Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004254.1 Hibiscus syriacus cultivar Beakdansim tig00009325_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: 146320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2378 original size:31 final size:31
Alignment explanation
Indices: 2340--2430 Score: 125
Period size: 30 Copynumber: 3.0 Consensus size: 31
2330 TGACTTTCAA
2340 TTACTATTCGGACTTTGAAACAACGCTACGC
1 TTACTATTCGGACTTTGAAACAACGCTACGC
2371 TTACTATTCGGACTTTG-AACAACGCTACG-
1 TTACTATTCGGACTTTGAAACAACGCTACGC
* * *
2400 TGGACTATTCGGACTTGGAAA-TACGCTACGC
1 T-TACTATTCGGACTTTGAAACAACGCTACGC
2431 GGATCACCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
29 1 0.02
30 34 0.63
31 19 0.35
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (31 bp):
TTACTATTCGGACTTTGAAACAACGCTACGC
Found at i:4304 original size:23 final size:24
Alignment explanation
Indices: 4278--4331 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
4268 TCAACTCAGT
**
4278 CTGCCTTCGGTGCCGGGAGCA-CC
1 CTGCCTTCGGTGCCGCAAGCACCC
4301 CTGCCTTCGGTGCCGCAAGCACCC
1 CTGCCTTCGGTGCCGCAAGCACCC
4325 CTGCCTT
1 CTGCCTT
4332 TGGTTCTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.09, C:0.43, G:0.28, T:0.20
Consensus pattern (24 bp):
CTGCCTTCGGTGCCGCAAGCACCC
Found at i:4402 original size:24 final size:24
Alignment explanation
Indices: 4370--4430 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
4360 AGCACTGGAA
* *
4370 CTGCATTTGGAGGATC-AAGCACAC
1 CTGCTTTTGGAGCATCTAA-CACAC
*
4394 CTGCTTTTGGCA-CATCTAACACTC
1 CTGCTTTTGG-AGCATCTAACACAC
4418 CTGCTTTTGGAGC
1 CTGCTTTTGGAGC
4431 CTCAGCTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.03
24 27 0.87
25 3 0.10
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (24 bp):
CTGCTTTTGGAGCATCTAACACAC
Found at i:13387 original size:2 final size:2
Alignment explanation
Indices: 13380--13407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13370 TATTTATTCA
13380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13408 TAGTGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22772 original size:2 final size:2
Alignment explanation
Indices: 22765--22797 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22755 TACATTTGTT
22765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22798 TCATTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28455 original size:17 final size:19
Alignment explanation
Indices: 28428--28469 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
28418 GAAATTGAAG
*
28428 GATATTTTTTGGTTG-TTT
1 GATATTATTTGGTTGATTT
*
28446 G-TATTATTTGTTTGATTT
1 GATATTATTTGGTTGATTT
28464 GATATT
1 GATATT
28470 CCATACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 11 0.55
18 5 0.25
19 4 0.20
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64
Consensus pattern (19 bp):
GATATTATTTGGTTGATTT
Found at i:36582 original size:12 final size:12
Alignment explanation
Indices: 36565--36594 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
36555 GACCTATTCC
36565 TATAAAAAAATA
1 TATAAAAAAATA
*
36577 TATAAAAATATA
1 TATAAAAAAATA
36589 TATAAA
1 TATAAA
36595 TTATTCAACA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TATAAAAAAATA
Found at i:43239 original size:40 final size:41
Alignment explanation
Indices: 43184--43265 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
43174 AAATAATTCT
* *
43184 AGCACTTAGTCTCCTCTCCACAC-TGTTCTTTTAATCCCGA
1 AGCACTTAGTCTCCTCTCCACACATGTTCTTTCAATACCGA
43224 AGCACTT-GATCTCCTCTCCACACTATGTTCTTTCAATACCGA
1 AGCACTTAG-TCTCCTCTCCACAC-ATGTTCTTTCAATACCGA
43266 GGCGTTAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 1 0.03
40 21 0.57
42 15 0.41
ACGTcount: A:0.22, C:0.34, G:0.10, T:0.34
Consensus pattern (41 bp):
AGCACTTAGTCTCCTCTCCACACATGTTCTTTCAATACCGA
Found at i:47089 original size:138 final size:139
Alignment explanation
Indices: 46841--47115 Score: 457
Period size: 138 Copynumber: 2.0 Consensus size: 139
46831 GTTGGAGTAG
*
46841 GTTTTCTTTGCAGCCTCCTAAATCTCCTTTTCGTTTTAGACAGTAGCAAAATCTCTCCAATATCA
1 GTTTTCTTTGCAGCCTCCCAAATCTCCTTTTCGTTTTAGACAGTAGCAAAATCTCTCCAATATCA
* *
46906 ATTGCCATAGAATTGATAGCCACGGTGTAACCATATGGTTCTCAACTC-CCAGGTGTGATATTTA
66 ATGGCCATAGAATTGATAGCCACGGTCTAACCATATGGTTCTCAACTCTCCAGGTGTGATATTTA
46970 GGATCATCA
131 GGATCATCA
*
46979 GTTTTCTTTGCAGCCTCCCAAATCTCC-TTTCGTTTT-GTACAGTAGGAAAATCTCTCCAATATC
1 GTTTTCTTTGCAGCCTCCCAAATCTCCTTTTCGTTTTAG-ACAGTAGCAAAATCTCTCCAATATC
* *
47042 AATGGCCATATAATTGATAAGCCATGGTCTAACCATATGGTTCTCAACTCTCCAGGTGTGATATT
65 AATGGCCATAGAATTGAT-AGCCACGGTCTAACCATATGGTTCTCAACTCTCCAGGTGTGATATT
47107 TAGGATCAT
129 TAGGATCAT
47116 ATGGTCTAAC
Statistics
Matches: 128, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
136 1 0.01
137 49 0.38
138 55 0.43
139 23 0.18
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (139 bp):
GTTTTCTTTGCAGCCTCCCAAATCTCCTTTTCGTTTTAGACAGTAGCAAAATCTCTCCAATATCA
ATGGCCATAGAATTGATAGCCACGGTCTAACCATATGGTTCTCAACTCTCCAGGTGTGATATTTA
GGATCATCA
Found at i:57168 original size:9 final size:9
Alignment explanation
Indices: 57156--57189 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
57146 AAATTTGGTT
57156 AATTAACCG
1 AATTAACCG
57165 AATTAACCG
1 AATTAACCG
57174 AATTAACCG
1 AATTAACCG
57183 AAATTAA
1 -AATTAA
57190 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:57581 original size:183 final size:183
Alignment explanation
Indices: 57195--57581 Score: 643
Period size: 183 Copynumber: 2.1 Consensus size: 183
57185 ATTAAATTTT
* *
57195 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAATAATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
* *
57260 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAACATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* *
57325 TATTTTGTAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
* *
57378 AAATATTAAATATATTATATATAACATATGGGTTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
*
57443 TTTAACATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATTT
66 TTTAACATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATTT
57508 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
* *
57562 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
57582 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
183 125 0.65
184 66 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAACATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:70257 original size:21 final size:20
Alignment explanation
Indices: 70233--70276 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
70223 CTAAAATTTA
*
70233 TAAATAATATATATTATATAT
1 TAAATAATAAATATT-TATAT
* *
70254 TAAATATTAAATATTTTTAT
1 TAAATAATAAATATTTATAT
70274 TAA
1 TAA
70277 TTCGATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATAATAAATATTTATAT
Found at i:70864 original size:2 final size:2
Alignment explanation
Indices: 70857--70903 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
70847 GACTATCTTT
70857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70899 TA TA T
1 TA TA T
70904 GGTTGTTCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:71780 original size:64 final size:64
Alignment explanation
Indices: 71679--71806 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
71669 TGGGACATCC
*
71679 CATGTTGAAGGGATACTGATAGAATTAGTTGAGTATGTCGAAGAGATTTCCGAGACATAATCGG
1 CATGTTGAAGGGATACTGATAGAATTAGTTGAGTATGTCGAAGAGATTTCCAAGACATAATCGG
* *
71743 CATGTTGAAGGGATACTGATAGAATTAGTTGAGTATGTTGAATAGATTTCCAAGACATAATCGG
1 CATGTTGAAGGGATACTGATAGAATTAGTTGAGTATGTCGAAGAGATTTCCAAGACATAATCGG
71807 GATGACATTA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.30
Consensus pattern (64 bp):
CATGTTGAAGGGATACTGATAGAATTAGTTGAGTATGTCGAAGAGATTTCCAAGACATAATCGG
Found at i:74253 original size:19 final size:19
Alignment explanation
Indices: 74229--74272 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
74219 TACCTCTCAA
74229 CTTGATCGTCACCATTTCG
1 CTTGATCGTCACCATTTCG
74248 CTTGATCGTCACCATTTCG
1 CTTGATCGTCACCATTTCG
74267 CTTGAT
1 CTTGAT
74273 TTTGAAGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.39
Consensus pattern (19 bp):
CTTGATCGTCACCATTTCG
Found at i:76216 original size:18 final size:17
Alignment explanation
Indices: 76193--76230 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
76183 TATATATATG
*
76193 ATTATCCTCTTCCTTATC
1 ATTATCCTCTT-ATTATC
76211 ATTATCCTCTTATTATC
1 ATTATCCTCTTATTATC
76228 ATT
1 ATT
76231 GATACCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATCCTCTTATTATC
Found at i:76583 original size:31 final size:31
Alignment explanation
Indices: 76545--76669 Score: 178
Period size: 31 Copynumber: 4.0 Consensus size: 31
76535 CCCGAAGGAC
* * * *
76545 CAGTCCATAGGTTCCGAAGAACCTAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
76576 CAGTCCATATATTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
76607 CATTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
76638 CAGTCCATATGTCCCCAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
76669 C
1 C
76670 CCTCAACCCT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:83074 original size:21 final size:21
Alignment explanation
Indices: 83048--83101 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
83038 GTTTCCAGAT
* *
83048 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTGGACTA
83069 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
83090 TCGCAATGCGAA
1 TCGCAATGCGAA
83102 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:83223 original size:92 final size:92
Alignment explanation
Indices: 83064--83247 Score: 257
Period size: 92 Copynumber: 2.0 Consensus size: 92
83054 CGCGAACTTT
* * * *
83064 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAA
1 GACTATCGCAACGCGAACTTCGACTATCGCAATGAGAATATGTAAATCGCAATGCGATAGTCCAA
*
83129 GTTCGCGTTGCGATTTATTCCAAATTC
66 GTTCGCATTGCGATTTATTCCAAATTC
* *
83156 GACTATCGCAACGCGAACTTCGACTATCGCATTGAG-AT-T-TACATATTCGCATTGCGATAGTC
1 GACTATCGCAACGCGAACTTCGACTATCGCAATGAGAATATGTA-A-A-TCGCAATGCGATAGTC
83218 CAAGTTCGCATTGCGATTTATTCCAAATTC
63 CAAGTTCGCATTGCGATTTATTCCAAATTC
83248 ATTGCGATAG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
89 2 0.02
90 2 0.02
91 3 0.04
92 75 0.91
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (92 bp):
GACTATCGCAACGCGAACTTCGACTATCGCAATGAGAATATGTAAATCGCAATGCGATAGTCCAA
GTTCGCATTGCGATTTATTCCAAATTC
Found at i:83227 original size:21 final size:21
Alignment explanation
Indices: 83200--83332 Score: 121
Period size: 21 Copynumber: 6.3 Consensus size: 21
83190 AGATTTACAT
83200 ATTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGTCCAA
* *
83221 GTTCGCATTGCGATTTATTCCAA
1 ATTCGCATTGCGA--TAGTCCAA
*
83244 ATT--CATTGCGATAGTCGAA
1 ATTCGCATTGCGATAGTCCAA
* * *
83263 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCATTGCGA--TAGTCCAA
*
83286 ATTCG--TTGCGATAGTCGAA
1 ATTCGCATTGCGATAGTCCAA
*
83305 ATTCGCGTTGCGATAGTCCAA
1 ATTCGCATTGCGATAGTCCAA
*
83326 AATCGCA
1 ATTCGCA
83333 ACGACTGGTG
Statistics
Matches: 89, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
19 19 0.21
21 51 0.57
23 19 0.21
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
ATTCGCATTGCGATAGTCCAA
Found at i:83265 original size:42 final size:42
Alignment explanation
Indices: 83205--83318 Score: 192
Period size: 42 Copynumber: 2.7 Consensus size: 42
83195 TACATATTCG
* *
83205 CATTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
83247 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
83289 CGTTGCGATAGTCGAAATTCGCGTTGCGAT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGAT
83319 AGTCCAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (42 bp):
CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:83426 original size:6 final size:6
Alignment explanation
Indices: 83415--83446 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
83405 GACACGTATT
83415 ACCACG ACCACG ACCACG ACC-CG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
83447 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:83441 original size:11 final size:11
Alignment explanation
Indices: 83415--83449 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
83405 GACACGTATT
83415 ACCACGACCACG
1 ACCACGACC-CG
83427 ACCACGACCCG
1 ACCACGACCCG
83438 ACCACGACCCG
1 ACCACGACCCG
83449 A
1 A
83450 GACGAGACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.31, C:0.51, G:0.17, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:83969 original size:5 final size:5
Alignment explanation
Indices: 83961--84003 Score: 59
Period size: 5 Copynumber: 8.0 Consensus size: 5
83951 TCTCGTCTCT
83961 GGTCG GGTCG GGTCG GGTCG GGTCG TGGTCG TGGTCG TGGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG -GGTCG -GGTCG -GGTCG
84004 TGGTAATACG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 20 0.54
6 17 0.46
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.26
Consensus pattern (5 bp):
GGTCG
Found at i:83992 original size:6 final size:6
Alignment explanation
Indices: 83960--84007 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
83950 GTCTCGTCTC
83960 TGGTCG -GGTCG -GGTCG -GGTCG -GGTCG TGGTCG TGGTCG TGGTCG
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG
84004 TGGT
1 TGGT
84008 AATACGTGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 20 0.49
6 21 0.51
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
TGGTCG
Found at i:83998 original size:12 final size:11
Alignment explanation
Indices: 83960--84007 Score: 64
Period size: 10 Copynumber: 4.4 Consensus size: 11
83950 GTCTCGTCTC
83960 TGGTCGGGTCG
1 TGGTCGGGTCG
83971 -GGTCGGGTCG
1 TGGTCGGGTCG
83981 -GGTCGTGGTCG
1 TGGTCG-GGTCG
83992 TGGTCGTGGTCG
1 TGGTCG-GGTCG
84004 TGGT
1 TGGT
84008 AATACGTGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 15 0.43
11 5 0.14
12 15 0.43
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (11 bp):
TGGTCGGGTCG
Found at i:84146 original size:33 final size:33
Alignment explanation
Indices: 84104--84212 Score: 128
Period size: 33 Copynumber: 3.0 Consensus size: 33
84094 ATTTTGGACT
84104 ATCGCAACGAATTTGGAATAAATCGCAATGCGA
1 ATCGCAACGAATTTGGAATAAATCGCAATGCGA
*
84137 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
1 ATCGCAACGAATTTGGAATAAAT-----CGC-AA-TGCGA
84177 CTATCGCAACGAATTTGGAATAAATCGCAATGCGA
1 --ATCGCAACGAATTTGGAATAAATCGCAATGCGA
84212 A
1 A
84213 CTTTGACTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
33 24 0.37
35 4 0.06
36 2 0.03
37 3 0.05
38 3 0.05
39 2 0.03
40 4 0.06
42 23 0.35
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (33 bp):
ATCGCAACGAATTTGGAATAAATCGCAATGCGA
Found at i:84162 original size:21 final size:21
Alignment explanation
Indices: 84136--84206 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
84126 TCGCAATGCG
84136 AATCGCAACGAATTTGGAATA
1 AATCGCAACGAATTTGGAATA
* * *
84157 AATCGCAACGCGAACTTCGACT-
1 AATCGCAA--CGAATTTGGAATA
84179 -ATCGCAACGAATTTGGAATA
1 AATCGCAACGAATTTGGAATA
84199 AATCGCAA
1 AATCGCAA
84207 TGCGAACTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 9 0.22
21 22 0.55
23 9 0.22
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
AATCGCAACGAATTTGGAATA
Found at i:84196 original size:42 final size:42
Alignment explanation
Indices: 84137--84278 Score: 185
Period size: 42 Copynumber: 3.2 Consensus size: 42
84127 CGCAATGCGA
84137 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* *
84179 ATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTTGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
84221 ATCGCAATGCGATAGTCGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 AT--C---GC-A-A--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT
84272 ATCGCAA
1 ATCGCAA
84279 TGCGAACTTC
Statistics
Matches: 87, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
42 42 0.48
44 2 0.02
45 1 0.01
46 2 0.02
47 2 0.02
48 1 0.01
49 2 0.02
51 35 0.40
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:84224 original size:21 final size:21
Alignment explanation
Indices: 84158--84232 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
84148 TTTGGAATAA
* *
84158 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTTGACT
*
84179 ATCGCAA--CGAA-TTTGGAAT
1 ATCGCAATGCGAACTTT-GACT
84198 AAATCGCAATGCGAACTTTGACT
1 --ATCGCAATGCGAACTTTGACT
84221 ATCGCAATGCGA
1 ATCGCAATGCGA
84233 TAGTCGAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
18 2 0.04
19 7 0.16
21 26 0.58
23 7 0.16
24 3 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTTGACT
Found at i:84266 original size:93 final size:89
Alignment explanation
Indices: 84144--84327 Score: 262
Period size: 93 Copynumber: 2.0 Consensus size: 89
84134 CGAATCGCAA
* *
84144 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-CGAATTTGGAATAAATCGCAAT
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAGCGAACTTCGAAT--ATCGCAAT
*
84208 GCGAACTTTGACTATCGCAATGCGATAGT
64 GCGAA-TATG--TATCGCAATGCGATAGT
*
84237 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTCGAATATCGCATTG
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-GCGAACTTCGAATATCGCAATG
*
84302 CGAATATGTGTCGCAATGCGATAGT
65 CGAATATGTATCGCAATGCGATAGT
84327 C
1 C
84328 CAAGTTCGCA
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
90 17 0.20
92 3 0.04
93 54 0.64
95 10 0.12
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (89 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAGCGAACTTCGAATATCGCAATGC
GAATATGTATCGCAATGCGATAGT
Found at i:84292 original size:51 final size:51
Alignment explanation
Indices: 84186--84283 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
84176 ACTATCGCAA
* *
84186 CGAATTTGGAATAAATCGCAATGCGAACTTTGACTATCGCAATGCGATAGT
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGATAGT
84237 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGA
84284 ACTTCGAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (51 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGATAGT
Found at i:84303 original size:21 final size:21
Alignment explanation
Indices: 84251--84305 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
84241 TTTGGAATAA
* *
84251 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGAAT
84272 ATCGCAATGCGAACTTCGAAT
1 ATCGCAATGCGAACTTCGAAT
*
84293 ATCGCATTGCGAA
1 ATCGCAATGCGAA
84306 TATGTGTCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGAAT
Found at i:84337 original size:21 final size:21
Alignment explanation
Indices: 84312--84385 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
84302 CGAATATGTG
*
84312 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
84333 TCGCATTGTGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
84354 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
84375 TCGCGTTGCGA
1 TCGCATTGCGA
84386 ATCTGGAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:87719 original size:16 final size:16
Alignment explanation
Indices: 87683--87713 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
87673 AAACATAAAA
87683 AATA-AATTTTAATAT
1 AATATAATTTTAATAT
87698 AATATAATTTTAATAT
1 AATATAATTTTAATAT
87714 CTTATATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATAATTTTAATAT
Found at i:95066 original size:14 final size:17
Alignment explanation
Indices: 95033--95068 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
95023 TCAATTAATG
95033 AATTTCTTAATAAGTTA
1 AATTTCTTAATAAGTTA
95050 AATTT-TTAAT-A-TTA
1 AATTTCTTAATAAGTTA
95064 AATTT
1 AATTT
95069 AAAATATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.42
15 1 0.05
16 5 0.26
17 5 0.26
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTCTTAATAAGTTA
Found at i:96399 original size:20 final size:21
Alignment explanation
Indices: 96369--96407 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
96359 AGCCGTTGGG
*
96369 GCCTGATGGTATTGATACTCT
1 GCCTGATGGTATCGATACTCT
96390 GCCT-ATGGTATCGATACT
1 GCCTGATGGTATCGATACT
96408 ACTATACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTCT
Found at i:99514 original size:2 final size:2
Alignment explanation
Indices: 99507--99534 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
99497 GAGGTATAAC
99507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99535 GTAGATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99609 original size:3 final size:3
Alignment explanation
Indices: 99601--99626 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
99591 GCTTACTTTT
99601 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
99627 TATTTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:108613 original size:29 final size:29
Alignment explanation
Indices: 108581--108646 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
108571 TTCTGAAAGT
*
108581 TACAAAATGATCACTCATTTAAAA-ATTAG
1 TACAAAATG-TCACTCAATTAAAATATTAG
* * *
108610 TACAAATATGTTACTGAATTAAAATATTAT
1 TACAAA-ATGTCACTCAATTAAAATATTAG
108640 TACAAAA
1 TACAAAA
108647 AAATTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (29 bp):
TACAAAATGTCACTCAATTAAAATATTAG
Found at i:112002 original size:18 final size:18
Alignment explanation
Indices: 111979--112051 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
111969 AGGGATTATC
111979 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
111997 AGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGGAC-A-T
*
112017 AGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
112035 AATGGTCCTTCAGGACA
1 AGTGGTCCTTCGGGACA
112052 AATATTCAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 29 0.64
19 2 0.04
20 14 0.31
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:112337 original size:4 final size:4
Alignment explanation
Indices: 112316--112361 Score: 69
Period size: 4 Copynumber: 11.8 Consensus size: 4
112306 TATATATATA
112316 TATT TATT TATT TA-- TATT TATT TATT TATT TATT TATT TATAT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TAT
112362 GTCTCACTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.05
4 33 0.85
5 4 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:112345 original size:26 final size:26
Alignment explanation
Indices: 112301--112359 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
112291 GAATGCATTG
*
112301 TTATATATATATATATATTTATTTAT
1 TTATATTTATATATATATTTATTTAT
* *
112327 TTATATTTATTTATTTATTTATTTAT
1 TTATATTTATATATATATTTATTTAT
112353 TTATATT
1 TTATATT
112360 ATGTCTCACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTATATTTATATATATATTTATTTAT
Found at i:112359 original size:22 final size:22
Alignment explanation
Indices: 112301--112358 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
112291 GAATGCATTG
*
112301 TTATATATATATATATATTTAT
1 TTATTTATATATATATATTTAT
* *
112323 TTATTTATATTTATTTATTTAT
1 TTATTTATATATATATATTTAT
*
112345 TTATTTATTTATAT
1 TTATTTATATATAT
112359 TATGTCTCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTTATATATATATATTTAT
Found at i:113423 original size:23 final size:23
Alignment explanation
Indices: 113393--113452 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
113383 ATGATTTATG
113393 GGTGCAATTCTACGCGGCACTCC
1 GGTGCAATTCTACGCGGCACTCC
* *
113416 GGTGCAATTCTACGTGGCACTTC
1 GGTGCAATTCTACGCGGCACTCC
*
113439 GGTGCAATTATACG
1 GGTGCAATTCTACG
113453 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCC
Found at i:115690 original size:21 final size:21
Alignment explanation
Indices: 115666--115710 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
115656 AGTAATGTAA
* *
115666 ATTTTTAATTCATATCAAAAT
1 ATTTTCAAGTCATATCAAAAT
* *
115687 ATTTTCAAGTCATTTTAAAAT
1 ATTTTCAAGTCATATCAAAAT
115708 ATT
1 ATT
115711 AAATTACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTTCAAGTCATATCAAAAT
Found at i:117639 original size:15 final size:15
Alignment explanation
Indices: 117619--117661 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
117609 CTCTATAAAA
117619 ACTCGACTTGAGATG
1 ACTCGACTTGAGATG
*
117634 ACTCGACTTGATATG
1 ACTCGACTTGAGATG
*
117649 ACTCGACTCGAGA
1 ACTCGACTTGAGA
117662 CCTTAACGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (15 bp):
ACTCGACTTGAGATG
Found at i:119065 original size:38 final size:38
Alignment explanation
Indices: 119014--119120 Score: 142
Period size: 38 Copynumber: 2.8 Consensus size: 38
119004 GAGAAACATG
* *
119014 TAAACAAACTTGTTCATGAACATAAATGAACGAGTCGA
1 TAAACAAACTTGTTCATGAACATAAATAAACAAGTCGA
*
119052 TAAACAAACTTGTTCATAAACATAAATAAACAAGTCGA
1 TAAACAAACTTGTTCATGAACATAAATAAACAAGTCGA
** * * *
119090 TAAATGAATTTGTTCATGAATATAAACAAAC
1 TAAACAAACTTGTTCATGAACATAAATAAAC
119121 TAAACACACA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (38 bp):
TAAACAAACTTGTTCATGAACATAAATAAACAAGTCGA
Found at i:119363 original size:28 final size:28
Alignment explanation
Indices: 119323--119410 Score: 176
Period size: 28 Copynumber: 3.1 Consensus size: 28
119313 ATTGGACCCA
119323 CAACCTTACATTGATTAAAGGAGTGGGC
1 CAACCTTACATTGATTAAAGGAGTGGGC
119351 CAACCTTACATTGATTAAAGGAGTGGGC
1 CAACCTTACATTGATTAAAGGAGTGGGC
119379 CAACCTTACATTGATTAAAGGAGTGGGC
1 CAACCTTACATTGATTAAAGGAGTGGGC
119407 CAAC
1 CAAC
119411 TCTAATAGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (28 bp):
CAACCTTACATTGATTAAAGGAGTGGGC
Found at i:124505 original size:15 final size:15
Alignment explanation
Indices: 124485--124513 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
124475 TGGCCGACCG
124485 AACCGAATTAACCAT
1 AACCGAATTAACCAT
124500 AACCGAATTAACCA
1 AACCGAATTAACCA
124514 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:124872 original size:179 final size:180
Alignment explanation
Indices: 124639--125009 Score: 592
Period size: 180 Copynumber: 2.1 Consensus size: 180
124629 ATTTTCTAAT
* * *
124639 TTATATA-AAAATTAAATATTTTTTAATTCAAAAAAAGTTATAATTAATTTAAAT-A-ATATAAT
1 TTATATATAATATTAAATATTTTTTAATTCAAAAAAAGTTACAAATAATTTAAATAATATATAAT
*
124701 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
124766 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATG
130 AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATG
*
124817 TTATATATAATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAA-TTAAATAATATATA
1 TTATATATAATATTAAATATTTTTTAATTCAAAAAA-AG-TTACAAATAATTTAAATAATATATA
*
124880 ATTATAAAATAAAAAATTTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
64 ATTATAAAATAAAAAATTTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
124945 TAGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATG
129 TAGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATG
124997 TTATATATAATAT
1 TTATATATAATAT
125010 ATTTAAAATT
Statistics
Matches: 179, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
178 13 0.07
179 29 0.16
180 111 0.62
181 26 0.15
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (180 bp):
TTATATATAATATTAAATATTTTTTAATTCAAAAAAAGTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTA
GATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATG
Found at i:128076 original size:29 final size:29
Alignment explanation
Indices: 128034--128092 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
128024 ACCATACATC
128034 AGCAACTATCAAAGTTGGGAAAAATAATT
1 AGCAACTATCAAAGTTGGGAAAAATAATT
*
128063 AGCAACTATCAAAGTTGGGAAAGATAATT
1 AGCAACTATCAAAGTTGGGAAAAATAATT
128092 A
1 A
128093 AAGAAGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (29 bp):
AGCAACTATCAAAGTTGGGAAAAATAATT
Found at i:139953 original size:6 final size:6
Alignment explanation
Indices: 139942--139971 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
139932 TTAAATTAAA
139942 TTAATT TTAATT TTAATT TTAATAT TTAAT
1 TTAATT TTAATT TTAATT TTAAT-T TTAAT
139972 AAATTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTAATT
Found at i:145719 original size:13 final size:13
Alignment explanation
Indices: 145703--145747 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
145693 CCTTATTATT
*
145703 TATATGTATATAA
1 TATATATATATAA
*
145716 TATATATATATAT
1 TATATATATATAA
*
145729 TATATATATTTAA
1 TATATATATATAA
145742 T-TATAT
1 TATATAT
145748 TTTATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 5 0.18
13 23 0.82
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TATATATATATAA
Found at i:145727 original size:15 final size:15
Alignment explanation
Indices: 145703--145737 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
145693 CCTTATTATT
*
145703 TATATGTATATAATA
1 TATATATATATAATA
*
145718 TATATATATATTATA
1 TATATATATATAATA
145733 TATAT
1 TATAT
145738 TTAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TATATATATATAATA
Found at i:145898 original size:109 final size:108
Alignment explanation
Indices: 145695--145901 Score: 237
Period size: 109 Copynumber: 1.9 Consensus size: 108
145685 TAATTTAACC
* * *
145695 TTATTATTTATATGTATATAATATATATATATATTATATATATTTAATTATATTTTATTTATTTA
1 TTATTATTTATATATATATAATATATATATATATTATATATATTT-ATTATATTTTACTTATGTA
* **
145760 TTATTTTTTTTCATTTTTCTTTGTGTTATATATTATTTTTCCTA
65 CTATTTTTTTTCATTTTTCTACGTGTTATATATTATTTTTCCTA
*
145804 TTATTATTTAT-TATATAT-ATATATATATATATTAT-TAT-TTT-TTCTATGTTTACTTATGTA
1 TTATTATTTATATATATATAATATATATATATATTATATATATTTATTATAT-TTTACTTATGTA
145864 CTATGTTTTTTTACTATATTTTCCTAACGT-TTATATAT
65 CTAT-TTTTTTT-C-AT-TTTT-CT-ACGTGTTATATAT
145902 ATATATATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
103 5 0.06
104 13 0.15
105 10 0.12
106 4 0.05
107 19 0.23
108 10 0.12
109 21 0.25
110 2 0.02
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (108 bp):
TTATTATTTATATATATATAATATATATATATATTATATATATTTATTATATTTTACTTATGTAC
TATTTTTTTTCATTTTTCTACGTGTTATATATTATTTTTCCTA
Found at i:145902 original size:2 final size:2
Alignment explanation
Indices: 145895--145919 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
145885 TCCTAACGTT
145895 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
145920 TCTTACTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:146052 original size:17 final size:17
Alignment explanation
Indices: 145984--146070 Score: 65
Period size: 17 Copynumber: 5.1 Consensus size: 17
145974 TATGTATATT
* *
145984 TATTTTCATTTATTTTA
1 TATTTTTATATATTTTA
*
146001 TATTGTTA-ATA-TTTA
1 TATTTTTATATATTTTA
146016 GTATTTTTTATTATACATTTTA
1 -TA-TTTTTA-TAT--ATTTTA
*
146038 TATTTTTATATATTTTT
1 TATTTTTATATATTTTA
146055 TA-TTTTAT-TATTTTA
1 TATTTTTATATATTTTA
146070 T
1 T
146071 TTATATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
15 11 0.19
16 10 0.18
17 18 0.32
19 5 0.09
20 6 0.11
21 3 0.05
22 4 0.07
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
TATTTTTATATATTTTA
Found at i:146053 original size:9 final size:9
Alignment explanation
Indices: 146026--146085 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
146016 GTATTTTTTA
*
146026 TTATACATT
1 TTATATATT
146035 TTATAT-TT
1 TTATATATT
146043 TTATATATT
1 TTATATATT
146052 TT-T-TATT
1 TTATATATT
146059 TTAT-TATT
1 TTATATATT
* *
146067 TTATTTATA
1 TTATATATT
*
146076 TTATTTATT
1 TTATATATT
146085 T
1 T
146086 ATTTTCATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
7 6 0.13
8 18 0.40
9 21 0.47
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATATATT
Found at i:146063 original size:22 final size:21
Alignment explanation
Indices: 146038--146137 Score: 53
Period size: 24 Copynumber: 4.4 Consensus size: 21
146028 ATACATTTTA
146038 TATTTTTATATATTTTTTATTT
1 TATTTTTATATATTTTTTA-TT
*
146060 TATTATTTTATTTATATTATTTATT
1 TA-T-TTTTA--TATATTTTTTATT
*
146085 TATTTTCAT-TATGTTTTTAGTT
1 TATTTTTATATAT-TTTTTA-TT
*
146107 TCTTTGCTTAT-TATTATTTTTATT
1 TATTT--TTATATA-T-TTTTTATT
146131 T-TTTTTA
1 TATTTTTA
146138 AAAACACTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
20 3 0.05
21 9 0.14
22 8 0.13
23 8 0.13
24 14 0.22
25 11 0.17
26 10 0.16
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (21 bp):
TATTTTTATATATTTTTTATT
Found at i:146070 original size:13 final size:14
Alignment explanation
Indices: 146046--146087 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 14
146036 TATATTTTTA
146046 TATATT-TTTTATT
1 TATATTATTTTATT
146059 T-TATTATTTTATT
1 TATATTATTTTATT
146072 TATATTA-TTTATT
1 TATATTATTTTATT
146085 TAT
1 TAT
146088 TTTCATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.15
13 18 0.67
14 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATATTATTTTATT
Found at i:146073 original size:17 final size:17
Alignment explanation
Indices: 145983--146085 Score: 56
Period size: 17 Copynumber: 5.9 Consensus size: 17
145973 ATATGTATAT
145983 TTATTTTCATTTATTTTA
1 TTATTTT-ATTTATTTTA
*
146001 -TATTGTTA-ATATTTAGTA
1 TTATT-TTATTTATTT--TA
146019 TT-TTTTATTATACATTTTA
1 TTATTTTATT-T--ATTTTA
*
146038 -TATTTTTATATATTTT-
1 TTA-TTTTATTTATTTTA
146054 TTATTTTA-TTATTTTA
1 TTATTTTATTTATTTTA
*
146070 TTTATATTATTTATTT
1 -TTATTTTATTTATTT
146086 ATTTTCATTA
Statistics
Matches: 66, Mismatches: 5, Indels: 28
0.67 0.05 0.28
Matches are distributed among these distances:
15 6 0.09
16 10 0.15
17 22 0.33
18 13 0.20
19 5 0.08
20 6 0.09
21 4 0.06
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TTATTTTATTTATTTTA
Found at i:146086 original size:17 final size:16
Alignment explanation
Indices: 146017--146103 Score: 69
Period size: 17 Copynumber: 5.6 Consensus size: 16
146007 TAATATTTAG
146017 TATTTTTTA-TTATA-
1 TATTTTTTATTTATAT
* * *
146031 CATTTTATATTTTTAT
1 TATTTTTTATTTATAT
146047 ATATTTTTTATTT-TAT
1 -TATTTTTTATTTATAT
146063 TA--TTTTATTTATAT
1 TATTTTTTATTTATAT
146077 TATTTATTTATTT-TCAT
1 TATTT-TTTATTTAT-AT
146094 TATGTTTTTA
1 TAT-TTTTTA
146104 GTTTCTTTGC
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
13 8 0.14
14 12 0.20
15 6 0.10
16 5 0.08
17 26 0.44
18 2 0.03
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.71
Consensus pattern (16 bp):
TATTTTTTATTTATAT
Found at i:146096 original size:13 final size:13
Alignment explanation
Indices: 146034--146087 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
146024 TATTATACAT
146034 TTTATATT-TTTA
1 TTTATATTATTTA
*
146046 --TATATTTTTTA
1 TTTATATTATTTA
146057 TTT-TATTATTTTA
1 TTTATATTA-TTTA
146070 TTTATATTATTTA
1 TTTATATTATTTA
146083 TTTAT
1 TTTAT
146088 TTTCATTATG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 6 0.17
11 4 0.11
12 4 0.11
13 17 0.47
14 5 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATATTATTTA
Found at i:146096 original size:26 final size:26
Alignment explanation
Indices: 146032--146085 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
146022 TTTATTATAC
* *
146032 ATTTTA-TATTTT-TATATATTTTTT
1 ATTTTATTATTTTATTTATATTATTT
146056 ATTTTATTATTTTATTTATATTATTT
1 ATTTTATTATTTTATTTATATTATTT
146082 ATTT
1 ATTT
146086 ATTTTCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 6 0.23
26 14 0.54
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (26 bp):
ATTTTATTATTTTATTTATATTATTT
Found at i:146175 original size:21 final size:22
Alignment explanation
Indices: 146151--146247 Score: 67
Period size: 21 Copynumber: 4.4 Consensus size: 22
146141 ACACTTTACC
146151 TTTTTTATTC-TTT-TTTGTATAT
1 TTTTTTATTCATTTATTT-TAT-T
*
146173 TTTTTTCTTCATTTATTTTA-T
1 TTTTTTATTCATTTATTTTATT
*
146194 TTTTTTATTTTATTTTATTTTATT
1 TTTTTTA-TTCA-TTTATTTTATT
* * * *
146218 TGTTTCATCCA-TTATTTTATG
1 TTTTTTATTCATTTATTTTATT
*
146239 TTTATTATT
1 TTTTTTATT
146248 ATTGGTTTCA
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
21 21 0.36
22 12 0.21
23 16 0.28
24 9 0.16
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTTTATTCATTTATTTTATT
Found at i:146198 original size:23 final size:22
Alignment explanation
Indices: 146151--146218 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
146141 ACACTTTACC
*
146151 TTTTTTATTC-TTT-TTTGTATAT
1 TTTTTTTTTCATTTATTT-TAT-T
*
146173 TTTTTTCTTCATTTATTTTATT
1 TTTTTTTTTCATTTATTTTATT
146195 TTTTTATTTT-ATTTTATTTTATT
1 TTTTT-TTTTCA-TTTATTTTATT
146218 T
1 T
146219 GTTTCATCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 16 0.40
23 21 0.52
24 3 0.08
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (22 bp):
TTTTTTTTTCATTTATTTTATT
Found at i:146200 original size:13 final size:13
Alignment explanation
Indices: 146184--146209 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
146174 TTTTTCTTCA
146184 TTTATTTTATTTT
1 TTTATTTTATTTT
146197 TTTATTTTATTTT
1 TTTATTTTATTTT
146210 ATTTTATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:146237 original size:5 final size:5
Alignment explanation
Indices: 146184--146218 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
146174 TTTTTCTTCA
146184 TTTAT TTTA- TTT-T TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
146219 GTTTCATCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 6 0.21
5 22 0.79
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:146256 original size:33 final size:31
Alignment explanation
Indices: 146198--146258 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 31
146188 TTTTATTTTT
*
146198 TTATTTTATTTTATTTTATTTGTTTCATCCA
1 TTATTTTATTTTATTTTATTGGTTTCATCCA
146229 TTATTTTATGTTTATTATTATTGGTTTCAT
1 TTATTTTAT-TTTATT-TTATTGGTTTCAT
146259 TTATTTCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 9 0.33
32 6 0.22
33 12 0.44
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (31 bp):
TTATTTTATTTTATTTTATTGGTTTCATCCA
Done.