Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009343.1 Hibiscus syriacus cultivar Beakdansim tig00113123_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: 2141224
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:394159 original size:23 final size:23
Alignment explanation
Indices: 394131--394207 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
394121 TACACTATCA
394131 GTGCATCGATACATCCTATGAAT
1 GTGCATCGATACATCCTATGAAT
*
394154 GTGCATCGATACAT-C-ATGAAG
1 GTGCATCGATACATCCTATGAAT
* *
394175 GTGCACCGATGCACTCCT-TGAAT
1 GTGCATCGATACA-TCCTATGAAT
394198 GTGCATCGAT
1 GTGCATCGAT
394208 GCACTCAGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
21 16 0.35
22 2 0.04
23 28 0.61
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (23 bp):
GTGCATCGATACATCCTATGAAT
Found at i:395823 original size:27 final size:27
Alignment explanation
Indices: 395776--395832 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
395766 CTTTGAATGC
* * *
395776 TTGAACTTATATTTATATATTTGGTTT
1 TTGAACTTATATTGATATATTAGATTT
* *
395803 TTGAACTTATATTGGTTTATTAGATTT
1 TTGAACTTATATTGATATATTAGATTT
395830 TTG
1 TTG
395833 CATCATTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.14, T:0.58
Consensus pattern (27 bp):
TTGAACTTATATTGATATATTAGATTT
Found at i:397224 original size:3 final size:3
Alignment explanation
Indices: 397216--397261 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
397206 CTACAAACTC
397216 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
397262 GTTTTATTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:398453 original size:21 final size:21
Alignment explanation
Indices: 398418--398481 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
398408 GACCGAAATT
398418 ACTGTAGCAAGGGTATCGATAC
1 ACTGTAG-AAGGGTATCGATAC
* *
398440 ACTGTAGTAGGGTATCAATATC
1 ACTGTAGAAGGGTATCGATA-C
*
398462 -CTGTAGCAGGGTATCGATAC
1 ACTGTAGAAGGGTATCGATAC
398482 CCCTATAGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.76
22 8 0.22
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
ACTGTAGAAGGGTATCGATAC
Found at i:398904 original size:26 final size:26
Alignment explanation
Indices: 398875--398943 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 26
398865 TGATATGCAC
398875 ATATAATATAAGATATATGTT-TATAA
1 ATATAATATAAGATATATGTTATAT-A
* * * *
398901 ATATGACATAGGTTATATGTTATATA
1 ATATAATATAAGATATATGTTATATA
*
398927 ATA-AATATGAACATATA
1 ATATAATAT-AAGATATA
398944 AGAATAAGAG
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
25 3 0.09
26 26 0.81
27 3 0.09
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (26 bp):
ATATAATATAAGATATATGTTATATA
Found at i:400473 original size:21 final size:21
Alignment explanation
Indices: 400436--400495 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
400426 TATAATGAAG
*
400436 GGTCAAATT-AAAGAATTAAAA
1 GGTCAATTTGAAA-AATTAAAA
* *
400457 GGTCAATTTGAAAAATTGAAT
1 GGTCAATTTGAAAAATTAAAA
*
400478 GGCCAATTTGAAAAATTA
1 GGTCAATTTGAAAAATTA
400496 GTGAGCATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (21 bp):
GGTCAATTTGAAAAATTAAAA
Found at i:402445 original size:26 final size:27
Alignment explanation
Indices: 402407--402472 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
402397 TCTCTGTATT
* *
402407 TTATATTTTTATTTTCTTTATCTTTAC
1 TTATATTTTTATTTCCTTTATATTTAC
*
402434 TTAT-TTTTTATTTCCTTTATATTTAT
1 TTATATTTTTATTTCCTTTATATTTAC
*
402460 TTTTATTTCTTAT
1 TTATATTT-TTAT
402473 ATATTTTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 22 0.67
27 7 0.21
28 4 0.12
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (27 bp):
TTATATTTTTATTTCCTTTATATTTAC
Found at i:402462 original size:22 final size:22
Alignment explanation
Indices: 402434--402489 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
402424 TTATCTTTAC
402434 TTATTTTTTATTTCCTT-TATAT
1 TTATTTTTTATTT-CTTATATAT
402456 TTA-TTTTTATTTCTTATATAT
1 TTATTTTTTATTTCTTATATAT
402477 TT-TTGTTTTATTT
1 TTATT-TTTTATTT
402490 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.10
21 17 0.55
22 11 0.35
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (22 bp):
TTATTTTTTATTTCTTATATAT
Found at i:402479 original size:17 final size:20
Alignment explanation
Indices: 402438--402502 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 20
402428 CTTTACTTAT
402438 TTTTTATTTCCTTTATATTTA
1 TTTTTATTTCCTTTATA-TTA
402459 TTTTTATTT-C-TTATA-TA
1 TTTTTATTTCCTTTATATTA
* **
402476 TTTTTGTTTTATTTAT-TTA
1 TTTTTATTTCCTTTATATTA
402495 TTTATTAT
1 TTT-TTAT
402503 ATTATTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 10 0.27
19 14 0.38
20 4 0.11
21 9 0.24
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTATTTCCTTTATATTA
Found at i:402620 original size:23 final size:23
Alignment explanation
Indices: 402570--402625 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
402560 TTTTATTTTC
* *
402570 TTTTATTTTTTGTTTATTTATTT
1 TTTTATTTTTTGTCTATTGATTT
*
402593 TTTTATTTTTT-TCTCTTGATTT
1 TTTTATTTTTTGTCTATTGATTT
*
402615 TATTTACTTTT
1 T-TTTATTTTT
402626 ATTACATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.12, C:0.05, G:0.04, T:0.79
Consensus pattern (23 bp):
TTTTATTTTTTGTCTATTGATTT
Found at i:403571 original size:18 final size:18
Alignment explanation
Indices: 403548--403583 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
403538 CTTTTCTTTC
403548 TTTATTTAATTATTTTTA
1 TTTATTTAATTATTTTTA
*
403566 TTTATTTATTTATTTTTA
1 TTTATTTAATTATTTTTA
403584 CTAACTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTAATTATTTTTA
Found at i:405879 original size:18 final size:19
Alignment explanation
Indices: 405856--405894 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
405846 ATTCCTTGTA
405856 TTTTATA-TTTCATGTTTT
1 TTTTATATTTTCATGTTTT
405874 TTTTATATTTTTCATGTTTT
1 TTTTATA-TTTTCATGTTTT
405894 T
1 T
405895 ACATTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTATATTTTCATGTTTT
Found at i:411741 original size:175 final size:175
Alignment explanation
Indices: 411450--411799 Score: 700
Period size: 175 Copynumber: 2.0 Consensus size: 175
411440 GAAACTAATA
411450 CTGGATCTTCTCGAAGAATTTGATGAAGTCACCTTCCACTATGTATCAAGAGAAGAAAATCAAAT
1 CTGGATCTTCTCGAAGAATTTGATGAAGTCACCTTCCACTATGTATCAAGAGAAGAAAATCAAAT
411515 GGCAGATGCTTTAGCTACCTTGGCAGCCGCATTCAAGGCTGGCGAGGAGTCTGAGATGATATCAA
66 GGCAGATGCTTTAGCTACCTTGGCAGCCGCATTCAAGGCTGGCGAGGAGTCTGAGATGATATCAA
411580 TTGATATGCAGTCATATGATTACCCGGCTCATTGTTACCAAATTG
131 TTGATATGCAGTCATATGATTACCCGGCTCATTGTTACCAAATTG
411625 CTGGATCTTCTCGAAGAATTTGATGAAGTCACCTTCCACTATGTATCAAGAGAAGAAAATCAAAT
1 CTGGATCTTCTCGAAGAATTTGATGAAGTCACCTTCCACTATGTATCAAGAGAAGAAAATCAAAT
411690 GGCAGATGCTTTAGCTACCTTGGCAGCCGCATTCAAGGCTGGCGAGGAGTCTGAGATGATATCAA
66 GGCAGATGCTTTAGCTACCTTGGCAGCCGCATTCAAGGCTGGCGAGGAGTCTGAGATGATATCAA
411755 TTGATATGCAGTCATATGATTACCCGGCTCATTGTTACCAAATTG
131 TTGATATGCAGTCATATGATTACCCGGCTCATTGTTACCAAATTG
411800 AGGAAGTGAA
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (175 bp):
CTGGATCTTCTCGAAGAATTTGATGAAGTCACCTTCCACTATGTATCAAGAGAAGAAAATCAAAT
GGCAGATGCTTTAGCTACCTTGGCAGCCGCATTCAAGGCTGGCGAGGAGTCTGAGATGATATCAA
TTGATATGCAGTCATATGATTACCCGGCTCATTGTTACCAAATTG
Found at i:413846 original size:26 final size:25
Alignment explanation
Indices: 413806--413854 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
413796 GGCATAAAAA
413806 TATAATATAAATATATATACATAAG
1 TATAATATAAATATATATACATAAG
*
413831 TATAGATATAAGTATATATACATA
1 TATA-ATATAAATATATATACATA
413855 TCTATATAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (25 bp):
TATAATATAAATATATATACATAAG
Found at i:413860 original size:26 final size:25
Alignment explanation
Indices: 413806--413860 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
413796 GGCATAAAAA
*
413806 TATAATATAAATATATATACATAAG
1 TATAATATAAATATATATACATAAC
* *
413831 TATAGATATAAGTATATATACATATC
1 TATA-ATATAAATATATATACATAAC
413857 TATA
1 TATA
413861 TAGGTCGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (25 bp):
TATAATATAAATATATATACATAAC
Found at i:415184 original size:78 final size:78
Alignment explanation
Indices: 415035--415186 Score: 184
Period size: 78 Copynumber: 1.9 Consensus size: 78
415025 AATACTTCGC
* * ** * * *
415035 TTAGGATGAAAACCCGAGAGGGCGTCCTAGGTTGAAGAAGAAAAAGAAAAAGAAAAGAACAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAACAAAAAGAAAAAGAAAAGAACAAAAA
415100 AGAGAAAAAATGT
66 AGAGAAAAAATGT
*
415113 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTAAAAAACAACAAAGAAAAA-AAAGAGAA-AAG
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAACAA-AAAGAAAAAGAAA-AGAACAA-
415176 AAAA-AGAAAAA
63 AAAAGAGAAAAA
415187 TAAGGTGGGT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 46 0.73
79 17 0.27
ACGTcount: A:0.57, C:0.11, G:0.22, T:0.10
Consensus pattern (78 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAACAAAAAGAAAAAGAAAAGAACAAAAA
AGAGAAAAAATGT
Found at i:416287 original size:88 final size:89
Alignment explanation
Indices: 416133--416330 Score: 283
Period size: 88 Copynumber: 2.2 Consensus size: 89
416123 ATCCACGATT
*
416133 TCAACTTCACGACGAAGGATATCGTGCCCACCAGCAATGTTCATCTTTAGATTGGATTTCAACTT
1 TCAACTTCACGACGAAGGATATCGTGCCCACCAACAA---TCATCTTTAGATTGGATTTCAACTT
416198 CACAACAAAGGATATCCAATTC-ATGGC
63 CACAACAAAGGATATCCAATTCGA-GGC
**
416225 TCAACTTCACGACGAAGGATATCGTGTTCACCAACAA-CATCTTTAGATTGGATTTCAACTTCAC
1 TCAACTTCACGACGAAGGATATCGTGCCCACCAACAATCATCTTTAGATTGGATTTCAACTTCAC
* * *
416289 GACGAATGATATCCAATTCGAGGC
66 AACAAAGGATATCCAATTCGAGGC
*
416313 TCAACTTCACAACGAAGG
1 TCAACTTCACGACGAAGG
416331 GGCCATCCAC
Statistics
Matches: 98, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
88 63 0.64
89 1 0.01
92 34 0.35
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (89 bp):
TCAACTTCACGACGAAGGATATCGTGCCCACCAACAATCATCTTTAGATTGGATTTCAACTTCAC
AACAAAGGATATCCAATTCGAGGC
Found at i:416415 original size:124 final size:119
Alignment explanation
Indices: 416225--416444 Score: 323
Period size: 124 Copynumber: 1.8 Consensus size: 119
416215 AATTCATGGC
** * *
416225 TCAACTTCACGACGAAGGATATCGTGTTCACCAACAACATCTTTAGATTGGATTTCAACTTCACG
1 TCAACTTCACGACGAAGGATATCGTGCCCACCAACAACAACTCTAGATTGGATTTCAACTTCACG
* *
416290 ACGAATGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCATCCACGATT
66 ACGAAGGATATCCAATTC-AAGCTCAACTTCACAACGAAGGGGCCATCCACGATT
* *
416345 TCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATACAACTCTATATTGGATTTCAACTT
1 TCAACTTCACGACGAAGGATATCGTGCCCAC---CAACA-ACAACTCTAGATTGGATTTCAACTT
416410 CACGACGAAGGATATCCAATTCAAGCTCAACTTCA
62 CACGACGAAGGATATCCAATTCAAGCTCAACTTCA
416445 TAGAGAAGGG
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
120 29 0.33
123 16 0.18
124 43 0.49
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (119 bp):
TCAACTTCACGACGAAGGATATCGTGCCCACCAACAACAACTCTAGATTGGATTTCAACTTCACG
ACGAAGGATATCCAATTCAAGCTCAACTTCACAACGAAGGGGCCATCCACGATT
Found at i:416427 original size:212 final size:211
Alignment explanation
Indices: 416060--416444 Score: 626
Period size: 212 Copynumber: 1.8 Consensus size: 211
416050 AAAACAATTC
* * *
416060 TTGGATTTCAACTTCACGACGAAGGATATCCAATTTGAGGCTCAACTTCACAACGAATGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCAT
* ** * * *
416125 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAATGTTCATCTTTAGATTGGAT
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACATACAACTCTAGATTGGAT
*
416190 TTCAACTTCACAACAAAGGATATCCAATTCATGGCTCAACTTCACGACGAAGGATATCGTGTTCA
131 TTCAACTTCACAACAAAGGATATCCAATTCA-AGCTCAACTTCACGACGAAGGATATCGTGTTCA
416255 CCAACAACATCTTTAGA
195 CCAACAACATCTTTAGA
*
416272 TTGGATTTCAACTTCACGACGAATGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCAT
* *
416337 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATACAACTCTATATTGGAT
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACATACAACTCTAGATTGGAT
* *
416402 TTCAACTTCACGACGAAGGATATCCAATTCAAGCTCAACTTCA
131 TTCAACTTCACAACAAAGGATATCCAATTCAAGCTCAACTTCA
416445 TAGAGAAGGG
Statistics
Matches: 158, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
211 11 0.07
212 147 0.93
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (211 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACATACAACTCTAGATTGGAT
TTCAACTTCACAACAAAGGATATCCAATTCAAGCTCAACTTCACGACGAAGGATATCGTGTTCAC
CAACAACATCTTTAGA
Found at i:418113 original size:22 final size:20
Alignment explanation
Indices: 418087--418137 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
418077 CAATTTAATC
*
418087 ATTTTTATTAGTATTTATTATT
1 ATTTTTATT-GTATTAATTA-T
*
418109 ATTTTTTATTTTATTAATTAT
1 A-TTTTTATTGTATTAATTAT
418130 ATTTTTAT
1 ATTTTTAT
418138 ATACTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
21 2 0.08
22 9 0.35
23 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTTTATTGTATTAATTAT
Found at i:418163 original size:3 final size:3
Alignment explanation
Indices: 418155--418234 Score: 76
Period size: 3 Copynumber: 27.7 Consensus size: 3
418145 GTTTATACGA
* * * *
418155 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT AAC TAT CAT TCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
418201 GAC TAT TAT TAT TAT TAT TAT TAT T-T TAC TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
418235 ACGTATATAT
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 6 0.10
3 54 0.90
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:418259 original size:6 final size:6
Alignment explanation
Indices: 418244--418515 Score: 64
Period size: 6 Copynumber: 43.2 Consensus size: 6
418234 AACGTATATA
* * *
418244 TTTTACT TTTTAT TTTT-T TATTTCT TTATT-T TTTAAT TTTTAT CTTTAT
1 TTTTA-T TTTTAT TTTTAT T-TTTAT TT-TTAT TTTTAT TTTTAT TTTTAT
* * * **
418293 TTTTA- TTTTCT TTATCT TTACTTAT TTTCTA- TTTCCT TTTTAT TTATT-T
1 TTTTAT TTTTAT TTTTAT TT--TTAT TTT-TAT TTTTAT TTTTAT TT-TTAT
* * *
418342 TGTTTCT TATTTAT TTTTA- TTTTGT TTTT-G TTTTATT TATTTAT TTATTA-
1 T-TTTAT T-TTTAT TTTTAT TTTTAT TTTTAT TTTTA-T T-TTTAT TT-TTAT
* * * *
418392 TATTAT TATTAGGT TCTTTAT TTTATTT ATTTTATT TTTTAT TTTTAC
1 TTTTAT TTTTA--T T-TTTAT TTT-TAT -TTTTA-T TTTTAT TTTTAT
* * *
418440 TTTTAT TCCTT-T TTTTAT TTTT-T TCTTT-T TGTTTAT TTATTTT TTTTCT
1 TTTTAT T-TTTAT TTTTAT TTTTAT T-TTTAT T-TTTAT TT-TTAT TTTTAT
*
418489 TTTTTT TCTCTTGA- TTTTAT TTTTAT T
1 TTTTAT T-T-TT-AT TTTTAT TTTTAT T
418516 ATCTTTTTTC
Statistics
Matches: 202, Mismatches: 30, Indels: 67
0.68 0.10 0.22
Matches are distributed among these distances:
5 23 0.11
6 111 0.55
7 48 0.24
8 17 0.08
9 3 0.01
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:418273 original size:16 final size:15
Alignment explanation
Indices: 418244--418485 Score: 92
Period size: 16 Copynumber: 15.3 Consensus size: 15
418234 AACGTATATA
*
418244 TTTTACTTTTTATTT
1 TTTTATTTTTTATTT
418259 TTTTATTTCTTTA-TT
1 TTTTATTT-TTTATTT
*
418274 TTTTAATTTTTA--T
1 TTTTATTTTTTATTT
*
418287 CTTTA-TTTTTATTT
1 TTTTATTTTTTATTT
418301 TCTTTATCTTTACTTATTT
1 T-TTTAT-TTT--TTATTT
418320 TCTATT-TCCTTTTTATTT
1 T-T-TTAT--TTTTTATTT
* *
418338 ATTTTGTTTCTTATTTAT
1 -TTTTATTTTTTA-TT-T
418356 TTTTATTTTGTT-TTT
1 TTTTATTTT-TTATTT
418371 GTTTTATTTATTTATTT
1 -TTTTATTT-TTTATTT
* *
418388 ATTATATTATTATTAGGTT
1 -TTTTATT-TT-TTA-TTT
*
418407 CTTTA--TTTTATTT
1 TTTTATTTTTTATTT
418420 ATTTTATTTTTTA--T
1 -TTTTATTTTTTATTT
*
418434 TTTTACTTTTATTCCTTT
1 TTTTA-TTTT-TT-ATTT
*
418452 TTTTATTTTTT-TCT
1 TTTTATTTTTTATTT
*
418466 TTTTGTTTATTTATTT
1 TTTTATTT-TTTATTT
418482 TTTT
1 TTTT
418486 TCTTTTTTTT
Statistics
Matches: 178, Mismatches: 18, Indels: 61
0.69 0.07 0.24
Matches are distributed among these distances:
12 6 0.03
13 12 0.07
14 26 0.15
15 28 0.16
16 34 0.19
17 29 0.16
18 24 0.13
19 13 0.07
20 6 0.03
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTATTTTTTATTT
Found at i:418338 original size:26 final size:24
Alignment explanation
Indices: 418280--418363 Score: 64
Period size: 26 Copynumber: 3.4 Consensus size: 24
418270 TATTTTTTAA
*
418280 TTTTTATCT-TTATTTT-TATTTTC
1 TTTTTATTTATTATTTTCTA-TTTC
* *
418303 TTTATCTTTACTTATTTTCTATTTCC
1 TTTTTATTTA-TTATTTTCTATTT-C
* *
418329 TTTTTATTTATTTTGTTTCTTATTTA
1 TTTTTATTTATTAT-TTTC-TATTTC
418355 TTTTTATTT
1 TTTTTATTT
418364 TGTTTTTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
23 6 0.12
25 13 0.27
26 24 0.50
27 5 0.10
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.75
Consensus pattern (24 bp):
TTTTTATTTATTATTTTCTATTTC
Found at i:420439 original size:5 final size:5
Alignment explanation
Indices: 420431--420459 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
420421 AGGAAAGGAA
420431 AGAAG AGAAG AGAAG AGAAG AGAAG AGAA
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAA
420460 AATTACCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:426538 original size:15 final size:15
Alignment explanation
Indices: 426520--426550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
426510 AAATTCTAAA
426520 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
426535 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
426550 T
1 T
426551 TTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:435151 original size:28 final size:28
Alignment explanation
Indices: 435106--435176 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
435096 TTTATTTTAT
* *
435106 GTAATCGAGTCAGTGCTTGAAACATGAC
1 GTAACCGAGCCAGTGCTTGAAACATGAC
*
435134 GTAGCCGAGCCAGTGCTTGAAACATGAC
1 GTAACCGAGCCAGTGCTTGAAACATGAC
*
435162 GTAATCGAGCCAGTG
1 GTAACCGAGCCAGTG
435177 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (28 bp):
GTAACCGAGCCAGTGCTTGAAACATGAC
Found at i:438466 original size:37 final size:37
Alignment explanation
Indices: 438425--438496 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
438415 GGCCAATAAT
* * *
438425 CTCTCAATTTTAGTACTCTTTTTGGTTGAATCTATCA
1 CTCTCAATTATAGTAATCTTTTTGATTGAATCTATCA
* *
438462 CTCTCCATTATAGTAATCTTTTTTATTGAATCTAT
1 CTCTCAATTATAGTAATCTTTTTGATTGAATCTAT
438497 TAACTATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (37 bp):
CTCTCAATTATAGTAATCTTTTTGATTGAATCTATCA
Found at i:438659 original size:63 final size:63
Alignment explanation
Indices: 438587--438712 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
438577 TAACAAATAT
* *
438587 GCTCTTTTCCTTCTAAAATTTACAAACATAACATTCAGTTAAAATATTATTATAAATAGATCA
1 GCTCTTTTCCTTCTAAAAATTACAAACATAACATTCAATTAAAATATTATTATAAATAGATCA
* *
438650 GCTCTTTTCCTTCTAAAAATTACAAGCATAGCATTCAATTAAAATATTATTATAAATAGATCA
1 GCTCTTTTCCTTCTAAAAATTACAAACATAACATTCAATTAAAATATTATTATAAATAGATCA
438713 CTTCGTCATT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (63 bp):
GCTCTTTTCCTTCTAAAAATTACAAACATAACATTCAATTAAAATATTATTATAAATAGATCA
Found at i:447000 original size:2 final size:2
Alignment explanation
Indices: 446993--447031 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
446983 TACATTCATT
446993 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
447032 AAACCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:448744 original size:26 final size:26
Alignment explanation
Indices: 448714--448792 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 26
448704 TTCTACATAA
448714 ATAATTGATTATCACATACTATAATT
1 ATAATTGATTATCACATACTATAATT
** * *
448740 ATAATT-AAAAT-AAAT-GTATTAA--
1 ATAATTGATTATCACATACTA-TAATT
448762 ATAATTGATTATCACATACTATAATT
1 ATAATTGATTATCACATACTATAATT
448788 ATAAT
1 ATAAT
448793 AATTCTAGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 6 0.15
23 5 0.13
24 12 0.31
25 5 0.13
26 11 0.28
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (26 bp):
ATAATTGATTATCACATACTATAATT
Found at i:459085 original size:5 final size:5
Alignment explanation
Indices: 459077--459156 Score: 56
Period size: 5 Copynumber: 14.8 Consensus size: 5
459067 CCTGAAAAGA
* *
459077 AAAAT AAAAT AAAGT -TAAT AAAAT AAAAT AAAAT AGAAA- AGGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT A--AAAT
459123 AAATAAT AATAAT AATAAT AATAAT AAAAT AAAA
1 -AA-AAT AA-AAT AA-AAT AA-AAT AAAAT AAAA
459157 ATATTTTCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
4 2 0.03
5 31 0.48
6 28 0.43
7 3 0.05
8 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:459132 original size:3 final size:3
Alignment explanation
Indices: 459124--459159 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
459114 AAAGGAAATA
*
459124 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAA AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
459160 TTTTCAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:459194 original size:37 final size:35
Alignment explanation
Indices: 459152--459478 Score: 323
Period size: 37 Copynumber: 8.9 Consensus size: 35
459142 AATAATAAAA
* *
459152 TAAAAATATTTTCAAAAACCTATATAATATATATTCT
1 TAAAAATGTTTT-AAAAA-CTATATAATATATATTTT
* *
459189 TAAAAATATTTTAAAAACTATATATTATATTTATTTT
1 TAAAAATGTTTTAAAAACTATATA--ATATATATTTT
* *** * *
459226 CAATTTTTTTTTTAAAACTATATAATATATATTTT
1 TAAAAATGTTTTAAAAACTATATAATATATATTTT
*
459261 TCAAAAATGTTTTAAAAACTTTATAATATATATTTT
1 T-AAAAATGTTTTAAAAACTATATAATATATATTTT
*
459297 TCAAAATGTTTTAAAAACTATATAATATATATATTTT
1 TAAAAATGTTTTAAAAACTATAT-A-ATATATATTTT
* * *
459334 TAAAAATGTTTTTAAAACTATATATTATATTTATTT
1 TAAAAATGTTTTAAAAACTATATAATATATAT-TTT
*
459370 TCAAAATGTTTTAAAAACTATATAATATATAAATGTTT
1 TAAAAATGTTTTAAAAACTATATAATATAT--AT-TTT
* * *
459408 TCAAACATGTTTTCAAAACTATATATTATATATGTTTT
1 T-AAAAATGTTTTAAAAACTATATA--ATATATATTTT
*
459446 TAAAAATGTTTT-TAAACTATAATATATATATAT
1 TAAAAATGTTTTAAAAACTAT-ATA-ATATATAT
459479 ATATGTGTGT
Statistics
Matches: 244, Mismatches: 34, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
35 43 0.18
36 81 0.33
37 84 0.34
38 9 0.04
39 21 0.09
41 6 0.02
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (35 bp):
TAAAAATGTTTTAAAAACTATATAATATATATTTT
Found at i:459268 original size:73 final size:73
Alignment explanation
Indices: 459154--459480 Score: 378
Period size: 73 Copynumber: 4.4 Consensus size: 73
459144 TAATAAAATA
* * *
459154 AAAATATTTTCAAAAACCTATATAATATATAT-TCTT-AAAAATATTTTAAAAACTATATATTAT
1 AAAATGTTTT-AAAAA-CTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTAT
459217 ATTTATTTTC
64 ATTTATTTTC
** * * * *
459227 AATTTTTTTTTTAAAACTATATAATATATAT-TTTTCAAAAATGTTTTAAAAACTTTATAATATA
1 AA-AATGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATA
*
459291 TAT-TTTTC
65 TTTATTTTC
* *
459299 AAAATGTTTTAAAAACTATATAATATATATATTTTTAAAAATGTTTTTAAAACTATATATTATAT
1 AAAATGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATAT
459364 TTATTTTC
66 TTATTTTC
* * *
459372 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAACATGTTTTCAAAACTATATATTAT
1 AAAATGTTTTAAAAACTATATAATATAT--ATATTTTCAAAAATGTTTTAAAAACTATATATTAT
*
459437 ATATGT-TTTTA
64 AT-T-TATTTTC
*
459448 AAAATGTTTT-TAAACTATAATATATATATATAT
1 AAAATGTTTTAAAAACTAT-ATA-ATATATATAT
459481 ATGTGTGTGT
Statistics
Matches: 219, Mismatches: 25, Indels: 18
0.84 0.10 0.07
Matches are distributed among these distances:
71 24 0.11
72 56 0.26
73 66 0.30
74 5 0.02
75 43 0.20
76 18 0.08
77 7 0.03
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (73 bp):
AAAATGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATAT
TTATTTTC
Found at i:459288 original size:108 final size:109
Alignment explanation
Indices: 459153--459480 Score: 401
Period size: 108 Copynumber: 3.0 Consensus size: 109
459143 ATAATAAAAT
* * *
459153 AAAAATATTTTCAAAAACCTATATAATATATATTCTTAAAAATATTTTAAAAACTATATATTATA
1 AAAAATGTTTT-AAAAA-CTATATAATATATATTTTTAAAAATGTTTTAAAAACTATATATTATA
* *** *
459218 TTTATTTTCAATTTTTTTTTTAAAACTATATAATATATAT-TTTTC
64 TATATTTTCAAAAATGTTTTTAAAACTATATAATATATATATTTTC
* * *
459263 AAAAATGTTTTAAAAACTTTATAATATATATTTTTCAAAATGTTTTAAAAACTATATAATATATA
1 AAAAATGTTTTAAAAACTATATAATATATATTTTTAAAAATGTTTTAAAAACTATATATTATATA
* * *
459328 TATTTTTAAAAATGTTTTTAAAACTATATATTATATTTATTTTC
66 TATTTTCAAAAATGTTTTTAAAACTATATAATATATATATTTTC
* *
459372 -AAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAACATGTTTTCAAAACTATATATTA
1 AAAAATGTTTTAAAAACTATATAATATAT--AT-TTTT-AAAAATGTTTTAAAAACTATATATTA
* *
459436 TATATGTTTTTAAAAATGTTTTT-AAACTATAATATATATATATAT
62 TATATATTTTCAAAAATGTTTTTAAAACTAT-ATA-ATATATATAT
459481 ATGTGTGTGT
Statistics
Matches: 189, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
108 101 0.53
109 10 0.05
110 12 0.06
111 11 0.06
112 47 0.25
113 8 0.04
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (109 bp):
AAAAATGTTTTAAAAACTATATAATATATATTTTTAAAAATGTTTTAAAAACTATATATTATATA
TATTTTCAAAAATGTTTTTAAAACTATATAATATATATATTTTC
Found at i:460174 original size:84 final size:83
Alignment explanation
Indices: 460070--460767 Score: 615
Period size: 84 Copynumber: 8.4 Consensus size: 83
460060 AATTTATTGA
* * * *
460070 CAGATAGCCCTTCTTGCCTTGAGCTATGCTATAAATGATATGCCCTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAA
* *
460135 CTCAAAGGTCTTTTATTGG
66 CTCGAAGGTC-TTTGTTGG
* * * * * *
460154 CAGATAACTCTTCTAGCCTTGCGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAA
460219 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTT-GTTGG
* * * * * * *
460238 CAGATAACCCTTCTCGACTTAAGTTATACTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAA
* *
460303 CTCGAAGGTCTTTTGGTGA
66 CTCGAAGGTC-TTTGTTGG
* * * * * *
460322 CAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCT-GGAGCTGAGCGTAGTCGA
*
460387 ACTCGAGGGTC--T-TTGG
65 ACTCGAAGGTCTTTGTTGG
* * * * * * ** * *
460403 CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAATCAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCT-GGAGCTGAGCGTAGTCGA
*
460468 ACTCGAGGGTC--T-TTGG
65 ACTCGAAGGTCTTTGTTGG
* * * * * * * ** *
460484 AAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTACAGCTGAGCGTAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAA
* *
460549 CTCAAAGGTCTTTGGTT-A
66 CTCGAAGGTCTTT-GTTGG
* * * * * * *
460567 CAGATAACCCTTTTAGCCTTGAGTTATACTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCT-GGAGCTGAGCGTAGTCGA
* *
460632 ACTCGAGGGTC--T-TCGG
65 ACTCGAAGGTCTTTGTTGG
* * * * * * * * *
460648 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTGGAGCTAAGCGTAGTCGAT
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAA
460713 CTCGAAGGTCTTTGTTGG
66 CTCGAAGGTCTTTGTTGG
* * *
460731 CAGATAACCCTTCTAGCCTTGAGTTACGCTGCAAATG
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATG
460768 TTGTCTTTAA
Statistics
Matches: 500, Mismatches: 102, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
80 45 0.09
81 151 0.30
82 4 0.01
83 71 0.14
84 201 0.40
85 28 0.06
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (83 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGTTGG
Found at i:460615 original size:164 final size:165
Alignment explanation
Indices: 460178--460756 Score: 650
Period size: 164 Copynumber: 3.5 Consensus size: 165
460168 AGCCTTGCGT
* *
460178 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* * * * * * *
460243 AACCCTTCTCGACTTAAGTTATACTGTAAATGAT-ATGCCTTGGAGCTGAGCGTAGTCGAACTCG
66 AACCCTTCTAGACTTAAGTTATACTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCG
* * * * * * *
460307 AAGGTCTTTTGGTGACAGATAACCCTTTTAGCCTTGAGT
131 AGGGTC-TTT-G-GA-AGATAGCCCTTCTCGACTTAAGC
* * * * * * *
460346 TATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGA
1 TATGCTGCAAATGATGTG-CCTTGCAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGA
* * * * * * * *
460407 TAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAATCAAACTC
65 TAACCCTTCTAGACTTAAGTTATACTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTC
460472 GAGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGC
130 GAGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGC
* * * *
460508 TATGCTGCAAATGATGTGCCTTACAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTT-ACAGAT
1 TATGCTGCAAATGATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* * *
460572 AACCCTTTTAGCCTTGAGTTATACTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCG
66 AACCCTTCTAGACTTAAGTTATACTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCG
* *
460637 AGGGTCTTCGGCAGATAGCCCTTCTCGACTTAAGC
131 AGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGC
* * * *
460672 TATGCTGCAAATAATGTGCCTTGGAGCTAAGCGTAGTCGATCTCGAAGGTCTTT-GTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* *
460736 AACCCTTCTAGCCTTGAGTTA
66 AACCCTTCTAGACTTAAGTTA
460757 CGCTGCAAAT
Statistics
Matches: 343, Mismatches: 61, Indels: 18
0.81 0.14 0.04
Matches are distributed among these distances:
161 25 0.07
162 33 0.10
163 6 0.02
164 165 0.48
165 45 0.13
166 25 0.07
167 1 0.00
168 16 0.05
169 27 0.08
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (165 bp):
TATGCTGCAAATGATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
AACCCTTCTAGACTTAAGTTATACTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCG
AGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGC
Found at i:460615 original size:245 final size:246
Alignment explanation
Indices: 460234--460691 Score: 756
Period size: 245 Copynumber: 1.9 Consensus size: 246
460224 AGGTCTTTGG
* * * **
460234 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGTAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGAAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTACAGCTGAGCGTAGT
* * *
460299 CGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGATATG
66 CAAACTCAAAGGTCTTTTGGTGACAGATAACCCTTTTAGCCTTGAGTTATACTGTAAATGATATG
*
460364 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTCGGCAGATAGCCCTTCTCGACTTAAGCTA
* *
460429 TGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAATCAAACTCGAGGGTCT
196 TGCTGCAAATAATGTGCCCTCGAAGCTAAGTATAATCAAACTCGAGGGTCT
* * *
460480 TTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTACAGCTGAGCGTAGT
1 TTGGAAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTACAGCTGAGCGTAGT
* * *
460545 CAAACTCAAAGGTC-TTTGGTTACAGATAACCCTTTTAGCCTTGAGTTATACTGTAAATGATGTT
66 CAAACTCAAAGGTCTTTTGGTGACAGATAACCCTTTTAGCCTTGAGTTATACTGTAAATGATATG
460609 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTCGGCAGATAGCCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTCGGCAGATAGCCCTTCTCGACTTAAGCTA
460674 TGCTGCAAATAATGTGCC
196 TGCTGCAAATAATGTGCC
460692 TTGGAGCTAA
Statistics
Matches: 195, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
245 126 0.65
246 69 0.35
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (246 bp):
TTGGAAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTACAGCTGAGCGTAGT
CAAACTCAAAGGTCTTTTGGTGACAGATAACCCTTTTAGCCTTGAGTTATACTGTAAATGATATG
CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTCGGCAGATAGCCCTTCTCGACTTAAGCTA
TGCTGCAAATAATGTGCCCTCGAAGCTAAGTATAATCAAACTCGAGGGTCT
Found at i:466031 original size:27 final size:26
Alignment explanation
Indices: 465991--466043 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
465981 ATCAAAAGAG
*
465991 AAATAGAAAATAAATAGAAAATATAT
1 AAATAGAAAATAAATAAAAAATATAT
*
466017 AAATATAAATATAAATAAAAAATATAT
1 AAATAGAAA-ATAAATAAAAAATATAT
466044 TAAACAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (26 bp):
AAATAGAAAATAAATAAAAAATATAT
Found at i:466043 original size:21 final size:20
Alignment explanation
Indices: 466019--466064 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
466009 AAATATATAA
*
466019 ATATAAATATAAATAAAAAAT
1 ATATAAA-ACAAATAAAAAAT
*
466040 ATATTAAACAAATAAAAAAT
1 ATATAAAACAAATAAAAAAT
466060 A-ATAA
1 ATATAA
466065 CAGAATAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 3 0.14
20 13 0.59
21 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
ATATAAAACAAATAAAAAAT
Found at i:466061 original size:27 final size:27
Alignment explanation
Indices: 466002--466057 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
465992 AATAGAAAAT
* * *
466002 AAATAGAAAATATATAAATATAAATAT
1 AAATAAAAAATATATAAATACAAATAA
*
466029 AAATAAAAAATATATTAA-ACAAATAA
1 AAATAAAAAATATATAAATACAAATAA
466055 AAA
1 AAA
466058 ATAATAACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (27 bp):
AAATAAAAAATATATAAATACAAATAA
Found at i:466103 original size:17 final size:17
Alignment explanation
Indices: 466083--466120 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
466073 CGAAGAGAAA
466083 AAAAT-AAAAAAAATGAT
1 AAAATGAAAAAAAAT-AT
*
466100 AAAATGAATAAAAATAT
1 AAAATGAAAAAAAATAT
466117 AAAA
1 AAAA
466121 AAATTAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAATGAAAAAAAATAT
Found at i:466268 original size:5 final size:6
Alignment explanation
Indices: 466253--466283 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
466243 CCTAGGTCAA
466253 AAAAAT AAAAAT AAAAAT -AAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
466284 GAATTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:466274 original size:11 final size:11
Alignment explanation
Indices: 466253--466283 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
466243 CCTAGGTCAA
466253 AAAAATAAAAAT
1 AAAAAT-AAAAT
466265 AAAAATAAAAT
1 AAAAATAAAAT
466276 AAAAATAA
1 AAAAATAA
466284 GAATTAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:468082 original size:30 final size:30
Alignment explanation
Indices: 468012--468093 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
468002 CCCGAAGGAC
*
468012 CTATCCAGAGGTCACAAAG-ACC-CGATAA
1 CTATCCAGAGGTCACAAAGAACCTCGACAA
*
468040 CTATCCAGAGGTCATAAAGAACCTCGACAA
1 CTATCCAGAGGTCACAAAGAACCTCGACAA
* * *
468070 CTGTCCATAGGTCCCAAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
468094 AGGTAAACTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.39
29 3 0.07
30 25 0.54
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGACAA
Found at i:468173 original size:63 final size:62
Alignment explanation
Indices: 468069--468192 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
468059 AACCTCGACA
* *
468069 ACTGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
468131 ACTGTCCATATGTCTCGAAAG-ACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTC-CCAAAGAACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
468193 AACCCTCGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 20 0.36
63 36 0.64
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:468188 original size:32 final size:31
Alignment explanation
Indices: 468068--468195 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
468058 GAACCTCGAC
* * ** *
468068 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
468099 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
468130 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
468162 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
468193 AAC
1 AAC
468196 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:473292 original size:31 final size:31
Alignment explanation
Indices: 473254--473378 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
473244 CCTCAGCAAT
* *
473254 TGTCCATAGGTCCCAAAGAACCTAGGTAAAC
1 TGTCCATATGTCCCAAAGAACATAGGTAAAC
* ** *
473285 TGTCCATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATATGTCCCAAAGAACATAGGTAAAC
*
473316 TGTCCATATGTCTCAAA-ATACATAGGTAAAAC
1 TGTCCATATGTCCCAAAGA-ACATAGGT-AAAC
* **
473348 TGTCCATATGTTCCGTAGAACATAGGTAAAC
1 TGTCCATATGTCCCAAAGAACATAGGTAAAC
473379 CCTCGACTCT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
30 1 0.01
31 50 0.66
32 24 0.32
33 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (31 bp):
TGTCCATATGTCCCAAAGAACATAGGTAAAC
Found at i:473359 original size:63 final size:62
Alignment explanation
Indices: 473254--473375 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 62
473244 CCTCAGCAAT
* *
473254 TGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAC
* *
473316 TGTCCATATGTCTCAAA-ATACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 TGTCCATAGGTCCCAAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
473376 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
61 1 0.02
62 22 0.41
63 31 0.57
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (62 bp):
TGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAC
Found at i:474596 original size:21 final size:22
Alignment explanation
Indices: 474570--474613 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
474560 TTAAGCTGAT
474570 GACAAGTCAAA-TGAACTTCAA
1 GACAAGTCAAATTGAACTTCAA
*
474591 GACAAGTCAAATTTAACTTCAA
1 GACAAGTCAAATTGAACTTCAA
474613 G
1 G
474614 TTCAACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (22 bp):
GACAAGTCAAATTGAACTTCAA
Found at i:475096 original size:66 final size:64
Alignment explanation
Indices: 475010--475134 Score: 171
Period size: 68 Copynumber: 1.9 Consensus size: 64
475000 ATCATATTTA
* *
475010 TTTCAAAATTTTTAAAACTATATATATATA-TTTTTCAAAATGTTTTAAAAATATATATAATGT
1 TTTCAAAATTTTTAAAACTATATATATATAGTTTTTAAAAATATTTTAAAAATATATATAATGT
* *
475073 TTTCAAACATGTTTTCAAAACTATATATATATATGTTTTTAAAAATATTTTTAAACTATATA
1 TTTCAAA-AT-TTTT-AAAACTATATATATATA-GTTTTTAAAAATATTTTAAAAATATATA
475135 ATATATATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
63 7 0.13
64 2 0.04
65 4 0.08
66 17 0.32
68 23 0.43
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (64 bp):
TTTCAAAATTTTTAAAACTATATATATATAGTTTTTAAAAATATTTTAAAAATATATATAATGT
Found at i:476211 original size:14 final size:15
Alignment explanation
Indices: 476194--476226 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
476184 AAAAACGTCT
476194 TTTTAA-AAAAATAA
1 TTTTAAGAAAAATAA
*
476208 TTTTAAGAAAAATCA
1 TTTTAAGAAAAATAA
476223 TTTT
1 TTTT
476227 TTAGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (15 bp):
TTTTAAGAAAAATAA
Found at i:476931 original size:22 final size:22
Alignment explanation
Indices: 476905--476958 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
476895 AAGATTATTT
* * *
476905 TTCATTTATATGTGTATATATA
1 TTCATATATATATATATATATA
476927 TTCATATATATATATATATATA
1 TTCATATATATATATATATATA
*
476949 TT-ATAAATAT
1 TTCATATATAT
476959 CTAACTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
TTCATATATATATATATATATA
Found at i:479264 original size:132 final size:135
Alignment explanation
Indices: 479005--479319 Score: 444
Period size: 133 Copynumber: 2.4 Consensus size: 135
478995 GTCGTCTAAG
* * * *
479005 GGTGGATGACACGACTCATACGTGATGAAGAGTTCT-GGTCTTCTTTAGGAAGGGTGATTACTCG
1 GGTGGATGACACGGCTCATACGTGATGAAGAGTT-TAGGCCATCTTTAGGAAGGGTGATAACTCG
** * * * *
479069 GTTCCTACGTGATGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGAT-
65 GTTCCTACGCCATGAGGACAACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATC
479133 TGGTC-
130 TGGTCA
*
479138 GGTGGATGACACGGCTCATACGTGAAGAAGAGTTTAGGCCATCTTTAGGAAGGGTGATAACTC-G
1 GGTGGATGACACGGCTCATACGTGATGAAGAGTTTAGGCCATCTTTAGGAAGGGTGATAACTCGG
*
479202 TTCCTACGCCATGAGGACAACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCT
66 TTCCTACGCCATGAGGACAACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCT
479267 GGTCA
131 GGTCA
* *
479272 GG-AGATGACACGGCTCATACGTTATGAAGAG-TTATGGCCATCTTTAGG
1 GGTGGATGACACGGCTCATACGTGATGAAGAGTTTA-GGCCATCTTTAGG
479320 GATAATGATT
Statistics
Matches: 163, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
132 61 0.37
133 100 0.61
134 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (135 bp):
GGTGGATGACACGGCTCATACGTGATGAAGAGTTTAGGCCATCTTTAGGAAGGGTGATAACTCGG
TTCCTACGCCATGAGGACAACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCT
GGTCA
Found at i:479727 original size:93 final size:92
Alignment explanation
Indices: 479553--479732 Score: 220
Period size: 93 Copynumber: 1.9 Consensus size: 92
479543 TTTCTCAAGA
* * * * *
479553 AAAAATGTCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGATTTTGGTTTTAA
1 AAAAATGTCTCAAGAGAAAAAAAACTTTGGTTCAAAAGAAACAAACTCAAAGAATTT-GTTTCAA
* *
479618 AAGAAATGACTTAAAGATTTTTTTTCAC
65 AAGAAATAACTCAAAGATTTTTTTTCAC
* * *
479646 AAAATTGTCTTAAGAGAAAAAAAACTTTGGTTCAAAAGAAACATACTCAAAGAATTT-TTTCAAA
1 AAAAATGTCTCAAGAGAAAAAAAACTTTGGTTCAAAAGAAACAAACTCAAAGAATTTGTTTCAAA
479710 A-AAATAACAACTCAAAGATTTTT
66 AGAAAT---AACTCAAAGATTTTT
479733 ATTTTAAAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
90 4 0.05
91 7 0.09
93 63 0.85
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (92 bp):
AAAAATGTCTCAAGAGAAAAAAAACTTTGGTTCAAAAGAAACAAACTCAAAGAATTTGTTTCAAA
AGAAATAACTCAAAGATTTTTTTTCAC
Found at i:479761 original size:29 final size:29
Alignment explanation
Indices: 479676--479786 Score: 102
Period size: 29 Copynumber: 3.8 Consensus size: 29
479666 AAAACTTTGG
*
479676 TTCAAAAGAAACATACTCAAAGA-ATTT-T
1 TTCAAAAGAAACA-ACTCAAAGACTTTTAT
* *
479704 TTCAAAAAAATAACAACTCAAAGATTTTTAT
1 TTC-AAAAGA-AACAACTCAAAGACTTTTAT
* *
479735 TTTAAAAGAAACAACTCACAA-ACTTTTGT
1 TTCAAAAGAAACAACTCA-AAGACTTTTAT
*
479764 TTCAAGAGAAACAAACTCAAAGA
1 TTCAAAAGAAAC-AACTCAAAGA
479787 TAGGTTTTGT
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
28 3 0.04
29 41 0.60
30 21 0.31
31 3 0.04
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.27
Consensus pattern (29 bp):
TTCAAAAGAAACAACTCAAAGACTTTTAT
Found at i:479798 original size:33 final size:31
Alignment explanation
Indices: 479718--479837 Score: 115
Period size: 33 Copynumber: 3.9 Consensus size: 31
479708 AAAAAATAAC
* * *
479718 AACTCAAAGAT-TTTTATTTTAAAAGAAAC-
1 AACTCAAAGATGTTTTGTTTCAAGAGAAACA
*
479747 AACTCACAA-A-CTTTTGTTTCAAGAGAAACA
1 AACTCA-AAGATGTTTTGTTTCAAGAGAAACA
*
479777 AACTCAAAGATAGGTTTTGTTTCAAGGGAAACA
1 AACTCAAAGAT--GTTTTGTTTCAAGAGAAACA
* *
479810 ATCTCAAAGATG-TTTGTTTTAAGAGAAA
1 AACTCAAAGATGTTTTGTTTCAAGAGAAA
479838 TTGCCTCAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 13
0.78 0.08 0.13
Matches are distributed among these distances:
29 24 0.32
30 23 0.30
31 1 0.01
33 28 0.37
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (31 bp):
AACTCAAAGATGTTTTGTTTCAAGAGAAACA
Found at i:479929 original size:66 final size:65
Alignment explanation
Indices: 479815--480025 Score: 228
Period size: 64 Copynumber: 3.2 Consensus size: 65
479805 AAACAATCTC
* * * * ** * *
479815 AAAGATGTTTGTTTTAAGAGAAATTGCCTCAAAAGAGACAAACCTTTGTTTTCAGTA-AAACAAA
1 AAAGAT-TTT-TTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCA-AAGAAACATA
479879 CTT
63 CTT
* *
479882 AAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACATACT
1 AAAGATTTTT-TTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACT
479947 T
65 T
* * * * * *
479948 AAAGA-TTCTTTCAAAAGAAACTTTCTCAAAAGAAACAAAATTTTGTTATCAAATAAACATACTC
1 AAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTT
480012 AAAGATTTTTTTCA
1 AAAGATTTTTTTCA
480026 TTTTGTTTTA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
64 53 0.43
65 12 0.10
66 51 0.42
67 6 0.05
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (65 bp):
AAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTT
Found at i:480527 original size:16 final size:16
Alignment explanation
Indices: 480506--480544 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
480496 CTCATGTAAT
**
480506 ATGTATGGATGTGTTG
1 ATGTATGGATGCATTG
*
480522 ATGTATGTATGCATTG
1 ATGTATGGATGCATTG
480538 ATGTATG
1 ATGTATG
480545 TTTTCTCGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.31, T:0.44
Consensus pattern (16 bp):
ATGTATGGATGCATTG
Found at i:484423 original size:31 final size:32
Alignment explanation
Indices: 484367--484427 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
484357 TGACAAAATG
484367 ACACAAACAAAAGAGAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTGT
484399 ACACAAACAAAAGAGAA-AAATAAGTTAGT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGT
484428 ACATGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTGT
Found at i:489153 original size:23 final size:23
Alignment explanation
Indices: 489127--489197 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
489117 TACCAAATGG
*
489127 CAGAGATAAACGTGCCACAAAGA
1 CAGAGATAAACGTGTCACAAAGA
* *
489150 CAGAGATAAATGTGTCATAAATG-
1 CAGAGATAAACGTGTCACAAA-GA
* *
489173 CAGAGATAATCATGTCACAAAGA
1 CAGAGATAAACGTGTCACAAAGA
489196 CA
1 CA
489198 TAATTAATCT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 1 0.03
23 37 0.95
24 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (23 bp):
CAGAGATAAACGTGTCACAAAGA
Found at i:493940 original size:27 final size:28
Alignment explanation
Indices: 493898--493956 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
493888 TAAATCATTG
* *
493898 TTATCTACATAGTTCATGATCATGTAAT
1 TTATCTACATAATTCATGATCATATAAT
* *
493926 TTATCT-CATAATTCATTATCATATAGT
1 TTATCTACATAATTCATGATCATATAAT
493953 TTAT
1 TTAT
493957 ATTTTGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (28 bp):
TTATCTACATAATTCATGATCATATAAT
Found at i:495798 original size:19 final size:18
Alignment explanation
Indices: 495770--495805 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
495760 AGTTTTGATG
495770 TTTTTGTTTAAATTACAA
1 TTTTTGTTTAAATTACAA
*
495788 TTTTATGTTTATATTACA
1 TTTT-TGTTTAAATTACA
495806 TTGCAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (18 bp):
TTTTTGTTTAAATTACAA
Found at i:501102 original size:31 final size:31
Alignment explanation
Indices: 501039--501116 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
501029 CTTTTAAAAC
** * * *
501039 TTGCAATACAGTCCCCCAACATTTATTTCAT
1 TTGCAATATGGTCCCTCAACATTTAGTCCAT
501070 TTGCAATATGGTCCCTCAACATTTAGTCCAT
1 TTGCAATATGGTCCCTCAACATTTAGTCCAT
**
501101 TTATAATATGGTCCCT
1 TTGCAATATGGTCCCT
501117 GACGTAACTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (31 bp):
TTGCAATATGGTCCCTCAACATTTAGTCCAT
Found at i:509207 original size:32 final size:33
Alignment explanation
Indices: 509139--509209 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
509129 ATGTTCAAAT
*
509139 TAAAAAGAATAAAAAAATGTTAAGATTAATAAA
1 TAAAAAGAATAAAAAAATGTTAAGATAAATAAA
* *
509172 TAAAAAGAATGAAGAACATGTTAA-A-AAATAAA
1 TAAAAAGAAT-AAAAAAATGTTAAGATAAATAAA
509204 TAAAAA
1 TAAAAA
509210 TAAATAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.35
33 11 0.32
34 11 0.32
ACGTcount: A:0.68, C:0.01, G:0.10, T:0.21
Consensus pattern (33 bp):
TAAAAAGAATAAAAAAATGTTAAGATAAATAAA
Found at i:509224 original size:18 final size:17
Alignment explanation
Indices: 509193--509227 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
509183 AAGAACATGT
509193 TAAAAAATAAATAAAAA
1 TAAAAAATAAATAAAAA
*
509210 TAAATAAATAGATAAAAA
1 TAAA-AAATAAATAAAAA
509228 AAGTAAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
TAAAAAATAAATAAAAA
Found at i:513168 original size:19 final size:18
Alignment explanation
Indices: 513144--513188 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
513134 GGATTGAACT
513144 TGAAATAATAAAAATAAAA
1 TGAAATAATAAAAAT-AAA
*
513163 TGAAATAA-ATAAATAAA
1 TGAAATAATAAAAATAAA
513180 T-AAATAATA
1 TGAAATAATA
513189 TAAACAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 5 0.21
18 5 0.21
19 8 0.33
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (18 bp):
TGAAATAATAAAAATAAA
Found at i:513331 original size:71 final size:72
Alignment explanation
Indices: 513256--513393 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 72
513246 TAAAAAATCG
*
513256 TTTAAAAAAAATATATTATACGTTTTC-AAATCATTT-AAAAAAACCATATACTATATGTTTTCA
1 TTTAAAAAAAATATATTATACGTTTTCAAAACCATTTCAAAAAAA-CATATACTATATGTTTTCA
513319 AAACCGTA
65 AAACCGTA
** * **
513327 TTTAAAAACTATATATTATACGTTTTCAAAACCATTTCAAAAAAATATATTTTATATGTTTTCAA
1 TTTAAAAAAAATATATTATACGTTTTCAAAACCATTTCAAAAAAACATATACTATATGTTTTCAA
513392 AA
66 AA
513394 ACTATATATT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 25 0.42
72 27 0.46
73 7 0.12
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.39
Consensus pattern (72 bp):
TTTAAAAAAAATATATTATACGTTTTCAAAACCATTTCAAAAAAACATATACTATATGTTTTCAA
AACCGTA
Found at i:513341 original size:36 final size:35
Alignment explanation
Indices: 513232--513393 Score: 159
Period size: 36 Copynumber: 4.6 Consensus size: 35
513222 TATATAATAT
* * * *
513232 TATATTATATGTTTTAAAAAATCGTTTAAAAAA-AA
1 TATATTATATGTTTT-CAAAACCATTTAAAAAACTA
* * *
513267 TATATTATACGTTTTC-AAATCATTTAAAAAAACCA
1 TATATTATATGTTTTCAAAACCATTT-AAAAAACTA
*
513302 TATACTATATGTTTTCAAAACCGTATTT-AAAAACTA
1 TATATTATATGTTTTCAAAACC--ATTTAAAAAACTA
* *
513338 TATATTATACGTTTTCAAAACCATTTCAAAAAAATA
1 TATATTATATGTTTTCAAAACCATTT-AAAAAACTA
*
513374 TATTTTATATGTTTTCAAAA
1 TATATTATATGTTTTCAAAA
513394 ACTATATATT
Statistics
Matches: 107, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
33 8 0.07
34 10 0.09
35 29 0.27
36 56 0.52
38 4 0.04
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (35 bp):
TATATTATATGTTTTCAAAACCATTTAAAAAACTA
Found at i:513399 original size:24 final size:24
Alignment explanation
Indices: 513361--513448 Score: 113
Period size: 24 Copynumber: 3.6 Consensus size: 24
513351 TTCAAAACCA
* *
513361 TTTCAAAAAAATATATTTTATATGT
1 TTTC-AAAAACTATATATTATATGT
*
513386 TTTCAAAAACTATATATTATACGT
1 TTTCAAAAACTATATATTATATGT
*
513410 TTTCAAAAACTATATATTATATAT
1 TTTCAAAAACTATATATTATATGT
* *
513434 TTTTAAAAATTATAT
1 TTTCAAAAACTATAT
513449 TTGAAATTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
24 52 0.93
25 4 0.07
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTCAAAAACTATATATTATATGT
Found at i:515385 original size:9 final size:10
Alignment explanation
Indices: 515339--515384 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
515329 AGTTTGTAAT
515339 TATTTAATAA
1 TATTTAATAA
515349 -ATTTAATAA
1 TATTTAATAA
*
515358 TTATTTAATAT
1 -TATTTAATAA
*
515369 TTTTTAA-AA
1 TATTTAATAA
515378 TATTTAA
1 TATTTAA
515385 ATAAATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
9 16 0.53
10 6 0.20
11 8 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATTTAATAA
Found at i:517270 original size:3 final size:3
Alignment explanation
Indices: 517262--517287 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
517252 CTTAACCTCT
517262 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
517288 AACCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:522374 original size:2 final size:2
Alignment explanation
Indices: 522367--522399 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
522357 AGTTGACATT
522367 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
522400 GGTACAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:522964 original size:27 final size:24
Alignment explanation
Indices: 522911--522995 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 24
522901 CGATTTTTAA
522911 AAAAAAACCGGATTTTT--T-CGG-
1 AAAAAAACCGG-TTTTTAATCCGGT
*
522932 ATAAAAAACCGGTTTTTTATCCGGTTT
1 A-AAAAAACCGGTTTTTAATCCGG--T
*
522959 GAAAAAAACCAGTTTTTAATCCGGT
1 -AAAAAAACCGGTTTTTAATCCGGT
522984 AAAAAAACCGGT
1 AAAAAAACCGGT
522996 CGTTCAATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
21 6 0.11
22 10 0.19
23 1 0.02
24 14 0.26
25 1 0.02
27 20 0.38
28 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (24 bp):
AAAAAAACCGGTTTTTAATCCGGT
Found at i:523558 original size:2 final size:2
Alignment explanation
Indices: 523551--523612 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
523541 TCCTAAATAA
523551 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
523593 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
523613 TAAAATTAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523725 original size:2 final size:2
Alignment explanation
Indices: 523718--523748 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
523708 TGATTTGATT
523718 TA TA TA 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 TA TA TA T
523749 TATTTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:537702 original size:133 final size:134
Alignment explanation
Indices: 537527--537823 Score: 384
Period size: 135 Copynumber: 2.2 Consensus size: 134
537517 TAAAGAGTAA
* * * * *
537527 TACTTTAGTGGCGTTTTTTAAACAAACACCGTAAAATGGTTGTATATTGTCATTTATAGC-G-GT
1 TACTTTAGTGGCGTTTTTGACATAAACACCATAAAATGGTTGTATATTATCATTTATAGCGGTGT
*
537590 ATTTTTAATCAAACACCGCAAAATACTATTAATTTAGTGGCGTTTATTACCAAACGCCGCTAAAA
66 ATTTTTAATCAAACACCGCAAAATACTATTAATTTAGTGGCATTTATTACCAAACGCCGCTAAAA
*
537655 AGTTG
131 A-ATG
* *
537660 TACTTTAGTGGCGTTTTTGACATAAACGCCATAATA-GAGTTGTATATTATCATTTATAGCGGTG
1 TACTTTAGTGGCGTTTTTGACATAAACACCATAAAATG-GTTGTATATTATCATTTATAGCGGTG
* * ** * * * *
537724 TTTTTTTAATTAAATGCCGTAAAATACTCTTAATTTAGTGGCATTTGTTACCAAACGTCGCTAAA
65 TATTTTTAATCAAACACCGCAAAATACTATTAATTTAGTGGCATTTATTACCAAACGCCGCTAAA
537789 AAATG
130 AAATG
* *
537794 TACTTTATTGGCATTTTTGACATAAACACC
1 TACTTTAGTGGCGTTTTTGACATAAACACC
537824 GCAATAACTG
Statistics
Matches: 141, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
132 1 0.01
133 51 0.36
134 30 0.21
135 59 0.42
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (134 bp):
TACTTTAGTGGCGTTTTTGACATAAACACCATAAAATGGTTGTATATTATCATTTATAGCGGTGT
ATTTTTAATCAAACACCGCAAAATACTATTAATTTAGTGGCATTTATTACCAAACGCCGCTAAAA
AATG
Found at i:539464 original size:46 final size:46
Alignment explanation
Indices: 539397--539526 Score: 224
Period size: 46 Copynumber: 2.8 Consensus size: 46
539387 AATAAAAAAT
*
539397 GAATAATGCTGAAAATGATTCCATGATTCAACATTCTATTTCTAGG
1 GAATAATGCTGAAAATGATTCCATGATTCAACATTCTATTTCTAAG
539443 GAATAATGCTGAAAATGATTCCATGATTCAACATTCTATTTCTAAG
1 GAATAATGCTGAAAATGATTCCATGATTCAACATTCTATTTCTAAG
* * *
539489 GAATAATGCTAAAAATGATTCCTTGATTCAGCATTCTA
1 GAATAATGCTGAAAATGATTCCATGATTCAACATTCTA
539527 AACTTGCAAG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (46 bp):
GAATAATGCTGAAAATGATTCCATGATTCAACATTCTATTTCTAAG
Found at i:540908 original size:11 final size:11
Alignment explanation
Indices: 540894--540918 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
540884 AGGGTAAAAG
540894 ACATTTGACTA
1 ACATTTGACTA
540905 ACATTTGACTA
1 ACATTTGACTA
540916 ACA
1 ACA
540919 ACCACATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (11 bp):
ACATTTGACTA
Found at i:544979 original size:2 final size:2
Alignment explanation
Indices: 544972--545005 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
544962 GAAAAAGATT
544972 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
545006 AATAAATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:546509 original size:18 final size:18
Alignment explanation
Indices: 546486--546524 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
546476 TTGAGGAGAA
546486 ATTATAT-TTAATATATAT
1 ATTATATATTAA-ATATAT
*
546504 ATTATATATTAAATTTAT
1 ATTATATATTAAATATAT
546522 ATT
1 ATT
546525 TTTAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATATATTAAATATAT
Found at i:546637 original size:18 final size:17
Alignment explanation
Indices: 546604--546647 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
546594 GGTAGTAAAA
546604 TATTATTTTAAATAATTAC
1 TATT-TTTTAAATAA-TAC
546623 -ATTTTTTACAATAATAC
1 TATTTTTTA-AATAATAC
546640 TATTTTTT
1 TATTTTTT
546648 TCATCCCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTTTTTAAATAATAC
Found at i:556079 original size:23 final size:23
Alignment explanation
Indices: 556049--556109 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
556039 CTCGTATAAA
556049 TACACCGAAGTGCCACATAGAAT
1 TACACCGAAGTGCCACATAGAAT
* *
556072 TACACCGAAGTGCCGCGTAGAAT
1 TACACCGAAGTGCCACATAGAAT
*
556095 TGCACCGAAGTGCCA
1 TACACCGAAGTGCCA
556110 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (23 bp):
TACACCGAAGTGCCACATAGAAT
Found at i:556436 original size:66 final size:66
Alignment explanation
Indices: 556364--556501 Score: 276
Period size: 66 Copynumber: 2.1 Consensus size: 66
556354 TAGAACATTT
556364 TCATATGATTCACATTTACATGTCACATAACTTATATACTTTCTCACGTAGTCACATAGATCCAT
1 TCATATGATTCACATTTACATGTCACATAACTTATATACTTTCTCACGTAGTCACATAGATCCAT
556429 G
66 G
556430 TCATATGATTCACATTTACATGTCACATAACTTATATACTTTCTCACGTAGTCACATAGATCCAT
1 TCATATGATTCACATTTACATGTCACATAACTTATATACTTTCTCACGTAGTCACATAGATCCAT
556495 G
66 G
556496 TCATAT
1 TCATAT
556502 AACATATATC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (66 bp):
TCATATGATTCACATTTACATGTCACATAACTTATATACTTTCTCACGTAGTCACATAGATCCAT
G
Found at i:560064 original size:17 final size:16
Alignment explanation
Indices: 560055--560133 Score: 65
Period size: 16 Copynumber: 5.1 Consensus size: 16
560045 GAAAAAACAC
560055 ACAAAAAGAAAGCAAAA
1 ACAAAAAGAAA-CAAAA
*
560072 ACAAAAAGAAAGAAAA
1 ACAAAAAGAAACAAAA
* ** *
560088 AGAAAAAGTGAGAAAA
1 ACAAAAAGAAACAAAA
560104 A-AAAAAGAAA-AAAA
1 ACAAAAAGAAACAAAA
* *
560118 AGAAAAA-AAAGAAAA
1 ACAAAAAGAAACAAAA
560133 A
1 A
560134 AGAATAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.15
15 17 0.31
16 18 0.33
17 11 0.20
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (16 bp):
ACAAAAAGAAACAAAA
Found at i:560071 original size:10 final size:9
Alignment explanation
Indices: 560058--560163 Score: 52
Period size: 9 Copynumber: 12.2 Consensus size: 9
560048 AAAACACACA
560058 AAAAGAAAG
1 AAAAGAAAG
*
560067 CAAAA-ACA-
1 -AAAAGAAAG
560075 AAAAGAAAG
1 AAAAGAAAG
560084 AAAAAGAAA-
1 -AAAAGAAAG
*
560093 AAGTGAGAAA-
1 AA--AAGAAAG
560103 AAAA-AAAG
1 AAAAGAAAG
*
560111 AAAAAAAAG
1 AAAAGAAAG
*
560120 AAAAAAAAG
1 AAAAGAAAG
560129 -AAA-AAAG
1 AAAAGAAAG
560136 AATAA-AAA-
1 AA-AAGAAAG
560144 AAGAA-AAAG
1 AA-AAGAAAG
560153 AAAAGAAAG
1 AAAAGAAAG
560162 AA
1 AA
560164 TATATAAAAC
Statistics
Matches: 80, Mismatches: 5, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
7 11 0.14
8 22 0.28
9 28 0.35
10 19 0.24
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:560104 original size:1 final size:1
Alignment explanation
Indices: 560100--560156 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
560090 AAAAAGTGAG
* * * * * * *
560100 AAAAAAAAAAGAAAAAAAAGAAAAAAAAGAAAAAAGAATAAAAAAAGAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
560157 GAAAGAATAT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (1 bp):
A
Found at i:560104 original size:27 final size:27
Alignment explanation
Indices: 560074--560160 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 27
560064 AAGCAAAAAC
*
560074 AAAAAGAAAGAAAAAGAAAAAGTGAGAAAAA
1 AAAAAGAAAGAAAAAG-AAAA---AGAAAGA
560105 AAAAAGAAA-AAAAAGAAAAA-AAAGA
1 AAAAAGAAAGAAAAAGAAAAAGAAAGA
*
560130 AAAAAGAATAAAAAAAGAAAAAGAAAAGA
1 AAAAAGAA-AGAAAAAGAAAAAG-AAAGA
560159 AA
1 AA
560161 GAATATATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
25 12 0.24
26 2 0.04
27 11 0.22
29 11 0.22
30 6 0.12
31 9 0.18
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (27 bp):
AAAAAGAAAGAAAAAGAAAAAGAAAGA
Found at i:560114 original size:9 final size:9
Alignment explanation
Indices: 560074--560163 Score: 80
Period size: 9 Copynumber: 9.9 Consensus size: 9
560064 AAGCAAAAAC
560074 AAAAAGAAA
1 AAAAAGAAA
560083 GAAAAAGAAA
1 -AAAAAGAAA
560093 AAGTGAGAA-AAA
1 AA---A-AAGAAA
560105 AAAAAGAAA
1 AAAAAGAAA
560114 AAAAAGAAA
1 AAAAAGAAA
560123 AAAAAG--A
1 AAAAAGAAA
*
560130 AAAAAGAAT
1 AAAAAGAAA
*
560139 AAAAA-AAG
1 AAAAAGAAA
560147 AAAAAGAAA
1 AAAAAGAAA
*
560156 AGAAAGAA
1 AAAAAGAA
560164 TATATAAAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 17
0.76 0.04 0.19
Matches are distributed among these distances:
7 7 0.10
8 9 0.13
9 35 0.51
10 9 0.13
12 6 0.09
13 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:560120 original size:36 final size:36
Alignment explanation
Indices: 560074--560160 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
560064 AAGCAAAAAC
560074 AAAAAGAAAGAAAAAGAAAAAGTGAGAAAAAAAAAAGAAA
1 AAAAAGAAA-AAAAAGAAAAA---AGAAAAAAAAAAGAAA
*
560114 AAAAAGAAAAAAAAGAAAAAAGAATAAAAAAAGAAAA
1 AAAAAGAAAAAAAAGAAAAAAGAAAAAAAAAAG-AAA
560151 AGAAAAGAAA
1 A-AAAAGAAA
560161 GAATATATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 12 0.27
37 4 0.09
38 8 0.18
39 11 0.25
40 9 0.20
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (36 bp):
AAAAAGAAAAAAAAGAAAAAAGAAAAAAAAAAGAAA
Found at i:560162 original size:33 final size:31
Alignment explanation
Indices: 560058--560163 Score: 117
Period size: 31 Copynumber: 3.4 Consensus size: 31
560048 AAAACACACA
*
560058 AAAAGAAAGCAAAAACAAAAAGAAAGAAAAAG
1 AAAAGAAAG-AAAAAAAAAAAGAAAGAAAAAG
**
560090 AAAA-AGTGAGAAAAAAAAAAGAAA-AAAAAG
1 AAAAGAAAGA-AAAAAAAAAAGAAAGAAAAAG
* *
560120 AAAAAAAAGAAAAAAGAATAAAAAAAGAAAAAG
1 AAAAGAAAGAAAAAA-AA-AAAGAAAGAAAAAG
560153 AAAAGAAAGAA
1 AAAAGAAAGAA
560164 TATATAAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
30 16 0.26
31 20 0.32
32 10 0.16
33 16 0.26
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (31 bp):
AAAAGAAAGAAAAAAAAAAAGAAAGAAAAAG
Found at i:561438 original size:20 final size:20
Alignment explanation
Indices: 561413--561483 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
561403 TCTTAATGAG
561413 TAAGTCTTTCGGGCCATCAA
1 TAAGTCTTTCGGGCCATCAA
* * *
561433 TAAGTCTTTCGAG-CATGATGTG
1 TAAGTCTTTCGGGCCATCA---A
*
561455 TAAGTCCTTCGGGCCATCAA
1 TAAGTCTTTCGGGCCATCAA
561475 TAAGTCTTT
1 TAAGTCTTT
561484 TGAGCATGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
22 11 0.28
23 4 0.10
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
TAAGTCTTTCGGGCCATCAA
Found at i:561465 original size:22 final size:22
Alignment explanation
Indices: 561433--561507 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
561423 GGGCCATCAA
*
561433 TAAGTCTTTCGAGCATGATGTG
1 TAAGTCCTTCGAGCATGATGTG
* * *
561455 TAAGTCCTTCGGGCCATCA---A
1 TAAGTCCTTCGAG-CATGATGTG
* *
561475 TAAGTCTTTTGAGCATGATGTG
1 TAAGTCCTTCGAGCATGATGTG
561497 TAAGTCCTTCG
1 TAAGTCCTTCG
561508 GGCCATCAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
19 4 0.11
20 10 0.26
22 20 0.53
23 4 0.11
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (22 bp):
TAAGTCCTTCGAGCATGATGTG
Found at i:561537 original size:42 final size:42
Alignment explanation
Indices: 561412--561520 Score: 200
Period size: 42 Copynumber: 2.6 Consensus size: 42
561402 TTCTTAATGA
*
561412 GTAAGTCTTTCGGGCCATCAATAAGTCTTTCGAGCATGATGT
1 GTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGT
*
561454 GTAAGTCCTTCGGGCCATCAATAAGTCTTTTGAGCATGATGT
1 GTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGT
561496 GTAAGTCCTTCGGGCCATCAATAAG
1 GTAAGTCCTTCGGGCCATCAATAAG
561521 ACCTTCGGGC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (42 bp):
GTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGT
Found at i:561614 original size:85 final size:85
Alignment explanation
Indices: 561504--561659 Score: 258
Period size: 85 Copynumber: 1.8 Consensus size: 85
561494 GTGTAAGTCC
*
561504 TTCGGGCCATCAATAAGACCTTCGGGCCGGATGTTTTCAACATTTCCTTTGCTCAATTCACAACA
1 TTCGGGCCATCAATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCAATTCACAACA
561569 CTTCGAATTAGCTTAAGTAT
66 CTTCGAATTAGCTTAAGTAT
* * ** *
561589 TTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTTGATTCACAATA
1 TTCGGGCCATCAATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCAATTCACAACA
561654 CTTCGA
66 CTTCGA
561660 TTCAATAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (85 bp):
TTCGGGCCATCAATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCAATTCACAACA
CTTCGAATTAGCTTAAGTAT
Found at i:561752 original size:20 final size:20
Alignment explanation
Indices: 561727--561772 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
561717 TGAATCAGCT
*
561727 TAAGTCATTCGGGCCATTAG
1 TAAGTCATTCGGGCCATCAG
*
561747 TAAGTCGTTCGGGCCATCAG
1 TAAGTCATTCGGGCCATCAG
561767 TAAGTC
1 TAAGTC
561773 TTTTAAGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (20 bp):
TAAGTCATTCGGGCCATCAG
Found at i:563128 original size:139 final size:134
Alignment explanation
Indices: 562831--563194 Score: 455
Period size: 139 Copynumber: 2.7 Consensus size: 134
562821 AGATGAACCA
* * *
562831 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-TGAAGGAGAAGAAGTTCA
* * * ** ** *
562896 TAATGAGAAGAGCTTATTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGATGCCTCGCT
65 TAATGAGAAGAACTTGTTCAACCT-TCACTCGATTCACGACATTTTGAATCAGCAACACCTCACT
*
562961 TGAGGG
129 CGAGGG
562967 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* *
563032 AATGAGAATAACTTGTTCAACCTT-AGCTCGATTCGTC-ACATATGGAGTTGAATCAGCAACACC
66 AATGAGAAGAACTTGTTCAACCTTCA-CTCGATTC-ACGACAT-T----TTGAATCAGCAACACC
563095 TCACTCGAGGG
124 TCACTCGAGGG
* *
563106 ATCAACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATG-AGGAAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGG-AGAAGAAGTTCA
* *
563170 TAATAAGTAGAACTTGTTCAACCTT
65 TAATGAGAAGAACTTGTTCAACCTT
563195 GGTAATTCCA
Statistics
Matches: 201, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
133 1 0.00
134 13 0.06
135 38 0.19
136 45 0.22
138 3 0.01
139 101 0.50
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (134 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTCACTCGATTCACGACATTTTGAATCAGCAACACCTCACTCG
AGGG
Found at i:565579 original size:20 final size:20
Alignment explanation
Indices: 565554--565607 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
565544 TGGAAGCTCG
*
565554 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
565574 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
565594 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
565608 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:565634 original size:19 final size:20
Alignment explanation
Indices: 565594--565644 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
565584 TTCTTTTTAA
*
565594 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
565614 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
*
565633 CGTTACGATTTT
1 CGTTGCGATTTT
565645 ATTGGTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:565824 original size:15 final size:14
Alignment explanation
Indices: 565797--565827 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
565787 TTCAAATTCA
565797 CTTTCTTTCTCTTC
1 CTTTCTTTCTCTTC
565811 CTTTCTTCTCTCTTC
1 CTTTCTT-TCTCTTC
565826 CT
1 CT
565828 CCATGGTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
CTTTCTTTCTCTTC
Found at i:567786 original size:13 final size:13
Alignment explanation
Indices: 567768--567806 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
567758 CAGTTTGATA
567768 GGCTGAATTTACG
1 GGCTGAATTTACG
567781 GGCTGAATTTACG
1 GGCTGAATTTACG
*
567794 GGCTCAATTTACG
1 GGCTGAATTTACG
567807 AGATAATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (13 bp):
GGCTGAATTTACG
Found at i:567927 original size:30 final size:30
Alignment explanation
Indices: 567891--567998 Score: 180
Period size: 30 Copynumber: 3.6 Consensus size: 30
567881 CTACAGTTCG
*
567891 AATGAAGGTCGCCAAGTGGTCTGGGCGACC
1 AATGAAGGTCGCCAGGTGGTCTGGGCGACC
*
567921 AATGAAGGTCGCCGGGTGGTCTGGGCGACC
1 AATGAAGGTCGCCAGGTGGTCTGGGCGACC
* *
567951 AATGAAGGTCGCCGGGTGTTCTGGGCGACC
1 AATGAAGGTCGCCAGGTGGTCTGGGCGACC
567981 AATGAAGGTCGCCAGGTG
1 AATGAAGGTCGCCAGGTG
567999 ATCCATGGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.40, T:0.18
Consensus pattern (30 bp):
AATGAAGGTCGCCAGGTGGTCTGGGCGACC
Found at i:568195 original size:50 final size:50
Alignment explanation
Indices: 568138--568239 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
568128 TTTATCCTAT
*
568138 TTTAGTATGTATTTATTTTAAAATTTATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
568188 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
568238 TT
1 TT
568240 CAATAATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:573155 original size:2 final size:2
Alignment explanation
Indices: 573148--573198 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
573138 GCTCTATCCC
573148 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
573190 TA TA TA TA T
1 TA TA TA TA T
573199 GAATAAATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:575429 original size:20 final size:20
Alignment explanation
Indices: 575404--575444 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
575394 GAAAAAACAT
575404 TCATTAAACCAAATTTTATA
1 TCATTAAACCAAATTTTATA
575424 TCATTAAACCAAATTTTATA
1 TCATTAAACCAAATTTTATA
575444 T
1 T
575445 TAGAGTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
TCATTAAACCAAATTTTATA
Found at i:577968 original size:3 final size:3
Alignment explanation
Indices: 577960--577998 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
577950 AGTTTTTGTG
577960 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
577999 CAAACCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:578219 original size:11 final size:11
Alignment explanation
Indices: 578185--578226 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
578175 AAACCAACCA
578185 CAAAATCAAAT
1 CAAAATCAAAT
578196 CAAAA-C--AT
1 CAAAATCAAAT
*
578204 AAAAATCAAAT
1 CAAAATCAAAT
578215 CAAAATCAAAT
1 CAAAATCAAAT
578226 C
1 C
578227 TAACAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 6 0.23
9 1 0.04
10 1 0.04
11 18 0.69
ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17
Consensus pattern (11 bp):
CAAAATCAAAT
Found at i:584398 original size:21 final size:21
Alignment explanation
Indices: 584372--584413 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
584362 CTCCCAAGAA
584372 TAGAAAATAGAAAAGCAACCT
1 TAGAAAATAGAAAAGCAACCT
584393 TAGAAAATAGAAAAGCAACCT
1 TAGAAAATAGAAAAGCAACCT
584414 AAAACTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (21 bp):
TAGAAAATAGAAAAGCAACCT
Found at i:585296 original size:53 final size:54
Alignment explanation
Indices: 585110--585802 Score: 669
Period size: 54 Copynumber: 12.9 Consensus size: 54
585100 TATGATGTCA
* * * *
585110 TCAAATGAATTTTTAAAGGAGTTAAGTCTGATTTTCAAGGGTTTCTTGATGTTT
1 TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* * * * * *
585164 ACAAATGGATTTTTAAATGAGCTAATCCTAATTTTCAGGGTTTTCTTAATGTTT
1 TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* * * * *
585218 ACAAATGGATTTTGAAA-GAAGCTAAGCCTGATTTTCAGGGGTTT-TTTATATTT
1 TCAAATGAATTTTTAAATG-AGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* *
585271 TCAAATG-ATTTTGTAAATGAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTTT
1 TCAAATGAATTTT-TAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* * * * * * *
585325 TCAAATGAATTTTGAAA-AAACTTAGCTTGACTTTCAGGGATTTCTTGATGTTT
1 TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* * * *
585378 TCAAATGAATGTTTAAATGAGCTAAGCCTAATTTTTAGGGG--T-TTGGTGTTT
1 TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* * * * * *
585429 TCAAATGAATTTTGAAA-AATTCTAAGCTTGATTTTTAGGGGTTTCTTAATGTTT
1 TCAAATGAATTTTTAAATGA-GCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* *
585483 T-AAATGAATTTTTAAATGAGCTAAGCCTGATTTTTAGGGGTTTCTTTATG-TT
1 TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* * * * * *
585535 TCAAATGAATTTTGAAATCAACTAATCTTGATTTTCTA-GGATTTCTTGATGTTT
1 TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTC-AGGGGTTTCTTGATGTTT
* * * * *
585589 TCAAATAAATGTTTAAATGAGCTAAGCTTTATTTTTAGGGGTTTCTTGATGTTT
1 TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* * * * *
585643 TCAAATGAATTTTGAAA-GAAGCTAAGCCTAATTTTCAAGGGTTTCTTGATATCT
1 TCAAATGAATTTTTAAATG-AGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
* * *
585697 TCAAATGGATTTTTAAA-GAGGCTAAGCCTGATTTTCAGGGGTTTCTTAATGATTACA
1 TCAAATGAATTTTTAAATGA-GCTAAGCCTGATTTTCAGGGGTTTCTTGATG-TT--T
* * * *
585754 TCAAATGAATTTTTAAAT-A-TTAAGTCTAATTTTTAGGGGTTTCTTGATG
1 TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATG
585803 ATATCTGTAA
Statistics
Matches: 525, Mismatches: 93, Indels: 41
0.80 0.14 0.06
Matches are distributed among these distances:
50 1 0.00
51 41 0.08
52 9 0.02
53 170 0.32
54 256 0.49
55 31 0.06
57 17 0.03
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.43
Consensus pattern (54 bp):
TCAAATGAATTTTTAAATGAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTT
Found at i:585323 original size:107 final size:108
Alignment explanation
Indices: 585110--585801 Score: 719
Period size: 107 Copynumber: 6.5 Consensus size: 108
585100 TATGATGTCA
* * * * * * *
585110 TCAAATGAATTTTTAAAGGAGTTAAGTCTGATTTTCAAGGGTTTCTTGATGTTTACAAATGGATT
1 TCAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGGATT
* * * * *
585175 TTTAAATGAGCTAATCCTAATTTTCAGGGTTTTCTTAATGTTT
66 TTTAAATGAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTT
* * *
585218 ACAAATGGATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTT-TTTATATTTTCAAAT-GATT
1 TCAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGGATT
*
585281 TTGTAAATGAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTTT
66 TT-TAAATGAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTT
* * * * * * * *
585325 TCAAATGAATTTTGAAA-AAACTTAGCTTGACTTTCAGGGATTTCTTGATGTTTTCAAATGAATG
1 TCAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGGATT
* *
585389 TTTAAATGAGCTAAGCCTAATTTTTAGGGG--T-TTGGTGTTT
66 TTTAAATGAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTT
* * * * * *
585429 TCAAATGAATTTTGAAA-AATTCTAAGCTTGATTTTTAGGGGTTTCTTAATGTTTT-AAATGAAT
1 TCAAATGAATTTTGAAAGAA-GCTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGGAT
*
585492 TTTTAAATGAGCTAAGCCTGATTTTTAGGGGTTTCTTTATG-TT
65 TTTTAAATGAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTT
* * * * * **
585535 TCAAATGAATTTTGAAATCAA-CTAATCTTGATTTTCTA-GGATTTCTTGATGTTTTCAAATAAA
1 TCAAATGAATTTTGAAA-GAAGCTAAGCCTGATTTTC-AGGGGTTTCTTGATATTTTCAAATGGA
* * *
585598 TGTTTAAATGAGCTAAGCTTTATTTTTAGGGGTTTCTTGATGTTT
64 TTTTTAAATGAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTT
* * *
585643 TCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAAGGGTTTCTTGATATCTTCAAATGGATT
1 TCAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGGATT
* * *
585708 TTTAAA-GAGGCTAAGCCTGATTTTCAGGGGTTTCTTAATGATTACA
66 TTTAAATGA-GCTAAGCCTGATTTTTAGGGGTTTCTTGATG-TT--T
* * * * * *
585754 TCAAATGAATTTTTAAA-TA-TTAAGTCTAATTTTTAGGGGTTTCTTGAT
1 TCAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGAT
585802 GATATCTGTA
Statistics
Matches: 496, Mismatches: 70, Indels: 35
0.83 0.12 0.06
Matches are distributed among these distances:
104 64 0.13
105 30 0.06
106 75 0.15
107 155 0.31
108 128 0.26
109 27 0.05
110 1 0.00
111 16 0.03
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.43
Consensus pattern (108 bp):
TCAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGGATT
TTTAAATGAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTT
Found at i:586805 original size:37 final size:37
Alignment explanation
Indices: 586719--586902 Score: 140
Period size: 37 Copynumber: 5.0 Consensus size: 37
586709 TAAGAAATTA
* * * * *
586719 TTGAGTCCTTCTTAGGACCTTTTCTCTA-TAAATTCAT
1 TTGAGTCTTTCTTAGGATCATTTCTCTAGAAAATT-GT
* * * * * *
586756 TAGAATCCTTCTTAGGAACGTTTTTCTAGAAAATTGT
1 TTGAGTCTTTCTTAGGATCATTTCTCTAGAAAATTGT
* * ** * **
586793 TTGAGTATTTCTTAAGATTGTTTCTCTATAATGTTGT
1 TTGAGTCTTTCTTAGGATCATTTCTCTAGAAAATTGT
* * *
586830 TTGAGTCCTTCTTAGGATCATTTATCTA-TAAATTGT
1 TTGAGTCTTTCTTAGGATCATTTCTCTAGAAAATTGT
586866 TTGAGTCCTTT-TTAGGATCATTTCTCTAGAAAATTGT
1 TTGAGT-CTTTCTTAGGATCATTTCTCTAGAAAATTGT
586903 AACAACCCAA
Statistics
Matches: 114, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
36 27 0.24
37 82 0.72
38 5 0.04
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (37 bp):
TTGAGTCTTTCTTAGGATCATTTCTCTAGAAAATTGT
Found at i:586805 original size:74 final size:73
Alignment explanation
Indices: 586719--586893 Score: 160
Period size: 74 Copynumber: 2.4 Consensus size: 73
586709 TAAGAAATTA
* * *
586719 TTGAGTC-CTTCTTAGGACCTTTTCTCTATAAAT-TCATTAGAATCCTTCTTAGGAACGTTTTTC
1 TTGAGTCATTTCTTAGGA-CTTTTCTCTAT-AATGTCATTAGAATCCTTCTTAGGAACATTTATC
586782 TAGAAAATTGT
64 TA-AAAATTGT
* * ** * * *
586793 TTGAGT-ATTTCTTAAGATTGTTTCTCTATAATGTTGTTTGAGTCCTTCTTAGGATCATTTATCT
1 TTGAGTCATTTCTTAGGACT-TTTCTCTATAATGTCATTAGAATCCTTCTTAGGAACATTTATCT
*
586857 ATAAATTGT
65 AAAAATTGT
* *
586866 TTGAGTCCTTT-TTAGGATCATTTCTCTA
1 TTGAGTCATTTCTTAGGA-CTTTTCTCTA
586894 GAAAATTGTA
Statistics
Matches: 81, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
73 30 0.37
74 51 0.63
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.47
Consensus pattern (73 bp):
TTGAGTCATTTCTTAGGACTTTTCTCTATAATGTCATTAGAATCCTTCTTAGGAACATTTATCTA
AAAATTGT
Found at i:589017 original size:23 final size:23
Alignment explanation
Indices: 588941--589019 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
588931 TACTATGTCA
*
588941 TTCGGGACA--TCTATGTGGTCC
1 TTCGGGACATTTCTACGTGGTCC
* * *
588962 TTCAGGACAATTCTACATGGT-C
1 TTCGGGACATTTCTACGTGGTCC
*
588984 TTCTGGGACATTTCTACGCGGTCC
1 TTC-GGGACATTTCTACGTGGTCC
589008 TTCGGGACATTT
1 TTCGGGACATTT
589020 TATATGGCAC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 8 0.17
22 4 0.09
23 31 0.66
24 4 0.09
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (23 bp):
TTCGGGACATTTCTACGTGGTCC
Found at i:589263 original size:21 final size:22
Alignment explanation
Indices: 589223--589264 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
589213 AAGATTATAT
589223 GATAAAAATGATTAATGATGAC
1 GATAAAAATGATTAATGATGAC
* *
589245 GATAAGAATG-TTGATGATGA
1 GATAAAAATGATTAATGATGA
589265 TAATGATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (22 bp):
GATAAAAATGATTAATGATGAC
Found at i:590401 original size:42 final size:42
Alignment explanation
Indices: 590291--590486 Score: 200
Period size: 42 Copynumber: 4.6 Consensus size: 42
590281 CTTTATTTGA
* * * *
590291 ATCCATCACAGAAGGGGTTGGATCAACATCAACATTTGACTT
1 ATCCATCACATAAGGAGTTGGATCAACATCATCATTTCACTT
* **
590333 GATTCCATTACATAAGGACATGGATCAACATCATCATTTCACTT
1 -A-TCCATCACATAAGGAGTTGGATCAACATCATCATTTCACTT
* * *
590377 ATCCATCACATAAGGAGTTTGATCAACATCATCATTTCGCTC
1 ATCCATCACATAAGGAGTTGGATCAACATCATCATTTCACTT
* *
590419 ATCCATCACATAAGGAGTTAGG--CAACATTACAT-TTTTCACTCG
1 ATCCATCACATAAGGAGTT-GGATCAACA-T-CATCATTTCACT-T
590462 ATTCCATCACATAAGGAGTTGGATC
1 A-TCCATCACATAAGGAGTTGGATC
590487 GGCACCAGCA
Statistics
Matches: 128, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
41 5 0.04
42 61 0.48
43 9 0.07
44 52 0.41
45 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (42 bp):
ATCCATCACATAAGGAGTTGGATCAACATCATCATTTCACTT
Found at i:590779 original size:239 final size:243
Alignment explanation
Indices: 590458--590935 Score: 632
Period size: 239 Copynumber: 2.0 Consensus size: 243
590448 ACATTTTTCA
* * * *
590458 CTCGATTCCATCACATAAGGAGTTGGATCGGCACCAGCACTACGTTTGATTCCATCACAAAAGGA
1 CTCGATTCCACCACATAAGGAGTTGGATCAGCACCAACACTACGTTTGATTCCATCACAAAAGAA
* *
590523 GGTGAATTAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTGTTCAACTTTA-GCTCAAT
66 GGTGAATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAAC---ACGCTCAAT
* * * *
590587 T-CATTACATAAGGAGTTGGATCAG-TGCTAGTACTACG-TTGATTTCATCACA-AAAAAG-GTG
128 TCCATCACATAAGGAGTTGGATCAGCAG-TAGCACTACGTTTGATTCCATCACATAAAAAGTGTG
* *
590647 GATCAATATTTCCAA-TGAAGAAGTTCATAACGAGAAGAACTTATTCAACATG
192 G-TCAACATTTCCAAGAGAAGAAGTTCATAACGAGAAGAACTTATTCAACATG
*** *
590699 CTCGATT-CACCACATAAGGAGTTGGATCATTGCCAACACTACG-TTGATTCCATCACAAAATAA
1 CTCGATTCCACCACATAAGGAGTTGGATCAGCACCAACACTACGTTTGATTCCATCACAAAAGAA
* *
590762 GGTGGATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAGCTTATTCAACACGCTCAATTCC
66 GGTGAATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAACACGCTCAATTCC
* * *
590827 ATCACATAAGGATTTGGATCAGCAGTAGCATTACGTTTGATTCCATCACATAAAAAGTTTGGTCA
131 ATCACATAAGGAGTTGGATCAGCAGTAGCACTACGTTTGATTCCATCACATAAAAAGTGTGGTCA
* * *
590892 ACGTTTCCAAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
196 ACATTTCCAAGAGAAGAAGTTCATAACGAGAAGAACTTATTCAA
590936 TTGGATCTTA
Statistics
Matches: 206, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
236 1 0.00
237 8 0.04
238 29 0.14
239 81 0.39
240 47 0.23
241 40 0.19
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (243 bp):
CTCGATTCCACCACATAAGGAGTTGGATCAGCACCAACACTACGTTTGATTCCATCACAAAAGAA
GGTGAATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAACACGCTCAATTCC
ATCACATAAGGAGTTGGATCAGCAGTAGCACTACGTTTGATTCCATCACATAAAAAGTGTGGTCA
ACATTTCCAAGAGAAGAAGTTCATAACGAGAAGAACTTATTCAACATG
Found at i:590814 original size:119 final size:120
Alignment explanation
Indices: 590462--590935 Score: 546
Period size: 120 Copynumber: 3.9 Consensus size: 120
590452 TTTTCACTCG
* ** * *
590462 ATTCCATCACATAAGGAGTTGGATCGGCACCAGCACTACGTTTGATTCCATCACAAAAGGAGGTG
1 ATTCCATCACATAAGGAGTTGGATCAGTGCCAACACTACGTTTGATTCCATCACAAAA-AAGGTG
* * * *
590527 AATTAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTGTTCAACTTTAGCTCA
65 GATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAAC-AT-GCTCA
* * ** *
590585 ATT-CATTACATAAGGAGTTGGATCAGTGCTAGTACTACG-TTGATTTCATCACAAAAAAGGTGG
1 ATTCCATCACATAAGGAGTTGGATCAGTGCCAACACTACGTTTGATTCCATCACAAAAAAGGTGG
* * * *
590648 ATCAATATTTCCAATGAAGAAGTTCATAACGAGAAGAACTTATTCAACATGCTCG
66 ATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAACATGCTCA
* *
590703 ATT-CACCACATAAGGAGTTGGATCATTGCCAACACTACG-TTGATTCCATCACAAAATAAGGTG
1 ATTCCATCACATAAGGAGTTGGATCAGTGCCAACACTACGTTTGATTCCATCACAAAA-AAGGTG
* *
590766 GATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAGCTTATTCAACACGCTCA
65 GATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAACATGCTCA
* * * * * *
590822 ATTCCATCACATAAGGATTTGGATCAGCAG-TAGCATTACGTTTGATTCCATCACATAAAAAGTT
1 ATTCCATCACATAAGGAGTTGGATCAG-TGCCAACACTACGTTTGATTCCATCACA-AAAAAG-G
* * * *
590886 TGG-TCAACGTTTCCAAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
63 TGGATCAACATTTCCAA-TGAAGAAGTTCATAATGAAAAGAACTTATTCAA
590936 TTGGATCTTA
Statistics
Matches: 302, Mismatches: 42, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
118 53 0.18
119 60 0.20
120 75 0.25
121 46 0.15
122 65 0.22
123 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (120 bp):
ATTCCATCACATAAGGAGTTGGATCAGTGCCAACACTACGTTTGATTCCATCACAAAAAAGGTGG
ATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAACATGCTCA
Found at i:590950 original size:122 final size:119
Alignment explanation
Indices: 590464--590961 Score: 490
Period size: 122 Copynumber: 4.1 Consensus size: 119
590454 TTCACTCGAT
* ** * *
590464 TCCATCACATAAGGAGTTGGATCGGCACCAGCACTACGTTTGATTCCATCACAAAAGGAGGTGAA
1 TCCATCACATAAGGAGTTGGATCAGCAGTAGCACTACG-TTGATTCCATCACAAAAGAAGGTGGA
* * *
590529 TTAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTGTTCAACTTTAGCTCAA
65 TCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAAC-TT-GATCAA
* * * * *
590586 TTCATTACATAAGGAGTTGGATCAG-TGCTAGTACTACGTTGATTTCATCACAAAA-AAGGTGGA
1 TCCATCACATAAGGAGTTGGATCAGCAG-TAGCACTACGTTGATTCCATCACAAAAGAAGGTGGA
* * * * * *
590649 TCAATATTTCCAATGAAGAAGTTCATAACGAGAAGAACTTATTCAACATGCTCGA
65 TCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAACTTGATCAA
* * *
590704 TTCACCACATAAGGAGTTGGATCATTGCCA--A-CACTACGTTGATTCCATCACAAAATAAGGTG
1 TCCATCACATAAGGAGTTGGATCA--G-CAGTAGCACTACGTTGATTCCATCACAAAAGAAGGTG
* ** *
590766 GATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAGCTTATTCAACACGCTCAA
63 GATCAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAACTTGATCAA
* * *
590823 TTCCATCACATAAGGATTTGGATCAGCAGTAGCATTACGTTTGATTCCATCACATAAA-AAGTTT
1 -TCCATCACATAAGGAGTTGGATCAGCAGTAGCACTACG-TTGATTCCATCACA-AAAGAAG-GT
* * * * *
590887 GG-TCAACGTTTCCAAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-TTGGATCTTA
62 GGATCAACATTTCCAA-TGAAGAAGTTCATAATGAAAAGAACTTATTCAACTT-GATC-AA
* *
590946 TCCATCATAGAAGGAG
1 TCCATCACATAAGGAG
590962 GTGCATTAAA
Statistics
Matches: 315, Mismatches: 45, Indels: 32
0.80 0.11 0.08
Matches are distributed among these distances:
117 2 0.01
118 50 0.16
119 60 0.19
120 76 0.24
121 45 0.14
122 81 0.26
123 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (119 bp):
TCCATCACATAAGGAGTTGGATCAGCAGTAGCACTACGTTGATTCCATCACAAAAGAAGGTGGAT
CAACATTTCCAATGAAGAAGTTCATAATGAAAAGAACTTATTCAACTTGATCAA
Found at i:591126 original size:3 final size:3
Alignment explanation
Indices: 591118--591149 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
591108 TTTTGATTTA
591118 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
591150 CCAACCGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.