTT
64 TCTATTTTAACAAT-AATATAAAAAA-TTCAACTTAAAATCAATTATGAGATTGTAAAACTATTT
* * *
5051 AAAGTGAGTAACAAGGC-TTCGAAGGAATGGGTGACTATAA
127 AAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAA
* * * * * *
5091 ATGGACTTTTTTTGTCAATGGATGGCTTCTACTTCACAT-TTTCTGAGGCCGATATTCAATTATA
1 ATGGACTTTTCTT-TCAATGGATGGCTTTTGCTT--CATGTTTCTAAGGCAGACATTCAATTATA
** * * *
5155 A--TATACT-A-AA-AATATAATAAAATACAACTTAAAATCAATTATGAGATTATAAAACCATTT
63 ATCTATTTTAACAATAATATAA-AAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATTT
* * * * * *
5215 AAAGCAAGTAATAATGATTTCGAAGGCATGAGTGAATACAA
127 AAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAA
* * *
5256 ATGGACTTTTCTCTTCAATGGATGGCTTTTGCTTTACAT-TTCCTGAGGTAGACATTCAATTATA
1 ATGGACTTTTCT-TTCAATGGATGGCTTTTGC-TT-CATGTTTCTAAGGCAGACATTCAATTATA
* * * * * * *
5320 ATCTATTTTTACCAACTAGATA-AAAAACTTCAACCTAAATTCAATTATAAGATTATAAAATTAT
63 ATCTA-TTTTAACAA-TA-ATATAAAAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTAT
* * *
5384 TTAAAGCGAGTAACAAGGGTTTGGAAGGCATGGGTGACTATAA
125 TTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAA
5427 ATGGACTTTTCTT
1 ATGGACTTTTCTT
5440 GTTGATGGTG
Statistics
Matches: 565, Mismatches: 99, Indels: 51
0.79 0.14 0.07
Matches are distributed among these distances:
164 52 0.09
165 76 0.13
166 5 0.01
167 3 0.01
168 5 0.01
169 6 0.01
170 203 0.36
171 205 0.36
172 7 0.01
173 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (167 bp):
ATGGACTTTTCTTTCAATGGATGGCTTTTGCTTCATGTTTCTAAGGCAGACATTCAATTATAATC
TATTTTAACAATAATATAAAAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATTTAAAG
CGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAA
Found at i:5311 original size:335 final size:334
Alignment explanation
Indices: 4580--5441 Score: 925
Period size: 335 Copynumber: 2.5 Consensus size: 334
4570 AAAACCATTC
* * * * ** * *
4580 ATGGATTTTTCTTTCTAATTGATGGCTTTTGCTTCATGTTTTTTAAGGGAGACATTCAATTATAA
1 ATGGACTTTTCTTTCAAATGGATGGCTTTTGCTTTACATTTTCTAAGGCAGACATTCAATTATAA
* *
4645 TCTATTTTAACCAACAATATAAATGAA-TTCAACTTAAAATCAATTATGAGATTGTAAAACTATT
66 TCTATTTTAA-CAATAATATAAA-AAACTTCAAC-TAAAATCAATTATGAGATTGTAAAACTATT
* * * * **
4709 TAAAGCAAGTAATAAGACTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTACCAATGAAT
128 TAAAGCGAGTAACAAGGC-TTCGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAAT
* * * ** *
4774 GTTTTTTCTTCATGTTTCCTATAGCAGACATTCAAATATAATATGTTTTAACTATAAATATACAA
192 GCTTCTACTTCACATTTCCTATAGCAGACATTCAAATATAATA----TTAACTAAAAATATACAA
* * * * * * *
4839 AAATTCAGCTTAACATCAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGTCTTTTAAA
253 AAATACAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGTATTTCAAA
* * * *
4904 GGCTTTAGTGACCATAA
318 GGCATGAGTGAACACAA
* * *
4921 ATGGACTTTTCTTACAAATGGATGGCTTTTGC-TT-CATGTTTCTCAAAGCAGACATTCAAATAT
1 ATGGACTTTTCTTTCAAATGGATGGCTTTTGCTTTACAT-TTTCT-AAGGCAGACATTCAATTAT
* *
4984 AATCTGTTTTAACAATGAATATAAAAAACTTTAACTGAAAATCAATTATGAGATTGTAAAACTAT
64 AATCTATTTTAACAAT-AATATAAAAAACTTCAACT-AAAATCAATTATGAGATTGTAAAACTAT
* * *
5049 TTAAAGTGAGTAACAAGGCTTCGAAGGAATGGGTGACTATAAATGGACTTTTTTTGTCAATGGAT
127 TTAAAGCGAGTAACAAGGCTTCGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAAT
* * * * *
5114 GGCTTCTACTTCACATTTTCTGA-GGCCGATATTCAATTATAATA-T-ACTAAAAATATA-ATAA
192 -GCTTCTACTTCACATTTCCT-ATAGCAGACATTCAAATATAATATTAACTAAAAATATACA-AA
*
5175 AATACAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAA-TGATTTCGAA
254 AATACAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGT-ATTTCAAA
*
5239 GGCATGAGTGAATACAA
318 GGCATGAGTGAACACAA
* * *
5256 ATGGACTTTTCTCTTC-AATGGATGGCTTTTGCTTTACATTTCCTGAGGTAGACATTCAATTATA
1 ATGGACTTTTCT-TTCAAATGGATGGCTTTTGCTTTACATTTTCTAAGGCAGACATTCAATTATA
* * * * * *
5320 ATCTATTTTTACCAACT-AGATAAAAAACTTCAACCTAAATTCAATTATAAGATTATAAAATTAT
65 ATCTA-TTTTAACAA-TAATATAAAAAACTTCAA-CTAAAATCAATTATGAGATTGTAAAACTAT
* * *
5384 TTAAAGCGAGTAACAAGGGTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGT
127 TTAAAGCGAGTAACAA-GGCTTCGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
5442 TGATGGTGCT
Statistics
Matches: 438, Mismatches: 67, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
334 2 0.00
335 180 0.41
336 56 0.13
337 4 0.01
339 1 0.00
340 52 0.12
341 142 0.32
342 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (334 bp):
ATGGACTTTTCTTTCAAATGGATGGCTTTTGCTTTACATTTTCTAAGGCAGACATTCAATTATAA
TCTATTTTAACAATAATATAAAAAACTTCAACTAAAATCAATTATGAGATTGTAAAACTATTTAA
AGCGAGTAACAAGGCTTCGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCTT
CTACTTCACATTTCCTATAGCAGACATTCAAATATAATATTAACTAAAAATATACAAAAATACAA
CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGTATTTCAAAGGCATGAG
TGAACACAA
Found at i:7431 original size:199 final size:201
Alignment explanation
Indices: 7180--7562 Score: 460
Period size: 199 Copynumber: 1.9 Consensus size: 201
7170 TTCATTTGTG
* ** *
7180 AGAAAAGTCCATTTATGGTCACTGAAGCCTTTAAAAGACGTATTACTCGCTTTAAAT-GTTTTTA
1 AGAAAAGTCCATTTATAGTCACCCAAGCCTTCAAAAGACGTATTACTCGCTTTAAATAG-TTTTA
* * * *
7244 CAATCTCATAA-TTGATGTTAAG-CTGAA-TTTTTGTACATTTAT-AGTTAAAACATATTATATT
65 CAAGCTCA-AATTTGATGTTAAGTC-AAAGTTTTT-TACATTTATGAG-TAAAACAGATTATAAT
* * * * *
7305 TGAATGTCT-GCTACAGGAA-ACATGAAGAAAAAG-TATTCATTGGTAAGAAAAGTCCATTTAAC
126 TGAATGTCTACCT--AGAAAGACATGAAGAAAAAGCTATTCACTAGCAAGAAAAGTCCATTTAAC
7367 CTATTCATTGGCA
189 CTATTCATTGGCA
* * * *
7380 AGAAAAGT-CATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
1 AGAAAAGTCCATTTATAGTCACCCAAGCCTTCAAAAGACGTATTACTCGCTTTAAATAGTTTTAC
* *
7444 AAGCTCAAATTTGATTTTAAGTCAAAGTTTTTTACATTTTTGAGTAAAACAGATTATAATTGAAT
66 AAGCTCAAATTTGATGTTAAGTCAAAGTTTTTTACATTTATGAGTAAAACAGATTATAATTGAAT
*
7509 GTCTACCTTGAAAGACATGAAGAAAAAGCTATTCACTAGCAAGAAAAGTCCATT
131 GTCTACCTAGAAAGACATGAAGAAAAAGCTATTCACTAGCAAGAAAAGTCCATT
7563 CATATTCACA
Statistics
Matches: 155, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
198 5 0.03
199 109 0.70
200 41 0.26
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (201 bp):
AGAAAAGTCCATTTATAGTCACCCAAGCCTTCAAAAGACGTATTACTCGCTTTAAATAGTTTTAC
AAGCTCAAATTTGATGTTAAGTCAAAGTTTTTTACATTTATGAGTAAAACAGATTATAATTGAAT
GTCTACCTAGAAAGACATGAAGAAAAAGCTATTCACTAGCAAGAAAAGTCCATTTAACCTATTCA
TTGGCA
Found at i:7697 original size:370 final size:371
Alignment explanation
Indices: 7002--7735 Score: 828
Period size: 370 Copynumber: 2.0 Consensus size: 371
6992 AGAAGCCATC
* ** *
7002 CATTGACAAAAAAAGTCCATTTATAGTCACCCATTCCTTTGAAGCCTTGTTACTCACTTTAAATA
1 CATTGACAAAAAAAGTCCATTTATAGTCACCCATGCCTTAAAAGCCTTATTACTCACTTTAAATA
* * * * *
7067 GTTTTACAATCTCATAATTAATTTTCAGTTAAATTTTTTTATATTCATGGTTAAAACAGATTATA
66 GTTTTACAAGCTCATAATTAATTTTAAGTCAAAGTTTTTTACATTCATGGTTAAAACAGATTATA
* * * * * ** * *
7132 TTTGAATGTCTGCTTAGAGAAACATGAAGCAAAAGTCATTCATTTGTGAGAAAAGTCCATTTATG
131 ATTGAATGTCTCCTTAGAGAAACATGAAGAAAAAGTCATTCACTAGCAAGAAAAGTCCATTCATA
* * **
7197 GTCACTGAAGCCTTTAAAAGACGTATTACTCGCTTTAAATGTTTTTACAATCTCATAATTGATGT
196 GTCACTGAACCCTTCAAAAGACGTATTACTAACTTTAAATGTTTTTACAATCTCATAATTGATGT
* * * * * *
7262 TAAGCTGAATTTTTGTACATTTATAGTTAAAACATATTATATTTGAATGTCTGCTACAGGAAACA
261 TAAGCTAAATTTTTGTACATTTATAGTTAAAACAGATTACAATTGAATGTCTACTACAAGAAACA
* **
7327 TGAAGAAAAAG-TATTCATTGGTAAGAAAAGTCCATTTAACCTATT
326 TAAAGAAAAAGCTATTCATTGACAAGAAAAGTCCATTTAACCTATT
* * *
7372 CATTGGCAAGAAAAGT-CATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAAAT
1 CATTGACAAAAAAAGTCCATTTATAGTCACCCATGCCTT-AAAAGCCTTATTACTCACTTTAAAT
* * **
7436 AGTTTTATAAGCTCA-AATTTGATTTTAAGTCAAAGTTTTTTACATTTTTGAG-TAAAACAGATT
65 AGTTTTACAAGCTCATAA-TTAATTTTAAGTCAAAGTTTTTTACATTCATG-GTTAAAACAGATT
7499 ATAATTGAATGTCTACCTT-GA-AAGACATGAAGAAAAAG-CTATTCACTAGCAAGAAAAGTCCA
128 ATAATTGAATGTCT-CCTTAGAGAA-ACATGAAGAAAAAGTC-ATTCACTAGCAAGAAAAGTCCA
* * * * *
7561 TTCATATTCACAT-ATCCCTTCAAAAGCCTTATTACTAATTTTAAATAGTTTTATA-AAT-TCAT
190 TTCATAGTCAC-TGAACCCTTCAAAAGACGTATTACTAACTTTAAAT-GTTTT-TACAATCTCAT
* * * * *
7623 AATTGATTTTAAGTTAAATTTTCT-TACATTTTTGGTTAAAACAGGTTACAATT-AAGTGTCTA-
252 AATTGATGTTAAGCTAAATTTT-TGTACATTTATAGTTAAAACAGATTACAATTGAA-TGTCTAC
*
7685 TTCAAAGAAACATAAAGAAAAAGCTATTCATTGACAAGAAAAGTCCATTTA
315 TAC-AAGAAACATAAAGAAAAAGCTATTCATTGACAAGAAAAGTCCATTTA
7736 TAGTTACTCA
Statistics
Matches: 302, Mismatches: 49, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
369 30 0.10
370 231 0.76
371 39 0.13
372 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (371 bp):
CATTGACAAAAAAAGTCCATTTATAGTCACCCATGCCTTAAAAGCCTTATTACTCACTTTAAATA
GTTTTACAAGCTCATAATTAATTTTAAGTCAAAGTTTTTTACATTCATGGTTAAAACAGATTATA
ATTGAATGTCTCCTTAGAGAAACATGAAGAAAAAGTCATTCACTAGCAAGAAAAGTCCATTCATA
GTCACTGAACCCTTCAAAAGACGTATTACTAACTTTAAATGTTTTTACAATCTCATAATTGATGT
TAAGCTAAATTTTTGTACATTTATAGTTAAAACAGATTACAATTGAATGTCTACTACAAGAAACA
TAAAGAAAAAGCTATTCATTGACAAGAAAAGTCCATTTAACCTATT
Found at i:8047 original size:342 final size:337
Alignment explanation
Indices: 7367--8250 Score: 962
Period size: 342 Copynumber: 2.6 Consensus size: 337
7357 TCCATTTAAC
* *
7367 CTATTCATTGGCAAGAAAAGT-CATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTT
1 CTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTTGCTT
* * * ** * *
7431 TAAATAGTTTTATAAGCTCAAATTTGATTTTAAGTCAAAGTTTTTTACATTTTTGAGTAAAACAG
66 TAAATAGTTTTACAAACTCTAA-TTGATTTTAAGTTGAA-TTTTTTACATTTTTG-TTAAAATAG
* * * *
7496 ATTATAATTGAATGTCTACCTTGA-AAGACATGAAGAAAAAGCTATTCACT-AGCAAGAAAAGTC
128 ATTATAATTGAATGTCTGCCTTGAGAA-ACATGAAGAAAAAGCCATTCATTGA-CTAGAAAAGTC
* * * *
7559 CATTCATATTCACATATCCCTTCAAAAGCCTTATTACTAATTTTAAATAGTTTTATAAATTCATA
191 CATTTATATTCACACATACCTTCAAAAGCCTTATTACTAACTTTAAATAGTTTTATAAATTCATA
* * * *
7624 ATTGATTTTAAGTTAAATTTTCTTACATTTTTGGTTAAAACAGGTTACAATTAAGTGTCTATTCA
256 ATTGATTTTAAGTTAAATTTTCTTACAATTTTGATTAAAACAGATTACAATTAAGTGTATATT-A
7689 AAGAAACATAAAGAAAAA
320 AAGAAACATAAAGAAAAA
* * * * *
7707 GCTATTCATTGACAAGAAAAGTCCATTTATAGTTACTCATGCCTTTGAAAGCC-TAGTTACTTAC
1 -CTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTA-TTACTTGC
* *
7771 TTTAAATAGTTTTACAAACTCGTAATTGATTTTAGGTTGAATTTTTTATTATTTTTGTTTAAAAT
64 TTTAAATAGTTTTACAAACTC-TAATTGATTTTAAGTTGAATTTTTTA-CATTTTTG-TTAAAAT
* * *
7836 AGATTATAATTGACTGTTTGCCTTCAGAAACATGAAGAAAAAGCCATTCATTGACTAGAAAAGTC
126 AGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGCCATTCATTGACTAGAAAAGTC
* * * * * **
7901 AATTTATGTTCACCCATACCTTCAAAAGCCTTGTTGCTCGCTTTAAATAGTTTTAT-AATCTCAT
191 CATTTATATTCACACATACCTTCAAAAGCCTTATTACTAACTTTAAATAGTTTTATAAAT-TCAT
* * * **
7965 AATTGATTTT-GGCTTAAATTTGT-TTATAATTTTGATTAAAATAGATTGTAATTGAA-TGTATA
255 AATTGATTTTAAG-TTAAATTT-TCTTACAATTTTGATTAAAACAGATTACAATT-AAGTGTATA
* * *
8027 CCTT-GAGAAACGTGAAGAAAAA
317 --TTAAAGAAACATAAAGAAAAA
* * *
8049 CTAATTCATTGGTAAGAAAAG-CCTATTTATAGTCACCCAAGCCTTCGAAAGCCTTAATACTTGC
1 CT-ATTCATTGGCAAGAAAAGTCC-ATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTTGC
* *
8113 TTTAAATAGTTTTACTATCTCATAATTGATTTTAAGTTGAATTGTTTTACATTTTTAGTTAAAAT
64 TTTAAATAGTTTTACAAACTC-TAATTGATTTTAAGTTGAATT-TTTTACATTTTT-GTTAAAAT
* * ** * * *
8178 ATATTATAATTGAATGTCTGCCTTGTGAAATGTGATGTAAAAGCCAATCATTGA-TATGAAAAGT
126 AGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGCCATTCATTGACTA-GAAAAGT
8242 CCATTTATA
190 CCATTTATA
8251 GCACTC
Statistics
Matches: 453, Mismatches: 72, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
341 39 0.09
342 396 0.87
343 16 0.04
344 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (337 bp):
CTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTTGCTT
TAAATAGTTTTACAAACTCTAATTGATTTTAAGTTGAATTTTTTACATTTTTGTTAAAATAGATT
ATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGCCATTCATTGACTAGAAAAGTCCATTT
ATATTCACACATACCTTCAAAAGCCTTATTACTAACTTTAAATAGTTTTATAAATTCATAATTGA
TTTTAAGTTAAATTTTCTTACAATTTTGATTAAAACAGATTACAATTAAGTGTATATTAAAGAAA
CATAAAGAAAAA
Found at i:8250 original size:171 final size:169
Alignment explanation
Indices: 7367--8251 Score: 843
Period size: 171 Copynumber: 5.2 Consensus size: 169
7357 TCCATTTAAC
7367 CTATTCATTGGCA-AGAAAAGT-CATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCT
1 CTATTCATT-G-ATAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCT
* *
7430 TTAAATAGTTTTATAAGCTCA-AATTTGATTTTAAGTCAAAGTTTTTTACATTTTTGAG-TAAAA
64 TTAAATAGTTTTATAATCTCATAA-TTGATTTTAAGTTAAA-TTTTTTACATTTTT-AGTTAAAA
*
7493 CAGATTATAATTGAATGTCTACCTTGA-AAGACATGAAGAAAAAG
126 TAGATTATAATTGAATGTCTACCTTGAGAA-ACATGAAGAAAAAG
* * * ** * ***
7537 CTATTCACTAGCA-AGAAAAGTCCATTCATATTCACATATCCCTTCAAAAGCCTTATTACTAATT
1 CTATTCA-TTG-ATAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCT
* *
7601 TTAAATAGTTTTATAAAT-TCATAATTGATTTTAAGTTAAATTTTCTTACATTTTTGGTTAAAAC
64 TTAAATAGTTTTAT-AATCTCATAATTGATTTTAAGTTAAATTTT-TTACATTTTTAGTTAAAAT
* * * *
7665 AGGTTACAATT-AAGTGTCTA--TTCAAAGAAACATAAAGAAAAAG
127 AGATTATAATTGAA-TGTCTACCTT--GAGAAACATGAAGAAAAAG
* * * ** **
7708 CTATTCATTGACAAGAAAAGTCCATTTATAGTTACTCATGCCTTTGAAAGCC-TAGTTACTTACT
1 CTATTCATTGA-TAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA-TTACTCGCT
* * * * * *
7772 TTAAATAGTTTTACAAACTCGTAATTGATTTTAGGTTGAATTTTTTATTATTTTT-GTTTAAAAT
64 TTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTA-CATTTTTAG-TTAAAAT
* * * *
7836 AGATTATAATTGACTGTTTGCCTTCAGAAACATGAAGAAAAAG
127 AGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAG
* * * * *
7879 CCATTCATTGACTAGAAAAGTCAATTTAT-GTTCACCCATACCTTCAAAAGCCTTGTTGCTCGCT
1 CTATTCATTGA-TAGAAAAGTCCATTTATAG-TCACCCATGCCTTCAAAAGCCTTATTACTCGCT
* * *
7943 TTAAATAGTTTTATAATCTCATAATTGATTTT-GGCTTAAATTTGTTTATAATTTT-GATTAAAA
64 TTAAATAGTTTTATAATCTCATAATTGATTTTAAG-TTAAATTT-TTTACATTTTTAG-TTAAAA
* * *
8006 TAGATTGTAATTGAATGTATACCTTGAGAAACGTGAAGAAAAA-
126 TAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAG
* * * * *
8049 CTAATTCATTGGTAAGAAAAG-CCTATTTATAGTCACCCAAGCCTTCGAAAGCCTTAATACTTGC
1 CT-ATTCATTGAT-AGAAAAGTCC-ATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGC
*
8113 TTTAAATAGTTTTACT-ATCTCATAATTGATTTTAAGTTGAATTGTTTTACATTTTTAGTTAAAA
63 TTTAAATAGTTTTA-TAATCTCATAATTGATTTTAAGTTAAATT-TTTTACATTTTTAGTTAAAA
* * * ** * *
8177 TATATTATAATTGAATGTCTGCCTTGTGAAATGTGATGTAAAAG
126 TAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAG
* *
8221 CCAATCATTGATATGAAAAGTCCATTTATAG
1 CTATTCATTGATA-GAAAAGTCCATTTATAG
8252 CACTC
Statistics
Matches: 591, Mismatches: 90, Indels: 67
0.79 0.12 0.09
Matches are distributed among these distances:
169 3 0.01
170 42 0.07
171 524 0.89
172 20 0.03
173 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (169 bp):
CTATTCATTGATAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTT
AAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTACATTTTTAGTTAAAATAGAT
TATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAG
Done.