Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 40 of 276
Found at i:12575516 original size:42 final size:43
Alignment explanation
Indices: 12575423--12575522 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 43
12575413 CGACTATGTT
* **
12575423 TGGCACTTAGTGTGCG-TTTTGAGATAGCTTTGGCTATATAGA
1 TGGCACTTAGTGTGCGAGTCGGAGATAGCTTTGGCTATATAGA
*
12575465 --GCACTTAGTGTGCGAGTCGGA-ATAG-TTTCGGCTATATATA
1 TGGCACTTAGTGTGCGAGTCGGAGATAGCTTT-GGCTATATAGA
12575505 TGGCACTTAGTGTGCGAG
1 TGGCACTTAGTGTGCGAG
12575523 ATTATAATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
39 3 0.06
40 28 0.56
41 3 0.06
42 16 0.32
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (43 bp):
TGGCACTTAGTGTGCGAGTCGGAGATAGCTTTGGCTATATAGA
Found at i:12578318 original size:24 final size:24
Alignment explanation
Indices: 12578285--12578350 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
12578275 GGCTGGTTGG
12578285 TAGGCA-AGGACTGAGTGTTTAGC
1 TAGGCAGAGGACTGAGTGTTTAGC
* * *
12578308 TGGGCAGAGGATTGAGTGTTTGGC
1 TAGGCAGAGGACTGAGTGTTTAGC
12578332 TAGGCAGAGGACTGAGTGT
1 TAGGCAGAGGACTGAGTGT
12578351 GAGTGTTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 5 0.14
24 32 0.86
ACGTcount: A:0.23, C:0.11, G:0.41, T:0.26
Consensus pattern (24 bp):
TAGGCAGAGGACTGAGTGTTTAGC
Found at i:12579550 original size:13 final size:13
Alignment explanation
Indices: 12579532--12579556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12579522 CCAGGGGACA
12579532 CATGACCGTGTAG
1 CATGACCGTGTAG
12579545 CATGACCGTGTA
1 CATGACCGTGTA
12579557 TCGCAAACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (13 bp):
CATGACCGTGTAG
Found at i:12580224 original size:28 final size:28
Alignment explanation
Indices: 12580193--12580250 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
12580183 CTCATAATTC
12580193 ATTCACAATTCAATCAATGTAATGCAAG
1 ATTCACAATTCAATCAATGTAATGCAAG
12580221 ATTCACAATTCAATCAATGTAATGCAAG
1 ATTCACAATTCAATCAATGTAATGCAAG
12580249 AT
1 AT
12580251 AATACAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (28 bp):
ATTCACAATTCAATCAATGTAATGCAAG
Found at i:12580578 original size:46 final size:49
Alignment explanation
Indices: 12580526--12580625 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 49
12580516 TGACCCGTAA
*
12580526 CCAAATCAAGG-TAACTC-C-TCCAAAGTGCCT-ATACCATGGCCTAAAG
1 CCAAATCAAGGATAACTCACACCCAAAGTG-CTGATACCATGGCCTAAAG
* *
12580572 CCAAATCAAGGCATAACTCACACCCAAAGTGCTGATATCATGGCCTGAAG
1 CCAAATCAAGG-ATAACTCACACCCAAAGTGCTGATACCATGGCCTAAAG
12580622 CCAA
1 CCAA
12580626 CTTAATACCC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
46 11 0.24
48 6 0.13
49 3 0.07
50 26 0.57
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (49 bp):
CCAAATCAAGGATAACTCACACCCAAAGTGCTGATACCATGGCCTAAAG
Found at i:12581814 original size:3 final size:3
Alignment explanation
Indices: 12581806--12581834 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12581796 GGCATTCAGC
12581806 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12581835 ATACATTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12583197 original size:40 final size:40
Alignment explanation
Indices: 12583149--12583365 Score: 364
Period size: 40 Copynumber: 5.5 Consensus size: 40
12583139 ATATATAATA
*
12583149 TAAA-TATATCCGGGTTAAATCCCACAGGCTTTGTGCTGG
1 TAAATTATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG
* *
12583188 TAAATTATATACGGGTTAAATCTCGCAGGCTTTGTGCTGG
1 TAAATTATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG
12583228 TAAATTATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG
1 TAAATTATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG
12583268 TAAATTATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG
1 TAAATTATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG
* * *
12583308 TAAAATATCTCCGGGTTAAATCCCACAGGCTTTGTGCTGG
1 TAAATTATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG
*
12583348 TAAAATATATCCGGGTTA
1 TAAATTATATCCGGGTTA
12583366 TAAACCTAGT
Statistics
Matches: 168, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 4 0.02
40 164 0.98
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (40 bp):
TAAATTATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG
Found at i:12588454 original size:2 final size:2
Alignment explanation
Indices: 12588441--12588504 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
12588431 CACTAAGTGT
* *
12588441 CA CA CT CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
12588483 CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA
12588505 TATATATATC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:12591066 original size:8 final size:8
Alignment explanation
Indices: 12591055--12591079 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12591045 TTTAATAAGA
12591055 TATTTTAT
1 TATTTTAT
12591063 TATTTTAT
1 TATTTTAT
12591071 TATTTTAT
1 TATTTTAT
12591079 T
1 T
12591080 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:12594603 original size:52 final size:52
Alignment explanation
Indices: 12594487--12594636 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 52
12594477 TATCATACTG
* * * **
12594487 ATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCACATTACACTG
1 ATGCCATAGCCCAGCTATGGTCTTATACGGAAGCACA-TATCACATTACACCA
* **
12594540 ATGCCATAGCCCAGCTATGGTCTTATAAGGGAA-CACATATCACATTGTACCA
1 ATGCCATAGCCCAGCTATGGTCTTAT-ACGGAAGCACATATCACATTACACCA
* *
12594592 ATGCCATAGCCCAACTATGGTCTTATATGGAAGCACATATCACAT
1 ATGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACAT
12594637 CTTTTCCGTC
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
51 5 0.06
52 48 0.56
53 28 0.33
54 5 0.06
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (52 bp):
ATGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATTACACCA
Found at i:12602122 original size:31 final size:31
Alignment explanation
Indices: 12602086--12602166 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
12602076 AATGTGTATG
12602086 ATTAAATCAAAATTAAAGTTTCAAGTATACA
1 ATTAAATCAAAATTAAAGTTTCAAGTATACA
* * * * * * *
12602117 TTTAAACCACAATTAGAGTTTTACGTATATA
1 ATTAAATCAAAATTAAAGTTTCAAGTATACA
*
12602148 ATTACATC-AAATTAAAGTT
1 ATTAAATCAAAATTAAAGTT
12602167 CATAATTACA
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
30 9 0.24
31 29 0.76
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (31 bp):
ATTAAATCAAAATTAAAGTTTCAAGTATACA
Found at i:12608487 original size:105 final size:104
Alignment explanation
Indices: 12608306--12608515 Score: 375
Period size: 105 Copynumber: 2.0 Consensus size: 104
12608296 CCTTTTCAGC
* *
12608306 TTTAAGCCGGTGTTAACCCGTCAAAAAACCGGTGAGTTACGAACTCGAGCTGTTTAACTCCCAAA
1 TTTAAGCCGGTGTTAACCCGTCAAAAAACCCGTGAGTTACGAACCCGAGCTGTTTAACTCCCAAA
12608371 TTTCGATATTTATTATTTCTCCGGATTAAGAGTATGACT
66 TTTCGATATTTATTATTTCTCCGGATTAAGAGTATGACT
*
12608410 TTTAAGTCGGTGTTAACCCCGTCAAAAAACCCGTGAGTTACGAACCCGAGCTGTTTAACTCCCAA
1 TTTAAGCCGGTGTTAA-CCCGTCAAAAAACCCGTGAGTTACGAACCCGAGCTGTTTAACTCCCAA
*
12608475 CTTTCGATATTTATTATTTCTCCGGATTAAGAGTATGACT
65 ATTTCGATATTTATTATTTCTCCGGATTAAGAGTATGACT
12608515 T
1 T
12608516 CGTCAACTCA
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 15 0.15
105 86 0.85
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (104 bp):
TTTAAGCCGGTGTTAACCCGTCAAAAAACCCGTGAGTTACGAACCCGAGCTGTTTAACTCCCAAA
TTTCGATATTTATTATTTCTCCGGATTAAGAGTATGACT
Found at i:12613162 original size:16 final size:15
Alignment explanation
Indices: 12613137--12613184 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
12613127 CTATTTTAAG
12613137 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
12613152 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
12613169 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
12613184 T
1 T
12613185 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:12614117 original size:18 final size:18
Alignment explanation
Indices: 12614073--12614117 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
12614063 TATTTTGTTA
12614073 TTTATTTTTATTTCATCT
1 TTTATTTTTATTTCATCT
12614091 TTT-TATTTTATTTCATCT
1 TTTAT-TTTTATTTCATCT
12614109 TTTATTTTT
1 TTTATTTTT
12614118 TACTTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTTATTTCATCT
Found at i:12614150 original size:21 final size:19
Alignment explanation
Indices: 12614073--12614165 Score: 73
Period size: 18 Copynumber: 4.8 Consensus size: 19
12614063 TATTTTGTTA
**
12614073 TTTAT-TTTTATTTCATCT
1 TTTATATTTTATTTCAGGT
**
12614091 TTT-TATTTTATTTCATCT
1 TTTATATTTTATTTCAGGT
* *
12614109 TTTATTTTTTACTTTTTAGGT
1 TTTATATTTTA--TTTCAGGT
*
12614130 TTTCTTATGTTTATTTCAGGT
1 TTT-ATAT-TTTATTTCAGGT
12614151 TTTATATTTTATTTC
1 TTTATATTTTATTTC
12614166 CCCCCTAAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.02
18 19 0.31
19 14 0.23
20 3 0.05
21 18 0.30
22 2 0.03
23 4 0.07
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTATATTTTATTTCAGGT
Found at i:12618367 original size:16 final size:15
Alignment explanation
Indices: 12618342--12618389 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
12618332 CTATTTTAAG
12618342 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
12618357 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
12618374 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
12618389 T
1 T
12618390 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:12619322 original size:18 final size:18
Alignment explanation
Indices: 12619278--12619322 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
12619268 TATTTTGTTA
12619278 TTTATTTTTATTTCATCT
1 TTTATTTTTATTTCATCT
12619296 TTT-TATTTTATTTCATCT
1 TTTAT-TTTTATTTCATCT
12619314 TTTATTTTT
1 TTTATTTTT
12619323 TACTTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTTATTTCATCT
Found at i:12619355 original size:21 final size:19
Alignment explanation
Indices: 12619278--12619370 Score: 73
Period size: 18 Copynumber: 4.8 Consensus size: 19
12619268 TATTTTGTTA
**
12619278 TTTAT-TTTTATTTCATCT
1 TTTATATTTTATTTCAGGT
**
12619296 TTT-TATTTTATTTCATCT
1 TTTATATTTTATTTCAGGT
* *
12619314 TTTATTTTTTACTTTTTAGGT
1 TTTATATTTTA--TTTCAGGT
*
12619335 TTTCTTATGTTTATTTCAGGT
1 TTT-ATAT-TTTATTTCAGGT
12619356 TTTATATTTTATTTC
1 TTTATATTTTATTTC
12619371 CCCCCTAAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.02
18 19 0.31
19 14 0.23
20 3 0.05
21 18 0.30
22 2 0.03
23 4 0.07
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTATATTTTATTTCAGGT
Found at i:12623526 original size:27 final size:26
Alignment explanation
Indices: 12623466--12623527 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
12623456 ATTTTATTTT
12623466 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * *
12623492 ATAATTATTAGGATTATTCAA-ATTTAGG
1 AT-TTTATTAGGATAATT-AATA-TTAAG
12623520 ATTTTATT
1 ATTTTATT
12623528 TTAATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:12627245 original size:5 final size:6
Alignment explanation
Indices: 12627230--12627316 Score: 74
Period size: 6 Copynumber: 14.7 Consensus size: 6
12627220 CCAATCTTTC
* ** *
12627230 TTTTTA TTTTTA TTTTTC TTTTTA TTTATTA TTTTCC TTTCT- TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA
*
12627278 TTTTTTA TTTATTA -TTTTA -TTTTA TTTCTA -TTTTA TTTT
1 -TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
12627317 AGTTAAATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
5 16 0.24
6 35 0.53
7 15 0.23
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:12627289 original size:35 final size:36
Alignment explanation
Indices: 12627236--12627316 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
12627226 TTTCTTTTTA
* *
12627236 TTTTTATTTTTCTTTTTATT-TATTATTTTCCTTTCT
1 TTTTTATTTTTCTATTTATTATATTATTTT-ATTTCT
*
12627272 TTTTTATTTTT-TATTTATTATTTTATTTTATTTCT
1 TTTTTATTTTTCTATTTATTATATTATTTTATTTCT
*
12627307 ATTTTATTTT
1 TTTTTATTTT
12627317 AGTTAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.52
36 19 0.47
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (36 bp):
TTTTTATTTTTCTATTTATTATATTATTTTATTTCT
Found at i:12627311 original size:16 final size:17
Alignment explanation
Indices: 12627280--12627317 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
12627270 CTTTTTTATT
*
12627280 TTTTATTTATTATTTTA
1 TTTTATTTACTATTTTA
12627297 TTTTATTT-CTATTTTA
1 TTTTATTTACTATTTTA
12627313 TTTTA
1 TTTTA
12627318 GTTAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTACTATTTTA
Found at i:12627487 original size:42 final size:43
Alignment explanation
Indices: 12627435--12627515 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
12627425 CAAACAATTC
**
12627435 TATTCCAGCCC-AGAATGCCAT-ATCTCTGCAGCCAAACAGTCT
1 TATTCCAGCCCTAGAAT-CCATAAAATCTGCAGCCAAACAGTCT
* *
12627477 TATTCTAGCCCTAGAATCCCTAAAATCTGCAGCCAAACA
1 TATTCCAGCCCTAGAATCCATAAAATCTGCAGCCAAACA
12627516 CCCATTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 13 0.39
43 20 0.61
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.23
Consensus pattern (43 bp):
TATTCCAGCCCTAGAATCCATAAAATCTGCAGCCAAACAGTCT
Found at i:12628522 original size:21 final size:19
Alignment explanation
Indices: 12628493--12628531 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
12628483 TATTTCTAAG
*
12628493 TAAATAAATAATAATAAAATT
1 TAAAAAAATAA-AA-AAAATT
12628514 TAAAAAAATAAAAAAAAT
1 TAAAAAAATAAAAAAAAT
12628532 AAAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAAAATAAAAAAAATT
Found at i:12629831 original size:88 final size:88
Alignment explanation
Indices: 12629704--12629957 Score: 411
Period size: 88 Copynumber: 2.9 Consensus size: 88
12629694 GTGAATTCAC
* * * *
12629704 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGACAGTGAGCTTTAAACCCCTAAGTAG
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACAGTGAGCCTTAAACCCCTAAGTAG
*
12629769 TAGGGTAACAGGTCGAAGATTGT
66 TAGGGTAACAGGCCGAAGATTGT
* * *
12629792 AGATCTTGTCTCTCTAAACAGTAGTGGAGCAAATCAAAGACAGTGAGCCTTAACCCCCTAAGTAG
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACAGTGAGCCTTAAACCCCTAAGTAG
12629857 TAGGGTAACAGGCCGAAGATTGT
66 TAGGGTAACAGGCCGAAGATTGT
*
12629880 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAGTCAAAGACAGTGAGCCTT-AACTCCCTAAGTA
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACAGTGAGCCTTAAAC-CCCTAAGTA
12629944 GTAGGGTAACAGGC
65 GTAGGGTAACAGGC
12629958 TGAAAATTAC
Statistics
Matches: 153, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
87 2 0.01
88 151 0.99
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (88 bp):
AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACAGTGAGCCTTAAACCCCTAAGTAG
TAGGGTAACAGGCCGAAGATTGT
Found at i:12629937 original size:44 final size:44
Alignment explanation
Indices: 12629708--12629947 Score: 141
Period size: 44 Copynumber: 5.5 Consensus size: 44
12629698 ATTCACAGAT
* *
12629708 CTTATCTCCCTAAGCAGTAGTGGAGC-AGATGAAAGACAGTGAGC
1 CTTAACTCCCTAAGCAGTAGTGGAGCAAG-TCAAAGACAGTGAGC
* * * * * ** *
12629752 TTTAAAC-CCCTAAGTAGTAG-GGTAACAGGTCGAAGATTGT-AGAT
1 CTT-AACTCCCTAAGCAGTAGTGG-AGCAAGTCAAAGACAGTGAG-C
** * * *
12629796 CTTGTCTCTCTAAACAGTAGTGGAGCAAATCAAAGACAGTGAGC
1 CTTAACTCCCTAAGCAGTAGTGGAGCAAGTCAAAGACAGTGAGC
* * * * * * ** *
12629840 CTTAACCCCCTAAGTAGTAG-GGTAACAGGCCGAAGATTGT-AGAT
1 CTTAACTCCCTAAGCAGTAGTGG-AGCAAGTCAAAGACAGTGAG-C
**
12629884 CTTGTCTCCCTAAGCAGTAGTGGAGCAAGTCAAAGACAGTGAGC
1 CTTAACTCCCTAAGCAGTAGTGGAGCAAGTCAAAGACAGTGAGC
*
12629928 CTTAACTCCCTAAGTAGTAG
1 CTTAACTCCCTAAGCAGTAG
12629948 GGTAACAGGC
Statistics
Matches: 134, Mismatches: 51, Indels: 22
0.65 0.25 0.11
Matches are distributed among these distances:
43 9 0.07
44 114 0.85
45 11 0.08
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (44 bp):
CTTAACTCCCTAAGCAGTAGTGGAGCAAGTCAAAGACAGTGAGC
Found at i:12632120 original size:21 final size:22
Alignment explanation
Indices: 12632102--12632142 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
12632092 TTCATATAGT
12632102 TGTTTTTAAAT-TATTTATATA
1 TGTTTTTAAATCTATTTATATA
12632123 TGTTTTTAAATCTA-TTATAT
1 TGTTTTTAAATCTATTTATAT
12632143 GTATAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (22 bp):
TGTTTTTAAATCTATTTATATA
Found at i:12632584 original size:24 final size:23
Alignment explanation
Indices: 12632552--12632596 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
12632542 TTAGTCATAC
*
12632552 TTAATTATTGGTTTTGTTAATTTG
1 TTAATTATTAG-TTTGTTAATTTG
12632576 TTAATTATTAGTTTGTTAATT
1 TTAATTATTAGTTTGTTAATT
12632597 GGCATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (23 bp):
TTAATTATTAGTTTGTTAATTTG
Found at i:12632962 original size:129 final size:127
Alignment explanation
Indices: 12632775--12633096 Score: 334
Period size: 129 Copynumber: 2.5 Consensus size: 127
12632765 TGAAGATTCA
* * * *
12632775 CTAAAACAAAGGTAATAGTT-GATGTTTGGGAACTCGAGGAATCGTGCCCAACGGTGCTGGGTTT
1 CTAAAAC-AAGGCAAT-GTTCGATGTTTGGAAATTCGAGGAATCGTGCCCTACGGTGCTGGGTTT
* * * * *
12632839 CGATTTGCTGTTTG-TCCAAATGATCAAATATTCCTTT-GAAATTTCA-TC-CGTACTTTGAAAA
64 CGATTTCCCGTTTGTTCAAAATAATCAAATATTCCTTTAG-AATTTCACTCACGTACTCT--AAA
*
12632900 TTT
126 -CT
12632903 CTTAAAACGAAGGCAATGTTCGATGTTTGGAAATTC-AGGAAATCGTGCCCTATC-GTGCTGGGT
1 C-TAAAAC-AAGGCAATGTTCGATGTTTGGAAATTCGAGG-AATCGTGCCCTA-CGGTGCTGGGT
* * * * * *
12632966 TGCAATTTCCCGTTTGTTCAAAATAATCGAATATTTCTTTAGAATTTCACTCATGTTCTCTAAAC
62 TTCGATTTCCCGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCACTCACGTACTCTAAAC
12633031 T
127 T
* **
12633032 CTAAAACAAGGCAATGTTCGATGTTTAGAAATTCGAGGAATCGTGCCCTACTATGCTGGGTTTCG
1 CTAAAACAAGGCAATGTTCGATGTTTGGAAATTCGAGGAATCGTGCCCTACGGTGCTGGGTTTCG
12633097 GTTTTTCGTT
Statistics
Matches: 163, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
126 1 0.01
127 48 0.29
128 16 0.10
129 60 0.37
130 30 0.18
131 3 0.02
132 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (127 bp):
CTAAAACAAGGCAATGTTCGATGTTTGGAAATTCGAGGAATCGTGCCCTACGGTGCTGGGTTTCG
ATTTCCCGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCACTCACGTACTCTAAACT
Found at i:12635122 original size:3 final size:3
Alignment explanation
Indices: 12635114--12635139 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12635104 ACAATTCACT
12635114 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
12635140 CCTGCCTAAC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12646434 original size:22 final size:20
Alignment explanation
Indices: 12646376--12646427 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
12646366 ATCACCCCAA
*
12646376 TTTTATTTTATTTTATTTAT
1 TTTTATTTTATATTATTTAT
*
12646396 TATTAATTGTTATATTATTTAT
1 T-TTTATT-TTATATTATTTAT
12646418 TTTTATTTTA
1 TTTTATTTTA
12646428 CTAATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.15
21 10 0.37
22 13 0.48
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTATTTTATATTATTTAT
Found at i:12646436 original size:4 final size:4
Alignment explanation
Indices: 12646429--12646453 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12646419 TTTATTTTAC
12646429 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
12646454 CTTATACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:12646485 original size:18 final size:16
Alignment explanation
Indices: 12646462--12646513 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
12646452 TTCTTATACT
12646462 TATATTTTAAATTTTTTA
1 TATATTTT-AA-TTTTTA
*
12646480 TATATTGTAATTTTTA
1 TATATTTTAATTTTTA
*
12646496 TATATTTTTTATTTTTA
1 TATA-TTTTAATTTTTA
12646513 T
1 T
12646514 TTTTATTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 10 0.33
17 13 0.43
18 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TATATTTTAATTTTTA
Found at i:12646516 original size:5 final size:6
Alignment explanation
Indices: 12646501--12646537 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
12646491 TTTTATATAT
12646501 TTTTTA TTTTTA TTTTTA TTTTGCTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTT--TA TTTTTA TTTTT
12646538 TTCTTTTTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 23 0.79
8 6 0.21
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:12646517 original size:14 final size:14
Alignment explanation
Indices: 12646498--12646545 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
12646488 AATTTTTATA
*
12646498 TATTTTT-TATTTT
1 TATTTTTATTTTTT
**
12646511 TATTTTTATTTTGC
1 TATTTTTATTTTTT
12646525 TATTTTTATTTTTT
1 TATTTTTATTTTTT
*
12646539 TCTTTTT
1 TATTTTT
12646546 CGTATTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.81
Consensus pattern (14 bp):
TATTTTTATTTTTT
Found at i:12648454 original size:30 final size:30
Alignment explanation
Indices: 12648418--12648478 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
12648408 GAGTTTTCAG
* * * *
12648418 GATCCACACGGGCTGGGCTCATGCCCATGT
1 GATCCACACGGACAGGCCACATGCCCATGT
12648448 GATCCACACGGACAGGCCACATGCCCATGT
1 GATCCACACGGACAGGCCACATGCCCATGT
12648478 G
1 G
12648479 CCATCCGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.34, G:0.28, T:0.16
Consensus pattern (30 bp):
GATCCACACGGACAGGCCACATGCCCATGT
Found at i:12650345 original size:46 final size:46
Alignment explanation
Indices: 12650145--12650451 Score: 180
Period size: 46 Copynumber: 6.5 Consensus size: 46
12650135 TTGCCGATAC
* * * *
12650145 CATGTCCCAGACATGGTCTCACACTTGCTA-TCATCATCGAGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGC-ACTCGTC-TCAAGGCCGATG
* * * * **
12650193 CCATGT-CCAAACATGGTCTTACACTAGCTCTCGTACTTACGTGTTGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCACTCGT-CTCAAG-GCCGATG
* * * * *
12650242 CCATGTCCCAGACATGGTCTAACACTAGCACAAC-TCT-TA-GTCAATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTCAAGGCCGATG
*
12650288 CATGTCCCAGACATGTCTTACACTAGCTTA-T-GTCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGC--ACTCGTCTCAAGGCCGATG
* * * *
12650334 CATGTCCCAGACATGTCTAACGCTGGCACTCGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAAGGCCGATG
* * * * *
12650380 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-ATGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCACTCGT-CTCAAGGCCGATG
* *
12650428 CATGTCCCACACATGCCTTACACT
1 CATGTCCCAGACATGTCTTACACT
12650452 GGCATACAAC
Statistics
Matches: 206, Mismatches: 37, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
44 16 0.08
45 16 0.08
46 57 0.28
47 27 0.13
48 47 0.23
49 20 0.10
50 22 0.11
51 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAAGGCCGATG
Found at i:12650398 original size:138 final size:143
Alignment explanation
Indices: 12650145--12650405 Score: 338
Period size: 138 Copynumber: 1.9 Consensus size: 143
12650135 TTGCCGATAC
*
12650145 CATGTCCCAGACATGGTCTCACACTTGCTATCATCATCGAGGCCGATGCCATGTCCAAACATGGT
1 CATGTCCCAGACATGGTCTCACACTAGCTATCATCATCGAGGCCGATGCCATGTCCAAACATGGT
* * * * **
12650210 CTTACACTAGCTCTCGTACTTACGTGTTGATGCCATGTCCCAGACATGGTCTAACACTAGCACAA
66 CTAACACTAGCACTCGTACTCACATGCCGATGCCATGTCCCAGACATGGTCTAACACTAGCACAA
12650275 CTCTTAGTCAATG
131 CTCTTAGTCAATG
* * *
12650288 CATGTCCCAGACAT-GTCTTACACTAGCTTAT-GTC-TCGAGGCCGATG-CATGTCCCAGACAT-
1 CATGTCCCAGACATGGTCTCACACTAGC-TATCATCATCGAGGCCGATGCCATGT-CCAAACATG
* * *
12650348 GTCTAACGCTGGCACTCGT-CTCA-ATGCCGATGCCATGTCCCAGACATGGTCTTACACT
64 GTCTAACACTAGCACTCGTACTCACATGCCGATGCCATGTCCCAGACATGGTCTAACACT
12650406 GGCTCTCATA
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
138 31 0.30
139 3 0.03
140 20 0.19
141 19 0.18
142 13 0.13
143 17 0.17
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (143 bp):
CATGTCCCAGACATGGTCTCACACTAGCTATCATCATCGAGGCCGATGCCATGTCCAAACATGGT
CTAACACTAGCACTCGTACTCACATGCCGATGCCATGTCCCAGACATGGTCTAACACTAGCACAA
CTCTTAGTCAATG
Found at i:12650424 original size:94 final size:92
Alignment explanation
Indices: 12650145--12650451 Score: 232
Period size: 94 Copynumber: 3.3 Consensus size: 92
12650135 TTGCCGATAC
* * * * * *
12650145 CATGTCCCAGACATGGTCTCACACTTGCTATCATCATCGAGGCCGATGCCATGT-CCAAACATGG
1 CATGTCCCAGACAT-GTCTAACACTAGC-A-CAAC-TCTAAGCCGATGCCATGTCCCAGACATGG
* * * **
12650209 TCTTACACTAGCTCTCGTACTTACGTGTTGATG
62 TCTTACACTAGCTCTCATA-ATATG-GCCGATG
* * *
12650242 CCATGTCCCAGACATGGTCTAACACTAGCACAACTCTTAGTCAATG-CATGTCCCAGACAT-GTC
1 -CATGTCCCAGACAT-GTCTAACACTAGCACAACTCTAAGCCGATGCCATGTCCCAGACATGGTC
* *
12650305 TTACACTAGCT-T-AT-GTCTCGAGGCCGATG
64 TTACACTAGCTCTCATAATAT---GGCCGATG
* * *
12650334 CATGTCCCAGACATGTCTAACGCTGGCAC-TCGTCTCAATGCCGATGCCATGTCCCAGACATGGT
1 CATGTCCCAGACATGTCTAACACTAGCACAAC-TCT-AA-GCCGATGCCATGTCCCAGACATGGT
*
12650398 CTTACACTGGCTCTCATAATATGGCCGATG
63 CTTACACTAGCTCTCATAATATGGCCGATG
* * *
12650428 CATGTCCCACACATGCCTTACACT
1 CATGTCCCAGACATGTCTAACACT
12650452 GGCATACAAC
Statistics
Matches: 169, Mismatches: 28, Indels: 28
0.75 0.12 0.12
Matches are distributed among these distances:
89 1 0.01
90 17 0.10
91 15 0.09
92 11 0.07
93 16 0.09
94 60 0.36
95 15 0.09
96 5 0.03
97 3 0.02
98 26 0.15
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (92 bp):
CATGTCCCAGACATGTCTAACACTAGCACAACTCTAAGCCGATGCCATGTCCCAGACATGGTCTT
ACACTAGCTCTCATAATATGGCCGATG
Found at i:12655034 original size:46 final size:46
Alignment explanation
Indices: 12654834--12655140 Score: 180
Period size: 46 Copynumber: 6.5 Consensus size: 46
12654824 TTGCCGATAC
* * * *
12654834 CATGTCCCAGACATGGTCTCACACTTGCTA-TCATCATCGAGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGC-ACTCGTC-TCAAGGCCGATG
* * * * **
12654882 CCATGT-CCAAACATGGTCTTACACTAGCTCTCGTACTTACGTGTTGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCACTCGT-CTCAAG-GCCGATG
* * * * *
12654931 CCATGTCCCAGACATGGTCTAACACTAGCACAAC-TCT-TA-GTCAATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTCAAGGCCGATG
*
12654977 CATGTCCCAGACATGTCTTACACTAGCTTA-T-GTCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGC--ACTCGTCTCAAGGCCGATG
* * * *
12655023 CATGTCCCAGACATGTCTAACGCTGGCACTCGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAAGGCCGATG
* * * * *
12655069 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-ATGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCACTCGT-CTCAAGGCCGATG
* *
12655117 CATGTCCCACACATGCCTTACACT
1 CATGTCCCAGACATGTCTTACACT
12655141 GGCATACAAC
Statistics
Matches: 206, Mismatches: 37, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
44 16 0.08
45 16 0.08
46 57 0.28
47 27 0.13
48 47 0.23
49 20 0.10
50 22 0.11
51 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAAGGCCGATG
Found at i:12655087 original size:138 final size:143
Alignment explanation
Indices: 12654834--12655094 Score: 338
Period size: 138 Copynumber: 1.9 Consensus size: 143
12654824 TTGCCGATAC
*
12654834 CATGTCCCAGACATGGTCTCACACTTGCTATCATCATCGAGGCCGATGCCATGTCCAAACATGGT
1 CATGTCCCAGACATGGTCTCACACTAGCTATCATCATCGAGGCCGATGCCATGTCCAAACATGGT
* * * * **
12654899 CTTACACTAGCTCTCGTACTTACGTGTTGATGCCATGTCCCAGACATGGTCTAACACTAGCACAA
66 CTAACACTAGCACTCGTACTCACATGCCGATGCCATGTCCCAGACATGGTCTAACACTAGCACAA
12654964 CTCTTAGTCAATG
131 CTCTTAGTCAATG
* * *
12654977 CATGTCCCAGACAT-GTCTTACACTAGCTTAT-GTC-TCGAGGCCGATG-CATGTCCCAGACAT-
1 CATGTCCCAGACATGGTCTCACACTAGC-TATCATCATCGAGGCCGATGCCATGT-CCAAACATG
* * *
12655037 GTCTAACGCTGGCACTCGT-CTCA-ATGCCGATGCCATGTCCCAGACATGGTCTTACACT
64 GTCTAACACTAGCACTCGTACTCACATGCCGATGCCATGTCCCAGACATGGTCTAACACT
12655095 GGCTCTCATA
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
138 31 0.30
139 3 0.03
140 20 0.19
141 19 0.18
142 13 0.13
143 17 0.17
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (143 bp):
CATGTCCCAGACATGGTCTCACACTAGCTATCATCATCGAGGCCGATGCCATGTCCAAACATGGT
CTAACACTAGCACTCGTACTCACATGCCGATGCCATGTCCCAGACATGGTCTAACACTAGCACAA
CTCTTAGTCAATG
Found at i:12655113 original size:94 final size:92
Alignment explanation
Indices: 12654834--12655140 Score: 232
Period size: 94 Copynumber: 3.3 Consensus size: 92
12654824 TTGCCGATAC
* * * * * *
12654834 CATGTCCCAGACATGGTCTCACACTTGCTATCATCATCGAGGCCGATGCCATGT-CCAAACATGG
1 CATGTCCCAGACAT-GTCTAACACTAGC-A-CAAC-TCTAAGCCGATGCCATGTCCCAGACATGG
* * * **
12654898 TCTTACACTAGCTCTCGTACTTACGTGTTGATG
62 TCTTACACTAGCTCTCATA-ATATG-GCCGATG
* * *
12654931 CCATGTCCCAGACATGGTCTAACACTAGCACAACTCTTAGTCAATG-CATGTCCCAGACAT-GTC
1 -CATGTCCCAGACAT-GTCTAACACTAGCACAACTCTAAGCCGATGCCATGTCCCAGACATGGTC
* *
12654994 TTACACTAGCT-T-AT-GTCTCGAGGCCGATG
64 TTACACTAGCTCTCATAATAT---GGCCGATG
* * *
12655023 CATGTCCCAGACATGTCTAACGCTGGCAC-TCGTCTCAATGCCGATGCCATGTCCCAGACATGGT
1 CATGTCCCAGACATGTCTAACACTAGCACAAC-TCT-AA-GCCGATGCCATGTCCCAGACATGGT
*
12655087 CTTACACTGGCTCTCATAATATGGCCGATG
63 CTTACACTAGCTCTCATAATATGGCCGATG
* * *
12655117 CATGTCCCACACATGCCTTACACT
1 CATGTCCCAGACATGTCTAACACT
12655141 GGCATACAAC
Statistics
Matches: 169, Mismatches: 28, Indels: 28
0.75 0.12 0.12
Matches are distributed among these distances:
89 1 0.01
90 17 0.10
91 15 0.09
92 11 0.07
93 16 0.09
94 60 0.36
95 15 0.09
96 5 0.03
97 3 0.02
98 26 0.15
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (92 bp):
CATGTCCCAGACATGTCTAACACTAGCACAACTCTAAGCCGATGCCATGTCCCAGACATGGTCTT
ACACTAGCTCTCATAATATGGCCGATG
Found at i:12659204 original size:23 final size:23
Alignment explanation
Indices: 12659174--12659221 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
12659164 TAAAATAGTA
* *
12659174 GAGAGAATTGAGAGAATATGATT
1 GAGAGAATTGAAAGAATAGGATT
12659197 GAGAGAATTGAAAGAATAGGATT
1 GAGAGAATTGAAAGAATAGGATT
12659220 GA
1 GA
12659222 ATGAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (23 bp):
GAGAGAATTGAAAGAATAGGATT
Found at i:12659244 original size:38 final size:38
Alignment explanation
Indices: 12659202--12659279 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
12659192 TGATTGAGAG
12659202 AATTGAAAGAATAGGATTGAATGAAGAAAAAAGAAAAT
1 AATTGAAAGAATAGGATTGAATGAAGAAAAAAGAAAAT
12659240 AATTGAAAGAATAGGATTGAATGAAGAAAAAAGAAAAT
1 AATTGAAAGAATAGGATTGAATGAAGAAAAAAGAAAAT
12659278 AA
1 AA
12659280 GTAGGGTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (38 bp):
AATTGAAAGAATAGGATTGAATGAAGAAAAAAGAAAAT
Found at i:12663410 original size:27 final size:28
Alignment explanation
Indices: 12663378--12663436 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
12663368 AATCGTCATG
*
12663378 TTATAAAAGTTTTATAATA-AT-ATTTAT
1 TTATAAAAG-GTTATAATACATAATTTAT
*
12663405 TTATAAAAGGTTATGATACATAATTTAT
1 TTATAAAAGGTTATAATACATAATTTAT
12663433 TTAT
1 TTAT
12663437 GTTTCCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.25
27 11 0.39
28 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (28 bp):
TTATAAAAGGTTATAATACATAATTTAT
Found at i:12664037 original size:104 final size:104
Alignment explanation
Indices: 12663928--12664118 Score: 319
Period size: 104 Copynumber: 1.8 Consensus size: 104
12663918 GTTGTTCTAA
* * * * *
12663928 AAAAATATTTCCTATAGCATAAAAAACGTTGAGTCATATTGACATATTGAGTATTTTATAATTTC
1 AAAAATATTTCCCACAGCATAAAAAACGTTGAGTCATACTGACATATTGAATATCTTATAATTTC
12663993 AATCATAGGTAAAATTGAGATGATTCATACTTCAAATCT
66 AATCATAGGTAAAATTGAGATGATTCATACTTCAAATCT
*
12664032 AAAAATATTTCCCACAGCATAAAAAATGTTGAGTCATACTGACATATTGAATATCTTATAATTTC
1 AAAAATATTTCCCACAGCATAAAAAACGTTGAGTCATACTGACATATTGAATATCTTATAATTTC
*
12664097 AATCATAGGTAGAATTGAGATG
66 AATCATAGGTAAAATTGAGATG
12664119 GCCTATACTT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 80 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (104 bp):
AAAAATATTTCCCACAGCATAAAAAACGTTGAGTCATACTGACATATTGAATATCTTATAATTTC
AATCATAGGTAAAATTGAGATGATTCATACTTCAAATCT
Found at i:12666034 original size:18 final size:18
Alignment explanation
Indices: 12666007--12666099 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
12665997 TACGACCGTT
12666007 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12666025 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12666043 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12666061 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12666079 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
12666097 TAC
1 TAC
12666100 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:12679556 original size:14 final size:14
Alignment explanation
Indices: 12679537--12679571 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12679527 CTAAAAATAC
12679537 TATAAATTTGTAAA
1 TATAAATTTGTAAA
12679551 TATAAATTTGTAAA
1 TATAAATTTGTAAA
*
12679565 TTTAAAT
1 TATAAAT
12679572 ATGAATTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (14 bp):
TATAAATTTGTAAA
Found at i:12680364 original size:29 final size:30
Alignment explanation
Indices: 12680310--12680374 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
12680300 TTTAATATAT
*
12680310 AATTGTATACATAAATTTTAATTTTG-TAC
1 AATTTTATACATAAATTTTAATTTTGATAC
* *
12680339 AATTTTATACATGAAATTTTGA-TTTGATTC
1 AATTTTATACAT-AAATTTTAATTTTGATAC
12680369 AATTTT
1 AATTTT
12680375 TATAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (30 bp):
AATTTTATACATAAATTTTAATTTTGATAC
Found at i:12682036 original size:38 final size:38
Alignment explanation
Indices: 12681985--12682062 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
12681975 GTATGAACAT
*
12681985 TATGTGACGTATACATTTAATCGCCATTAGAGATTTAA
1 TATGTGACGTATACATTTAACCGCCATTAGAGATTTAA
*
12682023 TATGTGACGTATACATTTAACCGCTATTAGAGATTTAA
1 TATGTGACGTATACATTTAACCGCCATTAGAGATTTAA
12682061 TA
1 TA
12682063 GTTCTATGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (38 bp):
TATGTGACGTATACATTTAACCGCCATTAGAGATTTAA
Found at i:12691782 original size:49 final size:49
Alignment explanation
Indices: 12691725--12691820 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
12691715 GCGATTTTCT
* ** *
12691725 TCCCTTCTTATAAAATGAGACTGTCGGAGTCGCGCGATATATAATTTAA
1 TCCCTTCTTATAAAATGAGACCGGAGGAGTCGCGCGATACATAATTTAA
12691774 TCCCTTCTTATAAAATGAGACCGGAGGAGTCGCGCGATACATAATTT
1 TCCCTTCTTATAAAATGAGACCGGAGGAGTCGCGCGATACATAATTT
12691821 TATCTCCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (49 bp):
TCCCTTCTTATAAAATGAGACCGGAGGAGTCGCGCGATACATAATTTAA
Found at i:12695611 original size:23 final size:23
Alignment explanation
Indices: 12695563--12695644 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
12695553 TTAAAGGACC
*
12695563 TTAGCGCTCTCCGATTATTAGCATA
1 TTAGTGCTCTCC-ATT-TTAGCATA
*
12695588 TTAGTGCTCTCCATTGTAGCATA
1 TTAGTGCTCTCCATTTTAGCATA
*
12695611 TTAGTGCTCTCCATTTTAGCACA
1 TTAGTGCTCTCCATTTTAGCATA
*
12695634 TTCGTGCTCTC
1 TTAGTGCTCTC
12695645 TGTATAGCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
23 38 0.73
24 3 0.06
25 11 0.21
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.39
Consensus pattern (23 bp):
TTAGTGCTCTCCATTTTAGCATA
Found at i:12704701 original size:28 final size:30
Alignment explanation
Indices: 12704651--12704715 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
12704641 TATTTCAAGC
** *
12704651 TCAATTTCAGTCAATATTTTTCAATATCAA
1 TCAATTTCAGTCAATATCATTCAATAACAA
*
12704681 TCAATTT-A-TCAATATCATTCAGTAACAA
1 TCAATTTCAGTCAATATCATTCAATAACAA
12704709 TCAATTT
1 TCAATTT
12704716 TTCACTAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 23 0.74
29 1 0.03
30 7 0.23
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (30 bp):
TCAATTTCAGTCAATATCATTCAATAACAA
Found at i:12704773 original size:36 final size:36
Alignment explanation
Indices: 12704694--12704776 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
12704684 ATTTATCAAT
* * *
12704694 ATCATTCAGTAACAATCAATTTTTCACTAGCAATTA
1 ATCATTCAGTAACAATCAATTATTCACTAACAATCA
* * * *
12704730 GTTATTCAGTAACAATCAATTATTCAGTAACAGTCA
1 ATCATTCAGTAACAATCAATTATTCACTAACAATCA
12704766 ATCATTCAGTA
1 ATCATTCAGTA
12704777 CCTTTATTCA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (36 bp):
ATCATTCAGTAACAATCAATTATTCACTAACAATCA
Found at i:12704774 original size:18 final size:18
Alignment explanation
Indices: 12704694--12704776 Score: 85
Period size: 18 Copynumber: 4.6 Consensus size: 18
12704684 ATTTATCAAT
12704694 ATCATTCAGTAACAATCA
1 ATCATTCAGTAACAATCA
** * * *
12704712 ATTTTTCACTAGCAATTA
1 ATCATTCAGTAACAATCA
* *
12704730 GTTATTCAGTAACAATCA
1 ATCATTCAGTAACAATCA
* *
12704748 ATTATTCAGTAACAGTCA
1 ATCATTCAGTAACAATCA
12704766 ATCATTCAGTA
1 ATCATTCAGTA
12704777 CCTTTATTCA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (18 bp):
ATCATTCAGTAACAATCA
Found at i:12704983 original size:43 final size:44
Alignment explanation
Indices: 12704929--12705019 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 44
12704919 TCGAAGTAAC
*
12704929 AGTAGCAGTACGACACACATTGTGCCTCATCGACTCGAA-GTCGA
1 AGTAGCAGTACGACACACATAGTGCCTCATCGACTC-AAGGTCGA
**
12704973 AGTA-CAGTACGACACTTATAGTGCCTCATCGACTCAAGGTCGA
1 AGTAGCAGTACGACACACATAGTGCCTCATCGACTCAAGGTCGA
12705016 AGTA
1 AGTA
12705020 TCCCTGAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 2 0.05
43 37 0.86
44 4 0.09
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (44 bp):
AGTAGCAGTACGACACACATAGTGCCTCATCGACTCAAGGTCGA
Found at i:12706394 original size:15 final size:15
Alignment explanation
Indices: 12706344--12706397 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
12706334 TTTATTCATT
12706344 AATATAATAAT-AT-
1 AATATAATAATAATA
12706357 AATATCAAT--TAATTA
1 AATAT-AATAATAA-TA
12706372 AATAATAATAATAATA
1 AAT-ATAATAATAATA
12706388 AATATAATAA
1 AATATAATAA
12706398 ATATATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
12 1 0.03
13 6 0.18
14 4 0.12
15 13 0.38
16 7 0.21
17 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAATAATAATA
Found at i:12706398 original size:9 final size:9
Alignment explanation
Indices: 12706344--12706402 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
12706334 TTTATTCATT
12706344 AATATAAT-
1 AATATAATA
12706352 AATATAATA
1 AATATAATA
*
12706361 TCAAT-TAATT
1 --AATATAATA
12706371 AA-ATAAT-
1 AATATAATA
12706378 AATAATAATA
1 AAT-ATAATA
12706388 AATATAATA
1 AATATAATA
12706397 AATATA
1 AATATA
12706403 TATTTAATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
7 2 0.05
8 14 0.33
9 17 0.40
10 7 0.16
11 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AATATAATA
Found at i:12706449 original size:15 final size:17
Alignment explanation
Indices: 12706420--12706451 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12706410 TAAAAAAATG
12706420 CATATATTACAATTGTT
1 CATATATTACAATTGTT
12706437 CATATA-TAC-ATTGTT
1 CATATATTACAATTGTT
12706452 ACATTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.47
Consensus pattern (17 bp):
CATATATTACAATTGTT
Found at i:12711293 original size:3 final size:3
Alignment explanation
Indices: 12711285--12711337 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
12711275 AACTTAAAAT
*
12711285 TAA TAA TAA TAA TAA TAA TAA T-A TAA -AA CT-A TAC TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA -TAA
12711329 TAA TAA TAA
1 TAA TAA TAA
12711338 AATCTTAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
2 5 0.12
3 35 0.81
4 3 0.07
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12717163 original size:51 final size:50
Alignment explanation
Indices: 12716976--12717213 Score: 221
Period size: 50 Copynumber: 4.8 Consensus size: 50
12716966 AGCCGAAACT
* * * *
12716976 ATCTGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCGAACC
* * * * **
12717025 ATCCGGTATACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACC
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCGAACC
* * * *
12717075 ATCTGATACACGTAGTAGTCTGCACTTAGTACTACACACGTGATCGAAGTC
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCGAA-CC
* * * * **
12717126 AT-TGAGTACGCATAGTAACCTGCACTTAGTACTACACATGCGACTTAA-C
1 ATCTGA-TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCGAACC
* * *
12717175 AGTATGGTACACACAGTAGCCTGCACTTAGTACTACACA
1 A-TCTGATACACATAGTAGCCTGCACTTAGTACTACACA
12717214 TGTGTATTCA
Statistics
Matches: 154, Mismatches: 30, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
49 40 0.26
50 76 0.49
51 38 0.25
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCGAACC
Found at i:12717253 original size:15 final size:15
Alignment explanation
Indices: 12717233--12717262 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12717223 ACAATGGGTC
12717233 ATTCGTATTGTTCCT
1 ATTCGTATTGTTCCT
12717248 ATTCGTATTGTTCCT
1 ATTCGTATTGTTCCT
12717263 GTTCCGAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (15 bp):
ATTCGTATTGTTCCT
Found at i:12720006 original size:20 final size:20
Alignment explanation
Indices: 12719976--12720030 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
12719966 ATTATTTAGT
*
12719976 CTAGAATTAGGTGGTAAAAA
1 CTAGGATTAGGTGGTAAAAA
*
12719996 TTAGGATTAGGTGGTAAAAA
1 CTAGGATTAGGTGGTAAAAA
12720016 CTAGGATTAGGTGGT
1 CTAGGATTAGGTGGT
12720031 CGGTTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.31, T:0.29
Consensus pattern (20 bp):
CTAGGATTAGGTGGTAAAAA
Found at i:12720070 original size:18 final size:18
Alignment explanation
Indices: 12720047--12720085 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12720037 TTAAATAACT
12720047 TAAAAT-GAACTTTAAAAA
1 TAAAATCGAA-TTTAAAAA
*
12720065 TAAAATCGAATTTGAAAA
1 TAAAATCGAATTTAAAAA
12720083 TAA
1 TAA
12720086 TTAAGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (18 bp):
TAAAATCGAATTTAAAAA
Found at i:12722345 original size:12 final size:13
Alignment explanation
Indices: 12722330--12722367 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
12722320 GTCATATAAA
12722330 AATTA-TTAATAT
1 AATTATTTAATAT
12722342 AATTTATTTAATA-
1 AA-TTATTTAATAT
12722355 AATTATTTAATAT
1 AATTATTTAATAT
12722368 TTCAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.52
13 5 0.22
14 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTATTTAATAT
Found at i:12722483 original size:34 final size:33
Alignment explanation
Indices: 12722426--12722490 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
12722416 TATTATTCAA
* *
12722426 TTATTCAATATTAAATCTTTTAATAATAAATAT
1 TTATTCAATATTAAATATATTAATAATAAATAT
*
12722459 TTATTACAATTTTAAATATATTAATAATAAAT
1 TTATT-CAATATTAAATATATTAATAATAAAT
12722491 GTTTTGTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (33 bp):
TTATTCAATATTAAATATATTAATAATAAATAT
Found at i:12722989 original size:15 final size:14
Alignment explanation
Indices: 12722951--12722989 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12722941 TCAGGAAAAT
*
12722951 AAGTCATTTTCTAG
1 AAGTCATTTTTTAG
* *
12722965 AAATCATTTTTCAG
1 AAGTCATTTTTTAG
12722979 AAGTCATTTTT
1 AAGTCATTTTT
12722990 AGTGAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (14 bp):
AAGTCATTTTTTAG
Found at i:12723497 original size:12 final size:13
Alignment explanation
Indices: 12723469--12723510 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
12723459 CACCTTCCAC
*
12723469 AATTTTTTTGCAT
1 AATTTTTTTTCAT
12723482 AATTTTTTTTCA-
1 AATTTTTTTTCAT
*
12723494 AATTGTTTTTTAAT
1 AATT-TTTTTTCAT
12723508 AAT
1 AAT
12723511 AAAAATCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.16
13 18 0.72
14 3 0.12
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (13 bp):
AATTTTTTTTCAT
Found at i:12727217 original size:10 final size:10
Alignment explanation
Indices: 12727202--12727251 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
12727192 TAATTTTATG
12727202 ATTTAT-TTT
1 ATTTATCTTT
12727211 CATTTATCTTT
1 -ATTTATCTTT
12727222 ATTTATCTTT
1 ATTTATCTTT
12727232 ATTTAT-TTGT
1 ATTTATCTT-T
12727242 ATTTATCTTT
1 ATTTATCTTT
12727252 TAGAATTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.05
10 30 0.81
11 5 0.14
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.70
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:12731061 original size:15 final size:15
Alignment explanation
Indices: 12731043--12731089 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
12731033 TTTTCTTAAT
12731043 TTTTATTATTTATTA
1 TTTTATTATTTATTA
12731058 --TT-TTA-TT-TTA
1 TTTTATTATTTATTA
12731068 TTTTATTATTTATTA
1 TTTTATTATTTATTA
12731083 TTTTATT
1 TTTTATT
12731090 TTAGTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
10 3 0.11
11 2 0.07
12 5 0.19
13 5 0.19
14 2 0.07
15 10 0.37
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTATTTATTA
Found at i:12731065 original size:5 final size:5
Alignment explanation
Indices: 12731055--12731092 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
12731045 TTATTATTTA
*
12731055 TTATT TTATT TTATT TTATT ATT-TA TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT -TTATT TTATT TTATT TTA
12731093 GTTATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 2 0.07
5 25 0.86
6 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:12731065 original size:12 final size:12
Alignment explanation
Indices: 12731048--12731090 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
12731038 TTAATTTTTA
12731048 TTATTTATTATT
1 TTATTTATTATT
12731060 TTATTTTATT-TT
1 TTA-TTTATTATT
12731072 ATTATTTATTATT
1 -TTATTTATTATT
12731085 TTATTT
1 TTATTT
12731091 TAGTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTATTATT
Found at i:12731071 original size:25 final size:25
Alignment explanation
Indices: 12731043--12731092 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12731033 TTTTCTTAAT
12731043 TTTTATTATTTATTATTTTATTTTA
1 TTTTATTATTTATTATTTTATTTTA
12731068 TTTTATTATTTATTATTTTATTTTA
1 TTTTATTATTTATTATTTTATTTTA
12731093 GTTATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTATTATTTATTATTTTATTTTA
Found at i:12732895 original size:23 final size:24
Alignment explanation
Indices: 12732851--12732896 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
12732841 ATTTTAATTA
*
12732851 TTTAGGATTTTTATTTAGATTTAAT
1 TTTAGGA-TTTTATTTACATTTAAT
*
12732876 TTTAGGA-TTTATTTTCATTTA
1 TTTAGGATTTTATTTACATTTA
12732897 TCCTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
25 7 0.37
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (24 bp):
TTTAGGATTTTATTTACATTTAAT
Found at i:12732917 original size:10 final size:10
Alignment explanation
Indices: 12732882--12732941 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
12732872 TAATTTTAGG
12732882 ATTTAT-TTT
1 ATTTATCTTT
12732891 CATTTATCCTTT
1 -ATTTAT-CTTT
12732903 -TTTATCTTT
1 ATTTATCTTT
* *
12732912 AATTATATTT
1 ATTTATCTTT
12732922 ATTTAT-TTGT
1 ATTTATCTT-T
12732932 ATTTATCTTT
1 ATTTATCTTT
12732942 TAGAATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
9 6 0.14
10 31 0.74
11 2 0.05
12 3 0.07
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:12738946 original size:20 final size:23
Alignment explanation
Indices: 12738904--12738946 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
12738894 ATACTCTTAC
*
12738904 ATTATATTATATTGTATATAAAA
1 ATTATATTATATTGTATAGAAAA
12738927 ATTATA-TAT-TTGTAT-GAAAA
1 ATTATATTATATTGTATAGAAAA
12738947 TATAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 3 0.16
23 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (23 bp):
ATTATATTATATTGTATAGAAAA
Found at i:12742195 original size:2 final size:2
Alignment explanation
Indices: 12742188--12742213 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12742178 TAGTTTCTCA
12742188 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
12742214 TTTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12742708 original size:31 final size:32
Alignment explanation
Indices: 12742649--12742708 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
12742639 AAAATTTATG
* *
12742649 ATTTTTAGTAATTTTTAGATATTCTTTTACCA
1 ATTTTAAGTAATTTTTAGATATTATTTTACCA
12742681 ATTTTAAG-AATTTTTAAGA-ATTATTTTA
1 ATTTTAAGTAATTTTT-AGATATTATTTTA
12742709 AAGCTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (32 bp):
ATTTTAAGTAATTTTTAGATATTATTTTACCA
Found at i:12743962 original size:66 final size:67
Alignment explanation
Indices: 12743887--12744029 Score: 198
Period size: 66 Copynumber: 2.1 Consensus size: 67
12743877 CATTTCTTTG
* * **
12743887 CAAATTTTTAGTATTGTATTGAAATCATCATGGTAACTATATT-GAATCACCATCCATTTGCATT
1 CAAAATTTTAGTATTGTATTGAAATCACCATGAAAACTATATTAGAATCACCATCCATTTGCATT
12743951 TA
66 TA
* * * * *
12743953 TAAAATTTTAGTATTGTATTGGAATCACCCTGAAAACTATATTAGAATCACTATTCATTTGCATT
1 CAAAATTTTAGTATTGTATTGAAATCACCATGAAAACTATATTAGAATCACCATCCATTTGCATT
12744018 TA
66 TA
12744020 CAAAATTTTA
1 CAAAATTTTA
12744030 ATACTGTAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
66 36 0.55
67 30 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (67 bp):
CAAAATTTTAGTATTGTATTGAAATCACCATGAAAACTATATTAGAATCACCATCCATTTGCATT
TA
Found at i:12743964 original size:104 final size:105
Alignment explanation
Indices: 12743782--12743976 Score: 284
Period size: 104 Copynumber: 1.9 Consensus size: 105
12743772 ATATTGGTTA
* * * * ** *
12743782 CAAAATTTTAGTATTGTATTGGAATCATCATGGTAATTGTTTTAGAATCATTATTCATTTGCATT
1 CAAAATTTTAGTATTGTATTGAAATCATCATGGTAACTATATTAGAATCACCATCCATTTGCATT
*
12743847 TGCAAAATCTTAGTATTGTATTGGAAATACCATTTCTTTG
66 TACAAAATCTTAGTATTGTATTGGAAATACCATTTCTTTG
*
12743887 CAAATTTTTAGTATTGTATTGAAATCATCATGGTAACTATATT-GAATCACCATCCATTTGCATT
1 CAAAATTTTAGTATTGTATTGAAATCATCATGGTAACTATATTAGAATCACCATCCATTTGCATT
* *
12743951 TATAAAATTTTAGTATTGTATTGGAA
66 TACAAAATCTTAGTATTGTATTGGAA
12743977 TCACCCTGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
104 41 0.52
105 38 0.48
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (105 bp):
CAAAATTTTAGTATTGTATTGAAATCATCATGGTAACTATATTAGAATCACCATCCATTTGCATT
TACAAAATCTTAGTATTGTATTGGAAATACCATTTCTTTG
Found at i:12746274 original size:27 final size:27
Alignment explanation
Indices: 12746210--12746275 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
12746200 ATAGCCCTTG
* *
12746210 TGGCAAACTCCGAAAGAATGGCCTTTA
1 TGGCGAACTCTGAAAGAATGGCCTTTA
* *
12746237 TGGCGAACTCTGAAAGGATGGTCTTTA
1 TGGCGAACTCTGAAAGAATGGCCTTTA
*
12746264 TGGTGAACTCTG
1 TGGCGAACTCTG
12746276 TGTTAACTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (27 bp):
TGGCGAACTCTGAAAGAATGGCCTTTA
Found at i:12747898 original size:42 final size:42
Alignment explanation
Indices: 12747835--12747949 Score: 162
Period size: 42 Copynumber: 2.7 Consensus size: 42
12747825 CTTCGTTTTC
* * *
12747835 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCA-CATAA
1 TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCATC-T-A
*
12747878 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATCTA
1 TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCATCTA
12747919 TCGATGCCATAGTCCAGCTATGGTCTTACAC
1 TCGATGCCATAGTCCAGCTATGGTCTTACAC
12747950 GAATCACATA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
41 2 0.03
42 61 0.94
43 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCATCTA
Found at i:12748091 original size:47 final size:47
Alignment explanation
Indices: 12747920--12748093 Score: 244
Period size: 47 Copynumber: 3.7 Consensus size: 47
12747910 ATTCATCTAT
* * * * *
12747920 CGATGCCATAGT-CCAGCTATGGTCTTACAC-GAATCACATATCTCAC
1 CGATGCCATA-TCCCAGATATGGTCTTATACGGAAGCATATATCACAC
* * *
12747966 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACGGAAGCATATATCACAC
12748013 CGATGCCATATCCCAGATATGGTCTTATACGGAAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACGGAAGCATATATCACAC
*
12748060 CGATGCCATATCCCAAATATGGTCTTATACGGAA
1 CGATGCCATATCCCAGATATGGTCTTATACGGAA
12748094 ATCACTTGTC
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 25 0.22
47 89 0.77
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTATACGGAAGCATATATCACAC
Found at i:12748143 original size:31 final size:31
Alignment explanation
Indices: 12748108--12748318 Score: 368
Period size: 31 Copynumber: 6.8 Consensus size: 31
12748098 CTTGTCACTT
*
12748108 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
12748139 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
12748170 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
12748201 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
12748232 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
12748263 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
12748294 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
12748319 TGTCATTTGT
Statistics
Matches: 174, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 174 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:12748400 original size:50 final size:51
Alignment explanation
Indices: 12748294--12748422 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
12748284 CACTGATCAG
* * *
12748294 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
12748345 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
12748395 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
12748423 TGCCATGGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:12754072 original size:14 final size:14
Alignment explanation
Indices: 12754053--12754082 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12754043 TATCTTATAA
12754053 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
12754067 ATATGCGTTAATCT
1 ATATGCGTGAATCT
12754081 AT
1 AT
12754083 CTTGAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:12761082 original size:62 final size:62
Alignment explanation
Indices: 12761000--12761154 Score: 274
Period size: 62 Copynumber: 2.5 Consensus size: 62
12760990 GGAATTGACG
* * *
12761000 GTAAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGTCCTCCCGAAGAATATGT
1 GTAAAATGGATTTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGT
12761062 GTAAAATGGATTTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGT
1 GTAAAATGGATTTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGT
*
12761124 GTAAAATGGATTTAGCCCGGACGGGTAATCC
1 GTAAAATGGATTTAGCCCGGACGGGTGATCC
12761155 GAATTAGGGT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 89 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (62 bp):
GTAAAATGGATTTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGT
Found at i:12761932 original size:14 final size:14
Alignment explanation
Indices: 12761913--12761942 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12761903 TATCTTATAA
12761913 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
12761927 ATATGCGTTAATCT
1 ATATGCGTGAATCT
12761941 AT
1 AT
12761943 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:12765151 original size:12 final size:13
Alignment explanation
Indices: 12765134--12765162 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12765124 CTCATATCTC
12765134 AATTTCAATTCA-
1 AATTTCAATTCAT
12765146 AATTTCAATTCAT
1 AATTTCAATTCAT
12765159 AATT
1 AATT
12765163 CCACTTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTTCAATTCAT
Found at i:12765155 original size:18 final size:19
Alignment explanation
Indices: 12765117--12765155 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
12765107 TGGTTCAAGC
*
12765117 TTTCAATCTCATATCTCAA
1 TTTCAATCTCAAATCTCAA
*
12765136 TTTCAAT-TCAAATTTCAA
1 TTTCAATCTCAAATCTCAA
12765154 TT
1 TT
12765156 CATAATTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCAAATCTCAA
Found at i:12765302 original size:23 final size:23
Alignment explanation
Indices: 12765271--12765339 Score: 129
Period size: 23 Copynumber: 3.0 Consensus size: 23
12765261 ATACATGGAT
12765271 TCCAACCAAACACACCAGAATGA
1 TCCAACCAAACACACCAGAATGA
*
12765294 TCCACCCAAACACACCAGAATGA
1 TCCAACCAAACACACCAGAATGA
12765317 TCCAACCAAACACACCAGAATGA
1 TCCAACCAAACACACCAGAATGA
12765340 CACCCAGTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.46, C:0.36, G:0.09, T:0.09
Consensus pattern (23 bp):
TCCAACCAAACACACCAGAATGA
Found at i:12765490 original size:17 final size:17
Alignment explanation
Indices: 12765448--12765490 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
12765438 ATTCCAATTC
*
12765448 TCAATTCAATTTCACTT
1 TCAATTCAAATTCACTT
12765465 TC-ATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
12765482 TCAATTCAA
1 TCAATTCAA
12765491 TATACAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:12765493 original size:23 final size:23
Alignment explanation
Indices: 12765449--12765502 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
12765439 TTCCAATTCT
*
12765449 CAATTCAATTTCACTTTCATAT-
1 CAATTCAATTTCACATTCATATA
*
12765471 CAAATTCACTTTCA-ATTCAATATA
1 C-AATTCAATTTCACATTC-ATATA
12765495 CAATTCAA
1 CAATTCAA
12765503 CTCAATACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 4 0.15
23 21 0.81
24 1 0.04
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (23 bp):
CAATTCAATTTCACATTCATATA
Found at i:12766291 original size:16 final size:15
Alignment explanation
Indices: 12766272--12766327 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
12766262 GAATGGTCTC
12766272 TGTTTCTTTTCTTCTT
1 TGTTTCTTTT-TTCTT
12766288 TGTTTCTTTATTTCTT
1 TGTTTCTTT-TTTCTT
*
12766304 T-TATTC-TTTTACTT
1 TGT-TTCTTTTTTCTT
*
12766318 TATTTCTTTT
1 TGTTTCTTTT
12766328 ATGTATTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 9 0.26
15 7 0.20
16 18 0.51
17 1 0.03
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.75
Consensus pattern (15 bp):
TGTTTCTTTTTTCTT
Found at i:12772005 original size:11 final size:11
Alignment explanation
Indices: 12771984--12772017 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12771974 TCAATTTCCC
12771984 CCTTTTTCTTT
1 CCTTTTTCTTT
* *
12771995 TCTTTTCCTTT
1 CCTTTTTCTTT
12772006 CCTTTTTCTTT
1 CCTTTTTCTTT
12772017 C
1 C
12772018 TCCATATTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
CCTTTTTCTTT
Found at i:12772086 original size:17 final size:18
Alignment explanation
Indices: 12772064--12772102 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
12772054 TTTCTTTCTT
*
12772064 TTTATTCTTTTA-GTTTC
1 TTTATTCTTTTATGTTTA
12772081 TTTATTCTTTTATGTTTA
1 TTTATTCTTTTATGTTTA
12772099 TTTA
1 TTTA
12772103 CTTTATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTATTCTTTTATGTTTA
Found at i:12772115 original size:23 final size:23
Alignment explanation
Indices: 12772072--12772115 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12772062 TTTTTATTCT
**
12772072 TTTAGTTTCTTTATTCTTTTATG
1 TTTAGTTTCTTTATTAATTTATG
12772095 TTTA-TTTACTTTATTAATTTA
1 TTTAGTTT-CTTTATTAATTTA
12772116 ATAATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTAGTTTCTTTATTAATTTATG
Found at i:12772152 original size:18 final size:17
Alignment explanation
Indices: 12772106--12772160 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
12772096 TTATTTACTT
12772106 TATTAATTTAATAAT-AA
1 TATT-ATTTAATAATAAA
12772123 TAATT-TTT-ATAATAAA
1 T-ATTATTTAATAATAAA
*
12772139 TATCTATTTAATAACAAA
1 TAT-TATTTAATAATAAA
12772157 TATT
1 TATT
12772161 TATATTACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
15 7 0.22
16 7 0.22
17 5 0.16
18 13 0.41
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTATTTAATAATAAA
Found at i:12778823 original size:20 final size:19
Alignment explanation
Indices: 12778798--12778841 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12778788 CGAAAAATGA
12778798 TTTCTAAAAAATAATTTATT
1 TTTCT-AAAAATAATTTATT
* *
12778818 TTTCTAGAAATAATTTGTT
1 TTTCTAAAAATAATTTATT
12778837 TTTCT
1 TTTCT
12778842 GGTGTTTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTCTAAAAATAATTTATT
Found at i:12778936 original size:28 final size:29
Alignment explanation
Indices: 12778894--12778959 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
12778884 GGAAAAGTTG
* *
12778894 TTTTTACATATATTTATATTTTAAATTAT
1 TTTTTACATAAATTTATACTTTAAATTAT
*
12778923 TTTTTA-ATAAATTTATACTTTAAATT-G
1 TTTTTACATAAATTTATACTTTAAATTAT
12778950 TTTTTACATA
1 TTTTTACATA
12778960 TACTGCAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 6 0.18
28 21 0.64
29 6 0.18
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTTACATAAATTTATACTTTAAATTAT
Found at i:12780243 original size:21 final size:21
Alignment explanation
Indices: 12780219--12780260 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12780209 TCAATATCAT
12780219 TATCCAACCA-AATAAATTCAA
1 TATCCAA-CATAATAAATTCAA
*
12780240 TATCTAACATAATAAATTCAA
1 TATCCAACATAATAAATTCAA
12780261 CAAGCTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (21 bp):
TATCCAACATAATAAATTCAA
Found at i:12780294 original size:21 final size:21
Alignment explanation
Indices: 12780229--12780294 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
12780219 TATCCAACCA
12780229 AATAAATTCAATATCTAACAT
1 AATAAATTCAATATCTAACAT
* *
12780250 AATAAATTCAACAAGCTTAAAACAT
1 AATAAATTCAA-TATC-T--AACAT
*
12780275 AATAAATTTAATATCTAACA
1 AATAAATTCAATATCTAACA
12780295 AATTCAAGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 15 0.42
22 2 0.06
23 2 0.06
24 2 0.06
25 15 0.42
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAAATTCAATATCTAACAT
Found at i:12782368 original size:18 final size:16
Alignment explanation
Indices: 12782345--12782388 Score: 63
Period size: 15 Copynumber: 2.7 Consensus size: 16
12782335 GTATTTTGGC
12782345 ATATATTTTGCTATGAT
1 ATATATTTTGCTAT-AT
12782362 AATATATTTTG-TATAT
1 -ATATATTTTGCTATAT
12782378 ATATATTTTGC
1 ATATATTTTGC
12782389 ATAAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
16 2 0.08
17 3 0.12
18 10 0.40
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (16 bp):
ATATATTTTGCTATAT
Found at i:12782923 original size:15 final size:17
Alignment explanation
Indices: 12782892--12782932 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
12782882 GGCCATGTAG
12782892 TTTTTT-TTATATCATA
1 TTTTTTGTTATATCATA
12782908 TTTTTTGTTAT-T-ATA
1 TTTTTTGTTATATCATA
*
12782923 TGTTTTGTTA
1 TTTTTTGTTA
12782933 ACTTCTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 12 0.52
16 7 0.30
17 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (17 bp):
TTTTTTGTTATATCATA
Found at i:12783618 original size:130 final size:132
Alignment explanation
Indices: 12783461--12783748 Score: 377
Period size: 130 Copynumber: 2.2 Consensus size: 132
12783451 AGATTTGATA
12783461 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAAT
1 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAAT
** * *
12783526 CGAATATCACTTCAAAATTTCACTCATATCTT-TTAAAATCCCTT-AAACGAAGGCGATATGCGA
66 AAAATATCACTTCAAAATTTCACTCAGATCTTCTAAAAATCCCTTAAAACGAAGGCGATATGCGA
12783589 TT
131 TT
* * * * * *
12783591 TTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGTTTAAAATAAT
1 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAAT
* * * **
12783656 AAAATATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTAAAACGAAGGTAATACT-CG
66 AAAATATCACTTCAAAATTTCACTCAGATCTTCTAAAAATCCCTTAAAACGAAGGCGATA-TGCG
* *
12783720 GTG
130 ATT
*
12783723 TTTGACAATTCG-GGAATCATGCCCTA
1 TTTGGCAATTCGCGGAATCATGCCCTA
12783749 TCATGCTTGG
Statistics
Matches: 136, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
130 86 0.63
131 23 0.17
132 26 0.19
133 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (132 bp):
TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAAT
AAAATATCACTTCAAAATTTCACTCAGATCTTCTAAAAATCCCTTAAAACGAAGGCGATATGCGA
TT
Found at i:12783769 original size:131 final size:130
Alignment explanation
Indices: 12783461--12783782 Score: 373
Period size: 130 Copynumber: 2.5 Consensus size: 130
12783451 AGATTTGATA
* * * *
12783461 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAAT
1 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGTTTAAAATAAT
** * * * *
12783526 CGAATATCACTTCAAAATTTCACTCATATCTTTTAAAATCCCTTAAACGAAGGCGATATGCGATT
66 AAAATATCACTTCAAAATTTCACTCAGATCTTTAAAAATCCCTTAAACGAAGGCAATATGCGATG
* *
12783591 TTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGTTTAAAATAAT
1 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGTTTAAAATAAT
* * * *
12783656 AAAATATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTAAAACGAAGGTAATACT-CG
66 AAAATATCACTTCAAAATTTCACTCAGATCTT-TAAAAATCCCTT-AAACGAAGGCAATA-TGCG
*
12783720 GTG
128 ATG
* * * **
12783723 TTTGACAATTCG-GGAATCATGCCCTATCATGCTT-GGTTGTGATTTCTCGTTT-TTTCAAAA
1 TTTGGCAATTCGCGGAATCATGCCCTAACGTG-TTGGGTTGCAATTTCTCGTTTGTTT-AAAA
12783783 CAATCGAATA
Statistics
Matches: 164, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
130 89 0.54
131 46 0.28
132 28 0.17
133 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (130 bp):
TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGTTTAAAATAAT
AAAATATCACTTCAAAATTTCACTCAGATCTTTAAAAATCCCTTAAACGAAGGCAATATGCGATG
Found at i:12783793 original size:131 final size:131
Alignment explanation
Indices: 12783461--12783859 Score: 414
Period size: 131 Copynumber: 3.0 Consensus size: 131
12783451 AGATTTGATA
* * **
12783461 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAAT
1 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTTTTCAAAATAAT
* * * * **
12783526 CGAATATCACTTCAAAATTTCACTCATATCTTTTAAAATCCCTT-AAACGAAGGCGATATGCGAT
66 CGAATATCCCTTCAAAATTTCACTCATGTCTTTAAAAATCCTTTAAAACGAAGGTAATATGCGAT
*
12783590 T
131 G
* *
12783591 TTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGTTT-AAAATAA
1 TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCTCGTTT-TTTCAAAATAA
** *
12783655 TAAAATATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTAAAACGAAGGTAATACT-C
65 TCGAATATCCCTTCAAAATTTCACTCATGTCTT-TAAAAATCCTTTAAAACGAAGGTAATA-TGC
*
12783719 GGTG
128 GATG
* * * ** *
12783723 TTTGACAATTCG-GGAATCATGCCCTATCATGCTT-GGTTGTGATTTCTCGTTTTTTCAAAACAA
1 TTTGGCAATTCGCGGAATCATGCCCTAACGTG-TTGGGTTGCAATTTCTCGTTTTTTCAAAATAA
* * ** * * * * *
12783786 TCGAATATTCCTTTAAGTTTTCATTCATGTTTATTAAAAA-CCTTTTAAAACGAAGGTGATGTTC
65 TCGAATATCCCTTCAAAATTTCACTCATGTCT-TTAAAAATCC-TTTAAAACGAAGGTAATATGC
12783850 GATG
128 GATG
12783854 TTTGGC
1 TTTGGC
12783860 GATTTAATAA
Statistics
Matches: 223, Mismatches: 37, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
130 90 0.40
131 103 0.46
132 29 0.13
133 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (131 bp):
TTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTTTTCAAAATAAT
CGAATATCCCTTCAAAATTTCACTCATGTCTTTAAAAATCCTTTAAAACGAAGGTAATATGCGAT
G
Found at i:12794372 original size:132 final size:132
Alignment explanation
Indices: 12794154--12794670 Score: 876
Period size: 132 Copynumber: 3.9 Consensus size: 132
12794144 GAATCCTACC
*
12794154 GATCTCGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCCTGAGATT
1 GATCTCGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCCTAAGATT
* * *
12794219 GCAGTGAAGCAGATTTGAGCCATCACCCTAGCTCCCTAAAGTTTTAGTGGAGTAGGTTCAAATTT
66 GCAGTGAAGCAGATTTAAGCCATCACCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTT
12794284 TA
131 TA
12794286 GATCTCGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCCTAAGATT
1 GATCTCGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCCTAAGATT
12794351 GCAGTGAAGCAGATTTAAGCCATCACCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTT
66 GCAGTGAAGCAGATTTAAGCCATCACCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTT
12794416 TA
131 TA
* * *
12794418 GATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCTTGAGATT
1 GATCTCGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCCTAAGATT
* *
12794483 GTAGTGAAGCAGATTTGAGCCATCACCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTT
66 GCAGTGAAGCAGATTTAAGCCATCACCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTT
12794548 TA
131 TA
* *
12794550 GATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCCTGATG-T
1 GATCTCGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCCT-AAGAT
* * *
12794614 TGCAGTGAAGCATATTTAAGCCATCACACTAGCTCCCTAATA-TTGTAATGGAGTAGG
65 TGCAGTGAAGCAGATTTAAGCCATCACCCTAGCTCCCTAA-AGTTGTAGTGGAGTAGG
12794671 CCGAAGATTG
Statistics
Matches: 366, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
132 364 0.99
133 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (132 bp):
GATCTCGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGTGAATCTAGGCTTCCTAAGATT
GCAGTGAAGCAGATTTAAGCCATCACCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTT
TA
Found at i:12795123 original size:20 final size:20
Alignment explanation
Indices: 12795095--12795144 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
12795085 GCGCGCACCT
* *
12795095 GTACACCAGCTCTCGTACCC
1 GTACGCCAGCTCTCATACCC
12795115 GTACGCCAGCTCTCATACCC
1 GTACGCCAGCTCTCATACCC
*
12795135 GAACGCCAGC
1 GTACGCCAGC
12795145 ACGTCTCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.44, G:0.18, T:0.16
Consensus pattern (20 bp):
GTACGCCAGCTCTCATACCC
Found at i:12796326 original size:18 final size:16
Alignment explanation
Indices: 12796303--12796346 Score: 63
Period size: 15 Copynumber: 2.7 Consensus size: 16
12796293 GTATTTTGGC
12796303 ATATATTTTGCTATGAT
1 ATATATTTTGCTAT-AT
12796320 AATATATTTTG-TATAT
1 -ATATATTTTGCTATAT
12796336 ATATATTTTGC
1 ATATATTTTGC
12796347 ATAAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
16 2 0.08
17 3 0.12
18 10 0.40
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (16 bp):
ATATATTTTGCTATAT
Found at i:12796634 original size:17 final size:17
Alignment explanation
Indices: 12796595--12796643 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
12796585 ACATATCAAT
* *
12796595 ATACTTATTACTTTAAT
1 ATACTTTTTACTTTAAA
* *
12796612 AGACTTTTTATTTTAAA
1 ATACTTTTTACTTTAAA
*
12796629 ATACTTTTTGCTTTA
1 ATACTTTTTACTTTA
12796644 TGATTTTTTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (17 bp):
ATACTTTTTACTTTAAA
Found at i:12796880 original size:15 final size:15
Alignment explanation
Indices: 12796868--12796899 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12796858 GTTTTTTTTA
12796868 TATCATATTTTTTGT
1 TATCATATTTTTTGT
*
12796883 TATCATATGTTTTGT
1 TATCATATTTTTTGT
12796898 TA
1 TA
12796900 ACTTCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.09, T:0.62
Consensus pattern (15 bp):
TATCATATTTTTTGT
Found at i:12796885 original size:17 final size:17
Alignment explanation
Indices: 12796859--12796899 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
12796849 GGTCATGTAG
12796859 TTTTTT-TTATATCATA
1 TTTTTTGTTATATCATA
12796875 TTTTTTG-T-TATCATA
1 TTTTTTGTTATATCATA
*
12796890 TGTTTTGTTA
1 TTTTTTGTTA
12796900 ACTTCTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (17 bp):
TTTTTTGTTATATCATA
Found at i:12797768 original size:21 final size:19
Alignment explanation
Indices: 12797728--12797766 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12797718 ATAGAGCACG
12797728 CGCCCGTGTGCTAGGGACA
1 CGCCCGTGTGCTAGGGACA
12797747 CGCCCGTGTGCTAGGGACA
1 CGCCCGTGTGCTAGGGACA
12797766 C
1 C
12797767 ACTCGTGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.33, G:0.36, T:0.15
Consensus pattern (19 bp):
CGCCCGTGTGCTAGGGACA
Found at i:12797773 original size:19 final size:19
Alignment explanation
Indices: 12797730--12797774 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
12797720 AGAGCACGCG
*
12797730 CCCGTGTGCTAGGGACACG
1 CCCGTGTGCTAGGGACACA
12797749 CCCGTGTGCTAGGGACACA
1 CCCGTGTGCTAGGGACACA
*
12797768 CTCGTGT
1 CCCGTGT
12797775 CCCGAACCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.31, G:0.33, T:0.20
Consensus pattern (19 bp):
CCCGTGTGCTAGGGACACA
Found at i:12800874 original size:131 final size:132
Alignment explanation
Indices: 12800564--12801008 Score: 363
Period size: 131 Copynumber: 3.4 Consensus size: 132
12800554 TGTTACAGGG
* * * * * *
12800564 TTGCAATTT-TGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATATCTTTT-A
1 TTGCAATTTCT-CATTTGTTCAAAACAATCAAATATCCCTCCAAAATTTCACTCATGTCTTTTAA
* * * * * *
12800627 AAATCCCTT-AAACGAAGGCGATATGCGATTTTTGGCAATTCGTGGAATCGTGCCCTATCGTGTT
65 AAATCCTTTAAAACGAAGGCAATATGCGATGTTTGACAATTCGTGGAATCATGCCCTATCGTGCT
*
12800691 GGG
130 GGA
* * * *
12800694 TTGCAATTTCTCGTTTGTTTAAAATAATCAAATATCCCTCCAAAATTTCACTCAGGTCTTTTAAA
1 TTGCAATTTCTCATTTGTTCAAAACAATCAAATATCCCTCCAAAATTTCACTCATGTCTTTTAAA
* *
12800759 AATCCTTTAAAACGAAGGTAATACT-CGGTGTTTGACAATTCG-GGAATCATGCCCTATCGTGCT
66 AATCCTTTAAAACGAAGGCAATA-TGCGATGTTTGACAATTCGTGGAATCATGCCCTATCGTGCT
12800822 GGA
130 GGA
** * * *** *
12800825 TTGTGATTTCTCATTTGTTCAAAACAATCGAATATTCCCT-TAGGTTTTCATTCATGT-TTATTA
1 TTGCAATTTCTCATTTGTTCAAAACAATCAAATA-TCCCTCCAAAATTTCACTCATGTCTT-TTA
* * * * * *
12800888 AAAA-CCTTTTAAAACGAAGGCGATGTTCGATGTTTGGCGATT--TGATAATCGA-GCCCTATCG
64 AAAATCC-TTTAAAACGAAGGCAATATGCGATGTTTGACAATTCGTG-GAATC-ATGCCCTATCG
*
12800949 TGCTGGG
126 TGCTGGA
* * * * * * * * *
12800956 TTGCACTTTTTCATTCGCTCAAAACAATCGAAGATTCCTTCAGAATTTCACTC
1 TTGCAATTTCTCATTTGTTCAAAACAATCAAATATCCCTCCAAAATTTCACTC
12801009 GTATTTTCTA
Statistics
Matches: 254, Mismatches: 49, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
130 62 0.24
131 159 0.63
132 32 0.13
133 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (132 bp):
TTGCAATTTCTCATTTGTTCAAAACAATCAAATATCCCTCCAAAATTTCACTCATGTCTTTTAAA
AATCCTTTAAAACGAAGGCAATATGCGATGTTTGACAATTCGTGGAATCATGCCCTATCGTGCTG
GA
Found at i:12805584 original size:20 final size:20
Alignment explanation
Indices: 12805559--12805596 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12805549 TTATTAGTAG
12805559 AATTGCAGCAAACAACAACA
1 AATTGCAGCAAACAACAACA
12805579 AATTGCAGCAAACAACAA
1 AATTGCAGCAAACAACAA
12805597 ACAGAGGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.24, G:0.11, T:0.11
Consensus pattern (20 bp):
AATTGCAGCAAACAACAACA
Found at i:12806257 original size:28 final size:28
Alignment explanation
Indices: 12806226--12806280 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
12806216 CATTACGATA
12806226 TATATAAATTA-TATTTT-TATTATATAAT
1 TATAT-AATTATTATTTTAT-TTATATAAT
12806254 TATATAATTATTATTTTATTTATATAA
1 TATATAATTATTATTTTATTTATATAA
12806281 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 5 0.20
28 19 0.76
29 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATAATTATTATTTTATTTATATAAT
Found at i:12806264 original size:19 final size:20
Alignment explanation
Indices: 12806226--12806267 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
12806216 CATTACGATA
**
12806226 TATATAAATTATATTTTTAT
1 TATATAAATTATATAATTAT
12806246 TATAT-AATTATATAATTAT
1 TATATAAATTATATAATTAT
12806265 TAT
1 TAT
12806268 TTTATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATAAATTATATAATTAT
Found at i:12806290 original size:28 final size:28
Alignment explanation
Indices: 12806231--12806295 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
12806221 CGATATATAT
* *
12806231 AAATTA-TATTTTTATTATATAATTATA
1 AAATTATTATTTTTATTATATAAATAAA
*
12806258 TAATTATTA-TTTTATTTATATAAATAAA
1 AAATTATTATTTTTA-TTATATAAATAAA
12806286 AAATTTATTA
1 AAA-TTATTA
12806296 ATTAAAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 10 0.32
28 15 0.48
29 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AAATTATTATTTTTATTATATAAATAAA
Done.