Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_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: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 21
Found at i:2399345 original size:40 final size:40
Alignment explanation
Indices: 2399269--2399345 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
2399259 TACAAAAAAT
* ** *
2399269 GCCGCAATAGGGTGGTTTATTGCGGCGTTTTTTACCAAAC
1 GCCGCAATAGAGTGGTAAATTGCGGCGTTTTATACCAAAC
*
2399309 GCCGCAATAGAGTGGTAAATTAGCGGTG-TTTATACCA
1 GCCGCAATAGAGTGGTAAATT-GCGGCGTTTTATACCA
2399346 CAAACTCCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 26 0.84
41 5 0.16
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (40 bp):
GCCGCAATAGAGTGGTAAATTGCGGCGTTTTATACCAAAC
Found at i:2399484 original size:41 final size:41
Alignment explanation
Indices: 2399437--2399591 Score: 170
Period size: 41 Copynumber: 3.8 Consensus size: 41
2399427 TTTATTCTTA
* *
2399437 AAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGAC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAC
* * * *
2399478 AAACGCCGTAATAGTGTTAATCACTAGTGGCGTTTTTAGAAA
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAG-AC
* * *
2399520 AAATGCCGCAATAGTTTTAATCAATAGTGACATTTTTTA-AC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCA-TTTTTAGAC
* *
2399561 AAATGCCACCAATAGTG-TAATCAATAGTGGC
1 AAACGCC-GCAATAGTGTTAATCAATAGTGGC
2399592 GTTATTTTTA
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
41 55 0.58
42 34 0.36
43 6 0.06
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (41 bp):
AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAC
Found at i:2399563 original size:83 final size:83
Alignment explanation
Indices: 2399436--2399594 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 83
2399426 ATTTATTCTT
* **
2399436 AAAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACGCC-GTAATAGTGTTAATC
1 AAAACGCCGCAATAGTGATAATAAATAGTGACATTTTTAGACAAACGCCACCAATAGTG-TAATC
*
2399500 ACTAGTGGCGTTTTTAGAA
65 AATAGTGGCGTTTTTAGAA
* ** * *
2399519 AAAATGCCGCAATAGTTTTAATCAATAGTGACATTTTTTA-ACAAATGCCACCAATAGTGTAATC
1 AAAACGCCGCAATAGTGATAATAAATAGTGACA-TTTTTAGACAAACGCCACCAATAGTGTAATC
2399583 AATAGTGGCGTT
65 AATAGTGGCGTT
2399595 ATTTTTATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 52 0.80
84 13 0.20
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (83 bp):
AAAACGCCGCAATAGTGATAATAAATAGTGACATTTTTAGACAAACGCCACCAATAGTGTAATCA
ATAGTGGCGTTTTTAGAA
Found at i:2399607 original size:42 final size:40
Alignment explanation
Indices: 2399436--2399609 Score: 125
Period size: 41 Copynumber: 4.2 Consensus size: 40
2399426 ATTTATTCTT
* * * *
2399436 AAAACGCCGCAATAGTGATAATAAATAGTGGC-ATTTTTAGA
1 AAAATGCCCCAATAGTG-TAATCAATAGTGGCGTTTTTTA-A
* * ** * *
2399477 CAAACGCCGTAATAGTGTTAATCACTAGTGGCGTTTTTAGAA
1 AAAATGCCCCAATAGTG-TAATCAATAGTGGCGTTTTT-TAA
* * * *
2399519 AAAATGCCGCAATAGTTTTAATCAATAGTGACATTTTTTAA
1 AAAATGCCCCAATAG-TGTAATCAATAGTGGCGTTTTTTAA
* *
2399560 CAAATGCCACCAATAGTGTAATCAATAGTGGCGTTATTTTTA
1 AAAATGCC-CCAATAGTGTAATCAATAGTGGCGTT-TTTTAA
*
2399602 TAAATGCC
1 AAAATGCC
2399610 GCAAAATGTT
Statistics
Matches: 106, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
41 52 0.49
42 52 0.49
43 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (40 bp):
AAAATGCCCCAATAGTGTAATCAATAGTGGCGTTTTTTAA
Found at i:2399607 original size:83 final size:82
Alignment explanation
Indices: 2399428--2399613 Score: 198
Period size: 83 Copynumber: 2.2 Consensus size: 82
2399418 ATAGTGGTAT
* * * **
2399428 TTATTCTTAAAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACGCCGTAATAGT
1 TTATTTTTAAAATGCCGCAATAGTGATAATAAATAGTGACATTTTTAGACAAACGCCCCAATAGT
*
2399493 GTTAATCACTAGTGGCG
66 GTTAATCAATAGTGGCG
** ** * *
2399510 TT-TTTAGAAAAAATGCCGCAATAGTTTTAATCAATAGTGACATTTTTTA-ACAAATGCCACCAA
1 TTATTT--TTAAAATGCCGCAATAGTGATAATAAATAGTGACA-TTTTTAGACAAACGCC-CCAA
2399573 TAGTG-TAATCAATAGTGGCG
62 TAGTGTTAATCAATAGTGGCG
2399593 TTATTTTTATAAATGCCGCAA
1 TTATTTTTA-AAATGCCGCAA
2399614 AATGTTAAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
81 2 0.02
82 3 0.04
83 63 0.75
84 16 0.19
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (82 bp):
TTATTTTTAAAATGCCGCAATAGTGATAATAAATAGTGACATTTTTAGACAAACGCCCCAATAGT
GTTAATCAATAGTGGCG
Found at i:2400936 original size:43 final size:43
Alignment explanation
Indices: 2400843--2400940 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
2400833 TAAAAGGTAA
* * * * *
2400843 TTAGCGGCGTTTGTATCCAGAAACGCCGCTATAGATCTGACAT
1 TTAGTGGCGTTTGTATCAAAAAACGCCGCTAAAGATATGACAT
*
2400886 TTTGTGGCGTTTGTATCAAAAAACGCCGCTAAAGAGTAAT-AC-T
1 TTAGTGGCGTTTGTATCAAAAAACGCCGCTAAAGA-T-ATGACAT
2400929 TTAGTGGCGTTT
1 TTAGTGGCGTTT
2400941 TTGAAACAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 42 0.91
44 3 0.07
45 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (43 bp):
TTAGTGGCGTTTGTATCAAAAAACGCCGCTAAAGATATGACAT
Found at i:2401174 original size:42 final size:41
Alignment explanation
Indices: 2401018--2401406 Score: 340
Period size: 41 Copynumber: 9.4 Consensus size: 41
2401008 TATAGGTACG
* * *
2401018 TACTTTAGTGGCATTTTTATACAAACGCCGCTATAGAATCG
1 TACTTTAGTGGCATTTTAATACAAACGCCGCTATAGACTCA
* * * * *
2401059 TAATTTAGTAGCATTTTTATGCAAACGCCGCTATATACT-A
1 TACTTTAGTGGCATTTTAATACAAACGCCGCTATAGACTCA
* * * *
2401099 GTACTTTAATGGCGTTTCT-ATACAAACGCCGCTAAATACTCA
1 -TACTTTAGTGGCATTT-TAATACAAACGCCGCTATAGACTCA
* *
2401141 TACTTTAGTGGCATTTTGAATCCAAACGCCGCTATAAACTCA
1 TACTTTAGTGGCATTTT-AATACAAACGCCGCTATAGACTCA
* * * * *
2401183 TACTTTAGTGGCGTTTTGAATGCAACCGCCGCTAAAGACTCG
1 TACTTTAGTGGCATTTT-AATACAAACGCCGCTATAGACTCA
* * * *
2401225 TACTTTAGTAGCATTTTTATATAAACGCCGCTATATACT-A
1 TACTTTAGTGGCATTTTAATACAAACGCCGCTATAGACTCA
* ** *
2401265 GTACTTTAGTGGCATTTTTATACAAATACCTCTATAGACT-A
1 -TACTTTAGTGGCATTTTAATACAAACGCCGCTATAGACTCA
** *
2401306 GTACTTTAGTGGCATTTTGAATGTAAACGCCGCTATAGACTCG
1 -TACTTTAGTGGCATTTT-AATACAAACGCCGCTATAGACTCA
* * **
2401349 TACTTTTA-TGGCGTTTTGAATACAAACACCGCTAATA-ACTTG
1 TAC-TTTAGTGGCATTTT-AATACAAACGCCGCT-ATAGACTCA
2401391 TACTTTAGTGGCATTT
1 TACTTTAGTGGCATTT
2401407 GTATTTATAA
Statistics
Matches: 286, Mismatches: 51, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
40 1 0.00
41 151 0.53
42 127 0.44
43 7 0.02
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (41 bp):
TACTTTAGTGGCATTTTAATACAAACGCCGCTATAGACTCA
Found at i:2401253 original size:166 final size:166
Alignment explanation
Indices: 2401018--2401406 Score: 507
Period size: 166 Copynumber: 2.3 Consensus size: 166
2401008 TATAGGTACG
* * * * * *
2401018 TACTTTAGTGGCATTTT-TATACAAACGCCGCTATAGAATCGTAATTTAGTAGCATTTTTATGCA
1 TACTTTAGTGGCGTTTTGAATACAAACGCCGCTAAAGACTCGTACTTTAGTAGCATTTTTATACA
* * *
2401082 AACGCCGCTATATACTAGTACTTTAATGGCGTTTCTATACAAACGCCGCTAAATACTCA-TACTT
66 AACGCCGCTATATACTAGTACTTTAATGGCATTTCTATACAAACACCGCTAAAGACT-AGTACTT
2401146 TAGTGGCATTTTGAATCCAAACGCCGCTATAAACTCA
130 TAGTGGCATTTTGAATCCAAACGCCGCTATAAACTCA
* * *
2401183 TACTTTAGTGGCGTTTTGAATGCAACCGCCGCTAAAGACTCGTACTTTAGTAGCATTTTTATATA
1 TACTTTAGTGGCGTTTTGAATACAAACGCCGCTAAAGACTCGTACTTTAGTAGCATTTTTATACA
* * * * *
2401248 AACGCCGCTATATACTAGTACTTTAGTGGCATTTTTATACAAATACCTCTATAGACTAGTACTTT
66 AACGCCGCTATATACTAGTACTTTAATGGCATTTCTATACAAACACCGCTAAAGACTAGTACTTT
** * *
2401313 AGTGGCATTTTGAATGTAAACGCCGCTATAGACTCG
131 AGTGGCATTTTGAATCCAAACGCCGCTATAAACTCA
* * *
2401349 TACTTTTA-TGGCGTTTTGAATACAAACACCGCTAATA-ACTTGTACTTTAGTGGCATTT
1 TAC-TTTAGTGGCGTTTTGAATACAAACGCCGCTAA-AGACTCGTACTTTAGTAGCATTT
2401407 GTATTTATAA
Statistics
Matches: 194, Mismatches: 26, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
165 17 0.09
166 172 0.89
167 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (166 bp):
TACTTTAGTGGCGTTTTGAATACAAACGCCGCTAAAGACTCGTACTTTAGTAGCATTTTTATACA
AACGCCGCTATATACTAGTACTTTAATGGCATTTCTATACAAACACCGCTAAAGACTAGTACTTT
AGTGGCATTTTGAATCCAAACGCCGCTATAAACTCA
Found at i:2404986 original size:2 final size:2
Alignment explanation
Indices: 2404981--2405030 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2404971 TTATTTTTTA
2404981 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
2405023 AT AT AT AT
1 AT AT AT AT
2405031 TGCTGAAGAA
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:2410472 original size:21 final size:21
Alignment explanation
Indices: 2410448--2410516 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
2410438 AAGCAAAGAA
** *
2410448 AGAAGCAGCGGTAGCACAAAG
1 AGAAGCAGCGACAACACAAAG
* *
2410469 AGAAGCAACGACAACACAGAG
1 AGAAGCAGCGACAACACAAAG
2410490 AGAAGCAGCGACAACACAAAG
1 AGAAGCAGCGACAACACAAAG
2410511 AGAAGC
1 AGAAGC
2410517 CACATATCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.49, C:0.22, G:0.28, T:0.01
Consensus pattern (21 bp):
AGAAGCAGCGACAACACAAAG
Found at i:2410478 original size:42 final size:42
Alignment explanation
Indices: 2410432--2410516 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
2410422 TCCAGAGCAA
** *
2410432 CAACGA-AAGCAAAGAAAGAAGCAGCGGTAGCACAAAGAGAAG
1 CAACGACAA-CAAAGAAAGAAGCAGCGACAACACAAAGAGAAG
* *
2410474 CAACGACAACACAGAGAGAAGCAGCGACAACACAAAGAGAAG
1 CAACGACAACAAAGAAAGAAGCAGCGACAACACAAAGAGAAG
2410516 C
1 C
2410517 CACATATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.52, C:0.21, G:0.26, T:0.01
Consensus pattern (42 bp):
CAACGACAACAAAGAAAGAAGCAGCGACAACACAAAGAGAAG
Found at i:2410994 original size:43 final size:42
Alignment explanation
Indices: 2410931--2411037 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 42
2410921 TGTTTTTAGC
* * *
2410931 AAAAACGCCTA-ATAAA-ATCAATACCTATTGCGACGTTTGTGAG
1 AAAAACGCC-ACA-AAACATCAAAACCTACTGCGACATTTGTG-G
* *
2410974 AAAAACGCCACAAAACATCAAAACCTACTGTGTCATTTGTGG
1 AAAAACGCCACAAAACATCAAAACCTACTGCGACATTTGTGG
*
2411016 AATAAACGCCGCAAAACATCAA
1 AA-AAACGCCACAAAACATCAA
2411038 CATCTACTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 7 0.13
43 48 0.87
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (42 bp):
AAAAACGCCACAAAACATCAAAACCTACTGCGACATTTGTGG
Found at i:2411045 original size:43 final size:42
Alignment explanation
Indices: 2410964--2411120 Score: 161
Period size: 42 Copynumber: 3.7 Consensus size: 42
2410954 CCTATTGCGA
* * * *
2410964 CGTTTGTGAGAAAAACGCCACAAAACATCAAAACCTACTGTGT
1 CGTTTGTG-GAAAAACGCCGCAAAACATCAACATCTACTGTGG
* **
2411007 CATTTGTGGAATAAACGCCGCAAAACATCAACATCTACTACGG
1 CGTTTGTGGAA-AAACGCCGCAAAACATCAACATCTACTGTGG
* * * * *
2411050 CGTTTGTGGGAAAATGTCGTAAAACTTCAACATCTACTGTGG
1 CGTTTGTGGAAAAACGCCGCAAAACATCAACATCTACTGTGG
* * *
2411092 CGTTTGTGGGAAAACGCCGCTAAATATCA
1 CGTTTGTGGAAAAACGCCGCAAAACATCA
2411121 TTACCTATTG
Statistics
Matches: 92, Mismatches: 21, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
42 51 0.55
43 41 0.45
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (42 bp):
CGTTTGTGGAAAAACGCCGCAAAACATCAACATCTACTGTGG
Found at i:2411155 original size:43 final size:43
Alignment explanation
Indices: 2411102--2411267 Score: 190
Period size: 43 Copynumber: 3.9 Consensus size: 43
2411092 CGTTTGTGGG
* **
2411102 AAAACGCCGCTAAATATCATTACCTATTGCGGCGTTTATCTAA
1 AAAACACCGCTAAATATCAACACCTATTGCGGCGTTTATCTAA
** * *
2411145 AAAACACCGCTAAATATCAACACCTATTGCGGTATTTTTCTGA
1 AAAACACCGCTAAATATCAACACCTATTGCGGCGTTTATCTAA
* * * *
2411188 CAAACGCCGCTAAATATCAACACCTATTGCGACGTTTGTC-ACA
1 AAAACACCGCTAAATATCAACACCTATTGCGGCGTTTATCTA-A
* * *
2411231 CAAACACCGTTAAATATCAATACCTATTGCGGCGTTT
1 AAAACACCGCTAAATATCAACACCTATTGCGGCGTTT
2411268 TTTGTTTAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
43 104 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (43 bp):
AAAACACCGCTAAATATCAACACCTATTGCGGCGTTTATCTAA
Found at i:2411206 original size:86 final size:86
Alignment explanation
Indices: 2411103--2411262 Score: 241
Period size: 86 Copynumber: 1.9 Consensus size: 86
2411093 GTTTGTGGGA
** *
2411103 AAACGCCGCTAAATATCATTACCTATTGCGGCGTTTATCTA-AAAAACACCGCTAAATATCAACA
1 AAACGCCGCTAAATATCAACACCTATTGCGACGTTTATC-ACAAAAACACCGCTAAATATCAACA
2411167 CCTATTGCGGTATTTTTCTGAC
65 CCTATTGCGGTATTTTTCTGAC
* * * *
2411189 AAACGCCGCTAAATATCAACACCTATTGCGACGTTTGTCACACAAACACCGTTAAATATCAATAC
1 AAACGCCGCTAAATATCAACACCTATTGCGACGTTTATCACAAAAACACCGCTAAATATCAACAC
2411254 CTATTGCGG
66 CTATTGCGG
2411263 CGTTTTTTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 1 0.02
86 65 0.98
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (86 bp):
AAACGCCGCTAAATATCAACACCTATTGCGACGTTTATCACAAAAACACCGCTAAATATCAACAC
CTATTGCGGTATTTTTCTGAC
Found at i:2412483 original size:20 final size:18
Alignment explanation
Indices: 2412422--2412501 Score: 65
Period size: 18 Copynumber: 4.3 Consensus size: 18
2412412 AGTGCTACAC
* *
2412422 AATGCACTGAATTG-CAA
1 AATGCACAGAAGTGCCAA
* *
2412439 TAATGCACTA-AAGTTCCAC
1 -AATGCAC-AGAAGTGCCAA
2412458 AATGCACAGAAGTGCTACAA
1 AATGCACAGAAGTGC--CAA
*
2412478 AATGCACCGAAGTGCCAA
1 AATGCACAGAAGTGCCAA
2412496 AATGCA
1 AATGCA
2412502 ACAACTAGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.02
18 31 0.62
19 2 0.04
20 16 0.32
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (18 bp):
AATGCACAGAAGTGCCAA
Found at i:2418214 original size:43 final size:43
Alignment explanation
Indices: 2418153--2418301 Score: 183
Period size: 43 Copynumber: 3.5 Consensus size: 43
2418143 TTGATATTTA
* *
2418153 GCAATAGGTGTTGATATTTAGCGGCTTTTTTCAGACAAACGCC
1 GCAATAGGTGTTGATATTTAGCGGCTTTTTTCATAAAAACGCC
* *
2418196 GCAATAGGTGTTGATATTTAGCGGCGTTTGTT-ATAAAAACACC
1 GCAATAGGTGTTGATATTTAGCGGC-TTTTTTCATAAAAACGCC
* * * * *
2418239 ACAATAGGTGTTGATATTTAGCGACGTTTTTCATAAAAATGCT
1 GCAATAGGTGTTGATATTTAGCGGCTTTTTTCATAAAAACGCC
* *
2418282 GAAATAGGTGTTAATATTTA
1 GCAATAGGTGTTGATATTTA
2418302 ATAGCGTTTC
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 4 0.04
43 81 0.90
44 5 0.06
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (43 bp):
GCAATAGGTGTTGATATTTAGCGGCTTTTTTCATAAAAACGCC
Found at i:2418330 original size:86 final size:86
Alignment explanation
Indices: 2418153--2418356 Score: 212
Period size: 86 Copynumber: 2.4 Consensus size: 86
2418143 TTGATATTTA
* * * * *
2418153 GCAATAGGTGTTGATATTTAGCGGCTTTTTTCAGACAAACGCCGCAATAGGTGTTGATATTTAGC
1 GCAATAGGTGTTGATATTTAGCGGCGTTTTTCAGAAAAACGCCGAAATAGGTGTTAATATTTAAC
* ***
2418218 GGCGTTTGTTATAAAAACACC
66 AGCGTTTCAAATAAAAACACC
* * * * * *
2418239 ACAATAGGTGTTGATATTTAGCGACGTTTTTCATAAAAATGCTGAAATAGGTGTTAATATTTAAT
1 GCAATAGGTGTTGATATTTAGCGGCGTTTTTCAGAAAAACGCCGAAATAGGTGTTAATATTTAAC
* **
2418304 AGCGTTTCAAATACAAATGCC
66 AGCGTTTCAAATAAAAACACC
* *
2418325 GCAATAGGT-TATGATGTTTCGCGGCGTTTTTC
1 GCAATAGGTGT-TGATATTTAGCGGCGTTTTTC
2418357 GCTAAAACGC
Statistics
Matches: 95, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
85 1 0.01
86 94 0.99
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (86 bp):
GCAATAGGTGTTGATATTTAGCGGCGTTTTTCAGAAAAACGCCGAAATAGGTGTTAATATTTAAC
AGCGTTTCAAATAAAAACACC
Found at i:2418369 original size:43 final size:42
Alignment explanation
Indices: 2418322--2418448 Score: 125
Period size: 43 Copynumber: 3.0 Consensus size: 42
2418312 AAATACAAAT
*
2418322 GCCGCAATAGGTTATGATGTTTCGCGGCGTTTTTCGCTAAAAC
1 GCCGCAATAGGTTATGATGTTTTGCGGCGTTTTT-GCTAAAAC
* * * *
2418365 GCCGCAGTTGGTGT-TGATGTTTTGCAGCGTTTTT-TTCACAAAC
1 GCCGCAATAGGT-TATGATGTTTTGCGGCGTTTTTGCT-A-AAAC
* *
2418408 GTCGCAATAGG-TATTGATGTTTTGCGGCGTTTCTGCTAAAA
1 GCCGCAATAGGTTA-TGATGTTTTGCGGCGTTTTTGCTAAAA
2418449 ACGCTGGTAC
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
41 2 0.03
42 4 0.06
43 59 0.88
44 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (42 bp):
GCCGCAATAGGTTATGATGTTTTGCGGCGTTTTTGCTAAAAC
Found at i:2418931 original size:21 final size:21
Alignment explanation
Indices: 2418850--2418933 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2418840 CTGCTGATAT
* * *
2418850 GTTGCTTCTCTCTGTGCTGCC
1 GTTGCTGCTCTCTCTGCTTCC
* *
2418871 GTTGCTTCTTTCTCTGCTTCC
1 GTTGCTGCTCTCTCTGCTTCC
* * ** *
2418892 GCTGCTGCTTTGGCTGCTTCT
1 GTTGCTGCTCTCTCTGCTTCC
2418913 GTTGCTGCTCTCTCTGCTTCC
1 GTTGCTGCTCTCTCTGCTTCC
2418934 CTTGATTCAT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.00, C:0.33, G:0.21, T:0.45
Consensus pattern (21 bp):
GTTGCTGCTCTCTCTGCTTCC
Found at i:2427180 original size:41 final size:40
Alignment explanation
Indices: 2427135--2427240 Score: 158
Period size: 41 Copynumber: 2.6 Consensus size: 40
2427125 CATCTATTAC
*
2427135 GGCGTTTGTATAAAAATGCCACTATAGATCCGCCCTTTAGT
1 GGCGTTTGT-TAAAAACGCCACTATAGATCCGCCCTTTAGT
* *
2427176 GGCGTTTGTCCAAAAACGCCACTATAGATCCGTCCTTTAGT
1 GGCGTTTGT-TAAAAACGCCACTATAGATCCGCCCTTTAGT
2427217 GGCGTTTGTTCAAAAACGCCACTA
1 GGCGTTTGTT-AAAAACGCCACTA
2427241 CAGTATGACT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
GGCGTTTGTTAAAAACGCCACTATAGATCCGCCCTTTAGT
Found at i:2428613 original size:41 final size:40
Alignment explanation
Indices: 2428549--2428668 Score: 131
Period size: 40 Copynumber: 3.0 Consensus size: 40
2428539 GTTTATACAA
* *
2428549 AAAAACGCCACTATTGATT-ACACTATTGTGGCGTTTGATT
1 AAAAACGCCACTATTAATTAACACTATTGAGGCGTTT-ATT
* * *
2428589 AAAAATGCCACTATTAATTAACACTATTGCGGTGTTTATCT
1 AAAAACGCCACTATTAATTAACACTATTGAGGCGTTTAT-T
* *
2428630 AAAAACG-CACTATTTATTATCACTATTGAGGC-TTT-TT
1 AAAAACGCCACTATTAATTAACACTATTGAGGCGTTTATT
2428667 AA
1 AA
2428669 GAATAAATGC
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
37 3 0.04
38 1 0.01
39 3 0.04
40 40 0.58
41 22 0.32
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (40 bp):
AAAAACGCCACTATTAATTAACACTATTGAGGCGTTTATT
Found at i:2428762 original size:41 final size:40
Alignment explanation
Indices: 2428709--2428832 Score: 146
Period size: 41 Copynumber: 3.0 Consensus size: 40
2428699 ACGGCATTTG
*
2428709 TGGTATAAACGCCGCTAATTTACCGATCTATTGTGGCGTTT
1 TGGTATAAACGCCACTAATTTACC-ATCTATTGTGGCGTTT
2428750 TGGCTA-AAACGCCACTATATGTTA--ATCTATTGTGGCGTTT
1 TGG-TATAAACGCCACTA-AT-TTACCATCTATTGTGGCGTTT
* *
2428790 ATGGTATAAACGTCACTAATTTACCATTCTATTGTGGCATTT
1 -TGGTATAAACGCCACTAATTTACCA-TCTATTGTGGCGTTT
2428832 T
1 T
2428833 TACAAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
39 3 0.04
40 20 0.28
41 28 0.39
42 18 0.25
43 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (40 bp):
TGGTATAAACGCCACTAATTTACCATCTATTGTGGCGTTT
Found at i:2428799 original size:82 final size:83
Alignment explanation
Indices: 2428677--2428832 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 83
2428667 AAGAATAAAT
* *
2428677 GCCACTATATGTGTAATCTATTACGGCATTTGTGGTATAAACGCCGCTAATTTACCGA-TCTATT
1 GCCACTATATGTGTAATCTATTACGGCATTTATGGTATAAACGCCACTAATTTACC-ATTCTATT
*
2428741 GTGGCGTTTTGGCTAAAAC
65 GTGGCATTTTGGCTAAAAC
** * *
2428760 GCCACTATATGT-TAATCTATTGTGGCGTTTATGGTATAAACGTCACTAATTTACCATTCTATTG
1 GCCACTATATGTGTAATCTATTACGGCATTTATGGTATAAACGCCACTAATTTACCATTCTATTG
2428824 TGGCATTTT
66 TGGCATTTT
2428833 TACAAAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 1 0.02
82 52 0.80
83 12 0.18
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (83 bp):
GCCACTATATGTGTAATCTATTACGGCATTTATGGTATAAACGCCACTAATTTACCATTCTATTG
TGGCATTTTGGCTAAAAC
Found at i:2428959 original size:136 final size:136
Alignment explanation
Indices: 2428715--2428976 Score: 420
Period size: 136 Copynumber: 1.9 Consensus size: 136
2428705 TTTGTGGTAT
* * *
2428715 AAACGCCGCTAATTTACCGATCTATTGTGGCGTTTTGGCTAAAACGCCACTATATGTTAATCTAT
1 AAACGCCGCTAATTTACCAATATATTGTGGCGTTTTGCCTAAAACGCCACTATATGTTAATCTAT
* *
2428780 TGTGGCGTTTATGGTATAAACGTCACTAATTTACCATTCTATTGTGGCATTT-TTACAAAAAAAT
66 TGTGACGTTTATGGTATAAACGTCACTAATTTACCATTCTATTGCGGCATTTGTTA-AAAAAAAT
2428844 GCCGTAA
130 GCCGTAA
*
2428851 AAACGCCGCTAATTTACCAATATATTGTGGCGTTTTGCCTAAAACGGCACTATATGTTAATCTAT
1 AAACGCCGCTAATTTACCAATATATTGTGGCGTTTTGCCTAAAACGCCACTATATGTTAATCTAT
* *
2428916 TGTGACGTTTATGGTATAAACG-CTGCTAATTTACCATTCTATTGCGGCGTTTGTTAAAAAA
66 TGTGACGTTTATGGTATAAACGTC-ACTAATTTACCATTCTATTGCGGCATTTGTTAAAAAA
2428977 CGCCGCAATA
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
135 1 0.01
136 112 0.97
137 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (136 bp):
AAACGCCGCTAATTTACCAATATATTGTGGCGTTTTGCCTAAAACGCCACTATATGTTAATCTAT
TGTGACGTTTATGGTATAAACGTCACTAATTTACCATTCTATTGCGGCATTTGTTAAAAAAAATG
CCGTAA
Found at i:2432674 original size:7 final size:7
Alignment explanation
Indices: 2432658--2432688 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2432648 AAAGTCAATA
*
2432658 GTCAATG
1 GTCAACG
2432665 GTCAACG
1 GTCAACG
2432672 GTCAACG
1 GTCAACG
2432679 GTCAACG
1 GTCAACG
2432686 GTC
1 GTC
2432689 GGGTTGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:2439740 original size:22 final size:22
Alignment explanation
Indices: 2439713--2439754 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2439703 ACAGTCAACG
*
2439713 GTCAACGGTCGGGTTGGGTCTT
1 GTCAACGGTCGGGTCGGGTCTT
2439735 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCGGGTCGGGTC
2439755 GGGTCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.43, T:0.26
Consensus pattern (22 bp):
GTCAACGGTCGGGTCGGGTCTT
Found at i:2442342 original size:2 final size:2
Alignment explanation
Indices: 2442335--2442391 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2442325 TAAATCAGGT
2442335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2442377 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2442392 TATTTCACAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2446086 original size:64 final size:65
Alignment explanation
Indices: 2446018--2446198 Score: 159
Period size: 64 Copynumber: 2.8 Consensus size: 65
2446008 TTGGAACACT
* * *
2446018 TGATGCATCGGTGCACCAAGTGTGCATCGATTCATGAAATGAATTCGATG-TTTGAAAAATAGCC
1 TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGAATTCGATGTTTTGAAAAATAGCC
***** * **
2446082 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTC
1 TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGAATTCGATGTTTTGAAAAATAGCC
* *** * * ** *
2446146 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGAATTCGATGTT
2446199 CAATTAATTC
Statistics
Matches: 97, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 50 0.52
65 47 0.48
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGAATTCGATGTTTTGAAAAATAGCC
Found at i:2446170 original size:19 final size:19
Alignment explanation
Indices: 2446146--2446196 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2446136 GAAAATATTC
2446146 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2446165 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2446184 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2446197 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2446172 original size:65 final size:65
Alignment explanation
Indices: 2446039--2446198 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
2446029 TGCACCAAGT
* * * ***
2446039 GTGCATCGATTCATGAAATGAATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
2446103 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
2446167 A
65 A
* *
2446168 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
2446199 CAATTAATTC
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 35 0.43
65 47 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:2446438 original size:20 final size:21
Alignment explanation
Indices: 2446415--2446454 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2446405 GAATCGAATA
2446415 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
2446435 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
2446455 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:2453034 original size:14 final size:15
Alignment explanation
Indices: 2453003--2453035 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2452993 GTGTTAATTA
*
2453003 ATTTTAAGATTTTAT
1 ATTTTAAGATTATAT
2453018 ATTTTAA-ATTATAT
1 ATTTTAAGATTATAT
2453032 ATTT
1 ATTT
2453036 GATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTTAAGATTATAT
Found at i:2461875 original size:21 final size:20
Alignment explanation
Indices: 2461860--2461897 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2461850 AATACTAAGT
*
2461860 CACTTAGTATCGATACTAAC
1 CACTGAGTATCGATACTAAC
*
2461880 CTCTGAGTATCGATACTA
1 CACTGAGTATCGATACTA
2461898 CTGACTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (20 bp):
CACTGAGTATCGATACTAAC
Found at i:2466842 original size:14 final size:15
Alignment explanation
Indices: 2466823--2466855 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2466813 GTTTTATGTG
*
2466823 TTTCACTCGTATAT-
1 TTTCACCCGTATATA
2466837 TTTCACCCGTATATA
1 TTTCACCCGTATATA
2466852 TTTC
1 TTTC
2466856 TATGTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.21, C:0.24, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTCACCCGTATATA
Found at i:2474485 original size:24 final size:25
Alignment explanation
Indices: 2474423--2474485 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
2474413 TTCGGGACAT
*
2474423 TTCTATGTGGCA-CTTCAGTGCATA
1 TTCTATGTGGTAGCTTCAGTGCATA
* * *
2474447 TTCTACGCGAT-GCTTCAGTGCA-A
1 TTCTATGTGGTAGCTTCAGTGCATA
2474470 TTCTATGTGGTAGCTT
1 TTCTATGTGGTAGCTT
2474486 TGACTGCAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (25 bp):
TTCTATGTGGTAGCTTCAGTGCATA
Found at i:2475330 original size:19 final size:18
Alignment explanation
Indices: 2475286--2475321 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2475276 TGAAAACAAT
2475286 GTAATTAAATCAAAAACA
1 GTAATTAAATCAAAAACA
2475304 GTAATTAAATCAAAAACA
1 GTAATTAAATCAAAAACA
2475322 TTTTTTTAAT
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:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (18 bp):
GTAATTAAATCAAAAACA
Found at i:2475817 original size:21 final size:21
Alignment explanation
Indices: 2475791--2475900 Score: 73
Period size: 20 Copynumber: 5.3 Consensus size: 21
2475781 TGATACTTGG
2475791 GTATCGATACCTATTCAAGTA
1 GTATCGATACCTATTCAAGTA
* * * *
2475812 GTATCGGTA-TTGTATGAA-TA
1 GTATCGATACCTAT-TCAAGTA
* *
2475832 ATATCGATACTTATTCAAGTA
1 GTATCGATACCTATTCAAGTA
* * * *
2475853 ATATTGATA-CTATGCTAGTA
1 GTATCGATACCTATTCAAGTA
* *
2475873 GTATCGATACCTAGTAAGAGTA
1 GTATCGATACCTATTCA-AGTA
2475895 GTATCG
1 GTATCG
2475901 GTACTGGGTG
Statistics
Matches: 66, Mismatches: 18, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
20 29 0.44
21 27 0.41
22 10 0.15
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (21 bp):
GTATCGATACCTATTCAAGTA
Found at i:2486942 original size:22 final size:23
Alignment explanation
Indices: 2486914--2486956 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2486904 AGGCAAATTA
*
2486914 GTATTAA-TGCTAATGCACTTGT
1 GTATTAAGTGCTAATACACTTGT
2486936 GTATTAAGTGCTAATACACTT
1 GTATTAAGTGCTAATACACTT
2486957 CCATATCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (23 bp):
GTATTAAGTGCTAATACACTTGT
Found at i:2486977 original size:22 final size:23
Alignment explanation
Indices: 2486942--2487001 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
2486932 TTGTGTATTA
**
2486942 AGTGCTAATACACTTCCA-TATC
1 AGTGCTAAGGCACTTCCAGTATC
* * *
2486964 AGTGTTGAGGCACTT-TAGTATC
1 AGTGCTAAGGCACTTCCAGTATC
2486986 AGTGCTAAGGCACTTC
1 AGTGCTAAGGCACTTC
2487002 AATTATTCGA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (23 bp):
AGTGCTAAGGCACTTCCAGTATC
Found at i:2487021 original size:2 final size:2
Alignment explanation
Indices: 2487014--2487068 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2487004 TTATTCGATG
2487014 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
2487056 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2487069 CACACCAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2496817 original size:98 final size:98
Alignment explanation
Indices: 2496628--2496852 Score: 290
Period size: 98 Copynumber: 2.3 Consensus size: 98
2496618 TTGATTCTGG
* * * *
2496628 TTATATCCAGATTGACTCGATCTCCTCAACGTGAAGGAGCAGTGTCATTCTTAGACAATCAGACT
1 TTATATCCAGATTGACTCGATATCCTCAACGCGAAGAAGCAGTGTCATTCTCAGACAATCAGACT
*
2496693 TCCCCAACACGAAGGAACCATATTGTCTCTAAA
66 TCCCCAACACGAAAGAACCATATTGTCTCTAAA
* * *
2496726 TTATTTCCAAATTGACTCGATATCCTTAACGCGAAGAAGCAGTGTCATTCTCAGACAATCAGACT
1 TTATATCCAGATTGACTCGATATCCTCAACGCGAAGAAGCAGTGTCATTCTCAGACAATCAGACT
* * ** *
2496791 TTCTCAACGTGAAAGAA-CATTGTTGTCTCTAAA
66 TCCCCAACACGAAAGAACCA-TATTGTCTCTAAA
* * *
2496824 TTATCTCCAGATTGACCCGATTTCCTCAA
1 TTATATCCAGATTGACTCGATATCCTCAA
2496853 TGAGAAGGAA
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 2 0.02
98 106 0.98
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (98 bp):
TTATATCCAGATTGACTCGATATCCTCAACGCGAAGAAGCAGTGTCATTCTCAGACAATCAGACT
TCCCCAACACGAAAGAACCATATTGTCTCTAAA
Found at i:2497325 original size:220 final size:219
Alignment explanation
Indices: 2496723--2497342 Score: 787
Period size: 218 Copynumber: 2.8 Consensus size: 219
2496713 TATTGTCTCT
* * * *
2496723 AAATTATTTCCAAATTGACTCGATATCCTTAACGCGAAGAAGCAGTGTCATTCTCAGACAATCAG
1 AAATTATCTCCAAATTGACTCGATCTCCTCAACGCGAAGGAGCAGTGTCATTCTCAGACAATCAG
* ** * * *
2496788 ACTTTCTCAACGTGAAAGAACATTGTTGTCTCTAAATTATCTCCAGATTGACCCGATTTCCTCAA
66 ACTTCCTCAACACGAATGACCA-TGTTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCAA
* * * * * *
2496853 TGAGAAGGAATAGTGTCATCTCCAGCAAACAATTTACTTGAAAACGATTAGATCTCATCAACATG
130 CGAGAAGGAATAATGTCATCTCCAGCAAACAATTTACCTGAAAACGATCAGATATCATCAACATA
2496918 GATGAGCAGTATCGTCTTCAACATC
195 GATGAGCAGTATCGTCTTCAACATC
* * * * *
2496943 AAATTATCTCCAAATTAACTTGATCTCATCAACGCGAAGGAGCAATGTCATTCTCAGAGAATC--
1 AAATTATCTCCAAATTGACTCGATCTCCTCAACGCGAAGGAGCAGTGTCATTCTCAGACAATCAG
* * *
2497006 ACTTCCTCAACACGAATGAACTC-TGTTGTCTCCAAATTATCTCCAAATTAACCTGATTTCCTCA
66 ACTTCCTCAACACGAATG-AC-CATGTTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCA
* * * *
2497070 ACGAGAATGAACAATGTCATCTCCAGCAAACAATTTACCTGAAAACGATCAGATATCTTCAAGAT
129 ACGAGAAGGAATAATGTCATCTCCAGCAAACAATTTACCTGAAAACGATCAGATATCATCAACAT
**
2497135 AGATGAGCAGTATTTTCTTCAACATC
194 AGATGAGCAGTATCGTCTTCAACATC
* * * * * *
2497161 AAATTATCTCTAGATTGACCCGATCTCCTCAACGCAAAGGAGCAGTGCCATTCTAAGACAATCAG
1 AAATTATCTCCAAATTGACTCGATCTCCTCAACGCGAAGGAGCAGTGTCATTCTCAGACAATCAG
**
2497226 ACTTCCTCAACACGAATGAGCCATGTTGTCTCCAAATTATCTTTAGATTGACCCGATTTCCTCAA
66 ACTTCCTCAACACGAATGA-CCATGTTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCAA
* * * * * *
2497291 CAAGCAGGATTAATGTCATCTTCAACAAACAATTTACCTGAAAACAATCAGA
130 CGAGAAGGAATAATGTCATCTCCAGCAAACAATTTACCTGAAAACGATCAGA
2497343 AATTGATGTA
Statistics
Matches: 340, Mismatches: 54, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
218 182 0.54
219 3 0.01
220 155 0.46
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (219 bp):
AAATTATCTCCAAATTGACTCGATCTCCTCAACGCGAAGGAGCAGTGTCATTCTCAGACAATCAG
ACTTCCTCAACACGAATGACCATGTTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCAAC
GAGAAGGAATAATGTCATCTCCAGCAAACAATTTACCTGAAAACGATCAGATATCATCAACATAG
ATGAGCAGTATCGTCTTCAACATC
Found at i:2500020 original size:7 final size:7
Alignment explanation
Indices: 2500008--2500034 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2499998 GAAATGAAAG
2500008 GGAGAAT
1 GGAGAAT
2500015 GGAGAAT
1 GGAGAAT
2500022 GGAGAAT
1 GGAGAAT
2500029 GGAGAA
1 GGAGAA
2500035 CATGAATCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (7 bp):
GGAGAAT
Found at i:2503782 original size:219 final size:219
Alignment explanation
Indices: 2503396--2503791 Score: 521
Period size: 219 Copynumber: 1.8 Consensus size: 219
2503386 GATCCATCAG
* * * *
2503396 ATCTCTTCAACATGGATGAACAGTATCGACTTCAACATCAAATTATGTCCATATTAACCCGATCT
1 ATCTCTTCAACACGAATGAACAATATCGACTTCAACATCAAATTATGTCCAGATTAACCCGATCT
* * * * *
2503461 CCTCAACGCGAAGGAGCAGTGTCATTCTCAAACAATCAAACTTCCTCAACGCGAATGAACTATTT
66 CCTCAACGCGAAAGAGCAATGTCATTCTCAAACAATCAAACTTCCTCAACACGAAGGAACCATTT
* * * *
2503526 GTCTCCAAATTATCTCTAGATTGACCCGATTTCCTCAATGGGAAGGAACAACGTCATCTTCAACA
131 ATCTCCAAATTATCTCCAGATTGACCCGATCTCCTCAATGCGAAGGAACAACGTCATCTTCAACA
2503591 AACAATTTACCCGAAAGAGACCAT
196 AACAATTTACCCGAAAGAGACCAT
* * * * * *
2503615 ATCTCTTCAACACGAATGAGCAATGTCGTCTTCAACA-CTAAA-TATTTCCAGATTGACTCGATC
1 ATCTCTTCAACACGAATGAACAATATCGACTTCAACATC-AAATTATGTCCAGATTAACCCGATC
* * *
2503678 TCCTCAACGCGAAAGAGCAATGTCATTCTCAGACAATCAGACTTTCC-CAACACGAAGGAACCGT
65 TCCTCAACGCGAAAGAGCAATGTCATTCTCAAACAATCAAAC-TTCCTCAACACGAAGGAACCAT
*
2503742 GTTATC-CTCAAATTATTTCCAGATTGACCCGATCTCCTCAATGCGAAGGA
129 -TTATCTC-CAAATTATCTCCAGATTGACCCGATCTCCTCAATGCGAAGGA
2503792 GTATTGTCAT
Statistics
Matches: 150, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
218 70 0.47
219 80 0.53
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (219 bp):
ATCTCTTCAACACGAATGAACAATATCGACTTCAACATCAAATTATGTCCAGATTAACCCGATCT
CCTCAACGCGAAAGAGCAATGTCATTCTCAAACAATCAAACTTCCTCAACACGAAGGAACCATTT
ATCTCCAAATTATCTCCAGATTGACCCGATCTCCTCAATGCGAAGGAACAACGTCATCTTCAACA
AACAATTTACCCGAAAGAGACCAT
Found at i:2503832 original size:98 final size:98
Alignment explanation
Indices: 2503657--2503868 Score: 282
Period size: 98 Copynumber: 2.2 Consensus size: 98
2503647 CAACACTAAA
* * *
2503657 TATTTCCAGATTGACTCGATCTCCTCAACGCGAAAGAGCAATGTCATTCTCAGACAATCAGACTT
1 TATTTCCAGATTGACCCGATCTCCTCAACGCGAAAGAGCAATGTCATCCTAAGACAATCAGACTT
*
2503722 TCCCAACACGAAGGAACCGTGTTATC-CTCAAAT
66 TCCCAACACGAAGGAACCATGTTATCTC-CAAAT
* * * * * *
2503755 TATTTCCAGATTGACCCGATCTCCTCAATGCGAAGGAGTATTGTCATCCTAAGACAATTAGATTT
1 TATTTCCAGATTGACCCGATCTCCTCAACGCGAAAGAGCAATGTCATCCTAAGACAATCAGACTT
* * *
2503820 TCTCAACGCGAAGGAACCATGTTGTCTCCAAAT
66 TCCCAACACGAAGGAACCATGTTATCTCCAAAT
*
2503853 TATCTCCAGATTGACC
1 TATTTCCAGATTGACC
2503869 TGATTTCCAC
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 98 0.99
99 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (98 bp):
TATTTCCAGATTGACCCGATCTCCTCAACGCGAAAGAGCAATGTCATCCTAAGACAATCAGACTT
TCCCAACACGAAGGAACCATGTTATCTCCAAAT
Found at i:2503900 original size:98 final size:98
Alignment explanation
Indices: 2503661--2503900 Score: 248
Period size: 98 Copynumber: 2.4 Consensus size: 98
2503651 ACTAAATATT
* * * * * * * * *
2503661 TCCAGATTGACTCGATCTCCTCAACGCGAAAGAGCAATGTCATTCTCAGACAATCAGACTTTCCC
1 TCCAGATTGACCCGATCTCCACAAAGAGAAGGAGCAGTATCATCCTAAGACAATCAGACTTTCCC
* *
2503726 AACACGAAGGAACCGTGTTATCCTCAAATTATT
66 AACACGAAGGAACCATGTTATCCTCAAATTATC
* * * * * * * * *
2503759 TCCAGATTGACCCGATCTCCTCAATGCGAAGGAGTATTGTCATCCTAAGACAATTAGATTTTCTC
1 TCCAGATTGACCCGATCTCCACAAAGAGAAGGAGCAGTATCATCCTAAGACAATCAGACTTTCCC
* *
2503824 AACGCGAAGGAACCATGTTGT-CTCCAAATTATC
66 AACACGAAGGAACCATGTTATCCT-CAAATTATC
* *
2503857 TCCAGATTGACCTGATTTCCACAAAGAGAAGGAGCAGTATCATC
1 TCCAGATTGACCCGATCTCCACAAAGAGAAGGAGCAGTATCATC
2503901 TTCAACAAAT
Statistics
Matches: 119, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
97 2 0.02
98 117 0.98
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (98 bp):
TCCAGATTGACCCGATCTCCACAAAGAGAAGGAGCAGTATCATCCTAAGACAATCAGACTTTCCC
AACACGAAGGAACCATGTTATCCTCAAATTATC
Found at i:2508610 original size:32 final size:33
Alignment explanation
Indices: 2508559--2508681 Score: 92
Period size: 32 Copynumber: 3.8 Consensus size: 33
2508549 TCACCGACTT
* *
2508559 ACTAACATCCTAA-CATTTATTTTATTGTTCGA
1 ACTAACATACTAATCATTTATTTTATTGTTCTA
* *
2508591 ACTAACATACTAATC-TTTA-TCTATTTGTTCTT
1 ACTAACATACTAATCATTTATTTTA-TTGTTCTA
* * * * *
2508623 ATTAACATACT-ATCTTTTATTTTGACTGTTATC
1 ACTAACATACTAATCATTTATTTT-ATTGTTCTA
* * *
2508656 ACTAACTTACTAACCCTTTATTTTAT
1 ACTAACATACTAATCATTTATTTTAT
2508682 CTCTCAAACT
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
31 6 0.08
32 36 0.51
33 18 0.25
34 11 0.15
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.48
Consensus pattern (33 bp):
ACTAACATACTAATCATTTATTTTATTGTTCTA
Found at i:2508804 original size:15 final size:15
Alignment explanation
Indices: 2508784--2508825 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
2508774 TCTTGTACGC
2508784 TTTAATTTTCCAG-CA
1 TTTAA-TTTCCAGTCA
2508799 TTTAATTT-CAGTCA
1 TTTAATTTCCAGTCA
2508813 TTTAATTTCCAGT
1 TTTAATTTCCAGT
2508826 ACTTTATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 13 0.52
15 9 0.36
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (15 bp):
TTTAATTTCCAGTCA
Found at i:2508831 original size:15 final size:15
Alignment explanation
Indices: 2508783--2508831 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2508773 TTCTTGTACG
*
2508783 CTTTAATTTTCCAGCA
1 CTTTAA-TTTCCAGTA
2508799 -TTTAATTT-CAGT-
1 CTTTAATTTCCAGTA
2508811 CATTTAATTTCCAGTA
1 C-TTTAATTTCCAGTA
2508827 CTTTA
1 CTTTA
2508832 TTTGTAGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
13 3 0.11
14 11 0.39
15 13 0.46
16 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (15 bp):
CTTTAATTTCCAGTA
Found at i:2509095 original size:2 final size:2
Alignment explanation
Indices: 2509088--2509119 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2509078 TTTTCCTCGC
2509088 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
2509120 TGTTTACACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2519468 original size:30 final size:30
Alignment explanation
Indices: 2519404--2519468 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
2519394 TTTTATAATC
*
2519404 TTAATTTATGCAAAATAATTATAGGTGAAA
1 TTAATTTATGCAAAATAATTATAGATGAAA
*
2519434 -TAATTTATGTCTAAATAATTGATA-AT-AAA
1 TTAATTTATG-CAAAATAATT-ATAGATGAAA
2519463 TTAATT
1 TTAATT
2519469 CATCTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
29 12 0.40
30 15 0.50
31 3 0.10
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (30 bp):
TTAATTTATGCAAAATAATTATAGATGAAA
Found at i:2520641 original size:64 final size:64
Alignment explanation
Indices: 2520510--2520696 Score: 200
Period size: 64 Copynumber: 2.9 Consensus size: 64
2520500 ACACTAGGGC
* * ** *
2520510 TGCATCGATGCATAAAATACATTCGATGTTTCAAATAAGCCT-GGAGTGCATCGATGCATGGTCT
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAATTA-TTTAGGAGTGCATCGATGCATGCTCT
2520574 G
64 G
*
2520575 TGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATCGAAGCATGC-CTTG
1 TGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATCGATGCATGCTC-TG
* * * ** * *
2520639 TGCATCGGTACACAAAATGCATTCGAAATTCAATTTATTCAAGG-GTGCATCGATGCAT
1 TGCATCGATGCATAAAATGCATTCGATGTTCAAATTATT-TAGGAGTGCATCGATGCAT
2520697 TATATAGTGC
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.02
64 73 0.70
65 30 0.29
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATCGATGCATGCTCTG
Found at i:2523286 original size:20 final size:22
Alignment explanation
Indices: 2523263--2523307 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
2523253 CGATGAGTAT
2523263 ATCAATGCACA-AC-AGAGTGC
1 ATCAATGCACATACAAGAGTGC
*
2523283 ATCAATGCACATTCAAGAGTGC
1 ATCAATGCACATACAAGAGTGC
2523305 ATC
1 ATC
2523308 GGTGCACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 1 0.05
22 10 0.45
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCAATGCACATACAAGAGTGC
Found at i:2523304 original size:22 final size:22
Alignment explanation
Indices: 2523276--2523358 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
2523266 AATGCACAAC
*
2523276 AGAGTGCATCAATGCACATTCA
1 AGAGTGCATCGATGCACATTCA
* *
2523298 AGAGTGCATCGGTGCACCTTCA
1 AGAGTGCATCGATGCACATTCA
* *
2523320 AG-GTGTATCGATGCATATTCA
1 AGAGTGCATCGATGCACATTCA
2523341 A-AGGATGCATCGATGCAC
1 AGA-G-TGCATCGATGCAC
2523359 TGTAATATCC
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 16 0.33
22 22 0.45
23 11 0.22
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
AGAGTGCATCGATGCACATTCA
Found at i:2525712 original size:22 final size:22
Alignment explanation
Indices: 2525684--2525743 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
2525674 GGGTCTACGT
*
2525684 GGTCCTTCGGGACATACTCATA
1 GGTCCTTCGGGACATACTCACA
2525706 GGTCCTTCGGGACATACTCACA
1 GGTCCTTCGGGACATACTCACA
*
2525728 GGTCATTCGGGACATA
1 GGTCCTTCGGGACATA
2525744 TTTCACATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCCTTCGGGACATACTCACA
Found at i:2530381 original size:21 final size:21
Alignment explanation
Indices: 2530355--2530394 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2530345 AAGACTATTT
2530355 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTGAAACA
**
2530376 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
2530395 TAGATTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAACA
Found at i:2532466 original size:19 final size:19
Alignment explanation
Indices: 2532442--2532486 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2532432 TATTTAGGTG
2532442 TGCATCGATGCATGCCTTC
1 TGCATCGATGCATGCCTTC
*
2532461 TGCATCGATTCATGCCTTC
1 TGCATCGATGCATGCCTTC
2532480 TGCATCG
1 TGCATCG
2532487 GTACATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCATGCCTTC
Found at i:2533418 original size:32 final size:32
Alignment explanation
Indices: 2533382--2533442 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
2533372 TTTTAAAACT
2533382 AATGAAAATGAATAATAAAA-AAATAAATATTA
1 AATGAAAAT-AATAATAAAATAAATAAATATTA
*
2533414 AATGAAAATAATGATAAAATAAATAAATA
1 AATGAAAATAATAATAAAATAAATAAATA
2533443 AAATAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.25
Consensus pattern (32 bp):
AATGAAAATAATAATAAAATAAATAAATATTA
Found at i:2536556 original size:13 final size:13
Alignment explanation
Indices: 2536533--2536568 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2536523 CTTAGTATTG
2536533 TGAAA-AAAATAA
1 TGAAAGAAAATAA
2536545 TGAAAGAAAATAA
1 TGAAAGAAAATAA
*
2536558 AGAAAGAAAAT
1 TGAAAGAAAAT
2536569 TGGAGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
TGAAAGAAAATAA
Found at i:2542450 original size:19 final size:19
Alignment explanation
Indices: 2542426--2542467 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2542416 TGACCCTTTA
*
2542426 GACCTTTGACCTGATCGTT
1 GACCTTTGACATGATCGTT
* *
2542445 GACCTTTTACATGTTCGTT
1 GACCTTTGACATGATCGTT
2542464 GACC
1 GACC
2542468 AAACCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (19 bp):
GACCTTTGACATGATCGTT
Found at i:2544798 original size:5 final size:5
Alignment explanation
Indices: 2544790--2544822 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2544780 AGACTACATA
*
2544790 CAATG CAATG CAATG CAATG CAATG CTATG CAA
1 CAATG CAATG CAATG CAATG CAATG CAATG CAA
2544823 GGTACCTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (5 bp):
CAATG
Found at i:2553768 original size:24 final size:24
Alignment explanation
Indices: 2553741--2553788 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2553731 GCAGTTGGGT
*
2553741 GTGGTACCCTCTAGGCAGCTAGGC
1 GTGGTACCCTCCAGGCAGCTAGGC
*
2553765 GTGGTCCCCTCCAGGCAGCTAGGC
1 GTGGTACCCTCCAGGCAGCTAGGC
2553789 ATGATTCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.19
Consensus pattern (24 bp):
GTGGTACCCTCCAGGCAGCTAGGC
Found at i:2557573 original size:19 final size:19
Alignment explanation
Indices: 2557551--2557598 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
2557541 TAATTTGTAA
*
2557551 TTAGGATTATCTCTTGTTT
1 TTAGGATTATCTCTTATTT
* *
2557570 TTAGGAATTGTCTTTTATTT
1 TTAGG-ATTATCTCTTATTT
2557590 TTAGGATTA
1 TTAGGATTA
2557599 AGTTTGAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.21, C:0.06, G:0.17, T:0.56
Consensus pattern (19 bp):
TTAGGATTATCTCTTATTT
Found at i:2559929 original size:25 final size:29
Alignment explanation
Indices: 2559893--2559947 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
2559883 CAAGTCTATT
2559893 TTTATCACATAT-T-TA-A-TTAAAATTG
1 TTTATCACATATATATATATTTAAAATTG
2559918 TTTAT-ACAATATATATATATTTAAAATTG
1 TTTATCAC-ATATATATATATTTAAAATTG
2559947 T
1 T
2559948 ATCCGTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
24 2 0.08
25 9 0.36
26 1 0.04
27 2 0.08
28 1 0.04
29 10 0.40
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTATCACATATATATATATTTAAAATTG
Found at i:2563103 original size:2 final size:2
Alignment explanation
Indices: 2563096--2563168 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
2563086 TTTGATTTTG
2563096 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
2563138 CT CT CT CT CT AT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2563169 ACTCACTCAC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.01, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2567411 original size:20 final size:20
Alignment explanation
Indices: 2567374--2567412 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2567364 AGATTGAGTG
* * *
2567374 GATTTTGATGTTGTTTGCAC
1 GATTTTCATGATGATTGCAC
2567394 GATTTTCATGATGATTGCA
1 GATTTTCATGATGATTGCA
2567413 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTCATGATGATTGCAC
Found at i:2567594 original size:21 final size:21
Alignment explanation
Indices: 2567568--2567607 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2567558 CAGAACCCCA
*
2567568 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2567589 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2567608 TTAAAGAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2578691 original size:32 final size:32
Alignment explanation
Indices: 2578655--2578991 Score: 273
Period size: 32 Copynumber: 12.0 Consensus size: 32
2578645 ACAACTACAA
2578655 TAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
*
2578687 TAATAAATTATTTAAAACAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
2578719 TAATAAATTATTTAAAATAAATCAAT-C---C
1 TAATAAATTATTTAAAATAAATCAATCCATAC
2578747 --AT--A-T-TTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
*
2578773 TGATAAATTATTTAAAATAAATCAAT-C---C
1 TAATAAATTATTTAAAATAAATCAATCCATAC
2578801 --AT--A-T-TTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
*
2578827 TAATAAATTATTTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
*
2578859 -AACTACA--A--T--AATAAATCAATCC--A-
1 TAA-TAAATTATTTAAAATAAATCAATCCATAC
* *
2578882 T-AT------TTTAAAATAAACCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
2578907 TAATAAATTATTTAAAATAAATCAAT-C---C
1 TAATAAATTATTTAAAATAAATCAATCCATAC
2578935 --AT--A-T-TTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
*
2578961 TAATAAATTATTTAAAATAAGTCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
2578992 TTTTATAATA
Statistics
Matches: 250, Mismatches: 9, Indels: 92
0.71 0.03 0.26
Matches are distributed among these distances:
20 1 0.00
22 60 0.24
23 7 0.03
24 5 0.02
25 1 0.00
26 23 0.09
28 10 0.04
30 4 0.02
31 8 0.03
32 131 0.52
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.34
Consensus pattern (32 bp):
TAATAAATTATTTAAAATAAATCAATCCATAC
Found at i:2578755 original size:22 final size:22
Alignment explanation
Indices: 2578729--2578771 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2578719 TAATAAATTA
2578729 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2578751 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2578772 CTGATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2578757 original size:54 final size:54
Alignment explanation
Indices: 2578697--2578857 Score: 295
Period size: 54 Copynumber: 3.0 Consensus size: 54
2578687 TAATAAATTA
*
2578697 TTTAAAACAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
2578751 TTTAAAATAAATCAATCCATACTGATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
2578805 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
2578858 CAACTACAAT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:2578780 original size:22 final size:22
Alignment explanation
Indices: 2578731--2578779 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2578721 ATAAATTATT
**
2578731 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATGA
2578753 TAAAATAAATCAATCCATACTGA
1 TAAAATAAATCAATCCATA-TGA
2578776 TAAA
1 TAAA
2578780 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATGA
Found at i:2578809 original size:22 final size:22
Alignment explanation
Indices: 2578783--2578825 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2578773 TGATAAATTA
2578783 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2578805 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2578826 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2578834 original size:22 final size:22
Alignment explanation
Indices: 2578785--2578833 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2578775 ATAAATTATT
**
2578785 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2578807 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2578830 TAAA
1 TAAA
2578834 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2578841 original size:86 final size:85
Alignment explanation
Indices: 2578655--2578937 Score: 314
Period size: 86 Copynumber: 3.4 Consensus size: 85
2578645 ACAACTACAA
*
2578655 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAATCCATACT
1 TAATAAATTATTTAAAATAAATCAATCCATACT-ATAAATTATTTAAAATAAATCAATCCATA-T
** * ** * *
2578720 AATAAATTATTTAAAATAAAT-C
64 TTTAAAATAAAT-CAATACATAC
**
2578742 -AATCCA-TATTTTAAAATAAATCAATCCATACTGATAAATTATTTAAAATAAATCAATCCATAT
1 TAATAAATTA-TTTAAAATAAATCAATCCATACT-ATAAATTATTTAAAATAAATCAATCCATAT
*
2578805 TTTAAAATAAATCAATCCATAC
64 TTTAAAATAAATCAATACATAC
* * *
2578827 TAATAAATTATTTAAAATAAATCAATACATAC----AACTA--CAATAATAAATCAATCCATATT
1 TAATAAATTATTTAAAATAAATCAATCCATACTATAAATTATTTAA-AATAAATCAATCCATATT
*
2578886 TTAAAATAAACCAATACATAC
65 TTAAAATAAATCAATACATAC
2578907 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
2578938 TTTTAAAATA
Statistics
Matches: 171, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
79 2 0.01
80 67 0.39
81 4 0.02
84 5 0.03
85 11 0.06
86 80 0.47
87 2 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (85 bp):
TAATAAATTATTTAAAATAAATCAATCCATACTATAAATTATTTAAAATAAATCAATCCATATTT
TAAAATAAATCAATACATAC
Found at i:2578889 original size:80 final size:80
Alignment explanation
Indices: 2578788--2578937 Score: 273
Period size: 80 Copynumber: 1.9 Consensus size: 80
2578778 AATTATTTAA
* *
2578788 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAAAATAAATCAAT
2578853 ACATACAACTACAAT
66 ACATACAACTACAAT
2578868 AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAAAATAAATCAAT
*
2578933 CCATA
66 ACATA
2578938 TTTTAAAATA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAAAATAAATCAAT
ACATACAACTACAAT
Found at i:2578926 original size:134 final size:137
Alignment explanation
Indices: 2578665--2578991 Score: 527
Period size: 134 Copynumber: 2.4 Consensus size: 137
2578655 TAATAAATTA
*
2578665 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAA-TA-
* * *
2578730 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTGATAAATTATTTAAAATAAAT
64 TT-AAATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAAAATAAAT
2578795 CAATCCATAT
128 CAATCCATAT
* *
2578805 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATAC-AACTACA-A-
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAA-TAAATAT
2578867 T-AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAAAATAAATCA
65 TAAATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAAAATAAATCA
2578931 ATCCATAT
130 ATCCATAT
*
2578939 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAGTCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
2578992 TTTTATAATA
Statistics
Matches: 178, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
134 119 0.67
136 1 0.01
138 1 0.01
139 2 0.01
140 55 0.31
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (137 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATATT
AAATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAAAATAAATCAA
TCCATAT
Found at i:2578937 original size:54 final size:54
Alignment explanation
Indices: 2578868--2579002 Score: 234
Period size: 54 Copynumber: 2.5 Consensus size: 54
2578858 CAACTACAAT
2578868 AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAA
* *
2578922 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAA
* *
2578976 AATAAGTCAATCCATATTTTATAATAA
1 AATAAATCAATCCATATTTTAAAATAA
2579003 TTTATTTTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAACCAATACATACTAATAAATTATTTAA
Found at i:2578943 original size:22 final size:22
Alignment explanation
Indices: 2578917--2578959 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2578907 TAATAAATTA
2578917 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2578939 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2578960 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2578968 original size:22 final size:22
Alignment explanation
Indices: 2578919--2578967 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2578909 ATAAATTATT
**
2578919 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2578941 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2578964 TAAA
1 TAAA
2578968 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2579010 original size:15 final size:15
Alignment explanation
Indices: 2578990--2579049 Score: 93
Period size: 15 Copynumber: 4.0 Consensus size: 15
2578980 AGTCAATCCA
* *
2578990 TATTTTATAATAATT
1 TATTTTAAAATAAAT
2579005 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
2579020 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
2579035 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
2579050 AACCTTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:2579024 original size:30 final size:30
Alignment explanation
Indices: 2578990--2579049 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2578980 AGTCAATCCA
*
2578990 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
2579020 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
2579050 AACCTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:2586116 original size:24 final size:23
Alignment explanation
Indices: 2586088--2586146 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
2586078 TTCGAGATAT
2586088 TTCTATGTGGCACTTCAGTGCATA
1 TTCTATGTGGCACTTCAGTGCA-A
* * *
2586112 TTCTATGCGACACTTCGGTGCAA
1 TTCTATGTGGCACTTCAGTGCAA
*
2586135 TTGTATGTGGCA
1 TTCTATGTGGCA
2586147 GTTTCGACTG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGCACTTCAGTGCAA
Found at i:2586728 original size:16 final size:17
Alignment explanation
Indices: 2586695--2586728 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2586685 AATTTTCAAC
2586695 AAGTTTTCAAAGAGTCA
1 AAGTTTTCAAAGAGTCA
*
2586712 AAGTTTTGAAA-AGTCA
1 AAGTTTTCAAAGAGTCA
2586728 A
1 A
2586729 TGTGACACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (17 bp):
AAGTTTTCAAAGAGTCA
Found at i:2589926 original size:42 final size:42
Alignment explanation
Indices: 2589844--2589927 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
2589834 AGAGATGATC
* *
2589844 GATCAAGCAAAAAAGCTCCAAGATGATTTAAATGAACAAATG
1 GATCAAGCAAAAAAACTCCAAGATGATTAAAATGAACAAATG
* * *
2589886 GATCAAGCAAAAAAATTCCAGGATGATTCAAAAT-AGCAAATG
1 GATCAAGCAAAAAAACTCCAAGATGATT-AAAATGAACAAATG
2589928 ACCAAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 32 0.89
43 4 0.11
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (42 bp):
GATCAAGCAAAAAAACTCCAAGATGATTAAAATGAACAAATG
Found at i:2590815 original size:19 final size:19
Alignment explanation
Indices: 2590787--2590830 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2590777 TTGGAAAAAT
*
2590787 AATCAACAAAAGACTAATC
1 AATCAACAAAAGACCAATC
* *
2590806 AATCAGCAAAATACCAATC
1 AATCAACAAAAGACCAATC
2590825 AATCAA
1 AATCAA
2590831 GAAGTGAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.23, G:0.05, T:0.16
Consensus pattern (19 bp):
AATCAACAAAAGACCAATC
Found at i:2593065 original size:7 final size:7
Alignment explanation
Indices: 2593048--2593126 Score: 76
Period size: 7 Copynumber: 11.4 Consensus size: 7
2593038 AAATAAGAAA
2593048 AAAAAAGG
1 AAAAAA-G
2593056 AAAAAAG
1 AAAAAAG
2593063 AAAAAAG
1 AAAAAAG
2593070 -AAAAAG
1 AAAAAAG
2593076 -AAAAAG
1 AAAAAAG
*
2593082 -AGAAAG
1 AAAAAAG
2593088 AAAAAAGG
1 AAAAAA-G
2593096 AGAAAAAG
1 A-AAAAAG
*
2593104 AAAATA-
1 AAAAAAG
*
2593110 AAAGAAG
1 AAAAAAG
2593117 AAAAAAG
1 AAAAAAG
2593124 AAA
1 AAA
2593127 TTGAATCAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
6 21 0.34
7 25 0.41
8 10 0.16
9 5 0.08
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:2593066 original size:6 final size:6
Alignment explanation
Indices: 2593042--2593126 Score: 61
Period size: 6 Copynumber: 14.0 Consensus size: 6
2593032 CAGAGAAAAT
* *
2593042 AAGAAA AA-AAA AGGAAAA AAGAAAA AAGAAA AAGAAA AAGAGA AAG-AA
1 AAGAAA AAGAAA AAG-AAA AAG-AAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
2593090 AA-AAG GAGAAA AAGAAA ATA-AAA GAAGAAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA A-AGAAA -AAG-AAA AAGAAA
2593127 TTGAATCAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
5 9 0.14
6 34 0.54
7 17 0.27
8 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:2593067 original size:19 final size:19
Alignment explanation
Indices: 2593036--2593126 Score: 96
Period size: 20 Copynumber: 4.6 Consensus size: 19
2593026 ATCCATCAGA
2593036 GAAAATAAG-AAAAAAAAAG
1 GAAAA-AAGAAAAAAAAAAG
*
2593055 GAAAAAAGAAAAAAGAAAAA
1 GAAAAAAGAAAAAA-AAAAG
*
2593075 GAAAAAGAGAAAGAAAAAAG
1 GAAAAA-AGAAAAAAAAAAG
2593095 GAGAAAAAGAAAATAAAAGAA-
1 GA-AAAAAGAAAA-AAAA-AAG
2593116 GAAAAAAGAAA
1 GAAAAAAGAAA
2593127 TTGAATCAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.05
19 10 0.16
20 30 0.48
21 17 0.27
22 2 0.03
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (19 bp):
GAAAAAAGAAAAAAAAAAG
Found at i:2593074 original size:26 final size:25
Alignment explanation
Indices: 2593035--2593126 Score: 96
Period size: 25 Copynumber: 3.5 Consensus size: 25
2593025 CATCCATCAG
*
2593035 AGAAAATAAGAAAAAAAAAGGAAAAA
1 AGAAAA-AAGAAAAAAAAAAGAAAAA
*
2593061 AGAAAAAAGAAAAAGAAAAAG-AGAA
1 AGAAAAAAGAAAAA-AAAAAGAAAAA
*
2593086 AGAAAAAAGGAGAAAAAGAAAATAAAAGA
1 AGAAAAAA-GA-AAAAA-AAAAGAAAA-A
2593115 AGAAAAAAGAAA
1 AGAAAAAAGAAA
2593127 TTGAATCAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
25 19 0.34
26 14 0.25
27 10 0.18
28 4 0.07
29 9 0.16
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.02
Consensus pattern (25 bp):
AGAAAAAAGAAAAAAAAAAGAAAAA
Found at i:2593119 original size:33 final size:32
Alignment explanation
Indices: 2593035--2593119 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
2593025 CATCCATCAG
*
2593035 AGAAAATAAGAAAAAAAAAGGAAAAAAGAAAAA
1 AGAAAATAA-AAAAAGAAAGGAAAAAAGAAAAA
2593068 AGAAAA-AGAAAAAGAGAAA-GAAAAAAGGAGAAAA
1 AGAAAATA-AAAAA-AGAAAGGAAAAAA-GA-AAAA
*
2593102 AGAAAATAAAAGAAGAAA
1 AGAAAATAAAAAAAGAAA
2593120 AAAGAAATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
32 12 0.27
33 18 0.40
34 14 0.31
35 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (32 bp):
AGAAAATAAAAAAAGAAAGGAAAAAAGAAAAA
Found at i:2594739 original size:52 final size:51
Alignment explanation
Indices: 2594628--2594816 Score: 256
Period size: 52 Copynumber: 3.7 Consensus size: 51
2594618 TATTATTCAC
* * * * *
2594628 GTGGGTATCTTGAAGGCTCACATCAGTATG-AAAAGATAGAAATGATCCAT
1 GTGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCAT
* *
2594678 GTGGGGCATCTTGAAGGCTTACATCAGGATGAAAAAGACAGAAGTAATCCAT
1 GT-GGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCAT
2594730 GTGGTGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCAT
1 GTGG-GCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCAT
*
2594782 GTAGGGCATCTTGAAGACTCACA-CTAGCATGAAAA
1 GT-GGGCATCTTGAAGGCTCACATC-AGCATGAAAA
2594817 GGTTGAGATA
Statistics
Matches: 125, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
50 2 0.02
51 28 0.22
52 93 0.74
53 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (51 bp):
GTGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCAT
Found at i:2596732 original size:177 final size:177
Alignment explanation
Indices: 2596428--2596842 Score: 688
Period size: 177 Copynumber: 2.4 Consensus size: 177
2596418 TTTCCCATAC
* * * *
2596428 TTGTAAGTCCTACGGGCCATCTATAAGACCTTAAGTGTAGGATGTTTTCAAATGAGATTTTAGAA
1 TTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAAATTTTAGAA
* * *
2596493 ACCAAGCCTTCAGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAACCTAATCCTAACAAA
66 ACCAAGCCTTCAGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGAAACCTAAACCTAACAAA
*
2596558 GGGGTTCCTTGACAACTAAGAAACCAAGTCTTCGGGGGTTTCTTGAT
131 GGGGTTCCTTGACAACTAAGAAACCAAGCCTTCGGGGGTTTCTTGAT
* *
2596605 TTGTAAGTCCTACGGGTCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAAATTTTAGAA
1 TTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAAATTTTAGAA
** **
2596670 ACCAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGAAAGTTAAACCTAACAAA
66 ACCAAGCCTTCAGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGAAACCTAAACCTAACAAA
*
2596735 GGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGAT
131 GGGGTTCCTTGACAACTAAGAAACCAAGCCTTCGGGGGTTTCTTGAT
2596782 TTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAT-AAATTTTA
1 TTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAAATTTTA
2596843 TCTCACTTGA
Statistics
Matches: 221, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
176 8 0.04
177 213 0.96
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (177 bp):
TTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAAATTTTAGAA
ACCAAGCCTTCAGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGAAACCTAAACCTAACAAA
GGGGTTCCTTGACAACTAAGAAACCAAGCCTTCGGGGGTTTCTTGAT
Found at i:2597197 original size:123 final size:124
Alignment explanation
Indices: 2596868--2597570 Score: 828
Period size: 123 Copynumber: 5.7 Consensus size: 124
2596858 TTTTTCTTAA
** *
2596868 AACATTTATAGACA-GAGTT-AGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAG
1 AACATTTCCAGACAGGAGTTCA-TAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
2596931 TCTGAAGAACTTATTCAACATTTTGCTTGACTCTATCGCAGAAGCAGATAGAGCAACA-G
65 TCTGAAGAACGTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATC
* ** *
2596990 ACCCATTTCCAGACAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAG
1 A-ACATTTCCAGACAGGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
2597055 TCTGAAGAACTTATTCAACCTTTTTCTTGACTCTATCGTAGAAGGAGATAGAGCAACA-G
65 TCTGAAGAACGTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATC
* **
2597114 AGCCATTTCCAGACA-GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 A-ACATTTCCAGACAGGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * * * * * *
2597178 TCTGAAGAACATAATCAACCTTTTTCTCGATTTTATCGCAGAAGAAGATAGAGCACCATC
65 TCTGAAGAACGTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATC
* *
2597238 AACATTTCCAGA-AGGAGTTCGTAATAAGAAGAATTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGACAGGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * * *
2597302 TTGAAGAACGTATTCAACCTTTTGGTCGATTCTATCGCAGAAGGAGATAGAGCAACATC
66 CTGAAGAACGTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATC
* * ** * *
2597361 AACGTTTCCA-AAAGGAGTTTGTAATAAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTTATAAT
1 AACATTTCCAGACAGGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * * * *
2597425 CTAAATATCGTATTCAACCTTTTGCTTGACTCTGTCGCAGAAGGAGATAGAGCAGCATC
66 CTGAAGAACGTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATC
* * * * ** *
2597484 AACGTTTCTAGA-AGGAGTTCGTAACAAGAAGAACTCATCTGAAGAATAAGAATAAGTTCATAAT
1 AACATTTCCAGACAGGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
** * * *
2597548 AAGAAGAACTTGTTCAACATTTT
66 CTGAAGAACGTATTCAACCTTTT
2597571 CATCTTAATC
Statistics
Matches: 511, Mismatches: 63, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
122 3 0.01
123 391 0.77
124 116 0.23
125 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (124 bp):
AACATTTCCAGACAGGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
CTGAAGAACGTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATC
Found at i:2597543 original size:369 final size:370
Alignment explanation
Indices: 2596882--2597556 Score: 919
Period size: 369 Copynumber: 1.8 Consensus size: 370
2596872 TTTATAGACA
* *
2596882 GAGTTAGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
1 GAGTTAGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACGTATTC
* * * *
2596947 AACATTTTGCTTGACTCTATCGCAGAAGCAGATAGAGCAACAGACCCATTTCCAGACAGGAGTTC
66 AACATTTTGCTCGACTCTATCGCAGAAGCAGATAGAGCAACACACACATTTCCAGAAAGGAGTTC
** * * *
2597012 ATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTT
131 ATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTAAAGAACGTATTCAACCTT
* * * * *
2597077 TTTCTTGACTCTATCGTAGAAGGAGATAGAGCAACAGAGCCATTTCCAGACAGAGTTCATAATCT
196 TTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACACAGACATTTCCAGACAGAGTTCATAATCA
* **
2597142 GAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACATAATCAACCTTTTTCTCG
261 GAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACATAATCAACCTTTTTCTCG
2597207 ATTTTATCGCAGAAGAAGATAGAGCACCATCAACATTTCCAGAAG
326 ATTTTATCGCAGAAGAAGATAGAGCACCATCAACATTTCCAGAAG
* * *
2597252 GAGTTCGTAATAAGAAGAATTCATCTGAAGAGGAAGAAGAAGTTCATAATTTGAAGAACGTATTC
1 GAGTTAGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACGTATTC
* * * * *
2597317 AACCTTTTGGTCGATTCTATCGCAGAAGGAGATAGAGCAACATCA-ACGTTTCCA-AAAGGAGTT
66 AACATTTTGCTCGACTCTATCGCAGAAGCAGATAGAGCAACA-CACACATTTCCAGAAAGGAGTT
** * * * *
2597380 TGTAATAAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTTATAATCTAAATATCGTATTCAACCT
130 CATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTAAAGAACGTATTCAACCT
* * * * *
2597445 TTTGCTTGACTCTGTCGCAGAAGGAGATAGAGCAGCATCA-ACGTTTCTAGA-AGGAGTTCGTAA
195 TTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACA-CAGACATTTCCAGACA-GAGTTCATAA
* *
2597508 -CAAGAAGAACTCATCTGAAGAATAAGAATAAGTTCATAATAAGAAGAAC
258 TC-AGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAAC
2597557 TTGTTCAACA
Statistics
Matches: 261, Mismatches: 40, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
368 2 0.01
369 153 0.59
370 105 0.40
371 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (370 bp):
GAGTTAGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACGTATTC
AACATTTTGCTCGACTCTATCGCAGAAGCAGATAGAGCAACACACACATTTCCAGAAAGGAGTTC
ATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTAAAGAACGTATTCAACCTT
TTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACACAGACATTTCCAGACAGAGTTCATAATCA
GAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACATAATCAACCTTTTTCTCG
ATTTTATCGCAGAAGAAGATAGAGCACCATCAACATTTCCAGAAG
Found at i:2597712 original size:17 final size:17
Alignment explanation
Indices: 2597690--2597722 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2597680 TTTTGTCCCA
2597690 TTTATTATTATTATTAT
1 TTTATTATTATTATTAT
*
2597707 TTTATTGTTATTATTA
1 TTTATTATTATTATTA
2597723 AATGATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATTATTATTATTAT
Found at i:2602699 original size:74 final size:74
Alignment explanation
Indices: 2602574--2602825 Score: 263
Period size: 74 Copynumber: 3.4 Consensus size: 74
2602564 CTTAACATAA
* * * ** *
2602574 ACCCACAAAGGGGAGTCATTCAAAGGATCAAGAATGATTTAAACCGCGAAGGAGAGTCATCTTAT
1 ACCCACGAAGGGGAGTCATCCAAAGAATCAAGAATGGCTTAAACCGTGAAGGAGAGTCATCTTAT
2602639 TTGACTTAG
66 TTGACTTAG
* * * * * *
2602648 ACCCACGAAGGGGAGTCATCCAAAGAATGAAGATTGGCTTAAACCATGAAGGAGTGTCATCTCAC
1 ACCCACGAAGGGGAGTCATCCAAAGAATCAAGAATGGCTTAAACCGTGAAGGAGAGTCATCTTAT
2602713 TTGACTTAG
66 TTGACTTAG
** * * * * * *
2602722 ACCTGCGAAGGGGAGTTATCCAAAGAATCTAA-ACTGGCTTAAACCGTGGAGGGGAGTCTTCTTG
1 ACCCACGAAGGGGAGTCATCCAAAGAATC-AAGAATGGCTTAAACCGTGAAGGAGAGTCATCTTA
* *
2602786 TTTGGGCTTAA
65 TTT-GACTTAG
**
2602797 ACCCGTGAAGGGGAGTCATCCAAAGAATC
1 ACCCACGAAGGGGAGTCATCCAAAGAATC
2602826 CTTCATTTGG
Statistics
Matches: 146, Mismatches: 30, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
74 113 0.77
75 33 0.23
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (74 bp):
ACCCACGAAGGGGAGTCATCCAAAGAATCAAGAATGGCTTAAACCGTGAAGGAGAGTCATCTTAT
TTGACTTAG
Found at i:2603209 original size:200 final size:199
Alignment explanation
Indices: 2602851--2603702 Score: 783
Period size: 201 Copynumber: 4.2 Consensus size: 199
2602841 TCATTTACAG
** * * * * *
2602851 CATAGCTTAAGTTGAGAAGAGCCATATGTCAACCAAATCTTTCAAGTTTAATTCCATTCAACTCA
1 CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAAGCTTTCAAGTTTGATTCCACTCAACTCG
* * * * *
2602916 AAAGCACATTAACCTCATGGTAGCAATGAGGAATTATCTT-TCTATCAAAATTCAAACTGAGGTC
66 AGAGCACATCAACCGCATGGTAGCAATGAGGAACTATCTTAT-GATCAAAATTCAAACTGAGGTC
** **
2602980 TTTAAGCCAAGAAGACTACCCAGGTTGGCTACGATTTAGCAATAATAAACCACTTCCCAGTTAGA
130 TTTAAGCCAAGAAGAAGACCCAGGTTGGCT-CGATTTAGCAATAAGGAACCACTTCCCAGTTAGA
2603045 TTTCGA
194 TTTCGA
* * * *
2603051 CATAACTTAAATCAAGAAGAGTTATATGTCAACCAAAGCTTTCAAGTTTGATTCTACTCAACTCG
1 CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAAGCTTTCAAGTTTGATTCCACTCAACTCG
* * * * *
2603116 AGAGCACACCAACCACATGGTAGCAATGAGGAGCTATCTTATGATAAAAATTCAAACTGATGTCT
66 AGAGCACATCAACCGCATGGTAGCAATGAGGAACTATCTTATGATCAAAATTCAAACTGAGGTCT
* * * * * * * *
2603181 TTAAGCCAAAAAGAAGACCCATGTTGGCTTGCATTTGGCAATAAGGATCCAATTCTCAATTCAGA
131 TTAAGCCAAGAAGAAGACCCAGGTTGGCTCG-ATTTAGCAATAAGGAACCACTTCCCAGTT-AGA
*
2603246 TTTCAA
194 TTTCGA
** * *
2603252 CATAGCTTAAGTCAAGAAGAGCTATATGTTGACCAAAGTTTTCAAGTTTGATTCCACTCAATTCG
1 CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAAGCTTTCAAGTTTGATTCCACTCAACTCG
* * * * * * * *
2603317 AGAGTAGATCGACCGCATGGTAGCAATAAAGAACTACCTTACGGTCAAAATTCAAACTGAGGTCT
66 AGAGCACATCAACCGCATGGTAGCAATGAGGAACTATCTTATGATCAAAATTCAAACTGAGGTCT
* * * * **
2603382 TTAAGCCAAGAAGAAGACTCGGGTTGGCTGCGATTTAGCAACAAGGAACCACTTTCTTGTCTAGA
131 TTAAGCCAAGAAGAAGACCCAGGTTGGCT-CGATTTAGCAATAAGGAACCACTTCCCAGT-TAGA
*
2603447 TTTTGA
194 TTTCGA
* * * * * * * *
2603453 CATAGCTTAAGTTAATAAGATCTATCTATCAACCAAAGATTTCAAGTTCGATTCCACTTAACTCG
1 CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAAGCTTTCAAGTTTGATTCCACTCAACTCG
** * ** * * * *
2603518 AGAGCACATTGACCGCATGGTAGCAACGACAAACTACCTTCT-AGTCAAAATTCAAACTAACGTC
66 AGAGCACATCAACCGCATGGTAGCAATGAGGAACTATCTTATGA-TCAAAATTCAAACTGAGGTC
* * * ** **** * * * * **
2603582 TTTAAG-TATAAAAGAATACCCAAATCAATTGCAATTTAGCAACAAGCAACTACTTCCCAACCTA
130 TTTAAGCCA-AGAAGAAGACCCAGGTTGGCT-CGATTTAGCAATAAGGAACCACTTCCC-AGTTA
*
2603646 GATGTCGA
192 GATTTCGA
* * * *
2603654 CGTAGCTTAAGTCAAGAAGAGCTATTTGACAACTAAAGCTTTCAAGTTT
1 CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAAGCTTTCAAGTTT
2603703 AACTCCATGA
Statistics
Matches: 520, Mismatches: 124, Indels: 15
0.79 0.19 0.02
Matches are distributed among these distances:
199 1 0.00
200 156 0.30
201 361 0.69
202 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (199 bp):
CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAAGCTTTCAAGTTTGATTCCACTCAACTCG
AGAGCACATCAACCGCATGGTAGCAATGAGGAACTATCTTATGATCAAAATTCAAACTGAGGTCT
TTAAGCCAAGAAGAAGACCCAGGTTGGCTCGATTTAGCAATAAGGAACCACTTCCCAGTTAGATT
TCGA
Found at i:2603668 original size:402 final size:401
Alignment explanation
Indices: 2602851--2603709 Score: 893
Period size: 402 Copynumber: 2.1 Consensus size: 401
2602841 TCATTTACAG
** * *
2602851 CATAGCTTAAGTTGAGAAGAGCCATATGTCAACCAAATCTTTCAAGTTTAATTCCATTCAACTCA
1 CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAATCTTTCAAGTTTAATTCCACTCAACTCA
* * * * * * * *
2602916 AAAGCACATTAACCTCATGGTAGCAATGAGGAATTATCTTTCTATCAAAATTCAAACTGAGGTCT
66 AAAGCACATCAACCGCATGGTAGCAATAAAGAACTACCTTACGATCAAAATTCAAACTGAGGTCT
** * *
2602981 TTAAGCCAAGAAGACTACCCAGGTTGGCTACGATTTAGCAATAATAAACCACTTCCCAGTTAGAT
131 TTAAGCCAAGAAGAAGACCCAGGTTGGCTACGATTTAGCAACAAGAAACCACTTCCCAGTTAGAT
* * * *
2603046 TTCGACATAACTTAAATCAAGAAGAGTTATATGTCAACCAAAGCTTTCAAGTTTGATTCTACTCA
196 TTCGACATAACTTAAATCAAGAAGAGTTATATATCAACCAAAGATTTCAAGTTCGATTCCACTCA
* ** * * *
2603111 ACTCGAGAGCACACCAACCACATGGTAGCAATGAGGAGCTATCTTATGATAAAAATTCAAACTGA
261 ACTCGAGAGCACACCAACCACATGGTAGCAACGACAAACTACCTTATGATAAAAATTCAAACTAA
* ** *** * * * * * *
2603176 TGTCTTTAAGCCAAAAAGAAGACCCATGTTGGCTTGCATTTGGCAATAAGGATCCAATTCTCAAT
326 CGTCTTTAAGCCAAAAAGAAGACCCATAATCAATTGCATTTAGCAACAAGCAACCAATTCCCAAC
*
2603241 TCAGATTTCAA
391 TCAGATGTCAA
** * *
2603252 CATAGCTTAAGTCAAGAAGAGCTATATGTTGACCAAAGT-TTTCAAGTTTGATTCCACTCAATTC
1 CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAA-TCTTTCAAGTTTAATTCCACTCAACTC
* * * * * *
2603316 GAGAGTAGATCGACCGCATGGTAGCAATAAAGAACTACCTTACGGTCAAAATTCAAACTGAGGTC
65 AAAAGCACATCAACCGCATGGTAGCAATAAAGAACTACCTTACGATCAAAATTCAAACTGAGGTC
* * * * * **
2603381 TTTAAGCCAAGAAGAAGACTCGGGTTGGCTGCGATTTAGCAACAAGGAACCACTTTCTTGTCTAG
130 TTTAAGCCAAGAAGAAGACCCAGGTTGGCTACGATTTAGCAACAAGAAACCACTTCCCAGT-TAG
* * * * * *
2603446 ATTTTGACATAGCTTAAGTTAATAAGA-TCTATCTATCAACCAAAGATTTCAAGTTCGATTCCAC
194 ATTTCGACATAACTTAAATCAAGAAGAGT-TATATATCAACCAAAGATTTCAAGTTCGATTCCAC
* *** * * *
2603510 TTAACTCGAGAGCACATTGACCGCATGGTAGCAACGACAAACTACCTTCT-AGTCAAAATTCAAA
258 TCAACTCGAGAGCACACCAACCACATGGTAGCAACGACAAACTACCTTATGA-TAAAAATTCAAA
* * * *
2603574 CTAACGTCTTTAAG-TATAAAAGAATACCCA-AATCAATTGCAATTTAGCAACAAGCAACTACTT
322 CTAACGTCTTTAAGCCA-AAAAGAAGACCCATAATCAATTGC-ATTTAGCAACAAGCAACCAATT
*
2603637 CCCAAC-CTAGATGTCGA
385 CCCAACTC-AGATGTCAA
* * * * * *
2603654 CGTAGCTTAAGTCAAGAAGAGCTATTTGACAACTAAAGCTTTCAAGTTTAACTCCA
1 CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAATCTTTCAAGTTTAATTCCA
2603710 TGACGGAGGA
Statistics
Matches: 367, Mismatches: 83, Indels: 15
0.79 0.18 0.03
Matches are distributed among these distances:
401 164 0.45
402 203 0.55
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (401 bp):
CATAGCTTAAGTCAAGAAGAGCTATATGTCAACCAAATCTTTCAAGTTTAATTCCACTCAACTCA
AAAGCACATCAACCGCATGGTAGCAATAAAGAACTACCTTACGATCAAAATTCAAACTGAGGTCT
TTAAGCCAAGAAGAAGACCCAGGTTGGCTACGATTTAGCAACAAGAAACCACTTCCCAGTTAGAT
TTCGACATAACTTAAATCAAGAAGAGTTATATATCAACCAAAGATTTCAAGTTCGATTCCACTCA
ACTCGAGAGCACACCAACCACATGGTAGCAACGACAAACTACCTTATGATAAAAATTCAAACTAA
CGTCTTTAAGCCAAAAAGAAGACCCATAATCAATTGCATTTAGCAACAAGCAACCAATTCCCAAC
TCAGATGTCAA
Found at i:2604846 original size:2 final size:2
Alignment explanation
Indices: 2604839--2604863 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2604829 ACGTATTCAT
2604839 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2604864 TTAATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2605008 original size:23 final size:23
Alignment explanation
Indices: 2604982--2605028 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2604972 ATATTATTAC
2604982 TTTTCGT-AATCTTAATTTTTATA
1 TTTTCGTGAAT-TTAATTTTTATA
* *
2605005 TTTTTGTGTATTTAATTTTTATA
1 TTTTCGTGAATTTAATTTTTATA
2605028 T
1 T
2605029 CTTTTAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.66
Consensus pattern (23 bp):
TTTTCGTGAATTTAATTTTTATA
Found at i:2606270 original size:16 final size:17
Alignment explanation
Indices: 2606245--2606277 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2606235 AACTATATAA
2606245 ATTATATTTTAA-AATT
1 ATTATATTTTAATAATT
*
2606261 ATTATTTTTTAATAATT
1 ATTATATTTTAATAATT
2606278 TTAGGTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATTTTAATAATT
Found at i:2609196 original size:16 final size:16
Alignment explanation
Indices: 2609175--2609206 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2609165 TGATGTTAAG
2609175 TTTAGTTCCTTAATTA
1 TTTAGTTCCTTAATTA
2609191 TTTAGTTCCTTAATTA
1 TTTAGTTCCTTAATTA
2609207 GTAGAAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAGTTCCTTAATTA
Found at i:2611197 original size:26 final size:25
Alignment explanation
Indices: 2611157--2611214 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
2611147 AAATAAATGA
*
2611157 TTTATATTATGTTATAAAATATATTT
1 TTTATATTATGTTATAAAACA-ATTT
*
2611183 TTTATATTGAT-TTATTAAACAATTT
1 TTTATATT-ATGTTATAAAACAATTT
2611208 TGTTATA
1 T-TTATA
2611215 ATTTTTGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 5 0.18
26 21 0.75
27 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (25 bp):
TTTATATTATGTTATAAAACAATTT
Found at i:2611769 original size:23 final size:23
Alignment explanation
Indices: 2611739--2611808 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
2611729 AGTCGAGGGT
2611739 TCTATGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
2611762 TCTATGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* * * *
2611785 CCTATGTGGTTCTTCAGTACAAA
1 TCTATGTGGTCCTTCGGGACAAA
2611808 T
1 T
2611809 ATGTGACACT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:2611820 original size:21 final size:22
Alignment explanation
Indices: 2611796--2611836 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2611786 CTATGTGGTT
2611796 CTTCAGTACAAA-TATGTGACA
1 CTTCAGTACAAATTATGTGACA
* *
2611817 CTTCGGTGCAAATTATGTGA
1 CTTCAGTACAAATTATGTGA
2611837 GCAGAGGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (22 bp):
CTTCAGTACAAATTATGTGACA
Found at i:2613271 original size:130 final size:130
Alignment explanation
Indices: 2612959--2613445 Score: 650
Period size: 131 Copynumber: 3.7 Consensus size: 130
2612949 AGAGAAAACA
* * * *
2612959 ATAATATCTAATTATTTCCAATAGAGAATATATGACCTTTCATGCCTTAAAACAATCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
* * * * * * * * *
2613024 CCCCAATTGAAATGAATAGATATCACTATTTCGCCTTAAAATTGAATATTGATTCGAGTGAAAAT
66 CTCCAATTGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAG-AAAAAT
2613089 G
130 G
* * *
2613090 ATAATATCTAATGATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTACTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
*
2613155 CTCCAATTGAATTGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGAAAAATG
66 CTCCAATTGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGAAAAATG
* * * *
2613220 ATAATATCTGATTATTTCCAATCGAGAATAAATGACCTATCATGCCTTAAAGTAGTCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
* *
2613285 CTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGAGAAAAC
66 CTCCAATTGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGA-AAAAT
2613350 G
130 G
* * * * *
2613351 GTAATATATAATTATTTCCAATCGAGAATAAATGACCTCTTATGCCTTAAAGTAGTCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
* ** ** *
2613416 CTTCAACCGAAATGTGGAGATATTACTATT
66 CTCCAATTGAAATGAAGAGATATCACTATT
2613446 TTCATTATCA
Statistics
Matches: 318, Mismatches: 37, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
130 121 0.38
131 197 0.62
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (130 bp):
ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
CTCCAATTGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGAAAAATG
Found at i:2613438 original size:261 final size:261
Alignment explanation
Indices: 2612959--2613445 Score: 677
Period size: 261 Copynumber: 1.9 Consensus size: 261
2612949 AGAGAAAACA
* *
2612959 ATAATATCTAATTATTTCCAATAGAGAATATATGACCTTTCATGCCTTAAAACAATCATTTATTA
1 ATAATATCTAATTATTTCCAATAGAGAATAAATGACCTATCATGCCTTAAAACAATCATTTATTA
* * * * * * * * *
2613024 CCCCAATTGAAATGAATAGATATCACTATTTCGCCTTAAAATTGAATATTGATTCGAGTGAAAAT
66 CCCCAATCGAAATGAAGAGATATCACTATTCCGCCTTAAAAATCAATATTAACTCGAGAGAAAAC
*
2613089 GATAATATCTAATGATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTACT
131 GATAATATATAATGATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTACT
** *
2613154 ACTCCAATTGAATTGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGAAAAAT
196 ACTCCAACCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGAAAAAT
2613219 G
261 G
* * ** *
2613220 ATAATATCTGATTATTTCCAATCGAGAATAAATGACCTATCATGCCTTAAAGTAGTCATTTATTA
1 ATAATATCTAATTATTTCCAATAGAGAATAAATGACCTATCATGCCTTAAAACAATCATTTATTA
* *
2613285 CTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGAGAAAAC
66 CCCCAATCGAAATGAAGAGATATCACTATTCCGCCTTAAAAATCAATATTAACTCGAGAGAAAAC
* * * * * * *
2613350 GGTAATATATAATTATTTCCAATCGAGAATAAATGACCTCTTATGCCTTAAAGTAGTCATTTATT
131 GATAATATATAATGATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTACT
* ** *
2613415 ACTTCAACCGAAATGTGGAGATATTACTATT
196 ACTCCAACCGAAATGAAGAGATATCACTATT
2613446 TTCATTATCA
Statistics
Matches: 193, Mismatches: 33, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
261 193 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (261 bp):
ATAATATCTAATTATTTCCAATAGAGAATAAATGACCTATCATGCCTTAAAACAATCATTTATTA
CCCCAATCGAAATGAAGAGATATCACTATTCCGCCTTAAAAATCAATATTAACTCGAGAGAAAAC
GATAATATATAATGATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTACT
ACTCCAACCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAACTCGAGAAAAAT
G
Found at i:2616162 original size:134 final size:135
Alignment explanation
Indices: 2615710--2616283 Score: 581
Period size: 134 Copynumber: 4.3 Consensus size: 135
2615700 TTCAGGGTAT
* * *
2615710 ATCAGAT-TAAGAAACATTGATTCATTCTACTGTTCTTCAGGGAAGATTGAATCGAGGCAA-ACT
1 ATCAGATAT-AGAGACATTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATCGAGG-AAGACT
** * * * * ** *
2615773 TGTTCCACTACTGCTCAGGGAAGATCAAATCTAGAAAGAAAGAA-GGATTTGTTCCGCTGTTTCT
64 TGTTCCACTGTTCCTCAGGGAAGATCAAATATAG-AA-AAAGAAGGGATCTATTCTACTGCTTCT
2615837 TGAGGGAAA
127 TGAGGGAAA
* * * * * **
2615846 ATCAGAT-TTGA-AAATGTTGATTCATTCCACTGTTCTTTAAGGAATATTGAACCGAGCTAGACT
1 ATCAGATATAGAGACA--TTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATCGAGGAAGACT
* * * * * * *
2615909 TGTTCCACTGTTCCTCAAGGAAGATAAAATATAGAAAAAG-GGGGATCTATTTTGCTGTTTATTG
64 TGTTCCACTGTTCCTCAGGGAAGATCAAATATAGAAAAAGAAGGGATCTATTCTACTGCTTCTTG
2615973 AGGG-AA
129 AGGGAAA
* * * * * * *
2615979 ATCAGATATGGGGACGTTGATTCATTCCACTATTCTTCAAGAAAGATTGAATTGAGGAAGGCTTG
1 ATCAGATATAGAGACATTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATCGAGGAAGACTTG
* * * * *
2616044 TTCCACTGTTTCTCAGGGAAGATCAAATCTAG-AAAAGAAGGTATTTGTTCCT-CTGCTTCTTGA
66 TTCCACTGTTCCTCAGGGAAGATCAAATATAGAAAAAGAAGGGATCTATT-CTACTGCTTCTTGA
2616107 GGGAAA
130 GGGAAA
* * * * *
2616113 ATCAGATATCGAGACATTGATTCATTCCACTGTTCTTCAGGGGAGATTGAATCGAGGTAGACTTA
1 ATCAGATATAGAGACATTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATCGAGGAAGACTTG
* *
2616178 TTCCACTGTTCCTCAGGGAAGATCAAATATGGAAAAAGAGGGGATCTATTCTACTGCTTCTTGAG
66 TTCCACTGTTCCTCAGGGAAGATCAAATATAGAAAAAGAAGGGATCTATTCTACTGCTTCTTGAG
2616243 GGAAA
131 GGAAA
* * * *
2616248 ATCAGATCTAGGGACATTGATTCGTTCCACTATTCT
1 ATCAGATATAGAGACATTGATTCATTCCACTGTTCT
2616284 GCGGAGAAAA
Statistics
Matches: 359, Mismatches: 68, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
132 5 0.01
133 96 0.27
134 117 0.33
135 67 0.19
136 74 0.21
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (135 bp):
ATCAGATATAGAGACATTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATCGAGGAAGACTTG
TTCCACTGTTCCTCAGGGAAGATCAAATATAGAAAAAGAAGGGATCTATTCTACTGCTTCTTGAG
GGAAA
Found at i:2616190 original size:267 final size:269
Alignment explanation
Indices: 2615723--2616283 Score: 747
Period size: 267 Copynumber: 2.1 Consensus size: 269
2615713 AGATTAAGAA
* * * *
2615723 ACATTGATTCATTCTACTGTTCTTCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTACTGCT
1 ACATTGATTCATTCCACTATTCTTCAAGAAAGATTGAATCGAGGCAAACTTGTTCCACTACTGCT
*
2615788 CAGGGAAGATCAAATCTAGAAAGAAAGAAGGATTTGTTCCGCTGTTTCTTGAGGGAAAATCAGAT
66 CAGGGAAGATCAAATCTAG-AAGAAAGAAGGATTTGTTCCGCTGCTTCTTGAGGGAAAATCAGAT
* * * *
2615853 TTGAAAATGTTGATTCATTCCACTGTTCTTTAAGGAATATTGAACCGAGCTAGACTTGTTCCACT
130 TCGAAAA-GTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAACCGAGCTAGACTTATTCCACT
* * *
2615918 GTTCCTCAAGGAAGATAAAATATAGAAAAAG-GGGGATCTATTTTGCTGTTTATTGAGGG-AAAT
194 GTTCCTCAAGGAAGATAAAATATAGAAAAAGAGGGGATCTATTCTACTGCTTATTGAGGGAAAAT
*
2615981 CAGATATGGGG
259 CAGATATAGGG
* * * ** *
2615992 ACGTTGATTCATTCCACTATTCTTCAAGAAAGATTGAATTGAGG-AAGGCTTGTTCCACTGTTTC
1 ACATTGATTCATTCCACTATTCTTCAAGAAAGATTGAATCGAGGCAA-ACTTGTTCCACTACTGC
*
2616056 TCAGGGAAGATCAAATCTAG-A-AAAGAAGGTATTTGTTCCTCTGCTTCTTGAGGGAAAATCAGA
65 TCAGGGAAGATCAAATCTAGAAGAAAGAAGG-ATTTGTTCCGCTGCTTCTTGAGGGAAAATCAGA
* * * * *
2616119 TATCGAGACA-TTGATTCATTCCACTGTTCTTCAGGGGAGATTGAATCGAGGTAGACTTATTCCA
129 T-TCGA-AAAGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAACCGAGCTAGACTTATTCCA
* * * *
2616183 CTGTTCCTCAGGGAAGATCAAATATGGAAAAAGAGGGGATCTATTCTACTGCTTCTTGAGGGAAA
192 CTGTTCCTCAAGGAAGATAAAATATAGAAAAAGAGGGGATCTATTCTACTGCTTATTGAGGGAAA
*
2616248 ATCAGATCTAGGG
257 ATCAGATATAGGG
*
2616261 ACATTGATTCGTTCCACTATTCT
1 ACATTGATTCATTCCACTATTCT
2616284 GCGGAGAAAA
Statistics
Matches: 254, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
266 8 0.03
267 110 0.43
268 29 0.11
269 107 0.42
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (269 bp):
ACATTGATTCATTCCACTATTCTTCAAGAAAGATTGAATCGAGGCAAACTTGTTCCACTACTGCT
CAGGGAAGATCAAATCTAGAAGAAAGAAGGATTTGTTCCGCTGCTTCTTGAGGGAAAATCAGATT
CGAAAAGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAACCGAGCTAGACTTATTCCACTGT
TCCTCAAGGAAGATAAAATATAGAAAAAGAGGGGATCTATTCTACTGCTTATTGAGGGAAAATCA
GATATAGGG
Found at i:2617564 original size:21 final size:21
Alignment explanation
Indices: 2617550--2617605 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 21
2617540 TTTTTGTTTC
*
2617550 TTTTTCATTCTTTTTCTCTCT
1 TTTTTCATTTTTTTTCTCTCT
*
2617571 TTTTTCATTTTTTTTCATTTTTCT
1 TTTTTCATTTTTTTTC---TCTCT
2617595 TTTTTCATTTT
1 TTTTTCATTTT
2617606 CAATTTCCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 15 0.50
24 15 0.50
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTCATTTTTTTTCTCTCT
Found at i:2617590 original size:10 final size:10
Alignment explanation
Indices: 2617550--2617592 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
2617540 TTTTTGTTTC
2617550 TTTTTCATTCT
1 TTTTTCATT-T
*
2617561 TTTTCTC-TCT
1 TTTT-TCATTT
2617571 TTTTTCATTT
1 TTTTTCATTT
2617581 TTTTTCATTT
1 TTTTTCATTT
2617591 TT
1 TT
2617593 CTTTTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 2 0.07
10 19 0.68
11 5 0.18
12 2 0.07
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:2628299 original size:131 final size:131
Alignment explanation
Indices: 2628123--2628623 Score: 612
Period size: 131 Copynumber: 3.8 Consensus size: 131
2628113 ATAATTTTAA
* * * *
2628123 GAGAGAAAACAATAATATCTAATT-TTTTCCAATCGAGAATAAATGACCTTTCCTGCCTTAAAAC
1 GAGAGAAAACGATAATATCTAATTATTTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * ** * *
2628187 AGTCATTTATTACCCCAATTGAAATGAAGATATATCACTATTTTTTCTTAAAATTCAATATTGAT
66 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAA-TCAATATTAAC
2628252 TC
130 TC
* * * * * * *
2628254 CAGTGAAAACGATAATAACTAATGATTTT-CAATCGAGAATGAATGACCTCTTATGCCTTAAAGT
1 GAGAGAAAACGATAATATCTAATTATTTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
*
2628318 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCAATATTTCGTCTTAGAAATCAATATTAAC
66 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTA-AAATCAATATTAAC
2628383 TC
130 TC
* * * *
2628385 GAGAGAAAACGGTAATATTTGATTA-TTTCCAATAGAGAATAAATGACCTCTCATGCCTTAAAGC
1 GAGAGAAAACGATAATATCTAATTATTTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * * * *
2628449 AGCCATTTAATACTCTAATCGAAAAGAAGAGATATCACTATTCCGTCTTAAAAATAAATATTAAC
66 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTT-AAAATCAATATTAAC
2628514 TC
130 TC
* * *
2628516 GAGAGAAAACGGTAATATCTGATTTTTTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
1 GAGAGAAAACGATAATATCTAATTATTTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * * * *
2628581 AATCATTTATTACTTCAACCAAAATGAGGAGATATTACTATTT
66 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTT
2628624 TCATTATCGA
Statistics
Matches: 314, Mismatches: 51, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
130 3 0.01
131 233 0.74
132 78 0.25
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAATCAATATTAACT
C
Found at i:2629259 original size:28 final size:28
Alignment explanation
Indices: 2629227--2629297 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
2629217 GACAAAGAAA
*
2629227 AAAATAAATAAAACATG-AGGGATAAATT
1 AAAATAAATAAAA-ATGCAGGGACAAATT
* * *
2629255 AAAATAAACTAAAATTGCATGGCCAAATT
1 AAAATAAA-TAAAAATGCAGGGACAAATT
2629284 AAAATAAATAAAAA
1 AAAATAAATAAAAA
2629298 AACATATTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (28 bp):
AAAATAAATAAAAATGCAGGGACAAATT
Found at i:2630670 original size:3 final size:3
Alignment explanation
Indices: 2630662--2630709 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
2630652 AATTAAAAAT
* * *
2630662 ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA AAA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2630710 TTATCGGGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2636720 original size:20 final size:20
Alignment explanation
Indices: 2636695--2636732 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2636685 TTGGGTTAGT
*
2636695 GTATCGATGTTGGATGAATA
1 GTATCGATGATGGATGAATA
2636715 GTATCGATGATGGATGAA
1 GTATCGATGATGGATGAA
2636733 ATGAGATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (20 bp):
GTATCGATGATGGATGAATA
Found at i:2645764 original size:23 final size:22
Alignment explanation
Indices: 2645738--2645780 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2645728 AGTAAAAACA
2645738 AATAAAATTAAAATTAATAAATT
1 AATAAAATTAAAA-TAATAAATT
*
2645761 AATAAATTTAAAATAATAAA
1 AATAAAATTAAAATAATAAA
2645781 AAATATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAAATTAAAATAATAAATT
Found at i:2647519 original size:18 final size:18
Alignment explanation
Indices: 2647496--2647542 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2647486 TATGAAATTA
2647496 TAGGGTTTATGTTCACAT
1 TAGGGTTTATGTTCACAT
2647514 TAGGGTTTATGTTCACAT
1 TAGGGTTTATGTTCACAT
*
2647532 TAGTGTTTATG
1 TAGGGTTTATG
2647543 GAATTGAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (18 bp):
TAGGGTTTATGTTCACAT
Found at i:2655505 original size:22 final size:22
Alignment explanation
Indices: 2655461--2655505 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2655451 CATTGTTTAT
* *
2655461 TATATATGATGTTTATCATGAA
1 TATACATGATGTTTATCACGAA
* *
2655483 TATACATGATGTTTTTTACGAA
1 TATACATGATGTTTATCACGAA
2655505 T
1 T
2655506 GTTATTTTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (22 bp):
TATACATGATGTTTATCACGAA
Found at i:2655739 original size:59 final size:59
Alignment explanation
Indices: 2655664--2655827 Score: 224
Period size: 59 Copynumber: 2.8 Consensus size: 59
2655654 GGGGTTGCAT
* * *
2655664 TAAAGTATAACTAGTGCATATGGTGGGCAAGACCTTATGTGTCATATTAAG-GATTATAC
1 TAAAGTATAACTAGTGCATATGGTGGGCAAGACCTTATGTGTCATATT-AGCGACTACAA
* * * *
2655723 TAAAGTATGACTAGTGCATATGGTGGGCACGACCTTATGTGTCATATTTGCGACTGCAA
1 TAAAGTATAACTAGTGCATATGGTGGGCAAGACCTTATGTGTCATATTAGCGACTACAA
*
2655782 TAAAGTATAACTAGTGCAGATGGTGGG-AACGACCTTATGTGTCATA
1 TAAAGTATAACTAGTGCATATGGTGGGCAA-GACCTTATGTGTCATA
2655828 CTCGGGTTAG
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.02
59 91 0.98
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (59 bp):
TAAAGTATAACTAGTGCATATGGTGGGCAAGACCTTATGTGTCATATTAGCGACTACAA
Done.