Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 51
Found at i:3013726 original size:27 final size:27
Alignment explanation
Indices: 3013637--3013726 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 27
3013627 TCTTTACTAA
* *
3013637 AATATTATTTAAATATATAAATAATAT
1 AATATTATTAAAATATAAAAATAATAT
*
3013664 ATTCATTATTAAATATATAAAAA-AATTATT
1 AAT-ATTATTAAA-ATATAAAAATAA-TA-T
3013694 ATATATTATTAAAATA-AAAATATAATAT
1 A-ATATTATTAAAATATAAAA-ATAATAT
3013722 AATAT
1 AATAT
3013727 CTTATATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
27 6 0.12
28 16 0.31
29 16 0.31
30 13 0.25
31 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
AATATTATTAAAATATAAAAATAATAT
Found at i:3013759 original size:28 final size:28
Alignment explanation
Indices: 3013714--3013797 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
3013704 AAAATAAAAA
*
3013714 TATAATATAATATCTTATATTATAT-TAT
1 TATAATATAAT-TATTATATTATATATAT
*
3013742 TATAATATAATTGATTATTTTATATAATAT
1 TATAATATAATT-ATTATATTATAT-ATAT
*
3013772 TAAAAATATAA-TATTATATTAT-TATA
1 T-ATAATATAATTATTATATTATATATA
3013798 AATATTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
27 4 0.08
28 22 0.46
29 9 0.19
30 5 0.10
31 8 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
TATAATATAATTATTATATTATATATAT
Found at i:3013789 original size:22 final size:23
Alignment explanation
Indices: 3013764--3013807 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3013754 GATTATTTTA
3013764 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
3013786 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
3013808 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:3013804 original size:12 final size:12
Alignment explanation
Indices: 3013787--3013839 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
3013777 ATATAATATT
3013787 ATATTATTATAA
1 ATATTATTATAA
3013799 ATATTA--ATAA
1 ATATTATTATAA
*
3013809 ATA-TATTTTAA
1 ATATTATTATAA
3013820 ATATT-TTAATAA
1 ATATTATT-ATAA
*
3013832 ATAATATT
1 ATATTATT
3013840 TTGATGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.06
10 7 0.21
11 8 0.24
12 14 0.42
13 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTATTATAA
Found at i:3013812 original size:22 final size:21
Alignment explanation
Indices: 3013768--3013839 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 21
3013758 ATTTTATATA
* *
3013768 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATA-AAT
3013789 ATTATTATAAATATTAATAAAT
1 A-TATTATAAATATTAATAAAT
*
3013811 ATATTTTAAATATTTTAATAAAT
1 ATATTATAAATA--TTAATAAAT
3013834 AATATT
1 -ATATT
3013840 TTGATGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 11 0.26
22 13 0.30
23 14 0.33
24 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTATAAATATTAATAAAT
Found at i:3013820 original size:21 final size:23
Alignment explanation
Indices: 3013791--3013841 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
3013781 AATATTATAT
*
3013791 TATTATAAATA-TTAATAAAT-A
1 TATTTTAAATATTTAATAAATAA
3013812 TATTTTAAATATTTTAATAAATAA
1 TATTTTAAATA-TTTAATAAATAA
3013836 TATTTT
1 TATTTT
3013842 GATGAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.38
23 9 0.35
24 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAAATATTTAATAAATAA
Found at i:3013825 original size:64 final size:64
Alignment explanation
Indices: 3013614--3013831 Score: 150
Period size: 64 Copynumber: 3.4 Consensus size: 64
3013604 AAAATATTAG
* *
3013614 TATATTTTAAATATCTTTACTAAAATATTATTTAAATATATAAATAATATATTCATTATTAAATA
1 TATATTTTAAATAT-TTTA-TATAATATTA---AAA-ATAT-AATATTATATT-ATTA-TAAATA
3013679 TATAA-AAA
57 T-TAATAAA
* * * * * *
3013687 -A-ATTATT--ATATATTAT-TAA-AATAAAAATATAATATAATA-TCTTATATTATATTATTAT
1 TATATT-TTAAATATTTTATATAATATTAAAAATATAATATTATATTATTATA-AATATTAATA-
3013745 AA
63 AA
* * *
3013747 TATA-ATTGATTATTTTATATAATATTAAAAATATAATATTATATTATTATAAATATTAATAAA
1 TATATTTTAAATATTTTATATAATATTAAAAATATAATATTATATTATTATAAATATTAATAAA
3013810 TATATTTTAAATATTTTA-ATAA
1 TATATTTTAAATATTTTATATAA
3013832 ATAATATTTT
Statistics
Matches: 114, Mismatches: 19, Indels: 34
0.68 0.11 0.20
Matches are distributed among these distances:
58 4 0.04
59 8 0.07
60 5 0.04
61 8 0.07
62 12 0.11
63 16 0.14
64 36 0.32
65 6 0.05
66 3 0.03
67 2 0.02
68 1 0.01
69 3 0.03
70 4 0.04
71 3 0.03
72 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.47
Consensus pattern (64 bp):
TATATTTTAAATATTTTATATAATATTAAAAATATAATATTATATTATTATAAATATTAATAAA
Found at i:3014072 original size:74 final size:75
Alignment explanation
Indices: 3013942--3014102 Score: 279
Period size: 74 Copynumber: 2.2 Consensus size: 75
3013932 AAATGACTTA
3013942 CGGAAAATGAATCCGTAAGTCATTTTACAAAAAAACACAAAGGAAATTCTGTTACTAGGAAAATG
1 CGGAAAATGAATCCGTAAGTCATTTTACAAAAAAACACAAAGGAAATTCTGTTACTAGGAAAATG
3014007 AATTACATTC
66 AATTACATTC
* * *
3014017 CGGAAAATGAATCTGTAAGTCATTTTA-TAGAAAACACAAAGGAAATTCTGTTACTAGGAAAATG
1 CGGAAAATGAATCCGTAAGTCATTTTACAAAAAAACACAAAGGAAATTCTGTTACTAGGAAAATG
3014081 AATTACATTC
66 AATTACATTC
*
3014091 CGGAAAACGAAT
1 CGGAAAATGAAT
3014103 TACGTGAAAC
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
74 56 0.68
75 26 0.32
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (75 bp):
CGGAAAATGAATCCGTAAGTCATTTTACAAAAAAACACAAAGGAAATTCTGTTACTAGGAAAATG
AATTACATTC
Found at i:3014677 original size:21 final size:21
Alignment explanation
Indices: 3014651--3014693 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3014641 TTTGTGTCAG
*
3014651 AATCGGAGGAGAAGAGGAAGA
1 AATCGGAAGAGAAGAGGAAGA
3014672 AATCGGAAGAGAAGAGGAAGA
1 AATCGGAAGAGAAGAGGAAGA
3014693 A
1 A
3014694 CGAAGGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.40, T:0.05
Consensus pattern (21 bp):
AATCGGAAGAGAAGAGGAAGA
Found at i:3022241 original size:4 final size:4
Alignment explanation
Indices: 3022234--3022258 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3022224 CTCTCTCTCT
3022234 CTCC CTCC CTCC CTCC CTCC CTCC C
1 CTCC CTCC CTCC CTCC CTCC CTCC C
3022259 ATTCTGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CTCC
Found at i:3026144 original size:18 final size:18
Alignment explanation
Indices: 3026102--3026145 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3026092 AATTAAATCT
*
3026102 TAAAAAATTATAAAAAAC
1 TAAAAATTTATAAAAAAC
*
3026120 TATAAATTTATAAAAATA-
1 TAAAAATTTATAAAAA-AC
3026138 TAAAAATT
1 TAAAAATT
3026146 AGTAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATTTATAAAAAAC
Found at i:3035277 original size:23 final size:23
Alignment explanation
Indices: 3035246--3035299 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
3035236 ATTCATGTAT
*
3035246 GTTTTTCTGCAGAAAAAACATCA
1 GTTTCTCTGCAGAAAAAACATCA
3035269 GTTTCTCTGCAGAAAAAACATCA
1 GTTTCTCTGCAGAAAAAACATCA
3035292 GTTTCTCT
1 GTTTCTCT
3035300 CCTCCAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
GTTTCTCTGCAGAAAAAACATCA
Found at i:3038366 original size:24 final size:25
Alignment explanation
Indices: 3038319--3038385 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 25
3038309 ATTTGAAATA
*
3038319 TGTTCTGATTTCTTAT-TCGAATTC
1 TGTTCTGATTTCTGATATCGAATTC
*
3038343 TGTTCTGATTTCTGATAT-GGATTC
1 TGTTCTGATTTCTGATATCGAATTC
* * *
3038367 TGTTTTGATATATGATATC
1 TGTTCTGATTTCTGATATC
3038386 TGATATATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.52
Consensus pattern (25 bp):
TGTTCTGATTTCTGATATCGAATTC
Found at i:3038379 original size:19 final size:20
Alignment explanation
Indices: 3038355--3038413 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
3038345 TTCTGATTTC
3038355 TGATATGGATTCTGTTTTGA
1 TGATATGGATTCTGTTTTGA
* *
3038375 T-ATAT-GATATCTGATAT-A
1 TGATATGGAT-TCTGTTTTGA
*
3038393 TGATATGAATTCTGTTTTGA
1 TGATATGGATTCTGTTTTGA
3038413 T
1 T
3038414 TTTTGATATC
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
18 5 0.17
19 20 0.67
20 5 0.17
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.49
Consensus pattern (20 bp):
TGATATGGATTCTGTTTTGA
Found at i:3038391 original size:14 final size:14
Alignment explanation
Indices: 3038372--3038398 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3038362 GATTCTGTTT
3038372 TGATATATGATATC
1 TGATATATGATATC
3038386 TGATATATGATAT
1 TGATATATGATAT
3038399 GAATTCTGTT
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:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TGATATATGATATC
Found at i:3038397 original size:38 final size:38
Alignment explanation
Indices: 3038346--3038424 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
3038336 CGAATTCTGT
* * *
3038346 TCTGATTTCTGATATGGATTCTGTTTTGATATATGATA
1 TCTGATATATGATATGAATTCTGTTTTGATATATGATA
* *
3038384 TCTGATATATGATATGAATTCTGTTTTGATTTTTGATA
1 TCTGATATATGATATGAATTCTGTTTTGATATATGATA
3038422 TCT
1 TCT
3038425 CCATTTATTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (38 bp):
TCTGATATATGATATGAATTCTGTTTTGATATATGATA
Found at i:3045773 original size:32 final size:31
Alignment explanation
Indices: 3045705--3045785 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
3045695 TGTGACTCTT
* *
3045705 AGGTAGGCTTTGCGTCCCTGAGATCATTCTC
1 AGGTAGGCCTTGCGGCCCTGAGATCATTCTC
* * **
3045736 GGGTAGGCCTTGCGGCCTTGAGATGTGTTCTC
1 AGGTAGGCCTTGCGGCCCTGAGAT-CATTCTC
* *
3045768 AGGTAGGCCCTGTGGCCC
1 AGGTAGGCCTTGCGGCCC
3045786 CAAAAACTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 20 0.51
32 19 0.49
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.28
Consensus pattern (31 bp):
AGGTAGGCCTTGCGGCCCTGAGATCATTCTC
Found at i:3048187 original size:16 final size:16
Alignment explanation
Indices: 3048166--3048205 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3048156 GGCCTTATAA
3048166 ATAATAATATTA-ATAT
1 ATAATAATATTATAT-T
*
3048182 ATAATATTATTATATT
1 ATAATAATATTATATT
3048198 ATAATAAT
1 ATAATAAT
3048206 GTATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATAATATTATATT
Found at i:3050327 original size:30 final size:27
Alignment explanation
Indices: 3050263--3050327 Score: 67
Period size: 30 Copynumber: 2.3 Consensus size: 27
3050253 ATAAATACTC
*
3050263 AAAATATTATTATTTTATACATTTAATA
1 AAAATA-TATTATTTTAAACATTTAATA
**
3050291 TTAATATATTATTTTAGAATCATTTTAATA
1 AAAATATATTATTTTA-AA-CA-TTTAATA
3050321 AAAATAT
1 AAAATAT
3050328 TAATTATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 10 0.34
28 5 0.17
29 2 0.07
30 12 0.41
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAATATATTATTTTAAACATTTAATA
Found at i:3050438 original size:21 final size:23
Alignment explanation
Indices: 3050380--3050441 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 23
3050370 ATTATATTAT
*
3050380 TTTAATGTTAGATAATATGTTCAA
1 TTTAATTTTA-ATAATATGTTCAA
3050404 -TTATATTATT-ATAATAT-TT-AA
1 TTTA-ATT-TTAATAATATGTTCAA
3050425 TTTAATTTTAATAATAT
1 TTTAATTTTAATAATAT
3050442 ACAATAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
20 2 0.06
21 12 0.36
22 5 0.15
23 10 0.30
24 2 0.06
25 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTAATTTTAATAATATGTTCAA
Found at i:3050599 original size:22 final size:22
Alignment explanation
Indices: 3050556--3050657 Score: 73
Period size: 22 Copynumber: 4.5 Consensus size: 22
3050546 TATAATATTT
* *
3050556 TTATTTTAATATGATAATATTATTA
1 TTATTTTAATAAG-T-A-ATTAATA
3050581 TTATTTTAATAAGTAATTAATA
1 TTATTTTAATAAGTAATTAATA
* * * * *
3050603 -TA-ATTAATAATTTATTAGTC
1 TTATTTTAATAAGTAATTAATA
*
3050623 TTATTTTAATAAATAATTAATA
1 TTATTTTAATAAGTAATTAATA
*
3050645 TAATTTGTAATAA
1 TTATTT-TAATAA
3050658 TTTTATTTTA
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
20 13 0.21
21 4 0.07
22 24 0.39
23 7 0.11
24 1 0.02
25 12 0.20
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (22 bp):
TTATTTTAATAAGTAATTAATA
Found at i:3050608 original size:25 final size:25
Alignment explanation
Indices: 3050539--3050608 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
3050529 TTTAGAATAA
* **
3050539 AATAAAAT-ATAATATTTTTATTTT
1 AATAAGATAATAATATAATTATTTT
* * *
3050563 AATATGATAATATTATTATTATTTT
1 AATAAGATAATAATATAATTATTTT
3050588 AATAAG-TAATTAATATAATTA
1 AATAAGATAA-TAATATAATTA
3050609 ATAATTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 9 0.24
25 28 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
AATAAGATAATAATATAATTATTTT
Found at i:3050756 original size:14 final size:14
Alignment explanation
Indices: 3050713--3050767 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
3050703 AACTGTAGAC
*
3050713 ATAATATTTTAAT-A
1 ATAATA-TTAAATAA
3050727 ATAATATTAACATAA
1 ATAATATTAA-ATAA
3050742 ATAATATTAAATAA
1 ATAATATTAAATAA
*
3050756 ATTAT-TTAAATA
1 ATAATATTAAATA
3050768 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 10 0.27
14 16 0.43
15 11 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATATTAAATAA
Found at i:3050764 original size:28 final size:29
Alignment explanation
Indices: 3050733--3050806 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
3050723 AATAATAATA
3050733 TTAACATAAATAATATTAAATAA-ATTA-T
1 TTAA-ATAAATAATATTAAATAATATTATT
** *
3050761 TTAAATATTTTAAAATT-AATAATATTATT
1 TTAAATA-AATAATATTAAATAATATTATT
*
3050790 TTTAATAAATAATATTA
1 TTAAATAAATAATATTA
3050807 TTTATTATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
27 8 0.23
28 20 0.57
29 7 0.20
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAAATAAATAATATTAAATAATATTATT
Found at i:3050808 original size:22 final size:21
Alignment explanation
Indices: 3050768--3050808 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3050758 TATTTAAATA
*
3050768 TTTTAAAATTAATAATATTAT
1 TTTTAAAAATAATAATATTAT
*
3050789 TTTTAATAAATAATATTATT
1 TTTTAA-AAATAATAATATT
3050809 TATTATATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTAAAAATAATAATATTAT
Found at i:3052112 original size:2 final size:2
Alignment explanation
Indices: 3052107--3052132 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3052097 TTTTTGTTTC
3052107 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
3052133 AAGTTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3054910 original size:171 final size:174
Alignment explanation
Indices: 3054624--3054972 Score: 668
Period size: 171 Copynumber: 2.0 Consensus size: 174
3054614 TTTAATATAA
3054624 AATTTTTAAATTTTATATTTTTTAGAATCATTTAATGAATGAAATAATCTACCGAGATTATCTTT
1 AATTTTTAAATTTTATATTTTTTAGAATCATTTAATGAATGAAATAATCTACCGAGATTATCTTT
3054689 TTATTTATTTTTTTTGAATATCTTCTCATTTTTCACTGTTAATTTTAACCGTTATTTTTGTTAAT
66 TTATTTATTTTTTTTGAATATCTTCTCATTTTTCACTGTTAATTTTAACCGTTATTTTTGTTAAT
3054754 CCAAAATTTCTAAAAGATATAAACTT-AAAAAA-ACACGACGTG
131 CCAAAATTTCTAAAAGATATAAACTTAAAAAAATACACGACGTG
3054796 AATTTTTAAATTTTATA-TTTTTAGAATCATTTAATGAATGAAATAATCTACCGAGATTATCTTT
1 AATTTTTAAATTTTATATTTTTTAGAATCATTTAATGAATGAAATAATCTACCGAGATTATCTTT
3054860 TTATTTATTTTTTTTGAATATCTTCTCATTTTTCACTGTTAATTTTAACCGTTATTTTTGTTAAT
66 TTATTTATTTTTTTTGAATATCTTCTCATTTTTCACTGTTAATTTTAACCGTTATTTTTGTTAAT
3054925 CCAAAATTTCTAAAAGATATAAACTTAAAAAAATTACACGACGTG
131 CCAAAATTTCTAAAAGATATAAACTTAAAAAAA-TACACGACGTG
3054970 AAT
1 AAT
3054973 GGATCTTACC
Statistics
Matches: 174, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
171 138 0.79
172 23 0.13
174 13 0.07
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (174 bp):
AATTTTTAAATTTTATATTTTTTAGAATCATTTAATGAATGAAATAATCTACCGAGATTATCTTT
TTATTTATTTTTTTTGAATATCTTCTCATTTTTCACTGTTAATTTTAACCGTTATTTTTGTTAAT
CCAAAATTTCTAAAAGATATAAACTTAAAAAAATACACGACGTG
Found at i:3055408 original size:7 final size:7
Alignment explanation
Indices: 3055393--3055423 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3055383 CCCCCTTCTC
3055393 TCCCCCT
1 TCCCCCT
*
3055400 TCTCCCT
1 TCCCCCT
3055407 TCCCCCT
1 TCCCCCT
3055414 TCCCCCT
1 TCCCCCT
3055421 TCC
1 TCC
3055424 ATAGTCATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (7 bp):
TCCCCCT
Found at i:3055412 original size:14 final size:14
Alignment explanation
Indices: 3055382--3055423 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
3055372 TCATGTCACA
3055382 TCCCCCTTCT--C-
1 TCCCCCTTCTCCCT
3055393 TCCCCCTTCTCCCT
1 TCCCCCTTCTCCCT
*
3055407 TCCCCCTTCCCCCT
1 TCCCCCTTCTCCCT
3055421 TCC
1 TCC
3055424 ATAGTCATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.37
13 1 0.04
14 16 0.59
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (14 bp):
TCCCCCTTCTCCCT
Found at i:3056620 original size:32 final size:31
Alignment explanation
Indices: 3056583--3056678 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 31
3056573 TTTAGGGACC
*
3056583 AATTTAGAATGAATGTCATAGTTTGGGGATGG
1 AATTTAGAATG-ATGTCATAGTTTGGGGATGA
* * *
3056615 AATTTA-AATG-T-TCAAAAGTTTGAGGAT-T
1 AATTTAGAATGATGTC-ATAGTTTGGGGATGA
* *
3056643 AATTTAGAATGATAGTCATAATTTAGGGATGA
1 AATTTAGAATGAT-GTCATAGTTTGGGGATGA
3056675 AATT
1 AATT
3056679 AAAACATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
28 8 0.16
29 16 0.32
30 1 0.02
31 13 0.26
32 12 0.24
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (31 bp):
AATTTAGAATGATGTCATAGTTTGGGGATGA
Found at i:3056647 original size:60 final size:61
Alignment explanation
Indices: 3056547--3056678 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 61
3056537 TGTATAGCTT
** * *
3056547 GGGATGAAATTGGAATGTTCAAAAAGTTTAGGGACCAATTTAGAATGA-ATGTCATAGTTTG
1 GGGATGAAATTTAAATGTTCAAAAAGTTTAGGGACCAATTTAGAATGATA-GTCATAATTTA
* **
3056608 GGGATGGAATTTAAATGTTC-AAAAGTTT-GAGGATTAATTTAGAATGATAGTCATAATTTA
1 GGGATGAAATTTAAATGTTCAAAAAGTTTAG-GGACCAATTTAGAATGATAGTCATAATTTA
3056668 GGGATGAAATT
1 GGGATGAAATT
3056679 AAAACATTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 42 0.69
61 18 0.30
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (61 bp):
GGGATGAAATTTAAATGTTCAAAAAGTTTAGGGACCAATTTAGAATGATAGTCATAATTTA
Found at i:3056714 original size:60 final size:61
Alignment explanation
Indices: 3056568--3056715 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 61
3056558 GGAATGTTCA
* * * * * * **
3056568 AAAAGTTTAGGGACCAATTTAGAATGA-ATGTCATAGTTTGGGGATGGAATTTAAATGTTC
1 AAAAGTTTAGAGATCAATTTAGAATGATATGTCATAATTTAGGGATGAAATTAAAACATTC
* *
3056628 AAAAGTTT-GAGGATTAATTTAGAATGATA-GTCATAATTTAGGGATGAAATTAAAACATTT
1 AAAAGTTTAGA-GATCAATTTAGAATGATATGTCATAATTTAGGGATGAAATTAAAACATTC
* *
3056688 AAAAGTTTAGAGATCAATTCAAAATGAT
1 AAAAGTTTAGAGATCAATTTAGAATGAT
3056716 GATCATTACT
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 1 0.01
60 68 0.94
61 3 0.04
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.33
Consensus pattern (61 bp):
AAAAGTTTAGAGATCAATTTAGAATGATATGTCATAATTTAGGGATGAAATTAAAACATTC
Found at i:3060167 original size:3 final size:3
Alignment explanation
Indices: 3060159--3060227 Score: 84
Period size: 3 Copynumber: 21.3 Consensus size: 3
3060149 TTTTTTAATA
*
3060159 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT T-AT
3060206 TAAT TAAT TAAT TAT TAT TAT T
1 T-AT T-AT T-AT TAT TAT TAT T
3060228 TACATTACAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 44 0.70
4 19 0.30
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3061920 original size:2 final size:2
Alignment explanation
Indices: 3061908--3061939 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3061898 ATTCCCATGA
*
3061908 AT AT GT 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
3061940 TAATCTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3064850 original size:227 final size:227
Alignment explanation
Indices: 3064449--3064904 Score: 862
Period size: 227 Copynumber: 2.0 Consensus size: 227
3064439 TTTTTCTTTG
*
3064449 TATACTTAATAAATATTTTGTTGATTGAACTTATGTCGTTTTCTAAGGTTATGAGCAATTAATAA
1 TATACTTAATAAATATTTTGTTGATTGAACTTATGTCGTTTTCTAAGGTTATGAGCAATAAATAA
3064514 AGTTTTAATCTTATAGTTCTTTGAATATTGAATGAATTAAAGGTTCTTTTACTACTTCATTAATT
66 AGTTTTAATCTTATAGTTCTTTGAATATTGAATGAATTAAAGGTTCTTTTACTACTTCATTAATT
3064579 ATATCTTTGACAAGGGGCAATATTAGACCTTCCATACCCCCCACCCAAAACCGAAATAACTA-TG
131 ATATCTTTGACAAGGGGCAATATTAGACCTTCCATA-CCCCCACCCAAAACCGAAATAACTATTG
3064643 GTGGATTTCTTACCCGAAATAACACATATTTAC
195 GTGGATTTCTTACCCGAAATAACACATATTTAC
3064676 TATACTTAATAAATATTTTGTTGATTGAACTTATGTCGTTTTCTAAGGTTATGAGCAATAAATAA
1 TATACTTAATAAATATTTTGTTGATTGAACTTATGTCGTTTTCTAAGGTTATGAGCAATAAATAA
3064741 AGTTTTAATCTTATAGTTCTTTGAATATTGAATGAATTAAAGGTTCTTTTACTACTTCATTAATT
66 AGTTTTAATCTTATAGTTCTTTGAATATTGAATGAATTAAAGGTTCTTTTACTACTTCATTAA-T
3064806 ATATATCTTTGACAAGGGGCAATATTAGACCTTCCATA-CCCCACCCAAAACCGAAATAACTATT
130 -TATATCTTTGACAAGGGGCAATATTAGACCTTCCATACCCCCACCCAAAACCGAAATAACTATT
3064870 GGTGGATTTCTTACCCGAAATAACACATATTTAC
194 GGTGGATTTCTTACCCGAAATAACACATATTTAC
3064904 T
1 T
3064905 CCCAAAAGAC
Statistics
Matches: 225, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
227 151 0.67
228 37 0.16
229 37 0.16
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (227 bp):
TATACTTAATAAATATTTTGTTGATTGAACTTATGTCGTTTTCTAAGGTTATGAGCAATAAATAA
AGTTTTAATCTTATAGTTCTTTGAATATTGAATGAATTAAAGGTTCTTTTACTACTTCATTAATT
ATATCTTTGACAAGGGGCAATATTAGACCTTCCATACCCCCACCCAAAACCGAAATAACTATTGG
TGGATTTCTTACCCGAAATAACACATATTTAC
Found at i:3068006 original size:55 final size:55
Alignment explanation
Indices: 3067897--3068006 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 55
3067887 ATAAACTTTC
* * * ** * *
3067897 AAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTTTTTAAATGATTTTTTT
1 AAAGAAGCTAAGCCTGAATTTTAGAGGTTTCTTGATAATTGTAAATGATCTTTTT
*
3067952 AAAGAAGCTGAGCCT-AATTTTAGAGGTTTCTTGATAATTGTAAATGAATCTTTTT
1 AAAGAAGCTAAGCCTGAATTTTAGAGGTTTCTTGATAATTGTAAATG-ATCTTTTT
3068007 GAATTTTCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 26 0.57
55 20 0.43
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (55 bp):
AAAGAAGCTAAGCCTGAATTTTAGAGGTTTCTTGATAATTGTAAATGATCTTTTT
Found at i:3069013 original size:140 final size:134
Alignment explanation
Indices: 3068710--3069063 Score: 403
Period size: 140 Copynumber: 2.6 Consensus size: 134
3068700 GATGCACGAG
* * * * *
3068710 TCAACATTTCCAATGGAGAGTTCATAATGAGAAAAACTAATCCGATG-AGGGAGAAGAAGTTCAT
1 TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTAATCCGAAGAAAGGA-AAGAAGTTCAT
* * ** * **
3068774 AATGATAAGAACTTGTTCAACCTTAACTCGATTCACGGTATTTCGAATTAGTGACACCTCACTCG
65 AATGAGAAGAACTTTTTCAACCTTAACTCGATTCACCATATTTCGAATCAGCAACACCTCACTCG
3068839 AGGGA
130 AGGGA
* *
3068844 TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTTATCCGAAGAAAGGATAAAAAGTTCAT
1 TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTAATCCGAAGAAAGGA-AAGAAGTTCAT
3068909 AATGAGAAGAACTTTTTCAACCTT-ACATCGATTCATCACATATGGAGTT-GAATCAGCAACACC
65 AATGAGAAGAACTTTTTCAACCTTAAC-TCGATTCA-C-CATAT----TTCGAATCAGCAACACC
3068972 TCACTCGAGGGA
123 TCACTCGAGGGA
* * * *
3068984 TCAACCTTTAC-AGTGGAGAGTTTATAATGAGAAGAACTCATCCGATA-AGAGAGAAAGAAGTTC
1 TCAACATTT-CTAGTGGAGAGTTCATAATGAGAAGAACTAATCCGA-AGAAAG-GAAAGAAGTTC
3069047 ATAATGAGAAGAACTTT
63 ATAATGAGAAGAACTTT
3069064 AGCTTGTTTC
Statistics
Matches: 189, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
134 44 0.23
135 44 0.23
136 1 0.01
137 3 0.02
140 91 0.48
141 6 0.03
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (134 bp):
TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTAATCCGAAGAAAGGAAAGAAGTTCATA
ATGAGAAGAACTTTTTCAACCTTAACTCGATTCACCATATTTCGAATCAGCAACACCTCACTCGA
GGGA
Found at i:3069124 original size:41 final size:42
Alignment explanation
Indices: 3069079--3069175 Score: 126
Period size: 41 Copynumber: 2.3 Consensus size: 42
3069069 GTTTCCATTG
* *
3069079 CATAAGGAGTTGGAACAACACCGA-CATTT-GTTATTCCATCA
1 CATAAGGAGTTGGAACAACACC-ATCATTTCGCTAGTCCATCA
* * *
3069120 CATAAGGAGTTTGATCAACATCATCATTTCGCTAGTCCATCA
1 CATAAGGAGTTGGAACAACACCATCATTTCGCTAGTCCATCA
3069162 CATAAGGAGTTGGA
1 CATAAGGAGTTGGA
3069176 TTAGAATCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.02
41 24 0.50
42 23 0.48
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (42 bp):
CATAAGGAGTTGGAACAACACCATCATTTCGCTAGTCCATCA
Found at i:3069384 original size:3 final size:3
Alignment explanation
Indices: 3069376--3069410 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
3069366 TTTTCTAATA
3069376 TAT TAT TAT TAT TAT TAT TAT TAAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T
3069411 TACATTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3071076 original size:2 final size:2
Alignment explanation
Indices: 3071069--3071108 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3071059 AGTCCCATGA
*
3071069 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3071109 CGTTTTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3073008 original size:14 final size:17
Alignment explanation
Indices: 3072989--3073025 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
3072979 AGGAATTTTG
3072989 GGGATTT-A-AATTT-A
1 GGGATTTAAGAATTTAA
3073003 GGGATTTAAGAATTTAA
1 GGGATTTAAGAATTTAA
3073020 GGGATT
1 GGGATT
3073026 GATAACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 1 0.05
16 5 0.25
17 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (17 bp):
GGGATTTAAGAATTTAA
Found at i:3076352 original size:28 final size:28
Alignment explanation
Indices: 3076320--3076381 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
3076310 TATTTGAAGC
3076320 GTTTATTTTCTCTAGTATATGATATAGT
1 GTTTATTTTCTCTAGTATATGATATAGT
3076348 GTTTATTTTCTCTAGTATATGATATAGT
1 GTTTATTTTCTCTAGTATATGATATAGT
3076376 GTTTAT
1 GTTTAT
3076382 GTAGCCGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (28 bp):
GTTTATTTTCTCTAGTATATGATATAGT
Found at i:3078490 original size:69 final size:69
Alignment explanation
Indices: 3078379--3078516 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
3078369 CTAAACTTGG
3078379 GTTCACTAGCTCGGGTTTAGGACTTATTCGTGGTGGCCTGAGCGAGAATGACCACCACTAAATGA
1 GTTCACTAGCTCGGGTTTAGGACTTATTCGTGGTGGCCTGAGCGAGAATGACCACCACTAAATGA
3078444 TGGC
66 TGGC
3078448 GTTCACTAGCTCGGGTTTAGGACTTATTCGTGGTGGCCTGAGCGAGAATGACCACCACTAAATGA
1 GTTCACTAGCTCGGGTTTAGGACTTATTCGTGGTGGCCTGAGCGAGAATGACCACCACTAAATGA
3078513 TGGC
66 TGGC
3078517 CTGCCGATGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (69 bp):
GTTCACTAGCTCGGGTTTAGGACTTATTCGTGGTGGCCTGAGCGAGAATGACCACCACTAAATGA
TGGC
Found at i:3083404 original size:17 final size:18
Alignment explanation
Indices: 3083378--3083417 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3083368 GATGAAAGCT
*
3083378 CTTTTGTAAGAA-TGTAA
1 CTTTTCTAAGAATTGTAA
*
3083395 CTTTTCTAAGAATTGTTA
1 CTTTTCTAAGAATTGTAA
3083413 CTTTT
1 CTTTT
3083418 GGAAATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (18 bp):
CTTTTCTAAGAATTGTAA
Found at i:3090797 original size:16 final size:17
Alignment explanation
Indices: 3090776--3090815 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3090766 TATGCTTGAA
*
3090776 AAAAAAAGGAACAAAT-
1 AAAAAAAGGAAAAAATG
*
3090792 AAAAAAATGAAAAAATG
1 AAAAAAAGGAAAAAATG
3090809 AAAAAAA
1 AAAAAAA
3090816 AAATTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (17 bp):
AAAAAAAGGAAAAAATG
Found at i:3092076 original size:72 final size:75
Alignment explanation
Indices: 3091990--3092159 Score: 247
Period size: 78 Copynumber: 2.3 Consensus size: 75
3091980 TAAAGGAGAA
*
3091990 AGTTCATAATGAGAAGAACTTATT-CC-T-TTCAAGTCCATCGCAGAAAGAGGTGACTCAACATT
1 AGTTCATAATGAGAAGAACTTATTACCTTGTTCAAGTCCACCGCAGAAAGAGGTGACTCAACATT
*
3092052 TTCAGTGGAG
66 TTCAGTGAAG
* * *
3092062 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCACCGCAGAAGGAGGTGACTCAAC
1 AGTTCATAATGAGAAGAACTTATT--ACCTT-GTTCAAGTCCACCGCAGAAAGAGGTGACTCAAC
3092127 ATTTTCAGTGAAG
63 ATTTTCAGTGAAG
3092140 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
3092160 CATCCAACAA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
72 23 0.26
75 2 0.02
76 1 0.01
78 61 0.70
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (75 bp):
AGTTCATAATGAGAAGAACTTATTACCTTGTTCAAGTCCACCGCAGAAAGAGGTGACTCAACATT
TTCAGTGAAG
Found at i:3092377 original size:3 final size:3
Alignment explanation
Indices: 3092369--3092394 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3092359 CATTTTAAAA
3092369 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3092395 ATTAACTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3094389 original size:2 final size:2
Alignment explanation
Indices: 3094384--3094416 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3094374 ATTAATTCGA
3094384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3094417 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3095235 original size:255 final size:255
Alignment explanation
Indices: 3094774--3095238 Score: 729
Period size: 255 Copynumber: 1.8 Consensus size: 255
3094764 TTCCCCACGC
**
3094774 GTAACCGACTCCCGAACCTATTTTAATTGAATCTTTGGTAAACGCAGACAAATTTTTGTCTTAAA
1 GTAACCGACTCCCGAACCTATTTTAATCAAATCTTTGGTAAACGCAGACAAATTTTTGTCTTAAA
* * ** *
3094839 AAATGATTTTTCTTAAAATTGTTTTTAAAAGATATTTTTAGGTATTCGACCTACCTAGCCCAAAT
66 AAATGATTTTTCTTAAAATTGTTTTTAAAAGACATTTTTAGGTATTCGACCTACCAAAACCAAAG
* * *
3094904 GTTGATGGCGACTCTTTTCAATTTTATTCAAATTAATCCAAAATCACCCATTTTTCAAAATTAAA
131 GTTGATGGCGACTCTTTTCAATTTAATTCAAATTAATCCAAAATCACCAATTTTCCAAAATTAAA
3094969 AGTCGTAACTGTTTTTTTAAACGATTGTCCCCGCCGAGAAAACGGTTACGTCACCCACTT
196 AGTCGTAACTGTTTTTTTAAACGATTGTCCCCGCCGAGAAAACGGTTACGTCACCCACTT
* * *
3095029 GTAACCGACTCCCGAATCC-GTTTTAATCAAATCTTTGGTAAACGGAGAC-CATCTTTTGTCTTA
1 GTAACCGACTCCCGAA-CCTATTTTAATCAAATCTTTGGTAAACGCAGACAAAT-TTTTGTCTTA
* * *
3095092 AAAAATGATTTTTCTTAAAATTGTTTTTAAAAGGCATTTTTAGGTGTTCGACCTACCAAAACTAA
64 AAAAATGATTTTTCTTAAAATTGTTTTTAAAAGACATTTTTAGGTATTCGACCTACCAAAACCAA
3095157 AGGTTGATGGCGACTCTTTTCAATTTAATTCAAATTAATCCAAAATCACCGAATTTTCCAAAATT
129 AGGTTGATGGCGACTCTTTTCAATTTAATTCAAATTAATCCAAAATCACC-AATTTTCCAAAATT
*
3095222 -AAAGTCTTAACTGTTTT
193 AAAAGTCGTAACTGTTTT
3095239 CTAAACAATT
Statistics
Matches: 190, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
254 2 0.01
255 174 0.92
256 14 0.07
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (255 bp):
GTAACCGACTCCCGAACCTATTTTAATCAAATCTTTGGTAAACGCAGACAAATTTTTGTCTTAAA
AAATGATTTTTCTTAAAATTGTTTTTAAAAGACATTTTTAGGTATTCGACCTACCAAAACCAAAG
GTTGATGGCGACTCTTTTCAATTTAATTCAAATTAATCCAAAATCACCAATTTTCCAAAATTAAA
AGTCGTAACTGTTTTTTTAAACGATTGTCCCCGCCGAGAAAACGGTTACGTCACCCACTT
Found at i:3100666 original size:75 final size:75
Alignment explanation
Indices: 3100563--3100766 Score: 245
Period size: 76 Copynumber: 2.7 Consensus size: 75
3100553 AATACGGAGG
* * *
3100563 ATTT-ATTTCACTGAAGATTGTTTTTCTTAAAACAGACTTTGTCTCACTTGAGAC-TGTTTTACT
1 ATTTCATTTCACTCAAGATTGTTTTTCTTAAAACAGA-TTTGTCTCGCTTGAGACAGGTTTTA-T
* *
3100626 T-GAAAGAAGAC
64 TCAAAACAAGAC
* * * *
3100637 ATTTCATTTGACTCAAGATTGTTTTTCTTAAAATAAGATTTTTCTCGCTTGGGACAGGTTTTATT
1 ATTTCATTTCACTCAAGATTGTTTTTCTTAAAA-CAGATTTGTCTCGCTTGAGACAGGTTTTATT
3100702 CAAAACAAGAC
65 CAAAACAAGAC
*
3100713 ATTTCATTTCACTACATG-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGA
1 ATTTCATTTCACT-CAAGATTGTTTTTCTTAAAAC-AGATTTGTCTCGCTTGAGA
3100767 TAGTTTCCCT
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
74 4 0.04
75 42 0.38
76 61 0.55
77 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (75 bp):
ATTTCATTTCACTCAAGATTGTTTTTCTTAAAACAGATTTGTCTCGCTTGAGACAGGTTTTATTC
AAAACAAGAC
Found at i:3100882 original size:78 final size:78
Alignment explanation
Indices: 3100747--3101299 Score: 493
Period size: 78 Copynumber: 7.5 Consensus size: 78
3100737 TTCTTAAAAC
* *
3100747 AAGA-TTTGTCTCGCTTGAGATAGTTTCCCTTGAAATAAAAGATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
3100811 TCCCTCGAAACAG
66 TCCCTCGAAACAG
** * *
3100824 AAGATTTTGTCTTACTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATATCGTTTGAGATAGTT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* *
3100889 TCCCTCAAAACAA
66 TCCCTCGAAACAG
*
3100902 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGCT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
3100967 TCCCTCGAAACAG
66 TCCCTCGAAACAG
* * *
3100980 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC--AA-ATTTTGTCTCCCTTGAGATAGTC
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* *
3101042 TCTCTTGAAACA-
66 TCCCTCGAAACAG
* * * * * * * *
3101054 CAGA-----ACT---TTGAGAAAGCTTCCCTTG-AA-ATAA-ATTTTGTCTCCCTTGAGACAGTT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* *
3101108 TCCCT-TAAA-AC
66 TCCCTCGAAACAG
* * * * * * *
3101119 AA-ATTTTGTCTCTCTTGAGACAATTTCCCTTTAAAC-G-A-ATTTTGTCTCCCTTGAGACAGTT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* *
3101180 TTCCTTGAAAC--
66 TCCCTCGAAACAG
* * * * * *
3101191 AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTTGTCTCTCTTAAGACAGTT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
*
3101252 TCCCTTGAAAC--
66 TCCCTCGAAACAG
* * **
3101263 AA-ATTTTGTCTCCCTTAAGATAGTTTATCTTGAAACA
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACA
3101300 CAGAACTTTG
Statistics
Matches: 410, Mismatches: 48, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
64 2 0.00
65 6 0.01
66 43 0.10
69 4 0.01
72 139 0.34
73 5 0.01
74 3 0.01
75 29 0.07
76 2 0.00
77 4 0.01
78 173 0.42
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (78 bp):
AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
TCCCTCGAAACAG
Found at i:3100890 original size:117 final size:116
Alignment explanation
Indices: 3100757--3101263 Score: 414
Period size: 117 Copynumber: 4.6 Consensus size: 116
3100747 AAGATTTGTC
*
3100757 TCGCTTGAGATAGTTTCCCTTGAAATAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 TCGCTTGAGATAGTTTCCCTTGAAA-AAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
3100822 AGAAGATTTTGTCTTACTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATA
65 AGAAGATTTTATCTCACTTGAGATAGCTTCCCTCGAAACAGAAGATTTTATA
* ** *
3100874 TCGTTTGAGATAGTTTCCCTCAAAACAAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
1 TCGCTTGAGATAGTTTCCCTTGAAA-AAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
3100939 AGAAGATTTTATCTCGCTTGAGATAGCTTCCCTCGAAACAGAAGATTTTGTC
65 AGAAGATTTTATCTCACTTGAGATAGCTTCCCTCGAAACAGAAGATTTTATA
* * * * *
3100991 TCGCTTGAGATAGTTTCCCTTG-AAACAA-ATTTTGTCTCCCTTGAGATAGTCTCTCTTGAAACA
1 TCGCTTGAGATAGTTTCCCTTGAAAAAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACA
* * * * * *
3101054 -CAGA----A-CT---TTGAGAAAGCTTCCCTTG-AA-ATAA-ATTTTGTC
66 GAAGATTTTATCTCACTTGAGATAGCTTCCCTCGAAACAGAAGATTTTATA
* * * * * * **
3101093 TCCCTTGAGACAGTTTCCCTT-AAAACAA-ATTTTGTCTCTCTTGAGACAATTTCCCTTTAAAC-
1 TCGCTTGAGATAGTTTCCCTTGAAAAAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACA
* * * * * * * *
3101155 G-A-ATTTTGTCTCCCTTGAGACAGTTTTCCTTGAAAC--AA-ATTTTGTC
66 GAAGATTTTATCTCACTTGAGATAGCTTCCCTCGAAACAGAAGATTTTATA
* * * * * * *
3101201 TCTCTTGAGACAGTTTCCCTTG-AAACAA-ATTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACA
1 TCGCTTGAGATAGTTTCCCTTGAAAAAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACA
3101264 AATTTTGTCT
Statistics
Matches: 336, Mismatches: 40, Indels: 36
0.82 0.10 0.09
Matches are distributed among these distances:
100 1 0.00
101 1 0.00
102 61 0.18
103 3 0.01
104 2 0.01
105 18 0.05
108 84 0.25
109 3 0.01
113 3 0.01
114 32 0.10
115 3 0.01
116 2 0.01
117 123 0.37
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (116 bp):
TCGCTTGAGATAGTTTCCCTTGAAAAAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACA
GAAGATTTTATCTCACTTGAGATAGCTTCCCTCGAAACAGAAGATTTTATA
Found at i:3101034 original size:36 final size:36
Alignment explanation
Indices: 3100743--3101299 Score: 509
Period size: 36 Copynumber: 15.1 Consensus size: 36
3100733 GTTTTTCTTA
3100743 AAACAAGA-TTTGTCTCGCTTGAGATAGTTTCCCTTG
1 AAACAA-ATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * *
3100779 AAATAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCG
1 -AA-ACAA-ATTTTGTCTCGCTTGAGATAGTTTCCCTTG
**
3100818 AAACAGAAGATTTTGTCTTACTTGAGATAGTTTCCCTTG
1 AAAC--AA-ATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * * **
3100857 AAACAGAAGATTTTATATCGTTTGAGATAGTTTCCCTCA
1 AAAC--AA-ATTTTGTCTCGCTTGAGATAGTTTCCCTTG
3100896 AAACAAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTG
1 AAAC--AA-ATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * *
3100935 AAACAGAAGATTTTATCTCGCTTGAGATAGCTTCCCTCG
1 AAAC--AA-ATTTTGTCTCGCTTGAGATAGTTTCCCTTG
3100974 AAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTG
1 AAAC--AA-ATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * *
3101013 AAACAAATTTTGTCTCCCTTGAGATAGTCTCTCTTG
1 AAACAAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * * *
3101049 AAACACA----GAACT---TTGAGAAAGCTTCCCTTG
1 AAACAAATTTTG-TCTCGCTTGAGATAGTTTCCCTTG
* * * *
3101079 AAATAAATTTTGTCTCCCTTGAGACAGTTTCCCTTA
1 AAACAAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * * *
3101115 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTT
1 AAACAAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * * *
3101151 AAACGAATTTTGTCTCCCTTGAGACAGTTTTCCTTG
1 AAACAAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* *
3101187 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * *
3101223 AAACAAATTTTGTCTCTCTTAAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
* * **
3101259 AAACAAATTTTGTCTCCCTTAAGATAGTTTATCTTG
1 AAACAAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
3101295 AAACA
1 AAACA
3101300 CAGAACTTTG
Statistics
Matches: 448, Mismatches: 60, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
30 19 0.04
32 1 0.00
33 4 0.01
34 1 0.00
36 216 0.48
37 5 0.01
38 7 0.02
39 195 0.44
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (36 bp):
AAACAAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
Found at i:3101264 original size:246 final size:250
Alignment explanation
Indices: 3100905--3101371 Score: 692
Period size: 246 Copynumber: 1.9 Consensus size: 250
3100895 AAAACAAAAG
* * *
3100905 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGCTTCC
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA-AAGATTTTATCTCGCTTGAGACAGCTTCC
* * *
3100970 CTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGA
65 CTCGAAACA-AAGATTTTGTCTCGCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTAA
* *
3101035 GATAGTCTCTCTTGAAACACAGAACTTTGAGAA-AGCTTCCCTTGAAATAAATTTTGTCTCCCTT
129 GATAGTCTATCTTGAAACACAGAACTTTGAGAACA-CTTCCCTTGAAACAAATTTTGTCTCCCTT
3101099 GAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTTAAACGA
193 GAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTTAAACGA
* * * *
3101157 ATTTTGTCTCCCTTGAGACAGTTTTCCTTGAAAC-AA-ATTTTGTCTCTCTTGAGACAGTTTCCC
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGATTTTATCTCGCTTGAGACAGCTTCCC
* *
3101220 TTGAAAC-AA-ATTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGA
66 TCGAAACAAAGATTTTGTCTCGCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGA
* * *
3101283 TAGTTTATCTTGAAACACAGAACTTTGAGAACATTTCCCTTGAAACGAATTTTGTCTCCCTTGAG
131 TAGTCTATCTTGAAACACAGAACTTTGAGAACACTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
* * *
3101348 ACAGTTTCTCTTGAAACAAGTTTT
196 ACAGTTTCCCTTAAAACAAATTTT
3101372 TGAGACAGTT
Statistics
Matches: 194, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
246 129 0.66
247 3 0.02
249 29 0.15
250 2 0.01
252 31 0.16
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (250 bp):
ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGATTTTATCTCGCTTGAGACAGCTTCCC
TCGAAACAAAGATTTTGTCTCGCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGA
TAGTCTATCTTGAAACACAGAACTTTGAGAACACTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
ACAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTTAAACGA
Found at i:3101383 original size:28 final size:29
Alignment explanation
Indices: 3101343--3101400 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
3101333 TTTGTCTCCC
3101343 TTGAGACAGTTTCTCTTGAAAC-AAGTTT
1 TTGAGACAGTTTCTCTTGAAACAAAGTTT
3101371 TTGAGACAGTTTCTCTTGAAACAAAGTTT
1 TTGAGACAGTTTCTCTTGAAACAAAGTTT
3101400 T
1 T
3101401 GTCTCCCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (29 bp):
TTGAGACAGTTTCTCTTGAAACAAAGTTT
Found at i:3101496 original size:76 final size:76
Alignment explanation
Indices: 3101402--3101544 Score: 225
Period size: 76 Copynumber: 1.9 Consensus size: 76
3101392 CAAAGTTTTG
*
3101402 TCTCCCTTAAGATGGTTTTTCTTAAAACCAACTTCGTCTTGCTTGAGACAACTTTCCCTT-GAAA
1 TCTCACTTAAGATGGTTTTTCTTAAAACCAACTTCGTCTTGCTTGAGACAA-TTTCCCTTCGAAA
3101466 CAAGAAATTGAA
65 CAAGAAATTGAA
* * * *
3101478 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTTGCTTGAGATAATTTTCCTTCGAAAC
1 TCTCACTTAAGATGGTTTTTCTTAAAACCAACTTCGTCTTGCTTGAGACAATTTCCCTTCGAAAC
3101543 AA
66 AA
3101545 AATTTATCTC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 7 0.11
76 54 0.89
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (76 bp):
TCTCACTTAAGATGGTTTTTCTTAAAACCAACTTCGTCTTGCTTGAGACAATTTCCCTTCGAAAC
AAGAAATTGAA
Found at i:3102187 original size:136 final size:136
Alignment explanation
Indices: 3101824--3102299 Score: 643
Period size: 131 Copynumber: 3.6 Consensus size: 136
3101814 AAACATATCA
* * ** *
3101824 ACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCTGATAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
*
3101889 GAGAAGAGCTTGTTCGACCTATCACTCGATTCATGGCATTTCGAATCAGTGACACCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
3101954 GGATTG
131 GGATTG
* **
3101960 CCATTTCCAATGGAGAGTTC---AT-A-AAGAACTCATCCATCAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
* *
3102020 GAGAAGAGCTTGTTCGACCTATCACTTGATTCACGGTATTTCGAATCAGTGACACCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
3102085 GGATTG
131 GGATTG
* *
3102091 ACATTTCCAATGGAGAGTTCATAAAGAGAAGAACTCATCCAAAAGAGGGAGAATAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
* * * * * *
3102156 GAGAAGATCTTGTTCGTCCTATCACTCGATTCACGACATTTCGAATTAGTGACGCCTCACTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
*
3102221 GGATTA
131 GGATTG
* * * *
3102227 ACATTTTC-A-GAAGAGTTCATAATGATAAGAACTCATCC-TAA-A-GGAG-A-AAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
*
3102285 GAGAAGAACTTGTTC
66 GAGAAGAGCTTGTTC
3102300 CTTTCGATTC
Statistics
Matches: 305, Mismatches: 30, Indels: 17
0.87 0.09 0.05
Matches are distributed among these distances:
129 25 0.08
130 1 0.00
131 123 0.40
132 2 0.01
133 4 0.01
134 27 0.09
135 2 0.01
136 121 0.40
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (136 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
GGATTG
Found at i:3102506 original size:20 final size:20
Alignment explanation
Indices: 3102443--3102507 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
3102433 TTTAATGGAG
3102443 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
3102463 CA-TTC--AAGGACGAAGAAAA
1 -AGTTCATAATGA-GAAGAACT
3102482 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
3102502 TGTTCA
1 AGTTCA
3102508 ATCCAATGCT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 14 0.42
21 5 0.15
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:3106205 original size:10 final size:10
Alignment explanation
Indices: 3106185--3106218 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3106175 ATTTTTCTAA
3106185 TTTTTAATTT
1 TTTTTAATTT
*
3106195 TTGTT-ATTT
1 TTTTTAATTT
3106204 TTTTTAATTT
1 TTTTTAATTT
3106214 TTTTT
1 TTTTT
3106219 TCTTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTAATTT
Found at i:3112007 original size:21 final size:21
Alignment explanation
Indices: 3111957--3112011 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3111947 TTTAATCTAA
* *
3111957 TATTATTTTATAATATTATTAT
1 TATTA-TTTATAATATTATAAC
*
3111979 TATCATTTATAATATTATAAC
1 TATTATTTATAATATTATAAC
3112000 TATTATTT-TAAT
1 TATTATTTATAAT
3112012 CCATACTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 4 0.14
21 21 0.72
22 4 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTATTTATAATATTATAAC
Found at i:3116702 original size:2 final size:2
Alignment explanation
Indices: 3116695--3116720 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3116685 TCTAAGAGAA
3116695 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
3116721 TATCCATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3116907 original size:30 final size:30
Alignment explanation
Indices: 3116867--3116929 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
3116857 GTTTCGAATT
*
3116867 ATTCATGGTGAGGTGGGATGTATGATTTTG
1 ATTCAAGGTGAGGTGGGATGTATGATTTTG
3116897 ATTCAAGGTGAGGTGGGATGTATGATTTTG
1 ATTCAAGGTGAGGTGGGATGTATGATTTTG
3116927 ATT
1 ATT
3116930 TTTGATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.03, G:0.35, T:0.40
Consensus pattern (30 bp):
ATTCAAGGTGAGGTGGGATGTATGATTTTG
Found at i:3117325 original size:2 final size:2
Alignment explanation
Indices: 3117318--3117408 Score: 52
Period size: 2 Copynumber: 47.0 Consensus size: 2
3117308 TAATAACATA
*
3117318 AT AT AT AT -T AT AT AT AT AT AA AT A- AT A- AT AT A- 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
* * *
3117356 AT CAT GT AT AT AT A- AGT A- AT GAT GT GAT AT AT AT CT -T AT AT
1 AT -AT AT AT AT AT AT A-T AT AT -AT AT -AT AT AT AT AT AT AT AT
*
3117397 AT AA AT AT AT AT
1 AT AT AT AT AT AT
3117409 TTAAAAATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
1 7 0.10
2 56 0.81
3 6 0.09
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3117345 original size:32 final size:32
Alignment explanation
Indices: 3117308--3117403 Score: 106
Period size: 32 Copynumber: 3.1 Consensus size: 32
3117298 GTGTCCAAAG
*
3117308 TAATAACATAATATATATTATATATATATAAA
1 TAATAACATAATATATATCATATATATATAAA
* * *
3117340 TAATAATATAATATATATCATGTATATATAAG
1 TAATAACATAATATATATCATATATATATAAA
* ** *
3117372 TAATGATGTGATATATATC-T-TATATATAAA
1 TAATAACATAATATATATCATATATATATAAA
3117402 TA
1 TA
3117404 TATATTTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 11 0.20
31 1 0.02
32 44 0.79
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (32 bp):
TAATAACATAATATATATCATATATATATAAA
Found at i:3117348 original size:25 final size:25
Alignment explanation
Indices: 3117310--3117357 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3117300 GTCCAAAGTA
*
3117310 ATAACATAATATATATTATATATAT
1 ATAACATAATATATAATATATATAT
3117335 ATAA-ATAATAATATAATATATAT
1 ATAACATAAT-ATATAATATATAT
3117358 CATGTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAACATAATATATAATATATATAT
Found at i:3118181 original size:16 final size:18
Alignment explanation
Indices: 3118150--3118182 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3118140 GAAGTATATG
3118150 ATAATTAATAAAATTTAT
1 ATAATTAATAAAATTTAT
3118168 ATAA-TAAT-AAATTTA
1 ATAATTAATAAAATTTA
3118183 ACTCTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTAATAAAATTTAT
Found at i:3133482 original size:20 final size:20
Alignment explanation
Indices: 3133454--3133501 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
3133444 ACAAACTAAG
*
3133454 CATATTCACGTAATATCAAA
1 CATAATCACGTAATATCAAA
3133474 CATAATCACGTAATATCAAA
1 CATAATCACGTAATATCAAA
3133494 CATAATCA
1 CATAATCA
3133502 TACTTCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.21, G:0.04, T:0.27
Consensus pattern (20 bp):
CATAATCACGTAATATCAAA
Found at i:3134006 original size:167 final size:167
Alignment explanation
Indices: 3133726--3134063 Score: 633
Period size: 167 Copynumber: 2.0 Consensus size: 167
3133716 AGTATACTAA
3133726 TTAA-TATATTCTAAACTATCATTTCTTAGGCTAAAAGAAAAGATATTTTCATCTCTTAATAAAC
1 TTAAGTATATTCTAAACTATCATTTCTTAGGCTAAAAGAAAAGATATTTTCATCTCTTAATAAAC
* *
3133790 GTATGCATCGATGTACTACACCATGTATCGATGCATCCCTTGACGGGTGCATCGATGCACTATCT
66 GTATGCATCGATGCAATACACCATGTATCGATGCATCCCTTGACGGGTGCATCGATGCACTATCT
3133855 ATGCATCGGTACATAAATCACATTCGATGTTTGTATT
131 ATGCATCGGTACATAAATCACATTCGATGTTTGTATT
*
3133892 TTAAGTATATTCTAAACTATCATTTCTTAGGCTAAAAGAAAAGCTATTTTCATCTCTTAATAAAC
1 TTAAGTATATTCTAAACTATCATTTCTTAGGCTAAAAGAAAAGATATTTTCATCTCTTAATAAAC
3133957 GTATGCATCGATGCAATACACCATGTATCGATGCATCCCTTGACGGGTGCATCGATGCACTATCT
66 GTATGCATCGATGCAATACACCATGTATCGATGCATCCCTTGACGGGTGCATCGATGCACTATCT
*
3134022 ATGCATCGGTACATAAATCCCATTCGATGTTTGTATT
131 ATGCATCGGTACATAAATCACATTCGATGTTTGTATT
3134059 TTAAG
1 TTAAG
3134064 GGGGTGCATC
Statistics
Matches: 167, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
166 4 0.02
167 163 0.98
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (167 bp):
TTAAGTATATTCTAAACTATCATTTCTTAGGCTAAAAGAAAAGATATTTTCATCTCTTAATAAAC
GTATGCATCGATGCAATACACCATGTATCGATGCATCCCTTGACGGGTGCATCGATGCACTATCT
ATGCATCGGTACATAAATCACATTCGATGTTTGTATT
Found at i:3136124 original size:22 final size:22
Alignment explanation
Indices: 3136098--3136198 Score: 103
Period size: 22 Copynumber: 4.5 Consensus size: 22
3136088 AACTTTTTTT
* *
3136098 GTCAAAGTAAACGGTTAGACCA
1 GTCAAAGTCAACGGTCAGACCA
* *
3136120 GTCAAAGTCAACGATCAGACAA
1 GTCAAAGTCAACGGTCAGACCA
* *
3136142 GTCAAAGTCAACTGTCAGACCG
1 GTCAAAGTCAACGGTCAGACCA
* * *
3136164 GTCAAAGATCAACGGATTAGGCCG
1 GTCAAAG-TCAACGG-TCAGACCA
3136188 GTCAAAGTCAA
1 GTCAAAGTCAA
3136199 TAGGTAGGGT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 43 0.65
23 10 0.15
24 13 0.20
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCAGACCA
Found at i:3136242 original size:19 final size:19
Alignment explanation
Indices: 3136187--3136247 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
3136177 GGATTAGGCC
*
3136187 GGTCAAAGTCAATAGGTAG
1 GGTCAAAGTCAATAGGTCG
*
3136206 GGTCAAAGTCAATGGGTCG
1 GGTCAAAGTCAATAGGTCG
**
3136225 GGTCAAAGTCAACCGGTCG
1 GGTCAAAGTCAATAGGTCG
3136244 GGTC
1 GGTC
3136248 GGGTTGACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (19 bp):
GGTCAAAGTCAATAGGTCG
Found at i:3140361 original size:28 final size:28
Alignment explanation
Indices: 3140326--3140411 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 28
3140316 GAATTAAAAA
3140326 TAAATTTATTATTTTTATATTTTTAAAT
1 TAAATTTATTATTTTTATATTTTTAAAT
* * *
3140354 TAAATTTA--A--TAT-TATTTTCATAT
1 TAAATTTATTATTTTTATATTTTTAAAT
* *
3140377 TAAATTTATTTGTTTTTATATTTCTAAAT
1 TAAATTTA-TTATTTTTATATTTTTAAAT
3140406 TAAATT
1 TAAATT
3140412 CAGTAGTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
23 17 0.39
24 2 0.05
26 1 0.02
28 10 0.23
29 14 0.32
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (28 bp):
TAAATTTATTATTTTTATATTTTTAAAT
Found at i:3145383 original size:21 final size:21
Alignment explanation
Indices: 3145358--3145398 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3145348 GAAGTGCCAC
3145358 ATATTTGTCCCAAATGACCAT
1 ATATTTGTCCCAAATGACCAT
*
3145379 ATATTTGTCCCGAATGACCA
1 ATATTTGTCCCAAATGACCA
3145399 CATAAGACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (21 bp):
ATATTTGTCCCAAATGACCAT
Found at i:3145562 original size:21 final size:21
Alignment explanation
Indices: 3145536--3145586 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3145526 CATAGATTTT
*
3145536 GTTCACATTCACTGGTTCAAA
1 GTTCACATTCACTGATTCAAA
*
3145557 GTTCACATTCACTTATTCAAA
1 GTTCACATTCACTGATTCAAA
3145578 GTTCACATT
1 GTTCACATT
3145587 TCCATAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:3146054 original size:53 final size:53
Alignment explanation
Indices: 3145972--3146094 Score: 174
Period size: 53 Copynumber: 2.3 Consensus size: 53
3145962 GATACTTCCC
* *
3145972 TTCAAGGGTATCGATACCTTCTCATGGTACCGATACCAAAATAGCATTCGATA
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGATA
** * * *
3146025 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATCTGGCATTTGATG
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGATA
3146078 TTCCAAGGGTATCGATA
1 TT-CAAGGGTATCGATA
3146095 TCATCCTTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
53 48 0.77
54 14 0.23
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (53 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGATA
Found at i:3147678 original size:3 final size:3
Alignment explanation
Indices: 3147670--3147694 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3147660 AATCACACAT
3147670 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
3147695 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:3147928 original size:14 final size:14
Alignment explanation
Indices: 3147909--3147947 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3147899 TAATGGGGAG
3147909 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
3147923 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
3147937 GAATCTCTGCA
1 TAATCCCTGCA
3147948 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:3154261 original size:21 final size:21
Alignment explanation
Indices: 3154236--3154378 Score: 175
Period size: 21 Copynumber: 6.7 Consensus size: 21
3154226 GTAATTTGCA
*
3154236 CCGAAGTG-CCACATAATTGTC
1 CCGAAG-GACCACATATTTGTC
*
3154257 CCGAAGGACCATATAGGTTTG-C
1 CCGAAGGACCACATA--TTTGTC
3154279 ACCGAAGTG-CCACATATTTGTC
1 -CCGAAG-GACCACATATTTGTC
3154301 CCGAAGGACCACATATTTGTC
1 CCGAAGGACCACATATTTGTC
3154322 CCGAAGGACCACATATTTGTC
1 CCGAAGGACCACATATTTGTC
* * *
3154343 CCGAAAGACCACGTATTTATC
1 CCGAAGGACCACATATTTGTC
3154364 CCGAAGGACCACATA
1 CCGAAGGACCACATA
3154379 AGACCCTCGA
Statistics
Matches: 107, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.02
21 87 0.81
22 2 0.02
23 15 0.14
24 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (21 bp):
CCGAAGGACCACATATTTGTC
Found at i:3154536 original size:21 final size:21
Alignment explanation
Indices: 3154512--3154558 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3154502 CATAGAGTTT
*
3154512 GTTCGCAGTCAC-TAGTTCAAA
1 GTTCACAGTCACTTA-TTCAAA
*
3154533 GTTCACATTCACTTATTCAAA
1 GTTCACAGTCACTTATTCAAA
3154554 GTTCA
1 GTTCA
3154559 TATTTTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (21 bp):
GTTCACAGTCACTTATTCAAA
Found at i:3155052 original size:52 final size:54
Alignment explanation
Indices: 3154947--3155070 Score: 155
Period size: 52 Copynumber: 2.3 Consensus size: 54
3154937 GATACTTCCC
*
3154947 TTCAAGGGTAGCGATACCTCCTCATAGTACCGATACCAAAATAGCATTCGATG-
1 TTCAAGGGTATCGATACCTCCTCATAGTACCGATACCAAAATAGCATTCGATGT
* ** * * *
3155000 TTCAAGGGTCTCG-TACCTCCTCA-AGGTACCGATACCAATCTGGTATTTGATGT
1 TTCAAGGGTATCGATACCTCCTCATA-GTACCGATACCAAAATAGCATTCGATGT
3155053 TTCAAGGGTATCGATACC
1 TTCAAGGGTATCGATACC
3155071 ATCTTTCAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
51 1 0.02
52 32 0.53
53 23 0.38
54 4 0.07
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCATAGTACCGATACCAAAATAGCATTCGATGT
Found at i:3156058 original size:53 final size:55
Alignment explanation
Indices: 3156000--3156107 Score: 130
Period size: 56 Copynumber: 2.0 Consensus size: 55
3155990 AATTTGAGCA
* * * * * * *
3156000 AATTG-ATAG-TATCCTACGCTTCCTTTAATCAATTTGTGATTAGCAAAGATGAT
1 AATTGAATAGTTATCCTACACCTCATTTAATCAACTTGTAAATAACAAAGATGAT
3156053 AATTGAATAGTTTATCCTACACCTCATTTAATCAACTTGTAAATAACAAAGATGA
1 AATTGAATAG-TTATCCTACACCTCATTTAATCAACTTGTAAATAACAAAGATGA
3156108 CACTTCCTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 5 0.11
54 4 0.09
56 36 0.80
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (55 bp):
AATTGAATAGTTATCCTACACCTCATTTAATCAACTTGTAAATAACAAAGATGAT
Found at i:3168927 original size:29 final size:33
Alignment explanation
Indices: 3168886--3168955 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
3168876 ATTTATTATT
* *
3168886 AAATATT-ATTTTTATA-ATTTTA-T-TAATAA
1 AAATATTAATTTTGATATATTTTAGTGAAATAA
*
3168915 AAATATTAATTTTGGTATATTTTAGTGAAATAA
1 AAATATTAATTTTGATATATTTTAGTGAAATAA
3168948 AAATATTA
1 AAATATTA
3168956 TAAATTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.21
30 7 0.21
31 6 0.18
32 1 0.03
33 13 0.38
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (33 bp):
AAATATTAATTTTGATATATTTTAGTGAAATAA
Found at i:3169046 original size:23 final size:23
Alignment explanation
Indices: 3168997--3169047 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3168987 GTGTTATATT
**
3168997 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
3169020 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
3169043 ATATT
1 ATATT
3169048 ATTATATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:3169117 original size:28 final size:28
Alignment explanation
Indices: 3169052--3169117 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
3169042 AATATTATTA
* *
3169052 TATTA-ATATTAAATATAGAAATAATAC
1 TATTATATATTAAATATAAAAAAAATAC
*
3169079 TATTCAT-TATTAAATATATAAAAAAAT-T
1 TATT-ATATATTAAATATA-AAAAAAATAC
3169107 TATTATATATT
1 TATTATATATT
3169118 TATTAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 6 0.19
28 20 0.62
29 6 0.19
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (28 bp):
TATTATATATTAAATATAAAAAAAATAC
Found at i:3169152 original size:8 final size:8
Alignment explanation
Indices: 3169141--3169208 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
3169131 ATATAATATC
3169141 TTATATTA
1 TTATATTA
*
3169149 TTATAATA
1 TTATATTA
3169157 -TA-ATTGA
1 TTATATT-A
*
3169164 TTATTTTA
1 TTATATTA
*
3169172 TTATAATA
1 TTATATTA
*
3169180 TTATAAATA
1 TTAT-ATTA
*
3169189 TAATA-TA
1 TTATATTA
3169196 TTATATTA
1 TTATATTA
3169204 TTATA
1 TTATA
3169209 AATATTAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
6 2 0.04
7 9 0.19
8 28 0.58
9 9 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (8 bp):
TTATATTA
Found at i:3169205 original size:24 final size:25
Alignment explanation
Indices: 3169107--3169240 Score: 77
Period size: 26 Copynumber: 5.4 Consensus size: 25
3169097 TAAAAAAATT
**
3169107 TATT-ATATATT-TATTAAAATAAA
1 TATTAATATATTATATTATTATAAA
* *
3169130 AATATAATATCTTATATTATTATAATA
1 TAT-TAATATATTATATTATTATAA-A
* *
3169157 TAATTGAT-TATTTTATTATAATATTATAA
1 T-ATTAATATATTATATTAT--TA-TA-AA
3169186 -ATATAATATATTATATTATTATAAA
1 TAT-TAATATATTATATTATTATAAA
*
3169211 TATTAATA-A--ATA-TATTTTAAA
1 TATTAATATATTATATTATTATAAA
3169232 TATTAATAT
1 TATTAATAT
3169241 TTTGATGAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 27
0.70 0.09 0.22
Matches are distributed among these distances:
21 16 0.18
22 3 0.03
23 2 0.02
24 2 0.02
25 13 0.15
26 22 0.25
27 8 0.09
28 7 0.08
29 13 0.15
30 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
TATTAATATATTATATTATTATAAA
Found at i:3169226 original size:29 final size:32
Alignment explanation
Indices: 3169141--3169224 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 32
3169131 ATATAATATC
* *
3169141 TTATATTATTAT-AATATAAT-TGATTATTTTA
1 TTATAATATTATAAATATAATAT-ATTATATTA
3169172 TTATAATATTATAAATATAATATATTATATTA
1 TTATAATATTATAAATATAATATATTATATTA
3169204 TTATAAATATTAATAAATATA
1 TTAT-AATATT-ATAAATATA
3169225 TTTTAAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
31 11 0.23
32 20 0.43
33 7 0.15
34 9 0.19
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
TTATAATATTATAAATATAATATATTATATTA
Found at i:3169468 original size:61 final size:61
Alignment explanation
Indices: 3169402--3169538 Score: 238
Period size: 61 Copynumber: 2.2 Consensus size: 61
3169392 TGTTGACCAT
* * *
3169402 GAAAATGAATTACGTTGATCAACCAGTTTTTCTCCAACCAAACACTGGAAAACATTTTCCG
1 GAAAATGAATTACGTTGACCAACCAGTTTTCCTCCAACCAAACACTGAAAAACATTTTCCG
3169463 GAAAATGAATTACGTTGACCAACCAGTTTTCCTCCAACCAAACACTGAAAAACATTTTCCG
1 GAAAATGAATTACGTTGACCAACCAGTTTTCCTCCAACCAAACACTGAAAAACATTTTCCG
*
3169524 GAAAACGAATTACGT
1 GAAAATGAATTACGT
3169539 GAAATAAACA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (61 bp):
GAAAATGAATTACGTTGACCAACCAGTTTTCCTCCAACCAAACACTGAAAAACATTTTCCG
Found at i:3169572 original size:43 final size:42
Alignment explanation
Indices: 3169501--3169636 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 42
3169491 TTCCTCCAAC
* * *
3169501 CAAACACTGAAAAACATTTTCCGGAAAACGAATTACGTGAAA
1 CAAACACGGAAAAACATTTTCCGAAAAACGAATTACATGAAA
* * * * *
3169543 TAAACACGGGAAAACATTTTTCGTAAAAACAAATTACTTGAAA
1 CAAACACGGAAAAACATTTTCCG-AAAAACGAATTACATGAAA
* * * *
3169586 CAAACAAGGAAAAATATTTTCCGAAAAACGAATTATACGAAA
1 CAAACACGGAAAAACATTTTCCGAAAAACGAATTACATGAAA
3169628 CAAACACGG
1 CAAACACGG
3169637 GATTTCGGGG
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 42 0.55
43 34 0.45
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (42 bp):
CAAACACGGAAAAACATTTTCCGAAAAACGAATTACATGAAA
Found at i:3173006 original size:2 final size:2
Alignment explanation
Indices: 3172999--3173027 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3172989 ACTCTATACC
3172999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3173028 TTGCATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3178216 original size:16 final size:18
Alignment explanation
Indices: 3178189--3178224 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3178179 TAATACTATT
3178189 TATTATTTTAATAA-AAA
1 TATTATTTTAATAATAAA
3178206 TATTA-TTTAATAATAAA
1 TATTATTTTAATAATAAA
3178223 TA
1 TA
3178225 GCATCCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATTTTAATAATAAA
Found at i:3178826 original size:17 final size:19
Alignment explanation
Indices: 3178788--3178827 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
3178778 AAGTTTTATT
3178788 TTTTTATATAATTTAAATA
1 TTTTTATATAATTTAAATA
*
3178807 TTTTTAT-TAA-TTATATA
1 TTTTTATATAATTTAAATA
3178824 TTTT
1 TTTT
3178828 AGTCCTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 3 0.15
19 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATATAATTTAAATA
Found at i:3183291 original size:24 final size:24
Alignment explanation
Indices: 3183264--3183310 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
3183254 TGCATGACAT
3183264 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
3183288 TGTACATAGATGTTTTATACATC
1 TGTACATAGATGTTTTATACATC
3183311 GACAGGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:3190318 original size:2 final size:2
Alignment explanation
Indices: 3190313--3190359 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3190303 AGAAACTCAA
3190313 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
3190355 AT AT A
1 AT AT A
3190360 AAATTTTAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3191845 original size:26 final size:26
Alignment explanation
Indices: 3191816--3191866 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3191806 TTAAAAATAT
*
3191816 GAATTAAAGTTATATATATATTATAA
1 GAATTAAAGTTATATAGATATTATAA
*
3191842 GAATTGAAGTTATATAGATATTATA
1 GAATTAAAGTTATATAGATATTATA
3191867 TAGTGTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (26 bp):
GAATTAAAGTTATATAGATATTATAA
Found at i:3197754 original size:6 final size:6
Alignment explanation
Indices: 3197743--3197773 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3197733 AAATGCTGAG
*
3197743 AGAGAT AGAGAT AGAGAT AGAGAG AGAGAT A
1 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT A
3197774 TGCATGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.35, T:0.13
Consensus pattern (6 bp):
AGAGAT
Found at i:3197760 original size:12 final size:12
Alignment explanation
Indices: 3197740--3197773 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3197730 AATAAATGCT
3197740 GAGAGAGATAGA
1 GAGAGAGATAGA
*
3197752 GATAGAGATAGA
1 GAGAGAGATAGA
3197764 GAGAGAGATA
1 GAGAGAGATA
3197774 TGCATGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (12 bp):
GAGAGAGATAGA
Found at i:3208885 original size:26 final size:26
Alignment explanation
Indices: 3208849--3208901 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3208839 ATGGGTTAAT
3208849 AGACTTGTGTTAGAATTAAAGATGCA
1 AGACTTGTGTTAGAATTAAAGATGCA
*
3208875 AGACTTGTGTTAGAATTGAAGATGCA
1 AGACTTGTGTTAGAATTAAAGATGCA
3208901 A
1 A
3208902 TGTATGTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (26 bp):
AGACTTGTGTTAGAATTAAAGATGCA
Found at i:3209225 original size:28 final size:28
Alignment explanation
Indices: 3209144--3209260 Score: 153
Period size: 28 Copynumber: 4.1 Consensus size: 28
3209134 TTGCCAATTG
3209144 TCACCACAAAACCTAACAATATCAGCTA
1 TCACCACAAAACCTAACAATATCAGCTA
* ***
3209172 TCCCTCACATGTCCTAACAATATCAGCTA
1 TCAC-CACAAAACCTAACAATATCAGCTA
* *
3209201 TCACAACAAAATCTAACAATATCAGCTA
1 TCACCACAAAACCTAACAATATCAGCTA
*
3209229 TCACCATAAAACCTAACAATATCAGCTGA
1 TCACCACAAAACCTAACAATATCAGCT-A
3209258 TCA
1 TCA
3209261 AAGCATTATA
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
28 46 0.62
29 28 0.38
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.22
Consensus pattern (28 bp):
TCACCACAAAACCTAACAATATCAGCTA
Found at i:3210047 original size:21 final size:21
Alignment explanation
Indices: 3210017--3210084 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
3210007 GAACCGATTC
*
3210017 CCCCCCAGAGGGGTACCAATT
1 CCCCCTAGAGGGGTACCAATT
*
3210038 CCCCCTAGAGGGGTACCGATT
1 CCCCCTAGAGGGGTACCAATT
*
3210059 --CCCTATGAGGGGGTATCAATT
1 CCCCCTA-GA-GGGGTACCAATT
3210080 CCCCC
1 CCCCC
3210085 CACGCTCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 5 0.13
20 2 0.05
21 29 0.74
23 3 0.08
ACGTcount: A:0.21, C:0.35, G:0.25, T:0.19
Consensus pattern (21 bp):
CCCCCTAGAGGGGTACCAATT
Found at i:3213541 original size:25 final size:25
Alignment explanation
Indices: 3213495--3213570 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
3213485 TCCGTATAAA
* * *
3213495 TTGCACTGAAGTGCCACATAGAATT
1 TTGCACCGAAGTGCCGCGTAGAATT
3213520 TTGCACCGAAGTGCCGCGTAGAAATT
1 TTGCACCGAAGTGCCGCGTAG-AATT
3213546 TAT-C-CCGAAG-GACCGCGTAGAATT
1 T-TGCACCGAAGTG-CCGCGTAGAATT
3213570 T
1 T
3213571 GTCCCGAAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
24 6 0.13
25 32 0.71
26 6 0.13
27 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (25 bp):
TTGCACCGAAGTGCCGCGTAGAATT
Found at i:3213575 original size:24 final size:25
Alignment explanation
Indices: 3213525--3213594 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
3213515 GAATTTTGCA
3213525 CCGAAGTG-CCGCGTAGAAATTTATC
1 CCGAAG-GACCGCGTAGAAATTTATC
*
3213550 CCGAAGGACCGCGTAG-AATTTGTC
1 CCGAAGGACCGCGTAGAAATTTATC
* *
3213574 CCGAAGGACCACATAGAAATT
1 CCGAAGGACCGCGTAGAAATT
3213595 CCTTAAGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
24 22 0.55
25 18 0.45
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (25 bp):
CCGAAGGACCGCGTAGAAATTTATC
Found at i:3215182 original size:21 final size:21
Alignment explanation
Indices: 3215138--3215221 Score: 132
Period size: 21 Copynumber: 4.0 Consensus size: 21
3215128 TTTTGTTCGT
* *
3215138 TTGAAGGGGTATCGGTTCCCCC
1 TTGAATGGGTATCGATT-CCCC
*
3215160 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTATCGATTCCCC
3215181 TTGAATGGGTATCGATTCCCC
1 TTGAATGGGTATCGATTCCCC
3215202 TTGAATGGGTATCGATTCCC
1 TTGAATGGGTATCGATTCCC
3215222 TTAACCCAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 44 0.76
22 14 0.24
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (21 bp):
TTGAATGGGTATCGATTCCCC
Found at i:3216152 original size:16 final size:17
Alignment explanation
Indices: 3216114--3216155 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3216104 TCATCAGTTC
*
3216114 TTATCACTCAAAATCAT
1 TTATCAATCAAAATCAT
* *
3216131 TAATCAATCAAATTC-T
1 TTATCAATCAAAATCAT
3216147 TTATCAATC
1 TTATCAATC
3216156 TTTAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATCAATCAAAATCAT
Found at i:3218509 original size:25 final size:25
Alignment explanation
Indices: 3218481--3218556 Score: 102
Period size: 25 Copynumber: 3.0 Consensus size: 25
3218471 CTCGTATAAA
*
3218481 TTGCACCGAAGTGCCACGTAGAATT
1 TTGCACCGAAGTGCCGCGTAGAATT
*
3218506 TTGCACCGAAGTGCCGCGTAGAAAT
1 TTGCACCGAAGTGCCGCGTAGAATT
3218531 TTGTC-CCGAAG-GACCGCGTAGAATT
1 TTG-CACCGAAGTG-CCGCGTAGAATT
3218556 T
1 T
3218557 GTCCCGAAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
24 1 0.02
25 44 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
TTGCACCGAAGTGCCGCGTAGAATT
Found at i:3218560 original size:24 final size:24
Alignment explanation
Indices: 3218497--3218569 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 24
3218487 CGAAGTGCCA
3218497 CGTAGAATTT-TGCACCGAAGTG-CCG
1 CGTAGAATTTGT-C-CCGAAG-GACCG
3218522 CGTAGAAATTTGTCCCGAAGGACCG
1 CGTAG-AATTTGTCCCGAAGGACCG
3218547 CGTAGAATTTGTCCCGAAGGACC
1 CGTAGAATTTGTCCCGAAGGACC
3218570 ACATAGAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
24 19 0.42
25 19 0.42
26 6 0.13
27 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (24 bp):
CGTAGAATTTGTCCCGAAGGACCG
Found at i:3218576 original size:24 final size:24
Alignment explanation
Indices: 3218528--3218577 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
3218518 GCCGCGTAGA
* *
3218528 AATTTGTCCCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGGACCACATAG
3218552 AATTTGTCCCGAAGGACCACATAG
1 AATTTGTCCCGAAGGACCACATAG
3218576 AA
1 AA
3218578 ATTCCTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACATAG
Found at i:3220175 original size:21 final size:21
Alignment explanation
Indices: 3220131--3220214 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
3220121 TTTTGTTCGT
* * *
3220131 TTGAAGGGGTATCGGTTCCCCC
1 TTGAATGGGTACCGATT-CCCC
3220153 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
3220174 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
*
3220195 TTGAATGGGTATCGATTCCC
1 TTGAATGGGTACCGATTCCC
3220215 TTAACCCAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 44 0.76
22 14 0.24
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCC
Found at i:3223547 original size:31 final size:31
Alignment explanation
Indices: 3223488--3223706 Score: 350
Period size: 31 Copynumber: 7.0 Consensus size: 31
3223478 CCCGAAGGAC
* * *
3223488 CAGTCCATA-GATTCCGAAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCG-AAGAACATAGGTAAA
3223520 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3223551 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
3223582 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
3223613 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3223644 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
3223675 TAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3223706 C
1 C
3223707 CCTCGACCTT
Statistics
Matches: 176, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
31 162 0.92
32 13 0.07
33 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:3224692 original size:21 final size:21
Alignment explanation
Indices: 3224662--3224706 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3224652 TTTTGTTTGT
* *
3224662 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3224683 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3224704 TTG
1 TTG
3224707 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3226422 original size:22 final size:23
Alignment explanation
Indices: 3226396--3226459 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
3226386 TTAGTGTAGA
* *
3226396 GGGAATCGATACTCCC-TTGAAG
1 GGGAACCGATACCCCCTTTGAAG
* *
3226418 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATACCCCCTTTGAAG
*
3226441 GGGAACCGATTCCCTCCTT
1 GGGAACCGATACCC-CCTT
3226460 GAGAGAATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.36
23 19 0.53
24 4 0.11
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (23 bp):
GGGAACCGATACCCCCTTTGAAG
Found at i:3226444 original size:23 final size:24
Alignment explanation
Indices: 3226407--3226459 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
3226397 GGAATCGATA
*
3226407 CTCCCTTGAAGGGGAACCGATTCC
1 CTCCTTTGAAGGGGAACCGATTCC
*
3226431 C-CCTTTGAATGGGAACCGATTCC
1 CTCCTTTGAAGGGGAACCGATTCC
3226454 CTCCTT
1 CTCCTT
3226460 GAGAGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.19, C:0.34, G:0.21, T:0.26
Consensus pattern (24 bp):
CTCCTTTGAAGGGGAACCGATTCC
Found at i:3228223 original size:16 final size:16
Alignment explanation
Indices: 3228202--3228235 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3228192 TTATGGAACT
3228202 AATGTTTGTGTTTTTA
1 AATGTTTGTGTTTTTA
3228218 AATGTTTGTGTTTTTA
1 AATGTTTGTGTTTTTA
3228234 AA
1 AA
3228236 GGGGAGAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (16 bp):
AATGTTTGTGTTTTTA
Found at i:3229447 original size:16 final size:16
Alignment explanation
Indices: 3229408--3229451 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3229398 AAGCTCCAAT
*
3229408 CAATCTAAAATAAATG
1 CAATCTAAAACAAATG
*
3229424 CAAGCTAAAACAAA-G
1 CAATCTAAAACAAATG
3229439 CTAATCTAAAACA
1 C-AATCTAAAACA
3229452 TATTGGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.18
Consensus pattern (16 bp):
CAATCTAAAACAAATG
Found at i:3230146 original size:13 final size:13
Alignment explanation
Indices: 3230128--3230225 Score: 101
Period size: 13 Copynumber: 7.5 Consensus size: 13
3230118 TCAATTATTC
3230128 CAATATGCAATAA
1 CAATATGCAATAA
3230141 CAATATGC-ATGAA
1 CAATATGCAAT-AA
*
3230154 CAATATGTAATAA
1 CAATATGCAATAA
*
3230167 CATTATGC-ATGAA
1 CAATATGCAAT-AA
3230180 CAATATGCAATAA
1 CAATATGCAATAA
* *
3230193 CATTATGCAGTAA
1 CAATATGCAATAA
**
3230206 CAATATATAATAA
1 CAATATGCAATAA
*
3230219 CAGTATG
1 CAATATG
3230226 TATGAAGAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
12 4 0.06
13 61 0.88
14 4 0.06
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (13 bp):
CAATATGCAATAA
Found at i:3230165 original size:26 final size:26
Alignment explanation
Indices: 3230128--3230240 Score: 147
Period size: 26 Copynumber: 4.3 Consensus size: 26
3230118 TCAATTATTC
* *
3230128 CAATATGCAATAACAATATGCATGAA
1 CAATATGTAATAACATTATGCATGAA
3230154 CAATATGTAATAACATTATGCATGAA
1 CAATATGTAATAACATTATGCATGAA
*
3230180 CAATATGCAATAACATTATGCA-GTAA
1 CAATATGTAATAACATTATGCATG-AA
* * *
3230206 CAATATATAATAACAGTATGTATGAA
1 CAATATGTAATAACATTATGCATGAA
*
3230232 GAATATGTA
1 CAATATGTA
3230241 TTAGCAAGTT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
25 1 0.01
26 74 0.97
27 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (26 bp):
CAATATGTAATAACATTATGCATGAA
Found at i:3230207 original size:39 final size:39
Alignment explanation
Indices: 3230131--3230238 Score: 103
Period size: 39 Copynumber: 2.8 Consensus size: 39
3230121 ATTATTCCAA
*
3230131 TATGCAATAACAATATGCATGAACAATATGTAATAACAT
1 TATGCAATAACAATATGCATGAACAATATGCAATAACAT
* * *
3230170 TATGC-ATGAACAATATGCAAT-AACATTATGCAGTAACAA
1 TATGCAAT-AACAATATGC-ATGAACAATATGCAATAACAT
** * * *
3230209 TATATAATAACAGTATGTATGAAGAATATG
1 TATGCAATAACAATATGCATGAACAATATG
3230239 TATTAGCAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
38 4 0.07
39 47 0.85
40 4 0.07
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (39 bp):
TATGCAATAACAATATGCATGAACAATATGCAATAACAT
Found at i:3232175 original size:30 final size:30
Alignment explanation
Indices: 3232139--3232241 Score: 154
Period size: 30 Copynumber: 3.4 Consensus size: 30
3232129 ATCAATTTTA
3232139 GGTTCATTAATTTCTAGCTCAGCTAGTTCT
1 GGTTCATTAATTTCTAGCTCAGCTAGTTCT
* * *
3232169 GGTTCATTAATTTTTGGCTCAGCTGGTTCT
1 GGTTCATTAATTTCTAGCTCAGCTAGTTCT
*
3232199 GGTTCATTAATTTC-AGGCTCACCTAGTTCT
1 GGTTCATTAATTTCTA-GCTCAGCTAGTTCT
3232229 GGTTCATTAATTT
1 GGTTCATTAATTT
3232242 TGGGTTCACT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (30 bp):
GGTTCATTAATTTCTAGCTCAGCTAGTTCT
Found at i:3232259 original size:30 final size:30
Alignment explanation
Indices: 3232139--3232264 Score: 148
Period size: 30 Copynumber: 4.2 Consensus size: 30
3232129 ATCAATTTTA
*
3232139 GGTTCATTAATTTCTA-GCTCAGCTAGTTCT
1 GGTTCATTAATTT-TAGGCTCACCTAGTTCT
* * *
3232169 GGTTCATTAATTTTTGGCTCAGCTGGTTCT
1 GGTTCATTAATTTTAGGCTCACCTAGTTCT
*
3232199 GGTTCATTAATTTCAGGCTCACCTAGTTCT
1 GGTTCATTAATTTTAGGCTCACCTAGTTCT
* * *
3232229 GGTTCATTAATTTTGGGTTCA-CTAATTTCT
1 GGTTCATTAATTTTAGGCTCACCT-AGTTCT
3232259 GGTTCA
1 GGTTCA
3232265 ACTGGTTCTG
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 3 0.04
30 81 0.96
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (30 bp):
GGTTCATTAATTTTAGGCTCACCTAGTTCT
Found at i:3232259 original size:60 final size:60
Alignment explanation
Indices: 3232139--3232264 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
3232129 ATCAATTTTA
* * *
3232139 GGTTCATTAATTTCTAGCTCAGCTAGTTCTGGTTCATTAATTTTTGGCTCAGCTGGTTCT
1 GGTTCATTAATTTCTAGCTCACCTAGTTCTGGTTCATTAATTTTGGGCTCAGCTAGTTCT
* *
3232199 GGTTCATTAATTTC-AGGCTCACCTAGTTCTGGTTCATTAATTTTGGGTTCA-CTAATTTCT
1 GGTTCATTAATTTCTA-GCTCACCTAGTTCTGGTTCATTAATTTTGGGCTCAGCT-AGTTCT
3232259 GGTTCA
1 GGTTCA
3232265 ACTGGTTCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 3 0.05
60 56 0.95
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (60 bp):
GGTTCATTAATTTCTAGCTCACCTAGTTCTGGTTCATTAATTTTGGGCTCAGCTAGTTCT
Found at i:3232262 original size:15 final size:15
Alignment explanation
Indices: 3232120--3232264 Score: 68
Period size: 15 Copynumber: 9.7 Consensus size: 15
3232110 CCTCAGTAGG
3232120 TTCTGGTTCA-TCAAT
1 TTCTGGTTCACT-AAT
*
3232135 TT-TAGGTTCATTAAT
1 TTCT-GGTTCACTAAT
* * *
3232150 TTCTAGCTCAGCT-AG
1 TTCTGGTTCA-CTAAT
*
3232165 TTCTGGTTCATTAAT
1 TTCTGGTTCACTAAT
* * **
3232180 TTTTGGCTCAGCT-GG
1 TTCTGGTTCA-CTAAT
*
3232195 TTCTGGTTCATTAAT
1 TTCTGGTTCACTAAT
* * *
3232210 TTCAGGCTCACCT-AG
1 TTCTGGTTCA-CTAAT
*
3232225 TTCTGGTTCATTAAT
1 TTCTGGTTCACTAAT
3232240 TT-TGGGTTCACTAAT
1 TTCT-GGTTCACTAAT
3232255 TTCTGGTTCA
1 TTCTGGTTCA
3232265 ACTGGTTCTG
Statistics
Matches: 92, Mismatches: 27, Indels: 22
0.65 0.19 0.16
Matches are distributed among these distances:
14 5 0.05
15 81 0.88
16 6 0.07
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.46
Consensus pattern (15 bp):
TTCTGGTTCACTAAT
Done.