Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009589.1 Hibiscus syriacus cultivar Beakdansim tig00116968_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: 660543
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:362738 original size:16 final size:17
Alignment explanation
Indices: 362702--362735 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
362692 GTAATAGTGC
*
362702 TATATTATATTTTAAAAA
1 TATAGTATATTTT-AAAA
362720 TATAGTATATTTTAAA
1 TATAGTATATTTTAAA
362736 TATCTTTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 3 0.20
18 12 0.80
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATAGTATATTTTAAAA
Found at i:362803 original size:29 final size:28
Alignment explanation
Indices: 362749--362822 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
362739 CTTTACTAAA
* *
362749 ATATTATTGAAAT-ATATAAATATATTAT
1 ATATTATT-AAATAAAAAAAATATATTAT
*
362777 -TCATTATTAAATATAAAAAAATTTATTAT
1 AT-ATTATTAAATA-AAAAAAATATATTAT
362806 ATATTATTAAATAAAAA
1 ATATTATTAAATAAAAA
362823 TATTATCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 5 0.13
28 10 0.26
29 23 0.59
30 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
ATATTATTAAATAAAAAAAATATATTAT
Found at i:362810 original size:26 final size:27
Alignment explanation
Indices: 362753--362845 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 27
362743 ACTAAAATAT
* *
362753 TATTGAAATATATAAATATATTATTCAT-
1 TATT-AAATATAAAAAAATATTATT-ATA
362781 TATTAAATATAAAAAAAT-TTATTATA
1 TATTAAATATAAAAAAATATTATTATA
*
362807 TATT-ATTA-AATAAAAATATTATCT-TA
1 TATTAAATATAA-AAAAATATTAT-TATA
362833 TATTATAATATAA
1 TATTA-AATATAA
362846 TTAATTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
24 2 0.04
25 11 0.20
26 19 0.35
27 13 0.24
28 7 0.13
29 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (27 bp):
TATTAAATATAAAAAAATATTATTATA
Found at i:362858 original size:25 final size:24
Alignment explanation
Indices: 362824--362906 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 24
362814 AAATAAAAAT
*
362824 ATTATCTTATATTATAATATAATTA
1 ATTATTTTATATTATAATATAA-TA
* *
362849 ATTATTTTATATAAT-AT-TAAAA
1 ATTATTTTATATTATAATATAATA
* *
362871 ATAATATTATATTATAAATATTAATA
1 ATTATTTTATATTAT-AATA-TAATA
362897 ATATATTTTA
1 AT-TATTTTA
362907 AATATTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
22 13 0.30
23 3 0.07
24 4 0.09
25 13 0.30
26 6 0.14
27 5 0.11
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTATTTTATATTATAATATAATA
Found at i:362877 original size:17 final size:17
Alignment explanation
Indices: 362857--362900 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
362847 TAATTATTTT
362857 ATATAATATTAAAAATA
1 ATATAATATTAAAAATA
* *
362874 ATATTATATTATAAATA
1 ATATAATATTAAAAATA
*
362891 TTAATAATAT
1 AT-ATAATAT
362901 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATATTAAAAATA
Found at i:362920 original size:22 final size:20
Alignment explanation
Indices: 362872--362912 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
362862 ATATTAAAAA
*
362872 TAATATTATATTATAAATAT
1 TAATAATATATTATAAATAT
*
362892 TAATAATATATTTTAAATAT
1 TAATAATATATTATAAATAT
362912 T
1 T
362913 TTAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATAATATATTATAAATAT
Found at i:363160 original size:42 final size:42
Alignment explanation
Indices: 363103--363215 Score: 192
Period size: 42 Copynumber: 2.7 Consensus size: 42
363093 TACATTTCGG
*
363103 AAAACGAATTACGTGAAACAAACACGGGAAAACGTTTTCCGA
1 AAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCCGA
* *
363145 AAAACAAATTACGTGAAACAAACACGGGAAAACATTTTCCGG
1 AAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCCGA
363187 AAAACGAATTACGTGAAAC-AACACGGGAA
1 AAAACGAATTACGTGAAACAAACACGGGAA
363216 TTCAGGGAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 10 0.15
42 57 0.85
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.15
Consensus pattern (42 bp):
AAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCCGA
Found at i:363685 original size:41 final size:42
Alignment explanation
Indices: 363597--363715 Score: 213
Period size: 41 Copynumber: 2.9 Consensus size: 42
363587 TTTCCCTGAA
*
363597 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
363639 TTCCCGTGTTTGTTTCACGTAATTTGTTTT-CGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
363680 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
363716 TGTAATTCAT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
41 39 0.53
42 34 0.47
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:363950 original size:22 final size:23
Alignment explanation
Indices: 363903--363994 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 23
363893 TAATTATTAA
* *
363903 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
363924 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
*
363947 -ATATTTTTAATATTATATAAAATAATT
1 AATATTTATAATA--ATAT--AAT-ATT
363974 AATTATATTATAATAATATAA
1 AA-TAT-TTATAATAATATAA
363995 GATATTATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
21 11 0.19
22 15 0.26
23 4 0.07
24 4 0.07
26 5 0.09
27 3 0.05
28 5 0.09
29 3 0.05
30 7 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:363960 original size:52 final size:52
Alignment explanation
Indices: 363903--364023 Score: 144
Period size: 52 Copynumber: 2.3 Consensus size: 52
363893 TAATTATTAA
*
363903 AATATTTAAAATATATTTATTAATATTTATAATAATAT-A-ATATTATATTTTT
1 AATATTTAAAATATATTAATT-ATA-TTATAATAATATAAGATATTATATTTTT
363955 AATATTATATAAA-ATAATTAATTATATTATAATAATATAAGATATTATATTTTT
1 AATATT-TA-AAATAT-ATTAATTATATTATAATAATATAAGATATTATATTTTT
364009 -AT-TTTAATAATATAT
1 AATATTTAA-AATATAT
364024 AATAAATTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 15
0.79 0.01 0.19
Matches are distributed among these distances:
50 1 0.02
51 6 0.10
52 22 0.36
53 10 0.16
54 22 0.36
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (52 bp):
AATATTTAAAATATATTAATTATATTATAATAATATAAGATATTATATTTTT
Found at i:363990 original size:18 final size:19
Alignment explanation
Indices: 363958--364003 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
363948 TATTTTTAAT
*
363958 ATTATA-TAAAATAAT-TA
1 ATTATATTATAATAATATA
363975 ATTATATTATAATAATATA
1 ATTATATTATAATAATATA
*
363994 A-GATATTATA
1 ATTATATTATA
364004 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTATATTATAATAATATA
Found at i:364026 original size:54 final size:52
Alignment explanation
Indices: 363907--364038 Score: 148
Period size: 54 Copynumber: 2.5 Consensus size: 52
363897 TATTAAAATA
*
363907 TTTAA-AATATATTTATTAA-TATTTATAATAATATAATATTATATTTTTAAT
1 TTTAATAATATA-TAATTAATTATTTATAATAATATAATATTATATTTTTAAT
*
363958 ATTATATAA-A-ATAATTAATTATATTATAATAATATAAGATATTATATTTTT-AT
1 TTTA-ATAATATATAATTAATTAT-TTATAATAATAT-A-ATATTATATTTTTAAT
* *
364011 TTTAATAATATATAATAAATTTTTTATA
1 TTTAATAATATATAATTAATTATTTATA
364039 TATTTAATAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
50 6 0.09
51 7 0.10
52 18 0.26
53 14 0.21
54 23 0.34
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (52 bp):
TTTAATAATATATAATTAATTATTTATAATAATATAATATTATATTTTTAAT
Found at i:364071 original size:59 final size:59
Alignment explanation
Indices: 363931--364076 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 59
363921 ATTAATATTT
* *
363931 ATAATAATATAATATTATAT-TTTTAATATTATATAAAATAATTAATTATATTATAATA
1 ATAATAATATTATATTATATATTTTAATAATATATAAAATAATTAATTATATTATAATA
* * ** *
363989 AT-ATAAGATATTATATT-TTTATTTTAATAATATATAATA-AATTTTTTATATATTTAATA
1 ATAAT-A-ATATTATATTATATATTTTAATAATATATAAAATAATTAATTATAT-TATAATA
*
364048 ATGAATAATATTAT-TTATATATTTCAATA
1 AT-AATAATATTATATTATATATTTTAATA
364077 TATTTTAGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
57 2 0.03
58 17 0.24
59 50 0.69
60 1 0.01
61 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (59 bp):
ATAATAATATTATATTATATATTTTAATAATATATAAAATAATTAATTATATTATAATA
Found at i:364123 original size:16 final size:18
Alignment explanation
Indices: 364093--364125 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
364083 AGTAAAGATA
364093 TTTAAATATACTAATATT
1 TTTAAATATACTAATATT
364111 TTTAAA-ATA-TAATAT
1 TTTAAATATACTAATAT
364126 AGCACTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAAATATACTAATATT
Found at i:364458 original size:20 final size:20
Alignment explanation
Indices: 364401--364450 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
364391 TTTCCAGATG
364401 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
364421 TTTTCCTGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
364441 TTTTCCAGAA
1 TTTTCCAGAA
364451 TTCAAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:364475 original size:29 final size:29
Alignment explanation
Indices: 364433--364494 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
364423 TTCCTGAAAT
** *
364433 GTAATTCATTTTCCAG-AATTCAAATTTCA
1 GTAATTCAAATTCCAGTAATTC-AATTCCA
364462 GTAATTCAAATTCCAGTAATTCAATTCCA
1 GTAATTCAAATTCCAGTAATTCAATTCCA
364491 GTAA
1 GTAA
364495 GGGTCTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (29 bp):
GTAATTCAAATTCCAGTAATTCAATTCCA
Found at i:364489 original size:14 final size:15
Alignment explanation
Indices: 364433--364494 Score: 83
Period size: 14 Copynumber: 4.3 Consensus size: 15
364423 TTCCTGAAAT
**
364433 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
364448 G-AATTCAAATTTCA
1 GTAATTCAAATTCCA
364462 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
364477 GTAATTC-AATTCCA
1 GTAATTCAAATTCCA
364491 GTAA
1 GTAA
364495 GGGTCTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
14 22 0.52
15 20 0.48
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:364632 original size:43 final size:42
Alignment explanation
Indices: 364545--364665 Score: 224
Period size: 43 Copynumber: 2.9 Consensus size: 42
364535 TTTCCCTGAA
*
364545 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
364587 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCG-TTTTCCGGAAAACGTT
364630 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
364666 TGTAATTCAT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
42 36 0.47
43 41 0.53
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:364874 original size:30 final size:28
Alignment explanation
Indices: 364840--364907 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
364830 TTCATCAAAA
*
364840 TATTAATTATTAAAATATTTAAAATATATT
1 TATTAA-TATTAAAATA-ATAAAATATATT
* *
364870 TATTAATATTATAATAATAATATATATT
1 TATTAATATTAAAATAATAAAATATATT
364898 T-TTAATATTA
1 TATTAATATTA
364908 TATAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.26
28 11 0.31
29 9 0.26
30 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTAATATTAAAATAATAAAATATATT
Found at i:364928 original size:31 final size:28
Alignment explanation
Indices: 364863--364918 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
364853 AATATTTAAA
*
364863 ATATATTTATTAATATTATAATAATAAT
1 ATATATTTATTAATATTATAAAAATAAT
364891 ATATATTT-TTAATATTATATAAAATAAT
1 ATATATTTATTAATATTATA-AAAATAAT
364919 CAATTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATATTTATTAATATTATAAAAATAAT
Found at i:364969 original size:24 final size:27
Alignment explanation
Indices: 364922--365024 Score: 84
Period size: 28 Copynumber: 3.6 Consensus size: 27
364912 AAATAATCAA
*
364922 TTATATTATAATAATATAAGATATTATATTT
1 TTATATT-TAATAATAT---ATATAATATTT
*
364953 TTAT-TTTAATAATATATAATAATTTTT
1 TTATATTTAATAATATAT-ATAATATTT
*
364980 TTATATTTAATAATGA-ATAATATTATTT
1 TTATATTTAATAAT-ATAT-ATAATATTT
*
365008 ATATATTTCAATAATAT
1 TTATATTT-AATAATAT
365025 TTTAGTAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
26 2 0.03
27 11 0.18
28 27 0.44
29 16 0.26
30 2 0.03
31 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (27 bp):
TTATATTTAATAATATATATAATATTT
Found at i:365263 original size:20 final size:20
Alignment explanation
Indices: 365185--365254 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
365175 TTTCCAGATG
365185 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
365205 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
365225 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
365245 TTTTCCAGAA
1 TTTTCCAGAA
365255 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:365263 original size:40 final size:40
Alignment explanation
Indices: 365185--365263 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
365175 TTTCCAGATG
* **
365185 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
365225 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
365264 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:365273 original size:15 final size:15
Alignment explanation
Indices: 365237--365318 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
365227 TTACAGAAAT
**
365237 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
365252 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
365266 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
365281 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
365296 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
365311 GTAATTCA
1 GTAATTCA
365319 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:365289 original size:30 final size:30
Alignment explanation
Indices: 365237--365318 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
365227 TTACAGAAAT
365237 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
365266 GTAATTCATTTTCCAGTAATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
365296 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
365319 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:365309 original size:45 final size:44
Alignment explanation
Indices: 365237--365323 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
365227 TTACAGAAAT
*
365237 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAATTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
365281 GTAATTCAAATTT-CAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTC-AATTTCCAG-AATTCAAATTCCAGTAATTCATTTTC
365324 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 10 0.25
45 30 0.75
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTCAATTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:365363 original size:60 final size:60
Alignment explanation
Indices: 365297--365419 Score: 176
Period size: 60 Copynumber: 2.0 Consensus size: 60
365287 CAAATTTCAG
* * *
365297 TAATTCAAATTCCAGTAATTCATTTTCTGGAAAACCAATTACA-GCTAAACAAACAAACCC
1 TAATTCAAATTCCAATAATTCATTTTCCGAAAAACCAATTACATGC-AAACAAACAAACCC
* **
365357 TAATTCAAATTCCAATAATTCATTTTCCGAAAAACCAATTATATGCAAACAAACCTACCC
1 TAATTCAAATTCCAATAATTCATTTTCCGAAAAACCAATTACATGCAAACAAACAAACCC
365417 TAA
1 TAA
365420 AATTACGTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 54 0.96
61 2 0.04
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.28
Consensus pattern (60 bp):
TAATTCAAATTCCAATAATTCATTTTCCGAAAAACCAATTACATGCAAACAAACAAACCC
Found at i:366306 original size:14 final size:15
Alignment explanation
Indices: 366282--366355 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
366272 AAATAGTTAT
* *
366282 TATTTTTTATATTAA
1 TATTATTTATATAAA
366297 TA-TATTTATATAAA
1 TATTATTTATATAAA
*
366311 TATTATTTTTTTTATTAAAA
1 TATTA---TTTATA-T-AAA
* *
366331 TAATATTTATATAAT
1 TATTATTTATATAAA
366346 TATTATTTAT
1 TATTATTTAT
366356 TTAGAATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
14 12 0.26
15 15 0.33
16 1 0.02
17 5 0.11
18 5 0.11
19 1 0.02
20 7 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTTATATAAA
Found at i:366320 original size:32 final size:34
Alignment explanation
Indices: 366279--366358 Score: 110
Period size: 35 Copynumber: 2.4 Consensus size: 34
366269 TTTAAATAGT
366279 TATTATTTTTTATATT-AAT-ATATTTATATAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
* *
366311 TATTATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATATT-AAATAATATTTATATAAA
366346 TATTATTTATTTA
1 TATTATTT-TTTA
366359 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
32 15 0.37
34 3 0.07
35 20 0.49
36 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:366322 original size:34 final size:33
Alignment explanation
Indices: 366246--366353 Score: 103
Period size: 35 Copynumber: 3.1 Consensus size: 33
366236 GTGGAAAGAA
* *
366246 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
366280 ATTATTTTTTATATTAATATATTTATATAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
366315 ATTTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
366350 ATTT
1 ATTT
366354 ATTTAGAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
33 1 0.02
34 27 0.42
35 29 0.45
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:368107 original size:21 final size:21
Alignment explanation
Indices: 368077--368124 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
368067 GCAGGGGTAC
* *
368077 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
368098 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
368119 ATGCCA
1 ATGCCA
368125 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:368154 original size:21 final size:21
Alignment explanation
Indices: 368128--368221 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
368118 TATGCCATCT
* *
368128 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
368149 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
368170 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
368191 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
368212 CCGCAGGGTT
1 CCGCAGGGTT
368222 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:368806 original size:27 final size:28
Alignment explanation
Indices: 368739--368832 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 28
368729 GATAAATGTT
* *
368739 TTTAAAATACAAATTATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
368767 TTTAAAATAAAAATAATATTATTC-AAA
1 TTTAAAATAAAAATAATATTATTCGAAA
*
368794 TTTAAATTTAAAATATAAATTATAGTATTCGAAA
1 TTTAAA-ATAAAA-AT-AA-TAT--TATTCGAAA
368828 TTTAA
1 TTTAA
368833 CATTAAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
27 9 0.16
28 27 0.48
29 2 0.04
30 2 0.04
31 3 0.05
33 5 0.09
34 8 0.14
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCGAAA
Found at i:369602 original size:128 final size:128
Alignment explanation
Indices: 369223--370234 Score: 1976
Period size: 128 Copynumber: 7.9 Consensus size: 128
369213 AAGTTATTCA
*
369223 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369288 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
369351 ACTGATATATCTAGTGTCCCCGA-GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369415 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
369478 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369543 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
369606 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369671 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
369734 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369799 GACGAAATAATGGAAGGCGCGCCCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
369861 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369926 GACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
369988 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
370053 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
370116 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
370181 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
370235 CCGATTATAG
Statistics
Matches: 877, Mismatches: 4, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
126 4 0.00
127 368 0.42
128 505 0.58
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:369831 original size:255 final size:256
Alignment explanation
Indices: 369223--370234 Score: 1976
Period size: 255 Copynumber: 4.0 Consensus size: 256
369213 AAGTTATTCA
*
369223 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369288 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
*
369353 TGATATATCTAGTGTCCCCGA-GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA
369417 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
369478 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369543 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
*
369608 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA
369673 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
369734 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
369799 GACGAAATAATGGAAGGCGCGCCCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
369863 TGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA
369928 CGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
369988 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
370053 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
370118 TGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA
370183 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
370235 CCGATTATAG
Statistics
Matches: 752, Mismatches: 2, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
254 132 0.18
255 393 0.52
256 227 0.30
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (256 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
TGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA
CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:374876 original size:10 final size:10
Alignment explanation
Indices: 374863--374912 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
374853 CATTTAAATG
*
374863 ATAAACGAAC
1 ATAAACAAAC
374873 ATAAACAAAC
1 ATAAACAAAC
* *
374883 GTAAACGAAC
1 ATAAACAAAC
374893 ATAAACAAAC
1 ATAAACAAAC
*
374903 A-ACACAAAC
1 ATAAACAAAC
374912 A
1 A
374913 CAAAAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
9 8 0.24
10 26 0.76
ACGTcount: A:0.64, C:0.22, G:0.06, T:0.08
Consensus pattern (10 bp):
ATAAACAAAC
Found at i:374889 original size:20 final size:20
Alignment explanation
Indices: 374864--374902 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
374854 ATTTAAATGA
374864 TAAACGAACATAAACAAACG
1 TAAACGAACATAAACAAACG
374884 TAAACGAACATAAACAAAC
1 TAAACGAACATAAACAAAC
374903 AACACAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.21, G:0.08, T:0.10
Consensus pattern (20 bp):
TAAACGAACATAAACAAACG
Found at i:378676 original size:32 final size:32
Alignment explanation
Indices: 378635--378702 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
378625 GCTTTTTGGT
378635 ATTATTTTCTAAAGGTACTCACGTGTCTCTGC
1 ATTATTTTCTAAAGGTACTCACGTGTCTCTGC
*
378667 ATTATTTTCTAAAGGTACTCATGTGTCTCTGC
1 ATTATTTTCTAAAGGTACTCACGTGTCTCTGC
378699 ATTA
1 ATTA
378703 CTCTCTAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (32 bp):
ATTATTTTCTAAAGGTACTCACGTGTCTCTGC
Found at i:380891 original size:36 final size:36
Alignment explanation
Indices: 380844--380915 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
380834 TATGTGCAGG
*
380844 GGGAACAGATTCCTCCCT-GGGGGGTATTGATTCCCC
1 GGGAACAGATTCC-CCCTGGGGGGGTATCGATTCCCC
*
380880 GGGAACAGATTCCCCTTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
380916 CCTAAATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 3 0.09
36 30 0.91
ACGTcount: A:0.17, C:0.28, G:0.32, T:0.24
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
Found at i:381545 original size:15 final size:15
Alignment explanation
Indices: 381527--381561 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
381517 CGAGGGTATT
*
381527 GTAGTCCTTCGGGAC
1 GTAGTCCTTCAGGAC
381542 GTAGTCCTTCAGGAC
1 GTAGTCCTTCAGGAC
381557 GTAGT
1 GTAGT
381562 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCAGGAC
Found at i:383628 original size:2 final size:2
Alignment explanation
Indices: 383621--383665 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
383611 TATCATTGGA
383621 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
383663 AT A
1 AT A
383666 ATAATTTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:384126 original size:2 final size:2
Alignment explanation
Indices: 384119--384164 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
384109 TATTTGGATC
384119 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
384161 AT AT
1 AT AT
384165 GATTAAGGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:386951 original size:36 final size:36
Alignment explanation
Indices: 386904--386973 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
386894 TGTGCAGGGG
386904 GAACAGATTCCCCCAT-GGGGGGTATCGATTCCCCGA
1 GAACAGATT-CCCCATGGGGGGGTATCGATTCCCCGA
*
386940 GAACAGATTCCCCTTGGGGGGGTATCGATTCCCC
1 GAACAGATTCCCCATGGGGGGGTATCGATTCCCC
386974 CTAAATGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 5 0.16
36 27 0.84
ACGTcount: A:0.20, C:0.30, G:0.29, T:0.21
Consensus pattern (36 bp):
GAACAGATTCCCCATGGGGGGGTATCGATTCCCCGA
Found at i:387605 original size:15 final size:15
Alignment explanation
Indices: 387587--387621 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
387577 CGAGGGTTTT
387587 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
387602 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
387617 GTAGT
1 GTAGT
387622 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:389322 original size:39 final size:39
Alignment explanation
Indices: 389279--389371 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
389269 AGACGTTGTA
*
389279 CACTCCTAGAGTC-TATACGCTTGGTATGAAGAAG-TCGTG
1 CACTCCTAGAGTCTTAT-CGATTGGTATGAAGAAGAT-GTG
* *
389318 CACTCCTAGAGTCTTATCGATTGGTCTGAAGATGATGTG
1 CACTCCTAGAGTCTTATCGATTGGTATGAAGAAGATGTG
389357 CACTCCT-GAAGTCTT
1 CACTCCTAG-AGTCTT
389372 TACGTTTAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 1 0.02
39 43 0.90
40 4 0.08
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (39 bp):
CACTCCTAGAGTCTTATCGATTGGTATGAAGAAGATGTG
Found at i:391007 original size:25 final size:25
Alignment explanation
Indices: 390960--391008 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
390950 TTATATATAT
* *
390960 TTTTAGACATTGGACTTTAAATTTA
1 TTTTAAACATTGAACTTTAAATTTA
* *
390985 TTTTAAACATTGAATTTTGAATTT
1 TTTTAAACATTGAACTTTAAATTT
391009 GAATTTGATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (25 bp):
TTTTAAACATTGAACTTTAAATTTA
Found at i:401038 original size:26 final size:26
Alignment explanation
Indices: 401002--401063 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
400992 AGAAGAAACT
401002 GCAACCATTGTATTTCACACGTGATA
1 GCAACCATTGTATTTCACACGTGATA
401028 GCAACCATTGTATTTCACACGTGATA
1 GCAACCATTGTATTTCACACGTGATA
401054 GCAACCATTG
1 GCAACCATTG
401064 CTTGATATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (26 bp):
GCAACCATTGTATTTCACACGTGATA
Found at i:402951 original size:20 final size:20
Alignment explanation
Indices: 402889--402958 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
402879 AGGCTTAAAA
**
402889 GTATCGATACTCATACATG-G
1 GTATCGATACT-ATAGGTGAG
402909 GTATCGATACTATAGGTGAG
1 GTATCGATACTATAGGTGAG
* *
402929 GTATCAATACTCATAGG-GTG
1 GTATCGATACT-ATAGGTGAG
402949 GTATCGATAC
1 GTATCGATAC
402959 CAAGTTCACT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
19 5 0.12
20 33 0.77
21 5 0.12
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (20 bp):
GTATCGATACTATAGGTGAG
Found at i:403223 original size:19 final size:18
Alignment explanation
Indices: 403196--403234 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
403186 TTCAATAAGG
403196 TATTAGTATCGATACCACA
1 TATTAGTATCGATACC-CA
*
403215 TATTCGTATCGATACCCA
1 TATTAGTATCGATACCCA
403233 TA
1 TA
403235 GGCCAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (18 bp):
TATTAGTATCGATACCCA
Found at i:404375 original size:219 final size:218
Alignment explanation
Indices: 403992--404428 Score: 833
Period size: 219 Copynumber: 2.0 Consensus size: 218
403982 TTATTTTGAA
403992 TGATTTGGAGCTTCCCATATTTTATAAACTTTAAATTATCACATTTTATTTAATTTTACTTGGAT
1 TGATTTGGAGCTTCCCATATTTTATAAACTTTAAATTATCACATTTTATTTAATTTTACTTGGAT
404057 GAATTTTATATGATATTTTAAAAAAAATTTGGGTTAGCCACTCTACAGATCTCGTGTGACATCGT
66 GAATTTTATATGATATTTTAAAAAAAATTTGGGTTAGCCACTCTACAGATCTCGTGTGACATCGT
404122 GATCTAATGATCTTTGGGTCGGACTGGATTAGGATGTTACATTT-TTGGTATCAAAGTGTAACAC
131 GATCTAATGATCTTTGGGTCGGACTGGATTAGGATGTTACATTTATTGGTATCAAAGTGTAACAC
404186 CCCATACCTGGTCTAGAAGATAG
196 CCCATACCTGGTCTAGAAGATAG
404209 TGATTTGGGAGCTTCCCATATTTTATAAACTTTAAATTATCACATTTTATTTAATTTTACTTGGA
1 TGATTT-GGAGCTTCCCATATTTTATAAACTTTAAATTATCACATTTTATTTAATTTTACTTGGA
404274 TGAA-TTTATATGATATTTTAAAGAAAAATTTTGGGTTAGCCACTCTACAGATCTCGTGTGACAT
65 TGAATTTTATATGATATTTTAAA-AAAAA-TTTGGGTTAGCCACTCTACAGATCTCGTGTGACAT
404338 CGTGATCTAATGATCTTTGGGTCGGACTGGATTAGGATGTTACATTTATTGGTATCAAAGTGTAA
128 CGTGATCTAATGATCTTTGGGTCGGACTGGATTAGGATGTTACATTTATTGGTATCAAAGTGTAA
404403 CACCCCATACCTGGTCTAGAAGATAG
193 CACCCCATACCTGGTCTAGAAGATAG
404429 ACTTGGATAC
Statistics
Matches: 216, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
217 24 0.11
218 67 0.31
219 82 0.38
220 43 0.20
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (218 bp):
TGATTTGGAGCTTCCCATATTTTATAAACTTTAAATTATCACATTTTATTTAATTTTACTTGGAT
GAATTTTATATGATATTTTAAAAAAAATTTGGGTTAGCCACTCTACAGATCTCGTGTGACATCGT
GATCTAATGATCTTTGGGTCGGACTGGATTAGGATGTTACATTTATTGGTATCAAAGTGTAACAC
CCCATACCTGGTCTAGAAGATAG
Found at i:409511 original size:25 final size:25
Alignment explanation
Indices: 409482--409538 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
409472 TTAGACTAAT
* * *
409482 TCAGTGGAAGGTTTAGATGGGTGTA
1 TCAGTGAAAAGTTCAGATGGGTGTA
*
409507 TCAGTGAAAAGTTCAGATTGGTGTA
1 TCAGTGAAAAGTTCAGATGGGTGTA
*
409532 TCGGTGA
1 TCAGTGA
409539 GAAAATAGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.07, G:0.35, T:0.32
Consensus pattern (25 bp):
TCAGTGAAAAGTTCAGATGGGTGTA
Found at i:413369 original size:21 final size:21
Alignment explanation
Indices: 413343--413409 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
413333 AATTCGCGTT
413343 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
*
413364 GTGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
*
413385 GCGATTTTCAATTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
413406 GCGA
1 GCGA
413410 AATGCAACGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:419882 original size:21 final size:18
Alignment explanation
Indices: 419843--419894 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
419833 TTTTTTTAAC
*
419843 AATAAACAAATAT-AATAT
1 AATAAA-AATTATAAATAT
419861 AAATAAATAATGTATAAATAT
1 -AATAAA-AAT-TATAAATAT
419882 AATAAAAATTATA
1 AATAAAAATTATA
419895 TAACAATACG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 11 0.38
20 9 0.31
21 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AATAAAAATTATAAATAT
Found at i:434042 original size:18 final size:18
Alignment explanation
Indices: 434019--434053 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
434009 AGTTGAAAAA
*
434019 AAAAGAGGAAAAAATAAT
1 AAAAGAAGAAAAAATAAT
*
434037 AAAAGAAGAGAAAATAA
1 AAAAGAAGAAAAAATAA
434054 GGTAGGTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (18 bp):
AAAAGAAGAAAAAATAAT
Found at i:435071 original size:98 final size:98
Alignment explanation
Indices: 434807--435605 Score: 1157
Period size: 98 Copynumber: 8.0 Consensus size: 98
434797 TTTACCCAGA
434807 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
434872 AGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGA
66 AGGGACCGCTGGTTGTCAA-TAA-A-----CAATTTCAGG
*
434912 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
434977 AGGGACCGCTGGTTGTCAATAAACAATTTCAGG
66 AGGGACCGCTGGTTGTCAATAAACAATTTCAGG
* *
435010 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
435075 AGGGACCGCTGGTTGTCAATAAACAATTTCAGG
66 AGGGACCGCTGGTTGTCAATAAACAATTTCAGG
*
435108 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
435173 AGGGACCGCTGGTTGTCAATAAACAATTTCAAG
66 AGGGACCGCTGGTTGTCAATAAACAATTTCAGG
435206 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
435271 AGGGACCGCTGGTTGTCAATAAACAATTTCAGA
66 AGGGACCGCTGGTTGTCAATAAACAATTTCAGG
*
435304 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
435369 AGGGACCGCTGGTTGTCAATAAACAATTTC---
66 AGGGACCGCTGGTTGTCAATAAACAATTTCAGG
435399 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC-A----ACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
435458 AGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAAT--A-AA-----CAATTTCAGG
* * * *
435499 GCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGACAACACAAGTTCA
1 GCCAA-TT-----------TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
*
435564 ACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTC
54 ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
435606 CCAATTCCAA
Statistics
Matches: 649, Mismatches: 16, Indels: 53
0.90 0.02 0.07
Matches are distributed among these distances:
89 27 0.04
91 1 0.00
92 2 0.00
93 1 0.00
94 50 0.08
97 7 0.01
98 391 0.60
101 4 0.01
102 2 0.00
103 1 0.00
104 2 0.00
105 83 0.13
110 7 0.01
113 41 0.06
114 1 0.00
115 2 0.00
116 1 0.00
118 26 0.04
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (98 bp):
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAATAAACAATTTCAGG
Found at i:435505 original size:12 final size:12
Alignment explanation
Indices: 435488--435520 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
435478 AAACAACTTC
435488 CCAATTTCAGAG
1 CCAATTTCAGAG
435500 CCAATTTCAGAG
1 CCAATTTCAGAG
435512 CCAATTTCA
1 CCAATTTCA
435521 ACTTCACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (12 bp):
CCAATTTCAGAG
Found at i:449062 original size:17 final size:19
Alignment explanation
Indices: 449040--449075 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
449030 ACTTTTGTAA
449040 TAAAAT-ATTTA-ATTTTT
1 TAAAATAATTTATATTTTT
449057 TAAAATAATTTATATTTTT
1 TAAAATAATTTATATTTTT
449076 AATAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAAAATAATTTATATTTTT
Found at i:449082 original size:20 final size:19
Alignment explanation
Indices: 449032--449084 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
449022 TGATTAATAC
449032 TTTTGTAATAAA-ATATTTAA
1 TTTT-TAATAAATA-ATTTAA
*
449052 TTTTTTA-AAATAATTTATA
1 TTTTTAATAAATAATTTA-A
449071 TTTTTAATAAATAA
1 TTTTTAATAAATAA
449085 AGTTTTGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 8 0.29
19 10 0.36
20 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTTAATAAATAATTTAA
Found at i:450599 original size:29 final size:29
Alignment explanation
Indices: 450555--450628 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
450545 TTACAGTGAG
450555 CTTGGAGGTCGCCATGGCATCCGAGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
* * *
450584 CTTGGAGGTTGTCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
450613 CTTGGAGGTCGCCATG
1 CTTGGAGGTCGCCATG
450629 CGAGCGACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.22
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGAGCGAC
Found at i:450988 original size:20 final size:20
Alignment explanation
Indices: 450960--451014 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
450950 GACCATCCGA
*
450960 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGAAT
* *
450980 CCGATGCCATCCGAGAGAAT
1 CCGAGGCCATCCGAAAGAAT
451000 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
451015 CGAGCTATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.35, G:0.25, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGAAT
Found at i:451055 original size:23 final size:23
Alignment explanation
Indices: 451007--451059 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
450997 AATCCGAGGC
*
451007 CATCCGAACGAGCTATGTGAGAG
1 CATCCGAACGAGCTATGCGAGAG
**
451030 CATCCGAACGAGCTATGCGATTG
1 CATCCGAACGAGCTATGCGAGAG
451053 CATCCGA
1 CATCCGA
451060 GGGCAACCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
CATCCGAACGAGCTATGCGAGAG
Found at i:451076 original size:33 final size:33
Alignment explanation
Indices: 451033--451107 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
451023 GTGAGAGCAT
* ** *
451033 CCGAACGAGCTATGCGATTGCATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
451066 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
451099 CCGAGCGAG
1 CCGAGCGAG
451108 GGTAGGTCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.27, C:0.27, G:0.36, T:0.11
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
Found at i:451143 original size:29 final size:29
Alignment explanation
Indices: 451108--451165 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
451098 ACCGAGCGAG
451108 GGTAGGTCGCCCGGAGTACATGGCGACCT
1 GGTAGGTCGCCCGGAGTACATGGCGACCT
** * *
451137 GGTAGGTCGCTGGGCGTGCATGGCGACCT
1 GGTAGGTCGCCCGGAGTACATGGCGACCT
451166 ACCCCAGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.26, G:0.41, T:0.19
Consensus pattern (29 bp):
GGTAGGTCGCCCGGAGTACATGGCGACCT
Found at i:451327 original size:1 final size:1
Alignment explanation
Indices: 451323--451384 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
451313 TTATTAGATT
* * * * * * * *
451323 AAAAAAATAAAAAATAAAAAATAAAAAAATAAAAAATAAAAAATAAAAATAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
451385 TAATTTTTTA
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (1 bp):
A
Found at i:451336 original size:7 final size:7
Alignment explanation
Indices: 451324--451384 Score: 106
Period size: 7 Copynumber: 8.7 Consensus size: 7
451314 TATTAGATTA
451324 AAAAAAT
1 AAAAAAT
451331 AAAAAAT
1 AAAAAAT
451338 AAAAAAT
1 AAAAAAT
451345 AAAAAAAT
1 -AAAAAAT
451353 AAAAAAT
1 AAAAAAT
451360 AAAAAAT
1 AAAAAAT
451367 -AAAAAT
1 AAAAAAT
451373 AAAAAAT
1 AAAAAAT
451380 AAAAA
1 AAAAA
451385 TAATTTTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.12
7 39 0.75
8 7 0.13
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:451350 original size:22 final size:22
Alignment explanation
Indices: 451322--451384 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
451312 ATTATTAGAT
451322 TAAAAAAATAAAAAATAAAAAA
1 TAAAAAAATAAAAAATAAAAAA
451344 TAAAAAAATAAAAAATAAAAAA
1 TAAAAAAATAAAAAATAAAAAA
451366 T--AAAAATAAAAAATAAAAA
1 TAAAAAAATAAAAAATAAAAA
451385 TAATTTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 18 0.44
22 23 0.56
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (22 bp):
TAAAAAAATAAAAAATAAAAAA
Found at i:461049 original size:3 final size:3
Alignment explanation
Indices: 461036--461067 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
461026 ATGGAGACAC
*
461036 AAG ACG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
461068 TTGTAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:478800 original size:23 final size:23
Alignment explanation
Indices: 478770--478817 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
478760 TGTTGAAAAA
*
478770 TCAAAATTTTCAGCTTACAATGG
1 TCAAAATTTTCAGCTTACAAAGG
478793 TCAAAATTTTCAGCTTACAAAGG
1 TCAAAATTTTCAGCTTACAAAGG
478816 TC
1 TC
478818 TTATTTTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (23 bp):
TCAAAATTTTCAGCTTACAAAGG
Found at i:479598 original size:18 final size:18
Alignment explanation
Indices: 479555--479601 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
479545 TATAATAAAT
*
479555 AAAAAGAAAAGAAAAAGA
1 AAAAACAAAAGAAAAAGA
479573 AAATAACAAAAGAAAGAA-A
1 AAA-AACAAAAGAAA-AAGA
479592 AAAAACAAAA
1 AAAAACAAAA
479602 ACTAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.38
19 14 0.54
20 2 0.08
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAACAAAAGAAAAAGA
Found at i:479616 original size:24 final size:24
Alignment explanation
Indices: 479589--479636 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
479579 CAAAAGAAAG
479589 AAAAAAAACAAAAACTAAAAATAT
1 AAAAAAAACAAAAACTAAAAATAT
* *
479613 AAAAATAACAAAAACTAATAATAT
1 AAAAAAAACAAAAACTAAAAATAT
479637 GTAGCGCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (24 bp):
AAAAAAAACAAAAACTAAAAATAT
Found at i:480092 original size:17 final size:17
Alignment explanation
Indices: 480070--480102 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
480060 CGTGTAGGTG
480070 AATATGTGATTTACGTT
1 AATATGTGATTTACGTT
480087 AATATGTGATTTACGT
1 AATATGTGATTTACGT
480103 CACGACGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (17 bp):
AATATGTGATTTACGTT
Found at i:484097 original size:18 final size:18
Alignment explanation
Indices: 484074--484108 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
484064 GTTCTTAAGG
484074 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
484092 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
484109 AATTTACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:486978 original size:26 final size:25
Alignment explanation
Indices: 486913--486986 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 25
486903 GTAAAAGTAT
*
486913 TAATTTAATTTTATTT--CATTAAAA
1 TAATTTAA-TTTATTTAATATTAAAA
*
486937 T-ATTTAATGGTA-TTAATATTATAAA
1 TAATTTAAT-TTATTTAATATTA-AAA
*
486962 TAATTTAATTTATTTAATAATAAAA
1 TAATTTAATTTATTTAATATTAAAA
486987 ATGAAATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 3 0.08
23 8 0.20
24 5 0.12
25 9 0.22
26 15 0.38
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (25 bp):
TAATTTAATTTATTTAATATTAAAA
Found at i:498265 original size:2 final size:2
Alignment explanation
Indices: 498260--498290 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
498250 TTTCAAAACC
498260 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 A
498291 ATGAGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:498599 original size:87 final size:87
Alignment explanation
Indices: 498449--498609 Score: 286
Period size: 87 Copynumber: 1.9 Consensus size: 87
498439 CAACGTACTC
* *
498449 TACCAACATATTTTATATATACGTATAGTTCGTTATAAACAATACAAAATGACAATTGACAAAGT
1 TACCAACATATTTTATATATACGTATAGTGCGGTATAAACAATACAAAATGACAATTGACAAAGT
498514 CCTAAAAGTTCATATGACTTTG
66 CCTAAAAGTTCATATGACTTTG
* *
498536 TACCAACATATTTTATATATACGTATAGTGCGGTATAAACAATACACAATGACAATTGGCAAAGT
1 TACCAACATATTTTATATATACGTATAGTGCGGTATAAACAATACAAAATGACAATTGACAAAGT
498601 CCTAAAAGT
66 CCTAAAAGT
498610 CCATCGATAC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (87 bp):
TACCAACATATTTTATATATACGTATAGTGCGGTATAAACAATACAAAATGACAATTGACAAAGT
CCTAAAAGTTCATATGACTTTG
Found at i:499274 original size:2 final size:2
Alignment explanation
Indices: 499267--499312 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
499257 ATTATATTTA
499267 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
499309 AT AT
1 AT AT
499313 GTTAAATTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:499644 original size:2 final size:2
Alignment explanation
Indices: 499637--499686 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
499627 TTACAATTCA
499637 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
499679 AT AT AT AT
1 AT AT AT AT
499687 GTGAGTGATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:518363 original size:23 final size:24
Alignment explanation
Indices: 518334--518378 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
518324 TTAAATTTTA
*
518334 TTTTATAACTA-TAAATTTATACT
1 TTTTATAACAATTAAATTTATACT
*
518357 TTTTATATCAATTAAATTTATA
1 TTTTATAACAATTAAATTTATA
518379 AAATTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTATAACAATTAAATTTATACT
Found at i:518656 original size:35 final size:35
Alignment explanation
Indices: 518609--518720 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
518599 AAAACATTCC
*
518609 TCAATTTCATTCTAAACCCCAAAATCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAAATCCAAAATAAT
* * *
518644 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAAATCCAAAATAAT
* * * * * *
518679 TCAATTACATTCTAAAACTCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAAATCCAAAATAAT
518714 TCAATTT
1 TCAATTT
518721 AAGGAGGAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAAATCCAAAATAAT
Found at i:519820 original size:35 final size:35
Alignment explanation
Indices: 519772--519883 Score: 122
Period size: 35 Copynumber: 3.2 Consensus size: 35
519762 AAAAAGACAA
*
519772 AAATTGAAGTATTTTAGAATTTGGATTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGATTTTAGAATG
* *
519807 TAATTGAATTATTTTAGAATTT--ATGGTTTAAAATG
1 AAATTGAATTATTTTAGAATTTGGAT--TTTAGAATG
* * *
519842 AAATTGAATTACTTTGGAATTTGTG-GTTTAGAATG
1 AAATTGAATTATTTTAGAATTTG-GATTTTAGAATG
519877 AAATTGA
1 AAATTGA
519884 GGATTGTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
33 2 0.03
35 62 0.97
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.44
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGGATTTTAGAATG
Found at i:522458 original size:84 final size:85
Alignment explanation
Indices: 522302--522470 Score: 277
Period size: 84 Copynumber: 2.0 Consensus size: 85
522292 AACTACAATA
* *
522302 TTGATTATTTTCGTTTAAGTTTTGTACACTTTTTCTTTTCAAATTCAGAAAATATAACATTTGGT
1 TTGATCATTTTCGTTTAAG-TTTGTACACTTATTCTTTTCAAATTCAGAAAATATAACATTTGGT
522367 TAGTTTCGTTTTTATTTAAGG
65 TAGTTTCGTTTTTATTTAAGG
* *
522388 TTGATCATTTTCGTTTAAG-TTGTACACTTATTCTTTTCAAATTCAGAAAATATAATATTTTGTT
1 TTGATCATTTTCGTTTAAGTTTGTACACTTATTCTTTTCAAATTCAGAAAATATAACATTTGGTT
*
522452 ATTTTCGTTTTTATTTAAG
66 AGTTTCGTTTTTATTTAAG
522471 ATATGATTAC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 60 0.77
86 18 0.23
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (85 bp):
TTGATCATTTTCGTTTAAGTTTGTACACTTATTCTTTTCAAATTCAGAAAATATAACATTTGGTT
AGTTTCGTTTTTATTTAAGG
Found at i:524657 original size:15 final size:15
Alignment explanation
Indices: 524637--524671 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
524627 AAGTTTATAA
524637 AATTTGAGTCGAGTC
1 AATTTGAGTCGAGTC
*
524652 AATTTGATTCGAGTC
1 AATTTGAGTCGAGTC
*
524667 GATTT
1 AATTT
524672 TTCGAGTTTT
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:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (15 bp):
AATTTGAGTCGAGTC
Found at i:527801 original size:29 final size:30
Alignment explanation
Indices: 527762--527823 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
527752 TTTGTAGACC
* * *
527762 CTAAACTTTTCAATATTTATACTTTAGTCA
1 CTAAACTTTTCAAAACTTACACTTTAGTCA
*
527792 CTAAA-TTTTCAAAACTTACATTTTAGTCA
1 CTAAACTTTTCAAAACTTACACTTTAGTCA
527821 CTA
1 CTA
527824 GCCAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (30 bp):
CTAAACTTTTCAAAACTTACACTTTAGTCA
Found at i:531376 original size:31 final size:32
Alignment explanation
Indices: 531338--531415 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
531328 AGGTGCGTGA
* * *
531338 GGCGCGAG-GGAACTCTGACCAAGGAAGTTGC
1 GGCGCGAGAGAAAATCTGACCAAGGAAGTTAC
*
531369 GGCGCGAGATGAAAATCTGACCAAGGGAGTTAC
1 GGCGCGAGA-GAAAATCTGACCAAGGAAGTTAC
531402 GGCGCGAGATGAAA
1 GGCGCGAGA-GAAA
531416 TGCTTGCTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 8 0.20
33 33 0.80
ACGTcount: A:0.31, C:0.19, G:0.37, T:0.13
Consensus pattern (32 bp):
GGCGCGAGAGAAAATCTGACCAAGGAAGTTAC
Found at i:531391 original size:33 final size:33
Alignment explanation
Indices: 531351--531415 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
531341 GCGAGGGAAC
*
531351 TCTGACCAAGGAAGTTGCGGCGCGAGATGAAAA
1 TCTGACCAAGGAAGTTACGGCGCGAGATGAAAA
*
531384 TCTGACCAAGGGAGTTACGGCGCGAGATGAAA
1 TCTGACCAAGGAAGTTACGGCGCGAGATGAAA
531416 TGCTTGCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.34, T:0.15
Consensus pattern (33 bp):
TCTGACCAAGGAAGTTACGGCGCGAGATGAAAA
Found at i:531529 original size:21 final size:21
Alignment explanation
Indices: 531504--531546 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
531494 AAAAATGTAA
*
531504 ATATAGTATA-ATTTATAATAT
1 ATATA-TATATATATATAATAT
531525 ATATATATATATATATAATAT
1 ATATATATATATATATAATAT
531546 A
1 A
531547 AGGATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATATATATATATATATAATAT
Found at i:531782 original size:20 final size:20
Alignment explanation
Indices: 531759--531800 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
531749 GAATCCTTCG
*
531759 TCGTGAAATTGAAATTGAAC
1 TCGTGAAATTGAAATCGAAC
*
531779 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
531799 TC
1 TC
531801 AGAGTTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:532061 original size:105 final size:105
Alignment explanation
Indices: 531879--532491 Score: 1118
Period size: 105 Copynumber: 5.8 Consensus size: 105
531869 AAATTATTTA
*
531879 TTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
531944 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTG
66 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTG
*
531984 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
532049 TTGTGGAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
66 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTG
*
532089 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
532154 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTG
66 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTG
*
532194 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
532259 TTGTGAAATTGAAATTGGCTCTGAAATTGAGAAATGTTTG
66 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTG
*
532299 GTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
532364 CTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTG
66 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTG
*
532404 GTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
532469 TTGTGAAGTTGAAATTGGCTCTG
66 TTGTGAAGTTGAAATTGGCTCTG
532492 GGTAAAACCT
Statistics
Matches: 490, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 490 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTG
Found at i:545225 original size:31 final size:32
Alignment explanation
Indices: 545187--545264 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 32
545177 AGGTGCGTGA
* *
545187 GGCGCGAG-GGAACTCTGACCAAGGAAGTTGC
1 GGCGCGAGAGAAACTCTGACCAAGGAAGTTAC
*
545218 GGCGCGAGATGAAACTCTGACCAAGGGAGTTAC
1 GGCGCGAGA-GAAACTCTGACCAAGGAAGTTAC
545251 GGCGCGAGATGAAA
1 GGCGCGAGA-GAAA
545265 TGCTTGCTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 8 0.19
33 34 0.81
ACGTcount: A:0.29, C:0.21, G:0.37, T:0.13
Consensus pattern (32 bp):
GGCGCGAGAGAAACTCTGACCAAGGAAGTTAC
Found at i:545237 original size:33 final size:33
Alignment explanation
Indices: 545197--545264 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
545187 GGCGCGAGGG
*
545197 AACTCTGACCAAGGAAGTTGCGGCGCGAGATGA
1 AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
*
545230 AACTCTGACCAAGGGAGTTACGGCGCGAGATGA
1 AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
545263 AA
1 AA
545265 TGCTTGCTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.32, T:0.15
Consensus pattern (33 bp):
AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
Found at i:547340 original size:20 final size:20
Alignment explanation
Indices: 547289--547379 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
547279 GCGATTTTCC
*
547289 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
547309 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
547329 GACTATCTCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
* *
547349 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
547369 GACTGTCGCAA
1 GACTATCGCAA
547380 CACTGAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.02
20 59 0.97
21 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:550533 original size:18 final size:18
Alignment explanation
Indices: 550510--550544 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
550500 AGAAAAAGGC
*
550510 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
550528 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
550545 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:550860 original size:140 final size:140
Alignment explanation
Indices: 550604--550869 Score: 478
Period size: 140 Copynumber: 1.9 Consensus size: 140
550594 AAACGTTGTA
550604 TTATGTGTAAAATTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAAATTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
*
550669 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACGCGAATTTGACTAT
550734 TATGTGTATT
131 TATGTGTATT
* * *
550744 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGTTA
1 TTATGTGTAAAATTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
* *
550809 TGATATGTTCAGTTGTTATTACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACGCGAATTTGA
550870 TTATCGCAAC
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 120 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAAATTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACGCGAATTTGACTAT
TATGTGTATT
Found at i:550869 original size:20 final size:20
Alignment explanation
Indices: 550844--551083 Score: 238
Period size: 20 Copynumber: 12.7 Consensus size: 20
550834 TTACACATTC
*
550844 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
550864 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
550884 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
550904 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
550923 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
550938 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
550958 ATTTGACTATCGCAATG-GCT
1 ATTTGACTATCGCAACGCG-A
550978 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
550998 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
551018 ATTTGATTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
551038 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
551052 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
551072 A-TTGACTTTCGC
1 ATTTGACTATCGC
551084 GTTGCGATTT
Statistics
Matches: 183, Mismatches: 23, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
14 20 0.11
15 3 0.02
16 1 0.01
18 1 0.01
19 12 0.07
20 145 0.79
21 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:550985 original size:74 final size:74
Alignment explanation
Indices: 550852--551034 Score: 235
Period size: 74 Copynumber: 2.4 Consensus size: 74
550842 TCATTTGAAT
550852 ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGC
1 ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGC
550917 AACGCAAAA
66 AACGCAAAA
** * *
550926 ATCGCAACGCGAATTTG-TCTATCGCAACGCGAATTTGACTATCGCAA-TGGCTATTTGACTATC
1 ATCGCAACGCGAATTTGAT-TATCGCAACGCGAATTTGACTATCGCAACACG-AATATGACTATC
*
550989 GCAACGCGAATTTGAGT
64 GCAACGC-AA----A-A
551006 ATCGCAACGCGAATTTGATTATCGCAACG
1 ATCGCAACGCGAATTTGATTATCGCAACG
551035 AGAAAATCGC
Statistics
Matches: 95, Mismatches: 5, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
73 2 0.02
74 62 0.65
75 2 0.02
79 1 0.01
80 27 0.28
81 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGC
AACGCAAAA
Found at i:551044 original size:114 final size:113
Alignment explanation
Indices: 550864--551083 Score: 325
Period size: 114 Copynumber: 1.9 Consensus size: 113
550854 CGCAACGCGA
*
550864 ATTTGATTATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATC
* * *
550929 GCAACGCGAATTTGTCTATCGCAACGCGAATTTGACTATCGCAATGGCT
66 GCAAAGCGAATTAGACTATCGCAACGCGAA-TTGACTATCGCAATGGCT
* * * *
550978 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAACG-AGAAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCA-AAAAT
* *
551042 CGCAAAGCGTATTAGACTATCGCAACGCGAATTGACTTTCGC
65 CGCAAAGCGAATTAGACTATCGCAACGCGAATTGACTATCGC
551084 GTTGCGATTT
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
113 11 0.12
114 84 0.88
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (113 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATC
GCAAAGCGAATTAGACTATCGCAACGCGAATTGACTATCGCAATGGCT
Found at i:551102 original size:20 final size:20
Alignment explanation
Indices: 551073--551130 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
551063 GCAACGCGAA
551073 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* * *
551093 TTGTCTTTCGCATTGTGATT
1 TTGACTTTCGCGTTGCGATT
* *
551113 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
551131 AAGTGTACCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:552739 original size:21 final size:21
Alignment explanation
Indices: 552713--552782 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
552703 TGACAGTGGC
*
552713 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
552734 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGA
552755 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
552776 CTCTTGA
1 CTCTTGA
552783 GGGATGATAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.08
21 33 0.85
22 3 0.08
ACGTcount: A:0.19, C:0.14, G:0.43, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:552747 original size:42 final size:42
Alignment explanation
Indices: 552701--552806 Score: 185
Period size: 42 Copynumber: 2.5 Consensus size: 42
552691 CCTTTTCAAC
* * *
552701 GATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
552743 GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
552785 GATGATAGGGGCCTCTTGAACG
1 GATGATAGGGGCCTCTTGAACG
552807 ATAGGGGAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
Found at i:552794 original size:21 final size:21
Alignment explanation
Indices: 552728--552803 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
552718 GAATGGTGGG
552728 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGAGGGATGAT
* * **
552749 AGGGGCCTCTTGAACGG-TGGG
1 AGGGGACTCTTG-AGGGATGAT
552770 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGAGGGATGAT
*
552791 AGGGGCCTCTTGA
1 AGGGGACTCTTGA
552804 ACGATAGGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.22
Consensus pattern (21 bp):
AGGGGACTCTTGAGGGATGAT
Found at i:552831 original size:42 final size:42
Alignment explanation
Indices: 552698--552831 Score: 162
Period size: 42 Copynumber: 3.2 Consensus size: 42
552688 GGACCTTTTC
* * *
552698 AACGATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTTG
1 AACGATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTG
**
552740 AGGGATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTG
1 AACGATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTG
** * * *
552782 AGGGATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTG
1 AACGATGATAGGGGCCTCTTGAACGGT-GGGAGGGGACTCTTG
552824 AACGATGA
1 AACGATGA
552832 CAGGTGAGTC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 78 0.96
43 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
AACGATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTG
Found at i:553357 original size:20 final size:20
Alignment explanation
Indices: 553332--553407 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
553322 TAGCAACACG
553332 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
553352 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
553372 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
553392 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
553408 AGAGAATCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:553475 original size:20 final size:20
Alignment explanation
Indices: 553450--553497 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
553440 GCGATTCTCT
553450 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
553470 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
553490 CGTTGCGA
1 CGTTGCGA
553498 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:555475 original size:19 final size:20
Alignment explanation
Indices: 555388--555494 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
555378 TCTGAAACTT
555388 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
555408 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** **
555428 ACTATCGCAACACGAATTTG
1 AAAATCGCAACACGAAAATG
** *
555448 ACTATCGCAACGC-AAAATG
1 AAAATCGCAACACGAAAATG
* *
555467 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
555486 AAAATCGCA
1 AAAATCGCA
555495 TTGCGATTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 24 0.32
20 52 0.68
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:555907 original size:22 final size:22
Alignment explanation
Indices: 555880--555922 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
555870 GAGATAGACG
555880 GATTTC-TCCGGAGATCGGGACT
1 GATTTCGT-CGGAGATCGGGACT
*
555902 GATTTCGTCGGAGATGGGGAC
1 GATTTCGTCGGAGATCGGGAC
555923 AGATGTCGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATCGGGACT
Found at i:556126 original size:20 final size:20
Alignment explanation
Indices: 556096--556189 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
556086 GCGCTTTGAA
* *
556096 AATCGCATTGCGATAGTCAC
1 AATCGCGTTGCGATAGTCAG
* *
556116 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
556136 AATCTCGTTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
556156 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
556176 ACTCGCATTGCGAT
1 AATCGCGTTGCGAT
556190 TTACATATTC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:561927 original size:21 final size:20
Alignment explanation
Indices: 561900--561997 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
561890 AATCAGTGTC
561900 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
561921 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
561941 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
561961 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
561982 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
561998 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:561950 original size:41 final size:41
Alignment explanation
Indices: 561841--561997 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
561831 AAATGACCAA
* **
561841 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
561880 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
561921 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
561962 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
561998 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:562007 original size:20 final size:20
Alignment explanation
Indices: 561984--562114 Score: 104
Period size: 20 Copynumber: 6.5 Consensus size: 20
561974 GCGAATATGA
561984 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
562004 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
562024 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
562044 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
562064 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
562084 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
562104 AAATCGCAACG
1 AAATCGCAACG
562115 AGAATATGTA
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
19 2 0.02
20 93 0.96
21 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:562049 original size:60 final size:60
Alignment explanation
Indices: 561964--562173 Score: 219
Period size: 60 Copynumber: 3.5 Consensus size: 60
561954 CGATTTTCCA
* ** * *
561964 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACACGTAAATCGCAATGCGTATCCGT
* ** * *
562024 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTC-CGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACACGTAAATCGCAATGCGTATCCGT
* * * *
562084 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATATGTAAATCGCAATG-ATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAACACGTAAATCGCAATGCGT-ATCCGT
* * *
562144 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
562174 ACTGAAATTT
Statistics
Matches: 123, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
59 1 0.01
60 120 0.98
61 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACACGTAAATCGCAATGCGTATCCGT
Found at i:562115 original size:20 final size:20
Alignment explanation
Indices: 562018--562173 Score: 156
Period size: 20 Copynumber: 7.8 Consensus size: 20
562008 CGCAATGCGT
*
562018 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
562038 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
562058 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
562078 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
562098 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
** *
562118 ATATGTAAATCGCAATGATA
1 ATCCGTAAATCGCAACGATA
*
562138 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
562158 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
562174 ACTGAAATTT
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 115 0.98
22 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:562155 original size:40 final size:40
Alignment explanation
Indices: 561984--562173 Score: 188
Period size: 40 Copynumber: 4.8 Consensus size: 40
561974 GCGAATATGA
* * * *
561984 AAATCGCAACGCGAA-CACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGCATATCCGT
* * * *
562024 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCATATCCGT
* * *
562064 ATATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCAT-ATCCGT
** *
562104 AAATCGCAACGAGAATATGTAAATCGCAATG-ATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCAT-ATCCGT
* *
562144 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
562174 ACTGAAATTT
Statistics
Matches: 130, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 128 0.98
41 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGCATATCCGT
Found at i:562889 original size:24 final size:24
Alignment explanation
Indices: 562850--562896 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
562840 AAATTTGGTC
562850 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
562874 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
562897 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:565387 original size:19 final size:19
Alignment explanation
Indices: 565365--565742 Score: 465
Period size: 19 Copynumber: 21.4 Consensus size: 19
565355 CGGAAATTAC
*
565365 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
565384 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
565398 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
565418 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
565432 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
565451 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
565470 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
565484 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
565503 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
565522 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
565536 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
565555 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
565574 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
565593 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
565607 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
565626 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
565645 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
565664 AATCGCAATGCTAAATGAA
1 AATCGCAATGCGAAATGAA
*
565683 AATCGCAATGCGAAATCAA
1 AATCGCAATGCGAAATGAA
565702 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
565716 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
565735 AATCGCAA
1 AATCGCAA
565743 CGAGAGAATC
Statistics
Matches: 314, Mismatches: 14, Indels: 62
0.81 0.04 0.16
Matches are distributed among these distances:
14 58 0.18
15 3 0.01
16 17 0.05
17 17 0.05
18 4 0.01
19 202 0.64
20 13 0.04
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:565516 original size:71 final size:69
Alignment explanation
Indices: 565432--565742 Score: 342
Period size: 71 Copynumber: 4.4 Consensus size: 69
565422 GCAACGAGAG
565432 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGA-AATCGCAATGCGA
565497 AATGAA
64 AATGAA
* * * * *
565503 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA-AAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAT-CGCAACGAGAAATCGCAATGCG
565567 AAATGAA
63 AAATGAA
* * * *
565574 AATCGCAATGCGAAATGAAAATCGCAACGAC-AGAATCGCAATGCGAAATGA-AAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAATG-CGA-AAT-GAAAT-CGCAACGAGAAATCGCAATGC
565637 GAAATGAA
62 GAAATGAA
* * * ** *
565645 AATCGCAATGCGAAATGAAAATCGCAATGCTAAATGAAAATCGCAATGCGAAATCAAAAT-CGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAAATCGCAATGCGAA
*
565709 ACGAAA
65 ATG-AA
565715 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
565743 CGAGAGAATC
Statistics
Matches: 217, Mismatches: 14, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
69 12 0.06
70 17 0.08
71 174 0.80
72 7 0.03
73 7 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (69 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAAATCGCAATGCGAAA
TGAA
Found at i:565721 original size:14 final size:14
Alignment explanation
Indices: 565702--565756 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
565692 GCGAAATCAA
565702 AATCGCAACGAAAG
1 AATCGCAACGAAAG
565716 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
565733 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
565749 AATCGCAA
1 AATCGCAA
565757 TGCGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 5 0.14
19 8 0.23
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:565780 original size:52 final size:52
Alignment explanation
Indices: 565393--565764 Score: 493
Period size: 52 Copynumber: 7.0 Consensus size: 52
565383 AAATCCCAAC
565393 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
565446 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
565498 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
565550 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* *
565600 ACGACAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
* * * ** *
565659 ATGAAAATCGCAATGCTAAATGAAAATCGCAATGCGA-AATCAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
565709 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATG-AA-AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
565763 AT
1 AT
565765 TATAAACGCA
Statistics
Matches: 280, Mismatches: 24, Indels: 29
0.84 0.07 0.09
Matches are distributed among these distances:
50 12 0.04
51 16 0.06
52 181 0.65
53 23 0.08
54 5 0.02
55 1 0.00
57 28 0.10
58 7 0.03
59 7 0.03
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:565879 original size:19 final size:19
Alignment explanation
Indices: 565771--565871 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
565761 AAATTATAAA
565771 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
565790 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
565810 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
565826 CG--TTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
565842 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
565861 CGCATTGCGAT
1 CGCATTGCGAT
565872 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 8 0.11
17 3 0.04
18 6 0.08
19 29 0.39
20 19 0.26
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:565997 original size:14 final size:14
Alignment explanation
Indices: 565978--566014 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
565968 CATCAATTAC
565978 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
565992 ACAAATCATCTTTT
1 ACAAATCAACTTTT
566006 ACAAATCAA
1 ACAAATCAA
566015 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:568023 original size:33 final size:33
Alignment explanation
Indices: 567977--568064 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
567967 ACCAAAAGCG
*
567977 CAACGCGAAATGAAAATCGCAACGACAGAATCA
1 CAACGCGAAATGAAAATCGCAACGAAAGAATCA
* *
568010 CAATGCGAAATGAAAATCGCAACGAAAGAATCG
1 CAACGCGAAATGAAAATCGCAACGAAAGAATCA
568043 CAACGCGAAATGAAAATCGCAA
1 CAACGCGAAATGAAAATCGCAA
568065 TGCGATTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (33 bp):
CAACGCGAAATGAAAATCGCAACGAAAGAATCA
Done.