Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003289.1 Hibiscus syriacus cultivar Beakdansim tig00006919_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: 94445
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:5396 original size:16 final size:17
Alignment explanation
Indices: 5375--5406 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5365 ATTACTCTTT
5375 AAACAT-AATTAAATAG
1 AAACATGAATTAAATAG
5391 AAACATGAATTAAATA
1 AAACATGAATTAAATA
5407 AAGAAAGGAT
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:0.06, G:0.06, T:0.25
Consensus pattern (17 bp):
AAACATGAATTAAATAG
Found at i:6673 original size:5 final size:5
Alignment explanation
Indices: 6665--6698 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
6655 TAATAAATAA
*
6665 TATAC TATAC TATAC TATAC TATAC TATAA TATA
1 TATAC TATAC TATAC TATAC TATAC TATAC TATA
6699 TAAATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAC
Found at i:6685 original size:15 final size:15
Alignment explanation
Indices: 6661--6698 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
6651 AATATAATAA
6661 ATAATATACTATACT
1 ATAATATACTATACT
*
6676 ATACTATACTATACT
1 ATAATATACTATACT
6691 ATAATATA
1 ATAATATA
6699 TAAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATATACTATACT
Found at i:7646 original size:65 final size:64
Alignment explanation
Indices: 7447--7657 Score: 234
Period size: 65 Copynumber: 3.3 Consensus size: 64
7437 TTAGTGCATC
* * ** *
7447 GGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCT
1 GGTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTT
* *
7511 GGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGG
1 GGTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGG
7574 TAT
63 T-T
*
7577 -GTGCATCGATGCATGAAATGCATTCGATG-TTCAATATAATTCATGGTGCATCGATGCATGGAT
1 GGTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-T
7640 T
64 T
* *
7641 GGTGCAACGGTGCATCA
1 GGTGCATCGATGCATCA
7658 CTCTGAAAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 53 0.43
65 62 0.50
66 1 0.01
67 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (64 bp):
GGTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTT
Found at i:7713 original size:24 final size:24
Alignment explanation
Indices: 7686--7744 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
7676 AGGCTTGATT
7686 TTGGTTCAAAATACTTTATGAAAA
1 TTGGTTCAAAATACTTTATGAAAA
*
7710 TTGGTTCAAAATACTTTGTGAAAA
1 TTGGTTCAAAATACTTTATGAAAA
*
7734 TTGTTTCAAAA
1 TTGGTTCAAAA
7745 ATATATTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (24 bp):
TTGGTTCAAAATACTTTATGAAAA
Found at i:14219 original size:22 final size:21
Alignment explanation
Indices: 14177--14216 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
14167 GAGTTTATTT
*
14177 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
14198 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
14217 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:16193 original size:18 final size:17
Alignment explanation
Indices: 16139--16187 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
16129 TTGGATCCTT
* *
16139 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
16157 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
16175 AGTGCATTCGATG
1 AGTGCA-TCGATG
16188 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:16292 original size:65 final size:64
Alignment explanation
Indices: 16133--16318 Score: 225
Period size: 65 Copynumber: 2.9 Consensus size: 64
16123 TGATCTTTGG
* *
16133 ATCCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAA
1 ATCCTTAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAA
16196 T
64 T
* ** * *
16197 AGCCAGAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ATCCTTAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
16262 -
64 T
* *
16262 ATCCTTAGTGCATCGGTGCATGGTATGTGCATTGATGCATGAAATGCATTCGATGTT
1 ATCCTTAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
16319 CAATTTAATT
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 45 0.44
65 53 0.51
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
ATCCTTAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:16358 original size:65 final size:63
Alignment explanation
Indices: 16159--16368 Score: 226
Period size: 65 Copynumber: 3.3 Consensus size: 63
16149 TGCACTAAGA
* * * *
16159 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCATAGTGCATCGATGCATGG-TT
* *
16223 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGGT-T
* * ** * *
16288 GTGCATTGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-TT
*
16352 GATGCATCGGTGCATCA
1 G-TGCATCGATGCATCA
16369 CTCTGAAAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
63 3 0.02
64 53 0.43
65 64 0.52
66 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTT
Found at i:16643 original size:26 final size:26
Alignment explanation
Indices: 16614--16750 Score: 121
Period size: 26 Copynumber: 5.5 Consensus size: 26
16604 GTTTTCAACA
16614 ATATATTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAACTATATATTAT
*
16640 ATATGTTTTCAAAAACTATATTATGTAT
1 ATATATTTTCAAAAACTATA-TAT-TAT
* * * *
16668 ATATA-TAT-ATATA-TATATATTAA
1 ATATATTTTCAAAAACTATATATTAT
*
16691 AAATATTTTCAAAAAC----TA-TAT
1 ATATATTTTCAAAAACTATATATTAT
*
16712 ATATATTTTCAAAAACTGTATATTAT
1 ATATATTTTCAAAAACTATATATTAT
*
16738 ATACA-TTTCAAAA
1 ATATATTTTCAAAA
16751 TATTTTCAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
21 17 0.19
22 2 0.02
23 6 0.07
24 5 0.06
25 17 0.19
26 29 0.33
27 5 0.06
28 7 0.08
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (26 bp):
ATATATTTTCAAAAACTATATATTAT
Found at i:16646 original size:40 final size:38
Alignment explanation
Indices: 16602--16717 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 38
16592 GAAACACAAA
16602 ATGTTTTCAACAATATATTTTCAAAAACTATATATTATAT
1 ATGTTTTCAA-AATATATTTTCAAAAACTATATA-TATAT
* *
16642 ATGTTTTCAAAAACTATATTATGT-ATATA-TATATATATAT
1 ATGTTTTC-AAAA-TATATT-T-TCAAAAACTATATATATAT
* *
16682 ATATATT-AAAA-ATATTTTCAAAAACTATATATATAT
1 ATGTTTTCAAAATATATTTTCAAAAACTATATATATAT
16718 TTTCAAAAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
34 1 0.02
35 4 0.06
36 16 0.25
38 4 0.06
40 20 0.31
41 14 0.22
42 4 0.06
43 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
ATGTTTTCAAAATATATTTTCAAAAACTATATATATAT
Found at i:16717 original size:21 final size:22
Alignment explanation
Indices: 16693--16739 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
16683 TATATTAAAA
16693 ATATTTTCAAAAACTATATA-T
1 ATATTTTCAAAAACTATATATT
*
16714 ATATTTTCAAAAACTGTATATT
1 ATATTTTCAAAAACTATATATT
16736 ATAT
1 ATAT
16740 ACATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTTTCAAAAACTATATATT
Found at i:16797 original size:39 final size:39
Alignment explanation
Indices: 16714--16891 Score: 179
Period size: 39 Copynumber: 4.7 Consensus size: 39
16704 AACTATATAT
* *
16714 ATATTTTCAAAAACTGTATATTATATACA---TTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATGTTTTCAAA
*
16750 ATATTTTCAAAAACTATATATTATATATATGTTTTCAAG
1 ATATTTTCAAAAACTATATATTATATATATGTTTTCAAA
* * *
16789 ATGTTTTCAAAAACTATAAATT-T-TATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATGTTTTCAAA
* * * *
16826 ATATTTT-TAACACTATATATTATATAAATGTTTTGAAA
1 ATATTTTCAAAAACTATATATTATATATATGTTTTCAAA
** ** *
16864 ACGTTTTTGAAAATTATATATTATATAT
1 ATATTTTCAAAAACTATATATTATATAT
16892 GCTTTCAAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
36 38 0.33
37 19 0.16
38 17 0.15
39 42 0.36
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (39 bp):
ATATTTTCAAAAACTATATATTATATATATGTTTTCAAA
Found at i:16870 original size:75 final size:74
Alignment explanation
Indices: 16717--16927 Score: 221
Period size: 75 Copynumber: 2.8 Consensus size: 74
16707 TATATATATA
* * * *
16717 TTTTCAAAAACTGTATATTATATACATTTCAAAATATTTTCAAAAACTATATATTATATATATGT
1 TTTTCAAAAACTATATATTATATATATTTCAAAATATTTT-TAAAACTATATATTATATAAATGT
* *
16782 TTTCAAGATG
65 TTTCAAAACG
* * *
16792 TTTTCAAAAACTATAAATTTTATATATTTTCAAAATATTTTTAACACTATATATTATATAAATGT
1 TTTTCAAAAACTATATATTATATATA-TTTCAAAATATTTTTAAAACTATATATTATATAAATGT
*
16857 TTTGAAAACG
65 TTTCAAAACG
** * * * *
16867 TTTTTGAAAATTATATATTATATATGCTTTCAAAAT-TTTATATATACTATATA-TAT-TAAAT
1 TTTTCAAAAACTATATATTATATAT-ATTTCAAAATATTTTTA-AAACTATATATTATATAAAT
16928 AACACCCTGG
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
73 5 0.04
74 8 0.07
75 88 0.77
76 14 0.12
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (74 bp):
TTTTCAAAAACTATATATTATATATATTTCAAAATATTTTTAAAACTATATATTATATAAATGTT
TTCAAAACG
Found at i:16978 original size:10 final size:10
Alignment explanation
Indices: 16963--17012 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
16953 TTCAAATTTA
16963 TTATTAAATT
1 TTATTAAATT
*
16973 TTATT-AA-C
1 TTATTAAATT
16981 TTATTCAAATAT
1 TTATT-AAAT-T
16993 TTATTAAATT
1 TTATTAAATT
*
17003 TCATTAAATT
1 TTATTAAATT
17013 ATTAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.15
9 2 0.06
10 17 0.52
11 4 0.12
12 5 0.15
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (10 bp):
TTATTAAATT
Found at i:16997 original size:20 final size:18
Alignment explanation
Indices: 16963--16999 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
16953 TTCAAATTTA
16963 TTATTAAATTTTATTAAC
1 TTATTAAATTTTATTAAC
16981 TTATTCAAATATTTATTAA
1 TTATT-AAAT-TTTATTAA
17000 ATTTCATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTAAATTTTATTAAC
Found at i:16999 original size:30 final size:31
Alignment explanation
Indices: 16953--17015 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
16943 AATGAGCGAC
* * *
16953 TTCAAATTTATTATTAAATTTTATTAACTTA
1 TTCAAATATATTATTAAATTTCATTAAATTA
16984 TTCAAATAT-TTATTAAATTTCATTAAATTA
1 TTCAAATATATTATTAAATTTCATTAAATTA
17014 TT
1 TT
17016 AAAAATAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (31 bp):
TTCAAATATATTATTAAATTTCATTAAATTA
Found at i:20403 original size:29 final size:31
Alignment explanation
Indices: 20369--20429 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
20359 CTTTGACTAA
20369 TCATTTCAACTA-AATTGA-TTCTTTTTGTC
1 TCATTTCAACTACAATTGATTTCTTTTTGTC
* *
20398 TCATTTCTACTACTATTGATTTCTTTTTGTC
1 TCATTTCAACTACAATTGATTTCTTTTTGTC
20429 T
1 T
20430 GGTCTTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.39
30 5 0.18
31 12 0.43
ACGTcount: A:0.20, C:0.18, G:0.07, T:0.56
Consensus pattern (31 bp):
TCATTTCAACTACAATTGATTTCTTTTTGTC
Found at i:22351 original size:19 final size:18
Alignment explanation
Indices: 22315--22366 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
22305 AAAAATAGAG
22315 AAAAAGAAATAAAG-AAGA
1 AAAAAGAAA-AAAGAAAGA
22333 AAAATAGAAAAAAGAAAGA
1 AAAA-AGAAAAAAGAAAGA
*
22352 AGAAAGAAAAGAAGA
1 AAAAAGAAAA-AAGA
22367 TATAAAACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAAGAAAGA
Found at i:22358 original size:26 final size:27
Alignment explanation
Indices: 22305--22361 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
22295 AATAACACAC
*
22305 AAAAATAGAGAAAAAGAAATAAAGAAG
1 AAAAATAGAGAAAAAGAAAGAAAGAAG
22332 AAAAATAGA-AAAAAGAAAG-AAGAAAG
1 AAAAATAGAGAAAAAGAAAGAAAG-AAG
22358 AAAA
1 AAAA
22362 GAAGATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 3 0.11
26 16 0.57
27 9 0.32
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (27 bp):
AAAAATAGAGAAAAAGAAAGAAAGAAG
Found at i:22373 original size:12 final size:12
Alignment explanation
Indices: 22325--22366 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
22315 AAAAAGAAAT
22325 AAAGAAGAAA-A
1 AAAGAAGAAAGA
* *
22336 ATAGAAAAAAG-
1 AAAGAAGAAAGA
22347 AAAGAAGAAAGA
1 AAAGAAGAAAGA
22359 AAAGAAGA
1 AAAGAAGA
22367 TATAAAACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
AAAGAAGAAAGA
Found at i:24558 original size:41 final size:42
Alignment explanation
Indices: 24448--24559 Score: 102
Period size: 42 Copynumber: 2.7 Consensus size: 42
24438 GGTTTTCTTT
* * * *
24448 ATGAGTAAGTCCTTTGGGCCATC-AGTAAGTCTTTTGAGCATG
1 ATGAATAAGTCCTTCGGGCCATCTA-TAAGTCTTTTAAGCAAG
** * ** * *
24490 ATGCTTAAATCCTTCGGGTTATTTATAAGTCTTTTAAGTAAG
1 ATGAATAAGTCCTTCGGGCCATCTATAAGTCTTTTAAGCAAG
24532 AT-AATAAGTCCTTCGGGCCATCTATAAG
1 ATGAATAAGTCCTTCGGGCCATCTATAAG
24560 ACATTTGTGC
Statistics
Matches: 53, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (42 bp):
ATGAATAAGTCCTTCGGGCCATCTATAAGTCTTTTAAGCAAG
Found at i:24713 original size:20 final size:20
Alignment explanation
Indices: 24680--24755 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
24670 CAAATAAGCT
* *
24680 TAAGTCCTTAGAGCCATCAG
1 TAAGTCTTTCGAGCCATCAG
*
24700 TAAGTCTTTCGAG-CATGATG
1 TAAGTCTTTCGAGCCATCA-G
* *
24720 CTTAAATCTTTCGGGCCATCTA-
1 --TAAGTCTTTCGAGCCATC-AG
24742 TAAGTCTTTCGAGC
1 TAAGTCTTTCGAGC
24756 AAGATAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
19 4 0.09
20 24 0.56
22 11 0.26
23 3 0.07
24 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
TAAGTCTTTCGAGCCATCAG
Found at i:24724 original size:42 final size:42
Alignment explanation
Indices: 24677--24756 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
24667 TTTCAAATAA
*
24677 GCTTAAGTCCTTAGAGCCATC-AGTAAGTCTTTCGAGCATGAT
1 GCTTAAATCCTTAGAGCCATCTA-TAAGTCTTTCGAGCATGAT
* * *
24719 GCTTAAATCTTTCGGGCCATCTATAAGTCTTTCGAGCA
1 GCTTAAATCCTTAGAGCCATCTATAAGTCTTTCGAGCA
24757 AGATAATAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (42 bp):
GCTTAAATCCTTAGAGCCATCTATAAGTCTTTCGAGCATGAT
Found at i:24917 original size:168 final size:168
Alignment explanation
Indices: 24639--24973 Score: 485
Period size: 168 Copynumber: 2.0 Consensus size: 168
24629 CCAGAGGGGT
24639 TAACATTTCCTTTGGTTGATTCACGACATTTCAAATAAGCTTAAGTCCTTAGAGCCATCAGTAAG
1 TAACATTTCCTTTGGTTGATTCACGACATTTCAAATAAGCTTAAGTCCTTAGAGCCATCAGTAAG
* * * *
24704 TCTTTCGAGCATGATGCTTAAATCTTTCGGGCCATCTATAAGTCTTTCGAGCAAGATAATAAGTA
66 TCTTTCGAGCATAATGCTTAAATCCTTCAGGCCATCTATAAGTCTTTCGAGAAAGATAATAAGTA
*
24769 ATTCGGACCATCCATAAGACCTTCAGGCAAGATGTTTA
131 ATTCGGACCACCCATAAGACCTTCAGGCAAGATGTTTA
* * * *
24807 TAACATTTCCTTT-GTTCGATTCACTG-CATTTCGAATCAGCTTAAGTCCTTCGGGCCATCAGTA
1 TAACATTTCCTTTGGTT-GATTCAC-GACATTTCAAATAAGCTTAAGTCCTTAGAGCCATCAGTA
* * *
24870 AGTCTTTCGAGCATAATGCTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGAAAGTTGATAAG
64 AGTCTTTCGAGCATAATGCTTAAATCCTTCAGGCCATCTATAAGTCTTTCGAGAAAGATAATAAG
** * * *
24935 TCCTTCGGGCGACCCATAAGACCTTCAGGCAGGATGTTT
129 TAATTCGGACCACCCATAAGACCTTCAGGCAAGATGTTT
24974 CCAATTGATT
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
167 3 0.02
168 144 0.97
169 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (168 bp):
TAACATTTCCTTTGGTTGATTCACGACATTTCAAATAAGCTTAAGTCCTTAGAGCCATCAGTAAG
TCTTTCGAGCATAATGCTTAAATCCTTCAGGCCATCTATAAGTCTTTCGAGAAAGATAATAAGTA
ATTCGGACCACCCATAAGACCTTCAGGCAAGATGTTTA
Found at i:25804 original size:136 final size:136
Alignment explanation
Indices: 25556--26275 Score: 705
Period size: 136 Copynumber: 5.3 Consensus size: 136
25546 CAATAAAGAG
* * * * *
25556 TAATGATAAGAACTCATCTAACTGAGGGAGAGGAAGTTCATAATGAGAAGAG-ATTGATCGACCT
1 TAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCA-TGTTCGACCT
* ** *
25620 ATCGTTCGATTCACGGTATTTTGAATCAGTGACACCTCGCTT-ATGGGATTAAAATTTCAAATGG
65 ATCGCTCGATTCACGACATTTTGAATCAGTGACGCCTCGCTTGA-GGGATTAAAATTTCAAATGG
25684 AGAGTTCA
129 AGAGTTCA
* * *
25692 TAATGAGAAGAAGTCATCCAACAGAGGGAGAAGAAGTTCATAATAATAAGAGCATGTTCGACCTA
1 TAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCATGTTCGACCTA
* ** * *
25757 TCACTCGATTCACGGTATTTTGAACCAGTGACGCCTCGCTTGAGGGATTAACATTTCAAATGGAG
66 TCGCTCGATTCACGACATTTTGAATCAGTGACGCCTCGCTTGAGGGATTAAAATTTCAAATGGAG
25822 AGTTCA
131 AGTTCA
* * * **
25828 TAATGAGAAGAACTCATTCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGTTTGTTCGACCTA
1 TAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCATGTTCGACCTA
* * * * * *
25893 TCTCTCGGTTCATGACATTTCGAATCAGTGACGCCTCACTTGAGGGATTAACATTTCAAATGGAG
66 TCGCTCGATTCACGACATTTTGAATCAGTGACGCCTCGCTTGAGGGATTAAAATTTCAAATGGAG
*
25958 AATTCA
131 AGTTCA
* * * * *
25964 TAATGAGAAGAACTCATCCGACAGAGGGAGAATAAGTTCATAATGAGAAGAACTTATTCGACCTA
1 TAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCATGTTCGACCTA
* * * * * ** * *
26029 TTGCTCGATTCACAACACTTTGAATTAGCT-ATGCCTCGCTTGAGGGATTGGCATTTTC-GATGG
66 TCGCTCGATTCACGACATTTTGAATCAG-TGACGCCTCGCTTGAGGGATT-AAAATTTCAAATGG
* *
26092 TGGGTTCA
129 AGAGTTCA
* * * * * *
26100 TAATGAGAATAACTCATCCAAAAGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTTTC-ACTT
1 TAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCATG-TTCGACCT
** * * * * * ** * * * * ** *
26164 ATTACTCGATTAACAACACTTCGAATAAGCAACGCTTCACTTGAGGGATTCATATTTTC-GTTGA
65 ATCGCTCGATTCACGACATTTTGAATCAGTGACGCCTCGCTTGAGGGATT-AAAATTTCAAATGG
*
26228 AGGGTTCA
129 AGAGTTCA
* * *
26236 TAATGAGAAGAACTTATCCGACAGAGGGAGAAAAAGTTCA
1 TAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCA
26276 ACATTTTGAA
Statistics
Matches: 498, Mismatches: 80, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
136 488 0.98
137 10 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (136 bp):
TAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCATGTTCGACCTA
TCGCTCGATTCACGACATTTTGAATCAGTGACGCCTCGCTTGAGGGATTAAAATTTCAAATGGAG
AGTTCA
Found at i:26067 original size:272 final size:272
Alignment explanation
Indices: 25556--26275 Score: 781
Period size: 272 Copynumber: 2.6 Consensus size: 272
25546 CAATAAAGAG
* * ** * *
25556 TAATGATAAGAACTCATCTAACTGAGGGAGAGGAAGTTCATAATGAGAAGAGATTGATCGACCTA
1 TAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGATTGTTCGACCTA
** * * *
25621 TCGT-TCGATTCACGGTATTTTGAATCAGTGACACCTCGCTT-ATGGGATTAAAATTTCAAATGG
66 TC-TCTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGA-GGGATTAAAATTTCAAATGG
* * * * * *
25684 AGAGTTCATAATGAGAAGAAGTCATCCAACAGAGGGAGAAGAAGTTCATAATAATAAGAGCATGT
129 AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATAAGAAGAACATAT
*** *
25749 TCGACCTATCACTCGATTCACGGTATTTTGAACCAGTGACGCCTCGCTTGAGGGATTAACA-TTT
194 TCGACCTATCACTCGATTCACAACACTTTGAACCAGTGACGCCTCGCTTGAGGGATTAACATTTT
25813 CAAATGGAGAGTTCA
259 C-AATGGAGAGTTCA
* * * *
25828 TAATGAGAAGAACTCATTCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGTTTGTTCGACCTA
1 TAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGATTGTTCGACCTA
* * *
25893 TCTCTCGGTTCATGACATTTCGAATCAGTGACGCCTCACTTGAGGGATTAACATTTCAAATGGAG
66 TCTCTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGGATTAAAATTTCAAATGGAG
* * * *
25958 AATTCATAATGAGAAGAACTCATCCGACAGAGGGAGAATAAGTTCATAATGAGAAGAACTTATTC
131 AGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATAAGAAGAACATATTC
** ** * **
26023 GACCTATTGCTCGATTCACAACACTTTGAATTAGCT-ATGCCTCGCTTGAGGGATTGGCATTTTC
196 GACCTATCACTCGATTCACAACACTTTGAACCAG-TGACGCCTCGCTTGAGGGATTAACATTTTC
* * *
26087 GATGGTGGGTTCA
260 AATGGAGAGTTCA
* * *
26100 TAATGAGAATAACTCATCCAAAAGAGGGAGAAGAAGTTCATAATGAGAATA-ACTTGTTTC-ACT
1 TAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGA-TTG-TTCGACC
* * * * ** * * * **
26163 TAT-TACTCGATTAACAACACTTCGAATAAGCAACGCTTCACTTGAGGGATTCATATTTTC-GTT
64 TATCT-CTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGGATT-AAAATTTCAAAT
* * *
26226 GAAGGGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAAAAGTTCA
127 GGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCA
26276 ACATTTTGAA
Statistics
Matches: 374, Mismatches: 66, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
271 2 0.01
272 358 0.96
273 14 0.04
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (272 bp):
TAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGATTGTTCGACCTA
TCTCTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGGATTAAAATTTCAAATGGAG
AGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATAAGAAGAACATATTC
GACCTATCACTCGATTCACAACACTTTGAACCAGTGACGCCTCGCTTGAGGGATTAACATTTTCA
ATGGAGAGTTCA
Found at i:28537 original size:15 final size:15
Alignment explanation
Indices: 28517--28560 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
28507 AATCCTTAAG
28517 CTTTAAATTTAGATT
1 CTTTAAATTTAGATT
* *
28532 CTTTAATTTTAGACT
1 CTTTAAATTTAGATT
*
28547 -TTTACATTTAGATT
1 CTTTAAATTTAGATT
28561 TTTGGATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.55
Consensus pattern (15 bp):
CTTTAAATTTAGATT
Found at i:28550 original size:29 final size:28
Alignment explanation
Indices: 28518--28576 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
28508 ATCCTTAAGC
28518 TTTAAATTTAGATTCTTT-AATTTTAGACT
1 TTTAAATTTAGATT-TTTGAATTTTAG-CT
* *
28547 TTTACATTTAGATTTTTGGATTTTAGCT
1 TTTAAATTTAGATTTTTGAATTTTAGCT
28575 TT
1 TT
28577 CTTACATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.58
Consensus pattern (28 bp):
TTTAAATTTAGATTTTTGAATTTTAGCT
Found at i:31490 original size:19 final size:18
Alignment explanation
Indices: 31450--31492 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
31440 GAAATTATTT
* *
31450 AAAACCTACCAATACCAC
1 AAAAACTACAAATACCAC
31468 AAAAACTACAAATACCAC
1 AAAAACTACAAATACCAC
31486 AAAAACT
1 AAAAACT
31493 TAAAACCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.58, C:0.30, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAACTACAAATACCAC
Found at i:31976 original size:11 final size:11
Alignment explanation
Indices: 31951--32018 Score: 79
Period size: 10 Copynumber: 6.4 Consensus size: 11
31941 TTTTCTAAAA
*
31951 ATTA-TAAAAT
1 ATTATTAAATT
*
31961 ATTATTAATTT
1 ATTATTAAATT
31972 ATTATTAAATT
1 ATTATTAAATT
31983 -TTATTAAATT
1 ATTATTAAATT
31993 ATTTATTAAATT
1 A-TTATTAAATT
*
32005 -TCATTAAATT
1 ATTATTAAATT
32015 ATTA
1 ATTA
32019 AAAATAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
10 23 0.47
11 16 0.33
12 10 0.20
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:31992 original size:22 final size:21
Alignment explanation
Indices: 31951--32018 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
31941 TTTTCTAAAA
* * *
31951 ATTATAAAATATTATTAATTT
1 ATTATTAAATTTTATTAAATT
31972 ATTATTAAATTTTATTAAATT
1 ATTATTAAATTTTATTAAATT
*
31993 ATTTATTAAATTTCATTAAATT
1 A-TTATTAAATTTTATTAAATT
32015 ATTA
1 ATTA
32019 AAAATAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 22 0.52
22 20 0.48
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATTAAATTTTATTAAATT
Found at i:33513 original size:23 final size:21
Alignment explanation
Indices: 33486--33535 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
33476 ATCCCGTCAT
33486 TCCCTTAAATTTAATATTTTATC
1 TCCCTTAAATTT--TATTTTATC
** *
33509 TCCCTTTGATTTTATTTTATT
1 TCCCTTAAATTTTATTTTATC
33530 TCCCTT
1 TCCCTT
33536 TTTGTTCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.58
23 10 0.42
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.58
Consensus pattern (21 bp):
TCCCTTAAATTTTATTTTATC
Found at i:33779 original size:29 final size:29
Alignment explanation
Indices: 33739--33817 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
33729 GTCCTTAAGC
* *
33739 TTTAAATTTAGATTCTTAAATTTTAGAC-T
1 TTTACATTTAGATCCTTAAATTTTAG-CTT
**
33768 TTTACATTTAGATCCTTGGATTTTAGCTT
1 TTTACATTTAGATCCTTAAATTTTAGCTT
33797 TCTTACATTTTAG-TCCTTAAA
1 T-TTACA-TTTAGATCCTTAAA
33818 ACTTCAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 1 0.02
29 24 0.59
30 11 0.27
31 5 0.12
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (29 bp):
TTTACATTTAGATCCTTAAATTTTAGCTT
Found at i:35916 original size:20 final size:22
Alignment explanation
Indices: 35877--35925 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
35867 CCTTGTTGCA
*
35877 TTTGCATCTCACATTTTGCATC
1 TTTGCATCTCACATTGTGCATC
35899 TTTGCATCT-ACA-TGTGCATC
1 TTTGCATCTCACATTGTGCATC
35919 TTTGCAT
1 TTTGCAT
35926 TTTTTGCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 14 0.54
21 3 0.12
22 9 0.35
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45
Consensus pattern (22 bp):
TTTGCATCTCACATTGTGCATC
Found at i:37002 original size:2 final size:2
Alignment explanation
Indices: 36995--37026 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
36985 ATCCTTTCAA
*
36995 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37027 CCCTTGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37317 original size:10 final size:9
Alignment explanation
Indices: 37302--37377 Score: 68
Period size: 8 Copynumber: 8.3 Consensus size: 9
37292 AAGAACACAC
37302 AAAAAGAGAG
1 AAAAAGA-AG
37312 AAAAAGAA-
1 AAAAAGAAG
*
37320 AGAAAGAAG
1 AAAAAGAAG
37329 AAAAAGAA-
1 AAAAAGAAG
*
37337 AGAAAGAAG
1 AAAAAGAAG
*
37346 AAAAA-TAG
1 AAAAAGAAG
37354 AAAAAGAAAG
1 AAAAAG-AAG
37364 AAAGAAAGAAG
1 -AA-AAAGAAG
37375 AAA
1 AAA
37378 TAAAATAGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
8 21 0.39
9 13 0.24
10 11 0.20
11 5 0.09
12 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:37323 original size:4 final size:4
Alignment explanation
Indices: 37314--37377 Score: 66
Period size: 4 Copynumber: 16.8 Consensus size: 4
37304 AAAGAGAGAA
*
37314 AAAG AAAG AAAG AAGAA AAAG AAAG AAAG -AAG AAA- AATAG -AA- AAAG
1 AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AA-AG AAAG AAAG
37360 AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAA
37378 TAAAATAGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
3 11 0.22
4 37 0.73
5 3 0.06
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:37330 original size:17 final size:17
Alignment explanation
Indices: 37304--37377 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
37294 GAACACACAA
37304 AAAGAGAGAAAAAGAAAG
1 AAAGA-AGAAAAAGAAAG
37322 AAAGAAGAAAAAGAAAG
1 AAAGAAGAAAAAGAAAG
*
37339 AAAGAAG-AAAA-ATAG
1 AAAGAAGAAAAAGAAAG
37354 AAA-AAG--AAAGAAAG
1 AAAGAAGAAAAAGAAAG
37368 AAAGAAGAAA
1 AAAGAAGAAA
37378 TAAAATAGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.06
14 9 0.18
15 9 0.18
16 4 0.08
17 20 0.40
18 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (17 bp):
AAAGAAGAAAAAGAAAG
Found at i:37355 original size:25 final size:26
Alignment explanation
Indices: 37314--37379 Score: 100
Period size: 25 Copynumber: 2.6 Consensus size: 26
37304 AAAGAGAGAA
*
37314 AAAGAAAGAAAGA-AGAAAAAGAAAG
1 AAAGAAAGAAAAATAGAAAAAGAAAG
37339 AAAG-AAGAAAAATAGAAAAAGAAAG
1 AAAGAAAGAAAAATAGAAAAAGAAAG
37364 AAAGAAAGAAGAAATA
1 AAAGAAAGAA-AAATA
37380 AAATAGATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 7 0.19
25 20 0.54
26 5 0.14
27 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (26 bp):
AAAGAAAGAAAAATAGAAAAAGAAAG
Found at i:39741 original size:42 final size:42
Alignment explanation
Indices: 39694--39778 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
39684 TTTCGAATCA
* *
39694 GCTTAAGTCCTTAGGGCCATC-AGTAAGTCTTTCGAGCATGAT
1 GCTTAAATCCTTAGGGCCATCTA-TAAGTCTTTCGAGCAAGAT
* *
39736 GCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGAT
1 GCTTAAATCCTTAGGGCCATCTATAAGTCTTTCGAGCAAGAT
39778 G
1 G
39779 ATAAGTCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (42 bp):
GCTTAAATCCTTAGGGCCATCTATAAGTCTTTCGAGCAAGAT
Found at i:40029 original size:41 final size:41
Alignment explanation
Indices: 39923--40036 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
39913 CGAATCAGCT
* * * * *
39923 TAAGTCATTCGGGCCATCAGTAAGTCTTTTGAACATGATGCT
1 TAAGTCCTTCGGGCCACCA-TAAGTCTTTCGAACAAGATGCA
* * * *
39965 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG-A
1 TAAGTCCTTCGGGCCA-CCATAAGTCTTTCGAACAAGATGCA
*
40006 TAAGTCCTTCGGGCCACCCATAAGTCATTCG
1 TAAGTCCTTCGGGCCA-CCATAAGTCTTTCG
40037 GGTGGGATGT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
41 26 0.46
42 30 0.53
43 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCACCATAAGTCTTTCGAACAAGATGCA
Found at i:40048 original size:226 final size:227
Alignment explanation
Indices: 39483--40048 Score: 868
Period size: 226 Copynumber: 2.5 Consensus size: 227
39473 AGTCCTTCAA
* * * * *
39483 GCCATCAGTAAGTCTTTCGATCATGATGCTTAAATCCTTAGGGTTATTTATAAG-CTTTTGAGCA
1 GCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
* * * *
39547 AGATGATAAGTCTTTCGGGTCATCCATAAGACATTTGGGCAGGATGTTTACAATATTTCCTTTTC
66 AGATGATAAGTCATTCGGGCCATCCATAAGACATTTGGGCAGGATGTTTACAACATTTCATTTTC
* *
39612 TCGATTCACAACAGTTCGAATCAGCAACGCCCCACCAGAAGGGTTAACATTTCCTTTGCTCGATT
131 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAAGGGTTAACATTTCATTTGCTCGATT
*
39677 CACGACATTTCGAATCAGCTTAAGTCCTTAGG
196 CACGACATTTCGAATCAGCTTAAGTCATTAGG
*
39709 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
1 GCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
* * *
39774 AGATGATAAGTCATTCAGGCCATCCATAAGACCTTTGGGCACGATGTTTACAACATTTCATTTTC
66 AGATGATAAGTCATTCGGGCCATCCATAAGACATTTGGGCAGGATGTTTACAACATTTCATTTTC
*
39839 TCGATTCATAACACTTCGAATCAGCAACGCCCCACCAG-AGGTGTTAACATTTCATTTG-TCGAT
131 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAAGG-GTTAACATTTCATTTGCTCGAT
* *
39902 TCACGTCATTTCGAATCAGCTTAAGTCATTCGG
195 TCACGACATTTCGAATCAGCTTAAGTCATTAGG
*
39935 GCCATCAGTAAGTCTTTTGAACATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
1 GCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
* * * * **
40000 AGATGATAAGTCCTTCGGGCCACCCATAAGTCATTCGGGTGGGATGTTT
66 AGATGATAAGTCATTCGGGCCATCCATAAGACATTTGGGCAGGATGTTT
40049 CCAATTGATT
Statistics
Matches: 309, Mismatches: 29, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
226 191 0.62
227 118 0.38
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (227 bp):
GCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
AGATGATAAGTCATTCGGGCCATCCATAAGACATTTGGGCAGGATGTTTACAACATTTCATTTTC
TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAAGGGTTAACATTTCATTTGCTCGATT
CACGACATTTCGAATCAGCTTAAGTCATTAGG
Found at i:40905 original size:136 final size:136
Alignment explanation
Indices: 40658--41377 Score: 823
Period size: 136 Copynumber: 5.3 Consensus size: 136
40648 CAATGAAGAG
* * * * * *
40658 TAATGAGAAGAACTCATCTGACTGAGGGAGAGGAAGTTCATAATGAGAAAAGCTTGCTCGATCTA
1 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA
* ** *** * * * ** *
40723 GCGTTCGATTCACGGTATTTTGAATCACTGATGCCTCATTTAAGGGATTAACATTTCAAATGGAG
66 TCACTCGATTCACAACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTAACATTTCAAATGGAG
*
40788 AGCTCA
131 AGTTCA
*
40794 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGATAAGAGCTTGTTCGACCTA
1 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA
*** *
40859 TCACTCGATTCACGGTATTTCGAATCAGTGACGCCTCGCTTGAGGGATTAACATTTCAAATGTAG
66 TCACTCGATTCACAACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTAACATTTCAAATGGAG
40924 AGTTCA
131 AGTTCA
* * * *
40930 TAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAATTCATAATGAGAAGTGCTTGTTCGACCTT
1 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA
* * *
40995 TCTCTCGGTTCACAACATTTTGAATCAGTGACGCCTCGCTTGAGGGATTAACATTTCAAATGGAG
66 TCACTCGATTCACAACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTAACATTTCAAATGGAG
41060 AGTTCA
131 AGTTCA
* ** *
41066 TAATGAAAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAAATTATTCGACCTA
1 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA
* ** * * ***
41131 TTACTCGATTCGTAACACTTT-GAATCAGCT-ACGCCTCACTTGAGGGATTGACATTTTTGATGG
66 TCACTCGATTCACAACA-TTTCGAATCAG-TGACGCCTCGCTTGAGGGATTAACATTTCAAATGG
*
41194 AGGGTTCA
129 AGAGTTCA
* * * * * *
41202 TAATGAGAATAACTTATCCAAAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTGACCTA
1 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA
* * * * * * * * ****
41267 TTACTCGATTAACAACACTTCGAATCAGTAACACTTCGCTTGGGGGATTGACATTTTTGTTGGAG
66 TCACTCGATTCACAACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTAACATTTCAAATGGAG
*
41332 GGTTCA
131 AGTTCA
* *
41338 TAATGAGAATAACTTATCCGACAGAGGGAGAAGAAGTTCA
1 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
41378 ACACTTCGAA
Statistics
Matches: 512, Mismatches: 68, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
135 3 0.01
136 505 0.99
137 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (136 bp):
TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA
TCACTCGATTCACAACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTAACATTTCAAATGGAG
AGTTCA
Found at i:43216 original size:10 final size:10
Alignment explanation
Indices: 43201--43229 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
43191 CCTTTCTCAT
43201 ATTTGTTTCA
1 ATTTGTTTCA
43211 ATTTGTTTCA
1 ATTTGTTTCA
43221 ATTTGTTTC
1 ATTTGTTTC
43230 TTCCTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (10 bp):
ATTTGTTTCA
Found at i:43666 original size:15 final size:15
Alignment explanation
Indices: 43646--43688 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43636 AATCCTTGAG
43646 CTTTAAATTTAGATT
1 CTTTAAATTTAGATT
* *
43661 CTTTAATTTTAGACT
1 CTTTAAATTTAGATT
*
43676 -TTTACATTTAGAT
1 CTTTAAATTTAGAT
43689 CCTTGGATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.53
Consensus pattern (15 bp):
CTTTAAATTTAGATT
Found at i:43679 original size:29 final size:28
Alignment explanation
Indices: 43647--43705 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
43637 ATCCTTGAGC
* *
43647 TTTAAATTTAGATTCTTTAATTTTAGACT
1 TTTAAATTTAGATCCTTGAATTTTAG-CT
* *
43676 TTTACATTTAGATCCTTGGATTTTAGCT
1 TTTAAATTTAGATCCTTGAATTTTAGCT
43704 TT
1 TT
43706 CTTACATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.54
Consensus pattern (28 bp):
TTTAAATTTAGATCCTTGAATTTTAGCT
Found at i:46071 original size:16 final size:16
Alignment explanation
Indices: 46050--46084 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
46040 GTCTATACAA
46050 GTCAAGTTCATAACAT
1 GTCAAGTTCATAACAT
*
46066 GTCAAGTTGATAACAT
1 GTCAAGTTCATAACAT
46082 GTC
1 GTC
46085 GAATAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (16 bp):
GTCAAGTTCATAACAT
Found at i:47148 original size:19 final size:18
Alignment explanation
Indices: 47108--47150 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
47098 GAAATTATTT
* *
47108 AAAACCTACCAATACCAC
1 AAAAACTACAAATACCAC
47126 AAAAACTACAAATACCAC
1 AAAAACTACAAATACCAC
47144 AAAAACT
1 AAAAACT
47151 TAAAACCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.58, C:0.30, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAACTACAAATACCAC
Found at i:47639 original size:29 final size:30
Alignment explanation
Indices: 47607--47670 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
47597 GTTTTTCTAA
* **
47607 AAATTATAAAATATTATTAATTTA-TTATT
1 AAATTATAAAACATTATTAAAATATTTATT
* *
47636 AAATTTTAATACATTATTAAAATATTTATT
1 AAATTATAAAACATTATTAAAATATTTATT
47666 AAATT
1 AAATT
47671 TCATTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
AAATTATAAAACATTATTAAAATATTTATT
Found at i:47662 original size:21 final size:21
Alignment explanation
Indices: 47609--47662 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 21
47599 TTTTCTAAAA
**
47609 ATTA-TAAAATATTATTAATTT
1 ATTATTAAAATATT-TTAATAC
47630 ATTATT--AA-ATTTTAATAC
1 ATTATTAAAATATTTTAATAC
47648 ATTATTAAAATATTT
1 ATTATTAAAATATTT
47663 ATTAAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
18 11 0.41
19 3 0.11
20 4 0.15
21 8 0.30
22 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATTAAAATATTTTAATAC
Found at i:47667 original size:30 final size:30
Alignment explanation
Indices: 47631--47687 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
47621 TATTAATTTA
* *
47631 TTATTAAATTTTAATACATTATTAAAATAT
1 TTATTAAATTTCAATAAATTATTAAAATAT
*
47661 TTATTAAATTTCATTAAATTATTAAAA
1 TTATTAAATTTCAATAAATTATTAAAA
47688 ATAATCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
TTATTAAATTTCAATAAATTATTAAAATAT
Found at i:78421 original size:16 final size:17
Alignment explanation
Indices: 78389--78423 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
78379 CCTCATAGAA
78389 TTTACAAATCAATTTTT
1 TTTACAAATCAATTTTT
78406 TTTACAAATC-ATTTTT
1 TTTACAAATCAATTTTT
78422 TT
1 TT
78424 CAAAAACTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTACAAATCAATTTTT
Found at i:89974 original size:20 final size:20
Alignment explanation
Indices: 89922--89978 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
89912 ACCAGTTAAA
* * *
89922 CATTGGCCATTAACTTTGAT
1 CATTGACCATTTACTTTGAC
89942 CATTGACCATTTACTTTGAC
1 CATTGACCATTTACTTTGAC
*
89962 CATTGACCGTTTACTTT
1 CATTGACCATTTACTTT
89979 TTGTTGACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (20 bp):
CATTGACCATTTACTTTGAC
Done.