Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012322.1 Kokia drynarioides strain JFW-HI SEQ_127324, 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: 238935
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:25 original size:16 final size:15
Alignment explanation
Indices: 4--47 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1 AAA
*
4 AAAAGAGAGAGAAAAT
1 AAAAGAGA-AGAAAAG
*
20 AAAAGAAAAGAAAAAG
1 AAAAGAGAAG-AAAAG
36 AAAAGAGAAGAA
1 AAAAGAGAAGAA
48 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (15 bp):
AAAAGAGAAGAAAAG
Found at i:36 original size:6 final size:6
Alignment explanation
Indices: 20--60 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
10 GAGAGAAAAT
*
20 AAAAG- AAAAGA AAAAGA AAAGAGA AGAAGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAA-AGA AAAAGA AAAAGA AAAAG
61 GAGAGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
5 5 0.16
6 22 0.69
7 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:51 original size:19 final size:18
Alignment explanation
Indices: 23--58 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
13 AGAAAATAAA
23 AGAAAAGAAAAAGAAAAG
1 AGAAAAGAAAAAGAAAAG
41 AGAAGAAGAAAAAGAAAA
1 AGAA-AAGAAAAAGAAAA
59 AGGAGAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AGAAAAGAAAAAGAAAAG
Found at i:1070 original size:49 final size:48
Alignment explanation
Indices: 915--1080 Score: 135
Period size: 49 Copynumber: 3.4 Consensus size: 48
905 ATAGAAGCCG
* *
915 CAACGGTGAACCTTGTACCATAG-GAATGTGAA-GGAAGAGATTAAAGCTA
1 CAACGGTGAACCTTATACCATAGAG-ATGTGAAGGGAA-AGATTGAAG-TA
* * * * *
964 CAA-TGTCGAATCTTATACCTTGGAGATGT-AATGGGAAAGGTTGAAGTCA
1 CAACGGT-GAACCTTATACCATAGAGATGTGAA-GGGAAAGATTGAAGT-A
*
1013 TAACGGTGAACCTTATAACC-TAGAGATGTGAAGGGAAAGATTGAAGTA
1 CAACGGTGAACCTTAT-ACCATAGAGATGTGAAGGGAAAGATTGAAGTA
* *
1061 GCAATGGTGAATCTTATACC
1 -CAACGGTGAACCTTATACC
1081 TTGAAGATGT
Statistics
Matches: 93, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
48 9 0.10
49 72 0.77
50 12 0.13
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (48 bp):
CAACGGTGAACCTTATACCATAGAGATGTGAAGGGAAAGATTGAAGTA
Found at i:1089 original size:49 final size:47
Alignment explanation
Indices: 940--1090 Score: 146
Period size: 49 Copynumber: 3.1 Consensus size: 47
930 TACCATAGGA
*
940 ATGTGAA-GGAAGAGATTAAAGCTACAAT-GTCGAATCTTATACCTTGGAG
1 ATGTGAAGGGAA-AGATTGAAG-TACAATGGT-GAATCTTATACCTT-GAG
* * * * *
989 ATGT-AATGGGAAAGGTTGAAGTCATAACGGTGAACCTTATAACCTAGAG
1 ATGTGAA-GGGAAAGATTGAAGT-ACAATGGTGAATCTTAT-ACCTTGAG
1038 ATGTGAAGGGAAAGATTGAAGTAGCAATGGTGAATCTTATACCTTGAAG
1 ATGTGAAGGGAAAGATTGAAGTA-CAATGGTGAATCTTATACCTTG-AG
1087 ATGT
1 ATGT
1091 AGAGAAGCAG
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
48 9 0.11
49 62 0.75
50 12 0.14
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (47 bp):
ATGTGAAGGGAAAGATTGAAGTACAATGGTGAATCTTATACCTTGAG
Found at i:1109 original size:98 final size:98
Alignment explanation
Indices: 916--1109 Score: 222
Period size: 98 Copynumber: 2.0 Consensus size: 98
906 TAGAAGCCGC
*
916 AACGGTGAACCTTGTACCATAGGAATGTGAAGGAAGAGATTAAAGCTACAATGTCGAATCTTATA
1 AACGGTGAACCTTATACCATAGGAATGTGAAGGAAGAGATTAAAGCTACAATGTCGAATCTTATA
* * * *
981 CCTTGGAGATGTAATGGGAAAGGTTGAAGTCAT
66 CCTTGAAGATGTAATGAGAAAGATTAAAGTCAT
*
1014 AACGGTGAACCTTATAACC-TA-GAGATGTGAAGGGAA-AGATTGAAG-TAGCAATGGT-GAATC
1 AACGGTGAACCTTAT-ACCATAGGA-ATGTGAA-GGAAGAGATTAAAGCTA-CAAT-GTCGAATC
1074 TTATACCTTGAAGATGT-A-GAGAAGCAGATTAAAGTC
61 TTATACCTTGAAGATGTAATGAGAA--AGATTAAAGTC
1110 GCAAAAGTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
96 4 0.05
97 5 0.06
98 65 0.78
99 9 0.11
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (98 bp):
AACGGTGAACCTTATACCATAGGAATGTGAAGGAAGAGATTAAAGCTACAATGTCGAATCTTATA
CCTTGAAGATGTAATGAGAAAGATTAAAGTCAT
Found at i:1421 original size:45 final size:45
Alignment explanation
Indices: 1367--1909 Score: 485
Period size: 45 Copynumber: 12.3 Consensus size: 45
1357 CCTTAACCAT
*
1367 GGGGTAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* * * * * * * *
1412 GGGGCAGATTGAAGTCACCGTCCAATATTTTACCCTTAATCCATA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* *
1457 GAGGCA-AGTTGAAGCCAT--TCCAATCTTTTACCCCTAATCAAGA
1 GGGGCAGA-TTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* * * *
1500 GGGGTAGATTGAAG--A-CTTCCAATCTTTTACCTCTAGTCATGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* *
1542 GGGGCAGATTGAAGCCATCTTCCAATCTTTTA-CCTTAGTCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* * * * *
1586 GGGGCAGATTGAAGTCAGT-GTCTAACCTTTTACCCCTAATCTAA-A
1 GGGGCAGATTGAAGCCA-TCATCCAATCTTTTACCCCTAGTC-AAGA
* *
1631 GGGGCA-AGTTGAAGCCAT--TCCAAACTTTTACTCCTAGTCAAGA
1 GGGGCAGA-TTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
** * * *
1674 GGGGCAGATTGAAGTTA-CTGTCCAATCTTTTACCCCTAATC--CA
1 GGGGCAGATTGAAGCCATC-ATCCAATCTTTTACCCCTAGTCAAGA
*
1717 --GGTAGATTGAAGCCATCATCCAATCTTTTA-CCCTAAAGTCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCT--AGTCAAGA
** * * *
1761 GTAGCAGATTAAAGCCATCATCCAATCTTTTACCCCAAAGTCAAGT
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCC-TAGTCAAGA
* * * *
1807 GGGGTAGATTTAAGCCATCATTCAATCTTTTACCCCTA-ACAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* * *
1851 GGGGAAAATTGAAGCAATCATCCAATCTTTTACCCCTAAGTCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCT-AGTCAAGA
*
1897 GGGGTAGATTGAA
1 GGGGCAGATTGAA
1910 CCTATTATCA
Statistics
Matches: 402, Mismatches: 69, Indels: 53
0.77 0.13 0.10
Matches are distributed among these distances:
40 4 0.01
41 25 0.06
42 41 0.10
43 63 0.16
44 78 0.19
45 105 0.26
46 83 0.21
47 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (45 bp):
GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
Found at i:1498 original size:88 final size:88
Alignment explanation
Indices: 1375--1889 Score: 441
Period size: 88 Copynumber: 5.8 Consensus size: 88
1365 ATGGGGTAGA
*
1375 TTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTCACCGTCCAATAT
1 TTGAAGCCAT--TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTCACCGTCCAATCT
* *
1440 TTTACCCTTAATCCATAGAGGCAAG
64 TTTACCCCTAATCCATAGGGGCAAG
* * *
1465 TTGAAGCCATTCCAATCTTTTACCCCTAATCAAGAGGGGTAGATTGAAG--A-CTTCCAATCTTT
1 TTGAAGCCATTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTCACCGTCCAATCTTT
* *
1527 TACCTCTAGT-CATGAGGGGC-AG
66 TACCCCTAATCCAT-AGGGGCAAG
* ** * *
1549 ATTGAAGCCATCTTCCAATCTTTTA-CCTTAGTCAAGAGGGGCAGATTGAAGTCAGTGTCTAACC
1 -TTGAAGCCA--TTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTCACCGTCCAATC
* *
1613 TTTTACCCCTAATCTAAAGGGGCAAG
63 TTTTACCCCTAATCCATAGGGGCAAG
* * * *
1639 TTGAAGCCATTCCAAACTTTTACTCCTAGTCAAGAGGGGCAGATTGAAGTTACTGTCCAATCTTT
1 TTGAAGCCATTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTCACCGTCCAATCTTT
*
1704 TACCCCTAATCC--A--GG-TAG
66 TACCCCTAATCCATAGGGGCAAG
** * * * *
1722 ATTGAAGCCATCATCCAATCTTTTA-CCCTAAAGTCAAGAGTAGCAGATTAAAGCCATCATCCAA
1 -TTGAAGCCAT--TCCAATCTTTTACCCCT--AGTCAAGAGGGGCAGATTGAAGTCACCGTCCAA
* **
1786 TCTTTTACCCCAAAGT-CA-AGTGGGGTAG
61 TCTTTTACCCCTAA-TCCATAG-GGGCAAG
* * * * * * *
1814 ATTTAAGCCATCATTCAATCTTTTACCCCTA-ACAAGAGGGGAAAATTGAAG-CAATCATCCAAT
1 -TTGAAGCCAT--TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTC-ACCGTCCAAT
1877 CTTTTACCCCTAA
62 CTTTTACCCCTAA
1890 GTCAAGAGGG
Statistics
Matches: 354, Mismatches: 48, Indels: 46
0.79 0.11 0.10
Matches are distributed among these distances:
83 2 0.01
84 17 0.05
85 34 0.10
86 36 0.10
87 64 0.18
88 87 0.25
89 32 0.09
90 49 0.14
91 3 0.01
92 26 0.07
93 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (88 bp):
TTGAAGCCATTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTCACCGTCCAATCTTT
TACCCCTAATCCATAGGGGCAAG
Found at i:1639 original size:174 final size:173
Alignment explanation
Indices: 1367--1909 Score: 587
Period size: 174 Copynumber: 3.1 Consensus size: 173
1357 CCTTAACCAT
* *
1367 GGGGTAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTCACCG
1 GGGGTAGATTGAAGCCATCATCCAATCTTTTACCCTTAGTCAAGAGGGGCAGATTGAAGTCA-TG
* * * *
1432 TCCAATATTTTACCCTTAATCCATAGAGGCAAGTTGAAGCCATTCCAATCTTTTACCCCTAATCA
65 TCCAATCTTTTACCCCTAAT-CAAAGGGGCAAGTTGAAGCCATTCCAATCTTTTACCCCTAATCA
* *
1497 AGAGGGGTAGATTGAAG-ACTTCCAATCTTTTACCTCTAGTCATGA
129 AGAGGGGAAGATTGAAGTACTTCCAATCTTTTACCCCTAGTCA-GA
* *
1542 GGGGCAGATTGAAGCCATCTTCCAATCTTTTA-CCTTAGTCAAGAGGGGCAGATTGAAGTCAGTG
1 GGGGTAGATTGAAGCCATCATCCAATCTTTTACCCTTAGTCAAGAGGGGCAGATTGAAGTCA-TG
* * * * *
1606 TCTAACCTTTTACCCCTAATCTAAAGGGGCAAGTTGAAGCCATTCCAAACTTTTACTCCTAGTCA
65 TCCAATCTTTTACCCCTAATC-AAAGGGGCAAGTTGAAGCCATTCCAATCTTTTACCCCTAATCA
* * *
1671 AGAGGGGCAGATTGAAGTTACTGTCCAATCTTTTACCCCTAATC-CA
129 AGAGGGGAAGATTGAAG-TACT-TCCAATCTTTTACCCCTAGTCAGA
* ** * *
1717 --GGTAGATTGAAGCCATCATCCAATCTTTTACCCTAAAGTCAAGAGTAGCAGATTAAAGCCATC
1 GGGGTAGATTGAAGCCATCATCCAATCTTTTACCCT-TAGTCAAGAGGGGCAGATTGAAGTCAT-
* * ** * *
1780 ATCCAATCTTTTACCCCAAAGTC-AAGTGGGGTAGATTTAAGCCATCATTCAATCTTTTACCCCT
64 GTCCAATCTTTTACCCCTAA-TCAAAG-GGGCAAG-TTGAAGCCAT--TCCAATCTTTTACCCCT
* * *
1844 AA-CAAGAGGGGAAAATTGAAGCAATCATCCAATCTTTTACCCCTAAGTCAAGA
124 AATCAAGAGGGGAAGATTGAAG-TA-CTTCCAATCTTTTACCCCT-AGTC-AGA
1897 GGGGTAGATTGAA
1 GGGGTAGATTGAA
1910 CCTATTATCA
Statistics
Matches: 307, Mismatches: 43, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
173 29 0.09
174 106 0.35
175 73 0.24
176 14 0.05
177 54 0.18
178 19 0.06
180 1 0.00
182 11 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (173 bp):
GGGGTAGATTGAAGCCATCATCCAATCTTTTACCCTTAGTCAAGAGGGGCAGATTGAAGTCATGT
CCAATCTTTTACCCCTAATCAAAGGGGCAAGTTGAAGCCATTCCAATCTTTTACCCCTAATCAAG
AGGGGAAGATTGAAGTACTTCCAATCTTTTACCCCTAGTCAGA
Found at i:1787 original size:46 final size:46
Alignment explanation
Indices: 1367--1909 Score: 460
Period size: 46 Copynumber: 12.3 Consensus size: 46
1357 CCTTAACCAT
*
1367 GGGGTAGATTGAAGCCATCATCCAATCTTTTACCCCT-AGTCAAGA
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
* * * * * *
1412 GGGGCAGATTGAAGTCACCGTCCAATATTTTACCCTTAA-TCCATAGA
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGT-CA-AGA
*
1459 -GGCAAG-TTGAAGCCAT--TCCAATCTTTTACCCCTAA-TCAAGA
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
* * * *
1500 GGGGTAGATTGAAG--A-CTTCCAATCTTTTACCTCT-AGTCATGA
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
* * *
1542 GGGGCAGATTGAAGCCATCTTCCAATCTTTTA--CCTTAGTCAAGA
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
* * * * *
1586 GGGGCAGATTGAAGTCAGT-GTCTAACCTTTTACCCCTAA-TCTAA-A
1 GGGGAAGATTGAAGCCA-TCATCCAATCTTTTACCCCTAAGTC-AAGA
* *
1631 GGGGCAAG-TTGAAGCCAT--TCCAAACTTTTACTCCT-AGTCAAGA
1 GGGG-AAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
* ** * *
1674 GGGGCAGATTGAAGTTA-CTGTCCAATCTTTTACCCCTAA-TC--CA
1 GGGGAAGATTGAAGCCATC-ATCCAATCTTTTACCCCTAAGTCAAGA
*
1717 --GGTAGATTGAAGCCATCATCCAATCTTTTA-CCCTAAAGTCAAGA
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCT-AAGTCAAGA
** * * * *
1761 GTAGCAGATTAAAGCCATCATCCAATCTTTTACCCCAAAGTCAAGT
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
* * *
1807 GGGGTAGATTTAAGCCATCATTCAATCTTTTACCCCTAA--CAAGA
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
* *
1851 GGGGAAAATTGAAGCAATCATCCAATCTTTTACCCCTAAGTCAAGA
1 GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
*
1897 GGGGTAGATTGAA
1 GGGGAAGATTGAA
1910 CCTATTATCA
Statistics
Matches: 405, Mismatches: 59, Indels: 67
0.76 0.11 0.13
Matches are distributed among these distances:
40 4 0.01
41 31 0.08
42 48 0.12
43 55 0.14
44 74 0.18
45 87 0.21
46 100 0.25
47 6 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (46 bp):
GGGGAAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGA
Found at i:2207 original size:160 final size:161
Alignment explanation
Indices: 2022--2460 Score: 548
Period size: 158 Copynumber: 2.8 Consensus size: 161
2012 GATCACAATG
* *
2022 ATGAAGCGGCCATCTTCCTGATGAGATACTGAGAAGTGGACCAAAACAATAAAGTGAAGCTCAAT
1 ATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATAAAGTGAAGCTCAAT
* * * **
2087 GTGAGTGAAAATTTAAACCCCTAT-TTCCTGATAAGATATAAAGAAGTGGGCCAAATCCGTCATC
66 GTGAGTGAAAATTCAAACCCCCATCTTCCTAATAAGATATAAAGAAGTGGGCCAAATCCACCATC
2151 CTAATAAGATACAGAGAAGTGGATTAAATCA
131 CTAATAAGATACAGAGAAGTGGATTAAATCA
* * * * *
2182 ATGAAGCAGTCATCTTCTTGATGAGATACAGAGAAGTGAACCAAAACAATGAAGTGAATC-CTAA
1 ATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATAAAGTGAAGCTC-AA
** * * * *
2246 TGTGAGTGAAACGTCAAACCCCCATCTTTCTAATAAG--ATACA-AAGTGGACCAAATCCACCTT
65 TGTGAGTGAAAATTCAAACCCCCATCTTCCTAATAAGATATAAAGAAGTGGGCCAAATCCACCAT
* * *
2308 CCTGATGAGATACAGAGAAGTGGATTAAATTA
130 CCTAATAAGATACAGAGAAGTGGATTAAATCA
* * * * **
2340 ATGAAGCGGTCATCTTCCTAACGAGATACAGAGAAGTAGACCAAATCAATAAAGCAAAGCTCAAT
1 ATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATAAAGTGAAGCTCAAT
* * *
2405 GTGAGT-AAAACTTCAAACCCCCATCTTCCTAATGAGATATAGAGAAGTGGGTCAAA
66 GTGAGTGAAAA-TTCAAACCCCCATCTTCCTAATAAGATATAAAGAAGTGGGCCAAA
2461 GCAATAAAGT
Statistics
Matches: 233, Mismatches: 39, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
157 3 0.01
158 125 0.54
159 6 0.03
160 80 0.34
161 19 0.08
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.23
Consensus pattern (161 bp):
ATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATAAAGTGAAGCTCAAT
GTGAGTGAAAATTCAAACCCCCATCTTCCTAATAAGATATAAAGAAGTGGGCCAAATCCACCATC
CTAATAAGATACAGAGAAGTGGATTAAATCA
Found at i:2554 original size:209 final size:209
Alignment explanation
Indices: 2288--3891 Score: 2085
Period size: 209 Copynumber: 7.7 Consensus size: 209
2278 ATAAGATACA
** *
2288 AAGTGGACCAAATCCACCTTCCTGATGAGATACAGAGAAGTGGATTAAATTAATGAAGCGGTCAT
1 AAGTGGACCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
* * * *
2353 CTTCCTAACGAGATACAGAGAAGTAGACCAAATCAATAAAGCAAAGCTCAATGTGAGTAAAACTT
66 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTT
* * *
2418 CAAACCCCCATCTTCCTAATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTAGTCATCTTTCT
131 CAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCT
2483 GATGAGATACAGAG
196 GATGAGATACAGAG
* * * * *
2497 AAGTGGACCAAATCTGCCTTCGTGATGAGATATAGAGAAGTGGAATAGATCAATGAAGCGATCAT
1 AAGTGGACCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
* *
2562 CTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATTTGAGTGAAACTT
66 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTT
* * * * * *
2627 CAAACCCCTAACTTCCTGATGAGATACAAAGAACTGGGTCAAAGCAATAAAGTGATCATCTTCCT
131 CAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCT
* * *
2692 AATGAGACACATAG
196 GATGAGATACAGAG
* * * * *
2706 AAGTGGACAAAATCTACCTTCTTGATGAGATACAGAGAAGTGGATTAAATCAATTAAGCGGTCAA
1 AAGTGGACCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
* * *
2771 CTTCTTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGTAAAGCTCAATGTGAGTGAAACTT
66 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTT
* * * *
2836 CAAACCCCTATCTTCTTGATGAGATACAGAGAAGTTGGTCAAAGCAATAAAGTGGTCATCTTCCT
131 CAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCT
* *
2901 GATGAGATATAAAG
196 GATGAGATACAGAG
* * * *
2915 AAGTGGACCAAATATGCCTTCCCGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATCAT
1 AAGTGGACCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
*
2980 CTTCCTGATGAGATACAGAGAAGTAGACCAAATTAATGAAGCAAAGCTCAATAG-GAGTGAAACT
66 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAAT-GTGAGTGAAACT
* * * * * * * *
3044 TCAAACCCCAATCATCCTAATGAGATATAAAAAAGTGGGTCAATGCAATAAAGCGGTCGTCTTCC
130 TCAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCC
*
3109 GGATGAGATACAGAG
195 TGATGAGATACAGAG
*
3124 AAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
1 AAGTGGACCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
* * * *
3189 CTTCTTGATGAGATACAGAGAAGTAAACCAAATCAAAGAAGCAAAGCTGAATGTGAGTGAAACTT
66 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTT
* *
3254 CAAA---CC--C--CC--AT---ACA-A-AGAAGTGGGTCAAAGCAATAAAGTGATCATCTTCCT
131 CAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCT
* *
3305 AATGAGACACAGAG
196 GATGAGATACAGAG
* * * * * * *
3319 AAGTGGACAAAATCCGCCTTCCTGATAAGATACAAAGAAGTGGATTAAATCAATTAATCGGTCAA
1 AAGTGGACCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
* * *
3384 CTTCTTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATGTGAGTGAAACTT
66 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTT
* *
3449 CAAACCCCCATCTTCTTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCT
131 CAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCT
3514 GATGAGATACAGAG
196 GATGAGATACAGAG
** * * * * ** *
3528 ATCTGGACCAAATCGGCCTTCTTGATGAGATACAAAGAAGTGGATTAAATCAATGAAACAATTAT
1 AAGTGGACCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
* *
3593 CTTCTTGATAAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTT
66 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTT
* * * * * *
3658 CAAACCCCCATCTTCCTTATGAGATA-CGAAGGAGTGAGTCAAAGCAATAAAGCGGTCATCTTCT
131 CAAACCCCCATCTTCCTGATGAGATATAG-AGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCC
3722 TGATGAGATACAGAG
195 TGATGAGATACAGAG
* * * * * * *
3737 AAGTGGGCCAAAT-TCGTCC-TCTTAATGAGATACAGAGAAGTAGATCAAAACAATGAAGTGGTC
1 AAGTGGACCAAATCT-G-CCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTC
* * * * ** *
3800 ATCTTCCTGATGAGATACAGAGAAGCAGACCAAGTAAATGACGTGAAGCTCAATGTGAGAGAAAC
64 ATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAAC
3865 TTCAAA-CCCCATCTTCCTGATGAGATA
129 TTCAAACCCCCATCTTCCTGATGAGATA
3892 CAAAAACGTG
Statistics
Matches: 1217, Mismatches: 159, Indels: 39
0.86 0.11 0.03
Matches are distributed among these distances:
195 165 0.14
196 1 0.00
197 2 0.00
198 2 0.00
200 3 0.00
202 3 0.00
204 3 0.00
206 1 0.00
207 2 0.00
208 23 0.02
209 1009 0.83
210 3 0.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (209 bp):
AAGTGGACCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCAT
CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTT
CAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCT
GATGAGATACAGAG
Found at i:3002 original size:85 final size:85
Alignment explanation
Indices: 2853--3012 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
2843 CTATCTTCTT
* * * *
2853 GATGAGATACAGAGAAGTTGGTCAAAGCAATAAAGTGGTCATCTTCCTGATGAGATATAAAGAAG
1 GATGAGATACAAAGAAGTTGGTCAAAGCAATAAAGCGATCATCTTCCTGATGAGATACAAAGAAG
*
2918 TGGACCAAATATGCCTTCCC
66 TAGACCAAATATGCCTTCCC
* * * *
2938 GATGAGATACAAAGAAG-TGGATTAAATCAATGAAGCGATCATCTTCCTGATGAGATACAGAGAA
1 GATGAGATACAAAGAAGTTGG-TCAAAGCAATAAAGCGATCATCTTCCTGATGAGATACAAAGAA
3002 GTAGACCAAAT
65 GTAGACCAAAT
3013 TAATGAAGCA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
84 3 0.05
85 62 0.95
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (85 bp):
GATGAGATACAAAGAAGTTGGTCAAAGCAATAAAGCGATCATCTTCCTGATGAGATACAAAGAAG
TAGACCAAATATGCCTTCCC
Found at i:3557 original size:613 final size:614
Alignment explanation
Indices: 2291--3874 Score: 2294
Period size: 613 Copynumber: 2.6 Consensus size: 614
2281 AGATACAAAG
* * * *
2291 TGGACCAAATCCACCTTCCTGATGAGATACAGAGAAGTGGATTAAATTAATGAAGCGGTCATCTT
1 TGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATCATCTT
* * * *
2356 CCTAACGAGATACAGAGAAGTAGACCAAATCAATAAAGCAAAGCTCAATGTGAGTAAAACTTCAA
66 CCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAA
* ** *
2421 ACCCCCATCTTCCTAATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGTAGTCATCTTTCTGAT
131 ACCCCCATCTTCCTAATGAGATATAAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGAT
* * * * *
2486 GAGATACAGAGAAGTGGACCAAATCTGCCTTCGTGATGAGATATAGAGAAGTGGAATAGATCAAT
196 GAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAAT
* * * *
2551 GAAGCGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATTT
261 GAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAAAGAAGCAAAGCTCAATGT
2616 GAGTGAAACTTCAAACCCCTAACTTCCTGATGAGATACAAAGAACTGGGTCAAAGCAATAAAGTG
326 GAGTGAAACTTCAAA--CC---C--CC------GATACAAAGAACTGGGTCAAAGCAATAAAGTG
* * * * *
2681 ATCATCTTCCTAATGAGACACATAGAAGTGGACAAAATCTACCTTCTTGATGAGATACAGAGAAG
378 ATCATCTTCCTAATGAGACACAGAGAAGTGGACAAAATCCACCTTCCTGATAAGATACAAAGAAG
2746 TGGATTAAATCAATTAAGCGGTCAACTTCTTGATGAGATATAGAGAAGTAGACCAAATCAATGAA
443 TGGATTAAATCAATTAAGCGGTCAACTTCTTGATGAGATATAGAGAAGTAGACCAAATCAATGAA
* * *
2811 GTAAAGCTCAATGTGAGTGAAACTTCAAACCCCTATCTTCTTGATGAGATACAGAGAAGTTGGTC
508 GAAAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGGTC
* * *
2876 AAAGCAATAAAGTGGTCATCTTCCTGATGAGATATAAAGAAG
573 AAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAAAGAAC
** *
2918 TGGACCAAATATGCCTTCCCGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATCATCTT
1 TGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATCATCTT
*
2983 CCTGATGAGATACAGAGAAGTAGACCAAATTAATGAAGCAAAGCTCAATAG-GAGTGAAACTTCA
66 CCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAAT-GTGAGTGAAACTTCA
* * * * * *
3047 AACCCCAATCATCCTAATGAGATATAAAAAAGTGGGTCAATGCAATAAAGCGGTCGTCTTCCGGA
130 AACCCCCATCTTCCTAATGAGATATAAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGA
3112 TGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAA
195 TGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAA
* * *
3177 TGAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTAAACCAAATCAAAGAAGCAAAGCTGAATG
260 TGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAAAGAAGCAAAGCTCAATG
*
3242 TGAGTGAAACTTCAAACCCCC-ATACAAAGAAGTGGGTCAAAGCAATAAAGTGATCATCTTCCTA
325 TGAGTGAAACTTCAAACCCCCGATACAAAGAACTGGGTCAAAGCAATAAAGTGATCATCTTCCTA
*
3306 ATGAGACACAGAGAAGTGGACAAAATCCGCCTTCCTGATAAGATACAAAGAAGTGGATTAAATCA
390 ATGAGACACAGAGAAGTGGACAAAATCCACCTTCCTGATAAGATACAAAGAAGTGGATTAAATCA
*
3371 ATTAATCGGTCAACTTCTTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAAT
455 ATTAAGCGGTCAACTTCTTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAAT
*
3436 GTGAGTGAAACTTCAAACCCCCATCTTCTTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAG
520 GTGAGTGAAACTTCAAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAG
* *
3501 CGGTCATCTTCCTGATGAGATACAGAGATC
585 CGGTCATCTTCCTGATGAGATACAAAGAAC
* * * * *
3531 TGGACCAAATCGGCCTTCTTGATGAGATACAAAGAAGTGGATTAAATCAATGAAACAATTATCTT
1 TGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATCATCTT
* *
3596 CTTGATAAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAA
66 CCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAA
* ** * * *
3661 ACCCCCATCTTCCTTATGAGATACGAAGGAGTGAGTCAAAGCAATAAAGCGGTCATCTTCTTGAT
131 ACCCCCATCTTCCTAATGAGATATAAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGAT
* * * * * * *
3726 GAGATACAGAGAAGTGGGCCAAATTCGTCC-TCTTAATGAGATACAGAGAAGTAGATCAAAACAA
196 GAGATACAGAGAAGTGGACCAAATCCG-CCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAA
* * * * **
3790 TGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGCAGACCAAGT-AAATGACGTGAAGCTCAAT
260 TGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAAA-GAAGCAAAGCTCAAT
*
3854 GTGAGAGAAACTTCAAACCCC
324 GTGAGTGAAACTTCAAACCCC
3875 ATCTTCCTGA
Statistics
Matches: 863, Mismatches: 90, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
612 4 0.00
613 547 0.63
614 2 0.00
620 2 0.00
622 1 0.00
625 2 0.00
627 304 0.35
628 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (614 bp):
TGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATCATCTT
CCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAA
ACCCCCATCTTCCTAATGAGATATAAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGAT
GAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAAT
GAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAAAGAAGCAAAGCTCAATGT
GAGTGAAACTTCAAACCCCCGATACAAAGAACTGGGTCAAAGCAATAAAGTGATCATCTTCCTAA
TGAGACACAGAGAAGTGGACAAAATCCACCTTCCTGATAAGATACAAAGAAGTGGATTAAATCAA
TTAAGCGGTCAACTTCTTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATG
TGAGTGAAACTTCAAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGC
GGTCATCTTCCTGATGAGATACAAAGAAC
Found at i:3622 original size:85 final size:85
Alignment explanation
Indices: 3460--3626 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 85
3450 AAACCCCCAT
* * * ** *
3460 CTTCTTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACA
1 CTTCTTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGCAATCATCTTCCTGATAAGATACA
* *
3525 GAGATCTGGACCAAATCGGC
66 GAGAACTAGACCAAATCGGC
* * * *
3545 CTTCTTGATGAGATACAAAGAAGTGGATTAAATCAATGAAA-CAATTATCTTCTTGATAAGATAC
1 CTTCTTGATGAGATACAAAGAAGTGGATCAAAGCAAT-AAAGCAATCATCTTCCTGATAAGATAC
*
3609 AGAGAAGTAGACCAAATC
65 AGAGAACTAGACCAAATC
3627 AATGAAGCAA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
85 65 0.96
86 3 0.04
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (85 bp):
CTTCTTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGCAATCATCTTCCTGATAAGATACA
GAGAACTAGACCAAATCGGC
Found at i:4716 original size:2 final size:2
Alignment explanation
Indices: 4709--4735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4699 TACATTCGTT
4709 TA 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 TA T
4736 TGTTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5524 original size:30 final size:29
Alignment explanation
Indices: 5457--5564 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 29
5447 AAAACCTCAT
**
5457 TTTGACCATCAAACTTTACAAAAATTT-AGA
1 TTTGACCCCCAAACTTT-CAAAAATTTGA-A
*
5487 TTTGACCCTCAAACTTTCAAAATATTTGAA
1 TTTGACCCCCAAACTTTCAAAA-ATTTGAA
* *
5517 TTTGACCCCCGAA-TTATCTAAAAATTTGGA
1 TTTGACCCCCAAACTT-TC-AAAAATTTGAA
*
5547 TTTAACCCCCAAACTTTC
1 TTTGACCCCCAAACTTTC
5565 CTCAAATTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
29 7 0.10
30 53 0.79
31 7 0.10
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (29 bp):
TTTGACCCCCAAACTTTCAAAAATTTGAA
Found at i:5602 original size:30 final size:30
Alignment explanation
Indices: 5476--5611 Score: 100
Period size: 30 Copynumber: 4.5 Consensus size: 30
5466 CAAACTTTAC
* *
5476 AAAAATTTAGATTTGACCCTCAAACTTTC-
1 AAAAATTTAGATTTGACCCTCGAACTTCCT
* *
5505 AAAATATTT-GAATTTGACCCCCGAA-TTATCT
1 AAAA-ATTTAG-ATTTGACCCTCGAACTT-CCT
* * * *
5536 AAAAATTTGGATTTAACCCCCAAACTTTCCT
1 AAAAATTTAGATTTGACCCTCGAAC-TTCCT
* *
5567 -CAAATTTAGATTTGACCCTTGAACTTCCT
1 AAAAATTTAGATTTGACCCTCGAACTTCCT
* *
5596 AAAAATTCAAATTTGA
1 AAAAATTTAGATTTGA
5612 TGCTTGAACA
Statistics
Matches: 85, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
29 12 0.14
30 64 0.75
31 7 0.08
32 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (30 bp):
AAAAATTTAGATTTGACCCTCGAACTTCCT
Found at i:6649 original size:93 final size:92
Alignment explanation
Indices: 6546--6734 Score: 297
Period size: 93 Copynumber: 2.0 Consensus size: 92
6536 AATCTCAAAC
* * *
6546 TCTTGTTAATAATTAATCCAAATTATAAAATTTAATTTATAATTAATATTAAGAATTAGCAAAAC
1 TCTTGATAATAATTAATACAAATTATAAAATTTAATTTATAATTAACATTAAGAATTAGCAAAAC
*
6611 TTTAAAAAATAAGAATTTAAATGAAAAA
66 TTTAAAAAATAAAAATTTAAATG-AAAA
* * *
6639 TCTTGATAATAATTAATATAAATTATAAATTTTAATTTATAATTAACATTAAGAATTATCAAAAC
1 TCTTGATAATAATTAATACAAATTATAAAATTTAATTTATAATTAACATTAAGAATTAGCAAAAC
*
6704 TTTGAAAAATAAAAATTTAAATGAAAA
66 TTTAAAAAATAAAAATTTAAATGAAAA
6731 TCTT
1 TCTT
6735 AATTCAAACT
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 8 0.09
93 80 0.91
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (92 bp):
TCTTGATAATAATTAATACAAATTATAAAATTTAATTTATAATTAACATTAAGAATTAGCAAAAC
TTTAAAAAATAAAAATTTAAATGAAAA
Found at i:6920 original size:19 final size:20
Alignment explanation
Indices: 6898--6945 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
6888 CAAACTCTTG
6898 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
*
6917 ATAA-AATTTAATTTATAATT
1 ATAATAA-TTAATATATAATT
6937 -TAAT-ATTAA
1 ATAATAATTAA
6946 GAATTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:7019 original size:149 final size:147
Alignment explanation
Indices: 6735--7005 Score: 361
Period size: 149 Copynumber: 1.8 Consensus size: 147
6725 TGAAAATCTT
* * * *
6735 AATTCAAACTTTTGATAATAATTAATATAATTTATAAAATTTAATTTATAATTCATATCAAGAGT
1 AATTCAAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATCAAGAAT
* *
6800 TATCAAAATTCAAAAAATAAAAATAACTTTAAATTCAAATGAAAATCTTTATTTAAATTTAAAAA
66 TATCAAAATTCAAAAAAAAAAAATAACTTTAAATTCAAATGAAAAACTTTATTT--ATTTAAAAA
6865 TTTAAAGAAAACAAATATC
129 TTTAAAGAAAACAAATATC
*
6884 AATTCAAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTTAATATTAAGAA
1 AATTCAAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAA-TTAATATCAAGAA
*
6949 TTATCAAAATTTTGAAAAGGTAAAAAAAGATAA-TTTAAA-T-AAAT-AAAAACTTTATTT
65 TTATCAAAA--TTCAAAA---AAAAAAA-ATAACTTTAAATTCAAATGAAAAACTTTATTT
7006 TTAGCTGTTT
Statistics
Matches: 107, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
149 49 0.46
150 19 0.18
152 18 0.17
153 4 0.04
154 1 0.01
155 12 0.11
156 4 0.04
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (147 bp):
AATTCAAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATCAAGAAT
TATCAAAATTCAAAAAAAAAAAATAACTTTAAATTCAAATGAAAAACTTTATTTATTTAAAAATT
TAAAGAAAACAAATATC
Found at i:8565 original size:25 final size:25
Alignment explanation
Indices: 8531--8583 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
8521 AAAAATAGTA
8531 CTTAGCATCATGAAGGAACTTCTTC
1 CTTAGCATCATGAAGGAACTTCTTC
8556 CTTAGCATCATGAAGGAACTTCTTC
1 CTTAGCATCATGAAGGAACTTCTTC
8581 CTT
1 CTT
8584 TGCTGATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (25 bp):
CTTAGCATCATGAAGGAACTTCTTC
Found at i:23371 original size:22 final size:22
Alignment explanation
Indices: 23339--23393 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
23329 TCTTCGAACT
*
23339 GATGTCACGACACTTTATAGCC
1 GATGTCGCGACACTTTATAGCC
23361 GATGTCGCGACACTTTATAGCC
1 GATGTCGCGACACTTTATAGCC
23383 GATGTCGCGAC
1 GATGTCGCGAC
23394 TTTGCTGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (22 bp):
GATGTCGCGACACTTTATAGCC
Found at i:25913 original size:28 final size:28
Alignment explanation
Indices: 25881--25938 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
25871 GTCTAAGAGA
25881 TAAAATTTAAATTCTTATCTTC-ACCTCT
1 TAAAATTTAAATTCTTATCTTCGA-CTCT
25909 TAAAATTTAAATTCTTATCTTCGACTCT
1 TAAAATTTAAATTCTTATCTTCGACTCT
25937 TA
1 TA
25939 GAAACGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.47
Consensus pattern (28 bp):
TAAAATTTAAATTCTTATCTTCGACTCT
Found at i:25999 original size:20 final size:20
Alignment explanation
Indices: 25953--26053 Score: 85
Period size: 20 Copynumber: 4.8 Consensus size: 20
25943 CGTTTCAAAC
* *
25953 AATTTTAAAATCAAGTTAAAGT
1 AATTTT-AAA-CAAGTCAAAAT
*
25975 GATTTTAAACAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* * *
25995 AATTTGAACCAAGTCAAAAA
1 AATTTTAAACAAGTCAAAAT
26015 AATTTAATTAAACAAGTCAAAAT
1 AA-TT--TTAAACAAGTCAAAAT
* *
26038 AATTTGAACCAAGTCA
1 AATTTTAAACAAGTCA
26054 GAATTTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 37 0.58
21 5 0.08
22 7 0.11
23 15 0.23
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:26030 original size:23 final size:21
Alignment explanation
Indices: 25977--26042 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 21
25967 GTTAAAGTGA
25977 TTTTAAACAAGTCAAAATAA-
1 TTTTAAACAAGTCAAAATAAT
* * *
25997 TTTGAACCAAGTCAAAAAAAT
1 TTTTAAACAAGTCAAAATAAT
26018 TTAATTAAACAAGTCAAAATAAT
1 TT--TTAAACAAGTCAAAATAAT
26041 TT
1 TT
26043 GAACCAAGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.46
21 2 0.05
23 18 0.49
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (21 bp):
TTTTAAACAAGTCAAAATAAT
Found at i:30885 original size:44 final size:44
Alignment explanation
Indices: 30822--30915 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
30812 ATTGAGCATC
* *
30822 CTATTTGTCAGTTTTACCGACCAGTGTTGGGCACATTTATCTGT
1 CTATTTGTCAGTTTTACCGACCAGTGCTAGGCACATTTATCTGT
* * *
30866 CTATTTGTCGGTTTTACCGACCAGTGCTAGGTACATTTATTTGT
1 CTATTTGTCAGTTTTACCGACCAGTGCTAGGCACATTTATCTGT
*
30910 CGATTT
1 CTATTT
30916 TACCGACTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (44 bp):
CTATTTGTCAGTTTTACCGACCAGTGCTAGGCACATTTATCTGT
Found at i:30917 original size:36 final size:36
Alignment explanation
Indices: 30867--31173 Score: 151
Period size: 36 Copynumber: 8.4 Consensus size: 36
30857 TTTATCTGTC
* *
30867 TATTTGTCGGTTTTACCGACCAGTGCTAGGTACATT
1 TATTTGTCGATTTTACCGACCAGTGCTAGGCACATT
* **
30903 TATTTGTCGATTTTACCGACTAGTGCCGGGCACATT
1 TATTTGTCGATTTTACCGACCAGTGCTAGGCACATT
* * * ** * *
30939 CATTTTTTTCTG-TTTT-CCTTATAAGTGTTGGGCACATT
1 --TATTTGTC-GATTTTACC-GACCAGTGCTAGGCACATT
* * * *
30977 TATTTATCGGTTTT-CTCGACCAGTG-TCAAGAACATT
1 TATTTGTCGATTTTAC-CGACCAGTGCT-AGGCACATT
* * * *
31013 TATTTTGTCGGTTTTCCCGTCCAGTG-TTGGACACATT
1 TA-TTTGTCGATTTTACCGACCAGTGCTAGG-CACATT
* * * * * **
31050 TATTTTTCAATTTTATCAACAAGAACT-GGACACATT
1 TATTTGTCGATTTTACCGACCAGTGCTAGG-CACATT
* * * *
31086 TATTTTATCTATTTTCCCAACCAGTGCTAGGCACATT
1 TA-TTTGTCGATTTTACCGACCAGTGCTAGGCACATT
* * * * *
31123 TATTTTTCGATTTTACCGATCAATGTTGGGCACATT
1 TATTTGTCGATTTTACCGACCAGTGCTAGGCACATT
31159 TA-TTGTCGATTTTAC
1 TATTTGTCGATTTTAC
31174 AACCGGCGTA
Statistics
Matches: 207, Mismatches: 51, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
35 14 0.07
36 108 0.52
37 57 0.28
38 27 0.13
39 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (36 bp):
TATTTGTCGATTTTACCGACCAGTGCTAGGCACATT
Found at i:31157 original size:73 final size:72
Alignment explanation
Indices: 30876--31162 Score: 184
Period size: 73 Copynumber: 3.9 Consensus size: 72
30866 CTATTTGTCG
* * * * * *
30876 GTTTTACCGACCAGTGCTAGGTACATTTATTTGTCGATTTTACCGACTAGTGCCGGGCACATTCA
1 GTTTTCCCAACCAGTGCTAGGCACATTTATTTTTCGATTTTACCGAC-AATGCCGGGCACATTTA
*
30941 TTTTTTTCT
65 -TTTTATCT
** ** * * * * * * ** *
30950 GTTTTCCTTATAAGTGTTGGGCACATTTATTTATCGGTTTT-CTCGACCAGTGTCAAGAACATTT
1 GTTTTCCCAACCAGTGCTAGGCACATTTATTTTTCGATTTTAC-CGA-CAATGCCGGGCACATTT
* *
31014 ATTTTGTCG
64 ATTTTATCT
** * * * * * *
31023 GTTTTCCCGTCCAGTG-TTGGACACATTTATTTTTCAATTTTATCAACAA-GAACTGGACACATT
1 GTTTTCCCAACCAGTGCTAGG-CACATTTATTTTTCGATTTTACCGACAATG--CCGGGCACATT
31086 TATTTTATCT
63 TATTTTATCT
* **
31096 ATTTTCCCAACCAGTGCTAGGCACATTTATTTTTCGATTTTACCGATCAATGTTGGGCACATTTA
1 GTTTTCCCAACCAGTGCTAGGCACATTTATTTTTCGATTTTACCGA-CAATGCCGGGCACATTTA
31161 TT
65 TT
31163 GTCGATTTTA
Statistics
Matches: 158, Mismatches: 46, Indels: 19
0.71 0.21 0.09
Matches are distributed among these distances:
71 1 0.01
72 5 0.03
73 98 0.62
74 52 0.33
75 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (72 bp):
GTTTTCCCAACCAGTGCTAGGCACATTTATTTTTCGATTTTACCGACAATGCCGGGCACATTTAT
TTTATCT
Found at i:33610 original size:45 final size:44
Alignment explanation
Indices: 33546--33662 Score: 144
Period size: 45 Copynumber: 2.6 Consensus size: 44
33536 ATTTAACCGG
* * * *
33546 AATGAATAAGACCATAGTTGAAAGATATTATGACATTAAGTCGGA
1 AATGAATAAGACCATAGTTGAAAAATACTATGACACTAAATC-GA
** *
33591 AATGTGTAAGACCATAGTTGAAAAATACTATGGCACTAAATCGA
1 AATGAATAAGACCATAGTTGAAAAATACTATGACACTAAATCGA
* *
33635 TATGAATAAGACCATAGTTGAAATATAC
1 AATGAATAAGACCATAGTTGAAAAATAC
33663 AATGGCACCA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 26 0.43
45 35 0.57
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.26
Consensus pattern (44 bp):
AATGAATAAGACCATAGTTGAAAAATACTATGACACTAAATCGA
Found at i:33668 original size:44 final size:45
Alignment explanation
Indices: 33518--33670 Score: 157
Period size: 44 Copynumber: 3.4 Consensus size: 45
33508 GAGAAAGACT
* * * * *
33518 GTTGAAAGACACTATGGCATTTAACCGG-AATGAATAAGACCATA
1 GTTGAAAAATACTATGGCACTAAATCGGAAATGAATAAGACCATA
* * * * * **
33562 GTTGAAAGATATTATGACATTAAGTCGGAAATGTGTAAGACCATA
1 GTTGAAAAATACTATGGCACTAAATCGGAAATGAATAAGACCATA
*
33607 GTTGAAAAATACTATGGCACTAAATC-GATATGAATAAGACCATA
1 GTTGAAAAATACTATGGCACTAAATCGGAAATGAATAAGACCATA
* *
33651 GTTGAAATATACAATGGCAC
1 GTTGAAAAATACTATGGCAC
33671 CACTTCAGGA
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 55 0.61
45 35 0.39
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (45 bp):
GTTGAAAAATACTATGGCACTAAATCGGAAATGAATAAGACCATA
Found at i:42753 original size:6 final size:6
Alignment explanation
Indices: 42742--42812 Score: 115
Period size: 6 Copynumber: 11.8 Consensus size: 6
42732 AAGAATGAAC
* * *
42742 GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GTGGCC GTGGCT GTGACC
1 GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT
42790 GTGGCT GTGGCT GTGGCT GTGGC
1 GTGGCT GTGGCT GTGGCT GTGGC
42813 CATGGCCATG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.01, C:0.20, G:0.49, T:0.30
Consensus pattern (6 bp):
GTGGCT
Found at i:52970 original size:24 final size:24
Alignment explanation
Indices: 52938--53012 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
52928 ATATACAGGT
52938 TAACCATTCTGGGCTCGTGAGAGC
1 TAACCATTCTGGGCTCGTGAGAGC
* *
52962 TAACCATTCTAGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTGAGAGC
*
52986 TAACCATTCTGGGCTTGTGAGAGC
1 TAACCATTCTGGGCTCGTGAGAGC
53010 TAA
1 TAA
53013 TATTATCTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTGAGAGC
Found at i:54820 original size:22 final size:23
Alignment explanation
Indices: 54790--54832 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
54780 TAAAATGGGT
54790 CATGCAAATTAAATTAATTAAAG
1 CATGCAAATTAAATTAATTAAAG
* *
54813 CATG-AAATTATATTATTTAA
1 CATGCAAATTAAATTAATTAA
54833 TGGACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGCAAATTAAATTAATTAAAG
Found at i:63554 original size:17 final size:16
Alignment explanation
Indices: 63520--63584 Score: 76
Period size: 17 Copynumber: 3.9 Consensus size: 16
63510 CTATAGTATA
*
63520 ATTGTCCCTGCATTTT
1 ATTGTCACTGCATTTT
63536 ATTGTCACTGCACTTTT
1 ATTGTCACTGCA-TTTT
**
63553 ATTGTCACTGCATCTAC
1 ATTGTCACTGCAT-TTT
*
63570 ATTGTCATTGCATTT
1 ATTGTCACTGCATTT
63585 CCATATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 13 0.31
17 29 0.69
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.46
Consensus pattern (16 bp):
ATTGTCACTGCATTTT
Found at i:116200 original size:18 final size:18
Alignment explanation
Indices: 116179--116213 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
116169 CTGCATTCAA
116179 GTATGTGATTGCATCTGG
1 GTATGTGATTGCATCTGG
*
116197 GTATGTTATTGCATCTG
1 GTATGTGATTGCATCTG
116214 ATCAGGCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.29, T:0.43
Consensus pattern (18 bp):
GTATGTGATTGCATCTGG
Found at i:122459 original size:13 final size:13
Alignment explanation
Indices: 122441--122470 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
122431 GGAATCATTG
122441 ATTAAATAGGTTA
1 ATTAAATAGGTTA
122454 ATTAAATAGGTTA
1 ATTAAATAGGTTA
122467 ATTA
1 ATTA
122471 GTAAAGGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (13 bp):
ATTAAATAGGTTA
Found at i:142186 original size:18 final size:18
Alignment explanation
Indices: 142163--142213 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
142153 AACATCATGA
142163 TCAGATGCAGCCACATAC
1 TCAGATGCAGCCACATAC
* * *
142181 TCAGATACAGTCACATGC
1 TCAGATGCAGCCACATAC
142199 TC-GTATGCAGCCACA
1 TCAG-ATGCAGCCACA
142214 ACAAATTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (18 bp):
TCAGATGCAGCCACATAC
Found at i:161557 original size:21 final size:22
Alignment explanation
Indices: 161524--161565 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
161514 TGAAGTTTAC
161524 TATGAATTTTTTTTATTTCTTT
1 TATGAATTTTTTTTATTTCTTT
161546 TATGAA-TTTTTTTATTTCTT
1 TATGAATTTTTTTTATTTCTT
161566 ATGGTTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (22 bp):
TATGAATTTTTTTTATTTCTTT
Found at i:165152 original size:25 final size:26
Alignment explanation
Indices: 165119--165168 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
165109 TATGTATGCT
*
165119 AACCTTGATAAACATG-CTATGTGTG
1 AACCCTGATAAACATGTCTATGTGTG
*
165144 AACCCTGATAAACATGTTTATGTGT
1 AACCCTGATAAACATGTCTATGTGT
165169 TATGTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (26 bp):
AACCCTGATAAACATGTCTATGTGTG
Found at i:166722 original size:24 final size:23
Alignment explanation
Indices: 166679--166724 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
166669 CAATGTTATC
166679 CAAATTTAGTTCAAACTCTTCAA
1 CAAATTTAGTTCAAACTCTTCAA
166702 CAAATTTTAGCTTCAAA-TCTTCA
1 CAAA-TTTAG-TTCAAACTCTTCA
166725 TTCTATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (23 bp):
CAAATTTAGTTCAAACTCTTCAA
Found at i:177625 original size:18 final size:18
Alignment explanation
Indices: 177602--177643 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
177592 TTCTTATCAC
177602 TGCATTTTGTTTTGTCAT
1 TGCATTTTGTTTTGTCAT
177620 TGCATTTTGTTTTGTCAT
1 TGCATTTTGTTTTGTCAT
177638 TGCATT
1 TGCATT
177644 CCTTTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.60
Consensus pattern (18 bp):
TGCATTTTGTTTTGTCAT
Found at i:179798 original size:13 final size:14
Alignment explanation
Indices: 179769--179798 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
179759 TTCAATATAT
179769 TGACATTTAACCTC
1 TGACATTTAACCTC
179783 TGACATTTAA-CTC
1 TGACATTTAACCTC
179796 TGA
1 TGA
179799 TTGGGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:188775 original size:3 final size:3
Alignment explanation
Indices: 188759--188817 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
188749 ACGCATGAGT
* *
188759 AGA AGA AGT GGA AGA AGA AGA AGA AGGA A-A AGA AGA AGA A-A GAGA
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA -AGA
* *
188804 GGA AGA AAA AGA AG
1 AGA AGA AGA AGA AG
188818 TAGAGGCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
2 3 0.07
3 37 0.84
4 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:190310 original size:17 final size:18
Alignment explanation
Indices: 190278--190312 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
190268 TCAAGTTATA
190278 TAGAAGTACATTTGATATT
1 TAGAAGTACA-TTGATATT
190297 TAGAAGTACA-TGATAT
1 TAGAAGTACATTGATAT
190313 CTATTTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (18 bp):
TAGAAGTACATTGATATT
Found at i:203390 original size:30 final size:30
Alignment explanation
Indices: 203332--203390 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
203322 TAATTGGAAA
* *
203332 TTAAAGTTTTTATAATTTTTTTATTTTTAT
1 TTAAAGTTTTTATAATTTATTTACTTTTAT
*
203362 TTAAA-TTTTTAGTGATTTATTTACTTTTA
1 TTAAAGTTTTTA-TAATTTATTTACTTTTA
203391 ATCGTCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (30 bp):
TTAAAGTTTTTATAATTTATTTACTTTTAT
Found at i:203539 original size:15 final size:16
Alignment explanation
Indices: 203506--203540 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
203496 TCTGATTCAA
203506 AAAAATTAATATTTAC
1 AAAAATTAATATTTAC
*
203522 AAAAATTATTATTT-C
1 AAAAATTAATATTTAC
203537 AAAA
1 AAAA
203541 GCATTCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATTAATATTTAC
Found at i:204106 original size:22 final size:22
Alignment explanation
Indices: 204081--204162 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
204071 AGAATTCGAA
204081 AAAAATAATATATATTTAATTT
1 AAAAATAATATATATTTAATTT
* **
204103 -AAAATAA-ATAAAGCT-A-TT
1 AAAAATAATATATATTTAATTT
204121 AAAAATTAATATATATTTAATTT
1 AAAAA-TAATATATATTTAATTT
* *
204144 TAAAACAATATATATTTAA
1 AAAAATAATATATATTTAA
204163 AAAAATTGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
18 2 0.04
19 5 0.11
20 8 0.17
21 12 0.26
22 14 0.30
23 6 0.13
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (22 bp):
AAAAATAATATATATTTAATTT
Found at i:204166 original size:41 final size:41
Alignment explanation
Indices: 204079--204168 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
204069 GTAGAATTCG
*
204079 AAAAAAATAATATATATTTAATTTAAAATAAATAAAGCTATT
1 AAAAAAATAATATATATTTAATTTAAAACAAATAAA-CTATT
* *
204121 -AAAAATTAATATATATTTAATTTTAAAAC-AATATA-TATTT
1 AAAAAAATAATATATATTTAA-TTTAAAACAAATAAACTA-TT
204161 AAAAAAAT
1 AAAAAAAT
204169 TGATTGGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
39 2 0.05
40 2 0.05
41 30 0.73
42 7 0.17
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (41 bp):
AAAAAAATAATATATATTTAATTTAAAACAAATAAACTATT
Found at i:205011 original size:3 final size:3
Alignment explanation
Indices: 204998--205067 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
204988 TCTCCATTTT
*
204998 TTC TT- TTC TTC TTC TTC TCC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
205045 TT- TT- TTC TT- TTC TT- TTT TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
205068 ATAAACCCTA
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
2 10 0.17
3 50 0.83
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:207218 original size:14 final size:14
Alignment explanation
Indices: 207199--207259 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
207189 AAAGTTAATT
* *
207199 GTCAACGGTCAACA
1 GTCAACAGTCAACG
*
207213 GTCAACAGTCAACT
1 GTCAACAGTCAACG
* * *
207227 ATCAATAGTCAATG
1 GTCAACAGTCAACG
207241 GTCAACTA-TCAACG
1 GTCAAC-AGTCAACG
207255 GTCAA
1 GTCAA
207260 TGGGTCAGGT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
14 36 0.97
15 1 0.03
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (14 bp):
GTCAACAGTCAACG
Found at i:207260 original size:21 final size:21
Alignment explanation
Indices: 207207--207262 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
207197 TTGTCAACGG
**
207207 TCAACAGTCAACAGTCAACTA
1 TCAACAGTCAATGGTCAACTA
*
207228 TCAATAGTCAATGGTCAACTA
1 TCAACAGTCAATGGTCAACTA
*
207249 TCAACGGTCAATGG
1 TCAACAGTCAATGG
207263 GTCAGGTCGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (21 bp):
TCAACAGTCAATGGTCAACTA
Found at i:208644 original size:3 final size:3
Alignment explanation
Indices: 208636--208680 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
208626 TTCTTTTCAC
* *
208636 CTT CTT CTT -TT CTT CTT TTT CTT CTT -TT CTT CTT TTT C-T CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
208681 AAACCCTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
CTT
Found at i:208657 original size:14 final size:14
Alignment explanation
Indices: 208623--208680 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
208613 GCATCTCCAT
**
208623 TTTTTCTTTTCACC
1 TTTTTCTTTTCTTC
*
208637 TTCTTCTTTTCTTC
1 TTTTTCTTTTCTTC
208651 TTTTTCTTCTTTTCTTC
1 --TTT-TTCTTTTCTTC
*
208668 TTTTTCTCTTCTT
1 TTTTTCTTTTCTT
208681 AAACCCTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 20 0.56
15 3 0.08
16 2 0.06
17 11 0.31
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTCTTTTCTTC
Found at i:208659 original size:17 final size:17
Alignment explanation
Indices: 208637--208674 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
208627 TCTTTTCACC
208637 TTCTTCTTTTCTTCTTT
1 TTCTTCTTTTCTTCTTT
208654 TTCTTCTTTTCTTCTTT
1 TTCTTCTTTTCTTCTTT
208671 TTCT
1 TTCT
208675 CTTCTTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTCTTTTCTTCTTT
Found at i:208677 original size:8 final size:9
Alignment explanation
Indices: 208637--208674 Score: 62
Period size: 8 Copynumber: 4.4 Consensus size: 9
208627 TCTTTTCACC
208637 TTCTTC-TT
1 TTCTTCTTT
208645 TTCTTCTTT
1 TTCTTCTTT
208654 TTCTTC-TT
1 TTCTTCTTT
208662 TTCTTCTTT
1 TTCTTCTTT
208671 TTCT
1 TTCT
208675 CTTCTTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:221853 original size:93 final size:93
Alignment explanation
Indices: 221744--221938 Score: 302
Period size: 93 Copynumber: 2.1 Consensus size: 93
221734 CTTTAACTTT
* * * *
221744 ACTGATCTTTTTCTTGTTCTTCTTCTCGGTTTTCTCTTTGACAACTTCCGGAATTTGTGAA-TCC
1 ACTGATCTTTTCCTTGTTCTTCTTCTCGGTTTTCTCTTGGACAACTTCCGAAATTAGTGAAGT-C
*
221808 CTTGGAGGTTCAACAGATTCTTCAGCTTC
65 CTTGGAGGTTCAACAGATTCTCCAGCTTC
*
221837 ACTGATCTTTTCCTTGTTCTTCTTCTCTGTTTTCTCTTGGACAACTTCCGAAATTAGTGAAGTCC
1 ACTGATCTTTTCCTTGTTCTTCTTCTCGGTTTTCTCTTGGACAACTTCCGAAATTAGTGAAGTCC
*
221902 TTGGAGGTTCAACAGATTCTCCAGCTTT
66 TTGGAGGTTCAACAGATTCTCCAGCTTC
*
221930 GCTGATCTT
1 ACTGATCTT
221939 CTTCTTGGTT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 92 0.99
94 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (93 bp):
ACTGATCTTTTCCTTGTTCTTCTTCTCGGTTTTCTCTTGGACAACTTCCGAAATTAGTGAAGTCC
TTGGAGGTTCAACAGATTCTCCAGCTTC
Found at i:221989 original size:81 final size:81
Alignment explanation
Indices: 221854--222002 Score: 201
Period size: 81 Copynumber: 1.8 Consensus size: 81
221844 TTTTCCTTGT
*
221854 TCTTCTTCTCTGTTTTCTCTTGGACAACTTCCGAAATTAGTGAAGTCCTTGGAGGTTCAACAGAT
1 TCTTCTTCTCTGTTTTCTCTTGGACAACTTCCGAAATTAGTGAAGTACTTGGAGGTTCAACAGAT
221919 TCTCCAGCTTTGCTGA
66 TCTCCAGCTTTGCTGA
* * * * ** * *
221935 TCTTCTTCT-TGGTTTTCTCTTTGACAACTTTCGGAGTTTTTGAAGTACTTGGAGGTTTAACGGA
1 TCTTCTTCTCT-GTTTTCTCTTGGACAACTTCCGAAATTAGTGAAGTACTTGGAGGTTCAACAGA
221999 TTCT
65 TTCT
222003 AGAGGCAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.02
81 57 0.98
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.42
Consensus pattern (81 bp):
TCTTCTTCTCTGTTTTCTCTTGGACAACTTCCGAAATTAGTGAAGTACTTGGAGGTTCAACAGAT
TCTCCAGCTTTGCTGA
Found at i:224019 original size:15 final size:16
Alignment explanation
Indices: 224001--224034 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
223991 TAACACTTAA
224001 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
224016 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
224032 AAA
1 AAA
224035 ATTACATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:224967 original size:24 final size:24
Alignment explanation
Indices: 224886--224968 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
224876 AAAATTTTAA
224886 ATTAATAATAATAAAATTATATTTT
1 ATTAA-AATAATAAAATTATATTTT
* ***
224911 AACTGTTTTAAAATAATAAAAATATAAACT
1 -A-----TTAAAATAATAAAATTATATTTT
224941 ATTAAAATAATAAAATTATATTTT
1 ATTAAAATAATAAAATTATATTTT
224965 ATTA
1 ATTA
224969 TCGTAAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
24 23 0.52
26 1 0.02
29 1 0.02
30 15 0.34
31 4 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (24 bp):
ATTAAAATAATAAAATTATATTTT
Done.