Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 174 of 186
Found at i:57926704 original size:88 final size:88
Alignment explanation
Indices: 57926555--57926716 Score: 252
Period size: 88 Copynumber: 1.8 Consensus size: 88
57926545 TACTACCTTG
* ** * * *
57926555 GAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCTGCTACAACGCCAGGGAAAAGAAGACTCG
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCCACTCCGCTACAACGCCAGGGAAAAAAAGACTCA
57926620 CTGTCTTCAGTCTTAACGCTAAA
66 CTGTCTTCAGTCTTAACGCTAAA
*
57926643 GAGATAAGATTCGCTGTCTTCAGCTTTAATCCACTCCGCTACAACGCCAGGGAAAAAAAGACTCA
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCCACTCCGCTACAACGCCAGGGAAAAAAAGACTCA
*
57926708 TTGTCTTCA
66 CTGTCTTCA
57926717 ATCTGCTTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 66 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (88 bp):
GAGATAAGATTCGCTGCCTTCAGCTTTAATCCACTCCGCTACAACGCCAGGGAAAAAAAGACTCA
CTGTCTTCAGTCTTAACGCTAAA
Found at i:57927366 original size:45 final size:45
Alignment explanation
Indices: 57927294--57927380 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
57927284 AGCTTGAACT
* * *
57927294 GAATGAATTAATCAAGATAGCAAATTTTGCTAGAATACAAAACGA
1 GAATAAATTAATCAAGATAGCAAATTTTGCCAAAATACAAAACGA
* * **
57927339 GAATAAATTAATCAAGGTGGCGTATTTTGCCAAAATACAAAA
1 GAATAAATTAATCAAGATAGCAAATTTTGCCAAAATACAAAA
57927381 ATGAATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.25
Consensus pattern (45 bp):
GAATAAATTAATCAAGATAGCAAATTTTGCCAAAATACAAAACGA
Found at i:57927692 original size:13 final size:14
Alignment explanation
Indices: 57927654--57927692 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
57927644 CACCTTGGCC
57927654 TCTTCTTTTTATTT
1 TCTTCTTTTTATTT
57927668 TCTCTCTTTTTATTT
1 TCT-TCTTTTTATTT
57927683 TCTT-TTTTTA
1 TCTTCTTTTTA
57927693 GGTAAAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.25
14 4 0.17
15 14 0.58
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTCTTTTTATTT
Found at i:57934275 original size:9 final size:9
Alignment explanation
Indices: 57934261--57934303 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
57934251 GTTTTCGAAT
57934261 TCGAATAAC
1 TCGAATAAC
57934270 TCGAATAAC
1 TCGAATAAC
*
57934279 TCGAATAAT
1 TCGAATAAC
* *
57934288 TCAAATAAT
1 TCGAATAAC
57934297 TCGAATA
1 TCGAATA
57934304 TCAAACTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (9 bp):
TCGAATAAC
Found at i:57934564 original size:30 final size:31
Alignment explanation
Indices: 57934516--57934575 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
57934506 AAACCTTTTA
*
57934516 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* * *
57934546 TTTTCCTCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
57934576 TCTCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:57938277 original size:16 final size:16
Alignment explanation
Indices: 57938256--57938291 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
57938246 CTTTTATAAT
*
57938256 AAAATGCCATGTAGTC
1 AAAATGCCATGTAGCC
57938272 AAAATGCCATGTAGCC
1 AAAATGCCATGTAGCC
57938288 AAAA
1 AAAA
57938292 CAAAACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (16 bp):
AAAATGCCATGTAGCC
Found at i:57939463 original size:16 final size:16
Alignment explanation
Indices: 57939428--57939467 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
57939418 TTAATAAAAT
* *
57939428 TAAAACTAATTGCTAT
1 TAAAATTAATTGCTAG
*
57939444 TAAAATTAATTGTTAG
1 TAAAATTAATTGCTAG
57939460 TAAAATTA
1 TAAAATTA
57939468 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (16 bp):
TAAAATTAATTGCTAG
Found at i:57939526 original size:66 final size:68
Alignment explanation
Indices: 57939456--57939598 Score: 245
Period size: 68 Copynumber: 2.1 Consensus size: 68
57939446 AAATTAATTG
* *
57939456 TTAGTAAAATTATCAAATTATTAA-T-TGTTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTATATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
57939519 TGA
66 TGA
*
57939522 TTAGTAAATTTATCAAATTATTAATTATATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTATATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
57939587 TGA
66 TGA
57939590 TTAGTAAAA
1 TTAGTAAAA
57939599 CAAACTTGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 23 0.32
67 1 0.01
68 47 0.66
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (68 bp):
TTAGTAAAATTATCAAATTATTAATTATATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
TGA
Found at i:57944356 original size:147 final size:147
Alignment explanation
Indices: 57944085--57944361 Score: 358
Period size: 147 Copynumber: 1.9 Consensus size: 147
57944075 GTAAAATTCG
** * * * * *
57944085 GGTTTACTCACACAAGCTGTAGGTTGGGGTTGTTGATATAAGTGTTATTTGATACTGCTCACAGA
1 GGTTTACTCACACAAGCTGTAGGTCAGGATTATTCATATAAGTGTTATTCGATACTGCTCACACA
** * * *
57944150 AGATGTAGAGAACCCGCAACATATGTTAGATCTCGGCCATCGATAACTAAGCCATTGACTAGCAC
66 AGATGTAGAGAACCCGCAACATATGCAAGATCTCAGCCATCAATAACTAAGCCACTGACTAGCAC
57944215 TTGAACTATATCATTTA
131 TTGAACTATATCATTTA
* ** *
57944232 GGTTTGCTCACACAAGCTGTAGGTCAGGATTATTCATATAAGTGTTATTCGATGTTGCTCGCACA
1 GGTTTACTCACACAAGCTGTAGGTCAGGATTATTCATATAAGTGTTATTCGATACTGCTCACACA
* * * *
57944297 AGCTGTAGAGTATCCGCAACATATGCAAGATCTCAGTCATCAATAACTAAGTCC-CTGACTAGCA
66 AGATGTAGAGAACCCGCAACATATGCAAGATCTCAGCCATCAATAACTAAG-CCACTGACTAGCA
57944361 C
130 C
57944362 CCAATTCCTT
Statistics
Matches: 109, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
147 107 0.98
148 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (147 bp):
GGTTTACTCACACAAGCTGTAGGTCAGGATTATTCATATAAGTGTTATTCGATACTGCTCACACA
AGATGTAGAGAACCCGCAACATATGCAAGATCTCAGCCATCAATAACTAAGCCACTGACTAGCAC
TTGAACTATATCATTTA
Found at i:57946227 original size:188 final size:188
Alignment explanation
Indices: 57945906--57946288 Score: 599
Period size: 188 Copynumber: 2.0 Consensus size: 188
57945896 AATATGAGGT
* * * *
57945906 GTCA-TCACAAGCACCTGTCAATAAGGAACACATGTTATTGCTAGCTGCATTTTACTTTGCAAAT
1 GTCACTCACAAGAACCTGTCAATAAGAAACACATGTTATTGCTAGCTACATTTTACTTTGCAAAC
* *
57945970 CACAAAAAAACTTAGGAAAAACTTAACAAAAGAACAGACCACAGTCTCCCACTATAAACTTCATC
66 CACAAAAAAACTTAGGAAAAACTTAACAAAAGAACAGACCAAAATCTCCCACTATAAACTTCATC
* * *
57946035 TTTCATCTTGAATAAGTTTCACTAACTAGTTCATTTCATTCCAATAGCATTCTTCAAA
131 TTTCATCTTGAATAAGTTTCACTAACTAGTTCATTTCATTCCAACAACATTCCTCAAA
*
57946093 GTCACTCACAAGAACCTGTCAGTAAGAAACACATGTTATTGCTAGCTACATTTTACTTTGCAAAC
1 GTCACTCACAAGAACCTGTCAATAAGAAACACATGTTATTGCTAGCTACATTTTACTTTGCAAAC
* * **
57946158 CACAAAAAAA-TTGAGGAAAAACTTAATAAAAGAACATACCAAAATCTCCTGCTATAAACTTCAT
66 CACAAAAAAACTT-AGGAAAAACTTAACAAAAGAACAGACCAAAATCTCCCACTATAAACTTCAT
*
57946222 CTTTCATCTTGAATAAGTTTCACTAACTAGTTCATTTCTTTCCAACAACATTCCTCAAA
130 CTTTCATCTTGAATAAGTTTCACTAACTAGTTCATTTCATTCCAACAACATTCCTCAAA
*
57946281 GTCCCTCA
1 GTCACTCA
57946289 AAAAAATTTG
Statistics
Matches: 178, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
187 6 0.03
188 172 0.97
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (188 bp):
GTCACTCACAAGAACCTGTCAATAAGAAACACATGTTATTGCTAGCTACATTTTACTTTGCAAAC
CACAAAAAAACTTAGGAAAAACTTAACAAAAGAACAGACCAAAATCTCCCACTATAAACTTCATC
TTTCATCTTGAATAAGTTTCACTAACTAGTTCATTTCATTCCAACAACATTCCTCAAA
Found at i:57949319 original size:27 final size:27
Alignment explanation
Indices: 57949282--57949338 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
57949272 AACATTGAAT
57949282 AAAACATTGAATTATCAAATAATAAGA
1 AAAACATTGAATTATCAAATAATAAGA
57949309 AAAACATTGAATTATCAAATAATAAGA
1 AAAACATTGAATTATCAAATAATAAGA
57949336 AAA
1 AAA
57949339 GTCAAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAACATTGAATTATCAAATAATAAGA
Found at i:57949703 original size:98 final size:97
Alignment explanation
Indices: 57949514--57949705 Score: 287
Period size: 98 Copynumber: 2.0 Consensus size: 97
57949504 ATATATGAAA
* * *
57949514 ATAAAGACACAACAATGAGTTCAGGCTAGTAGAATACAAGCAATGGAAAAATCAACATTGTACTC
1 ATAAAGACACAACAAGGAGTTCAGGATAGTAGAATACAAGCAATGAAAAAATCAACATTGTACTC
*
57949579 GAAATAGAAAAATTAGAGATAACAATGTTCAC
66 GAAATAGAAAAATCAGAGATAACAATGTTCAC
* * *
57949611 ATAAAGACACAACAGGGAGTTCATGATAGTAGAATACTAAGTAATGAAAAAATCAACATTGTACT
1 ATAAAGACACAACAAGGAGTTCAGGATAGTAGAATAC-AAGCAATGAAAAAATCAACATTGTACT
*
57949676 C-AGAATAGAAAAATCAGAGATAGCAATGTT
65 CGA-AATAGAAAAATCAGAGATAACAATGTT
57949706 GGTAGTGGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
97 34 0.40
98 51 0.60
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.21
Consensus pattern (97 bp):
ATAAAGACACAACAAGGAGTTCAGGATAGTAGAATACAAGCAATGAAAAAATCAACATTGTACTC
GAAATAGAAAAATCAGAGATAACAATGTTCAC
Found at i:57951038 original size:18 final size:19
Alignment explanation
Indices: 57951011--57951046 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
57951001 CCCTTGCACC
*
57951011 CACCATGTTGAAG-ATCAA
1 CACCAAGTTGAAGTATCAA
57951029 CACCAAGTTGAAGTATCA
1 CACCAAGTTGAAGTATCA
57951047 GAATCCATTG
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:0.22, G:0.17, T:0.22
Consensus pattern (19 bp):
CACCAAGTTGAAGTATCAA
Found at i:57956651 original size:12 final size:13
Alignment explanation
Indices: 57956627--57956651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57956617 AGAGAATTCA
57956627 TATGAAAATTTTT
1 TATGAAAATTTTT
57956640 TATGAAAATTTT
1 TATGAAAATTTT
57956652 ACTGATTACA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TATGAAAATTTTT
Found at i:57959293 original size:55 final size:55
Alignment explanation
Indices: 57959232--57959335 Score: 190
Period size: 55 Copynumber: 1.9 Consensus size: 55
57959222 AATTATCCAA
* *
57959232 GTCAGTATGCTCACACGGCTTAGCACACGGGTGTGTGGCTTGGCAGTGTGACCAT
1 GTCAGTATGCTCACACGGCCTAGCACACGGGCGTGTGGCTTGGCAGTGTGACCAT
57959287 GTCAGTATGCTCACACGGCCTAGCACACGGGCGTGTGGCTTGGCAGTGT
1 GTCAGTATGCTCACACGGCCTAGCACACGGGCGTGTGGCTTGGCAGTGT
57959336 AACGAAGCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.24
Consensus pattern (55 bp):
GTCAGTATGCTCACACGGCCTAGCACACGGGCGTGTGGCTTGGCAGTGTGACCAT
Found at i:57961552 original size:64 final size:63
Alignment explanation
Indices: 57961447--57961572 Score: 153
Period size: 64 Copynumber: 2.0 Consensus size: 63
57961437 AGCATGCTGG
* * * * * * * * * *
57961447 TCGGTATTGATCTGCATGTGTTGTAGACATACTGTAGCTCTTTGTGAGTGTCCTGGTATATGA
1 TCGGTATGGATCTGCATATATTGCAGACATACCGTAACTCTTTATGAGCGTCCCGATATATGA
57961510 TCGGTATGGATCCTGCATATATTGCAGACATACCGTAACTCTTTATGAGCGTCCCGATATATG
1 TCGGTATGGAT-CTGCATATATTGCAGACATACCGTAACTCTTTATGAGCGTCCCGATATATG
57961573 GCTCTTAATG
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
63 10 0.19
64 42 0.81
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (63 bp):
TCGGTATGGATCTGCATATATTGCAGACATACCGTAACTCTTTATGAGCGTCCCGATATATGA
Found at i:57973682 original size:3 final size:3
Alignment explanation
Indices: 57973674--57973702 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
57973664 CCTTTAATTT
57973674 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
57973703 ATGAACATGT
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:57974004 original size:16 final size:16
Alignment explanation
Indices: 57973983--57974013 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
57973973 TCTTCTAAGG
57973983 TAGCTAAGGGTTAAAT
1 TAGCTAAGGGTTAAAT
57973999 TAGCTAAGGGTTAAA
1 TAGCTAAGGGTTAAA
57974014 ATGTTCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
TAGCTAAGGGTTAAAT
Found at i:57976383 original size:8 final size:8
Alignment explanation
Indices: 57976369--57976472 Score: 192
Period size: 8 Copynumber: 13.1 Consensus size: 8
57976359 CATATTTATT
57976369 TTTTAAAA
1 TTTTAAAA
*
57976377 TTAT-AAA
1 TTTTAAAA
57976384 TTTTAAAA
1 TTTTAAAA
57976392 TTTTAAAA
1 TTTTAAAA
57976400 TTTTAAAA
1 TTTTAAAA
57976408 TTTTAAAA
1 TTTTAAAA
57976416 TTTTAAAA
1 TTTTAAAA
57976424 TTTTAAAA
1 TTTTAAAA
57976432 TTTTAAAA
1 TTTTAAAA
57976440 TTTTAAAA
1 TTTTAAAA
57976448 TTTTAAAA
1 TTTTAAAA
57976456 TTTTAAAA
1 TTTTAAAA
57976464 TTTTAAAA
1 TTTTAAAA
57976472 T
1 T
57976473 ATAAAAATAT
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
7 6 0.06
8 87 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTTAAAA
Found at i:57976701 original size:23 final size:23
Alignment explanation
Indices: 57976674--57976717 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57976664 TGAATTGTAA
*
57976674 AATTT-TAAAATTATATATATTTG
1 AATTTATAAAAGTATA-ATATTTG
57976697 AATTTATAAAAGTATAATATT
1 AATTTATAAAAGTATAATATT
57976718 ATTTAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
AATTTATAAAAGTATAATATTTG
Found at i:57976849 original size:19 final size:18
Alignment explanation
Indices: 57976832--57976876 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
57976822 TATTTTTTAA
57976832 ATAATATTTTA-GTTTTT
1 ATAATATTTTAGGTTTTT
*
57976849 ATATTATTTTAGGTTTTTT
1 ATAATATTTTAGG-TTTTT
*
57976868 TTAATATTT
1 ATAATATTT
57976877 ATATAACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 10 0.43
18 1 0.04
19 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (18 bp):
ATAATATTTTAGGTTTTT
Found at i:57978974 original size:316 final size:315
Alignment explanation
Indices: 57978353--57978984 Score: 1039
Period size: 316 Copynumber: 2.0 Consensus size: 315
57978343 CGTGTAGAAG
* * *
57978353 AGCTGTAGCCATTTGGTTCACGAATTAGCCTGAGGTTTTAAAGGCACATGGTCGTGTGGTGGCCA
1 AGCTATAGCCATTTGGTTCACGAACTAGCCTGAGGTTTTAAAGGCACATAGTCGTGTGGTGGCCA
* *
57978418 TGTGGTCCACCTATGTAGAAGACCGTGTGGCCCTAATCTTACACACGATAAACACTGATTCACTT
66 TGTGGTCCACCTATGTAGAAGACCGTGTGGCCCTAATCCTACAAACGATAAACACTGATTCACTT
* * * *
57978483 GGGAACGATCACACGCCTTTCATCAGTGTTCTGATTGACGTTCTTCACGATCAAACCTGATCTAA
131 GGGAAAGATCACACGCCTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACCTGATCCAA
* * *
57978548 TACACTTAAATTCGATCCTTCAGAAATATGTACACAATTAGTTATTAATGTCAAGATTGACGAGA
196 TACACTTAAATTCGATCCTTCAGAAATATGTACACAATTAGTGATTAACGTCAAGAATGACGAGA
*
57978613 TTTGCAAAAGATTTATCAAGATTTCAAATAGATCGATTCATCGAATTAAAGATTA
261 TTTGCAAAAGATCTATCAAGATTTCAAATAGATCGATTCATCGAATTAAAGATTA
*
57978668 AGCTATAGCCATTTGGTTCACGAACTAGCCTGAGGTTTTAAGAGGCACATAGTCGTGTGGTTGCC
1 AGCTATAGCCATTTGGTTCACGAACTAGCCTGAGGTTTTAA-AGGCACATAGTCGTGTGGTGGCC
** *
57978733 ATGTGGTCCACCTATGTAGAAGATTGTGTGGCCCTAATCCTACAAACGATAAGCACTGATTCACT
65 ATGTGGTCCACCTATGTAGAAGACCGTGTGGCCCTAATCCTACAAACGATAAACACTGATTCACT
* *
57978798 TGGGAAAGATCACACGCCTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACTTGATCCG
130 TGGGAAAGATCACACGCCTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACCTGATCCA
* *
57978863 ATACACTTAAATTCGATCCTTTAGACATATGTACACAATTAGTGATTAACGTCAAGAATGACGAG
195 ATACACTTAAATTCGATCCTTCAGAAATATGTACACAATTAGTGATTAACGTCAAGAATGACGAG
* * *
57978928 ATTTTCAAAAGATCTATCAATATTTCAAATAGATCGATTGATCGAATTAAAGATTA
260 ATTTGCAAAAGATCTATCAAGATTTCAAATAGATCGATTCATCGAATTAAAGATTA
57978984 A
1 A
57978985 AGGTTGGAGA
Statistics
Matches: 292, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
315 39 0.13
316 253 0.87
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (315 bp):
AGCTATAGCCATTTGGTTCACGAACTAGCCTGAGGTTTTAAAGGCACATAGTCGTGTGGTGGCCA
TGTGGTCCACCTATGTAGAAGACCGTGTGGCCCTAATCCTACAAACGATAAACACTGATTCACTT
GGGAAAGATCACACGCCTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACCTGATCCAA
TACACTTAAATTCGATCCTTCAGAAATATGTACACAATTAGTGATTAACGTCAAGAATGACGAGA
TTTGCAAAAGATCTATCAAGATTTCAAATAGATCGATTCATCGAATTAAAGATTA
Found at i:57980823 original size:5 final size:5
Alignment explanation
Indices: 57980808--57980842 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
57980798 TTCCATTTGC
*
57980808 TCTTT TTTTT TCTTT TCTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
57980843 CTGTATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:57982568 original size:29 final size:29
Alignment explanation
Indices: 57982525--57982647 Score: 131
Period size: 29 Copynumber: 4.2 Consensus size: 29
57982515 CAAAAAATAA
*
57982525 AAAATTATATTTTAACCCCTAAACTTTTT
1 AAAATTACATTTTAACCCCTAAACTTTTT
* * *
57982554 GAAATTGCATTTTAACCCCTAAA-TTTCAT
1 AAAATTACATTTTAACCCCTAAACTTT-TT
* * *
57982583 AAAATTACATTTTGACCCATGAACTTTTT
1 AAAATTACATTTTAACCCCTAAACTTTTT
* * *
57982612 AAAATTACGTTTTGACCCCTAAACTTTCTC
1 AAAATTACATTTTAACCCCTAAACTTT-TT
57982642 AAAATT
1 AAAATT
57982648 TTGTTTCAGC
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.04
29 64 0.83
30 10 0.13
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTAACCCCTAAACTTTTT
Found at i:57982588 original size:58 final size:59
Alignment explanation
Indices: 57982525--57982647 Score: 151
Period size: 58 Copynumber: 2.1 Consensus size: 59
57982515 CAAAAAATAA
* * * *
57982525 AAAATTATATTTTAACCCCTAAACTTTTTGAAATTGCATTTTAACCCCTAAA-TTTCAT-
1 AAAATTACATTTTAACCCATAAACTTTTTAAAATTACATTTTAACCCCTAAACTTTC-TC
* * * *
57982583 AAAATTACATTTTGACCCATGAACTTTTTAAAATTACGTTTTGACCCCTAAACTTTCTC
1 AAAATTACATTTTAACCCATAAACTTTTTAAAATTACATTTTAACCCCTAAACTTTCTC
57982642 AAAATT
1 AAAATT
57982648 TTGTTTCAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 45 0.82
59 10 0.18
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAATTACATTTTAACCCATAAACTTTTTAAAATTACATTTTAACCCCTAAACTTTCTC
Found at i:57982987 original size:3 final size:3
Alignment explanation
Indices: 57982979--57983048 Score: 62
Period size: 3 Copynumber: 24.7 Consensus size: 3
57982969 CCAAGGCGTA
57982979 AAG AAG AAG AAG AAG AAG AAGG AAG AA- AA- AAG AAG AAGG AAG AA-
1 AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AA-G AAG AAG
* *
57983023 AA- AAG AAA AAG -AG AA- AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
57983049 AAAATAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 12 0.21
3 39 0.68
4 6 0.11
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:57983013 original size:17 final size:17
Alignment explanation
Indices: 57982981--57983048 Score: 82
Period size: 17 Copynumber: 3.8 Consensus size: 17
57982971 AAGGCGTAAA
57982981 GAAGAAGAAGAAGAAGAAG
1 GAAGAA-AA-AAGAAGAAG
57983000 GAAGAAAAAAGAAGAAG
1 GAAGAAAAAAGAAGAAG
*
57983017 GAAGAAAAAAGAAAAAG
1 GAAGAAAAAAGAAGAAG
*
57983034 AGAAAAGAAAAAGAA
1 -GAAGA-AAAAAGAA
57983049 AAAATAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 25 0.56
18 6 0.13
19 14 0.31
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
GAAGAAAAAAGAAGAAG
Found at i:57983034 original size:13 final size:13
Alignment explanation
Indices: 57983018--57983052 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
57983008 AAGAAGAAGG
57983018 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
*
57983031 AAGAGAAAAGAAA
1 AAGAAAAAAGAAA
57983044 AAGAAAAAA
1 AAGAAAAAA
57983053 TAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:57983037 original size:8 final size:7
Alignment explanation
Indices: 57983001--57983052 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
57982991 AAGAAGAAGG
57983001 AAGAAAA
1 AAGAAAA
57983008 AAGAAGAA
1 AAGAA-AA
57983016 GGAAGAAAA
1 --AAGAAAA
57983025 AAG-AAA
1 AAGAAAA
*
57983031 AAGAGAA
1 AAGAAAA
57983038 AAG-AAA
1 AAGAAAA
57983044 AAGAAAA
1 AAGAAAA
57983051 AA
1 AA
57983053 TAATAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 11 0.29
7 18 0.47
8 2 0.05
9 2 0.05
10 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:57983052 original size:20 final size:22
Alignment explanation
Indices: 57982985--57983052 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
57982975 CGTAAAGAAG
*
57982985 AAGAAGAAGAAGAAGGAAGAAAA
1 AAGAAGAAGAAGAA-AAAGAAAA
57983008 AAGAAGAAGGAAGAAAAA-AGAAA
1 AAGAAGAA-GAAGAAAAAGA-AAA
57983031 AAG-AGAA-AAGAAAAAGAAAA
1 AAGAAGAAGAAGAAAAAGAAAA
57983051 AA
1 AA
57983053 TAATAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 13 0.32
21 1 0.02
22 5 0.12
23 16 0.39
24 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (22 bp):
AAGAAGAAGAAGAAAAAGAAAA
Found at i:57983133 original size:17 final size:18
Alignment explanation
Indices: 57983101--57983140 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
57983091 CCGGCTCAAA
57983101 ACCCAACCCGAGCAGAAG
1 ACCCAACCCGAGCAGAAG
*
57983119 ACCCGACCC-AGCAGAAG
1 ACCCAACCCGAGCAGAAG
57983136 -CCCAA
1 ACCCAA
57983141 AGCAGCCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 4 0.20
17 8 0.40
18 8 0.40
ACGTcount: A:0.38, C:0.42, G:0.20, T:0.00
Consensus pattern (18 bp):
ACCCAACCCGAGCAGAAG
Found at i:57983261 original size:26 final size:26
Alignment explanation
Indices: 57983210--57983262 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
57983200 AGGGGGCAGG
** *
57983210 CCAACAGCAGGCCCAATTCCAGCAGC
1 CCAACAGCAGGCCCAAGCCCAACAGC
*
57983236 CCAACAGCAGGCCCTAGCCCAACAGC
1 CCAACAGCAGGCCCAAGCCCAACAGC
57983262 C
1 C
57983263 AGCCTGTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.45, G:0.19, T:0.06
Consensus pattern (26 bp):
CCAACAGCAGGCCCAAGCCCAACAGC
Found at i:57983358 original size:11 final size:11
Alignment explanation
Indices: 57983342--57983415 Score: 80
Period size: 11 Copynumber: 6.6 Consensus size: 11
57983332 GGAGCCCAGC
*
57983342 AGAAAATGAAA
1 AGAAAAAGAAA
57983353 AGAAAAAAGAAA
1 AG-AAAAAGAAA
*
57983365 A-AAAGAAAAAA
1 AGAAA-AAGAAA
57983376 AGAAAAA-AAA
1 AGAAAAAGAAA
*
57983386 AGAAAAAAGAAG
1 AG-AAAAAGAAA
57983398 AGAAAAAGAAA
1 AGAAAAAGAAA
57983409 AGAAAAA
1 AGAAAAA
57983416 TTCAATTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.15
11 30 0.56
12 16 0.30
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:57983362 original size:7 final size:7
Alignment explanation
Indices: 57983350--57983409 Score: 61
Period size: 7 Copynumber: 8.3 Consensus size: 7
57983340 GCAGAAAATG
57983350 AAAAGAA
1 AAAAGAA
57983357 AAAAGAAA
1 AAAAG-AA
57983365 AAAAGAAA
1 AAAAG-AA
57983373 AAAAGAA
1 AAAAGAA
57983380 AAAA-AA
1 AAAAGAA
57983386 AGAAA-AA
1 A-AAAGAA
*
57983393 AGAAGAGA
1 AAAAGA-A
57983401 AAAAGAA
1 AAAAGAA
57983408 AA
1 AA
57983410 GAAAAATTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
6 5 0.11
7 21 0.45
8 21 0.45
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:57983368 original size:8 final size:8
Alignment explanation
Indices: 57983350--57983415 Score: 73
Period size: 8 Copynumber: 8.2 Consensus size: 8
57983340 GCAGAAAATG
57983350 AAAAG-AA
1 AAAAGAAA
57983357 AAAAGAAA
1 AAAAGAAA
57983365 AAAAGAAA
1 AAAAGAAA
57983373 AAAAGAAA
1 AAAAGAAA
*
57983381 AAAAAAGAA
1 AAAAGA-AA
57983390 AAAAGAAGA
1 AAAAGAA-A
* *
57983399 GAAA-AAG
1 AAAAGAAA
57983406 AAAAGAAA
1 AAAAGAAA
57983414 AA
1 AA
57983416 TTCAATTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
7 8 0.16
8 30 0.61
9 11 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:57983380 original size:28 final size:30
Alignment explanation
Indices: 57983344--57983415 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 30
57983334 AGCCCAGCAG
*
57983344 AAAATGAAAAGAAAAAAG-AAAAA-AAGAA
1 AAAAAGAAAAGAAAAAAGAAAAAAGAAGAA
*
57983372 AAAAAG-AAA-AAAAAAGAAAAAAGAAGAG
1 AAAAAGAAAAGAAAAAAGAAAAAAGAAGAA
57983400 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
57983416 TTCAATTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 7 0.18
27 8 0.21
28 15 0.39
29 3 0.08
30 5 0.13
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.01
Consensus pattern (30 bp):
AAAAAGAAAAGAAAAAAGAAAAAAGAAGAA
Found at i:57983390 original size:33 final size:33
Alignment explanation
Indices: 57983350--57983415 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
57983340 GCAGAAAATG
57983350 AAAAGAAAAAAGAA-AAAAAGAAAAAAAGAAAAA
1 AAAAGAAAAAAGAAGAAAAA-AAAAAAAGAAAAA
* *
57983383 AAAAGAAAAAAGAAGAGAAAAAGAAAAGAAAAA
1 AAAAGAAAAAAGAAGAAAAAAAAAAAAGAAAAA
57983416 TTCAATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (33 bp):
AAAAGAAAAAAGAAGAAAAAAAAAAAAGAAAAA
Found at i:57983807 original size:21 final size:20
Alignment explanation
Indices: 57983775--57983816 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
57983765 TCGGGTTTCG
57983775 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
57983795 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
57983816 A
1 A
57983817 TAAAGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:57983817 original size:19 final size:19
Alignment explanation
Indices: 57983775--57983816 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
57983765 TCGGGTTTCG
57983775 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
57983795 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
57983815 AA
1 AA
57983817 TAAAGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:57983972 original size:35 final size:35
Alignment explanation
Indices: 57983922--57984051 Score: 154
Period size: 35 Copynumber: 3.7 Consensus size: 35
57983912 AAAAAATTAG
*
57983922 AAAATTTTTCGTGTTTTCAAAAAATTCCAATTTTC
1 AAAATTTTTCGTGTTTTCAAAAAATTCCAGTTTTC
* * *
57983957 AAAATTTTTCATGTTTTCAGAAAATTCCCGTGTTTC
1 AAAATTTTTCGTGTTTTCAAAAAATTCCAGT-TTTC
* * * * *
57983993 AAAAATTCTCGTGTTTTCAAAAATTTCGATGTTTTG
1 AAAATTTTTCGTGTTTTCAAAAAATTCCA-GTTTTC
57984029 AAAA-TTTTCGTGTTTTCAAAAAA
1 AAAATTTTTCGTGTTTTCAAAAAA
57984052 AATCTCGTGT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
35 44 0.56
36 33 0.42
37 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (35 bp):
AAAATTTTTCGTGTTTTCAAAAAATTCCAGTTTTC
Found at i:57983975 original size:18 final size:18
Alignment explanation
Indices: 57983922--57984080 Score: 114
Period size: 17 Copynumber: 8.9 Consensus size: 18
57983912 AAAAAATTAG
*
57983922 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* ***
57983940 AAAAA-ATTCCAATTTTC
1 AAAAATTTTCGTGTTTTC
* *
57983957 AAAATTTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
**
57983975 AGAAAATTCCCGTG-TTTC
1 A-AAAATTTTCGTGTTTTC
*
57983993 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
57984011 AAAAA-TTTCGATGTTTT-
1 AAAAATTTTCG-TGTTTTC
*
57984028 GAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
57984046 AAAAAAAATCTCGTG-TTTC
1 --AAAAATTTTCGTGTTTTC
*
57984065 ATAAATTTTCGT-TTTT
1 AAAAATTTTCGTGTTTT
57984081 TAGACAAAAT
Statistics
Matches: 109, Mismatches: 23, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
17 49 0.45
18 38 0.35
19 12 0.11
20 10 0.09
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:57983999 original size:17 final size:18
Alignment explanation
Indices: 57983968--57984050 Score: 82
Period size: 18 Copynumber: 4.7 Consensus size: 18
57983958 AAATTTTTCA
57983968 TGTTTTCAGAAAATTCCCG
1 TGTTTTCA-AAAATTCCCG
*
57983987 TG-TTTCAAAAATTCTCG
1 TGTTTTCAAAAATTCCCG
*
57984004 TGTTTTCAAAAATT-TCG
1 TGTTTTCAAAAATTCCCG
* **
57984021 ATGTTTT-GAAAATTTTCG
1 -TGTTTTCAAAAATTCCCG
57984039 TGTTTTCAAAAA
1 TGTTTTCAAAAA
57984051 AAATCTCGTG
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
17 26 0.46
18 29 0.51
19 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (18 bp):
TGTTTTCAAAAATTCCCG
Found at i:57984105 original size:34 final size:34
Alignment explanation
Indices: 57983985--57984126 Score: 117
Period size: 34 Copynumber: 4.0 Consensus size: 34
57983975 AGAAAATTCC
* * * *
57983985 CGTGTTTCAAAAATTCTCGTGTTTT-CAAAAATTT
1 CGTGTTTC-AAAATTTTCGTTTTTTAAAAAAAATT
* *
57984019 CGATGTTTTGAAAATTTTCGTGTTTTCAAAAAAAATCT
1 CG-TG-TTTCAAAATTTTCGT-TTTTTAAAAAAAAT-T
* *
57984057 CGTGTTTCATAAATTTTCGTTTTTTAGACAAAATT
1 CGTGTTTCA-AAATTTTCGTTTTTTAAAAAAAATT
* *
57984092 -GTGTTTCCAAAATTCTCGTGTTTTAAAAAAAATT
1 CGTGTTT-CAAAATTTTCGTTTTTTAAAAAAAATT
57984126 C
1 C
57984127 TCGTGTTTTA
Statistics
Matches: 86, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
34 29 0.34
35 15 0.17
36 21 0.24
37 18 0.21
38 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (34 bp):
CGTGTTTCAAAATTTTCGTTTTTTAAAAAAAATT
Found at i:57984114 original size:17 final size:17
Alignment explanation
Indices: 57983971--57984134 Score: 100
Period size: 17 Copynumber: 9.2 Consensus size: 17
57983961 TTTTTCATGT
*
57983971 TTTCAGAAAATTCCCGTG
1 TTTCA-AAAATTCTCGTG
57983989 TTTCAAAAATTCTCGTG
1 TTTCAAAAATTCTCGTG
57984006 TTTTCAAAAATT-TCGATG
1 -TTTCAAAAATTCTCG-TG
** *
57984024 TTTTGAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
*
57984041 TTTTCAAAAAAAATCTCGTG
1 -TTTC--AAAAATTCTCGTG
* * *
57984061 TTTCATAAATTTTCGTT
1 TTTCAAAAATTCTCGTG
* *
57984078 TTTTAGACAAAAT-T-GTG
1 TTTCA-A-AAATTCTCGTG
*
57984095 TTTCCAAAATTCTCGTG
1 TTTCAAAAATTCTCGTG
*
57984112 TTTTAAAAAAAATTCTCGTG
1 -TTT--CAAAAATTCTCGTG
57984132 TTT
1 TTT
57984135 TAATCGGATC
Statistics
Matches: 113, Mismatches: 20, Indels: 25
0.72 0.13 0.16
Matches are distributed among these distances:
15 4 0.04
16 2 0.02
17 46 0.41
18 28 0.25
19 11 0.10
20 22 0.19
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:57984125 original size:20 final size:20
Alignment explanation
Indices: 57984100--57984137 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
57984090 TTGTGTTTCC
57984100 AAAATTCTCGTGTTTTAAAA
1 AAAATTCTCGTGTTTTAAAA
57984120 AAAATTCTCGTGTTTTAA
1 AAAATTCTCGTGTTTTAA
57984138 TCGGATCACG
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:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (20 bp):
AAAATTCTCGTGTTTTAAAA
Found at i:57990821 original size:80 final size:80
Alignment explanation
Indices: 57990660--57990821 Score: 299
Period size: 79 Copynumber: 2.0 Consensus size: 80
57990650 TCAAGAAATA
57990660 TTTTTAAAATTCTATTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAAATTCTATTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
57990725 CACGCTGAGGTATTT
66 CACGCTGAGGTATTT
* *
57990740 TTTTTAAAATTCTGTTTTTTTC-AAAAAATCAACTCATAATACAGATGTGAGTTGAGCCTCGGGT
1 TTTTTAAAATTCTATTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
57990804 CACGCTGAGGTATTT
66 CACGCTGAGGTATTT
57990819 TTT
1 TTT
57990822 AAATTGAGTT
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
79 59 0.74
80 21 0.26
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (80 bp):
TTTTTAAAATTCTATTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
CACGCTGAGGTATTT
Found at i:57990842 original size:118 final size:119
Alignment explanation
Indices: 57990708--57990947 Score: 405
Period size: 122 Copynumber: 2.0 Consensus size: 119
57990698 AATACAGAGG
*
57990708 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTT-AA-AA-TTCTGTTTTTTTCAAAAAATC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATAATTTATG-TTTTTTCAAAAAATC
*
57990770 AACTCATAATACAGATGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTAAAT
65 AACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTTTTAAAT
57990826 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTAATTTATGTTTTTTCAAAAAAT
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAA--TAATTTATGTTTTTTCAAAAAAT
57990891 CAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAAT
64 CAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAAT
57990947 T
1 T
57990948 TCTGCTTTTT
Statistics
Matches: 115, Mismatches: 2, Indels: 7
0.93 0.02 0.06
Matches are distributed among these distances:
118 37 0.32
119 2 0.02
121 10 0.09
122 62 0.54
123 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (119 bp):
TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATAATTTATGTTTTTTCAAAAAATCA
ACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAAT
Found at i:57990988 original size:77 final size:77
Alignment explanation
Indices: 57990826--57992672 Score: 2321
Period size: 77 Copynumber: 23.4 Consensus size: 77
57990816 TTTTTTAAAT
* ** *
57990826 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTAATTTATGTTTTTTCAAAAAAT
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTA---TTTTTAAATTT--CTGCT-TTTTTTAAAAAAAT
57990891 CAACTCATAATACAGAGG
60 CAACTCATAATACAGAGG
57990909 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57990974 ATAATACAGAGG
66 ATAATACAGAGG
57990986 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57991051 ATAATACAGAGG
66 ATAATACAGAGG
*
57991063 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAATTTAATTTCTG-TTTTTTTCAAAAAAT
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTA--TTTTT-A---AATTTCTGCTTTTTTTAAAAAAAT
57991127 CAACTCATAATACAGAGG
60 CAACTCATAATACAGAGG
*
57991145 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTCAAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57991210 ATAATACAGAGG
66 ATAATACAGAGG
* *
57991222 TGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTTAAATTTCTGC-TTTTTTCAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57991286 ATAATACAGAGG
66 ATAATACAGAGG
57991298 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57991363 ATAATACAGAGG
66 ATAATACAGAGG
57991375 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57991440 ATAATACAGAGG
66 ATAATACAGAGG
57991452 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57991517 ATAATACAGAGG
66 ATAATACAGAGG
57991529 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57991594 ATAATACAGAGG
66 ATAATACAGAGG
57991606 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
57991671 ATAATACAGAGG
66 ATAATACAGAGG
* * *
57991683 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT-AATTTATG-TCTTTTTTCAAAAAAGCAACT
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCT-TTTTTTAAAAAAATCAACT
57991746 CATAATACAGAGG
65 CATAATACAGAGG
* * *
57991759 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT-AATTTATG-TCTTTTTTCAAAAAAGCAACT
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCT-TTTTTTAAAAAAATCAACT
57991822 CATAATACAGAGG
65 CATAATACAGAGG
* * *
57991835 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT-AATTTATG-TCTTTTTTCAAAAAAGCAACT
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCT-TTTTTTAAAAAAATCAACT
57991898 CATAATACAGAGG
65 CATAATACAGAGG
*
57991911 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT-AATTTAT--TTTTTTTAAAAAAAATCAACT
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTT-AAAAAAATCAACT
57991973 CATAATACAGAGG
65 CATAATACAGAGG
* * * * *
57991986 TGAGTTGAGCCTCGGGTCACACCGAGGTATTTCTTTTAAATTTATG----TTTTCAAAAAATTAA
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTTAAATTTCTGCTTTTTTTAAAAAAATCAA
* * *
57992047 CTCATATTGCGAGAAG
63 CTCATAATAC-AGAGG
* * * **
57992063 TGAGTTGAGCCTCGAGTCGCATGCTGAGGTATTTTTTTTAAATTTCT-ATTTTTTTTCAAAAATC
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTA---TTTTTAAATTTCTGCTTTTTTTAAAAAAATC
* *
57992127 AACTCATATTGCGAGAGG
61 AACTCATAATAC-AGAGG
* * * * ** **
57992145 TGAGTTGAGTCTCGGATCACACGCTAAGGTATTTTTTTTAATTTCTATTTTTTTTTCAAAAATCA
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTA--TTTTTAAATTTCTGCTTTTTTTAAAAAAATCA
* * * *
57992210 ACTCATATTGCAATAAG
62 ACTCATAATAC-AGAGG
* * * **
57992227 TGAGTTGAGCCTCGGGTCGCACGTTGAGGTATTTTTTTAAATTTTTGTTTTTTTTTCAAAAATCA
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTA--TTTTTAAATTTCTGCTTTTTTTAAAAAAATCA
* * *
57992292 ACTCATATTGCGAGAAG
62 ACTCATAATAC-AGAGG
* **
57992309 TGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTAAAATTTCTGTTTTTTTTTCAAAAATC
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTA--TTTTT-AAATTTCTGCTTTTTTTAAAAAAATC
* * *
57992374 AACTCATATTGCGAGAAG
61 AACTCATAATAC-AGAGG
*
57992392 TGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATTTCTGC--TTTTTCAAAAAATC
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTA--T-TTTTAAATTTCTGCTTTTTTTAAAAAAATC
* * *
57992455 AACTCATATTGCGAGAAG
61 AACTCATAATAC-AGAGG
* **
57992473 TGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATTTTTG-TTTTTCAAAAAAAATC
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTA--T-TTTTAAATTTCTGCTTTTTTTAAAAAAATC
* * *
57992537 AACTCATATTGCGAGAAG
61 AACTCATAATAC-AGAGG
* **
57992555 TGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATTTTTG-TTTTTCAAAAAAAATC
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTA--T-TTTTAAATTTCTGCTTTTTTTAAAAAAATC
* * *
57992619 AACTCATATTGCGAGAAG
61 AACTCATAATAC-AGAGG
57992637 TGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTT
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTTT
57992673 TTAAATTAAT
Statistics
Matches: 1673, Mismatches: 63, Indels: 60
0.93 0.04 0.03
Matches are distributed among these distances:
74 6 0.00
75 53 0.03
76 328 0.20
77 609 0.36
78 6 0.00
79 37 0.02
80 21 0.01
81 91 0.05
82 395 0.24
83 123 0.07
84 4 0.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (77 bp):
TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTAAAAAAATCAACTC
ATAATACAGAGG
Found at i:57992710 original size:21 final size:21
Alignment explanation
Indices: 57992668--57992710 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
57992658 CGCTGAGGTA
* *
57992668 TTTTTTTAAATTAATTTCTAT
1 TTTTTTTAAATCAATCTCTAT
57992689 TTTTTTTAAATCAA-CTCATAT
1 TTTTTTTAAATCAATCTC-TAT
57992710 T
1 T
57992711 GCGAGAAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTTTAAATCAATCTCTAT
Found at i:57992931 original size:86 final size:86
Alignment explanation
Indices: 57992809--57994312 Score: 2111
Period size: 86 Copynumber: 17.9 Consensus size: 86
57992799 TTTTTTTCAA
57992809 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57992874 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
* *
57992895 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTT-TTTTAAA
* **
57992960 TTTCTGCTTTTTCA-------AA
65 TTTCTG-TTTTTTATGTTTTTTT
57992976 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993041 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993062 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993127 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993148 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993213 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993234 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993299 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993320 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993385 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993406 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993471 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993492 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993557 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993578 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993643 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993664 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
57993729 TTCTGTTTTTTATGTTTTTTT
66 TTCTGTTTTTTATGTTTTTTT
57993750 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
* ** ***
57993815 TTCTGTTTCTGCT-TTTTCAAA
66 TTCTGTTTTTTATGTTTT-TTT
* *
57993836 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTT-TTTTAAA
* * ****
57993901 TTTTTGTTTTTCA-----AAAA
65 TTTCTGTTTTTTATGTTTTTTT
* * *
57993918 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTAAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTT-TTTTAAA
* * ******
57993983 TTTCTATTTTTCA---AAAAAA
65 TTTCTGTTTTTTATGTTTTTTT
* * * *
57994002 AAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTT-TTTTAAA
****
57994064 TTTCTGTTTTTT-T-TTTCAAA
65 TTTCTGTTTTTTATGTTTTTTT
* * ** ** * *
57994084 AAATCAACTAATATTGCGAGAGGTGAGTTGAGTCTC-GAAC-CATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTT-TTTTAAA
* *
57994147 TTTCTGTTTTTCA--------A
65 TTTCTGTTTTTTATGTTTTTTT
* * * *
57994161 AAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTTGCACGCTGAGGTA---TTTTAAAT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
**
57994223 TTC-------TAT-TTTTTCAA
66 TTCTGTTTTTTATGTTTTT-TT
* * * *
57994237 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTT-TTTTAAA
57994302 TTTCTGTTTTT
65 TTTCTGTTTTT
57994313 CAAAAAAAAA
Statistics
Matches: 1323, Mismatches: 56, Indels: 77
0.91 0.04 0.05
Matches are distributed among these distances:
68 1 0.00
75 11 0.01
76 51 0.04
77 33 0.02
78 1 0.00
79 16 0.01
80 24 0.02
81 87 0.07
82 97 0.07
83 70 0.05
84 20 0.02
85 4 0.00
86 873 0.66
87 29 0.02
88 6 0.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (86 bp):
AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTTTTTTAAAT
TTCTGTTTTTTATGTTTTTTT
Found at i:57993949 original size:82 final size:80
Alignment explanation
Indices: 57993750--57994526 Score: 719
Period size: 82 Copynumber: 9.7 Consensus size: 80
57993740 ATGTTTTTTT
* *
57993750 AAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGTCGCAAGCTGAGGTATTT-TTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
57993814 TTTCTGTTTCTGCTTTTTCAAA
66 ----T-TTT-TG-TTTTTCAAA
57993836 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
57993901 TTTTTGTTTTTCAAAAA
66 TTTTTGTTTTTC--AAA
*
57993918 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTAAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
* *
57993983 TTTCTATTTTTCAAAAAAA
66 TTTTTGTTTTTC----AAA
* *
57994002 AAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
*
57994064 TTTCTGTTTTTTTTTTCAAA
66 ----T-TTTTGTTTTTCAAA
* * * ** * *
57994084 AAATCAACTAATATTGCGAGAGGTGAGTTGAGTCTC-GAAC-CATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
*
57994147 TTTCTGTTTTTC-AA
66 TTTTTGTTTTTCAAA
* *
57994161 AAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTTGCACGCTGAGGTA----TTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
57994222 TTTCTAT-TTTTTC-AA
66 TTT-T-TGTTTTTCAAA
* *
57994237 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
*
57994302 TTTCTGTTTTTCAAAAAAA
66 TTTTTGTTTTTC----AAA
* * * * * *
57994321 AAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTTGGGT--CACGCTGAGGTATTTTTAATTTC
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCT--TTTA
** *
57994383 GGTCTTTT-TTTTT--TA
64 AAT-TTTTGTTTTTCAAA
* * * *
57994398 AAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT--CACACTGAGGTA-TT-TTTT-AA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
* ***
57994457 TTTATGTTTTT-TTT
66 TTTTTGTTTTTCAAA
* * * * *
57994471 AAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG-CGACACTCCGAGGTATTT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCG-CACGCTGAGGTATTT
57994527 TCAATTTCTG
Statistics
Matches: 604, Mismatches: 52, Indels: 80
0.82 0.07 0.11
Matches are distributed among these distances:
71 3 0.00
72 6 0.01
73 42 0.07
75 21 0.03
76 62 0.10
77 85 0.14
78 11 0.02
79 17 0.03
80 16 0.03
81 40 0.07
82 99 0.16
83 89 0.15
84 41 0.07
85 1 0.00
86 64 0.11
87 7 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (80 bp):
AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAA
TTTTTGTTTTTCAAA
Found at i:57994755 original size:29 final size:29
Alignment explanation
Indices: 57994713--57994825 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
57994703 AAAAAATAAA
57994713 AAATTACATTTTAACCCCTAAACTTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTTG
* * * *
57994742 AAATTTCATTTTAACGCCTAAA-TTTCATA
1 AAATTACATTTTAACCCCTAAACTTT-TTG
* * *
57994771 AAATTACATTTTGACCCATAAAATTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTTG
* * *
57994800 AAATTACGTTTTGACCACTAAACTTT
1 AAATTACATTTTAACCCCTAAACTTT
57994826 CTCAAAATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.04
29 62 0.91
30 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (29 bp):
AAATTACATTTTAACCCCTAAACTTTTTG
Found at i:57994821 original size:58 final size:59
Alignment explanation
Indices: 57994712--57994834 Score: 153
Period size: 58 Copynumber: 2.1 Consensus size: 59
57994702 CAAAAAATAA
* * *
57994712 AAAATTACATTTTAACCCCTAAACTTTTTGAAATTTCATTTTAACGCCTAAA-TTTCAT-
1 AAAATTACATTTTAACCCATAAAATTTTTGAAATTACATTTTAACGCCTAAACTTTC-TC
* * *
57994770 AAAATTACATTTTGACCCATAAAATTTTTGAAATTACGTTTTGAC-CACTAAACTTTCTC
1 AAAATTACATTTTAACCCATAAAATTTTTGAAATTACATTTTAACGC-CTAAACTTTCTC
57994829 AAAATT
1 AAAATT
57994835 TTGTTTCGGC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 1 0.02
58 45 0.80
59 10 0.18
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAATTACATTTTAACCCATAAAATTTTTGAAATTACATTTTAACGCCTAAACTTTCTC
Found at i:57995176 original size:3 final size:3
Alignment explanation
Indices: 57995168--57995246 Score: 76
Period size: 3 Copynumber: 26.7 Consensus size: 3
57995158 CCAAGGCGTA
57995168 AAG AAG AAG AAG AAG AAG AAG AAGG AAG AAG AAAG AAG AAGG AAG AA-
1 AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG -AAG AAG AA-G AAG AAG
* * *
57995215 AA- AAG AAA AAG -AG AA- AAG AAA AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
57995247 AAATAATAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
2 8 0.12
3 47 0.73
4 9 0.14
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:57995249 original size:7 final size:7
Alignment explanation
Indices: 57995196--57995249 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
57995186 AAGAAGGAAG
*
57995196 AAGAAAG
1 AAGAAAA
**
57995203 AAGAAGG
1 AAGAAAA
57995210 AAGAAAA
1 AAGAAAA
57995217 AAG-AAA
1 AAGAAAA
*
57995223 AAGAGAA
1 AAGAAAA
57995230 AAG-AAA
1 AAGAAAA
57995236 AAG-AAA
1 AAGAAAA
57995242 AAGAAAA
1 AAGAAAA
57995249 A
1 A
57995250 TAATAAAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 17 0.43
7 23 0.57
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:57995257 original size:19 final size:19
Alignment explanation
Indices: 57995193--57995249 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
57995183 AAGAAGAAGG
*
57995193 AAGAAGAAAGAAGAAG-GAA
1 AAGAA-AAAGAAAAAGAGAA
*
57995212 GA-AAAAAGAAAAAGAGAA
1 AAGAAAAAGAAAAAGAGAA
57995230 AAGAAAAAGAAAAAGA-AA
1 AAGAAAAAGAAAAAGAGAA
57995248 AA
1 AA
57995250 TAATAAAGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 9 0.27
18 10 0.30
19 14 0.42
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAGAAAAAGAAAAAGAGAA
Found at i:57995545 original size:16 final size:15
Alignment explanation
Indices: 57995515--57995548 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
57995505 CCGGCCCAAC
*
57995515 AGAAAAAAAAGAGAA
1 AGAAAAAAAAAAGAA
57995530 AGAAAGAAAAAAAGAA
1 AGAAA-AAAAAAAGAA
57995546 AGA
1 AGA
57995549 NNTTTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAGAA
Found at i:57995792 original size:21 final size:21
Alignment explanation
Indices: 57995766--57995808 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
57995756 TCGGGTTTCG
*
57995766 AAATTTTTCGTGTCTTCAAAA
1 AAATTTCTCGTGTCTTCAAAA
*
57995787 AAATTTCTCGTGTTTTCAAAA
1 AAATTTCTCGTGTCTTCAAAA
57995808 A
1 A
57995809 TAAAGTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (21 bp):
AAATTTCTCGTGTCTTCAAAA
Found at i:57995991 original size:17 final size:18
Alignment explanation
Indices: 57995963--57996000 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
57995953 TTTTTCATGT
57995963 TTTCAGAAAATTCCCGTG
1 TTTCAGAAAATTCCCGTG
*
57995981 TTTCA-AAAATTCTCGTG
1 TTTCAGAAAATTCCCGTG
57995998 TTT
1 TTT
57996001 TATAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (18 bp):
TTTCAGAAAATTCCCGTG
Found at i:57996000 original size:36 final size:35
Alignment explanation
Indices: 57995922--57996001 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
57995912 AGAAAATTTT
* *
57995922 TCGTGTTTTCAAAAAATTCCAATTTTCAAAATTTT
1 TCGTGTTTTCAAAAAATTCCAATTTTCAAAAATTC
* * **
57995957 TCATGTTTTCAGAAAATTCCCGTGTTTCAAAAATTC
1 TCGTGTTTTCAAAAAATTCCAAT-TTTCAAAAATTC
57995993 TCGTGTTTT
1 TCGTGTTTT
57996002 ATAAATTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 19 0.51
36 18 0.49
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (35 bp):
TCGTGTTTTCAAAAAATTCCAATTTTCAAAAATTC
Found at i:57996007 original size:17 final size:17
Alignment explanation
Indices: 57995969--57996074 Score: 81
Period size: 17 Copynumber: 6.1 Consensus size: 17
57995959 ATGTTTTCAG
* *
57995969 AAAATTCCCGTGTTTCA
1 AAAATTCTCGTGTTTTA
57995986 AAAATTCTCGTGTTTTA
1 AAAATTCTCGTGTTTTA
* * *
57996003 TAAATTTTCGTTTTTTA
1 AAAATTCTCGTGTTTTA
* **
57996020 GACAAAAT-T-GTGTTTCC
1 -A-AAATTCTCGTGTTTTA
57996037 AAAATTCTCGTGTTTTAAAA
1 AAAATTCTCGTGTTTT---A
57996057 AAAATTCTCGTGTTTTA
1 AAAATTCTCGTGTTTTA
57996074 A
1 A
57996075 TCGGATCACG
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
15 4 0.06
16 2 0.03
17 42 0.61
18 1 0.01
19 4 0.06
20 16 0.23
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAATTCTCGTGTTTTA
Found at i:57996062 original size:20 final size:20
Alignment explanation
Indices: 57996037--57996074 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
57996027 TTGTGTTTCC
57996037 AAAATTCTCGTGTTTTAAAA
1 AAAATTCTCGTGTTTTAAAA
57996057 AAAATTCTCGTGTTTTAA
1 AAAATTCTCGTGTTTTAA
57996075 TCGGATCACG
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:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (20 bp):
AAAATTCTCGTGTTTTAAAA
Found at i:58006107 original size:5 final size:5
Alignment explanation
Indices: 58006097--58006122 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
58006087 GAGATGGAAT
58006097 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
58006123 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:58006650 original size:19 final size:20
Alignment explanation
Indices: 58006626--58006664 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
58006616 AAAGGGTGAG
58006626 AAAT-AAAAGTTTAGGGGAA
1 AAATAAAAAGTTTAGGGGAA
*
58006645 AAATAAAAAGTTTTGGGGAA
1 AAATAAAAAGTTTAGGGGAA
58006665 TAAAAGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (20 bp):
AAATAAAAAGTTTAGGGGAA
Found at i:58009364 original size:80 final size:80
Alignment explanation
Indices: 58009231--58009509 Score: 558
Period size: 80 Copynumber: 3.5 Consensus size: 80
58009221 TCACTTCGAG
58009231 AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGGCTGCAATCTAACAAAGTAAATGAAAA
1 AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGGCTGCAATCTAACAAAGTAAATGAAAA
58009296 AAATTGTAACCCTTA
66 AAATTGTAACCCTTA
58009311 AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGGCTGCAATCTAACAAAGTAAATGAAAA
1 AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGGCTGCAATCTAACAAAGTAAATGAAAA
58009376 AAATTGTAACCCTTA
66 AAATTGTAACCCTTA
58009391 AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGGCTGCAATCTAACAAAGTAAATGAAAA
1 AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGGCTGCAATCTAACAAAGTAAATGAAAA
58009456 AAATTGTAACCCTTA
66 AAATTGTAACCCTTA
58009471 AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGG
1 AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGG
58009510 TCAAATGCTA
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 199 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (80 bp):
AAGCATTGAAGGTCAGATGCTATTGTATTGGTGTTAAGGCTGCAATCTAACAAAGTAAATGAAAA
AAATTGTAACCCTTA
Found at i:58009517 original size:27 final size:27
Alignment explanation
Indices: 58009479--58009536 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
58009469 TAAAGCATTG
* *
58009479 AAGGTCAGATGCTATTGTATTGGTGTT
1 AAGGTCAAATGCTACTGTATTGGTGTT
58009506 AAGGTCAAATGCTACTGTATTGGTGTT
1 AAGGTCAAATGCTACTGTATTGGTGTT
58009533 AAGG
1 AAGG
58009537 CTGCAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (27 bp):
AAGGTCAAATGCTACTGTATTGGTGTT
Found at i:58009810 original size:13 final size:13
Alignment explanation
Indices: 58009792--58009817 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58009782 CCAGAAACTG
58009792 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
58009805 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
58009818 TCCCATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:58009993 original size:14 final size:14
Alignment explanation
Indices: 58009974--58010003 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
58009964 AACAAAACTA
58009974 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
58009988 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
58010002 GC
1 GC
58010004 TGCAATCAAT
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:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:58010063 original size:24 final size:24
Alignment explanation
Indices: 58010026--58010071 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
58010016 GGTGAAGAGA
* *
58010026 GTGAAGAGAGGAGCTGTGGAAAGG
1 GTGAAGAAAAGAGCTGTGGAAAGG
58010050 GTGAAGAAAAGAGCTGTGGAAA
1 GTGAAGAAAAGAGCTGTGGAAA
58010072 TGGTTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.13
Consensus pattern (24 bp):
GTGAAGAAAAGAGCTGTGGAAAGG
Found at i:58011249 original size:29 final size:29
Alignment explanation
Indices: 58011217--58011326 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 29
58011207 TAATAAAAAT
58011217 ATATAATTTAATAAAATTCTTAATATTAA
1 ATATAATTTAATAAAATTCTTAATATTAA
* *
58011246 ATATTAATTTACTAAAA-TCATAATATATAA
1 ATA-TAATTTAATAAAATTCTTAATAT-TAA
* ** *
58011276 TACTATAAAATATAATTTAAAATAATTATTATTAA
1 -A-TAT--AATTTAA--TAAAATTCTTAATATTAA
58011311 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
58011327 ATATATAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
29 16 0.25
30 15 0.24
31 8 0.13
32 2 0.03
33 8 0.13
34 1 0.02
35 8 0.13
36 5 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATAATTTAATAAAATTCTTAATATTAA
Found at i:58011303 original size:112 final size:116
Alignment explanation
Indices: 58011179--58011393 Score: 357
Period size: 112 Copynumber: 1.9 Consensus size: 116
58011169 TTAATCATAT
*
58011179 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-T-TAA-T
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCATATAATT
*
58011241 ATT-AAATATTAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 ATTCAAATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
58011291 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCAATATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-ATATAAT
**
58011356 TATTCTTATATGAATTTACTAAAATCATAATATATAAT
65 TATTCAAATATGAATTTACTAAAATCATAATATATAAT
58011394 NAGGTTTAGA
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
112 56 0.60
114 1 0.01
115 3 0.03
116 4 0.04
117 30 0.32
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (116 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCATATAATT
ATTCAAATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:58011346 original size:10 final size:10
Alignment explanation
Indices: 58011284--58011356 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
58011274 AATACTATAA
58011284 AATATAATTT
1 AATATAATTT
*
58011294 AAAATAA-TT
1 AATATAATTT
*
58011303 -AT-T-ATTA
1 AATATAATTT
58011310 AATATAATTT
1 AATATAATTT
**
58011320 AATA-AAAAT
1 AATATAATTT
58011329 -ATATAATTT
1 AATATAATTT
* *
58011338 AATAAAATTC
1 AATATAATTT
58011348 AATATAATT
1 AATATAATT
58011357 ATTCTTATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 6 0.13
9 9 0.20
10 28 0.61
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATAATTT
Found at i:58013697 original size:12 final size:12
Alignment explanation
Indices: 58013682--58013715 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
58013672 ACTTAACAGA
58013682 AACCAAAACATG
1 AACCAAAACATG
58013694 AACCAAAACATG
1 AACCAAAACATG
58013706 AACCAAAACA
1 AACCAAAACA
58013716 ATAGAGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.62, C:0.26, G:0.06, T:0.06
Consensus pattern (12 bp):
AACCAAAACATG
Found at i:58014195 original size:20 final size:20
Alignment explanation
Indices: 58014154--58014213 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
58014144 AAACAGGAAA
* *
58014154 AAATTTGGAAGAAGAAGCAG
1 AAATCTGGAAGAAGAAGAAG
58014174 AAATCTGGAGAGAAGAA-AAG
1 AAATCTGGA-AGAAGAAGAAG
*
58014194 AAATGTGAGAAGAA-AAGAAG
1 AAATCTG-GAAGAAGAAGAAG
58014214 CGTACCGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 23 0.68
21 9 0.26
ACGTcount: A:0.55, C:0.03, G:0.30, T:0.12
Consensus pattern (20 bp):
AAATCTGGAAGAAGAAGAAG
Found at i:58016086 original size:17 final size:17
Alignment explanation
Indices: 58016066--58016121 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
58016056 TCGCACATTG
*
58016066 ACACAAATCGCATATAA
1 ACACAACTCGCATATAA
* * *
58016083 ACACAACTCACAAATAG
1 ACACAACTCGCATATAA
*
58016100 ACACAGCTCGCATATAA
1 ACACAACTCGCATATAA
58016117 ACACA
1 ACACA
58016122 TATATGTATA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.50, C:0.29, G:0.07, T:0.14
Consensus pattern (17 bp):
ACACAACTCGCATATAA
Found at i:58030021 original size:26 final size:26
Alignment explanation
Indices: 58029985--58030046 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
58029975 CTTGTAAGTG
58029985 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* **
58030011 TTCTGAAACTGATATATTTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
*
58030037 TTTTGAAACT
1 TTCTGAAACT
58030047 ACTATAGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:58034333 original size:17 final size:17
Alignment explanation
Indices: 58034311--58034344 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58034301 GTTTTTTCCC
*
58034311 TTTTTGTTCCCTTTTGG
1 TTTTTGTTCCCCTTTGG
58034328 TTTTTGTTCCCCTTTGG
1 TTTTTGTTCCCCTTTGG
58034345 CCGAGTCTTG
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:0.00, C:0.21, G:0.18, T:0.62
Consensus pattern (17 bp):
TTTTTGTTCCCCTTTGG
Found at i:58040036 original size:15 final size:14
Alignment explanation
Indices: 58040014--58040054 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
58040004 ATGAAAATAC
58040014 AAAAATTAAATTAT
1 AAAAATTAAATTAT
* *
58040028 ATTAAATTAAAATAT
1 A-AAAATTAAATTAT
58040043 AAAAATTAAATT
1 AAAAATTAAATT
58040055 TTATAGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATTAAATTAT
Found at i:58047719 original size:26 final size:26
Alignment explanation
Indices: 58047690--58047751 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
58047680 CCTGTAAGTG
*
58047690 TTCTGAAACTGATACATGCTGTGATA
1 TTCTGAAACTGATACATGCTATGATA
* **
58047716 TTCTGAAACTGATATATTTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
58047742 TTCTGAAACT
1 TTCTGAAACT
58047752 ACTATAGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:58053893 original size:40 final size:39
Alignment explanation
Indices: 58053801--58054023 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
58053791 TCCTCGTTCA
* * * *
58053801 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
58053840 AACGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
58053879 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * * *
58053919 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGTAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
58053959 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
58054000 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
58054024 CAGCATTCAA
Statistics
Matches: 153, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
39 38 0.25
40 104 0.68
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:58062626 original size:18 final size:19
Alignment explanation
Indices: 58062603--58062641 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
58062593 AACAAACTTT
*
58062603 ACATAAT-TCACATTCTTC
1 ACATAATATCACATTATTC
58062621 ACATAATAATCACATTATTC
1 ACATAAT-ATCACATTATTC
58062641 A
1 A
58062642 TTTGCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (19 bp):
ACATAATATCACATTATTC
Found at i:58065588 original size:15 final size:14
Alignment explanation
Indices: 58065566--58065606 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
58065556 ATGAAAATAC
58065566 AAAAATTAAATTAT
1 AAAAATTAAATTAT
* *
58065580 ATTAAATTAAAATAT
1 A-AAAATTAAATTAT
58065595 AAAAATTAAATT
1 AAAAATTAAATT
58065607 TTATAGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATTAAATTAT
Found at i:58065706 original size:21 final size:20
Alignment explanation
Indices: 58065680--58065720 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
58065670 CATTTGATAT
58065680 AAAAAAAATTAGTATATTAAA
1 AAAAAAAATTAGTAT-TTAAA
* *
58065701 AAAAAATATTTGTATTTAAA
1 AAAAAAAATTAGTATTTAAA
58065721 TTGATTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAAAAATTAGTATTTAAA
Found at i:58067647 original size:51 final size:51
Alignment explanation
Indices: 58067587--58067687 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
58067577 AATTCATATC
*
58067587 AAAATGTATTTAATTGTTTCGAGTTGAATTTTAGTAACTATATATGTGTAG
1 AAAATGTATTTAATTGTTCCGAGTTGAATTTTAGTAACTATATATGTGTAG
58067638 AAAATGTATTTAATTGTTCCGAGTTGAATTTTAGTAACTATATATGTGTA
1 AAAATGTATTTAATTGTTCCGAGTTGAATTTTAGTAACTATATATGTGTA
58067688 TGTCGAATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.45
Consensus pattern (51 bp):
AAAATGTATTTAATTGTTCCGAGTTGAATTTTAGTAACTATATATGTGTAG
Found at i:58068860 original size:90 final size:90
Alignment explanation
Indices: 58068707--58068885 Score: 322
Period size: 90 Copynumber: 2.0 Consensus size: 90
58068697 TAGAGTTTCG
* * *
58068707 GAGACTTGCTCGGGTTGGAAGTCATAGGAGACCTCATCACACTATCCAGTTATCGCTTCGGTAAA
1 GAGACTTGCTCAGATTGGAAATCATAGGAGACCTCATCACACTATCCAGTTATCGCTTCGGTAAA
58068772 TATAAGCTTTGAGTTTTTGGTTATA
66 TATAAGCTTTGAGTTTTTGGTTATA
*
58068797 GAGACTTGCTCAGATTGGAAATCATAGGAGACCTCATCACACTATCCGGTTATCGCTTCGGTAAA
1 GAGACTTGCTCAGATTGGAAATCATAGGAGACCTCATCACACTATCCAGTTATCGCTTCGGTAAA
58068862 TATAAGCTTTGAGTTTTTGGTTAT
66 TATAAGCTTTGAGTTTTTGGTTAT
58068886 GTGGGATGTA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (90 bp):
GAGACTTGCTCAGATTGGAAATCATAGGAGACCTCATCACACTATCCAGTTATCGCTTCGGTAAA
TATAAGCTTTGAGTTTTTGGTTATA
Found at i:58075502 original size:58 final size:58
Alignment explanation
Indices: 58075406--58075518 Score: 183
Period size: 58 Copynumber: 1.9 Consensus size: 58
58075396 TGACGAGCAC
*
58075406 CTTAGGTTTGTTCTTCAAAACTTGAGGGAAAATCAGCTCTATGCTAAGTTCAGCACAG
1 CTTAGCTTTGTTCTTCAAAACTTGAGGGAAAATCAGCTCTATGCTAAGTTCAGCACAG
**
58075464 CTTAGCTTTGTTCTTCAAATTTTGAGGGAAAAGT-AGCTCTATGCTAAGTTCAGCA
1 CTTAGCTTTGTTCTTCAAAACTTGAGGGAAAA-TCAGCTCTATGCTAAGTTCAGCA
58075519 GGTGCGAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
58 50 0.98
59 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (58 bp):
CTTAGCTTTGTTCTTCAAAACTTGAGGGAAAATCAGCTCTATGCTAAGTTCAGCACAG
Found at i:58078017 original size:17 final size:17
Alignment explanation
Indices: 58077985--58078018 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58077975 GTTTTCTCCT
*
58077985 TTTTTGTTCACTTTTGG
1 TTTTTGTTCACCTTTGG
*
58078002 TTTTTGTTCTCCTTTGG
1 TTTTTGTTCACCTTTGG
58078019 CCCAATCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.15, G:0.18, T:0.65
Consensus pattern (17 bp):
TTTTTGTTCACCTTTGG
Found at i:58084993 original size:15 final size:14
Alignment explanation
Indices: 58084971--58085011 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
58084961 TAAAAAATAC
58084971 AAAAATTAAATTAT
1 AAAAATTAAATTAT
* *
58084985 ATTAAATTAAAATAT
1 A-AAAATTAAATTAT
58085000 AAAAATTAAATT
1 AAAAATTAAATT
58085012 TTATAGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATTAAATTAT
Found at i:58085016 original size:31 final size:29
Alignment explanation
Indices: 58084964--58085021 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
58084954 TTTAAACTAA
*
58084964 AAAATACAAAAATTAAATTATATTAAATT
1 AAAATACAAAAATTAAATTATAGTAAATT
*
58084993 AAAATATAAAAATTAAATTTTATAGTAAA
1 AAAATACAAAAATTAAA--TTATAGTAAA
58085022 AAATCATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.64
31 9 0.36
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATACAAAAATTAAATTATAGTAAATT
Found at i:58085067 original size:63 final size:63
Alignment explanation
Indices: 58084993--58085112 Score: 240
Period size: 63 Copynumber: 1.9 Consensus size: 63
58084983 ATATTAAATT
58084993 AAAATATAAAAATTAAATTTTATAGTAAAAAATCATAATCACAGTGTGACTTAAAACAGGACC
1 AAAATATAAAAATTAAATTTTATAGTAAAAAATCATAATCACAGTGTGACTTAAAACAGGACC
58085056 AAAATATAAAAATTAAATTTTATAGTAAAAAATCATAATCACAGTGTGACTTAAAAC
1 AAAATATAAAAATTAAATTTTATAGTAAAAAATCATAATCACAGTGTGACTTAAAAC
58085113 GATGTATGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (63 bp):
AAAATATAAAAATTAAATTTTATAGTAAAAAATCATAATCACAGTGTGACTTAAAACAGGACC
Found at i:58090279 original size:18 final size:19
Alignment explanation
Indices: 58090247--58090287 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
58090237 ACTTCATGGT
58090247 TTTGAATTATGATTTATGA
1 TTTGAATTATGATTTATGA
* *
58090266 TTTG-ATTATTATTTATTA
1 TTTGAATTATGATTTATGA
58090284 TTTG
1 TTTG
58090288 GGTTGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (19 bp):
TTTGAATTATGATTTATGA
Found at i:58099534 original size:36 final size:36
Alignment explanation
Indices: 58099487--58099558 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
58099477 GTATGAGTCT
58099487 TAGTCTCGGCACTAAGGTTTTGATGGGGTGGTTGTG
1 TAGTCTCGGCACTAAGGTTTTGATGGGGTGGTTGTG
58099523 TAGTCTCGGCACTAAGGTTTTGATGGGGTGGTTGTG
1 TAGTCTCGGCACTAAGGTTTTGATGGGGTGGTTGTG
58099559 ATATATTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.14, C:0.11, G:0.39, T:0.36
Consensus pattern (36 bp):
TAGTCTCGGCACTAAGGTTTTGATGGGGTGGTTGTG
Found at i:58105396 original size:26 final size:24
Alignment explanation
Indices: 58105348--58105398 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
58105338 TTTAAAATAC
* *
58105348 TTTTAAAATATTTTTATTTTTTAT
1 TTTTAAAATATTTTTAATGTTTAT
58105372 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAAT-A-TTTTTAATGTTTAT
58105398 T
1 T
58105399 AAAAAATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAAAATATTTTTAATGTTTAT
Found at i:58107525 original size:17 final size:17
Alignment explanation
Indices: 58107493--58107526 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58107483 GTTTTCTCCC
*
58107493 TTTTTGTTCACTTTTGG
1 TTTTTGTTCACCTTTGG
*
58107510 TTTTTGTTCCCCTTTGG
1 TTTTTGTTCACCTTTGG
58107527 CCGAATCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.18, G:0.18, T:0.62
Consensus pattern (17 bp):
TTTTTGTTCACCTTTGG
Found at i:58109558 original size:18 final size:17
Alignment explanation
Indices: 58109532--58109567 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
58109522 AATTTTGGGT
*
58109532 TTTTATTTATTTATTTA
1 TTTTATTTATTGATTTA
58109549 TTTTACTTTATTGATTTA
1 TTTTA-TTTATTGATTTA
58109567 T
1 T
58109568 ACCTGCTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTATTTATTGATTTA
Found at i:58114194 original size:15 final size:14
Alignment explanation
Indices: 58114172--58114212 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
58114162 ATGAAAATAC
58114172 AAAAATTAAATTAT
1 AAAAATTAAATTAT
* *
58114186 ATTAAATTAAAATAT
1 A-AAAATTAAATTAT
58114201 AAAAATTAAATT
1 AAAAATTAAATT
58114213 TTATAGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATTAAATTAT
Found at i:58116426 original size:85 final size:86
Alignment explanation
Indices: 58116265--58116428 Score: 199
Period size: 86 Copynumber: 1.9 Consensus size: 86
58116255 ATATGAGTTA
* * * ** *
58116265 TCGTGTAAGACCAAGTCTGGGACATTGGCGTCGATTTGAGATTTACGTGTAAGACCATGTCTGGT
1 TCGTGTAAGACCAAGTCTGGGACAGTGGCATCGATTTGAGATTTACATGTAAGACCACATCTGGG
58116330 ACTTCGGCATTGTATACAATT
66 ACTTCGGCATTGTATACAATT
** *
58116351 TCGTGTAAGACCTTGTCTGGGACAGTGGCATCGATATT-TG-TTTACATGTAAGACCACATCTGG
1 TCGTGTAAGACCAAGTCTGGGACAGTGGCATCGAT-TTGAGATTTACATGTAAGACCACATCTGG
*
58116414 GA-TGTTGGCATTGTA
65 GACT-TCGGCATTGTA
58116429 AGAGCTTCCA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
84 1 0.02
85 31 0.47
86 32 0.48
87 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (86 bp):
TCGTGTAAGACCAAGTCTGGGACAGTGGCATCGATTTGAGATTTACATGTAAGACCACATCTGGG
ACTTCGGCATTGTATACAATT
Found at i:58119605 original size:15 final size:15
Alignment explanation
Indices: 58119585--58119616 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58119575 CATTTCACTA
*
58119585 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
58119600 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
58119615 TT
1 TT
58119617 TGCAGGCATA
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:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:58121887 original size:13 final size:13
Alignment explanation
Indices: 58121869--58121895 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58121859 ATTTCTCGTC
58121869 TTTTTGAATGATT
1 TTTTTGAATGATT
58121882 TTTTTGAATGATT
1 TTTTTGAATGATT
58121895 T
1 T
58121896 GATTACATAG
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:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (13 bp):
TTTTTGAATGATT
Found at i:58138051 original size:30 final size:31
Alignment explanation
Indices: 58138017--58138076 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
58138007 AAACCTTTTA
*
58138017 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
58138047 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
58138077 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:58149745 original size:16 final size:17
Alignment explanation
Indices: 58149724--58149755 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58149714 CTATGTATTT
58149724 TGAAAT-TAAAAATATA
1 TGAAATGTAAAAATATA
58149740 TGAAATGTAAAAATAT
1 TGAAATGTAAAAATAT
58149756 GATTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (17 bp):
TGAAATGTAAAAATATA
Found at i:58150173 original size:131 final size:131
Alignment explanation
Indices: 58150022--58150444 Score: 672
Period size: 131 Copynumber: 3.2 Consensus size: 131
58150012 AGTTTAGAAC
* * * *
58150022 TAAAAGTTTAGAGGGAAAATAAAAATTTTTGAGGATTTTGT-GGGGAGTAAAATTTTAGGGGAAA
1 TAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTT-TAGGGGAGTAAAATTTTAGGGGAAA
58150086 TAGGTTTGGGGTAGATGGGGGATGGGATGGGAGGGGAGTAAAAGATTTAGGGGAAAGTGGCAGGG
65 TAGGTTTGGGGTAGATGGGGGATGGGATGGGAGGGGAGTAAAAGATTTAGGGGAAAGTGGCAGGG
58150151 AG
130 AG
*
58150153 TAAAAGTTTTGGGGGGAAATAAAAAGTTTTGAGGGTTTTTAGGGGAGTAAAATTTTAGGGGAAAT
1 TAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTTTAGGGGAGTAAAATTTTAGGGGAAAT
58150218 AGGTTTGGGGTAGATGGGGGATGGGATGGGAGGGGAGTAAAAGATTTAGGGGAAAGTGGCAGGGA
66 AGGTTTGGGGTAGATGGGGGATGGGATGGGAGGGGAGTAAAAGATTTAGGGGAAAGTGGCAGGGA
58150283 G
131 G
*
58150284 TAAAAGTTTTGGGGGGAAATAAAAAGTTTTGAGGGTTTTTAGGGGAGTAAAATTTTAGGGGAAAT
1 TAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTTTAGGGGAGTAAAATTTTAGGGGAAAT
* * * * * * *
58150349 AGGTTTGGGGTAGATGGGGGGTGAGATGGG-GGGCACTAAAAGTTTTAGAGGGAAATTGG-AAGG
66 AGGTTTGGGGTAGATGGGGGATGGGATGGGAGGGGAGTAAAAGATTTAG-GGGAAAGTGGCAGGG
58150412 AG
130 AG
58150414 TAAAAGTTTTGGGGGAAAAGTAAAAATGTTT
1 TAAAAGTTTTGGGGGAAAA-TAAAAA-GTTT
58150445 GGGGTAAAAA
Statistics
Matches: 275, Mismatches: 13, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
130 39 0.14
131 232 0.84
132 4 0.01
ACGTcount: A:0.33, C:0.01, G:0.40, T:0.26
Consensus pattern (131 bp):
TAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTTTAGGGGAGTAAAATTTTAGGGGAAAT
AGGTTTGGGGTAGATGGGGGATGGGATGGGAGGGGAGTAAAAGATTTAGGGGAAAGTGGCAGGGA
G
Found at i:58150437 original size:20 final size:21
Alignment explanation
Indices: 58150412--58150462 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
58150402 AATTGGAAGG
*
58150412 AGTAAAAGT-TTTGGGGGAAA
1 AGTAAAAATGTTTGGGGGAAA
*
58150432 AGTAAAAATGTTTGGGGTAAA
1 AGTAAAAATGTTTGGGGGAAA
*
58150453 AATATAAAAT
1 AGTA-AAAAT
58150463 ATTATAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 8 0.31
21 13 0.50
22 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.27
Consensus pattern (21 bp):
AGTAAAAATGTTTGGGGGAAA
Found at i:58150454 original size:22 final size:20
Alignment explanation
Indices: 58150412--58150454 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
58150402 AATTGGAAGG
* *
58150412 AGTAAAAGTTTTGGGGGAAA
1 AGTAAAAATTTTGGGGAAAA
58150432 AGTAAAAATGTTTGGGGTAAAA
1 AGTAAAAAT-TTTGGGG-AAAA
58150454 A
1 A
58150455 TATAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (20 bp):
AGTAAAAATTTTGGGGAAAA
Found at i:58150754 original size:20 final size:21
Alignment explanation
Indices: 58150729--58150767 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
58150719 TAAACCTATT
*
58150729 CAAAATATATCAA-AACATGC
1 CAAAATATACCAATAACATGC
58150749 CAAAATATACCAATAACAT
1 CAAAATATACCAATAACAT
58150768 TCAACCTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (21 bp):
CAAAATATACCAATAACATGC
Found at i:58152152 original size:21 final size:21
Alignment explanation
Indices: 58152128--58152180 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
58152118 TAACAAAGGA
58152128 ACCGAAGTGCAAAATAGAGAC
1 ACCGAAGTGCAAAATAGAGAC
** **
58152149 ACCGAAGTGC-TTATAGAGGT
1 ACCGAAGTGCAAAATAGAGAC
58152169 ACCGAAGTGCAA
1 ACCGAAGTGCAA
58152181 TCCCGTACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (21 bp):
ACCGAAGTGCAAAATAGAGAC
Found at i:58153216 original size:24 final size:23
Alignment explanation
Indices: 58153170--58153216 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
58153160 AGGTGATGGC
*
58153170 TTTATTTGTTTTATCTTATATTT
1 TTTATTTGTTTTATATTATATTT
58153193 TTTATCTTGTTTTATTATTA-ATTT
1 TTTAT-TTGTTTTA-TATTATATTT
58153217 AATATTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTATTTGTTTTATATTATATTT
Found at i:58154412 original size:17 final size:17
Alignment explanation
Indices: 58154382--58154425 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
58154372 TTTTGTTAGT
58154382 TTTTG-TTT-TTATTTA
1 TTTTGTTTTATTATTTA
58154397 TTTTGTTTTATTATTTA
1 TTTTGTTTTATTATTTA
*
58154414 TTTTCTTTTATT
1 TTTTGTTTTATT
58154426 CACGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 5 0.19
16 3 0.12
17 18 0.69
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTGTTTTATTATTTA
Found at i:58157123 original size:38 final size:38
Alignment explanation
Indices: 58157072--58157149 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
58157062 TTTTGCCCTA
58157072 AAGGTCCAAGGTATCAATACCTAGCTTAATTGTTGCGG
1 AAGGTCCAAGGTATCAATACCTAGCTTAATTGTTGCGG
58157110 AAGGTCCAAGGTATCAATACCTAGCTTAATTGTTGCGG
1 AAGGTCCAAGGTATCAATACCTAGCTTAATTGTTGCGG
58157148 AA
1 AA
58157150 CAACTGAGTG
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:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (38 bp):
AAGGTCCAAGGTATCAATACCTAGCTTAATTGTTGCGG
Found at i:58158275 original size:20 final size:20
Alignment explanation
Indices: 58158250--58158314 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
58158240 GTTGTATTGG
58158250 TACTTCTCTAGAGGTACCTA
1 TACTTCTCTAGAGGTACCTA
* * * *
58158270 TACTTCACCCACAAGGTACCTG
1 TACTTC-TCTA-GAGGTACCTA
58158292 TACTTCT-TCAGAGGTACCTA
1 TACTTCTCT-AGAGGTACCTA
58158312 TAC
1 TAC
58158315 CTCTATTCAG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 17 0.50
21 3 0.09
22 14 0.41
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (20 bp):
TACTTCTCTAGAGGTACCTA
Found at i:58165748 original size:44 final size:44
Alignment explanation
Indices: 58165638--58166795 Score: 760
Period size: 44 Copynumber: 25.7 Consensus size: 44
58165628 ATTAAAGTTT
* * *
58165638 CAAATCTTATCTCCTTAAAGTTGCAGTGGAGCAGATCGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* ** * * *
58165682 GCAAATCTTCTCTATCTAAAGTTGCAGTAGAGCAGATTGAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * ** *
58165727 AAAATCTTATCTCTCTGAAGTTGTAGTAAAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* ** * *
58165771 AAAATCTTATCTCCCTGAAGTTATAGTAGAGCAGATTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * ** *
58165815 CAAATCTTATCTCCCTAAAGTTACAGTGGAATAGATTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * *
58165859 CAAATCTCATCTCCTTAAAGTTGCAGTGGAGCAGATTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * * *
58165903 GCGAATCTTATTTCCCTAAAGTTGTAGTGGAACAGATTAAAGCTACTAATTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG------A-TA
* * * * *
58165955 CAAATCTTATTTGCCTGAAGTTGCAGTGAAGCAGATTGAATATG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * * *
58165999 CTAATCTTATTTCTCTGAAGTTACAGTGGAACAGATTAAAGCTACAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G----AAGATA
* * * *
58166050 CAAATCTTATCTCCCTAAAGTGGCAGTGGAGTAGATTGAAGATG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * ** *
58166094 CGAATCTTATTTCCCTGGAGTTGCAGTGTAATAGATTAAAGCTACAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G----AAGATA
* *
58166145 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-A
* * * *
58166190 CAAATCTTATCTCTCTGAAGTGGCAGTAGAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * *
58166234 CAAAACTTATCTCTCTGAAGTTGCAGTGAAGCAGATTGTAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* *** * * * * * *
58166278 GAAAATCTTATCAATCTAAAGCTGAAGTAGAGCATATTGAATATA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
** * * * * *
58166323 GTGAATCTTATCTCCCTTAATTTTCAATGGAACAGATTGAAGATA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
** * * * * *
58166368 GTGAATCTTATCTCCCTTAATTTTCAATGGAACAGATTGAAGATA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
** * *
58166413 GTGAATCTTATTTCCCTGAAGTTACAGTGGAGCAGATTGAAGATA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * * * *
58166458 GTAAATCTTATTTCCCTGAAGTGGTAGTGGAACAGATTAAAGTTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * * *
58166503 CAAGT-TACATCTCCCTAAAGTTGCTGTGGAGCATATTGAAGTTA
1 CAAATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * ** * *
58166547 CAAAT-TTATCTCCCTAAATTTGTAGTAAAACGGATTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * *
58166590 GCAAATCTTATCTCCTTGAAGTTGCAATGGAACAGATTGAAGTTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * *
58166635 CAAATCTTATCTCCATGAAGTTGCAGTGGAGTAGATT-AAAATTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TA
* * * * * * * *
58166679 CAAATCTCATCCCCCTAAAGTTGCAGTGAAGCAGAATAAAGCTG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * *
58166723 CAAATCTAATCTCTCTGAAGTTGCAGTGGAGTAGATTAAAGCA-A
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-ATA
* *
58166767 CAAATTTTATAC-CTCTGAAGTTGCAGTGG
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGG
58166796 GTTAGAATGA
Statistics
Matches: 892, Mismatches: 190, Indels: 63
0.78 0.17 0.06
Matches are distributed among these distances:
43 30 0.03
44 428 0.48
45 328 0.37
47 2 0.00
48 2 0.00
51 100 0.11
52 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
Found at i:58165990 original size:51 final size:49
Alignment explanation
Indices: 58165906--58166236 Score: 210
Period size: 51 Copynumber: 6.9 Consensus size: 49
58165896 GAAGATAGCG
* *
58165906 AATCTTATTTCCCTAAAGTTGTAGTGGAACAGATTAAAGCTACTAATTACA
1 AATCTTATTTCCCTGAAGTTGCAGT-GAACAGATTAAAGCTAC-AATTACA
* * * *
58165957 AATCTTATTTGCCTGAAGTTGCAGTGAAGCAGATTGAA--T---A-TGCT
1 AATCTTATTTCCCTGAAGTTGCAGTGAA-CAGATTAAAGCTACAATTACA
* *
58166001 AATCTTATTTCTCTGAAGTTACAGTGGAACAGATTAAAGCTACAAGTTACA
1 AATCTTATTTCCCTGAAGTTGCAGT-GAACAGATTAAAGCTACAA-TTACA
* * * ** * * *
58166052 AATCTTATCTCCCTAAAGTGGCAGTGGAGTAGATTGAAG-----A-TGCG
1 AATCTTATTTCCCTGAAGTTGCAGT-GAACAGATTAAAGCTACAATTACA
* *
58166096 AATCTTATTTCCCTGGAGTTGCAGTGTAATAGATTAAAGCTACAAGTTACA
1 AATCTTATTTCCCTGAAGTTGCAGTG-AACAGATTAAAGCTACAA-TTACA
* * * *
58166147 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT---G-TA-GATAACA
1 AATCTTATTTCCCTGAAGTTGCAGT-GAACAGATTAAAGCTACAATTACA
* * * * *
58166192 AATCTTATCTCTCTGAAGTGGCAGTAGAGCAGATTGAAGCTACAA
1 AATCTTATTTCCCTGAAGTTGCAGT-GAACAGATTAAAGCTACAA
58166237 AACTTATCTC
Statistics
Matches: 218, Mismatches: 39, Indels: 47
0.72 0.13 0.15
Matches are distributed among these distances:
43 1 0.00
44 65 0.30
45 41 0.19
46 3 0.01
47 2 0.01
48 2 0.01
49 5 0.02
50 4 0.02
51 94 0.43
52 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (49 bp):
AATCTTATTTCCCTGAAGTTGCAGTGAACAGATTAAAGCTACAATTACA
Found at i:58166038 original size:95 final size:95
Alignment explanation
Indices: 58165772--58166769 Score: 525
Period size: 95 Copynumber: 10.9 Consensus size: 95
58165762 TTGAAGCTAA
** * * * * *
58165772 AAATCTTATCTCCCTGAAGTTATAGT-AGAGCAGATTGAAGTTACAAATCTTATCTCCCTAAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGT
* *
58165836 TACAGTGGAATAGATT---G----AAGTTAC
65 TGCAGTGGAACAGATTAAAGCTACAAGTTAC
* * * * *
58165860 AAATCTCATCTCCTTAAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATTTCCCTAAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGAT-GCGAATCTTATTTCCCTGAAGT
*
58165925 TGTAGTGGAACAGATTAAAGCTACTAA-TTAC
65 TGCAGTGGAACAGATTAAAGCTAC-AAGTTAC
* * * * *
58165956 AAATCTTATTTGCCTGAAGTTGCAGTGAAGCAGATTGAATATGCTAATCTTATTTCTCTGAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGTT
*
58166021 ACAGTGGAACAGATTAAAGCTACAAGTTAC
66 GCAGTGGAACAGATTAAAGCTACAAGTTAC
* * * * *
58166051 AAATCTTATCTCCCTAAAGTGGCAGTGGAGTAGATTGAAGATGCGAATCTTATTTCCCTGGAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGTT
* *
58166116 GCAGTGTAATAGATTAAAGCTACAAGTTAC
66 GCAGTGGAACAGATTAAAGCTACAAGTTAC
* * * * *
58166146 AAATCTTATCTCCCTGAAGTTGCAGT-AGAGCAGATTGTAGATAACAAATCTTATCTCTCTGAAG
1 AAATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTGAAGAT-GCGAATCTTATTTCCCTGAAG
* * * *
58166210 TGGCAGTAGAGCAGATTGAAGCTAC-----A-
64 TTGCAGTGGAACAGATTAAAGCTACAAGTTAC
* * ** **** * *
58166236 AAA-CTTATCTCTCTGAAGTTGCAGTGAAGCAGATTGTAGATAGAAAATCTTATCAATCTAAAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGAT-GCGAATCTTATTTCCCTGAAGT
* * * * * *
58166300 TGAAGTAGAGCATATTGAA--TA-TAG-T--
65 TGCAGTGGAACAGATTAAAGCTACAAGTTAC
* * * * * * * * *
58166325 GAATCTTATCTCCCTTAATTTTCAATGGAA-CAGATTGAAGATAGTGAATCTTATCTCCCTTAAT
1 AAATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTGAAGAT-GCGAATCTTATTTCCCTGAAG
* * * *
58166389 TTTCAATGGAACAGATTGAAG--A-TAG-T--
64 TTGCAGTGGAACAGATTAAAGCTACAAGTTAC
* * * * **
58166415 GAATCTTATTTCCCTGAAGTTACAGTGGAGCAGATTGAAGATAGTAAATCTTATTTCCCTGAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGAT-GCGAATCTTATTTCCCTGAAGT
* * *
58166480 GGTAGTGGAACAGATTAAAGTTACAAGTT--
65 TGCAGTGGAACAGATTAAAGCTACAAGTTAC
* * * * * * * * * *
58166509 --A-C--ATCTCCCTAAAGTTGCTGTGGAGCATATTGAAGTTACAAAT-TTATCTCCCTAAATTT
1 AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGTT
* ** * * *
58166568 GTAGTAAAACGGATTGAAG--A-TAG---C
66 GCAGTGGAACAGATTAAAGCTACAAGTTAC
* * * * * * *
58166592 AAATCTTATCTCCTTGAAGTTGCAATGGAA-CAGATTGAAGTTACAAATCTTATCTCCATGAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGT
**
58166656 TGCAGTGGAGTAGATT--A---A-AA-TTAC
65 TGCAGTGGAACAGATTAAAGCTACAAGTTAC
* * * * * * * * * *
58166680 AAATCTCATCCCCCTAAAGTTGCAGTGAAGCAGAATAAAGCTGCAAATCTAATCTCTCTGAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGTT
** *
58166745 GCAGTGGAGTAGATTAAAGCAACAA
66 GCAGTGGAACAGATTAAAGCTACAA
58166770 ATTTTATACC
Statistics
Matches: 720, Mismatches: 146, Indels: 82
0.76 0.15 0.09
Matches are distributed among these distances:
84 2 0.00
85 2 0.00
86 3 0.00
87 33 0.05
88 135 0.19
89 157 0.22
90 133 0.18
91 5 0.01
92 3 0.00
93 3 0.00
94 5 0.01
95 163 0.23
96 74 0.10
97 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (95 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGTT
GCAGTGGAACAGATTAAAGCTACAAGTTAC
Found at i:58166307 original size:89 final size:89
Alignment explanation
Indices: 58166143--58166318 Score: 241
Period size: 89 Copynumber: 2.0 Consensus size: 89
58166133 AGCTACAAGT
* ** *
58166143 TACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAACAAATCTTATCTCTCTGA
1 TACAAAACTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAACAAATCTTATCAATCTAA
*
58166208 AGTGGCAGTAGAGCAGATTGAAGC
66 AGTGGAAGTAGAGCAGATTGAAGC
*
58166232 TACAAAACTTATCTCTCTGAAGTTGCAGT-GAAGCAGATTGTAGATAGA-AAATCTTATCAATCT
1 TACAAAACTTATCTCCCTGAAGTTGCAGTAG-AGCAGATTGTAGATA-ACAAATCTTATCAATCT
*
58166295 AAAGCT-GAAGTAGAGCATATTGAA
64 AAAG-TGGAAGTAGAGCAGATTGAA
58166319 TATAGTGAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
88 1 0.01
89 74 0.96
90 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (89 bp):
TACAAAACTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAACAAATCTTATCAATCTAA
AGTGGAAGTAGAGCAGATTGAAGC
Found at i:58166375 original size:90 final size:90
Alignment explanation
Indices: 58166239--58166468 Score: 221
Period size: 90 Copynumber: 2.6 Consensus size: 90
58166229 AGCTACAAAA
* * * * * * *
58166239 CTTATCTCTCTGAAGTTGCAGT-GAAGCAGATTGTAGATAGAAAATCTTATCAATC-TAAAGCTG
1 CTTATCTCCCTGAAGTTACAATGGAA-CAGATTGAAGATAGTAAATCTTATCAACCTTAAAGCTC
* * *
58166302 AAGTAGAGCATATTGAATATAGTGAAT
65 AA-TAGAACAGATTGAAGATAGTGAAT
* * * * ** ***
58166329 CTTATCTCCCTTAATTTTCAATGGAACAGATTGAAGATAGTGAATCTTATCTCCCTTAATTTTCA
1 CTTATCTCCCTGAAGTTACAATGGAACAGATTGAAGATAGTAAATCTTATCAACCTTAAAGCTCA
*
58166394 ATGGAACAGATTGAAGATAGTGAAT
66 ATAGAACAGATTGAAGATAGTGAAT
* * *
58166419 CTTATTTCCCTGAAGTTACAGTGGAGCAGATTGAAGATAGTAAATCTTAT
1 CTTATCTCCCTGAAGTTACAATGGAACAGATTGAAGATAGTAAATCTTAT
58166469 TTCCCTGAAG
Statistics
Matches: 112, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
90 103 0.92
91 9 0.08
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (90 bp):
CTTATCTCCCTGAAGTTACAATGGAACAGATTGAAGATAGTAAATCTTATCAACCTTAAAGCTCA
ATAGAACAGATTGAAGATAGTGAAT
Found at i:58167432 original size:14 final size:14
Alignment explanation
Indices: 58167402--58167448 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
58167392 TTGAAAACAA
* *
58167402 AAAAAAAG-GGAAG
1 AAAAAAAGAGAAAT
58167415 AAAAAAAGA-AAAT
1 AAAAAAAGAGAAAT
*
58167428 AAAAAAAGAGATAT
1 AAAAAAAGAGAAAT
58167442 AAAAAAA
1 AAAAAAA
58167449 CACCACAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (14 bp):
AAAAAAAGAGAAAT
Found at i:58168517 original size:21 final size:22
Alignment explanation
Indices: 58168492--58168541 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
58168482 ATGTTGTTCA
*
58168492 TATTTATACA-TTTTCGCTCAT
1 TATTTATACATTTTTCACTCAT
*
58168513 TATTTGTACATTTTTCACTCAT
1 TATTTATACATTTTTCACTCAT
58168535 TATTTAT
1 TATTTAT
58168542 TTATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (22 bp):
TATTTATACATTTTTCACTCAT
Found at i:58170072 original size:9 final size:9
Alignment explanation
Indices: 58170058--58170083 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
58170048 ACTACCCAAC
58170058 CTATGTTGT
1 CTATGTTGT
58170067 CTATGTTGT
1 CTATGTTGT
58170076 CTATGTTG
1 CTATGTTG
58170084 AATAATTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.54
Consensus pattern (9 bp):
CTATGTTGT
Found at i:58170101 original size:24 final size:24
Alignment explanation
Indices: 58170069--58170117 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
58170059 TATGTTGTCT
58170069 ATGTTGTCTATGTTGAATAATTAG
1 ATGTTGTCTATGTTGAATAATTAG
58170093 ATGTTGTCTATGTTGAATAATTAG
1 ATGTTGTCTATGTTGAATAATTAG
58170117 A
1 A
58170118 GTATTAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (24 bp):
ATGTTGTCTATGTTGAATAATTAG
Found at i:58170855 original size:37 final size:40
Alignment explanation
Indices: 58170762--58170880 Score: 109
Period size: 37 Copynumber: 3.0 Consensus size: 40
58170752 TTCAACCTCG
* *
58170762 AGTCGATGACACACTGGGTGTCAATCTATTACTTCGAATTA
1 AGTCGATGAGACACTGGGTGCCAA-CTATTACTTCGAATTA
* * * * *
58170803 ATTTGATGAGGCACTGGGTGCCAA-T-TTACTTCG-GTTT
1 AGTCGATGAGACACTGGGTGCCAACTATTACTTCGAATTA
* * *
58170840 AGTCGATGAGACACTGGGTGTCACCTTATTACTTGGAATTA
1 AGTCGATGAGACACTGGGTGCCAAC-TATTACTTCGAATTA
58170881 TCCGACGAGG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
37 21 0.36
38 8 0.14
39 2 0.03
40 7 0.12
41 21 0.36
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (40 bp):
AGTCGATGAGACACTGGGTGCCAACTATTACTTCGAATTA
Done.