Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 15
Found at i:2206554 original size:34 final size:35
Alignment explanation
Indices: 2206502--2206573 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
2206492 AATTAAGAGT
*
2206502 TAGTTTAATAAAAGAACT-AGTTTGA-TGAATGAAC
1 TAGTTTAATAAAAGAACTAAGTTT-ATTCAATGAAC
* **
2206536 TAGTTTAATTAATTAACTAAGTTTATTCAATGAAC
1 TAGTTTAATAAAAGAACTAAGTTTATTCAATGAAC
2206571 TAG
1 TAG
2206574 AACTTTATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.38
Consensus pattern (35 bp):
TAGTTTAATAAAAGAACTAAGTTTATTCAATGAAC
Found at i:2206582 original size:20 final size:20
Alignment explanation
Indices: 2206557--2206594 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2206547 ATTAACTAAG
2206557 TTTATTCAATGAACTAGAAC
1 TTTATTCAATGAACTAGAAC
2206577 TTTATTCAATGAACTAGA
1 TTTATTCAATGAACTAGA
2206595 TGTATGAATG
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:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
TTTATTCAATGAACTAGAAC
Found at i:2209460 original size:19 final size:18
Alignment explanation
Indices: 2209420--2209466 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
2209410 ATAAAATTTT
*
2209420 AAAATAAATATTATCAAC
1 AAAATAAATATTATCAAA
2209438 AAAATAAATAATTAAT-AAA
1 AAAATAAAT-ATT-ATCAAA
2209457 AAAATTAAAT
1 AAAA-TAAAT
2209467 TTTAGCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 9 0.36
20 7 0.28
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATAAATATTATCAAA
Found at i:2209646 original size:23 final size:23
Alignment explanation
Indices: 2209614--2209667 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
2209604 TTGTATAAAT
* *
2209614 TTTAATTTATATAATTTTTTTTA
1 TTTAAATTATATAATTTTATTTA
2209637 TTTAAATTATATAATTTTATTTA
1 TTTAAATTATATAATTTTATTTA
2209660 TTTAAATT
1 TTTAAATT
2209668 TTAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTAAATTATATAATTTTATTTA
Found at i:2209862 original size:31 final size:31
Alignment explanation
Indices: 2209827--2209886 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2209817 TTTTATCCCT
*
2209827 CTATTTTTCTA-TATTAATTATTCTTTGTCTC
1 CTATTTTT-TATTATTAATTATACTTTGTCTC
*
2209858 CTATTTTTTATTGTTAATTATACTTTGTC
1 CTATTTTTTATTATTAATTATACTTTGTC
2209887 ACCTTGAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.20, C:0.13, G:0.05, T:0.62
Consensus pattern (31 bp):
CTATTTTTTATTATTAATTATACTTTGTCTC
Found at i:2211384 original size:16 final size:17
Alignment explanation
Indices: 2211352--2211385 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2211342 GCATCGGATT
2211352 GCATCCTAATCTCTCTAA
1 GCATCCTAA-CTCTCTAA
2211370 GCATCCTAA-TCTCTAA
1 GCATCCTAACTCTCTAA
2211386 CGACTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.32, G:0.06, T:0.32
Consensus pattern (17 bp):
GCATCCTAACTCTCTAA
Found at i:2214883 original size:9 final size:9
Alignment explanation
Indices: 2214869--2214894 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2214859 CCGGATCGGT
2214869 CGGTTCAAC
1 CGGTTCAAC
2214878 CGGTTCAAC
1 CGGTTCAAC
2214887 CGGTTCAA
1 CGGTTCAA
2214895 TCGAGAATCG
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:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (9 bp):
CGGTTCAAC
Found at i:2223582 original size:32 final size:32
Alignment explanation
Indices: 2223537--2223600 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2223527 TGCTAACATG
* *
2223537 ACATTTTTTAATTATGTTTGGATGTTGGACTA
1 ACATATTTTAATTATGTTCGGATGTTGGACTA
2223569 ACATATTTTAATTATGTTCGGATGTTGGACTA
1 ACATATTTTAATTATGTTCGGATGTTGGACTA
2223601 TGTAATTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.47
Consensus pattern (32 bp):
ACATATTTTAATTATGTTCGGATGTTGGACTA
Found at i:2224391 original size:25 final size:23
Alignment explanation
Indices: 2224341--2224390 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
2224331 TAAATTATGA
*
2224341 ATTATATATATATATATAATATT
1 ATTATATATAAATATATAATATT
2224364 ATTATATAATAAAT-TAT-ATATT
1 ATTATAT-ATAAATATATAATATT
2224386 ATTAT
1 ATTAT
2224391 TTCAGGACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 10 0.40
24 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATATATAAATATATAATATT
Found at i:2224435 original size:18 final size:18
Alignment explanation
Indices: 2224414--2224449 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2224404 CTACCAGCTG
2224414 GCCCAAGGAACTACAAGC
1 GCCCAAGGAACTACAAGC
2224432 GCCCAAGGAACTACAAGC
1 GCCCAAGGAACTACAAGC
2224450 CTAGTGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.22, T:0.06
Consensus pattern (18 bp):
GCCCAAGGAACTACAAGC
Found at i:2232067 original size:35 final size:35
Alignment explanation
Indices: 2232017--2232087 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
2232007 ACGTTTTATG
* *
2232017 TATTTCCTTTCATTCAGCACTTACCATTTACTTTT
1 TATTTACTTTCATTCAACACTTACCATTTACTTTT
* *
2232052 TATTTACTTTTATTCAATACTTACCATTTACTTTT
1 TATTTACTTTCATTCAACACTTACCATTTACTTTT
2232087 T
1 T
2232088 TTCATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.55
Consensus pattern (35 bp):
TATTTACTTTCATTCAACACTTACCATTTACTTTT
Found at i:2233040 original size:65 final size:65
Alignment explanation
Indices: 2232936--2233096 Score: 259
Period size: 65 Copynumber: 2.5 Consensus size: 65
2232926 TGAAAACGAC
* * *
2232936 GCCTTCGTGGGAATTTATTCTCCGTATGGGCTTAGCAAGTAACCTTCGGGATTCATATACCTTAT
1 GCCTTCGTGTGAATTTATTCTCCGTATGGGCCTAGCAAGTAACCTTCAGGATTCATATACCTTAT
* *
2233001 GCCTTCGTGTGAATTTATTCTCTGTATGGGCCTAGCAAGTAATCTTCAGGATTCATATACCTTAT
1 GCCTTCGTGTGAATTTATTCTCCGTATGGGCCTAGCAAGTAACCTTCAGGATTCATATACCTTAT
* *
2233066 GCCTTCGTGTGAATTCATTTTCCGTATGGGC
1 GCCTTCGTGTGAATTTATTCTCCGTATGGGC
2233097 ATAAGGGAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 88 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (65 bp):
GCCTTCGTGTGAATTTATTCTCCGTATGGGCCTAGCAAGTAACCTTCAGGATTCATATACCTTAT
Found at i:2236290 original size:110 final size:110
Alignment explanation
Indices: 2236089--2236516 Score: 624
Period size: 110 Copynumber: 3.9 Consensus size: 110
2236079 TGATGGTGGT
* *
2236089 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGTGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
2236154 CAATTTCAACTTCACAGCAAAGGATATTGGACTCGATACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
2236199 AGCTCAACTTCATAGCGAAGGGGTGACTAACTGTCAACAAAAAACTTTTTAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGTGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * * *
2236264 CAATTTCAACTTCACAACGAATGATATTGGACTTGAGAGAACATA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
2236309 AACTCAACTTCACAGCGAAGGGGTGACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGTGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * *
2236374 CAATTTTAACTTCACAGCGAATGATATTGGACTCGGGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * ** *
2236419 AGCTCAACTTCACAGCGAAGGGG-CAGCTAGCTGTCAACAAACAACTTCCCAGTTTCATTAAGAG
1 AGCTCAACTTCACAGCGAAGGGGTGA-CTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAG
*
2236483 CCAATTTCAACTTCACAGCGAAGGATATTGGACT
65 TCAATTTCAACTTCACAGCGAAGGATATTGGACT
2236517 TGAAACAATA
Statistics
Matches: 282, Mismatches: 35, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
109 1 0.00
110 281 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (110 bp):
AGCTCAACTTCACAGCGAAGGGGTGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
Found at i:2237020 original size:173 final size:177
Alignment explanation
Indices: 2236724--2237045 Score: 465
Period size: 173 Copynumber: 1.8 Consensus size: 177
2236714 TTCAGAGCCA
* * *
2236724 ATTTCAACTTCACGGCGCAGGATATTGGACTCGAAACAATACAACTTACTTGGATTTCAACTTCA
1 ATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAATACAAC-TACTTGGATTTCAACTTCA
* * * * * * *
2236789 CGATGAAGGATATCCAATTTAAGGCTCAACTTCACGATGGAGGGGCCATCCGCGGTTTCAACTTC
65 CGACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTC
*
2236854 ACGACGGAGGGAATCGTGCACACAAGCAGCATCTATCTCCATATTTGG
130 ACGACGAAGGGAATCGTGCACACAAGCAGCATCTATCTCCATATTTGG
*
2236902 ATTTCAACTTCACGACGAAGGATATTGTACTCAAAAC-A-AC-AC-A-TTGGATTTCAACTTCAC
1 ATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAATACAACTACTTGGATTTCAACTTCAC
*
2236962 TACGAAAGATATCCAATTCCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTC
66 GACGAAAGATATCCAATT-CAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTC
*
2237027 ACGACGAAGGGAATTGTGC
130 ACGACGAAGGGAATCGTGC
2237046 TCACCATTGT
Statistics
Matches: 129, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
172 32 0.25
173 59 0.46
175 2 0.02
176 2 0.02
177 1 0.01
178 33 0.26
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (177 bp):
ATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAATACAACTACTTGGATTTCAACTTCAC
GACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCA
CGACGAAGGGAATCGTGCACACAAGCAGCATCTATCTCCATATTTGG
Found at i:2237097 original size:21 final size:21
Alignment explanation
Indices: 2237072--2237121 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2237062 TGAGACAGTT
2237072 TCTCTTGAAACAAATTTAGTC
1 TCTCTTGAAACAAATTTAGTC
2237093 TCTCTTGAAACAAATTTAGTC
1 TCTCTTGAAACAAATTTAGTC
2237114 TCTCTTGA
1 TCTCTTGA
2237122 GACAGTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTAGTC
Found at i:2237136 original size:36 final size:37
Alignment explanation
Indices: 2237096--2237177 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
2237086 TTTAGTCTCT
2237096 CTTGAAACAAA-TTTAGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAAGTTTAGTCTCTCTTGAGACAGTTTCC
* *
2237132 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAAGTTTAGTCTCTCTTGAGACAGTTTCC
2237169 CTTGAAACA
1 CTTGAAACA
2237178 CTAATCTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 11 0.26
37 32 0.74
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
CTTGAAACAAAGTTTAGTCTCTCTTGAGACAGTTTCC
Found at i:2237294 original size:33 final size:33
Alignment explanation
Indices: 2237231--2237342 Score: 140
Period size: 33 Copynumber: 3.4 Consensus size: 33
2237221 CTTGAGACAG
*
2237231 TTTCTCTTGAAACACAAAAAGAAACCTTTGAAATTG
1 TTTCTCTTGAAACAC--AAA-AAACCTTTGAAATTA
2237267 TTTCTCTTGAAACACAAAAAACCTTTGAAATTA
1 TTTCTCTTGAAACACAAAAAACCTTTGAAATTA
* *
2237300 TTTCTCTCGAAACAC--AAAACCTTTGAGATTA
1 TTTCTCTTGAAACACAAAAAACCTTTGAAATTA
2237331 TTT-TCCTTGAAA
1 TTTCT-CTTGAAA
2237343 AATATTTGTC
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
30 1 0.01
31 24 0.34
33 28 0.39
34 3 0.04
36 15 0.21
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (33 bp):
TTTCTCTTGAAACACAAAAAACCTTTGAAATTA
Found at i:2237439 original size:68 final size:66
Alignment explanation
Indices: 2237300--2237474 Score: 208
Period size: 66 Copynumber: 2.6 Consensus size: 66
2237290 TTTGAAATTA
* * * * *
2237300 TTTCTCTCGAAACACAAAACCTTTGAGATTATTTTCCTTGAAAAATATTTGTCTCCCTTGAGACA
1 TTTCTCTTGAAACACAAAATCTTTGAGATTATTTCCCTTAAAAAAGATTTGTCTCCCTTGAGACA
2237365 G
66 G
*
2237366 TTTCTCTTGAAACACAAAATCTTTGA-ATTTATTTCCCTTAAAACAAGATTTTGTTTCCCTTGAG
1 TTTCTCTTGAAACACAAAATCTTTGAGA-TTATTTCCCTTAAAA-AAGA-TTTGTCTCCCTTGAG
*
2237430 ACCG
63 ACAG
* **
2237434 TTTCTCATGAAACAACAAATATCTTTGAGATCGTTTCCCTT
1 TTTCTCTTGAAAC-ACAAA-ATCTTTGAGATTATTTCCCTT
2237475 GAAACGAATT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
65 1 0.01
66 37 0.40
67 3 0.03
68 29 0.31
69 5 0.05
70 17 0.18
71 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (66 bp):
TTTCTCTTGAAACACAAAATCTTTGAGATTATTTCCCTTAAAAAAGATTTGTCTCCCTTGAGACA
G
Found at i:2238011 original size:2 final size:2
Alignment explanation
Indices: 2238004--2238048 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
2237994 AATTATGAAT
*
2238004 TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA TA TA -A TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2238042 TA TA TA T
1 TA TA TA T
2238049 TATTATTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2238053 original size:10 final size:10
Alignment explanation
Indices: 2238002--2238054 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 10
2237992 TGAATTATGA
2238002 ATTATATATAT
1 ATTAT-TATAT
2238013 ATATATATATAT
1 AT-TAT-TATAT
2238025 ATTATTATAT
1 ATTATTATAT
*
2238035 AATAAATTATAT
1 -AT-TATTATAT
2238047 ATTATTAT
1 ATTATTAT
2238055 TTCAGGACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 10 0.27
11 9 0.24
12 18 0.49
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTATTATAT
Found at i:2239313 original size:39 final size:37
Alignment explanation
Indices: 2239264--2239346 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 37
2239254 ATTGAGCATA
* *
2239264 TTACGTTTTATATATTTCCTTTCATTCAGCACTTACCAT
1 TTAC-TTTT-TATATTTACTTTCATTCAACACTTACCAT
* *
2239303 TTAC-TTTT-TATTTACTTTTATTCAATACTTACCAT
1 TTACTTTTTATATTTACTTTCATTCAACACTTACCAT
2239338 TTACTTTTT
1 TTACTTTTT
2239347 TTCATATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
35 27 0.69
36 5 0.13
37 3 0.08
39 4 0.10
ACGTcount: A:0.23, C:0.19, G:0.02, T:0.55
Consensus pattern (37 bp):
TTACTTTTTATATTTACTTTCATTCAACACTTACCAT
Found at i:2239326 original size:35 final size:35
Alignment explanation
Indices: 2239276--2239346 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
2239266 ACGTTTTATA
* *
2239276 TATTTCCTTTCATTCAGCACTTACCATTTACTTTT
1 TATTTACTTTCATTCAACACTTACCATTTACTTTT
* *
2239311 TATTTACTTTTATTCAATACTTACCATTTACTTTT
1 TATTTACTTTCATTCAACACTTACCATTTACTTTT
2239346 T
1 T
2239347 TTCATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.55
Consensus pattern (35 bp):
TATTTACTTTCATTCAACACTTACCATTTACTTTT
Found at i:2241901 original size:17 final size:17
Alignment explanation
Indices: 2241879--2241936 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
2241869 TCTGAACCGG
*
2241879 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
2241896 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2241913 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2241930 GTTGACC
1 GTTGACC
2241937 GTTGACCGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:2241936 original size:7 final size:7
Alignment explanation
Indices: 2241926--2241962 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2241916 GACCCGACCC
2241926 GACCGTT
1 GACCGTT
2241933 GACCGTT
1 GACCGTT
2241940 GACCG-T
1 GACCGTT
2241946 GACCGTT
1 GACCGTT
2241953 GACCGTT
1 GACCGTT
2241960 GAC
1 GAC
2241963 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:2241950 original size:13 final size:13
Alignment explanation
Indices: 2241926--2241958 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2241916 GACCCGACCC
2241926 GACCGTTGACCGTT
1 GACCG-TGACCGTT
2241940 GACCGTGACCGTT
1 GACCGTGACCGTT
2241953 GACCGT
1 GACCGT
2241959 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:2249160 original size:17 final size:17
Alignment explanation
Indices: 2249138--2249195 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
2249128 TCTGAACCGG
*
2249138 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
2249155 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2249172 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2249189 GTTGACC
1 GTTGACC
2249196 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:2249195 original size:7 final size:7
Alignment explanation
Indices: 2249185--2249228 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
2249175 GACCCGACCC
2249185 GACCGTT
1 GACCGTT
2249192 GACCGTT
1 GACCGTT
2249199 GACCGTT
1 GACCGTT
2249206 GACCG-T
1 GACCGTT
2249212 GACCGTT
1 GACCGTT
2249219 GACCGTT
1 GACCGTT
2249226 GAC
1 GAC
2249229 TTTCTTTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:2249216 original size:20 final size:21
Alignment explanation
Indices: 2249185--2249228 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
2249175 GACCCGACCC
2249185 GACCGTTGACCGTTGACCGTT
1 GACCGTTGACCGTTGACCGTT
2249206 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCGTTGACCGTT
2249226 GAC
1 GAC
2249229 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.25
Consensus pattern (21 bp):
GACCGTTGACCGTTGACCGTT
Found at i:2260641 original size:31 final size:31
Alignment explanation
Indices: 2260603--2260758 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
2260593 CCCGAAGGAC
* *
2260603 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
2260634 CAGTCCATATGTCCCGAAGAACTTAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2260665 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2260696 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2260727 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2260758 C
1 C
2260759 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2263014 original size:26 final size:26
Alignment explanation
Indices: 2262978--2263034 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
2262968 GGGGAACCTA
2262978 GGGTTTCCTTTAAACCCAAGTAGCTT
1 GGGTTTCCTTTAAACCCAAGTAGCTT
2263004 GGGTTTCCTTTAAACCCAAGTAGCTT
1 GGGTTTCCTTTAAACCCAAGTAGCTT
2263030 GGGTT
1 GGGTT
2263035 ACATCTGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (26 bp):
GGGTTTCCTTTAAACCCAAGTAGCTT
Found at i:2264133 original size:13 final size:13
Alignment explanation
Indices: 2264115--2264140 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2264105 GGCTTGTTCT
2264115 CTAACTCATTTTA
1 CTAACTCATTTTA
2264128 CTAACTCATTTTA
1 CTAACTCATTTTA
2264141 TGAATTTCTT
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:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
CTAACTCATTTTA
Found at i:2271769 original size:6 final size:6
Alignment explanation
Indices: 2271758--2271783 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2271748 AATGACTTTT
2271758 AGTGTC AGTGTC AGTGTC AGTGTC AG
1 AGTGTC AGTGTC AGTGTC AGTGTC AG
2271784 ATATAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (6 bp):
AGTGTC
Found at i:2281005 original size:22 final size:22
Alignment explanation
Indices: 2280977--2281039 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
2280967 GAATGACCAC
* *
2280977 TATGTCCCGAAGAACCATTGTA
1 TATGTCCCGAAGGACCACTGTA
2280999 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
2281021 TATGTCCCGAAGGACCACT
1 TATGTCCCGAAGGACCACT
2281040 CCTTAAGAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:2286878 original size:12 final size:12
Alignment explanation
Indices: 2286861--2286915 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
2286851 AAATATGGTA
2286861 TGAACAGTACCG
1 TGAACAGTACCG
*
2286873 TGAACAGTA--A
1 TGAACAGTACCG
* * *
2286883 TAAACAATAACG
1 TGAACAGTACCG
*
2286895 TGAATAGTACCG
1 TGAACAGTACCG
2286907 TGAACAGTA
1 TGAACAGTA
2286916 ACATGTTACA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
10 7 0.22
12 25 0.78
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:2287588 original size:18 final size:18
Alignment explanation
Indices: 2287565--2287621 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 18
2287555 ACTGAATAGT
2287565 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
* *
2287583 TGTCCCGAAGGACAACTGTATA
1 TGTCCCAAAGGACCAC----TA
2287605 TGTCCCAAAGGACCACT
1 TGTCCCAAAGGACCACT
2287622 CTTTAAGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 15 0.48
22 16 0.52
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:2295323 original size:17 final size:17
Alignment explanation
Indices: 2295301--2295335 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2295291 CAGAGGCAAC
2295301 TCGGTTCGTGCGCCACA
1 TCGGTTCGTGCGCCACA
2295318 TCGGTTCGTGCGCCACA
1 TCGGTTCGTGCGCCACA
2295335 T
1 T
2295336 TTAATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.34, G:0.29, T:0.26
Consensus pattern (17 bp):
TCGGTTCGTGCGCCACA
Found at i:2299047 original size:23 final size:23
Alignment explanation
Indices: 2299021--2299139 Score: 193
Period size: 23 Copynumber: 5.2 Consensus size: 23
2299011 TTCAAAATGT
2299021 ACTGTTTTGCTGAATCATTCAGC
1 ACTGTTTTGCTGAATCATTCAGC
2299044 ACTGTTTTGCTGAATCATTCAGC
1 ACTGTTTTGCTGAATCATTCAGC
*
2299067 ACTGTTTTGCTAAATCATTCAGC
1 ACTGTTTTGCTGAATCATTCAGC
*
2299090 ACTGTTTTGCTGAATCATTCAGT
1 ACTGTTTTGCTGAATCATTCAGC
* * *
2299113 ACTGTTTTGTTGAATCAATCAGT
1 ACTGTTTTGCTGAATCATTCAGC
2299136 ACTG
1 ACTG
2299140 CATCATTCAG
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 91 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (23 bp):
ACTGTTTTGCTGAATCATTCAGC
Found at i:2305605 original size:13 final size:13
Alignment explanation
Indices: 2305587--2305616 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2305577 TACTGTCTAA
2305587 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
*
2305600 TTCTTTTCTTTTT
1 TTCTTTTCTTTCT
2305613 TTCT
1 TTCT
2305617 CTCGATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTCTTTCT
Found at i:2305661 original size:22 final size:21
Alignment explanation
Indices: 2305636--2305680 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2305626 TCTCTTGGTA
2305636 TTTTATTGTTTGACT-CTTTCTC
1 TTTTATTGTTT-ACTGCTTT-TC
*
2305658 TTTTTTTGTTTACTGCTTTTC
1 TTTTATTGTTTACTGCTTTTC
2305679 TT
1 TT
2305681 CCTCTGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.07, C:0.16, G:0.09, T:0.69
Consensus pattern (21 bp):
TTTTATTGTTTACTGCTTTTC
Found at i:2308534 original size:21 final size:22
Alignment explanation
Indices: 2308502--2308544 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2308492 TTTAAATTTT
2308502 TATTATTATTGGAT-GAAGAAA
1 TATTATTATTGGATAGAAGAAA
2308523 TATTAATT-TTGGATAGAAGAAA
1 TATT-ATTATTGGATAGAAGAAA
2308545 CGTCTAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (22 bp):
TATTATTATTGGATAGAAGAAA
Found at i:2311655 original size:32 final size:32
Alignment explanation
Indices: 2311619--2311683 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2311609 TTAATTGCCA
2311619 ATACCAATATCTTATTCCTTCTCGAAATTCTT
1 ATACCAATATCTTATTCCTTCTCGAAATTCTT
* *
2311651 ATACCAATCTCTTATTCCTTCTCGAAGTTCTT
1 ATACCAATATCTTATTCCTTCTCGAAATTCTT
2311683 A
1 A
2311684 CTCTGACGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.43
Consensus pattern (32 bp):
ATACCAATATCTTATTCCTTCTCGAAATTCTT
Found at i:2315227 original size:32 final size:32
Alignment explanation
Indices: 2315191--2315255 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2315181 TTAATTGCCA
2315191 ATACCAATATCTTATTCCTTCTCGAAATTCTT
1 ATACCAATATCTTATTCCTTCTCGAAATTCTT
* *
2315223 ATACCAATCTCTTATTCCTTCTCGAAGTTCTT
1 ATACCAATATCTTATTCCTTCTCGAAATTCTT
2315255 A
1 A
2315256 CTCTGACGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.43
Consensus pattern (32 bp):
ATACCAATATCTTATTCCTTCTCGAAATTCTT
Found at i:2316272 original size:22 final size:22
Alignment explanation
Indices: 2316244--2316285 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2316234 GAAGAAAATA
*
2316244 CCATAA-TACCCTTTCAATCCTT
1 CCATAATTACCATTT-AATCCTT
2316266 CCATAATTACCATTTAATCC
1 CCATAATTACCATTTAATCC
2316286 AATACTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (22 bp):
CCATAATTACCATTTAATCCTT
Found at i:2318566 original size:27 final size:27
Alignment explanation
Indices: 2318536--2318588 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2318526 TTAAAAAAAA
2318536 TTAT-AAACAAATAAAAAATAATTAAAT
1 TTATGAAACAAA-AAAAAATAATTAAAT
** *
2318563 TTATGAAATTAAAAAAAATCATTAAA
1 TTATGAAACAAAAAAAAATAATTAAA
2318589 AAATACCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (27 bp):
TTATGAAACAAAAAAAAATAATTAAAT
Found at i:2318843 original size:31 final size:31
Alignment explanation
Indices: 2318805--2318864 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2318795 TTGAGTGTGT
*
2318805 ACCAAATTACCGGATTTATCCGGTAATAAAC
1 ACCAAATTACCAGATTTATCCGGTAATAAAC
* *
2318836 ACCAAATTATCAGATTTATCTGGTAATAA
1 ACCAAATTACCAGATTTATCCGGTAATAA
2318865 TACCCCTCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (31 bp):
ACCAAATTACCAGATTTATCCGGTAATAAAC
Found at i:2321460 original size:44 final size:44
Alignment explanation
Indices: 2321412--2321498 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
2321402 GCCCTCTCTC
2321412 TGTTCCGTCTCTTGCTCTCCGTTTTTCTCTGTTGCCTTCTTCTA
1 TGTTCCGTCTCTTGCTCTCCGTTTTTCTCTGTTGCCTTCTTCTA
**
2321456 TGTTCCGTCTCTTGCTCTTTGTTTTTCTCTGTTGCCTTCTTCT
1 TGTTCCGTCTCTTGCTCTCCGTTTTTCTCTGTTGCCTTCTTCT
2321499 CTTTTTCTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.01, C:0.30, G:0.14, T:0.55
Consensus pattern (44 bp):
TGTTCCGTCTCTTGCTCTCCGTTTTTCTCTGTTGCCTTCTTCTA
Found at i:2321500 original size:15 final size:15
Alignment explanation
Indices: 2321436--2321500 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
2321426 CTCTCCGTTT
2321436 TTCTCTGTTGCCTTC
1 TTCTCTGTTGCCTTC
*
2321451 TTCTATGTT-CCGTCTC
1 TTCTCTGTTGCC-T-TC
*
2321467 TTGCTCT-TTG--TTT
1 TT-CTCTGTTGCCTTC
2321480 TTCTCTGTTGCCTTC
1 TTCTCTGTTGCCTTC
2321495 TTCTCT
1 TTCTCT
2321501 TTTTCTGCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
12 4 0.10
13 6 0.15
14 3 0.08
15 17 0.44
16 6 0.15
17 3 0.08
ACGTcount: A:0.02, C:0.29, G:0.12, T:0.57
Consensus pattern (15 bp):
TTCTCTGTTGCCTTC
Found at i:2321883 original size:3 final size:3
Alignment explanation
Indices: 2321875--2321937 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
2321865 GGCATGTTTG
**
2321875 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
2321920 TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA
2321938 AAAAATGGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2322412 original size:113 final size:113
Alignment explanation
Indices: 2322276--2322724 Score: 708
Period size: 113 Copynumber: 4.0 Consensus size: 113
2322266 ATAGAGTCAT
* *
2322276 GCAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * **
2322341 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGGATTTGA
* * ** *
2322389 ACAAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2322454 ATTATGAACTTTCTCTGGAAAAGCTGA-CCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
2322501 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCGTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2322566 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
2322614 GCAAAAGGTTGAACAAGCTCTTCTCAGTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTTTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
2322679 ATTATGAACTTTCTCTGGAAAAGCTGATCCAT--TGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
2322725 ATCCCTGCTA
Statistics
Matches: 314, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
111 15 0.05
112 99 0.32
113 200 0.64
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:2322558 original size:225 final size:224
Alignment explanation
Indices: 2322276--2322724 Score: 704
Period size: 225 Copynumber: 2.0 Consensus size: 224
2322266 ATAGAGTCAT
* *
2322276 GCAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCGTCCTTCTTCAGATGAGTTCTTCTC
*
2322341 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAAACAAAAGGTTAAACAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGAATTCAAACAAAAGGTTAAACAA
* * *
2322405 ATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
130 ACTCTTCTCAGTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
2322470 GGAAAAGCTGA-CCATCAAGTGATGGATTTGA
195 GGAAAAGCTGATCCAT--AGTGATGGATTTGA
* *
2322501 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCGTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCGTCCTTCTTCAGATGAGTTCTTCTC
* ** * * *
2322566 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTAAACAAA
* *
2322631 CTCTTCTCAGTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTTTCATTATGAACTTTCTCTG
131 CTCTTCTCAGTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
2322696 GAAAAGCTGATCCATTGTGATGGATTTGA
196 GAAAAGCTGATCCATAGTGATGGATTTGA
2322725 ATCCCTGCTA
Statistics
Matches: 205, Mismatches: 17, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
224 15 0.07
225 186 0.91
226 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (224 bp):
GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCGTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTAAACAAA
CTCTTCTCAGTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATAGTGATGGATTTGA
Found at i:2325693 original size:7 final size:7
Alignment explanation
Indices: 2325681--2325724 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
2325671 GTCAAAGGAA
2325681 GTCAACG
1 GTCAACG
2325688 GTCAACG
1 GTCAACG
2325695 GTC-ACG
1 GTCAACG
2325701 GTCAACG
1 GTCAACG
*
2325708 GTCAACA
1 GTCAACG
2325715 GTCAACG
1 GTCAACG
2325722 GTC
1 GTC
2325725 GAGTCGGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2325706 original size:20 final size:21
Alignment explanation
Indices: 2325682--2325724 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
2325672 TCAAAGGAAG
*
2325682 TCAACGGTCAACGGTC-ACGG
1 TCAACGGTCAACAGTCAACGG
2325702 TCAACGGTCAACAGTCAACGG
1 TCAACGGTCAACAGTCAACGG
2325723 TC
1 TC
2325725 GAGTCGGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
TCAACGGTCAACAGTCAACGG
Found at i:2325749 original size:9 final size:9
Alignment explanation
Indices: 2325731--2325811 Score: 81
Period size: 10 Copynumber: 8.3 Consensus size: 9
2325721 GGTCGAGTCG
*
2325731 GGTCAGACC
1 GGTCAAACC
2325740 GGTCAAACC
1 GGTCAAACC
2325749 GGTCAGAACC
1 GGTCA-AACC
*
2325759 GATCGAAACC
1 GGTC-AAACC
2325769 GGTCAGAACC
1 GGTCA-AACC
2325779 GGTCGAAACC
1 GGTC-AAACC
*
2325789 GGTTGAAAACC
1 GG-T-CAAACC
2325800 GGTCAAACC
1 GGTCAAACC
2325809 GGT
1 GGT
2325812 TTCCAGCCCT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
9 22 0.36
10 29 0.48
11 10 0.16
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.12
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2325781 original size:30 final size:30
Alignment explanation
Indices: 2325737--2325811 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
2325727 GTCGGGTCAG
2325737 ACCGGTCAAACCGGTC-AGAACCGATCG-AA
1 ACCGGTCAAACCGGTCGA-AACCGATCGAAA
* *
2325766 ACCGGTCAGAACCGGTCGAAACCGGTTGAAA
1 ACCGGTCA-AACCGGTCGAAACCGATCGAAA
2325797 ACCGGTCAAACCGGT
1 ACCGGTCAAACCGGT
2325812 TTCCAGCCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
29 8 0.20
30 22 0.54
31 11 0.27
ACGTcount: A:0.32, C:0.29, G:0.27, T:0.12
Consensus pattern (30 bp):
ACCGGTCAAACCGGTCGAAACCGATCGAAA
Found at i:2325812 original size:20 final size:20
Alignment explanation
Indices: 2325731--2325811 Score: 105
Period size: 20 Copynumber: 4.2 Consensus size: 20
2325721 GGTCGAGTCG
2325731 GGTCAG-ACCGGTC-AAACC
1 GGTCAGAACCGGTCGAAACC
*
2325749 GGTCAGAACCGATCGAAACC
1 GGTCAGAACCGGTCGAAACC
2325769 GGTCAGAACCGGTCGAAACC
1 GGTCAGAACCGGTCGAAACC
* *
2325789 GGTTGAAAACCGGTC-AAACC
1 GG-TCAGAACCGGTCGAAACC
2325809 GGT
1 GGT
2325812 TTCCAGCCCT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
18 6 0.11
19 7 0.12
20 33 0.59
21 10 0.18
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.12
Consensus pattern (20 bp):
GGTCAGAACCGGTCGAAACC
Found at i:2330024 original size:21 final size:21
Alignment explanation
Indices: 2329991--2330032 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2329981 ACAAGTGTGT
*
2329991 GTATATTTAAAAAAATAAAAA
1 GTATATTTAAAAAAAGAAAAA
2330012 GTAT-TTTAGAAAAAAGAAAAA
1 GTATATTTA-AAAAAAGAAAAA
2330033 TTAAGAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (21 bp):
GTATATTTAAAAAAAGAAAAA
Found at i:2335665 original size:15 final size:15
Alignment explanation
Indices: 2335645--2335677 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2335635 AACTCCATTA
2335645 GAGCTATTCGATATG
1 GAGCTATTCGATATG
2335660 GAGCTATTCGATATG
1 GAGCTATTCGATATG
2335675 GAG
1 GAG
2335678 ATATAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (15 bp):
GAGCTATTCGATATG
Found at i:2338588 original size:18 final size:18
Alignment explanation
Indices: 2338561--2338603 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2338551 AGTATGTCGA
*
2338561 AATGCGCCTATGACTCTC
1 AATGCACCTATGACTCTC
2338579 AATGCACCTATGACTCTC
1 AATGCACCTATGACTCTC
2338597 AATGCAC
1 AATGCAC
2338604 ATACAATGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.26
Consensus pattern (18 bp):
AATGCACCTATGACTCTC
Found at i:2344590 original size:38 final size:38
Alignment explanation
Indices: 2344520--2344830 Score: 156
Period size: 37 Copynumber: 8.3 Consensus size: 38
2344510 ATAAATATAG
**
2344520 TATAATTTTTA-AAAA-TATTTTTAGAAAA-ATATAATA
1 TATAATTTTTAGAAAACGGTTTTT-GAAAACATATAATA
2344556 TATAATTTTTAGAAAACGGTTTTTGAAAACATATAATA
1 TATAATTTTTAGAAAACGGTTTTTGAAAACATATAATA
** **
2344594 TAGTTTTTTTTTTAAAATCGG-TTTTG--AA-ATAT-ATA
1 TA-TAATTTTTAGAAAA-CGGTTTTTGAAAACATATAATA
* ***
2344629 TATAATATGGTTTTGAAAACACATTTT-AAAACATATAATA
1 TATAAT-T--TTTAGAAAACGGTTTTTGAAAACATATAATA
*
2344669 TATAA-TTTT-GAAAAC-ATATTTTGAAAACGTATATAATA
1 TATAATTTTTAGAAAACGGT-TTTTGAAAAC--ATATAATA
* * *
2344707 TATAGTTTTTA-AAATCGGTTTTAGAAAACATATAATA
1 TATAATTTTTAGAAAACGGTTTTTGAAAACATATAATA
** **
2344744 TATGTTTTTTA-AAATA---TTTTTGAAAATGTATATATAA
1 TATAATTTTTAGAAA-ACGGTTTTTGAAAACATATA-AT-A
* ** *
2344781 TATAGTTTTT-GAAAACATATTTTTTTGGAAACATATAATA
1 TATAATTTTTAGAAAAC---GGTTTTTGAAAACATATAATA
2344821 TAT-ATTTTTA
1 TATAATTTTTA
2344831 AAACATATAT
Statistics
Matches: 215, Mismatches: 29, Indels: 58
0.71 0.10 0.19
Matches are distributed among these distances:
34 2 0.01
35 29 0.13
36 27 0.13
37 55 0.26
38 30 0.14
39 41 0.19
40 16 0.07
41 2 0.01
42 13 0.06
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (38 bp):
TATAATTTTTAGAAAACGGTTTTTGAAAACATATAATA
Found at i:2344665 original size:35 final size:36
Alignment explanation
Indices: 2344615--2344708 Score: 111
Period size: 35 Copynumber: 2.6 Consensus size: 36
2344605 TTAAAATCGG
* **
2344615 TTTTGAAATATATATATAATATGGTTTTGAAAACACA
1 TTTTGAAA-ACATATATAATATAATTTTGAAAACACA
*
2344652 TTTT-AAAACATATA-ATATATAATTTTGAAAACATA
1 TTTTGAAAACATATATA-ATATAATTTTGAAAACACA
*
2344687 TTTTGAAAACGTATATAATATA
1 TTTTGAAAACATATATAATATA
2344709 TAGTTTTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
34 1 0.02
35 26 0.53
36 17 0.35
37 5 0.10
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (36 bp):
TTTTGAAAACATATATAATATAATTTTGAAAACACA
Found at i:2344702 original size:75 final size:73
Alignment explanation
Indices: 2344514--2344838 Score: 224
Period size: 75 Copynumber: 4.4 Consensus size: 73
2344504 ATATATATAA
* * *
2344514 ATATAGTATA-ATTTTTAAAA-ATATTTTTAGAAAAATATAATATATAAT-T--TTTAGAAAACG
1 ATATAATATATATTTTTAAAACATA-TTTT-G-AAAATAT-ATATATAATATGGTTTTGAAAACA
**
2344574 GTTTTTGAAAAC
62 CATTTTGAAAAC
* **
2344586 ATATAATATAGTTTTTTTTTTAAAATC-GGTTTTG-AAATATATATATAATATGGTTTTGAAAAC
1 ATATAATATA----TATTTTTAAAA-CATATTTTGAAAATATATATATAATATGGTTTTGAAAAC
2344649 ACATTTT-AAAAC
61 ACATTTTGAAAAC
* * *
2344661 ATATAATATATAATTTTGAAAACATATTTTGAAAACGTATATA-AT-ATATAGTTTTTAAAATC-
1 ATATAATATAT-ATTTTTAAAACATATTTTGAAAA--TATATATATAATATGGTTTTGAAAA-CA
**
2344723 GGTTTTAGAAAAC
62 CATTTT-GAAAAC
* * * * *
2344736 ATATAATATATGTTTTTTAAA-ATATTTTTGAAAATGTATATATAATATAGTTTTTGAAAACATA
1 ATATAATATATATTTTTAAAACATA-TTTTGAAAATATATATATAATAT-GGTTTTGAAAACACA
*
2344800 TTTTTTTGGAAAC
64 ---TTTTGAAAAC
2344813 ATATAATATATATTTTTAAAACATAT
1 ATATAATATATATTTTTAAAACATAT
2344839 ATAATATATA
Statistics
Matches: 198, Mismatches: 28, Indels: 49
0.72 0.10 0.18
Matches are distributed among these distances:
71 2 0.01
72 27 0.14
73 34 0.17
74 31 0.16
75 45 0.23
76 14 0.07
77 38 0.19
78 7 0.04
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (73 bp):
ATATAATATATATTTTTAAAACATATTTTGAAAATATATATATAATATGGTTTTGAAAACACATT
TTGAAAAC
Found at i:2344807 original size:16 final size:16
Alignment explanation
Indices: 2344786--2344816 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2344776 TATAATATAG
2344786 TTTTTGAAAACATATT
1 TTTTTGAAAACATATT
*
2344802 TTTTTGGAAACATAT
1 TTTTTGAAAACATAT
2344817 AATATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTTTGAAAACATATT
Found at i:2344834 original size:22 final size:24
Alignment explanation
Indices: 2344809--2344858 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
2344799 ATTTTTTTGG
2344809 AAAC-ATATAATATAT-ATTTTTA
1 AAACAATATAATATATAATTTTTA
2344831 AAACATATATAATATATAATTTTTA
1 AAACA-ATATAATATATAATTTTTA
2344856 AAA
1 AAA
2344859 ATCGATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.16
24 11 0.44
25 10 0.40
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACAATATAATATATAATTTTTA
Found at i:2344834 original size:38 final size:36
Alignment explanation
Indices: 2344514--2344838 Score: 197
Period size: 38 Copynumber: 8.7 Consensus size: 36
2344504 ATATATATAA
*
2344514 ATATAGTATA-ATTTTTAAAA-ATATTTTTAGAAAA-
1 ATATAATATATATTTTTAAAACATATTTTT-GAAAAC
**
2344548 ATATAATATATAATTTTTAGAAA-ACGGTTTTTGAAAAC
1 ATATAATATAT-ATTTTTA-AAACA-TATTTTTGAAAAC
* * ** *
2344586 ATATAATATAGTTTTTTTTTTAAA-ATCGGTTTTG-AAAT
1 ATATAATATA---TATTTTTAAAACAT-ATTTTTGAAAAC
*
2344624 ATAT-ATATAATATGGTTTTGAAAACACA-TTTT-AAAAC
1 ATATAATAT-ATAT--TTTT-AAAACATATTTTTGAAAAC
*
2344661 ATATAATATATAATTTTGAAAACATA-TTTTGAAAAC
1 ATATAATATAT-ATTTTTAAAACATATTTTTGAAAAC
** *
2344697 GTATATAATATATAGTTTTTAAAATC-GGTTTTAGAAAAC
1 --ATATAATATATA-TTTTTAAAA-CATATTTTTGAAAAC
* * *
2344736 ATATAATATATGTTTTTTAAA-ATATTTTTGAAAAT
1 ATATAATATATATTTTTAAAACATATTTTTGAAAAC
* *
2344771 GTATATATAATATAGTTTTTGAAAACATATTTTTTTGGAAAC
1 ATATA-AT-ATATA-TTTTT-AAAACATA--TTTTTGAAAAC
2344813 ATATAATATATATTTTTAAAACATAT
1 ATATAATATATATTTTTAAAACATAT
2344839 ATAATATATA
Statistics
Matches: 229, Mismatches: 31, Indels: 60
0.72 0.10 0.19
Matches are distributed among these distances:
34 9 0.04
35 26 0.11
36 26 0.11
37 46 0.20
38 64 0.28
39 29 0.13
40 13 0.06
41 3 0.01
42 13 0.06
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
ATATAATATATATTTTTAAAACATATTTTTGAAAAC
Found at i:2344963 original size:29 final size:27
Alignment explanation
Indices: 2344930--2344984 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
2344920 TTTTCAATTG
2344930 GTTTTTGAAAATATA-ATGTATGTTATATA
1 GTTTTT-AAAATATATAT-TAT-TTATATA
2344959 GTTTTTAAAATATATATTATTTATAT
1 GTTTTTAAAATATATATTATTTATAT
2344985 TTCTATATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 11 0.44
29 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (27 bp):
GTTTTTAAAATATATATTATTTATATA
Found at i:2345012 original size:21 final size:21
Alignment explanation
Indices: 2344968--2345030 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
2344958 AGTTTTTAAA
* *
2344968 ATATATATTAT-TTATATTTCT
1 ATATTTATTATATTATA-TTAT
2344989 ATATTGT-TTATTATT-TATTAT
1 ATATT-TATTA-TATTATATTAT
2345010 ATATTTATTATATTATATTAT
1 ATATTTATTATATTATATTAT
2345031 GTTGTTACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
20 5 0.14
21 24 0.69
22 4 0.11
23 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
ATATTTATTATATTATATTAT
Found at i:2345934 original size:2 final size:2
Alignment explanation
Indices: 2345894--2345920 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2345884 TGTATATCAA
2345894 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2345921 AACTCTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2352530 original size:77 final size:79
Alignment explanation
Indices: 2352431--2352575 Score: 183
Period size: 78 Copynumber: 1.9 Consensus size: 79
2352421 GGAAAAAAAA
* **
2352431 TATTTAATTAATTCAAATTAAATAT-ATATT-AAAGATTTATAATCTGAATTAAAATC-TTTAAT
1 TATTTAATTAATTCAAATTAAATATCA-ATTAAAAGAGTTATAATCAAAATTAAAATCTTTTAAT
2352493 GTTTATTTAAAATCT
65 GTTTATTTAAAATCT
* *
2352508 TATTTAATT-ATTCCGAAA-TAAATATCAATTAAAAGAGTTGTAATCAAAATTAAATTCTTTTAA
1 TATTTAATTAATT-C-AAATTAAATATCAATTAAAAGAGTTATAATCAAAATTAAAATCTTTTAA
2352571 TGTTT
64 TGTTT
2352576 TTATACTATA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
76 3 0.05
77 20 0.34
78 25 0.43
79 10 0.17
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (79 bp):
TATTTAATTAATTCAAATTAAATATCAATTAAAAGAGTTATAATCAAAATTAAAATCTTTTAATG
TTTATTTAAAATCT
Found at i:2361051 original size:199 final size:200
Alignment explanation
Indices: 2360638--2361147 Score: 655
Period size: 199 Copynumber: 2.6 Consensus size: 200
2360628 TAGAGGAACC
** * * * ** ** *
2360638 ATTTACAACATTGCTTAAGTTGATAAAAGTTATCTGTCAACGAAATTCCGAGTTTTATTTCATTC
1 ATTTACAACATAACTTAAGTCGAGAAAAGATATCTGTCAACGAAATTTTGAGTTCGATTCCATTC
* * *
2360703 AGCTCGAGGGCATATCAACTGCAGGGTAGTATCGATGAACTACTTTCCTCGTTGAAGTTTAAACT
66 AGCTCGAGGGCATATCAACTGCAGGGTAGCATCGAGGAACTACTTTCCTCGTTAAAGTTTAAACT
* * * *
2360768 GAGGTCTTTAGGCCAAGAAGAATACCTAGGTTAGTTGCGATTTAGCAACAAGGAACTATCTTACA
131 GAGGTCTTTAAGCCAAGAAAAATACCTAGGTTAGTAGCGATTTAGCAACAAGGAACTACCTTACA
2360833 GCCTA
196 GCCTA
* * * * * * *
2360838 ATTCATAGCATAACTTAAGTCAAGAAAAGCTATCTGTCAATGAAATTTTGAGTTCGACTCCATTC
1 ATTTACAACATAACTTAAGTCGAGAAAAGATATCTGTCAACGAAATTTTGAGTTCGATTCCATTC
*
2360903 AGCTCGAGGGCATATCAACTGCAGGGTAGCATCGAGGAACTACTTT-CTGGTTAAAGTTTAAACT
66 AGCTCGAGGGCATATCAACTGCAGGGTAGCATCGAGGAACTACTTTCCTCGTTAAAGTTTAAACT
* * *
2360967 GAGGTCTTTAAGTCAAGAAAAATACCTAGGTTA-TCAGCGATTTAGCAATAAGGAACTACCTTCC
131 GAGGTCTTTAAGCCAAGAAAAATACCTAGGTTAGT-AGCGATTTAGCAACAAGGAACTACCTTAC
*
2361031 AGTCTA
195 AGCCTA
* * *
2361037 ATTTACAACATAACTTATGTCGAGAAAAGATATATGTCAACAAAATTTTGAGTTCGATTCCATTC
1 ATTTACAACATAACTTAAGTCGAGAAAAGATATCTGTCAACGAAATTTTGAGTTCGATTCCATTC
* * ** * *
2361102 AGCTCGAGGGCGTATCAACCGCATAGTAGCAGCAAGGAACTACTTT
66 AGCTCGAGGGCATATCAACTGCAGGGTAGCATCGAGGAACTACTTT
2361148 TCGGTTGAAC
Statistics
Matches: 265, Mismatches: 44, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
198 1 0.00
199 171 0.65
200 93 0.35
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (200 bp):
ATTTACAACATAACTTAAGTCGAGAAAAGATATCTGTCAACGAAATTTTGAGTTCGATTCCATTC
AGCTCGAGGGCATATCAACTGCAGGGTAGCATCGAGGAACTACTTTCCTCGTTAAAGTTTAAACT
GAGGTCTTTAAGCCAAGAAAAATACCTAGGTTAGTAGCGATTTAGCAACAAGGAACTACCTTACA
GCCTA
Found at i:2361640 original size:39 final size:38
Alignment explanation
Indices: 2361575--2361951 Score: 270
Period size: 37 Copynumber: 9.9 Consensus size: 38
2361565 ATAAATATAG
* * *
2361575 TATATTTTTTGAAAA-TA-TTTTTGAAAAACATATAATC
1 TATAGTTTTTGAAAACAAGTTTTTG-AAAACATATAATA
*
2361612 TATAGTTTTTAGAAAAC-GGTTTTTGAAAACATATAATA
1 TATAGTTTTT-GAAAACAAGTTTTTGAAAACATATAATA
* * *
2361650 TATAGTTTTTAAAAAAAAATCAGTTTTTG-AAATATAT-ATAA
1 TATAGTTTTT--GAAAACA--AGTTTTTGAAAACATATAAT-A
*
2361691 TATAG-TTTTGAAAACACG-TTTT-AAAACATATAATA
1 TATAGTTTTTGAAAACAAGTTTTTGAAAACATATAATA
2361726 TATAG-TTTTGAAAACATA-TTTTTGAAAACGAATATAATA
1 TATAGTTTTTGAAAACA-AGTTTTTGAAAAC--ATATAATA
* *** *
2361765 TATAGTTTGT-AAAATTCGTTTTGGAAAACATATAATA
1 TATAGTTTTTGAAAACAAGTTTTTGAAAACATATAATA
* **
2361802 TAT-GATTTTT-AAAA-TA-TTTTTGAAAATGTATATATAA
1 TATAG-TTTTTGAAAACAAGTTTTTGAAAACATATA-AT-A
* *
2361839 TATAGTTTTTGAAAACATAATTTTTGGAAACATATAATA
1 TATAGTTTTTGAAAACA-AGTTTTTGAAAACATATAATA
*
2361878 TATA-ATTTTGAAAACATA-TTTTTGAAAACATATCTAATA
1 TATAGTTTTTGAAAACA-AGTTTTTGAAAACATA--TAATA
*
2361917 TATAGTTTTT-AAAA-AATGATTTTGGAAAACATATA
1 TATAGTTTTTGAAAACAA-G-TTTTTGAAAACATATA
2361952 TAGTTTTGAA
Statistics
Matches: 279, Mismatches: 30, Indels: 61
0.75 0.08 0.16
Matches are distributed among these distances:
35 41 0.15
36 11 0.04
37 56 0.20
38 53 0.19
39 56 0.20
40 29 0.10
41 26 0.09
42 7 0.03
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (38 bp):
TATAGTTTTTGAAAACAAGTTTTTGAAAACATATAATA
Found at i:2361760 original size:76 final size:76
Alignment explanation
Indices: 2361581--2361951 Score: 287
Period size: 76 Copynumber: 4.9 Consensus size: 76
2361571 ATAGTATATT
* *
2361581 TTTTG-AAA-ATATTTTTGAAAAAC-ATATA-AT-CTATAGTTTTTAGAAAAC-GGTTTTTGAAA
1 TTTTGAAAACATATTTTTG-AAAACGATATATATAATATAG-TTTT-GAAAACACG-TTTTGAAA
2361640 ACATATAATATATAG
62 ACATATAATATATAG
* *
2361655 TTTTTAAAAAAAAATCAGTTTTTG--AA--ATATATATAATATAGTTTTGAAAACACGTTTT-AA
1 -TTTT--GAAAACAT-A-TTTTTGAAAACGATATATATAATATAGTTTTGAAAACACGTTTTGAA
2361715 AACATATAATATATAG
61 AACATATAATATATAG
**
2361731 TTTTGAAAACATATTTTTGAAAACGA-ATATA-ATATATAG-TTTGTAAAATTCGTTTTGGAAAA
1 TTTTGAAAACATATTTTTGAAAACGATATATATA-ATATAGTTTTG-AAAACACGTTTT-GAAAA
2361793 CATATAATATAT-G
63 CATATAATATATAG
* * ** *
2361806 ATTTT-TAAA-ATATTTTTGAAAATG-TATATATAATATAGTTTTTGAAAACATAATTTTTGGAA
1 -TTTTGAAAACATATTTTTGAAAACGATATATATAATATAG-TTTTGAAAAC--ACGTTTTGAAA
*
2361868 ACATATAATATATAA
62 ACATATAATATATAG
* * * *
2361883 TTTTGAAAACATATTTTTGAAAAC-ATATCTA-ATATATAGTTTTTAAAAAATGATTTTGGAAAA
1 TTTTGAAAACATATTTTTGAAAACGATATATATA-ATATAGTTTTGAAAACACG-TTTT-GAAAA
2361946 CATATA
63 CATATA
2361952 TAGTTTTGAA
Statistics
Matches: 242, Mismatches: 23, Indels: 60
0.74 0.07 0.18
Matches are distributed among these distances:
71 6 0.02
72 1 0.00
73 13 0.05
74 46 0.19
75 19 0.08
76 66 0.27
77 41 0.17
78 36 0.15
79 7 0.03
80 1 0.00
81 6 0.02
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (76 bp):
TTTTGAAAACATATTTTTGAAAACGATATATATAATATAGTTTTGAAAACACGTTTTGAAAACAT
ATAATATATAG
Found at i:2361794 original size:152 final size:149
Alignment explanation
Indices: 2361581--2361951 Score: 422
Period size: 152 Copynumber: 2.4 Consensus size: 149
2361571 ATAGTATATT
* * *
2361581 TTTTG-AAA-ATATTTTTGAAAA-ACATATAATCTATAGTTTTTAGAAAACGGTTTTTGAAAACA
1 TTTTGAAAACATATTTTTGAAAACACATATAATATATAGTTTTTA-AAATC-GTTTTGGAAAACA
2361643 TATAATATAT-AGTTTTTAAAAAAAAATCAGTTTTTG-AAA-TATATATAATATAG-TTTTGAAA
64 TATAATATATGA-TTTTT-----AAAAT-A-TTTTTGAAAAGTATATATAATATAGTTTTTGAAA
* *
2361704 AC-ACGTTTT-AAAACATATAATATATAG
121 ACAAAGTTTTGAAAACATATAATATATAA
*
2361731 TTTTGAAAACATATTTTTGAAAACGA-ATATAATATATAGTTTGTAAAATTCGTTTTGGAAAACA
1 TTTTGAAAACATATTTTTGAAAAC-ACATATAATATATAGTTTTTAAAA-TCGTTTTGGAAAACA
*
2361795 TATAATATATGATTTTTAAAATATTTTTGAAAATGTATATATAATATAGTTTTTGAAAACATAAT
64 TATAATATATGATTTTTAAAATATTTTTGAAAA-GTATATATAATATAGTTTTTGAAAACA-AAG
*
2361860 TTTTGGAAACATATAATATATAA
127 TTTTGAAAACATATAATATATAA
* *
2361883 TTTTGAAAACATATTTTTGAAAACATATCTAATATATAGTTTTTAAAAAAT-GATTTTGGAAAAC
1 TTTTGAAAACATATTTTTGAAAACACATATAATATATAGTTTTT--AAAATCG-TTTTGGAAAAC
2361947 ATATA
63 ATATA
2361952 TAGTTTTGAA
Statistics
Matches: 194, Mismatches: 10, Indels: 31
0.83 0.04 0.13
Matches are distributed among these distances:
145 6 0.03
146 4 0.02
147 5 0.03
148 14 0.07
149 10 0.05
150 5 0.03
151 9 0.05
152 100 0.52
153 36 0.19
154 5 0.03
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (149 bp):
TTTTGAAAACATATTTTTGAAAACACATATAATATATAGTTTTTAAAATCGTTTTGGAAAACATA
TAATATATGATTTTTAAAATATTTTTGAAAAGTATATATAATATAGTTTTTGAAAACAAAGTTTT
GAAAACATATAATATATAA
Found at i:2361902 original size:14 final size:14
Alignment explanation
Indices: 2361883--2361910 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2361873 TAATATATAA
2361883 TTTTGAAAACATAT
1 TTTTGAAAACATAT
2361897 TTTTGAAAACATAT
1 TTTTGAAAACATAT
2361911 CTAATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTTGAAAACATAT
Found at i:2361983 original size:56 final size:55
Alignment explanation
Indices: 2361897--2362009 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 55
2361887 GAAAACATAT
2361897 TTTTGAAAACATATCTAATATATAGTTTTTAAAAAATGATTTTGGAAAACATATA-TAG
1 TTTTGAAAACATA-CTAATATATAGTTTTT--AAAAT-ATTTTGGAAAACATATAGTAG
* *
2361955 TTTTGAAAACATA-TAATATATGGTTTTTAAAATATTTTTGAAAACATATAGTAG
1 TTTTGAAAACATACTAATATATAGTTTTTAAAATATTTTGGAAAACATATAGTAG
2362009 T
1 T
2362010 ATATAGTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
53 16 0.31
54 9 0.17
56 14 0.27
58 13 0.25
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (55 bp):
TTTTGAAAACATACTAATATATAGTTTTTAAAATATTTTGGAAAACATATAGTAG
Found at i:2362033 original size:93 final size:90
Alignment explanation
Indices: 2361843--2362043 Score: 246
Period size: 92 Copynumber: 2.2 Consensus size: 90
2361833 ATATAATATA
*
2361843 GTTTTTGAAAACATAATTTTTGGAAACATATAATATATAATTTTGAAAACATATTTTTGAAAACA
1 GTTTTTGAAAACATAATTTTTGAAAACATATAATATATAATTTTGAAAACATATTTTTGAAAACA
2361908 TATCTAATATATAGTTTTTAAAAAAT
66 TATCTAATATATAGTTTTT-AAAAAT
* ** *
2361934 GATTTTGGAAAACATATATAGTTTTGAAAACATATAATATATGGTTTT-TAAA-ATATTTTTGAA
1 G-TTTTTGAAAACATA-AT--TTTTGAAAACATATAATATATAATTTTGAAAACATATTTTTGAA
* *
2361997 AACATATAGTAGTATATAGTTTTT-AAAAT
62 AACATAT-CTAATATATAGTTTTTAAAAAT
*
2362026 GGTTTTTGAAAATATAAT
1 -GTTTTTGAAAACATAAT
2362044 GTATGTTATA
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
91 3 0.03
92 30 0.32
93 21 0.22
94 17 0.18
95 24 0.25
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (90 bp):
GTTTTTGAAAACATAATTTTTGAAAACATATAATATATAATTTTGAAAACATATTTTTGAAAACA
TATCTAATATATAGTTTTTAAAAAT
Found at i:2362060 original size:41 final size:38
Alignment explanation
Indices: 2361955--2362067 Score: 135
Period size: 38 Copynumber: 3.0 Consensus size: 38
2361945 ACATATATAG
*
2361955 TTTTGAAAACATATA--A-TATATGGTTTTTAAAATAT
1 TTTTGAAAACATATAGTAGTATATAGTTTTTAAAATAT
*
2361990 TTTTGAAAACATATAGTAGTATATAGTTTTTAAAATGGT
1 TTTTGAAAACATATAGTAGTATATAGTTTTTAAAAT-AT
*
2362029 TTTTGAAAATATA-ATGTATGTTATATAGTTTTTAAAATA
1 TTTTGAAAACATATA-GTA-G-TATATAGTTTTTAAAATA
2362068 AATATTATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
35 15 0.22
37 1 0.01
38 17 0.25
39 16 0.24
40 1 0.01
41 17 0.25
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.46
Consensus pattern (38 bp):
TTTTGAAAACATATAGTAGTATATAGTTTTTAAAATAT
Found at i:2362095 original size:17 final size:19
Alignment explanation
Indices: 2362069--2362111 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
2362059 TTTAAAATAA
2362069 ATATTATTTA-TATTTA-T
1 ATATTATTTATTATTTATT
*
2362086 ATATTGTTTATTATTTATT
1 ATATTATTTATTATTTATT
2362105 ATATTAT
1 ATATTAT
2362112 ATTACGTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATATTATTTATTATTTATT
Found at i:2365044 original size:55 final size:54
Alignment explanation
Indices: 2364945--2365052 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 54
2364935 GAAAATAAGT
*
2364945 TATAAACGGTAAATGTTATAAATACTTTAACATTTTAGGTTGCACCTAAAATGG
1 TATAAACGGTAAATGTTATAAATACTTTAACATTTCAGGTTGCACCTAAAATGG
* * *
2364999 TATAAACGGTGAATGTTATGAATATTATTAACATTTCAGGTTGCACCTAAAATG
1 TATAAACGGTAAATGTTATAAATACT-TTAACATTTCAGGTTGCACCTAAAATG
2365053 TTACCAAAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 23 0.47
55 26 0.53
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (54 bp):
TATAAACGGTAAATGTTATAAATACTTTAACATTTCAGGTTGCACCTAAAATGG
Found at i:2372580 original size:31 final size:31
Alignment explanation
Indices: 2372516--2372581 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 31
2372506 ACATCCTTAA
*
2372516 AAAAATAATAATAATTTATTTTAATTATTTT
1 AAAAATAATAATAATTTATTTTAATTATATT
2372547 AAAAATACATAA-AATTTATGATTT-A-TATATT
1 AAAAATA-ATAATAATTTAT--TTTAATTATATT
2372578 AAAA
1 AAAA
2372582 TTTTAATAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
31 23 0.74
32 5 0.16
33 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
AAAAATAATAATAATTTATTTTAATTATATT
Found at i:2374951 original size:27 final size:27
Alignment explanation
Indices: 2374905--2374956 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2374895 AGATACTTTA
* * *
2374905 GGTCATTTTACCCTTTAGGGGAATTTT
1 GGTCATTTTACACTTCAGGGCAATTTT
2374932 GGTCATTTTACACTTCAGGGCAATT
1 GGTCATTTTACACTTCAGGGCAATT
2374957 CTAAATCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTCATTTTACACTTCAGGGCAATTTT
Found at i:2380504 original size:29 final size:29
Alignment explanation
Indices: 2380471--2380582 Score: 145
Period size: 29 Copynumber: 3.9 Consensus size: 29
2380461 ACCAACCCAT
*
2380471 AGGTCGCCATGCCCTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCGGGCGACCAAGG
2380500 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCGGGCGACCAAGG
* * * *
2380529 AGGTCGTCATGCACGCCAGGCGA-CATGG
1 AGGTCGCCATGCACTCCGGGCGACCAAGG
* *
2380557 TAGGTCGCCATGCACGCCAGGCGACC
1 -AGGTCGCCATGCACTCCGGGCGACC
2380583 TTGTCCTGTG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.05
29 70 0.93
30 1 0.01
ACGTcount: A:0.20, C:0.35, G:0.34, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCGGGCGACCAAGG
Found at i:2380622 original size:22 final size:22
Alignment explanation
Indices: 2380594--2380668 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
2380584 TGTCCTGTGC
* *
2380594 CCTGCTCCCCGCTACATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
2380616 CCTGCTCCCCACTGCATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
2380638 CCTGCTCCCCACTGCATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
*
2380660 CTTGCTCCC
1 CCTGCTCCC
2380669 GCTGCTCCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.08, C:0.51, G:0.17, T:0.24
Consensus pattern (22 bp):
CCTGCTCCCCACTGCATGCTCG
Found at i:2380746 original size:22 final size:22
Alignment explanation
Indices: 2380718--2380772 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
2380708 TAATTTTCGC
2380718 TGCTTCATGCAACATCATTTGT
1 TGCTTCATGCAACATCATTTGT
2380740 TGCTTCATGCAACATCATTTGT
1 TGCTTCATGCAACATCATTTGT
2380762 TGCTTCATGCA
1 TGCTTCATGCA
2380773 GCAATTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (22 bp):
TGCTTCATGCAACATCATTTGT
Found at i:2381247 original size:30 final size:30
Alignment explanation
Indices: 2381179--2381280 Score: 134
Period size: 30 Copynumber: 3.3 Consensus size: 30
2381169 TTTAGTTAAT
* *
2381179 TAGTTTTTTAGTAGTGAA-TTATAATTAAAAAA
1 TAGTTTATTAGT--TGAAGTTAT-ATTAAAGAA
* *
2381211 TCGTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
2381241 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
2381271 TAGTTTATTA
1 TAGTTTATTA
2381281 ATTGTTTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
30 49 0.78
31 4 0.06
32 10 0.16
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:2381279 original size:15 final size:16
Alignment explanation
Indices: 2381226--2381281 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 16
2381216 TATTAGTTTA
2381226 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
2381242 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
2381256 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
2381272 AGTT-TATTAA
1 AGTTATATTAA
2381282 TTGTTTAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 18 0.56
16 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:2381366 original size:15 final size:16
Alignment explanation
Indices: 2381338--2381371 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2381328 GTTTGTTACT
2381338 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
2381354 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
2381369 TTA
1 TTA
2381372 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:2383679 original size:17 final size:17
Alignment explanation
Indices: 2383649--2383687 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2383639 ATTAGTATCA
*
2383649 AATAATTAAATATTAAT
1 AATAAATAAATATTAAT
*
2383666 AATAAATAATTATTAAT
1 AATAAATAAATATTAAT
2383683 AATAA
1 AATAA
2383688 TTAGTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATAAATATTAAT
Found at i:2383755 original size:59 final size:59
Alignment explanation
Indices: 2383603--2383755 Score: 147
Period size: 59 Copynumber: 2.6 Consensus size: 59
2383593 TTAGTATCAA
* * *
2383603 ATAATTAAATATTTAGT-AATTCGACTATTTTAAATCATTAGTATCAAATAATTAAATATT
1 ATAA-TAAATAATTA-TAAATTCAACTATTATAAATCATTAGTATCAAATAATTAAATATT
* *
2383663 AATAATAAATAATTATTAA-T-AA-TAATTAGTAAATCATTAGTATCAAATCATTAAATATT
1 -ATAATAAATAATTATAAATTCAACT-ATTA-TAAATCATTAGTATCAAATAATTAAATATT
*
2383722 -TAA-AAATCATTAATAAATTCAACTATGTATAAAT
1 ATAATAAATAATT-ATAAATTCAACTAT-TATAAAT
2383756 TTAAACTCGA
Statistics
Matches: 78, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
56 7 0.09
57 8 0.10
58 5 0.06
59 40 0.51
60 14 0.18
61 4 0.05
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.40
Consensus pattern (59 bp):
ATAATAAATAATTATAAATTCAACTATTATAAATCATTAGTATCAAATAATTAAATATT
Found at i:2383839 original size:14 final size:14
Alignment explanation
Indices: 2383820--2383846 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2383810 TAGAAATAAT
2383820 TATTAAATCATTAG
1 TATTAAATCATTAG
2383834 TATTAAATCATTA
1 TATTAAATCATTA
2383847 TTATCATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:2383854 original size:9 final size:9
Alignment explanation
Indices: 2383840--2383894 Score: 78
Period size: 9 Copynumber: 6.2 Consensus size: 9
2383830 TTAGTATTAA
2383840 ATCATTATT
1 ATCATTATT
2383849 ATCATTATT
1 ATCATTATT
2383858 ATCATTATT
1 ATCATTATT
*
2383867 A-CAATTA-A
1 ATC-ATTATT
2383875 ATCATTATT
1 ATCATTATT
2383884 ATCATTATT
1 ATCATTATT
2383893 AT
1 AT
2383895 TAAATCATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 6 0.15
9 35 0.85
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (9 bp):
ATCATTATT
Found at i:2383875 original size:49 final size:47
Alignment explanation
Indices: 2383821--2384046 Score: 172
Period size: 49 Copynumber: 4.6 Consensus size: 47
2383811 AGAAATAATT
* * * *
2383821 ATTAAATCATTAGTATTAAATCATTATTATCATTATTATCATTATTACA
1 ATTAAATCATTATTA-T-AATCATTATTATCATTATTATAATGATTATA
* * *
2383870 ATTAAATCATTATTATCATTATTATTAAATCATTATTATAATGATTATT
1 ATTAAATCATTATTATAATCATTATT--ATCATTATTATAATGATTATA
* * * * * *
2383919 ACTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATTAAATCATTATTATAATCATTATTATC--ATTATTA-T-AATGAT--TATA
*
2383972 ATTAAAT-A-T-TTA-AATCATTATTAAATCATTATTATAATGATTATT
1 ATTAAATCATTATTATAATCATTATT--ATCATTATTATAATGATTATA
* *
2384017 ACTAAATCATTATTATAATGATTATTATCA
1 ATTAAATCATTATTATAATCATTATTATCA
2384047 AATCATTAAT
Statistics
Matches: 141, Mismatches: 22, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
45 8 0.06
46 1 0.01
47 21 0.15
48 5 0.04
49 84 0.60
50 4 0.03
51 9 0.06
52 1 0.01
53 8 0.06
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (47 bp):
ATTAAATCATTATTATAATCATTATTATCATTATTATAATGATTATA
Found at i:2383890 original size:23 final size:24
Alignment explanation
Indices: 2383849--2383908 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
2383839 AATCATTATT
2383849 ATCATTATTATCATTATTACAATTAA
1 ATCATTATTATC--TATTACAATTAA
**
2383875 ATCATTATTATC-ATTATTATTAA
1 ATCATTATTATCTATTACAATTAA
2383898 ATCATTATTAT
1 ATCATTATTAT
2383909 AATGATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 20 0.62
26 12 0.38
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (24 bp):
ATCATTATTATCTATTACAATTAA
Found at i:2383935 original size:26 final size:25
Alignment explanation
Indices: 2383849--2384080 Score: 212
Period size: 26 Copynumber: 9.3 Consensus size: 25
2383839 AATCATTATT
* * **
2383849 ATCATTATTATCATTATTACAATTAA
1 ATCATTATTATAATGATTATTA-TAA
* *
2383875 ATCATTATTATCATTATTA-T-TAA
1 ATCATTATTATAATGATTATTATAA
2383898 ATCATTATTATAATGATTATTACTAA
1 ATCATTATTATAATGATTATTA-TAA
2383924 ATCATTATTATAATGATTATTATCAA
1 ATCATTATTATAATGATTATTAT-AA
* * * *
2383950 ATCATTACTA-AATCATCAAATCATTAA
1 ATCATTATTATAATGAT--TATTA-TAA
*
2383977 AT-A-T-TTA-AATCATTA-T-TAA
1 ATCATTATTATAATGATTATTATAA
2383996 ATCATTATTATAATGATTATTACTAA
1 ATCATTATTATAATGATTATTA-TAA
2384022 ATCATTATTATAATGATTATTATCAA
1 ATCATTATTATAATGATTATTAT-AA
*
2384048 ATCATTAATATAATGATTATTATCAA
1 ATCATTATTATAATGATTATTAT-AA
2384074 ATCATTA
1 ATCATTA
2384081 CTAAATCATC
Statistics
Matches: 179, Mismatches: 12, Indels: 30
0.81 0.05 0.14
Matches are distributed among these distances:
19 5 0.03
20 1 0.01
21 1 0.01
22 4 0.02
23 27 0.15
24 10 0.06
25 8 0.04
26 115 0.64
27 7 0.04
28 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (25 bp):
ATCATTATTATAATGATTATTATAA
Found at i:2384035 original size:124 final size:123
Alignment explanation
Indices: 2383870--2384153 Score: 438
Period size: 124 Copynumber: 2.3 Consensus size: 123
2383860 CATTATTACA
2383870 ATTAAATCATTA-T-T-ATCATTATTATTAAATCATTATTATAATGATTATTA-CTAAATCATTA
1 ATTAAATCATTATTATAATCATTATTA-TAAATCATTATTATAATGATTATTATC-AAATCATTA
*
2383931 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAA-TCATT
64 ATATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA-TTAAATTCATT
*
2383991 ATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAA
1 ATTAAATCATTATTATAATCATTATTA-TAAATCATTATTATAATGATTATTATCAAATCATTAA
2384056 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCATT
65 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCATT
* *
2384115 ATTAAATTCATTATTA-AATTATTATT-TAAATTATTATTA
1 ATTAAA-TCATTATTATAATCATTATTATAAATCATTATTA
2384154 AATCATTTTT
Statistics
Matches: 152, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
121 12 0.08
122 13 0.09
123 6 0.04
124 111 0.73
125 10 0.07
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (123 bp):
ATTAAATCATTATTATAATCATTATTATAAATCATTATTATAATGATTATTATCAAATCATTAAT
ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCATT
Found at i:2384107 original size:52 final size:52
Alignment explanation
Indices: 2383991--2384107 Score: 132
Period size: 52 Copynumber: 2.2 Consensus size: 52
2383981 TTAAATCATT
* * * * *
2383991 ATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATT
1 ATTAAATCATTAATATAATGATTATTACTAAATCATTACTATAATCATAATC
*
2384043 ATCAAATCATTAATATAATGATTATTA-TCAAATCATTACTA-AATCATCAAATC
1 ATTAAATCATTAATATAATGATTATTACT-AAATCATTACTATAATCAT--AATC
2384096 ATTAAAT-ATTAA
1 ATTAAATCATTAA
2384108 ATTCATTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
51 6 0.11
52 41 0.75
53 8 0.15
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (52 bp):
ATTAAATCATTAATATAATGATTATTACTAAATCATTACTATAATCATAATC
Found at i:2384119 original size:12 final size:12
Alignment explanation
Indices: 2384102--2384160 Score: 88
Period size: 12 Copynumber: 5.1 Consensus size: 12
2384092 AATCATTAAA
2384102 TATTAAATTCAT
1 TATTAAATTCAT
2384114 TATTAAATTCAT
1 TATTAAATTCAT
2384126 TATTAAATT-AT
1 TATTAAATTCAT
2384137 TATTTAAATT-AT
1 TA-TTAAATTCAT
2384149 TATTAAA-TCAT
1 TATTAAATTCAT
2384160 T
1 T
2384161 TTTATGGTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
10 1 0.02
11 12 0.27
12 32 0.71
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:2384121 original size:98 final size:94
Alignment explanation
Indices: 2383896--2384159 Score: 261
Period size: 98 Copynumber: 2.7 Consensus size: 94
2383886 CATTATTATT
* *
2383896 AAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTAA
1 AAATCATTAATATAA-GATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAATAA
* *
2383961 ATCATCAAATCATTAAATATTTAAATCATTATT
65 ATCAT-AAATCATCAAATATTTAAATC--TATC
*
2383994 AAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAATAT
1 AAATCATTAATATAA-GATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAATA-
* * *
2384059 AATGAT-TATTATCAAATCATTACTAAATC-ATC
64 AATCATAAATCATCAAAT-ATT--TAAATCTATC
* * * *
2384091 AAATCATTAAATATTAA-ATTCATTATTAAATTCATTATTA-AATTATTATT-T-AAATTATTAT
1 AAATCATT-AATA-TAAGATT-ATTACTAAA-TCATTATTATAATGATTATTATCAAATCATTAA
2384152 TAAATCAT
62 TAAATCAT
2384160 TTTTATGGTT
Statistics
Matches: 146, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
95 5 0.03
96 10 0.07
97 22 0.15
98 86 0.59
99 17 0.12
100 6 0.04
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (94 bp):
AAATCATTAATATAAGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAATAAA
TCATAAATCATCAAATATTTAAATCTATC
Found at i:2384355 original size:17 final size:18
Alignment explanation
Indices: 2384335--2384369 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2384325 TATTAGTAAA
2384335 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
2384352 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
2384370 ACTAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:2384424 original size:49 final size:49
Alignment explanation
Indices: 2384367--2384603 Score: 420
Period size: 49 Copynumber: 4.8 Consensus size: 49
2384357 ATTATTAATA
*
2384367 ATTACTAATAATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
2384416 ATTACTAATAATTACTATCAAATTATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
2384465 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
2384514 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
2384563 ATAACTAATCATTACTATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
2384604 GATGGGTGCC
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 181 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:2387871 original size:17 final size:17
Alignment explanation
Indices: 2387816--2387876 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
2387806 ACAATATAAA
*
2387816 TTAAACAAAATATTTTT
1 TTAAACACAATATTTTT
* *
2387833 TTAAAACAACACTAAATATTT
1 TT-AAAC-ACA--ATATTTTT
2387854 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
2387871 TTAAAC
1 TTAAAC
2387877 GGAAATTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.40
18 4 0.11
19 5 0.14
20 4 0.11
21 8 0.23
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:2388350 original size:42 final size:46
Alignment explanation
Indices: 2388294--2388395 Score: 140
Period size: 46 Copynumber: 2.3 Consensus size: 46
2388284 GTTTAAAGAC
* * *
2388294 ACTAACAAATTAATTAA-T-ATTTTTTTAT-ATTTA-ATAACTTAA
1 ACTAACAAACTAATTAACTAATTTTTATATAATATATATAACTTAA
*
2388336 ACTAATAAACTAATTAACTAATTTTTATATAATATATATAACTTAA
1 ACTAACAAACTAATTAACTAATTTTTATATAATATATATAACTTAA
2388382 ACTAACAAACTAAT
1 ACTAACAAACTAAT
2388396 AATTTATACT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 15 0.29
43 1 0.02
44 9 0.18
45 4 0.08
46 22 0.43
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (46 bp):
ACTAACAAACTAATTAACTAATTTTTATATAATATATATAACTTAA
Found at i:2388406 original size:21 final size:20
Alignment explanation
Indices: 2388373--2388420 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
2388363 TATAATATAT
2388373 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAAC-AACTA
* *
2388394 ATAATTTATACTAACAACTA
1 ATAACTTAAACTAACAACTA
2388414 ATTAACT
1 A-TAACT
2388421 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAACTTAAACTAACAACTA
Found at i:2389063 original size:29 final size:29
Alignment explanation
Indices: 2389031--2389090 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
2389021 ACATGCATCG
2389031 CTCCCATGTCGCCCGGAAGGCATGGCGAC
1 CTCCCATGTCGCCCGGAAGGCATGGCGAC
** *
2389060 CTCCTTTGTTGCCCGGAAGGCATGGCGAC
1 CTCCCATGTCGCCCGGAAGGCATGGCGAC
2389089 CT
1 CT
2389091 ACGGCAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.15, C:0.35, G:0.30, T:0.20
Consensus pattern (29 bp):
CTCCCATGTCGCCCGGAAGGCATGGCGAC
Found at i:2396765 original size:22 final size:20
Alignment explanation
Indices: 2396739--2396778 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
2396729 AATGATTTTG
2396739 AAACAAAATAATTAAATAATTA
1 AAACAAAATAA--AAATAATTA
*
2396761 AAACAGAATAAAAATAAT
1 AAACAAAATAAAAATAAT
2396779 AATTAAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (20 bp):
AAACAAAATAAAAATAATTA
Found at i:2403715 original size:22 final size:22
Alignment explanation
Indices: 2403690--2403747 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
2403680 ATTTTTTTCA
2403690 TAATAATAAT-TATAATTATTAT
1 TAAT-ATAATATATAATTATTAT
*
2403712 TAATATAATATATTATTATTAT
1 TAATATAATATATAATTATTAT
*
2403734 T-TTATTAATATATA
1 TAATA-TAATATATA
2403748 TATATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATATAATATATAATTATTAT
Found at i:2403748 original size:2 final size:2
Alignment explanation
Indices: 2403741--2403768 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2403731 TATTTTATTA
2403741 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2403769 TAATATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2413454 original size:114 final size:114
Alignment explanation
Indices: 2413254--2413587 Score: 562
Period size: 114 Copynumber: 2.9 Consensus size: 114
2413244 CATGTTCTCG
*
2413254 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGA-CATGGTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC-TGGTT
* *
2413318 TGGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
65 TGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCA
*
2413368 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
*
2413433 GGTATAAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCA
* *
2413482 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* * *
2413547 GGTAGGAACCCCAGAACCAATCATTAGAATTGAAAGATGAA
66 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAA
2413588 ATGCATGATC
Statistics
Matches: 207, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
114 206 1.00
115 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCA
Found at i:2415947 original size:22 final size:22
Alignment explanation
Indices: 2415920--2415972 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
2415910 CTACACTCTT
*
2415920 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTTTC
*
2415942 TAAAGATGATAGATTCTCTTTC
1 CAAAGATGATAGATTCTCTTTC
2415964 CAAAGATGA
1 CAAAGATGA
2415973 AAGCTTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTTTC
Found at i:2417126 original size:76 final size:76
Alignment explanation
Indices: 2416995--2417511 Score: 936
Period size: 76 Copynumber: 6.9 Consensus size: 76
2416985 CTATTTCCCA
*
2416995 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTCTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2417060 AACCTTAGGGT
66 AGCCTTAGGGT
2417071 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2417136 AACCTTAGGGT
66 AGCCTTAGGGT
2417147 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2417212 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2417223 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2417288 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2417299 CATCTGTGAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC-GG-G---TTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2417359 AGCCTTAGGGT
66 AGCCTTAGGGT
2417370 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2417435 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2417446 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCTTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2417511 A
66 A
2417512 CATTTTCATC
Statistics
Matches: 429, Mismatches: 7, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
71 67 0.16
72 2 0.00
73 1 0.00
74 1 0.00
75 2 0.00
76 356 0.83
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2417462 original size:223 final size:226
Alignment explanation
Indices: 2416995--2417511 Score: 941
Period size: 223 Copynumber: 2.3 Consensus size: 226
2416985 CTATTTCCCA
* *
2416995 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTCTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
2417060 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG--TTTT
2417125 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
129 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
2417190 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
194 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
2417223 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
* *
2417288 AGCCTTAGGGTCATCTGTGAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC-GG-G-TTTGA
66 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTGA
*
2417350 TGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGG
131 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGG
2417415 GAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
196 GAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
*
2417446 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCTTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
2417511 A
66 A
2417512 CATTTTCATC
Statistics
Matches: 283, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
223 165 0.58
226 1 0.00
227 2 0.01
228 115 0.41
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (226 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTGA
TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGG
GAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:2417676 original size:22 final size:24
Alignment explanation
Indices: 2417635--2417681 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
2417625 TTTTTCATAA
2417635 TAATAATAATAATATAATTATTAT
1 TAATAATAATAATATAATTATTAT
*
2417659 TAAT-ATAAT-ATATTATTATTAT
1 TAATAATAATAATATAATTATTAT
2417681 T
1 T
2417682 TATTATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 5 0.23
24 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATAATAATATAATTATTAT
Found at i:2421284 original size:2 final size:2
Alignment explanation
Indices: 2421217--2421266 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2421207 TTTATATTGA
2421217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2421259 AT AT AT AT
1 AT AT AT AT
2421267 TTTTTTTAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2422217 original size:12 final size:12
Alignment explanation
Indices: 2422202--2422228 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2422192 ACTCAATGTC
2422202 AAAAACAATCCA
1 AAAAACAATCCA
2422214 AAAAACAATCCA
1 AAAAACAATCCA
2422226 AAA
1 AAA
2422229 TTTTTAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.22, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAACAATCCA
Found at i:2422590 original size:278 final size:272
Alignment explanation
Indices: 2421935--2422475 Score: 830
Period size: 277 Copynumber: 1.9 Consensus size: 272
2421925 TACAAAATTC
* * *
2421935 CAAAAAACAATCCAAAATTTTTAGATAATGACCGAGCATCAATCCAATTTTCGTGTAAATCCAAC
1 CAAAAAACAATCCAAAAGTGTTAGATAATGAACGA-CAT-AAT-CAATTTTCGTGTAAAT-CAAC
* * *
2422000 CGAGTAATGATCACAATCATTAATGACAGTTATTTTACTGATAATTTTATTCAAATTATTTTAAT
62 CGAGTAATGATCACAATCATAAATGAAAGTTATTTAACTGATAATTTTATTCAAATTATTTTAAT
2422065 AAAAATTAAAATACCGAAGATCAAAATGTTTAAAAATATATAAACTAACATGATATTTTAAGGCT
127 AAAAATTAAAATACCGAAGATCAAAATGTTTAAAAATATATAAACTAACATGATATTTTAAGGCT
*
2422130 TAATATTAAAATAAGAGTTTCGATTATACCAGTTTTTTAAATAGATACCTAAATTAATTTTGACT
192 TAATATTAAAATAAGAGTTCCGATTATACCAGTTTTTTAAATAGATACCTAAATTAATTTTGACT
*
2422195 CAATGTCAAAAACAATC
257 CAATGTC-AAAACAATA
* * *
2422212 CAAAAAACAATCCAAAATTTTTAGATAATGACCGAGCATCAATCCAATTTTCGTGTAAATCAACC
1 CAAAAAACAATCCAAAAGTGTTAGATAATGAACGA-CAT-AAT-CAATTTTCGTGTAAATCAACC
* *
2422277 GAGTAATGATCACAATCATTAATGACAGTTATTTAACTGATAATTTTATTCAAATTATTTTAATT
63 GAGTAATGATCACAATCATAAATGAAAGTTATTTAACTGATAATTTTATTCAAATTATTTTAA-T
* *
2422342 AAAATTTAAAATATCGAAGATCAAAATGTTTAAAAATATATAAACTAACATGATATTTTTAAGGC
127 AAAAATTAAAATACCGAAGATCAAAATGTTTAAAAATATATAAACTAACATGATA-TTTTAAGGC
* *
2422407 TTAATATTAAAATAAGTGTTCCGATTATACCAGTTTTTTAAATAGATACCTAAATTAGTTTTTGA
191 TTAATATTAAAATAAGAGTTCCGATTATACCAGTTTTTTAAATAGATACCTAAATTA-ATTTTGA
2422472 CTCA
255 CTCA
2422476 TCTAGATGTC
Statistics
Matches: 255, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
276 67 0.26
277 114 0.45
278 64 0.25
279 10 0.04
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (272 bp):
CAAAAAACAATCCAAAAGTGTTAGATAATGAACGACATAATCAATTTTCGTGTAAATCAACCGAG
TAATGATCACAATCATAAATGAAAGTTATTTAACTGATAATTTTATTCAAATTATTTTAATAAAA
ATTAAAATACCGAAGATCAAAATGTTTAAAAATATATAAACTAACATGATATTTTAAGGCTTAAT
ATTAAAATAAGAGTTCCGATTATACCAGTTTTTTAAATAGATACCTAAATTAATTTTGACTCAAT
GTCAAAACAATA
Found at i:2424913 original size:2 final size:2
Alignment explanation
Indices: 2424906--2424960 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
2424896 AGATCTAAAT
*
2424906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2424947 TA TT TA TT TA TA TA
1 TA TA TA TA TA TA TA
2424961 CATAGTGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2441446 original size:100 final size:102
Alignment explanation
Indices: 2441271--2441475 Score: 378
Period size: 100 Copynumber: 2.0 Consensus size: 102
2441261 CTAATGGTTT
*
2441271 TTTTGCCCCAATACTAGGGTATTGGGCCAACATAGATTTCATTTTGGAAACTACGGCATTCTCTA
1 TTTTGCCCCAATACTAGGGTATTGGGCCAACATA-ATTTCATTTTGGAAACTACGACATTCTCTA
2441336 CAGTGAATACTAATTTTTTA-CCATTTTTTTATTGTTA
65 CAGTGAATACTAATTTTTTACCCATTTTTTTATTGTTA
2441373 TTTTGCCCCAATACTAGGGTATTGGGCCAACAT-ATTTCATTTTGGAAACTACGACATTCTCTAC
1 TTTTGCCCCAATACTAGGGTATTGGGCCAACATAATTTCATTTTGGAAACTACGACATTCTCTAC
2441437 AGTGAATACTAATTTTTTACCCATTTTTTTATTGTTA
66 AGTGAATACTAATTTTTTACCCATTTTTTTATTGTTA
2441474 TT
1 TT
2441476 ATTATTATTA
Statistics
Matches: 101, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
100 49 0.49
101 19 0.19
102 33 0.33
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (102 bp):
TTTTGCCCCAATACTAGGGTATTGGGCCAACATAATTTCATTTTGGAAACTACGACATTCTCTAC
AGTGAATACTAATTTTTTACCCATTTTTTTATTGTTA
Found at i:2441477 original size:3 final size:3
Alignment explanation
Indices: 2441465--2441524 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
2441455 ACCCATTTTT
*
2441465 TTA TTG TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
**
2441510 AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
2441525 CAAACAGGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2441684 original size:17 final size:17
Alignment explanation
Indices: 2441662--2441709 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
2441652 TCCAGAAGGC
* *
2441662 CAGCCGCCGCCTCTGCT
1 CAGCCGCCACCTCCGCT
*
2441679 CAGCCGGCACCTCCGCT
1 CAGCCGCCACCTCCGCT
2441696 CAGCCGCCACCTCC
1 CAGCCGCCACCTCC
2441710 ACGTTGTCGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.10, C:0.56, G:0.21, T:0.12
Consensus pattern (17 bp):
CAGCCGCCACCTCCGCT
Found at i:2441959 original size:29 final size:29
Alignment explanation
Indices: 2441927--2441992 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
2441917 AGAAGAAGGC
*
2441927 AACAGAGAAAAACGGAGAGCAAGAGACGG
1 AACAGAGAAAAACAGAGAGCAAGAGACGG
*
2441956 AACAGAGAAAAACAGAGAGCAAGAGATGG
1 AACAGAGAAAAACAGAGAGCAAGAGACGG
2441985 AACAGAGA
1 AACAGAGA
2441993 GAGGGCAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.55, C:0.12, G:0.32, T:0.02
Consensus pattern (29 bp):
AACAGAGAAAAACAGAGAGCAAGAGACGG
Found at i:2450998 original size:9 final size:9
Alignment explanation
Indices: 2450984--2451033 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
2450974 AGGGCTGGAA
2450984 ACCGGTTTG
1 ACCGGTTTG
2450993 ACCGGTTTCG
1 ACCGGTTT-G
*
2451003 ACCGGTTCG
1 ACCGGTTTG
2451012 AACCGGTTTG
1 -ACCGGTTTG
* *
2451022 GCCGGTCTG
1 ACCGGTTTG
2451031 ACC
1 ACC
2451034 CGACCCGATC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.12, C:0.30, G:0.32, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Done.