Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008257.1 Hibiscus syriacus cultivar Beakdansim tig00110910_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: 140121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4548 original size:13 final size:12
Alignment explanation
Indices: 4513--4550 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
4503 CCTTCTGATC
4513 TTTTTATCTTC-
1 TTTTTATCTTCA
*
4524 TTTTTGTCTTCA
1 TTTTTATCTTCA
4536 TTTTCTATCTTCA
1 TTTT-TATCTTCA
4549 TT
1 TT
4551 CAGAGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 4 0.17
13 9 0.39
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTTATCTTCA
Found at i:7795 original size:58 final size:59
Alignment explanation
Indices: 7695--8008 Score: 347
Period size: 58 Copynumber: 5.4 Consensus size: 59
7685 AGACACTATA
* * * * * *
7695 TGTGCT-AAATAATAAGG-AATCATACTGAATATATGAAATTCCATATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTAAG
* *
7752 TGTGCTAAAATGATAAGGAAATCATA-TGAGTGTATGGATTTCCATATGGAGTACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTAAG
* *
7810 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTAAG
* * * * *
7869 TGTGCTAAAATGATAAGGAAATGATATTGA--ATATGGATTTCCAGATAG-GCATTATA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTA-AG
* * * * * *
7925 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGA-TTCCAGAAAAATCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTAAG
* * *
7983 GGTGCTACAAGGATAAGGAAATCATA
1 TGTGCTAAAATGATAAGGAAATCATA
8009 TATAGTATGG
Statistics
Matches: 218, Mismatches: 31, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
56 30 0.14
57 31 0.14
58 92 0.42
59 65 0.30
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTAAG
Found at i:7854 original size:117 final size:113
Alignment explanation
Indices: 7691--8027 Score: 378
Period size: 117 Copynumber: 2.9 Consensus size: 113
7681 CCAAAGACAC
* * * *
7691 TATATGTGCT-AAATAATAAGGAATCATACTGAATATATGAAATTCCATATAGAGCACTGAGTGT
1 TATATGTGCTAAAATGATAAGGAATCATACTGAGTGTATG-GATTCCATATAGAGCACTGAGTGT
7755 GCTAAAATGATAAGGAAATCATATGAGTGTATGGATTTCCATAT-GG-AG
65 GCTAAAATGATAAGGAAATCATATGA-TGTATGGATTTCCATATAGGCAG
*
7803 TACTAAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGA
1 TA-T-A-TGTGCTAAAATGATAAGG-AATCATACTGAGTGTATGGA-TTCCATATAGAGCACTGA
* * * *
7868 GTGTGCTAAAATGATAAGGAAATGATATTGA-ATATGGATTTCCAGATAGGCAT
61 GTGTGCTAAAATGATAAGGAAATCATA-TGATGTATGGATTTCCATATAGGCAG
* * * * * * *
7921 TATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTCCAGAAAAATCACTAAGGGT
1 TATATGTGCTAAAATGATAA-GGAATCATACTGAGTGTATGGATTCCATATAGAGCACTGAGTGT
* * *
7986 GCTACAAGGATAAGGAAATCATAT-ATAGTATGGATTTTCATA
65 GCTAAAATGATAAGGAAATCATATGAT-GTATGGATTTCCATA
8028 GGGCACTTCA
Statistics
Matches: 190, Mismatches: 23, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
112 3 0.02
113 2 0.01
114 48 0.25
115 41 0.22
116 28 0.15
117 62 0.33
118 6 0.03
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (113 bp):
TATATGTGCTAAAATGATAAGGAATCATACTGAGTGTATGGATTCCATATAGAGCACTGAGTGTG
CTAAAATGATAAGGAAATCATATGATGTATGGATTTCCATATAGGCAG
Found at i:8066 original size:114 final size:113
Alignment explanation
Indices: 7694--8054 Score: 331
Period size: 114 Copynumber: 3.2 Consensus size: 113
7684 AAGACACTAT
** * * * * * * * * *
7694 ATGTGCT-AAATAATAAGGAATCATACTGAATATATGAAATTCCATATAGAGCACTGAGTGTGCT
1 ATGTGCTAAAATGGTAAGGAATCATACTGAGTGTATGGATTTCCAGAAAAAGCACTAAGGGTGCT
*
7758 AAAATGATAAGGAAATCATATGAGT-GTATGGATTTCCATATGGAGTAC-TA
66 AAAATGATAAGGAAATCATAT-A-TAGTATGGATTTCCATA-GG-GCACTTA
* * *** * *
7808 AGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTG
1 A-TGTGCTAAAATGGTAAGG-AATCATACTGAGTGTATGGATTTCCAGAAAAAGCACTAAGGGTG
* *
7873 CTAAAATGATAAGGAAATGATAT-TGAATATGGATTTCCAGATA-GGCA-TTA
64 CTAAAATGATAAGGAAATCATATAT-AGTATGGATTTCC--ATAGGGCACTTA
*
7923 TATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGA-TTCCAGAAAAATCACTAAGGGTG
1 -ATGTGCTAAAATGGTAA-GGAATCATACTGAGTGTATGGATTTCCAGAAAAAGCACTAAGGGTG
* * * *
7987 CTACAAGGATAAGGAAATCATATATAGTATGGATTTTCATAGGGCACTTC
64 CTAAAATGATAAGGAAATCATATATAGTATGGATTTCCATAGGGCACTTA
8037 ATGTGCTAAAAATGGTAA
1 ATGTGCT-AAAATGGTAA
8055 ATGGATCATA
Statistics
Matches: 210, Mismatches: 23, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
112 3 0.01
113 11 0.05
114 61 0.29
115 46 0.22
116 25 0.12
117 61 0.29
118 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (113 bp):
ATGTGCTAAAATGGTAAGGAATCATACTGAGTGTATGGATTTCCAGAAAAAGCACTAAGGGTGCT
AAAATGATAAGGAAATCATATATAGTATGGATTTCCATAGGGCACTTA
Found at i:8091 original size:60 final size:60
Alignment explanation
Indices: 8025--8167 Score: 223
Period size: 60 Copynumber: 2.4 Consensus size: 60
8015 ATGGATTTTC
* *
8025 ATAGGGCACTTCATGTGCTAAAAATGGTAAATGGATCATACTAATGGTATAGATTCTCGA
1 ATAGGGCACTTCATGTGCTAAAAATGGTAAATGAATCATACTAATGGTATAGAATCTCGA
* * * *
8085 ATAGGGCATTTCATGTGCTAAAAATGGTAAATGAATCGTATTAATGGTATGGAATCTCGA
1 ATAGGGCACTTCATGTGCTAAAAATGGTAAATGAATCATACTAATGGTATAGAATCTCGA
*
8145 ATAGGGCACTTCGTGTGCTAAAA
1 ATAGGGCACTTCATGTGCTAAAA
8168 TGGAAGAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (60 bp):
ATAGGGCACTTCATGTGCTAAAAATGGTAAATGAATCATACTAATGGTATAGAATCTCGA
Found at i:8417 original size:44 final size:44
Alignment explanation
Indices: 8368--8847 Score: 664
Period size: 44 Copynumber: 11.0 Consensus size: 44
8358 TATGAAATTG
8368 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
8412 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
8456 TGAAATAATAGTAAGTATATTGGTAAAATAAGATTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
8500 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACAAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
8544 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * * * *
8588 TGGAGTAATTGTAAGTATATTGGTAAAATAAGCTTACGTGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * *
8632 TGAAATTATAGTAAG--TATTAGTGAAATAAGCTTACGAACTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * *
8674 TGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * * * *
8718 TGGAATAATGGTAAGTATATTAGTAAAATAAGCTTACGATCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * *
8762 TGGAATAAT-GCTAAGT-TATTGGTAAAAAAAGCTTACGAGCTTA
1 TGAAATTATAG-TAAGTATATTGGTAAAATAAGCTTACGAGCTTA
** * * *
8805 -GGGATTAATGGTAAGTAGATTGGTAAATTAAGCTTACGAGCTT
1 TGAAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
8848 TGATTAAATG
Statistics
Matches: 395, Mismatches: 35, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
42 39 0.10
43 32 0.08
44 324 0.82
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
Found at i:8484 original size:23 final size:23
Alignment explanation
Indices: 8458--8530 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
8448 CGAGCTTATG
8458 AAATAATAGTAAGTATATTGGTA
1 AAATAATAGTAAGTATATTGGTA
* * * ** * *
8481 AAATAAGATTACG-AGCTT-ATG
1 AAATAATAGTAAGTATATTGGTA
*
8502 AAATTATAGTAAGTATATTGGTA
1 AAATAATAGTAAGTATATTGGTA
8525 AAATAA
1 AAATAA
8531 GCTTACAAGC
Statistics
Matches: 32, Mismatches: 16, Indels: 4
0.62 0.31 0.08
Matches are distributed among these distances:
21 10 0.31
22 6 0.19
23 16 0.50
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33
Consensus pattern (23 bp):
AAATAATAGTAAGTATATTGGTA
Found at i:14560 original size:118 final size:118
Alignment explanation
Indices: 14341--14645 Score: 316
Period size: 118 Copynumber: 2.6 Consensus size: 118
14331 TCATTTGAAT
* * * * *
14341 GTATGAATTTCCATATAGAGCACTGA-GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATG
1 GTATGAATTTCCAGATAGGGCACT-ACATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATG
*** * * * *
14405 GATTTTCATGTGGAGCACTGAGTGTGCTAAAATGATAAGGAAATCATATTGAATA
65 GATTTTCATGAAAAGCACTAAGGGTGCTAAAAGGATAAGGAAATCATACT-AATA
* * *
14460 -TATGGATTTCCAGATAGGGCATTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGG
1 GTATGAATTTCCAGATAGGGCACTACATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGG
* * *
14524 A-TTTC-TAGAAAAATCACTAAGGGTTCTACAAGGATAAGGAAATCATACTAATA
66 ATTTTCAT-G-AAAAGCACTAAGGGTGCTAAAAGGATAAGGAAATCATACTAATA
* * *
14577 GTATGAATTTTCATATAGGGCACTACATGTGCTAAAAATGGTAAAGGG-ATCATACT-AATGGTA
1 GTATGAATTTCCAGATAGGGCACTACATGTGCT-AAAATGGT-AAGGGAATCATACTGAGT-GTA
14640 TGGATT
63 TGGATT
14646 CTCGAATAGG
Statistics
Matches: 155, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
116 1 0.01
117 10 0.06
118 115 0.74
119 23 0.15
120 6 0.04
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.30
Consensus pattern (118 bp):
GTATGAATTTCCAGATAGGGCACTACATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGG
ATTTTCATGAAAAGCACTAAGGGTGCTAAAAGGATAAGGAAATCATACTAATA
Found at i:14601 original size:59 final size:59
Alignment explanation
Indices: 14336--14673 Score: 239
Period size: 59 Copynumber: 5.7 Consensus size: 59
14326 TAACATCATT
* * * * *
14336 TGAATGTATGAATTTCCATATAGAGCACTGAGTGTGCTAAAATGATAAGGAAATCATAC
1 TGAATGTATGGATTTTCATATAGGGCACTAAGTGTGCTAAAAGGATAAGGAAATCATAC
* * * * *
14395 TGAGTGTATGGATTTTCATGT-GGAGCACTGAGTGTGCTAAAATGATAAGGAAATCATAT
1 TGAATGTATGGATTTTCATATAGG-GCACTAAGTGTGCTAAAAGGATAAGGAAATCATAC
* * * * *
14454 TGAATATATGGATTTCCAGATAGGGCATTATA-TGTGCTAAAATGG-TAAGGGAATCATAC
1 TGAATGTATGGATTTTCATATAGGGCACTA-AGTGTGCTAAAA-GGATAAGGAAATCATAC
* * * *** * * *
14513 TGAGTGTATGGA-TTTCTAGAAAAATCACTAAGGGTTCTACAAGGATAAGGAAATCATAC
1 TGAATGTATGGATTTTC-ATATAGGGCACTAAGTGTGCTAAAAGGATAAGGAAATCATAC
* *
14572 T-AATAGTATGAATTTTCATATAGGGCACTACA-TGTGCTAAAAATGG-TAAAGG-GATCATAC
1 TGAAT-GTATGGATTTTCATATAGGGCACTA-AGTGTGCT-AAAA-GGAT-AAGGAAATCATAC
* *
14632 T-AATGGTATGGATTCTCGA-ATAGGGCACTTCA-TGTGCTAAAA
1 TGAAT-GTATGGATTTTC-ATATAGGGCAC-TAAGTGTGCTAAAA
14674 ATGGTAAAGG
Statistics
Matches: 221, Mismatches: 43, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
58 9 0.04
59 154 0.70
60 50 0.23
61 8 0.04
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (59 bp):
TGAATGTATGGATTTTCATATAGGGCACTAAGTGTGCTAAAAGGATAAGGAAATCATAC
Found at i:14634 original size:60 final size:60
Alignment explanation
Indices: 14559--14733 Score: 244
Period size: 60 Copynumber: 2.9 Consensus size: 60
14549 CTACAAGGAT
* * *
14559 AAGGAAATCATACTAATAGTATGAATTTTC-ATATAGGGCACTACATGTGCTAAAAATGGTA
1 AAGG-AATCATACTAATGGTATGAATTCTCGA-ATAGGGCACTTCATGTGCTAAAAATGGTA
* *
14620 AAGGGATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
* * * *
14680 AAGGAATTATATTAATGGTATGTATTCTCGAATAGGGCACTTCGTGTGCTAAAA
1 AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAA
14734 TGAGAAGAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
60 98 0.95
61 5 0.05
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (60 bp):
AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
Found at i:14766 original size:60 final size:60
Alignment explanation
Indices: 14591--14779 Score: 199
Period size: 60 Copynumber: 3.2 Consensus size: 60
14581 GAATTTTCAT
* ** * * *
14591 ATAGGGCACTACATGTGCTAAAAATGGTAAAGGGATCATACTAATGGTATGGATTCTCGA
1 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
* * *
14651 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATTATATTAATGGTATGTATTCTCGA
1 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
* *
14711 ATAGGGCACTTCGTGTGCT-AAAAT-G-AGAAGAAAATCATATTAA-GTATATGATATTC-CAA
1 ATAGGGCACTTCATGTGCTAAAAATGGTA-AAG-AAATCATATTAATG-ATATG-TATTCTCGA
*
14770 ATAGAGCACT
1 ATAGGGCACT
14780 GAGAGTGCTA
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 30 0.26
60 78 0.68
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (60 bp):
ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
Found at i:16951 original size:18 final size:17
Alignment explanation
Indices: 16897--16945 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
16887 TTGGACCCTT
* *
16897 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
16915 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
16933 AGTGCATTCGATG
1 AGTGCA-TCGATG
16946 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:17517 original size:60 final size:60
Alignment explanation
Indices: 17435--17609 Score: 235
Period size: 60 Copynumber: 2.9 Consensus size: 60
17425 CTACAAGGAT
* * *
17435 AAGGAAATCATACTAATAGTATGAATTTTC-ATATAGGGCACTACATGTGCTAAAAATGGTA
1 AAGG-AATCATACTAATGGTATGAATTCTCGA-ATAGGGCACTTCATGTGCTAAAAATGGTA
* *
17496 AAGGGATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
* * * * *
17556 AAGGAATTATATTAATGATATGTATTCTCGAATAGGGCACTTCGTGTGCTAAAA
1 AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAA
17610 TGAGAAGAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 97 0.95
61 5 0.05
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (60 bp):
AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
Found at i:17642 original size:60 final size:60
Alignment explanation
Indices: 17467--17655 Score: 208
Period size: 60 Copynumber: 3.2 Consensus size: 60
17457 GAATTTTCAT
* ** * * *
17467 ATAGGGCACTACATGTGCTAAAAATGGTAAAGGGATCATACTAATGGTATGGATTCTCGA
1 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
* *
17527 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATTATATTAATGATATGTATTCTCGA
1 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
* *
17587 ATAGGGCACTTCGTGTGCT-AAAAT-G-AGAAGAAAATCATATTAA-GTATATGATATTC-CAA
1 ATAGGGCACTTCATGTGCTAAAAATGGTA-AAG-AAATCATATTAATG-ATATG-TATTCTCGA
*
17646 ATAGAGCACT
1 ATAGGGCACT
17656 GAGAGTGCTA
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 31 0.27
60 77 0.68
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (60 bp):
ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
Found at i:17649 original size:59 final size:60
Alignment explanation
Indices: 17438--17655 Score: 205
Period size: 60 Copynumber: 3.6 Consensus size: 60
17428 CAAGGATAAG
* * * * *
17438 GAAATCATACTAAT-AGTATGAATTTTCATATAGGGCACTACATGTGCTAAAAATGGTAAA
1 GAAATCATATTAATGA-TATGTATTCTCAAATAGGGCACTTCATGTGCTAAAAATGGTAAA
** * * * *
17498 GGGATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTAAA
1 GAAATCATATTAATGATATGTATTCTCAAATAGGGCACTTCATGTGCTAAAAATGGTAAA
* * * *
17558 GGAATTATATTAATGATATGTATTCTCGAATAGGGCACTTCGTGTGCT-AAAAT-G-AGAA
1 GAAATCATATTAATGATATGTATTCTCAAATAGGGCACTTCATGTGCTAAAAATGGTA-AA
*
17616 GAAAATCATATTAA-GTATATGATATTC-CAAATAGAGCACT
1 G-AAATCATATTAATG-ATATG-TATTCTCAAATAGGGCACT
17656 GAGAGTGCTA
Statistics
Matches: 135, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 31 0.23
60 98 0.73
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (60 bp):
GAAATCATATTAATGATATGTATTCTCAAATAGGGCACTTCATGTGCTAAAAATGGTAAA
Found at i:17824 original size:44 final size:44
Alignment explanation
Indices: 17761--18101 Score: 445
Period size: 44 Copynumber: 8.0 Consensus size: 44
17751 TCAGTGATGC
*
17761 AAATTATAGTAAGTCTATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* *
17805 AAATTATAGTGAGTATATTGGAAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
17849 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
17893 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
17937 AAATTACAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
17981 --------G-AA-TA-A-TAGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * *
18013 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGACCTTAGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * * *
18057 GATTTAATGGTAAGTATATTGGTATATTAAGCTTTCGAGCTTATG
1 AAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
18102 GATTAAATGG
Statistics
Matches: 267, Mismatches: 17, Indels: 25
0.86 0.06 0.08
Matches are distributed among these distances:
32 25 0.09
33 1 0.00
34 2 0.01
35 2 0.01
36 1 0.00
40 1 0.00
41 2 0.01
42 2 0.01
43 1 0.00
44 196 0.73
45 34 0.13
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:17994 original size:32 final size:32
Alignment explanation
Indices: 17957--18024 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
17947 AAGTATATTG
17957 GTAAAATAAGCTTACGAGCTTATGGAATAATA
1 GTAAAATAAGCTTACGAGCTTATGGAATAATA
*
17989 GTAAAATAAGCTTACGAGCTTATGGAATAATG
1 GTAAAATAAGCTTACGAGCTTATGGAATAATA
18021 GTAA
1 GTAA
18025 GTATATTGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (32 bp):
GTAAAATAAGCTTACGAGCTTATGGAATAATA
Found at i:18003 original size:76 final size:76
Alignment explanation
Indices: 17913--18054 Score: 239
Period size: 76 Copynumber: 1.9 Consensus size: 76
17903 AAGTATATTG
* *
17913 GTAAAATAAGCTTACGAGCTTATGAAATTACAGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
1 GTAAAATAAGCTTACGAGCTTATGAAATAACAGTAAGTATATTGGTAAAATAAGCTTACGACCTT
17978 ATGGAATAATA
66 ATGGAATAATA
* **
17989 GTAAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGACCTT
1 GTAAAATAAGCTTACGAGCTTATGAAATAACAGTAAGTATATTGGTAAAATAAGCTTACGACCTT
18054 A
66 A
18055 GGGATTTAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 61 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (76 bp):
GTAAAATAAGCTTACGAGCTTATGAAATAACAGTAAGTATATTGGTAAAATAAGCTTACGACCTT
ATGGAATAATA
Found at i:18033 original size:120 final size:120
Alignment explanation
Indices: 17869--18103 Score: 355
Period size: 120 Copynumber: 1.9 Consensus size: 120
17859 AAGTATATTG
* *
17869 GTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
1 GTAAAATAAGCTTACGAGCTTATGAAATAATAGTAAGTATATTGGTAAAATAAGCTTACGACCTT
*
17934 ATGAAATTACA-GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATA
66 AGGAAATTA-AGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATA
* *
17989 GTAAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGACCTT
1 GTAAAATAAGCTTACGAGCTTATGAAATAATAGTAAGTATATTGGTAAAATAAGCTTACGACCTT
* * * * *
18054 AGGGATTTAATGGTAAGTATATTGGTATATTAAGCTTTCGAGCTTATGGA
66 AGGAAATTAA-GGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
18104 TTAAATGGTA
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
119 1 0.01
120 67 0.65
121 35 0.34
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (120 bp):
GTAAAATAAGCTTACGAGCTTATGAAATAATAGTAAGTATATTGGTAAAATAAGCTTACGACCTT
AGGAAATTAAGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATA
Found at i:18077 original size:45 final size:45
Alignment explanation
Indices: 17989--18122 Score: 189
Period size: 45 Copynumber: 3.0 Consensus size: 45
17979 TGGAATAATA
*
17989 GTAAAATAAGCTTACGAGCTTATGGA-ATAATGGTAAGTATATTG
1 GTAAAATAAGCTTACGAGCTTATGGATTTAATGGTAAGTATATTG
* *
18033 GTAAAATAAGCTTACGACCTTAGGGATTTAATGGTAAGTATATTG
1 GTAAAATAAGCTTACGAGCTTATGGATTTAATGGTAAGTATATTG
* * * * *
18078 GTATATTAAGCTTTCGAGCTTATGGATTAAATGGTATGTATATTG
1 GTAAAATAAGCTTACGAGCTTATGGATTTAATGGTAAGTATATTG
18123 ATAAGAAACT
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 24 0.30
45 55 0.70
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.36
Consensus pattern (45 bp):
GTAAAATAAGCTTACGAGCTTATGGATTTAATGGTAAGTATATTG
Found at i:24497 original size:3 final size:3
Alignment explanation
Indices: 24489--24519 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
24479 TTATAACATT
24489 CAA CAA CAAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA C-AA CAA CAA CAA CAA CAA CAA CAA
24520 AACCCAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:30327 original size:47 final size:47
Alignment explanation
Indices: 30270--30365 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
30260 AAAACTTAAC
* * *
30270 TTGAAACTAAACCTAAACTAAACTAAACAATTCAGCCGCATTTGCTT
1 TTGAAACTAAACCTAAAATAAAATAAACAATTCAGCCACATTTGCTT
* *
30317 TTGAACCTAAACCTAAAATAAAATAAACAATTCAGCCACATTTTCTT
1 TTGAAACTAAACCTAAAATAAAATAAACAATTCAGCCACATTTGCTT
30364 TT
1 TT
30366 TCACTCTCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (47 bp):
TTGAAACTAAACCTAAAATAAAATAAACAATTCAGCCACATTTGCTT
Found at i:31459 original size:22 final size:22
Alignment explanation
Indices: 31434--31503 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
31424 AGACATGGTT
*
31434 GTTGCAACCGGGTTCGGGTTAG
1 GTTGCAACCGGGTTCGGGTCAG
* *
31456 GTTGTAACCAGGTTCGGGTCAG
1 GTTGCAACCGGGTTCGGGTCAG
*
31478 GTTGCAACCGGG-TCTGGGTCGG
1 GTTGCAACCGGGTTC-GGGTCAG
31500 GTTG
1 GTTG
31504 GGTCGTAACC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.13, C:0.19, G:0.41, T:0.27
Consensus pattern (22 bp):
GTTGCAACCGGGTTCGGGTCAG
Found at i:33133 original size:54 final size:55
Alignment explanation
Indices: 33057--33182 Score: 139
Period size: 55 Copynumber: 2.3 Consensus size: 55
33047 TACCTTCACA
* *
33057 TGTACCAACAC-CTAAATTACATTCAAAATGGCAAGGGTATC-ATACACTCCTCAG
1 TGTACCAATACAC-AAATAACATTCAAAATGGCAAGGGTATCAATACACTCCTCAG
* * ** ****
33111 TGTACCGATACACAAATAACATTCGATGTTTTGAGGGTATCAATACACTCCTCAG
1 TGTACCAATACACAAATAACATTCAAAATGGCAAGGGTATCAATACACTCCTCAG
33166 TGTACCAATACACAAAT
1 TGTACCAATACACAAAT
33183 GGAATTCGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 29 0.49
55 30 0.51
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (55 bp):
TGTACCAATACACAAATAACATTCAAAATGGCAAGGGTATCAATACACTCCTCAG
Found at i:33170 original size:55 final size:53
Alignment explanation
Indices: 33090--33234 Score: 193
Period size: 55 Copynumber: 2.7 Consensus size: 53
33080 CAAAATGGCA
33090 AGGGTATCATACACTCCTCAGTGTACCGATACACAAAT-AACATTCGATGTTTT
1 AGGGTATCATACACTCCTCAGTGTACCGATACACAAATGAA-ATTCGATGTTTT
* *
33143 GAGGGTATCAATACACTCCTCAGTGTACCAATACACAAATGGAATTCGATGTTTT
1 -AGGGTATC-ATACACTCCTCAGTGTACCGATACACAAATGAAATTCGATGTTTT
* * *
33198 ACGGGTATCGATACACTCTTTAGTGTACTGATACACA
1 A-GGGTATC-ATACACTCCTCAGTGTACCGATACACA
33235 CCCATACAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
54 9 0.11
55 71 0.88
56 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (53 bp):
AGGGTATCATACACTCCTCAGTGTACCGATACACAAATGAAATTCGATGTTTT
Found at i:38029 original size:25 final size:25
Alignment explanation
Indices: 37975--38029 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
37965 AACAAATGGG
**
37975 CTGATCGGATACCTTGATTTCTTGG
1 CTGATCGGATACCTTGATTTCTTAC
*
38000 ATGATCGGATACCTTGATTTCTTAC
1 CTGATCGGATACCTTGATTTCTTAC
38025 CTGAT
1 CTGAT
38030 TTGTATCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (25 bp):
CTGATCGGATACCTTGATTTCTTAC
Found at i:39815 original size:27 final size:27
Alignment explanation
Indices: 39784--39851 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
39774 TCTATTTACA
39784 AAATCACATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
*
39811 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
39838 AAAT--CATCTCTATA
1 AAATCACATCTCTATA
39852 ATTCCTACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 9 0.23
27 30 0.77
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (27 bp):
AAATCACATCTCTATAGGAATGGTAAC
Found at i:47348 original size:9 final size:9
Alignment explanation
Indices: 47334--47393 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
47324 TGAACCAGTT
47334 GAGCCGACC
1 GAGCCGACC
47343 GAGCCGACC
1 GAGCCGACC
*
47352 GAGCTGACC
1 GAGCCGACC
*
47361 TA-CCGAGCC
1 GAGCCGA-CC
*
47370 GA-CCGAGCT
1 GAGCCGA-CC
47379 GA-CCGACC
1 GAGCCGACC
47387 GAGCCGA
1 GAGCCGA
47394 ACTACCGAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
8 6 0.14
9 37 0.86
ACGTcount: A:0.23, C:0.40, G:0.32, T:0.05
Consensus pattern (9 bp):
GAGCCGACC
Found at i:47365 original size:13 final size:13
Alignment explanation
Indices: 47346--47390 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
47336 GCCGACCGAG
47346 CCGACCGAGCTGA
1 CCGACCGAGCTGA
*
47359 CCTACCGA---G-
1 CCGACCGAGCTGA
47368 CCGACCGAGCTGA
1 CCGACCGAGCTGA
47381 CCGACCGAGC
1 CCGACCGAGC
47391 CGAACTACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
9 7 0.27
10 1 0.04
12 1 0.04
13 17 0.65
ACGTcount: A:0.22, C:0.42, G:0.29, T:0.07
Consensus pattern (13 bp):
CCGACCGAGCTGA
Found at i:47368 original size:22 final size:22
Alignment explanation
Indices: 47337--47393 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
47327 ACCAGTTGAG
47337 CCGACCGAGCCGACCGAGCTGA
1 CCGACCGAGCCGACCGAGCTGA
*
47359 CCTACCGAGCCGACCGAGCTGA
1 CCGACCGAGCCGACCGAGCTGA
47381 CCGACCGAGCCGA
1 CCGACCGAGCCGA
47394 ACTACCGAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.23, C:0.42, G:0.30, T:0.05
Consensus pattern (22 bp):
CCGACCGAGCCGACCGAGCTGA
Found at i:47436 original size:19 final size:19
Alignment explanation
Indices: 47414--47452 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
47404 CGCTTAGACT
*
47414 GAACCGCCTGGACCGGACC
1 GAACCGCCTGGACCGAACC
47433 GAACCGCCTGGACCGAACC
1 GAACCGCCTGGACCGAACC
47452 G
1 G
47453 TTGACCGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.41, G:0.31, T:0.05
Consensus pattern (19 bp):
GAACCGCCTGGACCGAACC
Found at i:48787 original size:18 final size:18
Alignment explanation
Indices: 48761--48795 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48751 TCGAAAGAAC
*
48761 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
48779 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
48796 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:52533 original size:22 final size:22
Alignment explanation
Indices: 52505--52594 Score: 92
Period size: 22 Copynumber: 4.1 Consensus size: 22
52495 TGAACCAGTT
*
52505 GAGCCGACCGACTGAGCCGATC
1 GAGCCGACCGACCGAGCCGATC
* *
52527 GAGCCGACTGAGCCGA-TCGATC
1 GAGCCGACCGA-CCGAGCCGATC
* * * *
52549 GAGCCGATCGACCAAACCGACC
1 GAGCCGACCGACCGAGCCGATC
*
52571 GAGCTGACCGACCGAGCCGATC
1 GAGCCGACCGACCGAGCCGATC
52593 GA
1 GA
52595 ACCGCTTAGA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
21 3 0.06
22 47 0.89
23 3 0.06
ACGTcount: A:0.26, C:0.36, G:0.30, T:0.09
Consensus pattern (22 bp):
GAGCCGACCGACCGAGCCGATC
Found at i:52535 original size:18 final size:18
Alignment explanation
Indices: 52512--52546 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52502 GTTGAGCCGA
52512 CCGACTGAGCCGATCGAG
1 CCGACTGAGCCGATCGAG
52530 CCGACTGAGCCGATCGA
1 CCGACTGAGCCGATCGA
52547 TCGAGCCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.34, G:0.31, T:0.11
Consensus pattern (18 bp):
CCGACTGAGCCGATCGAG
Found at i:53968 original size:18 final size:18
Alignment explanation
Indices: 53942--53976 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53932 TCGAAAGGAA
*
53942 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
53960 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
53977 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:56523 original size:68 final size:70
Alignment explanation
Indices: 56411--56563 Score: 238
Period size: 68 Copynumber: 2.2 Consensus size: 70
56401 TTATGAAATA
56411 ATATATATTATATCACAGCTAAATACAGAAAGTAAAGGCATTGTAACACTAGTTAGGAACTTCAT
1 ATATATA-TATAT-ACAGCTAAATACAGAAAGTAAAGGCATTGTAACACTAGTTAGGAACTTCAT
56476 AGTT-GT
64 AGTTAGT
* *
56482 ATATATATATAT-CAGCTAAATACAGAAAGTAAAGGCATTGTAATATTAGTTAGGAACTTCATAG
1 ATATATATATATACAGCTAAATACAGAAAGTAAAGGCATTGTAACACTAGTTAGGAACTTCATAG
*
56546 TTATT
66 TTAGT
*
56551 TTATATATATATA
1 ATATATATATATA
56564 TATATATATA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
68 52 0.68
69 12 0.16
70 5 0.07
71 7 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (70 bp):
ATATATATATATACAGCTAAATACAGAAAGTAAAGGCATTGTAACACTAGTTAGGAACTTCATAG
TTAGT
Found at i:58756 original size:64 final size:64
Alignment explanation
Indices: 58620--58803 Score: 174
Period size: 64 Copynumber: 2.8 Consensus size: 64
58610 ACTAGATATA
* * *
58620 TTTTAATATTCAAATTTAAACAGATAATAATACCTTTTAATTTGAAATATTCAAAAGATATAAAC
1 TTTTAATATTCAAACTTAAATAGAT-AT--TA-TTTTTAATTTGAAATATTCAAAAGATATAAAC
*
58685 TCC
62 TAC
* * * * *
58688 TTTTAGTATTCCAACTTAAATAGATATTATTTTTAATTTTAAATATTCAAAAGGATAT-AATTAT
1 TTTTAATATTCAAACTTAAATAGATATTATTTTTAATTTGAAATATTCAAAA-GATATAAACTAC
* * * *
58752 TTTTAATATTCAAATTTAAATAGGTAATACCTTTTT-ATTTGACATATTCAAA
1 TTTTAATATTCAAACTTAAATAGATATTA--TTTTTAATTTGAAATATTCAAA
58804 GAATAATTAT
Statistics
Matches: 97, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
64 48 0.49
65 21 0.22
66 5 0.05
67 2 0.02
68 21 0.22
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.43
Consensus pattern (64 bp):
TTTTAATATTCAAACTTAAATAGATATTATTTTTAATTTGAAATATTCAAAAGATATAAACTAC
Found at i:62598 original size:63 final size:60
Alignment explanation
Indices: 62492--62699 Score: 169
Period size: 63 Copynumber: 3.4 Consensus size: 60
62482 TAATAATACC
* * *
62492 TTTT-ATTTGAAATATTCAAAA-AAT-ATAAACTCCTTTTACTATTCAAACTTAAATAGATATTA
1 TTTTAATTTAAAATATTCAAAAGAATAAT-TA-TCC-TTTAATATTCAAA-TTAAATAGATA-TA
*
62554 TTTTAATTTAAAATATTCAAAAGTATATAATTAT-CTTTAATATTCAAATTTAAATAGGTAATA
1 TTTTAATTTAAAATATTCAAAAG-A-ATAATTATCCTTTAATATTCAAA-TTAAATAGAT-ATA
* * * *
62617 CCTTTTAATTTGACATATTC-AAAGAATAATTATCCTATTAATATTTAAATTAAA-A-ATATC
1 --TTTTAATTTAAAATATTCAAAAGAATAATTATCCT-TTAATATTCAAATTAAATAGATATA
* *
62677 TTTTAATTTATAATATTTAAAAG
1 TTTTAATTTAAAATATTCAAAAG
62700 GAACATGAAT
Statistics
Matches: 121, Mismatches: 14, Indels: 25
0.76 0.09 0.16
Matches are distributed among these distances:
58 14 0.12
59 4 0.03
60 2 0.02
61 1 0.01
62 13 0.11
63 47 0.39
64 17 0.14
65 18 0.15
66 3 0.02
67 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (60 bp):
TTTTAATTTAAAATATTCAAAAGAATAATTATCCTTTAATATTCAAATTAAATAGATATA
Found at i:62693 original size:58 final size:62
Alignment explanation
Indices: 62459--62699 Score: 157
Period size: 63 Copynumber: 3.8 Consensus size: 62
62449 CTAGATATAT
* *
62459 TTTAATATTCAAATTTAAAAAAATAATAATACCTTTT-ATTTGAAATATTCAAAA-AATATAA--
1 TTTAATATTCAAATTT----AAAT-AGAATACCTTTTAATTT-AAATATTCAAAAGTATATAATT
62520 ACTCC
60 A-T-C
* *
62525 TTTTACTATTCAAACTTAAATAGATATTA--TTTTAATTTAAAATATTCAAAAGTATATAATTAT
1 -TTTAATATTCAAATTTAAATAGA-A-TACCTTTTAATTT-AAATATTCAAAAGTATATAATTAT
62588 C
62 C
*
62589 TTTAATATTCAAATTTAAATAGGTAATACCTTTTAATTTGACATATTC-AAAG-A-ATAATTATC
1 TTTAATATTCAAATTTAAATA-G-AATACCTTTTAATTT-AAATATTCAAAAGTATATAATTAT-
62651 C
62 C
* * *
62652 TATTAATATTTAAA-TT-AA-A-AATATCTTTTAATTTATAATATTTAAAAG
1 T-TTAATATTCAAATTTAAATAGAATACCTTTTAATTTA-AATATTCAAAAG
62700 GAACATGAAT
Statistics
Matches: 147, Mismatches: 13, Indels: 36
0.75 0.07 0.18
Matches are distributed among these distances:
57 1 0.01
58 19 0.13
59 4 0.03
61 1 0.01
62 16 0.11
63 47 0.32
64 26 0.18
65 18 0.12
66 1 0.01
67 14 0.10
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (62 bp):
TTTAATATTCAAATTTAAATAGAATACCTTTTAATTTAAATATTCAAAAGTATATAATTATC
Found at i:67483 original size:31 final size:32
Alignment explanation
Indices: 67448--67510 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
67438 ATAATGTTAC
* *
67448 AAATAAAA-TCACTCCAATGTGGGTGTATTAT
1 AAATAAAAGGCACTCAAATGTGGGTGTATTAT
67479 AAATAAAAGGCACTCAAATGTGGGTGTATTAT
1 AAATAAAAGGCACTCAAATGTGGGTGTATTAT
67511 GAAGTGGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (32 bp):
AAATAAAAGGCACTCAAATGTGGGTGTATTAT
Found at i:68949 original size:45 final size:45
Alignment explanation
Indices: 68898--68993 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
68888 GAAGAGAAGC
* * *
68898 AATTTGCTTTGTTTATGAAAGGTGGGTGGCTGGTTGCTTTGAGAG
1 AATTTGCTTTGTTTAAGAAAGGTGGGTGGCTAGTTGCTTCGAGAG
68943 AATTTGCTTTGTTTAAGAAAGGTGGGTGGCTAGTTGCTTCGAGAG
1 AATTTGCTTTGTTTAAGAAAGGTGGGTGGCTAGTTGCTTCGAGAG
68988 AGATTT
1 A-ATTT
68994 CTATTCTAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 43 0.91
46 4 0.09
ACGTcount: A:0.21, C:0.07, G:0.33, T:0.39
Consensus pattern (45 bp):
AATTTGCTTTGTTTAAGAAAGGTGGGTGGCTAGTTGCTTCGAGAG
Found at i:69567 original size:328 final size:333
Alignment explanation
Indices: 68965--69625 Score: 1262
Period size: 328 Copynumber: 2.0 Consensus size: 333
68955 TTAAGAAAGG
68965 TGGGTGGCTAGTTGCTTCGAGAGAGATTTCTATTCTAAGTGTTTAAGATTGTAGGAACATATGGC
1 TGGGTGGCTAGTTGCTTCGAGAGAGATTTCTATTCTAAGTGTTTAAGATTGTAGGAACATATGGC
*
69030 TTTACAGGGGCACGAACAATCTGGCGAAGCTGTTGTTGGGGATGATGGCAGAGGACGAAGAATAT
66 TTTACAGGGGCACGAACAATCTGGCGAAGCTGTTGTTGGGGAAGATGGCAGAGGACGAAGAATAT
69095 AACGTTCTAAAATCTGGGTTAGTAGAATCGAGTAATTTTCGTGATTTCTGGTAAAATCAAAATTT
131 AACGTTCTAAAATCTGGGTTAGTAGAATCGAGTAATTTTCGTGATTTCTGGTAAAATCAAAATTT
69160 TGAATTAAAATATGAGAAATATTTTTAAATACTAAAATATGATTTTTGAAATATTAAAAATAATA
196 TGAATTAAAATATGAGAAATATTTTTAAATACTAAAATATGATTTTTGAAATATTAAAAATAATA
69225 TTATTCAGATTTAATGGAATTTTAGAAGTGATTAAATTGCAATTTTTGCAAAGTATGAATTTTAG
261 TTATTCAGATTTAATGGAATTTTAGAAGTGATTAAATTGCAATTTTTGCAAAGTATGAATTTTAG
69290 TGACTAAA
326 TGACTAAA
69298 TGGGTGGCTAGTTGCTTCGAGAGAGATTTCTATTCTAAGTGTTTTAAGATTGTAGGAACATATGG
1 TGGGTGGCTAGTTGCTTCGAGAGAGATTTCTATTCTAAGTG-TTTAAGATTGTAGGAACATATGG
69363 CTTTACA-GGGCACGAAC-ATCTGGCG-AGCTGTTGTTGGGGAAGATGGCAGAGGACGAAG-ATA
65 CTTTACAGGGGCACGAACAATCTGGCGAAGCTGTTGTTGGGGAAGATGGCAGAGGACGAAGAATA
69424 TAACGTTCTAAAATCTGGGTTAGT-GAATCGAGTAATTTTCGTGATTTCTGGTAAAATCAAAATT
130 TAACGTTCTAAAATCTGGGTTAGTAGAATCGAGTAATTTTCGTGATTTCTGGTAAAATCAAAATT
69488 TTGAATT-AAATATGAGAAATATTTTTAAATACTAAAATATGATTTTTGAAATATTAAAAATAAT
195 TTGAATTAAAATATGAGAAATATTTTTAAATACTAAAATATGATTTTTGAAATATTAAAAATAAT
69552 ATTATTCAGATTTAATGGAATTTTAGAAGTGATTAAATTGCAATTTTTGCAAAGTATGAATTTTA
260 ATTATTCAGATTTAATGGAATTTTAGAAGTGATTAAATTGCAATTTTTGCAAAGTATGAATTTTA
69617 GTGACTAAA
325 GTGACTAAA
69626 CTGTAAATGA
Statistics
Matches: 326, Mismatches: 1, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
328 131 0.40
329 47 0.14
330 27 0.08
331 32 0.10
332 8 0.02
333 51 0.16
334 30 0.09
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (333 bp):
TGGGTGGCTAGTTGCTTCGAGAGAGATTTCTATTCTAAGTGTTTAAGATTGTAGGAACATATGGC
TTTACAGGGGCACGAACAATCTGGCGAAGCTGTTGTTGGGGAAGATGGCAGAGGACGAAGAATAT
AACGTTCTAAAATCTGGGTTAGTAGAATCGAGTAATTTTCGTGATTTCTGGTAAAATCAAAATTT
TGAATTAAAATATGAGAAATATTTTTAAATACTAAAATATGATTTTTGAAATATTAAAAATAATA
TTATTCAGATTTAATGGAATTTTAGAAGTGATTAAATTGCAATTTTTGCAAAGTATGAATTTTAG
TGACTAAA
Found at i:72200 original size:21 final size:20
Alignment explanation
Indices: 72176--72215 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
72166 GCTCAAGTTC
*
72176 ATTTTTAATGGACTTTGAATT
1 ATTTTTAA-GAACTTTGAATT
*
72197 ATTTTTGAGAACTTTGAAT
1 ATTTTTAAGAACTTTGAAT
72216 AAATTCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (20 bp):
ATTTTTAAGAACTTTGAATT
Found at i:75454 original size:17 final size:18
Alignment explanation
Indices: 75420--75454 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
75410 ATTTGGTTTG
75420 AAATTTTAGCCTTCAACA
1 AAATTTTAGCCTTCAACA
*
75438 AAATTTTGGCC-TCAACA
1 AAATTTTAGCCTTCAACA
75455 TGTTCGACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (18 bp):
AAATTTTAGCCTTCAACA
Found at i:82946 original size:13 final size:13
Alignment explanation
Indices: 82905--82939 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
82895 TGCGTCAAAA
82905 ATTTATGACGCAC
1 ATTTATGACGCAC
*
82918 ATTTATGACGCGC
1 ATTTATGACGCAC
82931 ATTTATGAC
1 ATTTATGAC
82940 TTACATTGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:83061 original size:85 final size:85
Alignment explanation
Indices: 82918--83083 Score: 287
Period size: 85 Copynumber: 2.0 Consensus size: 85
82908 TATGACGCAC
* * *
82918 ATTTATGACGCGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
*
82983 CACACATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
*
83003 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
83068 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
83084 GTGATTGTAT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
CACACATTCGTGTGTCATAA
Found at i:101112 original size:17 final size:16
Alignment explanation
Indices: 101090--101141 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
101080 TATTTTCATC
101090 TTTTTCATTGCATTTGT
1 TTTTTCATTGCATTT-T
*
101107 TTTTTCATTGAATGTTT
1 TTTTTCATTGCAT-TTT
*
101124 ATTTTCATTGCATTTT
1 TTTTTCATTGCATTTT
101140 TT
1 TT
101142 ATTATTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 4 0.13
17 24 0.80
18 2 0.07
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (16 bp):
TTTTTCATTGCATTTT
Found at i:101232 original size:17 final size:17
Alignment explanation
Indices: 101210--101266 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
101200 TCATTATTAG
*
101210 TGCATTCATTTTGTCAT
1 TGCATTCATATTGTCAT
*
101227 TGCATTCATATTGTCAC
1 TGCATTCATATTGTCAT
* *
101244 TACATAT-GTATTGTCAT
1 TGCAT-TCATATTGTCAT
101261 TGCATT
1 TGCATT
101267 ATTGTTGCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (17 bp):
TGCATTCATATTGTCAT
Found at i:111853 original size:54 final size:54
Alignment explanation
Indices: 111743--111949 Score: 234
Period size: 54 Copynumber: 3.8 Consensus size: 54
111733 CCATACGGTC
* * * ** * * * * **
111743 ATTCATAAACATATTATGAATTATGTGGTTTGCACACATAATGCCAAAATTATT
1 ATTCATCAACATATGATGAATTACGTACTTTGTACACTTAGTGCCGAAACGATT
* * * * * *
111797 ATTCATCAACCTATGATGAATTCCGTACTTTATAAACTTAGTGCCGAAATGTTT
1 ATTCATCAACATATGATGAATTACGTACTTTGTACACTTAGTGCCGAAACGATT
*
111851 ATTCATCAACATATGATGAATTACATACTTTGTACACTTAGTGCCGAAACGATT
1 ATTCATCAACATATGATGAATTACGTACTTTGTACACTTAGTGCCGAAACGATT
* *
111905 ATTCATCAACATATGATGAATTTCGTACTTTGCACACTTAGTGCC
1 ATTCATCAACATATGATGAATTACGTACTTTGTACACTTAGTGCC
111950 TATTTGGTCA
Statistics
Matches: 128, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 128 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTACGTACTTTGTACACTTAGTGCCGAAACGATT
Found at i:111870 original size:108 final size:108
Alignment explanation
Indices: 111743--111949 Score: 261
Period size: 108 Copynumber: 1.9 Consensus size: 108
111733 CCATACGGTC
* ** ** ** *
111743 ATTCATAAACATATTATGAATTATGTGGTTTGCACACATAATGCCAAAATTATTATTCATCAACC
1 ATTCATAAACATATGATGAATTACATACTTTGCACACATAATGCCAAAACGATTATTCATCAACA
*
111808 TATGATGAATTCCGTACTTTATAAACTTAGTGCCGAAATGTTT
66 TATGATGAATTCCGTACTTTACAAACTTAGTGCCGAAATGTTT
* * * * *
111851 ATTCATCAACATATGATGAATTACATACTTTGTACACTTAGTGCCGAAACGATTATTCATCAACA
1 ATTCATAAACATATGATGAATTACATACTTTGCACACATAATGCCAAAACGATTATTCATCAACA
* * *
111916 TATGATGAATTTCGTACTTTGCACACTTAGTGCC
66 TATGATGAATTCCGTACTTTACAAACTTAGTGCC
111950 TATTTGGTCA
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
108 82 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (108 bp):
ATTCATAAACATATGATGAATTACATACTTTGCACACATAATGCCAAAACGATTATTCATCAACA
TATGATGAATTCCGTACTTTACAAACTTAGTGCCGAAATGTTT
Found at i:112022 original size:15 final size:15
Alignment explanation
Indices: 112002--112030 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
111992 TGAGTAGTAT
112002 AACATATAGTTACAC
1 AACATATAGTTACAC
112017 AACATATAGTTACA
1 AACATATAGTTACA
112031 TAATTAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (15 bp):
AACATATAGTTACAC
Found at i:115778 original size:8 final size:9
Alignment explanation
Indices: 115749--115778 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
115739 AAATAAATTG
115749 AAATAAATAA
1 AAAT-AATAA
115759 AAATAATAA
1 AAATAATAA
115768 AAATAATAA
1 AAATAATAA
115777 AA
1 AA
115779 GTATATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAATAA
Found at i:116583 original size:40 final size:37
Alignment explanation
Indices: 116524--116608 Score: 134
Period size: 40 Copynumber: 2.2 Consensus size: 37
116514 AATAATTAAT
116524 TCCTAAATAAAATAATAATAAAATAATCAAACTAAAAA
1 TCCTAAATAAAATAATAATAAAATAATCAAA-TAAAAA
*
116562 TCCTAAATAAAAAATAATAATAAAATGATCAAATAAAAA
1 TCCTAAAT--AAAATAATAATAAAATAATCAAATAAAAA
116601 TCCTAAAT
1 TCCTAAAT
116609 CTAAAAGGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
38 8 0.18
39 14 0.32
40 22 0.50
ACGTcount: A:0.64, C:0.11, G:0.01, T:0.25
Consensus pattern (37 bp):
TCCTAAATAAAATAATAATAAAATAATCAAATAAAAA
Found at i:117893 original size:21 final size:21
Alignment explanation
Indices: 117867--117910 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
117857 TATGAGAAAT
117867 ATTTTT-AAATACTAAAATATA
1 ATTTTTGAAATA-TAAAATATA
*
117888 ATTTTTGAAATATTAAATATA
1 ATTTTTGAAATATAAAATATA
117909 AT
1 AT
117911 ATTATTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTTTTGAAATATAAAATATA
Found at i:118464 original size:13 final size:13
Alignment explanation
Indices: 118446--118471 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
118436 AGAATAACTC
118446 TCTTTAATTAAAA
1 TCTTTAATTAAAA
118459 TCTTTAATTAAAA
1 TCTTTAATTAAAA
118472 CTAATTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TCTTTAATTAAAA
Found at i:118628 original size:36 final size:36
Alignment explanation
Indices: 118583--118667 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 36
118573 CTTTTCTTTT
* *
118583 ATCTCTAAAAAGTCAAATTCCCTTATCTTGAACTTA
1 ATCTCTAAAAAGTCAAATTCCCATATCTTCAACTTA
* * * *
118619 ATCTATAAAAATTCAAATTCTCATATCTTCAGCTTA
1 ATCTCTAAAAAGTCAAATTCCCATATCTTCAACTTA
*
118655 ATCTCCAAAAAGT
1 ATCTCTAAAAAGT
118668 TGAGAAGATT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (36 bp):
ATCTCTAAAAAGTCAAATTCCCATATCTTCAACTTA
Found at i:119447 original size:31 final size:32
Alignment explanation
Indices: 119401--119477 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
119391 TAATGTTAAA
* *
119401 TAAAATAAAACAAAACAA-AATAAA-AATGTAT
1 TAAATTAAAAGAAAACAACAATAAAGAATG-AT
*
119432 TAAATTAAAAGAAAACAACCATTAAAGAATGAT
1 TAAATTAAAAGAAAACAA-CAATAAAGAATGAT
*
119465 TAAATTGAAAGAA
1 TAAATTAAAAGAA
119478 TTTAAAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 16 0.41
33 19 0.49
34 4 0.10
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (32 bp):
TAAATTAAAAGAAAACAACAATAAAGAATGAT
Found at i:120889 original size:40 final size:40
Alignment explanation
Indices: 120846--120921 Score: 120
Period size: 38 Copynumber: 1.9 Consensus size: 40
120836 AAGAAACTAT
* *
120846 ATATATTATTTATGTTTT-CAAAAA-CATTTTAAAAAATC
1 ATATATTATATATGTTTTCCAAAAACCATTTAAAAAAATC
120884 ATATATTATATATGTTTTCCAAAAACCATTTAAAAAAA
1 ATATATTATATATGTTTTCCAAAAACCATTTAAAAAAA
120922 ACCATATACG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 17 0.50
39 6 0.18
40 11 0.32
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (40 bp):
ATATATTATATATGTTTTCCAAAAACCATTTAAAAAAATC
Found at i:120935 original size:34 final size:33
Alignment explanation
Indices: 120891--120954 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
120881 ATCATATATT
*
120891 ATATATGTTTTCCAAAAACCATTTAAAAAAAACC
1 ATATACGTTTT-CAAAAACCATTTAAAAAAAACC
* **
120925 ATATACGTTTTCAAAATCGTTTTAAAAAAA
1 ATATACGTTTTCAAAAACCATTTAAAAAAA
120955 TTTTGAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 16 0.62
34 10 0.38
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (33 bp):
ATATACGTTTTCAAAAACCATTTAAAAAAAACC
Found at i:121019 original size:22 final size:22
Alignment explanation
Indices: 120991--121035 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
120981 CAAAAATACG
**
120991 TTTTCAAATCCTATACTATATA
1 TTTTCAAAAACTATACTATATA
*
121013 TTTTCAAAAACTATATTATATA
1 TTTTCAAAAACTATACTATATA
121035 T
1 T
121036 ATTATGCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTCAAAAACTATACTATATA
Found at i:121769 original size:58 final size:58
Alignment explanation
Indices: 121706--121843 Score: 249
Period size: 58 Copynumber: 2.4 Consensus size: 58
121696 TTTGAGTCGG
* *
121706 ATATCCTTCGTTGTGAAGTTGAGATCCCACTTTAATCTTGAGTGTTCTTTTGAGTTCA
1 ATATCCTTCGTTGTGAAGTTGAGATCCAACTTTAATCTTAAGTGTTCTTTTGAGTTCA
121764 ATATCCTTCGTTGTGAAGTTGAGATCCAACTTTAATCTTAAGTGTTCTTTTGAGTTCA
1 ATATCCTTCGTTGTGAAGTTGAGATCCAACTTTAATCTTAAGTGTTCTTTTGAGTTCA
*
121822 ATATCCTTCGTTGTGAACTTGA
1 ATATCCTTCGTTGTGAAGTTGA
121844 AAATTGACTC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 77 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (58 bp):
ATATCCTTCGTTGTGAAGTTGAGATCCAACTTTAATCTTAAGTGTTCTTTTGAGTTCA
Found at i:129352 original size:24 final size:24
Alignment explanation
Indices: 129325--129378 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
129315 AGATTTTACT
*
129325 TTTGCAGCCGATGAAGCTTGTGCC
1 TTTGCAGCAGATGAAGCTTGTGCC
* * *
129349 TTTGCAGTATATGAAGCTTGTGCT
1 TTTGCAGCAGATGAAGCTTGTGCC
129373 TTTGCA
1 TTTGCA
129379 ATAGATGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (24 bp):
TTTGCAGCAGATGAAGCTTGTGCC
Found at i:129386 original size:24 final size:24
Alignment explanation
Indices: 129334--129386 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
129324 TTTTGCAGCC
*
129334 GATGAAGCTTGTGCCTTTGCAGTA
1 GATGAAGCTTGTGCCTTTGCAATA
* *
129358 TATGAAGCTTGTGCTTTTGCAATA
1 GATGAAGCTTGTGCCTTTGCAATA
129382 GATGA
1 GATGA
129387 GTCTCCTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (24 bp):
GATGAAGCTTGTGCCTTTGCAATA
Found at i:133065 original size:5 final size:5
Alignment explanation
Indices: 133055--133088 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
133045 AAATTATGTT
*
133055 AAATA AAATA AAATA AAATA AAACA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAATA AAAT
133089 GTATTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:134789 original size:76 final size:74
Alignment explanation
Indices: 134507--134822 Score: 304
Period size: 76 Copynumber: 4.2 Consensus size: 74
134497 AAACTATATA
* * *
134507 TATAATATATATGTTTTT-AAAAATA-TTTTAAAAAATCATATATTATATGTTTTCAAAAATACG
1 TATATTATATAT-TTTTTCAAAAATACTTTTAAAAACT-ATATATTATACGTTTTCAAAAATACG
*
134570 TTTTCAAAAAT
64 TTTTCAAAAAC
* * ** * * *
134581 TAAATTATATATGTTTTCCAAAAACCTTTTTTTTTTAAAAACCACATATTATACATTTTC-AAAA
1 TATATTATATAT-TTTTTCAAAAA-----TACTTTTAAAAACTATATATTATACGTTTTCAAAAA
134645 T-CGTTTT-AAAAAC
60 TACGTTTTCAAAAAC
** ** *
134658 TATA-TATAATACATTTTCAAAACCA-TTTTAAAAAACTATATATTATATGTTTTCAAAAATACG
1 TATATTAT-ATATTTTTTCAAAAATACTTTT-AAAAACTATATATTATACGTTTTCAAAAATACG
*
134721 CTTTCAAAAAC
64 TTTTCAAAAAC
134732 TATATTATATATTTTTTCAAAAATACGTTTTCAAAAACTATATATTATACGTTTTCAAAAATACG
1 TATATTATATATTTTTTCAAAAATAC-TTTT-AAAAACTATATATTATACGTTTTCAAAAATACG
*
134797 TTTTCAAAACC
64 TTTTCAAAAAC
*
134808 TATACTATATATTTT
1 TATATTATATATTTT
134823 CAAAAACTAT
Statistics
Matches: 196, Mismatches: 31, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
70 4 0.02
71 20 0.10
72 5 0.03
73 5 0.03
74 38 0.19
75 8 0.04
76 70 0.36
77 11 0.06
78 6 0.03
79 5 0.03
80 15 0.08
81 9 0.05
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (74 bp):
TATATTATATATTTTTTCAAAAATACTTTTAAAAACTATATATTATACGTTTTCAAAAATACGTT
TTCAAAAAC
Found at i:134797 original size:14 final size:14
Alignment explanation
Indices: 134778--134805 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
134768 ACTATATATT
134778 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
134792 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
134806 CCTATACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATACGTTTTCAAAA
Found at i:134811 original size:38 final size:38
Alignment explanation
Indices: 134505--134828 Score: 269
Period size: 38 Copynumber: 8.6 Consensus size: 38
134495 AGAAACTATA
* *
134505 TATATAATATATATGTTTTTAAAAATA--TTTT-AAAAAA
1 TATAT-AT-TATATGTTTTCAAAAATACGTTTTCAAAAAC
*
134542 TCATATATTATATGTTTTCAAAAATACGTTTTCAAAAAT
1 T-ATATATTATATGTTTTCAAAAATACGTTTTCAAAAAC
* *** *
134581 TAAAT-TATATATGTTTTCCAAAAACCTTTTTTTTTTAAAAAC
1 TATATAT-TATATGTTTT-CAAAAA---TACGTTTTCAAAAAC
* * **
134623 CACATATTATACATTTTC-AAAAT-CGTTTT-AAAAAC
1 TATATATTATATGTTTTCAAAAATACGTTTTCAAAAAC
* ** * * *
134658 TATATATAATACATTTTC-AAAA-CCATTTTAAAAAAC
1 TATATATTATATGTTTTCAAAAATACGTTTTCAAAAAC
*
134694 TATATATTATATGTTTTCAAAAATACGCTTTCAAAAAC
1 TATATATTATATGTTTTCAAAAATACGTTTTCAAAAAC
*
134732 TATAT-TATATATTTTTTCAAAAATACGTTTTCAAAAAC
1 TATATAT-TATATGTTTTCAAAAATACGTTTTCAAAAAC
* *
134770 TATATATTATACGTTTTCAAAAATACGTTTTCAAAACC
1 TATATATTATATGTTTTCAAAAATACGTTTTCAAAAAC
134808 TATACTA-TATA--TTTTCAAAAA
1 TATA-TATTATATGTTTTCAAAAA
134829 CTATATTACA
Statistics
Matches: 240, Mismatches: 30, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
35 30 0.12
36 52 0.22
37 10 0.04
38 106 0.44
39 15 0.06
40 4 0.02
41 1 0.00
42 21 0.09
43 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (38 bp):
TATATATTATATGTTTTCAAAAATACGTTTTCAAAAAC
Found at i:134841 original size:22 final size:22
Alignment explanation
Indices: 134797--134841 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
134787 CAAAAATACG
* *
134797 TTTTCAAAACCTATACTATATA
1 TTTTCAAAAACTATACTACATA
*
134819 TTTTCAAAAACTATATTACATA
1 TTTTCAAAAACTATACTACATA
134841 T
1 T
134842 ATTATGCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTCAAAAACTATACTACATA
Found at i:136171 original size:24 final size:25
Alignment explanation
Indices: 136124--136177 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
136114 CTAATGAAAT
*
136124 TAAAAAATTAACAACCTAACTAAAA
1 TAAAAAATTAACAACCAAACTAAAA
136149 TAAAAAATTAA-AA-CAAACATAAAA
1 TAAAAAATTAACAACCAAAC-TAAAA
*
136173 GAAAA
1 TAAAA
136178 TTCAAAGGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 11 0.42
25 11 0.42
ACGTcount: A:0.70, C:0.11, G:0.02, T:0.17
Consensus pattern (25 bp):
TAAAAAATTAACAACCAAACTAAAA
Done.