Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000519.1 Hibiscus syriacus cultivar Beakdansim tig00000986_pilon, 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: 92596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9253 original size:233 final size:233
Alignment explanation
Indices: 8842--9965 Score: 1520
Period size: 233 Copynumber: 4.8 Consensus size: 233
8832 AATTGTCTTT
* * * *
8842 TTTTCAAAAATTTCAATTTTTATATTTAAAT--GAAATTTTTTTCTTTTTTTCGAAGAAACATGT
1 TTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTC-ATTTTTCGAA-AAACATGT
* * * * * * * * * *
8905 GAAAACATCTTACCTGATGGTCTTATGAATGGCCCGAATGCCTTATCATCTTCCTCAAAATG-CT
64 GAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTTGCTCGAAA-GACT
* * * ** *
8969 TATAAATGACCTGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
128 TACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAC
*
9034 CAATTTTGGAAATAGTTTACTATGTAAGAAACTTTTCGTAC
193 CAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCGTAC
* *
9075 TTTTCAAAAATTTCAATTTTTAGATTAAAATGAGAAACTTTTCTCATTTTTCGAAAAATATGTG-
1 TTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGA
* * * *
9139 ACACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAAGTCTTTATTATCTTGCTCGAAAGACTTA
66 AAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGAC-TTATCATCTTGCTCGAAAGACTTA
* * * * * * *
9204 TAAATGACCCGAAGGATTTAAACATCATGCTCGAAACAATTATTGATGGCCCGAAGGACTTACCA
130 CAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCA
* * *
9269 AATTTCGAAATAGTTTACTAGGTAAGAAACTTTTCTTAC
195 ATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCGTAC
*
9308 TTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATATGA
1 TTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGA
* * * * **
9373 AAATATCCTGTCCGAAGGTCTTATAGATGGCTAGAAGGACTTATCATCTTGCTCGAAAGACTTAC
66 AAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
* * * * *
9438 AGATTACTCGAAGGATTTAAGCATCATGCTCCAAAGACTTACTAATAGCCCGAAGGACTTACCAA
131 AGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAA
* *
9503 TTTTGGAAATAGTTTAATAGGTAAGAAACGTTTCGTAC
196 TTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCGTAC
* * * *
9541 TTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCACTTTTCAAAAAAATATGTG
1 TTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTC-GAAAAACATGTG
*
9606 AAAACATCCTGCCCGAAGGTCTTGTGGATGGCCC-AATGGACTTATCATCCTGCTCGAAAGACTT
65 AAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAA-GGACTTATCATCTTGCTCGAAAGACTT
* *
9670 ACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAACACTTACTGATGGCTCGAAGGACTTACC
129 ACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACC
*
9735 AATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTAC
194 AATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCGTAC
* * *
9775 TTTTCAAAAATTTCAATTTTCAGATTTAAATGTGAAACTTTTCTCATTTTTGGAAAAACATGTGA
1 TTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGA
* * * ** * *
9840 AAACATCTTGCCCAAAGATCTTGTGGATGGATCGAAGGACTTATCATCTTGCTTGATAGACTTAC
66 AAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
* *
9905 AGTTGACTCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTA
131 AGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTA
9966 TCATCTTGCT
Statistics
Matches: 787, Mismatches: 96, Indels: 16
0.88 0.11 0.02
Matches are distributed among these distances:
232 32 0.04
233 496 0.63
234 249 0.32
235 10 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (233 bp):
TTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGA
AAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
AGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAA
TTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCGTAC
Found at i:9806 original size:467 final size:464
Alignment explanation
Indices: 8842--9965 Score: 1580
Period size: 467 Copynumber: 2.4 Consensus size: 464
8832 AATTGTCTTT
* * * *
8842 TTTTCAAAAATTTCAATTTTTATATTTAAAT-GAAATTTTTTTCTTTTTTTCGAAGAAACATGTG
1 TTTTCAAAAATTTCAATTTTTAGATTTAAATGGAAACTTTTCTC-ATTTTTCGAA-AAACATGTG
* * * * * *
8906 AAAACAT-CT-TACCTGATGGTCTTATGAATGGCCCGAATGCCTTATCATCTTCCTCAAAATG-C
64 AAAACATCCTGT-CC-GAAGGTCTTATG-ATGGCTCGAAGGACTTATCATCTTGCTCGAAA-GAC
* * * ** *
8968 TTATAAATGAC-CTGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
125 TTACAGATTACTC-GAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
* * * *
9032 ACCAATTTTGGAAATAGTTTACTATGTAAGAAACTTTTCGTACTTTTCAAAAATTTCAATTTTTA
189 ACCAATTTTGGAAATAGTTTAATAGGTAAGAAACGTTTCGTACTTTTCAAAAATTTCAATTTTCA
* * *
9097 GATTAAAATGAGAAACTTTTCTCATTTTTCGAAAAATATGTGACACATCCTGCCCGAAGGTCTTG
254 GATTAAAATGAGAAACTTTTCTCACTTTTCAAAAAATATGTGAAACATCCTGCCCGAAGGTCTTG
* * * *
9162 TGGATGGCCCGAAAGTCTTTATTATCTTGCTCGAAAGACTTATAAATGACCCGAAGGATTTAAAC
319 TGGATGGCCCGAAAGACTTTATCATCCTGCTCGAAAGACTTACAAATGACCCGAAGGATTTAAAC
* *
9227 ATCATGCTCGAAACAATTATTGATGGCCCGAAGGACTTACCAAATTTCGAAATAGTTTACTAGGT
384 ATCATGCTCAAAACAATTACTGATGGCCCGAAGGACTTACCAAATTTCGAAATAGTTTACTAGGT
9292 AAGAAACTTTTCTTAC
449 AAGAAACTTTTCTTAC
*
9308 TTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATATGA
1 TTTTCAAAAATTTCAATTTTTAGATTTAAATG-GAAACTTTTCTCATTTTTCGAAAAACATGTGA
* *
9373 AAATATCCTGTCCGAAGGTCTTATAGATGGCTAGAAGGACTTATCATCTTGCTCGAAAGACTTAC
65 AAACATCCTGTCCGAAGGTCTTAT-GATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
* * *
9438 AGATTACTCGAAGGATTTAAGCATCATGCTCCAAAGACTTACTAATAGCCCGAAGGACTTACCAA
129 AGATTACTCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAA
*
9503 TTTTGGAAATAGTTTAATAGGTAAGAAACGTTTCGTACTTTTCAAAAATTTCAATTTTCAGATTT
194 TTTTGGAAATAGTTTAATAGGTAAGAAACGTTTCGTACTTTTCAAAAATTTCAATTTTCAGATTA
9568 AAATGAGAAACTTTTCTCACTTTTCAAAAAAATATGTGAAAACATCCTGCCCGAAGGTCTTGTGG
259 AAATGAGAAACTTTTCTCACTTTTC-AAAAAATATGTG-AAACATCCTGCCCGAAGGTCTTGTGG
* * *
9633 ATGGCCC-AATGGAC-TTATCATCCTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCAT
322 ATGGCCCGAA-AGACTTTATCATCCTGCTCGAAAGACTTACAAATGACCCGAAGGATTTAAACAT
* * * *
9696 CATGCTCAAAACACTTACTGATGGCTCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAA
386 CATGCTCAAAACAATTACTGATGGCCCGAAGGACTTACCAAATTTCGAAATAGTTTACTAGGTAA
9761 GAAACTTTTCTTAC
451 GAAACTTTTCTTAC
* *
9775 TTTTCAAAAATTTCAATTTTCAGATTTAAATGTGAAACTTTTCTCATTTTTGGAAAAACATGTGA
1 TTTTCAAAAATTTCAATTTTTAGATTTAAATG-GAAACTTTTCTCATTTTTCGAAAAACATGTGA
* * * * * * * *
9840 AAACATCTTGCCCAAAGATCTTGTGGATGGATCGAAGGACTTATCATCTTGCTTGATAGACTTAC
65 AAACATCCTGTCCGAAGGTCTTAT-GATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
9905 AG-TTGACTCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTA
129 AGATT-ACTCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTA
9966 TCATCTTGCT
Statistics
Matches: 587, Mismatches: 60, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
465 1 0.00
466 226 0.39
467 315 0.54
468 45 0.08
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (464 bp):
TTTTCAAAAATTTCAATTTTTAGATTTAAATGGAAACTTTTCTCATTTTTCGAAAAACATGTGAA
AACATCCTGTCCGAAGGTCTTATGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTACAG
ATTACTCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAATT
TTGGAAATAGTTTAATAGGTAAGAAACGTTTCGTACTTTTCAAAAATTTCAATTTTCAGATTAAA
ATGAGAAACTTTTCTCACTTTTCAAAAAATATGTGAAACATCCTGCCCGAAGGTCTTGTGGATGG
CCCGAAAGACTTTATCATCCTGCTCGAAAGACTTACAAATGACCCGAAGGATTTAAACATCATGC
TCAAAACAATTACTGATGGCCCGAAGGACTTACCAAATTTCGAAATAGTTTACTAGGTAAGAAAC
TTTTCTTAC
Found at i:9946 original size:42 final size:42
Alignment explanation
Indices: 9871--10029 Score: 160
Period size: 42 Copynumber: 3.8 Consensus size: 42
9861 TGTGGATGGA
* * * * *
9871 TCGAAGGACTT-ATCATCTTGCTTGATAGACTTACAGTTGAC
1 TCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGTTGAC
* * * *
9912 TCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGC
1 TCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGTTGAC
* * * * *
9954 CCGAAGGACTT-ATCATCTTGCTCGAAAGACTTACAATTGAC
1 TCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGTTGAC
**
9995 TTTAAGGATTTAAGCATCATGCTCGAAAGACTTAC
1 TCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
10030 TGATGGCCCG
Statistics
Matches: 92, Mismatches: 24, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
41 40 0.43
42 52 0.57
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (42 bp):
TCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGTTGAC
Found at i:10004 original size:83 final size:83
Alignment explanation
Indices: 9872--10041 Score: 286
Period size: 83 Copynumber: 2.0 Consensus size: 83
9862 GTGGATGGAT
* * *
9872 CGAAGGACTTATCATCTTGCTTGATAGACTTACAGTTGACTCGAAGGATTTAAGCATCATGCTCA
1 CGAAGGACTTATCATCTTGCTCGAAAGACTTACAATTGACTCGAAGGATTTAAGCATCATGCTCA
9937 AAAGACTTACTGATGGCC
66 AAAGACTTACTGATGGCC
** *
9955 CGAAGGACTTATCATCTTGCTCGAAAGACTTACAATTGACTTTAAGGATTTAAGCATCATGCTCG
1 CGAAGGACTTATCATCTTGCTCGAAAGACTTACAATTGACTCGAAGGATTTAAGCATCATGCTCA
10020 AAAGACTTACTGATGGCC
66 AAAGACTTACTGATGGCC
10038 CGAA
1 CGAA
10042 AGGCTTACCA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (83 bp):
CGAAGGACTTATCATCTTGCTCGAAAGACTTACAATTGACTCGAAGGATTTAAGCATCATGCTCA
AAAGACTTACTGATGGCC
Found at i:10205 original size:316 final size:314
Alignment explanation
Indices: 9632--10280 Score: 960
Period size: 316 Copynumber: 2.1 Consensus size: 314
9622 AGGTCTTGTG
9632 GATGGCCCAATGGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCAA-GGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
*
9697 ATGCTCAAAACACTTACTGATGGCTCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
65 ATGCTCAAAACACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
* * * *
9762 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGTGAAACTTTTCTCATTTTTG
130 AAACGTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCATTTTTC
* * * *
9827 GAAAAACATGTGAAAACATCTTGCCCAAAGATCTTGTGGATGGATCGAAGGACTTATCATCTTGC
195 GAAAAACATATAAAAACATCCTGCCCAAAGATCTTGTGGATGGACCGAAGGACTTATCATCTTGC
* * * * * *
9892 TTGATAGACTTACAGTTGACTCGAAGGATTTAAGCATCATGCTCAAAAGACTTACT
260 TCGAAAGACTTAC-GATAACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTACT
* ***
9948 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACA-ATTGACTTTAAGGATTTAAGCAT
1 GATGGCCC-AAGGACTTATCATCCTGCTCGAAAGACTTACAGA-TGACCCGAAGGATTTAAGCAT
* *
10012 CATGCTCGAAAGACTTACTGATGGCCCGAAAGG-CTTACCAATTTTGGAAATAGTTTACTAGGTA
64 CATGCTCAAAACACTTACTGATGGCCCG-AAGGACTTACCAATTTTGGAAATAGTTTACTAGGTA
*
10076 AGAAACGTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAATTTTCTCATTTT
128 AGAAACGTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCATTTT
* * * * *
10141 TCTAAAAATATATAAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTT
193 TCGAAAAACATATAAAAACATCCTGCCCAAAGATCTTGTGGATGGACCGAAGGACTTATCATCTT
*
10206 GCTCGAAAGACTTACGATAACCCGAAGGATTTAAGAATCATGCTCGAAAGACTTACT
258 GCTCGAAAGACTTACGATAACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTACT
* *
10263 GATAGCTCAAAGGACTTA
1 GATGGC-CCAAGGACTTA
10281 CCAATTCTGG
Statistics
Matches: 299, Mismatches: 30, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
315 52 0.17
316 241 0.81
317 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (314 bp):
GATGGCCCAAGGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCA
TGCTCAAAACACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGA
AACGTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCATTTTTCG
AAAAACATATAAAAACATCCTGCCCAAAGATCTTGTGGATGGACCGAAGGACTTATCATCTTGCT
CGAAAGACTTACGATAACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTACT
Found at i:10355 original size:232 final size:232
Alignment explanation
Indices: 9948--11116 Score: 1605
Period size: 232 Copynumber: 5.0 Consensus size: 232
9938 AAGACTTACT
* ***
9948 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAATTGACTTTAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACGA-TGACCCGAAGGATTTAAGCATC
10013 ATGCTCGAAAGACTTACTGATGGCCCGAAAGG-CTTACCAATTTTGGAAATAGTTTACTAGGTAA
65 ATGCTCGAAAGACTTACTGATGGCCCG-AAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAA
* *
10077 GAAACGTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAATTTTCTCATTTTT
129 GAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCATTTTT
* * * *
10142 CTAAAAATATATAAAAACATCCTGCCCGAAGGTCTTGTG
194 CGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTG
* *
10181 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACGATAACCCGAAGGATTTAAGAATCA
1 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACGATGACCCGAAGGATTTAAGCATCA
* * * *
10246 TGCTCGAAAGACTTACTGATAGCTCAAAGGACTTACCAATTCTGGAAATAGTTTACTAGGTAAGA
66 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGA
*
10311 AACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTCG
131 AACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCATTTTTCG
*
10376 AAAAACATGTGAAAACATCCT-CTCCTAAGGTCTTGTG
196 AAAAACATGTGAAAACATCCTGC-CCGAAGGTCTTGTG
* * * *
10413 GATGGCCCAAAGGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCAAAGGATTTAAGCATA
1 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC-GATGACCCGAAGGATTTAAGCATC
* *
10478 ATGCTTGAAACACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
65 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
** * *
10543 AAGTTTTTCTTACTTTTAAAAAATTTCAATTTTTAGATTTAAATGA-AAAACTTTTCTCATTTTT
130 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAA-TTTTCTCATTTTT
* * * **
10607 AGAAAAACATGT-AAAACATCCTACCCAAAAATCTTGTG
194 CGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTG
* * *
10645 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAC-TACAGTTGATCTGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC-GATGACCCGAAGGATTTAAGCATC
** * * * * * * *
10709 ATGCTCGAAAGACTTTTTAATAGCCCGAATGACTTACAAATTTTGGAAATTGTTTAGTATGTAAG
65 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
* * * *
10774 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTAAGATTTAAATGAGGAAACTTTCCCATTTTTC
130 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCATTTTTC
* *
10839 GAAAAACATTTGAAAACATCCTGCCCGAAGGTCTTGTC
195 GAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTG
* * *
10877 GATGGCCCGAAGGACTTACCATCTTGCTC-AAACGAATTATAGATGACCCGAAGGATTTAAGCAT
1 GATGGCCCGAAGGACTTATCATCTTGCTCGAAA-GACTTA-CGATGACCCGAAGGATTTAAGCAT
* * * *
10941 CATGCTCGAAAGACTTACTGATGGCCTGAAGGAATTTACCAATTTTGGAAGTAGTTTAGTAGGTA
64 CATGCTCGAAAGACTTACTGATGGCCCGAAGG-ACTTACCAATTTTGGAAATAGTTTACTAGGTA
* *
11006 AGAAACTTTTCTTACTTTTAAAAAATTTCAATTTGCAGATTTAAATGAG-AAATATTTCTCATTT
128 AGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAAT-TTTCTCATTT
* * * * *
11070 TTCGAGAGACATGTGAAAACATCATGCCTGAAGGTCTTATG
192 TTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTG
*
11111 AATGGC
1 GATGGC
11117 TTGAAAAATT
Statistics
Matches: 823, Mismatches: 101, Indels: 23
0.87 0.11 0.02
Matches are distributed among these distances:
231 148 0.18
232 316 0.38
233 238 0.29
234 121 0.15
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (232 bp):
GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACGATGACCCGAAGGATTTAAGCATCA
TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGA
AACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCATTTTTCG
AAAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTG
Found at i:10451 original size:548 final size:550
Alignment explanation
Indices: 9406--10513 Score: 1787
Period size: 548 Copynumber: 2.0 Consensus size: 550
9396 TAGATGGCTA
9406 GAAGGACTTATCATCTTGCTCGAAAGACTTACAGATTACTCGAAGGATTTAAGCATCATGCTCCA
1 GAAGGACTTATCATCTTGCTCGAAAGACTTACAGATTACTCGAAGGATTTAAGCATCATGCTCCA
9471 AAGACTTACTAATAGCCCGAAGGACTTACCAATTTTGGAAATAGTTTAATAGGTAAGAAACGTTT
66 AAGACTTACTAATAGCCCGAAGGACTTACCAATTTTGGAAATAGTTTAATAGGTAAGAAACGTTT
*
9536 CGTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCACTTTTCAAAAAAAT
131 CGTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCACTTTTCAAAAAAAT
* *
9601 ATGTGAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCAATGGACTTATCATCCTGCTCGAAAG
196 ATATAAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCAATGGACTTATCATCCTGCTCGAAAG
* * * *
9666 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAACACTTACTGATGGCTCGAAGGACT
261 ACTTACAGATAACCCGAAGGATTTAAGAATCATGCTCAAAACACTTACTGATAGCTCAAAGGACT
*
9731 TACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTC
326 TACCAATTCTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTC
* * *
9796 AGATTTAAATGTGAAACTTTTCTCATTTTTGGAAAAACATGTGAAAACATCTTGCCCAAAGATCT
391 AGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCAAAGATCT
* * * * * * * *
9861 TGTGGATGGATCGAAGGACTTATCATCTTGCTTGATAGACTTACAGTTGACTCGAAGGATTTAAG
456 TGTGGATGGACCAAAGGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCAAAGGATTTAAG
* *
9926 CATCATGCTCAAAAGACTTACTGATGGCCC
521 CATAATGCTCAAAACACTTACTGATGGCCC
** *
9956 GAAGGACTTATCATCTTGCTCGAAAGACTTACA-ATTGACTTTAAGGATTTAAGCATCATGCTCG
1 GAAGGACTTATCATCTTGCTCGAAAGACTTACAGATT-ACTCGAAGGATTTAAGCATCATGCTCC
* * *
10020 AAAGACTTACTGATGGCCCGAAAGG-CTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACGT
65 AAAGACTTACTAATAGCCCG-AAGGACTTACCAATTTTGGAAATAGTTTAATAGGTAAGAAACGT
* * * *
10084 TTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAATTTTCTCATTTTTC-TAAAA
129 TTCGTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCACTTTTCAAAAAA
*
10148 ATATATAAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAA-GGACTTATCATCTTGCTCGA
194 ATATATAAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCC-AATGGACTTATCATCCTGCTCGA
* *
10212 AAGACTTAC-GATAACCCGAAGGATTTAAGAATCATGCTCGAAAGACTTACTGATAGCTCAAAGG
258 AAGACTTACAGATAACCCGAAGGATTTAAGAATCATGCTCAAAACACTTACTGATAGCTCAAAGG
10276 ACTTACCAATTCTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATT
323 ACTTACCAATTCTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATT
*
10341 TTCAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACATCCT-CTCCTAAG
388 TTCAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACATCCTGC-CCAAAG
* *
10405 GTCTTGTGGATGGCCCAAAGGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCAAAGGATT
452 ATCTTGTGGATGGACCAAAGGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCAAAGGATT
**
10470 TAAGCATAATGCTTGAAACACTTACTGATGGCCC
517 TAAGCATAATGCTCAAAACACTTACTGATGGCCC
10504 GAAGGACTTA
1 GAAGGACTTA
10514 CCAATTTTGG
Statistics
Matches: 515, Mismatches: 39, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
547 1 0.00
548 266 0.52
549 74 0.14
550 170 0.33
551 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (550 bp):
GAAGGACTTATCATCTTGCTCGAAAGACTTACAGATTACTCGAAGGATTTAAGCATCATGCTCCA
AAGACTTACTAATAGCCCGAAGGACTTACCAATTTTGGAAATAGTTTAATAGGTAAGAAACGTTT
CGTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATTTTCTCACTTTTCAAAAAAAT
ATATAAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCAATGGACTTATCATCCTGCTCGAAAG
ACTTACAGATAACCCGAAGGATTTAAGAATCATGCTCAAAACACTTACTGATAGCTCAAAGGACT
TACCAATTCTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTC
AGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCAAAGATCT
TGTGGATGGACCAAAGGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCAAAGGATTTAAG
CATAATGCTCAAAACACTTACTGATGGCCC
Found at i:10463 original size:41 final size:41
Alignment explanation
Indices: 10413--10513 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
10403 AGGTCTTGTG
* ** *
10413 GATGGCCCAAAGGACTTATCATCCTGCTCGAAAGACTTACA
1 GATGGCCCAAAGGACTTAGCATAATGCTCGAAACACTTACA
* * * *
10454 GATGACCCAAAGGATTTAAGCATAATGCTTGAAACACTTACT
1 GATGGCCCAAAGGACTT-AGCATAATGCTCGAAACACTTACA
*
10496 GATGGCCCGAAGGACTTA
1 GATGGCCCAAAGGACTTA
10514 CCAATTTTGG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 16 0.33
42 32 0.67
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (41 bp):
GATGGCCCAAAGGACTTAGCATAATGCTCGAAACACTTACA
Found at i:23865 original size:17 final size:17
Alignment explanation
Indices: 23843--23876 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23833 TAAAAACAGT
*
23843 AAATAAATAGAAAATAA
1 AAATAAAAAGAAAATAA
*
23860 AAATAAAAAGAAGATAA
1 AAATAAAAAGAAAATAA
23877 TCCTCACCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (17 bp):
AAATAAAAAGAAAATAA
Found at i:24397 original size:24 final size:24
Alignment explanation
Indices: 24352--24401 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
24342 ATAAAGAACC
*
24352 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
24376 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
24400 AA
1 AA
24402 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:26754 original size:15 final size:15
Alignment explanation
Indices: 26721--26763 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
26711 AAAATAATAT
* *
26721 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
26736 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
26750 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
26764 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:27748 original size:24 final size:24
Alignment explanation
Indices: 27703--27752 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
27693 ATAAAGAACC
*
27703 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
27727 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
27751 AA
1 AA
27753 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:35133 original size:12 final size:12
Alignment explanation
Indices: 35116--35142 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35106 CACTTTTATT
35116 TCATACTAGATG
1 TCATACTAGATG
35128 TCATACTAGATG
1 TCATACTAGATG
35140 TCA
1 TCA
35143 ACTGATCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (12 bp):
TCATACTAGATG
Found at i:37231 original size:12 final size:12
Alignment explanation
Indices: 37214--37240 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
37204 CACTTTTATT
37214 TCATACTAGATG
1 TCATACTAGATG
37226 TCATACTAGATG
1 TCATACTAGATG
37238 TCA
1 TCA
37241 ACTGATCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (12 bp):
TCATACTAGATG
Found at i:49461 original size:60 final size:60
Alignment explanation
Indices: 49368--49486 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
49358 TCCACGATGC
* * * *
49368 CGACATTTAGGTCGAACAAGCTAGTAGTTGAATGCCTTCCCCC-TGAACTTTAAGGCATCT
1 CGACATTGAGGTCGAACAAGCTAGCAGTTGAATGCC-TCCCCCAGGAACTTGAAGGCATCT
* * *
49428 CGACATTGAGGTCGAAGAAGCTCGCAGTTGAATGGCTCCCCCAGGAACTTGAAGGCATC
1 CGACATTGAGGTCGAACAAGCTAGCAGTTGAATGCCTCCCCCAGGAACTTGAAGGCATC
49487 AAGTCAAATG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 6 0.12
60 45 0.88
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (60 bp):
CGACATTGAGGTCGAACAAGCTAGCAGTTGAATGCCTCCCCCAGGAACTTGAAGGCATCT
Found at i:50397 original size:15 final size:15
Alignment explanation
Indices: 50379--50421 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
50369 AAATTTGTTC
*
50379 AAATAATTAAATATA
1 AAATAAATAAATATA
*
50394 AAATAAATATATATA
1 AAATAAATAAATATA
*
50409 ATAAAAAATAAAT
1 A-AATAAATAAAT
50422 TTACCTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAATAAATATA
Found at i:52178 original size:25 final size:25
Alignment explanation
Indices: 52144--52191 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
52134 TTGTCATCTT
52144 AAACCCCATTCCCACAGGACCTTGA
1 AAACCCCATTCCCACAGGACCTTGA
*
52169 AAACCCCATTCCCACCGGACCTT
1 AAACCCCATTCCCACAGGACCTT
52192 ATATTAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.44, G:0.10, T:0.17
Consensus pattern (25 bp):
AAACCCCATTCCCACAGGACCTTGA
Found at i:53717 original size:32 final size:32
Alignment explanation
Indices: 53640--53758 Score: 107
Period size: 32 Copynumber: 3.7 Consensus size: 32
53630 ACCTAAATCG
* ** *
53640 AAAATCAATCGAT-TCGATATTGACATGATCCA
1 AAAATCAATCGATCT-AATATTGACCCGACCCA
* * *
53672 AAAATCAACCGATCAAATATTGACTCGACCCGA
1 AAAATCAATCGATCTAATATTGACCCGACCC-A
* ** *
53705 AATAT-AATCGATCTGGTATTAACCCGACCCA
1 AAAATCAATCGATCTAATATTGACCCGACCCA
53736 AAAATCAATCGATCTAATATTGA
1 AAAATCAATCGATCTAATATTGA
53759 TACGAACCGA
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
31 5 0.07
32 57 0.85
33 5 0.07
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (32 bp):
AAAATCAATCGATCTAATATTGACCCGACCCA
Found at i:53815 original size:21 final size:21
Alignment explanation
Indices: 53789--53838 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 21
53779 ATCCAATAGT
53789 CACCCGACCTAAAAATTGACC
1 CACCCGACCTAAAAATTGACC
53810 CACCCG-----AAAATTGACC
1 CACCCGACCTAAAAATTGACC
53826 CGACCCGACCTAA
1 C-ACCCGACCTAA
53839 TTTACCATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 11
0.68 0.00 0.32
Matches are distributed among these distances:
16 11 0.48
17 5 0.22
21 6 0.26
22 1 0.04
ACGTcount: A:0.36, C:0.40, G:0.12, T:0.12
Consensus pattern (21 bp):
CACCCGACCTAAAAATTGACC
Found at i:53821 original size:16 final size:17
Alignment explanation
Indices: 53790--53833 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
53780 TCCAATAGTC
**
53790 ACCCGACCTAAAAATTG
1 ACCCGACCCGAAAATTG
53807 ACCC-ACCCGAAAATTG
1 ACCCGACCCGAAAATTG
53823 ACCCGACCCGA
1 ACCCGACCCGA
53834 CCTAATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.36, C:0.39, G:0.14, T:0.11
Consensus pattern (17 bp):
ACCCGACCCGAAAATTG
Found at i:56852 original size:17 final size:17
Alignment explanation
Indices: 56825--56863 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
56815 AATTTACAAT
56825 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
*
56841 TAATTATAAATATTATC
1 TAATTATAAATAATATC
56858 TAATTA
1 TAATTA
56864 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:57565 original size:21 final size:20
Alignment explanation
Indices: 57539--57583 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
57529 GTCATACTTT
57539 TAAATAAATTTTAACAT-AAAA
1 TAAAT-AATTTTAA-ATGAAAA
*
57560 TAAATATTTTTAAATGAAAA
1 TAAATAATTTTAAATGAAAA
57580 TAAA
1 TAAA
57584 AATAAATACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 15 0.68
21 5 0.23
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAATAATTTTAAATGAAAA
Found at i:57587 original size:26 final size:25
Alignment explanation
Indices: 57556--57606 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
57546 ATTTTAACAT
*
57556 AAAATAAATATTTTTAAATGAAAATA
1 AAAATAAATACTTTTAAAT-AAAATA
57582 AAAATAAATACTTTTAAATAAAATA
1 AAAATAAATACTTTTAAATAAAATA
57607 TTCTCTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAATAAATACTTTTAAATAAAATA
Found at i:62765 original size:2 final size:2
Alignment explanation
Indices: 62758--62829 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
62748 AGAATTATTG
62758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62830 GTGTGTGTGT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63141 original size:2 final size:2
Alignment explanation
Indices: 63134--63184 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
63124 AAGTATGTGA
63134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63176 AT AT AT AT A
1 AT AT AT AT A
63185 AAGCCACATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63502 original size:32 final size:30
Alignment explanation
Indices: 63432--63550 Score: 123
Period size: 30 Copynumber: 3.9 Consensus size: 30
63422 GAGTCGAGGG
* * * *
63432 TTACCTATGTCTTTCGAG-CATATGGATAGT
1 TTACCTATGTCCTTCGGGACATATGGACA-A
* *
63462 TTACCTATGTCCTTTGGGATATATGGACAAGA
1 TTACCTATGTCCTTCGGGACATATGGAC-A-A
63494 TTACCTATGTCCTTCGGGACATATGGACAA
1 TTACCTATGTCCTTCGGGACATATGGACAA
* * *
63524 TTACCTATGTTCTCCGGAACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
63551 TAGGTCATTC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
30 40 0.53
31 8 0.11
32 28 0.37
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (30 bp):
TTACCTATGTCCTTCGGGACATATGGACAA
Found at i:63548 original size:62 final size:62
Alignment explanation
Indices: 63432--63550 Score: 141
Period size: 62 Copynumber: 1.9 Consensus size: 62
63422 GAGTCGAGGG
* * * ** * *
63432 TTACCTATGTCTTTCGAGCATATGGATAGTTTACCTATGTCCTTTGGGATATATGGACAAGA
1 TTACCTATGTCCTTCGAGCATATGGACAGATTACCTATGTCCTCCGGAACATATGGACAAGA
* *
63494 TTACCTATGTCCTTCGGGACATATGGACA-ATTACCTATGTTCTCCGGAACATATGGA
1 TTACCTATGTCCTTCGAG-CATATGGACAGATTACCTATGTCCTCCGGAACATATGGA
63551 TAGGTCATTC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 38 0.81
63 9 0.19
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (62 bp):
TTACCTATGTCCTTCGAGCATATGGACAGATTACCTATGTCCTCCGGAACATATGGACAAGA
Found at i:65410 original size:24 final size:23
Alignment explanation
Indices: 65374--65435 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
65364 GTGAGAGTCT
65374 ACCAGCACGAAATCAACTACCATC
1 ACCAGCAC-AAATCAACTACCATC
* **
65398 ACCAGCATCAAATCAGCTGTCATC
1 ACCAGCA-CAAATCAACTACCATC
65422 ACCAGCACCAAATC
1 ACCAGCA-CAAATC
65436 CGTTCGTCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.39, C:0.37, G:0.10, T:0.15
Consensus pattern (23 bp):
ACCAGCACAAATCAACTACCATC
Found at i:66033 original size:32 final size:32
Alignment explanation
Indices: 65997--66091 Score: 113
Period size: 32 Copynumber: 2.9 Consensus size: 32
65987 TCACTAGCTT
*
65997 ACTAACATTATAACTTTTATTTTATTGTTCGA
1 ACTAACATTATAACTTTTATTTTATTGTTCCA
* *
66029 ACTAACATTCTAACTTTTA-TTTATTTGTTCCT
1 ACTAACATTATAACTTTTATTTTA-TTGTTCCA
66061 ACTAACA-TACTAACTTTTTATTTTTATTGTT
1 ACTAACATTA-TAAC-TTTTA-TTTTATTGTT
66092 ATTACTTACT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
31 5 0.09
32 35 0.65
33 5 0.09
34 5 0.09
35 4 0.07
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (32 bp):
ACTAACATTATAACTTTTATTTTATTGTTCCA
Found at i:66324 original size:30 final size:30
Alignment explanation
Indices: 66290--66373 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
66280 TTTTCTAGCA
* *
66290 CTTTAAATTCCAACATTTTATTTTCA-TGCC
1 CTTTAATTTCCAGCATTTTATTTTCAGT-CC
* *
66320 CTTTAGTTTTCATGCATTTTA-TTTCAGTCC
1 CTTTAATTTCCA-GCATTTTATTTTCAGTCC
*
66350 CTTTAATTTCCAGCATTTAATTTT
1 CTTTAATTTCCAGCATTTTATTTT
66374 ATATATTTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 7 0.16
30 29 0.66
31 8 0.18
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (30 bp):
CTTTAATTTCCAGCATTTTATTTTCAGTCC
Found at i:66340 original size:16 final size:15
Alignment explanation
Indices: 66303--66343 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
66293 TAAATTCCAA
66303 CATTTTATTTTCATG
1 CATTTTATTTTCATG
**
66318 CCCTTTAGTTTTCATG
1 CATTTTA-TTTTCATG
66334 CATTTTATTT
1 CATTTTATTT
66344 CAGTCCCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (15 bp):
CATTTTATTTTCATG
Found at i:66835 original size:28 final size:29
Alignment explanation
Indices: 66803--66861 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
66793 TCATTTCATT
*
66803 TTGTTTTATTATATTA-TATTA-TTTTATC
1 TTGTTCTATT-TATTATTATTATTTTTATC
*
66831 TTGTTCTATTTTTTATTATTATTTTTATC
1 TTGTTCTATTTATTATTATTATTTTTATC
66860 TT
1 TT
66862 TGATGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 14 0.52
29 9 0.33
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.71
Consensus pattern (29 bp):
TTGTTCTATTTATTATTATTATTTTTATC
Found at i:68997 original size:44 final size:44
Alignment explanation
Indices: 68929--69017 Score: 137
Period size: 43 Copynumber: 2.0 Consensus size: 44
68919 GAAAAATATT
68929 AAGACGTACTGATACCTCTATGAATGAGTATCAATACCCCTATGA
1 AAGACGTACTGATACCTCTATGAATG-GTATCAATACCCCTATGA
*
68974 AAGA-GTACTGATACC-CATATGAATGGTATTAATACCCCTATGA
1 AAGACGTACTGATACCTC-TATGAATGGTATCAATACCCCTATGA
69017 A
1 A
69018 GGCTCAAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 19 0.45
44 19 0.45
45 4 0.10
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (44 bp):
AAGACGTACTGATACCTCTATGAATGGTATCAATACCCCTATGA
Found at i:69010 original size:21 final size:22
Alignment explanation
Indices: 68940--69017 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
68930 AGACGTACTG
* *
68940 ATACCTCTATGAATGAGTATCA
1 ATACCCCTATGAATGAGTATTA
* * *
68962 ATACCCCTATGAAAGAGTACTG
1 ATACCCCTATGAATGAGTATTA
*
68984 ATACCCATATGAATG-GTATTA
1 ATACCCCTATGAATGAGTATTA
69005 ATACCCCTATGAA
1 ATACCCCTATGAA
69018 GGCTCAAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
21 16 0.35
22 30 0.65
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (22 bp):
ATACCCCTATGAATGAGTATTA
Found at i:69062 original size:19 final size:19
Alignment explanation
Indices: 69038--69074 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
69028 TTGAATGCAA
69038 AAAGGGTA-CTGATACCATG
1 AAAGGGTATC-GATACCATG
69057 AAAGGGTATCGATACCAT
1 AAAGGGTATCGATACCAT
69075 AGTGCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (19 bp):
AAAGGGTATCGATACCATG
Found at i:70568 original size:3 final size:3
Alignment explanation
Indices: 70558--70596 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
70548 GGAAGAAGGT
* *
70558 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
70597 GTAGGCATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:72517 original size:22 final size:22
Alignment explanation
Indices: 72485--72570 Score: 127
Period size: 22 Copynumber: 3.9 Consensus size: 22
72475 AATATTAAGA
*
72485 GGTATCGATACCCCTATGAATG
1 GGTATCAATACCCCTATGAATG
*
72507 TGTATCAATACCCCTATGAATG
1 GGTATCAATACCCCTATGAATG
* *
72529 GGTACCGATACCCCTATGAATG
1 GGTATCAATACCCCTATGAATG
*
72551 GGTGTCAATACCCCTATGAA
1 GGTATCAATACCCCTATGAA
72571 GGCTCAAACA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (22 bp):
GGTATCAATACCCCTATGAATG
Found at i:72559 original size:44 final size:44
Alignment explanation
Indices: 72485--72570 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
72475 AATATTAAGA
* *
72485 GGTATCGATACCCCTATGAATGTGTATCAATACCCCTATGAATG
1 GGTACCGATACCCCTATGAATGGGTATCAATACCCCTATGAATG
*
72529 GGTACCGATACCCCTATGAATGGGTGTCAATACCCCTATGAA
1 GGTACCGATACCCCTATGAATGGGTATCAATACCCCTATGAA
72571 GGCTCAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (44 bp):
GGTACCGATACCCCTATGAATGGGTATCAATACCCCTATGAATG
Found at i:75522 original size:25 final size:24
Alignment explanation
Indices: 75470--75536 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 24
75460 AGAAAGGGGC
75470 AATATGTTTTC-AAATTTTTTATTA
1 AATAT-TTTTCAAAATTTTTTATTA
75494 AATATTTTTCAAAATTCTTTTAATT-
1 AATATTTTTCAAAATT-TTTT-ATTA
75519 AATATTTTTCAAAATTTT
1 AATATTTTTCAAAATTTT
75537 GAAAATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.12
24 12 0.30
25 20 0.50
26 3 0.08
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (24 bp):
AATATTTTTCAAAATTTTTTATTA
Found at i:78312 original size:83 final size:83
Alignment explanation
Indices: 78123--78305 Score: 269
Period size: 83 Copynumber: 2.2 Consensus size: 83
78113 ATAGCTAGAT
* * *
78123 TTCCTCAACACGAAGGAACAATGTCGTCAACCGATCATATCTTCTCAACACGAAGGAGCAGTGTC
1 TTCCTCAACACGAAGGAACAATGTCGTAAACCGACCATATCTCCTCAACACGAAGGAGCAGTGTC
* *
78188 ATCTTCAGACAATCAGAC
66 ATCCTCAGACAACCAGAC
* *
78206 TTCCTCAACACGAAGGAACAATGTTGTAAACCGACCATATCTCCTCAATACGAAGGAGCAGT-TC
1 TTCCTCAACACGAAGGAACAATGTCGTAAACCGACCATATCTCCTCAACACGAAGGAGCAGTGT-
*
78270 CATCCTCAGACAACCATAC
65 CATCCTCAGACAACCAGAC
*
78289 TTCCTCAACAAGAAGGA
1 TTCCTCAACACGAAGGA
78306 GTAATGTCAT
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
82 1 0.01
83 89 0.99
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (83 bp):
TTCCTCAACACGAAGGAACAATGTCGTAAACCGACCATATCTCCTCAACACGAAGGAGCAGTGTC
ATCCTCAGACAACCAGAC
Found at i:81102 original size:25 final size:25
Alignment explanation
Indices: 81039--81110 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
81029 TACATTTAAC
*** *
81039 ATTTTATAGAATAAAGTTGTTTATTT
1 ATTTTATAGAATAAA-TTAAATATAT
* *
81065 ATTCTATAAAATAAATTAAATATAT
1 ATTTTATAGAATAAATTAAATATAT
81090 ATTTTATAGAATAAATTAAAT
1 ATTTTATAGAATAAATTAAAT
81111 TTATTCTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 25 0.66
26 13 0.34
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (25 bp):
ATTTTATAGAATAAATTAAATATAT
Found at i:81140 original size:25 final size:23
Alignment explanation
Indices: 81061--81149 Score: 115
Period size: 25 Copynumber: 3.7 Consensus size: 23
81051 AAAGTTGTTT
81061 ATTTATTCTATAAAATAAATTAA
1 ATTTATTCTATAAAATAAATTAA
* *
81084 ATATATATTTTATAGAATAAATTAA
1 AT-T-TATTCTATAAAATAAATTAA
*
81109 ATTTATTCTATAAAATATATATTTA
1 ATTTATTCTATAAAATA-A-ATTAA
81134 ATTTATTCTATAAAAT
1 ATTTATTCTATAAAAT
81150 GGCATGTGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
23 14 0.25
24 3 0.05
25 40 0.70
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (23 bp):
ATTTATTCTATAAAATAAATTAA
Done.