Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002576.1 Hibiscus syriacus cultivar Beakdansim tig00005221_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: 98619
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8639 original size:60 final size:60
Alignment explanation
Indices: 8525--8704 Score: 150
Period size: 60 Copynumber: 3.0 Consensus size: 60
8515 TCATATGTCT
* * * * *
8525 TCAAACTATGACA-TGCAATCTAAATTAGTCCTCAAAATTTGT-ATTAC-TCTAATTTCATCC
1 TCAAACTATGACACT-CATTCTAAATTAATCCCCAAAATTT-TAAAT-CTTCCAATTTCATCC
* * * * ** * * *
8585 TCATACTATGATACTCATTTTAAATTATTCCTTAAAATTTTGAATGTTCCAATTTTATCC
1 TCAAACTATGACACTCATTCTAAATTAATCCCCAAAATTTTAAATCTTCCAATTTCATCC
* * * *
8645 TTAAACTATGACCCTCATTCTAAATTAATCCCCAAACTTTTAAATCTTTCAATTTCATCC
1 TCAAACTATGACACTCATTCTAAATTAATCCCCAAAATTTTAAATCTTCCAATTTCATCC
8705 CTAAATTCAT
Statistics
Matches: 94, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
59 1 0.01
60 92 0.98
61 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (60 bp):
TCAAACTATGACACTCATTCTAAATTAATCCCCAAAATTTTAAATCTTCCAATTTCATCC
Found at i:8924 original size:60 final size:60
Alignment explanation
Indices: 8831--8946 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
8821 TAGTATATAC
* * * *
8831 ATATAATTTGGGATGAAATTGAAATGTTGAAAAAGTTTG-GGAACTAATTTAGAATGAAGG
1 ATATAATTTGGGATGAAACTAAAATGTTGAAAAACTTTGAGG-ACAAATTTAGAATGAAGG
* *
8891 ATATAGTTTGGGGATGAAACTAAAATGTT-AAAAACTTTGAGGACAAATTTGGAATG
1 ATATAATTT-GGGATGAAACTAAAATGTTGAAAAACTTTGAGGACAAATTTAGAATG
8947 GTAGTCATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 29 0.60
61 19 0.40
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (60 bp):
ATATAATTTGGGATGAAACTAAAATGTTGAAAAACTTTGAGGACAAATTTAGAATGAAGG
Found at i:10910 original size:40 final size:40
Alignment explanation
Indices: 10866--11100 Score: 123
Period size: 41 Copynumber: 5.7 Consensus size: 40
10856 CAAACGTCAG
* * * *
10866 TAAATATTGTTAAATATTATATTTTAGTGGCGTTTTTGTA
1 TAAATATCGTTAAATATTATATTTTAATGGCATTTTTATA
* * * *
10906 TAAATACCGTTAAAAACTCATATTTTAATGGTATTTTTATA
1 TAAATATCGTTAAATA-TTATATTTTAATGGCATTTTTATA
** * *
10947 TAAACGTCGTTAAATATTGTATTTTAATGACTTATGGTATTTTTATA
1 TAAATATCGTTAAATATTATA-TTT--T-A---ATGGCATTTTTATA
** * * *
10994 TAAACGTCGTTAAATATTGTATTTTAATGAC-TTTTTTTAA
1 TAAATATCGTTAAATATTATATTTTAATGGCATTTTTAT-A
* * * ** * **
11034 CAAATGA-GGGTAAATACTCGTATTTTAGTGGTGTTTTTATA
1 TAAAT-ATCGTTAAATA-TTATATTTTAATGGCATTTTTATA
*
11075 TAAATATCGCTAAATATTATATTTTA
1 TAAATATCGTTAAATATTATATTTTA
11101 GTAGTTCGTA
Statistics
Matches: 150, Mismatches: 32, Indels: 26
0.72 0.15 0.12
Matches are distributed among these distances:
39 6 0.04
40 39 0.26
41 57 0.38
42 6 0.04
43 2 0.01
44 2 0.01
46 3 0.02
47 35 0.23
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (40 bp):
TAAATATCGTTAAATATTATATTTTAATGGCATTTTTATA
Found at i:10964 original size:24 final size:24
Alignment explanation
Indices: 10937--11011 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
10927 ATTTTAATGG
10937 TATTTTTATATAAACGTCGTTAAA
1 TATTTTTATATAAACGTCGTTAAA
* * * * * **
10961 TA-TTGTATTTTAATGAC-TTATGG
1 TATTTTTATATAAACGTCGTTA-AA
10984 TATTTTTATATAAACGTCGTTAAA
1 TATTTTTATATAAACGTCGTTAAA
11008 TATT
1 TATT
11012 GTATTTTAAT
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
22 3 0.09
23 12 0.35
24 16 0.47
25 3 0.09
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (24 bp):
TATTTTTATATAAACGTCGTTAAA
Found at i:10986 original size:47 final size:47
Alignment explanation
Indices: 10933--11026 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
10923 TCATATTTTA
10933 ATGGTATTTTTATATAAACGTCGTTAAATATTGTATTTTAATGACTT
1 ATGGTATTTTTATATAAACGTCGTTAAATATTGTATTTTAATGACTT
10980 ATGGTATTTTTATATAAACGTCGTTAAATATTGTATTTTAATGACTT
1 ATGGTATTTTTATATAAACGTCGTTAAATATTGTATTTTAATGACTT
11027 TTTTTAACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (47 bp):
ATGGTATTTTTATATAAACGTCGTTAAATATTGTATTTTAATGACTT
Found at i:24860 original size:23 final size:24
Alignment explanation
Indices: 24833--24881 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
24823 GAGTCTAAAA
24833 TATTTGAATCAAA-TTAAATATTT
1 TATTTGAATCAAATTTAAATATTT
* *
24856 TATTTGAATTAAATTTTAATATTT
1 TATTTGAATCAAATTTAAATATTT
24880 TA
1 TA
24882 CTCGCAGACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TATTTGAATCAAATTTAAATATTT
Found at i:42011 original size:6 final size:6
Alignment explanation
Indices: 42000--42043 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
41990 GTGCCAAGTC
42000 CCAACT CCAACT CCAACT CCAACT CCAACT CCAACT CCAACT CC
1 CCAACT CCAACT CCAACT CCAACT CCAACT CCAACT CCAACT CC
42044 GACCTTCTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CCAACT
Found at i:48583 original size:41 final size:41
Alignment explanation
Indices: 48454--48585 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
48444 CTGGTTCTCC
48454 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
* * *** **
48495 CCATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCC
1 CCATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGG
48538 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
48579 CCATGCA
1 CCATGCA
48586 GTGGAATAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 3 0.04
41 27 0.40
42 2 0.03
43 20 0.30
44 3 0.04
45 3 0.04
46 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (41 bp):
CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
Found at i:48598 original size:27 final size:27
Alignment explanation
Indices: 48568--48650 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
48558 AGTGCGAGCC
48568 ATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCGAGGTGGCCATGCAGTGGAATAG
* * * * * ***
48595 ATGCATACG-AGCCATACGAGTGCAAGCC
1 ATGC-GAGGTGGCCATGC-AGTGGAATAG
48623 ATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCGAGGTGGCCATGCAGTGGAATAG
48650 A
1 A
48651 GAGGTCGTTC
Statistics
Matches: 37, Mismatches: 16, Indels: 6
0.63 0.27 0.10
Matches are distributed among these distances:
27 19 0.51
28 18 0.49
ACGTcount: A:0.29, C:0.19, G:0.35, T:0.17
Consensus pattern (27 bp):
ATGCGAGGTGGCCATGCAGTGGAATAG
Found at i:48600 original size:55 final size:55
Alignment explanation
Indices: 48540--48650 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
48530 CGAGGTCCCC
*
48540 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCCATGCAGTGGAATAG
48595 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCCATGCAGTGGAATAG
48650 A
1 A
48651 GAGGTCGTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.33, T:0.16
Consensus pattern (55 bp):
ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCCATGCAGTGGAATAG
Found at i:48626 original size:28 final size:28
Alignment explanation
Indices: 48538--48626 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
48528 TGCGAGGTCC
*
48538 CCATGCATACGAGCCATACGAGTGCGAG
1 CCATGCATACGAGCCATACGAGTGCAAG
* * * * * *
48566 CCATGC-GAGGTGGCCATGC-AGTGGAAT
1 CCATGCATACG-AGCCATACGAGTGCAAG
**
48593 AGATGCATACGAGCCATACGAGTGCAAG
1 CCATGCATACGAGCCATACGAGTGCAAG
48621 CCATGC
1 CCATGC
48627 GAGGTGGCCA
Statistics
Matches: 41, Mismatches: 17, Indels: 6
0.64 0.27 0.09
Matches are distributed among these distances:
27 17 0.41
28 24 0.59
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.16
Consensus pattern (28 bp):
CCATGCATACGAGCCATACGAGTGCAAG
Found at i:48636 original size:28 final size:28
Alignment explanation
Indices: 48550--48637 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
48540 ATGCATACGA
*
48550 GCCATACGAGTGCGAGCCATGCGAGGTG
1 GCCATACGAGTGCAAGCCATGCGAGGTG
* * *** * * *
48578 GCCATGC-AGTGGAATAGATGCATACG-A
1 GCCATACGAGTGCAAGCCATGC-GAGGTG
48605 GCCATACGAGTGCAAGCCATGCGAGGTG
1 GCCATACGAGTGCAAGCCATGCGAGGTG
48633 GCCAT
1 GCCAT
48638 GCAGTGGAAT
Statistics
Matches: 40, Mismatches: 17, Indels: 6
0.63 0.27 0.10
Matches are distributed among these distances:
27 17 0.43
28 23 0.57
ACGTcount: A:0.26, C:0.24, G:0.34, T:0.16
Consensus pattern (28 bp):
GCCATACGAGTGCAAGCCATGCGAGGTG
Found at i:48706 original size:139 final size:139
Alignment explanation
Indices: 48456--48731 Score: 543
Period size: 139 Copynumber: 2.0 Consensus size: 139
48446 GGTTCTCCCC
*
48456 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
1 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
48521 CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
66 CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
48586 GTGGAATAG
131 GTGGAATAG
48595 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
1 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
48660 CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
66 CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
48725 GTGGAAT
131 GTGGAAT
48732 GGTGGCCATG
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.17
Consensus pattern (139 bp):
ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
GTGGAATAG
Found at i:48722 original size:41 final size:41
Alignment explanation
Indices: 48595--48724 Score: 106
Period size: 41 Copynumber: 3.1 Consensus size: 41
48585 AGTGGAATAG
48595 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCC
* * *** **
48636 ATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCCCC
1 ATGCA-TACGAGCCATA-CGA-GT-G--CAAGCCATGCGAGGTGGCC
*
48679 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCC
48720 ATGCA
1 ATGCA
48725 GTGGAATGGT
Statistics
Matches: 65, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.05
39 3 0.05
40 3 0.05
41 25 0.38
42 2 0.03
43 20 0.31
44 3 0.05
45 3 0.05
46 3 0.05
ACGTcount: A:0.25, C:0.27, G:0.32, T:0.17
Consensus pattern (41 bp):
ATGCATACGAGCCATACGAGTGCAAGCCATGCGAGGTGGCC
Found at i:48737 original size:19 final size:19
Alignment explanation
Indices: 48713--48750 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
48703 AGCCATGCGA
48713 GGTGGCCATGCAGTGGAAT
1 GGTGGCCATGCAGTGGAAT
48732 GGTGGCCATGCAGTGGAAT
1 GGTGGCCATGCAGTGGAAT
48751 AGGAGAGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (19 bp):
GGTGGCCATGCAGTGGAAT
Found at i:48795 original size:29 final size:29
Alignment explanation
Indices: 48758--48866 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
48748 AATAGGAGAG
* * *
48758 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTAT
48787 AGGTCGCCATGTAGTCCCGGCGACCTTAT
1 AGGTCGCCATGTAGTCCCGGCGACCTTAT
48816 AGGTCGCCATGTAGTCCCGGCGACCTTAT
1 AGGTCGCCATGTAGTCCCGGCGACCTTAT
48845 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
48867 CCATTCCCAT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 74 0.97
30 2 0.03
ACGTcount: A:0.17, C:0.31, G:0.30, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTAT
Found at i:48937 original size:27 final size:23
Alignment explanation
Indices: 48872--48931 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
48862 CGGCGCCATT
*
48872 CCCATCGTCCATTCACATGCAGC
1 CCCATCATCCATTCACATGCAGC
48895 CCCATCATCCATTCACATGCAGC
1 CCCATCATCCATTCACATGCAGC
48918 CCCATCATCCATTC
1 CCCATCATCCATTC
48932 CTTCACGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.45, G:0.08, T:0.23
Consensus pattern (23 bp):
CCCATCATCCATTCACATGCAGC
Found at i:49070 original size:25 final size:25
Alignment explanation
Indices: 49042--49092 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
49032 TGTACAATTA
*
49042 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
49067 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
49092 T
1 T
49093 ATAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:49163 original size:4 final size:4
Alignment explanation
Indices: 49154--49211 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
49144 ATTGCAGCCG
** **
49154 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A-GAA
*
49204 AGTA AGAA
1 AGAA AGAA
49212 GAATTCGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:49181 original size:17 final size:16
Alignment explanation
Indices: 49153--49184 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
49143 GATTGCAGCC
49153 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
49169 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
49185 AAAGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:49182 original size:25 final size:25
Alignment explanation
Indices: 49154--49211 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
49144 ATTGCAGCCG
49154 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
49179 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
*
49204 AGTAAGAA
1 AGAAAGAA
49212 GAATTCGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAGAAAGGGAGAAAGGAA
Found at i:49472 original size:44 final size:47
Alignment explanation
Indices: 49415--49503 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 47
49405 TTATATAGTT
49415 AAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
49459 AAAAATTATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
49504 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
44 22 0.55
45 3 0.08
46 7 0.17
47 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (47 bp):
AAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:51868 original size:17 final size:17
Alignment explanation
Indices: 51846--51878 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
51836 CAATGATTTT
*
51846 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
51863 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
51879 GATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:51916 original size:12 final size:12
Alignment explanation
Indices: 51899--51923 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51889 AAATCAACTA
51899 TTTTAAATCATG
1 TTTTAAATCATG
51911 TTTTAAATCATG
1 TTTTAAATCATG
51923 T
1 T
51924 ATCCCAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTTAAATCATG
Found at i:53623 original size:16 final size:16
Alignment explanation
Indices: 53572--53626 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
53562 AATGTAAATT
*
53572 AACAAAATATTTTTTA
1 AACACAATATTTTTTA
*
53588 AACAACACTAAATATTTTTA
1 AAC-ACA--ATAT-TTTTTA
53608 AACACAATATTTTTTA
1 AACACAATATTTTTTA
53624 AAC
1 AAC
53627 GGAAATTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 12 0.38
17 5 0.16
19 6 0.19
20 9 0.28
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (16 bp):
AACACAATATTTTTTA
Found at i:54144 original size:27 final size:27
Alignment explanation
Indices: 54102--54185 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 27
54092 TTTTTATATA
54102 ATATATATATAACTTAAACTAATAAACT
1 ATATA-ATATAACTTAAACTAATAAACT
* *
54130 ATATAATATAACTTAAACTTACAAACT
1 ATATAATATAACTTAAACTAATAAACT
* * *
54157 A-ATAATTTATACTACAAACTAATTAACT
1 ATATAATATA-ACT-TAAACTAATAAACT
54185 A
1 A
54186 GATTTTAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
26 7 0.15
27 24 0.51
28 16 0.34
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (27 bp):
ATATAATATAACTTAAACTAATAAACT
Found at i:54149 original size:33 final size:34
Alignment explanation
Indices: 54096--54161 Score: 84
Period size: 33 Copynumber: 1.9 Consensus size: 34
54086 ACTAATTTTT
54096 TATATAATATATATATAACTT-AAACTAATAAAC
1 TATATAATATATATATAACTTAAAACTAATAAAC
54129 TATATAATATA-ACT-TAAACTTACAAACTAATAA
1 TATATAATATATA-TAT-AACTTA-AAACTAATAA
54162 TTTATACTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
32 2 0.07
33 17 0.59
35 10 0.34
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (34 bp):
TATATAATATATATATAACTTAAAACTAATAAAC
Found at i:54161 original size:21 final size:20
Alignment explanation
Indices: 54137--54184 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
54127 ACTATATAAT
54137 ATAACTTAAACTTACAAACTA
1 ATAACTTAAAC-TACAAACTA
* *
54158 ATAATTTATACTACAAACTA
1 ATAACTTAAACTACAAACTA
54178 ATTAACT
1 A-TAACT
54185 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTTAAACTACAAACTA
Found at i:54615 original size:15 final size:15
Alignment explanation
Indices: 54592--54773 Score: 118
Period size: 15 Copynumber: 11.4 Consensus size: 15
54582 ACCGTGACCA
*
54592 TCCCTCCCCATGCAT
1 TCCCACCCCATGCAT
54607 TCCCACCCCATGCAT
1 TCCCACCCCATGCAT
* *
54622 T-CCACGTCCAATACACCAT
1 TCCCAC--CCCAT---GCAT
* *
54641 CCCCTCCCCCATGCAT
1 TCCC-ACCCCATGCAT
54657 T-CCACCCCATGCAT
1 TCCCACCCCATGCAT
54671 TCCCACGTCCCATGCAT
1 TCCCAC--CCCATGCAT
* *
54688 CCCCTCCCCCATGCAT
1 TCCC-ACCCCATGCAT
*
54704 TCCCACATCCCATG-TT
1 TCCCAC--CCCATGCAT
*
54720 GATCCCTCCCCATGCAT
1 --TCCCACCCCATGCAT
54737 TCCCACCCCATGCAT
1 TCCCACCCCATGCAT
* *
54752 CCCCTCCCCCATGCAT
1 TCCC-ACCCCATGCAT
54768 TCCCAC
1 TCCCAC
54774 GTCCCATGTT
Statistics
Matches: 129, Mismatches: 21, Indels: 34
0.70 0.11 0.18
Matches are distributed among these distances:
14 15 0.12
15 40 0.31
16 39 0.30
17 19 0.15
18 6 0.05
19 7 0.05
20 2 0.02
21 1 0.01
ACGTcount: A:0.18, C:0.53, G:0.07, T:0.22
Consensus pattern (15 bp):
TCCCACCCCATGCAT
Found at i:54662 original size:49 final size:48
Alignment explanation
Indices: 54588--54706 Score: 165
Period size: 47 Copynumber: 2.5 Consensus size: 48
54578 GACCACCGTG
54588 ACCAT-CCCT-CCCCATGCATTCCCACCCCATGCATT-CCACGTCCAAT
1 ACCATCCCCTCCCCCATGCATT-CCACCCCATGCATTCCCACGTCCAAT
*
54634 ACACCATCCCCTCCCCCATGCATTCCACCCCATGCATTCCCACGTCCCAT
1 --ACCATCCCCTCCCCCATGCATTCCACCCCATGCATTCCCACGTCCAAT
*
54684 -GCATCCCCTCCCCCATGCATTCC
1 ACCATCCCCTCCCCCATGCATTCC
54707 CACATCCCAT
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
47 22 0.33
48 5 0.08
49 18 0.27
50 21 0.32
ACGTcount: A:0.19, C:0.53, G:0.07, T:0.21
Consensus pattern (48 bp):
ACCATCCCCTCCCCCATGCATTCCACCCCATGCATTCCCACGTCCAAT
Found at i:54698 original size:16 final size:16
Alignment explanation
Indices: 54638--54767 Score: 90
Period size: 16 Copynumber: 8.2 Consensus size: 16
54628 TCCAATACAC
54638 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
* *
54654 CAT-TCC-ACCCCATG
1 CATCCCCTCCCCCATG
* * *
54668 CATTCCCACGTCCCATG
1 CATCCCCTC-CCCCATG
54685 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
* * *
54701 CATTCCCACATCCCATG
1 CATCCCCTC-CCCCATG
*
54718 TTGAT-CCCT-CCCCATG
1 --CATCCCCTCCCCCATG
* *
54734 CATTCCC-ACCCCATG
1 CATCCCCTCCCCCATG
54749 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
54765 CAT
1 CAT
54768 TCCCACGTCC
Statistics
Matches: 88, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
14 12 0.14
15 20 0.23
16 32 0.36
17 19 0.22
18 3 0.03
19 2 0.02
ACGTcount: A:0.17, C:0.53, G:0.08, T:0.22
Consensus pattern (16 bp):
CATCCCCTCCCCCATG
Found at i:54702 original size:33 final size:33
Alignment explanation
Indices: 54661--54781 Score: 178
Period size: 33 Copynumber: 3.7 Consensus size: 33
54651 ATGCATTCCA
54661 CCCCATGCATTCCCACGTCCCATGCATCCCCTC
1 CCCCATGCATTCCCACGTCCCATGCATCCCCTC
* *
54694 CCCCATGCATTCCCACATCCCATGTTGAT-CCCT-
1 CCCCATGCATTCCCACGTCCCATG--CATCCCCTC
54727 CCCCATGCATTCCCAC--CCCATGCATCCCCTC
1 CCCCATGCATTCCCACGTCCCATGCATCCCCTC
54758 CCCCATGCATTCCCACGTCCCATG
1 CCCCATGCATTCCCACGTCCCATG
54782 TTGATTGCAT
Statistics
Matches: 79, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
29 2 0.03
30 4 0.05
31 22 0.28
33 45 0.57
34 4 0.05
35 2 0.03
ACGTcount: A:0.17, C:0.52, G:0.09, T:0.22
Consensus pattern (33 bp):
CCCCATGCATTCCCACGTCCCATGCATCCCCTC
Found at i:54783 original size:64 final size:65
Alignment explanation
Indices: 54661--54786 Score: 227
Period size: 64 Copynumber: 1.9 Consensus size: 65
54651 ATGCATTCCA
54661 CCCCATGCATTCCCACGTCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCC
1 CCCCATGCATTCCCACG-CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCC
54726 T
65 T
*
54727 CCCCATGCATTCCCAC-CCCATGCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGAT
1 CCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGAT
54787 TGCATGCATC
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 43 0.73
66 16 0.27
ACGTcount: A:0.17, C:0.50, G:0.10, T:0.24
Consensus pattern (65 bp):
CCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCCT
Found at i:54847 original size:18 final size:18
Alignment explanation
Indices: 54807--54848 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
54797 CCCTCCCCCA
*
54807 TGCACGTCCCATGTTGAT
1 TGCATGTCCCATGTTGAT
54825 TGCATGTCCCATGTTGAT
1 TGCATGTCCCATGTTGAT
54843 TGCATG
1 TGCATG
54849 GCCCTATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (18 bp):
TGCATGTCCCATGTTGAT
Found at i:54903 original size:29 final size:29
Alignment explanation
Indices: 54870--54987 Score: 236
Period size: 29 Copynumber: 4.1 Consensus size: 29
54860 TAATACACAC
54870 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
54899 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
54928 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
54957 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
54986 AG
1 AG
54988 ACCACTGTAG
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:61636 original size:20 final size:20
Alignment explanation
Indices: 61611--61650 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
61601 TCCCACAATG
61611 TCATAATCATTCACAACCAC
1 TCATAATCATTCACAACCAC
61631 TCATAATCATTCACAACCAC
1 TCATAATCATTCACAACCAC
61651 CAACAGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (20 bp):
TCATAATCATTCACAACCAC
Found at i:62882 original size:69 final size:69
Alignment explanation
Indices: 62751--62955 Score: 279
Period size: 69 Copynumber: 3.0 Consensus size: 69
62741 TATAAAGCTA
* * *
62751 ACGTAAATTTATATAGGGTAAAGTGTAC--ATGATCTCTTGATTATATGTTGTTGTTTTGTTAAA
1 ACGTAAATTTATATAGGGTAAAGTTTACAAATGGTCTCTTGATTATAAGTTGTTGTTTTGTTAAA
62814 TTTT
66 TTTT
* * * * *
62818 ACGTAAATTTATATAGGGTAAAATTTACAAATGGTCTCCTGATTACAGGTTGTTGTTTTATTAAA
1 ACGTAAATTTATATAGGGTAAAGTTTACAAATGGTCTCTTGATTATAAGTTGTTGTTTTGTTAAA
62883 TTTT
66 TTTT
* * * * *
62887 ACCTAAACTTATATAGGGTAAAGTTTACAAATGGTCTTTTGATTATAAGATGTTGTTTTGTTAAT
1 ACGTAAATTTATATAGGGTAAAGTTTACAAATGGTCTCTTGATTATAAGTTGTTGTTTTGTTAAA
62952 TTTT
66 TTTT
62956 TTTATTATTA
Statistics
Matches: 119, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
67 26 0.22
69 93 0.78
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (69 bp):
ACGTAAATTTATATAGGGTAAAGTTTACAAATGGTCTCTTGATTATAAGTTGTTGTTTTGTTAAA
TTTT
Found at i:69610 original size:22 final size:22
Alignment explanation
Indices: 69562--69624 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
69552 AAAATACGGT
**
69562 ATGAACAGTACCGTATGAGCAGTG
1 ATGAACAGTACCG--TGAATAGTG
*
69586 ATGAACAGTACTGTGAATAGTG
1 ATGAACAGTACCGTGAATAGTG
69608 ATGAACAGTACCGTGAA
1 ATGAACAGTACCGTGAA
69625 AAGTACCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 23 0.66
24 12 0.34
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (22 bp):
ATGAACAGTACCGTGAATAGTG
Found at i:70069 original size:2 final size:2
Alignment explanation
Indices: 70064--70098 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
70054 AATAAAATGC
70064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
70099 CACCATCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70412 original size:18 final size:18
Alignment explanation
Indices: 70385--70419 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
70375 CTACGTAGAA
70385 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
*
70403 ATGTCTCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
70420 ATATCACATA
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:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:79443 original size:5 final size:5
Alignment explanation
Indices: 79435--79459 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
79425 TGTCACCATA
79435 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
79460 ATGTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:84130 original size:60 final size:60
Alignment explanation
Indices: 84046--84192 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 60
84036 AGTCTGATGG
* * * *
84046 TCATTTTGTAACTCTTGATAGTCGAGGGAATAAAAAAAAGCAACTTCATATAGTTA-GAGA
1 TCATTTTGTAACTTTTAATAGTCGAGGGAATAAAAAAAA-CAACTCCATATAGTCAGGAGA
* * * * * * *
84106 -CTATTTTTTAACTTTTAATTGTCGAGCGATTCAACAAAACAACTCCATATTGTCAGGAGA
1 TC-ATTTTGTAACTTTTAATAGTCGAGGGAATAAAAAAAACAACTCCATATAGTCAGGAGA
*
84166 TCATTTTGTAACTTTTTATAGTCGAGG
1 TCATTTTGTAACTTTTAATAGTCGAGG
84193 TAATCCACAA
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
59 14 0.20
60 54 0.78
61 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (60 bp):
TCATTTTGTAACTTTTAATAGTCGAGGGAATAAAAAAAACAACTCCATATAGTCAGGAGA
Found at i:88993 original size:15 final size:15
Alignment explanation
Indices: 88955--88994 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
88945 GGTTTAGTAA
88955 TAACCGGAGGAACTG
1 TAACCGGAGGAACTG
* *
88970 TTACTGGAGGAACTG
1 TAACCGGAGGAACTG
88985 TAACCGGAGG
1 TAACCGGAGG
88995 GAGGCCAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.17, G:0.35, T:0.17
Consensus pattern (15 bp):
TAACCGGAGGAACTG
Done.