Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008004.1 Hibiscus syriacus cultivar Beakdansim tig00110465_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: 236824
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1220 original size:13 final size:12
Alignment explanation
Indices: 1180--1224 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1170 GTAGTCTAAT
*
1180 AATATTTTAATA
1 AATATTTAAATA
**
1192 AATATAAAAATA
1 AATATTTAAATA
1204 AATATTTAAATTA
1 AATATTTAAA-TA
1217 AATATTTA
1 AATATTTA
1225 TTCTAGTAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATTTAAATA
Found at i:3084 original size:20 final size:20
Alignment explanation
Indices: 3040--3254 Score: 175
Period size: 20 Copynumber: 10.6 Consensus size: 20
3030 AATGACCAAT
* * *
3040 AAAATCGCAACACGATAT-C
1 AAAATCGCAACGCGATTTAG
3059 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
3079 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
3099 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
3119 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
3139 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
3159 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
3180 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* *
3203 AAAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
3223 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
3243 AGAATCGCAACG
1 AAAATCGCAACG
3255 GTCAAAAGAA
Statistics
Matches: 161, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
19 16 0.10
20 117 0.73
21 14 0.09
23 14 0.09
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:3353 original size:6 final size:6
Alignment explanation
Indices: 3342--3373 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3332 GACACGTATT
3342 ACCACG ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG AC
3374 GGCGCGCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4060 original size:6 final size:6
Alignment explanation
Indices: 4033--4140 Score: 195
Period size: 6 Copynumber: 18.5 Consensus size: 6
4023 TCTCGTCTCG
4033 GGTCG- GGTCG- GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
4078 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
4126 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
4141 AATACGTGTC
Statistics
Matches: 101, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.15
6 86 0.85
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:10038 original size:32 final size:33
Alignment explanation
Indices: 10002--10069 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
9992 AATTAAATAT
* * *
10002 AATCTAAGTTTGGTGTATTCAATTAC-TAATCA
1 AATCTAAGTTAGGTGTATACAATTACACAATCA
*
10034 AATCTAAGTTAGTTGTATACAATTACACAATCA
1 AATCTAAGTTAGGTGTATACAATTACACAATCA
10067 AAT
1 AAT
10070 TTCATGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (33 bp):
AATCTAAGTTAGGTGTATACAATTACACAATCA
Found at i:15138 original size:28 final size:26
Alignment explanation
Indices: 15075--15138 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
15065 TTAGGGATGA
*
15075 ATTTATAAAATTTTAAGAGATAATAT
1 ATTTATAAAATTTTAAGAGATAAAAT
15101 ATTTATAAAATTTTAAG-GATAAAAAT
1 ATTTATAAAATTTTAAGAGAT-AAAAT
15127 ATATTATCAAAA
1 AT-TTAT-AAAA
15139 GAAATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 3 0.09
26 23 0.68
27 4 0.12
28 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (26 bp):
ATTTATAAAATTTTAAGAGATAAAAT
Found at i:22166 original size:15 final size:15
Alignment explanation
Indices: 22143--22182 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
22133 TTTCTCACCT
*
22143 CTGAATGATTCAGTG
1 CTGACTGATTCAGTG
22158 CTGACTGATTCAGTG
1 CTGACTGATTCAGTG
*
22173 TTGACTGATT
1 CTGACTGATT
22183 TAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (15 bp):
CTGACTGATTCAGTG
Found at i:22283 original size:16 final size:16
Alignment explanation
Indices: 22262--22292 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
22252 ATACAGAGCC
22262 TTTGAATCATTCAGCA
1 TTTGAATCATTCAGCA
22278 TTTGAATCATTCAGC
1 TTTGAATCATTCAGC
22293 GCTTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (16 bp):
TTTGAATCATTCAGCA
Found at i:33428 original size:33 final size:32
Alignment explanation
Indices: 33386--33489 Score: 93
Period size: 34 Copynumber: 3.1 Consensus size: 32
33376 GTGGTAAGAA
* * *
33386 ATTTATTTTTATGTTAGTATTT-TTTAAATAGTT
1 ATTT-TTTTTATATTAATATTTATGTAAATA-TT
33419 ATTATTTTTTATATTAATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATTTATGTAAATATT
* * * *
33452 ATTTTTTTATTAAAATAATATTTATATAATTATT
1 A-TTTTTT-TTATATTAATATTTATGTAAATATT
33486 ATTT
1 ATTT
33490 ATTTAGAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
33 28 0.47
34 32 0.53
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (32 bp):
ATTTTTTTTATATTAATATTTATGTAAATATT
Found at i:33471 original size:34 final size:34
Alignment explanation
Indices: 33410--33494 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
33400 TAGTATTTTT
* * * *
33410 TAAATAGTTATTATTTT-TTATATTAATATTTATG
1 TAAATA-TTATTTTTTTATTAAAATAATATTTATA
33444 TAAATATTATTTTTTTATTAAAATAATATTTATA
1 TAAATATTATTTTTTTATTAAAATAATATTTATA
* *
33478 TAATTATTATTTATTTA
1 TAAATATTATTTTTTTA
33495 GAATTATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
33 9 0.20
34 35 0.80
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (34 bp):
TAAATATTATTTTTTTATTAAAATAATATTTATA
Found at i:35242 original size:21 final size:21
Alignment explanation
Indices: 35212--35259 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
35202 GCAGGGGTAC
* *
35212 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
35233 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
35254 ATGCCA
1 ATGCCA
35260 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:35274 original size:21 final size:21
Alignment explanation
Indices: 35250--35356 Score: 101
Period size: 21 Copynumber: 5.1 Consensus size: 21
35240 GCCCACCAGT
*
35250 TTATATGCC-ATCTCCGCAGGG
1 TTATATGCCGAGC-CCGCAGGG
*
35271 TTATATTCCGAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
* *
35292 TTACATTCCGAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
* * *
35313 TTACATTCCTAGCCCGCTA-GG
1 TTATATGCCGAGCCCGC-AGGG
* *
35334 TTACATGCCTAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
35355 TT
1 TT
35357 TTATACCATA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
20 1 0.01
21 74 0.95
22 3 0.04
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (21 bp):
TTATATGCCGAGCCCGCAGGG
Found at i:35310 original size:42 final size:42
Alignment explanation
Indices: 35263--35356 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
35253 TATGCCATCT
* *
35263 CCGCAGGGTTATATTCCGAGCCCGC-AGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGCCCGCTA-GGTTACATGCCGAGC
* *
35305 CCGCAGGGTTACATTCCTAGCCCGCTAGGTTACATGCCTAGC
1 CCGCAGGGTTACATTCCGAGCCCGCTAGGTTACATGCCGAGC
35347 CCGCAGGGTT
1 CCGCAGGGTT
35357 TTATACCATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (42 bp):
CCGCAGGGTTACATTCCGAGCCCGCTAGGTTACATGCCGAGC
Found at i:35921 original size:28 final size:28
Alignment explanation
Indices: 35873--35950 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
35863 GATAAATGTT
* *
35873 TTTAAAAT-AAAATTATATTATTTGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
35900 TTTAAAATAAAAATAATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
*
35928 TTTAAATTTAAAATATAA-ATTAT
1 TTTAAA-ATAAAA-ATAATATTAT
35951 AGTATTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 8 0.18
28 23 0.51
29 10 0.22
30 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCGAAA
Found at i:35962 original size:28 final size:28
Alignment explanation
Indices: 35873--35975 Score: 84
Period size: 34 Copynumber: 3.5 Consensus size: 28
35863 GATAAATGTT
**
35873 TTTAAAATA-AAATTATATTATTTGAAA
1 TTTAAAATATAAATTATATTATTCAAAA
* *
35900 TTTAAAATAAAAATAATATTATTCGAAATTTAAA
1 TTTAAAATATAAATTATATTATTC---A---AAA
*
35934 TTTAAAATATAAATTATAGTATTCAAAA
1 TTTAAAATATAAATTATATTATTCAAAA
*
35962 TTTAACAT-TAAATT
1 TTTAAAATATAAATT
35976 TCAACTTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
27 15 0.24
28 22 0.35
31 1 0.02
34 24 0.39
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTAAAATATAAATTATATTATTCAAAA
Found at i:35973 original size:34 final size:34
Alignment explanation
Indices: 35892--35966 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
35882 AAATTATATT
* *
35892 ATTTGAAATTTAAAATAAAAATAATATTATTCGAA
1 ATTT-AAATTTAAAATAAAAATAATAGTATTCAAA
* *
35927 ATTTAAATTTAAAATATAAATTATAGTATTCAAA
1 ATTTAAATTTAAAATAAAAATAATAGTATTCAAA
35961 ATTTAA
1 ATTTAA
35967 CATTAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 32 0.89
35 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (34 bp):
ATTTAAATTTAAAATAAAAATAATAGTATTCAAA
Found at i:36749 original size:128 final size:128
Alignment explanation
Indices: 36366--37242 Score: 1468
Period size: 128 Copynumber: 6.9 Consensus size: 128
36356 TTACCTGATT
*
36366 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *** *
36431 TGACAAAATAATGGAA-G-TCGCCCCCGGGAACGCGCCTTCATGTCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
36491 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAA-ATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* * * *** *
36554 ATGACAAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
65 CTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
36618 TACTGGTATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
36683 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
36746 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
36811 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* * *
36874 TACTGATAAATCTAGTGTCCCAGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
36939 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
37002 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
37067 TGACGAAATAATGGAA-G-GCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
37128 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
37193 TGACGAAATAATGGAAGGCGCGCCCCCGGGAA--CGCATTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
37243 ACTCCGATTA
Statistics
Matches: 719, Mismatches: 24, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
124 24 0.03
125 53 0.07
126 166 0.23
127 71 0.10
128 405 0.56
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:37326 original size:8 final size:8
Alignment explanation
Indices: 37313--37353 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
37303 TCACAATCTT
37313 TCAAATTC
1 TCAAATTC
37321 TCAAATTC
1 TCAAATTC
* *
37329 CCAAACTC
1 TCAAATTC
37337 T-AAATTC
1 TCAAATTC
37344 TCAAATTC
1 TCAAATTC
37352 TC
1 TC
37354 TGAAAACGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:46611 original size:18 final size:18
Alignment explanation
Indices: 46559--46611 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
46549 ATGATCCTTG
46559 AATTTTAGATAAAATATT
1 AATTTTAGATAAAATATT
*
46577 AA-TTT-GAT---CTA-T
1 AATTTTAGATAAAATATT
46589 AATTTTAGATAAAATATT
1 AATTTTAGATAAAATATT
46607 AATTT
1 AATTT
46612 GATTCTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 3 0.11
13 5 0.19
14 3 0.11
16 3 0.11
17 5 0.19
18 8 0.30
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (18 bp):
AATTTTAGATAAAATATT
Found at i:46775 original size:28 final size:25
Alignment explanation
Indices: 46720--46777 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 25
46710 ATTTATTATA
* *
46720 TAAATGGATAAGTGATAATTTATTT
1 TAAATGGATAAGTGATAATGTATCT
*
46745 TAAATGGATAATTTGTGATAATGTGTCT
1 TAAATGGATAA---GTGATAATGTATCT
46773 TAAAT
1 TAAAT
46778 TGATGTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.41
28 16 0.59
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (25 bp):
TAAATGGATAAGTGATAATGTATCT
Found at i:46963 original size:25 final size:25
Alignment explanation
Indices: 46930--46978 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
46920 ATTATTATAA
46930 TATTATAAATGGATACGTGATAATT
1 TATTATAAATGGATACGTGATAATT
* **
46955 TATTTTAAATGGATTTGTGATAAT
1 TATTATAAATGGATACGTGATAAT
46979 GTGTCTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (25 bp):
TATTATAAATGGATACGTGATAATT
Found at i:46987 original size:25 final size:25
Alignment explanation
Indices: 46935--46989 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
46925 TATAATATTA
* *
46935 TAAATGGATACGTGATAATTTATTT
1 TAAATGGATACGTGATAATGTATCT
** *
46960 TAAATGGATTTGTGATAATGTGTCT
1 TAAATGGATACGTGATAATGTATCT
46985 TAAAT
1 TAAAT
46990 TGATGTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.44
Consensus pattern (25 bp):
TAAATGGATACGTGATAATGTATCT
Found at i:47285 original size:20 final size:20
Alignment explanation
Indices: 47224--47589 Score: 447
Period size: 20 Copynumber: 18.4 Consensus size: 20
47214 GATTTTCCAT
* ** *
47224 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
47244 AATCGCAACGCG-A-ACATA
1 AATCGCAACGCGTATCCGTA
47262 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
47282 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
47302 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
47322 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
47342 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
47362 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
47382 AACCGC-ACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
47401 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
47421 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
47441 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
47461 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
47481 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
47501 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
47521 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
47541 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
47561 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
47581 AATCACAAC
1 AATCGCAAC
47590 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
18 14 0.05
19 21 0.07
20 267 0.88
21 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:50486 original size:14 final size:15
Alignment explanation
Indices: 50451--50479 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
50441 TTTGATATGA
50451 AAATAAA-TTTAAAT
1 AAATAAATTTTAAAT
50465 AAATAAATTTTAAAT
1 AAATAAATTTTAAAT
50480 GATAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAAATTTTAAAT
Found at i:53700 original size:13 final size:13
Alignment explanation
Indices: 53682--53708 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53672 TTGCTAAACC
53682 TTAAGAACACATT
1 TTAAGAACACATT
53695 TTAAGAACACATT
1 TTAAGAACACATT
53708 T
1 T
53709 GCTAAAGTTC
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:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TTAAGAACACATT
Found at i:56571 original size:17 final size:18
Alignment explanation
Indices: 56515--56571 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
56505 TTTATGAGGA
56515 AATT-GAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
*
56532 AATTGGAATCTGTGAAAG
1 AATTGGAATCTGTGAAGG
* *
56550 AATTGGGATCTGT-CAGG
1 AATTGGAATCTGTGAAGG
56567 AATTG
1 AATTG
56572 TAATTCAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 11 0.31
18 24 0.69
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (18 bp):
AATTGGAATCTGTGAAGG
Found at i:66876 original size:68 final size:65
Alignment explanation
Indices: 66747--66894 Score: 156
Period size: 67 Copynumber: 2.2 Consensus size: 65
66737 TTTAAAGAGT
* * * * *
66747 TAAAATATAATAGTTTCCTTATCATGAATTAAAAAATTATTTCTCCATTACTGAATATTTAAATG
1 TAAAATATAA-AGTTTCCTCATCATGAATTAAAAAATAATATCTCCATTACCGAATATTT-AATC
66812 AA
64 AA
*
66814 TAAAATATAAAGTTTCCTCATCAAT-ATATTAAAAAAATAAATAT-TCCATTACCGAGTATTTAA
1 TAAAATATAAAGTTTCCTCATC-ATGA-ATT-AAAAAAT-AATATCTCCATTACCGAATATTTAA
66877 TCAA
62 TCAA
* *
66881 TTAGATATAAAGTT
1 TAAAATATAAAGTT
66895 CTAAGTTTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
66 12 0.17
67 32 0.46
68 22 0.32
69 3 0.04
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (65 bp):
TAAAATATAAAGTTTCCTCATCATGAATTAAAAAATAATATCTCCATTACCGAATATTTAATCAA
Found at i:67070 original size:15 final size:16
Alignment explanation
Indices: 67028--67070 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
67018 TATTGACCAA
*
67028 ATATTTAAAT-ATAAT
1 ATATTTATATAATAAT
*
67043 ATATTTGTATAATAAT
1 ATATTTATATAATAAT
67059 AT-TTTATATAAT
1 ATATTTATATAAT
67071 TATTGATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATTTATATAATAAT
Found at i:69541 original size:23 final size:23
Alignment explanation
Indices: 69510--69561 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
69500 CTTAAACTCG
69510 ATACTTGCTTAAGTGATATTACA
1 ATACTTGCTTAAGTGATATTACA
*
69533 CTACTTGCTTAAGTGATATTACA
1 ATACTTGCTTAAGTGATATTACA
69556 ATACTT
1 ATACTT
69562 ACCACTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (23 bp):
ATACTTGCTTAAGTGATATTACA
Found at i:71611 original size:26 final size:26
Alignment explanation
Indices: 71575--71627 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
71565 AAAGTTAACT
71575 ATCCAACCCTATATCGACATCGACTC
1 ATCCAACCCTATATCGACATCGACTC
71601 ATCCAACCCTATATCGACATCGACTC
1 ATCCAACCCTATATCGACATCGACTC
71627 A
1 A
71628 ATAGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.23
Consensus pattern (26 bp):
ATCCAACCCTATATCGACATCGACTC
Found at i:75080 original size:18 final size:19
Alignment explanation
Indices: 75039--75080 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
75029 TTGGTTCACG
75039 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAG-GA
75059 GAATGTAAGATTACCA-GA
1 GAATGTAAGATTACCAGGA
75077 GAAT
1 GAAT
75081 AGGATTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (19 bp):
GAATGTAAGATTACCAGGA
Found at i:75305 original size:37 final size:37
Alignment explanation
Indices: 75232--75306 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
75222 GTTGGAAAAT
* *
75232 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
75269 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
75306 A
1 A
75307 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:83746 original size:20 final size:20
Alignment explanation
Indices: 83721--83775 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
83711 GAAATGGTGT
*
83721 GTGCATCGATGCATCAAAGA
1 GTGCATCGGTGCATCAAAGA
83741 GTGCATCGGTGCATCAAAGA
1 GTGCATCGGTGCATCAAAGA
83761 GTGCATCGGTGCATC
1 GTGCATCGGTGCATC
83776 CCTTCACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (20 bp):
GTGCATCGGTGCATCAAAGA
Found at i:84230 original size:23 final size:24
Alignment explanation
Indices: 84204--84251 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
84194 TTCTCCGAGC
*
84204 CATTTTTTTCT-TCTTCTT-TTTCT
1 CATTCTTTTCTCTC-TCTTATTTCT
84227 CATTCTTTTCTCTCTCTTATTTCT
1 CATTCTTTTCTCTCTCTTATTTCT
84251 C
1 C
84252 TCTCTCTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (24 bp):
CATTCTTTTCTCTCTCTTATTTCT
Found at i:91771 original size:16 final size:17
Alignment explanation
Indices: 91719--91783 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 17
91709 AAAATTATAT
91719 TAAAA-AATTTAAAATA
1 TAAAATAATTTAAAATA
* * **
91735 TGAAATTATACAATCAATA
1 TAAAATAATTTAA--AATA
91754 TAAAAT-ATTTAAAATA
1 TAAAATAATTTAAAATA
91770 TAAAATAATTTAAA
1 TAAAATAATTTAAA
91784 TTTTTTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 14 0.37
17 11 0.29
18 4 0.11
19 9 0.24
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAAATAATTTAAAATA
Found at i:91783 original size:26 final size:26
Alignment explanation
Indices: 91719--91793 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
91709 AAAATTATAT
* *
91719 TAAAA-AATTTAAAATA-TGAAATTA
1 TAAAATAATTTAAAATATTTAAAATA
* *
91743 TACAATCAATATAAAATATTTAAAATA
1 TAAAAT-AATTTAAAATATTTAAAATA
* *
91770 TAAAATAATTTAAATTTTTTAAAA
1 TAAAATAATTTAAAATATTTAAAA
91794 ATACCTATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 4 0.10
26 25 0.62
27 11 0.28
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (26 bp):
TAAAATAATTTAAAATATTTAAAATA
Found at i:95198 original size:24 final size:25
Alignment explanation
Indices: 95150--95198 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
95140 TACTTTTTTT
* *
95150 AATTTTATAAATTCATCATCTCTTAA
1 AATTTTAAAAATTCATCA-CACTTAA
95176 AATTTTAAAAATTCATC-CACTTA
1 AATTTTAAAAATTCATCACACTTA
95199 TATAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
26 16 0.76
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTTTAAAAATTCATCACACTTAA
Found at i:103719 original size:21 final size:21
Alignment explanation
Indices: 103682--103735 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
103672 CATTAAGTTG
* *
103682 AATAT-TTGAATAGAATTTAT
1 AATATATTAAATAGAATTTAA
*
103702 AATATATTAAATATAATTTAA
1 AATATATTAAATAGAATTTAA
*
103723 AACTATAGTAAAT
1 AA-TATATTAAAT
103736 CAATAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (21 bp):
AATATATTAAATAGAATTTAA
Found at i:105375 original size:22 final size:21
Alignment explanation
Indices: 105344--105397 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
105334 CCCGAACCGA
*
105344 AAAAAGATTTAATCGATACAAT
1 AAAAATATTTAA-CGATACAAT
* *
105366 AAAAATATTTTAAGGATTCAAT
1 AAAAATA-TTTAACGATACAAT
*
105388 TAAAATATTT
1 AAAAATATTT
105398 TAAAGTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.11
22 19 0.70
23 5 0.19
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAAATATTTAACGATACAAT
Found at i:105377 original size:23 final size:22
Alignment explanation
Indices: 105351--105400 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
105341 CGAAAAAAGA
105351 TTTAATCGATACAATAAAAATAT
1 TTTAA-CGATACAATAAAAATAT
* * *
105374 TTTAAGGATTCAATTAAAATAT
1 TTTAACGATACAATAAAAATAT
105396 TTTAA
1 TTTAA
105401 AGTTTAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (22 bp):
TTTAACGATACAATAAAAATAT
Found at i:109520 original size:27 final size:27
Alignment explanation
Indices: 109481--109546 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
109471 TACCAGCTTA
109481 TTGTCT-GCTATTGCAATCTATATTGC
1 TTGTCTGGCTATTGCAATCTATATTGC
109507 TTGTCTGGCTATTGCAATCTATATTGC
1 TTGTCTGGCTATTGCAATCTATATTGC
109534 TTGTCTGGCTATT
1 TTGTCTGGCTATT
109547 TCTTATTGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
26 6 0.15
27 33 0.85
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (27 bp):
TTGTCTGGCTATTGCAATCTATATTGC
Found at i:110793 original size:97 final size:97
Alignment explanation
Indices: 110623--110815 Score: 332
Period size: 97 Copynumber: 2.0 Consensus size: 97
110613 AACTCAAGTA
*
110623 TTTGGTTAATAAACTCACAAAGCAGGTTCGAATTCTTCTGGTTCCTCCTTTCTAAATTTAAACAT
1 TTTGGTTAATAAACTCACAAAGCAGGTTCAAATTCTTCTGGTTCCTCCTTTCTAAATTTAAACAT
* *
110688 GGCTTCTATAGTCTACTATAGTATGTCTGAGT
66 GGCGTCTATAGTCTACCATAGTATGTCTGAGT
* **
110720 TTTGGTTAATAAACTCACAAAGCAGGTTTAAATTCTTCTGGTTCCTCCTTTCTGGATTTAAACAT
1 TTTGGTTAATAAACTCACAAAGCAGGTTCAAATTCTTCTGGTTCCTCCTTTCTAAATTTAAACAT
110785 GGCGTCTATAGTCTACCATAGTATGTCTGAG
66 GGCGTCTATAGTCTACCATAGTATGTCTGAG
110816 AGTTTTTCTG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (97 bp):
TTTGGTTAATAAACTCACAAAGCAGGTTCAAATTCTTCTGGTTCCTCCTTTCTAAATTTAAACAT
GGCGTCTATAGTCTACCATAGTATGTCTGAGT
Found at i:115472 original size:7 final size:7
Alignment explanation
Indices: 115462--115486 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
115452 AAATTACATT
115462 TTAATTG
1 TTAATTG
115469 TTAATTG
1 TTAATTG
115476 TTAATTG
1 TTAATTG
115483 TTAA
1 TTAA
115487 ATCGGTGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (7 bp):
TTAATTG
Found at i:115834 original size:19 final size:19
Alignment explanation
Indices: 115791--115837 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
115781 TCTAATATAT
*
115791 TATTTAATATTTGAATTTAG
1 TATTT-ATATTTAAATTTAG
115811 T-TTTATAGTTTAAATTTA-
1 TATTTATA-TTTAAATTTAG
115829 TATTTATAT
1 TATTTATAT
115838 ATATTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 5 0.21
19 18 0.75
20 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TATTTATATTTAAATTTAG
Found at i:119081 original size:18 final size:20
Alignment explanation
Indices: 119035--119081 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
119025 CGTGCTATGA
*
119035 ATTTTCTATGAATTTAATCC
1 ATTTTTTATGAATTTAATCC
* *
119055 ATTTATTAT-AATTTCAT-C
1 ATTTTTTATGAATTTAATCC
119073 ATTTTTTAT
1 ATTTTTTAT
119082 TTATTTAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 9 0.39
19 7 0.30
20 7 0.30
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTTTATGAATTTAATCC
Found at i:129771 original size:4 final size:4
Alignment explanation
Indices: 129762--129792 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
129752 TCCTTTGGTC
129762 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
129793 CTTTTCAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:131518 original size:18 final size:19
Alignment explanation
Indices: 131487--131530 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
131477 TATTCTCTTA
*
131487 TTTTT-TTTACTTTAATTG
1 TTTTTATTTACTTTAATCG
131505 TTTTTATTTA-TTTAATCG
1 TTTTTATTTACTTTAATCG
131523 TTTTTATT
1 TTTTTATT
131531 ACTACTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTTTATTTACTTTAATCG
Found at i:135285 original size:18 final size:18
Alignment explanation
Indices: 135262--135305 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
135252 AATGTTGAAT
*
135262 AAAAAAACAGCAGTTCGA
1 AAAAAAAAAGCAGTTCGA
**
135280 AAAAAAAAAGTTGTTCGA
1 AAAAAAAAAGCAGTTCGA
135298 AAGAAAAA
1 AA-AAAAA
135306 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.61, C:0.09, G:0.16, T:0.14
Consensus pattern (18 bp):
AAAAAAAAAGCAGTTCGA
Found at i:136513 original size:16 final size:16
Alignment explanation
Indices: 136492--136523 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
136482 CAATTCCAAC
136492 GGGAGAATTGAAACGG
1 GGGAGAATTGAAACGG
136508 GGGAGAATTGAAACGG
1 GGGAGAATTGAAACGG
136524 TCCTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.44, T:0.12
Consensus pattern (16 bp):
GGGAGAATTGAAACGG
Found at i:137016 original size:18 final size:19
Alignment explanation
Indices: 136986--137028 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
136976 TATTCTCTTA
*
136986 TTTT-TTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
137004 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
137022 TTTTATT
1 TTTTATT
137029 ACTACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:138617 original size:18 final size:17
Alignment explanation
Indices: 138594--138642 Score: 80
Period size: 18 Copynumber: 2.8 Consensus size: 17
138584 AGAGTACACT
138594 AAATAATTTAAAAATTAA
1 AAATAATTTAAAAATT-A
138612 AAATAATTTAAAAATTA
1 AAATAATTTAAAAATTA
*
138629 TAATAATTTAAAAA
1 AAATAATTTAAAAA
138643 ATATAATACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATAATTTAAAAATTA
Found at i:138643 original size:18 final size:17
Alignment explanation
Indices: 138595--138650 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
138585 GAGTACACTA
*
138595 AATAATTTAAAAATTAAA
1 AATAATTTAAAAATT-AT
138613 AATAATTTAAAAATTAT
1 AATAATTTAAAAATTAT
*
138630 AATAATTTAAAAAATAT
1 AATAATTTAAAAATTAT
138647 AATA
1 AATA
138651 CTATAATAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 21 0.58
18 15 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATTTAAAAATTAT
Found at i:149334 original size:20 final size:22
Alignment explanation
Indices: 149311--149353 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
149301 CTTTAAAAAA
*
149311 ATTATTTTATTAA-AAA-AATT
1 ATTAATTTATTAATAAATAATT
149331 ATTAATTTATTAATAAATAATT
1 ATTAATTTATTAATAAATAATT
149353 A
1 A
149354 AAAATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 3 0.15
22 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATTTATTAATAAATAATT
Found at i:149368 original size:38 final size:36
Alignment explanation
Indices: 149326--149410 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 36
149316 TTTATTAAAA
*
149326 AAATTATTAATTTATTAATAAATAAT-TAAAAATATGAT
1 AAATTATTAATTT-TTAATAAATAATAAAAAAATA-G-T
*
149364 AAATTAATAATTTTTAATAAATAATAAAAAAATAGT
1 AAATTATTAATTTTTAATAAATAATAAAAAAATAGT
149400 AAA-TATTAATT
1 AAATTATTAATT
149411 AATATTTTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 7 0.16
36 4 0.09
37 13 0.30
38 19 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (36 bp):
AAATTATTAATTTTTAATAAATAATAAAAAAATAGT
Found at i:149688 original size:23 final size:23
Alignment explanation
Indices: 149658--149731 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
149648 GAAGCGAACT
149658 ACGAGCATCGAGCTTAATGAGCA
1 ACGAGCATCGAGCTTAATGAGCA
*
149681 ACGAGCATCGAGATTAATGAGCA
1 ACGAGCATCGAGCTTAATGAGCA
* **
149704 ACGAGCATCGAACTTAACAAGCA
1 ACGAGCATCGAGCTTAATGAGCA
149727 ACGAG
1 ACGAG
149732 TCGAGCAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (23 bp):
ACGAGCATCGAGCTTAATGAGCA
Found at i:156290 original size:21 final size:21
Alignment explanation
Indices: 156264--156357 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
156254 TATGTCATCT
156264 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
156285 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
156306 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
156327 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
*
156348 CCGTAGGGTT
1 CCGCAGGGTT
156358 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 1 0.01
21 65 0.96
22 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:176106 original size:26 final size:26
Alignment explanation
Indices: 176071--176123 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
176061 CTCGTATAAG
176071 ATATAGTGAAAATTATTTTTTAAACT
1 ATATAGTGAAAATTATTTTTTAAACT
*
176097 ATATATTGAAAATTATTTTTTAAACT
1 ATATAGTGAAAATTATTTTTTAAACT
176123 A
1 A
176124 GGATCTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (26 bp):
ATATAGTGAAAATTATTTTTTAAACT
Found at i:176297 original size:21 final size:20
Alignment explanation
Indices: 176260--176357 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
176250 AATCAGTTTC
*
176260 CAAAATCGCAACACGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
176281 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
176301 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
176321 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
176342 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
176358 ACACATAAAT
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.52
21 29 0.48
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:176367 original size:20 final size:20
Alignment explanation
Indices: 176344--176517 Score: 109
Period size: 20 Copynumber: 8.7 Consensus size: 20
176334 GCGAATATGA
176344 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
176364 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
176384 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
176404 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* ** *
176424 AAATCGCAATGCGTATTCGT
1 AAATCGCAACGCGTAACCAT
* * **
176444 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
176464 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
176484 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
176505 AAATCGCAACGCG
1 AAATCGCAACGCG
176518 ATATTTAAAG
Statistics
Matches: 125, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
19 2 0.02
20 106 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:176371 original size:61 final size:62
Alignment explanation
Indices: 176221--176376 Score: 149
Period size: 61 Copynumber: 2.5 Consensus size: 62
176211 AATGACCAAC
* * * * * * *
176221 AAAATCGCAACGCGATCCCCAGAATCGTAAAT-C-AGTTTCCAAAATCGCAACACGATTCTTG
1 AAAATCGCAACGCGATACACAAAATCG-CAATGCGATTTTCCAAAATCGCAACACGAATCATG
* ** * * *
176282 AAAATCGCAATGCGATAGTCAAATTCGCATTGCGATTTTCCAAAATCGCAACGCGAAT-ATG
1 AAAATCGCAACGCGATACACAAAATCGCAATGCGATTTTCCAAAATCGCAACACGAATCATG
176343 AAAATCGCAACGCGA-ACACATAAATCGCAATGCG
1 AAAATCGCAACGCGATACACA-AAATCGCAATGCG
176377 TATCCGTAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
60 5 0.07
61 49 0.65
62 21 0.28
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (62 bp):
AAAATCGCAACGCGATACACAAAATCGCAATGCGATTTTCCAAAATCGCAACACGAATCATG
Found at i:176388 original size:40 final size:40
Alignment explanation
Indices: 176324--176518 Score: 185
Period size: 40 Copynumber: 4.8 Consensus size: 40
176314 CGATTTTCCA
* ** *
176324 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * * *
176364 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
** * * ** *
176404 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATTCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * ** *
176444 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
176484 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
176519 TATTTAAAGC
Statistics
Matches: 124, Mismatches: 28, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
40 92 0.74
41 32 0.26
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:176409 original size:60 final size:60
Alignment explanation
Indices: 176324--176517 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
176314 CGATTTTCCA
* ** * *
176324 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * *** *
176384 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATTCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
176444 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
176505 AAATCGCAACGCG
1 AAATCGCAACGCG
176518 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 80 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:176938 original size:33 final size:33
Alignment explanation
Indices: 176900--176970 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
176890 TTCACTTAGA
*
176900 TTTCATTTTGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
176933 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
176966 TTTCA
1 TTTCA
176971 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:177107 original size:41 final size:41
Alignment explanation
Indices: 177049--177126 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
177039 TTGCAGAAGA
*
177049 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
177090 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
177127 CGCAAAGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:177123 original size:21 final size:21
Alignment explanation
Indices: 177050--177125 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
177040 TGCAGAAGAG
*
177050 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
177071 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
177091 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
177112 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
177126 TCGCAAAGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:177129 original size:14 final size:14
Alignment explanation
Indices: 177110--177166 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
177100 GAGAAATGAA
177110 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
177124 AATCGCAAAGCGATATGAA
1 AATCGC-AA-CG--A-GAG
177143 AATCGCAACGAGAG
1 AATCGCAACGAGAG
177157 AATCGCAACG
1 AATCGCAACG
177167 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 8 0.22
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:177143 original size:33 final size:33
Alignment explanation
Indices: 177105--177169 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
177095 AACGAGAGAA
177105 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
*
177138 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGA
177170 AACCAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
Found at i:177178 original size:33 final size:33
Alignment explanation
Indices: 177108--177182 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
177098 GAGAGAAATG
* **
177108 AAAATCGCAACGAGAGAATCGCAAAGCGATATG
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
*
177141 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
177174 AAAATCGCA
1 AAAATCGCA
177183 TTGCGATTTT
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:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
Found at i:177200 original size:19 final size:19
Alignment explanation
Indices: 177178--177275 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
177168 GAAACCAAAA
*
177178 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
177197 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
177211 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
177230 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
177244 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
177263 TCGCGTTGCGATT
1 TCGCGTTGCGATT
177276 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:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:177219 original size:14 final size:14
Alignment explanation
Indices: 177200--177289 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
177190 TTTCATTTCG
177200 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
177214 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
177233 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
177247 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
177266 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
177280 CGTTGCGATT
1 CGTTGCGATT
177290 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:177225 original size:33 final size:33
Alignment explanation
Indices: 177183--177297 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
177173 CAAAATCGCA
177183 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
177216 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
177249 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
177282 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
177298 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:179154 original size:93 final size:93
Alignment explanation
Indices: 178995--179370 Score: 736
Period size: 93 Copynumber: 4.1 Consensus size: 93
178985 TAGATTGCTT
*
178995 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179060 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
179088 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179153 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
179181 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179246 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
179274 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179339 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
179366 AGTAA
1 AGTAA
179371 TGCAATCCAT
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 276 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:179478 original size:33 final size:32
Alignment explanation
Indices: 179435--179527 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
179425 ACGAAACTTA
**
179435 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
179467 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
179500 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
179528 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:179527 original size:19 final size:19
Alignment explanation
Indices: 179418--179527 Score: 87
Period size: 19 Copynumber: 6.3 Consensus size: 19
179408 TAGTTTACTT
* *
179418 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
179438 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
179457 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
179471 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
179490 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
179504 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
179523 TCGCA
1 TCGCA
179528 TTGCGATTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.26
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 29 0.40
20 12 0.17
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:179545 original size:19 final size:19
Alignment explanation
Indices: 179523--179657 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
179513 GAAACCAAAA
*
179523 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
179542 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
179558 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
179575 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
179591 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
179608 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
179627 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
179647 TCGTGTTGCGA
1 TCGCGTTGCGA
179658 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:179564 original size:14 final size:14
Alignment explanation
Indices: 179545--179601 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
179535 TTTCATTTCG
179545 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
179559 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
179576 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
179592 CGTTGCGATT
1 CGTTGCGATT
179602 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:179570 original size:33 final size:33
Alignment explanation
Indices: 179528--179620 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
179518 CAAAATCGCA
*
179528 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
179561 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
179594 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
179621 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:181601 original size:14 final size:14
Alignment explanation
Indices: 181582--181631 Score: 91
Period size: 14 Copynumber: 3.6 Consensus size: 14
181572 ATTGTTTAAT
181582 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
181596 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
181610 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
181624 TGATTTGT
1 TGATTTGT
181632 GTAATTGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:181754 original size:19 final size:19
Alignment explanation
Indices: 181738--181835 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
181728 AAAAATGACT
181738 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
181757 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
181776 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
181790 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
181809 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
181829 ATCGCAA
1 ATCGCAA
181836 CGAGAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.15
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 40 0.56
20 16 0.23
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:181867 original size:53 final size:53
Alignment explanation
Indices: 181740--181853 Score: 203
Period size: 53 Copynumber: 2.2 Consensus size: 53
181730 AAATGACTAT
* *
181740 CGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGAGAGAAT
1 CGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAAC
181792 CGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAAC
1 CGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAAC
181845 CGCAATGCG
1 CGCAATGCG
181854 TTTATAATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 27 0.46
53 32 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (53 bp):
CGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAAC
Found at i:181897 original size:33 final size:34
Alignment explanation
Indices: 181860--182013 Score: 149
Period size: 33 Copynumber: 4.5 Consensus size: 34
181850 TGCGTTTATA
181860 ATTTCGCATTGCGATTCTCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGATTGCGATTTTC
*
181893 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG-ATTGCGATT-T-TC
* * *
181933 GTTGCG-ATTTTC-ATT-TC-CGTATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCG-ATTGCGATTTTC
*
181965 ATTTCGCATTGCGATTCTATCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGATTGCGATTTTC
181998 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
182014 TTCATTTCGC
Statistics
Matches: 99, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
32 9 0.09
33 46 0.46
34 12 0.12
35 6 0.06
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTCTCGATTGCGATTTTC
Found at i:181906 original size:19 final size:19
Alignment explanation
Indices: 181882--182098 Score: 231
Period size: 19 Copynumber: 12.4 Consensus size: 19
181872 GATTCTCTCG
181882 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
181901 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
181920 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
181934 TTGCGATTTTCATTTCCGTA
1 TTGCGATTTTCATTT-CGCA
181954 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
181973 TTGCGA--TTC-TATCG--
1 TTGCGATTTTCATTTCGCA
181987 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
182006 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
182025 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
182039 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
182058 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
182072 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
182091 TTGCGATT
1 TTGCGATT
182099 GTAATTTCCG
Statistics
Matches: 168, Mismatches: 9, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 21 0.12
18 2 0.01
19 78 0.46
20 15 0.09
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:181991 original size:105 final size:104
Alignment explanation
Indices: 181860--182070 Score: 395
Period size: 105 Copynumber: 2.0 Consensus size: 104
181850 TGCGTTTATA
*
181860 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
181925 ATTCTCTCGTTGCGATTTTCATTTCCGTATTGCGATTTTC
66 ATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
181965 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
182030 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
182069 AT
1 AT
182071 GTTGGGATTT
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
104 16 0.15
105 88 0.85
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (104 bp):
ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:182043 original size:33 final size:33
Alignment explanation
Indices: 181901--182098 Score: 188
Period size: 33 Copynumber: 5.8 Consensus size: 33
181891 TCATTTCGCA
181901 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
181934 TTGCGATTTTCATTTCCGTATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTT-CGCATTGCGA--TTC-TCTCG
* * * * *
181971 CATTGCGATTCTATCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
182006 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
182039 TTGCGATTTTCATTTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
* *
182072 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
182099 GTAATTTCCG
Statistics
Matches: 136, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
31 9 0.07
32 5 0.04
33 81 0.60
34 10 0.07
35 2 0.01
36 3 0.02
37 6 0.04
39 10 0.07
40 6 0.04
41 4 0.03
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:182106 original size:52 final size:52
Alignment explanation
Indices: 181860--182070 Score: 395
Period size: 52 Copynumber: 4.0 Consensus size: 52
181850 TGCGTTTATA
181860 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
181912 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGTATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
*
181965 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
182017 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
182069 AT
1 AT
182071 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
52 104 0.68
53 50 0.32
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:182884 original size:20 final size:20
Alignment explanation
Indices: 182856--183065 Score: 197
Period size: 20 Copynumber: 10.5 Consensus size: 20
182846 AAATTTCAGT
* * *
182856 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
182876 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* * *
182896 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
182916 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
182936 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
182956 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
** *
182976 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
182996 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
183016 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
183036 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
183056 GTTGCGATTT
1 GTTGCGATTT
183066 TGGAAAATCG
Statistics
Matches: 160, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
20 159 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:183082 original size:21 final size:20
Alignment explanation
Indices: 183032--183129 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
183022 ATTTATGTGT
* * * *
183032 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
183052 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
183073 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
183093 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
183114 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
183130 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:183105 original size:61 final size:60
Alignment explanation
Indices: 183032--183188 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
183022 ATTTATGTGT
*
183032 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
183093 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
183154 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
183189 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:183124 original size:41 final size:41
Alignment explanation
Indices: 183032--183188 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
183022 ATTTATGTGT
* * *
183032 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
183073 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
183114 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
183154 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
183189 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:185811 original size:23 final size:23
Alignment explanation
Indices: 185793--185853 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
185783 CTCGTATAAA
185793 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
185816 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
185839 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
185854 TATAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:186112 original size:30 final size:31
Alignment explanation
Indices: 186078--186136 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
186068 TATTGTATAG
186078 ACATATAAT-TTCCAT-ACCTTTATCACATGA
1 ACATATAATGTTCCATCA-CTTTATCACATGA
*
186108 ACATATCATGTTCCATCACTTTATCACAT
1 ACATATAATGTTCCATCACTTTATCACAT
186137 AGCTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (31 bp):
ACATATAATGTTCCATCACTTTATCACATGA
Found at i:187945 original size:20 final size:21
Alignment explanation
Indices: 187896--187947 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
187886 AAATAACCAA
187896 CAAATTCGCAACGCGATTCTC
1 CAAATTCGCAACGCGATTCTC
* *
187917 CAAAATCGCAGCGCGATTCT-
1 CAAATTCGCAACGCGATTCTC
187937 CAAATTCGCAA
1 CAAATTCGCAA
187948 TGTGAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTCTC
Found at i:188114 original size:99 final size:99
Alignment explanation
Indices: 187917--188153 Score: 341
Period size: 99 Copynumber: 2.4 Consensus size: 99
187907 CGCGATTCTC
* * * * * *
187917 CAAAATCGCAGCGCGATTCT-CAAATTCGCAATGTGAATTTCGTTTTAGCAACGCTAATTACCGA
1 CAAATTCGCAACGCGATTCTCCAAAATCGCAACGCGAATTTCGTTTTAGCAACGCTAACTACCGA
*
187981 TATAGGTAAACACAACTATTCACAAGTCAATTTT
66 TATAGGTAAACACAACTATTCACAACTCAATTTT
* * *
188015 CAAATTTGCAACGCGATTCTCCAAAATCGCAGCGCGAATTTCGTTTTCGCAACGCTAACTACCGA
1 CAAATTCGCAACGCGATTCTCCAAAATCGCAACGCGAATTTCGTTTTAGCAACGCTAACTACCGA
*
188080 TATAGGTAAACACAACTATTCACAACTCAGTTTT
66 TATAGGTAAACACAACTATTCACAACTCAATTTT
** *
188114 CAAATTCGCAACGCGATTCTCCAAGTTCGCAACGCTAATT
1 CAAATTCGCAACGCGATTCTCCAAAATCGCAACGCGAATT
188154 ACCGATATAG
Statistics
Matches: 122, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
98 17 0.14
99 105 0.86
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (99 bp):
CAAATTCGCAACGCGATTCTCCAAAATCGCAACGCGAATTTCGTTTTAGCAACGCTAACTACCGA
TATAGGTAAACACAACTATTCACAACTCAATTTT
Found at i:188477 original size:91 final size:91
Alignment explanation
Indices: 188317--188497 Score: 290
Period size: 91 Copynumber: 2.0 Consensus size: 91
188307 CGAATAGTTG
* * *
188317 TGTTTACCTATATCGGTAATTAGCGTTGTGAAAACGAAATTCACGTTACGATTTTGGAGAATCGT
1 TGTTTACCCATATCGGTAATTAGCGTTGCGAAAACGAAATTCACGTTACGATTTTGGAGAATCGC
188382 GTTGCGAATTTGAAAACTGAGTTGCA
66 GTTGCGAATTTGAAAACTGAGTTGCA
* * **
188408 TGTTTACCCATGTCGGTAATTAGCGTTGCGAAAACGAAATTCGCGTTGTGATTTTGGAGAATCGC
1 TGTTTACCCATATCGGTAATTAGCGTTGCGAAAACGAAATTCACGTTACGATTTTGGAGAATCGC
*
188473 GTTGCGAATTTGAAAACTGTGTTGC
66 GTTGCGAATTTGAAAACTGAGTTGC
188498 GAAACTGGTG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (91 bp):
TGTTTACCCATATCGGTAATTAGCGTTGCGAAAACGAAATTCACGTTACGATTTTGGAGAATCGC
GTTGCGAATTTGAAAACTGAGTTGCA
Found at i:207971 original size:6 final size:6
Alignment explanation
Indices: 207960--207993 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
207950 TCTGGCACTA
207960 GGTTCG GGTTCG GGTTCG GGTTCG GGTTCG GGTT
1 GGTTCG GGTTCG GGTTCG GGTTCG GGTTCG GGTT
207994 TCTTTGTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GGTTCG
Found at i:214323 original size:6 final size:6
Alignment explanation
Indices: 214312--214389 Score: 156
Period size: 6 Copynumber: 13.0 Consensus size: 6
214302 TACATATCAT
214312 CATTGG CATTGG CATTGG CATTGG CATTGG CATTGG CATTGG CATTGG
1 CATTGG CATTGG CATTGG CATTGG CATTGG CATTGG CATTGG CATTGG
214360 CATTGG CATTGG CATTGG CATTGG CATTGG
1 CATTGG CATTGG CATTGG CATTGG CATTGG
214390 GAGTTGGGGC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 72 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
CATTGG
Found at i:216787 original size:25 final size:26
Alignment explanation
Indices: 216741--216793 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
216731 TTTTTAACTT
*
216741 AAAATATATTAAATTATAAGATATATA
1 AAAATATATTAAA-TATAAGATAAATA
*
216768 AAAATATATTAAA-ATTAGATAAATA
1 AAAATATATTAAATATAAGATAAATA
216793 A
1 A
216794 TCATACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.46
27 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (26 bp):
AAAATATATTAAATATAAGATAAATA
Found at i:216825 original size:20 final size:18
Alignment explanation
Indices: 216799--216850 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
216789 AATAATCATA
*
216799 CTATTTTTTTGTAATTTTT
1 CTATTTTTTTAT-ATTTTT
216818 CGTATTTTTTTATATTTTT
1 C-TATTTTTTTATATTTTT
216837 CTGA-TTTTTTATAT
1 CT-ATTTTTTTATAT
216851 CCGTAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.37
19 9 0.30
20 10 0.33
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
CTATTTTTTTATATTTTT
Found at i:216833 original size:10 final size:10
Alignment explanation
Indices: 216800--216846 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
216790 ATAATCATAC
216800 TATTTTTTTG
1 TATTTTTTTG
* *
216810 TAATTTTTCG
1 TATTTTTTTG
*
216820 TATTTTTTTA
1 TATTTTTTTG
*
216830 TATTTTTCTG
1 TATTTTTTTG
216840 -ATTTTTT
1 TATTTTTT
216847 ATATCCGTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
9 6 0.21
10 23 0.79
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (10 bp):
TATTTTTTTG
Found at i:223856 original size:16 final size:16
Alignment explanation
Indices: 223835--223869 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
223825 TTTTATATAA
*
223835 TTTTCTGTGTTGTTGT
1 TTTTCTGTGTTCTTGT
*
223851 TTTTCTTTGTTCTTGT
1 TTTTCTGTGTTCTTGT
223867 TTT
1 TTT
223870 GCAATAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.17, T:0.74
Consensus pattern (16 bp):
TTTTCTGTGTTCTTGT
Found at i:224112 original size:20 final size:20
Alignment explanation
Indices: 224087--224127 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
224077 AACTTTCAAA
224087 ATAATTA-TAGAAATATTATT
1 ATAATTATTA-AAATATTATT
*
224107 ATAATTATTAAATTATTATT
1 ATAATTATTAAAATATTATT
224127 A
1 A
224128 AACTTACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATAATTATTAAAATATTATT
Found at i:224143 original size:20 final size:20
Alignment explanation
Indices: 224097--224144 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
224087 ATAATTATAG
**
224097 AAATATTATTATAATTATTA
1 AAATATTATTATAATTACCA
*
224117 AATTATTATTA-AACTTACCA
1 AAATATTATTATAA-TTACCA
224137 AAATATTA
1 AAATATTA
224145 CAAGAGATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATATTATTATAATTACCA
Found at i:226243 original size:19 final size:19
Alignment explanation
Indices: 226211--226255 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
226201 CTGACATCTG
226211 CAGCA-GGGCAGCATGGTC
1 CAGCATGGGCAGCATGGTC
* *
226229 CAGCATGGGCGGCATGGTG
1 CAGCATGGGCAGCATGGTC
226248 CAGCATGG
1 CAGCATGG
226256 CATTTGCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.20, C:0.24, G:0.42, T:0.13
Consensus pattern (19 bp):
CAGCATGGGCAGCATGGTC
Found at i:226245 original size:9 final size:10
Alignment explanation
Indices: 226209--226255 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
226199 ACCTGACATC
226209 TGCAGCA-GG
1 TGCAGCATGG
226218 -GCAGCATGG
1 TGCAGCATGG
*
226227 TCCAGCATGG
1 TGCAGCATGG
*
226237 -GCGGCATGG
1 TGCAGCATGG
226246 TGCAGCATGG
1 TGCAGCATGG
226256 CATTTGCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
8 6 0.19
9 9 0.29
10 16 0.52
ACGTcount: A:0.19, C:0.23, G:0.43, T:0.15
Consensus pattern (10 bp):
TGCAGCATGG
Found at i:233258 original size:14 final size:14
Alignment explanation
Indices: 233226--233275 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
233216 AAGTGGTATA
233226 TATAAAATAA-ATAT
1 TATAAAATAATA-AT
233240 T-TAAAA-AAGTAAT
1 TATAAAATAA-TAAT
*
233253 TATAAAATAATATT
1 TATAAAATAATAAT
233267 TATAAAATA
1 TATAAAATA
233276 TGAAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 2 0.06
13 8 0.26
14 19 0.61
15 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TATAAAATAATAAT
Done.