Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014759.1 Corchorus capsularis cultivar CVL-1 contig14780, 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: 29703
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:12206 original size:29 final size:30
Alignment explanation
Indices: 12169--12296 Score: 114
Period size: 35 Copynumber: 4.0 Consensus size: 30
12159 TAAATAATAA
* *
12169 AATATAATTAAATAA-TTATATTTATACAT
1 AATAAAATTAAATAATTTATATGTATACAT
*
12198 AATAAAATTGAATAATTTATATGTATACAATTAAT
1 AATAAAATTAAATAATTTATATGTATAC-----AT
*
12233 AATAAAATTGAATAATTTATATGTATACAATTAAT
1 AATAAAATTAAATAATTTATATGTATAC-----AT
*
12268 AATAAAATTGAATAATTTATATGTATACA
1 AATAAAATTAAATAATTTATATGTATACA
12297 ATTAATTAGA
Statistics
Matches: 90, Mismatches: 3, Indels: 11
0.87 0.03 0.11
Matches are distributed among these distances:
29 13 0.14
30 12 0.13
35 65 0.72
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (30 bp):
AATAAAATTAAATAATTTATATGTATACAT
Found at i:12239 original size:35 final size:35
Alignment explanation
Indices: 12196--12302 Score: 214
Period size: 35 Copynumber: 3.1 Consensus size: 35
12186 ATATTTATAC
12196 ATAATAAAATTGAATAATTTATATGTATACAATTA
1 ATAATAAAATTGAATAATTTATATGTATACAATTA
12231 ATAATAAAATTGAATAATTTATATGTATACAATTA
1 ATAATAAAATTGAATAATTTATATGTATACAATTA
12266 ATAATAAAATTGAATAATTTATATGTATACAATTA
1 ATAATAAAATTGAATAATTTATATGTATACAATTA
12301 AT
1 AT
12303 TAGAACTTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 72 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (35 bp):
ATAATAAAATTGAATAATTTATATGTATACAATTA
Found at i:14518 original size:663 final size:661
Alignment explanation
Indices: 13307--14863 Score: 1477
Period size: 660 Copynumber: 2.4 Consensus size: 661
13297 ATTAGTATAT
* * * * * * *
13307 GATTTCGGCTAAAAATTTTGTAAAAATTGATCCGAAAGATATTTTC-TC-AATTTTTGCCTAGAA
1 GATTTCGGCT-AAAATTTTGCAAAAAATGACCCGAAAAATATTGTCGTCAAATTTTAGCC-AAAA
* * ** * * * * * *
13370 TACTCATAAAAAGTATATAATTCGACATCAAAAAGA-TTGAAGGGCTTTTAACCCTTCTAATATT
64 TACTCATAAAAAATATATAATTCAACGCCAGAAAGATTTGAA-GACTTCTCACACTTCTAATATC
* * * * **
13434 GTTTTTCATAATTTTT-TCCGAATTAATTTCTAATTAAATC-AAGACAAGTTTCCGATGCTCGTA
128 GTTTTTCAT-ATTTTTCT-C-AAATAGTTTATAATTAAATCGAA-ACAAGATTCAAATGCTCGTA
* * * * * * * * *
13497 AAAACAAATCCTTAAATCTAATGTGGTTGAGATTTG-TTAGATGAAT--ATAGATATTTT-AAGA
189 AAAACAAATCCTTAAATCCAAAGTCGCTAAGATTTGATTAGATGAATACAAATATATTTTCGAGG
* ** * * * * **
13558 AGTCTTGGC-ACCAAAAATCATGCAAAACTGAGTC--GAGCCCCAGAACGCGTTTTTAGCCGAAA
254 AGT-TTTGCTACCAAAAATCATGCAAAACT-AACCAGGGGCCTCGGAACGCGTTATTAGCAAAAA
***** *** ** * * *
13620 ACCGTGTACACAAT-TTCGGAT-AAAATTTTGTAAAAATTGATCGAAAGATTTTTCCTCGATTTC
317 AAAAAAT-CGTGATGGACGGCTAAAAATTTTGCAAAAATTGATCGAAAGATTTTTCCTCAATTTC
*
13683 TAGCGAAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAAATTGAAAGTGTTTTTCACGTT
381 TAGCCAAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAAATTGAAAGTGTTTTTCACGTT
* * * * *
13748 TTAAATATCGTTTTTCCTATTTTATTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTTAGA
446 TTAAATATCGTTTTTCATATTTTATCTCCAAA-TAATTTCTAATTAAAACGAAACAAGATTTAGA
*
13813 AACTCGTAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAACATAGATATAT
510 AACTCGTAAAAACAAATCCTTAAATACAAAGTGGCTGAGATTTGATTAGATGAACATAG--ATAT
* * * *
13878 TTTAAGGAGTCTTGACGCCAAAAATCATGCAAAACTAACCAGGG-CCCTGGAACGCGTTTTTAGA
573 TTGAAGGAGTCTCGACGCCAAAAATCATGCAAAACTAACCAGGGACCCCGAAACGCGTTTTTAG-
*
13942 AAAAAAAAAAAAACCAT-GATACTACAT
637 ---AAAAAAAAAACCATGGATACTACAC
* * * * *
13969 GATTTCGGCTAAAATTTTGCAAAAATTGA-CCGAAATATATT-TC-TGAATTTTTAGCCACAATA
1 GATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATATTGTCGTCAAATTTTAGCCAAAATA
14031 CTCATAAAAAAATATATAATTCAACGCCA-AAAGGA-TTGAAGA-TTCCTCACACTTCTAATATC
66 CTCAT-AAAAAATATATAATTCAACGCCAGAAA-GATTTGAAGACTT-CTCACACTTCTAATATC
* * * *
14093 GTTTTTCCTATGTTCTT-TCAAATTGATTTATAATTAAATCGAAATATGATTCAAATGCTCGTAA
128 GTTTTTCATAT-TT-TTCTCAAATAG-TTTATAATTAAATCGAAACAAGATTCAAATGCTCGTAA
* *
14157 AAACAAATTCTTAAATCCAATGTCGCTAAGATTT-AGTTAGATGAATACAAATATATTTTCGAGG
190 AAACAAATCCTTAAATCCAAAGTCGCTAAGATTTGA-TTAGATGAATACAAATATATTTTCGAGG
14221 AGTTTTGCTACCAAAAATCATGCAAAACTAACCAGGGGCCTCGGAACGCGTTATTAGCAAAAAAA
254 AGTTTTGCTACCAAAAATCATGCAAAACTAACCAGGGGCCTCGGAACGCGTTATTAGCAAAAAAA
* * *
14286 AAAATCGTGATGGACGGCTAAAAATTTT-CAAAAATTGATCCGAAATATTTTTCTTCAATTTTTA
319 AAAATCGTGATGGACGGCTAAAAATTTTGCAAAAATTGAT-CGAAAGATTTTTCCTCAATTTCTA
** * * * * *
14350 GCCCCAATACTCATTATATATATATATAATTCAATGCCAAAAAGATTG-GAG-GATTTTTCACGG
383 GCCAAAATACTCA-TA-AAAAATATATAATTCAAAGCCAAAAAAATTGAAAGTG-TTTTTCAC-G
* *
14413 TTTT-AATATTGTTTTTCATATTTT-TCT-GAAGA-AATTTCTAATTAAAACGAAACAAGATTTA
444 TTTTAAATATCGTTTTTCATATTTTATCTCCAA-ATAATTTCTAATTAAAACGAAACAAGATTTA
* * ** * *
14474 -AATGCTCTTAAAAACAAATCCTTAAATTTAAAGTGGCTGAGATTTGATTATATGAATATAGATA
508 GAA-ACTCGTAAAAACAAATCCTTAAATACAAAGTGGCTGAGATTTGATTAGATGAACATAGATA
* * * *
14538 TTTGAAGGAGTCTCGGCTCCAAAAATCATGCAAAACTAAGCTGGGACCCCGAAACGCGTTTTTAG
572 TTTGAAGGAGTCTCGACGCCAAAAATCATGCAAAACTAACCAGGGACCCCGAAACGCGTTTTTAG
*** ***** * *
14603 TCCAAAACCGTGATGGTTAGTACAC
637 AAAAAAAAAACCATGGATACTACAC
* * *
14628 GATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTTTGTCGTCAAATTTTGGCTAAAATA
1 GATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATATTGTCGTCAAATTTTAGCCAAAATA
* * * * * *
14693 CTCATAAAATATATATAATTTAACGCCAGAAAGATTTGAGGACTTTTCACGCTTTTAATATCGTT
66 CTCATAAAAAATATATAATTCAACGCCAGAAAGATTTGAAGACTTCTCACACTTCTAATATCGTT
* * * * *
14758 TTTCATATTTTTCTGAAATAGTTTCTAATTAAATCGAAACAAGATTTATATGCTCTTAAAAACAA
131 TTTCATATTTTTCTCAAATAGTTTATAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAA
* * *
14823 ATCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATA
196 ATCCTTAAATCCAAAGTCGCTAAGATTTGATTAGATGAATA
14864 TAGAGCCTTC
Statistics
Matches: 732, Mismatches: 128, Indels: 72
0.79 0.14 0.08
Matches are distributed among these distances:
658 13 0.02
659 134 0.18
660 144 0.20
661 94 0.13
662 96 0.13
663 107 0.15
664 40 0.05
665 42 0.06
666 30 0.04
667 32 0.04
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (661 bp):
GATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATATTGTCGTCAAATTTTAGCCAAAATA
CTCATAAAAAATATATAATTCAACGCCAGAAAGATTTGAAGACTTCTCACACTTCTAATATCGTT
TTTCATATTTTTCTCAAATAGTTTATAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAA
ATCCTTAAATCCAAAGTCGCTAAGATTTGATTAGATGAATACAAATATATTTTCGAGGAGTTTTG
CTACCAAAAATCATGCAAAACTAACCAGGGGCCTCGGAACGCGTTATTAGCAAAAAAAAAAATCG
TGATGGACGGCTAAAAATTTTGCAAAAATTGATCGAAAGATTTTTCCTCAATTTCTAGCCAAAAT
ACTCATAAAAAATATATAATTCAAAGCCAAAAAAATTGAAAGTGTTTTTCACGTTTTAAATATCG
TTTTTCATATTTTATCTCCAAATAATTTCTAATTAAAACGAAACAAGATTTAGAAACTCGTAAAA
ACAAATCCTTAAATACAAAGTGGCTGAGATTTGATTAGATGAACATAGATATTTGAAGGAGTCTC
GACGCCAAAAATCATGCAAAACTAACCAGGGACCCCGAAACGCGTTTTTAGAAAAAAAAAACCAT
GGATACTACAC
Found at i:14751 original size:332 final size:329
Alignment explanation
Indices: 13286--15326 Score: 1631
Period size: 332 Copynumber: 6.2 Consensus size: 329
13276 TCGACCTGCT
* * * * *
13286 AAACCGTGATGATTAGTATATGATTTCGGCTAAAAATTTTGTAAAAATTGATCCGAAAGATATTT
1 AAACCGTGATGGTTAGTACACGATTTCGGCT-AAAATTTTGTAAAAATTGACCCGAAAAAT-TTT
* * * **
13351 T-CTCAATTTTTGCCTAGAATACTCATAAAA-AGTATATAATTCGACATCAAAAAGA-TTGAAGG
64 TCCTCAATTTTTGGCTAAAATACTCATAAAATA-TATATAATTCAACGCCAAAAAGATTTG-AGG
* * * * * * *
13413 GCTTTTAACCCTTCTAATATTGTTTTTCATAATTTTTTCCGAATTAATTTCTAATTAAATC-AAG
127 ACTTTTCACGCTTTTAATATCGTTTTTCAT-A-TTTTTCTGAA-AAATTTCTAATTAAATCGAA-
* * *
13477 ACAAG-TTTCCGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGAGATTTG-TTAGATG
188 ACAAGATTT-AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * ** *
13540 AATATAGATATTTTAAGAAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGAG-CCCC-AGAA
252 AATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAACCCGGGACCCCGA-AA
*
13603 CGCGTTTTTAGCCGA
316 CGCGTTTTTAG-CAA
* * * *
13618 AAACC------G-T-GTACACAATTTCGGATAAAATTTTGTAAAAATTGA-TCGAAAGATTTTTC
1 AAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAAATTTTTC
* * * * * * *
13674 CTCGATTTCTAGCGAAAATACTCATAAAAAATATATAATTCAAAGCCAAAAA-AATTGAAAGTG-
66 CTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTTG--AG-GA
* * * * *
13737 TTTTTCACG-TTTTAAATATCGTTTTTCCTATTTTATTTCCAAATTAATTTCTGATTAAATCGAA
128 CTTTTCACGCTTTT-AATATCGTTTTTCATATTTT-TCT-GAAA--AATTTCTAATTAAATCGAA
* ** *
13801 ATAAGATTTAGAAACTCGTAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGA
188 ACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
* * * * * *
13866 ACATAGATATATTTTAAGGAGTCTTGACGCCAAAAATCATGCAAAACTAACCAGGG-CCCTGGAA
253 ATATAG--ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAACCCGGGACCCCGAAA
*
13930 CGCGTTTTTAGAAAAAAAA
316 CGCGTTTTTAG-----CAA
***** * * * * * *
13949 AAAAAACCAT-GATACTACATGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGAAATATATTT-
1 AAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAAATTTTTC
* * * * * * *
14011 CTGAATTTTTAGCCACAATACTCATAAAAAAATATATAATTCAACGCCAAAAGGA-TTGAAGA-T
66 CTCAATTTTTGGCTAAAATACTCAT-AAAATATATATAATTCAACGCCAAAAAGATTTGAGGACT
* * * * * * * *
14074 TCCTCACACTTCTAATATCGTTTTTCCTATGTTCTT-TCAAATTGATTTATAATTAAATCGAAAT
130 T-TTCACGCTTTTAATATCGTTTTTCATAT-TT-TTCTGAAA--AATTTCTAATTAAATCGAAAC
* * * * * *
14138 ATGATTCAAATGCTCGTAAAAACAAATTCTTAAATCCAATGTCGCTAAGATTT-AGTTAGATGAA
190 AAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA-TTAGATGAA
* * * * * * * * *
14202 TACAAATATATTTTCGAGGAGT-TTTGCTACCAAAAATCATGCAAAACTAACCAGGGGCCTCGGA
254 T--ATAGATA-TTTCAAGGAGTCTTGGC-GCCAAAAATCATGCAAAACTAACCCGGGACCCCGAA
*
14266 ACGCGTTATTAGCAA
315 ACGCGTTTTTAGCAA
***** * ** * * *
14281 AAAAAAAAATCG-T-G-A-TGGA---CGGCTAAAAATTTT-CAAAAATTGATCCGAAATATTTTT
1 AAACCGTGATGGTTAGTACACGATTTCGGCT-AAAATTTTGTAAAAATTGACCCGAAAAATTTTT
* * *** * * *
14338 CTTCAATTTTTAGCCCCAATACTCATTATATATATATATAATTCAATGCCAAAAAGATTGGAGGA
65 CCTCAATTTTTGGCTAAAATACTCA-TA-AAATATATATAATTCAACGCCAAAAAGATTTGAGGA
* * * *
14403 TTTTTCACGGTTTTAATATTGTTTTTCATATTTTTCTGAAGAAATTTCTAATTAAAACGAAACAA
128 CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAA-AAATTTCTAATTAAATCGAAACAA
* * ** * *
14468 GATTTAAATGCTCTTAAAAACAAATCCTTAAATTTAAAGTGGCTGAGATTTGATTATATGAATAT
192 GATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
* * * * *
14533 AGATATTTGAAGGAGTCTCGGCTCCAAAAATCATGCAAAACTAAGCTGGGACCCCGAAACGCGTT
257 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAACCCGGGACCCCGAAACGCGTT
*
14598 TTTAGTCCA
322 TTTAG-CAA
* *
14607 AAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTTTGT
1 AAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAAATTTT-T
* * * *
14672 CGTCAAATTTTGGCTAAAATACTCATAAAATATATATAATTTAACGCCAGAAAGATTTGAGGACT
65 CCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTTGAGGACT
*
14737 TTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAAATAGTTTCTAATTAAATCGAAACAAGA
130 TTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAAA-AATTTCTAATTAAATCGAAACAAGA
* * * *
14802 TTTATATGCTCTTAAAAACAAATCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATATAG
194 TTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG
*** * * * *
14867 AGCCTTCAGGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCC-GGAGCCCC-AAGATGCGTT
259 ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAACCCGGGA-CCCCGAA-ACGCGTT
*
14930 TTTAGCCCA
322 TTTAG-CAA
* * * **
14939 AAACCGTGGTGGTTAGTACACGATTTCGGTTAAAATTTTGTAAAAAATGACCCGAAATTTTTTTC
1 AAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAAATTTTTC
* * * * ** *
15004 ATCAATTTTTGGATAAAATACCCATAATATATATATATATATAATTTAACGGAAAAAAGATTGGA
66 CTCAATTTTTGGCTAAAATA--C-TCATA-A-A-ATATATATAATTCAACGCCAAAAAGATTTGA
* *
15069 AGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGTAATAATTTCTAATTAAATCGAAA
125 GGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTG-AAAAATTTCTAATTAAATCGAAA
* * ** * *
15134 CAAGATTCAGATGTTCGTAAAAACAAATTTTTAAATGCAATGTAGCTGAGATTTGATTAGATGAA
189 CAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * * * * * **
15199 TATGGATATCTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACAT
254 TATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAACCCGGGACCCCGAAACGC
*
15264 GTTATTAGCCAA
319 GTTTTTAG-CAA
* * * * **
15276 AACCCGTGATGATTATTACACGATTTCGGCTAGAATTTTACAAAAATTGAC
1 AAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGAC
15327 TTGGAAGTTA
Statistics
Matches: 1403, Mismatches: 232, Indels: 143
0.79 0.13 0.08
Matches are distributed among these distances:
321 9 0.01
322 56 0.04
323 44 0.03
324 73 0.05
325 69 0.05
326 31 0.02
327 77 0.05
328 95 0.07
329 34 0.02
330 31 0.02
331 31 0.02
332 291 0.21
333 29 0.02
334 25 0.02
335 87 0.06
336 61 0.04
337 285 0.20
338 74 0.05
339 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (329 bp):
AAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAAATTTTTC
CTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTTGAGGACTT
TTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAAAAATTTCTAATTAAATCGAAACAAGATT
TAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
ATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAACCCGGGACCCCGAAACGCGTTTTTA
GCAA
Found at i:15350 original size:337 final size:331
Alignment explanation
Indices: 12777--15326 Score: 1493
Period size: 332 Copynumber: 7.7 Consensus size: 331
12767 CAAATTTTTG
* * *
12777 TTTCATATTTTT-TGAATTAATTTTTAATTAAATCGAAACAAGATATAAATGCTCGTAAAAACAA
1 TTTCATATTTTTCTGAA-TAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCTTAAAAACAA
* ** * * * * * *
12841 ATTCTTAAATAGAATA-TGTCTGAGATTTTATTAGAT-AATATAGATATTTTAAGGAGTTTCGGT
65 ATCCTTAAATTCAA-AGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGC
* ** * * * *
12904 GCCAAAAATCATGCAAAACTAAGCCGGGACCCATAACGTGTTTTTAGCCAAAAACCCTTGCTGGT
129 GCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAACATGTTTTTAGCCCAAAA-CCGTGATGGT
* * * *** * ** * *
12969 AAAAATCACCCGAAAGATTTTTCCTCAAATTTTGGC--AAAAT-ACTCATAAAATATAT-AT-AA
193 --TAGT-A--C--ACGATTTCGGCTAAAATTTT-GCAAAAAATGAC-CCGAAAATTTTTCATCAA
*** * * * *
13029 TTCTTTTTTTAGAA-A-T-A-A-A-AGATATATATAATTCAACACCAAAAAGATTGGAGGACTTT
249 TT-TTTGGATAAAATACTAATATATATATATATATAATTTAACGCCAAAAAGATTGGAGGACTTT
13088 TCACGCTTTTAATATCGTT
313 TCACGCTTTTAATATCGTT
*
13107 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAGCAAGACCAAAACAAGA-TTAAGATGC
1 TTTCATATTTTTCTGAA-TAATTTCTAATTAAAT-----C--G----AAACAAGATTTAA-ATGC
* * * ** * * * *
13171 ACATAAAAACAAATCCTTAAATCCAATTTGACAGAGATTTGATTAGATTAATA-AGGATATTTCA
53 TCTTAAAAACAAATCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATATA-GATATCTCA
* ** * * * *
13235 AGGAGTCTCAGCGCCAAAAATCATGCAAAAC-AGAGTTGTGG--TCG-AC------CT-G--CTA
117 AGGAGTCTCGGCGCCAAAAATCATGCAAAACTA-AGCCGGGGCCCCGAACATGTTTTTAGCCCAA
* * * * * *
13287 AACCGTGATGATTAGTATATGATTTCGGCTAAAAATTTTGTAAAAATTGATCCGAAAGATATTTT
181 AACCGTGATGGTTAGTACACGATTTCGGCT-AAAATTTTGCAAAAAATGACCCGAAA-AT-TTTT
** * * ** ** *
13352 C-TCAATTTTTGCCTAGAATACTCATA-A-A-A-AGTATATAATTCGACATCAAAAAGATTGAAG
243 CATCAATTTTTGGATAAAATACTAATATATATATA-TATATAATTTAACGCCAAAAAGATTGGAG
* * * * *
13412 GGCTTTTAACCCTTCTAATATTGTT
307 GACTTTTCACGCTTTTAATATCGTT
* ** *
13437 TTTCATAATTTTTTCCGAATTAATTTCTAATTAAATC-AAGACAAG-TTTCCGATGCTCGTAAAA
1 TTTCAT-A-TTTTTCTGAA-TAATTTCTAATTAAATCGAA-ACAAGATTT-AAATGCTCTTAAAA
* * * * *
13500 ACAAATCCTTAAA-TCTAATGTGGTTGAGATTTG-TTAGATGAATATAGATATTTTAAGAAGTCT
61 ACAAATCCTTAAATTC-AAAGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCT
* * * * * ** *
13563 TGGCACCAAAAATCATGCAAAACTGAGTC-GAGCCCCAGAACGCGTTTTTAGCCGAAAACC----
125 CGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCC-GAACATGTTTTTAGCCCAAAACCGTGA
* * * * * * * *
13623 --G-T-GTACACAATTTCGGATAAAATTTTGTAAAAATTGA-TCGAAAGATTTTTCCTCGATTTC
189 TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAA-ATTTTTCATCAATTTT
* ** * * * * * * *
13683 TAGCGAAAATACTCATA-A-A-AAATATATAATTCAAAGCCAAAAAAATTGAAAGTG-TTTTTCA
253 TGGATAAAATACTAATATATATATATATATAATTTAACGCCAAAAAGATTG-GAG-GACTTTTCA
13744 CG-TTTTAAATATCGTT
316 CGCTTTT-AATATCGTT
* ** * * * *
13760 TTTCCTATTTTATTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTTAGAA-ACTCGTAAAA
1 TTT-C-ATATT-TTTCTGAA-TAATTTCTAATTAAATCGAAACAAGATTTA-AATGCTCTTAAAA
* * * * *
13824 ACAAATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAACATAGATATATTTTAAGGAGTC
61 ACAAATCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATATAG--ATATCTCAAGGAGTC
* * * * ** *** *
13889 TTGACGCCAAAAATCATGCAAAACTAA-CCAGGGCCCTGGAACGCGTTTTTAGAAAAAAAAAAAA
124 TCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCC-CGAACATGTTTTTAG----CCCAAAAC
**** * * * * * *
13953 AACCAT-GATACTACATGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGAAATATATTTC-TGA
184 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAA-ATTTTTCATCA
* ** * * * * * * *
14015 ATTTTTAGCCACAATACTCATA-A-AAAAATATATAATTCAACGCCAAAAGGATT-GAAGA-TTC
248 ATTTTTGGATAAAATACTAATATATATATATATATAATTTAACGCCAAAAAGATTGGAGGACTT-
* * *
14076 CTCACACTTCTAATATCGTT
312 TTCACGCTTTTAATATCGTT
* * * * * * * *
14096 TTTCCTATGTTCTT-TCAAATTGATTTATAATTAAATCGAAATATGATTCAAATGCTCGTAAAAA
1 TTTCATAT-TT-TTCT-GAA-TAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCTTAAAAA
* * * * * * * * *
14160 CAAATTCTTAAATCCAATGTCGCTAAGATTT-AGTTAGATGAATACAAATATATTTTCGAGGAGT
62 CAAATCCTTAAATTCAAAGTGGCTGAGATTTGA-TTAGATGAAT--ATAGATA-TCTCAAGGAGT
** * * ** * * **
14224 -TTTGCTACCAAAAATCATGCAAAACTAA-CCAGGGGCCTCGGAACGCGTTATTAG-CAAAAAAA
123 CTCGGC-GCCAAAAATCATGCAAAACTAAGCC-GGGGCC-CCGAACATGTTTTTAGCCCAAAACC
*** * ** * * *
14286 AAAATCG-T-G-A-TGGA---CGGCTAAAAATTTT-CAAAAATTGATCCGAAATATTTTTCTTCA
185 GTGATGGTTAGTACACGATTTCGGCT-AAAATTTTGCAAAAAATGACCCGAAA-ATTTTTCATCA
* **** * * * *
14343 ATTTTTAGCCCCAATACTCAT-TATATATATATATAATTCAATGCCAAAAAGATTGGAGGATTTT
248 ATTTTTGGATAAAATACTAATATATATATATATATAATTTAACGCCAAAAAGATTGGAGGACTTT
* *
14407 TCACGGTTTTAATATTGTT
313 TCACGCTTTTAATATCGTT
* *
14426 TTTCATATTTTTCTGAAGAAATTTCTAATTAAAACGAAACAAGATTTAAATGCTCTTAAAAACAA
1 TTTCATATTTTTCTGAA-TAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCTTAAAAACAA
* * * * *
14491 ATCCTTAAATTTAAAGTGGCTGAGATTTGATTATATGAATATAGATATTTGAAGGAGTCTCGGCT
65 ATCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGCG
* * ** *
14556 CCAAAAATCATGCAAAACTAAGCTGGGACCCCGAAACGCGTTTTTAGTCCAAAACCGTGATGGTT
130 CCAAAAATCATGCAAAACTAAGCCGGGGCCCCG-AACATGTTTTTAGCCCAAAACCGTGATGGTT
* * *
14621 AGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTTTGTCGTCAAATTTTGGC
194 AGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCG-AAAATTTT-TCATCAATTTTTGGA
* * *
14686 TAAAATACTCATA-A-A-ATATATATAATTTAACGCCAGAAAGATTTGAGGACTTTTCACGCTTT
257 TAAAATACTAATATATATATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTT
14748 TAATATCGTT
322 TAATATCGTT
* *
14758 TTTCATATTTTTCTGAAATAGTTTCTAATTAAATCGAAACAAGATTTATATGCTCTTAAAAACAA
1 TTTCATATTTTTCTG-AATAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCTTAAAAACAA
** *
14823 ATCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATATAGA-GCCTTCAGGGAGTCTCGGC
65 ATCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATATAGATATC-TCAAGGAGTCTCGGC
* * *
14887 GCCAAAAATCATGCAAAACTAAGCCGGAGCCCC-AAGATGCGTTTTTAGCCCAAAACCGTGGTGG
129 GCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAACAT--GTTTTTAGCCCAAAACCGTGATGG
* * *
14951 TTAGTACACGATTTCGGTTAAAATTTTGTAAAAAATGACCCGAAATTTTTTTCATCAATTTTTGG
192 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAA-ATTTTTCATCAATTTTTGG
** *
15016 ATAAAATACCCATAATATATATATATATATAATTTAACGGAAAAAAGATTGGAAGACTTTTCACG
256 ATAAAATA--C-TAATATATATATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACG
15081 CTTTTAATATCGTT
318 CTTTTAATATCGTT
* * * *
15095 TTTCATATTTTTCTGTAATAATTTCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAA
1 TTTCATATTTTTCTG-AATAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCTTAAAAACAA
** * * * * * *
15160 ATTTTTAAATGCAATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAAGAGTCTTGGCG
65 ATCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGCG
* * *
15225 CCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACATGTTATTAG-CCAAAACCCGTGATGAT
130 CCAAAAATCATGCAAAACTAAGCCGGGGCCCC-GAACATGTTTTTAGCCCAAAA-CCGTGATGGT
* * * *
15289 TATTACACGATTTCGGCTAGAATTTTACAAAAATTGAC
193 TAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGAC
15327 TTGGAAGTTA
Statistics
Matches: 1786, Mismatches: 300, Indels: 261
0.76 0.13 0.11
Matches are distributed among these distances:
319 1 0.00
320 51 0.03
321 50 0.03
322 55 0.03
323 53 0.03
324 89 0.05
325 78 0.04
326 36 0.02
327 92 0.05
328 105 0.06
329 36 0.02
330 105 0.06
331 55 0.03
332 308 0.17
333 28 0.02
334 36 0.02
335 89 0.05
336 58 0.03
337 287 0.16
338 69 0.04
339 4 0.00
340 2 0.00
341 3 0.00
342 52 0.03
343 44 0.02
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (331 bp):
TTTCATATTTTTCTGAATAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCTTAAAAACAAA
TCCTTAAATTCAAAGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGCGC
CAAAAATCATGCAAAACTAAGCCGGGGCCCCGAACATGTTTTTAGCCCAAAACCGTGATGGTTAG
TACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTCATCAATTTTTGGATAAA
ATACTAATATATATATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAAT
ATCGTT
Found at i:16323 original size:973 final size:975
Alignment explanation
Indices: 13454--16910 Score: 2816
Period size: 973 Copynumber: 3.5 Consensus size: 975
13444 ATTTTTTCCG
* * * *
13454 AATTAATTTCTAATTAAATC-AAGACAAGTTTCCGATGCTCGTAAAAACAAATCCTTAAATCTAA
1 AATTAATTTCTAATTAAATCGAA-ACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAA
* * * * *
13518 TGTGGTTGAGATTTG-TTAGATGAATATAGATATTTTAAGAAGTCTTGGCACCAAAAATCATGCA
65 TGTGGATGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCA
** * * *
13582 AAACTG-AGTCGAGCCCCAGAACGCGTTTTTAGCCGAAAACC-----G--T-GTACACAATTTCG
130 AAACTGAACCCGGGCCCCGGAACGCGTTTTTAGCC-AAAACCGTGATGATTAGTACACGATTTCG
* * * * * * *
13638 GATAAAATTTTGTAAAAATTGA-TCGAAAGATTTTTCCTCGATTTCTAGCGAAAATACTCATAAA
194 GCTAAAATTTTGTAAAAA-TGACCCGAAAAATTTTTCCTCAATTT-TTGCTAAAATACTCATAAG
* *
13702 AAATATATAATTCAAAGCCAAAAAA-A-TTGAAAGTG-TTTTTCACG-TTTTAAATATCGTTTTT
257 ATATATATAATT-AAA-CCAAAAAAGATTTG--AG-GACTTTTCACGCTTTT-AATATCGTTTTT
* * * * ** *
13763 CCTATTTTATTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTTAGAAACTCGTAAAAACAA
316 CATATTTT-TCT-GAAA-TAATTTCTAATTAAATCGAAATAAGATTTAGATTCTCATAAAAACAA
* * * * * *
13828 ATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAACATAGATATATTTTAAGGAGTCTTGA
378 ATCCTTAAATGCAATATGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTCTCGG
* * * * * * ****
13893 CGCCAAAAATCATGCAAAACT-AACCAGGGCCCTGGAACGCGTTTTTAGAAAAAAAAAAAAAACC
441 TGCCAAAAATCATGCAAAACTGAGCC-GGACCC-GAAATGCGTTTTTAGCAAAAAAAACCGTA--
* * * * * * * * *
13957 AT-GATACTACATGATTTCGGCTAAAATTTTGCAAAAATTGACC-G-AAATATATTTC-TGAATT
502 ATGGTTAATACACGATTTCGGTTAAAAGTTAGCAAAAAATGACCAGAAAAAAT-TTTCATCAATT
* ** * * * *
14018 TTTAGCCACAATACTCATAA-A-A-A-A-ATATATAATTCAACGCCAAAAGGATT-GAAGA-TTC
566 TTTGGATAAAATAC-CATAATAGATATATATATATAATTTAACGCAAAAAAGATTGGAAGACTT-
* * * ** * * *
14076 CTCACACTTCT-AATATCGTTTTTCCTATGTTCTT-TCAAATTGATTTATAATTAAATCGAAATA
629 TTCACGCTT-TGAATATCGTTTTTCATAT-TT-TTCTGTAA-TAATTTCTAATTAAATCGAAACA
* * * ** * *
14139 TGATTCAAATGCTCGTAAAAACAAATTCTTAAATCCAATGTCGCTAAGATTT-AGTTAGATGAAT
690 AGATTCAGATGCTCATAAAAACAAAAACTTAAATGCAATGTAGCTAAGATTTGA-TTAGATGAAT
*** * * * * * * *
14203 ACAAATATATTTTCGAGGAGT-TTTGCTACCAAAAATCATGCAAAACT-AACCAGGGGCCTCGGA
754 --ATGGATA-TCTCAAAGAGTCTTGGC-GCCAAAAATCATGCAAAACTGACCCA-GGGCCCCGGA
* ** ** *
14266 ACGCGTTATTAGCAAAAAA--A--A--AA-A-T-CGTGATGGACGGCTAAAAATTTT-CAAAAAT
814 ACACGTTATTAGCAAAAAACCATGATGAATATTACACGAT-TTCAGCT-AAAATTTTACAAAAAT
** * ** * * *
14321 TGA-TCCGAA-ATATTTTTCTTCAATTTTTAGCCCCAATACTCATTATATATATATATAATTCAA
877 TGACTTGGAAGATA--TTTCCTCAATTTTTAGCCAAAATAATCA-TA-AAAAATATAT-ATTCAA
* * * * ** ** *
14384 TGCCAAAAAGATTGGAGGATTTTTCACGGTTTTAATATTGTTTTTCATATTTTTCT
937 CG-C----ATATT-GAAG-TTTTT-TC---TTCCATATCATTTTTCCTA------T
** * * * * **
14440 GAAGAAATTTCTAATTAAAACGAAACAAGATTTAAATGCTCTTAAAAACAAATCCTTAAATTTAA
1 -AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAA
* * * * *
14505 AGTGGCTGAGATTTGATTATATGAATATAGATATTTGAAGGAGTCTCGGCTCCAAAAATCATGCA
65 TGTGGATGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCA
* * * *
14570 AAACT-AAGCTGGGACCCCGAAACGCGTTTTTAGTCCAAAACCGTGATGGTTAGTACACGATTTC
130 AAACTGAACCCGGG-CCCCGGAACGCGTTTTTAG-CCAAAACCGTGATGATTAGTACACGATTTC
* * *
14634 GGCTAAAATTTTGCAAAAAATGACCCGAAAAATTTTGTCGTCAAATTTTGGCTAAAATACTCATA
193 GGCTAAAATTTTG-TAAAAATGACCCGAAAAATTTT-TCCTC-AATTTTTGCTAAAATACTCATA
* * * *
14699 AAATATATATAATTTAACGCCAGAAAGATTTGAGGACTTTTCACGCTTTTAATATCGTTTTTCAT
255 AGATATATATAATTAAAC-CAAAAAAGATTTGAGGACTTTTCACGCTTTTAATATCGTTTTTCAT
* * * * *
14764 ATTTTTCTGAAATAGTTTCTAATTAAATCGAAACAAGATTTATATGCTCTTAAAAACAAATCCTT
319 ATTTTTCTGAAATAATTTCTAATTAAATCGAAATAAGATTTAGATTCTCATAAAAACAAATCCTT
* *** * *
14829 AAATTCAA-AGTGGCTGAGATTTGATTAGATGAATATAGAGCCTTCAGGGAGTCTCGGCGCCAAA
384 AAATGCAATA-TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAA
* * ** ** *
14893 AATCATGCAAAACTAAGCCGGAGCCCCAAGATGCGTTTTTAGC--CCAAAACCGTGGTGGTTAGT
448 AATCATGCAAAACTGAGCCGGA-CCCGAA-ATGCGTTTTTAGCAAAAAAAACCGTAATGGTTAAT
* * * * ***
14956 ACACGATTTCGGTTAAAATTTTGTAAAAAATGACCCGAAATTTTTTTCATCAATTTTTGGATAAA
511 ACACGATTTCGGTTAAAAGTTAGCAAAAAATGACCAGAAAAAATTTTCATCAATTTTTGGATAAA
* * *
15021 ATACCCATAATATATATATATATATAATTTAACGGAAAAAAGATTGGAAGACTTTTCACGCTTTT
576 ATA-CCATAATAGATATATATATATAATTTAACGCAAAAAAGATTGGAAGACTTTTCACGCTTTG
* *
15086 AATATCGTTTTTCATATTTTTCTGTAATAATTTCTAATTAAATCGAAACAAGATTCAGATGTTCG
640 AATATCGTTTTTCATATTTTTCTGTAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCA
*** *
15151 TAAAAACAAATTTTTAAATGCAATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAAGA
705 TAAAAACAAAAACTTAAATGCAATGTAGCTAAGATTTGATTAGATGAATATGGATATCTCAAAGA
* * * * * *
15216 GTCTTGGCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACATGTTATTAGCCAAAACCC
770 GTCTTGGCGCCAAAAATCATGCAAAACTGACCCAGGGCCCCGGAACACGTTATTAGCAAAAAACC
* * * * * *
15281 GTGATGATTATTACACGATTTCGGCTAGAATTTTACAAAAATTGACTTGGAAGTTATTTCCTTAA
835 ATGATGAATATTACACGATTTCAGCTAAAATTTTACAAAAATTGACTTGGAAGATATTTCCTCAA
** * * *
15346 TTTTTAGCCACAAA-AAT-ATTGAAGGACT-T-T-TTC-ATGC-T-TTTAA-TTTTTT-TT-C-T
900 TTTTTAGCCA-AAATAATCA-T-AAAAAATATATATTCAACGCATATTGAAGTTTTTTCTTCCAT
*
15399 ATTA-TTTTCC-A-
962 ATCATTTTTCCTAT
* * ***
15410 AATTAATTTCTAATTAAATCGAAACATGATTCAGATGCAT-GTAATTTTCAAATCCTTAAATCCA
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC-TCATAA-AAACAAATCCTTAAATCCA
* * * *
15474 ATGTGGATGAGATTTGCTTAGAGGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAATTCATGC
64 ATGTGGATGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGC
* ** *
15539 AACACTGAACCCGGGCCCCGGAACATGTTTTTAGCCAAAACCTGTGATTTCGACTAACGTACACG
129 AAAACTGAACCCGGGCCCCGGAACGCGTTTTTAGCCAAAACC-GTGA--T-GA-TTA-GTACACG
* * * *
15604 ATTTCGGCTAATATTTTGTAGAAAATGACCAGAAATATTTTTCCCCAATTTTTGTCTAAAATACT
188 ATTTCGGCTAAAATTTTGTA-AAAATGACCCGAAAAATTTTTCCTCAATTTTTG-CTAAAATACT
* * *
15669 CATAAGATATATATAATTCAACTTAAAAAAGATTGGAGGAC-TTTCACGCTTTTAATATCGTTTT
251 CATAAGATATATATAATTAAAC-CAAAAAAGATTTGAGGACTTTTCACGCTTTTAATATCGTTTT
* * *
15733 TCATATTTTTCTGAAATAATTTCTAATTAAATCGAAATAAAATTCAGATTCTCACAAAAACAAAT
315 TCATATTTTTCTGAAATAATTTCTAATTAAATCGAAATAAGATTTAGATTCTCATAAAAACAAAT
* *
15798 CCTTAAATGCAATATGGCTGAGATTTGGTTAGATGAATAT-GAATATTTCAAGGAGTCTCGATGC
380 CCTTAAATGCAATATGGCTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTCTCGGTGC
* *
15862 CAAAAATCATGTAAAACTGAGCCGGGACCGCGAAATGCGTTTTTAGCAAAAAAAATCGTAATGGT
444 CAAAAATCATGCAAAACTGAGCC-GGACC-CGAAATGCGTTTTTAGCAAAAAAAACCGTAATGGT
* *** * *
15927 TAATACACGATTTTGGTTAAAAGTTAGCAAAAAATGGTGAGAAAAAATTTTCCTCAATTTTTGGG
507 TAATACACGATTTCGGTTAAAAGTTAGCAAAAAATGACCAGAAAAAATTTTCATCAATTTTTGGA
* ** *
15992 TAAAATA-C-TCAT-GA-A-ATATATATAATTTAACGCTGAAAAGATT-GAAGGACTTTTCGCGC
572 TAAAATACCATAATAGATATATATATATAATTTAACGCAAAAAAGATTGGAA-GACTTTTCACGC
* *
16051 TTTGCATATCGTTTTTCATATTTTTTCTG-AATTAATTTCTAATTAAATCGAAACAAGATTTAGA
636 TTTGAATATCGTTTTTCATA-TTTTTCTGTAA-TAATTTCTAATTAAATCGAAACAAGATTCAGA
* *
16115 TGCTCATAAAAATAAAAACTTAATTAGTGCAATGTGGCTAAGATTTGATTAGATGAATATGGATA
699 TGCTCATAAAAACAAAAACTTAA--A-TGCAATGTAGCTAAGATTTGATTAGATGAATATGGATA
* * * * *
16180 TTTCAAGGAGTCTTGGCGCCAAAAATGATGCAAAACTGACCCAGGG-TCCTGACACACGTT-TCT
761 TCTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCAGGGCCCCGGA-ACACGTTAT-T
*
16243 AGCAAAAAACTATGATGAATATTACACGATTTCAGCTAAAATTTTGTA-AAAAATT-AC-TGGAA
824 AGCAAAAAACCATGATGAATATTACACGATTTCAGCTAAAA-TTT-TACAAAAATTGACTTGG-A
* * *
16305 AGATATTTTCTCAATTTTTGGCTAAAATAATCATAAAAAATATATAATTCAACGCAAAAAATATT
886 AGATATTTCCTCAATTTTTAGCCAAAATAATCATAAAAAATATAT-ATTCAACGC-----ATATT
16370 GAAGGTTTTTTACGCTTCCAATATCATTTTTCCTACTTTT
945 GAA-GTTTTTT---CTTCC-ATATCATTTTTCCTA----T
*
16410 CGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCA
1 --AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCA
* * * **
16475 ATAT-GACCGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGTTAAAAATCATG
64 ATGTGGA-TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATG
** * *
16539 CAAAACTG-ACCCGGGGCCCTAGAACGCGTTTTTAGCAAAAAACCGTGATGATTATTACACGATT
128 CAAAACTGAACCC-GGGCCCCGGAACGCGTTTTTAGC-CAAAACCGTGATGATTAGTACACGATT
* * * * * * *
16603 TCAGCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCTCAATTCTTAGCCATAGTACTCAT
191 TCGGCTAAAATTTTGTAAAAA-TGACCCGAAAAATTTTTCCTCAATT-TTTGCTAAAATACTCAT
* * * * *
16668 AAGAAATATATAATTAAACGACAAAAAGATTTAAGCG-CTTTTCACGTTTTTAATACCGTTTTTC
254 AAGATATATATAATTAAACCA-AAAAAGATTTGAG-GACTTTTCACGCTTTTAATATCGTTTTTC
* *
16732 ATATTTTTCT-AAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGT-TCGTAAAAATAAAT
317 ATATTTTTCTGAAA-TAATTTCTAATTAAATCGAAATAAGATTTAGAT-TCTCATAAAAACAAAT
* * * * * *
16795 CCTTAAATGCAATGTGACTAAGATTTTATTAGACGAATATAGATATTTCAAGGAGTGTCGGTGCC
380 CCTTAAATGCAATATGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCC
* *
16860 AAAAATCATGCAAAACTGAACAGGACCCTGAAATGCGTTTTTAGCAAAAAA
445 AAAAATCATGCAAAACTGAGCCGGACCC-GAAATGCGTTTTTAGCAAAAAA
16911 CCATGATGAT
Statistics
Matches: 2017, Mismatches: 323, Indels: 251
0.78 0.12 0.10
Matches are distributed among these distances:
968 3 0.00
969 99 0.05
970 153 0.08
971 7 0.00
972 21 0.01
973 321 0.16
974 69 0.03
975 113 0.06
976 3 0.00
977 4 0.00
978 5 0.00
979 4 0.00
981 2 0.00
983 1 0.00
984 4 0.00
986 11 0.01
987 65 0.03
988 56 0.03
989 25 0.01
990 5 0.00
991 36 0.02
992 9 0.00
993 63 0.03
994 77 0.04
995 100 0.05
996 122 0.06
997 266 0.13
998 85 0.04
999 67 0.03
1000 17 0.01
1001 112 0.06
1002 80 0.04
1003 10 0.00
1004 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (975 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAAT
GTGGATGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAA
AACTGAACCCGGGCCCCGGAACGCGTTTTTAGCCAAAACCGTGATGATTAGTACACGATTTCGGC
TAAAATTTTGTAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGCTAAAATACTCATAAGATAT
ATATAATTAAACCAAAAAAGATTTGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTC
TGAAATAATTTCTAATTAAATCGAAATAAGATTTAGATTCTCATAAAAACAAATCCTTAAATGCA
ATATGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGC
AAAACTGAGCCGGACCCGAAATGCGTTTTTAGCAAAAAAAACCGTAATGGTTAATACACGATTTC
GGTTAAAAGTTAGCAAAAAATGACCAGAAAAAATTTTCATCAATTTTTGGATAAAATACCATAAT
AGATATATATATATAATTTAACGCAAAAAAGATTGGAAGACTTTTCACGCTTTGAATATCGTTTT
TCATATTTTTCTGTAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAAA
ACTTAAATGCAATGTAGCTAAGATTTGATTAGATGAATATGGATATCTCAAAGAGTCTTGGCGCC
AAAAATCATGCAAAACTGACCCAGGGCCCCGGAACACGTTATTAGCAAAAAACCATGATGAATAT
TACACGATTTCAGCTAAAATTTTACAAAAATTGACTTGGAAGATATTTCCTCAATTTTTAGCCAA
AATAATCATAAAAAATATATATTCAACGCATATTGAAGTTTTTTCTTCCATATCATTTTTCCTAT
Found at i:16547 original size:329 final size:329
Alignment explanation
Indices: 15410--16952 Score: 1498
Period size: 329 Copynumber: 4.6 Consensus size: 329
15400 TTATTTTCCA
* * * *** *
15410 AATTAATTTCTAATTAAATCGAAACATGATTCAGATGCAT-GTAATTTTCAAATCCTTAAATCCA
1 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGC-TCATAA-AAACAAATCCTTAAATGCA
* * * *
15474 ATGTGGA-TGAGATTTGCTTAGAGGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAATTCATG
64 ATGT-GACTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATG
* * ** * * *
15538 CAACACTGAACCCGGGCCCCGGAACATGTTTTTAGC-CAAAACCTGTGATTTCGACTAACGTACA
128 CAAAACTG-ACCCGGG-CCCTGAACGCGTTTTTAGCAAAAAACC-ATGA--T-GAAT-A-GTACA
* * * * * * * *
15602 CGATTTCGGCTAATATTTTGTAGAAAATGACCAGAAATAT-TTTTCCCCAATTTTTGTCTAAAAT
185 CGATTTCAGCTAAAATTTTGTAAAAAATTACCGGAAAGATATTTTCCTCAATTTTTGGCTAAAAT
* * ** * *
15666 ACTCATAAGATATATATAATTCAACTTAAAAAAGATTGGAGGAC-TTTCACGCTTTTAATATCGT
250 ACTCATAAAAAATATATAATTCAACGCAAAAAAGATTGAAGG-CTTTTCACGCTTTCAATATCGT
15730 TTTTCATATTTTTCTG
314 TTTTCATATTTTTCTG
* * * * * *
15746 AAATAATTTCTAATTAAATCGAAATAAAATTCAGATTCTCACAAAAACAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATGCAAT
* * * ** *
15811 ATGGCTGAGATTTGGTTAGATGAATAT-GAATATTTCAAGGAGTCTCGATGCCAAAAATCATGTA
66 GTGACTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCA
* * * ** *
15875 AAACTGAGCCGGGACCGC-GAAATGCGTTTTTAGCAAAAAA-AATCGTAATGGTTAATACACGAT
130 AAACTGACCCGGG-CC-CTG-AACGCGTTTTTAGCAAAAAACCAT-G--ATGAATAGTACACGAT
** * * * * *** * *
15938 TTTGGTTAAAAGTTAGCAAAAAA-TGGTGAGAAA-AAATTTTCCTCAATTTTTGGGTAAAATACT
189 TTCAGCTAAAATTTTGTAAAAAATTACCG-GAAAGATATTTTCCTCAATTTTTGGCTAAAATACT
* * * ** *
16001 CATGAAATATATATAATTTAACGCTGAAAAGATTGAAGGACTTTTCGCGCTTTGC-ATATCGTTT
253 CATAAAAAATATATAATTCAACGCAAAAAAGATTGAAGG-CTTTTCACGCTTT-CAATATCGTTT
16065 TTCATATTTTTTCTG
316 TTCATA-TTTTTCTG
* **
16080 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAATAAAAACTTAATTAGTGC
1 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAA--A-TGC
* * * * *
16145 AATGTGGCTAAGATTTGATTAGATGAATATGGATATTTCAAGGAGTCTTGGCGCCAAAAATGATG
63 AATGTGACTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATG
* * * * *
16210 CAAAACTGACCCAGGGTCCTGACACACGTTTCTAGCAAAAAACTATGATGAATATTACACGATTT
128 CAAAACTGACCC-GGGCCCTGA-ACGCGTTTTTAGCAAAAAACCATGATGAATAGTACACGATTT
* *
16275 CAGCTAAAATTTTGTAAAAAATTACTGGAAAGATATTTT-CTCAATTTTTGGCTAAAATAATCAT
191 CAGCTAAAATTTTGTAAAAAATTACCGGAAAGATATTTTCCTCAATTTTTGGCTAAAATACTCAT
* * * * * *
16339 AAAAAATATATAATTCAACGCAAAAAATATTGAAGGTTTTTTACGCTTCCAATATCATTTTTCCT
256 AAAAAATATATAATTCAACGCAAAAAAGATTGAAGGCTTTTCACGCTTTCAATATCGTTTTTCAT
*
16404 ACTTTTC-G
321 ATTTTTCTG
*
16412 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATGCAAT
* * * **
16477 ATGACCGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGTTAAAAATCATGCAA
66 GTGACTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAA
* * *
16542 AACTGACCCGGGGCCCTAGAACGCGTTTTTAGCAAAAAACCGTGATGATTATTACACGATTTCAG
131 AACTGACCC-GGGCCCT-GAACGCGTTTTTAGCAAAAAACCATGATGAATAGTACACGATTTCAG
* * * * * *
16607 CTAAAATTTTGT-AAAAATTGACCCGAAAGATA-TTTCCTCAATTCTTAGCCATAGTACTCATAA
194 CTAAAATTTTGTAAAAAATT-ACCGGAAAGATATTTTCCTCAATTTTTGGCTAAAATACTCATAA
* * * * * *
16670 GAAATATATAATTAAACG-ACAAAAAGATTTAAGCGCTTTTCACGTTTTTAATACCGTTTTTCAT
258 AAAATATATAATTCAACGCA-AAAAAGATTGAAG-GCTTTTCACGCTTTCAATATCGTTTTTCAT
*
16734 ATTTTTCTA
321 ATTTTTCTG
* * * *
16743 AATTAATTTCTAATTAAATCGAAATAAGATTTAGATGTTCGTAAAAATAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATGCAAT
* * * * *
16808 GTGACTAAGATTTTATTAGACGAATATAGATATTTCAAGGAGTGTCGGTGCCAAAAATCATGCAA
66 GTGACTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAA
* * * *
16873 AACTGAACAGGACCCTGAAATGCGTTTTTAGCAAAAAACCATGATGATTATTAGTACACGATTTT
131 AACTGACCCGGGCCCTG-AACGCGTTTTTAGCAAAAAACCATGATGA--A-TAGTACACGA-TTT
**
16938 TTGCTAAAATTTTGT
191 CAGCTAAAATTTTGT
16953 GTTGGTAACC
Statistics
Matches: 998, Mismatches: 173, Indels: 74
0.80 0.14 0.06
Matches are distributed among these distances:
328 11 0.01
329 188 0.19
330 64 0.06
331 123 0.12
332 141 0.14
333 41 0.04
334 109 0.11
335 175 0.18
336 51 0.05
337 89 0.09
338 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (329 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATGCAAT
GTGACTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAA
AACTGACCCGGGCCCTGAACGCGTTTTTAGCAAAAAACCATGATGAATAGTACACGATTTCAGCT
AAAATTTTGTAAAAAATTACCGGAAAGATATTTTCCTCAATTTTTGGCTAAAATACTCATAAAAA
ATATATAATTCAACGCAAAAAAGATTGAAGGCTTTTCACGCTTTCAATATCGTTTTTCATATTTT
TCTG
Found at i:25812 original size:2 final size:2
Alignment explanation
Indices: 25805--25835 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25795 AAATGATCAA
25805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25836 CAAATATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26191 original size:6 final size:6
Alignment explanation
Indices: 26180--26205 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
26170 AAAAGATTAA
26180 ACTAAC ACTAAC ACTAAC ACTAAC AC
1 ACTAAC ACTAAC ACTAAC ACTAAC AC
26206 GTACAATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
ACTAAC
Found at i:26385 original size:22 final size:22
Alignment explanation
Indices: 26343--26446 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 22
26333 TATGTAGCTA
* *
26343 TCAAAATTTCATA-AGATGGTTG
1 TCAAAATTCCATAGTGA-GGTTG
* * *
26365 TTATAATTCCATGAG-GAGGTTA
1 TCAAAATTCCAT-AGTGAGGTTG
26387 TCAAAATTCCATAGTGAGGTTG
1 TCAAAATTCCATAGTGAGGTTG
* * * *
26409 CCAAAATTTCATAGTGTGGTTA
1 TCAAAATTCCATAGTGAGGTTG
* *
26431 CCAAAATTTCATAGTG
1 TCAAAATTCCATAGTG
26447 TAGTTACCAA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.03
22 63 0.93
23 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (22 bp):
TCAAAATTCCATAGTGAGGTTG
Found at i:26447 original size:22 final size:22
Alignment explanation
Indices: 26382--26488 Score: 160
Period size: 22 Copynumber: 4.9 Consensus size: 22
26372 TCCATGAGGA
* * *
26382 GGTTATCAAAATTCCATAGTGA
1 GGTTACCAAAATTTCATAGTGT
*
26404 GGTTGCCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
26426 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
* *
26448 AGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAATTTCATAGTGT
26470 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
26489 GATCAGATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 77 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:26527 original size:22 final size:22
Alignment explanation
Indices: 26411--26542 Score: 111
Period size: 22 Copynumber: 5.9 Consensus size: 22
26401 TGAGGTTGCC
* **
26411 AAAATTTCATAGTGTGGTTACC
1 AAAATTTCATAGGGTGGTTATT
* * **
26433 AAAATTTCATAGTGTAGTTACC
1 AAAATTTCATAGGGTGGTTATT
* **
26455 AAAATTTCATAGAGTGGTTACC
1 AAAATTTCATAGGGTGGTTATT
* *
26477 AAAATTTCATAGGATCAGATTATT
1 AAAATTTCATAGGGT--GGTTATT
* *
26501 AAAATTTCTTAGGTTGGTTATT
1 AAAATTTCATAGGGTGGTTATT
*
26523 GAAATTTCATAGGGTGGTTA
1 AAAATTTCATAGGGTGGTTA
26543 ATTATCACAA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
22 77 0.82
24 17 0.18
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAGGGTGGTTATT
Found at i:26631 original size:22 final size:22
Alignment explanation
Indices: 26580--26995 Score: 170
Period size: 22 Copynumber: 18.7 Consensus size: 22
26570 AAAAAAGATT
* *
26580 TCAAAATGTCATAGCGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* *
26602 T-ACGAATTTCATAGTGTGGTTA
1 TCA-AAATTTCATAGTGAGGTTA
* *
26624 ACAAAATTTCATTAG-AAGGTTA
1 TCAAAATTTCA-TAGTGAGGTTA
* * * * *
26646 TTAATACTTCATCGGGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* *
26668 TCAAAATTTTATAGTGTGGTTA
1 TCAAAATTTCATAGTGAGGTTA
26690 TCAAAATTTCATA-TGAAGGTTA
1 TCAAAATTTCATAGTG-AGGTTA
* * *
26712 T-AAAAGTCTCAATTTCA-TAAGGAGTA
1 TCAAAA-TTTC-A--T-AGTGAGG-TTA
* * *
26738 CCAAAATTTGATAG-AAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* * * *
26759 TC-AAATCTCATAGAGTGATTA
1 TCAAAATTTCATAGTGAGGTTA
*
26780 TCGAAATTTCATAAAGAT-AGGATTA
1 TCAAAATTTCAT--AG-TGAGG-TTA
*
26805 TCAAAATTT-ATA-TGAAGATTA
1 TCAAAATTTCATAGTG-AGGTTA
* **
26826 TCAAAATTACATAGTGTTGTTA
1 TCAAAATTTCATAGTGAGGTTA
* *
26848 TCAAAATTTCAAAGCGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* * * *
26870 TCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAGTGAGGTTA
* * * *
26892 TTAAAATTTCATAGAGGGGTCA
1 TCAAAATTTCATAGTGAGGTTA
* * ** *
26914 ACAAAATTTTATAAAGATGTTA
1 TCAAAATTTCATAGTGAGGTTA
**
26936 TCAAAATTTCATAAAGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* * * * *
26958 TCAAATTTTCAAAATGTGATTA
1 TCAAAATTTCATAGTGAGGTTA
26980 -CAAAAATTTCATAGTG
1 TC-AAAATTTCATAGTG
26996 GTATTTCTAG
Statistics
Matches: 288, Mismatches: 82, Indels: 48
0.69 0.20 0.11
Matches are distributed among these distances:
20 10 0.03
21 30 0.10
22 209 0.73
23 8 0.03
24 5 0.02
25 16 0.06
26 6 0.02
27 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAGTGAGGTTA
Found at i:27104 original size:19 final size:19
Alignment explanation
Indices: 27082--27118 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27072 GAGGATACCA
27082 AAATTCAGGGAGAATATCG
1 AAATTCAGGGAGAATATCG
* *
27101 AAATTCAGTGAGGATATC
1 AAATTCAGGGAGAATATC
27119 AAACTTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (19 bp):
AAATTCAGGGAGAATATCG
Found at i:27209 original size:44 final size:41
Alignment explanation
Indices: 27134--27239 Score: 106
Period size: 44 Copynumber: 2.4 Consensus size: 41
27124 TTCATATGAA
* * *
27134 GGTTATCAAATTTTCATAGTTTAGTTTTCAGAATTTTATAAGAG
1 GGTTATCAAAATTTCATAGTTTAG-TATCAGAATTTCAT-AG-G
27178 GGTTATCAAAATTTCATAGTATGTAG-ATCAGAATTTCATAGG
1 GGTTATCAAAATTTCATAGT-T-TAGTATCAGAATTTCATAGG
*
27220 GAGATTAACAAAATTTCATA
1 G-G-TTATCAAAATTTCATA
27240 ATGAGGTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
42 2 0.04
43 3 0.06
44 45 0.83
45 1 0.02
46 3 0.06
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (41 bp):
GGTTATCAAAATTTCATAGTTTAGTATCAGAATTTCATAGG
Found at i:27337 original size:23 final size:23
Alignment explanation
Indices: 27284--27385 Score: 93
Period size: 23 Copynumber: 4.5 Consensus size: 23
27274 AAATTTGTAG
* * * *
27284 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
27306 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
*
27329 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
27352 TTATCAAAATTTAATAGCGAAG--
1 TTATCAAAATTTTATAG-GAAGAT
*
27374 TTATCACAATTT
1 TTATCAAAATTT
27386 CATACTGTGA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 27 0.41
23 35 0.53
24 4 0.06
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:27377 original size:22 final size:22
Alignment explanation
Indices: 27284--27385 Score: 91
Period size: 22 Copynumber: 4.5 Consensus size: 22
27274 AAATTTGTAG
* * *
27284 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTAT-AGGAAGT
*
27306 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATA-GGAAGT
*
27329 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAG-T
*
27352 TTATCAAAATTTAATAGCGAAG-
1 TTATCAAAATTTTATAG-GAAGT
*
27374 TTATCACAATTT
1 TTATCAAAATTT
27386 CATACTGTGA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
21 1 0.01
22 31 0.46
23 31 0.46
24 4 0.06
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAAGT
Done.