Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001966.1 Hibiscus syriacus cultivar Beakdansim tig00003973_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: 458221
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:148366 original size:17 final size:17
Alignment explanation
Indices: 148344--148396 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
148334 ATAATTAAAA
148344 TTAAATAAATTATATAT
1 TTAAATAAATTATATAT
*
148361 TTAAAT-AATT-TAAAT
1 TTAAATAAATTATATAT
*
148376 TTAAGGTAAATTATATAT
1 TTAA-ATAAATTATATAT
148394 TTA
1 TTA
148397 CTATTTAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.27
16 5 0.17
17 10 0.33
18 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
TTAAATAAATTATATAT
Found at i:148366 original size:31 final size:33
Alignment explanation
Indices: 148331--148396 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
148321 GGAGGAAAAA
148331 TAAATAA-TTAAAATTAA-ATAAATTATATATT
1 TAAATAATTTAAAATTAAGATAAATTATATATT
* *
148362 TAAATAATTTAAATTTAAGGTAAATTATATATT
1 TAAATAATTTAAAATTAAGATAAATTATATATT
148395 TA
1 TA
148397 CTATTTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 7 0.23
32 9 0.29
33 15 0.48
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (33 bp):
TAAATAATTTAAAATTAAGATAAATTATATATT
Found at i:148496 original size:23 final size:21
Alignment explanation
Indices: 148463--148520 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
148453 AATTTAAAAT
148463 TAATATTATTTCAAATAAATAAA
1 TAATA-TATTT-AAATAAATAAA
*
148486 TAATATGATTTTAATAAATAAA
1 TAATAT-ATTTAAATAAATAAA
*
148508 AAATATATTTAAA
1 TAATATATTTAAA
148521 AATAGTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 6 0.19
22 16 0.52
23 9 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TAATATATTTAAATAAATAAA
Found at i:156506 original size:65 final size:65
Alignment explanation
Indices: 156376--156506 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 65
156366 TTTTAGATAT
* * * * * * *
156376 ATCGTGATATATCTATAGCGTTTTATTAATAAAACCGCAATAATAATGACATTTTTTTAACAAAC
1 ATCGCGATATATCTATAACATTTTATCAATAAAACCGCAATAATAATGACATTTATTGAAAAAAC
* * * *
156441 ATCGCGATATATTTATAACATTTTATCAATAAAGCCGCAATAATAGTGACGTTTATTGAAAAAAC
1 ATCGCGATATATCTATAACATTTTATCAATAAAACCGCAATAATAATGACATTTATTGAAAAAAC
156506 A
1 A
156507 CCACTATATA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (65 bp):
ATCGCGATATATCTATAACATTTTATCAATAAAACCGCAATAATAATGACATTTATTGAAAAAAC
Found at i:158499 original size:18 final size:19
Alignment explanation
Indices: 158476--158518 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
158466 CAGTAATCCT
*
158476 ATTCC-CTGATAATGTTAC
1 ATTCCACTGATAATCTTAC
*
158494 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGATAATCTTAC
158514 ATTCC
1 ATTCC
158519 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:166628 original size:26 final size:26
Alignment explanation
Indices: 166592--166646 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
166582 GTGACTATTT
166592 TTTTTTTGACAAAGCCAAAGCGACTA
1 TTTTTTTGACAAAGCCAAAGCGACTA
*
166618 TTTTTTTGACAAAGCCAAAGTGACTA
1 TTTTTTTGACAAAGCCAAAGCGACTA
166644 TTT
1 TTT
166647 ATTCAAACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (26 bp):
TTTTTTTGACAAAGCCAAAGCGACTA
Found at i:168923 original size:30 final size:31
Alignment explanation
Indices: 168880--168941 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
168870 AAAATAGAAA
* **
168880 TTTTATGTTAAAT-ATATTTTAATAATTATAT
1 TTTTATGTAAAATAATATTAAAAT-ATTATAT
168911 TTTTAT-TAAAATAATATTAAAATATTATAT
1 TTTTATGTAAAATAATATTAAAATATTATAT
168941 T
1 T
168942 AATATGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
TTTTATGTAAAATAATATTAAAATATTATAT
Found at i:170237 original size:24 final size:23
Alignment explanation
Indices: 170210--170261 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
170200 TATTTTGTTC
170210 TTATCTTAACTTAAAATATATATT
1 TTATCTTAACTTAAAA-ATATATT
* * *
170234 TTATTTTTATCTTGAAAATATATT
1 TTA-TCTTAACTTAAAAATATATT
170258 TTAT
1 TTAT
170262 TATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 13 0.54
25 10 0.42
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (23 bp):
TTATCTTAACTTAAAAATATATT
Found at i:177175 original size:47 final size:51
Alignment explanation
Indices: 177099--177205 Score: 136
Period size: 47 Copynumber: 2.2 Consensus size: 51
177089 CACGTAGGGG
*
177099 TATAGCGC-GGATCAGGTACCGCGCTATACCTTTA-T-TG-CATAATTTTA
1 TATAGCGCGGGATCAGGTACCACGCTATACCTTTACTCTGACATAATTTTA
177146 TATAGCGCGGGA-CAGGTACCACGAC-ATACCTTTACTCCTGACATAATTTTA
1 TATAGCGCGGGATCAGGTACCACG-CTATACCTTTACT-CTGACATAATTTTA
*
177197 TATAACGCG
1 TATAGCGCG
177206 AGGCATGTAC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
47 27 0.52
48 5 0.10
50 2 0.04
51 18 0.35
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (51 bp):
TATAGCGCGGGATCAGGTACCACGCTATACCTTTACTCTGACATAATTTTA
Found at i:181363 original size:18 final size:18
Alignment explanation
Indices: 181340--181376 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
181330 AAAGGCAATG
181340 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
181358 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
181376 G
1 G
181377 TGGTGGCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:183079 original size:110 final size:111
Alignment explanation
Indices: 182885--183105 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 111
182875 ATTACAAAAA
* * * *
182885 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
182950 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
182996 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
183060 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
183106 ATGATTTCTA
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 33 0.32
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:183243 original size:12 final size:10
Alignment explanation
Indices: 183229--183269 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
183219 ACCTTAAAAA
*
183229 GAGAGTATTT
1 GAGAGAATTT
183239 GAGAGAAATTT
1 GAGAG-AATTT
183250 -AGAGAATTT
1 GAGAGAATTT
183259 GAGAGAATTT
1 GAGAGAATTT
183269 G
1 G
183270 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:183330 original size:11 final size:11
Alignment explanation
Indices: 183314--183339 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
183304 TAGGAAGGAT
183314 GGGGGAGGGGA
1 GGGGGAGGGGA
183325 GGGGGAGGGGA
1 GGGGGAGGGGA
183336 GGGG
1 GGGG
183340 TCGGTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.85, T:0.00
Consensus pattern (11 bp):
GGGGGAGGGGA
Found at i:183407 original size:50 final size:51
Alignment explanation
Indices: 183353--183477 Score: 189
Period size: 51 Copynumber: 2.5 Consensus size: 51
183343 GTAATTAGGG
* * **
183353 GTATAGCGCGCTGCAGGGGCCGCGCTATA-CCCACGTGACGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACC
* *
183403 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACC
183454 GTATAGCGCGGTGCAGGGGGCGCG
1 GTATAGCGCGGTGCAGGGGGCGCG
183478 TTTTACTGCT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 27 0.40
51 41 0.60
ACGTcount: A:0.18, C:0.32, G:0.36, T:0.14
Consensus pattern (51 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACC
Found at i:184252 original size:30 final size:30
Alignment explanation
Indices: 184216--184283 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
184206 CAGATTGCTT
*
184216 GGCGTCTTTGTATGGAAGCTTAGAGCTCTC
1 GGCGTCTTTGCATGGAAGCTTAGAGCTCTC
* *
184246 GGCGTCTTTGCATGGAAGGTTGGAGCTCTC
1 GGCGTCTTTGCATGGAAGCTTAGAGCTCTC
184276 GGCGTCTT
1 GGCGTCTT
184284 CAACACAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.13, C:0.21, G:0.34, T:0.32
Consensus pattern (30 bp):
GGCGTCTTTGCATGGAAGCTTAGAGCTCTC
Found at i:184837 original size:30 final size:30
Alignment explanation
Indices: 184797--184863 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
184787 AATTGTGTTG
*
184797 AAGACACCGAGAGCTCCAAGCTTCCATGCA
1 AAGACGCCGAGAGCTCCAAGCTTCCATGCA
*
184827 AAGACGCCGAGAGCTCCAAGCTTCTATGCA
1 AAGACGCCGAGAGCTCCAAGCTTCCATGCA
184857 AAGACGC
1 AAGACGC
184864 ATCTGCTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.13
Consensus pattern (30 bp):
AAGACGCCGAGAGCTCCAAGCTTCCATGCA
Found at i:186833 original size:19 final size:20
Alignment explanation
Indices: 186787--186833 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
186777 CAAGCAAATC
186787 TATATT-TTTATTGAATAAA
1 TATATTATTTATTGAATAAA
* * *
186806 AATAATATTT-TTTAATAAA
1 TATATTATTTATTGAATAAA
186825 TATATTATT
1 TATATTATT
186834 CCGGGTCGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TATATTATTTATTGAATAAA
Found at i:197813 original size:31 final size:31
Alignment explanation
Indices: 197750--197852 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
197740 TAGTGTATCG
* *
197750 AAAGTGATGATATAACACATA-CTATATGTAA
1 AAAGTGATGATGTAATACATATC-ATATGTAA
* *
197781 AAAGTGATGATGTAATACATATCATTTATAA
1 AAAGTGATGATGTAATACATATCATATGTAA
* * * * * *
197812 AAAATGATGACGTGATACATGTCATGTGTCA
1 AAAGTGATGATGTAATACATATCATATGTAA
197843 AAAGTGATGA
1 AAAGTGATGA
197853 ATTGAAGTGA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (31 bp):
AAAGTGATGATGTAATACATATCATATGTAA
Found at i:198671 original size:40 final size:40
Alignment explanation
Indices: 198627--198720 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
198617 ATAACGAAAT
* *
198627 TGAGAAAACCGAACCCAAGACTAGGACCGAGTTATTAAAC
1 TGAGAAAACCGAACCCAAGACTAGAACCGAGTAATTAAAC
**
198667 TGAGAAAACCGAACCGGAGACTAGAACCGAGTAATTAAAC
1 TGAGAAAACCGAACCCAAGACTAGAACCGAGTAATTAAAC
198707 TGAGAAAACCGAAC
1 TGAGAAAACCGAAC
198721 TGAACCAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (40 bp):
TGAGAAAACCGAACCCAAGACTAGAACCGAGTAATTAAAC
Found at i:204823 original size:2 final size:2
Alignment explanation
Indices: 204816--204853 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
204806 AGGTTCTGGT
204816 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
204854 AGAACAAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:208193 original size:3 final size:3
Alignment explanation
Indices: 208169--208210 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
208159 TACAAAAGCG
* *
208169 TAA TATA TAT TAA TAA -AA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
208211 AATTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:208690 original size:134 final size:135
Alignment explanation
Indices: 208424--208766 Score: 424
Period size: 134 Copynumber: 2.6 Consensus size: 135
208414 GTGACACAGT
* * * *
208424 TCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGC
1 TCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTAGC
* *
208489 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGAATGGTTATCTAGGGGTGAC
66 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGAATAGTTATCTAGGCGTGAC
208554 ACGAC
131 ACGAC
* * *
208559 TCTTACGCGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTC-TAGT
1 TCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTAGC
* ** * * *
208623 CATCTTTAGG-AGTGGTGATAACTTGGTTCCTACTTGATGAGGACGACTAGTTATCTATGCTTGA
66 CATCTTTAGGAAG-GGTGATAACTCGGTTCCTACGCGATGAGGACGAATAGTTATCTAGGCGTGA
*
208687 CACGGC
130 CACGAC
* * * * * * * *
208693 TCCTACGTGATGAGGAGGTTTAGTCAGGGGATGACACGGTTCCTACGTGATGAGGA-TGAC-TAG
1 TCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGT-TCTTAG
208756 CCATCTTTAGG
65 CCATCTTTAGG
208767 GACTATGGTT
Statistics
Matches: 179, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
133 3 0.02
134 121 0.68
135 55 0.31
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (135 bp):
TCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTAGC
CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGAATAGTTATCTAGGCGTGAC
ACGAC
Found at i:208814 original size:28 final size:28
Alignment explanation
Indices: 208774--208873 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
208764 AGGGACTATG
* *
208774 GTTTCAAGAGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
* *
208802 GTTTCAAAAGAAACGGACTCAGAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
* *
208830 GTTTCAAGAA-AAACAAACTCAAAGGTGATGT
1 GTTTCAA-AAGAAACAGACTCAAA---GATTT
208861 GTTTCAAAAGAAA
1 GTTTCAAAAGAAA
208874 ATGTGACAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
28 42 0.70
29 2 0.03
30 2 0.03
31 14 0.23
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:209021 original size:32 final size:33
Alignment explanation
Indices: 208981--209113 Score: 117
Period size: 38 Copynumber: 3.8 Consensus size: 33
208971 CAAAGATCGG
*
208981 TGTTTCAAGATAAACAAACTCAAAGATGT-TTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTATTT
* * *
209013 TGTTTCAAGAAAAACATACTCAAAGATTTTGTTTGTTT
1 TGTTTCAAGAGAAACAAACTCAAAGA---TG--TATTT
*
209051 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT--ATTT
*
209087 TGTTTCCAA-AGAAACAGACTCAAAGAT
1 TGTTT-CAAGAGAAACAAACTCAAAGAT
209114 TTTTCTTAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
32 24 0.29
34 1 0.01
35 3 0.04
36 25 0.30
37 4 0.05
38 26 0.31
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTATTT
Found at i:209066 original size:70 final size:72
Alignment explanation
Indices: 208981--209116 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 72
208971 CAAAGATCGG
* *
208981 TGTTTCAAGATAAACAAACTCAAAGAT-GT-TTTTGTTT-CAAGAAAAACATACTCAAAGATTTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGGTATTTTGTTTCCAA-AAAAACAGACTCAAAGATTTT
209043 GTTTGTTT
65 GTTTGTTT
* *
209051 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGGT--ATTTTGTTTCCAAAAAAACAGACTCAAAGATTT
209116 T
64 T
209117 TCTTAAAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 25 0.44
71 2 0.04
74 27 0.47
75 3 0.05
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (72 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGGTATTTTGTTTCCAAAAAAACAGACTCAAAGATTTTG
TTTGTTT
Found at i:209151 original size:65 final size:63
Alignment explanation
Indices: 209081--209219 Score: 179
Period size: 65 Copynumber: 2.2 Consensus size: 63
209071 CAAAGATGGT
*
209081 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTTAAAAGAAACTATCTCAAAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTC--AAAAGAAACTATCTCAAAAGAGAAA
* * * * * * *
209146 AAATTTTGTTTCCAAAGAAACATATTTAATGATTTTTCAAAAGAAATTGTCTCAAGAGAGAAA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGAAA
*
209209 AAACTTTGTTT
1 AAATTTTGTTT
209220 TTCATAAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 31 0.48
65 34 0.52
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (63 bp):
AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGAAA
Found at i:209467 original size:31 final size:31
Alignment explanation
Indices: 209399--209459 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
209389 AAGGGAAACG
209399 ACTCAAAGATGGTTTTATTTCAAGAGAAACAA
1 ACTCAAAGAT-GTTTTATTTCAAGAGAAACAA
*
209431 ACTCAAAGAT-TTTGTATTTCTAGAGAAAC
1 ACTCAAAGATGTTT-TATTTCAAGAGAAAC
209460 TGTCTCAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.11
31 14 0.52
32 10 0.37
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (31 bp):
ACTCAAAGATGTTTTATTTCAAGAGAAACAA
Found at i:209518 original size:98 final size:96
Alignment explanation
Indices: 209319--209525 Score: 215
Period size: 98 Copynumber: 2.1 Consensus size: 96
209309 TAAAACCTTG
* * *
209319 TTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGAGAAAACTTTTCAAGAGTCAAAATTC
1 TTTCAAGAGAAACAAACTCAAAGAT-ATCTTGTTTTAAGAGAAAACTTCTCAAGAGACAAAATTC
* * *
209384 ATTTTAAGGGAAACGACTCAAAGATGGTTTTA
65 ATTTTAAGAGAAACGACTCAAAGATGGGTATA
*
209416 TTTCAAGAGAAACAAACTCAAAGAT-T-TTGTATTTCTAGAG-AAACTGTCTCAAGGGAGACAAA
1 TTTCAAGAGAAACAAACTCAAAGATATCTTGT-TTT-AAGAGAAAACT-TCTCAA--GAGACAAA
** * *
209478 ATTTGTTTTAATAGAAACGATCTCAAAGGTGGGTAT-
61 ATTCATTTTAAGAGAAACGA-CTCAAAGATGGGTATA
*
209514 TTTCAAAAGAAA
1 TTTCAAGAGAAA
209526 TTGTCTCGAA
Statistics
Matches: 92, Mismatches: 12, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
94 4 0.04
95 9 0.10
96 9 0.10
97 24 0.26
98 34 0.37
99 12 0.13
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (96 bp):
TTTCAAGAGAAACAAACTCAAAGATATCTTGTTTTAAGAGAAAACTTCTCAAGAGACAAAATTCA
TTTTAAGAGAAACGACTCAAAGATGGGTATA
Found at i:210032 original size:20 final size:21
Alignment explanation
Indices: 210007--210046 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
209997 CATAATTTGG
210007 AAAATT-GTCTCAAGAGAAAC
1 AAAATTCGTCTCAAGAGAAAC
*
210027 AAAATTCGTTTCAAGAGAAA
1 AAAATTCGTCTCAAGAGAAA
210047 AAGATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (21 bp):
AAAATTCGTCTCAAGAGAAAC
Found at i:210273 original size:103 final size:104
Alignment explanation
Indices: 210147--210341 Score: 243
Period size: 104 Copynumber: 1.9 Consensus size: 104
210137 AATTTTGAAA
* * * ** * * *
210147 ATCTCAAGTGAGATTAATTTTGTTTCAA-GT-ACAACAAATT-TTAATTTTTATTTCATAGAAAA
1 ATCTCAAATGAGATCAACTTTGTTT-AATGTGA-AACAAATTCGAAATTTGTATCTCAAAGAAAA
* *
210209 AATTTCTCAAGCGAGACGAAGTTTGTTTTTTTGAGAAAGCG
64 AATGTCTCAAGCGAGACGAAATTTGTTTTTTTGAGAAAGCG
*
210250 ATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAGGAAAAA
1 ATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAGAAAAAA
*
210315 TGTCTCAAGTGAGACGAAATTTGTTTT
66 TGTCTCAAGCGAGACGAAATTTGTTTT
210342 GAAAGAAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
102 2 0.03
103 32 0.42
104 43 0.56
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (104 bp):
ATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAGAAAAAA
TGTCTCAAGCGAGACGAAATTTGTTTTTTTGAGAAAGCG
Found at i:210371 original size:36 final size:35
Alignment explanation
Indices: 210309--210449 Score: 183
Period size: 36 Copynumber: 3.9 Consensus size: 35
210299 TATCTCAAAG
* * *
210309 GAAAAATGTCTCAAGTGAGACGAAATTTGTTTTGA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
* * *
210344 AAGAAATTGTCTCAAGCAAGACAAAATTTGTTTTTA
1 GA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
*
210380 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
*
210415 GATAAATTGTCTCAAGCGAGAAAATAATTTGTTTT
1 GA-AAATTGTCTCAAGCGAGACAA-AATTTGTTTT
210450 AAAATTCTCA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
35 33 0.36
36 48 0.53
37 10 0.11
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (35 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
Found at i:210392 original size:71 final size:72
Alignment explanation
Indices: 210309--210449 Score: 212
Period size: 71 Copynumber: 2.0 Consensus size: 72
210299 TATCTCAAAG
* * *
210309 GAAAAATGTCTCAAGTGAGACGAAATTTGTTTTGAAAGAAATTGTCTCAAGCAAGACAA-AATTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAATTGTCTCAAGCAAGAAAATAATTT
210373 GTTTTTA
66 GTTTTTA
* * * *
210380 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGATAAATTGTCTCAAGCGAGAAAATAATTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAATTGTCTCAAGCAAGAAAATAATTT
210445 GTTTT
66 GTTTT
210450 AAAATTCTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 52 0.84
72 10 0.16
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (72 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAATTGTCTCAAGCAAGAAAATAATTT
GTTTTTA
Found at i:211266 original size:24 final size:22
Alignment explanation
Indices: 211238--211293 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
211228 TTCAAAAGTA
211238 TGAAAATATCAATTAAAAGAGTTT
1 TGAAAATATCAA-TAAAA-AGTTT
* * *
211262 TGAAAATGTTTAATCAAAAGTTT
1 TGAAAAT-ATCAATAAAAAGTTT
211285 TGAAAATAT
1 TGAAAATAT
211294 TACTCCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 1 0.04
23 12 0.44
24 11 0.41
25 3 0.11
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (22 bp):
TGAAAATATCAATAAAAAGTTT
Found at i:212161 original size:7 final size:7
Alignment explanation
Indices: 212149--212250 Score: 51
Period size: 7 Copynumber: 15.4 Consensus size: 7
212139 TTGTCTGTGC
212149 TCTTTGT
1 TCTTTGT
*
212156 TCTTTGC
1 TCTTTGT
212163 TC-TT-T
1 TCTTTGT
212168 TCTTTGT
1 TCTTTGT
212175 T-TTTGT
1 TCTTTGT
*
212181 T-TTTGC
1 TCTTTGT
*
212187 T-TTTCT
1 TCTTTGT
* *
212193 TTTTTTT
1 TCTTTGT
*
212200 TCTTTGC
1 TCTTTGT
212207 TCTTTG-
1 TCTTTGT
212213 T-TTT-T
1 TCTTTGT
212218 TCTTTGCT
1 TCTTTG-T
212226 TCTTT-T
1 TCTTTGT
212232 CTCTTTGT
1 -TCTTTGT
*
212240 TTTTATGT
1 TCTT-TGT
212248 TCT
1 TCT
212251 CTTTGCTTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
5 6 0.08
6 24 0.32
7 32 0.43
8 12 0.16
ACGTcount: A:0.01, C:0.16, G:0.10, T:0.74
Consensus pattern (7 bp):
TCTTTGT
Found at i:212192 original size:22 final size:21
Alignment explanation
Indices: 212155--212226 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 21
212145 GTGCTCTTTG
212155 TTCTTTGCTCTTTTCTTTGTTTT
1 TTCTTTG--CTTTTCTTTGTTTT
*
212178 TGTTTTTGCTTTTCTTT-TTTT
1 T-TCTTTGCTTTTCTTTGTTTT
212199 TTCTTTGC---TCTTTGTTTT
1 TTCTTTGCTTTTCTTTGTTTT
212217 TTCTTTGCTT
1 TTCTTTGCTT
212227 CTTTTCTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
17 5 0.12
18 12 0.28
20 6 0.14
21 5 0.12
22 9 0.21
23 1 0.02
24 5 0.12
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (21 bp):
TTCTTTGCTTTTCTTTGTTTT
Found at i:212217 original size:33 final size:32
Alignment explanation
Indices: 212165--212239 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
212155 TTCTTTGCTC
* * *
212165 TTTTCTTTGTTTTTGTTTTTGCTTTTCTTTTT
1 TTTTCTTTGTCTTTGTTTTTGCTTTGCTTCTT
*
212197 TTTTCTTTGCTCTTTGTTTTTTCTTTGCTTCTT
1 TTTTCTTTG-TCTTTGTTTTTGCTTTGCTTCTT
*
212230 TTCTCTTTGT
1 TTTTCTTTGT
212240 TTTTATGTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 10 0.27
33 27 0.73
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (32 bp):
TTTTCTTTGTCTTTGTTTTTGCTTTGCTTCTT
Found at i:212917 original size:28 final size:27
Alignment explanation
Indices: 212874--212927 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
212864 GGTCGGAAAG
*
212874 AATGTTTCAAAATCTCAAGGATAAATGC
1 AATGTTTCAAAATCTCAAAGA-AAATGC
**
212902 AATGTTTCAAGGTCTCAAAGAAAATG
1 AATGTTTCAAAATCTCAAAGAAAATG
212928 AATATCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (27 bp):
AATGTTTCAAAATCTCAAAGAAAATGC
Found at i:217088 original size:21 final size:22
Alignment explanation
Indices: 217062--217102 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
217052 TGCAAATGAC
*
217062 AAATAA-AATATTTACAATATT
1 AAATAAGAACATTTACAATATT
217083 AAATAAGAACATTTACAATA
1 AAATAAGAACATTTACAATA
217103 CATGCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (22 bp):
AAATAAGAACATTTACAATATT
Found at i:218986 original size:21 final size:23
Alignment explanation
Indices: 218962--219010 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
218952 ACAAAAGTGT
*
218962 AATAC-ATATTAATAA-AATAAC
1 AATACAATACTAATAATAATAAC
*
218983 AATACTAATACTAATAATAATAAT
1 AATAC-AATACTAATAATAATAAC
219007 AATA
1 AATA
219011 ATAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
23 9 0.39
24 9 0.39
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (23 bp):
AATACAATACTAATAATAATAAC
Found at i:219002 original size:3 final size:3
Alignment explanation
Indices: 218961--219014 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
218951 TACAAAAGTG
* * * *
218961 TAA TACA TAT TAA TAA -AA TAA CAA TAC TAA TAC TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
219006 TAA TAA TAA
1 TAA TAA TAA
219015 AATTAAATAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:221801 original size:2 final size:2
Alignment explanation
Indices: 221796--221827 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
221786 TTTTTTTAAA
221796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
221828 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222251 original size:32 final size:32
Alignment explanation
Indices: 222210--222280 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
222200 TCTAAGTTAT
* *
222210 ATTTTTTAATCAACATACCCATGTCTCATTTA
1 ATTTTTTAATAAACATACCAATGTCTCATTTA
222242 ATTTTTTAATAAACATACCAATGTCTCATTTA
1 ATTTTTTAATAAACATACCAATGTCTCATTTA
222274 ATTTTTT
1 ATTTTTT
222281 TTATTTTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.48
Consensus pattern (32 bp):
ATTTTTTAATAAACATACCAATGTCTCATTTA
Found at i:223016 original size:3 final size:3
Alignment explanation
Indices: 223002--223035 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
222992 TTTTGTTTAA
223002 ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
223036 CTTTTTACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:226380 original size:27 final size:26
Alignment explanation
Indices: 226350--226401 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
226340 ATGTTTTTTA
*
226350 ATTTT-CAAAAAGTTAACAATGAAAACT
1 ATTTTCCAAAAA-TGAA-AATGAAAACT
226377 ATTTTCCAAAAATGAAAATGAAAAC
1 ATTTTCCAAAAATGAAAATGAAAAC
226402 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 8 0.35
28 6 0.26
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.27
Consensus pattern (26 bp):
ATTTTCCAAAAATGAAAATGAAAACT
Found at i:227212 original size:25 final size:26
Alignment explanation
Indices: 227184--227232 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
227174 TATTGAAATT
* *
227184 ATAGTTTAT-TTTTTATTTTTAAAAA
1 ATAGTTTATATTTATATATTTAAAAA
227209 ATAGTTTATATTTATATATTTAAA
1 ATAGTTTATATTTATATATTTAAA
227233 TTTATTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (26 bp):
ATAGTTTATATTTATATATTTAAAAA
Found at i:227972 original size:23 final size:21
Alignment explanation
Indices: 227946--227996 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
227936 GTTTAATGTC
*
227946 TAATTATAAATATAATATATATA
1 TAATTATAAA-ATAAAATATA-A
227969 TAATT-TAAAATAAAATATAA
1 TAATTATAAAATAAAATATAA
227989 TAATTATA
1 TAATTATA
227997 TTTGGATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 11 0.42
22 4 0.15
23 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATTATAAAATAAAATATAA
Found at i:234478 original size:5 final size:5
Alignment explanation
Indices: 234468--234524 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
234458 ATATGAAATT
* * * *
234468 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATATA ATTAA ATGAA ATGAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
*
234518 ATGAA AT
1 ATAAA AT
234525 GATAAGGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (5 bp):
ATAAA
Found at i:241808 original size:31 final size:31
Alignment explanation
Indices: 241773--241863 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
241763 AGCATTTACT
* *
241773 AATTGGATTACACCATTTAACGACGAAAATG
1 AATTGGATTACATCATTTAATGACGAAAATG
* *
241804 AATTGGATTGCATCATTTAATGACAAAAATG
1 AATTGGATTACATCATTTAATGACGAAAATG
*
241835 AATCGGATTACATCATTTAATGA-GAAAAT
1 AATTGGATTACATCATTTAATGACGAAAAT
241864 TTAATTTGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 5 0.09
31 48 0.91
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (31 bp):
AATTGGATTACATCATTTAATGACGAAAATG
Found at i:243342 original size:13 final size:13
Alignment explanation
Indices: 243324--243350 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
243314 GGAAAGACGC
243324 ATGGTGGTCCAGA
1 ATGGTGGTCCAGA
243337 ATGGTGGTCCAGA
1 ATGGTGGTCCAGA
243350 A
1 A
243351 AGCGGGGAGT
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:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (13 bp):
ATGGTGGTCCAGA
Found at i:249038 original size:49 final size:50
Alignment explanation
Indices: 248955--249051 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 50
248945 AGTAAAGTAC
248955 GATATGTTCAGAAAGCGATATGGACTCAGACAAGCATTTTACTCTATCAT
1 GATATGTTCAGAAAGCGATATGGACTCAGACAAGCATTTTACTCTATCAT
** *
249005 GATATGTTTGGAAAGCG-TATGGACTCAGGCAAGCATTTTACTCTATC
1 GATATGTTCAGAAAGCGATATGGACTCAGACAAGCATTTTACTCTATC
249052 GGAAATCGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 29 0.66
50 15 0.34
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (50 bp):
GATATGTTCAGAAAGCGATATGGACTCAGACAAGCATTTTACTCTATCAT
Found at i:254374 original size:156 final size:157
Alignment explanation
Indices: 254077--254375 Score: 575
Period size: 156 Copynumber: 1.9 Consensus size: 157
254067 CAAAGAAGAG
254077 CCAATTATATTACTTTGCCACAAAACTATTCCTTAACAAGGATAAGCGGACAATGTTTATGTCAT
1 CCAATTATATTACTTTGCCACAAAACTATTCCTTAACAAGGATAAGCGGACAATGTTTATGTCAT
254142 TGTCGACCGATATTAGAGCTTGGTGGCTTAAAATGGAGATGGAGGAGAGCTCCATGGTCGCTTAA
66 TGTCGACCGATATTAGAGCTTGGTGGCTTAAAATGGAGATGGAGGAGAGCTCCATGGTCGCTTAA
254207 AGCTATAAATGAAAACATCAGCCAAGT
131 AGCTATAAATGAAAACATCAGCCAAGT
254234 CCAATT-TA-TACTTTTGCCACAAAACTATTCCTTAACAAGGATAAGCGGACAATGTTTATGTCA
1 CCAATTATATTAC-TTTGCCACAAAACTATTCCTTAACAAGGATAAGCGGACAATGTTTATGTCA
254297 TTGTCGACCGATATTAGAGCTTGGTGGCTTAAAATGGAGATGGAGGAGAGCTCCATGGTCGCTTA
65 TTGTCGACCGATATTAGAGCTTGGTGGCTTAAAATGGAGATGGAGGAGAGCTCCATGGTCGCTTA
254362 AAGCTATAAATGAA
130 AAGCTATAAATGAA
254376 CAGCGGTGAA
Statistics
Matches: 141, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
155 3 0.02
156 132 0.94
157 6 0.04
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (157 bp):
CCAATTATATTACTTTGCCACAAAACTATTCCTTAACAAGGATAAGCGGACAATGTTTATGTCAT
TGTCGACCGATATTAGAGCTTGGTGGCTTAAAATGGAGATGGAGGAGAGCTCCATGGTCGCTTAA
AGCTATAAATGAAAACATCAGCCAAGT
Found at i:254549 original size:118 final size:118
Alignment explanation
Indices: 254341--254573 Score: 405
Period size: 118 Copynumber: 2.0 Consensus size: 118
254331 TGGAGATGGA
* * * * *
254341 GGAGAGCTCCATGGTCGCTTAAAGCTATAAATGAACAGCGGTGAATGCCACGGTAGTTTTTTATG
1 GGAGAGCTCCAAGGTCGCTTAAAGCTATAAATAAACAGCGATGAATGCCACGGTAGTTCTTTATA
254406 TCTTCATTTCAATGTATTTTGATCAAGATTCAAGATGATGATCATAATGCCAG
66 TCTTCATTTCAATGTATTTTGATCAAGATTCAAGATGATGATCATAATGCCAG
254459 GGAGAGCTCCAAGGTCGCTTAAAGCTATAAATAAAC-GACGATGAATGCCACGGTAGTTCTTTAT
1 GGAGAGCTCCAAGGTCGCTTAAAGCTATAAATAAACAG-CGATGAATGCCACGGTAGTTCTTTAT
254523 ATCTTCATTTCAATGTATTTTGATCAAGATTCAAGATGATGATCATAATGC
65 ATCTTCATTTCAATGTATTTTGATCAAGATTCAAGATGATGATCATAATGC
254574 TAGGAACTTA
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
117 1 0.01
118 108 0.99
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (118 bp):
GGAGAGCTCCAAGGTCGCTTAAAGCTATAAATAAACAGCGATGAATGCCACGGTAGTTCTTTATA
TCTTCATTTCAATGTATTTTGATCAAGATTCAAGATGATGATCATAATGCCAG
Found at i:269451 original size:24 final size:23
Alignment explanation
Indices: 269419--269467 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
269409 TGACAAGGCG
* *
269419 GGGGTGGGGGTCAGAAGAGGTGAA
1 GGGGCGGGGGCCAGAAGAGGT-AA
269443 GGGGCGGGGGCCAGAAGAGGTAA
1 GGGGCGGGGGCCAGAAGAGGTAA
269466 GG
1 GG
269468 CAGTGGGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.24, C:0.08, G:0.59, T:0.08
Consensus pattern (23 bp):
GGGGCGGGGGCCAGAAGAGGTAA
Found at i:269915 original size:32 final size:31
Alignment explanation
Indices: 269859--269945 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 31
269849 CTACCGCACA
* * *
269859 TTTTCATTTAAGTAATAAAGTATACCCATTT
1 TTTTCATTTAAGTACTAAAGTATACACACTT
269890 TTTTCATTTAAGTACCTAAAGTATACACACTT
1 TTTTCATTTAAGTA-CTAAAGTATACACACTT
* *
269922 TTTTCAATGAAGTAACTAAAGTAT
1 TTTTCATTTAAGT-ACTAAAGTAT
269946 TTTTTGTCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 14 0.29
32 34 0.69
33 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (31 bp):
TTTTCATTTAAGTACTAAAGTATACACACTT
Found at i:270212 original size:29 final size:29
Alignment explanation
Indices: 270119--270219 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 29
270109 AAAATTGAAC
* * *
270119 ACTTTATGTACCTATTTTAACC-AAAAAT
1 ACTTTAGGTACTTATTTTGACCAAAAAAT
* *
270147 GC-TTAGGTACCTATTTTGACCAAAAAATT
1 ACTTTAGGTACTTATTTTGACCAAAAAA-T
* *
270176 AACTTTAGGCACTTATTTTGATCAAAAAAT
1 -ACTTTAGGTACTTATTTTGACCAAAAAAT
270206 ACTTTAGGTACTTA
1 ACTTTAGGTACTTA
270220 AATAAAAAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 17 0.28
28 6 0.10
29 14 0.23
30 2 0.03
31 22 0.36
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (29 bp):
ACTTTAGGTACTTATTTTGACCAAAAAAT
Found at i:273450 original size:47 final size:47
Alignment explanation
Indices: 273397--273486 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
273387 ATTAACATTT
* * *
273397 TTTTCTTTTTGAGAAAATGAAAGATTGATACTATATTTGAGCCGTTG
1 TTTTCTTTTTGAGAAAATGAAAGAATGATACCAGATTTGAGCCGTTG
*
273444 TTTTCTTTTTGAGAAAATGAAAGAATGGTACCAGATTTGAGCC
1 TTTTCTTTTTGAGAAAATGAAAGAATGATACCAGATTTGAGCC
273487 ATTATTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (47 bp):
TTTTCTTTTTGAGAAAATGAAAGAATGATACCAGATTTGAGCCGTTG
Found at i:285938 original size:2 final size:2
Alignment explanation
Indices: 285931--285971 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
285921 TGACAAACTT
285931 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
285972 AATAGTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:286691 original size:185 final size:183
Alignment explanation
Indices: 286339--286701 Score: 584
Period size: 185 Copynumber: 2.0 Consensus size: 183
286329 AATATTAAAT
* * * * * *
286339 ATATATTATATATAACATATGGGCTTAGTCCAAACTATTTAAAATCTAATTAATAATTTAATATT
1 ATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCAAATTAATAATTTAAGATC
*
286404 CAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTTTATTTTATA
66 CAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTTTATTTTATA
*
286469 ATTATATATTATTTAAATTAATTGTAAACTATTTTTTTGAATTAAAAAATATGAA
131 ATTATATATTATTTAAATTAATTATAAAC-ATTTTTTT-AATTAAAAAATATGAA
286524 ATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCAAATTAATAATTTAAGATC
1 ATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCAAATTAATAATTTAAGATC
* * *
286589 CAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAATATTTATCTGAAATTTTTATTTTAT
66 CAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAA-AATTATATAAAATTTTTATTTTAT
286654 AATTTATATATTATTTAAATTAATTATAAAC-TTTTTTTAATTAAAAAA
130 AA-TTATATATTATTTAAATTAATTATAAACATTTTTTTAATTAAAAAA
286702 CATTTAATTT
Statistics
Matches: 165, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
184 10 0.06
185 105 0.64
186 23 0.14
187 27 0.16
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (183 bp):
ATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCAAATTAATAATTTAAGATC
CAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTTTATTTTATA
ATTATATATTATTTAAATTAATTATAAACATTTTTTTAATTAAAAAATATGAA
Found at i:288793 original size:14 final size:14
Alignment explanation
Indices: 288774--288817 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
288764 ACACTTTTAA
288774 TATTTATTTTTATT
1 TATTTATTTTTATT
288788 TATTTATTTTTATT
1 TATTTATTTTTATT
* *
288802 AATTTTATTTTCATT
1 TA-TTTATTTTTATT
288817 T
1 T
288818 TAATTGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (14 bp):
TATTTATTTTTATT
Found at i:290751 original size:21 final size:21
Alignment explanation
Indices: 290727--290767 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
290717 AGAAATATAT
*
290727 ATTAACAGGAGTGTAGACTAC
1 ATTAACAGGAGTATAGACTAC
290748 ATTAACAGGAGTATAGACTA
1 ATTAACAGGAGTATAGACTA
290768 TAGAGACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (21 bp):
ATTAACAGGAGTATAGACTAC
Found at i:291942 original size:31 final size:31
Alignment explanation
Indices: 291907--291973 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
291897 TTAAAACTTA
* *
291907 CAATACAAT-CCTCCAATATTTAGTCTATTTG
1 CAATACAATCCCT-CAACATTTAGTCCATTTG
***
291938 CAATATGGTCCCTCAACATTTAGTCCATTTG
1 CAATACAATCCCTCAACATTTAGTCCATTTG
291969 CAATA
1 CAATA
291974 TGGTCCCTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (31 bp):
CAATACAATCCCTCAACATTTAGTCCATTTG
Found at i:292850 original size:14 final size:14
Alignment explanation
Indices: 292831--292881 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
292821 TTAAATACAC
292831 TTTTATTTATTTAT
1 TTTTATTTATTTAT
292845 TTTTATTTATTTAT
1 TTTTATTTATTTAT
*
292859 TTTTATTAATTTTAT
1 TTTTATTTA-TTTAT
*
292874 TTTCATTT
1 TTTTATTT
292882 TAATTGTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:294107 original size:26 final size:26
Alignment explanation
Indices: 294078--294133 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
294068 AAAGTTAACG
294078 TTTTTAATATTCGTTCTAATTATTAT
1 TTTTTAATATTCGTTCTAATTATTAT
* * * *
294104 TTTTTAATATTCTTTTTTATTTTTAT
1 TTTTTAATATTCGTTCTAATTATTAT
294130 TTTT
1 TTTT
294134 CCCTATCTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTTTAATATTCGTTCTAATTATTAT
Found at i:299030 original size:2 final size:2
Alignment explanation
Indices: 299023--299069 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
299013 TGACAAACTT
299023 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
299065 AG AG A
1 AG AG A
299070 AATAGTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:299787 original size:185 final size:183
Alignment explanation
Indices: 299426--299797 Score: 584
Period size: 185 Copynumber: 2.0 Consensus size: 183
299416 ATTAAATTTT
* * * * *
299426 AAATATTAAATATATTATATATAACATATGAGCTTAGTCCAAACTATTTAAAATCTAATTAATAA
1 AAATATGAAATATATTATATATAACATATGAGCTAAGTCCAAACCATTTAAAACCCAATTAATAA
* * * *
299491 TTTAATATTCAATAATTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
*
299556 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTGAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAAC-GTTTTTTT-AATTAAA
*
299611 AAATATGAAATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAATTAATAA
1 AAATATGAAATATATTATATATAACATATGAGCTAAGTCCAAACCATTTAAAACCCAATTAATAA
* *
299676 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATTT
299741 TTATTTTATAATTTATATATTATTTAAATTAATTATAAAC-TTTTTTTAATTAAA
130 TTATTTTATAA-TTATATATTATTTAAATTAATTATAAACGTTTTTTTAATTAAA
299795 AAA
1 AAA
299798 CATTTAATTT
Statistics
Matches: 172, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
184 10 0.06
185 113 0.66
186 22 0.13
187 27 0.16
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATGAAATATATTATATATAACATATGAGCTAAGTCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACGTTTTTTTAATTAAA
Found at i:300454 original size:20 final size:20
Alignment explanation
Indices: 300360--300728 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
300350 GATTTTCCAT
* ** *
300360 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
300380 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
300400 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
300420 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
300440 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
300460 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
300480 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
300500 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
300520 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
300540 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
300560 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
300580 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
300600 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
300620 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
300640 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
300660 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
300680 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
300700 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
300720 AATCACAAC
1 AATCGCAAC
300729 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:301441 original size:24 final size:24
Alignment explanation
Indices: 301402--301448 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
301392 AAATTTGGTC
301402 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
301426 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
301449 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:301640 original size:12 final size:12
Alignment explanation
Indices: 301623--301647 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
301613 ATATAATCCT
301623 GAAGAAGAAAAA
1 GAAGAAGAAAAA
301635 GAAGAAGAAAAA
1 GAAGAAGAAAAA
301647 G
1 G
301648 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:303975 original size:19 final size:19
Alignment explanation
Indices: 303953--304259 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
303943 CGGAAAATAC
*
303953 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
303972 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
303986 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
304006 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
304020 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
304039 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
304058 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
304072 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
304091 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
304110 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
304124 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
304143 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
304162 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
304181 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
304200 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
304214 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
304233 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
304252 AATCGCAA
1 AATCGCAA
304260 CGAGATAATC
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 16 0.06
17 15 0.06
18 5 0.02
19 151 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:304068 original size:52 final size:53
Alignment explanation
Indices: 303981--304259 Score: 358
Period size: 52 Copynumber: 5.2 Consensus size: 53
303971 AAATCCCAAC
*
303981 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
304034 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
304086 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
304138 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
304195 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
304247 ATGAAAATCGCAA
1 ATGAAAATCGCAA
304260 CGAGATAATC
Statistics
Matches: 212, Mismatches: 8, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
51 2 0.01
52 156 0.74
53 18 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:304104 original size:71 final size:71
Alignment explanation
Indices: 304020--304259 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
304010 GCAACGAGAG
*
304020 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
304085 AATGAA
66 AATGAA
* * *
304091 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
304151 TACGAAATGAA
61 TGCGAAATGAA
304162 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
304227 AATGAA
66 AATGAA
304233 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
304260 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 113 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:304205 original size:142 final size:137
Alignment explanation
Indices: 303953--304291 Score: 497
Period size: 142 Copynumber: 2.4 Consensus size: 137
303943 CGGAAAATAC
* * * *
303953 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
304016 AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 AGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
304081 GCGAAATGAA
128 GCGAAATGAA
304091 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
304156 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 -A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
304221 ATGCGAAATGAA
126 ATGCGAAATGAA
304233 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
304292 TTGCGATTTT
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 33 0.18
139 3 0.02
141 1 0.01
142 123 0.66
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGAGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:304397 original size:19 final size:19
Alignment explanation
Indices: 304288--304389 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
304278 AAATTATAAA
304288 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
304307 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
304327 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
304343 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
304360 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
304379 CGCATTGCGAT
1 CGCATTGCGAT
304390 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:304515 original size:14 final size:14
Alignment explanation
Indices: 304496--304532 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
304486 CATCAATTAC
304496 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
304510 ACAAATCATCTTTT
1 ACAAATCAACTTTT
304524 ACAAATCAA
1 ACAAATCAA
304533 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:304544 original size:12 final size:12
Alignment explanation
Indices: 304527--304599 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
304517 ATCTTTTACA
304527 AATCAATTAAAC
1 AATCAATTAAAC
*
304539 AATCAA--AAATTG
1 AATCAATTAAA--C
**
304551 AATCAACTTTTAC
1 AATCAA-TTAAAC
304564 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
304577 AATCAA-AAAAC
1 AATCAATTAAAC
304588 AATCAATTAAAC
1 AATCAATTAAAC
304600 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:304561 original size:38 final size:38
Alignment explanation
Indices: 304513--304585 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
304503 AACTTTTACA
*
304513 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
304551 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
304586 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:306477 original size:14 final size:14
Alignment explanation
Indices: 306458--306514 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
306448 GCGAAATGAA
*
306458 AATCGCAACGACAG
1 AATCGCAACGAAAG
306472 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
306489 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
306505 AATCGCAACG
1 AATCGCAACG
306515 CGAAATGAAA
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:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:306485 original size:33 final size:33
Alignment explanation
Indices: 306439--306531 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
306429 GCGAAACCAA
*
306439 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
306472 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
306505 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
306532 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:306496 original size:19 final size:19
Alignment explanation
Indices: 306402--306536 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
306392 TAGTTTACTT
* *
306402 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
306422 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
306441 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
306460 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
306474 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
306493 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
306507 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
306526 TCGCAATGCGA
1 TCGCAACGCGA
306537 TTTTGGTTTC
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:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:306554 original size:19 final size:19
Alignment explanation
Indices: 306532--306660 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
306522 AAAATCGCAA
306532 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
306551 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
306565 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
306584 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
306598 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
306617 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
306636 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
306656 TGCGA
1 TGCGA
306661 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:306574 original size:33 final size:33
Alignment explanation
Indices: 306532--306623 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
306522 AAAATCGCAA
306532 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
306565 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
306598 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
306624 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:306994 original size:92 final size:93
Alignment explanation
Indices: 306704--307175 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
306694 TTGAATGGAT
306704 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
306769 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
306797 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
306862 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
306890 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
306954 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
306982 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
307046 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
307074 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
307139 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
307167 AAATTTACT
1 AAATTTACT
307176 AAGCAATCTA
Statistics
Matches: 378, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.49
93 194 0.51
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:307017 original size:185 final size:185
Alignment explanation
Indices: 306704--307175 Score: 928
Period size: 185 Copynumber: 2.6 Consensus size: 185
306694 TTGAATGGAT
306704 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
306769 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
306834 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
306890 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
306954 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
307019 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
307074 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
307139 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
307176 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 92 0.32
185 154 0.54
186 39 0.14
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:308794 original size:45 final size:45
Alignment explanation
Indices: 308730--308815 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
308720 ATTGAGCCGA
308730 AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATATACC
1 AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATATACC
308775 AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATA
1 AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATA
308816 AACATAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (45 bp):
AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATATACC
Found at i:308825 original size:45 final size:45
Alignment explanation
Indices: 308730--308825 Score: 167
Period size: 45 Copynumber: 2.1 Consensus size: 45
308720 ATTGAGCCGA
*
308730 AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATATACC
1 AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATATAAC
308775 AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATA-AAC
1 AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATATAAC
308819 ATAAAAA
1 A-AAAAA
308826 GTAGTAGTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 3 0.06
45 46 0.94
ACGTcount: A:0.59, C:0.16, G:0.04, T:0.21
Consensus pattern (45 bp):
AAAAAATTTCTACAAAAACAATAAACATACCAAGTTAGATATAAC
Found at i:308906 original size:14 final size:14
Alignment explanation
Indices: 308887--308943 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
308877 TTGAAATGAA
308887 AATCGCAACGAGAG
1 AATCGCAACGAGAG
308901 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
308918 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
308934 AATCGCAACG
1 AATCGCAACG
308944 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:308924 original size:33 final size:33
Alignment explanation
Indices: 308879--308963 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
308869 TCTTTTGGTT
308879 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
308912 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
308945 GAAATGAAAAATCGCAACG
1 GAAATG-AAAATCGCAACG
308964 CGAAATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 36 0.77
34 11 0.23
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:308959 original size:20 final size:19
Alignment explanation
Indices: 308901--308985 Score: 90
Period size: 19 Copynumber: 4.7 Consensus size: 19
308891 GCAACGAGAG
* *
308901 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
308920 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
308934 AATCGCAACGCGAAATGAAA
1 AATCGCAACGCGAAATG-AA
308954 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
308973 AATCGCAATGCGA
1 AATCGCAACGCGA
308986 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 23 0.40
20 18 0.32
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:309016 original size:14 final size:14
Alignment explanation
Indices: 308997--309051 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
308987 TTTGGTTTCG
308997 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
309011 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
309030 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
309044 CGTTGCGA
1 CGTTGCGA
309052 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:309214 original size:33 final size:33
Alignment explanation
Indices: 309172--309242 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
309162 AATACTAACT
309172 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
309205 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
309238 TGAAA
1 TGAAA
309243 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:309476 original size:22 final size:22
Alignment explanation
Indices: 309424--309478 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
309414 TGGTTGTGAG
**
309424 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
309446 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
309468 GGATTTCTTCG
1 GGATTTCTTCG
309479 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:309649 original size:20 final size:20
Alignment explanation
Indices: 309624--309817 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
309614 CTTTAAATAT
309624 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
309644 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
309666 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
309685 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
309705 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
309725 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
309745 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
309765 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
309785 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
309805 CGCGTTGCGATTT
1 CGCGTTGCGATTT
309818 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:309811 original size:60 final size:60
Alignment explanation
Indices: 309624--309817 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
309614 CTTTAAATAT
**
309624 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
309685 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
309745 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
309805 CGCGTTGCGATTT
1 CGCGTTGCGATTT
309818 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:309834 original size:21 final size:20
Alignment explanation
Indices: 309810--309886 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
309800 ATATTCGCGT
309810 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
309831 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
309851 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
309873 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
309887 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:309897 original size:20 final size:20
Alignment explanation
Indices: 309872--309923 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
309862 AAGAATCGCG
*
309872 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
309892 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
309912 TTGCGATTCTGG
1 TTGCGATTCTGG
309924 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:310870 original size:20 final size:20
Alignment explanation
Indices: 310822--310870 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
310812 ATATTTTTAG
*
310822 TCGAATTGAATTTATAAAAT
1 TCGAATCGAATTTATAAAAT
* * *
310842 TTGATTCGAGTTTATAAAAT
1 TCGAATCGAATTTATAAAAT
310862 TCGAATCGA
1 TCGAATCGA
310871 TATTCTGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (20 bp):
TCGAATCGAATTTATAAAAT
Found at i:311864 original size:167 final size:167
Alignment explanation
Indices: 311588--311924 Score: 629
Period size: 167 Copynumber: 2.0 Consensus size: 167
311578 AACATTAGAT
311588 AAATTCGAGAGAATGTTTAAAGAATCGAAAATAAAATGTTAGCTTTTTCTTAATATTTTTTCAGT
1 AAATTCGAGAGAATGTTTAAAGAATCGAAAATAAAATGTTAGCTTTTTCTTAATATTTTTTCAGT
*
311653 TGTGCACTCGGTTCAACTGAAAAAGTTAAAAATTAACATTTTAAGTTAATCTCAACTAAAAATGT
66 TGTGCACTCGGTTCAACTGAAAAAGTTAAAAATTAACATTTTAAGTTAATCTCAACTAAAAATGG
311718 TATGCCATTTTATAACATTTTAAGTTACTCTCAACCG
131 TATGCCATTTTATAACATTTTAAGTTACTCTCAACCG
*
311755 AAATTCGAGAGAATGTTTAAAGAATCGAAAATAAAATGTTAGTTTTTTCTTAATATTTTTTCAGT
1 AAATTCGAGAGAATGTTTAAAGAATCGAAAATAAAATGTTAGCTTTTTCTTAATATTTTTTCAGT
* *
311820 TGTGCACTCGGTTCAACTGAAAAAGTTAAAAATTAATATTTTAAGTTACTCTCAACTAAAAATGG
66 TGTGCACTCGGTTCAACTGAAAAAGTTAAAAATTAACATTTTAAGTTAATCTCAACTAAAAATGG
*
311885 TATGCCATTTTATAACATTTTAAGTTACTCTCAATCG
131 TATGCCATTTTATAACATTTTAAGTTACTCTCAACCG
311922 AAA
1 AAA
311925 ATGTTAAAAA
Statistics
Matches: 165, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
167 165 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (167 bp):
AAATTCGAGAGAATGTTTAAAGAATCGAAAATAAAATGTTAGCTTTTTCTTAATATTTTTTCAGT
TGTGCACTCGGTTCAACTGAAAAAGTTAAAAATTAACATTTTAAGTTAATCTCAACTAAAAATGG
TATGCCATTTTATAACATTTTAAGTTACTCTCAACCG
Found at i:316001 original size:21 final size:21
Alignment explanation
Indices: 315977--316017 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
315967 AGAAATATAT
*
315977 ATTAACAGGAGTGTAGACTAC
1 ATTAACAGGAGTATAGACTAC
315998 ATTAACAGGAGTATAGACTA
1 ATTAACAGGAGTATAGACTA
316018 TAGAGACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (21 bp):
ATTAACAGGAGTATAGACTAC
Found at i:317191 original size:31 final size:31
Alignment explanation
Indices: 317153--317222 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
317143 CTTTTAAAAC
* *
317153 TTGCAATACAATCCTTCAACATTTAGTCTAT
1 TTGCAATACAATCCCTCAACATTTAGTCCAT
***
317184 TTGCAATATGGTCCCTCAACATTTAGTCCAT
1 TTGCAATACAATCCCTCAACATTTAGTCCAT
317215 TTGCAATA
1 TTGCAATA
317223 TGGTCCCTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (31 bp):
TTGCAATACAATCCCTCAACATTTAGTCCAT
Found at i:317223 original size:31 final size:31
Alignment explanation
Indices: 317168--317230 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
317158 ATACAATCCT
*
317168 TCAACATTTAGTCTATTTGCAATATGGTCCC
1 TCAACATTTAGTCCATTTGCAATATGGTCCC
317199 TCAACATTTAGTCCATTTGCAATATGGTCCC
1 TCAACATTTAGTCCATTTGCAATATGGTCCC
317230 T
1 T
317231 GATGTAACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (31 bp):
TCAACATTTAGTCCATTTGCAATATGGTCCC
Found at i:318826 original size:31 final size:31
Alignment explanation
Indices: 318791--318851 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
318781 GCAATCCCCC
* *
318791 AACATTTAGTTTGTTTGCAATATGGTCCCTT
1 AACATTTAGTCTATTTGCAATATGGTCCCTT
318822 AACATTTAGTCTATTTGCAATATGGTCCCT
1 AACATTTAGTCTATTTGCAATATGGTCCCT
318852 GACGTAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (31 bp):
AACATTTAGTCTATTTGCAATATGGTCCCTT
Found at i:319878 original size:16 final size:15
Alignment explanation
Indices: 319841--319882 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
319831 TCAATAGTGA
319841 ATTAGGGTTTTGTGG
1 ATTAGGGTTTTGTGG
* *
319856 AGT-GGGTGTTTTTGG
1 ATTAGGGT-TTTGTGG
319871 ATTAGGGTTTTG
1 ATTAGGGTTTTG
319883 ATTGGCTTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
14 4 0.19
15 13 0.62
16 4 0.19
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (15 bp):
ATTAGGGTTTTGTGG
Found at i:322546 original size:20 final size:19
Alignment explanation
Indices: 322509--322555 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
322499 AATAATATTT
322509 AAATATTAGTTGTACAATTA
1 AAATATTAGTTGTACAA-TA
*
322529 AAATATTA-TTGTGCCAATA
1 AAATATTAGTTGT-ACAATA
*
322548 ATATATTA
1 AAATATTA
322556 AACACTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (19 bp):
AAATATTAGTTGTACAATA
Found at i:328550 original size:33 final size:34
Alignment explanation
Indices: 328513--328578 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
328503 AAACTAATTT
*
328513 GATGTCATTACTTACATC-AATTTGTTAGGTGAA
1 GATGTCATTACTTACATCAAATTAGTTAGGTGAA
*
328546 GATGTCATTGCTTACATCAAATTAGTTAGGTGA
1 GATGTCATTACTTACATCAAATTAGTTAGGTGA
328579 GAGTTAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (34 bp):
GATGTCATTACTTACATCAAATTAGTTAGGTGAA
Found at i:330437 original size:61 final size:60
Alignment explanation
Indices: 330359--330527 Score: 170
Period size: 60 Copynumber: 2.8 Consensus size: 60
330349 ATACGTATAA
330359 TTTAGGATGA-AACTGAAATATTCTAAAAGTTTGGGGACTAATTCAAAAT-GA-AGATCATAG
1 TTTAGGATGATAA-TGAAATATTCTAAAAGTTTGGGGACTAATT-AAAATCGATAG-TCATAG
* * *
330419 TTTAGGGATGATAATGAAATATTC-AAAAGTTTGAGGACTAATTTAGATCGATAGTCATAG
1 TTTA-GGATGATAATGAAATATTCTAAAAGTTTGGGGACTAATTAAAATCGATAGTCATAG
* * * *
330479 TTTAAGGATAAT-ATTAATATATT-TAAAAGTTTAGGGACCAATTTAAAAT
1 TTT-AGGATGATAATGAA-ATATTCTAAAAGTTTGGGGACTAA-TTAAAAT
330528 AATGGTCAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
59 7 0.08
60 58 0.64
61 24 0.26
62 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (60 bp):
TTTAGGATGATAATGAAATATTCTAAAAGTTTGGGGACTAATTAAAATCGATAGTCATAG
Found at i:334176 original size:12 final size:12
Alignment explanation
Indices: 334161--334215 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
334151 GTTATTTAAA
334161 CGGGTATTGGGC
1 CGGGTATTGGGC
*
334173 CGGGTATTGGGT
1 CGGGTATTGGGC
334185 CGGGTATTGGGC
1 CGGGTATTGGGC
* * * *
334197 TGAGAATCGGGC
1 CGGGTATTGGGC
334209 CGGGTAT
1 CGGGTAT
334216 ATATATATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:334286 original size:2 final size:2
Alignment explanation
Indices: 334275--334311 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
334265 AAATTTATTA
334275 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
334312 TATTTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:334584 original size:2 final size:2
Alignment explanation
Indices: 334577--334625 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
334567 CCGCCAAGAA
*
334577 AC AC AC AC AC AC AC AC AC TC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
334619 AC AC AC A
1 AC AC AC A
334626 TTTATGAGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:335081 original size:25 final size:25
Alignment explanation
Indices: 335035--335082 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
335025 CTTAACGATA
* *
335035 AAGGCATCTTTGTTGTAGTAGAATT
1 AAGGCATCTTTATCGTAGTAGAATT
* *
335060 AAGGTATCTTTATCGTATTAGAA
1 AAGGCATCTTTATCGTAGTAGAA
335083 ACATGAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (25 bp):
AAGGCATCTTTATCGTAGTAGAATT
Found at i:341807 original size:2 final size:2
Alignment explanation
Indices: 341802--341828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
341792 TAAAACACTC
341802 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
341829 CACATTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:347974 original size:23 final size:23
Alignment explanation
Indices: 347941--348008 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
347931 AACCTTATAT
347941 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
347964 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
347987 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
348009 AGCTATGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:351190 original size:17 final size:17
Alignment explanation
Indices: 351159--351212 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
351149 CAAGTTTATT
**
351159 TTTTATAATAATAAATA
1 TTTTATAATTTTAAATA
*
351176 TTTTATAATTTTAAAAA
1 TTTTATAATTTTAAATA
* *
351193 TTATA-AATTTCAAATA
1 TTTTATAATTTTAAATA
351209 TTTT
1 TTTT
351213 TGAAAAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTATAATTTTAAATA
Found at i:352471 original size:20 final size:19
Alignment explanation
Indices: 352448--352509 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
352438 AATTGAACCT
*
352448 AAAATCTAATGATTGACCCG
1 AAAATCTAA-GGTTGACCCG
* *
352468 AAAATATGAAGGTTGACTCG
1 AAAATCT-AAGGTTGACCCG
352488 AAAATCTAAAGGTTGACCCG
1 AAAATCT-AAGGTTGACCCG
352508 AA
1 AA
352510 TTAAAATCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (19 bp):
AAAATCTAAGGTTGACCCG
Found at i:355734 original size:22 final size:22
Alignment explanation
Indices: 355683--355724 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
355673 ACAATTTCAT
*
355683 AAATTTAATAATTATTTTATTA
1 AAATTGAATAATTATTTTATTA
355705 AAATTGAATAATTATTTTAT
1 AAATTGAATAATTATTTTAT
355725 GATATCTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAATTGAATAATTATTTTATTA
Found at i:356665 original size:24 final size:25
Alignment explanation
Indices: 356622--356730 Score: 64
Period size: 25 Copynumber: 4.4 Consensus size: 25
356612 TATTTACTCT
* *
356622 TATATATAAATCATATAAATTTAGAC
1 TATA-ATAAATTATAAAAATTTAGAC
* *
356648 TATAATAAATT-TAAAAATAT-GAA
1 TATAATAAATTATAAAAATTTAGAC
* ** *
356671 TATATATGAATTATATCAATTTAAAC
1 TATA-ATAAATTATAAAAATTTAGAC
* *
356697 TATAATAAA-AATATAAAATTATA-AT
1 TATAATAAATTATA-AAAATT-TAGAC
356722 TATAATAAA
1 TATAATAAA
356731 AATATATTTT
Statistics
Matches: 63, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
23 6 0.10
24 16 0.25
25 30 0.48
26 11 0.17
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (25 bp):
TATAATAAATTATAAAAATTTAGAC
Found at i:364436 original size:16 final size:17
Alignment explanation
Indices: 364412--364445 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
364402 ACAGGTAACT
364412 TAATATAT-ATTTTTTA
1 TAATATATAATTTTTTA
*
364428 TAATTTATAATTTTTTA
1 TAATATATAATTTTTTA
364445 T
1 T
364446 TTCTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATATATAATTTTTTA
Found at i:385091 original size:20 final size:21
Alignment explanation
Indices: 385066--385158 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
385056 TTTTCCCAAT
*
385066 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
** **
385086 TCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
385107 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
385127 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
385148 TCGCAATGCGA
1 TCGCAATGCGA
385159 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:385111 original size:41 final size:41
Alignment explanation
Indices: 385066--385158 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
385056 TTTTCCCAAT
385066 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
*
385107 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
385148 TCGCAATGCGA
1 TCGCAATGCGA
385159 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
Found at i:385171 original size:41 final size:41
Alignment explanation
Indices: 385085--385219 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
385075 GAATAAGTAA
* * *
385085 ATCGCAACACGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
385126 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
385167 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
385208 TTCGCAACGCGA
1 ATCGCAACGCGA
385220 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:385172 original size:20 final size:20
Alignment explanation
Indices: 385147--385241 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
385137 AATTGGGAAA
*
385147 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
385167 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
385188 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
385208 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
385228 TTCGCAACGCGATA
1 ATCGCAACGCGATA
385242 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Done.