Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009367.1 Hibiscus syriacus cultivar Beakdansim tig00113198_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58309
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6786 original size:15 final size:14
Alignment explanation
Indices: 6766--6804 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
6756 TCAACGACAG
6766 AAGAAAGATTTTTTT
1 AAGAAA-ATTTTTTT
6781 AAG-AAATTTTTTT
1 AAGAAAATTTTTTT
*
6794 AAGAACATTTT
1 AAGAAAATTTT
6805 AGTCCAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 11 0.50
14 8 0.36
15 3 0.14
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (14 bp):
AAGAAAATTTTTTT
Found at i:6793 original size:14 final size:14
Alignment explanation
Indices: 6773--6804 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
6763 CAGAAGAAAG
6773 ATTTTTTTAAGAA-
1 ATTTTTTTAAGAAC
6786 ATTTTTTTAAGAAC
1 ATTTTTTTAAGAAC
6800 ATTTT
1 ATTTT
6805 AGTCCAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (14 bp):
ATTTTTTTAAGAAC
Found at i:9522 original size:35 final size:36
Alignment explanation
Indices: 9456--9956 Score: 644
Period size: 37 Copynumber: 13.8 Consensus size: 36
9446 AACTATTTCC
* * *
9456 AAAACACTATATAATATATATTTTTTCAAAAATATTTT
1 AAAA-ACTATATATTATATA-ATTTTCAAAAATGTTTT
* *
9494 AAAATCTATATATTATATAATTTTAAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
*
9530 CAAAAACTATATATTATATAAGTTTTC-AAAATAATTTT
1 -AAAAACTATATATTATATAA-TTTTCAAAAAT-GTTTT
*
9568 AAAAACTATATATTATATATATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATA-ATTTTCAAAAATGTTTT
9605 -AAAACTATATATTATATAATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
* *
9640 AAAAACTATGTAATATAT-ATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
*
9675 -AAAACTATATATTATAT-ATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
9709 AAAAAC--TATA-TATATAATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
9742 AAAAACTATATA-TATATAATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
* * *
9777 AAAAACTTTGTAATATATATATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATA-ATTTTCAAAAATGTTTT
*
9814 AAAAACTATATATTATATATATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATA-ATTTTCAAAAATGTTTT
* *
9851 AAATACTATATTTTATATAATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
* * *
9887 AAAAACTGTATAATATAT-ATATTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
9922 AAAAAAACTATATATTATATACGTATTTTCAAAAA
1 --AAAAACTATATATTATATA---ATTTTCAAAAA
9957 CCGTTTGCAA
Statistics
Matches: 412, Mismatches: 33, Indels: 33
0.86 0.07 0.07
Matches are distributed among these distances:
32 5 0.01
33 26 0.06
34 31 0.08
35 91 0.22
36 83 0.20
37 148 0.36
38 18 0.04
41 10 0.02
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
AAAAACTATATATTATATAATTTTCAAAAATGTTTT
Found at i:10671 original size:165 final size:162
Alignment explanation
Indices: 10484--11575 Score: 554
Period size: 165 Copynumber: 6.6 Consensus size: 162
10474 AGCTGAAGGG
*
10484 AATCGAACTCGACA-ATTTTGTTGACATATAGCTCTTCTTACCTTGAGCTATGTTGTAAATTTGA
1 AATCGAACTCGA-AGGTTTTGTTGACATATAGCTCTTCTTACCTTGAGCTATGTTGTAAA--TGA
* * * * *
10548 TTTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTT-AA
63 TATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTAGCAGATAACCCTTCTAGCCTTGAG
*
10612 TATATGCTGCAAATAACAGTGCATTGGAGTTGAGCGT
128 T-TATGCTGCAAATAA-AGTGCATTGGAGCTGAGCGT
* ** *
10649 AATCGAACTCGAAGGTTTTGTTGACGGATA-ACCT-TTC-TAGCCTTGATTTATGCTGTAAATGA
1 AATCGAACTCGAAGGTTTTGTTGAC--ATATAGCTCTTCTTA-CCTTGAGCTATGTTGTAAATGA
* ** * * *
10711 TATACCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCTTAGCAGATAACCCCTCTAGCCT
63 TATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTAGCAGATAACCCTTCTAGCCT
* * * *
10776 TGAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGT
124 TGAGTTATGCTGCAAATAAAGTGCATTGGAGCTGAGCGT
* * * * * * * * *
10815 AGTCAAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGA-CTTAAGCTAT-TCTGCAAATA
1 AATCGAACTCGAAGGT-TTT-GTTGACATATAGCTCTTCT-TACCTTGAGCTATGT-TGTAAATG
* * * * *
10878 ATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTG
62 AT-ATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTAGCAGATAACCCTTCTAGCCTTG
* * * **
10943 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGATTGT
126 AGTTATGCTGCAAATAAAGTGCATTGGAGCTGAGCGT
* * * * * * * **
10980 AGTCAAACTCGAAGGTCTTTGGTTGGA-AGATAACCCTTCTCGA-CTTAAGCTATGTTACAAATG
1 AATCGAACTCGAAGGT-TTT-GTT-GACATATAGCTCTTCT-TACCTTGAGCTATGTTGTAAATG
* * * * * *
11043 ATGTG-CTTTGGAGCTGAGCGTAGTC-AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGA
62 ATATGCCTTT-GAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTAGCAGATAACCCTTCTAGC
* * * * * * * **
11106 TTTAAGCTATGCTACAAATGATAGTGCCTCT-AAGCTGAGTAT
122 CTTGAGTTATGCTGCAAAT-AAAGTGCAT-TGGAGCTGAGCGT
* * * * *
11148 AATCGAACTCGAATGTCTTTAG-T-AGATA-A-CCCTTC-TAGCCTTGAGTTATGCTT-CAAATG
1 AATCGAACTCGAAGGT-TTT-GTTGACATATAGCTCTTCTTA-CCTTGAGCTATG-TTGTAAATG
* * * * * * * * *
11207 ATGTGCCTTTAAGATGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCAAATAGCCTTTCTTGCC
62 ATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTAGCAGATAACCCTTCTAGCC
* * *** * *
11272 TTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAACGT
123 TTGAGTTATGCTGCAAATAAAGTGCATTGGAGCTGAGCGT
* * * * * * * * *
11312 AGTTGAACTCGAAGGTCTTTTGCTGGCAGATAGCCCTTCTCGA-CTTAAGCTATGCTT-CAAATG
1 AATCGAACTCGAAGG--TTTTGTTGACATATAGCTCTTCT-TACCTTGAGCTATG-TTGTAAATG
* * * * * * *
11375 ATGGTGCCTCTGAGCTGAGTATAATCGAACTCGAAGGACTTTGGCAGATAACCCTTATAGCCTTA
62 AT-ATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTAGCAGATAACCCTTCTAGCCTTG
* * * * * * * *
11440 AGTTATGCTACAAATGATGTTCCTTTGAGCCGAGTGT
126 AGTTATGCTGCAAATAAAGTGCATTGGAGCTGAGCGT
* * * * * *
11477 AGTCAAACTCGAAGGTCTTTTGTTGGCAAATAGC-CATTCTTGCCTTGAGCTATGTTGCAAAT-A
1 AATCGAACTCGAAGG--TTTTGTTGACATATAGCTC-TTCTTACCTTGAGCTATGTTGTAAATGA
* * * *
11540 GTGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
63 -TATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
11576 CCTTAACTGA
Statistics
Matches: 742, Mismatches: 139, Indels: 93
0.76 0.14 0.10
Matches are distributed among these distances:
162 1 0.00
163 50 0.07
164 116 0.16
165 310 0.42
166 47 0.06
167 76 0.10
168 83 0.11
169 57 0.08
170 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (162 bp):
AATCGAACTCGAAGGTTTTGTTGACATATAGCTCTTCTTACCTTGAGCTATGTTGTAAATGATAT
GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTAGCAGATAACCCTTCTAGCCTTGAGTTA
TGCTGCAAATAAAGTGCATTGGAGCTGAGCGT
Found at i:10793 original size:84 final size:84
Alignment explanation
Indices: 10524--11575 Score: 899
Period size: 84 Copynumber: 12.7 Consensus size: 84
10514 GCTCTTCTTA
* * * * * *
10524 CCTTGAGCTATGTTGTAAATTTGATTTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T
1 CCTTGAGCTATGCTGCAAA--TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
* * *
10586 -TTAGCAGATAGCCCTTCTCG
64 GTTGGCAGATAACCCTTCTAG
* * ** * * * * *
10606 ACTTAATATATGCTGCAAATAACAGTGCATTGGAGTTGAGCGTAATCGAACTCGAAGG--TTTTG
1 CCTTGAGCTATGCTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* * *
10669 TTGACGGATAACCTTTCTAG
65 TTGGCAGATAACCCTTCTAG
** * * * ** *
10689 CCTTGATTTATGCTGTAAATGATATACCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
10754 TAGCAGATAACCCCTCTAG
66 TGGCAGATAACCCTTCTAG
* * * *
10773 CCTTGAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
10838 TGGCAGATAGCCCTTCTCG
66 TGGCAGATAACCCTTCTAG
* * * * ** * *
10857 ACTTAAGCTATTCTGCAAATAATGGTGCCTCT-GAGCTGAGTATAATCAAACTCGAAGGTC---T
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
10918 -TTGGCAGATAACCCTTCTAG
64 GTTGGCAGATAACCCTTCTAG
* ** * *
10938 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGATTGTAGTCAAACTCGAAGGTCTTTGGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
11003 TGGAAGATAACCCTTCTCG
66 TGGCAGATAACCCTTCTAG
* * * * *
11022 ACTTAAGCTATGTTACAAATGATGTGCTTTGGAGCTGAGCGTAGTC-AACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
*
11086 TGGCAGATAACCCTTCTCG
66 TGGCAGATAACCCTTCTAG
** * * * ** * * *
11105 ATTTAAGCTATGCTACAAATGATAGTGCCTCT-AAGCTGAGTATAATCGAACTCGAATGTCTTTA
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
11169 G-T---AGATAACCCTTCTAG
64 GTTGGCAGATAACCCTTCTAG
* * ** *
11186 CCTTGAGTTATGCTTCAAATGATGTGCCTTTAAGATGAGCGTAGTCGAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * * * *
11251 TAGCAAATAGCCTTTCTTG
66 TGGCAGATAACCCTTCTAG
* * * * *
11270 CCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAACGTAGTTGAACTCGAAGGTCTTTTGC
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
11335 TGGCAGATAGCCCTTCTCG
66 TGGCAGATAACCCTTCTAG
* * * ** * *
11354 ACTTAAGCTATGCTTCAAATGATGGTGCCTCT-GAGCTGAGTATAATCGAACTCGAAGGAC---T
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
*
11415 -TTGGCAGATAACCCTTATAG
64 GTTGGCAGATAACCCTTCTAG
* * * * * * * *
11435 CCTTAAGTTATGCTACAAATGATGTTCCTTTGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * * *
11500 TGGCAAATAGCCATTCTTG
66 TGGCAGATAACCCTTCTAG
*
11519 CCTTGAGCTATGTTGCAAAT-AGTGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1 CCTTGAGCTATGCTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
11576 CCTTAACTGA
Statistics
Matches: 779, Mismatches: 161, Indels: 58
0.78 0.16 0.06
Matches are distributed among these distances:
79 3 0.00
80 94 0.12
81 134 0.17
82 42 0.05
83 89 0.11
84 340 0.44
85 75 0.10
86 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (84 bp):
CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
TGGCAGATAACCCTTCTAG
Found at i:10991 original size:249 final size:249
Alignment explanation
Indices: 10517--11575 Score: 1299
Period size: 249 Copynumber: 4.3 Consensus size: 249
10507 ACATATAGCT
* * * * * *
10517 CTTCTTACCTTGAGCTATGTTGTAAATTTGATTTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CTTCTTGCCTTGAGCTATGTTGCAAA--TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* ** * * *
10582 GTC---T-TTAGCAGATAGCCCTTCTCGACTTAATATATGCTGCAAATAACAGTGCAT-TGGAGT
64 GTCTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCT-GAGC
** * * * *
10642 TGAGCGTAATCGAACTCGAAGGT-TTTGTTGACGGATAACCTTTCTAGCCTTGATTTATGCTGTA
128 TGAGTATAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCA
* * * * * *
10706 AATGATATACCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCTTAGCAGATAACC
190 AATGATGTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAAATAACC
* * * ** *
10766 CCTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGT
1 CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * *
10831 CTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATAATGGTGCCTCTGAGCTGA
66 CTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCTGAGCTGA
*
10896 GTATAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
131 GTATAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
** ** * *
10961 GTGCCTTGGAGCTGATTGTAGTCAAACTCGAAGGTCTTTGGTT-GGAAGATAACC
196 GTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAA-ATAACC
* * * * *
11015 CTTCTCGACTTAAGCTATGTTACAAATGATGTGCTTTGGAGCTGAGCGTAGTC-AACTCGAAGGT
1 CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * * * *
11079 CTTTTGTTGGCAGATAACCCTTCTCGATTTAAGCTATGCTACAAATGATAGTGCCTCTAAGCTGA
66 CTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCTGAGCTGA
* * * *
11144 GTATAATCGAACTCGAATGTCTTTAGTAGATAACCCTTCTAGCCTTGAGTTATGCTTCAAATGAT
131 GTATAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * *
11209 GTGCCTTTAAGATGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCAAATAGCC
196 GTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAAATAACC
* * * *
11263 TTTCTTGCCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAACGTAGTTGAACTCGAAGGT
1 CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * * *
11328 CTTTTGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGGTGCCTCTGAGCTGA
66 CTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCTGAGCTGA
* * * *
11393 GTATAATCGAACTCGAAGGACTTTGGCAGATAACCCTTATAGCCTTAAGTTATGCTACAAATGAT
131 GTATAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * * * * *
11458 GTTCCTTTGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAATAGCC
196 GTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAAATAACC
*
11512 ATTCTTGCCTTGAGCTATGTTGCAAAT-AGTGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1 CTTCTTGCCTTGAGCTATGTTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
11576 CCTTAACTGA
Statistics
Matches: 697, Mismatches: 103, Indels: 20
0.85 0.13 0.02
Matches are distributed among these distances:
247 35 0.05
248 215 0.31
249 375 0.54
250 1 0.00
251 66 0.09
252 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (249 bp):
CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
CTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCTGAGCTGA
GTATAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
GTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAAATAACC
Found at i:11275 original size:497 final size:498
Alignment explanation
Indices: 10550--11575 Score: 1381
Period size: 497 Copynumber: 2.1 Consensus size: 498
10540 AAATTTGATT
* * * * * *
10550 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTAGCAGATAGCCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTA
** * * * * * * ** *
10611 ATATATGCTGCAAATAACAGTGCAT-TGGAGTTGAGCGTAATCGAACTCGAAGGT-TTT-GTTGA
66 AGCTATGCTACAAATGATAGTGCCTCT-AAGCTGAGTATAATCGAACTCGAATGTCTTTAG-T-A
* * *
10673 CGGATAACCTTTCTAGCCTTGATTTATGCTGTAAATGATATACCTTAAAGCTGAGCGTAGTCGAA
128 --GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATACCTTAAAGATGAGCGTAGTCGAA
* *
10738 CTCGAAGGTCTTTTCTTAGCAGATAACCCCTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTT
191 CTCGAAGGTCTTTTCTTAGCAAATAACCCCTCTAGCCTTGAGCTATACTGCAAATGATGTGCCTT
* *
10803 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
256 GGAGCTGAACGTAGTCAAACTCGAAGGTCTTTGGCTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* *
10868 TCTGCAAATAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGTCTTTGGCAGATAACCCT
321 GCTGCAAATAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGACTTTGGCAGATAACCCT
* * * * *
10933 TCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGATTGTAGTCAAACTCGAAGGTCT
386 TATAGCCTTAAGTTATGCTACAAATGATGTGCCTTGGAGCCGAGTGTAGTCAAACTCGAAGGTCT
*
10998 TTGGTTGG-AAGATAACCCTTCTCGACTTAAGCTATGTTACAAAT-GATG
451 TTGGTTGGCAA-ATAACCATTCTCGACTTAAGCTATGTTACAAATAG-TG
*
11046 TGCTTTGGAGCTGAGCGTAGTC-AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTA
11110 AGCTATGCTACAAATGATAGTGCCTCTAAGCTGAGTATAATCGAACTCGAATGTCTTTAGTAGAT
66 AGCTATGCTACAAATGATAGTGCCTCTAAGCTGAGTATAATCGAACTCGAATGTCTTTAGTAGAT
* * *
11175 AACCCTTCTAGCCTTGAGTTATGCT-TCAAATGATGTGCCTTTAAGATGAGCGTAGTCGAACTCG
131 AACCCTTCTAGCCTTGAGTTATGCTGT-AAATGATATACCTTAAAGATGAGCGTAGTCGAACTCG
* * ** * ** *
11239 AAGGTCTTTTGTTAGCAAATAGCCTTTCTTGCCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAG
195 AAGGTCTTTTCTTAGCAAATAACCCCTCTAGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAG
** * *
11304 CTGAACGTAGTTGAACTCGAAGGTCTTTTGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTT
260 CTGAACGTAGTCAAACTCGAAGGTCTTTGGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
* *
11369 CAAATGATGGTGCCTCTGAGCTGAGTATAATCGAACTCGAAGGACTTTGGCAGATAACCCTTATA
325 CAAATAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGACTTTGGCAGATAACCCTTATA
* * *
11434 GCCTTAAGTTATGCTACAAATGATGTTCCTTTGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTTG
390 GCCTTAAGTTATGCTACAAATGATGTGCCTTGGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTGG
* * * * *
11499 TTGGCAAATAGCCATTCTTGCCTTGAGCTATGTTGCAAATAGTG
455 TTGGCAAATAACCATTCTCGACTTAAGCTATGTTACAAATAGTG
11543 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
11576 CCTTAACTGA
Statistics
Matches: 460, Mismatches: 59, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
495 12 0.03
496 19 0.04
497 345 0.75
498 14 0.03
499 64 0.14
500 5 0.01
501 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (498 bp):
TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTA
AGCTATGCTACAAATGATAGTGCCTCTAAGCTGAGTATAATCGAACTCGAATGTCTTTAGTAGAT
AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATACCTTAAAGATGAGCGTAGTCGAACTCGA
AGGTCTTTTCTTAGCAAATAACCCCTCTAGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGC
TGAACGTAGTCAAACTCGAAGGTCTTTGGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
AAATAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGACTTTGGCAGATAACCCTTATAG
CCTTAAGTTATGCTACAAATGATGTGCCTTGGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTGGT
TGGCAAATAACCATTCTCGACTTAAGCTATGTTACAAATAGTG
Found at i:12875 original size:82 final size:87
Alignment explanation
Indices: 12769--12990 Score: 233
Period size: 95 Copynumber: 2.5 Consensus size: 87
12759 AGCTGAATCT
* *
12769 ATAAAGCCGGGGCATTTAAACAATTGCTCTAGAGGGACAACTCAA-TAT-GTA-AA-CACCTTTA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACCTTTA
* *
12830 TTAGG-TGAGCTGAATCTTATCC
66 TCAGGCT-AGCTGAATATTATCC
* *
12852 AT-GAGTCGGGGCGTTTAACCAATTGC-CTTAGAGGGACAACTCAACCTTTATTGTATAGTATAA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----A-T-TATAGTATAA
*
12915 TCGCCTTTATCAGGCTAGCTGAATATTATCC
57 TCACCTTTATCAGGCTAGCTGAATATTATCC
*
12946 ATAAAGCCGGGGCGTGTAACCAATTGCTCTAGAGGGACAACTCAA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
12991 GCTTTATTGT
Statistics
Matches: 113, Mismatches: 10, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
81 1 0.01
82 34 0.30
83 3 0.03
88 1 0.01
89 1 0.01
91 3 0.03
92 3 0.03
93 2 0.02
94 28 0.25
95 36 0.32
96 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (87 bp):
ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACCTTTA
TCAGGCTAGCTGAATATTATCC
Found at i:12986 original size:95 final size:93
Alignment explanation
Indices: 12824--13007 Score: 264
Period size: 95 Copynumber: 2.0 Consensus size: 93
12814 TATGTAAACA
* * * * *
12824 CCTTTATTAGGTGAGCTGAATCTTATCCATGAGTCGGGGCGTTTAACCAATTGCCTTAGAGGGAC
1 CCTTTATCAGGTGAGCTGAATATTATCCATAAGCCGGGGCGTGTAACCAATTGCCTTAGAGGGAC
12889 AACTCAACCTTTATTGTATAGTATAATCG
66 AACTCAACCTTTATTGTATA-TATAATCG
12918 CCTTTATCAGGCT-AGCTGAATATTATCCATAAAGCCGGGGCGTGTAACCAATTG-CTCTAGAGG
1 CCTTTATCAGG-TGAGCTGAATATTATCCAT-AAGCCGGGGCGTGTAACCAATTGCCT-TAGAGG
*
12981 GACAACTCAAGCTTTATTGTATATATA
63 GACAACTCAACCTTTATTGTATATATA
13008 TAATTATAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
94 32 0.40
95 49 0.60
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (93 bp):
CCTTTATCAGGTGAGCTGAATATTATCCATAAGCCGGGGCGTGTAACCAATTGCCTTAGAGGGAC
AACTCAACCTTTATTGTATATATAATCG
Found at i:16456 original size:10 final size:11
Alignment explanation
Indices: 16433--16457 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16423 TTTGTGACTG
16433 TTTTTATGGTT
1 TTTTTATGGTT
16444 TTTTTATGGTT
1 TTTTTATGGTT
16455 TTT
1 TTT
16458 GTGATTCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (11 bp):
TTTTTATGGTT
Found at i:18146 original size:17 final size:16
Alignment explanation
Indices: 18115--18148 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
18105 CACGTGAGGA
18115 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
18131 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
18148 T
1 T
18149 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:24545 original size:20 final size:20
Alignment explanation
Indices: 24503--24551 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
24493 TAACTTTTTC
*
24503 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
24523 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
*
24542 TTTTACCTTT
1 TTTTATCTTT
24552 TCTCTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:28399 original size:17 final size:16
Alignment explanation
Indices: 28368--28401 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28358 CACGTGAGGA
28368 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
28384 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
28401 T
1 T
28402 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:28929 original size:3 final size:3
Alignment explanation
Indices: 28921--28948 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28911 GGAAAAAACA
28921 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28949 TATTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29020 original size:37 final size:36
Alignment explanation
Indices: 28975--29096 Score: 147
Period size: 37 Copynumber: 3.3 Consensus size: 36
28965 CTATTTCCAC
* *
28975 AAAACTATATAATATATATTTTTTCAAAAATATTTTT
1 AAAACTATATATTATATA-ATTTTCAAAAATATTTTT
* * *
29012 AAATCTATATATTATATAATTTTAAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTCAAAAATATTTTT
*
29048 AAAAACTATATATTATATAAGTTTTC-AAAATGATTTTA
1 -AAAACTATATATTATATAA-TTTTCAAAAAT-ATTTTT
29086 AAAACTATATA
1 AAAACTATATA
29097 GAGAAAATCG
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
36 15 0.21
37 50 0.68
38 8 0.11
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (36 bp):
AAAACTATATATTATATAATTTTCAAAAATATTTTT
Found at i:29223 original size:20 final size:20
Alignment explanation
Indices: 29179--29566 Score: 370
Period size: 20 Copynumber: 19.2 Consensus size: 20
29169 AATGACCAAC
*
29179 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
29198 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
29218 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
29238 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
29258 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
29280 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
29300 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
29322 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAG
29342 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
29362 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
29382 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
29402 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
29422 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
29442 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
29462 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
29482 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
29502 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
29522 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
29542 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
29562 AAAAT
1 AAAAT
29567 GAGTAAATTC
Statistics
Matches: 312, Mismatches: 30, Indels: 53
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.01
19 26 0.08
20 241 0.77
21 10 0.03
22 28 0.09
23 2 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:29249 original size:40 final size:40
Alignment explanation
Indices: 29179--29559 Score: 456
Period size: 40 Copynumber: 9.4 Consensus size: 40
29169 AATGACCAAC
* * *
29179 AAAATCGCAACGCGAAAT--AAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTAAG
* **** *
29218 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT-TA-AG
*
29258 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAG
* * *
29300 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG
29342 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
29382 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
*
29422 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
*
29462 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
29502 AAAATCGCAACGCGATT--AAGAAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATTCCAAG--AATCGCAACGCGATT--AAG
29544 --AATCGCAACGCGATTC
1 AAAATCGCAACGCGATTC
29560 AGAAAATGAG
Statistics
Matches: 307, Mismatches: 18, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
38 4 0.01
39 16 0.05
40 215 0.70
41 5 0.02
42 64 0.21
43 2 0.01
44 1 0.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:29673 original size:6 final size:6
Alignment explanation
Indices: 29662--29736 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
29652 GACACGTATT
29662 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
29710 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
29737 CGAGACGAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:30248 original size:6 final size:6
Alignment explanation
Indices: 30237--30281 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
30227 TCTCGTCTCG
30237 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
30282 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:30410 original size:20 final size:20
Alignment explanation
Indices: 30385--30563 Score: 222
Period size: 20 Copynumber: 8.8 Consensus size: 20
30375 TCATTTTCTT
30385 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
30405 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
30425 AATCGCGTTGCGATTTTCTT--
1 AATCGCGTTGCGA--TTCTTGG
30445 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
30465 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
*
30485 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
30505 AAGATCGCGTTGCGATTCTCT-T
1 -A-ATCGCGTTGCGATTCT-TGG
*
30527 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
30547 AATATCGCGTTGCGATT
1 -A-ATCGCGTTGCGATT
30564 TTCTTTTGAC
Statistics
Matches: 139, Mismatches: 8, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
18 5 0.04
19 3 0.02
20 92 0.66
21 5 0.04
22 33 0.24
23 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTTGG
Found at i:30470 original size:60 final size:60
Alignment explanation
Indices: 30377--30568 Score: 253
Period size: 60 Copynumber: 3.1 Consensus size: 60
30367 GAATTTACTC
30377 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* *
30437 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATT-TTCTGAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*** * *
30497 ATTCTTGGAAGATCGCGTTGCGATTCTCT-TAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCT-TGGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
30561 ATTTTCTT
1 ATTTTCTT
30569 TTGACCGTTG
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
59 2 0.02
60 58 0.51
61 3 0.03
62 31 0.27
63 6 0.05
64 13 0.12
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.40
Consensus pattern (60 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:30580 original size:42 final size:40
Alignment explanation
Indices: 30385--30644 Score: 264
Period size: 40 Copynumber: 6.4 Consensus size: 40
30375 TCATTTTCTT
30385 AATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTTGG
30425 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
* *
30465 AATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
* *
30505 AAGATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGG
1 -A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
* **
30547 AATATCGCGTTGCGATTTTCTT--TTGACCGTTGCGATT-TTCT
1 -A-ATCGCGTTGCGATTTTCTTAATCG--CGTTGCGATTCTTGG
** * * *
30588 TTTCAACGTTGCGATTTTCTAAATCGCGTTGCGATT-TT-T
1 AATC-GCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
*
30627 ATTTCGCGTTGCGATTTT
1 A-ATCGCGTTGCGATTTT
30645 GTTGGTCATT
Statistics
Matches: 193, Mismatches: 17, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
39 15 0.08
40 102 0.53
41 3 0.02
42 73 0.38
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (40 bp):
AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
Found at i:30617 original size:20 final size:20
Alignment explanation
Indices: 30377--30644 Score: 181
Period size: 20 Copynumber: 13.2 Consensus size: 20
30367 GAATTTACTC
*
30377 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
30397 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
30417 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
30437 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
30457 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
* *
30477 ATTTTCTGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
30497 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
30519 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
30539 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
30561 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
30581 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
30601 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
30621 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
30640 ATTTT
1 ATTTT
30645 GTTGGTCATT
Statistics
Matches: 202, Mismatches: 33, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.01
19 21 0.10
20 136 0.67
21 17 0.08
22 26 0.13
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:30791 original size:36 final size:37
Alignment explanation
Indices: 30727--30878 Score: 220
Period size: 36 Copynumber: 4.2 Consensus size: 37
30717 CGATTTTCTC
*
30727 AACTATATATTATATATATTTTCTAAAATGTTTTAAA
1 AACTATATATTATATATATTTTCAAAAATGTTTTAAA
*
30764 ACCTATATATTATATA-ATTTTCAAAAATGTTTTAAA
1 AACTATATATTATATATATTTTCAAAAATGTTTTAAA
* *
30800 AACTATGTAATATATAT-TTTTCAAAAATGCTTTT-AA
1 AACTATATATTATATATATTTTCAAAAATG-TTTTAAA
* *
30836 AACTATATATTATATATATTTTCTAAAATATTTTAAA
1 AACTATATATTATATATATTTTCAAAAATGTTTTAAA
30873 AACTAT
1 AACTAT
30879 GAGAAAATAA
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
36 65 0.64
37 37 0.36
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (37 bp):
AACTATATATTATATATATTTTCAAAAATGTTTTAAA
Found at i:30857 original size:73 final size:73
Alignment explanation
Indices: 30727--30879 Score: 229
Period size: 73 Copynumber: 2.1 Consensus size: 73
30717 CGATTTTCTC
* * *
30727 AACTATATATTATATATATTTTCTAAAATGTTTTAAAACCTATATATTATATAATTTTCAAAAAT
1 AACTATGTAATATATATATTTTCAAAAATGTTTTAAAACCTATATATTATATAATTTTCAAAAAT
*
30792 GTTTTAAA
66 ATTTTAAA
*
30800 AACTATGTAATATATAT-TTTTCAAAAATGCTTTTAAAA-CTATATATTATATATATTTTCTAAA
1 AACTATGTAATATATATATTTTCAAAAATG-TTTTAAAACCTATATATTATATA-ATTTTCAAAA
30863 ATATTTTAAA
64 ATATTTTAAA
30873 AACTATG
1 AACTATG
30880 AGAAAATAAC
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
72 25 0.34
73 48 0.66
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (73 bp):
AACTATGTAATATATATATTTTCAAAAATGTTTTAAAACCTATATATTATATAATTTTCAAAAAT
ATTTTAAA
Found at i:31095 original size:21 final size:21
Alignment explanation
Indices: 31063--31159 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
31053 GATTTACATA
*
31063 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* **
31084 TTTGCGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
31105 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
31126 TTTGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
31147 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
31160 TTATTACAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:31115 original size:42 final size:42
Alignment explanation
Indices: 31063--31191 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
31053 GATTTACATA
* * **
31063 TTCGCATTGCGATAGTCCAAGTTTGCGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATAGTCCAAATTTGCGTTGCGATAGTCCAAG
**
31105 TTCGCGTTGCGATTTTCCAAATTTGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAATTTGCGTTGCGATAGTCCAAG
* * *
31147 TTCGCGTTGCGATTTATTACAAA-TT-CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA--TAGTCCAAATTTGCGTTGCGATAGTCCAAG
31189 TTC
1 TTC
31192 TCTAAAAAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
42 67 0.88
43 2 0.03
44 7 0.09
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TTCGCGTTGCGATAGTCCAAATTTGCGTTGCGATAGTCCAAG
Found at i:32074 original size:42 final size:42
Alignment explanation
Indices: 32012--32202 Score: 337
Period size: 42 Copynumber: 4.5 Consensus size: 42
32002 TGCGATTTTG
*
32012 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
32054 GACTATCGCAACGAGCTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
32096 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
32138 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
32180 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
32203 CTATCGCAAC
Statistics
Matches: 142, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
42 132 0.93
44 10 0.07
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:32106 original size:63 final size:61
Alignment explanation
Indices: 32009--32295 Score: 325
Period size: 63 Copynumber: 4.6 Consensus size: 61
31999 CGTTGCGATT
* *
32009 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-CGAGC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAACCGAAC
* * * * *
32070 TTGGAATAAATCGCAACGCGAACTTCGACT-ATCGCAA--CGAACTTGGAATAAATCGCAACGCG
1 TTGGACT--ATCGCAA--CGAACTTGGAATAATCGCAACGCGAACTTCGACT--ATCGCAAC-CG
32132 AAC
59 AAC
32135 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAAC-CGAAC
*
32198 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAACCGAAC
* *
32259 TTGGACTATCGTAACGCGAACTTGGACT-ATCGCAACG
1 TTGGACTATCGCAA--CGAACTTGGAATAATCGCAACG
32296 AATTTGGAAA
Statistics
Matches: 196, Mismatches: 16, Indels: 28
0.82 0.07 0.12
Matches are distributed among these distances:
61 53 0.27
63 114 0.58
65 29 0.15
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (61 bp):
TTGGACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTCGACTATCGCAACCGAAC
Found at i:32230 original size:42 final size:42
Alignment explanation
Indices: 32184--32311 Score: 192
Period size: 40 Copynumber: 3.1 Consensus size: 42
32174 AACTTCGACT
32184 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
* * *
32226 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACT--
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
*
32266 ATCGTAACGCGAACTTGGACTATCGCAACGAATTTGG-A-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
32306 ATCGCA
1 ATCGCA
32312 TTGCGATAGT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
40 39 0.51
42 37 0.49
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:32250 original size:21 final size:21
Alignment explanation
Indices: 32009--32295 Score: 283
Period size: 21 Copynumber: 13.8 Consensus size: 21
31999 CGTTGCGATT
*
32009 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
32028 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
32051 TTCGACTATCGCAA--CGAGC
1 TTGGACTATCGCAACGCGAAC
*
32070 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
32093 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
32112 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
32135 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
32154 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
32177 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
32198 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
32217 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
32240 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
32259 TTGGACTATCGTAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
32280 TTGGACTATCGCAACG
1 TTGGACTATCGCAACG
32296 AATTTGGAAA
Statistics
Matches: 221, Mismatches: 25, Indels: 42
0.77 0.09 0.15
Matches are distributed among these distances:
19 63 0.29
21 110 0.50
23 48 0.22
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:32336 original size:21 final size:21
Alignment explanation
Indices: 32307--32359 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
32297 ATTTGGAAAA
*
32307 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
32328 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
*
32349 TCGTGTTGCGA
1 TCGCGTTGCGA
32360 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:36031 original size:40 final size:42
Alignment explanation
Indices: 35987--36067 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
35977 AATAAGTTCT
*
35987 TTGGTTGTAGATT-G-ATATATTATTTTTATTAGTATATATA
1 TTGGTTGTAGATTGGTATATATTATTTTTATTAGCATATATA
* *
36027 TTGGTTGTAGATTGGTGTATATTGTTTTTATTAGCATATAT
1 TTGGTTGTAGATTGGTATATATTATTTTTATTAGCATATAT
36068 TATAATGTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 13 0.36
41 1 0.03
42 22 0.61
ACGTcount: A:0.26, C:0.01, G:0.19, T:0.54
Consensus pattern (42 bp):
TTGGTTGTAGATTGGTATATATTATTTTTATTAGCATATATA
Found at i:36068 original size:40 final size:39
Alignment explanation
Indices: 35987--36068 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
35977 AATAAGTTCT
*
35987 TTGGTTGTAGATTGATATATTATTTTTATTAGTATATATA
1 TTGGTTGTAGATTGATATATTATTTTTATTAG-ACATATA
* *
36027 TTGGTTGTAGATTGGTGTATATTGTTTTTATTAG-CATATA
1 TTGGTTGTAGATT-G-ATATATTATTTTTATTAGACATATA
36067 TT
1 TT
36069 ATAATGTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 20 0.54
41 1 0.03
42 16 0.43
ACGTcount: A:0.26, C:0.01, G:0.18, T:0.55
Consensus pattern (39 bp):
TTGGTTGTAGATTGATATATTATTTTTATTAGACATATA
Found at i:45253 original size:24 final size:24
Alignment explanation
Indices: 45226--45272 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
45216 AGAAAACAAC
* *
45226 AAAGATGAGGTTTAGTTCAAAAAT
1 AAAGACGAGGTTTAGGTCAAAAAT
45250 AAAGACGAGGTTTAGGTCAAAAA
1 AAAGACGAGGTTTAGGTCAAAAA
45273 CTCAAACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.23
Consensus pattern (24 bp):
AAAGACGAGGTTTAGGTCAAAAAT
Found at i:50613 original size:25 final size:26
Alignment explanation
Indices: 50577--50631 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
50567 AAATTAAAAA
50577 AATATTTATCTAATGACAA-ATATTT
1 AATATTTATCTAATGACAATATATTT
* *
50602 AATATATT-TCTAATGATAATATTTTT
1 AATAT-TTATCTAATGACAATATATTT
50628 AATA
1 AATA
50632 ACTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (26 bp):
AATATTTATCTAATGACAATATATTT
Found at i:50793 original size:7 final size:7
Alignment explanation
Indices: 50778--50863 Score: 74
Period size: 7 Copynumber: 12.9 Consensus size: 7
50768 CTTTACATTG
50778 AACCCTA
1 AACCCTA
*
50785 AAACCTA
1 AACCCTA
50792 AACCCTA
1 AACCCTA
***
50799 AATTTTA
1 AACCCTA
50806 AACCCTA
1 AACCCTA
50813 AACCCTA
1 AACCCTA
50820 AA--CTA
1 AACCCTA
*
50825 AA-ACTA
1 AACCCTA
50831 AACCCTA
1 AACCCTA
*
50838 AA-CATA
1 AACCCTA
50844 AACCCT-
1 AACCCTA
50850 AACCACTA
1 AACC-CTA
50858 AACCCT
1 AACCCT
50864 TAATCCAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
5 5 0.08
6 14 0.22
7 40 0.63
8 4 0.06
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.19
Consensus pattern (7 bp):
AACCCTA
Found at i:52713 original size:18 final size:18
Alignment explanation
Indices: 52692--52765 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
52682 TAAAATAAAT
52692 AATAATTGTAAATATTAA
1 AATAATTGTAAATATTAA
*
52710 AATAATTTGT-ATTATTTAA
1 AATAA-TTGTAAATA-TTAA
*
52729 AATAA--ATAAA-A-T--
1 AATAATTGTAAATATTAA
52741 AATAATTGTAAATATTAA
1 AATAATTGTAAATATTAA
52759 AATAATT
1 AATAATT
52766 AAATATAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
12 5 0.12
14 5 0.12
15 1 0.02
16 3 0.07
17 1 0.02
18 15 0.35
19 13 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
AATAATTGTAAATATTAA
Done.