Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000428.1 Hibiscus syriacus cultivar Beakdansim tig00000787_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: 74931
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:2498 original size:15 final size:15
Alignment explanation
Indices: 2478--2527 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
2468 ATATTTTTCA
*
2478 TGAAAATGTTCTATG
1 TGAAAATGTTCTAAG
*
2493 TGAAAATGTGCTAAG
1 TGAAAATGTTCTAAG
*
2508 TGAAAA--TTCTACG
1 TGAAAATGTTCTAAG
2521 TGAAAAT
1 TGAAAAT
2528 AACCTATGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.37
15 19 0.63
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (15 bp):
TGAAAATGTTCTAAG
Found at i:2699 original size:24 final size:25
Alignment explanation
Indices: 2657--2710 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
2647 GAGTCGAGGG
2657 TTCTACGCGGTCCTACGGGACAAAA
1 TTCTACGCGGTCCTACGGGACAAAA
* *
2682 TTCTACG-TGTCCTTCGGGACAAAA
1 TTCTACGCGGTCCTACGGGACAAAA
2706 TTCTA
1 TTCTA
2711 GGTAGTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (25 bp):
TTCTACGCGGTCCTACGGGACAAAA
Found at i:7230 original size:2 final size:2
Alignment explanation
Indices: 7223--7254 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7213 TTTAAAACGA
*
7223 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7255 GACTAAGATG
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:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:8661 original size:3 final size:3
Alignment explanation
Indices: 8653--8720 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
8643 GGGCTGTTTG
*
8653 TAA TAA TAA TAA TAT TAA TAA TAA -AA TAAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
8697 TAA TAA TAA TAA TAAA TAA -AA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA
8721 AAAATAAACA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.10
3 46 0.79
4 6 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:8721 original size:9 final size:9
Alignment explanation
Indices: 8672--8734 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
8662 TAATATTAAT
8672 AATAAAATA
1 AATAAAATA
*
8681 AATAATAT-
1 AATAAAATA
8689 AATAATAATAA
1 AATAA-AAT-A
8700 TAATAATAATA
1 -AATAA-AATA
8711 AATAAAAT-
1 AATAAAATA
8719 AA-AAAATA
1 AATAAAATA
*
8727 AACAAAAT
1 AATAAAAT
8735 GAAAAAAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
7 5 0.11
8 9 0.20
9 17 0.37
10 5 0.11
11 1 0.02
12 9 0.20
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (9 bp):
AATAAAATA
Found at i:8725 original size:12 final size:12
Alignment explanation
Indices: 8672--8728 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
8662 TAATATTAAT
*
8672 AATAAAATAAAT
1 AATAAAATAAAA
*
8684 AATATAATAATAA
1 AATAAAATAA-AA
*
8697 TAATAATAATAATA
1 -AATAA-AATAAAA
8711 AATAAAATAAAA
1 AATAAAATAAAA
8723 AATAAA
1 AATAAA
8729 CAAAATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
12 21 0.57
13 6 0.16
14 5 0.14
15 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:9261 original size:121 final size:117
Alignment explanation
Indices: 9075--9504 Score: 469
Period size: 118 Copynumber: 3.7 Consensus size: 117
9065 TGAATTAAAG
* *
9075 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCTTCCTCTTCAGATAAGTTCTTCTCACTATG
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
* *
9140 AACTTTATCTGGAAATGTTGGTCTGATTTATCTTCTTCTGTGATAGAGTCAAACA
66 AACTCTATCTGGAAATGTTGGTCTGATCTATC-TCTT-TGTGATAGAGTC-AACA
9195 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * *
9260 GAACTTTCTCTGGAAAAGTTGATGT-TGATCTATCTCTTTCTGATAGAGTCATGCA
65 GAACTCTATCTGGAAATGTTG--GTCTGATCTATCTCTTTGTGATAGAGTCA-ACA
* * *
9315 AA-GTTGAACAAG-TCTTCTCATTATGAACTTCTTCTCCCACTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * *** *
9378 GAACTCTACCT-GCAA---T-G-CTGATCCATC-GAATGATGAATTGAG-C-A-A
65 GAACTCTATCTGGAAATGTTGGTCTGATCTATCTCTTTG-TG-ATAGAGTCAACA
*
9423 AAGGTTGAACAAGTTCTTCTCATTATGAAC--TTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
*
9486 AACTCT-TCCGGAAATGTTG
66 AACTCTATCTGGAAATGTTG
9505 ATCCATCGAA
Statistics
Matches: 269, Mismatches: 27, Indels: 37
0.81 0.08 0.11
Matches are distributed among these distances:
106 1 0.00
107 40 0.15
108 3 0.01
109 10 0.04
110 18 0.07
111 12 0.04
112 5 0.02
114 1 0.00
117 3 0.01
118 55 0.20
119 11 0.04
120 47 0.17
121 53 0.20
122 8 0.03
123 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (117 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
AACTCTATCTGGAAATGTTGGTCTGATCTATCTCTTTGTGATAGAGTCAACA
Found at i:9507 original size:107 final size:108
Alignment explanation
Indices: 9192--9528 Score: 360
Period size: 107 Copynumber: 3.0 Consensus size: 108
9182 ATAGAGTCAA
*
9192 ACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCAT
1 ACAAAGGTTGAACAAGTTCTTCTCATTATGAAC---TTCTTCCTCTTCAGATGAGTTCTTCTCAT
* *** ** *
9257 TATGAACT-TTCTCTGGAAAAGTTGATGTTGATCTATCTCTTTCTG-ATAGAGTC
63 TATGAACTCTTC-C-GG--AA----ATGTTGATCCATCGAATGATGAATTGAG-C
*
9310 ATGCAAA-GTTGAACAAG-TCTTCTCATTATGAACTTCTTCTCCCACTTCAGATGAGTTCTTCTC
1 A--CAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-T-T-CCTCTTCAGATGAGTTCTTCTC
* * * *
9373 ATTATGAACTCTACCTGCAATGCTGATCCATCGAATGATGAATTGAGC
61 ATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATTGAGC
9421 A-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 ACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
9485 GAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATTCGAGC
66 GAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATT-GAGC
9529 CTTTGCTGAA
Statistics
Matches: 191, Mismatches: 18, Indels: 30
0.80 0.08 0.13
Matches are distributed among these distances:
107 61 0.32
108 8 0.04
109 11 0.06
110 19 0.10
111 16 0.08
112 5 0.03
115 4 0.02
116 1 0.01
117 2 0.01
118 48 0.25
119 12 0.06
120 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (108 bp):
ACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATTGAGC
Found at i:9920 original size:22 final size:22
Alignment explanation
Indices: 9893--10003 Score: 213
Period size: 22 Copynumber: 5.0 Consensus size: 22
9883 CATATTTAAA
9893 AGAGAATCTATCATCTTTGAAG
1 AGAGAATCTATCATCTTTGAAG
9915 AGAGAATCTATCATCTTTGAAG
1 AGAGAATCTATCATCTTTGAAG
9937 AGAGAATCTATCATCTTTGAAG
1 AGAGAATCTATCATCTTTGAAG
*
9959 AGAGACTCTATCATCTTTGAAG
1 AGAGAATCTATCATCTTTGAAG
9981 AGAGAATCTATCATCTTTGAAG
1 AGAGAATCTATCATCTTTGAAG
10003 A
1 A
10004 ATGTAGATGT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
AGAGAATCTATCATCTTTGAAG
Found at i:11475 original size:73 final size:72
Alignment explanation
Indices: 11330--11513 Score: 257
Period size: 73 Copynumber: 2.6 Consensus size: 72
11320 GATATGGATC
* * *
11330 TTCAGCATG-CCCAACATTGGCTAATACAAACGTTCAAAAATATAACATTCATGATTCTAATTGA
1 TTCAGCATGCCCCAACATTGGCTGATACAGACGTTCAAAAATATAACATTCATGATTATAATTGA
11394 AAGGGGCT
66 AA-GGGCT
* *
11402 TTCAACATGCCCCAACATTGGCTGATACAGACGTTCAAAATATATCAACATTCATGATTATGATT
1 TTCAGCATGCCCCAACATTGGCTGATACAGACGTTCAAAA-ATAT-AACATTCATGATTATAATT
11467 GAAA-GGCT
64 GAAAGGGCT
* *
11475 TTCAGTATGCCCCAACATTGGCTGATACAGATGTT-AAAA
1 TTCAGCATGCCCCAACATTGGCTGATACAGACGTTCAAAA
11514 GTGTGCTCAA
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
72 12 0.12
73 64 0.63
74 4 0.04
75 21 0.21
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (72 bp):
TTCAGCATGCCCCAACATTGGCTGATACAGACGTTCAAAAATATAACATTCATGATTATAATTGA
AAGGGCT
Found at i:15393 original size:13 final size:15
Alignment explanation
Indices: 15377--15410 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
15367 AAGCAAACAA
15377 AAAATGCAAA-ATG-
1 AAAATGCAAAGATGC
15390 AAAATGCAAAGATGC
1 AAAATGCAAAGATGC
15405 AAAATG
1 AAAATG
15411 TAAATGCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 3 0.16
15 6 0.32
ACGTcount: A:0.59, C:0.09, G:0.18, T:0.15
Consensus pattern (15 bp):
AAAATGCAAAGATGC
Found at i:15404 original size:8 final size:7
Alignment explanation
Indices: 15377--15410 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
15367 AAGCAAACAA
15377 AAAATGC
1 AAAATGC
15384 AAAATG-
1 AAAATGC
15390 AAAATGC
1 AAAATGC
15397 AAAGATGC
1 AAA-ATGC
15405 AAAATG
1 AAAATG
15411 TAAATGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.59, C:0.09, G:0.18, T:0.15
Consensus pattern (7 bp):
AAAATGC
Found at i:16085 original size:35 final size:36
Alignment explanation
Indices: 16021--16088 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
16011 CTTACTGTAG
* **
16021 ACTTTTGGTATCAATTTGGCAGGATCTTTGTGTAAT
1 ACTTTTGGTATCAATATAACAGGATCTTTGTGTAAT
16057 ACTTTTGGTAT-AATATAACAGGATCTTTGTGT
1 ACTTTTGGTATCAATATAACAGGATCTTTGTGT
16089 GCATAGCTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 18 0.62
36 11 0.38
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (36 bp):
ACTTTTGGTATCAATATAACAGGATCTTTGTGTAAT
Found at i:16392 original size:15 final size:15
Alignment explanation
Indices: 16367--16404 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
16357 ATCCTAACCT
*
16367 CATGATTTCTAGTTC
1 CATGCTTTCTAGTTC
*
16382 TATGCTTTCTAGTTC
1 CATGCTTTCTAGTTC
16397 CATGCTTT
1 CATGCTTT
16405 GTTTGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (15 bp):
CATGCTTTCTAGTTC
Found at i:17379 original size:13 final size:13
Alignment explanation
Indices: 17361--17389 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17351 GTTGATTATA
17361 AATTGTCTCTAAT
1 AATTGTCTCTAAT
17374 AATTGTCTCTAAT
1 AATTGTCTCTAAT
17387 AAT
1 AAT
17390 AGAATTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (13 bp):
AATTGTCTCTAAT
Found at i:17597 original size:2 final size:2
Alignment explanation
Indices: 17590--17623 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17580 TTTAAAATGA
17590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17624 GACTAAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19100 original size:3 final size:3
Alignment explanation
Indices: 19092--19151 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
19082 GGCCTGTTTG
* *
19092 TAA TAA TAA TAA TAT TAA TAA TAA AAA TAAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
19137 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
19152 ACAAATAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19158 original size:14 final size:14
Alignment explanation
Indices: 19096--19179 Score: 54
Period size: 14 Copynumber: 6.1 Consensus size: 14
19086 TGTTTGTAAT
*
19096 AATAATAATATTAAT
1 AATAATAATA-TAAA
* *
19111 AATAAAAATAAATAAT
1 AATAATAAT--ATAAA
*
19127 AATAATAATATAAT
1 AATAATAATATAAA
19141 AATAATAATA-AACA
1 AATAATAATATAA-A
19155 AATAA-AAT-TAAA
1 AATAATAATATAAA
19167 AA-AA-AATA-AAA
1 AATAATAATATAAA
19178 AA
1 AA
19180 AAAACAAATG
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
11 10 0.16
12 3 0.05
13 7 0.11
14 20 0.33
15 8 0.13
16 12 0.20
17 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATAATATAAA
Found at i:19158 original size:17 final size:16
Alignment explanation
Indices: 19107--19188 Score: 78
Period size: 16 Copynumber: 5.1 Consensus size: 16
19097 ATAATAATAT
*
19107 TAATAATAAAAATAAA
1 TAATAATAAAAACAAA
* *
19123 TAATAATAATAATATAA
1 TAATAATAAAAACA-AA
19140 TAATAATAATAAACAAA
1 TAATAATAA-AAACAAA
*
19157 TAA-AATTAAAAAAAAA
1 TAATAA-TAAAAACAAA
*
19173 TAA-AAAAAAAACAAA
1 TAATAATAAAAACAAA
19188 T
1 T
19189 GAAAAAACTA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
15 9 0.16
16 26 0.46
17 19 0.33
18 3 0.05
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (16 bp):
TAATAATAAAAACAAA
Found at i:19193 original size:16 final size:15
Alignment explanation
Indices: 19150--19195 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
19140 TAATAATAAT
19150 AAACAAATAAAATTAAA
1 AAACAAATAAAA--AAA
19167 AAA-AAATAAAAAAA
1 AAACAAATAAAAAAA
19181 AAACAAATGAAAAAA
1 AAACAAAT-AAAAAA
19196 CTAGTGTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 14 0.52
17 3 0.11
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (15 bp):
AAACAAATAAAAAAA
Found at i:21861 original size:15 final size:15
Alignment explanation
Indices: 21843--21880 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
21833 AATATTCTAT
21843 GTGAAAATGTGCTAA
1 GTGAAAATGTGCTAA
* *
21858 GTGAAAATGTTCTAC
1 GTGAAAATGTGCTAA
21873 GTGAAAAT
1 GTGAAAAT
21881 ACCCTATGCG
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:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (15 bp):
GTGAAAATGTGCTAA
Found at i:22056 original size:25 final size:26
Alignment explanation
Indices: 22028--22080 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
22018 CATTTGAGAC
* *
22028 AAAATTCTAC-ATGTCATTCGGGGCA
1 AAAATTCTACGAGGTCATTCGGGACA
*
22053 AAAATTCTACGCGGTCATTCGGGACA
1 AAAATTCTACGAGGTCATTCGGGACA
22079 AA
1 AA
22081 TCTATGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (26 bp):
AAAATTCTACGAGGTCATTCGGGACA
Found at i:22108 original size:24 final size:24
Alignment explanation
Indices: 22077--22134 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
22067 TCATTCGGGA
22077 CAAA-TCTATGTGGAACTTCGATG
1 CAAATTCTATGTGGAACTTCGATG
* * * *
22100 CATATTCTACGTGGCACTTCGGTG
1 CAAATTCTATGTGGAACTTCGATG
*
22124 CAAATTATATG
1 CAAATTCTATG
22135 AGCAGTGTGA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (24 bp):
CAAATTCTATGTGGAACTTCGATG
Found at i:22709 original size:16 final size:17
Alignment explanation
Indices: 22676--22709 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22666 AATTTTCAAC
22676 AAGTTTTCAAAGAGTCA
1 AAGTTTTCAAAGAGTCA
*
22693 AAGTTTTGAAA-AGTCA
1 AAGTTTTCAAAGAGTCA
22709 A
1 A
22710 TGTGACACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (17 bp):
AAGTTTTCAAAGAGTCA
Found at i:27125 original size:65 final size:64
Alignment explanation
Indices: 27009--27130 Score: 165
Period size: 65 Copynumber: 1.9 Consensus size: 64
26999 TTCGAATGTT
* * * * *
27009 TTTTGTGTACCGATGCACAGTCATGCATCGATGCACTCTTGATTTTATTGAAACATCAAAGGCA
1 TTTTATGTACCGATGCACAGTAATGCATCGATACACTCTGGATCTTATTGAAACATCAAAGGCA
*
27073 TTTTATGTACTGATGCACAGATAATGCATCGATACACTCCTGGATCTT-TTGAAACATC
1 TTTTATGTACCGATGCACAG-TAATGCATCGATACACT-CTGGATCTTATTGAAACATC
27131 GAATGTAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 18 0.36
65 25 0.50
66 7 0.14
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (64 bp):
TTTTATGTACCGATGCACAGTAATGCATCGATACACTCTGGATCTTATTGAAACATCAAAGGCA
Found at i:27153 original size:65 final size:64
Alignment explanation
Indices: 27013--27155 Score: 148
Period size: 65 Copynumber: 2.2 Consensus size: 64
27003 AATGTTTTTT
* * * * *
27013 GTGTACCGATGCACAGTCATGCATCGATGCACTCTTGATTTTATTGAAACATCAAAGGCATTTTA
1 GTGTA-CGATGCACAGTAATGCATCGATACACTCTGGATCTTATTGAAACATCAAAGGCATATTA
* * *
27078 -TGTACTGATGCACAGATAATGCATCGATACACTCCTGGATCTT-TTGAAACATCGAATGTA-AT
1 GTGTAC-GATGCACAG-TAATGCATCGATACACT-CTGGATCTTATTGAAACATCAAAGGCATAT
27140 TA
63 TA
27142 GTGTAGCGATGCAC
1 GTGTA-CGATGCAC
27156 CCCAAGTGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
63 1 0.02
64 16 0.25
65 40 0.62
66 8 0.12
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (64 bp):
GTGTACGATGCACAGTAATGCATCGATACACTCTGGATCTTATTGAAACATCAAAGGCATATTA
Found at i:28101 original size:22 final size:22
Alignment explanation
Indices: 28064--28132 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 22
28054 GGGGTAGTGT
*
28064 ATCGATGCACATGTTAAGGGATGC
1 ATCGATG-ACATGTT-AGAGATGC
28088 ATCGATG-CATGTTAGAGATGC
1 ATCGATGACATGTTAGAGATGC
*
28109 -TCGAT-AC-TG-TAGA-ATGT
1 ATCGATGACATGTTAGAGATGC
28126 ATCGATG
1 ATCGATG
28133 CACTTCAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
17 3 0.08
18 9 0.22
19 2 0.05
20 6 0.15
21 7 0.17
22 6 0.15
24 7 0.17
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (22 bp):
ATCGATGACATGTTAGAGATGC
Found at i:29525 original size:23 final size:23
Alignment explanation
Indices: 29462--29525 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
29452 AGTATTAAAT
29462 AAATAATAATAGAAAATA-AGAA
1 AAATAATAATAGAAAATATAGAA
*
29484 ATAT-AT-ATAGAAACATATAGACA
1 AAATAATAATAGAAA-ATATAGA-A
29507 AAATAATAATA-AAAATATA
1 AAATAATAATAGAAAATATA
29526 CATAGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 7 0.20
21 5 0.14
22 6 0.17
23 9 0.26
24 5 0.14
25 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.23
Consensus pattern (23 bp):
AAATAATAATAGAAAATATAGAA
Found at i:29677 original size:2 final size:2
Alignment explanation
Indices: 29666--29697 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29656 GTATATTTAA
29666 AT AT -T 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 A
29698 CTAATATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31200 original size:107 final size:107
Alignment explanation
Indices: 31027--31259 Score: 324
Period size: 107 Copynumber: 2.2 Consensus size: 107
31017 ATCTTCTGTC
* * * * * **
31027 GTGAAGTTGAAGTTGGTTCTGGAACTGGGAAATTGTTTTGTTGACAGTCAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGATTTGTTGACAACCAGCCGTCCCTTCGTTG
*
31092 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATGCCCTTCAAT
66 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
*
31134 GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATT-ATTTGTTGACAACCAGCCGTCCCTTCGTTT
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGATTTGTTGACAACCAGCCGTCCCTTCG-TT
* * * **
31198 GTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCT
65 GTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
31241 GTGAAGTTGAAATTGGCTC
1 GTGAAGTTGAAATTGGCTC
31260 TAGCTAAACC
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 24 0.22
107 87 0.78
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (107 bp):
GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGATTTGTTGACAACCAGCCGTCCCTTCGTTG
TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
Found at i:31582 original size:34 final size:36
Alignment explanation
Indices: 31544--31628 Score: 147
Period size: 34 Copynumber: 2.4 Consensus size: 36
31534 GTTTAAATGA
*
31544 TGTTTCAAGAGAAACATTTTCAAAGG-TT-TTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
31578 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
31614 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
31629 TGTATCAAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
34 25 0.52
35 2 0.04
36 21 0.44
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (36 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
Found at i:31709 original size:37 final size:35
Alignment explanation
Indices: 31668--32167 Score: 185
Period size: 37 Copynumber: 14.9 Consensus size: 35
31658 CAAGGATTGA
31668 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAA-GGAGAC-AAATTT
* * *
31705 TGTTTTAAGA-AAACATGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAAC-TGTCTCAAG-GAGACAAATTT
31741 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGAC-AAATTT
*
31777 TGTTT-AATGTA-AAACATAT-TCAA--AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGGAGACAAATTT
* *
31806 TGTTTCAAGGGAAACTGTTTTCAA--AG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGAGACAAATTT
* *
31835 ATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTC-AAGGAGACAAATTT
* *
31872 TGTTT-AAGGGAAACTATCTCAAGAGAGACAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAATTT
** * * * *
31906 CATTTCAAGGGAAA-TGTTTCAA--TG-----TTA
1 TGTTTCAAGAGAAACTGTCTCAAGGAGACAAATTT
*
31933 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAA-GGAGAC-AAATTT
* *
31970 TGTTTCAAGGGAAACTATCTCAAGAGAGAC-AA-TT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAATTT
* * * *
32004 TATTTCAAGGGAAA-TGCTTTCAA--TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGAGACAAATTT
32032 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAA-GGAGAC-AAATTT
* * * *
32070 TGTTCCAAGGGAAA-TGTTTTCAA--TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGAGACAAATTT
32098 ATGTTTCAAGAGAAAC-GTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAA-GGAGAC-AAATTT
* *
32135 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAA
32168 ATTCATTTCA
Statistics
Matches: 353, Mismatches: 48, Indels: 125
0.67 0.09 0.24
Matches are distributed among these distances:
27 12 0.03
28 19 0.05
29 49 0.14
30 27 0.08
31 4 0.01
32 3 0.01
33 3 0.01
34 35 0.10
35 32 0.09
36 75 0.21
37 91 0.26
38 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGGAGACAAATTT
Found at i:31831 original size:30 final size:30
Alignment explanation
Indices: 31795--31853 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
31785 GTAAAACATA
*
31795 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
31825 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
31854 CTCAAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:31916 original size:35 final size:35
Alignment explanation
Indices: 31846--31919 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
31836 TGTTTCAATA
* **
31846 GAAACTGTCTCAAAGGAGACAAAATTTGTTTAAGG
1 GAAACTATCTCAAAGGAGACAAAATTCATTTAAGG
31881 GAAACTATCTC-AAGAGAGAC-AAATTCATTTCAAGG
1 GAAACTATCTCAAAG-GAGACAAAATTCATTT-AAGG
31916 GAAA
1 GAAA
31920 TGTTTCAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 11 0.32
35 23 0.68
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (35 bp):
GAAACTATCTCAAAGGAGACAAAATTCATTTAAGG
Found at i:32066 original size:100 final size:97
Alignment explanation
Indices: 31741--32083 Score: 439
Period size: 100 Copynumber: 3.5 Consensus size: 97
31731 AGACAAAATT
* * **
31741 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAATGTAAAACATAT-TC-A-A-AG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAA-GGGAAAC-TATCTCAAGAGAG
* * *
31802 --ATTTTGTTTCAAGGGAAACTGTTTTCAAAGTTTA
64 ACAATTTATTTCAAGGGAAA-TG-TTTCAATGTTTA
* *
31836 TGTTTCAATAGAAACTGTCTCAAAGGAGACAAAATTTGTTTAAGGGAAACTATCTCAAGAGAGAC
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAGGGAAACTATCTCAAGAGAGAC
*
31901 AAATTCATTTCAAGGGAAATGTTTCAATG-TTA
66 -AATTTATTTCAAGGGAAATGTTTCAATGTTTA
*
31933 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTT-AAGGGAAACTATCTCAAGAGAG
31998 ACAATTTATTTCAAGGGAAATGCTTTCAATGTTTA
64 ACAATTTATTTCAAGGGAAATG-TTTCAATGTTTA
*
32033 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTT-TAAGGGAAA
32084 TGTTTTCAAT
Statistics
Matches: 220, Mismatches: 16, Indels: 19
0.86 0.06 0.07
Matches are distributed among these distances:
93 3 0.01
94 7 0.03
95 40 0.18
96 1 0.00
97 36 0.16
98 33 0.15
99 34 0.15
100 66 0.30
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (97 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAGGGAAACTATCTCAAGAGAGAC
AATTTATTTCAAGGGAAATGTTTCAATGTTTA
Found at i:32081 original size:164 final size:161
Alignment explanation
Indices: 31872--32249 Score: 541
Period size: 165 Copynumber: 2.3 Consensus size: 161
31862 AGACAAAATT
* *
31872 TGTTTAAGGGAAACTATCTCAAGAGAGAC-AAATTCATTTCAAGGGAAATG-TTTCAATG-TTAT
1 TGTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
*
31934 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
66 GTTTCAAGAGAAA-CGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
*
31999 C-AATTTATTTCAAGGGAAATGCTTTCAATGTTTA
130 CAAATTCATTTCAAGGG-AAT--TTTCAATGTTTA
* *
32033 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TTGTTCCAAGGGAAATGTTTTCAATGTT
1 TGTTT-AAGAGAAACTGTCTCAAGAGAGACAAAATTCAT-TT-CAAGGGAAATGTTTTCAATGTT
32097 TATGTTTCAAGAGAAACGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
63 TATGTTTCAAGAGAAACGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
32162 GACAAAATTCATTTCAAGGGAATTTTCAATGTTTA
128 GAC-AAATTCATTTCAAGGGAATTTTCAATGTTTA
* *
32197 TGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTATTTCGAGGGAAA
1 TGTTT-AAGAGAAACTGTCTCAAGAGAGACAAAA--TTC-ATTTCAAGGGAAA
32250 CTATCTCAAG
Statistics
Matches: 195, Mismatches: 10, Indels: 19
0.87 0.04 0.08
Matches are distributed among these distances:
161 5 0.03
162 22 0.11
163 7 0.04
164 55 0.28
165 59 0.30
166 30 0.15
167 16 0.08
168 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (161 bp):
TGTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
GTTTCAAGAGAAACGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
AAATTCATTTCAAGGGAATTTTCAATGTTTA
Found at i:32130 original size:65 final size:65
Alignment explanation
Indices: 31970--32148 Score: 267
Period size: 66 Copynumber: 2.8 Consensus size: 65
31960 GACAAAATTT
* * *
31970 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTAT-TTCAAGGGAAATGCTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-TGTTCAAGGGAAATGCTTTCAATGTTT
32032 A
65 A
*
32033 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT-CAAGGGAAATGCTTTCAATGTTT
32098 A
65 A
32099 TGTTTCAAGAGAAAC-GTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTCAAGGGAAA
32149 CTATCTCAAG
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
63 27 0.25
64 1 0.01
65 39 0.36
66 40 0.37
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:32168 original size:37 final size:35
Alignment explanation
Indices: 32099--32183 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 35
32089 TCAATGTTTA
* * *
32099 TGTTTCAAGAGAAACGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACATCTCAAGAGAGACAAAA-TT
32135 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAAC-ATCTCAAGAGAGACAAAATT
**
32171 CATTTCAAGGGAA
1 TGTTTCAAGGGAA
32184 TTTTCAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 27 0.63
37 16 0.37
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (35 bp):
TGTTTCAAGGGAAACATCTCAAGAGAGACAAAATT
Found at i:32270 original size:101 final size:98
Alignment explanation
Indices: 32035--32270 Score: 303
Period size: 101 Copynumber: 2.3 Consensus size: 98
32025 AATGTTTATG
* * * *
32035 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TTGTTCCAAGGGAAATGTTTTCAATGTTTA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT-TT-CAAGGG-AA--TTTTCAATGTTTA
* *
32099 TGTTTCAAGAGAAACGTCTCAAGGGAGACAAAATTTTG
61 TGTTTAAAGAGAAACGTCTCAAGGGAGACAAAATTTTA
32137 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAATTTTCAATGTTTATGTTT
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAATTTTCAATGTTTATGTTT
*
32202 AAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTA
66 AAAGAGAAAC-GTCTCAAGGGAGACAAAA-TTT-TA
* * *
32238 TTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
32271 CTTGTTTTAA
Statistics
Matches: 120, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
98 27 0.22
99 17 0.14
100 5 0.04
101 37 0.31
102 33 0.28
103 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (98 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAATTTTCAATGTTTATGTTT
AAAGAGAAACGTCTCAAGGGAGACAAAATTTTA
Found at i:33776 original size:182 final size:182
Alignment explanation
Indices: 33469--33817 Score: 617
Period size: 182 Copynumber: 1.9 Consensus size: 182
33459 GGTTTAACTA
* **
33469 AAGGGTTCATCTCATCACGAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAATGCCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* **
33534 AGTGTCCGAGAAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGAAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
33599 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGAAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGAAAATCACTG
*
33651 AAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* *
33716 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGAAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
33781 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
33818 CGGATTTAAT
Statistics
Matches: 158, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 158 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (182 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
AGTGTCCGAGAAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGAAAATCACTG
Found at i:37824 original size:21 final size:21
Alignment explanation
Indices: 37786--37846 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
37776 ACATAGTATT
37786 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
37806 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
* *
37827 ACATATAGAACAAAATAATA
1 AAATA-AGAA-ATAATAATA
37847 ACAAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 9 0.26
21 14 0.41
22 4 0.12
23 4 0.12
24 3 0.09
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:43259 original size:18 final size:18
Alignment explanation
Indices: 43232--43296 Score: 96
Period size: 18 Copynumber: 3.6 Consensus size: 18
43222 GGATTTTCAA
*
43232 TGGTCTTTCGGAACATAC
1 TGGTCCTTCGGAACATAC
43250 TGGTCCTTCGGAACATAC
1 TGGTCCTTCGGAACATAC
*
43268 TGGTCCTTCGTGAA-ATAG
1 TGGTCCTTCG-GAACATAC
43286 TGGTCCTTCGG
1 TGGTCCTTCGG
43297 GATAAATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
17 1 0.02
18 40 0.91
19 3 0.07
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.32
Consensus pattern (18 bp):
TGGTCCTTCGGAACATAC
Found at i:43796 original size:16 final size:16
Alignment explanation
Indices: 43775--43821 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 16
43765 ATATATAGGA
*
43775 ATAAGAATAAGAATAT
1 ATAAGAATAAGATTAT
43791 ATAAG-ATAAG-TTAT
1 ATAAGAATAAGATTAT
43805 AT-AGAA-AAGATTAT
1 ATAAGAATAAGATTAT
43819 ATA
1 ATA
43822 TTTCAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 5 0.19
14 12 0.44
15 5 0.19
16 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (16 bp):
ATAAGAATAAGATTAT
Found at i:47434 original size:4 final size:4
Alignment explanation
Indices: 47427--48420 Score: 1890
Period size: 4 Copynumber: 252.0 Consensus size: 4
47417 TGTTAAGGTT
47427 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47475 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47523 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47571 TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47617 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47665 TATG T-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47712 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47760 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47808 TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47855 TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47901 TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47947 --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47993 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48041 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48089 TATG TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48135 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48183 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48231 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48279 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48327 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48375 TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48421 GTATATGAAA
Statistics
Matches: 976, Mismatches: 0, Indels: 28
0.97 0.00 0.03
Matches are distributed among these distances:
2 12 0.01
3 6 0.01
4 958 0.98
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:48699 original size:30 final size:30
Alignment explanation
Indices: 48665--49037 Score: 683
Period size: 30 Copynumber: 12.4 Consensus size: 30
48655 GGTTTTTCGG
* *
48665 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48695 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48725 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
48755 GAACTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48785 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48815 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48845 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48875 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
48905 GACCTTTGGATAGTTACCGAGGATCTGTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48935 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
48965 GACCTCTGGATAGTTACCGAGGATCTCTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
48995 GACCTCTGGATAGTTACCGAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
49025 GACCTCTGGATAG
1 GACCTCTGGATAG
49038 GTCCTTCGGA
Statistics
Matches: 332, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 332 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:56428 original size:65 final size:65
Alignment explanation
Indices: 56294--56436 Score: 157
Period size: 65 Copynumber: 2.2 Consensus size: 65
56284 AATGCTTTTT
* * * *
56294 GTGTACCGATGCACAGCCATGCATCGATGCACTCCTGATTTTATTGAAACATCAAAAGCATTTTA
1 GTGTACCGATGCACAGCAATGCATCGATACACTCCTGATCTTATTGAAACATCAAAAGCATATTA
* * * * * *
56359 -TGTACCGATGCACAGATAATGCATCGATATACTCCTGGCTCTT-TTGAAACATCGAATGTA-AT
1 GTGTACCGATGCACAG-CAATGCATCGATACACTCCT-GATCTTATTGAAACATCAAAAGCATAT
56421 TA
64 TA
56423 GTGTACCGATGCAC
1 GTGTACCGATGCAC
56437 CCCAAGTGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
64 18 0.28
65 43 0.66
66 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (65 bp):
GTGTACCGATGCACAGCAATGCATCGATACACTCCTGATCTTATTGAAACATCAAAAGCATATTA
Found at i:59474 original size:856 final size:856
Alignment explanation
Indices: 57822--59540 Score: 3420
Period size: 856 Copynumber: 2.0 Consensus size: 856
57812 TTAGAGATTG
57822 TAGTTGTCAATGATAATTCTCAACAAATCGATACAACATTACCTTTCTGTACAACCAAGTTTTCA
1 TAGTTGTCAATGATAATTCTCAACAAATCGATACAACATTACCTTTCTGTACAACCAAGTTTTCA
57887 ATGTTCTATTCATTAACTCGCACCGTTGTGTAGTCCTCATTACTGCACACCAAATTATACATATA
66 ATGTTCTATTCATTAACTCGCACCGTTGTGTAGTCCTCATTACTGCACACCAAATTATACATATA
57952 TAATAATTTTCTTAAATACAATAAATAAATATAATATTAAATACAATTAATGTTACATGTATAAA
131 TAATAATTTTCTTAAATACAATAAATAAATATAATATTAAATACAATTAATGTTACATGTATAAA
*
58017 ATTATCCTTGCAAATATGCTTCTGCCCATTTCTCTTTATCTTCATATAATTTTCGAACCCATCTC
196 ATTATCCTTGCAAATATGCTTCTGCCCATTTCTCTTTATCTTCATACAATTTTCGAACCCATCTC
58082 CTTCGTTCAACCTTTTGTTTCTCTACTAATTCTTTTTAAGCCCTTTAAAAATTGGATTTAGTTCT
261 CTTCGTTCAACCTTTTGTTTCTCTACTAATTCTTTTTAAGCCCTTTAAAAATTGGATTTAGTTCT
58147 ACACATGTCAGCGTATCTCAAAAACCTGTCGAGAAAATTTTGATTAACACTATACTGTATATTCC
326 ACACATGTCAGCGTATCTCAAAAACCTGTCGAGAAAATTTTGATTAACACTATACTGTATATTCC
58212 TCATGATATGTCATAAACACAATCTATGTTTTAGCCCGGGTAGTACTTCAGCAATTGCATTTGTC
391 TCATGATATGTCATAAACACAATCTATGTTTTAGCCCGGGTAGTACTTCAGCAATTGCATTTGTC
58277 ATGTTCTTATCTCTATCAGTAATAACAGTAAGAGGTTTGTGGCCATCTCCAGCTTTAATCAATTG
456 ATGTTCTTATCTCTATCAGTAATAACAGTAAGAGGTTTGTGGCCATCTCCAGCTTTAATCAATTG
58342 TTGTAAAACCCACACATAAGTATCCTCTTTCTCATTCACAACCAATGCACATCCAAATGACACTG
521 TTGTAAAACCCACACATAAGTATCCTCTTTCTCATTCACAACCAATGCACATCCAAATGACACTG
*
58407 TGTTTTGATGATGATTAACATCAACCAAAACAACGAACGGCTTGTTGCTTGAGTTGTACTTATAA
586 TGTTTTGATGATGATTAACATCAACCAAAACAACGAACGGCTTGTTGCTTGAGTTGCACTTATAA
58472 GTCGTATCAAATGCAAGAACATGCCTGAATTCTTTATAATCTACGCGTGATATACCATCAGCCCA
651 GTCGTATCAAATGCAAGAACATGCCTGAATTCTTTATAATCTACGCGTGATATACCATCAGCCCA
58537 AAATAACTTCTCTAAGTTTCCGAATTCATACCTCGTGTGGCTCACAAAAAGAAAGGGTCAGATTT
716 AAATAACTTCTCTAAGTTTCCGAATTCATACCTCGTGTGGCTCACAAAAAGAAAGGGTCAGATTT
58602 TTGCTTCCTATTTAAATACGTCATCATCGTTTCAGCATCACCATCTTGCACTTCTTCTCATTTGA
781 TTGCTTCCTATTTAAATACGTCATCATCGTTTCAGCATCACCATCTTGCACTTCTTCTCATTTGA
58667 TTCTATATAGA
846 TTCTATATAGA
58678 TAGTTGTCAATGATAATTCTCAACAAATCGATACAACATTACCTTTCTGTACAACCAAGTTTTCA
1 TAGTTGTCAATGATAATTCTCAACAAATCGATACAACATTACCTTTCTGTACAACCAAGTTTTCA
58743 ATGTTCTATTCATTAACTCGCACCGTTGTGTAGTCCTCATTACTGCACACCAAATTATACATATA
66 ATGTTCTATTCATTAACTCGCACCGTTGTGTAGTCCTCATTACTGCACACCAAATTATACATATA
58808 TAATAATTTTCTTAAATACAATAAATAAATATAATATTAAATACAATTAATGTTACATGTATAAA
131 TAATAATTTTCTTAAATACAATAAATAAATATAATATTAAATACAATTAATGTTACATGTATAAA
58873 ATTATCCTTGCAAATATGCTTCTGCCCATTTCTCTTTATCTTCATACAATTTTCGAACCCATCTC
196 ATTATCCTTGCAAATATGCTTCTGCCCATTTCTCTTTATCTTCATACAATTTTCGAACCCATCTC
58938 CTTCGTTCAACCTTTTGTTTCTCTACTAATTCTTTTTAAGCCCTTTAAAAATTGGATTTAGTTCT
261 CTTCGTTCAACCTTTTGTTTCTCTACTAATTCTTTTTAAGCCCTTTAAAAATTGGATTTAGTTCT
59003 ACACATGTCAGCGTATCTCAAAAACCTGTCGAGAAAATTTTGATTAACACTATACTGTATATTCC
326 ACACATGTCAGCGTATCTCAAAAACCTGTCGAGAAAATTTTGATTAACACTATACTGTATATTCC
59068 TCATGATATGTCATAAACACAATCTATGTTTTAGCCCGGGTAGTACTTCAGCAATTGCATTTGTC
391 TCATGATATGTCATAAACACAATCTATGTTTTAGCCCGGGTAGTACTTCAGCAATTGCATTTGTC
59133 ATGTTCTTATCTCTATCAGTAATAACAGTAAGAGGTTTGTGGCCATCTCCAGCTTTAATCAATTG
456 ATGTTCTTATCTCTATCAGTAATAACAGTAAGAGGTTTGTGGCCATCTCCAGCTTTAATCAATTG
59198 TTGTAAAACCCACACATAAGTATCCTCTTTCTCATTCACAACCAATGCACATCCAAATGACACTG
521 TTGTAAAACCCACACATAAGTATCCTCTTTCTCATTCACAACCAATGCACATCCAAATGACACTG
59263 TGTTTTGATGATGATTAACATCAACCAAAACAACGAACGGCTTGTTGCTTGAGTTGCACTTATAA
586 TGTTTTGATGATGATTAACATCAACCAAAACAACGAACGGCTTGTTGCTTGAGTTGCACTTATAA
59328 GTCGTATCAAATGCAAGAACATGCCTGAATTCTTTATAATCTACGCGTGATATACCATCAGCCCA
651 GTCGTATCAAATGCAAGAACATGCCTGAATTCTTTATAATCTACGCGTGATATACCATCAGCCCA
59393 AAATAACTTCTCTAAGTTTCCGAATTCATACCTCGTGTGGCTCACAAAAAGAAAGGGTCAGATTT
716 AAATAACTTCTCTAAGTTTCCGAATTCATACCTCGTGTGGCTCACAAAAAGAAAGGGTCAGATTT
59458 TTGCTTCCTATTTAAATACGTCATCATCGTTTCAGCATCACCATCTTGCACTTCTTCTCATTTGA
781 TTGCTTCCTATTTAAATACGTCATCATCGTTTCAGCATCACCATCTTGCACTTCTTCTCATTTGA
59523 TTCTATATAGA
846 TTCTATATAGA
59534 TAGTTGT
1 TAGTTGT
59541 ACAAATCCTT
Statistics
Matches: 861, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
856 861 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (856 bp):
TAGTTGTCAATGATAATTCTCAACAAATCGATACAACATTACCTTTCTGTACAACCAAGTTTTCA
ATGTTCTATTCATTAACTCGCACCGTTGTGTAGTCCTCATTACTGCACACCAAATTATACATATA
TAATAATTTTCTTAAATACAATAAATAAATATAATATTAAATACAATTAATGTTACATGTATAAA
ATTATCCTTGCAAATATGCTTCTGCCCATTTCTCTTTATCTTCATACAATTTTCGAACCCATCTC
CTTCGTTCAACCTTTTGTTTCTCTACTAATTCTTTTTAAGCCCTTTAAAAATTGGATTTAGTTCT
ACACATGTCAGCGTATCTCAAAAACCTGTCGAGAAAATTTTGATTAACACTATACTGTATATTCC
TCATGATATGTCATAAACACAATCTATGTTTTAGCCCGGGTAGTACTTCAGCAATTGCATTTGTC
ATGTTCTTATCTCTATCAGTAATAACAGTAAGAGGTTTGTGGCCATCTCCAGCTTTAATCAATTG
TTGTAAAACCCACACATAAGTATCCTCTTTCTCATTCACAACCAATGCACATCCAAATGACACTG
TGTTTTGATGATGATTAACATCAACCAAAACAACGAACGGCTTGTTGCTTGAGTTGCACTTATAA
GTCGTATCAAATGCAAGAACATGCCTGAATTCTTTATAATCTACGCGTGATATACCATCAGCCCA
AAATAACTTCTCTAAGTTTCCGAATTCATACCTCGTGTGGCTCACAAAAAGAAAGGGTCAGATTT
TTGCTTCCTATTTAAATACGTCATCATCGTTTCAGCATCACCATCTTGCACTTCTTCTCATTTGA
TTCTATATAGA
Found at i:65046 original size:87 final size:87
Alignment explanation
Indices: 64900--65075 Score: 307
Period size: 87 Copynumber: 2.0 Consensus size: 87
64890 TGACAACAAC
*
64900 GGATATCCTGCGCTTGCAGAAGATCCTGAAGAGAATTTTCTACTCGATGGCATGACCCCGAAGTT
1 GGATATCCTGCGCTTCCAGAAGATCCTGAAGAGAATTTTCTACTCGATGGCATGACCCCGAAGTT
64965 TATTGGACCTGATCCAAGCAAA
66 TATTGGACCTGATCCAAGCAAA
* * * *
64987 GGATATCCTGGGCTTCCAGAGGATCCTGAAGAGGATTTTCTACTCGATGGCTTGACCCCGAAGTT
1 GGATATCCTGCGCTTCCAGAAGATCCTGAAGAGAATTTTCTACTCGATGGCATGACCCCGAAGTT
65052 TATTGGACCTGATCCAAGCAAA
66 TATTGGACCTGATCCAAGCAAA
65074 GG
1 GG
65076 TTGGGAGTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.26
Consensus pattern (87 bp):
GGATATCCTGCGCTTCCAGAAGATCCTGAAGAGAATTTTCTACTCGATGGCATGACCCCGAAGTT
TATTGGACCTGATCCAAGCAAA
Found at i:66385 original size:6 final size:6
Alignment explanation
Indices: 66374--66398 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
66364 TTGGACATTC
66374 AGGCAT AGGCAT AGGCAT AGGCAT A
1 AGGCAT AGGCAT AGGCAT AGGCAT A
66399 TACGCTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (6 bp):
AGGCAT
Found at i:70492 original size:20 final size:21
Alignment explanation
Indices: 70454--70493 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
70444 CGTGGCGTTC
* *
70454 GGGAGGGGACGGGGAGAGAAG
1 GGGAGGGAAAGGGGAGAGAAG
70475 GGGAGGGAAAGGGG-GAGAA
1 GGGAGGGAAAGGGGAGAGAA
70494 ACAGTGGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.03, G:0.65, T:0.00
Consensus pattern (21 bp):
GGGAGGGAAAGGGGAGAGAAG
Found at i:71097 original size:20 final size:21
Alignment explanation
Indices: 71074--71125 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
71064 ATTTCCCAAT
*
71074 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
71094 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
71115 TCGCAATGCGA
1 TCGCAATGCGA
71126 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:71139 original size:20 final size:20
Alignment explanation
Indices: 71114--71228 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
71104 AATTGGGAAA
*
71114 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
71134 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
71155 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
71175 TTCGTAACGCGATACGGACT
1 ATCGCAACGCGATACTGACT
* *
71195 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
71215 TTCGCAACGCGATA
1 ATCGCAACGCGATA
71229 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:71156 original size:41 final size:41
Alignment explanation
Indices: 71111--71248 Score: 136
Period size: 41 Copynumber: 3.4 Consensus size: 41
71101 GCGAATTGGG
* * *
71111 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * * **
71152 AAAATCGCAACGAGATACTTACTTTCGTAACGCGATACGGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
71194 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
71233 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
71249 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 2 0.03
40 29 0.39
41 42 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:71444 original size:22 final size:22
Alignment explanation
Indices: 71416--71459 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
71406 CACTCTCTCA
71416 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
71438 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
71460 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:71731 original size:20 final size:20
Alignment explanation
Indices: 71702--71745 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
71692 GCGATTTTAG
71702 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
71722 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
71742 TTTC
1 TTTC
71746 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:73065 original size:18 final size:18
Alignment explanation
Indices: 73044--73088 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
73034 TCCACTTCGG
* *
73044 GAGCCATCACCTCGCCTA
1 GAGCCATCACCTCACCCA
*
73062 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
73080 GAGCCATCA
1 GAGCCATCA
73089 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:73500 original size:12 final size:13
Alignment explanation
Indices: 73483--73511 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
73473 TTTGTTAGTA
73483 TTTGTTTTTGT-T
1 TTTGTTTTTGTCT
73495 TTTGTTTTTGTCT
1 TTTGTTTTTGTCT
73508 TTTG
1 TTTG
73512 GTTGAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.79
Consensus pattern (13 bp):
TTTGTTTTTGTCT
Found at i:73629 original size:19 final size:19
Alignment explanation
Indices: 73607--73702 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
73597 GGAAATGGCT
*
73607 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATCAAA
73626 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
* *
73640 ATCACAATGCGAAAT-GAA
1 ATCGCAATGCGAAATCAAA
73658 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
* *
73672 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
73691 ATCGCAATGCGA
1 ATCGCAATGCGA
73703 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 6 0.10
17 2 0.03
18 10 0.17
19 21 0.36
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:73642 original size:14 final size:14
Alignment explanation
Indices: 73623--73680 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
73613 ATGCGAAATA
73623 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
73637 AAAATCACAATGCGAA
1 AAAATCGCAA--CGAC
73653 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
73669 AAAATCGCAACG
1 AAAATCGCAACG
73681 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:73665 original size:32 final size:32
Alignment explanation
Indices: 73611--73697 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
73601 ATGGCTATCG
*
73611 CAATGCGAAATAAAAATCGCAACGACAAAATCA
1 CAATGCGAAAT-GAAATCGCAACGACAAAATCA
*
73644 CAATGCGAAATGAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAATCGCAACGACAAAATCA
*
73676 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATG-AAATCGCAA
73698 TGCGATTTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 30 0.60
33 20 0.40
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.11
Consensus pattern (32 bp):
CAATGCGAAATGAAATCGCAACGACAAAATCA
Found at i:73734 original size:14 final size:14
Alignment explanation
Indices: 73715--73771 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
73705 TGTGTTTCGG
73715 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
*
73729 GTTGCGATTTCATTTCGC
1 GTTGCGATTT--TGT--C
73747 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
73761 GTTGCGATTTT
1 GTTGCGATTTT
73772 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.49
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:73751 original size:32 final size:33
Alignment explanation
Indices: 73709--73787 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
73699 GCGATTTGTG
*
73709 TTTCGGGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
73741 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
73774 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
73788 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:73806 original size:20 final size:19
Alignment explanation
Indices: 73772--73827 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
73762 TTGCGATTTT
*
73772 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
73791 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
73811 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
73828 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:74914 original size:10 final size:9
Alignment explanation
Indices: 74891--74918 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
74881 GTTAGTGTTT
74891 ATTTTTTAA
1 ATTTTTTAA
74900 ATTTTTTAA
1 ATTTTTTAA
74909 ATTTTTTAA
1 ATTTTTTAA
74918 A
1 A
74919 GTGTTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTTAA
Done.