Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001767.1 Hibiscus syriacus cultivar Beakdansim tig00003566_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: 54978
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:409 original size:122 final size:122
Alignment explanation
Indices: 127--451 Score: 482
Period size: 122 Copynumber: 2.7 Consensus size: 122
117 TGAATCATCT
* *
127 AAGGTCGAACAAATTCTTCTCA-TATGAACTTCTTCTTCCTCTTC--ATGAGTT-TTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
188 GAACTCTACCTGGAAATGTTGGTGTGATCTATCTCATTATGTGATAGAATCAAGCAA
66 GAACTCTATCTGGAAATGTTGATGTGATCTATCTCATTATGTGATAGAATCAAGCAA
* *
245 AAGGTTGAACAAGTTCTTCTCATTATAAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
310 GAACTCTATCTGGAAATGTTGATGTTGGTCTCTCCTCCTTCTGTGATAGAAT-GAGCAA
66 GAACTCTATCTGGAAATGTTGATG-TGATCTAT-CTCATTATGTGATAGAATCAAGCAA
*
368 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTCTTCAGATGAGTTCTTCTCATTAG
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
432 GAACTCTATCTGGAAATGTT
66 GAACTCTATCTGGAAATGTT
452 TTAAGAAAAA
Statistics
Matches: 187, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
118 20 0.11
119 20 0.11
121 7 0.04
122 79 0.42
123 45 0.24
124 16 0.09
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTATCTGGAAATGTTGATGTGATCTATCTCATTATGTGATAGAATCAAGCAA
Found at i:564 original size:70 final size:72
Alignment explanation
Indices: 448--631 Score: 284
Period size: 70 Copynumber: 2.6 Consensus size: 72
438 TATCTGGAAA
*
448 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCTAGCG-A
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCCAGCGAA
*
512 AACGGTT
66 AACAGTT
*
519 TG-TTTAAGAAAAATAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCCAGCGAT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCCAGCG--
583 AAAACAGTT
64 AAAACAGTT
* *
592 TGTTTTAAG-AAAACAATCTTAAGTGAGATAAATTGCTATT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATT
632 AAAACATCAT
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
70 58 0.56
71 2 0.02
73 37 0.36
74 6 0.06
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (72 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCCAGCGAA
AACAGTT
Found at i:5014 original size:10 final size:10
Alignment explanation
Indices: 4965--5014 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
4955 CTTGATTCAA
*
4965 TTTTTTCTTT
1 TTTTTTCTCT
4975 TCTTTTTCATCT
1 T-TTTTTC-TCT
*
4987 TTTTTTCCCT
1 TTTTTTCTCT
4997 TTTTTTCTCT
1 TTTTTTCTCT
5007 TTTTTTCT
1 TTTTTTCT
5015 TATGATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 20 0.57
11 12 0.34
12 3 0.09
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:6946 original size:11 final size:12
Alignment explanation
Indices: 6919--6948 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6909 TTATGCAAAG
6919 ATGCAAATGTAA
1 ATGCAAATGTAA
6931 ATGCAAATGT-A
1 ATGCAAATGTAA
6942 ATGCAAA
1 ATGCAAA
6949 CATGCGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (12 bp):
ATGCAAATGTAA
Found at i:6966 original size:31 final size:31
Alignment explanation
Indices: 6911--6969 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
6901 AAATGTAATT
* *
6911 ATGCAAAGATGCAAATGTAAATGCAAATGTA
1 ATGCAAACATGCAAATGCAAATGCAAATGTA
* *
6942 ATGCAAACATGCGAATGCAGATGCAAAT
1 ATGCAAACATGCAAATGCAAATGCAAAT
6970 ATATGAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (31 bp):
ATGCAAACATGCAAATGCAAATGCAAATGTA
Found at i:7162 original size:43 final size:43
Alignment explanation
Indices: 7114--7199 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
7104 CGGTACATCA
* * * *
7114 AACAAAACTTTACTTATAGGGGATAATTTTCACTCCTAACTTC
1 AACAAAACTTTACATATAAGGGATAACTTTCACTCATAACTTC
7157 AACAAAACTTTACATATAAGGGATAACTTTCACTCATAACTTC
1 AACAAAACTTTACATATAAGGGATAACTTTCACTCATAACTTC
7200 TCTAAAGACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (43 bp):
AACAAAACTTTACATATAAGGGATAACTTTCACTCATAACTTC
Found at i:7253 original size:24 final size:24
Alignment explanation
Indices: 7209--7254 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
7199 CTCTAAAGAC
* *
7209 AAGTTAGTTTTCATTCATGCTTAA
1 AAGTTAGTTATCAATCATGCTTAA
7233 AAGTTGAGTTATCAATC-TGCTT
1 AAGTT-AGTTATCAATCATGCTT
7255 CAATTTCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (24 bp):
AAGTTAGTTATCAATCATGCTTAA
Found at i:7768 original size:36 final size:36
Alignment explanation
Indices: 7669--7771 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
7659 CCATAAACTG
* * * *
7669 CTTTTGGTACCAATTTAATAGGATCTTGGTGGAATA
1 CTTTTGGTATCAATATAACAGGATCTTTGTGGAATA
*
7705 CTTTTGGTATCAATCTAACAGGATCTTTGTGGAATA
1 CTTTTGGTATCAATATAACAGGATCTTTGTGGAATA
*
7741 CTTTTGGTATTAATATAACAGGATCTTTGTG
1 CTTTTGGTATCAATATAACAGGATCTTTGTG
7772 TGCATAGCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (36 bp):
CTTTTGGTATCAATATAACAGGATCTTTGTGGAATA
Found at i:9358 original size:18 final size:17
Alignment explanation
Indices: 9335--9375 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
9325 AAAAATGAGG
*
9335 TAAATATATATATTTTT
1 TAAATATAGATATTTTT
9352 ATAAATA-AGATATTTTT
1 -TAAATATAGATATTTTT
9369 TAAATAT
1 TAAATAT
9376 CATAATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 6 0.29
17 9 0.43
18 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAAATATAGATATTTTT
Found at i:10835 original size:3 final size:3
Alignment explanation
Indices: 10827--10907 Score: 51
Period size: 3 Copynumber: 27.0 Consensus size: 3
10817 GTATGGCCTG
* * * * *
10827 TAA TAA TAA TAA T-A TTA TTA TTA TTA TTA TAA TTAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* *
10871 TAA TGA T-A GAA TAA TAA TAAA TAA TAA TAA TGAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA
10908 AATGGAGAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
2 5 0.07
3 54 0.79
4 9 0.13
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:10885 original size:11 final size:10
Alignment explanation
Indices: 10863--10900 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
10853 TTATAATTAA
10863 AATAAT-AAT
1 AATAATAAAT
*
10872 AATGATAGAAT
1 AATAATA-AAT
10883 AATAATAAAT
1 AATAATAAAT
10893 AATAATAA
1 AATAATAA
10901 TGAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 5 0.20
10 11 0.44
11 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (10 bp):
AATAATAAAT
Found at i:11006 original size:13 final size:13
Alignment explanation
Indices: 10988--11016 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10978 TAGTTACAAA
10988 TTTAAAAATATAT
1 TTTAAAAATATAT
11001 TTTAAAAATATAT
1 TTTAAAAATATAT
11014 TTT
1 TTT
11017 TAAATTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:11152 original size:119 final size:119
Alignment explanation
Indices: 10933--11362 Score: 446
Period size: 119 Copynumber: 3.5 Consensus size: 119
10923 GATGTCTACA
* *
10933 ATATATTCAATAAATTAAGAAAAA-AATAAAAAATAAATATTTTTATAGTTACA-AATTTAAAAA
1 ATATATTCGATAAATTAA-AAAAATAAT--AAAATATATATTTTTATAGTTA-AGAATTT---AA
* * * ** *
10996 TATATTTTAAAAATATATTTTTAAATTAAATGGTAAACTTGGCGTACTTTAAACCAAAATAT
59 -ATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAATAT
*
11058 ATATATTCGATAAATTAATAAAAATAATAATATATATATTTTTATAGTTAAGAATTT-AATATTT
1 ATATATTCGATAAATTAA-AAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTT
11122 TAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAATAT
65 TAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAATAT
11177 ATATATTCGATAAATT---AAAA-AATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTA
1 ATATATTCGATAAATTAAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATA--T-
* * *
11238 AAAAATATATATATATATATATTCTTACCTCAAATAATAAACTTGACCTACTTTAAA-CAAAA-A
63 -----T-T-TA-A-ATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAATA
*
11301 A
119 T
* *
11302 ATATATTTGATAAATTAAGAAAAAATAATAAAAAATATATTTTTTATAGTTAAGAATTTAA
1 ATATATTCGATAAATT-A-AAAAAATAATAAAATATATA-TTTTTATAGTTAAGAATTTAA
11363 GAGTATACTA
Statistics
Matches: 266, Mismatches: 17, Indels: 37
0.83 0.05 0.12
Matches are distributed among these distances:
114 31 0.12
115 8 0.03
117 1 0.00
119 71 0.27
120 1 0.00
123 2 0.01
124 26 0.10
125 40 0.15
126 9 0.03
127 40 0.15
130 4 0.02
131 12 0.05
132 21 0.08
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.39
Consensus pattern (119 bp):
ATATATTCGATAAATTAAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTT
AAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAATAT
Found at i:11306 original size:127 final size:128
Alignment explanation
Indices: 11125--11362 Score: 347
Period size: 127 Copynumber: 1.8 Consensus size: 128
11115 AATATTTTAA
* * * *
11125 ATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAATATATATATTCGATAA
1 ATATATATTCTTAACTCAAATAATAAACTTGACCTACTTTAAA-CAAAA-AAATATATTTGATAA
*
11190 ATT-AAAA-AATAAAATATATA-TTTTTATAGTTAAGAATTTAAATATTTAAAAAATATATATAT
64 ATTAAAAATAATAAAAAATATATTTTTTATAGTTAAGAATTTAAATATTTAAAAAATATATATAT
*
11252 ATATATATTCTTACCTCAAATAATAAACTTGACCTACTTTAAACAAAAAAATATATTTGATAAAT
1 ATATATATTCTTAACTCAAATAATAAACTTGACCTACTTTAAACAAAAAAATATATTTGATAAAT
11317 TAAGAAAAAATAATAAAAAATATATTTTTTATAGTTAAGAATTTAA
66 T----AAAAATAATAAAAAATATATTTTTTATAGTTAAGAATTTAA
11363 GAGTATACTA
Statistics
Matches: 98, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
125 16 0.16
126 5 0.05
127 40 0.41
130 4 0.04
131 12 0.12
132 21 0.21
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (128 bp):
ATATATATTCTTAACTCAAATAATAAACTTGACCTACTTTAAACAAAAAAATATATTTGATAAAT
TAAAAATAATAAAAAATATATTTTTTATAGTTAAGAATTTAAATATTTAAAAAATATATATAT
Found at i:13456 original size:2 final size:2
Alignment explanation
Indices: 13439--13501 Score: 62
Period size: 2 Copynumber: 32.5 Consensus size: 2
13429 AGTATAATAC
* *
13439 TA TA TA CTA TA CTA TA TA TA TA -A TA TA -A TT TA CA TA TA -A TA
1 TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13480 TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
13502 GTTTTCAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
1 4 0.08
2 43 0.84
3 4 0.08
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13519 original size:28 final size:28
Alignment explanation
Indices: 13486--13541 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 28
13476 AATATATATA
13486 TATATATATATTATATGTTTTCAAAAACAT
1 TATATAT-TA-TATATGTTTTCAAAAACAT
13516 TATATATTATATATGTTTTCAAAAAC
1 TATATATTATATATGTTTTCAAAAAC
13542 CATTTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 17 0.65
29 2 0.08
30 7 0.27
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (28 bp):
TATATATTATATATGTTTTCAAAAACAT
Found at i:13683 original size:70 final size:71
Alignment explanation
Indices: 13525--13827 Score: 271
Period size: 70 Copynumber: 4.2 Consensus size: 71
13515 TTATATATTA
* * ** *
13525 TATATGTTTTCAAAAACCATTTTTTCAAAAACTATATATCATATGTTTTCCAAAAACCGTTTTAA
1 TATATGTTTTC-AAAATCATTTTTT-AAAAACAATATATTTTATGTTTT-C--AAACCATTTTAA
*
13590 AAACTACATAC
61 AAACTATATAC
* * *
13601 TATATGTTTTCAAAATCATTTTTTTAAAATCAATATATTTTATGTTTTCAAATC-TTTT-TAAAC
1 TATATGTTTTCAAAATCA-TTTTTTAAAAACAATATATTTTATGTTTTCAAACCATTTTAAAAAC
13664 TATATAC
65 TATATAC
* * * *
13671 TATATGTTTTCAAAGTCATTTTTTAAAAACTATATATTGTACG-TTTCAAACCATTTTAAAAACT
1 TATATGTTTTCAAAATCATTTTTTAAAAACAATATATTTTATGTTTTCAAACCATTTTAAAAACT
13735 ATATTA-
66 ATA-TAC
* * * * *
13741 TACAAGTTTTCAAAA-C-TGTTTTAAAAA-ATATATATTATATGTTTTCAAAACTATTTTAAAAA
1 TATATGTTTTCAAAATCATTTTTTAAAAACA-ATATATTTTATGTTTTC-AAACCATTTT--AAA
*
13803 AACTATATAT
62 AACTATATAC
13813 TATATGCTTTT-AAAA
1 TATATG-TTTTCAAAA
13828 CCCTTTGAAA
Statistics
Matches: 191, Mismatches: 25, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
68 28 0.15
69 30 0.16
70 56 0.29
71 8 0.04
72 22 0.12
73 4 0.02
74 1 0.01
75 25 0.13
76 17 0.09
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (71 bp):
TATATGTTTTCAAAATCATTTTTTAAAAACAATATATTTTATGTTTTCAAACCATTTTAAAAACT
ATATAC
Found at i:13701 original size:37 final size:36
Alignment explanation
Indices: 13516--13871 Score: 266
Period size: 37 Copynumber: 9.8 Consensus size: 36
13506 TCAAAAACAT
13516 TATATATTATATATGTTTTCAAAAACCATTTTTTCAAAAAC
1 TATATA-T-TATATGTTTTC-AAAA-CATTTTTT-AAAAAC
* **
13557 TATATATCATATGTTTTCCAAAA-ACCGTTTTAAAAAC
1 TATATATTATATGTTTT-CAAAACA-TTTTTTAAAAAC
* * *
13594 TACATACTATATGTTTTCAAAATCATTTTTTTAAAATC
1 TATATATTATATGTTTTCAAAA-CA-TTTTTTAAAAAC
* * *
13632 AATATATTTTATGTTTTCAAATC--TTTTT--AAAC
1 TATATATTATATGTTTTCAAAACATTTTTTAAAAAC
* *
13664 TATATACTATATGTTTTCAAAGTCATTTTTTAAAAAC
1 TATATATTATATGTTTTCAAA-ACATTTTTTAAAAAC
* * *
13701 TATATATTGTACG-TTTCAAACCA--TTTTAAAAAC
1 TATATATTATATGTTTTCAAAACATTTTTTAAAAAC
* * * *
13734 TATAT-TATACAAGTTTTCAAAAC-TGTTTTAAAAAA
1 TATATAT-TATATGTTTTCAAAACATTTTTTAAAAAC
**
13769 TATATATTATATGTTTTCAAAACTATTTTAAAAAAAC
1 TATATATTATATGTTTTCAAAAC-ATTTTTTAAAAAC
** **
13806 TATATATTATATGCTTTT-AAAACCCTTTGAAAAAAC
1 TATATATTATATG-TTTTCAAAACATTTTTTAAAAAC
**
13842 TATATTATATATATGTTTAAAAAACATTTT
1 TATA-TAT-TATATGTTTTCAAAACATTTT
13872 CAAAATCAAA
Statistics
Matches: 255, Mismatches: 40, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
32 22 0.09
33 20 0.08
34 13 0.05
35 35 0.14
36 27 0.11
37 68 0.27
38 49 0.19
39 13 0.05
40 2 0.01
41 6 0.02
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATATTATATGTTTTCAAAACATTTTTTAAAAAC
Found at i:13788 original size:105 final size:104
Alignment explanation
Indices: 13644--13850 Score: 249
Period size: 105 Copynumber: 2.0 Consensus size: 104
13634 TATATTTTAT
* * * **
13644 GTTTTCAAATCTTTTTAAACTATATACTATATGTTTTC-AAAGTCATTTTTTAAAAACTATATAT
1 GTTTTCAAAACTTTTTAAAATATATACTATATGTTTTCAAAACT-ATTTTAAAAAAACTATATAT
* * *
13708 TGTA-CGTTTCAAACCATTT-TAAAAACTATATTATACAA
65 TATAGCGTTTAAAACCATTTGAAAAAACTATATTATACAA
*
13746 GTTTTCAAAACTGTTTTAAAAAATATATATTATATGTTTTCAAAACTATTTTAAAAAAACTATAT
1 GTTTTCAAAACT-TTTT--AAAATATATACTATATGTTTTCAAAACTATTTTAAAAAAACTATAT
* *
13811 ATTATATGCTTTTAAAACCCTTTGAAAAAACTATATTATA
63 ATTATA-GCGTTTAAAACCATTTGAAAAAACTATATTATA
13851 TATATGTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
102 11 0.13
103 4 0.05
105 41 0.47
106 4 0.05
107 12 0.14
108 15 0.17
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (104 bp):
GTTTTCAAAACTTTTTAAAATATATACTATATGTTTTCAAAACTATTTTAAAAAAACTATATATT
ATAGCGTTTAAAACCATTTGAAAAAACTATATTATACAA
Found at i:13866 original size:38 final size:38
Alignment explanation
Indices: 13799--13893 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 38
13789 AACTATTTTA
* * *
13799 AAAAAACTATA-TAT-TATATGCTTTTAAAACCCTTTG
1 AAAAAACTATATTATATATATGCTTTAAAAACACTTTC
*
13835 AAAAAACTATATTATATATATG-TTTAAAAAACATTTTC
1 AAAAAACTATATTATATATATGCTTT-AAAAACACTTTC
*
13873 AAAATCAAATATATTATATAT
1 AAAA--AACTATATTATATAT
13894 TCTCAAAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
36 11 0.22
37 6 0.12
38 18 0.37
40 14 0.29
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (38 bp):
AAAAAACTATATTATATATATGCTTTAAAAACACTTTC
Found at i:25359 original size:3 final size:3
Alignment explanation
Indices: 25351--25397 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
25341 AGTTAGTAAG
25351 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
25398 GAAAATAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:26318 original size:71 final size:69
Alignment explanation
Indices: 26229--26489 Score: 255
Period size: 70 Copynumber: 3.7 Consensus size: 69
26219 AAAAATATTA
* *
26229 TATATTATATATGGTTTCAAACATCGTTTTGTAAAAAACTATATATTATACGTTTTCAAATAGTT
1 TATA-TATATATGTTTTCAAA-A-CCTTTTGTAAAAAACTATATATTATACGTTTTCAAATAGTT
26294 TT-AAAC
63 TTAAAAC
** * * **
26300 TATATACTATATGTTTTCAAAATTATTTTTTTAAAAACTATATATTATACGTTTTCAAACCGTTT
1 TATATA-TATATGTTTTCAAAA-CCTTTTGTAAAAAACTATATATTATACGTTTTCAAATAGTTT
26365 TAAAAAC
64 T-AAAAC
* * *
26372 TATATTATACATGTTTTCAAAACCATTT-T-AAAAACTATATATTATATGTTTTCAAAACTA-TT
1 TATA-TATATATGTTTTCAAAACCTTTTGTAAAAAACTATATATTATACGTTTTC-AAA-TAGTT
26434 TTAAAAAAC
63 TT--AAAAC
*
26443 TATATATTATAT-TCTTTCAAAACCCTTTG-AAAAAACTATATATTATA
1 TATATA-TATATGT-TTTCAAAACCTTTTGTAAAAAACTATATATTATA
26490 TTCTTTCAAA
Statistics
Matches: 163, Mismatches: 16, Indels: 21
0.81 0.08 0.10
Matches are distributed among these distances:
69 23 0.14
70 52 0.32
71 47 0.29
72 39 0.24
73 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.44
Consensus pattern (69 bp):
TATATATATATGTTTTCAAAACCTTTTGTAAAAAACTATATATTATACGTTTTCAAATAGTTTTA
AAAC
Found at i:26448 original size:36 final size:36
Alignment explanation
Indices: 26260--26527 Score: 254
Period size: 35 Copynumber: 7.6 Consensus size: 36
26250 CATCGTTTTG
* *
26260 TAAAAAACTATATATTATACGTTTTCAAATA--GTTT
1 TAAAAAACTATATATTATATGTTTTCAAA-ACCATTT
* **
26295 T---AAACTATATACTATATGTTTTCAAAATTATTTTT
1 TAAAAAACTATATATTATATGTTTTCAAAACCA--TTT
* * *
26330 TTAAAAACTATATATTATACGTTTTC-AAACCGTTT
1 TAAAAAACTATATATTATATGTTTTCAAAACCATTT
*
26365 T-AAAAACTATAT-TATACATGTTTTCAAAACCATTT
1 TAAAAAACTATATAT-TATATGTTTTCAAAACCATTT
*
26400 T-AAAAACTATATATTATATGTTTTCAAAACTATTT
1 TAAAAAACTATATATTATATGTTTTCAAAACCATTT
*
26435 TAAAAAACTATATATTATAT-TCTTTCAAAACCCTTT
1 TAAAAAACTATATATTATATGT-TTTCAAAACCATTT
* *
26471 GAAAAAACTATATATTATAT-TCTTTC-AAACCCTTT
1 TAAAAAACTATATATTATATGT-TTTCAAAACCATTT
*
26506 GAAAAAACTATATTATATATAT
1 TAAAAAACTATA-TAT-TATAT
26528 ATATATATAT
Statistics
Matches: 203, Mismatches: 16, Indels: 26
0.83 0.07 0.11
Matches are distributed among these distances:
31 1 0.00
32 23 0.11
33 1 0.00
34 20 0.10
35 71 0.35
36 59 0.29
37 8 0.04
38 20 0.10
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (36 bp):
TAAAAAACTATATATTATATGTTTTCAAAACCATTT
Found at i:26497 original size:107 final size:106
Alignment explanation
Indices: 26256--26527 Score: 274
Period size: 107 Copynumber: 2.5 Consensus size: 106
26246 CAAACATCGT
* * *
26256 TTTGTAAAAAACTATATATTATACGTTTTCAAATA--GTTTT--AAACTATATACTATATGTTTT
1 TTTG-AAAAAACTATATATTATA-TTTTTCAAA-ACCATTTTAAAAACTATATATTATATGTTTT
* * *
26317 CAAAATTATTTTTTTAAAAACTATATATTATACGTTTTCAAACCG
63 CAAAACTA-TTTTTAAAAAACTATATATTATACGTTTTCAAACCC
* *
26362 TTT-TAAAAACTATAT-TATACATGTTTTCAAAACCATTTTAAAAACTATATATTATATGTTTTC
1 TTTGAAAAAACTATATAT-TATAT-TTTTCAAAACCATTTTAAAAACTATATATTATATGTTTTC
*
26425 AAAACTA-TTTTAAAAAACTATATATTATA-TTCTTTCAAAACCC
64 AAAACTATTTTTAAAAAACTATATATTATACGT-TTTC-AAACCC
* *
26468 TTTGAAAAAACTATATATTATATTCTTTC-AAACCCTTTGAAAAAACTATATTATATATAT
1 TTTGAAAAAACTATATATTATATT-TTTCAAAACCATTT-TAAAAACTATA-TAT-TATAT
26528 ATATATATAT
Statistics
Matches: 139, Mismatches: 13, Indels: 25
0.79 0.07 0.14
Matches are distributed among these distances:
103 2 0.01
104 23 0.17
105 29 0.21
106 20 0.14
107 56 0.40
108 4 0.03
109 5 0.04
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (106 bp):
TTTGAAAAAACTATATATTATATTTTTCAAAACCATTTTAAAAACTATATATTATATGTTTTCAA
AACTATTTTTAAAAAACTATATATTATACGTTTTCAAACCC
Found at i:26511 original size:71 final size:69
Alignment explanation
Indices: 26260--26527 Score: 226
Period size: 72 Copynumber: 3.8 Consensus size: 69
26250 CATCGTTTTG
* * * *
26260 TAAAAAACTATATATTATACGTTTTCAAA-TAGTTT--TAAACTATATA-CTATATGTTTTCAAA
1 TAAAAAACTATATATTATA-TTTTTCAAACCA-TTTAAAAAACTATATATATATATGTTTTCAAA
**
26321 ATTATTTTT
64 ACCA---TT
* * * * *
26330 TTAAAAACTATATATTATACGTTTTCAAACCGTTTTAAAAACTATAT-TATACATGTTTTCAAAA
1 TAAAAAACTATATATTATA-TTTTTCAAACCATTTAAAAAACTATATATATATATGTTTTCAAAA
26394 CCATT
65 CCATT
* *
26399 TTAAAAACTATATATTATATGTTTTCAAAACTATTTTAAAAAACTATATAT-TATAT-TCTTTCA
1 TAAAAAACTATATATTATAT-TTTTC-AAACCA-TTTAAAAAACTATATATATATATGT-TTTCA
*
26462 AAACCCTT
62 AAACCATT
*
26470 TGAAAAAACTATATATTATATTCTTTCAAACCCTTTGAAAAAACTATATTATATATAT
1 T-AAAAAACTATATATTATATT-TTTCAAACCATTT-AAAAAACTATA-TATATATAT
26528 ATATATATAT
Statistics
Matches: 167, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
69 26 0.16
70 39 0.23
71 47 0.28
72 50 0.30
73 5 0.03
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (69 bp):
TAAAAAACTATATATTATATTTTTCAAACCATTTAAAAAACTATATATATATATGTTTTCAAAAC
CATT
Found at i:26524 original size:2 final size:2
Alignment explanation
Indices: 26514--26555 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
26504 TTGAAAAAAC
26514 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26555 T
1 T
26556 GTGTGTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26560 original size:2 final size:2
Alignment explanation
Indices: 26555--26589 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
26545 TATATATATA
26555 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
26590 TTAAAAACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:30996 original size:13 final size:13
Alignment explanation
Indices: 30978--31004 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30968 TTACAGATTC
30978 GCATATGAAGACT
1 GCATATGAAGACT
30991 GCATATGAAGACT
1 GCATATGAAGACT
31004 G
1 G
31005 TTCAACCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:31735 original size:14 final size:13
Alignment explanation
Indices: 31708--31793 Score: 50
Period size: 12 Copynumber: 7.3 Consensus size: 13
31698 GCTTTATATA
31708 TTCTTTCATCTTC
1 TTCTTTCATCTTC
31721 TTCTCTTCA--TT-
1 TTCT-TTCATCTTC
31732 TTCTTT-A--TTC
1 TTCTTTCATCTTC
31742 -TCATTTC-TCTTC
1 TTC-TTTCATCTTC
*
31754 TTCCTTCA-CTTC
1 TTCTTTCATCTTC
*
31766 TTCCTTC-TCTTC
1 TTCTTTCATCTTC
*
31778 TTCCTTC-TCTTC
1 TTCTTTCATCTTC
31790 TTCT
1 TTCT
31794 CCAAGTGCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
9 5 0.08
10 5 0.08
11 4 0.06
12 38 0.61
13 6 0.10
14 4 0.06
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (13 bp):
TTCTTTCATCTTC
Found at i:31793 original size:15 final size:12
Alignment explanation
Indices: 31746--31792 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
31736 TTATTCTCAT
31746 TTCTCTTCTTCC
1 TTCTCTTCTTCC
*
31758 TTCACTTCTTCC
1 TTCTCTTCTTCC
31770 TTCTCTTCTTCC
1 TTCTCTTCTTCC
31782 TTCTCTTCTTC
1 TTCTCTTCTTC
31793 TCCAAGTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (12 bp):
TTCTCTTCTTCC
Found at i:32239 original size:21 final size:21
Alignment explanation
Indices: 32215--32254 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32205 GGTAAGTAAG
32215 ATCGATACTAGTAATAGTAGT
1 ATCGATACTAGTAATAGTAGT
* *
32236 ATCGATATTGGTAATAGTA
1 ATCGATACTAGTAATAGTA
32255 ACACAAGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (21 bp):
ATCGATACTAGTAATAGTAGT
Found at i:32268 original size:42 final size:42
Alignment explanation
Indices: 32222--32304 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
32212 AAGATCGATA
* * *
32222 CTAGTAATAGTAGTATC-GATATTGGTAATAGTAACACAAGTT
1 CTAGTAATAGTAGTACCAG-TACTGGAAATAGTAACACAAGTT
*
32264 CTAGTAATAGTAGTACCAGTACTGGAAATAGTAATACAAGT
1 CTAGTAATAGTAGTACCAGTACTGGAAATAGTAACACAAGT
32305 AATGGTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (42 bp):
CTAGTAATAGTAGTACCAGTACTGGAAATAGTAACACAAGTT
Found at i:32293 original size:21 final size:21
Alignment explanation
Indices: 32269--32321 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
32259 AAGTTCTAGT
* * *
32269 AATAGTAGTACCAGTACTGGA
1 AATAGTAATACAAGTAATGGA
*
32290 AATAGTAATACAAGTAATGGT
1 AATAGTAATACAAGTAATGGA
*
32311 AATATTAATAC
1 AATAGTAATAC
32322 TAATACTAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.28
Consensus pattern (21 bp):
AATAGTAATACAAGTAATGGA
Found at i:32313 original size:42 final size:42
Alignment explanation
Indices: 32223--32314 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
32213 AGATCGATAC
* * * **
32223 TAGTAATAGTAGTATCGATATTGGTAATAGTAACACAAGTTC
1 TAGTAATAGTAGTACCGATACTGGAAATAGTAACACAAGTAA
*
32265 TAGTAATAGTAGTACC-AGTACTGGAAATAGTAATACAAGTAA
1 TAGTAATAGTAGTACCGA-TACTGGAAATAGTAACACAAGTAA
*
32307 TGGTAATA
1 TAGTAATA
32315 TTAATACTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (42 bp):
TAGTAATAGTAGTACCGATACTGGAAATAGTAACACAAGTAA
Found at i:35374 original size:47 final size:44
Alignment explanation
Indices: 35302--35427 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 44
35292 TATAAAATCT
*
35302 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
35347 CTTACCATTTAAATTCTATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCA-TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
35394 CTTGCCATTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
35428 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 37 0.52
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:40924 original size:283 final size:283
Alignment explanation
Indices: 40418--41249 Score: 1292
Period size: 283 Copynumber: 2.9 Consensus size: 283
40408 AATATTATGG
40418 AGAGCTATGCACCCAAAGATCGTATGTCAGATGAAGAGCAAAAGGAGATAAGAGATATGAGA-GG
1 AGAGCTATGCACCCAAAGATCGTATGTCAGATGAAGAGCAAAAGGAGATAAGAGATATGAGAGGG
* *
40482 CAAATGTCCAAAATGATGGATAAAATATCTGTTTTGGCCAAAGGAAAAGATACTTTTACACAAGA
66 CAAATGTCCAAAATGATGGATAAAATATCTGTTTTGGCCAAAGGAAAAGATACTTCTGCACAAGA
40547 AGAGAAAGAGCTCGATAAACACAATCCTGCAATGTCAGATGCATAAGGGATTACTTTAGAACAAG
131 AGAGAAAGAGCTCGATAAACACAATCCTGCAATGTCAGATGCATAAGGGATTACTTTAGAACAAG
*
40612 TGGATCCTAGTCAATCTGAGAGATCACACACGATCACCATTCATATCAACAAATTATCTAGAAAT
196 TGGATCCTAGTCAATCTGAGAGATCACACATGATCACCATTCATATCAACAAATTATCTAGAAAT
* * * *
40677 ACCGAATATCATTTGTTAAATGA
261 ACCAAAGATCATATGTCAAATGA
* * * *
40700 AGAGCTATGCACCCAAAGATCGTATGTTAAATGAAAAGCAAAAGGAAATAAGAGATATGAGAGGG
1 AGAGCTATGCACCCAAAGATCGTATGTCAGATGAAGAGCAAAAGGAGATAAGAGATATGAGAGGG
* ** *
40765 AAAATGTATAAAATGATGGATAAAATATCTGCTTTGGCCAAAGGAAAAGATACTTCTGCACAAGA
66 CAAATGTCCAAAATGATGGATAAAATATCTGTTTTGGCCAAAGGAAAAGATACTTCTGCACAAGA
* * *
40830 AGAGAAAGAGCTCGATAAACACAATCTTGCAATGTCAGATGCATAAGGGGTTACTTTAGAACAAA
131 AGAGAAAGAGCTCGATAAACACAATCCTGCAATGTCAGATGCATAAGGGATTACTTTAGAACAAG
*
40895 TGGATCCTAGTCAATCTGAGAGATCACACATGATTACCATTCATATCAACAAATTATCTAGAAAT
196 TGGATCCTAGTCAATCTGAGAGATCACACATGATCACCATTCATATCAACAAATTATCTAGAAAT
* *
40960 ACCAAAGATCGTATGTCAGATGA
261 ACCAAAGATCATATGTCAAATGA
* * *
40983 AGAGCTATGAACCCAAAGATCGTATGTCAGATGAAGAGCAAAAGGAGATACGAGAGATG-GAGGG
1 AGAGCTATGCACCCAAAGATCGTATGTCAGATGAAGAGCAAAAGGAGATAAGAGATATGAGAGGG
* * *
41047 CAAATGTCCAAAATGATGGATAGAATATCTTTTTTGGCCAAAGGAAAAGATACTTCTGTACAAGA
66 CAAATGTCCAAAATGATGGATAAAATATCTGTTTTGGCCAAAGGAAAAGATACTTCTGCACAAGA
* * * * *
41112 AGAGAAAGTGCTCGATAAACACAATCCTGTAATATCAAATGCATAAGGGATTGA-TGTAGAACAA
131 AGAGAAAGAGCTCGATAAACACAATCCTGCAATGTCAGATGCATAAGGGATT-ACTTTAGAACAA
* * * * *
41176 GTGGATCCCAGTCAATCTGAGGGATCACTCATGATCACCATTCGTATCAACAAATTATCTGGAAA
195 GTGGATCCTAGTCAATCTGAGAGATCACACATGATCACCATTCATATCAACAAATTATCTAGAAA
*
41241 TACAAAAGA
260 TACCAAAGA
41250 AATGGTGGCA
Statistics
Matches: 498, Mismatches: 50, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
282 242 0.49
283 256 0.51
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (283 bp):
AGAGCTATGCACCCAAAGATCGTATGTCAGATGAAGAGCAAAAGGAGATAAGAGATATGAGAGGG
CAAATGTCCAAAATGATGGATAAAATATCTGTTTTGGCCAAAGGAAAAGATACTTCTGCACAAGA
AGAGAAAGAGCTCGATAAACACAATCCTGCAATGTCAGATGCATAAGGGATTACTTTAGAACAAG
TGGATCCTAGTCAATCTGAGAGATCACACATGATCACCATTCATATCAACAAATTATCTAGAAAT
ACCAAAGATCATATGTCAAATGA
Found at i:45193 original size:8 final size:8
Alignment explanation
Indices: 45180--45233 Score: 65
Period size: 8 Copynumber: 6.6 Consensus size: 8
45170 GAAAATATAT
45180 AAAAAGAA
1 AAAAAGAA
45188 AAAAAGAGA
1 AAAAAGA-A
*
45197 AAAAATAA
1 AAAAAGAA
45205 AAAGAA-AA
1 AAA-AAGAA
*
45213 AAAGAGAA
1 AAAAAGAA
45221 AAAAAGAA
1 AAAAAGAA
45229 AAAAA
1 AAAAA
45234 TAGGAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 1 0.03
8 30 0.75
9 9 0.22
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:45197 original size:10 final size:9
Alignment explanation
Indices: 45180--45233 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 9
45170 GAAAATATAT
45180 AAAAAGAAA
1 AAAAAGAAA
45189 AAAAGAGAAAA
1 AAAA-AG-AAA
*
45200 AATAAAAAGAA
1 AA-AAAGA-AA
45211 AAAAAGAGAA
1 AAAAAGA-AA
45221 AAAAAGAAA
1 AAAAAGAAA
45230 AAAA
1 AAAA
45234 TAGGAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 10 0.26
10 17 0.44
11 10 0.26
12 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:45230 original size:23 final size:23
Alignment explanation
Indices: 45169--45224 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 23
45159 AAAGGAGAAA
45169 AGAAAATATATAAAAAGAAAAAAAG
1 AGAAAA-A-ATAAAAAGAAAAAAAG
45194 AGAAAAAATAAAAAGAAAAAAAG
1 AGAAAAAATAAAAAGAAAAAAAG
45217 AGAAAAAA
1 AGAAAAAA
45225 AGAAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 24 0.77
24 1 0.03
25 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (23 bp):
AGAAAAAATAAAAAGAAAAAAAG
Found at i:45241 original size:18 final size:18
Alignment explanation
Indices: 45180--45233 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 18
45170 GAAAATATAT
45180 AAAAAGAAAAAAAGAGAAAAAA
1 AAAAAGAAAAAAAGAG----AA
45202 TAAAAAGAAAAAAAGAGAA
1 -AAAAAGAAAAAAAGAGAA
45221 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
45234 TAGGAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 13 0.42
19 2 0.06
23 16 0.52
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAAAGAGAA
Found at i:45246 original size:23 final size:20
Alignment explanation
Indices: 45180--45233 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 20
45170 GAAAATATAT
45180 AAAAAGAAAAAAAGAGAAAAA
1 AAAAAGAAAAAAA-AGAAAAA
*
45201 ATAAAA-AGAAAAAAAG-AGAA
1 A-AAAAGA-AAAAAAAGAAAAA
45221 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
45234 TAGGAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 10 0.34
20 5 0.17
21 4 0.14
22 10 0.34
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAAAAGAAAAA
Found at i:47527 original size:42 final size:41
Alignment explanation
Indices: 47457--47545 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 41
47447 AGTCTTCTGT
* *
47457 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCAAGCAAGATGA-TAAATCCTTCGG
* * *
47499 GTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCAAGCAAGATGATAAATCCTTCGG
47540 GCCATC
1 GCCATC
47546 CTTAAAACCT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 16 0.39
42 25 0.61
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (41 bp):
GCCATCAGTAAGTCTTTCAAGCAAGATGATAAATCCTTCGG
Found at i:47755 original size:22 final size:22
Alignment explanation
Indices: 47730--47797 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
47720 CAGTAAGTCT
47730 TTCGAGCATAATGATTAAATCC
1 TTCGAGCATAATGATTAAATCC
* * * *
47752 TTCGGGTCAT-CTG--TAAGTCT
1 TTCGAG-CATAATGATTAAATCC
47772 TTCGAGCATAATGATTAAATCC
1 TTCGAGCATAATGATTAAATCC
47794 TTCG
1 TTCG
47798 GGTCATCTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 12 0.35
22 16 0.47
23 3 0.09
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (22 bp):
TTCGAGCATAATGATTAAATCC
Found at i:47769 original size:42 final size:42
Alignment explanation
Indices: 47717--47838 Score: 203
Period size: 42 Copynumber: 2.9 Consensus size: 42
47707 TCCTTTGAGC
*
47717 CATCAGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGT
1 CATCTGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGT
47759 CATCTGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGT
1 CATCTGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGT
*
47801 CATCTGTAAGTCTTTCGAGCA-AGATGA-TAAGTCCTTCG
1 CATCTGTAAGTCTTTCGAGCATA-ATGATTAAATCCTTCG
47839 AGCCATCCGT
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
41 11 0.14
42 66 0.86
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (42 bp):
CATCTGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGT
Found at i:48006 original size:300 final size:300
Alignment explanation
Indices: 47459--48079 Score: 1048
Period size: 300 Copynumber: 2.1 Consensus size: 300
47449 TCTTCTGTGC
* *
47459 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAG
1 CATCTGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAG
* * *
47524 ATGATAAGTCCTTCGGGCCATCCTTAAAACCTTCGGGTAGGATGTTTTTACATGAATTGTGAAAA
66 ATGATAAGTCCTTCGAGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTGTGAAAA
47589 TGAGAAAGCGATTTCCAAAGTTTCTCAGTTAAATCTTTTTTGAAAATGAAATTTTTGAAAAGTAA
131 TGAGAAAGCGATTTCCAAAGTTTCTCAGTTAAATCTTTTTTGAAAATGAAATTTTTGAAAAGTAA
* * *
47654 GAAAGCGATTACCAAAGTTTCTTACACAGTAAACTATTTCCCAAATTGGTAAGTCCTTTGAGCCA
196 GAAAGCAATTACCAAAGTTTCTTACACAGTAAACTATTTCCCAAATTGGTAAGTCATTCGAGCCA
* *
47719 TC-AGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGT
261 TCGA-TAAGTCTTTCAAGCATAATGATTAAATCCTTCGAGT
*
47759 CATCTGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAG
1 CATCTGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAG
*
47824 ATGATAAGTCCTTCGAGCCATCCGTAAAACCTTTGGGTAGGATGTTTTCACATGAATTGTGAAAA
66 ATGATAAGTCCTTCGAGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTGTGAAAA
* *
47889 TGAGAAAGCGATTTCCAAAGTTTGTCATTTAAATCTTTTTTGAAAATGAAATTTTTGAAAAGTAA
131 TGAGAAAGCGATTTCCAAAGTTTCTCAGTTAAATCTTTTTTGAAAATGAAATTTTTGAAAAGTAA
*
47954 GAAAGCAATTACCAAAGTTTCTTATC-CAGTAAACTATTTCCCAAATTGGTAAGTCATTCGGGCC
196 GAAAGCAATTACCAAAGTTTCTTA-CACAGTAAACTATTTCCCAAATTGGTAAGTCATTCGAGCC
* * *
48018 ATCGATAAGTCTTTCAAGCATGATGATTAAATTCTTTGAGT
260 ATCGATAAGTCTTTCAAGCATAATGATTAAATCCTTCGAGT
48059 CATCTGTAAGTCTTTCGAGCA
1 CATCTGTAAGTCTTTCGAGCA
48080 AGATGATAAG
Statistics
Matches: 301, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
300 299 0.99
301 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (300 bp):
CATCTGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAG
ATGATAAGTCCTTCGAGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTGTGAAAA
TGAGAAAGCGATTTCCAAAGTTTCTCAGTTAAATCTTTTTTGAAAATGAAATTTTTGAAAAGTAA
GAAAGCAATTACCAAAGTTTCTTACACAGTAAACTATTTCCCAAATTGGTAAGTCATTCGAGCCA
TCGATAAGTCTTTCAAGCATAATGATTAAATCCTTCGAGT
Found at i:48231 original size:258 final size:258
Alignment explanation
Indices: 47752--48517 Score: 1171
Period size: 258 Copynumber: 3.0 Consensus size: 258
47742 GATTAAATCC
* *
47752 TTCGGGTCATCTG-TAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGTCATCTGTAAGTCTTT
1 TTCGGGCCATC-GATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTT
* *
47816 CGAGCAAGATGATAAGTCCTTCGAGCCATCCGTAAAACCTTTGGGTAGGATGTTTTCACATGAAT
65 CGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAAT
* * *
47881 TGTGAAAATGAGAAAGCGATTTCCAAAGTTTGTCATTTAAATCTTTTTTGAAAATGAAATTTTTG
130 TATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTATGAAAATGAAATTTTTG
* * *
47946 AAAAGTAAGAAAGCAATTACCAAAGTTTCTTATCCAGTAAACTATTTCCCAAATTGGTAAGTCA
195 AAAAGTAAGAAAGCGATTACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCA
* * * *
48010 TTCGGGCCATCGATAAGTCTTTCAAGCATGATGATTAAATTCTTTGAGTCATCTGTAAGTCTTTC
1 TTCGGGCCATCGATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTC
* ** *
48075 GAGCAAGATGATAAGTCATTCGGGCCATCCGTAGGACCTTCGGGTAGGATGTTTTCACATAAATT
66 GAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATT
48140 ATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTATGAAAATGAAATTTTTGA
131 ATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTATGAAAATGAAATTTTTGA
* * * * *
48205 AAAGTAAGAAAGTGGTTACAAAAGTTTCTCACCCAGTAAATTATTTCCCAAATTGGTAAGTCC
196 AAAGTAAGAAAGCGATTACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCA
*
48268 TTCGGGCTATC-AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTT
1 TTCGGGCCATCGA-TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTT
* * * *
48332 CAAGCAAGATGATTAGTCCTTTGGGCCATCTGTAAAACCTTCGGGTAGGATGTTTTCACATGAAT
65 CGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAAT
* *
48397 TGA-GAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATGTTTTCA-GAAAATTAAATTTT
130 T-ATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTT-ATGAAAATGAAATTTT
* * *
48460 TGAAAAGTAAGAAAGCGATTTCAAAAGTTTCTTACCCAGTAAAGTATTTCCAAAATTG
193 TGAAAAGTAAGAAAGCGATTACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTG
48518 ATCTGATTAC
Statistics
Matches: 460, Mismatches: 44, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
257 2 0.00
258 456 0.99
259 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (258 bp):
TTCGGGCCATCGATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTC
GAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATT
ATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTATGAAAATGAAATTTTTGA
AAAGTAAGAAAGCGATTACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCA
Found at i:48364 original size:41 final size:42
Alignment explanation
Indices: 48261--48366 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
48251 CCCAAATTGG
* * * *
48261 TAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGATGAT
* *
48303 TAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGAT
1 TAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGATGAT
*
48345 T-AGTCCTTTGGGCCATCTGTAA
1 TAAGTCCTTCGGGCCATCTGTAA
48367 AACCTTCGGG
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
41 18 0.33
42 37 0.67
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGATGAT
Found at i:48796 original size:3 final size:3
Alignment explanation
Indices: 48788--48872 Score: 161
Period size: 3 Copynumber: 28.3 Consensus size: 3
48778 TTTTCGTCCC
48788 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
48836 TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
48873 TTGTTAAATA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.