Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 91 of 290
Found at i:27965962 original size:16 final size:16
Alignment explanation
Indices: 27965941--27965971 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27965931 CCTTTATTTA
27965941 ATAATACAAAATCATT
1 ATAATACAAAATCATT
*
27965957 ATAATACAAAGTCAT
1 ATAATACAAAATCAT
27965972 AACCGTCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (16 bp):
ATAATACAAAATCATT
Found at i:27970662 original size:47 final size:47
Alignment explanation
Indices: 27970610--27970955 Score: 500
Period size: 47 Copynumber: 7.3 Consensus size: 47
27970600 TGTACAAGTA
* * *
27970610 TATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAA-AGTA
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
27970657 TATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
27970706 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
27970753 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
27970800 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
27970847 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
* *
27970894 TATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAA-GTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATG
*
27970941 TATAAATGTGATAAG
1 TATATATGTGATAAG
27970956 TCCCGAAGGG
Statistics
Matches: 280, Mismatches: 14, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 235 0.84
48 3 0.01
49 40 0.14
50 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
Found at i:27970833 original size:22 final size:22
Alignment explanation
Indices: 27970806--27970927 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
27970796 CATGTGTATG
27970806 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
27970828 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
27970853 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
27970875 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
27970900 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
27970922 TGTGAT
1 TGTGAT
27970928 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:27978430 original size:6 final size:6
Alignment explanation
Indices: 27978412--27978506 Score: 79
Period size: 6 Copynumber: 15.3 Consensus size: 6
27978402 AAGAAATATT
*
27978412 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAGT ATCAGGTA A-CAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* * *
27978461 ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATC-AGA ATCAGA AT
27978507 GTGAATGCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 18
0.73 0.08 0.18
Matches are distributed among these distances:
5 5 0.07
6 53 0.74
7 12 0.17
8 2 0.03
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:27978461 original size:31 final size:31
Alignment explanation
Indices: 27978426--27978506 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
27978416 GAACTAGAAT
*
27978426 CAGAATCAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGTATCAGGTAA
27978457 CAGAATCAAAATCAGAATCAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGTATCAGGTAA
27978488 CAGAATCAAAAATCAGAAT
1 CAGAATC-AAAATCAGAAT
27978507 GTGAATGCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 37 0.77
32 11 0.23
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (31 bp):
CAGAATCAAAATCAGAATCAGTATCAGGTAA
Found at i:27978899 original size:22 final size:22
Alignment explanation
Indices: 27978871--27978935 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
27978861 GCAAATACGT
*
27978871 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
27978893 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
27978915 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
27978936 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:27980032 original size:27 final size:27
Alignment explanation
Indices: 27979970--27980047 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
27979960 GGGCATATTC
27979970 GTCTTTTTACCATACAGGGGTATTACA
1 GTCTTTTTACCATACAGGGGTATTACA
** * **
27979997 GTCACTTTACCCTACAGGGGCT-TTATG
1 GTCTTTTTACCATACAGGGG-TATTACA
*
27980024 GTCTTTTTACC-TATTAGGGGTATT
1 GTCTTTTTACCATA-CAGGGGTATT
27980048 TTAGTCATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 3 0.08
27 36 0.90
28 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (27 bp):
GTCTTTTTACCATACAGGGGTATTACA
Found at i:27980121 original size:27 final size:27
Alignment explanation
Indices: 27980065--27980397 Score: 251
Period size: 27 Copynumber: 12.3 Consensus size: 27
27980055 TTTCATCCTA
* * * *
27980065 CAAGGGTGTTTTGGTAAATCTACAAGC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* **
27980092 CAAGGGTATTTTCGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *** * *
27980119 CAATGGTATTTCCATAATTTTTAGAAAGT
1 CAAGGGTATTTTGGTAA-TTTTACAAA-C
** *
27980148 CAAGGGTATTTCT-GTAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAC
* *
27980175 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
** *
27980202 TGAGGGTATTTTGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
27980229 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTGGTAATTTTACAAAC
* * *
27980256 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
** **
27980283 TGAGGGTATTTCAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * * *
27980310 C-AGAGGTATCTTAGCAATTTTACAGA-
1 CAAG-GGTATTTTGGTAATTTTACAAAC
* **
27980336 CTAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
** *
27980363 CAAGGGTATTTTGGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
27980390 CAAGGGTA
1 CAAGGGTA
27980398 AAACAGTAAT
Statistics
Matches: 248, Mismatches: 49, Indels: 18
0.79 0.16 0.06
Matches are distributed among these distances:
26 22 0.09
27 198 0.80
28 15 0.06
29 13 0.05
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:27980269 original size:81 final size:81
Alignment explanation
Indices: 27980176--27980382 Score: 290
Period size: 81 Copynumber: 2.6 Consensus size: 81
27980166 TTTGTAAATC
* *
27980176 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAACCAGAGGTATCTT
* *
27980241 GGTAATTTTACAAACT
66 AGCAATTTTACAAACT
** *
27980257 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAACCAGAGGTATCTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAACCAGAGGTATCTT
*
27980322 AGCAATTTTACAGACT
66 AGCAATTTTACAAACT
** ***
27980338 A-GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTT
27980383 TGTAAATCAA
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 37 0.33
81 74 0.67
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAACCAGAGGTATCTT
AGCAATTTTACAAACT
Found at i:27980406 original size:27 final size:27
Alignment explanation
Indices: 27980376--27980505 Score: 163
Period size: 27 Copynumber: 4.8 Consensus size: 27
27980366 GGGTATTTTG
*
27980376 GTAATTTTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCAAGGGTAAAACA
*
27980403 GTAATTCTGTAAATCAAGGGTAAAAAA
1 GTAATTCTGTAAATCAAGGGTAAAACA
* * *
27980430 ATAATTCTATAAATCGAGGGTAAAAC-
1 GTAATTCTGTAAATCAAGGGTAAAACA
* *
27980456 GATAATTTTGTAAATCAAGGGTAAAACG
1 G-TAATTCTGTAAATCAAGGGTAAAACA
* *
27980484 GTAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAATCAAGGGTA
27980506 CTTTGGTAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 87 0.99
28 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCAAGGGTAAAACA
Found at i:27980518 original size:54 final size:54
Alignment explanation
Indices: 27980348--27980505 Score: 190
Period size: 54 Copynumber: 2.9 Consensus size: 54
27980338 AGGGTATTTT
* **** * * *
27980348 GGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTGTAAATCAAGGGTAAAAC
1 GGTAATTTTGTAAATCAAGGGTAAAAAGGTAATTCTATAAATCGAGGGTAAAAC
* * **
27980402 AGTAATTCTGTAAATCAAGGGTAAAAAAATAATTCTATAAATCGAGGGTAAAAC
1 GGTAATTTTGTAAATCAAGGGTAAAAAGGTAATTCTATAAATCGAGGGTAAAAC
* *
27980456 GATAATTTTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
1 GGTAATTTTGTAAATCAAGGGTAAAAAGGTAATTCTATAAATCGAGGGTA
27980506 CTTTGGTAAT
Statistics
Matches: 86, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.30
Consensus pattern (54 bp):
GGTAATTTTGTAAATCAAGGGTAAAAAGGTAATTCTATAAATCGAGGGTAAAAC
Found at i:27983921 original size:34 final size:34
Alignment explanation
Indices: 27983874--27983951 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
27983864 ACCATCCACT
* *
27983874 ATCATGCTCACAACTTTTATCCTGCCCCAAATGG
1 ATCATGCTAACAACATTTATCCTGCCCCAAATGG
27983908 ATCATGCTAACAACATTTATCCTGCCCCAAATGG
1 ATCATGCTAACAACATTTATCCTGCCCCAAATGG
27983942 ATCATGCTAA
1 ATCATGCTAA
27983952 TTTCACATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (34 bp):
ATCATGCTAACAACATTTATCCTGCCCCAAATGG
Found at i:27989430 original size:19 final size:19
Alignment explanation
Indices: 27989406--27989443 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
27989396 AAAAAAATAG
27989406 AACACATTATGAATTTGTT
1 AACACATTATGAATTTGTT
*
27989425 AACACATTGTGAATTTGTT
1 AACACATTATGAATTTGTT
27989444 CTAACTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (19 bp):
AACACATTATGAATTTGTT
Found at i:27997252 original size:13 final size:12
Alignment explanation
Indices: 27997226--27997250 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27997216 TTATTAAAAC
27997226 TACTTTTATTTT
1 TACTTTTATTTT
27997238 TACTTTTATTTT
1 TACTTTTATTTT
27997250 T
1 T
27997251 TAGCATATTT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TACTTTTATTTT
Found at i:27999202 original size:22 final size:23
Alignment explanation
Indices: 27999177--27999230 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
27999167 ATGTTTTGTA
27999177 TTCTTTA-TT-CTTATGAGATGTT
1 TTCTTTATTTACTTA-GAGATGTT
*
27999199 TTC-TTATTTAGTTAGAGATGTT
1 TTCTTTATTTACTTAGAGATGTT
27999221 TTC-TTATTTA
1 TTCTTTATTTA
27999231 GTTATGAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 3 0.10
22 23 0.79
23 3 0.10
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.59
Consensus pattern (23 bp):
TTCTTTATTTACTTAGAGATGTT
Found at i:27999231 original size:22 final size:22
Alignment explanation
Indices: 27999191--27999234 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27999181 TTATTCTTAT
27999191 GAGATGTTTTCTTATTTAGTTA
1 GAGATGTTTTCTTATTTAGTTA
27999213 GAGATGTTTTCTTATTTAGTTA
1 GAGATGTTTTCTTATTTAGTTA
27999235 TGAACTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.55
Consensus pattern (22 bp):
GAGATGTTTTCTTATTTAGTTA
Found at i:28000326 original size:390 final size:391
Alignment explanation
Indices: 27999606--28000387 Score: 1139
Period size: 390 Copynumber: 2.0 Consensus size: 391
27999596 TTGAATAGGG
* *
27999606 ATAATAACATAACTTAGGGATCTCTATGGAACAAGTTGAATGAATAAATCGTCCGATTCGGAGCC
1 ATAATAACATAACTTAGGGATCTCTACGGAACAAGTTGAATGAATAAATCGTCCGATTCAGAGCC
* *
27999671 AGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTAGGTATTGTCTTAAGTCAATCGATTTTTCC
66 AGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTACGTATTGTCTTAAGTCAATCGAGTTTTCC
* * * * *
27999736 CAAAAGTAATTCCCCAATTAGTTTCTCTGTGCGTTCTTAGTTTAGATAATTAGTTAATTAAAACA
131 AAAAAGTAATTCCCAAATTACTTTCTCTATGAGTTCTTAGTTTAGATAATTAGTTAATTAAAACA
*
27999801 AAACCTCTCTATTCTTAGGCTAGATAATAAAAAGACAGTTATTACTAGTACTTTTAGTTCCTTTG
196 AAACCTCTCTATTCTTAGGCTAGATAATAAAAAGAAAGTTATTACTAGTACTTTTAGTTCCTTTG
* *
27999866 GGTTCGACAATCCGGTCTTGCTAAAACTATACTACTGTTCGATAGGTACACTTGCCTACATCACG
261 GGTTCGACAATCCGGTCTTACTAAAACTATACTACTATTCGATAGGTACACTTGCCTACATCACG
* *
27999931 ATAATAGTTAG-TTCAAGAACGAGTAATTATAAATATTTAAAACCTATCATGAA-ATCATGCGAT
326 ATAATAGCTAGTTTCAAGAACGAGTAATTATAAATATTTAAAACCTATCATGAATATCACGC-AT
27999994 CA
390 CA
* * *
27999996 ATAATAATATAACTTAGGGATCTCTACGGAACAAGTTGAATGAATAAATCGTTCGATTCAGAGTC
1 ATAATAACATAACTTAGGGATCTCTACGGAACAAGTTGAATGAATAAATCGTCCGATTCAGAGCC
*
28000061 A-AATAACAAGTGAAGTCTAGGTGGATTTTTCCTTACGTATTGTCTTAA-TCAATCGAGTTTTCC
66 AGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTACGTATTGTCTTAAGTCAATCGAGTTTTCC
* * * * *
28000124 AAAAAGTATTTTCCCTAAATTTCTTT-TCTATGATTTCTTAGTTTAGTTAATTATTTAGA-T-AA
131 AAAAAGTA-ATTCCC-AAATTACTTTCTCTATGAGTTCTTAGTTTAGATAATTAGTTA-ATTAAA
* * *
28000186 ACAAAACCCTTTTTATTTTTTAGGCTAGATAATAAAAAGAAAGTTGA-TACTAGTACTTTTAGTT
193 ACAAAA-CCTCTCTA-TTCTTAGGCTAGATAATAAAAAGAAAGTT-ATTACTAGTACTTTTAGTT
* * *
28000250 CCTTTGGGTTCGATAATCCGGTCTTACTAAAGCTATACTACTATTCGATAGGTACACTTGCCTTC
255 CCTTTGGGTTCGACAATCCGGTCTTACTAAAACTATACTACTATTCGATAGGTACACTTGCCTAC
** * * *
28000315 ATCGTGATAATAGCTAGTTTCAAGAACGATTCATTATAAATATTTAAAACCTGTCATGAATATCA
320 ATCACGATAATAGCTAGTTTCAAGAACGAGTAATTATAAATATTTAAAACCTATCATGAATATCA
28000380 CGCATCA
385 CGCATCA
28000387 A
1 A
28000388 ATTTTTGGCA
Statistics
Matches: 350, Mismatches: 34, Indels: 15
0.88 0.09 0.04
Matches are distributed among these distances:
388 29 0.08
389 83 0.24
390 187 0.53
391 45 0.13
392 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (391 bp):
ATAATAACATAACTTAGGGATCTCTACGGAACAAGTTGAATGAATAAATCGTCCGATTCAGAGCC
AGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTACGTATTGTCTTAAGTCAATCGAGTTTTCC
AAAAAGTAATTCCCAAATTACTTTCTCTATGAGTTCTTAGTTTAGATAATTAGTTAATTAAAACA
AAACCTCTCTATTCTTAGGCTAGATAATAAAAAGAAAGTTATTACTAGTACTTTTAGTTCCTTTG
GGTTCGACAATCCGGTCTTACTAAAACTATACTACTATTCGATAGGTACACTTGCCTACATCACG
ATAATAGCTAGTTTCAAGAACGAGTAATTATAAATATTTAAAACCTATCATGAATATCACGCATC
A
Found at i:28009412 original size:19 final size:19
Alignment explanation
Indices: 28009376--28009412 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28009366 AGATTGTTTA
**
28009376 CAATTTTAAAGCCTAAATT
1 CAATTTTAAAGCAGAAATT
28009395 CAATTTTAAAGCAGAAAT
1 CAATTTTAAAGCAGAAAT
28009413 CACTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (19 bp):
CAATTTTAAAGCAGAAATT
Found at i:28013830 original size:13 final size:13
Alignment explanation
Indices: 28013812--28013836 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28013802 CCATGGTCCG
28013812 TTTCTTTTTCATT
1 TTTCTTTTTCATT
28013825 TTTCTTTTTCAT
1 TTTCTTTTTCAT
28013837 CAATCATGCA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTTTCATT
Found at i:28019552 original size:43 final size:44
Alignment explanation
Indices: 28019488--28019616 Score: 138
Period size: 46 Copynumber: 2.9 Consensus size: 44
28019478 CTTTTATTCA
* * * *
28019488 TTCACCGGTATT-TCGCCTGCTAGGCTCG-AGGCCTGATATCAT-
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGA-ATAATG
28019530 TTCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATAATG
1 TTCACCGGCATTATAGCCTGCTAGGCTCG-AAGGCCCGAATAATG
* * * *
28019575 TCTCACCGGCATAATAGTCTGTTAGGCTCAAAGGCCCGAATA
1 T-TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
28019617 TAATACCAGC
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
42 11 0.15
43 15 0.20
44 4 0.05
45 20 0.27
46 24 0.32
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (44 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAATG
Found at i:28019665 original size:38 final size:38
Alignment explanation
Indices: 28019609--28019769 Score: 268
Period size: 38 Copynumber: 4.2 Consensus size: 38
28019599 GGCTCAAAGG
* * *
28019609 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
28019647 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
28019685 CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
28019723 CTCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
28019761 CCCGGATAT
1 CCCGGATAT
28019770 CATATTTCGA
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 114 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.20
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:28023780 original size:18 final size:17
Alignment explanation
Indices: 28023740--28023782 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28023730 CACTTTTTCA
*
28023740 ATCATCCCTCATCCCTC
1 ATCATCCCTCATCACTC
*
28023757 ATTCATCCCTCACTCATTC
1 A-TCATCCCTCA-TCACTC
28023776 ATCATCC
1 ATCATCC
28023783 TCGCCTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.21, C:0.47, G:0.00, T:0.33
Consensus pattern (17 bp):
ATCATCCCTCATCACTC
Found at i:28029719 original size:30 final size:30
Alignment explanation
Indices: 28029684--28029740 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28029674 AAGACAAATT
28029684 CCACACAGGCT-GAGCACACGCCCATGTGAG
1 CCACACAGGCTAGA-CACACGCCCATGTGAG
* *
28029714 CCACACGGGCTAGACACATGCCCATGT
1 CCACACAGGCTAGACACACGCCCATGT
28029741 TGCAGCCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.26, C:0.37, G:0.25, T:0.12
Consensus pattern (30 bp):
CCACACAGGCTAGACACACGCCCATGTGAG
Found at i:28030482 original size:20 final size:20
Alignment explanation
Indices: 28030457--28030496 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28030447 AAAGTCAGAA
28030457 TAATAAGTGAAGTCTAGGTG
1 TAATAAGTGAAGTCTAGGTG
28030477 TAATAAGTGAAGTCTAGGTG
1 TAATAAGTGAAGTCTAGGTG
28030497 GATTCTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (20 bp):
TAATAAGTGAAGTCTAGGTG
Found at i:28033409 original size:38 final size:37
Alignment explanation
Indices: 28033359--28033433 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 37
28033349 ATCTCAACAT
28033359 ATACTGGCCGAAGCCTTTTCATATTTCATATTTCATA
1 ATACTGGCCGAAGCCTTTTCATATTTCATATTTCATA
28033396 ATACTAGGCCGAAGCCTTTTCATATTTCATATTTCATA
1 ATACT-GGCCGAAGCCTTTTCATATTTCATATTTCATA
28033434 TTTCATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (37 bp):
ATACTGGCCGAAGCCTTTTCATATTTCATATTTCATA
Found at i:28033425 original size:7 final size:7
Alignment explanation
Indices: 28033413--28033442 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
28033403 GCCGAAGCCT
28033413 TTTCATA
1 TTTCATA
28033420 TTTCATA
1 TTTCATA
28033427 TTTCATA
1 TTTCATA
28033434 TTTCATA
1 TTTCATA
28033441 TT
1 TT
28033443 ACTGGGCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTCATA
Found at i:28033705 original size:26 final size:25
Alignment explanation
Indices: 28033676--28033758 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 25
28033666 GGCCTTGCCT
28033676 TTTTTTAATAACTGGGGCATAAGCCC
1 TTTTTT-ATAACTGGGGCATAAGCCC
*
28033702 TTTTCGGTA-AACTGGGGCATAAGCCC
1 TTTT--TTATAACTGGGGCATAAGCCC
*
28033728 TTTTTCGGTA-AACTAGGGCATAAG-CC
1 TTTTT---TATAACTGGGGCATAAGCCC
28033754 TTTTT
1 TTTTT
28033759 GCACTTCCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
26 32 0.65
27 16 0.33
28 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (25 bp):
TTTTTTATAACTGGGGCATAAGCCC
Found at i:28033740 original size:27 final size:27
Alignment explanation
Indices: 28033685--28033758 Score: 125
Period size: 26 Copynumber: 2.8 Consensus size: 27
28033675 TTTTTTTAAT
28033685 AACTGGGGCATAAGCCC-TTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTTCGGTA
28033711 AACTGGGGCATAAGCCCTTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTTCGGTA
*
28033738 AACTAGGGCATAAG-CCTTTTT
1 AACTGGGGCATAAGCCCTTTTT
28033759 GCACTTCCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 24 0.52
27 22 0.48
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (27 bp):
AACTGGGGCATAAGCCCTTTTTCGGTA
Found at i:28033871 original size:20 final size:20
Alignment explanation
Indices: 28033808--28033874 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
28033798 TTATGAATAC
*
28033808 ATCATGTTCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28033828 AACATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28033848 ATCATGTGCATGTCATATCA-
1 ATCATGTGCATATCATA-CAT
28033868 ATCATGT
1 ATCATGT
28033875 ATATCAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28041534 original size:38 final size:38
Alignment explanation
Indices: 28041484--28041577 Score: 172
Period size: 38 Copynumber: 2.5 Consensus size: 38
28041474 ATCTCAACAT
28041484 ATACT-GGCCGAAGCCTTTTCATATTTCATATTTCATA
1 ATACTGGGCCGAAGCCTTTTCATATTTCATATTTCATA
28041521 ATACTGGGCCGAAGCCTTTTCATATTTCATATTTCATA
1 ATACTGGGCCGAAGCCTTTTCATATTTCATATTTCATA
*
28041559 TTACTGGGCCGAAGCCTTT
1 ATACTGGGCCGAAGCCTTT
28041578 ACTGCAAACG
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 5 0.09
38 50 0.91
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (38 bp):
ATACTGGGCCGAAGCCTTTTCATATTTCATATTTCATA
Found at i:28041859 original size:27 final size:27
Alignment explanation
Indices: 28041804--28041877 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
28041794 TCTTTTTAAT
*
28041804 AACTGGGGCATAAGCCC-TTTTCTGTA
1 AACTGGGGCATAAGCCCTTTTTCAGTA
28041830 AACTGGGGCATAAGCCCTTTTTCAGTA
1 AACTGGGGCATAAGCCCTTTTTCAGTA
* *
28041857 AACTAGGGCATAAGCGCTTTT
1 AACTGGGGCATAAGCCCTTTT
28041878 GCACTTCCTC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 17 0.39
27 27 0.61
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (27 bp):
AACTGGGGCATAAGCCCTTTTTCAGTA
Found at i:28041990 original size:20 final size:20
Alignment explanation
Indices: 28041927--28041993 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
28041917 TTATAAATAC
*
28041927 ATCATGTACATATCATACAT
1 ATCATGTGCATATCATACAT
*
28041947 AACATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28041967 ATCATGTGCATGTCATATCA-
1 ATCATGTGCATATCATA-CAT
28041987 ATCATGT
1 ATCATGT
28041994 ATATCAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28046203 original size:29 final size:29
Alignment explanation
Indices: 28046161--28046218 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28046151 ACCAATGTGA
28046161 AAAATTATTTTTGGGAGGATCATTTTCTT
1 AAAATTATTTTTGGGAGGATCATTTTCTT
28046190 AAAATTATTTTTGGGAGGATCATTTTCTT
1 AAAATTATTTTTGGGAGGATCATTTTCTT
28046219 TTTCGTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (29 bp):
AAAATTATTTTTGGGAGGATCATTTTCTT
Found at i:28048001 original size:86 final size:86
Alignment explanation
Indices: 28047855--28048028 Score: 226
Period size: 86 Copynumber: 2.0 Consensus size: 86
28047845 ACACACAGAC
* * *
28047855 GTGTCCTAGGTCGTGTGAAAACTGAAGCTAAATTCCTAACTTTTAAACAAGTAAATGAGCTCCAC
1 GTGTCCAAGGCCGTGTGAAAACTGAAGCTAAATTCCTAAATTTTAAACAAGTAAATGAGCTCCAC
* *
28047920 GGCCGAGGCACATGGCCATGT
66 GGCCGAAGCACATGACCATGT
* * * *
28047941 GTGTCCAAGGCCGTGTGAAAATTGAAGTTAAATT-TTCAAATTTTAAACAAGTCAGA-GAGCTCC
1 GTGTCCAAGGCCGTGTGAAAACTGAAGCTAAATTCCT-AAATTTTAAACAAGT-AAATGAGCTCC
*
28048004 ACGGGCGAAGCACATGACCATGT
64 ACGGCCGAAGCACATGACCATGT
28048027 GT
1 GT
28048029 TCAGACACAT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
85 1 0.01
86 73 0.96
87 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (86 bp):
GTGTCCAAGGCCGTGTGAAAACTGAAGCTAAATTCCTAAATTTTAAACAAGTAAATGAGCTCCAC
GGCCGAAGCACATGACCATGT
Found at i:28048417 original size:15 final size:15
Alignment explanation
Indices: 28048393--28048426 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
28048383 ATCCTCTCTT
28048393 TTCTTCTCTTTTCTC
1 TTCTTCTCTTTTCTC
*
28048408 TTCTTTTCTTTTCTC
1 TTCTTCTCTTTTCTC
28048423 TTCT
1 TTCT
28048427 CTCCCATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTTCTCTTTTCTC
Found at i:28048754 original size:23 final size:22
Alignment explanation
Indices: 28048724--28048766 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
28048714 TTTTCCCTTT
28048724 TCTTTTA-TTCATTTATTATTAC
1 TCTTTTATTTC-TTTATTATTAC
28048746 TCTTATTATTTCTTTATTATT
1 TCTT-TTATTTCTTTATTATT
28048767 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 12 0.63
24 3 0.16
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (22 bp):
TCTTTTATTTCTTTATTATTAC
Found at i:28050451 original size:6 final size:6
Alignment explanation
Indices: 28050440--28050533 Score: 127
Period size: 6 Copynumber: 15.7 Consensus size: 6
28050430 TTGAGTCCAA
* * *
28050440 TTATTT TTATTT TTATTT TTATAT TTATGT TTATGT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
* *
28050488 TTA-TC TTATATT TTATTT TTATTT TTATTT TTATTT TTCTTT TTAT
1 TTATTT TTAT-TT TTATTT TTATTT TTATTT TTATTT TTATTT TTAT
28050534 GTCTATTTTG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
5 4 0.05
6 70 0.89
7 5 0.06
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:28063063 original size:26 final size:26
Alignment explanation
Indices: 28063034--28063141 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28063024 TGATACAAAT
28063034 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28063060 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28063086 TAATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28063112 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28063138 TGAT
1 TGAT
28063142 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28064805 original size:27 final size:27
Alignment explanation
Indices: 28064762--28064902 Score: 155
Period size: 27 Copynumber: 5.2 Consensus size: 27
28064752 AGGAAGCGTC
28064762 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
* * * *
28064789 CTGGTGGCTTTGTCAC-ATATATTTGTT
1 CTGGTGGCTATGCCACAAT-TATCTGAT
*
28064816 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
*
28064843 CTGGTGGCTCTGCCAC-ATATATCT-ATT
1 CTGGTGGCTATGCCACAAT-TATCTGA-T
*
28064870 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTATGCCACAATTATCTG-AT
28064897 CTGGTG
1 CTGGTG
28064903 ACTTCGTCAC
Statistics
Matches: 98, Mismatches: 9, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
26 10 0.10
27 84 0.86
28 4 0.04
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:28064844 original size:54 final size:53
Alignment explanation
Indices: 28064762--28064919 Score: 210
Period size: 54 Copynumber: 2.9 Consensus size: 53
28064752 AGGAAGCGTC
* *
28064762 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTTGTCACATATATTTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTTTGTCACATATATCTATT
* *
28064816 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTTTGTCACATATATCTATT
* * * *
28064870 CTGGTGGCTCTGCCACAATATCTGTATCTGGTGACTTCGTCACA-ATATCT
1 CTGGTGGCTATGCCACATTATCTG-ATCTGGTGGCTTTGTCACATATATCT
28064920 GGTAGCCTCG
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 13 0.14
54 79 0.86
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTTTGTCACATATATCTATT
Found at i:28064913 original size:27 final size:27
Alignment explanation
Indices: 28064762--28064920 Score: 127
Period size: 27 Copynumber: 5.9 Consensus size: 27
28064752 AGGAAGCGTC
28064762 CTGGTGGCTAT-GCCACAATTATCTG-AT
1 CTGGTGGCT-TCGCCACAA-TATCTGTAT
* * *
28064789 CTGGTGGCTTTGTCACATATATTTGT-T
1 CTGGTGGCTTCGCCACA-ATATCTGTAT
*
28064816 CTGGTGGCTAT-GCCACGATTATCTG-AT
1 CTGGTGGCT-TCGCCAC-AATATCTGTAT
*
28064843 CTGGTGGC-TCTGCCACATATATCTAT-T
1 CTGGTGGCTTC-GCCACA-ATATCTGTAT
28064870 CTGGTGGC-TCTGCCACAATATCTGTAT
1 CTGGTGGCTTC-GCCACAATATCTGTAT
* *
28064897 CTGGTGACTTCGTCACAATATCTG
1 CTGGTGGCTTCGCCACAATATCTG
28064921 GTAGCCTCGT
Statistics
Matches: 110, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.01
26 9 0.08
27 95 0.86
28 5 0.05
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTTCGCCACAATATCTGTAT
Found at i:28066847 original size:42 final size:43
Alignment explanation
Indices: 28066751--28066849 Score: 105
Period size: 43 Copynumber: 2.3 Consensus size: 43
28066741 AACGTCCTAG
* * * *
28066751 ACATGGTCTTACATGTAATCAAATATCGATCCCACTGTCCTAG
1 ACATGGTCTTACACGAAATCAAATATCGATCCCACTGTCCCAA
* *
28066794 ACAAT-TTCTTACACGAAATCAAATA-CGATGCCGA-TGTCCCAA
1 AC-ATGGTCTTACACGAAATCAAATATCGAT-CCCACTGTCCCAA
28066836 ACATGGTCTTACAC
1 ACATGGTCTTACAC
28066850 ATAAATCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
41 2 0.04
42 20 0.43
43 22 0.48
44 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.27
Consensus pattern (43 bp):
ACATGGTCTTACACGAAATCAAATATCGATCCCACTGTCCCAA
Found at i:28073622 original size:15 final size:15
Alignment explanation
Indices: 28073602--28073639 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
28073592 ATAAAGAAAT
28073602 TGGGGCACACGACCG
1 TGGGGCACACGACCG
28073617 TGGGGCACACGACCG
1 TGGGGCACACGACCG
28073632 TGGGGCAC
1 TGGGGCAC
28073640 GCCCGTGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.32, G:0.42, T:0.08
Consensus pattern (15 bp):
TGGGGCACACGACCG
Found at i:28073645 original size:13 final size:14
Alignment explanation
Indices: 28073602--28073646 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
28073592 ATAAAGAAAT
28073602 TGGGGCACACGACCG
1 TGGGG-ACACGACCG
28073617 TGGGGCACACGACCG
1 TGGGG-ACACGACCG
*
28073632 TGGGG-CACGCCCG
1 TGGGGACACGACCG
28073645 TG
1 TG
28073647 TGCCCTCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 9 0.31
15 20 0.69
ACGTcount: A:0.16, C:0.33, G:0.42, T:0.09
Consensus pattern (14 bp):
TGGGGACACGACCG
Found at i:28080118 original size:40 final size:40
Alignment explanation
Indices: 28079880--28080104 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
28079870 TCGAATGATG
* * * *
28079880 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28079920 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28079960 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28079999 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28080039 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28080080 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28080105 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28080126 original size:119 final size:119
Alignment explanation
Indices: 28079880--28080137 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
28079870 TCGAATGATG
* *
28079880 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
28079945 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
28079999 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
28080062 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
28080119 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28080138 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:28090911 original size:13 final size:13
Alignment explanation
Indices: 28090876--28090911 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
28090866 TGGGTGCACG
28090876 CGGCTGTGTCGCA
1 CGGCTGTGTCGCA
*
28090889 CGGCTATGTCGCA
1 CGGCTGTGTCGCA
*
28090902 CGGCCGTGTC
1 CGGCTGTGTC
28090912 TTGCTTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.08, C:0.33, G:0.36, T:0.22
Consensus pattern (13 bp):
CGGCTGTGTCGCA
Found at i:28096189 original size:47 final size:48
Alignment explanation
Indices: 28096082--28096212 Score: 137
Period size: 47 Copynumber: 2.8 Consensus size: 48
28096072 TGGGTAAGGT
** *
28096082 GTCGATGCCATGTCCCAGACATGGTCTTACACTAAC-TATCATCTAGTA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCATCAAG-A
* *
28096130 GTCGATG-GATGTCCCAGACAT-GTCATACACTGGCTTACGTC-TCAAG-
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTA--TCATCAAGA
* *
28096176 GTCGATGCCATGTCCAAGACATGGTCTTTCACTGGCT
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
28096213 CTCATAATGT
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
46 17 0.25
47 27 0.39
48 23 0.33
49 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (48 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCATCAAGA
Found at i:28106031 original size:14 final size:14
Alignment explanation
Indices: 28106014--28106044 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28106004 GATTGGTGCT
28106014 TGTTGATTCTTAAG
1 TGTTGATTCTTAAG
28106028 TGTTGATTCTTAAG
1 TGTTGATTCTTAAG
28106042 TGT
1 TGT
28106045 CATTCAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (14 bp):
TGTTGATTCTTAAG
Found at i:28112717 original size:47 final size:47
Alignment explanation
Indices: 28112648--28112876 Score: 220
Period size: 47 Copynumber: 4.9 Consensus size: 47
28112638 TGGGTAAGGT
*
28112648 GTCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCAT-ATCTCAA
1 GTCGATG-CATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA
* **
28112695 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTTGTA
1 GTCGATG-CATGTCCCAGACATGGTCTTACACTGGCTCATCATC-TCAA
* * * * *
28112743 GCCGATGCATGTCCCAGACAT-GTCTTATACTGGCTTA-CTTCTCGA
1 GTCGATGCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA
* * * * *
28112788 GGCTGATGCATGTCCCATACAT-GTCTTATACTAGCTC-TCGTCTCAA
1 GTC-GATGCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA
*
28112834 TTCTGATGTCATGTCCCAGACATGGTCTTACACTGGCTC-TCAT
1 GTC-GATG-CATGTCCCAGACATGGTCTTACACTGGCTCATCAT
28112877 AATGTGGCTG
Statistics
Matches: 153, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
45 4 0.03
46 59 0.39
47 66 0.43
48 24 0.16
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (47 bp):
GTCGATGCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA
Found at i:28112894 original size:47 final size:46
Alignment explanation
Indices: 28112651--28112918 Score: 164
Period size: 47 Copynumber: 5.7 Consensus size: 46
28112641 GTAAGGTGTC
*
28112651 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCAT-ATCTCAA-GT-C-
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGCTC-TCA--T-AATGTGCT
* * ** *
28112698 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTTGTAGCC
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGT-GCT
* *
28112746 GATG-CATGTCCCAGACATGTCTTATACTGGCTTACTTC-TCGA-G-GCT
1 GATGCCATGTCCCAGACATGTCTTACACTGGC-T-C-TCAT-AATGTGCT
* * * *
28112792 GATG-CATGTCCCATACATGTCTTATACTAGCTCTCGTCTCAAT-T-CT
1 GATGCCATGTCCCAGACATGTCTTACACTGGCTCTC--AT-AATGTGCT
*
28112838 GATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCT
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGT-GCT
* * *
28112886 GATG-CATGTCCTAGAAATGTCTTACACTAGCTC
1 GATGCCATGTCCCAGACATGTCTTACACTGGCTC
28112919 ACAAAAAAAT
Statistics
Matches: 181, Mismatches: 21, Indels: 39
0.75 0.09 0.16
Matches are distributed among these distances:
43 2 0.01
44 1 0.01
45 7 0.04
46 68 0.38
47 74 0.41
48 27 0.15
49 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGCT
Found at i:28112915 original size:94 final size:92
Alignment explanation
Indices: 28112746--28112918 Score: 224
Period size: 94 Copynumber: 1.9 Consensus size: 92
28112736 TCTTGTAGCC
* ** * *
28112746 GATGCATGTCCCAGACATGTCTTATACTGGCTTACTTCTCGAGGCTGATGCATGTCCCATACATG
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACTAATCGAGGCTGATGCATGTCCCAGAAATG
*
28112811 TCTTATACTAGCTCTCGTCTCAATTCT
66 TCTTACACTAGCTCTCGTCTCAATTCT
* *
28112838 GATGTCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCTGATGCATGTCCTAGA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TAC-TAATCGAGGCTGATGCATGTCCCAGA
28112901 AATGTCTTACACTAGCTC
62 AATGTCTTACACTAGCTC
28112919 ACAAAAAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
92 4 0.06
93 14 0.20
94 48 0.70
95 3 0.04
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTACTAATCGAGGCTGATGCATGTCCCAGAAATG
TCTTACACTAGCTCTCGTCTCAATTCT
Found at i:28119614 original size:43 final size:43
Alignment explanation
Indices: 28119519--28119637 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 43
28119509 GACTTATGTT
* * *
28119519 TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATCGA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGATAATCGA
** ** *
28119562 TTTTGTGTAAGACCCTGTCTGGGACAGTGGCATCGATGTTTGA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGATAATCGA
*
28119605 TTACATGTAAGACCAC-GTCTGGGAC-GTTGGCAT
1 TTACGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
28119638 TGTATTTACT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 61 0.97
44 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGATAATCGA
Found at i:28121240 original size:27 final size:27
Alignment explanation
Indices: 28121180--28121232 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28121170 ACGGTCATTT
* * *
28121180 TACCCTACAAGGGTATTTCGGTGATCC
1 TACCCTACAGGGGTATTTCAGTAATCC
28121207 TACCCTACAGGGGTATTTCAGTAATC
1 TACCCTACAGGGGTATTTCAGTAATC
28121233 TTGTCCTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (27 bp):
TACCCTACAGGGGTATTTCAGTAATCC
Found at i:28122208 original size:47 final size:46
Alignment explanation
Indices: 28122106--28122284 Score: 259
Period size: 46 Copynumber: 3.9 Consensus size: 46
28122096 TTATCTTCGA
* * * * * *
28122106 CATGATGCCATAGTATCTTTCAACTATGGTCTTACTCGTTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGT
*
28122152 CATGTTGCCATGGTATCTTTCAACCATGGACTTATTCATTTCCCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTT-CCTGT
*
28122199 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGT
* *
28122245 CACGGTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
28122285 GTATGTTTCA
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
46 77 0.64
47 44 0.36
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGT
Found at i:28122270 original size:93 final size:93
Alignment explanation
Indices: 28122106--28122284 Score: 270
Period size: 93 Copynumber: 1.9 Consensus size: 93
28122096 TTATCTTCGA
* * * *
28122106 CATGATGCCATAGTATCTTTCAACTATGGTCTTACTCGTTTTCTGTCATGTTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCGATTTCTGTCACGGTGCCATGGTATCTT
28122171 TCAACCATGGACTTATTCATTTCCCTGT
66 TCAACCATGGACTTATTCATTTCCCTGT
* * *
28122199 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-ATTTCATGTCACGGTGCCATGGTATCT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCGATTTC-TGTCACGGTGCCATGGTATCT
*
28122263 TTCAACCATGGTCTTATTCATT
65 TTCAACCATGGACTTATTCATT
28122285 GTATGTTTCA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 4 0.05
93 73 0.95
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (93 bp):
CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCGATTTCTGTCACGGTGCCATGGTATCTT
TCAACCATGGACTTATTCATTTCCCTGT
Found at i:28122318 original size:28 final size:28
Alignment explanation
Indices: 28122257--28122312 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28122247 CGGTGCCATG
*
28122257 GTATCTTTCAACCATGGTCTTATTCATT
1 GTATGTTTCAACCATGGTCTTATTCATT
28122285 GTATGTTTCAACCATGGTCTTATTCATT
1 GTATGTTTCAACCATGGTCTTATTCATT
28122313 TCATGTCACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (28 bp):
GTATGTTTCAACCATGGTCTTATTCATT
Found at i:28122337 original size:74 final size:74
Alignment explanation
Indices: 28122211--28122352 Score: 266
Period size: 74 Copynumber: 1.9 Consensus size: 74
28122201 TGTTGCCATG
28122211 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGGTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGGTGCCATGGTATCTTTCAACCATGGTC
28122276 TTATTCATT
66 TTATTCATT
* *
28122285 GTATGTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGGTGCCATGGTATCTTTCAACCATGGTC
28122350 TTA
66 TTA
28122353 CACATTTCAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (74 bp):
GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGGTGCCATGGTATCTTTCAACCATGGTC
TTATTCATT
Found at i:28122342 original size:46 final size:46
Alignment explanation
Indices: 28122285--28122454 Score: 286
Period size: 46 Copynumber: 3.7 Consensus size: 46
28122275 CTTATTCATT
* ** * *
28122285 GTATGTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
28122331 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
28122377 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
*
28122423 GTATCTTTCAACCATGGTTTTACACATTTCAT
1 GTATCTTTCAACCATGGTCTTACACATTTCAT
28122455 TTCAAAAAGC
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
Found at i:28122383 original size:120 final size:121
Alignment explanation
Indices: 28122164--28122398 Score: 382
Period size: 120 Copynumber: 2.0 Consensus size: 121
28122154 TGTTGCCATG
* *
28122164 GTATCTTTCAACCATGGACTTATTCATTTCCCTGTCATGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATGGACTTATTCATTTCCATGTCACGTTGCCATGGTATCTTTCAACCATGGT
** *
28122229 CTTATTCATTTCATGTCACGGTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
66 CTTACACATTTCATATCACGGTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
* *
28122285 GTATGTTTCAACCATGGTCTTATTCATTT-CATGTCACGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATGGACTTATTCATTTCCATGTCACGTTGCCATGGTATCTTTCAACCATGGT
* *
28122349 CTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
66 CTTACACATTTCATATCACGGTGCCATGGTATCTTTCAACCATGGTCTTA
28122399 CACATTTCAT
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
120 78 0.74
121 27 0.26
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (121 bp):
GTATCTTTCAACCATGGACTTATTCATTTCCATGTCACGTTGCCATGGTATCTTTCAACCATGGT
CTTACACATTTCATATCACGGTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
Found at i:28122407 original size:166 final size:167
Alignment explanation
Indices: 28122118--28122440 Score: 488
Period size: 166 Copynumber: 1.9 Consensus size: 167
28122108 TGATGCCATA
* * *
28122118 GTATCTTTCAACTATGGTCTTACTCGTTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGAC
1 GTATCTTTCAACCATGGTCTTACTCGATTTCTGTCACGTTGCCATGGTATCTTTCAACCATGGAC
** * * ** *
28122183 TTATTCATTTCCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCAC
66 TTACACATTTCCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAC
28122248 GGTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
131 GGTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
* * *
28122285 GTATGTTTCAACCATGGTCTTATTC-ATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATGGTCTTACTCGATTTC-TGTCACGTTGCCATGGTATCTTTCAACCATGGA
28122349 CTTACACATTT-CATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
65 CTTACACATTTCCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
* *
28122413 TGTTGCCATGGTATCTTTCAACCATGGT
130 CGGTGCCATGGTATCTTTCAACCATGGT
28122441 TTTACACATT
Statistics
Matches: 140, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
166 78 0.56
167 62 0.44
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.41
Consensus pattern (167 bp):
GTATCTTTCAACCATGGTCTTACTCGATTTCTGTCACGTTGCCATGGTATCTTTCAACCATGGAC
TTACACATTTCCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAC
GGTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
Found at i:28125140 original size:27 final size:27
Alignment explanation
Indices: 28125098--28125312 Score: 225
Period size: 27 Copynumber: 8.0 Consensus size: 27
28125088 TGGGATATTA
*
28125098 CAGGGTTATTTCGGTAATTTTACAAAT
1 CAGGGGTATTTCGGTAATTTTACAAAT
*
28125125 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAGGGGTATTTCGGTAATTTTACAAAT
* ** * *
28125152 CGGGGGTATTTCAATCATTTTGCAAAT
1 CAGGGGTATTTCGGTAATTTTACAAAT
* *
28125179 C-GAGGGTATTTTGGTAATTTTAAAAAT
1 CAG-GGGTATTTCGGTAATTTTACAAAT
** * * *
28125206 CAGGGGTATTTCATTAATTTCACGAGT
1 CAGGGGTATTTCGGTAATTTTACAAAT
* *
28125233 TAGGGGTATTTCAGTAATTTTACAAAT
1 CAGGGGTATTTCGGTAATTTTACAAAT
* * *
28125260 CAAGGGTATTTCGGTAATTTCACACAT
1 CAGGGGTATTTCGGTAATTTTACAAAT
* *
28125287 CGGGGGTATTTCGATAATTTTACAAA
1 CAGGGGTATTTCGGTAATTTTACAAA
28125313 CTGGGGTCTT
Statistics
Matches: 150, Mismatches: 36, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
26 1 0.01
27 148 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (27 bp):
CAGGGGTATTTCGGTAATTTTACAAAT
Found at i:28125195 original size:81 final size:81
Alignment explanation
Indices: 28125099--28125312 Score: 259
Period size: 81 Copynumber: 2.6 Consensus size: 81
28125089 GGGATATTAC
* * *
28125099 AGGGTTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCGGGGGTATTTC
1 AGGG-TATTTCGGTAATTTTACAAATCAGGGGTATTTCGATAATTTTACAAATCAGGGGTATTTC
* * *
28125164 AATCATTTTGCAAATCG
65 AATAATTTTACAAATCA
* * * * * *
28125181 AGGGTATTTTGGTAATTTTAAAAATCAGGGGTATTTC-ATTAATTTCACGAGTTAGGGGTATTTC
1 AGGGTATTTCGGTAATTTTACAAATCAGGGGTATTTCGA-TAATTTTACAAATCAGGGGTATTTC
*
28125245 AGTAATTTTACAAATCA
65 AATAATTTTACAAATCA
* * *
28125262 AGGGTATTTCGGTAATTTCACACATCGGGGGTATTTCGATAATTTTACAAA
1 AGGGTATTTCGGTAATTTTACAAATCAGGGGTATTTCGATAATTTTACAAA
28125313 CTGGGGTCTT
Statistics
Matches: 109, Mismatches: 21, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
81 104 0.95
82 5 0.05
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (81 bp):
AGGGTATTTCGGTAATTTTACAAATCAGGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCA
ATAATTTTACAAATCA
Found at i:28129423 original size:43 final size:43
Alignment explanation
Indices: 28129362--28129537 Score: 284
Period size: 43 Copynumber: 4.1 Consensus size: 43
28129352 CTGGCATTAC
* *
28129362 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACTAA
28129405 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACTAA
*
28129448 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACTAA
* * *
28129491 GCCTGCTAGGCACGAAGGCCCAAATATA-AT-ACCAGCACTAG
1 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACTAA
28129532 GCCTGC
1 GCCTGC
28129538 AAGATTTATC
Statistics
Matches: 126, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
41 15 0.12
42 2 0.02
43 109 0.87
ACGTcount: A:0.31, C:0.34, G:0.23, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACTAA
Found at i:28136135 original size:17 final size:17
Alignment explanation
Indices: 28136113--28136146 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28136103 GATAAGAATA
*
28136113 TATTGTCATTGCATTTT
1 TATTGTCATTACATTTT
28136130 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
28136147 CATGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:28140853 original size:17 final size:17
Alignment explanation
Indices: 28140831--28140864 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28140821 TAAGTTGATC
28140831 AATGTGTTACCCCCATA
1 AATGTGTTACCCCCATA
*
28140848 AATGTGTTACCCTCATA
1 AATGTGTTACCCCCATA
28140865 GGATATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (17 bp):
AATGTGTTACCCCCATA
Found at i:28146725 original size:20 final size:21
Alignment explanation
Indices: 28146702--28146744 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28146692 ATAAGCATGT
*
28146702 ATTTTG-ATGTTTGATGATAG
1 ATTTTGAATGCTTGATGATAG
*
28146722 ATTTTGAATGCTTGTTGATAG
1 ATTTTGAATGCTTGATGATAG
28146743 AT
1 AT
28146745 ATACAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (21 bp):
ATTTTGAATGCTTGATGATAG
Found at i:28151274 original size:27 final size:26
Alignment explanation
Indices: 28151230--28151281 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28151220 CTTGCTACAA
*
28151230 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
28151257 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
28151282 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:28153332 original size:17 final size:17
Alignment explanation
Indices: 28153310--28153350 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
28153300 TGAAGCATAC
28153310 AGAAAGACAGAATCGTG
1 AGAAAGACAGAATCGTG
28153327 AGAAAGACAGAATCGTG
1 AGAAAGACAGAATCGTG
28153344 AGAAAGA
1 AGAAAGA
28153351 TCGAAACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.29, T:0.10
Consensus pattern (17 bp):
AGAAAGACAGAATCGTG
Found at i:28158173 original size:33 final size:32
Alignment explanation
Indices: 28158124--28158187 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
28158114 CTCGCTGCAA
* *
28158124 TCTGGTGGCTTCGCCACATATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
28158157 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
28158188 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:28158201 original size:27 final size:26
Alignment explanation
Indices: 28158149--28158208 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
28158139 ACATATATAT
*
28158149 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
28158175 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
28158202 ATATCTG
1 ATATCTG
28158209 GTAGCATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:28165348 original size:58 final size:58
Alignment explanation
Indices: 28165277--28165388 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
28165267 AAATTCACAT
* * * *
28165277 ACCTGTATCTGGCCCATTATGCCC-AATCATATTCACATGGCCCCTTTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATCACATTCACATGG-CCCGTTAGGCCCAAATC
* *
28165335 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAGGCCCAAATCACATTCACATGGCCCGTTAGGCCCA
28165389 GTCACATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 34 0.72
59 13 0.28
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (58 bp):
ACCTGTATATGGCCCATTAGGCCCAAATCACATTCACATGGCCCGTTAGGCCCAAATC
Found at i:28165354 original size:29 final size:29
Alignment explanation
Indices: 28165280--28165388 Score: 114
Period size: 29 Copynumber: 3.8 Consensus size: 29
28165270 TTCACATACC
* * *
28165280 TGTATCTGGCCCATTATGCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* * *
28165308 T-TCACATGGCCCCTTTAGGCCCAAATCACC
1 TGT-ATATGG-CCCATTAGGCCCAAATCACA
28165338 TGTATATGGCCCATTAGGCCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
28165367 TTTATATGGCCCGTTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
28165389 GTCACATTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 1 0.02
28 5 0.08
29 48 0.73
30 11 0.17
31 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.28
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:28170138 original size:18 final size:20
Alignment explanation
Indices: 28170115--28170163 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
28170105 AGTGTTTTAG
*
28170115 TGAAAACCTTATTTT-CA-T
1 TGAAAACCTTATTTTGAATT
28170133 TGAAAACCCTT-TTTTGAATT
1 TGAAAA-CCTTATTTTGAATT
28170153 TGAAAACCTTA
1 TGAAAACCTTA
28170164 ATTACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 10 0.38
19 9 0.35
20 7 0.27
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (20 bp):
TGAAAACCTTATTTTGAATT
Found at i:28171295 original size:29 final size:29
Alignment explanation
Indices: 28171228--28171348 Score: 149
Period size: 29 Copynumber: 4.2 Consensus size: 29
28171218 AAGTCTACAT
*
28171228 ACATGCATATGGCCCACTAGG-CCAAAT-
1 ACATTCATATGGCCCACTAGGCCCAAATC
*
28171255 ATCATTCATATGGCCCATTAGGCCCAAATC
1 A-CATTCATATGGCCCACTAGGCCCAAATC
* * *
28171285 ACATTCGTATGGCCCACTAGGTCCAAACC
1 ACATTCATATGGCCCACTAGGCCCAAATC
*
28171314 ACATTCATATGGCCCATTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
*
28171342 TCATTCA
1 ACATTCA
28171349 CAGTCATGCT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
27 1 0.01
28 27 0.34
29 51 0.64
30 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:28171298 original size:57 final size:57
Alignment explanation
Indices: 28171235--28171347 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 57
28171225 CATACATGCA
*
28171235 TATGGCCCACTAGG-CCAAA-TATCATTCATATGGCCCATTAGGCCCAAATCACATTCG
1 TATGGCCCACTAGGTCCAAACCA-CATTCATATGGCCCATTAGGCCC-AATCACATTCG
*
28171292 TATGGCCCACTAGGTCCAAACCACATTCATATGGCCCATTAGGCCCAATCTCATTC
1 TATGGCCCACTAGGTCCAAACCACATTCATATGGCCCATTAGGCCCAATCACATTC
28171348 ACAGTCATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
57 23 0.44
58 28 0.54
59 1 0.02
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (57 bp):
TATGGCCCACTAGGTCCAAACCACATTCATATGGCCCATTAGGCCCAATCACATTCG
Found at i:28174251 original size:40 final size:40
Alignment explanation
Indices: 28174017--28174237 Score: 288
Period size: 40 Copynumber: 5.5 Consensus size: 40
28174007 ATAATGTACA
* * * *
28174017 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG
* * *
28174057 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
28174097 GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
28174136 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
28174176 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
28174216 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
28174238 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 117 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:28182589 original size:102 final size:104
Alignment explanation
Indices: 28182413--28182676 Score: 399
Period size: 102 Copynumber: 2.6 Consensus size: 104
28182403 AACCGTTATT
* * * *
28182413 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
* ** *
28182478 ATTAGCACATAGCAACCCCCTTT-TTA-TTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
28182515 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
28182579 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
28182619 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
28182677 TTATGTACAA
Statistics
Matches: 147, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
101 1 0.01
102 81 0.55
103 1 0.01
104 63 0.43
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:28183036 original size:29 final size:29
Alignment explanation
Indices: 28183003--28183066 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
28182993 TAATCCACCA
28183003 CCCAACTTTTTGAAAAATTACAATTTTG-C
1 CCCAAC-TTTTGAAAAATTACAATTTTGTC
* * *
28183032 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGTC
28183062 CCCAA
1 CCCAA
28183067 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGTC
Found at i:28183040 original size:30 final size:30
Alignment explanation
Indices: 28183010--28183066 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
28183000 CCACCCAACT
28183010 TTTTGAAAAATTACAATTTTG-CCCCAAAC
1 TTTTGAAAAATTACAATTTTGTCCCCAAAC
* * *
28183039 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGTCCCCAA
28183067 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGTCCCCAAAC
Found at i:28190085 original size:103 final size:104
Alignment explanation
Indices: 28189906--28190170 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
28189896 AACCGTTATT
* * * *
28189906 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
28189971 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
28190009 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
28190073 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
28190113 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
28190171 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:28190532 original size:30 final size:29
Alignment explanation
Indices: 28190498--28190562 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
28190488 TAATCCACCA
28190498 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
28190528 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
28190558 CCCAA
1 CCCAA
28190563 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:28190536 original size:31 final size:30
Alignment explanation
Indices: 28190505--28190562 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28190495 CCACCCAACT
28190505 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
28190535 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
28190563 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:28191422 original size:40 final size:40
Alignment explanation
Indices: 28191377--28191562 Score: 261
Period size: 40 Copynumber: 4.7 Consensus size: 40
28191367 GCTGTTACAT
* *
28191377 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
* *
28191417 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
28191456 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
28191496 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* *
28191537 A-CAGGGCTATGTCCCGAAGGCATTTG
1 ATCCGGGCTAAGTCCCGAAGGCATTTG
28191563 AATGAGTAGC
Statistics
Matches: 133, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
39 34 0.26
40 97 0.73
41 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:28191580 original size:80 final size:80
Alignment explanation
Indices: 28191391--28191595 Score: 229
Period size: 80 Copynumber: 2.6 Consensus size: 80
28191381 GGACTAAGAT
** * * *
28191391 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA
* *
28191455 AATCCGGGTTAAGTC
66 AATCAGGGCTAAGTC
** *
28191470 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA
*
28191535 TAA-CAGGGCTATGTC
66 -AATCAGGGCTAAGTC
* * * *
28191550 CCGAAGGCATTTGAATGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGG
28191596 TACGTGATTT
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
79 51 0.46
80 57 0.52
81 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA
AATCAGGGCTAAGTC
Found at i:28196012 original size:17 final size:17
Alignment explanation
Indices: 28195980--28196013 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28195970 CTCTCATGCA
28195980 TTATTTTTTGTGGCTTT
1 TTATTTTTTGTGGCTTT
28195997 TTATTCTTTTGT-GCTTT
1 TTATT-TTTTGTGGCTTT
28196014 CTTTTGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.06, C:0.09, G:0.15, T:0.71
Consensus pattern (17 bp):
TTATTTTTTGTGGCTTT
Found at i:28202872 original size:19 final size:21
Alignment explanation
Indices: 28202840--28202878 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
28202830 TGTAACATAG
*
28202840 AAAATTTATTTATGT-TTTGA
1 AAAATTTATGTATGTGTTTGA
28202860 AAAATTT-TGTATGTGTTTG
1 AAAATTTATGTATGTGTTTG
28202879 GCTTGGTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (21 bp):
AAAATTTATGTATGTGTTTGA
Found at i:28208122 original size:48 final size:48
Alignment explanation
Indices: 28208048--28208153 Score: 158
Period size: 48 Copynumber: 2.2 Consensus size: 48
28208038 CAAGATAAAT
* * *
28208048 ATATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAG
* *
28208096 ATATGTATATGTGGTAAAGCCGAATGGCTAATTTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAG
*
28208144 ATGTGTATAT
1 ATATGTATAT
28208154 ATTGTGGCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAG
Found at i:28208339 original size:37 final size:37
Alignment explanation
Indices: 28208289--28208429 Score: 225
Period size: 37 Copynumber: 3.9 Consensus size: 37
28208279 AATATATTCC
28208289 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
*
28208326 GGGTAAGACCCGATGACTACGTGTGGAGATT-TGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
*
28208362 GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCT
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
* *
28208399 GGGTAAGA--CGATAACTACGTGTGGGGATTAT
1 GGGTAAGACCCGATGACTACGTGTGGAGATTAT
28208430 TCGAGCTAAA
Statistics
Matches: 98, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
35 20 0.20
36 35 0.36
37 43 0.44
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
Found at i:28208405 original size:73 final size:71
Alignment explanation
Indices: 28208286--28208427 Score: 239
Period size: 73 Copynumber: 2.0 Consensus size: 71
28208276 GGAAATATAT
*
28208286 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCTGGGTAAGACCCGATGACTACGTGTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCTGGGTAAGA--CGATAACTACGTGTG
28208351 GAGATTTG
64 GAGATTTG
* *
28208359 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCTGGGTAAGACGATAACTACGTGTGGG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCTGGGTAAGACGATAACTACGTGTGGA
28208424 GATT
66 GATT
28208428 ATTCGAGCTA
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 19 0.29
73 47 0.71
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (71 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCTGGGTAAGACGATAACTACGTGTGGA
GATTTG
Found at i:28210343 original size:43 final size:43
Alignment explanation
Indices: 28210122--28210331 Score: 384
Period size: 43 Copynumber: 4.9 Consensus size: 43
28210112 GCATGAAACT
*
28210122 CGGTGATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
28210165 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
*
28210208 CAGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
28210251 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* *
28210294 CGGTGATATGTATTCGGGTCTTCGTCCCTAGCAGGCTT
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTT
28210332 AATACCGGTG
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 162 1.00
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.31
Consensus pattern (43 bp):
CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
Found at i:28210561 original size:29 final size:29
Alignment explanation
Indices: 28210529--28210634 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 29
28210519 CGTTAACCGA
28210529 GCACTATGTGTGCGAGATCAATAATTGAG
1 GCACTATGTGTGCGAGATCAATAATTGAG
* ** **
28210558 GCACTCTGTGTGCGA-ATTCCTTTAACCGA-
1 GCACTATGTGTGCGAGA-T-CAATAATTGAG
* ***
28210587 GCATTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGATCAATAATTGAG
*
28210616 GCACTGTGTGTGCGAGATC
1 GCACTATGTGTGCGAGATC
28210635 GGTCAGTGGG
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
28 6 0.10
29 45 0.78
30 7 0.12
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTATGTGTGCGAGATCAATAATTGAG
Found at i:28210629 original size:58 final size:57
Alignment explanation
Indices: 28210475--28210630 Score: 203
Period size: 58 Copynumber: 2.8 Consensus size: 57
28210465 ACGAATATGG
*
28210475 GCATTATGTGTGCGA-A-TG--ATTAGAGGCACTGTGTGTGCAAATTCCGTTAACCGA
1 GCATTATGTGTGCGAGATTGTAATT-GAGGCACTGTGTGTGCGAATTCCGTTAACCGA
* ** * *
28210529 GCACTATGTGTGCGAGATCAATAATTGAGGCACTCTGTGTGCGAATTCCTTTAACCGA
1 GCATTATGTGTGCGAGAT-TGTAATTGAGGCACTGTGTGTGCGAATTCCGTTAACCGA
28210587 GCATTATGTGTGCGAGATTGGTAATTGAGGCACTGTGTGTGCGA
1 GCATTATGTGTGCGAGATT-GTAATTGAGGCACTGTGTGTGCGA
28210631 GATCGGTCAG
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
54 14 0.16
55 1 0.01
58 68 0.79
59 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (57 bp):
GCATTATGTGTGCGAGATTGTAATTGAGGCACTGTGTGTGCGAATTCCGTTAACCGA
Found at i:28210655 original size:28 final size:29
Alignment explanation
Indices: 28210594--28210655 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
28210584 CGAGCATTAT
* * **
28210594 GTGTGCGAGATTGGTAATTGAGGCACTGT
1 GTGTGCGAGATCGGTAAGTGAGGCACTAA
*
28210623 GTGTGCGAGATCGGTCAGTG-GGCACTAA
1 GTGTGCGAGATCGGTAAGTGAGGCACTAA
28210651 GTGTG
1 GTGTG
28210656 TGAAATGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.19, C:0.13, G:0.40, T:0.27
Consensus pattern (29 bp):
GTGTGCGAGATCGGTAAGTGAGGCACTAA
Found at i:28214164 original size:48 final size:48
Alignment explanation
Indices: 28214024--28214266 Score: 371
Period size: 48 Copynumber: 5.0 Consensus size: 48
28214014 CAAGATAAAT
* *
28214024 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
28214072 ATATGTATATGTGGTAAAGCC-AATGGCTAATATGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
**
28214119 ATATATATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
28214167 ATATATATATATGTGGTAAATCCGAATGGCTATTGTGAAATATGTATGAG
1 --ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
28214217 ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
28214265 AT
1 AT
28214267 GTGTATATAT
Statistics
Matches: 178, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
47 44 0.25
48 90 0.51
50 44 0.25
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (48 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:28214243 original size:98 final size:97
Alignment explanation
Indices: 28214024--28214281 Score: 376
Period size: 98 Copynumber: 2.7 Consensus size: 97
28214014 CAAGATAAAT
* * *
28214024 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG--ATATGTATATGTGGT
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATATATATATGTGGT
28214087 AAAGCCAATGGCTAATATGAAATATGTATGAG
66 AAAGCCAATGGCTAATATGAAATATGTATGAG
**
28214119 ATATATATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGATATATATATATGTGGT
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATATATATATGTGGT
* * *
28214184 AAATCCGAATGGCTATTGTGAAATATGTATGAG
66 AAAGCC-AATGGCTAATATGAAATATGTATGAG
* * * *
28214217 ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATGTGTATATATTGTGG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATATATATA-TGTGG
28214282 CCGAATGACC
Statistics
Matches: 145, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
95 44 0.30
97 19 0.13
98 77 0.53
99 5 0.03
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (97 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATATATATATGTGGT
AAAGCCAATGGCTAATATGAAATATGTATGAG
Found at i:28214301 original size:145 final size:144
Alignment explanation
Indices: 28214022--28214293 Score: 420
Period size: 145 Copynumber: 1.9 Consensus size: 144
28214012 TACAAGATAA
*
28214022 ATATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGT
1 ATATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGT
* * *
28214087 AAAGCCAATGGCTAATATGAAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAACA
66 AAAGCCAATGGCTAATATGAAATATGTATGAGATATATATATATGGT-AAGCCGAATGACCAACA
28214152 TGAAATATGTATGAG
130 TGAAATATGTATGAG
* *
28214167 ATATATATATATGTGGTAAATCCGAATGGCTATTGTGAAATATGTATGAGATATGTATATGTGGT
1 ATATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGT
* * * * *
28214232 AAAGCCAAATGGCTAATGTGAAATATGTATGAGATGTGTATATATTGT-GGCCGAATGACCAA
66 AAAGCC-AATGGCTAATATGAAATATGTATGAGATATATATATATGGTAAGCCGAATGACCAA
28214294 ATGTGAAAGG
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
144 11 0.10
145 68 0.59
146 36 0.31
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.32
Consensus pattern (144 bp):
ATATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGT
AAAGCCAATGGCTAATATGAAATATGTATGAGATATATATATATGGTAAGCCGAATGACCAACAT
GAAATATGTATGAG
Found at i:28214462 original size:37 final size:37
Alignment explanation
Indices: 28214410--28214553 Score: 225
Period size: 37 Copynumber: 3.9 Consensus size: 37
28214400 AATATATTCT
28214410 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* *
28214447 GGGTAAGACCTGATGACTACGTGTGGAGATTTTGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* * *
28214484 GAGTAAGACTCGATGACTACGTGTGGAGATTTTGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* *
28214521 GGGTAAGACCCGATAACTACGTGTGGGGATTAT
1 GGGTAAGACCCGATGACTACGTGTGGAGATTAT
28214554 TCGAGCTAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
Found at i:28218252 original size:16 final size:16
Alignment explanation
Indices: 28218231--28218263 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28218221 TATTGATGAA
28218231 AGTGTAGCTCAGGAAC
1 AGTGTAGCTCAGGAAC
*
28218247 AGTGTAGCTCCGGAAC
1 AGTGTAGCTCAGGAAC
28218263 A
1 A
28218264 ATCTTAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.18
Consensus pattern (16 bp):
AGTGTAGCTCAGGAAC
Found at i:28226367 original size:23 final size:23
Alignment explanation
Indices: 28226341--28226389 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
28226331 GCATGTGTAT
28226341 TTTTCATTTTC-TATTTGTTTTGG
1 TTTTCATTTTCAT-TTTGTTTTGG
** *
28226364 TTTTGGTTTTCATTTTGTTTTTG
1 TTTTCATTTTCATTTTGTTTTGG
28226387 TTT
1 TTT
28226390 AGTTTGCCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.06, C:0.06, G:0.14, T:0.73
Consensus pattern (23 bp):
TTTTCATTTTCATTTTGTTTTGG
Found at i:28228672 original size:22 final size:21
Alignment explanation
Indices: 28228644--28228686 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
28228634 GTCTTCAGGG
28228644 CTGTGTCACGACACCCTATGGT
1 CTGTGTCACGACACCCT-TGGT
*
28228666 CTGTGTCACGACAGCCTTGGT
1 CTGTGTCACGACACCCTTGGT
28228687 AGATTGCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.16, C:0.30, G:0.26, T:0.28
Consensus pattern (21 bp):
CTGTGTCACGACACCCTTGGT
Found at i:28230171 original size:18 final size:19
Alignment explanation
Indices: 28230140--28230175 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28230130 TTCCATTAGG
28230140 TTAATTTAGGTTAATTAAT
1 TTAATTTAGGTTAATTAAT
*
28230159 TTAA-TTAGTTTAATTAA
1 TTAATTTAGGTTAATTAA
28230176 AATATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTAATTTAGGTTAATTAAT
Found at i:28233620 original size:23 final size:23
Alignment explanation
Indices: 28233593--28233640 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
28233583 CTGTACACCT
*
28233593 TCTTCTTTACTT-GTCTATCTGAA
1 TCTTCTTTACTTCGT-TAGCTGAA
28233616 TCTTCTTTACTTCGTTAGCTGAA
1 TCTTCTTTACTTCGTTAGCTGAA
28233639 TC
1 TC
28233641 ATAACCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (23 bp):
TCTTCTTTACTTCGTTAGCTGAA
Found at i:28234243 original size:20 final size:19
Alignment explanation
Indices: 28234218--28234258 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
28234208 CATGGCCTGA
*
28234218 GGTCAAATTGGGCCGTGGTG
1 GGTCAAAATGGGCCGT-GTG
*
28234238 GGTCAAAATGGGTCGTGTG
1 GGTCAAAATGGGCCGTGTG
28234257 GG
1 GG
28234259 CCTTACGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.17, C:0.12, G:0.46, T:0.24
Consensus pattern (19 bp):
GGTCAAAATGGGCCGTGTG
Found at i:28234723 original size:18 final size:18
Alignment explanation
Indices: 28234660--28234724 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
28234650 AGGACTTGTA
* *
28234660 TACTGTTATTGCATTGAT
1 TACTGTTACTGCACTGAT
*
28234678 TACTATTACTGCACTGAT
1 TACTGTTACTGCACTGAT
*
28234696 TACTGCTACTGCACTG-T
1 TACTGTTACTGCACTGAT
*
28234713 TCATTGTTACTG
1 T-ACTGTTACTG
28234725 AATTGGGCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 2 0.05
18 37 0.95
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (18 bp):
TACTGTTACTGCACTGAT
Found at i:28234773 original size:33 final size:34
Alignment explanation
Indices: 28234715--28234782 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
28234705 TGCACTGTTC
*
28234715 ATTGTTACTGAATTGGGCTAAGGCCC-ACACTAAT
1 ATTGTTACTGAATTAGGCTAAGGCCCTA-ACTAAT
*
28234749 ATTGTTACTGAA-TAGGCTATGGCCCTAACTAAT
1 ATTGTTACTGAATTAGGCTAAGGCCCTAACTAAT
28234782 A
1 A
28234783 CTAGACTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (34 bp):
ATTGTTACTGAATTAGGCTAAGGCCCTAACTAAT
Found at i:28238452 original size:40 final size:41
Alignment explanation
Indices: 28238401--28238503 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 41
28238391 GAAACTATCT
*
28238401 CAATATCGCACACTTAGTGCCA-CATATAGCCGAAGCTATTC
1 CAAT-TCGCACACTTAGTGCCATCATATAGCCAAAGCTATTC
* * *
28238442 CAATTCGCACACTTAGTGCTATTTATATAGCCAAAGCTATTT
1 CAATTCGCACACTTAGTGCCA-TCATATAGCCAAAGCTATTC
*
28238484 CAAATCGCACACTTAGTGCC
1 CAATTCGCACACTTAGTGCC
28238504 GAATGATCGC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
40 16 0.30
41 4 0.07
42 34 0.63
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (41 bp):
CAATTCGCACACTTAGTGCCATCATATAGCCAAAGCTATTC
Found at i:28238691 original size:20 final size:20
Alignment explanation
Indices: 28238662--28238701 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28238652 GTACTAGTAA
28238662 TGACTATCTTTTTATTATCT
1 TGACTATCTTTTTATTATCT
*
28238682 TGACTGTCTTTTTATTATCT
1 TGACTATCTTTTTATTATCT
28238702 AGCCTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.07, T:0.60
Consensus pattern (20 bp):
TGACTATCTTTTTATTATCT
Found at i:28242306 original size:44 final size:44
Alignment explanation
Indices: 28242241--28242325 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
28242231 AACATGTGTA
28242241 ACATATATCATGAACTGAGACCACAACTCATGAGTTCAGATGTC
1 ACATATATCATGAACTGAGACCACAACTCATGAGTTCAGATGTC
*
28242285 ACATATATCATGAACTTAGACCACAACTCATGAGTTCAGAT
1 ACATATATCATGAACTGAGACCACAACTCATGAGTTCAGAT
28242326 CACATAGTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (44 bp):
ACATATATCATGAACTGAGACCACAACTCATGAGTTCAGATGTC
Found at i:28242329 original size:20 final size:20
Alignment explanation
Indices: 28242262--28242329 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
28242252 GAACTGAGAC
28242262 CACAACTCATGAGTTCAGATGT
1 CACAACTCATGAGTTCAGA--T
* * *
28242284 CACATATATCATGAACTT-AGAC
1 CACA-A-CTCATG-AGTTCAGAT
28242306 CACAACTCATGAGTTCAGAT
1 CACAACTCATGAGTTCAGAT
28242326 CACA
1 CACA
28242330 TAGTTCCTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
21 1 0.03
22 8 0.22
23 1 0.03
24 8 0.22
25 3 0.08
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (20 bp):
CACAACTCATGAGTTCAGAT
Found at i:28245768 original size:13 final size:13
Alignment explanation
Indices: 28245750--28245776 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28245740 GTTTAATTAG
28245750 TTAATTAGTTTAA
1 TTAATTAGTTTAA
28245763 TTAATTAGTTTAA
1 TTAATTAGTTTAA
28245776 T
1 T
28245777 AAACAACCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTAATTAGTTTAA
Found at i:28245776 original size:9 final size:9
Alignment explanation
Indices: 28245737--28245765 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28245727 ACTCTTTGCT
28245737 TTAGTTTAA
1 TTAGTTTAA
28245746 TTAG-TTAA
1 TTAGTTTAA
28245754 TTAGTTTAA
1 TTAGTTTAA
28245763 TTA
1 TTA
28245766 ATTAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (9 bp):
TTAGTTTAA
Found at i:28251195 original size:12 final size:11
Alignment explanation
Indices: 28251178--28251222 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
28251168 CCTCCTATCT
28251178 TTTTATTTTTA
1 TTTTATTTTTA
28251189 GTTTTATTTTTA
1 -TTTTATTTTTA
**
28251201 TTTTCATTTCAA
1 TTTT-ATTTTTA
28251213 TTTTATTTTT
1 TTTTATTTTT
28251223 TTCTTTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:28251200 original size:18 final size:17
Alignment explanation
Indices: 28251177--28251222 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
28251167 TCCTCCTATC
*
28251177 TTTTTATTTTTAGTTTTA
1 TTTTTATTTTTA-TTTCA
*
28251195 TTTTTATTTTCATTTCA
1 TTTTTATTTTTATTTCA
*
28251212 ATTTTATTTTT
1 TTTTTATTTTT
28251223 TTCTTTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTATTTCA
Found at i:28254140 original size:13 final size:13
Alignment explanation
Indices: 28254122--28254150 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28254112 TTTAGTTTAA
28254122 TTAGTTAATTAGT
1 TTAGTTAATTAGT
28254135 TTAGTTAATTAGT
1 TTAGTTAATTAGT
28254148 TTA
1 TTA
28254151 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:28254459 original size:48 final size:48
Alignment explanation
Indices: 28254396--28254717 Score: 403
Period size: 48 Copynumber: 6.7 Consensus size: 48
28254386 CACATGTCAC
* * * * ** *
28254396 CGATGCCATGTCCCAGACATGGTCTTACACTAGTTCTCGTCTCAATGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATAACATTGT
* * * *
28254444 CAATGCCATGTCCCAGACATGGTCTTACTCTAGCTCTCATAACATTGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATAACATTGT
* * *
28254492 CAATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCAAAACATTGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATAACATTGT
* *
28254540 CGATGTCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG-
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATAACATTGT
* *
28254587 CTGATGCCATGTTTCAAACATGGTCTTACACTGGCTCTCATAACATTGT
1 C-GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATAACATTGT
* * ** * *
28254636 CGATGCCATATTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGA
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATAACATTGT
*
28254684 CGATGCCATGTCCCAAACATGGTCTTACACTAGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGC
28254718 ACACATATCA
Statistics
Matches: 246, Mismatches: 26, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
47 1 0.00
48 244 0.99
49 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATAACATTGT
Found at i:28254517 original size:96 final size:95
Alignment explanation
Indices: 28254356--28254717 Score: 422
Period size: 96 Copynumber: 3.8 Consensus size: 95
28254346 CACGCGATCA
* * * ** * *
28254356 CCATGTCCCAAACATGGTATTACACTGGCTCACATGTCA--CCGATGCCATGTCCCAGACATGGT
1 CCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTGCGATGCCATGTCCCAAACATGGT
* * ** * *
28254419 CTTACACTAGTTCTCGTCTCAATGTCAATG
66 CTTACACTAGCTCTCATAACATTGTCGATG
* * * * * *
28254449 CCATGTCCCAGACATGGTCTTACTCTAGCTCTCATAACATTGTCAATGCCATGTTCCAAACATGG
1 CCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG-CGATGCCATGTCCCAAACATGG
* *
28254514 TCTTACACTGGCTCTCAAAACATTGTCGATG
65 TCTTACACTAGCTCTCATAACATTGTCGATG
* **
28254545 TCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTGCTGATGCCATGTTTCAAACATGG
1 CCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTGC-GATGCCATGTCCCAAACATGG
*
28254610 TCTTACACTGGCTCTCATAACATTGTCGATG
65 TCTTACACTAGCTCTCATAACATTGTCGATG
* ** *
28254641 CCATATTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGACGATGCCATGTCCCAAACATGG
1 CCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG-CGATGCCATGTCCCAAACATGG
28254706 TCTTACACTAGC
65 TCTTACACTAGC
28254718 ACACATATCA
Statistics
Matches: 229, Mismatches: 35, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
93 32 0.14
95 1 0.00
96 195 0.85
97 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (95 bp):
CCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTGCGATGCCATGTCCCAAACATGGT
CTTACACTAGCTCTCATAACATTGTCGATG
Found at i:28262594 original size:20 final size:20
Alignment explanation
Indices: 28262528--28262595 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
28262518 ATCATGAACG
*
28262528 CAGACCACAACTCATGAGTT
1 CAGACCACAAATCATGAGTT
* * **
28262548 CAAATGTCACATATATCATGAACT
1 CAGA--CCACA-A-ATCATGAGTT
28262572 CAGACCACAAATCATGAGTT
1 CAGACCACAAATCATGAGTT
28262592 CAGA
1 CAGA
28262596 TCAAATGGTT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
20 15 0.43
21 1 0.03
22 8 0.23
23 1 0.03
24 10 0.29
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (20 bp):
CAGACCACAAATCATGAGTT
Found at i:28263666 original size:13 final size:13
Alignment explanation
Indices: 28263648--28263687 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
28263638 GCTCGGCAGG
*
28263648 GACACGCCCTTGT
1 GACACGCCCGTGT
28263661 GACACGCCCGTGT
1 GACACGCCCGTGT
*
28263674 GGCACGCCCGTGT
1 GACACGCCCGTGT
28263687 G
1 G
28263688 CAATTACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.12, C:0.38, G:0.33, T:0.17
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:28283507 original size:47 final size:47
Alignment explanation
Indices: 28283446--28283699 Score: 373
Period size: 47 Copynumber: 5.4 Consensus size: 47
28283436 CAGCCAACAC
28283446 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
28283493 AGTGTATATTTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
28283540 AGTGCATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
28283587 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
28283634 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
28283681 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
28283700 TCCTGAAGGG
Statistics
Matches: 187, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 187 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Done.