Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005366.1 Hibiscus syriacus cultivar Beakdansim tig00012198_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: 66383
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1514 original size:32 final size:31
Alignment explanation
Indices: 1447--1516 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
1437 GTTTCGGCCA
* * * **
1447 ACCCGACCCGACCCAAAACTTTATATCCTTT
1 ACCCGACCCGACCAAAAAATTTATACCCTCC
1478 ACCCGACCCGACTCAAAAAATTTATACCCTCC
1 ACCCGACCCGAC-CAAAAAATTTATACCCTCC
1510 ACCCGAC
1 ACCCGAC
1517 TCGAACTCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 12 0.36
32 21 0.64
ACGTcount: A:0.31, C:0.41, G:0.07, T:0.20
Consensus pattern (31 bp):
ACCCGACCCGACCAAAAAATTTATACCCTCC
Found at i:2492 original size:23 final size:22
Alignment explanation
Indices: 2466--2508 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2456 AAATATAACA
*
2466 TTTGAAAAAATAATAAGGAAAAT
1 TTTGAAAAAA-AAAAAGGAAAAT
2489 TTTGAAAAAAAAAAAGGAAA
1 TTTGAAAAAAAAAAAGGAAA
2509 GAAAATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.21
Consensus pattern (22 bp):
TTTGAAAAAAAAAAAGGAAAAT
Found at i:3590 original size:17 final size:17
Alignment explanation
Indices: 3568--3604 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3558 ACTAGATTTT
3568 TAATAATTAAGTTTAAC
1 TAATAATTAAGTTTAAC
*
3585 TAATAATTAAGTTTATC
1 TAATAATTAAGTTTAAC
3602 TAA
1 TAA
3605 ATTAATCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (17 bp):
TAATAATTAAGTTTAAC
Found at i:9055 original size:32 final size:31
Alignment explanation
Indices: 9019--9094 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
9009 GGGGCCGTGA
*
9019 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
*** **
9051 GGCCTACCCGTGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
9082 AGCCTACCTAAGA
1 GGCCTACCTAAGA
9095 GTCACATTAG
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 23 0.68
32 11 0.32
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:9977 original size:7 final size:7
Alignment explanation
Indices: 9965--9995 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
9955 GTCAAAGAAA
9965 GTCAACG
1 GTCAACG
9972 GTCAACG
1 GTCAACG
9979 GTCAACG
1 GTCAACG
9986 GTCAACG
1 GTCAACG
9993 GTC
1 GTC
9996 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:10007 original size:17 final size:17
Alignment explanation
Indices: 9985--10040 Score: 94
Period size: 17 Copynumber: 3.3 Consensus size: 17
9975 AACGGTCAAC
*
9985 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
10002 GGTCAACAGTCGGGCCG
1 GGTCAACAGTCGGGTCG
10019 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
10036 GGTCA
1 GGTCA
10041 GTCGGGTCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.16, C:0.25, G:0.43, T:0.16
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:10078 original size:19 final size:19
Alignment explanation
Indices: 10054--10102 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
10044 GGGTCAGGTT
10054 AACCCGGTTCAGACCGGTC
1 AACCCGGTTCAGACCGGTC
10073 AACCCGGTTCAGACCGGTC
1 AACCCGGTTCAGACCGGTC
*
10092 AAACCGGTTCA
1 AACCCGGTTCA
10103 AAACTGGTCA
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:0.24, C:0.35, G:0.24, T:0.16
Consensus pattern (19 bp):
AACCCGGTTCAGACCGGTC
Found at i:10103 original size:10 final size:10
Alignment explanation
Indices: 10057--10120 Score: 62
Period size: 9 Copynumber: 6.6 Consensus size: 10
10047 TCAGGTTAAC
*
10057 CCGGTTCAGA
1 CCGGTTCAAA
*
10067 CCGG-TCAAC
1 CCGGTTCAAA
*
10076 CCGGTTCAGA
1 CCGGTTCAAA
10086 CCGG-TCAAA
1 CCGGTTCAAA
10095 CCGGTTCAAAA
1 CCGGTTC-AAA
*
10106 CTGG-TCAAA
1 CCGGTTCAAA
10115 CCGGTT
1 CCGGTT
10121 TTCCAGCATC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
9 21 0.49
10 16 0.37
11 6 0.14
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (10 bp):
CCGGTTCAAA
Found at i:10111 original size:20 final size:19
Alignment explanation
Indices: 10057--10120 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
10047 TCAGGTTAAC
* *
10057 CCGGTTCAGACCGGTCAAC
1 CCGGTTCAAACCGGTCAAA
*
10076 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAAACCGGTCAAA
*
10095 CCGGTTCAAAACTGGTCAAA
1 CCGGTTC-AAACCGGTCAAA
10115 CCGGTT
1 CCGGTT
10121 TTCCAGCATC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (19 bp):
CCGGTTCAAACCGGTCAAA
Found at i:13938 original size:5 final size:5
Alignment explanation
Indices: 13930--13961 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
13920 CTCTCTACAA
*
13930 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
13962 GAGAGCTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:16360 original size:98 final size:98
Alignment explanation
Indices: 16180--16377 Score: 274
Period size: 98 Copynumber: 2.0 Consensus size: 98
16170 CTGAACATTG
*
16180 TTGGTATGCTCCGGGGATCGACTCACAAGGTTGATAAAAACAATTATCTCTTAAAAAATTTAAAT
1 TTGGTATGCTCCGGGGATCGACTCACAAGATTGATAAAAACAATTATCTCTTAAAAAATTTAAAT
16245 TTTTATGTAATTTAATTTTTTCTAATACGTTTTA
66 TTTTATGTAATTTAA-TTTTTCTAATACGTTTTA
* * * * * * * *
16279 TTGGTATGCT-CTGGGATCGACTCACGAGATTGATAGAAACAGTTGTTTCTTAAAAATTTTAAGT
1 TTGGTATGCTCCGGGGATCGACTCACAAGATTGATAAAAACAATTATCTCTTAAAAAATTTAAAT
*
16343 TTTT-TGTAATTTAAATTTTTCTAATACTTTTTA
66 TTTTATGTAATTT-AATTTTTCTAATACGTTTTA
16376 TT
1 TT
16378 TGATAATTTA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
97 27 0.31
98 51 0.58
99 10 0.11
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (98 bp):
TTGGTATGCTCCGGGGATCGACTCACAAGATTGATAAAAACAATTATCTCTTAAAAAATTTAAAT
TTTTATGTAATTTAATTTTTCTAATACGTTTTA
Found at i:19071 original size:59 final size:57
Alignment explanation
Indices: 19008--19673 Score: 644
Period size: 59 Copynumber: 11.3 Consensus size: 57
18998 TTACCAAATG
* *
19008 GCACTATATGTGCAAAAATGATAAGGAAATCATACTAAGTGTATGGATTTCCATATGGA
1 GCACTA-ATGTGCTAAAATGTTAAGGAAATCATACTAA-TGTATGGATTTCCATATGGA
*
19067 GCACTGAATGTGCTAAAATGATAA-GAAATCATACTAAGTGTATGGATTTCCATATGGA
1 GCACT-AATGTGCTAAAATGTTAAGGAAATCATACTAA-TGTATGGATTTCCATATGGA
* * * *
19125 GCACTAAGTATGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCACATAGG-
1 GCACTAA-TGTGCTAAAATGTTAAGGAAATCATACT-AATGTATGGATTTCCATAT-GGA
* * *
19184 GCATTATATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGGATTTCCATATGGA
1 GCACTA-ATGTGCTAAAATGTTAAGGAAATCATACTAA-TGTATGGATTTCCATATGGA
* * * *
19243 GCACTAAGTGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGG-
1 GCACTAA-TGTGCTAAAATGTTAAGGAAATCATACT-AATGTATGGATTTCCATAT-GGA
* * ** *
19302 GCATTATATGTGCTAAAATGGTAAGGGGATCATACTAAGTGTATGTATTTCCATATGGA
1 GCACTA-ATGTGCTAAAATGTTAAGGAAATCATACTAA-TGTATGGATTTCCATATGGA
* * * *
19361 GCACTAATTGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGG-
1 GCACTAA-TGTGCTAAAATGTTAAGGAAATCATACT-AATGTATGGATTTCCATAT-GGA
* ** *
19420 GCATTATATGTGCTAAAATAG-TAAGGGGATCATACTAAGTGTATGTATTTCCATATGGA
1 GCACTA-ATGTGCTAAAAT-GTTAAGGAAATCATACTAA-TGTATGGATTTCCATATGGA
* * * * *
19479 GCACTAATTGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCAAAATAGG-
1 GCACTAA-TGTGCTAAAATGTTAAGGAAATCATACT-AATGTATGGATTTCCATAT-GGA
* * * ** * *
19538 GCATTATGTGTGCTAAAATGATAAGGGGATCATACTAACTGTATGTATTTCCATGTGGA
1 GCACTA-ATGTGCTAAAATGTTAAGGAAATCATACTAA-TGTATGGATTTCCATATGGA
* *
19597 GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAGG-
1 GCACTAA-TGTGCTAAAATGTTAAGGAAATCATACT-AATGTATGGATTTCCATAT-GGA
*
19656 GCATTATATGTGCTAAAA
1 GCACTA-ATGTGCTAAAA
19674 ATGGTAAAAG
Statistics
Matches: 498, Mismatches: 77, Indels: 64
0.78 0.12 0.10
Matches are distributed among these distances:
57 2 0.00
58 73 0.15
59 397 0.80
60 26 0.05
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (57 bp):
GCACTAATGTGCTAAAATGTTAAGGAAATCATACTAATGTATGGATTTCCATATGGA
Found at i:19257 original size:118 final size:118
Alignment explanation
Indices: 19008--19760 Score: 1036
Period size: 118 Copynumber: 6.4 Consensus size: 118
18998 TTACCAAATG
* * * * *
19008 GCACTATA-TGTGCAAAAATGATAAGGAAATCATACT-AAGTGTATGGATTTCCATAT-GGAGCA
1 GCACTA-AGTGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCCAAATAGG-GCA
* * * *
19070 CTGA-ATGTGCTAAAATGATAA-GAAATCATACTAAGTGTATGGATTTCCATATGGA
63 -TTATATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGTATTTCCATATGGA
* *
19125 GCACTAAGTATGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCACATAGGGCATTA
1 GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTA
*
19190 TATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGGATTTCCATATGGA
66 TATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGTATTTCCATATGGA
*
19243 GCACTAAGTGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTA
1 GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTA
*
19308 TATGTGCTAAAATGGTAAGGGGATCATACTAAGTGTATGTATTTCCATATGGA
66 TATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGTATTTCCATATGGA
* *
19361 GCACTAATTGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTA
1 GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTA
* *
19426 TATGTGCTAAAATAGTAAGGGGATCATACTAAGTGTATGTATTTCCATATGGA
66 TATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGTATTTCCATATGGA
* * *
19479 GCACTAATTGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCAAAATAGGGCATTA
1 GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTA
* * * * *
19544 TGTGTGCTAAAATGATAAGGGGATCATACTAACTGTATGTATTTCCATGTGGA
66 TATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGTATTTCCATATGGA
*
19597 GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAGGGCATTA
1 GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTA
** * * **
19662 TATGTGCTAAAAATGGTAAAAGAATCATAC-AAATGGTATGAATTCTTGA-ATAGG-
66 TATGTGCT-AAAATGGTAAGGGAATCATACTAAGT-GTATGTATT-TCCATAT-GGA
** ** *
19716 GCACTTTGTGTGCTAAAATGAGAAGGAAATCATATTGAGTATATG
1 GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATG
19761 ATAATTCAAA
Statistics
Matches: 586, Mismatches: 41, Indels: 16
0.91 0.06 0.02
Matches are distributed among these distances:
116 3 0.01
117 64 0.11
118 449 0.77
119 66 0.11
120 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (118 bp):
GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTA
TATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGTATTTCCATATGGA
Found at i:19773 original size:59 final size:59
Alignment explanation
Indices: 19007--19779 Score: 496
Period size: 59 Copynumber: 13.1 Consensus size: 59
18997 ATTACCAAAT
* * * * *
19007 GGCAC-TATATGTGCAAAAATGATAAGGAAATCATACT-AAGTGTATGGATTTC-CATATG
1 GGCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCAAATA-G
* * * * *
19065 GAGCACTGA-ATGTGCTAAAATGATAA-GAAATCATACT-AAGTGTATGGATTTC-CATATG
1 G-GCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCAAATA-G
* *
19123 GAGCAC-TA-AGTATGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCACATAG
1 G-GCACTTATA-TGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTT-CAAATAG
* * * * *
19183 GGCA-TTATATGTGCTAAAATGGTAAGGGAATCATACT-AAGTGTATGGATTTC-CATATG
1 GGCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCAAATA-G
*
19241 GAGCAC-TA-AGTGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAG
1 G-GCACTTATA-TGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTT-CAAATAG
* ** * * * *
19301 GGCA-TTATATGTGCTAAAATGGTAAGGGGATCATACT-AAGTGTATGTATTTC-CATATG
1 GGCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCAAATA-G
* *
19359 GAGCACTAAT-TGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCCAAATAG
1 G-GCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTT-CAAATAG
** * * * *
19419 GGCA-TTATATGTGCTAAAATAG-TAAGGGGATCATACT-AAGTGTATGTATTTC-CATATG
1 GGCACTTATATGTGCTAAAAT-GTTAAGGAAATCATATTGAA-TATATGGATTTCAAATA-G
* *
19477 GAGCACTAAT-TGTGCTAAAACGTTAAGGAAATCATATTGAATATATGGATTTCAAAATAG
1 G-GCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTC-AAATAG
* * ** * * * * *
19537 GGCA-TTATGTGTGCTAAAATGATAAGGGGATCATACT-AACTGTATGTATTTC-CATGTG
1 GGCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCAAAT-AG
*
19595 GAGCAC-TA-AGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
1 G-GCACTTATA-TGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTT-CAAATAG
* * ** * * **
19655 GGCA-TTATATGTGCTAAAAATGGTAA-AAGAATCATA-CAAATGGTATGAATTCTTGAATAG
1 GGCACTTATATGTGCT-AAAATGTTAAGGA-AATCATATTGAAT-ATATGGATT-TCAAATAG
* ** *
19715 GGCACTT-TGTGTGCTAAAATGAGAAGGAAATCATATTGAGTATAT-GATAATTCAAATAG
1 GGCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGAT--TTCAAATAG
*
19774 AGCACT
1 GGCACT
19780 GAGAGTGCTA
Statistics
Matches: 568, Mismatches: 91, Indels: 111
0.74 0.12 0.14
Matches are distributed among these distances:
57 14 0.02
58 82 0.14
59 377 0.66
60 77 0.14
61 18 0.03
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (59 bp):
GGCACTTATATGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCAAATAG
Found at i:20010 original size:43 final size:43
Alignment explanation
Indices: 19889--21072 Score: 1495
Period size: 43 Copynumber: 27.2 Consensus size: 43
19879 GTGATGCAAT
* * *
19889 AATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATAGAAT
1 AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
* *
19933 AATGGTATGCATATTGGTAAAATAAGCTTACGAGCTTATGGAAA
1 AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
*
19977 AATGATAAGTATATTGTAAAATAAGCTTACGAGCTTAT-GAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
** * *
20019 TAATGGGGAGTAGATTGGTAAAATAAGCTTACGAGCTTATGGAAT
1 -AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
*
20064 AATGATGAA-TATAATTGTAAAATAAGCTTACGAGCTTAT-GAAA
1 AATGGT-AAGTAT-ATTGTAAAATAAGCTTACGAGCTTATGGAAA
** * * *
20107 TAATGGGGAGTAGATTGGTAAAATAAGCTTATGAGCTTATGGAAT
1 -AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
* * *
20152 AATGATGAA-TATAATGGTAAAATAAGCTTACGAGCTTATGGAAT
1 AATGGT-AAGTAT-ATTGTAAAATAAGCTTACGAGCTTATGGAAA
* * *
20196 AATGATAACTATATTGGTAAAATAAGCTTACGAGCTTATGGAAT
1 AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
** *
20240 AATAATGAA-TATATTGGTAAAATAACCTTACGAGCTTAT-GAAA
1 AATGGT-AAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
* *
20283 TAATGGTAAATATATTGTAAAATAAGCTTACGAGCTTATAGAAA
1 -AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
* * *
20327 AATAGTAAGTAGATTGTAAAATAAGCTTAAGAGCTTATGGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
*
20370 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATAGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
* * *
20413 AATAGTAAGTAGATTGTAAAATAAGCTTAAGAGCTTATGGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
*
20456 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATAGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
* * * *
20499 AATAGTAAGTAGATTGTAAAATAAGCTTAAGGGCTTATGGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
* * *
20542 AATGGTAAGTATATTATAAAATAAGCATACGAGCTTATAGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
* *
20585 AATAGTAAGTAGATTGTAAAATAAGCTTACGAGCTTATGGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
* *
20628 AATGGTAAGTAGATTGTAAAATAAGCTTAAGAGCTTATGGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
*
20671 AATGGTAAGTATATTGGTAAAATAAGCTTAAGAGCTTATGGAAA
1 AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
*
20715 AATGGTAAGTATATTGGTAAAATAAGCTTAAGAGCTTAT-GAAA
1 AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
* *
20758 TAATGGTGAGTGTATTGGTAAAATAAGCTTACGAGCTTAT-GAAA
1 -AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
* *
20802 TAATGGTAATTATATTGGTAAAATAAGCTTACAAGCTTATGG-AA
1 -AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
20846 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
* * * * * *
20889 AATTGTAATTATATTGGAAAATAGGCTTAAGAGCTTATAGAAA
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
* * * * * *
20932 AATGGTAAGTAGAATGTAAAATAAGTTTACGAGCTTATAGTAT
1 AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
*
20975 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAAT
1 AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTATGGAAA
* *
21019 AATGATAAGTATATTAGTAAAATAAGCTTACGAGCTTATGGGATA
1 AATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTAT-GGAAA
21064 AATGGTAAG
1 AATGGTAAG
21073 AAGTTTGATA
Statistics
Matches: 1008, Mismatches: 109, Indels: 45
0.87 0.09 0.04
Matches are distributed among these distances:
42 28 0.03
43 497 0.49
44 456 0.45
45 27 0.03
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (43 bp):
AATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATGGAAA
Found at i:20736 original size:21 final size:21
Alignment explanation
Indices: 20668--20736 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
20658 GAGCTTATGG
20668 AAAAATGGTAAGTATATTGGT
1 AAAAATGGTAAGTATATTGGT
* *
20689 AAAATAAGCTTAAG-AGCT-TATGG-
1 AAAA-ATG-GTAAGTA--TAT-TGGT
20712 AAAAATGGTAAGTATATTGGT
1 AAAAATGGTAAGTATATTGGT
20733 AAAA
1 AAAA
20737 TAAGCTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
20 4 0.11
21 13 0.36
22 6 0.17
23 9 0.25
24 4 0.11
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.29
Consensus pattern (21 bp):
AAAAATGGTAAGTATATTGGT
Found at i:21489 original size:21 final size:21
Alignment explanation
Indices: 21465--21507 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
21455 TTCGAAAATT
*
21465 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAATGCATCGATGC
21486 ACTGTAGCAATGCATCGATGC
1 ACTGTAGCAATGCATCGATGC
21507 A
1 A
21508 TATTTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAATGCATCGATGC
Found at i:22912 original size:9 final size:9
Alignment explanation
Indices: 22895--22959 Score: 71
Period size: 10 Copynumber: 7.0 Consensus size: 9
22885 TGGGGAACAT
22895 GCTG-ACCG
1 GCTGAACCG
22903 GCT-AGACCG
1 GCTGA-ACCG
22912 GTCTGAACCG
1 G-CTGAACCG
22922 GCTGAACCG
1 GCTGAACCG
22931 GTCTGAACCG
1 G-CTGAACCG
*
22941 GCTGGACCG
1 GCTGAACCG
22950 GTCTGAACCG
1 G-CTGAACCG
22960 AGCCGTTCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
8 3 0.06
9 22 0.45
10 23 0.47
11 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.15
Consensus pattern (9 bp):
GCTGAACCG
Found at i:22923 original size:19 final size:18
Alignment explanation
Indices: 22899--22959 Score: 95
Period size: 19 Copynumber: 3.2 Consensus size: 18
22889 GAACATGCTG
22899 ACCGGCTAGACCGGTCTGA
1 ACCGGCT-GACCGGTCTGA
22918 ACCGGCTGAACCGGTCTGA
1 ACCGGCTG-ACCGGTCTGA
22937 ACCGGCTGGACCGGTCTGA
1 ACCGGCT-GACCGGTCTGA
22956 ACCG
1 ACCG
22960 AGCCGTTCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.03
19 38 0.95
20 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.15
Consensus pattern (18 bp):
ACCGGCTGACCGGTCTGA
Found at i:22936 original size:10 final size:10
Alignment explanation
Indices: 22908--22959 Score: 81
Period size: 10 Copynumber: 5.4 Consensus size: 10
22898 GACCGGCTAG
22908 ACCGGTCTGA
1 ACCGGTCTGA
22918 ACCGG-CTGA
1 ACCGGTCTGA
22927 ACCGGTCTGA
1 ACCGGTCTGA
*
22937 ACCGG-CTGG
1 ACCGGTCTGA
22946 ACCGGTCTGA
1 ACCGGTCTGA
22956 ACCG
1 ACCG
22960 AGCCGTTCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 17 0.45
10 21 0.55
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.15
Consensus pattern (10 bp):
ACCGGTCTGA
Found at i:22992 original size:22 final size:23
Alignment explanation
Indices: 22950--22992 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
22940 GGCTGGACCG
**
22950 GTCTGAACCGAGCCGTTCGAGCC
1 GTCTGAACCGAGCCGACCGAGCC
22973 GTCTG-ACCGAGCCGACCGAG
1 GTCTGAACCGAGCCGACCGAG
22993 GCACTCGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.19, C:0.35, G:0.33, T:0.14
Consensus pattern (23 bp):
GTCTGAACCGAGCCGACCGAGCC
Found at i:47005 original size:105 final size:105
Alignment explanation
Indices: 46870--47836 Score: 1242
Period size: 105 Copynumber: 9.1 Consensus size: 105
46860 GTATAAGACA
* *
46870 CGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAACATCTT
1 CGAA-AATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
*
46935 CAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
65 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * *
46976 CGAAAATCTTCTGCGAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCTTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
* * * *
47041 AAACGGGTTCGCTTCCTCTTTCTTCAGGAAGTATAGAACT
66 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * *
47081 CGAACATCTTC-T-T-ACGGGTCCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
*
47143 AAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACT
66 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* *
47183 CGAAAATCTTCTGCGAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
* * *
47248 AAACGGGTTCGCTCCCTCTTTTTTTAGGAAGTATAGAACT
66 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * *
47288 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACTCGAAAATATTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG--AACA-TC
** * * *
47353 TTCTTACGGGTTCACTCCTTCTTTCTTTAAGGAGTATGGAACT
63 TTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * *
47396 CGGACATCTTCTTCTTACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA---TC
** * *
47461 TTCTTACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACT
63 TTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * * *
47504 CGGACATCTTCTTCTTAA-GGATTCGCTCCTTCTTTCTTTAAGGAGTATGAAACTCGAACATCTT
1 CGAAAATCTTCTTC-TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
*
47568 CAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACT
65 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * *
47609 CGAAAATCTTCTGCGAACGGATTCGCTCACTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTT
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
* * *
47674 AAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
66 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * *
47714 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATATTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG--AACA-TC
** * * *
47779 TTCTTATGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACT
63 TTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
47822 CGAATAATCTT-TTCT
1 CGAA-AATCTTCTTCT
47837 GCTTCACTAT
Statistics
Matches: 756, Mismatches: 91, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
102 90 0.12
104 2 0.00
105 413 0.55
106 7 0.01
107 6 0.01
108 230 0.30
109 8 0.01
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (105 bp):
CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
Found at i:47018 original size:54 final size:53
Alignment explanation
Indices: 46870--47825 Score: 1114
Period size: 54 Copynumber: 18.1 Consensus size: 53
46860 GTATAAGACA
* *
46870 CGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACT
1 CGAAC-ATCTTC-TCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* *
46925 CGAACATC-T-TCAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
1 CGAACATCTTCTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* *
46976 CGAAAATCTTCTGCGAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
1 CGAACATCTTCT-CTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * * *
47030 CGAATATC-T-TCAAACGGGTTCGCTTCCTCTTTCTTCAGGAAGTATAGAACT
1 CGAACATCTTCTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * *
47081 CGAACATCTTCT-T-ACGGGTCCGCTCCTTCTTTCTTTAAGGAGTATGGAACT
1 CGAACATCTTCTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* *
47132 CGAACATC-T-TCAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACT
1 CGAACATCTTCTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* *
47183 CGAAAATCTTCTGCGAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
1 CGAACATCTTCT-CTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * *
47237 CGAACATC-T-TCAAACGGGTTCGCTCCCTCTTTTTTTAGGAAGTATAGAACT
1 CGAACATCTTCTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * *
47288 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACT
1 CGAACATCTTC-TCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * * *
47342 CGAAAATATTCTTCTTACGGGTTCACTCCTTCTTTCTTTAAGGAGTATGGAACT
1 CGAACATCTTC-TCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * *
47396 CGGACATCTTCTTCTTACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACT
1 CGAACATCTTC-TCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * *
47450 CGAACATCTTCTTCTTACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACT
1 CGAACATCTTC-TCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * *
47504 CGGACATCTTCTTCTTAA-GGATTCGCTCCTTCTTTCTTTAAGGAGTATGAAACT
1 CGAACATCTTC-TC-TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* *
47558 CGAACATC-T-TCAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACT
1 CGAACATCTTCTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * *
47609 CGAAAATCTTCTGCGAACGGATTCGCTCACTCTTTCTTTAGGGAGTATGGAACT
1 CGAACATCTTCT-CTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * *
47663 CGAACATCTT-T-AAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
1 CGAACATCTTCTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * *
47714 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACT
1 CGAACATCTTC-TCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * * *
47768 CGAAAATATTCTTCTTATGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACT
1 CGAACATCTTC-TCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
47822 CGAA
1 CGAA
47826 TAATCTTTTC
Statistics
Matches: 793, Mismatches: 87, Indels: 43
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.00
50 3 0.00
51 295 0.37
52 7 0.01
53 10 0.01
54 470 0.59
55 7 0.01
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (53 bp):
CGAACATCTTCTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
Found at i:47598 original size:426 final size:420
Alignment explanation
Indices: 46870--47832 Score: 1515
Period size: 426 Copynumber: 2.3 Consensus size: 420
46860 GTATAAGACA
*
46870 CGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCT-TCAGGGAGTATGGAACTCG--AACA-
1 CGAA-AATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAAAATAT
** * *
46931 TCTTCAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTTCTGCGAACGG
64 TCTTCTTATGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGCGAACGG
*
46996 GTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCTTCAAACGGGTTCGCTTCCTCTT
129 GTTCGCTCCCTCTTTCTTTAAGGAGTATGGAACTCGAATATCTTCAAACGGGTTCGCTTCCTCTT
* * *
47061 TCTTCAGGAAGTATAGAACTCGAACATCTTCTTACGGGTCCGCTCCTTCTTTCTTTAAGGAGTAT
194 TCTTAAGGAAGTATAGAACTCGAACATCTTCTTAAGGATCCGCTCCTTCTTTCTTTAAGGAGTAT
*
47126 GGAACTCGAACATCTTCAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATC
259 GAAACTCGAACATCTTCAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATC
* *
47191 TTCTGCGAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCAAACGGGT
324 TTCTGCGAACGGATTCGCTCACTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCAAACGGGT
* *
47256 TCGCTCCCTCTTTTTTTAGGAAGTATAGAACT
389 TCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
*
47288 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACTCGAAAATATTC
1 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATATTC
* * * * * **
47353 TTCTTACGGGTTCACTCCTTCTTTCTTTAAGGAGTATGGAACTCGGACATCTTCTTCTTACGGGT
66 TTCTTATGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGCGAACGGGT
* * **
47418 TCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGC-TCCTTC
131 TCGCTCCCTCTTTCTTTAAGGAGTATGGAACTCG-A-AT-ATCTTCAAACGGGTTCGCTTCC-TC
* * *
47482 TTTCTTTAAGG-AGTATGGAACTCGGACATCTTCTTCTTAAGGATTCGCTCCTTCTTTCTTTAAG
192 TTTC-TTAAGGAAGTATAGAACTC-GA-A-CATCTTCTTAAGGATCCGCTCCTTCTTTCTTTAAG
47546 GAGTATGAAACTCGAACATCTTCAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACTCG
253 GAGTATGAAACTCGAACATCTTCAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACTCG
*
47611 AAAATCTTCTGCGAACGGATTCGCTCACTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTTAA
318 AAAATCTTCTGCGAACGGATTCGCTCACTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCAA
47676 ACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
383 ACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
47714 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATATTC
1 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATATTC
47779 TTCTTATGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAATAATCTT
66 TTCTTATGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAA-AATCTT
47833 TTCTGCTTCA
Statistics
Matches: 497, Mismatches: 35, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
417 49 0.10
418 5 0.01
419 3 0.01
420 88 0.18
421 1 0.00
422 5 0.01
423 32 0.06
424 7 0.01
425 1 0.00
426 301 0.61
427 5 0.01
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (420 bp):
CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATATTC
TTCTTATGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGCGAACGGGT
TCGCTCCCTCTTTCTTTAAGGAGTATGGAACTCGAATATCTTCAAACGGGTTCGCTTCCTCTTTC
TTAAGGAAGTATAGAACTCGAACATCTTCTTAAGGATCCGCTCCTTCTTTCTTTAAGGAGTATGA
AACTCGAACATCTTCAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAATCTT
CTGCGAACGGATTCGCTCACTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTC
GCTCCCTCTTTCTTCAGGAAGTATAGAACT
Found at i:48315 original size:36 final size:36
Alignment explanation
Indices: 48204--48398 Score: 176
Period size: 36 Copynumber: 5.4 Consensus size: 36
48194 ACTCTTCCTA
* * * * **
48204 GAAGGCTTAAAATGGATTTCCTTCACGACTCTTTTAT
1 GAAGGCTTAAGATGG-TTTGCTTCACTATTCTTTGGT
* ** *
48241 GAAGACACAAGATGGTTTACTTCACTATTCTTTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* * *
48277 GAAGGCTTAAGATGGTTTGCTTCCCTACTCTTTAGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* **
48313 GAAGGCTTAAGATTG-TTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* * * **
48348 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
*
48384 GAAGGCTTCAGATGG
1 GAAGGCTTAAGATGG
48399 ACTTTGCCCC
Statistics
Matches: 133, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
35 29 0.22
36 93 0.70
37 11 0.08
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
Found at i:48386 original size:71 final size:71
Alignment explanation
Indices: 48260--48396 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 71
48250 AGATGGTTTA
** * * **
48260 CTTCACTATTCTTTGGTGAAGGCTTAAGATGGTTTGCTTCCCTACTCTTTAGTGAAGGCTTAAGA
1 CTTCACTATTCTCCGGTGAAGGCTTAAGATGGATTGCTTCACTACTCTCCAGTGAAGGCTTAAGA
48325 TTGTTG
66 TTGTTG
* * * * *
48331 CTTCACTATTCTCCGGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGTGAAGGCTTCAGA
1 CTTCACTATTCTCCGGTGAAGGCTTAAGATGGATTGCTTCACTACTCTCCAGTGAAGGCTTAAGA
48396 T
66 T
48397 GGACTTTGCC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (71 bp):
CTTCACTATTCTCCGGTGAAGGCTTAAGATGGATTGCTTCACTACTCTCCAGTGAAGGCTTAAGA
TTGTTG
Found at i:49929 original size:125 final size:125
Alignment explanation
Indices: 49703--49958 Score: 368
Period size: 125 Copynumber: 2.0 Consensus size: 125
49693 ACTAGTGCTG
*** * * * *
49703 CAACATTATCTTATACTGGTATGGGCCTTCAAAATGCCTCAACACCTCAATTTGTAAGGCTCATT
1 CAACATTATCTTATACTGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAAGCCCATT
* * *
49768 CTCAACGCCTTCTTGGTCTGAATCTCATCATTTCAACATGATGTTGGTTCAGTCGTGCCC
66 CTCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATGTGGGTTCAGTCGTGCCC
* *
49828 CAACATTATCTTATACTGGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAAGCCCGTT
1 CAACATTATCTTATACTGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAAGCCCATT
* * **
49893 CTTAATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
66 CTCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATGTGGGTTCAGTCGTGCCC
49953 CAACAT
1 CAACAT
49959 ATCACAACTT
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
125 115 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (125 bp):
CAACATTATCTTATACTGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAAGCCCATT
CTCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATGTGGGTTCAGTCGTGCCC
Found at i:58076 original size:10 final size:10
Alignment explanation
Indices: 58061--58104 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
58051 GTATTTGTGT
58061 TGTTCGTTTA
1 TGTTCGTTTA
58071 TGTTCGTTTA
1 TGTTCGTTTA
58081 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
58094 TGTTCATTTA
1 TGTTCGTTTA
58104 T
1 T
58105 TATGTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 20 0.67
13 10 0.33
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:58090 original size:23 final size:23
Alignment explanation
Indices: 58061--58141 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
58051 GTATTTGTGT
58061 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCGTTTATTG
* *
58084 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCGTTTATTG
**
58107 TGTTATTTTATGTTCGTTCGT-TTG
1 TGTTCGTTTATGTTCGTT--TATTG
*
58131 CGTTCGTTTAT
1 TGTTCGTTTAT
58142 CATTTAATTG
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 36 0.77
24 10 0.21
25 1 0.02
ACGTcount: A:0.11, C:0.10, G:0.19, T:0.60
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTTATTG
Done.