Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008312.1 Hibiscus syriacus cultivar Beakdansim tig00111005_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: 1258310
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:860366 original size:57 final size:57
Alignment explanation
Indices: 860276--860383 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 57
860266 ATTTCAGAAT
*
860276 TTATTTTCTGAATCAAAACTTATTTCTAAATTCA-GAACTTATTTCCAAATTAATAAC
1 TTATTTTCAGAATCAAAACTTATTTCTAAATTCATG-ACTTATTTCCAAATTAATAAC
* * * * *
860333 TTATTTTCAGACTCATAACTTATTGTC-AGATTCATGGCTTATTTTCAAATT
1 TTATTTTCAGAATCAAAACTTATT-TCTAAATTCATGACTTATTTCCAAATT
860384 CATAGCCCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
57 40 0.93
58 3 0.07
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.44
Consensus pattern (57 bp):
TTATTTTCAGAATCAAAACTTATTTCTAAATTCATGACTTATTTCCAAATTAATAAC
Found at i:860384 original size:19 final size:19
Alignment explanation
Indices: 860292--860387 Score: 95
Period size: 19 Copynumber: 5.1 Consensus size: 19
860282 TCTGAATCAA
*
860292 AACTTA-TTTCTAAATTCAG
1 AACTTATTTTC-AAATTCAT
* *
860311 AACTTATTTCCAAATTAAT
1 AACTTATTTTCAAATTCAT
* *
860330 AACTTATTTTCAGACTCAT
1 AACTTATTTTCAAATTCAT
* *
860349 AACTTATTGTCAGATTCAT
1 AACTTATTTTCAAATTCAT
**
860368 GGCTTATTTTCAAATTCAT
1 AACTTATTTTCAAATTCAT
860387 A
1 A
860388 GCCCAACATA
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
19 59 0.95
20 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (19 bp):
AACTTATTTTCAAATTCAT
Found at i:870380 original size:27 final size:28
Alignment explanation
Indices: 870322--870386 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
870312 AATTTTGGGA
870322 TTTTTTATAATTTCAGAGAAATTAGTGT
1 TTTTTTATAATTTCAGAGAAATTAGTGT
870350 TTTTTTATAATTTCAGAGAAATTAGTG-
1 TTTTTTATAATTTCAGAGAAATTAGTGT
870377 TTTTTTATAA
1 TTTTTTATAA
870387 ATATAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.27
28 27 0.73
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.52
Consensus pattern (28 bp):
TTTTTTATAATTTCAGAGAAATTAGTGT
Found at i:881510 original size:15 final size:16
Alignment explanation
Indices: 881492--881521 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
881482 TTGATTCGAT
881492 TCGAAATAA-TTCAAC
1 TCGAAATAACTTCAAC
881507 TCGAAATAACTTCAA
1 TCGAAATAACTTCAA
881522 GTTGTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (16 bp):
TCGAAATAACTTCAAC
Found at i:881762 original size:2 final size:2
Alignment explanation
Indices: 881755--881839 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
881745 AATGGATTGT
881755 TA TA TA 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
881797 TA TA TA 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
881839 T
1 T
881840 GATCATAAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:881963 original size:2 final size:2
Alignment explanation
Indices: 881952--881987 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
881942 AAAATCATAG
881952 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
881988 ATTATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:882080 original size:15 final size:15
Alignment explanation
Indices: 882060--882089 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
882050 ACACAAACTC
*
882060 AAAAATTTAACTCAA
1 AAAAATTTAAATCAA
882075 AAAAATTTAAATCAA
1 AAAAATTTAAATCAA
882090 CTCCAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATTTAAATCAA
Found at i:891178 original size:23 final size:25
Alignment explanation
Indices: 891147--891194 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
891137 AAAATTATAT
*
891147 TAAATTTTTAA-AGATAT-AAATTA
1 TAAAATTTTAATAGATATGAAATTA
*
891170 TAAAATTTTAATAGGTATGAAATTA
1 TAAAATTTTAATAGATATGAAATTA
891195 AATAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 5 0.24
25 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (25 bp):
TAAAATTTTAATAGATATGAAATTA
Found at i:891441 original size:11 final size:11
Alignment explanation
Indices: 891425--891468 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
891415 ATATAAATAA
891425 ATTTAAAAAAT
1 ATTTAAAAAAT
891436 ATTTAAAAAAGT
1 ATTTAAAAAA-T
*
891448 ATTAATAAAAAT
1 ATTTA-AAAAAT
891460 A-TTAAAAAA
1 ATTTAAAAAA
891469 ACTAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 5 0.17
11 12 0.41
12 7 0.24
13 5 0.17
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
ATTTAAAAAAT
Found at i:891450 original size:12 final size:10
Alignment explanation
Indices: 891413--891468 Score: 53
Period size: 10 Copynumber: 5.3 Consensus size: 10
891403 ATAAAATTTT
891413 AAATA-TAAA
1 AAATATTAAA
891422 TAAAT-TTAAA
1 -AAATATTAAA
891432 AAATATTTAAA
1 AAATA-TTAAA
891443 AAAGTATTAATAA
1 AAA-TATT-A-AA
891456 AAATATTAAA
1 AAATATTAAA
891466 AAA
1 AAA
891469 ACTAAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 4 0.10
10 13 0.32
11 11 0.28
12 7 0.17
13 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAATATTAAA
Found at i:891469 original size:11 final size:11
Alignment explanation
Indices: 891413--891469 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 11
891403 ATAAAATTTT
*
891413 AAATA-TAAAT
1 AAATATTAAAA
891423 AAAT-TT-AAA
1 AAATATTAAAA
891432 AAATATTTAAAA
1 AAATA-TTAAAA
*
891444 AAGTATTAATAA
1 AAATATTAA-AA
891456 AAATATTAAAA
1 AAATATTAAAA
891467 AAA
1 AAA
891470 CTAAAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.15
10 5 0.13
11 11 0.28
12 17 0.44
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AAATATTAAAA
Found at i:891786 original size:21 final size:20
Alignment explanation
Indices: 891743--891787 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
891733 AACCTTTAAA
*
891743 AATTATTTTATAAAAATATT
1 AATTATTTTATAAAAATAAT
*
891763 AATTATTTTGTAAAAAGTAAT
1 AATTATTTTATAAAAA-TAAT
891784 AATT
1 AATT
891788 TTGCCACGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
AATTATTTTATAAAAATAAT
Found at i:892199 original size:20 final size:20
Alignment explanation
Indices: 892174--892219 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
892164 GTTTTAGGGT
892174 TTAGGGTTTAGGGTTTTAAA
1 TTAGGGTTTAGGGTTTTAAA
892194 TTAGGGTTTAGGGTTTTAAA
1 TTAGGGTTTAGGGTTTTAAA
892214 TTAGGG
1 TTAGGG
892220 ATAGAGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (20 bp):
TTAGGGTTTAGGGTTTTAAA
Found at i:892778 original size:15 final size:16
Alignment explanation
Indices: 892758--892798 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
892748 GTTTACTTCA
*
892758 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
892773 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
892789 GAATGATTCA
1 GAATGATTCA
892799 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:896454 original size:15 final size:16
Alignment explanation
Indices: 896417--896460 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
896407 TATTTTTTTT
*
896417 ATTTTTTTGAAATAAA
1 ATTTTTTTTAAATAAA
* *
896433 ATATTTTTTAAA-AAC
1 ATTTTTTTTAAATAAA
896448 ATTTTTTTTAAAT
1 ATTTTTTTTAAAT
896461 CTGAACATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTTTTTAAATAAA
Found at i:897185 original size:6 final size:6
Alignment explanation
Indices: 897145--897183 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
897135 CATATCAGTA
* *
897145 TCCTAT TCCTAT TCCTAT TCCTAT TTCTAT TCCCAT TCC
1 TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT TCC
897184 CACGCTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.36, G:0.00, T:0.49
Consensus pattern (6 bp):
TCCTAT
Found at i:905047 original size:64 final size:63
Alignment explanation
Indices: 904967--905187 Score: 257
Period size: 64 Copynumber: 3.5 Consensus size: 63
904957 TTGAAGGTGT
** *
904967 ATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAA-AATAAATACATCGAATGCAATTCATGC
1 ATCGATGCATAAGTAGTGCATCGATGCA-TCTATTAATAATAAA-ACATCGAATGCAATTCATGC
* * **
905031 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCAT-CTATTAATAATAAAACATCGAATGCAATTCATGC
* ** * * *
905095 ATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCT-ATTAATAATAAAACATCGAATGCAATTCATGC
*
905159 A-CAGATGCATCAGTAGTGCATCGATGCAT
1 ATC-GATGCATAAGTAGTGCATCGATGCAT
905188 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
63 3 0.02
64 127 0.94
65 5 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCTATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:906030 original size:31 final size:31
Alignment explanation
Indices: 905844--906015 Score: 335
Period size: 31 Copynumber: 5.5 Consensus size: 31
905834 AGGGTCGAGG
905844 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
905875 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
905906 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
905937 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
905968 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
905999 GTTTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
906016 AGAATCTATG
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 140 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:907036 original size:36 final size:35
Alignment explanation
Indices: 906996--907292 Score: 126
Period size: 36 Copynumber: 8.6 Consensus size: 35
906986 AACTATTTTC
906996 TAAAAATCTATATAATATATATTTTCAAAATTATTT
1 TAAAAA-CTATATAATATATATTTTCAAAATTATTT
* * * *
907032 T-AAAAGTATAT-ATATTATAATTTTTTAAAAATGTTT
1 TAAAAACTATATAATA-TAT-A-TTTTCAAAATTATTT
* * * **
907068 TCAAAA-T-TAT-GTA-GT-TTTAAAAAATGT-TTT
1 TAAAAACTATATAATATATATTTTCAAAAT-TATTT
* *
907098 T-AAAACTATATATTATATAAGTTTTCAAAATGA-TT
1 TAAAAACTATATAATATAT-A-TTTTCAAAATTATTT
* * *
907133 TCAAAACTATATAATATATATGTTTTCAAACTTTTTTT
1 TAAAAACTATATAATATATA--TTTTCAAA-ATTATTT
**
907171 TAAAAAC--TAT-A-A-A-ATTTTCAAAA-CGTTT
1 TAAAAACTATATAATATATATTTTCAAAATTATTT
* * *
907199 TAAAAAATATATAATATATATATTTTTAAAAATATTT
1 TAAAAACTATAT-A-ATATATATTTTCAAAATTATTT
* *
907236 TAAAAACTATATATTATAATTATTTTCAAAATGT-TTA
1 TAAAAACTATATAATAT-A-TATTTTCAAAAT-TATTT
* *
907273 AAAAAATTATATAATATATA
1 TAAAAACTATATAATATATA
907293 AATGTTTTCG
Statistics
Matches: 198, Mismatches: 34, Indels: 59
0.68 0.12 0.20
Matches are distributed among these distances:
28 9 0.05
29 4 0.02
30 23 0.12
31 4 0.02
32 3 0.02
33 7 0.04
34 10 0.05
35 21 0.11
36 63 0.32
37 45 0.23
38 9 0.05
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (35 bp):
TAAAAACTATATAATATATATTTTCAAAATTATTT
Found at i:907116 original size:102 final size:100
Alignment explanation
Indices: 906997--907277 Score: 255
Period size: 102 Copynumber: 2.8 Consensus size: 100
906987 ACTATTTTCT
* *
906997 AAAAATCTATATAATATATATTTTCAAAATTATTTTAAAAGTATATATATTATAATTTTTTAAAA
1 AAAAATATATATTATATATATTTTCAAAATTATTTTAAAA-TATATATATTATAATTTTTTAAAA
* * ** * * *
907062 ATGTTTTCAAAATTATGTAGTTTTAAAAAATGTTTTT
65 ATGTTTTAAAAACTATAAAATTTT-AAAAACGTTTTA
* * * *
907099 AAAACTATATATTATATA-AGTTTTCAAAATGATTTCAAAACTATATA-A-TATATATGTTTTCA
1 AAAAATATATATTATATATA-TTTTCAAAATTATTTTAAAA-TATATATATTATA-AT-TTTTTA
** * *
907161 AACTTTTTTTTAAAAACTATAAAATTTTCAAAACGTTTTA
62 AA-AATGTTTTAAAAACTATAAAATTTTAAAAACGTTTTA
* * * *
907201 AAAAATATATAATATATATATTTTTAAAAATATTTTAAAA-ACTATATATTATAATTATTTTCAA
1 AAAAATATATATTATATATATTTTCAAAATTATTTTAAAATA-TATATATTATAATT-TTTTAAA
*
907265 AATGTTTAAAAAA
64 AATGTTTTAAAAA
907278 ATTATATAAT
Statistics
Matches: 140, Mismatches: 30, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
100 5 0.04
101 18 0.13
102 95 0.68
103 22 0.16
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (100 bp):
AAAAATATATATTATATATATTTTCAAAATTATTTTAAAATATATATATTATAATTTTTTAAAAA
TGTTTTAAAAACTATAAAATTTTAAAAACGTTTTA
Found at i:907210 original size:66 final size:65
Alignment explanation
Indices: 907119--907246 Score: 166
Period size: 66 Copynumber: 2.0 Consensus size: 65
907109 ATTATATAAG
* * * * ** *
907119 TTTTCAAAATGATTTCAAAACTATATAATATATATGTTTTCAAACTTTTTTTTAAAAACTATAAA
1 TTTTCAAAACGATTTAAAAAATATATAATATATATATTTTCAAA-AATATTTTAAAAACTATAAA
907184 A
65 A
* *
907185 TTTTCAAAACGTTTTAAAAAATATATAATATATATATTTTTAAAAATATTTTAAAAACTATA
1 TTTTCAAAACGATTTAAAAAATATATAATATATATATTTTCAAAAATATTTTAAAAACTATA
907247 TATTATAATT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
65 15 0.28
66 38 0.72
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (65 bp):
TTTTCAAAACGATTTAAAAAATATATAATATATATATTTTCAAAAATATTTTAAAAACTATAAAA
Found at i:907284 original size:35 final size:37
Alignment explanation
Indices: 907088--907344 Score: 144
Period size: 36 Copynumber: 7.1 Consensus size: 37
907078 GTAGTTTTAA
* * *
907088 AAAATGTTTT-TAAAACTATATATTATATA-AGTTTTC
1 AAAATGTTTTAAAAAATTATATAATATATATA-TTTTC
* * * *
907124 AAAATGATTT-CAAAACTATATAATATATATGTTTTC
1 AAAATGTTTTAAAAAATTATATAATATATATATTTTC
* * ** *
907160 AAACTTTTTTTTAAAA--A-CT-ATA-A-A-ATTTTC
1 AAAATGTTTTAAAAAATTATATAATATATATATTTTC
* *
907190 AAAACGTTTTAAAAAA-TATATAATATATATATTTTTA
1 AAAATGTTTTAAAAAATTATATAATATATATA-TTTTC
* * *
907227 AAAATATTTT-AAAAACTATATATTATA-ATTATTTTC
1 AAAATGTTTTAAAAAATTATATAATATATA-TATTTTC
* *
907263 AAAATGTTTAAAAAAATTATATAATATATAAATGTTTTC
1 AAAATGTTTTAAAAAATTATATAATATAT--ATATTTTC
* * * * *
907302 GAACATGTTTTCAAAACTATATATTATATATATTTTTTC
1 -AAAATGTTTTAAAAAAT-TATATAATATATATATTTTC
907341 AAAA
1 AAAA
907345 AACCATTTGT
Statistics
Matches: 171, Mismatches: 33, Indels: 32
0.72 0.14 0.14
Matches are distributed among these distances:
30 16 0.09
31 2 0.01
32 2 0.01
33 6 0.04
34 2 0.01
35 2 0.01
36 57 0.33
37 43 0.25
38 3 0.02
39 13 0.08
40 14 0.08
41 11 0.06
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAAATTATATAATATATATATTTTC
Found at i:907323 original size:39 final size:37
Alignment explanation
Indices: 907178--907344 Score: 158
Period size: 37 Copynumber: 4.4 Consensus size: 37
907168 TTTTAAAAAC
* * *
907178 TATAAAATTTTCAAAACGTTTTAAAAAATATATAATA
1 TATAAATTTTTCAAAATGTTTTAAAAACTATATAATA
* * *
907215 TATATATTTTTAAAAATATTTTAAAAACTATAT-AT-
1 TATAAATTTTTCAAAATGTTTTAAAAACTATATAATA
* * *
907250 TATAATTATTTTCAAAATGTTTAAAAAAATTATATAATA
1 TATAAAT-TTTTCAAAATGTTT-TAAAAACTATATAATA
* * *
907289 TATAAATGTTTTCGAACATGTTTTCAAAACTATATATTA
1 TATAAAT-TTTTC-AAAATGTTTTAAAAACTATATAATA
*
907328 TATATATTTTTTCAAAA
1 TATA-AATTTTTCAAAA
907345 AACCATTTGT
Statistics
Matches: 103, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
35 5 0.05
36 14 0.14
37 37 0.36
38 5 0.05
39 32 0.31
40 10 0.10
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (37 bp):
TATAAATTTTTCAAAATGTTTTAAAAACTATATAATA
Found at i:907323 original size:74 final size:72
Alignment explanation
Indices: 907184--907344 Score: 187
Period size: 76 Copynumber: 2.1 Consensus size: 72
907174 AAACTATAAA
* *
907184 ATTTTCAAAACGTTTTAAAAAATATATAATATATATATTTTTAAAAATATTTTAAAAACTATATA
1 ATTTTCAAAACGTTTAAAAAAATATATAATATATAAATTTTTAAAAATATTTTAAAAAC-ATATA
907249 TTATAATT
65 TTATAATT
* * * * *
907257 ATTTTCAAAATGTTTAAAAAAATTATATAATATATAAATGTTTTCGAACATGTTTTCAAAACTAT
1 ATTTTCAAAACGTTTAAAAAAA-TATATAATATATAAAT-TTTT-AAAAATATTTTAAAAAC-AT
907322 ATATTATATATAT
62 ATATTATA-AT-T
*
907335 TTTTTCAAAA
1 ATTTTCAAAA
907345 AACCATTTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
73 20 0.27
74 15 0.20
75 4 0.05
76 24 0.32
77 2 0.03
78 10 0.13
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (72 bp):
ATTTTCAAAACGTTTAAAAAAATATATAATATATAAATTTTTAAAAATATTTTAAAAACATATAT
TATAATT
Found at i:907382 original size:12 final size:12
Alignment explanation
Indices: 907365--907392 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
907355 AAACTATATA
907365 ATATATAGACAT
1 ATATATAGACAT
907377 ATATATAGACAT
1 ATATATAGACAT
907389 ATAT
1 ATAT
907393 GTAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (12 bp):
ATATATAGACAT
Found at i:911806 original size:38 final size:38
Alignment explanation
Indices: 911745--911833 Score: 126
Period size: 38 Copynumber: 2.3 Consensus size: 38
911735 AATATTCGGT
**
911745 TCGGGTCGGG-TTTTTTAAGTGTGATATTTGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
* *
911782 TCGGGTCGGGTTTTTTTAAGTGTGATATTCATGTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
911820 TCGGGTTCGGGTTT
1 TCGGG-TCGGGTTT
911834 AGGGTGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 10 0.22
38 28 0.61
39 8 0.17
ACGTcount: A:0.11, C:0.10, G:0.37, T:0.42
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
Found at i:927430 original size:14 final size:14
Alignment explanation
Indices: 927413--927442 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
927403 GAGGTTATGA
927413 TTTAGGGTTTAAAG
1 TTTAGGGTTTAAAG
*
927427 TTTAGGGTTTTAAG
1 TTTAGGGTTTAAAG
927441 TT
1 TT
927443 ATAGAACGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTAAAG
Found at i:944571 original size:22 final size:24
Alignment explanation
Indices: 944546--944591 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
944536 ATGCAGTATC
*
944546 ATGTTCGTAAA-GTT-AAATGAAT
1 ATGTTCATAAATGTTAAAATGAAT
*
944568 ATGTTTATAAATGTTAAAATGAAT
1 ATGTTCATAAATGTTAAAATGAAT
944592 CGAACACGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.39
Consensus pattern (24 bp):
ATGTTCATAAATGTTAAAATGAAT
Found at i:947533 original size:2 final size:2
Alignment explanation
Indices: 947526--947581 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
947516 TACCATTTCC
947526 AT AT AT AT 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 AT AT AT AT
947568 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
947582 CGGTTTAGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:949473 original size:25 final size:25
Alignment explanation
Indices: 949442--949496 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
949432 TTAAAGGTAA
949442 GAATTCTTCTAGTTGGTTATTTCTT
1 GAATTCTTCTAGTTGGTTATTTCTT
949467 GAATTCTTCTAGTTGGTTATTTCTT
1 GAATTCTTCTAGTTGGTTATTTCTT
949492 GAATT
1 GAATT
949497 TTTAAGTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (25 bp):
GAATTCTTCTAGTTGGTTATTTCTT
Found at i:949998 original size:16 final size:16
Alignment explanation
Indices: 949977--950011 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
949967 TGGATGAGCA
949977 GTATCGATACCATAAG
1 GTATCGATACCATAAG
949993 GTATCGATACCATAAG
1 GTATCGATACCATAAG
950009 GTA
1 GTA
950012 AAAGTTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (16 bp):
GTATCGATACCATAAG
Found at i:956220 original size:4 final size:4
Alignment explanation
Indices: 956211--956241 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
956201 TTCAACTATG
956211 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
956242 ACATGCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:957151 original size:23 final size:24
Alignment explanation
Indices: 957086--957152 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
957076 AAAAATAATT
*
957086 AAATAAATATTTATATATTTTATA
1 AAATTAATATTTATATATTTTATA
* * *
957110 AACTTAATATTAATTTATTTTA-A
1 AAATTAATATTTATATATTTTATA
957133 AAATTAA-ATTTATGATATTT
1 AAATTAATATTTAT-ATATTT
957153 GTTACGGTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
22 5 0.14
23 12 0.34
24 18 0.51
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (24 bp):
AAATTAATATTTATATATTTTATA
Found at i:957712 original size:63 final size:64
Alignment explanation
Indices: 957613--957747 Score: 182
Period size: 63 Copynumber: 2.1 Consensus size: 64
957603 GTTCCATTTC
* *
957613 AAATATAAATTTTTGAAAGTTTAAGTACTAAAATGT-ATAAAGTAAAACCTTAAGTACTAAATT
1 AAATATAAATTTTTAAAAGTTTAAGTACTAAAATGTAAAAAAGTAAAACCTTAAGTACTAAATT
* * *
957676 AAATATAATTTTTTAAAAGTTTAAGTATTAAAATGTAAAAAAAAAAGTAAAACCTTAAGTAGTAA
1 AAATATAAATTTTTAAAAGTTTAAGTACTAAAATGT----AAAAAAGTAAAACCTTAAGTACTAA
957741 ATT
62 ATT
957744 AAAT
1 AAAT
957748 GTGTAGTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
63 33 0.53
68 29 0.47
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (64 bp):
AAATATAAATTTTTAAAAGTTTAAGTACTAAAATGTAAAAAAGTAAAACCTTAAGTACTAAATT
Found at i:965570 original size:21 final size:22
Alignment explanation
Indices: 965532--965572 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
965522 CCCTTCTACT
965532 TTTAATCTTTTGAATTTAATCC
1 TTTAATCTTTTGAATTTAATCC
*
965554 TTTATTCTTTT-AATTTAAT
1 TTTAATCTTTTGAATTTAAT
965573 AATTGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTAATCTTTTGAATTTAATCC
Found at i:966936 original size:11 final size:11
Alignment explanation
Indices: 966920--966958 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
966910 GTTCAGCGTC
966920 CATTTAGTGTT
1 CATTTAGTGTT
*
966931 CATTTAATGTT
1 CATTTAGTGTT
*
966942 CTTTTAGTGTT
1 CATTTAGTGTT
*
966953 CGTTTA
1 CATTTA
966959 TCATTGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.56
Consensus pattern (11 bp):
CATTTAGTGTT
Found at i:969396 original size:67 final size:67
Alignment explanation
Indices: 969283--969414 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
969273 TTACTGGTGT
* *
969283 TTGTAGACTTTCGGTGTAGGTTTTTTTATCTGGTCTTCTTCTTGGTCTGTGATTTTACATGAATA
1 TTGTAGACTTCCGGTGCAGGTTTTTTTATCTGGTCTTCTTCTTGGTCTGTGATTTTACATGAATA
969348 TA
66 TA
*
969350 TTGTGGACTTCCGGTGCAGGTTTTTTTATCTGGTCTTCTTCTTGGTCTGTGATTTTACATGAATA
1 TTGTAGACTTCCGGTGCAGGTTTTTTTATCTGGTCTTCTTCTTGGTCTGTGATTTTACATGAATA
969415 CATGGTTGGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.15, C:0.14, G:0.22, T:0.49
Consensus pattern (67 bp):
TTGTAGACTTCCGGTGCAGGTTTTTTTATCTGGTCTTCTTCTTGGTCTGTGATTTTACATGAATA
TA
Found at i:970956 original size:17 final size:17
Alignment explanation
Indices: 970934--970970 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
970924 ACTGGAGTAG
*
970934 TTTACCCTAAAATTAAT
1 TTTACCATAAAATTAAT
*
970951 TTTACCATTAAATTAAT
1 TTTACCATAAAATTAAT
970968 TTT
1 TTT
970971 TTTTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTACCATAAAATTAAT
Found at i:973679 original size:22 final size:20
Alignment explanation
Indices: 973645--973715 Score: 54
Period size: 22 Copynumber: 3.4 Consensus size: 20
973635 TTATAAAAAT
*
973645 ATTT-TTTATTTTATTTAATA
1 ATTTATTTAATTTATTTAA-A
*
973665 ATTTAATTTAATTTAATTTTAA
1 ATTT-ATTTAATTT-ATTTAAA
* *
973687 ATTTATCTTTATTTATTTCTAA
1 ATTTAT-TTAATTTATTT-AAA
973709 ATTTATT
1 ATTTATT
973716 ATTTAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
20 4 0.09
21 7 0.16
22 27 0.63
23 5 0.12
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTATTTAATTTATTTAAA
Found at i:973691 original size:12 final size:10
Alignment explanation
Indices: 973648--973725 Score: 50
Period size: 12 Copynumber: 7.0 Consensus size: 10
973638 TAAAAATATT
*
973648 TTTTATTTTA
1 TTTTAATTTA
973658 TTTAATAATTTA
1 TTT--TAATTTA
*
973670 ATTTAATTTAA
1 TTTTAATTT-A
973681 TTTTAAATTTA
1 TTTT-AATTTA
973692 TCTTT-ATTTA
1 T-TTTAATTTA
973702 TTTCTAAATTTA
1 TTT-T-AATTTA
973714 TTATTTAATTTA
1 -T-TTTAATTTA
973726 ATATTCATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
9 2 0.04
10 16 0.29
11 6 0.11
12 27 0.49
13 2 0.04
14 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:975693 original size:27 final size:27
Alignment explanation
Indices: 975663--975714 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
975653 TTTGACCCAT
975663 ATAATTTTACTATTCGTCGACGTTTTA
1 ATAATTTTACTATTCGTCGACGTTTTA
975690 ATAATTTTACTATTCGTCGACGTTT
1 ATAATTTTACTATTCGTCGACGTTT
975715 ACACGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (27 bp):
ATAATTTTACTATTCGTCGACGTTTTA
Found at i:977351 original size:39 final size:39
Alignment explanation
Indices: 977303--977383 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
977293 AGCCATCAGA
977303 AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAG
1 AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAG
977342 AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAG
1 AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAG
977381 AAA
1 AAA
977384 CGTGTGAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (39 bp):
AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAG
Found at i:978177 original size:26 final size:26
Alignment explanation
Indices: 978148--978243 Score: 165
Period size: 26 Copynumber: 3.7 Consensus size: 26
978138 TGAGCAGAGA
*
978148 AGGATCTCTCGGCGTCTTGGGCATGC
1 AGGATCTCTCGGCGTCTTGTGCATGC
*
978174 AGGATCTCTCGGCGTCTTGTGCATGG
1 AGGATCTCTCGGCGTCTTGTGCATGC
*
978200 AGTATCTCTCGGCGTCTTGTGCATGC
1 AGGATCTCTCGGCGTCTTGTGCATGC
978226 AGGATCTCTCGGCGTCTT
1 AGGATCTCTCGGCGTCTT
978244 CTTCAGCCTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.11, C:0.26, G:0.31, T:0.31
Consensus pattern (26 bp):
AGGATCTCTCGGCGTCTTGTGCATGC
Found at i:978280 original size:36 final size:36
Alignment explanation
Indices: 978232--978322 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
978222 ATGCAGGATC
978232 TCTCGGCGTCTTC-T--TCAGCCTT-GTGGGTGGAGT
1 TCTCGGCGTCTTCTTCATCAGCCTTGGT-GGTGGAGT
978265 TCTCGGCGTCTTCTTCATCAGCCTTGGTGGTGGAGT
1 TCTCGGCGTCTTCTTCATCAGCCTTGGTGGTGGAGT
978301 TCTCGGCGTCTTCTTCATCAGC
1 TCTCGGCGTCTTCTTCATCAGC
978323 ATCATTCATC
Statistics
Matches: 54, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
33 13 0.24
34 1 0.02
36 38 0.70
37 2 0.04
ACGTcount: A:0.08, C:0.27, G:0.29, T:0.36
Consensus pattern (36 bp):
TCTCGGCGTCTTCTTCATCAGCCTTGGTGGTGGAGT
Found at i:979299 original size:14 final size:14
Alignment explanation
Indices: 979233--979324 Score: 87
Period size: 14 Copynumber: 7.3 Consensus size: 14
979223 ATAATAATAA
979233 TTAACTTTAATGAT
1 TTAACTTTAATGAT
*
979247 TTAA---TAAT-AA
1 TTAACTTTAATGAT
979257 TT-ACTTTAATGAT
1 TTAACTTTAATGAT
*
979270 TTAA---TAAT-AA
1 TTAACTTTAATGAT
979280 TT-ACTTTAATGAT
1 TTAACTTTAATGAT
979293 TTAACTTTAATGAT
1 TTAACTTTAATGAT
*
979307 TTAATTTTAATGAT
1 TTAACTTTAATGAT
979321 TTAA
1 TTAA
979325 TAATAATTAC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
9 2 0.03
10 6 0.10
11 8 0.13
12 8 0.13
13 6 0.10
14 33 0.52
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (14 bp):
TTAACTTTAATGAT
Found at i:979331 original size:20 final size:20
Alignment explanation
Indices: 979308--979355 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
979298 TTTAATGATT
979308 TAATTTTAATGATTTAATAA
1 TAATTTTAATGATTTAATAA
*
979328 TAATTACTTTAATGCTTTAATAA
1 TAA-T--TTTAATGATTTAATAA
979351 TAATT
1 TAATT
979356 ACTTTAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 4 0.17
21 1 0.04
22 1 0.04
23 18 0.75
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (20 bp):
TAATTTTAATGATTTAATAA
Found at i:979364 original size:23 final size:23
Alignment explanation
Indices: 979224--979296 Score: 137
Period size: 23 Copynumber: 3.1 Consensus size: 23
979214 CCAGTATGGA
979224 TAATAATAATTAACTTTAATGATT
1 TAATAATAATT-ACTTTAATGATT
979248 TAATAATAATTACTTTAATGATT
1 TAATAATAATTACTTTAATGATT
979271 TAATAATAATTACTTTAATGATT
1 TAATAATAATTACTTTAATGATT
979294 TAA
1 TAA
979297 CTTTAATGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 38 0.78
24 11 0.22
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
TAATAATAATTACTTTAATGATT
Found at i:981843 original size:173 final size:173
Alignment explanation
Indices: 981549--981907 Score: 612
Period size: 173 Copynumber: 2.1 Consensus size: 173
981539 CATCAAATAT
* *
981549 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
981614 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
*
981679 TTTTTATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
981722 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAACTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* *
981786 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATATCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
981851 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
981895 AAAACGGTCCCTA
1 AAAACGATCCCTA
981908 CAACTTTACA
Statistics
Matches: 175, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
172 1 0.01
173 174 0.99
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (173 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:982387 original size:23 final size:23
Alignment explanation
Indices: 982361--982404 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
982351 ATTGCATGCC
982361 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
982384 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
982405 CCCCTGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:982543 original size:34 final size:34
Alignment explanation
Indices: 982500--982584 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
982490 CATGCACAGC
*
982500 ACTGAAGACGCCGAGATTTCCTATGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
982534 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
982568 ACTGAAGACGCCGAGAG
1 ACTGAAGACGCCGAGAG
982585 ATCAATCATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (34 bp):
ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
Found at i:982686 original size:30 final size:30
Alignment explanation
Indices: 982650--982710 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
982640 AAATTGCGTT
*
982650 AAAGACGCCGAGATATCCA-GCCTTCCATGC
1 AAAGACGCCGAGAGATCCACG-CTTCCATGC
*
982680 AAAGACGCGGAGAGATCCACGCTTCCATGC
1 AAAGACGCCGAGAGATCCACGCTTCCATGC
982710 A
1 A
982711 CATCTGCTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (30 bp):
AAAGACGCCGAGAGATCCACGCTTCCATGC
Found at i:984249 original size:102 final size:102
Alignment explanation
Indices: 984068--984274 Score: 351
Period size: 102 Copynumber: 2.0 Consensus size: 102
984058 ACACGCCTCT
* * *
984068 TCAATTTTCAAAACGAATATATATTGGTGGGAAATGAGGGGGACCAAAGGTGTAATTTTCCCCTT
1 TCAACTTTCAAAACGAATATACATTGGTGGGAAATGAGGGGGACCAAAGGTGTAATCTTCCCCTT
* *
984133 TGAGATAGAGTAGGCCGAAAATATATGATTAACCTTA
66 CGAGATAGAGTAGGCCGAAAAGATATGATTAACCTTA
*
984170 TCAACTTTCAAAATGAATATACATTGGTGGGAAATGAGGGGGACCAAAGGTGTAATCTTCCCCTT
1 TCAACTTTCAAAACGAATATACATTGGTGGGAAATGAGGGGGACCAAAGGTGTAATCTTCCCCTT
*
984235 CGAGATAGAGTAGGCTGAAAAGATATGATTAACCTTA
66 CGAGATAGAGTAGGCCGAAAAGATATGATTAACCTTA
984272 TCA
1 TCA
984275 CATTTTCATT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (102 bp):
TCAACTTTCAAAACGAATATACATTGGTGGGAAATGAGGGGGACCAAAGGTGTAATCTTCCCCTT
CGAGATAGAGTAGGCCGAAAAGATATGATTAACCTTA
Found at i:988850 original size:60 final size:60
Alignment explanation
Indices: 988767--988902 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
988757 AATTTTGAGT
* * * * *
988767 AAATTACACAAATGGTCTCTCGACTATA-AAGTATTATTTTATTAAGTCTTTCGATTATTAA
1 AAATTACA-AAATGATGTTTCGACTATAGAA-TATTATTTTATTAAGTCCTTCGACTATTAA
* * *
988828 AAATTATAAAATGATGTTTCGACTATAGAATGTTGTTTTATTAAGTCCTTCGACTATTAA
1 AAATTACAAAATGATGTTTCGACTATAGAATATTATTTTATTAAGTCCTTCGACTATTAA
*
988888 AAGTTACAAAATGAT
1 AAATTACAAAATGAT
988903 CACCTGACTA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 55 0.86
61 9 0.14
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (60 bp):
AAATTACAAAATGATGTTTCGACTATAGAATATTATTTTATTAAGTCCTTCGACTATTAA
Found at i:990958 original size:23 final size:23
Alignment explanation
Indices: 990921--990997 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
990911 CACTGAAGCG
*
990921 CCACATAGAATTTGTCCCGAATGA
1 CCACATAG-ATTTGTCCCGAAGGA
*
990945 CCATATAGATTTGTCCCGAAGGA
1 CCACATAGATTTGTCCCGAAGGA
* *
990968 CCACATAGGTTTGTCCCGAAGAA
1 CCACATAGATTTGTCCCGAAGGA
990991 CCACATA
1 CCACATA
990998 AAACCCTCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 41 0.85
24 7 0.15
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (23 bp):
CCACATAGATTTGTCCCGAAGGA
Found at i:1005472 original size:31 final size:31
Alignment explanation
Indices: 1005437--1005513 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1005427 AAAAATTAAA
* * *
1005437 AGTTTAGGTACTAAAACAGACCTAAATTGAT
1 AGTTTAGGTATTAAAACAGACCTAAACTAAT
* **
1005468 AGTTTAAGTATTAAAATGGACCTAAACTAAT
1 AGTTTAGGTATTAAAACAGACCTAAACTAAT
1005499 AGTTTAGGTATTAAA
1 AGTTTAGGTATTAAA
1005514 CGTATAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (31 bp):
AGTTTAGGTATTAAAACAGACCTAAACTAAT
Found at i:1007490 original size:151 final size:151
Alignment explanation
Indices: 1007216--1007516 Score: 575
Period size: 151 Copynumber: 2.0 Consensus size: 151
1007206 TTAGTGACCA
1007216 AAATAGGAGTGAGAAAATATTTGAATGATATGATGTAATTTACTCATAAAAATGTGTCACGTGCA
1 AAATAGGAGTGAGAAAATATTTGAATGATATGATGTAATTTACTCATAAAAATGTGTCACGTGCA
*
1007281 AATCATCTCTTAAGTTTTTAACGGTGAGGTACTAAAACGAAACAAAAATTAAATGTTAAGTATGA
66 AATCACCTCTTAAGTTTTTAACGGTGAGGTACTAAAACGAAACAAAAATTAAATGTTAAGTATGA
1007346 ATTAAGAGTTTAAATATTAAG
131 ATTAAGAGTTTAAATATTAAG
1007367 AAATAGGAGTGAGAAAATATTTGAATGATATGATGTAATTTACTCATAAAAATGTGTCACGTGCA
1 AAATAGGAGTGAGAAAATATTTGAATGATATGATGTAATTTACTCATAAAAATGTGTCACGTGCA
* *
1007432 AATCACCTCTTAAGTTTTTAACGGTGAGGTACTAAATCGAAGCAAAAATTAAATGTTAAGTATGA
66 AATCACCTCTTAAGTTTTTAACGGTGAGGTACTAAAACGAAACAAAAATTAAATGTTAAGTATGA
1007497 ATTAAGAGTTTAAATATTAA
131 ATTAAGAGTTTAAATATTAA
1007517 AATAACATAA
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 147 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (151 bp):
AAATAGGAGTGAGAAAATATTTGAATGATATGATGTAATTTACTCATAAAAATGTGTCACGTGCA
AATCACCTCTTAAGTTTTTAACGGTGAGGTACTAAAACGAAACAAAAATTAAATGTTAAGTATGA
ATTAAGAGTTTAAATATTAAG
Found at i:1007858 original size:2 final size:2
Alignment explanation
Indices: 1007851--1007886 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1007841 AATGAAAATG
1007851 AT 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 AT
1007887 TTGTTCTAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1008606 original size:25 final size:24
Alignment explanation
Indices: 1008564--1008610 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1008554 TATACTAGAG
1008564 ATTTAAGGAGTATAAAATTATAAA
1 ATTTAAGGAGTATAAAATTATAAA
*
1008588 ATTTAACGGATTATAAAATTATA
1 ATTTAA-GGAGTATAAAATTATA
1008611 CTAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (24 bp):
ATTTAAGGAGTATAAAATTATAAA
Found at i:1018647 original size:20 final size:20
Alignment explanation
Indices: 1018622--1018662 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1018612 AAACTAGGTA
1018622 CTTAAACTATTATATGTAAT
1 CTTAAACTATTATATGTAAT
1018642 CTTAAACTATTATATGTAAT
1 CTTAAACTATTATATGTAAT
1018662 C
1 C
1018663 ACTTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (20 bp):
CTTAAACTATTATATGTAAT
Found at i:1018957 original size:23 final size:22
Alignment explanation
Indices: 1018896--1018955 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
1018886 TATTTTTATC
*
1018896 TAATT-ATAAATAATAATTTAA
1 TAATTAATCAATAATAATTTAA
* *
1018917 TAAATTATTCAAAAATAATTTAA
1 T-AATTAATCAATAATAATTTAA
1018940 TAATTAA--AATAATAAT
1 TAATTAATCAATAATAAT
1018956 AAATCAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.25
21 1 0.03
22 9 0.28
23 14 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATTAATCAATAATAATTTAA
Found at i:1023318 original size:15 final size:15
Alignment explanation
Indices: 1023298--1023327 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1023288 CTTGCTAATG
1023298 AGCTTTTTTTTTTCA
1 AGCTTTTTTTTTTCA
1023313 AGCTTTTTTTTTTCA
1 AGCTTTTTTTTTTCA
1023328 CAACATGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
AGCTTTTTTTTTTCA
Found at i:1023645 original size:14 final size:14
Alignment explanation
Indices: 1023626--1023653 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1023616 TGGCTATCAT
1023626 TAATGAGAAGGCCA
1 TAATGAGAAGGCCA
1023640 TAATGAGAAGGCCA
1 TAATGAGAAGGCCA
1023654 GATTTAGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (14 bp):
TAATGAGAAGGCCA
Found at i:1034447 original size:2 final size:2
Alignment explanation
Indices: 1034440--1034514 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
1034430 AACAACCATT
*
1034440 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA GA 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
*
1034481 GA 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
1034515 ATCTGATCTG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1035323 original size:20 final size:18
Alignment explanation
Indices: 1035286--1035326 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1035276 TATCATCTAT
*
1035286 TTTATTTTTTATTTAAAA
1 TTTATTTTTCATTTAAAA
1035304 TTTATTTTTACATCTTAAAA
1 TTTATTTTT-CAT-TTAAAA
1035324 TTT
1 TTT
1035327 TATAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATTTTTCATTTAAAA
Found at i:1037539 original size:174 final size:178
Alignment explanation
Indices: 1037322--1037670 Score: 532
Period size: 174 Copynumber: 2.0 Consensus size: 178
1037312 TTAAATATAT
*
1037322 TATATAACATATGGGTTCAGCCCAAACAATTTAAAACCCAATTAAT-ATTTAAGATCCAATAACT
1 TATATAACATATGGGCTCAGCCCAAACAATTTAAAACCCAATTAATAATTTAAGATCCAATAACT
**
1037386 TTT-CTAAATCAATATTAATTAATTAAAA-AATTATAT-ATTTTTTTA-TTTATAATT-TATATT
66 TTTACTAAATCAATATTAATTAATTAAAATAATTATATAACATTTTTATTTTATAATTATATATT
1037446 ATTTAAATTAATT-GTAAACTATTTTTTTAAATTTAAAAAATATTATATTA
131 ATTTAAATTAATTAG-AAACTA-TTTTTTAAA-TTAAAAAATATTATATTA
*
1037496 TATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAACT
1 TATATAACATATGGGCTCAGCCCAAACAATTTAAAACCCAATTAATAATTTAAGATCCAATAACT
**
1037561 TTTAAACCTAAATCAATATTAATTAATTAAAATTTTTATATAACATTTTTATTTTATAATTATAT
66 TTT--A-CTAAATCAATATTAATTAATTAAAATAATTATATAACATTTTTATTTTATAATTATAT
*
1037626 ATTATTTAAATTAATTAGAAACTATTTTTTGAATTAAAAAATATT
128 ATTATTTAAATTAATTAGAAACTATTTTTTAAATTAAAAAATATT
1037671 TACTTTTTAT
Statistics
Matches: 158, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
174 44 0.28
175 21 0.13
179 25 0.16
180 6 0.04
181 19 0.12
182 17 0.11
183 25 0.16
184 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.43
Consensus pattern (178 bp):
TATATAACATATGGGCTCAGCCCAAACAATTTAAAACCCAATTAATAATTTAAGATCCAATAACT
TTTACTAAATCAATATTAATTAATTAAAATAATTATATAACATTTTTATTTTATAATTATATATT
ATTTAAATTAATTAGAAACTATTTTTTAAATTAAAAAATATTATATTA
Found at i:1038167 original size:42 final size:43
Alignment explanation
Indices: 1038072--1038397 Score: 369
Period size: 43 Copynumber: 7.7 Consensus size: 43
1038062 TTGAGAACAA
* * *
1038072 AAACGCCGCAAAAGGTCGAGATCTAGAGCGGCGCTTTTAGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * *
1038115 AAACGTCGCAAAAGGTCGAGATCTATAGCGGCG-CTTTAGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* **
1038157 AAACGCCGCAAAAGGTTGAGATCTATAGCGGTATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
*
1038200 AAACGCCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
1038243 AAA-GCTGTAAAAGATC-AGATCTATAGTGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * ** * *
1038284 AAACGCCACAAAAAGTCGAGATCTATAGTAGTGTTTTTCGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * *
1038327 AAACACCGCAAAAGGTC-AGATCTATAGCGGTGTTTTTCGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
*
1038369 AAATC-CCACAAAAGGT--ATGATCTATAGCG
1 AAA-CGCCGCAAAAGGTCGA-GATCTATAGCG
1038398 ACATTTTTTT
Statistics
Matches: 248, Mismatches: 30, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
41 28 0.11
42 103 0.42
43 117 0.47
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
Found at i:1038378 original size:85 final size:85
Alignment explanation
Indices: 1038072--1038397 Score: 349
Period size: 85 Copynumber: 3.8 Consensus size: 85
1038062 TTGAGAACAA
* * * * * *
1038072 AAACGCCGCAAAAGGTCGAGATCTAGAGCGGCGCTTTTAGAACAAACGTCGCAAAAGGTCGAGAT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCGAGAT
*
1038137 CTATAGCGGCG-CTTTAGAAC
65 CTATAGCGGCGTTTTTAGAAC
* ** *
1038157 AAACGCCGCAAAAGGTTGAGATCTATAGCGGTATTTTTGGAACAAACGCCGC-AAAAGATCGAGA
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAG-TCGAGA
*
1038221 TCTATAGCGGCGTTTTTGGAAC
64 TCTATAGCGGCGTTTTTAGAAC
* * * *
1038243 AAA-GCTGTAAAAGATCAGATCTATAGTGGCGTTTTTGGAACAAACGCCACAAAAAGTCGAGATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCGAGATC
** * *
1038307 TATAGTAGTGTTTTTCGAAC
66 TATAGCGGCGTTTTTAGAAC
* * * *
1038327 AAACACCGCAAAAGGTCAGATCTATAGCGGTGTTTTTCGAACAAATC-CCACAAAAGGT--ATGA
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAA-CGCCACAAAAAGTCGA-GA
1038389 TCTATAGCG
64 TCTATAGCG
1038398 ACATTTTTTT
Statistics
Matches: 202, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
83 1 0.00
84 71 0.35
85 118 0.58
86 12 0.06
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (85 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCGAGATC
TATAGCGGCGTTTTTAGAAC
Found at i:1038405 original size:42 final size:42
Alignment explanation
Indices: 1038080--1038405 Score: 167
Period size: 42 Copynumber: 7.7 Consensus size: 42
1038070 AAAAACGCCG
* * ** * ** *
1038080 CAAAAGGTCGAGATCTAGAGCGGCGCTTTTAGAACAAACGTCG
1 CAAAAGGTC-AGATCTATAGCGACATTTTTCGAACAAACACCA
* ** * * *
1038123 CAAAAGGTCGAGATCTATAGCGGC-GCTTTAGAACAAACGCCG
1 CAAAAGGTC-AGATCTATAGCGACATTTTTCGAACAAACACCA
* ** * * *
1038165 CAAAAGGTTGAGATCTATAGCGGTATTTTTGGAACAAACGCCG
1 CAAAAGG-TCAGATCTATAGCGACATTTTTCGAACAAACACCA
* * * * * **
1038208 CAAAAGATCGAGATCTATAGCGGCGTTTTTGGAACAAA-GCTG
1 CAAAAGGTC-AGATCTATAGCGACATTTTTCGAACAAACACCA
* * * * * * *
1038250 TAAAAGATCAGATCTATAGTGGCGTTTTTGGAACAAACGCCA
1 CAAAAGGTCAGATCTATAGCGACATTTTTCGAACAAACACCA
* * ** *
1038292 CAAAAAGTCGAGATCTATAG-TAGTGTTTTTCGAACAAACACCG
1 CAAAAGGTC-AGATCTATAGCGA-CATTTTTCGAACAAACACCA
***
1038335 CAAAAGGTCAGATCTATAGCGGTGTTTTTCGAACAAATC-CCA
1 CAAAAGGTCAGATCTATAGCGACATTTTTCGAACAAA-CACCA
1038377 CAAAAGGT-ATGATCTATAGCGACATTTTT
1 CAAAAGGTCA-GATCTATAGCGACATTTTT
1038406 TTGATACAAA
Statistics
Matches: 240, Mismatches: 34, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
41 28 0.12
42 106 0.44
43 106 0.44
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (42 bp):
CAAAAGGTCAGATCTATAGCGACATTTTTCGAACAAACACCA
Found at i:1038593 original size:16 final size:15
Alignment explanation
Indices: 1038567--1038596 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1038557 TAACAACAAA
1038567 ATAAAATTAAAATTT
1 ATAAAATTAAAATTT
1038582 ATAAACATTAAAATT
1 ATAAA-ATTAAAATT
1038597 AAATGTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAATTAAAATTT
Found at i:1039696 original size:29 final size:30
Alignment explanation
Indices: 1039629--1039703 Score: 134
Period size: 29 Copynumber: 2.5 Consensus size: 30
1039619 AACCGACAGA
1039629 ACCGAATTAGTTCGGTTAATTCGGCCGGCC
1 ACCGAATTAGTTCGGTTAATTCGGCCGGCC
*
1039659 ACCGAATTAGTTCGGTTAATTC-GTCGGCC
1 ACCGAATTAGTTCGGTTAATTCGGCCGGCC
1039688 ACCGAATTAGTTCGGT
1 ACCGAATTAGTTCGGT
1039704 CAGGGTACGA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 22 0.50
30 22 0.50
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.29
Consensus pattern (30 bp):
ACCGAATTAGTTCGGTTAATTCGGCCGGCC
Found at i:1043296 original size:29 final size:28
Alignment explanation
Indices: 1043239--1043296 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
1043229 AAAATGAAAC
***
1043239 AAAAACTAAATATTAGGTATGATTTTGA
1 AAAAACTAAATATTAGGTATGAAAATGA
1043267 AAAAACTGAAA-ATTTAGGTATGAAAATGA
1 AAAAACT-AAATA-TTAGGTATGAAAATGA
1043296 A
1 A
1043297 TCAAAATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (28 bp):
AAAAACTAAATATTAGGTATGAAAATGA
Found at i:1047470 original size:2 final size:2
Alignment explanation
Indices: 1047465--1047496 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1047455 AAAAGAACCT
1047465 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1047497 TATGAACCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1051429 original size:22 final size:22
Alignment explanation
Indices: 1051401--1051444 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1051391 CAATTTTTAT
*
1051401 TGATTATCACATCCCATTCTAC
1 TGATTATCACATCACATTCTAC
*
1051423 TGATTATCACATCATATTCTAC
1 TGATTATCACATCACATTCTAC
1051445 GTCTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.39
Consensus pattern (22 bp):
TGATTATCACATCACATTCTAC
Found at i:1051779 original size:188 final size:188
Alignment explanation
Indices: 1051464--1051845 Score: 723
Period size: 188 Copynumber: 2.0 Consensus size: 188
1051454 TAATGACAAA
1051464 ACTATAGCATTCATCACTCAACTATGTATCCCTTTTACTTACTACCGATCTTTTAATTTTATCAA
1 ACTATAGCATTCATCACTCAACTATGTATCCCTTTTACTTACTACCGATCTTTTAATTTTATCAA
1051529 TCATACCACTTAATTATTTAATTATGTTCAATCAAACCTCTTATTGTTAACAATTGATGGAAATG
66 TCATACCACTTAATTATTTAATTATGTTCAATCAAACCTCTTATTGTTAACAATTGATGGAAATG
1051594 CCGACCTGACATTTAAAAAATTAGCATGCTTC-ATATTTAGTCCTTAATATT-TATAT
131 CCGACCTGACATTTAAAAAATTAGCATGCTTCAATATTTAGTCCTTAATATTATATAT
1051650 ACTATAGCATTCATCACTCAACTATGTATCCCTTTTACATTTACTACCGATCTTTTAATTTTATC
1 ACTATAGCATTCATCACTCAACTATGTATCCCTTTTAC--TTACTACCGATCTTTTAATTTTATC
1051715 AATCATACCACTTAATTATTTAATTATGTTCAATCAAACCTCTTATTGTTAACAATTGATGGAAA
64 AATCATACCACTTAATTATTTAATTATGTTCAATCAAACCTCTTATTGTTAACAATTGATGGAAA
1051780 TGCCGACCTGACATTTAAAAAATTAGCATGCTTCAATATTTAGTCCTTAATATTATATAT
129 TGCCGACCTGACATTTAAAAAATTAGCATGCTTCAATATTTAGTCCTTAATATTATATAT
*
1051840 TCTATA
1 ACTATA
1051846 AATTTGGTCA
Statistics
Matches: 191, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
186 38 0.20
188 124 0.65
189 19 0.10
190 10 0.05
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (188 bp):
ACTATAGCATTCATCACTCAACTATGTATCCCTTTTACTTACTACCGATCTTTTAATTTTATCAA
TCATACCACTTAATTATTTAATTATGTTCAATCAAACCTCTTATTGTTAACAATTGATGGAAATG
CCGACCTGACATTTAAAAAATTAGCATGCTTCAATATTTAGTCCTTAATATTATATAT
Found at i:1054797 original size:20 final size:20
Alignment explanation
Indices: 1054758--1054811 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1054748 CAGAGATTTT
1054758 GTTCTCTTTACATGATGAAAAG
1 GTTC-CTTTAC-TGATGAAAAG
*
1054780 GTTCCTTTACTTATGAAAAG
1 GTTCCTTTACTGATGAAAAG
*
1054800 GTTCTTTTACTG
1 GTTCCTTTACTG
1054812 TTAATTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 19 0.66
21 6 0.21
22 4 0.14
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (20 bp):
GTTCCTTTACTGATGAAAAG
Found at i:1060621 original size:14 final size:14
Alignment explanation
Indices: 1060602--1060628 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1060592 GTTCGTGAAC
1060602 GTTCGGTTATGTTT
1 GTTCGGTTATGTTT
1060616 GTTCGGTTATGTT
1 GTTCGGTTATGTT
1060629 CGTTTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.30, T:0.56
Consensus pattern (14 bp):
GTTCGGTTATGTTT
Found at i:1060629 original size:24 final size:24
Alignment explanation
Indices: 1060602--1060666 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
1060592 GTTCGTGAAC
* *
1060602 GTTCGGTTATGTTTGTTCGGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
*
1060626 GTTCGTTTATGTTCGTTCAGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
1060650 GTTCGGTTATGTTCGTT
1 GTTCGGTTATGTTCGTT
1060667 TATGTTCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.09, C:0.11, G:0.26, T:0.54
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:1060630 original size:10 final size:10
Alignment explanation
Indices: 1060615--1060673 Score: 64
Period size: 10 Copynumber: 5.5 Consensus size: 10
1060605 CGGTTATGTT
1060615 TGTTCGGTTA
1 TGTTCGGTTA
*
1060625 TGTTCGTTTA
1 TGTTCGGTTA
1060635 TGTTCGTTCAGTTA
1 TGTTCG----GTTA
1060649 TGTTCGGTTA
1 TGTTCGGTTA
*
1060659 TGTTCGTTTA
1 TGTTCGGTTA
1060669 TGTTC
1 TGTTC
1060674 ATTCATTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 33 0.79
14 9 0.21
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.54
Consensus pattern (10 bp):
TGTTCGGTTA
Found at i:1060630 original size:34 final size:34
Alignment explanation
Indices: 1060592--1060665 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
1060582 GTTCATTTAC
1060592 GTTCGTGAACGTTCGGTT-ATGTT-TGTTCGGTTAT
1 GTTCGTGAACGTTC-GTTCA-GTTATGTTCGGTTAT
** *
1060626 GTTCGTTTATGTTCGTTCAGTTATGTTCGGTTAT
1 GTTCGTGAACGTTCGTTCAGTTATGTTCGGTTAT
1060660 GTTCGT
1 GTTCGT
1060666 TTATGTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 6 0.17
34 29 0.83
ACGTcount: A:0.11, C:0.12, G:0.27, T:0.50
Consensus pattern (34 bp):
GTTCGTGAACGTTCGTTCAGTTATGTTCGGTTAT
Found at i:1060643 original size:14 final size:14
Alignment explanation
Indices: 1060601--1060654 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
1060591 CGTTCGTGAA
*
1060601 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
* *
1060615 TGTTCGGTTATGTT
1 CGTTCAGTTATGTT
1060629 CG-T---TTATGTT
1 CGTTCAGTTATGTT
1060639 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
1060653 CG
1 CG
1060655 GTTATGTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.09, C:0.13, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:1060666 original size:34 final size:34
Alignment explanation
Indices: 1060615--1060686 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
1060605 CGGTTATGTT
*
1060615 TGTTCGGTTATGTTCGTTTATGTTCGTTCAGTTA
1 TGTTCGGTTATGTTCGTTTATGTTCATTCAGTTA
*
1060649 TGTTCGGTTATGTTCGTTTATGTTCATTCATTTA
1 TGTTCGGTTATGTTCGTTTATGTTCATTCAGTTA
1060683 TGTT
1 TGTT
1060687 TAACCCAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (34 bp):
TGTTCGGTTATGTTCGTTTATGTTCATTCAGTTA
Found at i:1061621 original size:16 final size:16
Alignment explanation
Indices: 1061602--1061656 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1061592 CCAATGTTTA
1061602 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1061618 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1061634 TGTTCGTTTATGTCCG
1 TGTTCGTTTATGTTCG
1061650 TGTTCGT
1 TGTTCGT
1061657 GTTCGTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.07, C:0.15, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1061970 original size:30 final size:28
Alignment explanation
Indices: 1061936--1062015 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 28
1061926 GATTTTCTAA
1061936 ATATTGTTTATCTGATATCTGATTTACTGT
1 ATATT-TTTATCTGATATCTGA-TTACTGT
* *
1061966 ATATTTCTGATATGATATCTGATTACTGT
1 ATATTT-TTATCTGATATCTGATTACTGT
*
1061995 AT-TTTTGTATCTGATTTCTGA
1 ATATTTT-TATCTGATATCTGA
1062016 GTATGAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.02
28 14 0.33
29 10 0.23
30 18 0.42
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (28 bp):
ATATTTTTATCTGATATCTGATTACTGT
Found at i:1062599 original size:2 final size:2
Alignment explanation
Indices: 1062592--1062623 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1062582 CGATTTTTGC
1062592 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
1062624 CGTATGAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1074780 original size:49 final size:49
Alignment explanation
Indices: 1074724--1074821 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1074714 ATATATTCTT
1074724 ACTCTCCTCTATTACCAATGTAACCTGATTCAGAATTATTCTTACTGAA
1 ACTCTCCTCTATTACCAATGTAACCTGATTCAGAATTATTCTTACTGAA
1074773 ACTCTCCTCTATTACCAATGTAACCTGATTCAGAATTATTCTTACTGAA
1 ACTCTCCTCTATTACCAATGTAACCTGATTCAGAATTATTCTTACTGAA
1074822 GTAAGTTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (49 bp):
ACTCTCCTCTATTACCAATGTAACCTGATTCAGAATTATTCTTACTGAA
Found at i:1083934 original size:21 final size:22
Alignment explanation
Indices: 1083893--1083945 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1083883 TAACGATAGG
*
1083893 TAAC-TAAAATGAAACCAAAAA
1 TAACATAAAAAGAAACCAAAAA
*
1083914 TAACATAAAAAGAGACC-AAAA
1 TAACATAAAAAGAAACCAAAAA
*
1083935 TAAAATAAAAA
1 TAACATAAAAA
1083946 TAATAATTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.70, C:0.11, G:0.06, T:0.13
Consensus pattern (22 bp):
TAACATAAAAAGAAACCAAAAA
Found at i:1084025 original size:17 final size:18
Alignment explanation
Indices: 1084003--1084044 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1083993 GACACATTTT
*
1084003 AAAATTTAAT-TTTCATA
1 AAAATTAAATATTTCATA
*
1084020 AAAATTAAATATTTTATA
1 AAAATTAAATATTTCATA
*
1084038 AATATTA
1 AAAATTA
1084045 TCATTTACGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTAAATATTTCATA
Found at i:1093700 original size:60 final size:59
Alignment explanation
Indices: 1093629--1093797 Score: 157
Period size: 60 Copynumber: 2.8 Consensus size: 59
1093619 ACGAACCTTG
*
1093629 TTCTAAATTAGTCCCTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTCTCA
1 TTCTAAATTAGTCCCTAAA-TTTTAAATATTTTAATTTCATCCCTAAACTATGACCCTCA
* * * * * *
1093689 TTCTAAATTAGTCCCTAAAATTTAAAAATTATGAA-TTCAT-CCTCAAATTGTGGCCCTCA
1 TTCTAAATTAGTCCCTAAATTTTAAATATT-TTAATTTCATCCCT-AAACTATGACCCTCA
* * * *
1093748 TTCTATATT-GATCCCCAAAATTTTTAATATTTTAATGTT-ATCCCCAAACT
1 TTCTAAATTAG-T-CCCTAAATTTTAAATATTTTAAT-TTCATCCCTAAACT
1093798 TTTGAATGAT
Statistics
Matches: 87, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
58 4 0.05
59 37 0.43
60 42 0.48
61 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (59 bp):
TTCTAAATTAGTCCCTAAATTTTAAATATTTTAATTTCATCCCTAAACTATGACCCTCA
Found at i:1093749 original size:59 final size:59
Alignment explanation
Indices: 1093629--1093770 Score: 146
Period size: 59 Copynumber: 2.4 Consensus size: 59
1093619 ACGAACCTTG
* * * *
1093629 TTCTAAATTAGTCCCTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTCTCA
1 TTCTAAATTAGTCCCTAAA-ATTTAAAAATTTGAATTTCATCCCTAAACTATGACCCTCA
* * *
1093689 TTCTAAATTAGTCCCTAAAATTTAAAAATTATGAA-TTCAT-CCTCAAATTGTGGCCCTCA
1 TTCTAAATTAGTCCCTAAAATTTAAAAATT-TGAATTTCATCCCT-AAACTATGACCCTCA
* *
1093748 TTCTATATT-GATCCCCAAAATTT
1 TTCTAAATTAG-TCCCTAAAATTT
1093771 TTAATATTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
58 4 0.06
59 44 0.63
60 22 0.31
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (59 bp):
TTCTAAATTAGTCCCTAAAATTTAAAAATTTGAATTTCATCCCTAAACTATGACCCTCA
Found at i:1093918 original size:60 final size:59
Alignment explanation
Indices: 1093848--1093992 Score: 152
Period size: 60 Copynumber: 2.4 Consensus size: 59
1093838 TTAGGAGACT
* * **
1093848 AATTTTGAATGAGGGTCATAGTTT-ATGGATGAATTTGGAAT-TTTCATAAGTTTAAGGACC
1 AATTTAGAATGAGGATCATAGTTTGA-GGATGAATTTAAAATATTT-A-AAGTTTAAGGACC
** * *
1093908 AATTTAGAATGAAAATCATAGTTTGAGGTTGAATTTAAAATATTTAAAGTTTAAGGACT
1 AATTTAGAATGAGGATCATAGTTTGAGGATGAATTTAAAATATTTAAAGTTTAAGGACC
*
1093967 AATTTA-AACTGAGGATCATAATTTGA
1 AATTTAGAA-TGAGGATCATAGTTTGA
1093993 AGACTATAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.03
59 32 0.45
60 33 0.46
61 4 0.06
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (59 bp):
AATTTAGAATGAGGATCATAGTTTGAGGATGAATTTAAAATATTTAAAGTTTAAGGACC
Found at i:1093985 original size:59 final size:60
Alignment explanation
Indices: 1093844--1093992 Score: 153
Period size: 59 Copynumber: 2.5 Consensus size: 60
1093834 AAAGTTAGGA
* * **
1093844 GACTAATTTTGAATGAGGGTCATAGTTT-ATGGATGAATTTGGAATTTTCATAAGTTTAAG
1 GACTAA-TTTAAATGAGGATCATAGTTTGATGGATGAATTTAAAATTTTCATAAGTTTAAG
* ** *
1093904 GACCAATTTAGAATGAAAATCATAGTTTGA-GGTTGAATTTAAAATATTT-A-AAGTTTAAG
1 GACTAATTTA-AATGAGGATCATAGTTTGATGGATGAATTTAAAAT-TTTCATAAGTTTAAG
*
1093963 GACTAATTTAAACTGAGGATCATAATTTGA
1 GACTAATTTAAA-TGAGGATCATAGTTTGA
1093993 AGACTATAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 9
0.78 0.13 0.10
Matches are distributed among these distances:
58 2 0.03
59 35 0.48
60 32 0.44
61 4 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (60 bp):
GACTAATTTAAATGAGGATCATAGTTTGATGGATGAATTTAAAATTTTCATAAGTTTAAG
Found at i:1107757 original size:15 final size:15
Alignment explanation
Indices: 1107737--1107766 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1107727 TTATTGTTGA
*
1107737 TTAAAAATAATATTT
1 TTAAAAAAAATATTT
1107752 TTAAAAAAAATATTT
1 TTAAAAAAAATATTT
1107767 AAAATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAAAAAAATATTT
Found at i:1113553 original size:18 final size:19
Alignment explanation
Indices: 1113530--1113573 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1113520 ACAGTAATCC
*
1113530 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
1113548 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
1113568 TATTCC
1 TATTCC
1113574 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:1113561 original size:20 final size:20
Alignment explanation
Indices: 1113536--1113573 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1113526 ATCCTATTCC
*
1113536 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
1113556 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
1113574 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:1113677 original size:30 final size:30
Alignment explanation
Indices: 1113641--1113709 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
1113631 GAATGAAATC
*
1113641 CACATTCCCCCGTTTTGTTAGCCCGGGAAT
1 CACATTCCCCCGTTTGGTTAGCCCGGGAAT
1113671 CACATTCCCCCGTTTGGTTAGCCCGGGAAT
1 CACATTCCCCCGTTTGGTTAGCCCGGGAAT
1113701 CACATTCCC
1 CACATTCCC
1113710 GGTAATGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.17, C:0.36, G:0.19, T:0.28
Consensus pattern (30 bp):
CACATTCCCCCGTTTGGTTAGCCCGGGAAT
Found at i:1114225 original size:15 final size:16
Alignment explanation
Indices: 1114205--1114237 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1114195 AAAATACAAC
1114205 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
*
1114220 ATTCCCTGGTAATCTT
1 ATTCCCTAGTAATCTT
1114236 AT
1 AT
1114238 ATTCCGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:1120936 original size:60 final size:60
Alignment explanation
Indices: 1120815--1120942 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
1120805 ATAGTCGGGT
* * ** **
1120815 GATCATTTTATAATTTTTAATAGTTGAGGGACTTAATAAAGTAATATTCTATGGTTAGAG
1 GATCATTTTATAACTTTTAATAGTTGAGGGACTTAATAAAATAATACCCTATGAATAGAG
* *
1120875 GATCATTTTATAACTTTTAATAGTTGAGGGACTTAATAAAATAATACCCTATTAATCGAG
1 GATCATTTTATAACTTTTAATAGTTGAGGGACTTAATAAAATAATACCCTATGAATAGAG
*
1120935 GACCATTT
1 GATCATTT
1120943 GTGTACTTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTTGAGGGACTTAATAAAATAATACCCTATGAATAGAG
Found at i:1121070 original size:37 final size:37
Alignment explanation
Indices: 1121005--1121081 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
1120995 TAGTTATTAA
**
1121005 TTTGATTTTATTTAATAAAAGACGAGTTTAACAAGAT
1 TTTGATTTTATTTAATAAAAGAAAAGTTTAACAAGAT
*
1121042 TTTGATTTTATTTAATAAATA-AAAAGTTTAGCAAGAT
1 TTTGATTTTATTTAATAAA-AGAAAAGTTTAACAAGAT
1121079 TTT
1 TTT
1121082 TTTAATGCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (37 bp):
TTTGATTTTATTTAATAAAAGAAAAGTTTAACAAGAT
Found at i:1124788 original size:15 final size:15
Alignment explanation
Indices: 1124770--1124799 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1124760 AAAACCATGT
1124770 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1124785 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1124800 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1124806 original size:15 final size:15
Alignment explanation
Indices: 1124773--1124807 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1124763 ACCATGTTAG
* *
1124773 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
1124788 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
1124803 ATAAA
1 ATAAA
1124808 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:1124874 original size:11 final size:11
Alignment explanation
Indices: 1124818--1124897 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
1124808 TAAATTAAAT
1124818 TAAAATAAAGA
1 TAAAATAAAGA
* *
1124829 GAAAA-CAA-A
1 TAAAATAAAGA
*
1124838 TTAAATAAAAGA
1 TAAAAT-AAAGA
*
1124850 TAAGATAAAG-
1 TAAAATAAAGA
1124860 -AAAATAAAGA
1 TAAAATAAAGA
1124870 TAAAATAGTAAG-
1 TAAAATA--AAGA
*
1124882 TAAAATAAATA
1 TAAAATAAAGA
1124893 TAAAA
1 TAAAA
1124898 AATAAAGAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
9 12 0.23
10 4 0.08
11 21 0.40
12 12 0.23
13 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.10, T:0.19
Consensus pattern (11 bp):
TAAAATAAAGA
Found at i:1124909 original size:23 final size:23
Alignment explanation
Indices: 1124854--1124908 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1124844 AAAAGATAAG
1124854 ATAAAGAAAATAAAGATAAAATA
1 ATAAAGAAAATAAAGATAAAATA
* *
1124877 GT-AAGTAAAATAAATATAAAA-A
1 ATAAAG-AAAATAAAGATAAAATA
1124899 ATAAAGAAAA
1 ATAAAGAAAA
1124909 AGAAGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (23 bp):
ATAAAGAAAATAAAGATAAAATA
Found at i:1124954 original size:5 final size:5
Alignment explanation
Indices: 1124801--1125000 Score: 50
Period size: 5 Copynumber: 40.6 Consensus size: 5
1124791 AAAAGGTAAG
* * * * *
1124801 AAAT- AAATA AATTA AATTA AAATA AAGAGA AAA-C AAATT AAATAA AAGATA
1 AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAAT-A AA-ATA
* * * *
1124852 AGAT- AAAGA AAATA AAGATA AAATA GTAAGTA AAAT- AAATA TAA-A
1 AAATA AAATA AAATA AA-ATA AAATA --AAATA AAATA AAATA AAATA
* * * * *
1124897 AAATA AAGA-A AAAGA AGA-A AAAGA AAA-A ATATA GAAATA AAA-C AAAT-
1 AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAATA
* * *
1124944 AAATA AAATA ATAAT- AAA-A AAGTAA AAATA ATATA TATATA AAAT-
1 AAATA AAATA A-AATA AAATA AAAT-A AAATA AAATA -AAATA AAATA
1124989 AAA-A AAATA AAA
1 AAATA AAATA AAA
1125001 AAAGTAAATA
Statistics
Matches: 148, Mismatches: 23, Indels: 49
0.67 0.10 0.22
Matches are distributed among these distances:
4 40 0.27
5 72 0.49
6 30 0.20
7 6 0.04
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1124972 original size:25 final size:24
Alignment explanation
Indices: 1124933--1125000 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
1124923 AAATATAGAA
* *
1124933 ATAAAACAAATAAATAAAATA-AT
1 ATAAAATAAAAAAATAAAATATAT
*
1124956 AATAAAA-AAGTAAAAATAATATATAT
1 -ATAAAATAA--AAAAATAAAATATAT
1124982 ATAAAATAAAAAAATAAAA
1 ATAAAATAAAAAAATAAAA
1125001 AAAGTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.05
24 15 0.41
25 16 0.43
26 4 0.11
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (24 bp):
ATAAAATAAAAAAATAAAATATAT
Found at i:1124986 original size:40 final size:41
Alignment explanation
Indices: 1124940--1125045 Score: 128
Period size: 39 Copynumber: 2.6 Consensus size: 41
1124930 GAAATAAAAC
1124940 AAATAAATAAAATAATAATAAAAAAGTAAAAATA-ATATAT
1 AAATAAATAAAATAATAATAAAAAAGTAAAAATATATATAT
* * *
1124980 ATATAAAATAAAAAAAT-A-AAAAAAGTAAATATATATATAT
1 AAAT-AAATAAAATAATAATAAAAAAGTAAAAATATATATAT
* *
1125020 AAATTAATAAAACTGATAATAAAAAA
1 AAATAAATAAAA-TAATAATAAAAAA
1125046 TAATATTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
39 21 0.39
40 15 0.28
41 12 0.22
42 6 0.11
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (41 bp):
AAATAAATAAAATAATAATAAAAAAGTAAAAATATATATAT
Found at i:1124992 original size:30 final size:31
Alignment explanation
Indices: 1124931--1125031 Score: 93
Period size: 30 Copynumber: 3.3 Consensus size: 31
1124921 AAAAATATAG
*
1124931 AAATAAAACAAA-TAAATAAAATAATAATAAAA
1 AAATAAAA-AAAGTAAAT-ATATAATAATAAAA
* *
1124963 AAGTAAAAATAA-TATATATATAA-AATAAAA
1 AAATAAAAA-AAGTAAATATATAATAATAAAA
*
1124993 AAATAAAAAAAGTAAATATAT-ATATATAAAT
1 AAATAAAAAAAGTAAATATATAATA-ATAAAA
*
1125024 TAATAAAA
1 AAATAAAA
1125032 CTGATAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
29 3 0.05
30 24 0.41
31 18 0.31
32 13 0.22
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (31 bp):
AAATAAAAAAAGTAAATATATAATAATAAAA
Found at i:1124994 original size:24 final size:22
Alignment explanation
Indices: 1124914--1124998 Score: 66
Period size: 25 Copynumber: 3.6 Consensus size: 22
1124904 GAAAAAGAAG
*
1124914 AAAAAGAAAAAAT-ATAGAA-AT
1 AAAAA-AAAAAATAATATAATAT
* *
1124935 AAAACAAATAAATAAAATAATAAT
1 AAAA-AAAAAAATAATATAAT-AT
1124959 AAAAAAGTAAAAATAATATATATAT
1 AAAAAA--AAAAATAATATA-ATAT
1124984 AAAATAAAAAAATAA
1 AAAA-AAAAAAATAA
1124999 AAAAAGTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
21 10 0.20
22 5 0.10
23 2 0.04
24 14 0.27
25 16 0.31
26 4 0.08
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (22 bp):
AAAAAAAAAAATAATATAATAT
Found at i:1125003 original size:9 final size:9
Alignment explanation
Indices: 1124882--1125008 Score: 53
Period size: 9 Copynumber: 13.4 Consensus size: 9
1124872 AAATAGTAAG
*
1124882 TAAAATAAA
1 TAAAAAAAA
*
1124891 TATAAAAAA
1 TAAAAAAAA
1124900 TAAAGAAAAA
1 TAAA-AAAAA
* *
1124910 GAAGAAAAA
1 TAAAAAAAA
* *
1124919 GAAAAAATA
1 TAAAAAAAA
1124928 TAGAAATAAAA
1 TA-AAA-AAAA
* *
1124939 -CAAATAAA
1 TAAAAAAAA
1124947 TAAAATAATAA
1 TAAAA-AA-AA
*
1124958 T-AAAAAAG
1 TAAAAAAAA
1124966 TAAAAATAATA
1 TAAAAA-AA-A
*
1124977 TATATATAAAA
1 TA-A-AAAAAA
1124988 T-AAAAAAA
1 TAAAAAAAA
*
1124996 TAAAAAAAG
1 TAAAAAAAA
1125005 TAAA
1 TAAA
1125009 TATATATATA
Statistics
Matches: 88, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
8 11 0.12
9 46 0.52
10 16 0.18
11 10 0.11
12 3 0.03
13 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.18
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1125014 original size:36 final size:40
Alignment explanation
Indices: 1124944--1125045 Score: 113
Period size: 36 Copynumber: 2.5 Consensus size: 40
1124934 TAAAACAAAT
*
1124944 AAATAAAATAATAATAAAAAAGTAAAAATAATATATATATA
1 AAATAAAAAAATAATAAAAAAGT-AAAATAATATATATATA
1124985 AAATAAAAAAAT-A-AAAAAAGT-AAAT-ATATATATATA
1 AAATAAAAAAATAATAAAAAAGTAAAATAATATATATATA
*
1125021 AATTAATAAAACTGATAATAAAAAA
1 AAATAA-AAAA---ATAATAAAAAA
1125046 TAATATTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
36 16 0.30
37 8 0.15
39 8 0.15
40 3 0.06
41 12 0.23
42 6 0.11
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (40 bp):
AAATAAAAAAATAATAAAAAAGTAAAATAATATATATATA
Found at i:1125051 original size:40 final size:34
Alignment explanation
Indices: 1124967--1125065 Score: 92
Period size: 40 Copynumber: 2.7 Consensus size: 34
1124957 ATAAAAAAGT
1124967 AAAAATAATATATATATA-AAATAAAAAAATAAA
1 AAAAATAATATATATATATAAATAAAAAAATAAA
*
1125000 AAAAGTAAATATATATATATAAATTAATAAAACTGATAATA
1 AAAAAT-AATATATATATATAAA-TAA-AAAA---ATAA-A
* * *
1125041 AAAAATAATATTTTTATATATATAA
1 AAAAATAATATATATATATAAATAA
1125066 TCTAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
33 5 0.09
34 12 0.23
35 3 0.06
36 3 0.06
37 4 0.08
39 3 0.06
40 17 0.32
41 6 0.11
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (34 bp):
AAAAATAATATATATATATAAATAAAAAAATAAA
Found at i:1125123 original size:24 final size:25
Alignment explanation
Indices: 1125056--1125127 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 25
1125046 TAATATTTTT
* *
1125056 ATATATATAATCTAAAAAAAATAAAA
1 ATATATAAAATGT-AAAAAAATAAAA
*
1125082 ATATATACTAAA-GT-AAAAAA-GAAA
1 ATATATA--AAATGTAAAAAAATAAAA
1125106 ATATATAAAATGTAAAAAAATA
1 ATATATAAAATGTAAAAAAATA
1125128 TTACATGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
22 3 0.08
23 2 0.05
24 16 0.43
25 6 0.16
26 7 0.19
27 1 0.03
28 2 0.05
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.25
Consensus pattern (25 bp):
ATATATAAAATGTAAAAAAATAAAA
Found at i:1125494 original size:34 final size:33
Alignment explanation
Indices: 1125398--1125518 Score: 121
Period size: 33 Copynumber: 3.7 Consensus size: 33
1125388 CTTGTGGATC
* *
1125398 CTATCTTTAGGAGTTTAAATCATAAAATTCTAT
1 CTATCTTTAGGAGTTTGAATCCTAAAATTCTAT
1125431 CCTA--TTT-----TTTGAATCCTAGCAAAATTCTAT
1 -CTATCTTTAGGAGTTTGAATCCT---AAAATTCTAT
1125461 CATATCTTTAGGAGTTTGAATCCTAAAATTCTAT
1 C-TATCTTTAGGAGTTTGAATCCTAAAATTCTAT
*
1125495 CTATTTTTAGGAGTTTGAATCCTA
1 CTATCTTTAGGAGTTTGAATCCTA
1125519 GTAGGACGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 23
0.74 0.03 0.23
Matches are distributed among these distances:
27 8 0.11
29 1 0.01
30 12 0.16
32 6 0.08
33 22 0.30
34 14 0.19
37 10 0.14
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (33 bp):
CTATCTTTAGGAGTTTGAATCCTAAAATTCTAT
Found at i:1131377 original size:33 final size:32
Alignment explanation
Indices: 1131340--1131404 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1131330 TAGTTTTTGA
1131340 ACACTTTTATCAAAAAAAATTTATAATATTTTT
1 ACACTTTTATC-AAAAAAATTTATAATATTTTT
* *
1131373 ACACTTTTATCAAAAATATTTATAATTTTTTT
1 ACACTTTTATCAAAAAAATTTATAATATTTTT
1131405 TGTTGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (32 bp):
ACACTTTTATCAAAAAAATTTATAATATTTTT
Found at i:1131405 original size:33 final size:33
Alignment explanation
Indices: 1131318--1131404 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 33
1131308 ATCTCTAAAT
* * **
1131318 AAAACATATTTATAGTTTTTGAACACTTTTATC
1 AAAAAATATTTATAATTTTTTTACACTTTTATC
* *
1131351 AAAAAAAATTTATAATATTTTTACACTTTTATC
1 AAAAAATATTTATAATTTTTTTACACTTTTATC
1131384 -AAAAATATTTATAATTTTTTT
1 AAAAAATATTTATAATTTTTTT
1131405 TGTTGTTATT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
32 19 0.41
33 27 0.59
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.48
Consensus pattern (33 bp):
AAAAAATATTTATAATTTTTTTACACTTTTATC
Found at i:1134956 original size:17 final size:17
Alignment explanation
Indices: 1134929--1134967 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1134919 AATTTACAAT
1134929 TAATT-TAAATAATATA
1 TAATTATAAATAATATA
*
1134945 TAATTATAAATAATATC
1 TAATTATAAATAATATA
1134962 TAATTA
1 TAATTA
1134968 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATA
Found at i:1136187 original size:31 final size:31
Alignment explanation
Indices: 1136152--1136218 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1136142 TTAATGCATT
1136152 TCTCAAGTCCAAATTCTTTTACGTTAATAAA
1 TCTCAAGTCCAAATTCTTTTACGTTAATAAA
*
1136183 TCTCAAGTCTAAATTCTTTTACGTTAATAAA
1 TCTCAAGTCCAAATTCTTTTACGTTAATAAA
1136214 TCTCA
1 TCTCA
1136219 CGTTTGCGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (31 bp):
TCTCAAGTCCAAATTCTTTTACGTTAATAAA
Found at i:1136286 original size:24 final size:24
Alignment explanation
Indices: 1136241--1136287 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1136231 ATGAGATCAG
* **
1136241 ACAAATTTCACTATATGTTACAAA
1 ACAAATTTCACTAAATACTACAAA
*
1136265 ACAACTTTCACTAAATACTACAA
1 ACAAATTTCACTAAATACTACAA
1136288 CAAATATCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (24 bp):
ACAAATTTCACTAAATACTACAAA
Found at i:1137651 original size:15 final size:15
Alignment explanation
Indices: 1137631--1137659 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1137621 TTTTAGAAGA
1137631 AAATTCATTTAAATT
1 AAATTCATTTAAATT
1137646 AAATTCATTTAAAT
1 AAATTCATTTAAAT
1137660 AAAGTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTCATTTAAATT
Found at i:1142090 original size:14 final size:14
Alignment explanation
Indices: 1142071--1142109 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
1142061 CTGTTCATCT
*
1142071 TCATCATTATTAAA
1 TCATCATTAATAAA
1142085 TCATCATTAATAAA
1 TCATCATTAATAAA
1142099 TCATCATTAAT
1 TCATCATTAAT
1142110 GTTAAAAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
TCATCATTAATAAA
Found at i:1143299 original size:11 final size:11
Alignment explanation
Indices: 1143283--1143311 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1143273 CACTTTTAAT
1143283 TATTTTTATTG
1 TATTTTTATTG
1143294 TATTTTTATTG
1 TATTTTTATTG
1143305 -ATTTTTA
1 TATTTTTA
1143312 AATATTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (11 bp):
TATTTTTATTG
Done.