Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 39
Found at i:6102182 original size:23 final size:23
Alignment explanation
Indices: 6102149--6102211 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
6102139 ATTATTATAT
*
6102149 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACAC
* *
6102172 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACAC
*
6102195 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
6102212 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACAC
Found at i:6105982 original size:34 final size:34
Alignment explanation
Indices: 6105919--6106011 Score: 89
Period size: 34 Copynumber: 2.7 Consensus size: 34
6105909 AATGGTAATA
* * *
6105919 AACAAAATTATCAAAATAAATTAAGAAAAAGTCC
1 AACAAAATAAACAAAATAAATTAAGAAAAAATCC
* * *
6105953 AATAAAATAAACAAAATAAATTTTA-AAAAAATTC
1 AACAAAATAAACAAAATAAA-TTAAGAAAAAATCC
* * *
6105987 AACCAAATTAACAAAATAAAGTAAG
1 AACAAAATAAACAAAATAAATTAAG
6106012 TATTTAATGA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
33 2 0.04
34 41 0.89
35 3 0.07
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.22
Consensus pattern (34 bp):
AACAAAATAAACAAAATAAATTAAGAAAAAATCC
Found at i:6106213 original size:9 final size:9
Alignment explanation
Indices: 6106196--6106234 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
6106186 TCATCATCAC
*
6106196 CATCATCGT
1 CATCGTCGT
*
6106205 CGTCGTCGT
1 CATCGTCGT
6106214 CATCGTCGT
1 CATCGTCGT
6106223 CATCGTCGT
1 CATCGTCGT
6106232 CAT
1 CAT
6106235 GAGCAGATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.13, C:0.33, G:0.21, T:0.33
Consensus pattern (9 bp):
CATCGTCGT
Found at i:6108315 original size:16 final size:16
Alignment explanation
Indices: 6108291--6108337 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
6108281 TATATATGTA
*
6108291 AAAAAATTAATTAAAT
1 AAAATATTAATTAAAT
*
6108307 AAAATATTAATAAAAT
1 AAAATATTAATTAAAT
* *
6108323 TAAAT-TTAAATAAAT
1 AAAATATTAATTAAAT
6108338 TACTAACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATATTAATTAAAT
Found at i:6110682 original size:18 final size:17
Alignment explanation
Indices: 6110654--6110692 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
6110644 GGACAAATGT
6110654 GATATGTGGTCCTTCGG
1 GATATGTGGTCCTTCGG
6110671 GATATAGTGGTCCTTCGG
1 GATAT-GTGGTCCTTCGG
6110689 GATA
1 GATA
6110693 AATATTCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (17 bp):
GATATGTGGTCCTTCGG
Found at i:6111006 original size:45 final size:46
Alignment explanation
Indices: 6110957--6111056 Score: 105
Period size: 45 Copynumber: 2.2 Consensus size: 46
6110947 TGTATTTCTT
* * *
6110957 TATGAAATGATAGATAATCACATATGTACATGTGTGGA-TTTGATA
1 TATGAAATGAAAGATAATCACATATGTACATGTATGCATTTTGATA
* *** *
6111002 TATG-AATAGAAATATAATGGTATATGTGCATGTATGCATTTTGATA
1 TATGAAAT-GAAAGATAATCACATATGTACATGTATGCATTTTGATA
6111048 TATGAAATG
1 TATGAAATG
6111057 TTTTATGGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
44 3 0.07
45 26 0.59
46 12 0.27
47 3 0.07
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (46 bp):
TATGAAATGAAAGATAATCACATATGTACATGTATGCATTTTGATA
Found at i:6111440 original size:21 final size:22
Alignment explanation
Indices: 6111416--6111463 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
6111406 AGCAGTACTG
6111416 TAGCA-GGGAATCGGTACCCTA
1 TAGCAGGGGAATCGGTACCCTA
*
6111437 TAGCAGGGGAATCGGTACCCTG
1 TAGCAGGGGAATCGGTACCCTA
6111459 TAGCA
1 TAGCA
6111464 ATCTGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (22 bp):
TAGCAGGGGAATCGGTACCCTA
Found at i:6122075 original size:11 final size:10
Alignment explanation
Indices: 6122049--6122107 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
6122039 TCACTTTTTA
6122049 AAAAATAAAT
1 AAAAATAAAT
*
6122059 ACAAATACAAT
1 AAAAATA-AAT
*
6122070 AAAAATGAATT
1 AAAAAT-AAAT
*
6122081 AAAAATGAAT
1 AAAAATAAAT
* *
6122091 AAAATTCAAT
1 AAAAATAAAT
6122101 AAAAATA
1 AAAAATA
6122108 TAATGTAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
10 21 0.55
11 16 0.42
12 1 0.03
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:6123390 original size:12 final size:11
Alignment explanation
Indices: 6123343--6123394 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 11
6123333 TTAGCTTTAC
*
6123343 ATTATATGTTT
1 ATTATATTTTT
6123354 ATTGA-A-TTTT
1 ATT-ATATTTTT
6123364 ATT-TATTTTT
1 ATTATATTTTT
6123374 ATTATATTTTT
1 ATTATATTTTT
6123385 ATT-TATTTTT
1 ATTATATTTTT
6123395 TAAAAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 1 0.03
10 20 0.56
11 14 0.39
12 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (11 bp):
ATTATATTTTT
Found at i:6123394 original size:10 final size:10
Alignment explanation
Indices: 6123360--6123394 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
6123350 GTTTATTGAA
6123360 TTTTATTTAT
1 TTTTATTTAT
6123370 TTTTATTATAT
1 TTTTATT-TAT
6123381 TTTTATTTAT
1 TTTTATTTAT
6123391 TTTT
1 TTTT
6123395 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:6123395 original size:11 final size:11
Alignment explanation
Indices: 6123360--6123396 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6123350 GTTTATTGAA
6123360 TTTTATTTA-T
1 TTTTATTTATT
6123370 TTTTA-TTATAT
1 TTTTATTTAT-T
6123381 TTTTATTTATT
1 TTTTATTTATT
6123392 TTTTA
1 TTTTA
6123397 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.12
10 5 0.21
11 12 0.50
12 4 0.17
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:6124226 original size:22 final size:20
Alignment explanation
Indices: 6124192--6124243 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
6124182 ATAATTATTT
*
6124192 AAAAAATTAAATAAAAATATA
1 AAAAAATTTAATAAAAA-ATA
6124213 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTTAATAAAAAATA
6124234 AAAAAATTTA
1 AAAAAATTTA
6124244 GGTTGAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 5 0.17
21 13 0.45
22 11 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAAATTTAATAAAAAATA
Found at i:6124230 original size:23 final size:21
Alignment explanation
Indices: 6124192--6124240 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
6124182 ATAATTATTT
6124192 AAAAA-ATTAAATAAAAATATA
1 AAAAATATTAAATAAAAATA-A
*
6124213 AAAAATATTTAATAAAAAATAA
1 AAAAATATTAAAT-AAAAATAA
6124235 AAAAAT
1 AAAAAT
6124241 TTAGGTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 13 0.52
23 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATATTAAATAAAAATAA
Found at i:6128363 original size:17 final size:18
Alignment explanation
Indices: 6128343--6128383 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6128333 AAATTATATT
6128343 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
6128360 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
6128378 ATTAAA
1 AGTAAA
6128384 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:6128438 original size:12 final size:12
Alignment explanation
Indices: 6128423--6128454 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
6128413 AACTTAAATA
6128423 GAGAGAATATTT
1 GAGAGAATATTT
6128435 GAGAG-A-ATTT
1 GAGAGAATATTT
6128445 GAGAGAATAT
1 GAGAGAATAT
6128455 GGTGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.50
11 2 0.11
12 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (12 bp):
GAGAGAATATTT
Found at i:6128529 original size:22 final size:23
Alignment explanation
Indices: 6128483--6128537 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
6128473 GATGATGAGA
6128483 TATTTATAGGGAGGTTAGGGGGG
1 TATTTATAGGGAGGTTAGGGGGG
*
6128506 TATTTATAGGGAGGTT-TGGGGG
1 TATTTATAGGGAGGTTAGGGGGG
6128528 TATTTATAGG
1 TATTTATAGG
6128538 TATAGCGCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (23 bp):
TATTTATAGGGAGGTTAGGGGGG
Found at i:6138532 original size:41 final size:41
Alignment explanation
Indices: 6138319--6138780 Score: 436
Period size: 41 Copynumber: 11.3 Consensus size: 41
6138309 ACATGTGCTA
* * *
6138319 TAGTGGCGTTTTTTTA-AAACGCCGCTAAATACTCATA-TT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
6138358 TAGTGGCG--TTTATATAAACGTCGCTAAAGA-TTGTAATT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
6138396 TAGTGGGGGTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * * *
6138437 TAGTGGCGTTTTTTTGTACAAACGCCGCTAAA-AATGAGTTCAT
1 TAGTGGCG--TTTTTATACAAACGCCGCTAAAGACT-CGTACTT
* * * * *
6138480 TATTGGTGTTTTTGTACAAACGTCGTTAACA-ACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAA-AGACTCGTACTT
* ** * *
6138521 TAGTGGCGTTTTTTGTACAAACGCCGCTAAA-ACGAGTTCAT
1 TAGTGGCG-TTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
6138562 TAGTGGCGTTTTTGTACAAACGCCGCTAACGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * * *
6138603 TAGTGGTGTTTGTGTTTACAAATGCTGCTAAAGACTCGTAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
* * * *
6138646 CAGTGGCGTTTTTATATAAACGCCGCTATAGACTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
6138687 CAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * *
6138728 CAGTGGTGTTTTTTATACAAACGCCGCTAAAGACTTGTACTT
1 TAGTGGCG-TTTTTATACAAACGCCGCTAAAGACTCGTACTT
6138770 TAGTGGCGTTT
1 TAGTGGCGTTT
6138781 GTAAACACAA
Statistics
Matches: 347, Mismatches: 62, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
37 8 0.02
38 22 0.06
39 8 0.02
40 41 0.12
41 142 0.41
42 63 0.18
43 63 0.18
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:6138640 original size:125 final size:125
Alignment explanation
Indices: 6138320--6138780 Score: 398
Period size: 125 Copynumber: 3.7 Consensus size: 125
6138310 CATGTGCTAT
* * * * * * *
6138320 AGTGGCGTTTTTTTA-AAACGCCGCTAAATACTCATA-TTTAGTGGCG---TTTATATAAACGTC
1 AGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTCAGTGGTGTTTTTTATACAAACGCC
* * ** * *
6138380 GCTAAAGA-TTGTAATTTAGTGG-GGGTTTTATACAAACGCCGCTA-AAGACTCGTACTTT
66 GCTAAAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAA-ACTCATACTTC
* * * * * *
6138438 AGTGGCGTTTTTTTGTACAAACGCCGCTAAA-AATGAGTTCATT-ATTGGTG-TTTTTGTACAAA
1 AGTGGCG--TTTTTATACAAACGCCGCTAAAGACT-CGTAC-TTCAGTGGTGTTTTTTATACAAA
* * * * *
6138500 CGTCGTTAACA-ACTCGTACTTTAGTGGCGTTTTTTGTACAAACGCCGCTA-AAAC-GAGTTCAT
62 CGCCGCTAA-AGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAAACTCA-TAC-T
6138562 T-
124 TC
* * * *
6138563 AGTGGCGTTTTTGTACAAACGCCGCTAACGACTCGTACTTTAGTGGTGTTTGTGTT-TACAAATG
1 AGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTCAGTGGTGTTT-T-TTATACAAACG
* * * * *
6138627 CTGCTAAAGACTCGTAATTCAGTGGCG-TTTTTATATAAACGCCGCTATAGACTCATACTTC
64 CCGCTAAAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAAACTCATACTTC
*
6138688 AGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTACTTCAGTGGTGTTTTTTATACAAACGCC
1 AGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTCAGTGGTGTTTTTTATACAAACGCC
*
6138753 GCTAAAGACTTGTACTTTAGTGGCGTTT
66 GCTAAAGACTCGTACTTTAGTGGCGTTT
6138781 GTAAACACAA
Statistics
Matches: 276, Mismatches: 43, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
118 7 0.03
120 9 0.03
121 14 0.05
122 7 0.03
123 34 0.12
124 73 0.26
125 106 0.38
126 26 0.09
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (125 bp):
AGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTCAGTGGTGTTTTTTATACAAACGCC
GCTAAAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAAACTCATACTTC
Found at i:6138694 original size:166 final size:164
Alignment explanation
Indices: 6138319--6138782 Score: 471
Period size: 166 Copynumber: 2.8 Consensus size: 164
6138309 ACATGTGCTA
* *
6138319 TAGTGGCGTTTTTTTAAAACGCCGCTAAATACTCATA-TTTAGTGGCG--TTTATATAAACGTCG
1 TAGTGGCGTTTTTATAAAACGCCGCTAAA-ACTCATACTTTAGTGGCGTTTTTATACAAACGTCG
* * * *
6138381 CT-AAA-GATTGTAATTTAGTGGGGGTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGC
65 CTAAAACGAGT-TCA-TTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGC
* *
6138444 GTTT-TTTTGTACAAACGCCGCTAAAAATGAGTTCAT
128 GTTTGTGTTGTACAAACGCCGCTAAAAATGAGTTAAT
* * * * * * * *
6138480 TATTGGTGTTTTTGTACAAACGTCGTTAACAACTCGTACTTTAGTGGCGTTTTTTGTACAAACGC
1 TAGTGGCGTTTTTATA-AAACGCCGCTAA-AACTCATACTTTAGTGGCG-TTTTTATACAAACGT
* * *
6138545 CGCTAAAACGAGTTCATTAGTGGCGTTTTTGTACAAACGCCGCTAACGACTCGTACTTTAGTGGT
63 CGCTAAAACGAGTTCATTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGC
* * * *
6138610 GTTTGTGTT-TACAAATGCTGCTAAAGACT-CG-TAAT
128 GTTTGTGTTGTACAAACGCCGCTAAA-AATGAGTTAAT
* *
6138645 TCAGTGGCGTTTTTATATAAACGCCGCTATAGACTCATACTTCAGTGGCGTTTTTATACAAACGT
1 T-AGTGGCGTTTTTATA-AAACGCCGCTA-AAACTCATACTTTAGTGGCGTTTTTATACAAACGT
** * * *
6138710 CGCTAAAGACTCGTAC-TTCAGTGGTGTTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
63 CGCTAAA-ACGAGTTCATT-AGTGGCG-TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
6138774 GGCGTTTGT
125 GGCGTTTGT
6138783 AAACACAAAC
Statistics
Matches: 247, Mismatches: 41, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
161 13 0.05
162 16 0.06
163 11 0.04
165 26 0.11
166 125 0.51
167 53 0.21
168 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (164 bp):
TAGTGGCGTTTTTATAAAACGCCGCTAAAACTCATACTTTAGTGGCGTTTTTATACAAACGTCGC
TAAAACGAGTTCATTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTT
TGTGTTGTACAAACGCCGCTAAAAATGAGTTAAT
Found at i:6141254 original size:42 final size:40
Alignment explanation
Indices: 6141193--6141304 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 40
6141183 TAATTAGCGG
6141193 CGTTTGTATCCACAAACGCCGCTATAGATATTGACCTTTTGTGA
1 CGTTTGT-TCCA-AAACGCCGCTATAGATATTGA-CTTTT-TGA
*
6141237 CGTTTGTTCCAAAACGCCGCTATAGCTATTGACTTTTTGA
1 CGTTTGTTCCAAAACGCCGCTATAGATATTGACTTTTTGA
* * * *
6141277 GGCTCGTTCCAAAAACGCAGCTATAGAT
1 CGTTTGTTCC-AAAACGCCGCTATAGAT
6141305 CTTCCTTTCG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
40 10 0.16
41 20 0.33
42 20 0.33
43 4 0.07
44 7 0.11
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (40 bp):
CGTTTGTTCCAAAACGCCGCTATAGATATTGACTTTTTGA
Found at i:6149919 original size:21 final size:21
Alignment explanation
Indices: 6149895--6149935 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6149885 CCATAACATG
*
6149895 GGGTATCGATACCCCTTCATA
1 GGGTATCGATACACCTTCATA
*
6149916 GGGTATCGGTACACCTTCAT
1 GGGTATCGATACACCTTCAT
6149936 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACACCTTCATA
Found at i:6150004 original size:20 final size:20
Alignment explanation
Indices: 6149979--6150049 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
6149969 TGCAGCCAGG
6149979 GTGTAT-GGATACACTGCAGA
1 GTGTATCGG-TACACTGCAGA
6149999 GTGTATCGGTACAC--C--A
1 GTGTATCGGTACACTGCAGA
*
6150015 GTGTAT-GGATACACTGCAGG
1 GTGTATCGG-TACACTGCAGA
6150035 GTGTATCGGTACACT
1 GTGTATCGGTACACT
6150050 AATTACATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
15 2 0.05
16 12 0.28
18 2 0.05
20 23 0.53
21 4 0.09
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (20 bp):
GTGTATCGGTACACTGCAGA
Found at i:6150019 original size:16 final size:17
Alignment explanation
Indices: 6149998--6150048 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
6149988 TACACTGCAG
6149998 AGTGTATCGGTACAC-C
1 AGTGTATCGGTACACGC
6150014 AGTGTAT-GGATACACTGC
1 AGTGTATCGG-TACAC-GC
6150032 AGGGTGTATCGGTACAC
1 A--GTGTATCGGTACAC
6150049 TAATTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
18 2 0.07
20 11 0.38
21 2 0.07
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (17 bp):
AGTGTATCGGTACACGC
Found at i:6150026 original size:36 final size:36
Alignment explanation
Indices: 6149979--6150148 Score: 142
Period size: 36 Copynumber: 4.9 Consensus size: 36
6149969 TGCAGCCAGG
6149979 GTGTATGGATACACTGCAGAGTGTATCGGTACACCA
1 GTGTATGGATACACTGCAGAGTGTATCGGTACACCA
*
6150015 GTGTATGGATACACTGCAGGGTGTATCGGTACA-C-
1 GTGTATGGATACACTGCAGAGTGTATCGGTACACCA
* * * * * * * **
6150049 -T-AAT---TACA-TTCGGTGTTTGAGCAGT-CATAA
1 GTGTATGGATACACTGCAGAGTGT-ATCGGTACACCA
* *
6150079 GGGTATGGATACACTGCAGTGTGTATCGGTACACCA
1 GTGTATGGATACACTGCAGAGTGTATCGGTACACCA
* *
6150115 ATGTATGGATACACTGCAGAGTGTATTGGTACAC
1 GTGTATGGATACACTGCAGAGTGTATCGGTACAC
6150149 TTTAGCATTT
Statistics
Matches: 102, Mismatches: 22, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
28 8 0.08
29 8 0.08
32 4 0.04
33 1 0.01
35 9 0.09
36 72 0.71
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (36 bp):
GTGTATGGATACACTGCAGAGTGTATCGGTACACCA
Found at i:6150111 original size:20 final size:18
Alignment explanation
Indices: 6150081--6150149 Score: 54
Period size: 20 Copynumber: 3.7 Consensus size: 18
6150071 AGTCATAAGG
6150081 GTATGGATACACTGCAGTGT
1 GTATGG-TACACTGCAG-GT
*
6150101 GTATCGGTACAC--CA-AT
1 GTAT-GGTACACTGCAGGT
6150117 GTATGGATACACTGCAGAGT
1 GTATGG-TACACTGCAG-GT
6150137 GTATTGGTACACT
1 GTA-TGGTACACT
6150150 TTAGCATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
15 2 0.05
16 10 0.25
18 4 0.10
20 19 0.47
21 5 0.12
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GTATGGTACACTGCAGGT
Found at i:6150582 original size:29 final size:28
Alignment explanation
Indices: 6150549--6150731 Score: 143
Period size: 29 Copynumber: 6.2 Consensus size: 28
6150539 TTATAATTAC
*
6150549 AAGGACCAGAATAGGAAAATAGAAACTTA
1 AAGGACCA-AATAGAAAAATAGAAACTTA
* * * *
6150578 AAGGACCAAAATAGTACAAACAGGAATTTA
1 AAGGACC-AAATAG-AAAAATAGAAACTTA
* *
6150608 AAGGTCCAAATTAAAAAAATAGAAACTTA
1 AAGGACCAAA-TAGAAAAATAGAAACTTA
* * * *
6150637 AGGGACTAGAAAACAAAAATAGAAACTTA
1 AAGGACCA-AATAGAAAAATAGAAACTTA
* *
6150666 AGGGACTAAAATAGGAAAAATAGAAACTTA
1 AAGGAC-CAAATA-GAAAAATAGAAACTTA
*
6150696 AAGGGA-TAAATAGAAAAAAATAGAAACTTA
1 AA-GGACCAAATAG--AAAAATAGAAACTTA
6150726 AAGGAC
1 AAGGAC
6150732 TAAAATAGTA
Statistics
Matches: 123, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
28 1 0.01
29 64 0.52
30 55 0.45
31 3 0.02
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.16
Consensus pattern (28 bp):
AAGGACCAAATAGAAAAATAGAAACTTA
Found at i:6150713 original size:88 final size:89
Alignment explanation
Indices: 6150564--6150733 Score: 218
Period size: 88 Copynumber: 1.9 Consensus size: 89
6150554 CCAGAATAGG
* * * * **
6150564 AAAATAGAAACTTAAAGGACCAAAATAGTACAAACAGGAATTTAAAGGTCCAAATT-AAAAAAAT
1 AAAATAGAAACTTAAAGGACCAAAATAGGAAAAACAGAAACTTAAAGGGACAAATTAAAAAAAAT
*
6150628 AGAAACTTAAGGGACTAGAAAACA
66 AGAAACTTAAAGGACTAGAAAACA
* * * *
6150652 AAAATAGAAACTTAAGGGACTAAAATAGGAAAAATAGAAACTTAAAGGGATAAA-TAGAAAAAAA
1 AAAATAGAAACTTAAAGGACCAAAATAGGAAAAACAGAAACTTAAAGGGACAAATTA-AAAAAAA
6150716 TAGAAACTTAAAGGACTA
65 TAGAAACTTAAAGGACTA
6150734 AAATAGTAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
87 1 0.01
88 44 0.64
89 24 0.35
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.17
Consensus pattern (89 bp):
AAAATAGAAACTTAAAGGACCAAAATAGGAAAAACAGAAACTTAAAGGGACAAATTAAAAAAAAT
AGAAACTTAAAGGACTAGAAAACA
Found at i:6150718 original size:60 final size:59
Alignment explanation
Indices: 6150622--6150739 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 59
6150612 TCCAAATTAA
* *
6150622 AAAAATAGAAACTTAAGGGACTAGAAAACAAAAATAGAAACTTAAGGGACTAAAATAGG
1 AAAAATAGAAACTTAAGGGACTAGAAAAAAAAAATAGAAACTTAAAGGACTAAAATAGG
6150681 AAAAATAGAAACTTAAAGGGA-TA-AATAGAAAAAAATAGAAACTTAAAGGACTAAAATAG
1 AAAAATAGAAACTT-AAGGGACTAGAA-A-AAAAAAATAGAAACTTAAAGGACTAAAATAG
6150740 TAATTACAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
58 2 0.04
59 17 0.31
60 35 0.65
ACGTcount: A:0.60, C:0.07, G:0.17, T:0.16
Consensus pattern (59 bp):
AAAAATAGAAACTTAAGGGACTAGAAAAAAAAAATAGAAACTTAAAGGACTAAAATAGG
Found at i:6151448 original size:64 final size:65
Alignment explanation
Indices: 6151240--6151449 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 65
6151230 TTTTTCAGAG
* * * **
6151240 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG--AACATCGAATGC
1 TGATGCATCGATGCACCAA-CCACGCATCGATGCACTCA-GGATTTTA-TGAAAACATCGAATGC
6151302 ATT
63 ATT
* ** * *
6151305 TCATGCATCGATGCACTTACCATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATT
1 TGATGCATCGATGCACCAACCACGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCATT
* * * *
6151370 TGATGCATCGATGCACCAACCACGTATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCAC
1 TGATGCATCGATGCACCAACCACGCATCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCAT
6151433 T
65 T
6151434 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
6151450 TTTTAGTGCA
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.02
64 52 0.42
65 67 0.54
66 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACCAACCACGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCATT
Found at i:6159454 original size:65 final size:65
Alignment explanation
Indices: 6159283--6159483 Score: 189
Period size: 65 Copynumber: 3.1 Consensus size: 65
6159273 TTTTCAGAGT
* ** * * *
6159283 GATGCACCA-ATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCAAATCCATTTTATGC
1 GATGCACCATA-CCATGCATCGATGCACTCA-GGATTTTA-TGAAACATCGAATGCATTTGATGC
6159345 ATC
63 ATC
*
6159348 GATGCA-CATACCATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCAT
1 GATGCACCATACCATGCATCGATGCACTCAGGATTTTATG-AAACATCGAATGCATTTGATGCAT
6159412 C
65 C
* * * * * *
6159413 GATGCACCA-GCTATGCATCGATGCACTCTGGCTATTT-TGAAATATCGAATGCACTTGATGCAT
1 GATGCACCATACCATGCATCGATGCACTCAGGAT-TTTATGAAACATCGAATGCATTTGATGCAT
6159476 C
65 C
*
6159477 AATGCAC
1 GATGCAC
6159484 TTTTAGTGCA
Statistics
Matches: 115, Mismatches: 15, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
63 2 0.02
64 52 0.45
65 56 0.49
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (65 bp):
GATGCACCATACCATGCATCGATGCACTCAGGATTTTATGAAACATCGAATGCATTTGATGCATC
Found at i:6166222 original size:20 final size:20
Alignment explanation
Indices: 6166197--6166236 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6166187 GCAGTACTTG
6166197 CATTGGTGGCTAGTTGGGAT
1 CATTGGTGGCTAGTTGGGAT
6166217 CATTGGTGGCTAGTTGGGAT
1 CATTGGTGGCTAGTTGGGAT
6166237 TTGCATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.40, T:0.35
Consensus pattern (20 bp):
CATTGGTGGCTAGTTGGGAT
Found at i:6167552 original size:22 final size:22
Alignment explanation
Indices: 6167524--6167567 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6167514 AGCTCGATCT
6167524 CGACTCGAGTTCTTAACGAGCC
1 CGACTCGAGTTCTTAACGAGCC
6167546 CGACTCGAGTTCTTAACGAGCC
1 CGACTCGAGTTCTTAACGAGCC
6167568 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.23
Consensus pattern (22 bp):
CGACTCGAGTTCTTAACGAGCC
Found at i:6167575 original size:21 final size:22
Alignment explanation
Indices: 6167529--6167575 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
6167519 GATCTCGACT
**
6167529 CGAGTTCTTAACGAGCCCGACT
1 CGAGTTCTTAACGAGCCCGAAA
6167551 CGAGTTCTTAACGAG-CCGAAA
1 CGAGTTCTTAACGAGCCCGAAA
6167572 CGAG
1 CGAG
6167576 CTACTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
CGAGTTCTTAACGAGCCCGAAA
Found at i:6167664 original size:14 final size:14
Alignment explanation
Indices: 6167645--6167674 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6167635 TTTAGATTTT
*
6167645 TTAAAATTACATTA
1 TTAAAAATACATTA
6167659 TTAAAAATACATTA
1 TTAAAAATACATTA
6167673 TT
1 TT
6167675 GATGATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:6169233 original size:21 final size:21
Alignment explanation
Indices: 6169207--6169305 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
6169197 AGATTACACC
6169207 CTAAACCCTTAATCCTAAACT
1 CTAAACCCTTAATCCTAAACT
* *
6169228 CTAAA-CTTTAAACCTTAAAC-
1 CTAAACCCTTAATCC-TAAACT
* *
6169248 CTTAAATCCTAAATCCTAAACT
1 C-TAAACCCTTAATCCTAAACT
* * *
6169270 ATAAACCCCTAAGTCCTAAACC
1 CTAAACCCTTAA-TCCTAAACT
6169292 CTAAACCCTTAATC
1 CTAAACCCTTAATC
6169306 TAATTATATG
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
20 8 0.13
21 29 0.48
22 24 0.39
ACGTcount: A:0.40, C:0.31, G:0.01, T:0.27
Consensus pattern (21 bp):
CTAAACCCTTAATCCTAAACT
Found at i:6169247 original size:35 final size:35
Alignment explanation
Indices: 6169208--6169276 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
6169198 GATTACACCC
*
6169208 TAAACCCTT-AATCCTAAA-CTCTAAACTTTAAACCT
1 TAAA-CCTTAAATCCTAAATC-CTAAACTATAAACCT
6169243 TAAACCTTAAATCCTAAATCCTAAACTATAAACC
1 TAAACCTTAAATCCTAAATCCTAAACTATAAACC
6169277 CCTAAGTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 4 0.13
35 26 0.84
36 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.29
Consensus pattern (35 bp):
TAAACCTTAAATCCTAAATCCTAAACTATAAACCT
Found at i:6169286 original size:22 final size:22
Alignment explanation
Indices: 6169255--6169299 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6169245 AACCTTAAAT
*
6169255 CCTAAATCCTAAACTATAAACC
1 CCTAAATCCTAAACCATAAACC
* *
6169277 CCTAAGTCCTAAACCCTAAACC
1 CCTAAATCCTAAACCATAAACC
6169299 C
1 C
6169300 TTAATCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.38, G:0.02, T:0.20
Consensus pattern (22 bp):
CCTAAATCCTAAACCATAAACC
Found at i:6169294 original size:7 final size:7
Alignment explanation
Indices: 6169204--6169300 Score: 68
Period size: 7 Copynumber: 13.7 Consensus size: 7
6169194 TTTAGATTAC
6169204 ACCCTAA
1 ACCCTAA
*
6169211 ACCCTTA
1 ACCCTAA
*
6169218 ATCCTAA
1 ACCCTAA
*
6169225 ACTCTAA
1 ACCCTAA
**
6169232 ACTTTAA
1 ACCCTAA
*
6169239 ACCTTAA
1 ACCCTAA
*
6169246 ACCTTAA
1 ACCCTAA
*
6169253 ATCCTAA
1 ACCCTAA
*
6169260 ATCCTAA
1 ACCCTAA
**
6169267 ACTATAA
1 ACCCTAA
6169274 ACCCCTAA
1 A-CCCTAA
**
6169282 GTCCTAA
1 ACCCTAA
6169289 ACCCTAA
1 ACCCTAA
6169296 ACCCT
1 ACCCT
6169301 TAATCTAATT
Statistics
Matches: 71, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
7 67 0.94
8 4 0.06
ACGTcount: A:0.40, C:0.33, G:0.01, T:0.26
Consensus pattern (7 bp):
ACCCTAA
Found at i:6171629 original size:30 final size:31
Alignment explanation
Indices: 6171593--6171653 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
6171583 GGAACTTAAT
6171593 TTGACATGTTGC-AATCTTTTGTAAGTAAAC
1 TTGACATGTTGCTAATCTTTTGTAAGTAAAC
*
6171623 TTGACATGTTGCTGTCATCTTTTGTAAGTAA
1 TTGACATGTTGC--TAATCTTTTGTAAGTAA
6171654 GCTTAACTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.44
33 15 0.56
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (31 bp):
TTGACATGTTGCTAATCTTTTGTAAGTAAAC
Found at i:6171679 original size:33 final size:33
Alignment explanation
Indices: 6171606--6171681 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
6171596 ACATGTTGCA
* * *
6171606 ATCTTTTGTAAGTAAACTTGACATGTTGCTGTC
1 ATCTTTTGTAAGTAAACTTAACATGTTGATATC
*
6171639 ATCTTTTGTAAGTAAGCTTAAC-TGGTTGATATC
1 ATCTTTTGTAAGTAAACTTAACAT-GTTGATATC
*
6171672 ATTTTTTGTA
1 ATCTTTTGTA
6171682 TTATTTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (33 bp):
ATCTTTTGTAAGTAAACTTAACATGTTGATATC
Found at i:6171768 original size:19 final size:19
Alignment explanation
Indices: 6171746--6171790 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
6171736 AAATAGTGTC
6171746 ATCTTGTATAAATTTGGAT
1 ATCTTGTATAAATTTGGAT
6171765 ATCTTGTATAAATTTGGAT
1 ATCTTGTATAAATTTGGAT
*
6171784 ATGTTGT
1 ATCTTGT
6171791 CATATTTGTC
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:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (19 bp):
ATCTTGTATAAATTTGGAT
Found at i:6172311 original size:55 final size:55
Alignment explanation
Indices: 6172225--6172363 Score: 224
Period size: 55 Copynumber: 2.5 Consensus size: 55
6172215 ACTGAAAAAC
* * *
6172225 CAGATTGCCCAGAGGGTACCGATACCACCATGTAAGATTTGGCTCCGAGAAATAA
1 CAGATTGCTCGGAGGGTACCGATACCCCCATGTAAGATTTGGCTCCGAGAAATAA
*
6172280 CAGATTGCTCGGAGGGTACCGATACCCCCATGTAAGATTTGGCTCCGATAAATAA
1 CAGATTGCTCGGAGGGTACCGATACCCCCATGTAAGATTTGGCTCCGAGAAATAA
* *
6172335 TAGATTGCTCGGAGGATACCGATACCCCC
1 CAGATTGCTCGGAGGGTACCGATACCCCC
6172364 CAGGAGTTAC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 78 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (55 bp):
CAGATTGCTCGGAGGGTACCGATACCCCCATGTAAGATTTGGCTCCGAGAAATAA
Found at i:6173168 original size:17 final size:17
Alignment explanation
Indices: 6173146--6173188 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
6173136 ATTCGAGTTT
*
6173146 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTCAATC
*
6173163 GAGTTCGAGTTTCAATC
1 GAGTTCGAGCTTCAATC
*
6173180 GAGCTCGAG
1 GAGTTCGAG
6173189 TCTCGAGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (17 bp):
GAGTTCGAGCTTCAATC
Found at i:6173200 original size:24 final size:23
Alignment explanation
Indices: 6173161--6173209 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
6173151 CGAGCTTGAA
*
6173161 TCGAGTTCGAGTTTCAATCGAGC
1 TCGAGTTCGAGCTTCAATCGAGC
6173184 TCGAGTCTCGAGCTTCAATCGAGC
1 TCGAGT-TCGAGCTTCAATCGAGC
6173208 TC
1 TC
6173210 CTGAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (23 bp):
TCGAGTTCGAGCTTCAATCGAGC
Found at i:6174673 original size:22 final size:22
Alignment explanation
Indices: 6174618--6174666 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
6174608 ATTTGAAAAT
*
6174618 TAATAATTAATTTTTTATAATAAA
1 TAAT-ATTAA-TTATTATAATAAA
*
6174642 TAATATTAATTATTATATTAAA
1 TAATATTAATTATTATAATAAA
6174664 TAA
1 TAA
6174667 ATATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 5 0.22
24 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATATTAATTATTATAATAAA
Found at i:6174709 original size:14 final size:13
Alignment explanation
Indices: 6174679--6174706 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6174669 ATAATAAAAT
6174679 AATTTTTAAATAA
1 AATTTTTAAATAA
6174692 AATTTTTAAATAA
1 AATTTTTAAATAA
6174705 AA
1 AA
6174707 ATTATTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTTTTAAATAA
Found at i:6177894 original size:20 final size:20
Alignment explanation
Indices: 6177871--6177938 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
6177861 GTTATCATTG
6177871 CCCTATTATGTCACTCATGT
1 CCCTATTATGTCACTCATGT
* *
6177891 CCCTCGGGGGTTATGTTA-TCAT-T
1 CCCT-----ATTATGTCACTCATGT
6177914 ACCCTATTATGTCACTCATGT
1 -CCCTATTATGTCACTCATGT
6177935 CCCT
1 CCCT
6177939 CGGGGGCACT
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
19 7 0.19
20 12 0.33
21 1 0.03
23 1 0.03
24 8 0.22
25 7 0.19
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.38
Consensus pattern (20 bp):
CCCTATTATGTCACTCATGT
Found at i:6177921 original size:44 final size:44
Alignment explanation
Indices: 6177858--6177944 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
6177848 TGTCAGAGAA
*
6177858 TATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGGT
1 TATGTTATCATTACCCTATTATGTCACTCATGTCCCTCGGGGGT
6177902 TATGTTATCATTACCCTATTATGTCACTCATGTCCCTCGGGGG
1 TATGTTATCATTACCCTATTATGTCACTCATGTCCCTCGGGGG
6177945 CACTATTCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (44 bp):
TATGTTATCATTACCCTATTATGTCACTCATGTCCCTCGGGGGT
Found at i:6178083 original size:44 final size:44
Alignment explanation
Indices: 6178019--6178106 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
6178009 TGTCAGAGAA
* ** *
6178019 TATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGGC
1 TATGTTATCATTACAATATTATGTCACTCATGTCCATCGGGGGC
*
6178063 TATGTTATCATTACAATATTATGTTACTCATGTCCATCGGGGGC
1 TATGTTATCATTACAATATTATGTCACTCATGTCCATCGGGGGC
6178107 ACTATTCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (44 bp):
TATGTTATCATTACAATATTATGTCACTCATGTCCATCGGGGGC
Found at i:6178085 original size:161 final size:160
Alignment explanation
Indices: 6177816--6178219 Score: 666
Period size: 161 Copynumber: 2.5 Consensus size: 160
6177806 TCATGTAAAG
* *
6177816 GCGCGTTCTCAGGGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
1 GCGCGTTCCCA-GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
* ** *
6177881 TCACTCATGTCCCTCGGGGGTTATGTTATCATTACCCTATTATGTCACTCATGTCCCTCGGGGGC
65 TCACTCATGTCCCTCGGGGGCTATGTTATCATTACAATATTATGTCACTCATGTCCATCGGGGGC
*
6177946 ACTATTCATGTCAATACCCAAAGTGGTGAAA
130 ACTATTCATATCAATACCCAAAGTGGTGAAA
6177977 GCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
1 GCGCGTTCCC-AGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
*
6178042 TCACTCATGTCCCTCGGGGGCTATGTTATCATTACAATATTATGTTACTCATGTCCATCGGGGGC
65 TCACTCATGTCCCTCGGGGGCTATGTTATCATTACAATATTATGTCACTCATGTCCATCGGGGGC
*
6178107 ACTATTCATATCAGTACCCAAAGTGGTGAAA
130 ACTATTCATATCAATACCCAAAGTGGTGAAA
* *
6178138 GCGTGTTCCCAGGG-GCGTACTTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTAT
1 GCGCGTTCCCAGGGCGCG--CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTAT
6178202 GTCACTCATGTCCCTCGG
64 GTCACTCATGTCCCTCGG
6178220 AGAACTATTC
Statistics
Matches: 229, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
159 3 0.01
160 4 0.02
161 221 0.97
162 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (160 bp):
GCGCGTTCCCAGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGT
CACTCATGTCCCTCGGGGGCTATGTTATCATTACAATATTATGTCACTCATGTCCATCGGGGGCA
CTATTCATATCAATACCCAAAGTGGTGAAA
Found at i:6178364 original size:60 final size:60
Alignment explanation
Indices: 6178265--6178410 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 60
6178255 CATAGTTGTG
* * * * * * *
6178265 AAAGCGCGTCCCCAGGGATGCACCTTACCCACGTAGCATCCGACTCAGC-AGATCTCATAT
1 AAAGCGCATCCCCGGGGATGCACCTTACACACGTAGCATCCCACTCAGCAAAAAC-CAGAT
* ** * * *
6178325 AAAGCGCATCCCCGGGGATGCGCCTTACACGTGTGGCATCCCAGTCAGCAAAAACCAGGT
1 AAAGCGCATCCCCGGGGATGCACCTTACACACGTAGCATCCCACTCAGCAAAAACCAGAT
*
6178385 AAAGCGCATCCACGGGGATGCACCTT
1 AAAGCGCATCCCCGGGGATGCACCTT
6178411 TGTGCCACCT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
60 67 0.96
61 3 0.04
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (60 bp):
AAAGCGCATCCCCGGGGATGCACCTTACACACGTAGCATCCCACTCAGCAAAAACCAGAT
Found at i:6191563 original size:97 final size:97
Alignment explanation
Indices: 6191397--6191589 Score: 350
Period size: 97 Copynumber: 2.0 Consensus size: 97
6191387 GATTTGCATT
* * *
6191397 ATAGCACTGATTTAAAGAAAAACTCTTCACCGATTTGGTCCATTTTAGAGACATAATGGAGTCGT
1 ATAGCACTGATTTAAAGAAAAACCCTTCACCGATTTAGTCCATTTTAGAGACATAATGGAGTCAT
6191462 CAGTGTAGTTTTAATAGGAAACCCTATCCTTA
66 CAGTGTAGTTTTAATAGGAAACCCTATCCTTA
6191494 ATAGCACTGATTTAAAGAAAAACCCTTCACCGATTTAGTCCATTTTAGAGACATAATGGAGTCAT
1 ATAGCACTGATTTAAAGAAAAACCCTTCACCGATTTAGTCCATTTTAGAGACATAATGGAGTCAT
*
6191559 CAGTGTAGTTTTTATAGGAAACCCTATCCTT
66 CAGTGTAGTTTTAATAGGAAACCCTATCCTT
6191590 CTCCTGAATT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (97 bp):
ATAGCACTGATTTAAAGAAAAACCCTTCACCGATTTAGTCCATTTTAGAGACATAATGGAGTCAT
CAGTGTAGTTTTAATAGGAAACCCTATCCTTA
Found at i:6192043 original size:9 final size:11
Alignment explanation
Indices: 6192018--6192043 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6192008 CTCTCTCTCT
6192018 CTCTCTCGAAC
1 CTCTCTCGAAC
6192029 CTCTCTCGAAC
1 CTCTCTCGAAC
6192040 CTCT
1 CTCT
6192044 TTTTGTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.46, G:0.08, T:0.31
Consensus pattern (11 bp):
CTCTCTCGAAC
Found at i:6194095 original size:11 final size:11
Alignment explanation
Indices: 6194079--6194125 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
6194069 CCAACAAATC
6194079 ATAACAAACTA
1 ATAACAAACTA
*
6194090 ATAACAAGCTA
1 ATAACAAACTA
*
6194101 ATAACAAAC-C
1 ATAACAAACTA
6194111 ATAACAAACTA
1 ATAACAAACTA
6194122 ATAA
1 ATAA
6194126 TACTCTAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.62, C:0.19, G:0.02, T:0.17
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:6194122 original size:21 final size:22
Alignment explanation
Indices: 6194071--6194125 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
6194061 GTATGAAACC
*
6194071 AACAAA-TCATAACAAACTAAT
1 AACAAACTAATAACAAACTAAT
* *
6194092 AACAAGCTAATAACAAAC-CAT
1 AACAAACTAATAACAAACTAAT
6194113 AACAAACTAATAA
1 AACAAACTAATAA
6194126 TACTCTAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.62, C:0.20, G:0.02, T:0.16
Consensus pattern (22 bp):
AACAAACTAATAACAAACTAAT
Found at i:6194349 original size:14 final size:15
Alignment explanation
Indices: 6194318--6194350 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6194308 GTATAATAAA
*
6194318 ATATAAATTATTTTT
1 ATATAAATTATTTAT
6194333 ATATAAA-TATTTAT
1 ATATAAATTATTTAT
6194347 ATAT
1 ATAT
6194351 TTGTAACTAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATAAATTATTTAT
Found at i:6195600 original size:22 final size:21
Alignment explanation
Indices: 6195558--6195601 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
6195548 AGAGAGAGAA
*
6195558 AAAGAAAAAACTTGAAGAAAG
1 AAAGAAAAAAATTGAAGAAAG
6195579 AAAGAAAAAAGATT-AAGCAAAG
1 AAAGAAAAAA-ATTGAAG-AAAG
6195601 A
1 A
6195602 TTCATGGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.09
Consensus pattern (21 bp):
AAAGAAAAAAATTGAAGAAAG
Found at i:6210945 original size:22 final size:22
Alignment explanation
Indices: 6210891--6210954 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
6210881 ACAGCTCGTA
*
6210891 TAAA-TGCACCTAAGTGCCACG
1 TAAATTGCACCAAAGTGCCACG
* *
6210912 TAGAATTACACCAAAGTGCCGCG
1 TA-AATTGCACCAAAGTGCCACG
*
6210935 TAAATTGCACCGAAGTGCCA
1 TAAATTGCACCAAAGTGCCA
6210955 TATAAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 2 0.06
22 17 0.49
23 16 0.46
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (22 bp):
TAAATTGCACCAAAGTGCCACG
Found at i:6214439 original size:20 final size:20
Alignment explanation
Indices: 6214414--6214452 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6214404 TTCCCATTGA
*
6214414 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
6214434 AGTGCATCGATGCATTCTT
1 AGTGCATCGATGCATTCTT
6214453 TAACATGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:6218561 original size:24 final size:20
Alignment explanation
Indices: 6218508--6218565 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
6218498 TTCCCATTGA
*
6218508 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
6218528 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
6218551 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
6218566 CTACCATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:6220515 original size:12 final size:12
Alignment explanation
Indices: 6220500--6220531 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
6220490 AATAGGAAGA
6220500 GGATTTGGAGGT
1 GGATTTGGAGGT
6220512 GGATTTGGAGGT
1 GGATTTGGAGGT
6220524 GGATTTGG
1 GGATTTGG
6220532 TTGATGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (12 bp):
GGATTTGGAGGT
Found at i:6220542 original size:12 final size:12
Alignment explanation
Indices: 6220527--6220554 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6220517 TGGAGGTGGA
6220527 TTTGGTTGATGG
1 TTTGGTTGATGG
6220539 TTTGGTTGATGG
1 TTTGGTTGATGG
6220551 TTTG
1 TTTG
6220555 AGCGACTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.39, T:0.54
Consensus pattern (12 bp):
TTTGGTTGATGG
Found at i:6228028 original size:17 final size:17
Alignment explanation
Indices: 6228006--6228038 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6227996 TCTAATTTCC
6228006 ATATAATAATATGCACA
1 ATATAATAATATGCACA
6228023 ATATAATAATATGCAC
1 ATATAATAATATGCAC
6228039 TCACCTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (17 bp):
ATATAATAATATGCACA
Found at i:6229998 original size:21 final size:21
Alignment explanation
Indices: 6229969--6230041 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
6229959 GGTGTCATCA
* *
6229969 AACCCTGCGGGCTGGGCATAT
1 AACCCTGCGGGCTGGGAATGT
* * *
6229990 AACCTTGCGGGATGGGTATGT
1 AACCCTGCGGGCTGGGAATGT
*
6230011 AACCTTGCGGGCTGGGAATGT
1 AACCCTGCGGGCTGGGAATGT
6230032 AACCCTGCGG
1 AACCCTGCGG
6230042 AGATGACATA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.22
Consensus pattern (21 bp):
AACCCTGCGGGCTGGGAATGT
Found at i:6234744 original size:4 final size:4
Alignment explanation
Indices: 6234731--6234764 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
6234721 CTGGTAATAT
6234731 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
6234765 GTGTTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:6236208 original size:20 final size:21
Alignment explanation
Indices: 6236170--6236208 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
6236160 ATATTTCCGT
6236170 AGGCAGAGTGCGAAGAGCTAC
1 AGGCAGAGTGCGAAGAGCTAC
6236191 AGGCGAGAGTG-G-AGAGCT
1 AGGC-AGAGTGCGAAGAGCT
6236209 TGGCGAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.31, C:0.15, G:0.44, T:0.10
Consensus pattern (21 bp):
AGGCAGAGTGCGAAGAGCTAC
Found at i:6248586 original size:19 final size:19
Alignment explanation
Indices: 6248562--6248599 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6248552 AATTTTACAC
6248562 TGAGTGTACCGATACACCT
1 TGAGTGTACCGATACACCT
6248581 TGAGTGTACCGATACACCT
1 TGAGTGTACCGATACACCT
6248600 ACGCCCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
TGAGTGTACCGATACACCT
Found at i:6255793 original size:496 final size:498
Alignment explanation
Indices: 6255129--6256124 Score: 1828
Period size: 496 Copynumber: 2.0 Consensus size: 498
6255119 TTATCACATC
6255129 TGATTCTTTAAACTTTATCCTTTCATTTCCTTATTCCATTATTCCTTTATTCATTCAAAATCTAA
1 TGATTCTTTAAACTTTATCCTTTCATTTCCTTATTCCATTATTCCTTTATTCATTCAAAATCTAA
6255194 ATCTCCTTATGCATAAATCATATATTTCCTTTCATGTTCACATACTCGTTTCCTATCACTTATAC
66 ATCTCCTTATGCATAAA-CATATATTTCCTTTCATGTTCACATACTCGTTTCCTATCACTTATAC
*
6255259 TTATCTGATTACCGATCTTTATCACCTTTCATACTTTGATAATTAATTTCACTTATACAAACCTC
130 TCATCTGATTACCGATCTTTATCACCTTTCATACTTTGATAATTAATTTCACTTATACAAACCTC
*
6255324 ATTATTACAATCTCTTATAC-T-TATTTCCTTCTTTAAAGCCCCCTTTTTAAAACATACTAATA-
195 ATTATTACAATCTCTTATACTTGTATTTCC-TCTTTAAAGCCCCCTTTTTAAAACATACCAATAC
6255386 TTATCTCCTTGCCTACATCATATCTGTATAATCAAATACATAACCACATCCAGATTCATATCATA
259 TTATCTCCTTGCCTACATCATATCTGTATAATCAAATACATAACCACATCCAGATTCATATCATA
6255451 CTTGATTAACTCCACTATA-TTTTCCTTCCAATCTTATAACTTTATCACATTTACTCTTACAGCT
324 CTTGATTAACTCCACTATATTTTTCCTTCCAATCTTATAACTTTATCACATTTACTCTTACAGCT
6255515 AGTCCATAACAACTGTTCAATCTAGGGCACAAGCCCTAATCAG-T-TCATATACACACTTTCACT
389 AGTCCATAACAACTGTTCAATCTAGGGCACAAGCCCTAATCAGTTATCATATACACACTTTCACT
6255578 AAGAATTATCTCAACCATAGTTTTACTTAACTTATCAAATTCATATT
454 AAGAATTATCTC-ACCATAG-TTTACTTAACTTATCAAATTCATATT
*
6255625 TGATTCTTTAAACTTTATCCTTTCATTTCCTTATTCCATTATTTCTTTATTCATTCAAAATCTAA
1 TGATTCTTTAAACTTTATCCTTTCATTTCCTTATTCCATTATTCCTTTATTCATTCAAAATCTAA
*
6255690 ATCTTCTTATGCAT-AA-ATATATTTCCTTTCATGTTCACATACTCGTTTCCTATCACTTATACT
66 ATCTCCTTATGCATAAACATATATTTCCTTTCATGTTCACATACTCGTTTCCTATCACTTATACT
6255753 CATCTTGATTACCGATCTTTATCACCTTTTCATAACTTTGATAATTAATTTCACTTATACAAACC
131 CATC-TGATTACCGATCTTTATCACC-TTTCAT-ACTTTGATAATTAATTTCACTTATACAAACC
6255818 TCATTATTACAATCTCTTATACTTGTATTTCCTCTTTAAAGCCCCCTTTTTAAAACATACCAATA
193 TCATTATTACAATCTCTTATACTTGTATTTCCTCTTTAAAGCCCCCTTTTTAAAACATACCAATA
6255883 CTTATCTCCTTGCCTACATCATATCTGTATAATCAAATACATAACCACATCCAGATTCATATCAT
258 CTTATCTCCTTGCCTACATCATATCTGTATAATCAAATACATAACCACATCCAGATTCATATCAT
6255948 ACTTGATTAACTCCACTATATTTTTCCTTCCAATCTTATAACTTTATCACATTTACTCTTACAGC
323 ACTTGATTAACTCCACTATATTTTTCCTTCCAATCTTATAACTTTATCACATTTACTCTTACAGC
6256013 TAGTCCATAACAACTGTTCAATCTAGGGCACAAGCCCTAATCAGTTAATCATATACACACTTTCA
388 TAGTCCATAACAACTGTTCAATCTAGGGCACAAGCCCTAATCAGTT-ATCATATACACACTTTCA
6256078 CTAAGAATTATCTCACCATAGTTTACTTAACTTATCAAATTCATATT
452 CTAAGAATTATCTCACCATAGTTTACTTAACTTATCAAATTCATATT
6256125 CATTCTCATA
Statistics
Matches: 486, Mismatches: 4, Indels: 16
0.96 0.01 0.03
Matches are distributed among these distances:
493 50 0.10
494 21 0.04
495 8 0.02
496 130 0.27
497 33 0.07
498 91 0.19
499 88 0.18
500 27 0.06
501 7 0.01
502 31 0.06
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.41
Consensus pattern (498 bp):
TGATTCTTTAAACTTTATCCTTTCATTTCCTTATTCCATTATTCCTTTATTCATTCAAAATCTAA
ATCTCCTTATGCATAAACATATATTTCCTTTCATGTTCACATACTCGTTTCCTATCACTTATACT
CATCTGATTACCGATCTTTATCACCTTTCATACTTTGATAATTAATTTCACTTATACAAACCTCA
TTATTACAATCTCTTATACTTGTATTTCCTCTTTAAAGCCCCCTTTTTAAAACATACCAATACTT
ATCTCCTTGCCTACATCATATCTGTATAATCAAATACATAACCACATCCAGATTCATATCATACT
TGATTAACTCCACTATATTTTTCCTTCCAATCTTATAACTTTATCACATTTACTCTTACAGCTAG
TCCATAACAACTGTTCAATCTAGGGCACAAGCCCTAATCAGTTATCATATACACACTTTCACTAA
GAATTATCTCACCATAGTTTACTTAACTTATCAAATTCATATT
Found at i:6257246 original size:23 final size:23
Alignment explanation
Indices: 6257204--6257270 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
6257194 CACCACAGCT
* *
6257204 CATATAAATACACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
* * * *
6257227 CGTAGAATTGCACCGTAGTGCCG
1 CATAGAAATGCACCGAAGTGCCA
6257250 CATAGAAATGCACCGAAGTGC
1 CATAGAAATGCACCGAAGTGC
6257271 TATATAAAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.18
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:6257926 original size:2 final size:2
Alignment explanation
Indices: 6257919--6258069 Score: 256
Period size: 2 Copynumber: 77.5 Consensus size: 2
6257909 TCATACAGTC
*
6257919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC 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
*
6257961 TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA 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
6258002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
6258043 TA TA TA TA TA TA TA -A TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6258070 CATAACTCCA
Statistics
Matches: 141, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
1 4 0.03
2 137 0.97
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6264171 original size:20 final size:20
Alignment explanation
Indices: 6264146--6264199 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
6264136 GACCAACAAA
6264146 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
6264166 TTCGCAAC-CTAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
6264186 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
6264200 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:6264300 original size:20 final size:20
Alignment explanation
Indices: 6264275--6264314 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6264265 AATTTGTAAA
6264275 TCGCAACAC-AGAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
6264295 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
6264315 GTTTTTACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:6264722 original size:13 final size:13
Alignment explanation
Indices: 6264704--6264734 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6264694 TTAGTATTTC
*
6264704 TTGTTTTGTCTTT
1 TTGTTTTGTCATT
6264717 TTGTTTTGTCATT
1 TTGTTTTGTCATT
6264730 TTGTT
1 TTGTT
6264735 GAAGAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.03, C:0.06, G:0.16, T:0.74
Consensus pattern (13 bp):
TTGTTTTGTCATT
Found at i:6264801 original size:19 final size:20
Alignment explanation
Indices: 6264763--6264805 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
6264753 AACACCAAAT
6264763 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
6264783 TCGCAACGC-AAAACT-AAAA
1 TCGCAACGCGAAAA-TGAAAA
6264802 TCGC
1 TCGC
6264806 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:6264843 original size:20 final size:20
Alignment explanation
Indices: 6264802--6264843 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6264792 AAAACTAAAA
* * *
6264802 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
6264822 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
6264842 TC
1 TC
6264844 AAAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:6266749 original size:21 final size:21
Alignment explanation
Indices: 6266691--6266790 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 21
6266681 GCCCCATGCA
* **
6266691 CCTATTATCATTCAAGAGGTG
1 CCTATCATCATTCAAGAGGCC
* *
6266712 CCT-CCTATCGTTCAAGAGGCC
1 CCTATC-ATCATTCAAGAGGCC
*
6266733 CCTATCATCA-TCGAAGAAGCC
1 CCTATCATCATTC-AAGAGGCC
** *
6266754 CCTCCCACCATTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCC
* *
6266775 CCTGTCATCGTTCAAG
1 CCTATCATCATTCAAG
6266791 TGGTCCTGCC
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.03
21 54 0.92
22 3 0.05
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (21 bp):
CCTATCATCATTCAAGAGGCC
Found at i:6268223 original size:14 final size:14
Alignment explanation
Indices: 6268204--6268243 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
6268194 TTTTGATTAA
6268204 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
6268218 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
6268232 TTGATTTGTAAA
1 TTGATTTGTAAA
6268244 TAAAGAATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:6268236 original size:61 final size:67
Alignment explanation
Indices: 6268153--6268294 Score: 172
Period size: 67 Copynumber: 2.2 Consensus size: 67
6268143 TTTTACATTG
6268153 AAAGTTGATTTG-TTACAATTGATGAGGAAAT-AAG-A-T-TTATTTT-TTGATTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAAGAATTATTATTTTCTTGATTAATTGATTTG
6268212 TA
66 TA
* ** * * *
6268214 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAAGAATTATTTTTTTGCTTGTTTAATTGATTT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAAGAATTATTATTTT-CTTGATTAATTGATTT
6268278 GTA
65 GTA
6268281 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
6268295 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
61 23 0.34
62 6 0.09
63 1 0.01
64 1 0.01
65 6 0.09
67 31 0.46
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.50
Consensus pattern (67 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAAGAATTATTATTTTCTTGATTAATTGATTTG
TA
Found at i:6268637 original size:34 final size:33
Alignment explanation
Indices: 6268592--6268676 Score: 89
Period size: 39 Copynumber: 2.4 Consensus size: 33
6268582 CTCAAGTTGT
*
6268592 AGATTTTGATTTCCTTTTTGCTTGGCACCATATG
1 AGATTTGGATTTCC-TTTTGCTTGGCACCATATG
6268626 AGATTTGGATTTTTTTTTCCTTTTGCTTGGCACCATATG
1 AGATTTGGA------TTTCCTTTTGCTTGGCACCATATG
*
6268665 AGCTTTGGATTT
1 AGATTTGGATTT
6268677 TGATGAGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
33 3 0.07
34 8 0.19
39 27 0.63
40 5 0.12
ACGTcount: A:0.16, C:0.15, G:0.19, T:0.49
Consensus pattern (33 bp):
AGATTTGGATTTCCTTTTGCTTGGCACCATATG
Found at i:6268660 original size:39 final size:40
Alignment explanation
Indices: 6268601--6268677 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
6268591 TAGATTTTGA
6268601 TTTCCTTTTTGCTTGGCACCATATGAGATTTGGATTTTTT
1 TTTCCTTTTTGCTTGGCACCATATGAGATTTGGATTTTTT
*
6268641 TTTCC-TTTTGCTTGGCACCATATGAGCTTTGGATTTT
1 TTTCCTTTTTGCTTGGCACCATATGAGATTTGGATTTT
6268678 GATGAGCATC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 31 0.86
40 5 0.14
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (40 bp):
TTTCCTTTTTGCTTGGCACCATATGAGATTTGGATTTTTT
Found at i:6269005 original size:18 final size:18
Alignment explanation
Indices: 6268982--6269018 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6268972 CGAAATTTAT
6268982 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
6269000 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
6269018 A
1 A
6269019 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:6269439 original size:25 final size:25
Alignment explanation
Indices: 6269405--6269454 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
6269395 ATTATTTTTC
*
6269405 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
6269430 CAAATAATGTACGCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
6269455 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:6269563 original size:34 final size:39
Alignment explanation
Indices: 6269520--6269606 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 39
6269510 TATTGAAGGT
6269520 AAATTCGCAACGCGAAA-T-AAA-CG-T-TGCGATAGTC
1 AAATTCGCAACGCGAAAGTAAAATCGCTATGCGATAGTC
6269554 AAATTCGCAACGCGAAAGTCAAAATCGCTATGCGATAGTC
1 AAATTCGCAACGCGAAAGT-AAAATCGCTATGCGATAGTC
*
6269594 AAATTCGTAACGC
1 AAATTCGCAACGC
6269607 TTATTTCGCA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
34 17 0.37
35 1 0.02
37 3 0.07
38 2 0.04
39 1 0.02
40 22 0.48
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (39 bp):
AAATTCGCAACGCGAAAGTAAAATCGCTATGCGATAGTC
Found at i:6269568 original size:20 final size:20
Alignment explanation
Indices: 6269545--6269606 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
6269535 AATAAACGTT
6269545 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* * * *
6269565 GCGAAAGTCAAAATCGCTAT
1 GCGATAGTCAAATTCGCAAC
*
6269585 GCGATAGTCAAATTCGTAAC
1 GCGATAGTCAAATTCGCAAC
6269605 GC
1 GC
6269607 TTATTTCGCA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:6269635 original size:20 final size:20
Alignment explanation
Indices: 6269610--6269656 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6269600 GTAACGCTTA
6269610 TTTCGCATTGT-GAATTTGAC
1 TTTCGCATT-TCGAATTTGAC
*
6269630 TTTCGCGTTTCGAATTTGAC
1 TTTCGCATTTCGAATTTGAC
*
6269650 TATCGCA
1 TTTCGCA
6269657 ACGCTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTCGCATTTCGAATTTGAC
Found at i:6269665 original size:54 final size:54
Alignment explanation
Indices: 6269602--6269747 Score: 224
Period size: 54 Copynumber: 2.7 Consensus size: 54
6269592 TCAAATTCGT
* *
6269602 AACGCTTATTTCGCATTGTGAATTTGACTTTCGCGTT-TCGAATTTGACTA-TCGC
1 AACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTGT-GAATTTGACTACT-GC
* *
6269656 AACGCTTATTTTGCGTTGCAAATTTGACTTTCGCGTTGTGAATTTGACTACTGC
1 AACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTGTGAATTTGACTACTGC
6269710 AACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTG
1 AACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTG
6269748 ATCGCAACAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
54 82 0.98
55 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (54 bp):
AACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTGTGAATTTGACTACTGC
Found at i:6272352 original size:24 final size:24
Alignment explanation
Indices: 6272325--6272371 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
6272315 CAAAATCCGA
6272325 GTATTGACCAAGATCAAAGTTCGT
1 GTATTGACCAAGATCAAAGTTCGT
*
6272349 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
6272372 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGT
Found at i:6272380 original size:24 final size:24
Alignment explanation
Indices: 6272329--6272380 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
6272319 ATCCGAGTAT
** *
6272329 TGACCAAGATCAAAGTTCGTGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
6272353 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
6272377 TGAC
1 TGAC
6272381 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:6273266 original size:20 final size:20
Alignment explanation
Indices: 6273231--6273378 Score: 144
Period size: 20 Copynumber: 7.5 Consensus size: 20
6273221 CTAAAATCTA
*
6273231 TTGCGAAATT-AAATTCGCG
1 TTGCGAATTTGAAATTCGCG
*
6273250 TTGCGAATTTGAAATTC-AG
1 TTGCGAATTTGAAATTCGCG
*
6273269 TTGCGAATTTGAAATTC-AG
1 TTGCGAATTTGAAATTCGCG
**
6273288 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGAAATTCGCG
*
6273308 TTGCGAATTTG-ACTATCGCG
1 TTGCGAATTTGAAAT-TCGCG
**
6273328 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGAAATTCGCG
* *
6273348 TTGAGAATTTG-ACTATCGCG
1 TTGCGAATTTGAAAT-TCGCG
*
6273368 TTGAGAATTTG
1 TTGCGAATTTG
6273379 GAAAATCGTA
Statistics
Matches: 112, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
19 46 0.41
20 65 0.58
21 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGAATTTGAAATTCGCG
Found at i:6273339 original size:40 final size:40
Alignment explanation
Indices: 6273245--6273378 Score: 175
Period size: 40 Copynumber: 3.4 Consensus size: 40
6273235 GAAATTAAAT
** * *
6273245 TCGCGTTGCGAATTTGAAATTC-AGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
*
6273283 TTC-AGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
1 -TCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
*
6273323 TCGCGTTGCGAATTTGACTTTCGCGTTGAGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
*
6273363 TCGCGTTGAGAATTTG
1 TCGCGTTGCGAATTTG
6273379 GAAAATCGTA
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
38 16 0.19
39 17 0.20
40 51 0.61
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
Found at i:6273436 original size:21 final size:21
Alignment explanation
Indices: 6273372--6273436 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
6273362 ATCGCGTTGA
*
6273372 GAATTTGGAAAATCGTAACGC
1 GAATTTGGAAAATCGCAACGC
*
6273393 AAATTTGGAAAATCGCAACGC
1 GAATTTGGAAAATCGCAACGC
* *
6273414 GAATTTGTAAAATCGCAATGC
1 GAATTTGGAAAATCGCAACGC
6273435 GA
1 GA
6273437 TTTACATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (21 bp):
GAATTTGGAAAATCGCAACGC
Found at i:6284399 original size:55 final size:55
Alignment explanation
Indices: 6284315--6284428 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
6284305 AATGGAAACG
6284315 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
1 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
6284370 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
1 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
6284425 AAAT
1 AAAT
6284429 TGAAACTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (55 bp):
AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
Found at i:6285157 original size:20 final size:20
Alignment explanation
Indices: 6285134--6285207 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
6285124 GAATATGTAA
* *
6285134 ATCGCAATGCGATTATAACT
1 ATCGCAATGCGATTCTGACT
*
6285154 ATCGCAATACGATTCTGACT
1 ATCGCAATGCGATTCTGACT
*
6285174 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATTCTGACT
*
6285194 GTCGCAATGCGATT
1 ATCGCAATGCGATT
6285208 TTCAAATTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATTCTGACT
Found at i:6285221 original size:40 final size:39
Alignment explanation
Indices: 6285050--6285220 Score: 128
Period size: 40 Copynumber: 4.2 Consensus size: 39
6285040 CAGTTTCCAG
* * *
6285050 ATTCGCAATGCGATTCTGACTATCACATTGCGATTTTTCAA
1 ATTCGCAATGCGATTCTGACTATCGCAATACGA-TTTT-AA
** * *
6285091 ATTCGCGTTGCGATTTTCCGACTATCGCAATACGAATATGTAA
1 ATTCGCAATGCGA--TTCTGACTATCGCAATACG-AT-TTTAA
* * * *
6285134 A-TCGCAATGCGATTATAACTATCGCAATACGATTCTGA
1 ATTCGCAATGCGATTCTGACTATCGCAATACGATTTTAA
* * * *
6285172 CTATCGCAACGCGATTCTGACTGTCGCAATGCGATTTTCAA
1 AT-TCGCAATGCGATTCTGACTATCGCAATACGATTTT-AA
6285213 ATTCGCAA
1 ATTCGCAA
6285221 CAGGTTTTAG
Statistics
Matches: 100, Mismatches: 23, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
38 3 0.03
39 2 0.02
40 51 0.51
41 13 0.13
42 9 0.09
43 19 0.19
44 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (39 bp):
ATTCGCAATGCGATTCTGACTATCGCAATACGATTTTAA
Found at i:6286072 original size:24 final size:24
Alignment explanation
Indices: 6286015--6286074 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
6286005 TAGTCGGTAT
6286015 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
6286039 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
6286063 TCGAATTTTGAT
1 TCGAAATTTGAT
6286075 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:6288681 original size:140 final size:140
Alignment explanation
Indices: 6288429--6288694 Score: 523
Period size: 140 Copynumber: 1.9 Consensus size: 140
6288419 AAACGTTGTA
6288429 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
6288494 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
6288559 TATGTGTATT
131 TATGTGTATT
6288569 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
6288634 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
6288695 TTATCACAAC
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:6288720 original size:34 final size:34
Alignment explanation
Indices: 6288677--6288772 Score: 165
Period size: 34 Copynumber: 2.8 Consensus size: 34
6288667 TCATTTGAAT
6288677 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
1 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
6288711 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
1 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
* * *
6288745 ATCGCAACGCAAATTTGACTATCGCAAC
1 ATCGCAACGCGAATTTGATTATCACAAC
6288773 ACGAATATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGATTATCACAACTCAAAA
Found at i:6288770 original size:20 final size:20
Alignment explanation
Indices: 6288745--6289005 Score: 220
Period size: 20 Copynumber: 14.0 Consensus size: 20
6288735 CAACTCAAAA
*
6288745 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
6288765 ATCGCAACACGAATATGACT
1 ATCGCAACGCGAATTTGACT
* *
6288785 ATCACAACGC-AA----A-A
1 ATCGCAACGCGAATTTGACT
*
6288799 ATCGCAACGCGAATTTGTCT
1 ATCGCAACGCGAATTTGACT
6288819 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
6288839 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
6288859 ATCGCAATAGC-TATTTGACT
1 ATCGCAA-CGCGAATTTGACT
*
6288879 ATCGCAACGAGAA----A--
1 ATCGCAACGCGAATTTGACT
6288893 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
6288913 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
6288933 ATCGCAACGAGTATTTGACT
1 ATCGCAACGCGAATTTGACT
*
6288953 ATCGCAACGAGAA----A--
1 ATCGCAACGCGAATTTGACT
* * *
6288967 ATCGCAAAGCGTATTAGACT
1 ATCGCAACGCGAATTTGACT
6288987 ATCGCAACGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACT
6289006 TTCGTGTTGC
Statistics
Matches: 192, Mismatches: 29, Indels: 41
0.73 0.11 0.16
Matches are distributed among these distances:
14 31 0.16
15 3 0.02
16 2 0.01
18 2 0.01
19 8 0.04
20 144 0.75
21 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:6288778 original size:54 final size:54
Alignment explanation
Indices: 6288711--6288848 Score: 213
Period size: 54 Copynumber: 2.6 Consensus size: 54
6288701 CAACTCAAAA
* *
6288711 ATCGCAACGCGAATTTGATTATCACAACTCAAAAATCGCAACGCAAATTTGACT
1 ATCGCAACGCGAATTTGACTATCACAACGCAAAAATCGCAACGCAAATTTGACT
* * * *
6288765 ATCGCAACACGAATATGACTATCACAACGCAAAAATCGCAACGCGAATTTGTCT
1 ATCGCAACGCGAATTTGACTATCACAACGCAAAAATCGCAACGCAAATTTGACT
*
6288819 ATCGCAACGCGAATTTGACTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCACAACGC
6288849 GAATTTGATT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCACAACGCAAAAATCGCAACGCAAATTTGACT
Found at i:6288897 original size:74 final size:74
Alignment explanation
Indices: 6288819--6289001 Score: 314
Period size: 74 Copynumber: 2.5 Consensus size: 74
6288809 GAATTTGTCT
*
6288819 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAA-TAGCTATTTGACTATCG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAG-TATTTGACTATCG
6288883 CAACGAGAAA
65 CAACGAGAAA
6288893 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAGTATTTGACTATCGC
6288958 AACGAGAAA
66 AACGAGAAA
* * *
6288967 ATCGCAAAGCGTATTAGACTATCGCAACGCGAATT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATT
6289002 GACTTTCGTG
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
74 102 0.98
75 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAGTATTTGACTATCGC
AACGAGAAA
Found at i:6288971 original size:54 final size:54
Alignment explanation
Indices: 6288711--6289005 Score: 199
Period size: 54 Copynumber: 5.4 Consensus size: 54
6288701 CAACTCAAAA
* * * * *
6288711 ATCGCAACGCGAATTTGATTATCACAACTCA-AAAATCGCAACGCAAATTTGACT
1 ATCGCAACGAGAATTTGACTATCGCAAC-GAGAAAATCGCAACGCGAATTTGACT
* * *
6288765 ATCGCAAC-ACGAATATGACTATCACAACGCA-AAAATCGCAACGCGAATTTGTCT
1 ATCGCAACGA-GAATTTGACTATCGCAACG-AGAAAATCGCAACGCGAATTTGACT
* * * *
6288819 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAATAGC-TATTTGACT
1 ATCGCAACGAGAATTTGACTATCGCAACGAGAA----A--ATCGCAA-CGCGAATTTGACT
* * * *** ** *
6288879 ATCGCAACGAGAAAATCG-C-AACGCGAATTTGACTATCGCAACGCGAATTTGATT
1 ATCGCAACGAG-AATTTGACTATCGC-AACGAGAAAATCGCAACGCGAATTTGACT
* * * *
6288933 ATCGCAACGAGTATTTGACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACT
1 ATCGCAACGAGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACT
*
6288987 ATCGCAACGCGAA-TTGACT
1 ATCGCAACGAGAATTTGACT
6289006 TTCGTGTTGC
Statistics
Matches: 185, Mismatches: 40, Indels: 33
0.72 0.16 0.13
Matches are distributed among these distances:
53 11 0.06
54 130 0.70
55 4 0.02
58 1 0.01
59 4 0.02
60 29 0.16
61 6 0.03
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAACGAGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACT
Found at i:6289055 original size:20 final size:20
Alignment explanation
Indices: 6289000--6289057 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
6288990 GCAACGCGAA
* *
6289000 TTGACTTTCGTGTTGCGATT
1 TTGACTTTAGCGTTGCGATT
* * *
6289020 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
6289040 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCGTTGCGA
6289058 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:6289216 original size:14 final size:14
Alignment explanation
Indices: 6289156--6289217 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
6289146 CACAAATAAG
*
6289156 AATTATTTACACATC
1 AATT-TTTACAAATC
**
6289171 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
6289186 AACTTTTACAAATC
1 AATTTTTACAAATC
*
6289200 AATTTTTATAAATC
1 AATTTTTACAAATC
6289214 AATT
1 AATT
6289218 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:6290716 original size:42 final size:42
Alignment explanation
Indices: 6290609--6290720 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
6290599 TCTAGAATGT
* *
6290609 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACAG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACAG
* * ** *
6290651 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAAC-G
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAG
6290692 ATAGGG-GAGGCCTCTTGAACGATGACAGG
1 -T-GGGAGAGGCCTCTTGAACGATGACAGG
6290721 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.02
42 50 0.89
43 5 0.09
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAG
Found at i:6291242 original size:20 final size:20
Alignment explanation
Indices: 6291217--6291272 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
6291207 TTGCAACACG
*
6291217 AATGACTATTGCAACGCGAA
1 AATGACTATCGCAACGCGAA
6291237 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
6291257 AATGACTATCGCAACG
1 AATGACTATCGCAACG
6291273 AGAGAATCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:6291512 original size:18 final size:18
Alignment explanation
Indices: 6291489--6291539 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
6291479 ATTTACTAAG
6291489 TAATCTAAGTGAAATGGT
1 TAATCTAAGTGAAATGGT
6291507 TAATCTAAGTGAAATGGT
1 TAATCTAAGTGAAATGGT
6291525 TAATCTAAGTGAAAT
1 TAATCTAAGTGAAAT
6291540 TACGAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (18 bp):
TAATCTAAGTGAAATGGT
Found at i:6293277 original size:20 final size:20
Alignment explanation
Indices: 6293254--6293309 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
6293244 TCTGAAACTT
6293254 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* *
6293274 AAAATCACAACACAAAAATG
1 AAAATCGCAACACGAAAATG
** *
6293294 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
6293310 TTTGACTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:6293722 original size:20 final size:21
Alignment explanation
Indices: 6293697--6293759 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
6293687 TCTGAGAGAT
6293697 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* * *
6293717 GGAGATGGGACTGATTTCGTC
1 GGAGATGAGACGGATTTCGCC
* *
6293738 GGAGATGGGGACGGATGTCGCC
1 GGAGAT-GAGACGGATTTCGCC
6293760 TTAGAGAGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 6 0.17
21 17 0.49
22 12 0.34
ACGTcount: A:0.21, C:0.17, G:0.41, T:0.21
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:6293952 original size:20 final size:20
Alignment explanation
Indices: 6293927--6293979 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
6293917 ACGCTTTGAA
6293927 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
6293947 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
6293967 AATCACGTTGCGA
1 AATCGCGTTGCGA
6293980 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:6297826 original size:31 final size:33
Alignment explanation
Indices: 6297778--6297856 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
6297768 TTTAAATAGT
*
6297778 TATTATATTTTATATT-AAT-ATAATTATATAAA
1 TATTAT-TTTTTTATTAAATAATAATTATATAAA
* *
6297810 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATAATTATATAAA
*
6297844 TATTATTTATTTA
1 TATTATTTTTTTA
6297857 AATTTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATAATTATATAAA
Found at i:6297848 original size:34 final size:31
Alignment explanation
Indices: 6297768--6297879 Score: 88
Period size: 34 Copynumber: 3.6 Consensus size: 31
6297758 CAGTTATTTT
* * *
6297768 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
6297800 ATTATATAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
* *
6297834 TTTATATAATTATTATTTATTTA--AATTTA
1 TTTATATAATTATTATTTTTTTATTAATATA
*
6297863 TTAAT-TAATTATT-TTTT
1 TTTATATAATTATTATTTT
6297880 GTGCTAATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
27 3 0.05
28 8 0.12
29 6 0.09
30 3 0.05
31 8 0.12
32 12 0.18
33 3 0.05
34 23 0.35
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:6299688 original size:21 final size:21
Alignment explanation
Indices: 6299662--6299734 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
6299652 TATGTCATCT
*
6299662 CCGCAGGGTTACATTTCTAGC
1 CCGCAGGGTTACATTCCTAGC
6299683 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
6299704 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
6299725 CCGCAGGGTT
1 CCGCAGGGTT
6299735 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:6300290 original size:34 final size:34
Alignment explanation
Indices: 6300247--6300353 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
6300237 ATAAATGTTT
**
6300247 TTAAAATACAAATTATAGTATTTGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* * *
6300281 TTAAAATACAAATAATATTATTCAAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* *
6300315 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
6300349 TTAAA
1 TTAAA
6300354 TTCAAGTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCAAAATTTAAAA
Found at i:6305447 original size:44 final size:46
Alignment explanation
Indices: 6305398--6305487 Score: 121
Period size: 49 Copynumber: 1.9 Consensus size: 46
6305388 AATCTGTTAA
*
6305398 TTTTAGTAAT-AA-ATTCTTTTAACAACTAAGATAAGTTAGTTCGT
1 TTTTAGTAATAAACATTCTTTTAACAACTAAGATAAATTAGTTCGT
*
6305442 TTTTAGTAATAACAACGATTCTTTTAACCACTAAGATAAATTAGTT
1 TTTTAGTAAT-A-AAC-ATTCTTTTAACAACTAAGATAAATTAGTT
6305488 TGTTCCCGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 10 0.26
47 2 0.05
49 27 0.69
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (46 bp):
TTTTAGTAATAAACATTCTTTTAACAACTAAGATAAATTAGTTCGT
Found at i:6311530 original size:22 final size:22
Alignment explanation
Indices: 6311476--6311523 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
6311466 GATTTATGTA
* *
6311476 GAGATAGTTTTGTAGGGATATT
1 GAGATAGTTTTGAAGGCATATT
6311498 GAGATAGTTTTGAAGGCATATT
1 GAGATAGTTTTGAAGGCATATT
6311520 GAGA
1 GAGA
6311524 GTTTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.35
Consensus pattern (22 bp):
GAGATAGTTTTGAAGGCATATT
Found at i:6313671 original size:19 final size:19
Alignment explanation
Indices: 6313643--6313705 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
6313633 AGTATTTTAG
*
6313643 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
6313662 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
6313681 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
6313702 TTTA
1 TTTA
6313706 GTTTAAATAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:6314327 original size:17 final size:17
Alignment explanation
Indices: 6314305--6314341 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6314295 CTTTAATTTG
6314305 TTTATTTAATTATTATT
1 TTTATTTAATTATTATT
*
6314322 TTTATTTAATTCTTATT
1 TTTATTTAATTATTATT
6314339 TTT
1 TTT
6314342 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTAATTATTATT
Found at i:6314444 original size:20 final size:17
Alignment explanation
Indices: 6314406--6314444 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
6314396 TTATTATTCA
6314406 ATTATTTTTCTTTTTTT
1 ATTATTTTTCTTTTTTT
*
6314423 ATTATTTATTC-TATTTT
1 ATTATTT-TTCTTTTTTT
6314440 ATTAT
1 ATTAT
6314445 ACATTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTATTTTTCTTTTTTT
Found at i:6314795 original size:33 final size:33
Alignment explanation
Indices: 6314753--6314829 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
6314743 AATAAAATGA
* * *
6314753 AGAGAGGGTTCTTTGTACCCTTTAGGATTTATC
1 AGAGAGGGTTCCTCGTACCCTTCAGGATTTATC
*
6314786 AGAGAGGGTTCCTCGTACCCTTCAGGGTTTATC
1 AGAGAGGGTTCCTCGTACCCTTCAGGATTTATC
*
6314819 AGAAAGGGTTC
1 AGAGAGGGTTC
6314830 GTGGCAATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (33 bp):
AGAGAGGGTTCCTCGTACCCTTCAGGATTTATC
Found at i:6318844 original size:157 final size:157
Alignment explanation
Indices: 6318558--6318845 Score: 576
Period size: 157 Copynumber: 1.8 Consensus size: 157
6318548 CATCTTGATC
6318558 CCATTGTCAGACCTCGACCGCTTGACTTTTAAACCAGTCTCATTTTCCACCATGACCTTCCATTT
1 CCATTGTCAGACCTCGACCGCTTGACTTTTAAACCAGTCTCATTTTCCACCATGACCTTCCATTT
6318623 TCTGAAGGTATCAAAGACTTCTGATTTCTTCTTCAGAAAATAAACCCACACCTTCCTTGTTGAAT
66 TCTGAAGGTATCAAAGACTTCTGATTTCTTCTTCAGAAAATAAACCCACACCTTCCTTGTTGAAT
6318688 CTGAATCTCCTATTTCTGTACTCTCCT
131 CTGAATCTCCTATTTCTGTACTCTCCT
6318715 CCATTGTCAGACCTCGACCGCTTGACTTTTAAACCAGTCTCATTTTCCACCATGACCTTCCATTT
1 CCATTGTCAGACCTCGACCGCTTGACTTTTAAACCAGTCTCATTTTCCACCATGACCTTCCATTT
6318780 TCTGAAGGTATCAAAGACTTCTGATTTCTTCTTCAGAAAATAAACCCACACCTTCCTTGTTGAAT
66 TCTGAAGGTATCAAAGACTTCTGATTTCTTCTTCAGAAAATAAACCCACACCTTCCTTGTTGAAT
6318845 C
131 C
6318846 ATCGATGAAG
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 131 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.35
Consensus pattern (157 bp):
CCATTGTCAGACCTCGACCGCTTGACTTTTAAACCAGTCTCATTTTCCACCATGACCTTCCATTT
TCTGAAGGTATCAAAGACTTCTGATTTCTTCTTCAGAAAATAAACCCACACCTTCCTTGTTGAAT
CTGAATCTCCTATTTCTGTACTCTCCT
Done.