Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004491.1 Hibiscus syriacus cultivar Beakdansim tig00009902_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: 69717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:775 original size:11 final size:12
Alignment explanation
Indices: 752--787 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
742 AAATTTAGTC
752 TAATAATTAAATA
1 TAATAA-TAAATA
765 TAA-AATAAATA
1 TAATAATAAATA
776 TAATAATAAATA
1 TAATAATAAATA
788 ATTTTACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.41
12 10 0.45
13 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:8637 original size:36 final size:36
Alignment explanation
Indices: 8569--8671 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
8559 CCAATTTAGG
*
8569 TTTCATAAGAAATTTGGGTATTTTTTCTTATTAAAGA
1 TTTCATAAGAAATTTGAGTA-TTTTTCTTATTAAAGA
*
8606 TTTCATAAGAAATTTGAGTATTTTTCTTATTAAAGG
1 TTTCATAAGAAATTTGAGTATTTTTCTTATTAAAGA
*
8642 TTTCATAAGAAATTTGTGTA-TTTTCTTATT
1 TTTCATAAGAAATTTGAGTATTTTTCTTATT
8672 GAATATTAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.16
36 34 0.54
37 19 0.30
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (36 bp):
TTTCATAAGAAATTTGAGTATTTTTCTTATTAAAGA
Found at i:11875 original size:31 final size:30
Alignment explanation
Indices: 11800--11882 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
11790 AGAAACCTAC
* * *
11800 CACAAC-AAACCAAAGAAAACAAAAACTCT
1 CACAACAAAAACAAAGGAAACAAAAACCCT
* * * *
11829 CACAGCAGAAGCAAAGGAAACAAAAGCCCTT
1 CACAACAAAAACAAAGGAAACAAAAACCC-T
11860 CACAACAAAAACAAA-GAAACAAA
1 CACAACAAAAACAAAGGAAACAAA
11883 TATAGGGGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
29 5 0.12
30 25 0.58
31 13 0.30
ACGTcount: A:0.60, C:0.25, G:0.10, T:0.05
Consensus pattern (30 bp):
CACAACAAAAACAAAGGAAACAAAAACCCT
Found at i:21899 original size:31 final size:31
Alignment explanation
Indices: 21864--21964 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 31
21854 ATCTATTTAG
21864 GTTATTTCTGTTTATATATTTAAATTTCTAT
1 GTTATTTCTGTTTATATATTTAAATTTCTAT
* *
21895 GTTATTT-TGATTTA-ATAAGTATT-ACTTT-TAAG
1 GTTATTTCTG-TTTATAT-A-T-TTAAATTTCT-AT
*
21927 GTTATTTCTTTTTATATATTTAAATTTCTAT
1 GTTATTTCTGTTTATATATTTAAATTTCTAT
21958 GTTATTT
1 GTTATTT
21965 TAATTTAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
30 6 0.11
31 26 0.46
32 19 0.34
33 5 0.09
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.60
Consensus pattern (31 bp):
GTTATTTCTGTTTATATATTTAAATTTCTAT
Found at i:21941 original size:63 final size:63
Alignment explanation
Indices: 21862--21985 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
21852 CTATCTATTT
*
21862 AGGTTATTTCTGTTTATATATTTAAATTTCTATGTTATTTTGATTTAATAAGTATTACTTTTA
1 AGGTTATTTCTGTTTATATATTTAAATTTCTATGTTATTTTAATTTAATAAGTATTACTTTTA
*
21925 AGGTTATTTCTTTTTATATATTTAAATTTCTATGTTATTTTAATTTAATAAGTATTACTTT
1 AGGTTATTTCTGTTTATATATTTAAATTTCTATGTTATTTTAATTTAATAAGTATTACTTT
21986 AATAAAAATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (63 bp):
AGGTTATTTCTGTTTATATATTTAAATTTCTATGTTATTTTAATTTAATAAGTATTACTTTTA
Found at i:25684 original size:198 final size:198
Alignment explanation
Indices: 25310--26075 Score: 846
Period size: 198 Copynumber: 3.8 Consensus size: 198
25300 CGTTATTTAC
* * ** * * *
25310 AAGTATCGACACAAATCTAA-AACGTGTCGATACACTATGTTCACCTATTTTCTCATAAAACCGG
1 AAGTATCGACACAAAT-TAACAA-GTGTCGACACATTATGTAGACCTATTCTCACATAAAACAGG
* * * * * * *
25374 TACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTAT-CAGTTTTGGTGTTTT
64 TATATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGA-TTTCGATGTTTC
* * *
25438 TGGGATCGATACTTTTTATAAATGTATCGCCA-CTTATGCGTTCACCCTTTTGGGCATTCATTAC
128 TGGGATCGATACTTTTTAAAAATGTATCGACACCTTATGCGTTCACCCTTTTGGGCATTCATTAG
25502 GACAAA
193 GACAAA
*
25508 AAGTATCGACACAATATTAACAAGTGTCAACACATTATGTAGACCTATTCTCACATAAAACAGGT
1 AAGTATCGACACAA-ATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACAGGT
* * *
25573 ATATTTATACCGGTTATATTACAAAATTACCTATTACA-TATATTTATGGATTTCGATGTTTCTG
65 ATATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGATTTCGATGTTTCTG
* * * * * * *
25637 GGATCGATACTGTTGAAAAATGTATCGACACCTTATGGGTGCACCCTTTTTGG-ATTTTCCTTGT
130 GGATCGATACTTTTTAAAAATGTATCGACACCTTATGCGTTCACCCTTTTGGGCA--TTCATT-A
*
25701 GGACCAA
192 GGACAAA
* * * * * * *
25708 AAGTATCGACACAAATTCTACAAGTGTCGATACATTATATATATCTATTTTCTCA-AAAAAAAAC
1 AAGTATCGACACAAATT-AACAAGTGTCGACACATTATGTAGACCTA--TTCTCACATAAAACA-
* * * * *
25772 GGTTTATTTAAACCGGTTACATTGTAAATTTACCTATTATATTATAATTATTGG-TTTCGATGTT
62 GGTATATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTA-TGGATTTCGATGTT
* * * * * *
25836 TTTGGGATCGATACTTTTTATAATTGTATCGATACTTTATGCGTTCACCCTTTTGGGCATTCATA
126 TCTGGGATCGATACTTTTTAAAAATGTATCGACACCTTATGCGTTCACCCTTTTGGGCATTCATT
25901 ATGGA-AAA
191 A-GGACAAA
25909 AAGTATCGACACAACATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACAGGT
1 AAGTATCGACACAA-ATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACAGGT
* * * * *
25974 ATATTTATACCGGTTATATTATAAAATTACCTATTACATTATATTTTTTGATTTTGATGTTTCTG
65 ATATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGATTTCGATGTTTCTG
* * * *
26039 AGATCGATACATTTTAAAACTGTATCGACACTTTATG
130 GGATCGATACTTTTTAAAAATGTATCGACACCTTATG
26076 GGAAACTTTA
Statistics
Matches: 468, Mismatches: 82, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
197 46 0.10
198 106 0.23
199 104 0.22
200 48 0.10
201 46 0.10
202 50 0.11
203 64 0.14
204 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (198 bp):
AAGTATCGACACAAATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACAGGTA
TATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGATTTCGATGTTTCTGG
GATCGATACTTTTTAAAAATGTATCGACACCTTATGCGTTCACCCTTTTGGGCATTCATTAGGAC
AAA
Found at i:26096 original size:15 final size:15
Alignment explanation
Indices: 26076--26115 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
26066 ACACTTTATG
*
26076 GGAAACTTTAAGTTT
1 GGAAACTTTAAGTAT
*
26091 GGAAACTTTATGTAT
1 GGAAACTTTAAGTAT
*
26106 GAAAACTTTA
1 GGAAACTTTA
26116 TTGTGGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (15 bp):
GGAAACTTTAAGTAT
Found at i:26402 original size:11 final size:11
Alignment explanation
Indices: 26386--26437 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
26376 TATACATAAC
26386 AATGTTCAAAT
1 AATGTTCAAAT
26397 AATGTTCAAAT
1 AATGTTCAAAT
* *
26408 AATTTATACATAAC
1 AATGT-T-CA-AAT
26422 AATGTTCAAAT
1 AATGTTCAAAT
26433 AATGT
1 AATGT
26438 AACCACAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 22 0.65
12 3 0.09
13 3 0.09
14 6 0.18
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:29306 original size:148 final size:148
Alignment explanation
Indices: 29120--29402 Score: 383
Period size: 148 Copynumber: 1.9 Consensus size: 148
29110 TTCCTTTTGG
* ** * * *
29120 ACAAAAAGTATCGACACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTCT-CATAA
1 ACAAAAAGTATCGACACAAAATAAAAAAGTATCGATACAT-TATGTAAACCTATTCT-TACATAA
** * *
29183 AATCGGTAT-TGTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTTATGGGTTTCGA
64 AATCGGTATAT-TTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGA
29247 TGTTTTTGAGATTCATTCTGA
128 TGTTTTTGAGATTCATTCTGA
*
29268 ACAAAAAGTATCGACACAAAATAAAAAAGTATCGATACATTATGTAAACCTATTCTTATATAAAA
1 ACAAAAAGTATCGACACAAAATAAAAAAGTATCGATACATTATGTAAACCTATTCTTACATAAAA
* * **
29333 TCGGTATATTTATACCGGTTATATTACAAAATTACCTATTATATTATAATTATTTGTTTCGATGT
66 TCGGTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
29398 TTTTG
131 TTTTG
29403 GGATCGACAC
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
147 2 0.02
148 114 0.97
149 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (148 bp):
ACAAAAAGTATCGACACAAAATAAAAAAGTATCGATACATTATGTAAACCTATTCTTACATAAAA
TCGGTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
TTTTGAGATTCATTCTGA
Found at i:29600 original size:200 final size:200
Alignment explanation
Indices: 29249--29633 Score: 621
Period size: 200 Copynumber: 1.9 Consensus size: 200
29239 GGTTTCGATG
*
29249 TTTTTGAGATTCATTCTGAACAAAAAGTATCGACACAAAATAAAAAAGTATCGATACATTATGTA
1 TTTTTGAGATTCATTCTGAACAAAAAGTATCGACACAAAATAAAAAAGTATCGAAACATTATGTA
* * * *
29314 AACCTATTCTTATATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTATATTA
66 AACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACATATTACATTA
* *
29379 TAATTATTTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTT
131 TAATTATTTGTTTCGATGTTTTTGGGATCGACACGTTTTATAAATGTATCAACACTTTATTCGTT
29444 CATCA
196 CATCA
* * *
29449 TTTTTG-GCATTCATTCTGGACAAAAAGTATCGACACAAAATAAAAAAGTGTTGAAACATTATGT
1 TTTTTGAG-ATTCATTCTGAACAAAAAGTATCGACACAAAATAAAAAAGTATCGAAACATTATGT
* **
29513 AGACCTATTCTCACATAAAA-CTGGTATATTTATAGTGGTTATATTACAAAATTACATATTACAT
65 AAACCTATTCTCACATAAAATC-GGTATATTTATACCGGTTATATTACAAAATTACATATTACAT
29577 TATAATTATTTGTTTCGATGTTTTTGGGATCGACACGTTTTATAAATGTATCAACAC
129 TATAATTATTTGTTTCGATGTTTTTGGGATCGACACGTTTTATAAATGTATCAACAC
29634 ATATGCTTAC
Statistics
Matches: 170, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
199 2 0.01
200 168 0.99
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (200 bp):
TTTTTGAGATTCATTCTGAACAAAAAGTATCGACACAAAATAAAAAAGTATCGAAACATTATGTA
AACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACATATTACATTA
TAATTATTTGTTTCGATGTTTTTGGGATCGACACGTTTTATAAATGTATCAACACTTTATTCGTT
CATCA
Found at i:29923 original size:19 final size:19
Alignment explanation
Indices: 29899--29947 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
29889 TTACATCCAC
29899 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
29918 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
29937 ATACAAAATTA
1 ATACAAAATTA
29948 ACTCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:31763 original size:33 final size:33
Alignment explanation
Indices: 31726--31788 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
31716 CTTAAGTTTA
31726 CCCCTCAACACCTCAACTTATTTCACCACTTTT
1 CCCCTCAACACCTCAACTTATTTCACCACTTTT
*
31759 CCCCTCAACACCTCAACTTCTTTCACCACT
1 CCCCTCAACACCTCAACTTATTTCACCACT
31789 CCATCTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (33 bp):
CCCCTCAACACCTCAACTTATTTCACCACTTTT
Found at i:31847 original size:21 final size:21
Alignment explanation
Indices: 31822--31886 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
31812 CCCATTATGC
*
31822 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
31843 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
31864 CTCTCAAGTTTCTCTCCGACT
1 CTCTCAAGTTTCTCTTCGACT
31885 CT
1 CT
31887 TGATTGTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.14, C:0.35, G:0.11, T:0.40
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:32024 original size:9 final size:9
Alignment explanation
Indices: 32007--32040 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
31997 CTTCTTCCTT
*
32007 CTCCTCTGC
1 CTCCACTGC
32016 CTCCACTGC
1 CTCCACTGC
*
32025 ATCCACTGC
1 CTCCACTGC
32034 CTCCACT
1 CTCCACT
32041 ACATACTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.12, C:0.53, G:0.09, T:0.26
Consensus pattern (9 bp):
CTCCACTGC
Found at i:34574 original size:182 final size:182
Alignment explanation
Indices: 34265--35227 Score: 1507
Period size: 182 Copynumber: 5.3 Consensus size: 182
34255 TACGCGTACT
*** * * *** *
34265 TATTAAAGTATCGACACTTTCAATATATCCGGTAGAGCTTTACCGGTTTTGTCATTTAGAGACTG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTATCTCTTTACCAGTTTTGTCTTTTCCTGACCG
* * * * *
34330 GTTTTATCATATTTTTACATGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
* * *
34395 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGAAACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * * * **
34447 TATTAAATTATCGATACTTTCAATATATCTGGTAGCGCTTTACCAGTTTTGTCTTTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTATCTCTTTACCAGTTTTGTCTTTTCCTGACCG
* * *
34512 GTTTTATCATATTTTTACATGTTATATCATTGTGGATCGATACATATTTATAAAGAATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
34577 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* **
34629 TATTAAAGTATCGACACTTGCAATATATCATGTATCTCTTTA-CAGGTTTTGTCTTTTCCTGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTATCTCTTTACCA-GTTTTGTCTTTTCCTGACC
*
34693 GGTTTTGTCATATTTTTACCTGTTATATTGTTGTGGATCGATACATATTTATAAAGAATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
34758 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* *
34811 TATTAAAGTATCGACACTTGT-AATATATCCGATATCTCTTTACCGGTTTTGTCTTTTCCTGACC
1 TATTAAAGTATCGACACTT-TCAATATATCCGGTATCTCTTTACCAGTTTTGTCTTTTCCTGACC
34875 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
* * *
34940 TTTATAGGCGTTAAAATTGCTTCTCCTTTAAATTCACAATGTGTCGGTACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * *
34993 TATTAAAGTATCGACACTTACAATATATCCAGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTATCTCTTTACCAGTTTTGTCTTTTCCTGACCG
* *
35058 GTTTTGTCATATTTTTACCTATTATATCGTTGTGGATTGATACATATTTATAAAGAATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
35123 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* *
35175 TATTAAAGTATCGACACTTGCAATATATCCAGTATCTCTTTACCAGTTTTGTC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTATCTCTTTACCAGTTTTGTC
35228 ATATTTTTAC
Statistics
Matches: 730, Mismatches: 47, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
181 2 0.00
182 727 1.00
183 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTATCTCTTTACCAGTTTTGTCTTTTCCTGACCG
GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
Found at i:34934 original size:364 final size:362
Alignment explanation
Indices: 34265--35465 Score: 1706
Period size: 364 Copynumber: 3.4 Consensus size: 362
34255 TACGCGTACT
* * * * *** *
34265 TATTAAAGTATCGACACTTTCAATATATCCGGTAGAGCTTTACCGGTTTTGTCATTTAGAGACTG
1 TATTAAAGTATCGACACTTGCAATATATCAGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACCG
* * * *
34330 GTTTTATCATATTTTTACATGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
* * * *
34395 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGAAACTTATATTAAATTATCG
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCG
* * * * * * *
34460 ATACTT-TCAATATATCTGGTAGCGCTTTACCAGTTTTGTCTTTTCGAGACCGGTTTTATCATAT
196 ACACTTGT-AATATATCCGATATCTCTTTACC-GTTTTGTCTTTTC-CGACCGGTTTTGTCATAT
*
34524 TTTTACATGTTATATCATTGTGGATCGATACATATTTATAAAGAATCGACACTTTATAGGCGCTA
258 TTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTATAGGCGCTA
34589 AAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
323 AAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * *
34629 TATTAAAGTATCGACACTTGCAATATATCATGTATCTCTTTACAGGTTTTGTCTTTTCCTGACCG
1 TATTAAAGTATCGACACTTGCAATATATCAGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACCG
* *
34694 GTTTTGTCATATTTTTACCTGTTATATTGTTGTGGATCGATACATATTTATAAAGAATCGACACT
66 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
34759 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCG
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCG
34824 ACACTTGTAATATATCCGATATCTCTTTACCGGTTTTGTCTTTTCCTGACCGGTTTTGTCATATT
196 ACACTTGTAATATATCCGATATCTCTTTACC-GTTTTGTCTTTTCC-GACCGGTTTTGTCATATT
* *
34889 TTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTATAGGCGTTAA
259 TTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTATAGGCGCTAA
* *
34954 AATTGCTTCTCCTTTAAATTCACAATGTGTCGGTACTTA
324 AACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * *
34993 TATTAAAGTATCGACACTTACAATATATCCA-GTATCTCTTTACCGGTTTTGTCTTTTCCTGACC
1 TATTAAAGTATCGACACTTGCAATATAT-CAGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACC
* * *
35057 GGTTTTGTCATATTTTTACCTATTATATCGTTGTGGATTGATACATATTTATAAAGAATCGACAC
65 GGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
35122 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATC
130 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATC
*
35187 GACACTTGCAATATATCC-AGTATCTCTTTA--------------CC-A---GTTTTGTCATATT
195 GACACTTGTAATATATCCGA-TATCTCTTTACCGTTTTGTCTTTTCCGACCGGTTTTGTCATATT
*
35233 TTTACATGTTATATCGTTGTGAATCGATACATATTTATAAAGAATCGACACTTTATAGGCGCTAA
259 TTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTATAGGCGCTAA
* *
35298 AACTGCTTCTCCTTTAAATTCACTATATGTCGATACTTA
324 AACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * *
35337 TATTAAAGTATCGACACGTGCAATATATCCGGTAGCGCTTTACTGGTTTTGTCTTTTCGTGACCG
1 TATTAAAGTATCGACACTTGCAATATATCAGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACCG
* * * * *
35402 GTTTTATCATATTTTTTTCCTGTTATATTGATGTGGATCGATACATTTTTATAAAGTATCGACA
66 GTTTTATCATA-TTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACA
35466 TAAACCGACA
Statistics
Matches: 768, Mismatches: 63, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
343 1 0.00
344 176 0.23
345 45 0.06
347 1 0.00
349 2 0.00
363 1 0.00
364 539 0.70
365 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (362 bp):
TATTAAAGTATCGACACTTGCAATATATCAGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACCG
GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCG
ACACTTGTAATATATCCGATATCTCTTTACCGTTTTGTCTTTTCCGACCGGTTTTGTCATATTTT
TACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTATAGGCGCTAAAA
CTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
Found at i:35236 original size:162 final size:162
Alignment explanation
Indices: 35058--35389 Score: 556
Period size: 162 Copynumber: 2.0 Consensus size: 162
35048 TTCCTGACCG
* * *
35058 GTTTTGTCATATTTTTACCTATTATATCGTTGTGGATTGATACATATTTATAAAGAATCGACACT
1 GTTTTGTCATATTTTTACATATTATATCGTTGTGAATCGATACATATTTATAAAGAATCGACACT
*
35123 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCG
66 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATATGTCGATACTTATATTAAAGTATCG
* * *
35188 ACACTTGCAATATATCCAGTATCTCTTTACCA
131 ACACGTGCAATATATCCAGTAGCGCTTTACCA
*
35220 GTTTTGTCATATTTTTACATGTTATATCGTTGTGAATCGATACATATTTATAAAGAATCGACACT
1 GTTTTGTCATATTTTTACATATTATATCGTTGTGAATCGATACATATTTATAAAGAATCGACACT
*
35285 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACTATATGTCGATACTTATATTAAAGTATCG
66 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATATGTCGATACTTATATTAAAGTATCG
* **
35350 ACACGTGCAATATATCCGGTAGCGCTTTACTG
131 ACACGTGCAATATATCCAGTAGCGCTTTACCA
35382 GTTTTGTC
1 GTTTTGTC
35390 TTTTCGTGAC
Statistics
Matches: 158, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 158 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (162 bp):
GTTTTGTCATATTTTTACATATTATATCGTTGTGAATCGATACATATTTATAAAGAATCGACACT
TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATATGTCGATACTTATATTAAAGTATCG
ACACGTGCAATATATCCAGTAGCGCTTTACCA
Found at i:38747 original size:20 final size:20
Alignment explanation
Indices: 38722--38773 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
38712 AACGCGATCC
38722 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
38742 CTAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
38762 CCAAAATCGCAA
1 CCAGAATCGCAA
38774 CGCGATTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.23
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:38854 original size:20 final size:20
Alignment explanation
Indices: 38829--39022 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
38819 GATTTTCCAT
* *
38829 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
38849 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
38869 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
38889 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
38909 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
38929 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
38949 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
38969 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
38990 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
39010 AATCGCAACGCGA
1 AATCGCAACGCGA
39023 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:38874 original size:40 final size:39
Alignment explanation
Indices: 38825--39022 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
38815 TTGCGATTTT
* ** *
38825 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
38863 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
38904 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
38944 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
38983 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
39023 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:38912 original size:60 final size:60
Alignment explanation
Indices: 38829--39021 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
38819 GATTTTCCAT
* ** * *
38829 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
38889 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
38949 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
39010 AATCGCAACGCG
1 AATCGCAACGCG
39022 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:39441 original size:33 final size:33
Alignment explanation
Indices: 39402--39472 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
39392 TTCACTTAGA
*
39402 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
39435 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
39468 TTTCA
1 TTTCA
39473 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:39612 original size:14 final size:14
Alignment explanation
Indices: 39593--39647 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
39583 AGAATGACTG
39593 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
39607 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
39626 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
39640 TCGCAACG
1 TCGCAACG
39648 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:39630 original size:33 final size:33
Alignment explanation
Indices: 39593--39663 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
39583 AGAATGACTG
**
39593 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
39626 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
39659 TCGCA
1 TCGCA
39664 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:39681 original size:19 final size:19
Alignment explanation
Indices: 39659--39756 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
39649 GAAACCAAAA
*
39659 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39678 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
39692 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39711 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
39725 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
39744 TCGCGTTGCGATT
1 TCGCGTTGCGATT
39757 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:39700 original size:14 final size:14
Alignment explanation
Indices: 39681--39770 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
39671 TTTCATTTCG
39681 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
39695 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
39714 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
39728 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
39745 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
39761 CGTTGCGATT
1 CGTTGCGATT
39771 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:39706 original size:33 final size:33
Alignment explanation
Indices: 39664--39778 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
39654 CAAAATCGCA
39664 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
39697 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
39730 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
39763 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
39779 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:41872 original size:178 final size:180
Alignment explanation
Indices: 41472--42027 Score: 976
Period size: 178 Copynumber: 3.0 Consensus size: 180
41462 TAGATTGCTT
*
41472 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41537 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTG----TT-GTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
41602 GTGTATTCTTTAACACTGTG-AA-ATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
126 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
41655 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41720 TTTGTCTTTGTTTTG-T-TTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA
66 TTTGTCTTTGTTTTGTTGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA
41783 TTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
41833 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41898 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTG----TT-GTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
41963 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
126 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
42019 AGTAAATTT
1 AGTAAATTT
42028 ATCCATTCAA
Statistics
Matches: 362, Mismatches: 1, Indels: 17
0.95 0.00 0.04
Matches are distributed among these distances:
176 62 0.17
177 2 0.01
178 112 0.31
183 80 0.22
185 67 0.19
186 39 0.11
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (180 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTTGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA
TTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:41962 original size:93 final size:93
Alignment explanation
Indices: 41472--42027 Score: 1026
Period size: 93 Copynumber: 6.1 Consensus size: 93
41462 TAGATTGCTT
*
41472 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41537 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41565 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41627 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41655 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41720 TTTGTCTTTGTTTTG-----T--TTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41741 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41805 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41833 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41898 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41926 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41991 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
42019 AGTAAATTT
1 AGTAAATTT
42028 ATCCATTCAA
Statistics
Matches: 451, Mismatches: 1, Indels: 22
0.95 0.00 0.05
Matches are distributed among these distances:
85 17 0.04
86 67 0.15
88 1 0.00
90 88 0.20
91 3 0.01
92 70 0.16
93 205 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:42111 original size:19 final size:19
Alignment explanation
Indices: 42071--42199 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
42061 TAGTTTACTT
* *
42071 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
42091 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
42110 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
42129 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
42143 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
42162 TCGCAA--CG--A-CAATA
1 TCGCAACGCGAAACCAAAA
42176 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
42195 TCGCA
1 TCGCA
42200 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:42150 original size:33 final size:32
Alignment explanation
Indices: 42107--42199 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
42097 CGCGAAACCA
**
42107 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
42139 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
42172 AATATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
42200 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:42197 original size:52 final size:52
Alignment explanation
Indices: 42071--42199 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
42061 TAGTTTACTT
**
42071 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
42123 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AATA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
42176 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
42200 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:42217 original size:19 final size:19
Alignment explanation
Indices: 42195--42329 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
42185 GAAACCAAAA
*
42195 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42214 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
42230 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
** *
42247 TCGTATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
42263 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
42280 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
42299 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
42319 TCGTGTTGCGA
1 TCGCGTTGCGA
42330 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 14 0.15
16 11 0.12
17 11 0.12
19 45 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:42236 original size:14 final size:14
Alignment explanation
Indices: 42217--42273 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
42207 TTTCATTTCG
42217 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
42231 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
42248 CGTATTGCGATTCTGT
1 CG--TTGCGATTCTTT
42264 CGTTGCGATT
1 CGTTGCGATT
42274 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:42242 original size:33 final size:33
Alignment explanation
Indices: 42200--42292 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
42190 CAAAATCGCA
*
42200 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
42233 TTGCGATTTTCATTTCGTATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
42266 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
42293 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:44274 original size:14 final size:14
Alignment explanation
Indices: 44255--44290 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
44245 ATTGTTTAAT
44255 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
44269 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
44283 TGATTTGT
1 TGATTTGT
44291 GTAATTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:44413 original size:19 final size:19
Alignment explanation
Indices: 44397--44498 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
44387 AAAAATGACT
44397 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
44416 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
44435 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
44449 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
44468 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
44488 ATCGCAATGCG
1 ATCGCAATGCG
44499 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:44547 original size:33 final size:33
Alignment explanation
Indices: 44505--44833 Score: 217
Period size: 33 Copynumber: 9.5 Consensus size: 33
44495 TGCGTTTATA
44505 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
44538 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
44574 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
44609 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* * *
44647 ATTTCGCATTGCGATTCTGTCGTTGCAATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
44680 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
44720 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
44751 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
44784 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
44818 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
44834 GTATTTTCCG
Statistics
Matches: 250, Mismatches: 23, Indels: 46
0.78 0.07 0.14
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 99 0.40
34 29 0.12
35 19 0.08
36 19 0.08
37 2 0.01
38 56 0.22
39 3 0.01
40 9 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:44551 original size:19 final size:19
Alignment explanation
Indices: 44527--44833 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
44517 GATTATCTCG
44527 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44546 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44565 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
44579 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44598 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44617 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44636 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44655 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
*
44669 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44688 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44707 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
44721 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44740 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44759 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
44773 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
44793 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
44807 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
44826 TTGCGATT
1 TTGCGATT
44834 GTATTTTCCG
Statistics
Matches: 250, Mismatches: 12, Indels: 52
0.80 0.04 0.17
Matches are distributed among these distances:
14 34 0.14
16 31 0.12
17 27 0.11
18 3 0.01
19 143 0.57
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:44602 original size:71 final size:71
Alignment explanation
Indices: 44527--44766 Score: 364
Period size: 71 Copynumber: 3.4 Consensus size: 71
44517 GATTATCTCG
44527 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
44592 TTCGCA
66 TTCGCA
*
44598 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
*
44661 TTC-TGTCG--
61 TTCATTTCGCA
* *
44669 TTGCAATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
44734 TTCGCA
66 TTCGCA
44740 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
44767 CTCTCGTTGC
Statistics
Matches: 152, Mismatches: 7, Indels: 20
0.85 0.04 0.11
Matches are distributed among these distances:
66 6 0.04
68 7 0.05
69 6 0.04
71 113 0.74
73 6 0.04
74 8 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:44678 original size:142 final size:137
Alignment explanation
Indices: 44489--44833 Score: 507
Period size: 142 Copynumber: 2.5 Consensus size: 137
44479 GAAATGAAAA
*
44489 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGAT
*
44553 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
63 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
*
44618 TGCGATTTTCATT
128 TGCGA--TTC-TC
*
44631 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCAATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGATT
44696 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
64 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
44761 GCGATTCTC
129 GCGATTCTC
* * *
44770 TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTAATTT-CGCATTGCGATTTTC--GTTGCGATTTTCATTTCGCATTGCGAT
44833 T
63 T
44834 GTATTTTCCG
Statistics
Matches: 189, Mismatches: 10, Indels: 12
0.90 0.05 0.06
Matches are distributed among these distances:
136 2 0.01
137 15 0.08
138 37 0.20
139 4 0.02
140 3 0.02
142 125 0.66
143 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (137 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCGTTGCGATTTTCATTTCGCATTGCGATTTT
CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTC
Found at i:44772 original size:52 final size:52
Alignment explanation
Indices: 44527--44805 Score: 379
Period size: 52 Copynumber: 5.2 Consensus size: 52
44517 GATTATCTCG
*
44527 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
44579 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
44636 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
44688 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
44740 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
44793 TTGCGATTTTCAT
1 TTGCGATTTTCAT
44806 GTTGGGATTT
Statistics
Matches: 215, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
52 159 0.74
53 17 0.08
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:47131 original size:12 final size:12
Alignment explanation
Indices: 47114--47138 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47104 TCTTCGGGGA
47114 CTTTTTCTTCTT
1 CTTTTTCTTCTT
47126 CTTTTTCTTCTT
1 CTTTTTCTTCTT
47138 C
1 C
47139 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:47347 original size:24 final size:24
Alignment explanation
Indices: 47313--47359 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47303 CTGAAACATC
47313 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
47337 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
47360 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:48070 original size:20 final size:20
Alignment explanation
Indices: 48042--48410 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
48032 AAATTTAAGT
* * * *
48042 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
48062 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
48082 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
48102 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
48122 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
48142 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
48162 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
48182 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
48202 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
48222 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
48242 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
48262 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
48282 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
48302 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
48322 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
48342 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
48362 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
48382 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
48402 GTTGCGATT
1 GTTGCGATT
48411 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:51538 original size:24 final size:24
Alignment explanation
Indices: 51494--51539 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
51484 TTAAAATTTT
*
51494 ATTTATACTCATCATAAATAAAAA
1 ATTTATACTCATAATAAATAAAAA
*
51518 ATTTATA-TCAATAATATATAAA
1 ATTTATACTC-ATAATAAATAAA
51540 TATATACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (24 bp):
ATTTATACTCATAATAAATAAAAA
Found at i:58024 original size:21 final size:21
Alignment explanation
Indices: 57998--58042 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57988 GATTTCTGGG
* *
57998 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAAACGATACCCATT
*
58019 CAAGGGGAAACGATACCCCTT
1 CAAGGGGAAACGATACCCATT
58040 CAA
1 CAA
58043 ATGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAAACGATACCCATT
Found at i:58605 original size:2 final size:2
Alignment explanation
Indices: 58598--58644 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
58588 CATGAGTTAG
58598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58640 AT AT A
1 AT AT A
58645 GGAATTGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59332 original size:31 final size:31
Alignment explanation
Indices: 59294--59371 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
59284 AGAGTCGAGG
*
59294 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
59325 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
* *
59356 GTTTACCGAGGATCTT
1 GTTTACCTAGGTTCTT
59372 TATGACCTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:59379 original size:31 final size:31
Alignment explanation
Indices: 59317--59419 Score: 118
Period size: 31 Copynumber: 3.4 Consensus size: 31
59307 TTTCGAGACA
* * ***
59317 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAGTTTACCGAGGATCTTTATGACC
59348 TATGGACAGTTTACCGAGGATCTTTATGACC
1 TATGGACAGTTTACCGAGGATCTTTATGACC
* *
59379 TCTGGATAG-TTACCGAGGATCTTTATGACC
1 TATGGACAGTTTACCGAGGATCTTTATGACC
* *
59409 TCTGGATAGTT
1 TATGGACAGTT
59420 AACGGGGTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
30 30 0.47
31 34 0.53
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGATCTTTATGACC
Found at i:59393 original size:30 final size:30
Alignment explanation
Indices: 59344--59446 Score: 145
Period size: 30 Copynumber: 3.4 Consensus size: 30
59334 GGTTCTTCGG
* *
59344 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGATAG-TTACCGAGGATCTTTAT
59375 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* * *
59405 GACCTCTGGATAGTTAACG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
59434 GACCTCTGGATAG
1 GACCTCTGGATAG
59447 GTCCTTCGGG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
29 21 0.31
30 35 0.52
31 11 0.16
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:66984 original size:21 final size:21
Alignment explanation
Indices: 66958--66997 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
66948 CCCCCTTTGA
*
66958 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
66979 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
66998 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Done.