Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001703.1 Hibiscus syriacus cultivar Beakdansim tig00003413_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: 104302
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1360 original size:32 final size:32
Alignment explanation
Indices: 1308--1403 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
1298 TTATAATATA
*
1308 ATTAAAATTTA-TAAATTATTATAAAATAATTT
1 ATTAAATTTTATTAAA-TATTATAAAATAATTT
** *
1340 ATTGGATTTTATTAAATATTATAAAGTAA-TT
1 ATTAAATTTTATTAAATATTATAAAATAATTT
* *
1371 ATTAAATTTTATTAAAATGTTATAAAATGATTT
1 ATTAAATTTTATT-AAATATTATAAAATAATTT
1404 TACACCAACT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
31 13 0.25
32 33 0.63
33 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (32 bp):
ATTAAATTTTATTAAATATTATAAAATAATTT
Found at i:2152 original size:8 final size:8
Alignment explanation
Indices: 2141--2176 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
2131 TTTTCTTTTT
2141 TTTTTTCA
1 TTTTTTCA
2149 TTTTTTCA
1 TTTTTTCA
2157 TTTTTTCA
1 TTTTTTCA
2165 TTTTTTCA
1 TTTTTTCA
2173 TTTT
1 TTTT
2177 AATTCTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3007 original size:9 final size:9
Alignment explanation
Indices: 2995--3190 Score: 63
Period size: 9 Copynumber: 21.2 Consensus size: 9
2985 AAAAGTAGCA
2995 AAAATAAAT
1 AAAATAAAT
*
3004 AAAATAAAG
1 AAAATAAAT
* *
3013 AAAGTAAAA
1 AAAATAAAT
*
3022 AAAACAAAT
1 AAAATAAAT
* *
3031 ACAATAAAG
1 AAAATAAAT
3040 AAGAGA-AAAT
1 AA-A-ATAAAT
*
3050 -AAA-AGA-
1 AAAATAAAT
3056 AAAATAGAAT
1 AAAATA-AAT
3066 AAAATAAA-
1 AAAATAAAT
*
3074 ATAATAAA-
1 AAAATAAAT
*
3082 CAAA-AAAT
1 AAAATAAAT
3090 AAAATAAAT
1 AAAATAAAT
*
3099 AAAAAAAAT
1 AAAATAAAT
*
3108 ATGTAAA-ATAT
1 A---AAATAAAT
3119 GCAATAATATAAT
1 --AA-AATA-AAT
*
3132 AAAATATAT
1 AAAATAAAT
3141 AACAATAATAT
1 AA-AATAA-AT
3152 AATAAT-AAT
1 AA-AATAAAT
3161 AATAAT-AAT
1 AA-AATAAAT
3170 ATAAAT-AAT
1 A-AAATAAAT
3179 AATAATAAAT
1 AA-AATAAAT
3189 AA
1 AA
3191 TAAAGACAAG
Statistics
Matches: 143, Mismatches: 23, Indels: 41
0.69 0.11 0.20
Matches are distributed among these distances:
7 9 0.06
8 15 0.10
9 71 0.50
10 26 0.18
11 15 0.10
12 4 0.03
13 3 0.02
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:3010 original size:5 final size:5
Alignment explanation
Indices: 2995--3108 Score: 57
Period size: 5 Copynumber: 24.2 Consensus size: 5
2985 AAAAGTAGCA
* * * * *
2995 AAAAT -AAAT AAAAT -AAAG AAAGT AAAA- AAAA- CAAAT ACAAT -AAAG
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * * *
3040 AAGAG AAAAT AAAAGA AAAAT AGAAT AAAAT AAAAT --AAT AAACAA AAAAT
1 AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT
3090 AAAAT -AAAT AAAA- AAAAT A
1 AAAAT AAAAT AAAAT AAAAT A
3109 TGTAAAATAT
Statistics
Matches: 81, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
3 3 0.04
4 24 0.30
5 46 0.57
6 8 0.10
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:3018 original size:27 final size:27
Alignment explanation
Indices: 2994--3097 Score: 84
Period size: 27 Copynumber: 3.7 Consensus size: 27
2984 TAAAAGTAGC
*
2994 AAAAATAAATAAAATAAAGAAAGTAAA
1 AAAAACAAATAAAATAAAGAAAGTAAA
* *
3021 AAAAACAAATACAATAAAGAAGAGAAAA
1 AAAAACAAATAAAATAAAGAA-AGTAAA
* * * *
3049 TAAAAGAAAAATAGAATAAAATAAAATAATA
1 -AAAA-ACAAATAAAAT-AAAGAAAGTAA-A
3080 AACAAA-AAATAAAATAAA
1 AA-AAACAAATAAAATAAA
3098 TAAAAAAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
27 19 0.31
28 8 0.13
29 12 0.19
30 15 0.24
31 8 0.13
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (27 bp):
AAAAACAAATAAAATAAAGAAAGTAAA
Found at i:3080 original size:29 final size:28
Alignment explanation
Indices: 3000--3102 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 28
2990 TAGCAAAAAT
* *
3000 AAATAAAATAAAGAAAGTAA-AAA-AAA
1 AAATAAAATAAATAAAATAATAAACAAA
* * *
3026 CAAATACAATAAAGAAGAGAAAATAAA-AGAA
1 -AAATAAAATAAATAA-A-ATAATAAACA-AA
*
3057 AAATAGAATAAAATAAAATAATAAACAAA
1 AAATAAAAT-AAATAAAATAATAAACAAA
3086 AAATAAAATAAATAAAA
1 AAATAAAATAAATAAAA
3103 AAAATATGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
27 14 0.22
28 9 0.14
29 19 0.30
30 14 0.22
31 7 0.11
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.14
Consensus pattern (28 bp):
AAATAAAATAAATAAAATAATAAACAAA
Found at i:3090 original size:19 final size:19
Alignment explanation
Indices: 2995--3106 Score: 79
Period size: 19 Copynumber: 5.9 Consensus size: 19
2985 AAAAGTAGCA
* *
2995 AAAATAAAT-AAAATAAAG
1 AAAATAAATAAAAAAAAAT
* *
3013 AAAGTAAA-AAAAACAAAT
1 AAAATAAATAAAAAAAAAT
* * * *
3031 ACAATAAAGAAGAGAAAAT
1 AAAATAAATAAAAAAAAAT
*
3050 AAAAGAAA-AATAGAATAAAAT
1 AAAATAAATAA-A-AA-AAAAT
3071 AAAAT-AATAAACAAAAAAT
1 AAAATAAATAAA-AAAAAAT
3090 AAAATAAATAAAAAAAA
1 AAAATAAATAAAAAAAA
3107 TATGTAAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
18 22 0.30
19 28 0.38
20 12 0.16
21 11 0.15
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.13
Consensus pattern (19 bp):
AAAATAAATAAAAAAAAAT
Found at i:3097 original size:16 final size:15
Alignment explanation
Indices: 2994--3104 Score: 63
Period size: 14 Copynumber: 7.6 Consensus size: 15
2984 TAAAAGTAGC
*
2994 AAAAATAAATAAAAT
1 AAAAAAAAATAAAAT
* *
3009 -AAAGAAAGT-AAA-
1 AAAAAAAAATAAAAT
* *
3021 AAAAACAAATACAAT
1 AAAAAAAAATAAAAT
* * *
3036 -AAAGAAGAGAAAAT
1 AAAAAAAAATAAAAT
*
3050 AAAAGAAAAATAGAAT
1 AAAA-AAAAATAAAAT
*
3066 AAAATAAAAT--AAT
1 AAAAAAAAATAAAAT
3079 AAACAAAAAATAAAAT
1 AAA-AAAAAATAAAAT
3095 AAATAAAAAA
1 AAA-AAAAAA
3105 AATATGTAAA
Statistics
Matches: 69, Mismatches: 19, Indels: 15
0.67 0.18 0.15
Matches are distributed among these distances:
13 15 0.22
14 23 0.33
15 8 0.12
16 23 0.33
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATAAAAT
Found at i:3104 original size:18 final size:18
Alignment explanation
Indices: 2995--3108 Score: 79
Period size: 18 Copynumber: 6.1 Consensus size: 18
2985 AAAAGTAGCA
* *
2995 AAAATAAATAAAATAAAG
1 AAAATAAATAAAAAAAAT
*
3013 AAAGTAAA-AAAAACAAAT
1 AAAATAAATAAAAA-AAAT
* * *
3031 ACAATAAAGAAGAGAAAAT
1 AAAATAAATAA-AAAAAAT
* *
3050 AAAAGAAAAATAGAATAAAAT
1 -AAA-ATAAATA-AAAAAAAT
3071 AAAAT-AATAAACAAAAAAT
1 AAAATAAAT-AA-AAAAAAT
3090 AAAATAAATAAAAAAAAT
1 AAAATAAATAAAAAAAAT
3108 A
1 A
3109 TGTAAAATAT
Statistics
Matches: 75, Mismatches: 12, Indels: 18
0.71 0.11 0.17
Matches are distributed among these distances:
17 4 0.05
18 28 0.37
19 21 0.28
20 10 0.13
21 11 0.15
22 1 0.01
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAATAAATAAAAAAAAT
Found at i:3133 original size:3 final size:3
Alignment explanation
Indices: 3121--3193 Score: 82
Period size: 3 Copynumber: 24.7 Consensus size: 3
3111 TAAAATATGC
*
3121 AAT AAT -AT AAT AA- AAT ATAT AAC AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
3164 AAT AAT -AT AAAT AAT AAT AAT AAAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AA
3194 AGACAAGAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
2 8 0.13
3 45 0.74
4 8 0.13
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3136 original size:20 final size:19
Alignment explanation
Indices: 3111--3194 Score: 59
Period size: 23 Copynumber: 4.2 Consensus size: 19
3101 AAAAAATATG
3111 TAAAATATGCAATAATATAA
1 TAAAATAT-CAATAATATAA
3131 TAAAATATATAACAATAATATAA
1 T-AAA-ATAT--CAATAATATAA
3154 TAATAATAAT-AATAATATAA
1 TAA-AAT-ATCAATAATATAA
*
3174 -ATAATAAT-AATAA-ATAA
1 TAAAAT-ATCAATAATATAA
3191 TAAA
1 TAAA
3195 GACAAGAGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
17 4 0.07
18 13 0.24
19 1 0.02
20 11 0.20
21 3 0.05
22 8 0.15
23 15 0.27
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (19 bp):
TAAAATATCAATAATATAA
Found at i:3318 original size:36 final size:33
Alignment explanation
Indices: 3277--3376 Score: 83
Period size: 38 Copynumber: 2.7 Consensus size: 33
3267 AAAAAACAAA
*
3277 AATAAAAAATAGAAAAAAATAAAAATAATATACAT
1 AATAAAAAATA-AAAAAAATAAAAAT-ATATAAAT
*
3312 ATATAAAATATATAAATAATAATGAAAAATATATAAAT
1 A-ATAAAA-A-ATAAA-AAAAAT-AAAAATATATAAAT
*
3350 AATAATAATAATAAAGAAAAAGAAAAA
1 AATAA-AA-AATAAA-AAAAATAAAAA
3377 ATGAAAACTA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
35 1 0.02
36 11 0.20
37 16 0.30
38 20 0.37
39 6 0.11
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (33 bp):
AATAAAAAATAAAAAAAATAAAAATATATAAAT
Found at i:3342 original size:21 final size:21
Alignment explanation
Indices: 3316--3355 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3306 ATACATATAT
3316 AAAATATATAAATAATAATGA
1 AAAATATATAAATAATAATGA
3337 AAAATATATAAATAATAAT
1 AAAATATATAAATAATAAT
3356 AATAATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAATATATAAATAATAATGA
Found at i:3362 original size:30 final size:30
Alignment explanation
Indices: 3310--3424 Score: 87
Period size: 30 Copynumber: 3.8 Consensus size: 30
3300 AATAATATAC
3310 ATATAT-AA-AATATATAAATAATAATGAAAA
1 ATATATAAATAATA-AT-AATAATAATGAAAA
*
3340 ATATATAAATAATAATAATAATAAAGAAAA
1 ATATATAAATAATAATAATAATAATGAAAA
* *
3370 AGA-AAAAATGAA-AACTAATAATAAT-AAAA
1 ATATATAAAT-AATAA-TAATAATAATGAAAA
* * *
3399 GATATAATTAATATTTATAATAATAA
1 -ATAT-ATAAATAATAATAATAATAA
3425 GGGACTAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
29 11 0.16
30 34 0.50
31 14 0.21
32 9 0.13
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (30 bp):
ATATATAAATAATAATAATAATAATGAAAA
Found at i:3847 original size:20 final size:20
Alignment explanation
Indices: 3822--3863 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3812 CGAATGTTCT
3822 TCAAGTCA-TTTCTTCAAAAA
1 TCAAGTCAGTTTCTT-AAAAA
*
3842 TCAAGTTAGTTTCTTAAAAA
1 TCAAGTCAGTTTCTTAAAAA
3862 TC
1 TC
3864 GCCTCGAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (20 bp):
TCAAGTCAGTTTCTTAAAAA
Found at i:5419 original size:86 final size:86
Alignment explanation
Indices: 5328--5593 Score: 344
Period size: 85 Copynumber: 3.1 Consensus size: 86
5318 TTTCTACTTA
* * * *
5328 AGTTAT-TCTGTAAATTTGACATGCCCTTGAGTTGAATGAAATCGAACTCAAAGGTCTTTTGTTG
1 AGTTATGT-TGTAAATTGGATATGCCTTTGAGCTGAATGAAATCGAACTCAAAGGTCTTTTGTTG
5392 ACAGATAACCCTTCTCACCTTG
65 ACAGATAACCCTTCTCACCTTG
* * * *
5414 AGTTATGTTGTAAATTGGATGTGCCTTTGAACTGAGTGTAATCGAACTCAAAGGT-TTTTGTTGA
1 AGTTATGTTGTAAATTGGATATGCCTTTGAGCTGAATGAAATCGAACTCAAAGGTCTTTTGTTGA
5478 CAGATAACCCTTCT-AGCCTTG
66 CAGATAACCCTTCTCA-CCTTG
* * *
5499 AGTTATGTTGTAAATTGGATATGCCTTTGAGCTGAAT-ATAATCGAACTCGAAGG-CCTTTGATG
1 AGTTATGTTGTAAATTGGATATGCCTTTGAGCTGAATGA-AATCGAACTCAAAGGTCTTTTGTTG
* * *
5562 ACATATAACCATTCTCGCCTTG
65 ACAGATAACCCTTCTCACCTTG
5584 AGTTATGTTG
1 AGTTATGTTG
5594 CACTGGGATG
Statistics
Matches: 157, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
84 1 0.01
85 110 0.70
86 45 0.29
87 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (86 bp):
AGTTATGTTGTAAATTGGATATGCCTTTGAGCTGAATGAAATCGAACTCAAAGGTCTTTTGTTGA
CAGATAACCCTTCTCACCTTG
Found at i:6107 original size:109 final size:109
Alignment explanation
Indices: 5964--6266 Score: 473
Period size: 109 Copynumber: 2.8 Consensus size: 109
5954 TGGCTCATTC
* * **
5964 GTTGAGCATTAAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAAG-ATTGTTGGCACGATAT
1 GTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCC-AAGTATTGTTGGCACGATAT
* * * * *
6028 CCTTAGTCGTGAAGTTGAAATCGTGGATGACTCTTTTGTTGTGAA
65 CCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTATGAA
* *
6073 GTTGAGCTTTGAATTGGATATCATTCATTGTGAAGTTGAAATCCAAGTATTGTTGGCACGATATC
1 GTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGTATTGTTGGCACGATATC
6138 CTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTATGAA
66 CTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTATGAA
*
6182 GTTGAGCTTTGAATTGAATATCCTTCGTTGTGAAGTTGAAATCCAAGTATTGTTGGCACGATATC
1 GTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGTATTGTTGGCACGATATC
*
6247 CTTCGTCTTGAAGTTGAAAT
66 CTTCGTCGTGAAGTTGAAAT
6267 TGACTCTGAA
Statistics
Matches: 178, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
108 3 0.02
109 175 0.98
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (109 bp):
GTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGTATTGTTGGCACGATATC
CTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTATGAA
Found at i:6310 original size:64 final size:64
Alignment explanation
Indices: 6242--6468 Score: 350
Period size: 64 Copynumber: 3.5 Consensus size: 64
6232 TGTTGGCACG
*
6242 ATATCCTTCGTCT-TGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTTTTTGTTGAGTCCA
1 ATATCCTTCG-CTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTTGAGTCCA
* *
6306 ATATCCTTCGCTGTGAAGTTAAAATTGACCCTGAATGAAACTGGAAAGTTATTTGTTGAGTCCA
1 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTTGAGTCCA
* * *
6370 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAATTGGAAAGTTGTTTGTTGAGTCCA
1 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTTGAGTCCA
* *
6434 ATATCCTTTGTTGTGAAGTTGAAATT-AGCTCTGAA
1 ATATCCTTCGCTGTGAAGTTGAAATTGA-CTCTGAA
6469 AGATACAAAA
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
63 3 0.02
64 147 0.98
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (64 bp):
ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTTGAGTCCA
Found at i:7529 original size:76 final size:76
Alignment explanation
Indices: 7419--7564 Score: 238
Period size: 76 Copynumber: 1.9 Consensus size: 76
7409 TCAGGTTAGT
* * *
7419 TGAATCTTATCTATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGGGACAACTTAAGCTTTATT
1 TGAATCTTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATT
7484 GTATAGATAGA
66 GTATAGATAGA
* * *
7495 TGAATCTTATCCATAAGGCCGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATT
1 TGAATCTTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATT
7560 GTATA
66 GTATA
7565 TATATGATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (76 bp):
TGAATCTTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATT
GTATAGATAGA
Found at i:9801 original size:10 final size:10
Alignment explanation
Indices: 9786--9810 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9776 ATAAATATAA
9786 TAATATTTTT
1 TAATATTTTT
9796 TAATATTTTT
1 TAATATTTTT
9806 TAATA
1 TAATA
9811 ATAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TAATATTTTT
Found at i:16131 original size:23 final size:23
Alignment explanation
Indices: 16105--16162 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
16095 CTCATATAAA
*
16105 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
16128 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
16151 TGCACCGTAGTG
1 TGCACCGTAGTG
16163 GCATATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:16360 original size:103 final size:102
Alignment explanation
Indices: 16181--16501 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 102
16171 TAATGTTCAT
* * *
16181 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
16246 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTC-CG
16284 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
16349 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGT-CCG
*
16387 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAATATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
16452 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCC-G
16490 AAGGACCACATA
1 AAGGACCACATA
16502 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
102 2 0.01
103 209 0.99
104 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCG
Found at i:21522 original size:23 final size:23
Alignment explanation
Indices: 21496--21553 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
21486 CTCATATAAA
*
21496 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
21519 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
21542 TGCACCGTAGTG
1 TGCACCGTAGTG
21554 GCATATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:21743 original size:103 final size:103
Alignment explanation
Indices: 21572--21892 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
21562 TAATGTCCAT
* * *
21572 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
21637 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
21675 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
21740 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
21778 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAATATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
21843 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
21881 AAGGACCACATA
1 AAGGACCACATA
21893 GACCCCCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:25708 original size:3 final size:3
Alignment explanation
Indices: 25690--25754 Score: 69
Period size: 3 Copynumber: 21.0 Consensus size: 3
25680 CTACAAAAAA
* * *
25690 TAT TAA TAT AAT TAT TAT TAT T-G TAGT TAT TAT TAT TAT TAT ATAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT -TA-T
25737 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
25755 AATAATTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 1 0.02
3 44 0.85
4 6 0.12
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:25738 original size:20 final size:20
Alignment explanation
Indices: 25700--25751 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
25690 TATTAATATA
*
25700 ATTATTATTATTGTAGTTATT
1 ATTATTATTA-TATAGTTATT
25721 ATTATTATTATATAGTTATT
1 ATTATTATTATATAGTTATT
25741 ATTATTATTAT
1 ATTATTATTAT
25752 TATAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
ATTATTATTATATAGTTATT
Found at i:28355 original size:21 final size:20
Alignment explanation
Indices: 28269--28426 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
28259 AAATGACCAA
**
28269 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
28288 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
28308 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
28328 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
28349 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
28370 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
28390 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
28411 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
28427 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:28455 original size:20 final size:20
Alignment explanation
Indices: 28393--28586 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
28383 CGATTTTCCA
* ** *
28393 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
28413 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
28433 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
28453 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
28473 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
28493 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
28513 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
28533 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
28553 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
28574 AAATCGCAACGCG
1 AAATCGCAACGCG
28587 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:28477 original size:60 final size:60
Alignment explanation
Indices: 28393--28586 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
28383 CGATTTTCCA
* ** * *
28393 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
28453 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
28513 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
28574 AAATCGCAACGCG
1 AAATCGCAACGCG
28587 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:29006 original size:33 final size:33
Alignment explanation
Indices: 28967--29037 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
28957 TTCACTTAGA
* *
28967 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
29000 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
29033 TTTCA
1 TTTCA
29038 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:29147 original size:20 final size:20
Alignment explanation
Indices: 29117--29221 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 20
29107 TGCAGAAGAG
29117 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
29138 TCGC-ACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
29157 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
29178 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
29192 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
29211 TCGCAACGAGA
1 TCGCAACGAGA
29222 GAATCGCAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
14 10 0.16
16 2 0.03
17 2 0.03
19 20 0.31
20 12 0.19
21 18 0.28
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:29173 original size:40 final size:41
Alignment explanation
Indices: 29116--29192 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
29106 TTGCAGAAGA
* *
29116 GTCGCAACGAGATAAATGAAAATCGC-ACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
29156 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
29193 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 24 0.71
41 10 0.29
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
Found at i:29182 original size:21 final size:21
Alignment explanation
Indices: 29118--29191 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
29108 GCAGAAGAGT
* *
29118 CGCAACGAGATAAATGAAAAT
1 CGCAACGAGAGAAATGAAAAG
**
29139 CGC-ACGAGAG-AATG-ACTG
1 CGCAACGAGAGAAATGAAAAG
29157 TCGCAACGAGAGAAATGAAAAG
1 -CGCAACGAGAGAAATGAAAAG
29179 CGCAACGAGAGAA
1 CGCAACGAGAGAA
29192 TCGCAACGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.02
19 7 0.16
20 13 0.30
21 20 0.47
22 2 0.05
ACGTcount: A:0.46, C:0.18, G:0.27, T:0.09
Consensus pattern (21 bp):
CGCAACGAGAGAAATGAAAAG
Found at i:29198 original size:14 final size:14
Alignment explanation
Indices: 29179--29232 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
29169 AAATGAAAAG
29179 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
29193 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
29212 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
29226 CGCAACG
1 CGCAACG
29233 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:29208 original size:33 final size:33
Alignment explanation
Indices: 29168--29237 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
29158 CGCAACGAGA
29168 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
29201 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
29234 GAAA
1 GAAA
29238 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:29244 original size:33 final size:33
Alignment explanation
Indices: 29174--29248 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
29164 GAGAGAAATG
* **
29174 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
29207 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
29240 AAAATCGCA
1 AAAATCGCA
29249 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:29266 original size:19 final size:19
Alignment explanation
Indices: 29244--29341 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
29234 GAAACCAAAA
*
29244 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29263 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
29277 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29296 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
29310 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
29329 TCGCGTTGCGATT
1 TCGCGTTGCGATT
29342 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:29285 original size:14 final size:14
Alignment explanation
Indices: 29266--29355 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
29256 TTTCATTTCG
29266 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
29280 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
29299 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
29313 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
29330 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
29346 CGTTGCGATT
1 CGTTGCGATT
29356 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:29291 original size:33 final size:33
Alignment explanation
Indices: 29249--29363 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
29239 CAAAATCGCA
29249 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29282 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
29315 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29348 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
29364 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:31219 original size:92 final size:92
Alignment explanation
Indices: 31062--31525 Score: 892
Period size: 92 Copynumber: 5.0 Consensus size: 92
31052 TTGCTTAGTA
*
31062 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
31127 TCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
31154 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
31219 TCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
31246 AAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTT
1 -AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTT
31311 GTCTTTGTTTTGTCTTTTGGTTGAAAGT
65 GTCTTTGTTTTGTCTTTTGGTTGAAAGT
*
31339 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
31404 TCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
31431 AAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTT
1 -AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTT
31496 GTCTTTGTTTTGTCTTTTGGTTGAAAGT
65 GTCTTTGTTTTGTCTTTTGGTTGAAAGT
31524 AA
1 AA
31526 ATTTATCCAT
Statistics
Matches: 367, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 184 0.50
93 183 0.50
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (92 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGT
Found at i:31288 original size:185 final size:185
Alignment explanation
Indices: 31058--31525 Score: 918
Period size: 185 Copynumber: 2.5 Consensus size: 185
31048 TAGATTGCTT
*
31058 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31123 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
*
31188 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31243 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31308 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
31373 TGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31428 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31493 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
31526 ATTTATCCAT
Statistics
Matches: 281, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 281 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31313 original size:93 final size:93
Alignment explanation
Indices: 31058--31529 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
31048 TAGATTGCTT
*
31058 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31123 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31151 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31215 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31243 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31308 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
31336 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31400 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31428 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31493 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31521 AGTAAATTT
1 AGTAAATTT
31530 ATCCATTCAA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 182 0.49
93 192 0.51
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31613 original size:19 final size:19
Alignment explanation
Indices: 31573--31701 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
31563 TAGTTTACTT
* *
31573 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
31593 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
31612 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
31631 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
31645 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
31664 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
31678 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
31697 TCGCA
1 TCGCA
31702 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:31652 original size:33 final size:32
Alignment explanation
Indices: 31609--31701 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
31599 CGCGAAACCA
**
31609 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
31641 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
31674 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
31702 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:31699 original size:52 final size:52
Alignment explanation
Indices: 31573--31701 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
31563 TAGTTTACTT
**
31573 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
31625 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
31678 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
31702 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:31719 original size:19 final size:19
Alignment explanation
Indices: 31697--31831 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
31687 GAAACCAAAA
*
31697 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31716 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
31732 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
31749 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
31765 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
31782 TCGCGTTGTGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
31801 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
31821 TCGTGTTGCGA
1 TCGCGTTGCGA
31832 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 44 0.47
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31738 original size:14 final size:14
Alignment explanation
Indices: 31719--31775 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
31709 TTTCATTTCG
31719 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
31733 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
31750 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
31766 CGTTGCGATT
1 CGTTGCGATT
31776 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:31744 original size:33 final size:33
Alignment explanation
Indices: 31702--31794 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
31692 CAAAATCGCA
*
31702 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
31735 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
31768 TTGCGATTTTCATTTCGCGTTGTGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
31795 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:33772 original size:14 final size:14
Alignment explanation
Indices: 33753--33788 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33743 ATTGTTTAAT
33753 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
33767 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
33781 TGATTTGT
1 TGATTTGT
33789 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:33919 original size:19 final size:19
Alignment explanation
Indices: 33895--33992 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
33885 AAAATTGACT
33895 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33914 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
33933 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
33947 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33966 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
33986 ATCGCAA
1 ATCGCAA
33993 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:34024 original size:53 final size:53
Alignment explanation
Indices: 33895--34011 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
33885 AAAATTGACT
33895 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
33947 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
34000 ATCGCAATGCGA
1 ATCGCAATGCGA
34012 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:36346 original size:12 final size:12
Alignment explanation
Indices: 36329--36353 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36319 TCTTCGGGGA
36329 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36341 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36353 C
1 C
36354 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:36562 original size:24 final size:24
Alignment explanation
Indices: 36528--36574 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
36518 CTGAAACATC
36528 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
36552 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
36575 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:37285 original size:20 final size:20
Alignment explanation
Indices: 37257--37506 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
37247 AAATTTCAGT
* * *
37257 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
37277 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
37297 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
37317 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
37337 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
37357 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
37377 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
37397 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
37417 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
37437 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
37457 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
37477 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
37497 GTTGCGATTT
1 GTTGCGATTT
37507 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:37523 original size:21 final size:21
Alignment explanation
Indices: 37493--37575 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
37483 ATTTTCATAT
*
37493 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
37514 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
37535 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
37556 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
37576 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:37566 original size:42 final size:43
Alignment explanation
Indices: 37473--37571 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
37463 ATTTATGTGT
* *
37473 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
37514 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
37556 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
37572 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:57286 original size:23 final size:23
Alignment explanation
Indices: 57232--57291 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
57222 ATATATGTAT
**
57232 CGAAGGACCATGTAGAATTGTCC
1 CGAAGGACCACATAGAATTGTCC
**
57255 CGATTGACCACATAGAATTGTCC
1 CGAAGGACCACATAGAATTGTCC
*
57278 CTAAGGACCACATA
1 CGAAGGACCACATA
57292 TATTCTAAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (23 bp):
CGAAGGACCACATAGAATTGTCC
Found at i:60748 original size:104 final size:104
Alignment explanation
Indices: 60550--60748 Score: 312
Period size: 104 Copynumber: 1.9 Consensus size: 104
60540 ATGACTCTAT
**
60550 TTGACTAGCTTGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGGTGTGATG
1 TTGACTAGCTCAGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGGTGTGATG
* *
60615 GGCTGACTCCCCTCGAAGCAGTGTTAAAAAAAACTTTAC
66 AGCTAACTCCCCTCGAAGCAGTGTTAAAAAAAACTTTAC
*
60654 TTGACTAGCTCAGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTA-GTGTTATG
1 TTGACTAGCTCAGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGGTGTGATG
* * *
60718 AGCTAACTCTCCTTGAAGTA-TGTTAAAAAAA
66 AGCTAACTCCCCTCGAAGCAGTGTTAAAAAAA
60749 TTTGAAGTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 11 0.13
103 22 0.25
104 54 0.62
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (104 bp):
TTGACTAGCTCAGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGGTGTGATG
AGCTAACTCCCCTCGAAGCAGTGTTAAAAAAAACTTTAC
Found at i:63739 original size:24 final size:24
Alignment explanation
Indices: 63712--63808 Score: 115
Period size: 24 Copynumber: 4.1 Consensus size: 24
63702 TGCCATATAT
* *
63712 AATTTGTCCCGAAGGACTGCTTAG
1 AATTTGTCCCGAAGGACCGCATAG
* *
63736 AATTTGTCTCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGGACCGCATAG
* *
63760 AATTTGTCCCTAAGGACCACATAG
1 AATTTGTCCCGAAGGACCGCATAG
* *
63784 -ATTTGTCCCGAACGACCGCGTAG
1 AATTTGTCCCGAAGGACCGCATAG
63807 AA
1 AA
63809 CCCTCAACTC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.31
24 42 0.69
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCGCATAG
Found at i:63805 original size:47 final size:48
Alignment explanation
Indices: 63712--63808 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 48
63702 TGCCATATAT
** * * *
63712 AATTTGTCCCGAAGGACTGCTTAGAATTTGTCTCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGGACCACATAGAATTTGTCCCGAACGACCGCGTAG
*
63760 AATTTGTCCCTAAGGACCACATAG-ATTTGTCCCGAACGACCGCGTAG
1 AATTTGTCCCGAAGGACCACATAGAATTTGTCCCGAACGACCGCGTAG
63807 AA
1 AA
63809 CCCTCAACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 23 0.53
48 20 0.47
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (48 bp):
AATTTGTCCCGAAGGACCACATAGAATTTGTCCCGAACGACCGCGTAG
Found at i:65997 original size:20 final size:21
Alignment explanation
Indices: 65972--66025 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
65962 TCTTACTTGG
65972 TAAGTCCTTCGGGC-GATCAT
1 TAAGTCCTTCGGGCAGATCAT
* * *
65992 TAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTCGGGCA-GATCAT
*
66014 TAAATCCTTCGG
1 TAAGTCCTTCGG
66026 ATCATCTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 12 0.46
22 14 0.54
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (21 bp):
TAAGTCCTTCGGGCAGATCAT
Found at i:66878 original size:133 final size:131
Alignment explanation
Indices: 66416--66913 Score: 540
Period size: 133 Copynumber: 3.8 Consensus size: 131
66406 AATCGAATTT
* * * * *
66416 GATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTGAGGA
1 GATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTTTCCAAATCTGA-TTTCCCTGA-AA
** * * * * *
66481 AGGAGCGGAACAGAT-CCCGTTTTCCAGATTTAATCTTCCCTGAGGAACATTGGAACAAGTCTTC
64 AATAGCAGAACATATCCCCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTTC
66545 CTC
129 CTC
* * * * * * *
66548 GATTCGATCTTCCTTAAAGAACAGTGGAATGAATTAACGTATCCAAATCTGGTTTTTCTTGAAAA
1 GATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTTTCCAAATCT-GATTTCCCTG-AAA
* * *
66613 AACAACAGAACATATCCCCTTTTTCTAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTTC
64 AATAGCAGAACATATCCCCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTTC
66678 CTC
129 CTC
* * *
66681 GATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACGTTTCCAGATCTGATTTTCCCTGAAAA
1 GATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTTTCCAAATCTGA-TTTCCCTGAAAA
* * * *
66746 AGTAGCAGAACATATCCCCTTTTTCCAGATTTGATCTTTCTTGAGGAATAGTGGAACAAGTCTAC
65 A-TAGCAGAACATATCCCCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTTC
66811 CTC
129 CTC
* * * * * * *
66814 GATTCAATATTCCCAAAAAAATAGTGGAAT-AAGTCAACGTTTCCAAATATGATATGCCTAGAAA
1 GATTCAATCTTCCCTAAAGAACAGTGGAATGAA-TCAACGTTTCCAAATCTGATTTCCCT-GAAA
*
66878 AATAGC-GAAGCATAT--CCTTTTT-CAGATTTCATCTTC
64 AATAGCAGAA-CATATCCCCTTTTTCCAGATTTGATCTTC
66914 AAGAATCTCT
Statistics
Matches: 308, Mismatches: 50, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
129 12 0.04
130 7 0.02
131 3 0.01
132 81 0.26
133 205 0.67
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (131 bp):
GATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTTTCCAAATCTGATTTCCCTGAAAAA
TAGCAGAACATATCCCCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTTCCT
C
Found at i:66894 original size:265 final size:262
Alignment explanation
Indices: 66416--66913 Score: 633
Period size: 266 Copynumber: 1.9 Consensus size: 262
66406 AATCGAATTT
* * **
66416 GATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTGAGGA
1 GATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTCCAGATCTGATTTTCCCTGAAAA
* * *
66481 AGGAGCGGAACAGATCCCGTTTTCCAGATTTAATCTTCCCTGAGGAACATTGGAACAAGTCTTCC
66 AGGAGCAGAACAGATCCCGTTTTCCAGATTTAATCTTCCCTGAGGAACAGTGGAACAAGTCTACC
* * ** * * * * * ** *
66546 TCGATTCGATCTTCCTTAAAGAACAGTGGAATGAATTAACGTATCCAAATCTGGTTTTTCTTGAA
131 TCGATTCAATATTCCCAAAAAAACAGTGGAATGAATCAACGTATCCAAATATGATATGCCTAGAA
*
66611 AAAACAACAGAACATATCCCCTTTTTCTAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCT
196 AAAACAACAGAACATAT--CCTTTTTC-AGATTTCATCTTCCCTGAGGAACAGTGGAACAAGTCT
66676 TCCTC
258 TCCTC
*
66681 GATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACGTTTCCAGATCTGATTTTCCCTGAAAA
1 GATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTCCAGATCTGATTTTCCCTGAAAA
* * * * * * *
66746 AGTAGCAGAACATATCCCCTTTTTCCAGATTTGATCTTTCTTGAGGAATAGTGGAACAAGTCTAC
66 AGGAGCAGAACAGAT-CCCGTTTTCCAGATTTAATCTTCCCTGAGGAACAGTGGAACAAGTCTAC
* *
66811 CTCGATTCAATATTCCCAAAAAAATAGTGGAAT-AAGTCAACGTTTCCAAATATGATATGCCTAG
130 CTCGATTCAATATTCCCAAAAAAACAGTGGAATGAA-TCAACGTATCCAAATATGATATGCCTAG
* *
66875 -AAAAATAGC-GAAGCATATCCTTTTTCAGATTTCATCTTC
194 AAAAAACAACAGAA-CATATCCTTTTTCAGATTTCATCTTC
66914 AAGAATCTCT
Statistics
Matches: 198, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
262 12 0.06
263 8 0.04
264 3 0.02
265 86 0.43
266 89 0.45
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (262 bp):
GATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTCCAGATCTGATTTTCCCTGAAAA
AGGAGCAGAACAGATCCCGTTTTCCAGATTTAATCTTCCCTGAGGAACAGTGGAACAAGTCTACC
TCGATTCAATATTCCCAAAAAAACAGTGGAATGAATCAACGTATCCAAATATGATATGCCTAGAA
AAAACAACAGAACATATCCTTTTTCAGATTTCATCTTCCCTGAGGAACAGTGGAACAAGTCTTCC
TC
Found at i:67225 original size:12 final size:13
Alignment explanation
Indices: 67203--67243 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
67193 ACATCAACCG
67203 GCCCAAACAGTGA
1 GCCCAAACAGTGA
67216 GCCC-AACAGT-A
1 GCCCAAACAGTGA
67227 GACCCAAACAGTGA
1 G-CCCAAACAGTGA
67241 GCC
1 GCC
67244 TAACAGCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 12 0.48
14 2 0.08
ACGTcount: A:0.37, C:0.34, G:0.22, T:0.07
Consensus pattern (13 bp):
GCCCAAACAGTGA
Found at i:67248 original size:12 final size:12
Alignment explanation
Indices: 67205--67249 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
67195 ATCAACCGGC
67205 CCAAACAGTGAG
1 CCAAACAGTGAG
* *
67217 CCCAACAGTAGAC
1 CCAAACAGT-GAG
67230 CCAAACAGTGAG
1 CCAAACAGTGAG
*
67242 CCTAACAG
1 CCAAACAG
67250 CTGGCCCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.40, C:0.31, G:0.20, T:0.09
Consensus pattern (12 bp):
CCAAACAGTGAG
Found at i:67746 original size:33 final size:32
Alignment explanation
Indices: 67705--67784 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
67695 ATAGAGAAAG
* * *
67705 AAAAAAAGAAAAATCGAGGGGGTTCAA-TTTAGA
1 AAAAAAAGAAAAAAC-AGCGAG-TCAATTTTAGA
*
67738 AAAAAAAGAGAAAAACAGCGAGTCAATTTTGGA
1 AAAAAAAGA-AAAAACAGCGAGTCAATTTTAGA
67771 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
67785 AATAAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.22
33 27 0.66
34 5 0.12
ACGTcount: A:0.60, C:0.06, G:0.20, T:0.14
Consensus pattern (32 bp):
AAAAAAAGAAAAAACAGCGAGTCAATTTTAGA
Found at i:67793 original size:18 final size:18
Alignment explanation
Indices: 67770--67813 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
67760 TCAATTTTGG
67770 AAAAAAAAGAAAAAAAAT
1 AAAAAAAAGAAAAAAAAT
* *
67788 AAAAAAGAGAAGAAAAAT
1 AAAAAAAAGAAAAAAAAT
67806 AAAAAAAA
1 AAAAAAAA
67814 CCAAAGCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAAT
Found at i:67843 original size:9 final size:9
Alignment explanation
Indices: 67769--67813 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
67759 GTCAATTTTG
67769 GAAAAAAAA
1 GAAAAAAAA
67778 GAAAAAAAA
1 GAAAAAAAA
* *
67787 TAAAAAAGA
1 GAAAAAAAA
*
67796 GAAGAAAAA
1 GAAAAAAAA
*
67805 TAAAAAAAA
1 GAAAAAAAA
67814 CCAAAGCAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.04
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:68959 original size:2 final size:2
Alignment explanation
Indices: 68952--68996 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
68942 ATTAATTTTA
*
68952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68991 AT AT AT
1 AT AT AT
68997 GGTATATGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70286 original size:13 final size:13
Alignment explanation
Indices: 70254--70280 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70244 AAAGTGTTAA
70254 TGAATTTTAAGAT
1 TGAATTTTAAGAT
70267 TGAATTTTAAGAT
1 TGAATTTTAAGAT
70280 T
1 T
70281 TTATTTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TGAATTTTAAGAT
Found at i:75509 original size:90 final size:90
Alignment explanation
Indices: 75377--75567 Score: 328
Period size: 90 Copynumber: 2.1 Consensus size: 90
75367 AGATTATGGA
* * *
75377 ATTGAAATTGGTACCATACCTATCAAGTGTGATAATATTAGAGTTATTTGTCTCACTAAAAATCC
1 ATTGAAATTAGTACCATACCTATCAAGTGTGACAATATTAGAGTTATTTATCTCACTAAAAATCC
*
75442 TATCCAACACTCTAGAACTAAGCAT
66 GATCCAACACTCTAGAACTAAGCAT
75467 ATTGAAATTAGTACCATACCTATCAAGTGTGACAATATTAGAGTTATTTATCTCACTAAAAATCC
1 ATTGAAATTAGTACCATACCTATCAAGTGTGACAATATTAGAGTTATTTATCTCACTAAAAATCC
*
75532 GATCTAACACTCTAGAACTAAGCAT
66 GATCCAACACTCTAGAACTAAGCAT
*
75557 ATTAAAATTAG
1 ATTGAAATTAG
75568 ACATCATTTC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 95 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (90 bp):
ATTGAAATTAGTACCATACCTATCAAGTGTGACAATATTAGAGTTATTTATCTCACTAAAAATCC
GATCCAACACTCTAGAACTAAGCAT
Found at i:76547 original size:20 final size:20
Alignment explanation
Indices: 76496--76547 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
76486 GAATGCTTGA
* *
76496 ATGGTACTGATACCCCCCAT
1 ATGGTACCGATACCCCCCAG
* * *
76516 A-GGTATCTATACCCCTCAG
1 ATGGTACCGATACCCCCCAG
76535 ATGGTACCGATAC
1 ATGGTACCGATAC
76548 TCTAAGCCAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (20 bp):
ATGGTACCGATACCCCCCAG
Found at i:81825 original size:22 final size:21
Alignment explanation
Indices: 81773--81832 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
81763 GATTTCTGGG
81773 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
81794 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
81814 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
81833 CTCAAGAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:81910 original size:23 final size:22
Alignment explanation
Indices: 81866--81910 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
81856 AATCTCATAG
*
81866 GGGAAACGATTCCCCCACAGGA
1 GGGAAACGATTCCCCCAAAGGA
* *
81888 GGGAATCGATTTCCCCTAAAGGA
1 GGGAAACGA-TTCCCCCAAAGGA
81911 AAAATGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (22 bp):
GGGAAACGATTCCCCCAAAGGA
Found at i:83388 original size:103 final size:103
Alignment explanation
Indices: 83204--83413 Score: 366
Period size: 103 Copynumber: 2.0 Consensus size: 103
83194 GGGTCTACGC
*
83204 GGTCATTCGGGACGTATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
83269 CCTTGGCATATGTATATGATTCTTAAGGAATGATATAT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
*
83307 GGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
83372 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
83410 GGTC
1 GGTC
83414 CTTATGGACA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
Found at i:83495 original size:23 final size:23
Alignment explanation
Indices: 83433--83484 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
83423 ATTATTATAT
*
83433 GGCACTACGGTGTAATTCTACGC
1 GGCACTCCGGTGTAATTCTACGC
* *
83456 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGTAATTCTACGC
83479 GGCACT
1 GGCACT
83485 TTGTTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTCCGGTGTAATTCTACGC
Found at i:85554 original size:23 final size:23
Alignment explanation
Indices: 85526--85623 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
85516 CTAAGACTGT
*
85526 TATCGATGCCCCCTTTGAATAGG
1 TATCGATACCCCCTTTGAATAGG
* *
85549 CATCGATA-CCCCTAT-AATAGG
1 TATCGATACCCCCTTTGAATAGG
* *
85570 TATCGATACCATCC-TTGAATGGG
1 TATCGATACC-CCCTTTGAATAGG
85593 TATCGATACCCCC-TTG-AT-GG
1 TATCGATACCCCCTTTGAATAGG
85613 TATCGATACCC
1 TATCGATACCC
85624 TCCACGGGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
20 13 0.20
21 15 0.23
22 13 0.20
23 23 0.36
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (23 bp):
TATCGATACCCCCTTTGAATAGG
Found at i:87935 original size:18 final size:19
Alignment explanation
Indices: 87897--87935 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
87887 TTTTTCAAAC
*
87897 TTGATTTCAAAAATTATTT
1 TTGATTTCAAAAATGATTT
87916 TTGATTTCAAAAATGATTT
1 TTGATTTCAAAAATGATTT
87935 T
1 T
87936 CAATTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (19 bp):
TTGATTTCAAAAATGATTT
Found at i:88364 original size:20 final size:21
Alignment explanation
Indices: 88306--88367 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
88296 CAGAATGCTC
*
88306 GAATGGTACCGATACCCCCAT
1 GAATGGTATCGATACCCCCAT
* *
88327 GCAATGGTATCTAAACCCCTCA-
1 G-AATGGTATCGATACCCC-CAT
88349 G-ATGGTATCGATACCCCCA
1 GAATGGTATCGATACCCCCA
88368 CGCTCCAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.06
20 14 0.41
21 1 0.03
22 15 0.44
23 2 0.06
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (21 bp):
GAATGGTATCGATACCCCCAT
Found at i:89609 original size:12 final size:12
Alignment explanation
Indices: 89571--89600 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
89561 GATCAAACCT
*
89571 ACCTCCAAACCC
1 ACCTCCAAATCC
89583 ACCTCCAAATCC
1 ACCTCCAAATCC
89595 ACCTCC
1 ACCTCC
89601 TATTCCACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.57, G:0.00, T:0.13
Consensus pattern (12 bp):
ACCTCCAAATCC
Found at i:90906 original size:23 final size:21
Alignment explanation
Indices: 90873--90915 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
90863 ATTTGTGTTT
*
90873 ATTTTGGATTTGTTTGTTTGG
1 ATTTTGGATTTGTTTATTTGG
90894 ATTTTGGATATTTGTTTATTTG
1 ATTTTGG--ATTTGTTTATTTG
90916 AATGATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (21 bp):
ATTTTGGATTTGTTTATTTGG
Found at i:91319 original size:13 final size:13
Alignment explanation
Indices: 91301--91327 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
91291 AAAGTTTTAA
91301 TGAATTTTAAGAT
1 TGAATTTTAAGAT
91314 TGAATTTTAAGAT
1 TGAATTTTAAGAT
91327 T
1 T
91328 TTATTCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TGAATTTTAAGAT
Found at i:91551 original size:21 final size:21
Alignment explanation
Indices: 91521--91598 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 21
91511 TTTATATAGT
*
91521 GGTACTGATACCTAGCTCAAA
1 GGTACCGATACCTAGCTCAAA
*
91542 GGTACCGATACC--CCTCTATATA
1 GGTACCGATACCTAGCTC-A-A-A
*
91564 GTGGTACCGATACCTAGATCAAA
1 --GGTACCGATACCTAGCTCAAA
91587 GGTACCGATACC
1 GGTACCGATACC
91599 CCTCGTGTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
19 3 0.07
20 1 0.02
21 24 0.52
22 1 0.02
23 1 0.02
24 13 0.28
25 1 0.02
26 2 0.04
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (21 bp):
GGTACCGATACCTAGCTCAAA
Found at i:91562 original size:45 final size:45
Alignment explanation
Indices: 91498--91602 Score: 183
Period size: 45 Copynumber: 2.3 Consensus size: 45
91488 AAATAGGGAT
* * *
91498 GTACCGATACCCCTTTATATAGTGGTACTGATACCTAGCTCAAAG
1 GTACCGATACCCCTCTATATAGTGGTACCGATACCTAGATCAAAG
91543 GTACCGATACCCCTCTATATAGTGGTACCGATACCTAGATCAAAG
1 GTACCGATACCCCTCTATATAGTGGTACCGATACCTAGATCAAAG
91588 GTACCGATACCCCTC
1 GTACCGATACCCCTC
91603 GTGTTGATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (45 bp):
GTACCGATACCCCTCTATATAGTGGTACCGATACCTAGATCAAAG
Found at i:91571 original size:24 final size:24
Alignment explanation
Indices: 91498--91577 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
91488 AAATAGGGAT
*
91498 GTACCGATACCCCTTTATATAGTG
1 GTACCGATACCCCTCTATATAGTG
* *
91522 GTACTGATACCTAGCTC-A-A-A--G
1 GTACCGATACC--CCTCTATATAGTG
91543 GTACCGATACCCCTCTATATAGTG
1 GTACCGATACCCCTCTATATAGTG
91567 GTACCGATACC
1 GTACCGATACC
91578 TAGATCAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
19 3 0.07
20 1 0.02
21 12 0.27
22 1 0.02
23 1 0.02
24 23 0.52
25 1 0.02
26 2 0.05
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (24 bp):
GTACCGATACCCCTCTATATAGTG
Found at i:92569 original size:69 final size:69
Alignment explanation
Indices: 92458--92609 Score: 250
Period size: 69 Copynumber: 2.2 Consensus size: 69
92448 ATTTACTTTG
* * * *
92458 TTTTATTTTACTGTTATTTATGTATTTGAATTTAACATTAATGAACTTTGTAATTGAGTTTTAAT
1 TTTTATTTTATTGTTATTTATATATTTGAATTTAAAATTAATGAACTTTGTAATTGAATTTTAAT
92523 ATTT
66 ATTT
92527 TTTTATTTTATTGTTATTTATATATTTGAATTTAAAATTAATGAACTTTGTAATTGAATTTTAAT
1 TTTTATTTTATTGTTATTTATATATTTGAATTTAAAATTAATGAACTTTGTAATTGAATTTTAAT
92592 ATTT
66 ATTT
*
92596 CTTTATTTTGATTG
1 TTTTATTTT-ATTG
92610 GAGTAAGAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 73 0.95
70 4 0.05
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (69 bp):
TTTTATTTTATTGTTATTTATATATTTGAATTTAAAATTAATGAACTTTGTAATTGAATTTTAAT
ATTT
Found at i:94834 original size:30 final size:29
Alignment explanation
Indices: 94745--94990 Score: 151
Period size: 30 Copynumber: 8.3 Consensus size: 29
94735 ACAAAACTTG
94745 AAGGGCTAAAATAGAAAAACAGAAATTTA
1 AAGGGCTAAAATAGAAAAACAGAAATTTA
** * * *
94774 AAGGATTAAAATAGAAAAATAAAAACTTA
1 AAGGGCTAAAATAGAAAAACAGAAATTTA
*
94803 AAGGGCTAAAACAGTAAAAACA-AAATTTTA
1 AAGGGCTAAAATAG-AAAAACAGAAA-TTTA
* *
94833 AAGGACTAAAATAGTAAAAATAGAAATTTA
1 AAGGGCTAAAATAG-AAAAACAGAAATTTA
* * **
94863 GAGGGCTAAAACAGCAAAAACAG-AGCTT-
1 AAGGGCTAAAATAG-AAAAACAGAAATTTA
*
94891 AAGGGACT-AAATAGCAAATACA-AACATTTA
1 AAGGG-CTAAAATAG-AAAAACAGAA-ATTTA
** * * *
94921 AAGGATTAAAATAATAAAAATAGAAACTTA
1 AAGGGCTAAAAT-AGAAAAACAGAAATTTA
* * * ** * *
94951 ATGGACTAAAATGGTATTAACAGAAACTAA
1 AAGGGCTAAAATAG-AAAAACAGAAATTTA
94981 AAGGGCTAAA
1 AAGGGCTAAA
94991 CATTAATTAC
Statistics
Matches: 165, Mismatches: 41, Indels: 21
0.73 0.18 0.09
Matches are distributed among these distances:
28 17 0.10
29 46 0.28
30 96 0.58
31 6 0.04
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.20
Consensus pattern (29 bp):
AAGGGCTAAAATAGAAAAACAGAAATTTA
Found at i:96450 original size:3 final size:3
Alignment explanation
Indices: 96442--96483 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
96432 TTAGATATGG
* * *
96442 TAA TAA TAA CAA TAA TAA CAA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
96484 ATATTTTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:96459 original size:12 final size:12
Alignment explanation
Indices: 96442--96483 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
96432 TTAGATATGG
96442 TAATAATAACAA
1 TAATAATAACAA
*
96454 TAATAACAACAA
1 TAATAATAACAA
*
96466 TAATAATAATAA
1 TAATAATAACAA
96478 TAATAA
1 TAATAA
96484 ATATTTTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
TAATAATAACAA
Found at i:99889 original size:23 final size:23
Alignment explanation
Indices: 99863--99908 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
99853 CACCACAGCT
*
99863 CGTATAAATGCACCGA-AGTGCCA
1 CGTAGAAATGCACC-ATAGTGCCA
99886 CGTAGAAATGCACCATAGTGCCA
1 CGTAGAAATGCACCATAGTGCCA
99909 TATATAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCATAGTGCCA
Found at i:102149 original size:226 final size:228
Alignment explanation
Indices: 101727--102181 Score: 808
Period size: 226 Copynumber: 2.0 Consensus size: 228
101717 TTTATCAAAA
* *
101727 TTGTTTCGAAAATATTTTAAGACTAAAACACAATTTTACACTTAAGTAAGGATTAAAATTTGCAT
1 TTGTTTCAAAAATATTTTAAGACTAAAACACAATTTTACACTTAAGTAAGGATTAAAATTGGCAT
*
101792 TTGAAAACTTGGAGTAATATTTTTGATATTCGAAAAATTTACTCGAATATTAATTTCAAAATCGA
66 TTGAAAACTTGGAGTAATATTTTTGATATTCGAAAAATTTACTCGAATATTAATTTCAAAATCAA
*
101857 ATATAAAATCTTAAAATTCAATAGGACTTTATTTGTTATATCGAAACATCAAAATGTTTTAACAA
131 ATATAAAATCTTAAAATTCAATAGGACTTTATTTGTTATATCGAAACATCAAAATATTTTAACAA
101922 TCTCCCCCTTTTTGATATAACAAAACATTTAAG
196 TCTCCCCCTTTTTGATATAACAAAACATTTAAG
101955 TTGTTTCAAAAATATTTTAAGACTAAAACACAA-TTTACACTTAAGTAAGGATTAAAATTGGCAT
1 TTGTTTCAAAAATATTTTAAGACTAAAACACAATTTTACACTTAAGTAAGGATTAAAATTGGCAT
* * *
102019 TTGAAAAC-TGGAGTATTATTTTTTATATTCGAATAATTTACTCGAATATTAATTTCAAAATCAA
66 TTGAAAACTTGGAGTAATATTTTTGATATTCGAAAAATTTACTCGAATATTAATTTCAAAATCAA
102083 ATATAAAATCTTAAAATT-AATAGGACTTTATTTGTTATATCGAAACATCAAAATATTTTCAACA
131 ATATAAAATCTTAAAATTCAATAGGACTTTATTTGTTATATCGAAACATCAAAATATTTT-AACA
*
102147 ATCTCCTCCTTTTTGATATAACAAAACATTTAAG
195 ATCTCCCCCTTTTTGATATAACAAAACATTTAAG
102181 T
1 T
102182 AATTTTAAGA
Statistics
Matches: 218, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
225 40 0.18
226 108 0.50
227 38 0.17
228 32 0.15
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (228 bp):
TTGTTTCAAAAATATTTTAAGACTAAAACACAATTTTACACTTAAGTAAGGATTAAAATTGGCAT
TTGAAAACTTGGAGTAATATTTTTGATATTCGAAAAATTTACTCGAATATTAATTTCAAAATCAA
ATATAAAATCTTAAAATTCAATAGGACTTTATTTGTTATATCGAAACATCAAAATATTTTAACAA
TCTCCCCCTTTTTGATATAACAAAACATTTAAG
Done.