Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022448.1 Corchorus olitorius cultivar O-4 contig22481, 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: 140121
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1597 original size:332 final size:330
Alignment explanation
Indices: 567--1933 Score: 1254
Period size: 332 Copynumber: 4.2 Consensus size: 330
557 TTGGTGTATA
* * * * * *
567 TTTTATGAGTATTGTGGCTAAAAATT-AAGAAAAACTATTTCGGGTCAATTTTTGTAAAATTTTA
1 TTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA-TCTTTCGGGTCAATTTTTGCAAAATTTTA
* * * *
631 GCCGAAATCATGTACCAATCA-CA-GTTTTTTTTTGGCTAAAAATGCGTTCCA-GGCCCCGGGTC
65 GCCGAAATCATGTACTAACCATCACG---GTTTTTGGCTAAAAACGCGTTCCATGG-CCC-GGTC
* * * * * * *
693 AGTTTTGCATGATTTTTTGTGGCAAAATTACTTGAAATATCTATATTCATCTAACAAAATCTTAG
125 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTTAA
* * *
758 GCATATTGGATTTAAGAATTT-TTTTTACGAGCATTTAAATCATT-TTTCGATTTAATTAAAAAT
190 GCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTAAATC-TTGTTTCGATTTAATTAAAAAT
* * * * * *
821 TAATT-TGAAAAAATAGGGAAAATGATATTAGAAGCGTCAGAAG-TCCTTCAATCTTTTTGGCTT
254 TAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAGCT-CTTCAATCTTTTTGGCGT
* *
884 TGGATTATATTTT
318 TGAATTATATATT
* * ** * * *
897 TTTTATGAGTATTGTGGTTAAAAATTGA-GAAAAATATTTCAGATCAATTTTTGCAAAATTTTAG
1 TTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAG
* * * * *
961 GCGAAATCTTGTA-T---CATCATGGTTTTTGGCTAATAACGCGTT-C-TGG-TC--TCAGTTTT
66 CCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCATGGCCCGGTCAGTTTT
* * * * *
1017 GCAAGATTTTTGGCGCCAAGACTCCTTAAAATATATCTATATTCATCAAACCAAATC-TCAG--C
131 GCATGATTTTTGGCGCCAAGACTCCTT-GAA-ATATCTATATTCATCTAACAAAATCTTAAGCAC
* ** * *
1079 A-T--ATTTAA-AGATTTGGTTTTACGAGTTTCTAAATCTTGTTTCGATTTAATCAGAAATTAAT
194 ATTAGATTTAAGA-ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAAT
* *
1140 TTGGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAGGCT-TTCGAT-TTATTTGGCGT
258 TCGG-AA-AAAATAGGAAAAACGATATTAGAAGCGT-AAAAA-GCTCTTCAATCTT-TTTGGCGT
1203 TGAATTATATATT
318 TGAATTATATATT
* ** * * *
1216 TTTTATGATTATTTTTA-TTATAAATCGAGGAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTA
1 TTTTATGAGTA-TTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTA
* *
1280 GCTGAAATCATGTACTAACCATCACGGTTTTAGGCTAAAAACGCGTTCCATGGCCCGGTTCAGTT
65 GCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCATGGCCCGG-TCAGTT
* * *
1345 TTGCATGATTTTTGGTGCCAAGACTCCTTGAAATACCTATATTCAT-TAAATCAAAAT-TTAACC
129 TTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT-AA-CAAAATCTTAAGC
* * * *
1408 ACATTAGATTTAAGAATTTGTTTTTATGAGCATCTGAATCTTGTCTCGATTTCATTAAAAATTAA
192 ACATTAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAA
* * * ***
1473 TTCGGAAAAAAATAGGATAAACAATATTAGAAGCGTTAAAAGCTCTTCAATCTTTTTTTTGTTGA
257 TTCGG-AAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAGCTCTTCAATCTTTTTGGCGTTGA
1538 ATTATATATT
321 ATTATATATT
**
1548 TTTTATGAGT-TTTATAGCCAAAAATTGAGGAATTATCTTTCGGGTCAATTTTTGCAAAATTTTA
1 TTTTATGAGTATTT-TAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTA
** * * * *
1612 GCCGAAATTGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTCCAAGGCCATGGCTCTGT
65 GCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCATGGCC-CGG-TCAGT
* * * * * *
1677 TTTGCATGATTTTTGACACCGAGACTCCTTGAATTATCTTTATTCATCTAATC-AAATCTCAAGC
128 TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAA-CAAAATCTTAAGC
* * * ** * * * * *
1741 ATATTAGATTTAGGGACCTGTTTTTA-TATACATCTGAATATTGTTTCGATTTAATTAGAAATTA
192 ACATTAGATTTAAGAATTTGTTTTTACGA-GCATCTAAATCTTGTTTCGATTTAATTAAAAATTA
* * * * * * * *
1805 ATTCAGAAAAAATAAGAAAAACGATATTAAAAACGTGAAAAGTTCTCCAATCTTTTTGGCATTGA
256 ATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAGCTCTTCAATCTTTTTGGCGTTGA
*
1870 ATTATATATA
321 ATTATATATT
* * * *
1880 TTTTATAAGTATTTTTGCCAAAAAAAATGAGAAAAAATCTTTCGGGTC-ATTTTT
1 TTTTATGAGTATTTTAGCC--AAAAATTGAGGAAAAATCTTTCGGGTCAATTTTT
1934 ACCATAATGG
Statistics
Matches: 852, Mismatches: 137, Indels: 93
0.79 0.13 0.09
Matches are distributed among these distances:
313 1 0.00
314 12 0.01
315 38 0.04
316 2 0.00
317 3 0.00
318 56 0.07
319 49 0.06
320 69 0.08
321 3 0.00
323 3 0.00
324 43 0.05
325 3 0.00
326 5 0.01
327 2 0.00
328 15 0.02
329 47 0.06
330 67 0.08
331 8 0.01
332 200 0.23
333 147 0.17
334 78 0.09
335 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (330 bp):
TTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAG
CCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCATGGCCCGGTCAGTTTT
GCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTTAAGCACAT
TAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCG
GAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAGCTCTTCAATCTTTTTGGCGTTGAATTAT
ATATT
Found at i:6633 original size:99 final size:99
Alignment explanation
Indices: 6462--6657 Score: 331
Period size: 99 Copynumber: 2.0 Consensus size: 99
6452 TTGGCCACTC
* * *
6462 CTTTGTTCCTGATGATTCTGATTTTATGACAAAATGGTTCTCCTTTTGGGACCCTATCCATAAAG
1 CTTTGCTCCTGATGATTCTGATTTTATGACAAAATGATTCTCCTTTTGGAACCCTATCCATAAAG
6527 CCACATCACGAACCATGTCATGCATTTTAACCCA
66 CCACATCACGAACCATGTCATGCATTTTAACCCA
6561 CTTTGCTCCTGATGATTCTGATTTTATGACAAAATGATTCTCCTTTTGGAACCCTATCCA-AAGA
1 CTTTGCTCCTGATGATTCTGATTTTATGACAAAATGATTCTCCTTTTGGAACCCTATCCATAA-A
* *
6625 GCCACATCATGAACCTTGTCATGCATTTTAACC
65 GCCACATCACGAACCATGTCATGCATTTTAACC
6658 AGCTTCTCCT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 2 0.02
99 89 0.98
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (99 bp):
CTTTGCTCCTGATGATTCTGATTTTATGACAAAATGATTCTCCTTTTGGAACCCTATCCATAAAG
CCACATCACGAACCATGTCATGCATTTTAACCCA
Found at i:8925 original size:13 final size:13
Alignment explanation
Indices: 8904--8947 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
8894 TCGATTTACT
8904 AATTTTTTGTATG
1 AATTTTTTGTATG
*
8917 AATTGTTTGT-TG
1 AATTTTTTGTATG
*
8929 CATTATTTTGTATG
1 AATT-TTTTGTATG
8943 AATTT
1 AATTT
8948 CTGTGGGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 5 0.20
13 15 0.60
14 5 0.20
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.59
Consensus pattern (13 bp):
AATTTTTTGTATG
Found at i:12885 original size:335 final size:330
Alignment explanation
Indices: 11118--15390 Score: 3340
Period size: 333 Copynumber: 12.8 Consensus size: 330
11108 TTTTTGGGCA
* * *
11118 AAAATACTTATAAAATATACATATAATTCAA-TGCCAAAAAGATTAAAGAACTTTTCACGCTTTT
1 AAAATACTCATAAAATAT--ATATAATTCAACT-CCAAAAAGATTGAAGGACTTTTCACGCTTTT
* *
11182 AATATCGTTTTTCATATTTTATTTTCTGAATTAACTTCTAATTAAATCGAAACAAGATTCAGATG
63 AATATCGTTTTTCATA---T-TTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
* * * * * * *
11247 CACATAAAAATAAATCCTTCAATCCAATGTGGCTGAGATTTGATTAGATGAAAAAAGATAATTCA
124 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC-
* * * * ** * * *
11312 AAAGAGTTTCAGCGCCAAAAATCAAGCAAAA-TAGAGCCATGGTCCTGGAACGCGTTTTTAGCCA
188 AAGGAGTCTCGGCGCCAAAAATCATGCAAAACTA-AGCCGGGGCCCCGAAACGCGTTTTTAGCCA
** * ** *
11376 AAAATCGTGATGGTTAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCTTAAAGATATTT
252 AAAAAAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAAT-TTT
*
11441 CCTCAATTTTTGGCT
316 CCTCAATTTTTAGCT
* *
11456 AAAATACTCATAAAA-AGTATACAATTCAACAT-CAAAAAGATTGGAAGG-CTTTTAACGCTTTT
1 AAAATACTCATAAAATA-TATATAATTCAAC-TCCAAAAAGATT-GAAGGACTTTTCACGCTTTT
* * *
11518 AATATTGTTTTTCCTATTTTTTTC-GAATTAATTTCTAATTAAATCGAGACAAGA-T----TGCT
63 AATATCGTTTTT-C-ATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* * * *
11577 CGTAAAAACAAATCCTTAAATCTACTGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG
126 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAG
* * * * * * * *
11642 GAGTCTTGGCACCAAAAATCATGCAAAACTAAGTC-GGGCCGCGGAATGCATTTTTAGCCGAAAA
191 GAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAA
** * * * * * * *
11706 CCGTGATGGTTTGTATATGATTTCGGCTAAAAGTTTGCAAAAATTGATCCGAAAGATTTTTTTCT
256 AAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-A-ATTTTCCT
* *
11771 CGATTTCTT-GCA
319 CAATTT-TTAGCT
* * * * * *
11783 AAAATAATCGTAAAAAATATATAATTCAA--CCAAAATA-ATTGAAAGCCTTTTTCACGCTTCTA
1 AAAATACTCATAAAATATATATAATTCAACTCCAAAA-AGATTGAAGGAC-TTTTCACGCTTTTA
* * * *
11845 ATATCGTTTTTCCTATTTTATTTTCA-AATTAATTTCTGATTAAATCGAAACAAGATTTAGAAAG
64 ATATCGTTTTT-C-A-TAT-TTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAG-ATG
* * * * *
11909 -TCGTAAAAACAAATCCTTAAATACAATGTGTCTTAGATTTGGTTAGAAGAATATAGATATATTT
124 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG--ATATTT
* * * * * * * * * *
11973 TAAAGAGTCTTGAC-CTTAAAAATCATGCAAAACTGA-CACAGGGCCTCGAAATGTGTTTTTAGC
187 CAAGGAGTCTCGGCGC-CAAAAATCATGCAAAACTAAGC-CGGGGCCCCGAAACGCGTTTTTAGC
** * * * * * *
12036 CAAAAAAA-CCAT-GATGGTACAAGATTTCGACTAAAATTTTGCAAAAATTGACCTGAAATATTT
250 CAAAAAAAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT
* * *
12099 TTCTCAATATTTAGCC
315 TCCTCAATTTTTAGCT
* * * * * * *
12115 ACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGCTTCTCAAG-TTTCTAA
1 AAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTT-TAA
* * * * * * * *
12179 TATCGTTTTCCCTTTTTTTCCA-AATTAATTTTTAATTAAATCGAGACATGATTCAAATACTCGT
65 TATCGTTTTTCATATTTTT-CAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
** * * * *
12243 AAAAACAAATTTTTAAATCCAATGTGGCTAAGATTCGGTTAGATGAATATTGATATTTCAAGGAG
129 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* * * * * *
12308 TTTTGCCACCAAAAATTCTTGCAAAAC--AGACCTGGGGCCCC-AGAACGAGTTTTTAGCCAAAA
194 TCTCGGCGCCAAAAA-TCATGCAAAACTAAG-CC-GGGGCCCCGA-AACGCGTTTTTAGCC-AAA
* * * * * * *
12370 AAAAATCG-TGATTGGTACACGATTTCAGCTAAAATTTTGCAAAAATTGATCCGATATATTTTTC
254 AAAAGT-GATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA-AAAATTTTC
*
12434 CTCAATTTTTAGCC
317 CTCAATTTTTAGCT
* * * *
12448 ATAATACTCATAAAATATATATAATTCAA-TGCCGAAAAGAATGGAGGACTTTTCACGCTTTTAA
1 AAAATACTCATAAAATATATATAATTCAACT-CCAAAAAGATTGAAGGACTTTTCACGCTTTTAA
** * * *
12512 TATTATTTTTCATATTTTTCTGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTA
65 TATCGTTTTTCATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * *
12577 AAAACAAATCCTTAAATTCAATTTCGTTGAGATTTGATTAGATGAATATAGATATTTTAAGGAGT
130 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
** * * **
12642 CTCGGCTTCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACACGTTTTTAGCCTAAAATTGT
195 CTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAAAGT
* * * * *
12707 GATGGTTAGTACACGATTTCAGCTGAAATTGTGCAAAAAAATGACCCGAAAAATTATGCCGTCAA
260 GATGGTTAGTACACGATTTCGGCTAAAATTTTGC-AAAAATTGACCCGAAAAATT-TTCC-TCAA
*
12772 TTTTTTGCT
322 TTTTTAGCT
* * *
12781 AAAATAATCATAATATATATATATAATTTAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTA
1 AAAATACTCATAA-A-ATATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTA
*
12846 ATATCATTTTTCATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGA-TCTAGATGCTCG
64 ATATCGTTTTTCATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTC-AGATGCTCG
* * * * *
12910 TAAAAACAAATTCTTAAATCCAATGTAGCCGAGATTTGATTAGATGAATATGGATATCTT-AAAG
128 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT-TTCAAGG
* * * * * * **
12974 AGTTTTGGCGCCAAAAATCATGCCAAACTTAGCC-AGG-CCCTAGATTGCGTTTTTAGCCAAAAA
192 AGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGA-AACGCGTTTTTAGCC--AAA
* * ** * ** * **
13037 AAAAGCCATGATGATTATTACACGATTTCGGCTGGAATTTTACAAAAATTGACTTGAGAGTTATT
254 AAAAG---TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAAT-TT
* *
13102 TCCTTAATTTTTAGCC
315 TCCTCAATTTTTAGCT
* * * * *
13118 ACAATACTCATAAAA-ATTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAA
1 AAAATACTCATAAAATA-TATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAA
* * *
13182 TATCGTTTTTCCTATTATTTTTC-GATTTAATTTCTAATTAAATCGCAACATGATTC-GAATGCT
65 TATCGTTTTT-C-A-TATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAG-ATGCT
* *** * * * *
13245 TGT-TTTACAAATCCTTAACTCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTT-TAG
126 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAG
* * *
13308 AGAGTCTCAGCGCCAAAAATCATTCAACA-TGAA-CCGGGG-CCCGAGAACGCGTTTTTAGCCAA
191 -GAGTCTCGGCGCCAAAAATCATGCAAAACT-AAGCCGGGGCCCCGA-AACGCGTTTTTAGCCAA
** * * * * * *
13370 AAACCGTGATTTTGACTAACATACACGATTTCGGCTAATATTTTGCAAAAATTGACCTGAAATAT
253 AAAAAGTGA---TG-GTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-AA
*
13435 TTTTCATCAATTTTT-GTCT
312 TTTTCCTCAATTTTTAG-CT
* *
13454 AAAATACTCATAAAATATATATAGTTCAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAAT
1 AAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
* *
13519 ATCGTTTTTCATATTTTTCCATAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
66 ATCGTTTTTCATATTTTT-CAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
13584 AAAACAAAT-CTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTCCAAGGAGT
130 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* ** * * * * * *
13648 CCCGATGACAAAAATCATGCAAAACTGAGCTGGGG-CCCGGATCGCATTTTTAG-CAAAAAAATC
195 CTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAAA--
* * * *
13711 TGTGATGGTCT-GTATACGATTTCGGCTAAAATTTTACAAAAAAATT-ACCAGAAAAATATTTCA
258 -GTGATGGT-TAGTACACGATTTCGGCTAAAATTTTGC--AAAAATTGACCCGAAAAAT-TTTCC
* *
13774 TCTACTTTTGGCTAAAATACTCAT
318 TC-A-ATTT---T----TA-GC-T
* * *
13798 GAAACACATACATACATAAATATATATATATATATAGTTTAACGT-CAAAAAGATTGGAGGAGTT
1 --AA-A-ATAC-T-CAT--A-A-A-ATATATATA-A-TTCAAC-TCCAAAAAGATTGAAGGACTT
* * *
13862 TTCACGCTTTTCATATCATTTTTCATATTTTTTATGAATTAATTTCCTAATTGGCTATGTTTCAT
52 TTCACGCTTTTAATATCGTTTTTCATATTTTTCA-GAATTAATTT-CTAA-T---TA------A-
* *
13927 ATCTGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCTTAAATGCAATGTGGCT-ATGATTTGA
104 ATC-GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA-GATTTGA
* * ** * * *
13991 TTAGATAAATA-AGGATATCTCAAGGAGTCTTAGCACCAAAAATAATGCAAAACTGA-CTCGGGG
167 TTAGATGAATATA-GATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGC-CGGGG
* ** ** * *
14054 CTCTAAAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCA
230 CCCCGAAACGCGTTTTTAGCCAAAAAAAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
* * * *
14119 ACAATTAACCGGAAAAATATTT-CTCAATTTTTAGTT
295 AAAATTGACCCGAAAAAT-TTTCCTCAATTTTTAGCT
* * * * ** * * *
14155 AAAATACTCATAAAAAATATATAATTAAACGCCAAAAATATTGAAGGGTTTTTTACGCATCTAAT
1 AAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
* * * * *
14220 ATAGTTTTTC-TACTTGTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATA
66 ATCGTTTTTCATA-TTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * *
14284 AAAACAAATCCTTCAATCCAATGTGGATGAGATTTGATTAAATGAATATAGATATTTCAAGGAGT
130 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* * * * *
14349 CAT-GGCGCAAAAAATCATGCAAAACT--GCCCGGGAGCCTCGTAACACGTTTTTAGCAAAAAAA
195 C-TCGGCGCCAAAAATCATGCAAAACTAAG-CCGGG-GCCCCGAAACGCGTTTTTAGCCAAAAAA
*** * * * * *
14411 AAAAACT-GTGATGTTACACGATTTCAGCTAATATTTTGCAAAAATTAACCCGAAATATTTTTCC
257 AGTGA-TGGTTA-G-TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-AATTTTCC
*
14475 TCAATTTTTAGCC
318 TCAATTTTTAGCT
** * * * * *
14488 GCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAAT
1 AAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
* * * * * * * *
14553 ATCGTTTTTCCTATTTTTTCCGAATTAATTTATAATTAAAACGAAACATGATTCACAAGCTTGT-
66 ATCGTTTTTCATA-TTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
14617 ------AA-----GAA--CAA--TGGCT-AGGATTTCG-TTTGATGAATATAGATATTTCAAGGA
130 AAAACAAATCCTTAAATCCAATGTGGCTGA-GATTT-GATTAGATGAATATAGATATTTCAAGGA
* * * * *
14665 GTCTCGGCGCCAAAAATCATTCAAAAATTGAA-CC-AGGCCCCGAAATGGGTTTTT-GCCCAAAA
193 GTCTCGGCGCCAAAAATCATGC-AAAACT-AAGCCGGGGCCCCGAAACGCGTTTTTAG-CCAAAA
** ** * **
14727 ACCGTGATAATTA-TCACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGGTATTTCC
255 AAAGTGATGGTTAGT-ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAAT-TTTCC
14791 TCAATTTTTAGCCT
318 TCAATTTTTAG-CT
* *
14805 --AATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGG-GTGTTTCACGCTTTTAA
1 AAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGAAGGACT-TTTCACGCTTTTAA
* * *
14867 TATCGTTTTTCATATTTTTTCAAAATTAATTTCTAATTAAATCGAAACAAGATCCAGATGCTTGT
65 TATCGTTTTTCATA-TTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * *
14932 AAAAACAAATCCTTAAATGCAATGTGGCTAATATTTTACTAGATGAATATAGATATTTCAAGGAG
129 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* * * *
14997 TGC-CGGCACCAAAAATCATGCAAAACTTCA-CCGGGGTCCCGAAACGCGTTTTTTTGCCAAAAA
194 T-CTCGGCGCCAAAAATCATGCAAAAC-TAAGCCGGGGCCCCGAAACGCG-TTTTTAGCCAAAAA
** ** * * * *
15060 AACCG-TAATAACGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTGTCCT
256 AAGTGATGGTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT-TCCT
* * **
15124 TAATTTTTGGAA
319 CAATTTTTAGCT
* * * * *
15136 AAAATACTCATAAAATATAAATAATTTAACACCAAAAAGATTCG-AGGACTATTCACGCTTTTAG
1 AAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATT-GAAGGACTTTTCACGCTTTTAA
* * * * **
15200 TATCATTTTTCATTTTTTTCTGAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGCTTTTA
65 TATCGTTTTTCATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * *
15265 AAAATAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA-AGGATATCTCAAGGAG
130 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA-GATATTTCAAGGAG
* * * * * * *
15329 TCTTGGCGCCAAAAATCATGCAAAAATGAGCTGGGGCCGC-AGAACGCTTTTTTAGCTAAAAA
194 TCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGA-AACGCGTTTTTAGCCAAAAA
15391 TTTTTTGACT
Statistics
Matches: 3175, Mismatches: 551, Indels: 425
0.76 0.13 0.10
Matches are distributed among these distances:
314 1 0.00
315 114 0.04
316 52 0.02
317 5 0.00
318 73 0.02
319 7 0.00
320 5 0.00
322 4 0.00
324 4 0.00
325 9 0.00
326 94 0.03
327 72 0.02
328 116 0.04
329 44 0.01
330 215 0.07
331 137 0.04
332 390 0.12
333 475 0.15
334 152 0.05
335 395 0.12
336 299 0.09
337 68 0.02
338 47 0.01
339 30 0.01
341 1 0.00
342 5 0.00
343 13 0.00
344 43 0.01
345 1 0.00
346 10 0.00
347 2 0.00
348 5 0.00
349 2 0.00
350 3 0.00
351 3 0.00
352 2 0.00
353 5 0.00
354 2 0.00
355 11 0.00
356 1 0.00
357 63 0.02
358 5 0.00
359 3 0.00
362 2 0.00
363 1 0.00
366 3 0.00
367 1 0.00
368 9 0.00
369 18 0.01
370 63 0.02
371 72 0.02
372 12 0.00
373 6 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (330 bp):
AAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
ATCGTTTTTCATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
TCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAAAGTG
ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTCAATTTT
TAGCT
Found at i:16560 original size:13 final size:13
Alignment explanation
Indices: 16542--16592 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
16532 ATATATATAT
16542 ATAGTAAGATAAG
1 ATAGTAAGATAAG
*
16555 ATAGTAAAATAAG
1 ATAGTAAGATAAG
16568 ATAGTAAGATAA-
1 ATAGTAAGATAAG
16580 A-A-TAAGATAAG
1 ATAGTAAGATAAG
16591 AT
1 AT
16593 TATATCCTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 8 0.24
11 2 0.06
12 1 0.03
13 23 0.68
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.24
Consensus pattern (13 bp):
ATAGTAAGATAAG
Found at i:16569 original size:18 final size:20
Alignment explanation
Indices: 16546--16592 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
16536 ATATATATAG
16546 TAAGATAAGAT-AG-TAAAA
1 TAAGATAAGATAAGATAAAA
16564 TAAGAT-AG-TAAGATAAAA
1 TAAGATAAGATAAGATAAAA
16582 TAAGATAAGAT
1 TAAGATAAGAT
16593 TATATCCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 4 0.16
18 17 0.68
19 2 0.08
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (20 bp):
TAAGATAAGATAAGATAAAA
Found at i:16637 original size:13 final size:14
Alignment explanation
Indices: 16619--16649 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
16609 AATTATTTTT
16619 AAAAGTAAATTT-G
1 AAAAGTAAATTTGG
16632 AAAAGTAAATTTGG
1 AAAAGTAAATTTGG
16646 AAAA
1 AAAA
16650 AAAAAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (14 bp):
AAAAGTAAATTTGG
Found at i:19060 original size:22 final size:22
Alignment explanation
Indices: 19032--19078 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
19022 AAAACTACCG
19032 TCTAGGTATGGTATTGATTAGT
1 TCTAGGTATGGTATTGATTAGT
19054 TCTAGGTATGGTATTGATTAGT
1 TCTAGGTATGGTATTGATTAGT
19076 TCT
1 TCT
19079 TGTCATGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (22 bp):
TCTAGGTATGGTATTGATTAGT
Found at i:20695 original size:43 final size:43
Alignment explanation
Indices: 20634--20716 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
20624 CATAGTTAGG
* * * * *
20634 TTATCAAAGTTTCTTATGGAGTTTATCACAATTTTATAGGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGTAA
*
20677 TTATCAAAATTTCATATGGTGGTTATCAAAATTTAATAGG
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGG
20717 GTGATTATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.42
Consensus pattern (43 bp):
TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGTAA
Found at i:20703 original size:22 final size:21
Alignment explanation
Indices: 20612--20724 Score: 82
Period size: 22 Copynumber: 5.2 Consensus size: 21
20602 ATAGGAAAGT
* * *
20612 TTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTCATAGGT-GA
* * * *
20634 TTATCAAAGTTTCTTATGGAGT
1 TTATCAAAATTTCATA-GGTGA
* * *
20656 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTCATAGGTGA
*
20677 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTCATA-GGTGA
*
20699 TTATCAAAATTTAATAGGGTGA
1 TTATCAAAATTTCATA-GGTGA
20721 TTAT
1 TTAT
20725 TGAAATTTTA
Statistics
Matches: 69, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
21 16 0.23
22 52 0.75
23 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGA
Found at i:21533 original size:20 final size:22
Alignment explanation
Indices: 21510--21549 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21500 TTAAAAATCA
21510 TAGG-AAGGTTA-CAAAATTCT
1 TAGGAAAGGTTATCAAAATTCT
*
21530 TAGGAAAGTTTATCAAAATT
1 TAGGAAAGGTTATCAAAATT
21550 TTATAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.33
Consensus pattern (22 bp):
TAGGAAAGGTTATCAAAATTCT
Found at i:21564 original size:22 final size:22
Alignment explanation
Indices: 21539--21602 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
21529 TTAGGAAAGT
21539 TTATCAAAATTTTATAGTTAGG
1 TTATCAAAATTTTATAGTTAGG
* * *
21561 TTATCAAAGTTTCT-TA-TGGAGT
1 TTATCAAAATTT-TATAGT-TAGG
*
21583 TTATCACAATTTTATAGTTA
1 TTATCAAAATTTTATAGTTA
21603 ATAATCAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTTAGG
Found at i:21634 original size:40 final size:42
Alignment explanation
Indices: 21539--21634 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 42
21529 TTAGGAAAGT
* * * *
21539 TTATCAAAATTTTATAGTTAGGTTATCAAAGTTTCTTATGGAGT
1 TTATCAAAATTTTATAGTTAGATAATCAAA--TTCATATGGAGA
* *
21583 TTATCACAATTTTATAGTTA-ATAATCAAA-TCATATGGTGA
1 TTATCAAAATTTTATAGTTAGATAATCAAATTCATATGGAGA
21623 TTATCAAAATTT
1 TTATCAAAATTT
21635 AACAGGGCAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
40 19 0.42
43 7 0.16
44 19 0.42
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (42 bp):
TTATCAAAATTTTATAGTTAGATAATCAAATTCATATGGAGA
Found at i:23360 original size:18 final size:18
Alignment explanation
Indices: 23337--23376 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
23327 ATAATAGAAG
23337 TTATCAAATTTACAGTAA
1 TTATCAAATTTACAGTAA
*
23355 TTATCAATTTTACAGTAA
1 TTATCAAATTTACAGTAA
23373 TTAT
1 TTAT
23377 TGAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (18 bp):
TTATCAAATTTACAGTAA
Found at i:23651 original size:38 final size:38
Alignment explanation
Indices: 23608--23680 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
23598 TTTACAATAC
*
23608 TTAATTACTCAAAAAGCTATAACGGTTATGAAAAAAAG
1 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAAAAG
23646 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAA
1 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAA
23681 GGTTATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (38 bp):
TTAATTACTCAAAAAGCTATAACAGTTATGAAAAAAAG
Found at i:24763 original size:22 final size:22
Alignment explanation
Indices: 24729--24820 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
24719 TTTCGATAAC
* *
24729 CTATGAAAATTTGATAAACGCA
1 CTATGAAATTTTGATAAACACA
* *
24751 CTGTGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAAACACA
* * *
24773 CTATGAAATTTTGATAATCTCC
1 CTATGAAATTTTGATAAACACA
*
24795 CTATGAAATTTTGATAATCACA
1 CTATGAAATTTTGATAAACACA
24817 CTAT
1 CTAT
24821 AAAACTGGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAAACACA
Found at i:24786 original size:44 final size:43
Alignment explanation
Indices: 24729--24866 Score: 143
Period size: 44 Copynumber: 3.2 Consensus size: 43
24719 TTTCGATAAC
*
24729 CTATGAAAATTTGATAAACGCACTGTGAAATTTTGATAACCACA
1 CTATG-AAATTTGATAAACGCACTATGAAATTTTGATAACCACA
* * * *
24773 CTATGAAATTTTGATAATCTCCCTATGAAATTTTGATAATCACA
1 CTATGAAA-TTTGATAAACGCACTATGAAATTTTGATAACCACA
** * * *
24817 CTAT-AAAACTGGTAACCGCATTATGAAAATTTTGATAACCACA
1 CTATGAAATTTGATAAACGCACTATG-AAATTTTGATAACCACA
*
24860 CCATGAA
1 CTATGAA
24867 GTTTCCCTTC
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
42 11 0.14
43 25 0.32
44 41 0.53
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (43 bp):
CTATGAAATTTGATAAACGCACTATGAAATTTTGATAACCACA
Found at i:25009 original size:26 final size:22
Alignment explanation
Indices: 24911--25206 Score: 171
Period size: 22 Copynumber: 13.3 Consensus size: 22
24901 CTCTTTATTT
* *
24911 AATTTTGATAACATCTCC-ATAA
1 AATTTTGATAACCT-TCCTATGA
24933 AATTTTTG-TAACCTTCCTATGA
1 AA-TTTTGATAACCTTCCTATGA
* *
24955 AATTTTGTTAACCTTCCTAGGA
1 AATTTTGATAACCTTCCTATGA
*
24977 AACTTTGATAACCTCCCTCCCTATGA
1 AATTTTGATAACCT---T-CCTATGA
*
25003 AATTTTGATAACC-ACACTAT-A
1 AATTTTGATAACCTTC-CTATGA
* *
25024 AATTTTGATAACCTTCATATAA
1 AATTTTGATAACCTTCCTATGA
* ** *
25046 AATTTTGTTAA-CGACACTAAGA
1 AATTTTGATAACCTTC-CTATGA
** *
25068 AATTTTGATAACCTTTTTATAA
1 AATTTTGATAACCTTCCTATGA
* * * *
25090 AATTTTGGTAA-CGTCTGTATGG
1 AATTTTGATAACCTTC-CTATGA
*
25112 AATTTTGATAA-CTACACTATGA
1 AATTTTGATAACCTTC-CTATGA
**
25134 CGTTTTGATAACC-TCCATATGA
1 AATTTTGATAACCTTCC-TATGA
*
25156 AATTTT-AGTAACC-ACACTATGA
1 AATTTTGA-TAACCTTC-CTATGA
** *
25178 AAAGTTGATAACCTTCCTATGT
1 AATTTTGATAACCTTCCTATGA
25200 AATTTTG
1 AATTTTG
25207 GTTTGATTGA
Statistics
Matches: 208, Mismatches: 47, Indels: 38
0.71 0.16 0.13
Matches are distributed among these distances:
21 32 0.15
22 147 0.71
23 10 0.05
25 1 0.00
26 18 0.09
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTTCCTATGA
Found at i:29845 original size:18 final size:19
Alignment explanation
Indices: 29813--29848 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29803 ACACCAAAAG
*
29813 GAAAATGAAACGAAAAACA
1 GAAAATGAAAAGAAAAACA
29832 GAAAAT-AAAAGAAAAAC
1 GAAAATGAAAAGAAAAAC
29849 TGCCCCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.72, C:0.08, G:0.14, T:0.06
Consensus pattern (19 bp):
GAAAATGAAAAGAAAAACA
Found at i:35749 original size:15 final size:15
Alignment explanation
Indices: 35729--35758 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35719 TGCGCCTCTT
*
35729 TTTTAATTTATTTTA
1 TTTTAAATTATTTTA
35744 TTTTAAATTATTTTA
1 TTTTAAATTATTTTA
35759 AGAAGGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAAATTATTTTA
Found at i:36293 original size:13 final size:13
Alignment explanation
Indices: 36275--36304 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
36265 TGTTTGTTAG
36275 TTATCTATAATAA
1 TTATCTATAATAA
*
36288 TTATCTATACTAA
1 TTATCTATAATAA
36301 TTAT
1 TTAT
36305 AAAGGCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATCTATAATAA
Found at i:36476 original size:18 final size:19
Alignment explanation
Indices: 36453--36499 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
36443 ATATCATTTT
36453 AAAAAACTATTCATTTAAA
1 AAAAAACTATTCATTTAAA
36472 AAAAAACTATTCATTT-AA
1 AAAAAACTATTCATTTAAA
36490 AAAAAACTAT
1 AAAAAACTAT
36500 CACAAACTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAACTATTCATTTAAA
Found at i:44116 original size:60 final size:60
Alignment explanation
Indices: 44052--44214 Score: 267
Period size: 60 Copynumber: 2.7 Consensus size: 60
44042 GCTAATTGCT
* *
44052 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
*
44112 CAAATAAGGGCCTAACGTTATTG--AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-T-TTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
44172 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTC
44215 TAGCATCAGT
Statistics
Matches: 95, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
58 3 0.03
59 1 0.01
60 87 0.92
61 1 0.01
62 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
Found at i:44150 original size:31 final size:30
Alignment explanation
Indices: 44048--44212 Score: 103
Period size: 31 Copynumber: 5.5 Consensus size: 30
44038 TAAGGCTAAT
* *
44048 TGCTCAAATAAGGGTCTAATG-TTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTTG--AAAA
* * **
44079 TGCTCAAATAAGGGTCCGATC-TTTT-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTTGAAAA
44108 TGGC-CAAATAAGGGCCTAACGTTATTGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TTGAAAA
* * **
44139 TGCTCAAATAAGGGCCCGATC-TTTT-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTTGAAAA
44168 TGGC-CAAATAAGGGCCTAACG-TTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTTG--AAAA
44199 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
44213 TCTAGCATCA
Statistics
Matches: 102, Mismatches: 18, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
28 11 0.11
29 28 0.27
30 12 0.12
31 42 0.41
32 9 0.09
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTTGAAAA
Found at i:44183 original size:29 final size:29
Alignment explanation
Indices: 44083--44183 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
44073 CCAAAATGCT
*
44083 CAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTTAATTTGGC
* * **
44112 CAAATAAGGG-CCTAACGTTATTGAAAAT-GC
1 CAAATAAGGGCCCGATC-TT-TT-AATTTGGC
44142 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
44172 CAAATAAGGGCC
1 CAAATAAGGGCC
44184 TAACGTTTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
28 4 0.07
29 27 0.47
30 8 0.14
31 15 0.26
32 4 0.07
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:44292 original size:31 final size:31
Alignment explanation
Indices: 44257--44421 Score: 121
Period size: 31 Copynumber: 5.5 Consensus size: 31
44247 CGATGTCAGA
* * *
44257 CCCTTATTTGAGCATTTTGGCAAATATTAGG
1 CCCTTATTTGAGCATATTGGAAAACATTAGG
* * *
44288 CCCTTATTTG-GTCAAATT--AAAAGA-TCGG
1 CCCTTATTTGAG-CATATTGGAAAACATTAGG
* * *
44316 ACCCTTATTTGAGCATTTTGGTAAACGTTAGG
1 -CCCTTATTTGAGCATATTGGAAAACATTAGG
* *
44348 CCCTTATTTG-GCCAAATT--AAAAGATT-GAG
1 CCCTTATTTGAG-CATATTGGAAAACATTAG-G
* *
44377 CCCTTATTTGAGCATATTGGCAAACATTAGA
1 CCCTTATTTGAGCATATTGGAAAACATTAGG
44408 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
44422 ATTAGCCTAC
Statistics
Matches: 102, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 4 0.04
29 39 0.38
30 4 0.04
31 51 0.50
32 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
CCCTTATTTGAGCATATTGGAAAACATTAGG
Found at i:44348 original size:60 final size:59
Alignment explanation
Indices: 44255--44417 Score: 245
Period size: 60 Copynumber: 2.7 Consensus size: 59
44245 TTCGATGTCA
* *
44255 GACCCTTATTTGAGCATTTTGGCAAATATTAGGCCCTTATTTGGTCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGAT-G
* * *
44315 GACCCTTATTTGAGCATTTTGGTAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATT
1 GACCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATG
* *
44374 GAGCCCTTATTTGAGCATATTGGCAAACATTAGACCCTTATTTG
1 GA-CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
44418 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 2 0.02
60 91 0.98
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (59 bp):
GACCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATG
Found at i:45263 original size:25 final size:26
Alignment explanation
Indices: 45235--45288 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
45225 GCTTGAATTA
* *
45235 AATTAAAATAAAAG-TAATACTGAAG
1 AATTAAAAAAAAAGATAATACTAAAG
45260 AATTAAAAAAAAAGACTAATACTAAAG
1 AATTAAAAAAAAAGA-TAATACTAAAG
45287 AA
1 AA
45289 AATGATTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.52
27 12 0.48
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.20
Consensus pattern (26 bp):
AATTAAAAAAAAAGATAATACTAAAG
Found at i:47411 original size:2 final size:2
Alignment explanation
Indices: 47404--47428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47394 AACCTTGCAC
47404 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
47429 GGGAAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48749 original size:62 final size:62
Alignment explanation
Indices: 48652--48899 Score: 487
Period size: 62 Copynumber: 4.0 Consensus size: 62
48642 AGTTATACAA
48652 GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTACATGTTTCTGTTATAACATGAATGACT
1 GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTACATGTTTCTGTTATAACATGAATGACT
48714 GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTACATGTTTCTGTTATAACATGAATGACT
1 GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTACATGTTTCTGTTATAACATGAATGACT
48776 GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTACATGTTTCTGTTATAACATGAATGACT
1 GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTACATGTTTCTGTTATAACATGAATGACT
*
48838 GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTAGATGTTTCTGTTATAACATGAATGACT
1 GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTACATGTTTCTGTTATAACATGAATGACT
48900 ATCCACTAGG
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 185 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (62 bp):
GTGCAAAGTAGGCCTGATGATCGGCTAATGCACTACATGTTTCTGTTATAACATGAATGACT
Found at i:48969 original size:13 final size:13
Alignment explanation
Indices: 48931--48973 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
48921 TTAGGAAAGG
48931 ATGAATTGTGTTT
1 ATGAATTGTGTTT
* *
48944 CATAAATTATGTTT
1 -ATGAATTGTGTTT
48958 ATGAATTGTGTTT
1 ATGAATTGTGTTT
48971 ATG
1 ATG
48974 TTTATATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (13 bp):
ATGAATTGTGTTT
Found at i:49607 original size:32 final size:32
Alignment explanation
Indices: 49528--49630 Score: 161
Period size: 32 Copynumber: 3.2 Consensus size: 32
49518 ACAAAAGGCA
49528 AAACATTGGTAAAAGACTATTGGAATTGTAAATG
1 AAACATTGGTAAAAGACTATTGGAATTGT-AA-G
* *
49562 AAACATTGGTAAAAGACTATTGAAATTGTTAG
1 AAACATTGGTAAAAGACTATTGGAATTGTAAG
*
49594 AAATATTGGTAAAAGACTATTGGAATTGTAAG
1 AAACATTGGTAAAAGACTATTGGAATTGTAAG
49626 AAACA
1 AAACA
49631 GAAACAAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 34 0.54
33 1 0.02
34 28 0.44
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (32 bp):
AAACATTGGTAAAAGACTATTGGAATTGTAAG
Found at i:49836 original size:17 final size:17
Alignment explanation
Indices: 49814--49848 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
49804 CCATATTTGG
49814 TTGGAGGAATCTAATTT
1 TTGGAGGAATCTAATTT
49831 TTGGAGGAATCTAATTT
1 TTGGAGGAATCTAATTT
49848 T
1 T
49849 AGGTGGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (17 bp):
TTGGAGGAATCTAATTT
Found at i:49856 original size:17 final size:17
Alignment explanation
Indices: 49816--49856 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
49806 ATATTTGGTT
*
49816 GGAGGAATCTAATTTTT
1 GGAGGAATCTAATTTTA
49833 GGAGGAATCTAATTTTA
1 GGAGGAATCTAATTTTA
*
49850 GGTGGAA
1 GGAGGAA
49857 ATGTCATTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (17 bp):
GGAGGAATCTAATTTTA
Found at i:51495 original size:4 final size:4
Alignment explanation
Indices: 51486--51523 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
51476 TAAATCATTG
* *
51486 CATA CATA CATA CATA CATA TAT- TATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
51524 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (4 bp):
CATA
Found at i:56953 original size:19 final size:19
Alignment explanation
Indices: 56920--56969 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
56910 CACTATTTAT
*
56920 TCAAACAGTGAATTAGTAAC
1 TCAAA-AGTGAATTAGAAAC
*
56940 TCAAAAGTGGATTAGAAAC
1 TCAAAAGTGAATTAGAAAC
* *
56959 TAAAAAATGAA
1 TCAAAAGTGAA
56970 AACTAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (19 bp):
TCAAAAGTGAATTAGAAAC
Found at i:64896 original size:2 final size:2
Alignment explanation
Indices: 64889--64922 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
64879 ATTCACTGAA
64889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64923 AGAAAACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65078 original size:2 final size:2
Alignment explanation
Indices: 65071--65102 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
65061 TAAGTTTTAC
65071 AT AT AT AT AT AT AT A- 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 AT A
65103 ATAGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:65091 original size:15 final size:15
Alignment explanation
Indices: 65071--65100 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
65061 TAAGTTTTAC
65071 ATATATATATATATA
1 ATATATATATATATA
65086 ATATATATATATATA
1 ATATATATATATATA
65101 TAATAGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:65093 original size:17 final size:17
Alignment explanation
Indices: 65071--65105 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
65061 TAAGTTTTAC
65071 ATATATATATATATAAT
1 ATATATATATATATAAT
65088 ATATATATATATATAAT
1 ATATATATATATATAAT
65105 A
1 A
65106 GTAAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATATATATATAAT
Found at i:68439 original size:115 final size:116
Alignment explanation
Indices: 68237--68476 Score: 385
Period size: 115 Copynumber: 2.1 Consensus size: 116
68227 AATTAAAATA
* * *
68237 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAATATTTAATTAAATAAAAGTAGAGTTTTTA
1 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATCAAATAAAAGTAGAGTTCTTA
*
68302 ATACAATAAAACTATAATAGTTTAAACAATGGCAC-TTAAGAAATATGTTT
66 ATACAATAAAACTATAATAGTTTAAACAATGACACTTTAAGAAATATGTTT
68352 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATCAAATAAAAGTAGAGTTCTTA
1 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATCAAATAAAAGTAGAGTTCTTA
*
68417 ATACAGTAAAGA-TATAATAGTTTAAACAATGACACTTATTAAGAAATATGTTT
66 ATACAATAAA-ACTATAATAGTTTAAACAATGACAC-T-TTAAGAAATATGTTT
*
68470 GAAAAAT
1 GTAAAAT
68477 AAATGTATGA
Statistics
Matches: 115, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
115 93 0.81
116 1 0.01
118 21 0.18
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (116 bp):
GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATCAAATAAAAGTAGAGTTCTTA
ATACAATAAAACTATAATAGTTTAAACAATGACACTTTAAGAAATATGTTT
Found at i:75719 original size:126 final size:126
Alignment explanation
Indices: 75492--75737 Score: 456
Period size: 126 Copynumber: 2.0 Consensus size: 126
75482 AATTGAAGTT
75492 AATACAAACTCTCTGCCACAAAATGATGGCAACCATGATCAACCAAAGAAGCCTACTGAGGAAAT
1 AATACAAACTCTCTGCCACAAAATGATGGCAACCATGATCAACCAAAGAAGCCTACTGAGGAAAT
* *
75557 ATACAAAAGTATAAGAGAAATTTTATCAGGCGCCTCTGTCTCCTCAGATCAGTGCGACTTC
66 ATACAAAAATATAAGAGAAATTTTATCAGGCACCTCTGTCTCCTCAGATCAGTGCGACTTC
*
75618 AATACAAACTCTCTGCCACAAAATGATGGCAACCATGATCAACCAAAGAAGCCTATTGAGGAAAT
1 AATACAAACTCTCTGCCACAAAATGATGGCAACCATGATCAACCAAAGAAGCCTACTGAGGAAAT
*
75683 ATACAAAAATATAAGAGAAATTTTATCAGGTACCTCTGTCTCCTCAGATCAGTGC
66 ATACAAAAATATAAGAGAAATTTTATCAGGCACCTCTGTCTCCTCAGATCAGTGC
75738 ACAATTCTAT
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 116 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (126 bp):
AATACAAACTCTCTGCCACAAAATGATGGCAACCATGATCAACCAAAGAAGCCTACTGAGGAAAT
ATACAAAAATATAAGAGAAATTTTATCAGGCACCTCTGTCTCCTCAGATCAGTGCGACTTC
Found at i:83328 original size:30 final size:30
Alignment explanation
Indices: 83292--83350 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
83282 GTAAGTACTC
83292 AAATCAAGTGAATTACTTAAGCACAGAAAG
1 AAATCAAGTGAATTACTTAAGCACAGAAAG
83322 AAATCAAGTGAATTACTTAAGCACAGAAA
1 AAATCAAGTGAATTACTTAAGCACAGAAA
83351 TTTTAGTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20
Consensus pattern (30 bp):
AAATCAAGTGAATTACTTAAGCACAGAAAG
Found at i:89345 original size:12 final size:13
Alignment explanation
Indices: 89318--89350 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
89308 ACTTTATTTG
*
89318 TATTATTAATTAA
1 TATTAATAATTAA
89331 TATTAATAA-TAA
1 TATTAATAATTAA
89343 TATTAATA
1 TATTAATA
89351 TATTGTGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTAATAATTAA
Found at i:90042 original size:16 final size:16
Alignment explanation
Indices: 90023--90059 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
90013 AAGTCAACGT
* *
90023 CCCGAAATTACCCGAG
1 CCCGAAAATACCCGAA
90039 CCCGAAAATACCCGAA
1 CCCGAAAATACCCGAA
90055 CCCGA
1 CCCGA
90060 GGCAGCCCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.35, C:0.41, G:0.16, T:0.08
Consensus pattern (16 bp):
CCCGAAAATACCCGAA
Found at i:91066 original size:16 final size:16
Alignment explanation
Indices: 91045--91134 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
91035 CATACTCGAG
91045 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
91061 CCCGAACCCG-ACATAA
1 CCCGAACCCGAAAAT-A
* *
91077 CCCGAGCCCGAAAAAA
1 CCCGAACCCGAAAATA
* **
91093 CCCGAATCCG-ACTTAA
1 CCCGAACCCGAAAAT-A
* *
91109 CCCGAGCCCGAAAAAA
1 CCCGAACCCGAAAATA
91125 CCCGAACCCG
1 CCCGAACCCG
91135 CCCAATTGCC
Statistics
Matches: 55, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
15 4 0.07
16 48 0.87
17 3 0.05
ACGTcount: A:0.38, C:0.41, G:0.16, T:0.06
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:91081 original size:32 final size:32
Alignment explanation
Indices: 91045--91134 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
91035 CATACTCGAG
* *
91045 CCCGAACCCGAAAATACCCGAACCCGACATAA
1 CCCGAGCCCGAAAAAACCCGAACCCGACATAA
* *
91077 CCCGAGCCCGAAAAAACCCGAATCCGACTTAA
1 CCCGAGCCCGAAAAAACCCGAACCCGACATAA
91109 CCCGAGCCCGAAAAAACCCGAACCCG
1 CCCGAGCCCGAAAAAACCCGAACCCG
91135 CCCAATTGCC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.38, C:0.41, G:0.16, T:0.06
Consensus pattern (32 bp):
CCCGAGCCCGAAAAAACCCGAACCCGACATAA
Found at i:92524 original size:2 final size:2
Alignment explanation
Indices: 92517--92556 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
92507 GGCATTTGAG
92517 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
92557 GGTCCAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101372 original size:8 final size:8
Alignment explanation
Indices: 101361--101390 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
101351 AATATAATTG
101361 ATTAATGA
1 ATTAATGA
101369 ATTAATGA
1 ATTAATGA
101377 ATTAATG-
1 ATTAATGA
101384 ATTAATG
1 ATTAATG
101391 TTAATGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (8 bp):
ATTAATGA
Found at i:101380 original size:16 final size:15
Alignment explanation
Indices: 101359--101396 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
101349 TTAATATAAT
101359 TGATTAATGAATTAA
1 TGATTAATGAATTAA
101374 TGAATTAATG-ATTAA
1 TG-ATTAATGAATTAA
101389 TG-TTAATG
1 TGATTAATG
101397 TTAAGTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
15 9 0.41
16 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (15 bp):
TGATTAATGAATTAA
Found at i:106888 original size:47 final size:47
Alignment explanation
Indices: 106829--106972 Score: 234
Period size: 47 Copynumber: 3.1 Consensus size: 47
106819 AGTGCCTACT
* *
106829 TTTTCACTGCTTTAATTTGATCTTGGAGTTAGTAAACTTGAGTTCTC
1 TTTTCACCGCTTTAATTTGATCTTGGAGTTAGTAAACTTTAGTTCTC
106876 TTTTCACCGCTTTAATTTGATCTTGGAGTTAGTAAACTTTAGTTCTC
1 TTTTCACCGCTTTAATTTGATCTTGGAGTTAGTAAACTTTAGTTCTC
** * *
106923 TTTTTGCCGCTTTAATTTGATCTTGGAGTTTGTAAACTTTAATTCTC
1 TTTTCACCGCTTTAATTTGATCTTGGAGTTAGTAAACTTTAGTTCTC
106970 TTT
1 TTT
106973 ACTTACGGCT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 91 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.49
Consensus pattern (47 bp):
TTTTCACCGCTTTAATTTGATCTTGGAGTTAGTAAACTTTAGTTCTC
Found at i:107003 original size:13 final size:13
Alignment explanation
Indices: 106985--107011 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
106975 TTACGGCTTC
106985 TAAATGACAAGGA
1 TAAATGACAAGGA
106998 TAAATGACAAGGA
1 TAAATGACAAGGA
107011 T
1 T
107012 TGTACTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (13 bp):
TAAATGACAAGGA
Found at i:109769 original size:29 final size:24
Alignment explanation
Indices: 109703--109753 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
109693 CCCTATAATA
109703 AGTTGATTCAACTCAAATAGGATT
1 AGTTGATTCAACTCAAATAGGATT
109727 AGTTGATTCAACTCAAATAGGATT
1 AGTTGATTCAACTCAAATAGGATT
109751 AGT
1 AGT
109754 CCTATTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (24 bp):
AGTTGATTCAACTCAAATAGGATT
Found at i:109909 original size:33 final size:34
Alignment explanation
Indices: 109861--109933 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 34
109851 GTAATAAATC
109861 ATTAACAATTAAATTGTGAATGGAGAAAATCATT
1 ATTAACAATTAAATTGTGAATGGAGAAAATCATT
109895 ATTAAC-ATTAAATTGTGAATGGAGAAAATCATT
1 ATTAACAATTAAATTGTGAATGGAGAAAATCATT
109928 ATTAAC
1 ATTAAC
109934 GGTGAATAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 33 0.85
34 6 0.15
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (34 bp):
ATTAACAATTAAATTGTGAATGGAGAAAATCATT
Found at i:117933 original size:1 final size:1
Alignment explanation
Indices: 117927--117952 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
117917 GAGAGTAGCC
117927 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
117953 CTGGCCTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:123123 original size:9 final size:9
Alignment explanation
Indices: 123109--123134 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
123099 TCCCTTTTCC
123109 CCTCTTTTA
1 CCTCTTTTA
123118 CCTCTTTTA
1 CCTCTTTTA
123127 CCTCTTTT
1 CCTCTTTT
123135 CCCATTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.58
Consensus pattern (9 bp):
CCTCTTTTA
Found at i:137209 original size:34 final size:34
Alignment explanation
Indices: 137166--137236 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
137156 GCTTTCAGGC
137166 AGCTCCTGCAATCTATGTCTAGTGCCAATCACAA
1 AGCTCCTGCAATCTATGTCTAGTGCCAATCACAA
137200 AGCTCCTGCAATCTATGTCTAGTGCCAATCACAA
1 AGCTCCTGCAATCTATGTCTAGTGCCAATCACAA
137234 AGC
1 AGC
137237 AGTAAGTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (34 bp):
AGCTCCTGCAATCTATGTCTAGTGCCAATCACAA
Found at i:139539 original size:70 final size:69
Alignment explanation
Indices: 139417--139576 Score: 268
Period size: 70 Copynumber: 2.3 Consensus size: 69
139407 ATTTCCCGCA
*
139417 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCT-A
139482 ACAGC
65 ACAGC
*
139487 ACAAGT-CTGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGTTCCTA
1 ACAAGTCCT-GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTA
139551 ACAGC
65 ACAGC
*
139556 CCAAGTCCTGGACAGGACTTG
1 ACAAGTCCTGGACAGGACTTG
139577 ACCAAGATCT
Statistics
Matches: 85, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
69 25 0.29
70 60 0.71
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (69 bp):
ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTAA
CAGC
Done.