Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008160.1 Hibiscus syriacus cultivar Beakdansim tig00110729_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: 1466564
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:527526 original size:64 final size:65
Alignment explanation
Indices: 527447--527605 Score: 227
Period size: 64 Copynumber: 2.5 Consensus size: 65
527437 TTATATGATA
* * * *
527447 TAAAATTAAATATCTATAATATATTTTTTAAAAATTAATATTTAATTTATTT-TAAAATTTAATA
1 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTTAATA
527511 T
65 T
527512 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAATTTAATA
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAAATTTAATA
527577 T
65 T
*
527578 TAAAATTAAAATC-A-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
527606 TTAAATATAA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
63 5 0.06
64 50 0.57
65 8 0.09
66 24 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (65 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTTAATAT
Found at i:527537 original size:14 final size:12
Alignment explanation
Indices: 527477--527609 Score: 74
Period size: 13 Copynumber: 10.7 Consensus size: 12
527467 ATATTTTTTA
527477 AAAATTAATATT
1 AAAATTAATATT
* * *
527489 -TAATTTATTTT
1 AAAATTAATATT
527500 AAAATTTAATATT
1 AAAA-TTAATATT
527513 AAAATTAATATCT
1 AAAATTAATAT-T
*
527526 ATAATATAATATT
1 AAAAT-TAATATT
527539 AAAAAATTAATATT
1 --AAAATTAATATT
* * * **
527553 TAATTTATTTAAA
1 AAAATTA-ATATT
527566 AAAATTTAATATT
1 AAAA-TTAATATT
*
527579 AAAATTAA-AAT
1 AAAATTAATATT
*
527590 CAAATATAATA-T
1 AAAAT-TAATATT
527602 AAAATTAA
1 AAAATTAA
527610 ATATAAAACA
Statistics
Matches: 90, Mismatches: 21, Indels: 21
0.68 0.16 0.16
Matches are distributed among these distances:
11 17 0.19
12 26 0.29
13 27 0.30
14 16 0.18
15 4 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:527556 original size:26 final size:26
Alignment explanation
Indices: 527505--527586 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
527495 ATTTTAAAAT
527505 TTAATATT--AAAATTAATATCTATAA
1 TTAATATTAAAAAATTAATAT-TATAA
527530 TATAATATTAAAAAATTAATATT-TAA
1 T-TAATATTAAAAAATTAATATTATAA
* *
527556 TTTAT-TTAAAAAAATTTAATATTAAAA
1 TTAATATT-AAAAAA-TTAATATTATAA
527583 TTAA
1 TTAA
527587 AATCAAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 2 0.04
25 10 0.21
26 19 0.40
27 6 0.12
28 11 0.23
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAATATTAAAAAATTAATATTATAA
Found at i:530115 original size:61 final size:61
Alignment explanation
Indices: 530020--530142 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
530010 AGGTAATTAT
*
530020 ACCTGTGATACGAGAGGTAAAAAGATTCTCCCAACATCCAAAGAGTGATACACCATATAAA
1 ACCTGTGATACGAGAGGTAAAAAGATACTCCCAACATCCAAAGAGTGATACACCATATAAA
530081 ACCTGTGATACGAGAGGTAAAAAGATACTCCCAACATCCAAAGAGTGATACACCATATAAA
1 ACCTGTGATACGAGAGGTAAAAAGATACTCCCAACATCCAAAGAGTGATACACCATATAAA
530142 A
1 A
530143 TTCAACGGCT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (61 bp):
ACCTGTGATACGAGAGGTAAAAAGATACTCCCAACATCCAAAGAGTGATACACCATATAAA
Found at i:549005 original size:105 final size:105
Alignment explanation
Indices: 548706--549537 Score: 1296
Period size: 105 Copynumber: 8.0 Consensus size: 105
548696 CATTGTTCCA
* * * ** * * * *
548706 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAATTTGTTTGTTAACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
548771 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
548812 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
548872 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
548912 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
548977 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
549017 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
549082 ATCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
549122 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
549187 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
549227 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
549292 AGCGGTCCCTTCGTCATAAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
549332 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
549397 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
549437 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
549502 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
549538 CCTCGAGTGC
Statistics
Matches: 680, Mismatches: 40, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 82 0.12
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 510 0.75
106 76 0.11
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:550296 original size:36 final size:35
Alignment explanation
Indices: 550245--550525 Score: 256
Period size: 36 Copynumber: 8.0 Consensus size: 35
550235 TTCAAAGGTT
* *
550245 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
550281 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
550316 CTTAG-TTCTAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTC-AAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
550354 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
550383 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
550418 TTTATTTCAAGGGAAACTATCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
550455 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
550490 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
550526 CTCTTCTAGT
Statistics
Matches: 202, Mismatches: 25, Indels: 36
0.77 0.10 0.14
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 132 0.65
37 33 0.16
38 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:550376 original size:138 final size:137
Alignment explanation
Indices: 550190--550499 Score: 381
Period size: 138 Copynumber: 2.3 Consensus size: 137
550180 TTGTTTCATG
* * * * ** * * * *
550190 AGAAACGGTCTCAAGGGAAACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGAAAACATATTCAAAGATTTTGTTTCAAG
* * *
550255 GGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
66 GGAAACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
550319 AG-TTCTAAA
129 AGTTTC-AAA
* ** *
550328 AGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGAAAACATATTCAAAGATTTTGTTTCAAG
* * * *
550393 GGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTATCTCAAGATAGACGAAATTTG
66 GGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAG
*
550458 TTTCAAG
131 TTTCAAA
550465 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA
550500 GGGAAACTGT
Statistics
Matches: 147, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
137 41 0.28
138 106 0.72
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGAAAACATATTCAAAGATTTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAG
TTTCAAA
Found at i:550469 original size:102 final size:102
Alignment explanation
Indices: 550281--550469 Score: 281
Period size: 102 Copynumber: 1.9 Consensus size: 102
550271 TAGACGAAAA
* *
550281 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTATCTCAAGAGA
*
550346 GACGGAATTTGTTTCAAAGAAAACATATTCAAATATT
66 GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
* * * ** *
550383 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTC-AAGGGAAACTATCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTATCTCAAGAGA
550447 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAA-AGAAA
550470 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 32 0.42
102 45 0.58
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTATCTCAAGAGA
GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
Found at i:550547 original size:35 final size:36
Alignment explanation
Indices: 550387--550559 Score: 163
Period size: 36 Copynumber: 4.8 Consensus size: 36
550377 AATATTTTGT
* * **
550387 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * * *
550423 TTCAAGGGAAACTATCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
550459 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
550495 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
550529 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
550560 TCTTGTTTTA
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 90 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:550567 original size:71 final size:72
Alignment explanation
Indices: 550387--550567 Score: 224
Period size: 72 Copynumber: 2.5 Consensus size: 72
550377 AATATTTTGT
* * *
550387 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTATCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACGA
** *
550452 AATTTGT
66 AAACTGC
*
550459 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACGA
550523 AAACT-C
66 AAACTGC
* * * *
550529 TTCTAGTGAAAACGGTCTCAAGCGAGAC-AAATCTTGTTT
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAAT-TTGTTT
550568 TAAGAAAAAC
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
70 10 0.10
71 27 0.28
72 59 0.61
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (72 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACGA
AAACTGC
Found at i:551031 original size:18 final size:18
Alignment explanation
Indices: 551004--551039 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
550994 TGTTGAATCC
* *
551004 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
551022 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
551040 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:551481 original size:22 final size:22
Alignment explanation
Indices: 551455--551503 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
551445 TTGTGTTTGG
* *
551455 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
551477 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
551499 TCAAA
1 TCAAA
551504 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:551510 original size:22 final size:22
Alignment explanation
Indices: 551467--551510 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
551457 AAAGGTTTGG
* * *
551467 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
551489 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
551511 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:552166 original size:23 final size:23
Alignment explanation
Indices: 552139--552220 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
552129 TTTTTGTCCC
*
552139 TTTTTCTTTTTGATTTTTGCTCT
1 TTTTTCTTTTTGTTTTTTGCTCT
* *
552162 TTTTTCCTTTTGTTCTTGTTTCTCT
1 TTTTTCTTTTTGTT-TT-TTGCTCT
*
552187 TTTTTTTTTTTGCTTTTTTGCT-T
1 TTTTTCTTTTTG-TTTTTTGCTCT
*
552210 CTTTTCTTTTT
1 TTTTTCTTTTT
552221 TGTTCTTGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 22 0.46
24 6 0.12
25 18 0.38
26 2 0.04
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.77
Consensus pattern (23 bp):
TTTTTCTTTTTGTTTTTTGCTCT
Found at i:552173 original size:39 final size:40
Alignment explanation
Indices: 552130--552205 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 40
552120 TGCATGTGCT
552130 TTTTGTCCCT-TTT-TCTTTTTGATTTTTGCTCTTTTTTCC
1 TTTTGTCCCTGTTTCTCTTTTTGATTTTTGCT-TTTTTTCC
* * **
552169 TTTTGTTCTTGTTTCTCTTTTTTTTTTTTGCTTTTTT
1 TTTTGTCCCTGTTTCTCTTTTTGATTTTTGCTTTTTT
552206 GCTTCTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 8 0.26
40 8 0.26
41 15 0.48
ACGTcount: A:0.01, C:0.16, G:0.08, T:0.75
Consensus pattern (40 bp):
TTTTGTCCCTGTTTCTCTTTTTGATTTTTGCTTTTTTTCC
Found at i:552197 original size:25 final size:25
Alignment explanation
Indices: 552158--552228 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
552148 TTGATTTTTG
**
552158 CTCTTTTTTCCTTTTGTTCTTGTTT
1 CTCTTTTTTTTTTTTGTTCTTGTTT
552183 CTCTTTTTTTTTTTTG--CTT-TTT
1 CTCTTTTTTTTTTTTGTTCTTGTTT
552205 -TGCTTCTTTTCTTTTTTGTTCTTG
1 CT-CTT-TTTT-TTTTTTGTTCTTG
552229 ATTGGATCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 1 0.03
22 6 0.16
23 7 0.18
24 7 0.18
25 14 0.37
26 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.08, T:0.75
Consensus pattern (25 bp):
CTCTTTTTTTTTTTTGTTCTTGTTT
Found at i:552203 original size:31 final size:30
Alignment explanation
Indices: 552161--552221 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
552151 ATTTTTGCTC
*
552161 TTTTTTCCTTTTGTT-CTTGTTTCTCTTTTTT
1 TTTTTTCCTTTT-TTGCTTCTTT-TCTTTTTT
*
552192 TTTTTTGCTTTTTTGCTTCTTTTCTTTTTT
1 TTTTTTCCTTTTTTGCTTCTTTTCTTTTTT
552222 GTTCTTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.79
Consensus pattern (30 bp):
TTTTTTCCTTTTTTGCTTCTTTTCTTTTTT
Found at i:555407 original size:34 final size:35
Alignment explanation
Indices: 555330--555427 Score: 144
Period size: 34 Copynumber: 2.8 Consensus size: 35
555320 ATAGTAGAAC
555330 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA--AAAAT
* * *
555367 TTTATCCTATTTTTAAGAGTTAGAATCCT-AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
555401 TCTATCCTATTTTTAGGAGTTTGAATC
1 TCTATCCTATTTTTAGGAGTTTGAATC
555428 ATAGTAGGAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 29 0.53
37 26 0.47
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:556685 original size:182 final size:183
Alignment explanation
Indices: 556378--556762 Score: 629
Period size: 182 Copynumber: 2.1 Consensus size: 183
556368 TTTTCTAATT
* *
556378 TATATAAAAT-TA-AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAAT
1 TATATAATATATATAATA-TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAAT
556441 TATAAAATAAAAATTCTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65 TATAAAATAAAAATTCTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
*
556506 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
*
556560 TATATAATATATATAATATTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAAT
1 TATATAATATATATAATATTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATAAATAAT
*
556624 TATAAAATAAAAAATT-TATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TATAAAAT-AAAAATTCTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*
556687 TGGATCTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATATGTTA
129 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
*
556742 TATATAATATATTTAATATTT
1 TATATAATATATATAATATTT
556763 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 7, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
181 2 0.01
182 127 0.66
183 51 0.27
184 11 0.06
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (183 bp):
TATATAATATATATAATATTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAATT
ATAAAATAAAAATTCTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:565621 original size:10 final size:10
Alignment explanation
Indices: 565592--565660 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
565582 GCTGCTGGAA
565592 AACCGGTTTG
1 AACCGGTTTG
*
565602 -ACCAGTTTTG
1 AACC-GGTTTG
565612 AACCGGTTTG
1 AACCGGTTTG
*
565622 -ACCGGTCTG
1 AACCGGTTTG
565631 AACCGGTTTG
1 AACCGGTTTG
*
565641 -ACCGGTCTG
1 AACCGGTTTG
*
565650 AACCGGGTTG
1 AACCGGTTTG
565660 A
1 A
565661 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:565634 original size:19 final size:19
Alignment explanation
Indices: 565592--565662 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
565582 GCTGCTGGAA
* *
565592 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
565612 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
565631 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
565650 AACCGGGTTGACC
1 AACCGGTTTGACC
565663 CGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:565677 original size:14 final size:14
Alignment explanation
Indices: 565658--565685 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
565648 TGAACCGGGT
565658 TGACCCGACCCGAC
1 TGACCCGACCCGAC
565672 TGACCCGACCCGAC
1 TGACCCGACCCGAC
565686 CCGACTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:565703 original size:17 final size:17
Alignment explanation
Indices: 565656--565732 Score: 100
Period size: 17 Copynumber: 4.4 Consensus size: 17
565646 TCTGAACCGG
565656 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
565673 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
*
565692 GTTGACCAGACCCGACT
1 GTTGACCCGACCCGACT
*
565709 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
565726 GTTGACC
1 GTTGACC
565733 GTTGACCGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
17 36 0.71
19 15 0.29
ACGTcount: A:0.19, C:0.43, G:0.23, T:0.14
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:566683 original size:63 final size:63
Alignment explanation
Indices: 566615--566738 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
566605 CTAATGTGAC
* ** * *
566615 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
566678 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
566739 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:572415 original size:12 final size:12
Alignment explanation
Indices: 572400--572424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
572390 TGTTGTATCG
572400 TGGTTTTCTGTT
1 TGGTTTTCTGTT
572412 TGGTTTTCTGTT
1 TGGTTTTCTGTT
572424 T
1 T
572425 CAAACAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.24, T:0.68
Consensus pattern (12 bp):
TGGTTTTCTGTT
Found at i:572974 original size:20 final size:19
Alignment explanation
Indices: 572949--573000 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
572939 GCTGCTGGAA
* *
572949 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
572969 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
572988 AACCGGGTTGACC
1 AACCGGTTTGACC
573001 CGACCCGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:572978 original size:10 final size:10
Alignment explanation
Indices: 572949--572998 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
572939 GCTGCTGGAA
572949 AACCGGTTTG
1 AACCGGTTTG
*
572959 -ACCAGTTTTG
1 AACC-GGTTTG
572969 AACCGGTTTG
1 AACCGGTTTG
*
572979 -ACCGGTCTG
1 AACCGGTTTG
*
572988 AACCGGGTTG
1 AACCGGTTTG
572998 A
1 A
572999 CCCGACCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.34
10 18 0.56
11 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:573015 original size:14 final size:14
Alignment explanation
Indices: 572996--573023 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
572986 TGAACCGGGT
572996 TGACCCGACCCGAC
1 TGACCCGACCCGAC
573010 TGACCCGACCCGAC
1 TGACCCGACCCGAC
573024 CCGACTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:573038 original size:17 final size:17
Alignment explanation
Indices: 572994--573053 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
572984 TCTGAACCGG
572994 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
573011 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
*
573030 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
573047 GTTGACC
1 GTTGACC
573054 GTTGACCGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 21 0.58
19 15 0.42
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.13
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:573038 original size:22 final size:19
Alignment explanation
Indices: 572997--573046 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 19
572987 GAACCGGGTT
572997 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
573016 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGAC---TGACCC
573038 GACCCGACC
1 GACCCGACC
573047 GTTGACCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.46
22 15 0.54
ACGTcount: A:0.20, C:0.50, G:0.22, T:0.08
Consensus pattern (19 bp):
GACCCGACCCGACTGACCC
Found at i:574004 original size:63 final size:63
Alignment explanation
Indices: 573936--574059 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
573926 CTAATGTGAC
* ** * *
573936 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
573999 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
574060 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:574947 original size:17 final size:17
Alignment explanation
Indices: 574925--574999 Score: 105
Period size: 17 Copynumber: 4.3 Consensus size: 17
574915 AACGGTCAAC
*
574925 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
574942 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
574959 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
**
574976 GGTCGGGTCAGTCGGGTCG
1 GGTC--AACAGTCGGGTCG
574995 GGTCA
1 GGTCA
575000 GCCCGGTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
17 37 0.71
19 15 0.29
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:574991 original size:14 final size:14
Alignment explanation
Indices: 574972--575000 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
574962 CAACAGTCGG
574972 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
574986 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
575000 G
1 G
575001 CCCGGTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:575026 original size:19 final size:19
Alignment explanation
Indices: 575002--575047 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
574992 TCGGGTCAGC
*
575002 CCGGTTCAGACCGATCCAA
1 CCGGTTCAGACCGATCAAA
*
575021 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGATCAAA
575040 CCGGTTCA
1 CCGGTTCA
575048 AAACTGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.17
Consensus pattern (19 bp):
CCGGTTCAGACCGATCAAA
Found at i:575035 original size:10 final size:10
Alignment explanation
Indices: 574997--575047 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
574987 TCGGGTCGGG
*
574997 TCAGCCCGGT
1 TCAGACCGGT
*
575007 TCAGACCGAT
1 TCAGACCGGT
*
575017 CCA-ACCGGT
1 TCAGACCGGT
575026 TCAGACCGG-
1 TCAGACCGGT
*
575035 TCAAACCGGT
1 TCAGACCGGT
575045 TCA
1 TCA
575048 AAACTGGTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 15 0.45
10 18 0.55
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:575058 original size:20 final size:19
Alignment explanation
Indices: 575002--575062 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
574992 TCGGGTCAGC
* * *
575002 CCGGTTCAGACCGATCCAA
1 CCGGTTCAAACCGGTCAAA
*
575021 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAAACCGGTCAAA
*
575040 CCGGTTCAAAACTGGTCAAA
1 CCGGTTC-AAACCGGTCAAA
575060 CCG
1 CCG
575063 ATTTTCCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 24 0.65
20 13 0.35
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (19 bp):
CCGGTTCAAACCGGTCAAA
Found at i:596774 original size:21 final size:21
Alignment explanation
Indices: 596750--596789 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
596740 TTTTCTCCTC
* *
596750 TACACTCAACCCAAAGAGGAT
1 TACACTAAACCAAAAGAGGAT
*
596771 TACATTAAACCAAAAGAGG
1 TACACTAAACCAAAAGAGG
596790 GTATTACCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.15
Consensus pattern (21 bp):
TACACTAAACCAAAAGAGGAT
Found at i:604546 original size:21 final size:23
Alignment explanation
Indices: 604522--604571 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
604512 TTATCCAAAT
*
604522 ATTAAGG-ATATTTAG-TCTTTA
1 ATTAAGGAATATTCAGCTCTTTA
*
604543 ATTAGGGAAATATTCAGCTCTTTA
1 ATTAAGG-AATATTCAGCTCTTTA
604567 ATTAA
1 ATTAA
604572 ACCCATAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.26
23 7 0.30
24 10 0.43
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (23 bp):
ATTAAGGAATATTCAGCTCTTTA
Found at i:605742 original size:45 final size:45
Alignment explanation
Indices: 605693--605778 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
605683 AAAAGCCTGG
* *
605693 GTGCATCGATGCATGGTCTGTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCACTGA
605738 GTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
1 GTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
605779 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (45 bp):
GTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCACTGA
Found at i:605826 original size:20 final size:20
Alignment explanation
Indices: 605798--605836 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
605788 CAAGAAATTA
605798 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
605818 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
605837 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:606205 original size:19 final size:20
Alignment explanation
Indices: 606167--606206 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
606157 TTTGAAATTA
*
606167 CTCCCCCTTACTATAACATTT
1 CTCCCCCTTA-TAAAACATTT
606188 CTCCCCCTT-TAAAACATTT
1 CTCCCCCTTATAAAACATTT
606207 TACACTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCCCCCTTATAAAACATTT
Found at i:608562 original size:44 final size:44
Alignment explanation
Indices: 608470--608566 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
608460 GACCCTATGC
* * *
608470 ATCGATGCACATTCAAGGCGTGCATCGGTGCATTAACATGATGA
1 ATCGATGCACATTCAAGGCGTGCATCGATGCACTAACAAGATGA
** *
608514 ATCGATGCACATTCAAAGG-GATGCATCGATGCACTATTAAG-TGT
1 ATCGATGCACATTC-AAGGCG-TGCATCGATGCACTAACAAGATGA
608558 ATCGATGCA
1 ATCGATGCA
608567 TGAAGCACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 26 0.58
45 19 0.42
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCGTGCATCGATGCACTAACAAGATGA
Found at i:612369 original size:22 final size:22
Alignment explanation
Indices: 612327--612370 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
612317 GAGTTTATTT
**
612327 TCATTTTTCAATTTTTGAAACA
1 TCATTTTTCAATTTTAAAAACA
612349 TCATTTTT-ATATTTTAAAAACA
1 TCATTTTTCA-ATTTTAAAAACA
612371 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.50
Consensus pattern (22 bp):
TCATTTTTCAATTTTAAAAACA
Found at i:622741 original size:41 final size:41
Alignment explanation
Indices: 622696--622836 Score: 273
Period size: 41 Copynumber: 3.4 Consensus size: 41
622686 ACGCGATAGT
622696 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
622737 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
*
622778 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGATAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
622819 CGAAGTTCGCATTGCGAT
1 CGAAGTTCGCATTGCGAT
622837 AGTCCAAATA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (41 bp):
CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:623764 original size:83 final size:83
Alignment explanation
Indices: 623565--623913 Score: 291
Period size: 83 Copynumber: 4.2 Consensus size: 83
623555 AATAGCGGCC
* * * * * * * * * *
623565 TTTTTAGAAAAACACCGCTAAAGACTCATACTATAGCGGCGTTTTTA-TAAAAACGACGCTAAAG
1 TTTTTATACAAACGCCGCTAAAGACGCATACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAAG
*
623629 AAT-GTACTGTAGTGGCG
66 AATAGTACTTTAGTGGCG
* * * * *
623646 TTTTTATACAAACACCGCTATAGAC-TAGTGA-TTTAGTGGCGTTTTTTA-TACAAACGCCGCTA
1 TTTTTATACAAACGCCGCTAAAGACGCA-T-ACTTTAGTGGCG-TTTTAAGCACAAACGCCGCTA
* *
623708 TAGACTAGTACTTTAGTGGCG
63 AAGAATAGTACTTTAGTGGCG
* * * * *
623729 TTTTTATACAAACGCTGCTAAAGACGCATACTTTAGTGGCGTTTTAAGCCCAAACGCCTCCAAAT
1 TTTTTATACAAACGCCGCTAAAGACGCATACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAAG
* **
623794 ACTCTTACTTTAGTGGCG
66 AATAGTACTTTAGTGGCG
* * * * *
623812 CTTTTATATAAACGCCGCTAAATACTG--TACTTTAATGGTGTTTTAAGCACAAACGCCGCTAAA
1 TTTTTATACAAACGCCGCTAAAGAC-GCATACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAA
* *
623875 TAATCA-TTCTTTAGTGGCG
65 GAAT-AGTACTTTAGTGGCG
*
623894 TTTTTATACAAACGCTGCTA
1 TTTTTATACAAACGCCGCTA
623914 TATATATACC
Statistics
Matches: 220, Mismatches: 39, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
80 1 0.00
81 31 0.14
82 92 0.42
83 94 0.43
84 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (83 bp):
TTTTTATACAAACGCCGCTAAAGACGCATACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAAG
AATAGTACTTTAGTGGCG
Found at i:623907 original size:41 final size:40
Alignment explanation
Indices: 623565--623913 Score: 295
Period size: 41 Copynumber: 8.5 Consensus size: 40
623555 AATAGCGGCC
* * * * *
623565 TTTTTAGAAAAACACCGCTAAAGACTCATACTATAGCGGCG
1 TTTTTATACAAACGCCGCTAAAGACT-ATACTTTAGTGGCG
* * * * *
623606 TTTTTATAAAAACGACGCTAAAGAATGTACTGTAGTGGCG
1 TTTTTATACAAACGCCGCTAAAGACTATACTTTAGTGGCG
* *
623646 TTTTTATACAAACACCGCTATAGACTAGTGA-TTTAGTGGCG
1 TTTTTATACAAACGCCGCTAAAGACTA-T-ACTTTAGTGGCG
*
623687 TTTTTTATACAAACGCCGCTATAGACTAGTACTTTAGTGGCG
1 -TTTTTATACAAACGCCGCTAAAGACTA-TACTTTAGTGGCG
* *
623729 TTTTTATACAAACGCTGCTAAAGACGCATACTTTAGTGGCG
1 TTTTTATACAAACGCCGCTAAAGAC-TATACTTTAGTGGCG
* ** * * * *
623770 TTTTAAGCCCAAACGCCTCCAAATACTCTTACTTTAGTGGCG
1 TTTTTA-TACAAACGCCGCTAAAGACT-ATACTTTAGTGGCG
* * * * * *
623812 CTTTTATATAAACGCCGCTAAATACTGTACTTTAATGGTG
1 TTTTTATACAAACGCCGCTAAAGACTATACTTTAGTGGCG
* * * * *
623852 TTTTAAGCACAAACGCCGCTAAATAATCATTCTTTAGTGGCG
1 TTTTTA-TACAAACGCCGCTAAAGACT-ATACTTTAGTGGCG
*
623894 TTTTTATACAAACGCTGCTA
1 TTTTTATACAAACGCCGCTA
623914 TATATATACC
Statistics
Matches: 250, Mismatches: 49, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
40 47 0.19
41 118 0.47
42 85 0.34
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (40 bp):
TTTTTATACAAACGCCGCTAAAGACTATACTTTAGTGGCG
Found at i:627408 original size:21 final size:22
Alignment explanation
Indices: 627384--627443 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
627374 TGATTTATTA
*
627384 TTATGGATTTCAATTTTCTTG-
1 TTATGGATTTCAAGTTTCTTGT
* *
627405 TTATGGATTTTAAGTTTGTTGT
1 TTATGGATTTCAAGTTTCTTGT
*
627427 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
627444 ATTGGAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (22 bp):
TTATGGATTTCAAGTTTCTTGT
Found at i:627681 original size:43 final size:42
Alignment explanation
Indices: 627634--627820 Score: 164
Period size: 43 Copynumber: 4.4 Consensus size: 42
627624 TATATACCAG
* * *
627634 ACCTATTGTGGCGTTTGTGTCAAACACGTCGCTAAATCTCAAC
1 ACCTATTGCGGCGTTTGTGTAAAACACG-CGCTAAATATCAAC
* * *
627677 ACCTATTGCAGCGTTTGTTGGAAAACAC-CACTAAATATCAAC
1 ACCTATTGCGGCGTTTG-TGTAAAACACGCGCTAAATATCAAC
* *
627719 ACCTATTGCGGCGTTTGGTGGACAA-ACGCCGCTAAATATCAAC
1 ACCTATTGCGGCGTTT-GTGTAAAACACG-CGCTAAATATCAAC
* ** * ***
627762 ACCTATTACGGCGTTTGTCCAATAA-ACGCCGCTATATATCGTT
1 ACCTATTGCGGCGTTTGTGTAA-AACACG-CGCTAAATATCAAC
627805 ACCTATTGCGGCGTTT
1 ACCTATTGCGGCGTTT
627821 TTTATTACCA
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.02
42 36 0.30
43 75 0.62
44 8 0.07
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (42 bp):
ACCTATTGCGGCGTTTGTGTAAAACACGCGCTAAATATCAAC
Found at i:627723 original size:42 final size:43
Alignment explanation
Indices: 627634--627779 Score: 172
Period size: 43 Copynumber: 3.4 Consensus size: 43
627624 TATATACCAG
* * * *
627634 ACCTATTGTGGCGTTTG-T-GTCAAACACGTCGCTAAATCTCAAC
1 ACCTATTGCGGCGTTTGTTGGACAAACAC--CACTAAATATCAAC
*
627677 ACCTATTGCAGCGTTTGTTGGA-AAACACCACTAAATATCAAC
1 ACCTATTGCGGCGTTTGTTGGACAAACACCACTAAATATCAAC
* * *
627719 ACCTATTGCGGCGTTTGGTGGACAAACGCCGCTAAATATCAAC
1 ACCTATTGCGGCGTTTGTTGGACAAACACCACTAAATATCAAC
*
627762 ACCTATTACGGCGTTTGT
1 ACCTATTGCGGCGTTTGT
627780 CCAATAAACG
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
42 32 0.36
43 49 0.55
44 7 0.08
45 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (43 bp):
ACCTATTGCGGCGTTTGTTGGACAAACACCACTAAATATCAAC
Found at i:628289 original size:5 final size:5
Alignment explanation
Indices: 628281--628324 Score: 70
Period size: 5 Copynumber: 8.6 Consensus size: 5
628271 TCGTCCCGTC
*
628281 TCGGG TCGGG TCGGG TCGGG TCGGG TCAGG TCGGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG
628325 TGGTAATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.02, C:0.20, G:0.55, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:628505 original size:41 final size:41
Alignment explanation
Indices: 628404--628577 Score: 276
Period size: 41 Copynumber: 4.2 Consensus size: 41
628394 GAAATATTTG
* * *
628404 GACTATCGCAACGAATTGGAATGAATCGCAATGTGATATTTG
1 GACTATCGCAACGAATTGGAATGAATCGCAATGCGA-ACTTC
628446 GACTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTC
*
628487 GCCTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTC
* * *
628528 GCCTGTCGCAACGAATTTGAATGAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTC
628569 GACTATCGC
1 GACTATCGC
628578 GTTGCGAATC
Statistics
Matches: 124, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 89 0.72
42 35 0.28
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (41 bp):
GACTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTC
Found at i:629587 original size:19 final size:19
Alignment explanation
Indices: 629563--629601 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
629553 TCAATGCCCT
629563 TGTTATCCCTTATGTCGAC
1 TGTTATCCCTTATGTCGAC
629582 TGTTATCCCTTATGTCGAC
1 TGTTATCCCTTATGTCGAC
629601 T
1 T
629602 CTATTTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (19 bp):
TGTTATCCCTTATGTCGAC
Found at i:634748 original size:16 final size:16
Alignment explanation
Indices: 634727--634761 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
634717 TGAGTACCGG
634727 TGAGTACCACTAATGA
1 TGAGTACCACTAATGA
*
634743 TGAGTACTACTAATGA
1 TGAGTACCACTAATGA
634759 TGA
1 TGA
634762 CCACATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (16 bp):
TGAGTACCACTAATGA
Found at i:635579 original size:58 final size:58
Alignment explanation
Indices: 635442--635568 Score: 218
Period size: 58 Copynumber: 2.2 Consensus size: 58
635432 ATTGATTGGG
* * **
635442 GAAAATAAGAAACATAATTTGACTGAATGTTTGAAGTCTATTTTATTTTATGTAGATT
1 GAAAATAAGAAACATAATTTGACTGAAAGTTGGAAGTCTATTCCATTTTATGTAGATT
635500 GAAAATAAGAAACATAATTTGACTGAAAGTTGGAAGTCTATTCCATTTTATGTAGATT
1 GAAAATAAGAAACATAATTTGACTGAAAGTTGGAAGTCTATTCCATTTTATGTAGATT
635558 GAAAATAAGAA
1 GAAAATAAGAA
635569 GCATGGTTTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (58 bp):
GAAAATAAGAAACATAATTTGACTGAAAGTTGGAAGTCTATTCCATTTTATGTAGATT
Found at i:636454 original size:71 final size:72
Alignment explanation
Indices: 636379--636521 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 72
636369 CAAAACATTT
*
636379 AAATTTAATTAAATTTCTTTATTTTAA-TTTTTAATAAACTTTATTTCAATTATGTAATTTGAAT
1 AAATTTAATTAAATTTATTTATTTTAATTTTTTAATAAACTTTATTTCAATTATGTAATTTGAAT
636443 TATTAAA
66 TATTAAA
** *
636450 AAATTTAATTTTATTTATTTATTTTAATTTTTTAATAAATTTTATTTCAATTATGTAATTTGAAT
1 AAATTTAATTAAATTTATTTATTTTAATTTTTTAATAAACTTTATTTCAATTATGTAATTTGAAT
*
636515 TTTTAAA
66 TATTAAA
636522 TTTTATGTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 24 0.36
72 42 0.64
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (72 bp):
AAATTTAATTAAATTTATTTATTTTAATTTTTTAATAAACTTTATTTCAATTATGTAATTTGAAT
TATTAAA
Found at i:636518 original size:36 final size:36
Alignment explanation
Indices: 636399--636520 Score: 147
Period size: 36 Copynumber: 3.4 Consensus size: 36
636389 AAATTTCTTT
* *
636399 ATTTTAATTTTTAATAAACTTTATTTCAATTATGTA
1 ATTTGAATTTTTAATAAATTTTATTTCAATTATGTA
* * * * * *
636435 ATTTGAATTATTAAAAAATTTAATTTTATTTAT-TT
1 ATTTGAATTTTTAATAAATTTTATTTCAATTATGTA
*
636470 ATTTTAATTTTTTAATAAATTTTATTTCAATTATGTA
1 ATTTGAA-TTTTTAATAAATTTTATTTCAATTATGTA
636507 ATTTGAATTTTTAA
1 ATTTGAATTTTTAA
636521 ATTTTATGTA
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
35 7 0.10
36 54 0.79
37 7 0.10
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.57
Consensus pattern (36 bp):
ATTTGAATTTTTAATAAATTTTATTTCAATTATGTA
Found at i:636657 original size:2 final size:2
Alignment explanation
Indices: 636646--636686 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
636636 TAATCCTAAC
636646 TA TA -A 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
636687 GTTAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:636773 original size:27 final size:27
Alignment explanation
Indices: 636688--636784 Score: 76
Period size: 27 Copynumber: 3.7 Consensus size: 27
636678 ATATATATAG
* *
636688 TTAAAAATATTTT-TATATTAACTT-A-
1 TTAAAAATATTTTAT-TTTTAAGTTCAT
* * *
636713 TTAAATATATTTTATTATTAAGTTCCT
1 TTAAAAATATTTTATTTTTAAGTTCAT
* **
636740 TTTAAAATATTTTATTTTTATTTTCAT
1 TTAAAAATATTTTATTTTTAAGTTCAT
*
636767 TTAAAAATA-TATATTTTT
1 TTAAAAATATTTTATTTTT
636785 GTTAAAATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
25 20 0.34
26 9 0.16
27 29 0.50
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (27 bp):
TTAAAAATATTTTATTTTTAAGTTCAT
Found at i:641538 original size:31 final size:31
Alignment explanation
Indices: 641457--641539 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 31
641447 CAATAGCCAC
** *
641457 TTTCGTTTTGTTTTAATTAAGATATGATCAT
1 TTTCGTTTCATTTTAATTAAGATGTGATCAT
641488 TTTCGTTTCA--TT--TTAAGATGTGATCAT
1 TTTCGTTTCATTTTAATTAAGATGTGATCAT
641515 TTTCGTTTCATTTTAATTAAGATGT
1 TTTCGTTTCATTTTAATTAAGATGT
641540 AGTCAATTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
27 24 0.53
29 4 0.09
31 17 0.38
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.54
Consensus pattern (31 bp):
TTTCGTTTCATTTTAATTAAGATGTGATCAT
Found at i:643644 original size:2 final size:2
Alignment explanation
Indices: 643639--643674 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
643629 TATTTTTTAA
643639 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
643675 TAATAATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:645539 original size:3 final size:3
Alignment explanation
Indices: 645531--645616 Score: 68
Period size: 3 Copynumber: 26.7 Consensus size: 3
645521 AGGAAAAATG
*
645531 AAT AAT AAT AAT AAGT AAT ATAT ATAT ATAT ATAT ATAT ATAT ATT AAT
1 AAT AAT AAT AAT AA-T AAT A-AT A-AT A-AT A-AT A-AT A-AT AAT AAT
*
645580 -AT AAT AA- AAT AAAC AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
645617 ATTCAAAACC
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.05
3 42 0.57
4 28 0.38
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:645555 original size:2 final size:2
Alignment explanation
Indices: 645548--645575 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
645538 ATAATAAGTA
645548 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
645576 TAATATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:645673 original size:38 final size:37
Alignment explanation
Indices: 645621--646046 Score: 392
Period size: 39 Copynumber: 11.2 Consensus size: 37
645611 TAATAAATTC
* * * *
645621 AAAACCATACATTATATACATTTTCAAAACTATTTTCA
1 AAAACTATATATTATATATATTTTCAAAA-TGTTTTCA
645659 AAAACTATATATTATATATATTTTTTCAAAATGTTTTCA
1 AAAACTATATATTATATATA--TTTTCAAAATGTTTTCA
*
645698 AAAACTATATA-TATATATA--TTCAAAAACGTTTTCA
1 AAAACTATATATTATATATATTTTC-AAAATGTTTTCA
* *
645733 AAAACTATATATTATATATGTTTT-AAAA--TTTTCC
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
* * *
645767 AAAACTATA-ATATATATATATATTCAAAATATTTTTA
1 AAAACTATATAT-TATATATATTTTCAAAATGTTTTCA
645804 AAAACTATATATTATATATATTTTTTCAAAATGTTTTCA
1 AAAACTATATATTATATATA--TTTTCAAAATGTTTTCA
*
645843 AAAACTATATATTATATATATTTTTTAAAAATGTTTTC-
1 AAAACTATATATTATATATA--TTTTCAAAATGTTTTCA
*
645881 AAAACTATA-ATATATATATATATTT-AAAACGTTTTCAA
1 AAAACTATATAT-TATATATAT-TTTCAAAATGTTTTC-A
* *
645919 AACTATAATATATATATATATATATATATTCGAAATGTTTTC-
1 AA--A-ACTATATAT-TATATATAT-T-TTCAAAATGTTTTCA
* *
645961 AAAACTATATAATATATATATTTTCGAAATTCGTTTTCTA
1 AAAACTATATATTATATATATTTTC-AAAAT-GTTTTC-A
* *
646001 AAAATTATATA-T-TATATATTTTCAAAAAATATTTTCA
1 AAAACTATATATTATATATATTTTC--AAAATGTTTTCA
646038 AAAACTATA
1 AAAACTATA
646047 CTATATTAAT
Statistics
Matches: 332, Mismatches: 28, Indels: 57
0.80 0.07 0.14
Matches are distributed among these distances:
33 2 0.01
34 27 0.08
35 26 0.08
36 25 0.08
37 39 0.12
38 79 0.24
39 81 0.24
40 21 0.06
41 5 0.02
42 16 0.05
43 2 0.01
44 9 0.03
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAATGTTTTCA
Found at i:645980 original size:46 final size:44
Alignment explanation
Indices: 645886--645981 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 44
645876 TTTTCAAAAC
*
645886 TATA-ATATATATATATATTTAAAACGTTTTCAAAACTATAATA
1 TATATATATATATATATATTCAAAACGTTTTCAAAACTATAATA
* *
645929 TATATATATATATATATATTCGAAATGTTTTCAAAACTAT-ATA
1 TATATATATATATATATATTCAAAACGTTTTCAAAACTATAATA
645972 -ATATATATAT
1 TATATATATAT
645982 TTTCGAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 10 0.20
43 7 0.14
44 32 0.65
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (44 bp):
TATATATATATATATATATTCAAAACGTTTTCAAAACTATAATA
Found at i:646034 original size:13 final size:13
Alignment explanation
Indices: 646016--646041 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
646006 TATATATTAT
646016 ATATTTTCAAAAA
1 ATATTTTCAAAAA
646029 ATATTTTCAAAAA
1 ATATTTTCAAAAA
646042 CTATACTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATTTTCAAAAA
Found at i:646797 original size:85 final size:85
Alignment explanation
Indices: 646653--646972 Score: 408
Period size: 85 Copynumber: 3.8 Consensus size: 85
646643 ATATGTCATC
* * * *
646653 GAGCTGAATGGAATTGAACTCGACA-GTTTTTGTTGACAGATAGCCCTTCTCACTTTGAGCAATG
1 GAGCTGAATGGAATCGAACTCGA-AGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* * *
646717 TTGTAAATTTAATACGCCTTT
65 TTGTAAATTTGATATGCCCTT
* * * * *
646738 GAGCTGAATGGAATTGAACTCGAAGGTTTTTGTTGACAAATAGTCCTTCTCGCCCTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGT
646803 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * * * * *
646823 GAGCTTAATGTAATCGAACTCGTAGGTTTTTGTTGACAGATAGTCCTTCTCTCCTTGATCTATGT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGT
646888 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * * * *
646908 GAGCTGAATGTAATCAAACTTGAAGGTTTTTTGCTGGCAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGAAGG-TTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
646973 CTGCGAATAG
Statistics
Matches: 205, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
84 1 0.00
85 171 0.83
86 33 0.16
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGT
TGTAAATTTGATATGCCCTT
Found at i:648348 original size:20 final size:20
Alignment explanation
Indices: 648310--648349 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
648300 AAGTCAGGGC
* **
648310 ATTTAACCGATTGGTCTAGA
1 ATTTAACCAATTGCACTAGA
648330 ATTTAACCAATTGCACTAGA
1 ATTTAACCAATTGCACTAGA
648350 GGGACAACTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATTTAACCAATTGCACTAGA
Found at i:648475 original size:99 final size:99
Alignment explanation
Indices: 648361--648567 Score: 326
Period size: 99 Copynumber: 2.1 Consensus size: 99
648351 GGACAACTCA
* * * *
648361 ATATTATAATCACCTTTATCAGGCTAGCTTAATCTTCTCCATAAAGCCGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
*
648426 GCTTTAGAGCGACAACTCAAGCTTTATTGTATAG
66 GCTCTAGAGCGACAACTCAAGCTTTATTGTATAG
* *
648460 ATATTATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCAGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
* *
648525 GCTCTAGAGGGACAACTCAAGCTTTATTGTATAT
66 GCTCTAGAGCGACAACTCAAGCTTTATTGTATAG
648559 ATA-TATAAT
1 ATATTATAAT
648568 ATTATAATAT
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 6 0.06
99 93 0.94
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
GCTCTAGAGCGACAACTCAAGCTTTATTGTATAG
Found at i:658742 original size:20 final size:20
Alignment explanation
Indices: 658714--658751 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
658704 ATTGTAAAAT
*
658714 AAAATAATAAAAAAATATGA
1 AAAAGAATAAAAAAATATGA
658734 AAAAGAATAAAAAAATAT
1 AAAAGAATAAAAAAATAT
658752 TAATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAGAATAAAAAAATATGA
Found at i:660193 original size:2 final size:2
Alignment explanation
Indices: 660181--660221 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
660171 TTTCAAAAAC
660181 TA TA T- 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
660222 AATGTTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:660260 original size:25 final size:27
Alignment explanation
Indices: 660210--660260 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
660200 TATATATATA
660210 TATATATATATAAATGTTTTCAAAAAC
1 TATATATATATAAATGTTTTCAAAAAC
*
660237 TATATAT-TATATATGTTTTCAAAA
1 TATATATATATAAATGTTTTCAAAA
660261 TTTTCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (27 bp):
TATATATATATAAATGTTTTCAAAAAC
Found at i:660284 original size:36 final size:37
Alignment explanation
Indices: 660198--660511 Score: 217
Period size: 38 Copynumber: 8.6 Consensus size: 37
660188 TATATATATA
* ** **
660198 TATATATATATATATATATATATAAATGTTTTCAAAAAC
1 TATATATATATATATAT-TTTCGAAACATTTTC-AAAAC
*
660237 TATATAT-TATATATGTTTTC-AAA-ATTTTCAAAAC
1 TATATATATATATATATTTTCGAAACATTTTCAAAAC
* *
660271 TATAATATATATATATATATAT--AATA-TTTTTCAAAAAAC
1 TAT-ATATATATATATAT-TTTCGAA-ACATTTTC--AAAAC
* * **
660310 TATTTAT-TATATATATTTTCAAAATGTTTTCAAAAC
1 TATATATATATATATATTTTCGAAACATTTTCAAAAC
* * **
660346 TATATA-ATATATACATATTCGAAATGTTTTCAAAAC
1 TATATATATATATATATTTTCGAAACATTTTCAAAAC
**
660382 --TATATA-ATATATATTTTCGAAATGTTTTCAAAAC
1 TATATATATATATATATTTTCGAAACATTTTCAAAAC
* *
660416 TATAT-GATATATATATTTTCGAATACCGTTTTCAAAAC
1 TATATATATATATATATTTTCGAA-A-CATTTTCAAAAC
*
660454 TATATA-ATATATATATTTTCGAAATCCATTTTCTAAAAA
1 TATATATATATATATATTTTCGAAA--CATTTTC-AAAAC
*
660493 T-TATATAT-TATATGTTTTC
1 TATATATATATATATATTTTC
660512 AAAAAAATAT
Statistics
Matches: 234, Mismatches: 21, Indels: 41
0.79 0.07 0.14
Matches are distributed among these distances:
34 38 0.16
35 11 0.05
36 69 0.29
37 22 0.09
38 72 0.31
39 22 0.09
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (37 bp):
TATATATATATATATATTTTCGAAACATTTTCAAAAC
Found at i:660486 original size:38 final size:36
Alignment explanation
Indices: 660198--660478 Score: 288
Period size: 36 Copynumber: 7.7 Consensus size: 36
660188 TATATATATA
* **
660198 TATATATATATATATATATATATAAATGTTTTCAAAAAC
1 TATATA-ATATATATAT-TTTCGAAATGTTTTC-AAAAC
* * *
660237 TATATATTATATATGTTTTC-AAA-ATTTTCAAAAC
1 TATATAATATATATATTTTCGAAATGTTTTCAAAAC
*
660271 TATAATATATATATATATATAT--AATAT-TTTTCAAAAAAC
1 TAT-ATA-ATATATATAT-TTTCGAA-ATGTTTTC--AAAAC
* * *
660310 TATTTATTATATATATTTTCAAAATGTTTTCAAAAC
1 TATATAATATATATATTTTCGAAATGTTTTCAAAAC
* *
660346 TATATAATATATACATATTCGAAATGTTTTCAAAAC
1 TATATAATATATATATTTTCGAAATGTTTTCAAAAC
660382 TATAT-A-ATATATATTTTCGAAATGTTTTCAAAAC
1 TATATAATATATATATTTTCGAAATGTTTTCAAAAC
* *
660416 TATATGATATATATATTTTCGAATACCGTTTTCAAAAC
1 TATATAATATATATATTTTCGAA-A-TGTTTTCAAAAC
660454 TATATAATATATATATTTTCGAAAT
1 TATATAATATATATATTTTCGAAAT
660479 CCATTTTCTA
Statistics
Matches: 207, Mismatches: 21, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
34 39 0.19
35 10 0.05
36 71 0.34
37 23 0.11
38 50 0.24
39 14 0.07
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATAATATATATATTTTCGAAATGTTTTCAAAAC
Found at i:660511 original size:38 final size:38
Alignment explanation
Indices: 660305--660505 Score: 231
Period size: 36 Copynumber: 5.4 Consensus size: 38
660295 TATTTTTCAA
* * *
660305 AAAACTATTTATTATATATATTTTCAAAAT--GTTTTC
1 AAAACTATATAATATATATATTTTCGAAATCCGTTTTC
* *
660341 AAAACTATATAATATATACATATTCGAAAT--GTTTTC
1 AAAACTATATAATATATATATTTTCGAAATCCGTTTTC
660377 AAAACTATAT-A-ATATATATTTTCGAAAT--GTTTTC
1 AAAACTATATAATATATATATTTTCGAAATCCGTTTTC
*
660411 AAAACTATATGATATATATATTTTCG-AATACCGTTTTC
1 AAAACTATATAATATATATATTTTCGAAAT-CCGTTTTC
*
660449 AAAACTATATAATATATATATTTTCGAAATCCATTTTC
1 AAAACTATATAATATATATATTTTCGAAATCCGTTTTC
* *
660487 TAAAAATTATATATTATAT
1 --AAAACTATATAATATAT
660506 GTTTTCAAAA
Statistics
Matches: 146, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
34 31 0.21
35 5 0.03
36 54 0.37
38 38 0.26
39 3 0.02
40 15 0.10
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (38 bp):
AAAACTATATAATATATATATTTTCGAAATCCGTTTTC
Found at i:670914 original size:25 final size:25
Alignment explanation
Indices: 670886--670939 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
670876 GACCCGGTTG
670886 CAGCAACCCATAATTGTGCCATTTC
1 CAGCAACCCATAATTGTGCCATTTC
**
670911 CAGCTCCCCATAATTGTGCCATTTC
1 CAGCAACCCATAATTGTGCCATTTC
670936 CAGC
1 CAGC
670940 TCCCACGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (25 bp):
CAGCAACCCATAATTGTGCCATTTC
Found at i:670940 original size:25 final size:25
Alignment explanation
Indices: 670892--670943 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
670882 GTTGCAGCAA
670892 CCCATAATTGTGCCATTTCCAGCTC
1 CCCATAATTGTGCCATTTCCAGCTC
670917 CCCATAATTGTGCCATTTCCAGCTC
1 CCCATAATTGTGCCATTTCCAGCTC
670942 CC
1 CC
670944 ACGTGAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.38, G:0.12, T:0.31
Consensus pattern (25 bp):
CCCATAATTGTGCCATTTCCAGCTC
Found at i:672453 original size:22 final size:22
Alignment explanation
Indices: 672427--672472 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
672417 CTGCAAGAGA
*
672427 AATAAAAAATAAAAATATTAAT
1 AATAAAAAATAAAAATAGTAAT
** *
672449 AATAATTAATAATAATAGTAAT
1 AATAAAAAATAAAAATAGTAAT
672471 AA
1 AA
672473 CATAAAAACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAAAAAATAAAAATAGTAAT
Found at i:676140 original size:43 final size:43
Alignment explanation
Indices: 676092--676179 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
676082 AAAAGAATAG
676092 TAAAAAATAAATAAGTCAGGAAAGAAAAACATTTTCAGACATA
1 TAAAAAATAAATAAGTCAGGAAAGAAAAACATTTTCAGACATA
676135 TAAAAAATAAATAAGTCAGGAAAGAAAAACATTTTCAGACATA
1 TAAAAAATAAATAAGTCAGGAAAGAAAAACATTTTCAGACATA
676178 TA
1 TA
676180 TGAACCTGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (43 bp):
TAAAAAATAAATAAGTCAGGAAAGAAAAACATTTTCAGACATA
Found at i:681184 original size:14 final size:13
Alignment explanation
Indices: 681162--681191 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
681152 AAAAATGTCG
681162 TTTTTTATTTTAA
1 TTTTTTATTTTAA
681175 TTTTTATATTTTAA
1 TTTTT-TATTTTAA
681189 TTT
1 TTT
681192 GTATCCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTTAA
Found at i:681573 original size:14 final size:14
Alignment explanation
Indices: 681544--681599 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
681534 CGTTCGTGAA
681544 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
681560 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
681574 CG----TTTATGTC
1 CGTTCATTTATGTT
681584 CGTTCATTTATGTT
1 CGTTCATTTATGTT
681598 CG
1 CG
681600 AACAAAGGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 9 0.26
14 17 0.50
15 3 0.09
16 5 0.15
ACGTcount: A:0.14, C:0.16, G:0.18, T:0.52
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:681587 original size:24 final size:26
Alignment explanation
Indices: 681545--681600 Score: 89
Period size: 24 Copynumber: 2.2 Consensus size: 26
681535 GTTCGTGAAC
*
681545 GTTCGATTATATGTTCGTTCATTTAT
1 GTTCGATTATATGTCCGTTCATTTAT
681571 GTTCG-TT-TATGTCCGTTCATTTAT
1 GTTCGATTATATGTCCGTTCATTTAT
681595 GTTCGA
1 GTTCGA
681601 ACAAAGGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 21 0.75
25 2 0.07
26 5 0.18
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (26 bp):
GTTCGATTATATGTCCGTTCATTTAT
Found at i:681880 original size:10 final size:10
Alignment explanation
Indices: 681867--681930 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
681857 GTGCTTGTGT
681867 TGTTCGTTTA
1 TGTTCGTTTA
*
681877 TGTTAGTTTA
1 TGTTCGTTTA
*
681887 TTGTGTTCGTTTT
1 ---TGTTCGTTTA
681900 TGTTCGTTTA
1 TGTTCGTTTA
* * *
681910 CGGTCGCTTA
1 TGTTCGTTTA
681920 TGTTCGTTTA
1 TGTTCGTTTA
681930 T
1 T
681931 CATTTAAATG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
10 33 0.80
13 8 0.20
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:682291 original size:23 final size:23
Alignment explanation
Indices: 682258--682335 Score: 138
Period size: 23 Copynumber: 3.4 Consensus size: 23
682248 TAAGTGTCCT
*
682258 TGGTTGATTGCTTTCCTGATGCA
1 TGGTTGTTTGCTTTCCTGATGCA
*
682281 TGGTCGTTTGCTTTCCTGATGCA
1 TGGTTGTTTGCTTTCCTGATGCA
682304 TGGTTGTTTGCTTTCCTGATGCA
1 TGGTTGTTTGCTTTCCTGATGCA
682327 TGGTTGTTT
1 TGGTTGTTT
682336 ACATATGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (23 bp):
TGGTTGTTTGCTTTCCTGATGCA
Found at i:688470 original size:19 final size:20
Alignment explanation
Indices: 688426--688470 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
688416 ACAACCGCGT
*
688426 AACATGTACCAAACAGCAGTGG
1 AACAAGTACCAAACAGCA--GG
688448 AACAAGTACCAAACAGC-GG
1 AACAAGTACCAAACAGCAGG
688467 AACA
1 AACA
688471 GAAAGGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
22 16 0.73
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (20 bp):
AACAAGTACCAAACAGCAGG
Found at i:688861 original size:23 final size:22
Alignment explanation
Indices: 688835--688895 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
688825 TTTCCGGCTC
688835 TGGTAAACAAAGTTTTTTCGGTT-
1 TGGTAAAC-AAGTTTTTT-GGTTA
688858 TGGT-AAC-AGTTTTTTGGTTA
1 TGGTAAACAAGTTTTTTGGTTA
*
688878 TAGTAAACAGAGTTTTTT
1 TGGTAAACA-AGTTTTTT
688896 TATTCTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 3 0.09
22 3 0.09
23 12 0.36
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (22 bp):
TGGTAAACAAGTTTTTTGGTTA
Found at i:688887 original size:21 final size:20
Alignment explanation
Indices: 688845--688883 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
688835 TGGTAAACAA
*
688845 AGTTTTTTCGGTTTGGTAAC
1 AGTTTTTTCGGTTTAGTAAC
688865 AGTTTTTT-GGTTATAGTAA
1 AGTTTTTTCGGTT-TAGTAA
688884 ACAGAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (20 bp):
AGTTTTTTCGGTTTAGTAAC
Found at i:703494 original size:3 final size:3
Alignment explanation
Indices: 703488--703552 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
703478 ATTTTTTTAT
*
703488 TTA TTA TTTG TTA TTA TTA -TA TTA TT- TTA TT- TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
**
703532 TTA TTA AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
703553 CAAACAGGCC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 6 0.12
3 40 0.78
4 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:703546 original size:35 final size:35
Alignment explanation
Indices: 703482--703548 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
703472 TTATCCATTT
* **
703482 TTTTATTTATTATTTGTTATTATTATATTATTTTA
1 TTTTATTTATTATTTATTATTAAAATATTATTTTA
703517 TTTTATTTATTA-TTATTATTAAAATTATTATT
1 TTTTATTTATTATTTATTATTAAAA-TATTATT
703549 ATTACAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 9 0.32
35 19 0.68
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (35 bp):
TTTTATTTATTATTTATTATTAAAATATTATTTTA
Found at i:703550 original size:28 final size:29
Alignment explanation
Indices: 703488--703551 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
703478 ATTTTTTTAT
* * **
703488 TTATTATTTGTTATTATTATATTATTTTA
1 TTATTATTTATTATTATTATATAAAATTA
703517 TT-TTATTTATTATTATTAT-TAAAATTA
1 TTATTATTTATTATTATTATATAAAATTA
703544 TTATTATT
1 TTATTATT
703552 ACAAACAGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 21 0.70
29 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (29 bp):
TTATTATTTATTATTATTATATAAAATTA
Found at i:703628 original size:26 final size:25
Alignment explanation
Indices: 703589--703638 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
703579 TATAGTTCCA
*
703589 GACCCAATTCAGATGGCCCAACAGT
1 GACCCAATTCAGATAGCCCAACAGT
703614 GACCCAACTTCAGATAGCCCAACAG
1 GACCCAA-TTCAGATAGCCCAACAG
703639 AGCCCAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.34, C:0.34, G:0.18, T:0.14
Consensus pattern (25 bp):
GACCCAATTCAGATAGCCCAACAGT
Found at i:703644 original size:25 final size:24
Alignment explanation
Indices: 703587--703645 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
703577 ATTATAGTTC
*
703587 CAGA-CCCAATTCAGATGGCCCAA
1 CAGAGCCCAATTCAGATAGCCCAA
*
703610 CAGTGACCCAACTTCAGATAGCCCAA
1 CAGAG-CCCAA-TTCAGATAGCCCAA
703636 CAGAGCCCAA
1 CAGAGCCCAA
703646 ATGTGTAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
25 10 0.33
26 17 0.57
ACGTcount: A:0.36, C:0.36, G:0.17, T:0.12
Consensus pattern (24 bp):
CAGAGCCCAATTCAGATAGCCCAA
Found at i:705499 original size:11 final size:13
Alignment explanation
Indices: 705462--705501 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
705452 TGTTTAATAA
705462 AATATA-TATATT
1 AATATATTATATT
*
705474 AATATATTATCTT
1 AATATATTATATT
705487 AA-A-ATTATATT
1 AATATATTATATT
705498 AATA
1 AATA
705502 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:715777 original size:113 final size:111
Alignment explanation
Indices: 715503--716414 Score: 596
Period size: 123 Copynumber: 7.8 Consensus size: 111
715493 ACAATAGATT
* * * *
715503 AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAGGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * *
715568 AGAAGAACTTGTTTAACCTTTTGTTCAAATCCATAAC-AATGGATC
66 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTGATGGATC
* *
715613 AACATTTCTAGAAGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * **
715678 AGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGTTTC
66 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCAC-TGATGGATC
* * * *
715725 AGCATTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAAT
1 AACATTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
* * * * *
715790 GAGAAGAATTTGTTTAACCTTTTTCTTAAATTCATCACTCGATGGACC
65 GAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACT-GATGGATC
* * *
715838 AACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-AGAGTTCATAA
1 AACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA-AATTCATAA
* * * * * * *
715902 TGAGAAGAACTTGTTCGACCTTTTACAT-GACTTTATCACAGAAGGAGATATATCATCATC
64 TGAGAAGAACTTGTTCAACCTTTTGC-TCAAATTCATCACTG-ATG-G----------ATC
* * * * *
715962 AACATTTCCAGAAGTGTTCATAATGAGAAGAAATCATCTGAAGAAAGAAGAAGGAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * * * *
716027 AGAAGAACTTGTTCGACCTTTTACAT-GACTTTATCACAGAAGGAGATATATCATCATC
66 AGAAGAACTTGTTCAACCTTTTGC-TCAAATTCATCACTG-ATG-G----------ATC
* * * * * *
716085 AACATTTCTAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATA
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * * **
716150 AGAAGAACTTGTTCGACCTTTTACAT-GACTTTATCAGAGAATGAGATATATCATCATC
66 AGAAGAACTTGTTCAACCTTTTGC-TCAAATTCATCACTG-ATG-G----------ATC
* * * *
716208 AACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * * * *
716273 AGAAGAACTTGTTCGACCTTTTACAT-GACTTTATCACAGAAGGAGATATATCATCATC
66 AGAAGAACTTGTTCAACCTTTTGC-TCAAATTCATCACTG-ATG-G----------ATC
* * *
716331 AACATTTCCAGAAGTGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
*
716395 AGAAGAATTTGTTCAACCTT
66 AGAAGAACTTGTTCAACCTT
716415 GCCTTAATTC
Statistics
Matches: 717, Mismatches: 65, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
110 90 0.13
112 16 0.02
113 175 0.24
114 2 0.00
122 37 0.05
123 384 0.54
124 13 0.02
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (111 bp):
AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTGATGGATC
Found at i:716004 original size:123 final size:123
Alignment explanation
Indices: 715854--716414 Score: 1007
Period size: 123 Copynumber: 4.6 Consensus size: 123
715844 TCCAGAGAAA
* *
715854 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAGAGTTCATAATGAGAAGAACTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATGAGAAGAACTTGTTCG
715919 ACCTTTTACATGACTTTATCACAGAAGGAGATATATCATCATCAACATTTCCAGAAGT
66 ACCTTTTACATGACTTTATCACAGAAGGAGATATATCATCATCAACATTTCCAGAAGT
*
715977 GTTCATAATGAGAAGAAATCATCTGAAGAAAGAAGAAGGAGTTCATAATGAGAAGAACTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATGAGAAGAACTTGTTCG
*
716042 ACCTTTTACATGACTTTATCACAGAAGGAGATATATCATCATCAACATTTCTAGAAGT
66 ACCTTTTACATGACTTTATCACAGAAGGAGATATATCATCATCAACATTTCCAGAAGT
*
716100 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATAAGAAGAACTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATGAGAAGAACTTGTTCG
* *
716165 ACCTTTTACATGACTTTATCAGAGAATGAGATATATCATCATCAACATTTCCAGAAGT
66 ACCTTTTACATGACTTTATCACAGAAGGAGATATATCATCATCAACATTTCCAGAAGT
716223 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATGAGAAGAACTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATGAGAAGAACTTGTTCG
716288 ACCTTTTACATGACTTTATCACAGAAGGAGATATATCATCATCAACATTTCCAGAAGT
66 ACCTTTTACATGACTTTATCACAGAAGGAGATATATCATCATCAACATTTCCAGAAGT
* * * * *
716346 GTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATGAGAAGAACTTGTTCG
716410 ACCTT
66 ACCTT
716415 GCCTTAATTC
Statistics
Matches: 421, Mismatches: 17, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
122 37 0.09
123 384 0.91
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (123 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGGAGTTCATAATGAGAAGAACTTGTTCG
ACCTTTTACATGACTTTATCACAGAAGGAGATATATCATCATCAACATTTCCAGAAGT
Found at i:716789 original size:3 final size:3
Alignment explanation
Indices: 716781--716831 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
716771 TATTTATTTG
**
716781 TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA AAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
716826 TTA TTA
1 TTA TTA
716832 CAAACAGGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:716907 original size:26 final size:25
Alignment explanation
Indices: 716868--716917 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
716858 TACAGTTCCA
*
716868 GACCCAATTCAGATGGCCCAACAGT
1 GACCCAATTCAGATAGCCCAACAGT
716893 GACCCAACTTCAGATAGCCCAACAG
1 GACCCAA-TTCAGATAGCCCAACAG
716918 AGCCCAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.34, C:0.34, G:0.18, T:0.14
Consensus pattern (25 bp):
GACCCAATTCAGATAGCCCAACAGT
Found at i:716923 original size:25 final size:24
Alignment explanation
Indices: 716866--716924 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
716856 ATTACAGTTC
*
716866 CAGA-CCCAATTCAGATGGCCCAA
1 CAGAGCCCAATTCAGATAGCCCAA
*
716889 CAGTGACCCAACTTCAGATAGCCCAA
1 CAGAG-CCCAA-TTCAGATAGCCCAA
716915 CAGAGCCCAA
1 CAGAGCCCAA
716925 ATGTGTAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
25 10 0.33
26 17 0.57
ACGTcount: A:0.36, C:0.36, G:0.17, T:0.12
Consensus pattern (24 bp):
CAGAGCCCAATTCAGATAGCCCAA
Found at i:718342 original size:16 final size:16
Alignment explanation
Indices: 718321--718351 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
718311 TTTTACTTTC
*
718321 ATATATTTATGATTAT
1 ATATATTTATCATTAT
718337 ATATATTTATCATTA
1 ATATATTTATCATTA
718352 GTATTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATATTTATCATTAT
Found at i:724401 original size:25 final size:26
Alignment explanation
Indices: 724372--724428 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
724362 TTGCAAGGTA
*
724372 ATTTTTT-AACTTCATTTATTTAATC
1 ATTTTTTGAACTTCATTAATTTAATC
* * *
724397 ATTTTTTGAATTTGATTAATTTAATT
1 ATTTTTTGAACTTCATTAATTTAATC
724423 ATTTTT
1 ATTTTT
724429 ATTTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (26 bp):
ATTTTTTGAACTTCATTAATTTAATC
Found at i:724451 original size:16 final size:17
Alignment explanation
Indices: 724430--724463 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
724420 ATTATTTTTA
724430 TTTATTTAT-AATATTT
1 TTTATTTATAAATATTT
*
724446 TTTATTTTTAAATATTT
1 TTTATTTATAAATATTT
724463 T
1 T
724464 AGATGGCGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTATAAATATTT
Found at i:724461 original size:17 final size:20
Alignment explanation
Indices: 724424--724463 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
724414 AATTTAATTA
724424 TTTTTATTTATTTATAATAT
1 TTTTTATTTATTTATAATAT
724444 TTTTTA-TT-TTTA-AATAT
1 TTTTTATTTATTTATAATAT
724461 TTT
1 TTT
724464 AGATGGCGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 2 0.10
20 6 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTATTTATTTATAATAT
Found at i:732248 original size:15 final size:15
Alignment explanation
Indices: 732228--732256 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
732218 CCATGGTGCT
732228 CCGGAATCCTGCGCC
1 CCGGAATCCTGCGCC
732243 CCGGAATCCTGCGC
1 CCGGAATCCTGCGC
732257 GATTGTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.45, G:0.28, T:0.14
Consensus pattern (15 bp):
CCGGAATCCTGCGCC
Found at i:733545 original size:30 final size:31
Alignment explanation
Indices: 733486--733548 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
733476 ACCACACAAC
733486 TAAAATGGAAGAAATTAAAGTAATAATAATAAA
1 TAAAATGGAAGAAATTAAAG--ATAATAATAAA
*
733519 TAAAATGGAAGATATTAAAG-TAATAATAAA
1 TAAAATGGAAGAAATTAAAGATAATAATAAA
733549 ACTCTTTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 10 0.34
33 19 0.66
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (31 bp):
TAAAATGGAAGAAATTAAAGATAATAATAAA
Found at i:734386 original size:102 final size:102
Alignment explanation
Indices: 734280--734515 Score: 321
Period size: 102 Copynumber: 2.3 Consensus size: 102
734270 AACCGTTTTT
* * *
734280 ATTATAAGATAAATCAAGTTTACATTTATAATAATATAGGTAGCACCTTCTTGAAATGGTAAATC
1 ATTATATGATAAATCAAGTTTACATTTATAATAATAAAGGTAACACCTTCTTGAAATGGTAAATC
* *
734345 GTATAAATTAAATTATATCAACCTTTTCTATTTTGAA
66 GTATAAATTAAATTATACCAACCTTTTCTATTTTAAA
* * *
734382 ATTATATGATAAATCAAGTTTACATTTATAACAATAAAGGTAACGCCTTCTTGTAATGGTAAATC
1 ATTATATGATAAATCAAGTTTACATTTATAATAATAAAGGTAACACCTTCTTGAAATGGTAAATC
* * ** *
734447 GTATAAATTACATTATGCCATTCTTTTTTATTTTAAA
66 GTATAAATTAAATTATACCAACCTTTTCTATTTTAAA
* *
734484 ATTATGTGATAAATAAAGTTTGA-ATTTATAAT
1 ATTATATGATAAATCAAGTTT-ACATTTATAAT
734516 TGTCATAACC
Statistics
Matches: 117, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
102 116 0.99
103 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (102 bp):
ATTATATGATAAATCAAGTTTACATTTATAATAATAAAGGTAACACCTTCTTGAAATGGTAAATC
GTATAAATTAAATTATACCAACCTTTTCTATTTTAAA
Found at i:737409 original size:35 final size:35
Alignment explanation
Indices: 737354--737432 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
737344 GAGATTTGAA
737354 CTGTAGATG--ATATATATATTTTGATTGGTTTTG
1 CTGTAGATGATATATATATATTTTGATTGGTTTTG
737387 CTGTAGATGATATATATATATTTTGATTGGTTTTG
1 CTGTAGATGATATATATATATTTTGATTGGTTTTG
*
737422 CTATAGATGAT
1 CTGTAGATGAT
737433 GATAGTAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
33 9 0.21
35 34 0.79
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (35 bp):
CTGTAGATGATATATATATATTTTGATTGGTTTTG
Found at i:737692 original size:3 final size:3
Alignment explanation
Indices: 737684--737728 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
737674 ATGTAAATTA
*
737684 AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT -AT AA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
737729 AAAAGACCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:738026 original size:84 final size:83
Alignment explanation
Indices: 737872--738108 Score: 329
Period size: 84 Copynumber: 2.9 Consensus size: 83
737862 GCGTGTTGGG
* * *
737872 GGGGACGACACTGCTCATACGTGATGAAGAGTTCTGGTCGTCTAAGGGTGACTCGGTTCCTACGT
1 GGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCATCTAAGGGTGACTCGGTTCCTACGT
737937 GATGAGGAAATCTGGTCA
66 GATGAGGAAATCTGGTCA
* *
737955 GGGGATGACACTGCTCATACGTGTTGAAGAGTTTTTGGCCATCTAAGGGTGACTCGGTTCCTACG
1 GGGGATGACACTGCTCATACGTGATGAAGAG-TTCTGGCCATCTAAGGGTGACTCGGTTCCTACG
738020 TGATGAGGAAATCTGGTCA
65 TGATGAGGAAATCTGGTCA
* * * * * *
738039 GGGGATGACACAGCTCCTACGTGATGAGGAGGTCTGG---TC-GAGGGATGACACGGTTCCTACG
1 GGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCATCTAAGGG-TGACTCGGTTCCTACG
738100 TGATGAGGA
65 TGATGAGGA
738109 CGGCTGGCCA
Statistics
Matches: 139, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
79 4 0.03
80 26 0.19
83 33 0.24
84 76 0.55
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (83 bp):
GGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCATCTAAGGGTGACTCGGTTCCTACGT
GATGAGGAAATCTGGTCA
Found at i:738058 original size:40 final size:40
Alignment explanation
Indices: 737920--738108 Score: 166
Period size: 40 Copynumber: 4.6 Consensus size: 40
737910 CGTCTAAGGG
* *
737920 TGACTCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGA
1 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCAGGGGA
* * * * ** * *
737960 TGACACTGCTCATACGTGTTGAAGAGTTTTTGGCCATCTAAGGG-
1 TGACACGGCTCCTACGTGATGAGGA-AATCTGG---TC-AGGGGA
* *
738004 TGACTCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGA
1 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCAGGGGA
* **
738044 TGACACAGCTCCTACGTGATGAGGAGGTCTGGTC-GAGGGA
1 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCAG-GGGA
*
738084 TGACACGGTTCCTACGTGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGA
738109 CGGCTGGCCA
Statistics
Matches: 115, Mismatches: 27, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
39 5 0.04
40 77 0.67
41 4 0.03
43 4 0.03
44 21 0.18
45 4 0.03
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (40 bp):
TGACACGGCTCCTACGTGATGAGGAAATCTGGTCAGGGGA
Found at i:738277 original size:31 final size:28
Alignment explanation
Indices: 738185--738280 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 28
738175 GGAGTTATGA
* * *
738185 TTTCAAGAGAAACCGATTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
738213 TTTCAAAAGAAACAGACTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
738241 TTTCAAGAA-AAACA-AGCTCAAAGATAATGTG
1 TTTCAA-AAGAAACAGA-CTCAAAGAT--T-TG
738272 TTTCAAAAG
1 TTTCAAAAG
738281 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 45 0.76
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTG
Found at i:738471 original size:66 final size:63
Alignment explanation
Indices: 738241--738464 Score: 153
Period size: 66 Copynumber: 3.4 Consensus size: 63
738231 CAAAGATTTG
** * * * *
738241 TTTCAAGAAAAACAAGCTCAAAGATAATGTGTTTCAAAAGCAACTGTCTCGAAAGAGACAAAATT
1 TTTCAAGGGAAACAATCTCAAAGATGA--TGTTT-AAAGGGAACTGTCTC-AAAGAGACAAAATT
*
738306 CG
62 CA
** * * * * *
738308 TTTCAAATGAAACAA-CTCAAAAGATGACGTTTAAAGGGAATTGTCTCAAGCGAGATAAAATTTG
1 TTTCAAGGGAAACAATCTC-AAAGATGATGTTTAAAGGGAACTGTCTCAA-AGAGACAAAA-TTC
*
738372 T
63 A
* ** * * * *
738373 TTTTAAGGGAAACGTTCTCAAATATCGGTGTTTCATGGGAAACTGTCTCAAATGAGACAAAATTC
1 TTTCAAGGGAAACAATCTCAAAGAT-GATGTTTAAAGGG-AACTGTCTCAAA-GAGACAAAATTC
738438 A
63 A
738439 TTTCAAGGGAAACAATCTCAAAGATG
1 TTTCAAGGGAAACAATCTCAAAGATG
738465 TTTGTTTTGT
Statistics
Matches: 119, Mismatches: 31, Indels: 16
0.72 0.19 0.10
Matches are distributed among these distances:
63 2 0.02
64 20 0.17
65 22 0.18
66 38 0.32
67 37 0.31
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (63 bp):
TTTCAAGGGAAACAATCTCAAAGATGATGTTTAAAGGGAACTGTCTCAAAGAGACAAAATTCA
Found at i:738749 original size:101 final size:100
Alignment explanation
Indices: 738564--738749 Score: 216
Period size: 101 Copynumber: 1.8 Consensus size: 100
738554 CTCGAGAGAA
* * ** *
738564 ACAAAATTTTGTTTCCAAAGAAAGAGATTCAATGATTTTTTTTTAAAGACATTTTCATAAGAGAC
1 ACAAAATTTTGTTTCCAAAGAAACAGACTCAATGATTTTTTTCAAAAGAAATTTT-ATAAGAGAC
* **
738629 AAAACTTTGTTTTTAAGAAAATTGTATCTTAGTGAG
65 AAAACCTTGTTTCCAAGAAAATTGTATCTTAGTGAG
*
738665 ACAAAATTTTGTTTCCAAAGAAACAGACTC-A-GATTTTTCTTCAAAAGAAACTGTTT-TAAGGG
1 ACAAAATTTTGTTTCCAAAGAAACAGACTCAATGATTTTT-TTCAAAAGAAA-T-TTTATAAGAG
*
738727 ATAAAACCTTGTTTCCAGAGAAA
63 ACAAAACCTTGTTTCCA-AGAAA
738750 CAAACTCAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
99 7 0.10
100 27 0.38
101 34 0.48
102 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (100 bp):
ACAAAATTTTGTTTCCAAAGAAACAGACTCAATGATTTTTTTCAAAAGAAATTTTATAAGAGACA
AAACCTTGTTTCCAAGAAAATTGTATCTTAGTGAG
Found at i:739318 original size:37 final size:37
Alignment explanation
Indices: 739267--739387 Score: 114
Period size: 37 Copynumber: 3.5 Consensus size: 37
739257 TTCAAAGATT
*
739267 TTTTTTTTCAAAAGAAAATATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAA
* * * *
739304 TTTTGTTTCCAAAGAAACAGA-C-TCA-A-AG----AT
1 TTTTGTTTCAAAAGAAA-ATATCTTAAGAGAGACAAAA
*
739334 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAA
*
739371 TTTTGTTTCCAAAGAAA
1 TTTTGTTTCAAAAGAAA
739388 CAGACTCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
29 1 0.02
30 18 0.28
31 2 0.03
32 1 0.02
33 2 0.03
34 2 0.03
35 1 0.02
36 2 0.03
37 33 0.52
38 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (37 bp):
TTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAA
Found at i:739338 original size:30 final size:30
Alignment explanation
Indices: 739304--739434 Score: 115
Period size: 30 Copynumber: 4.1 Consensus size: 30
739294 AGAGACAAAA
*
739304 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
**
739334 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAA-A-
1 TTTTGTTTCAAAAG-AA--A-C-----AGACTCAAAGAT
*
739371 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
739401 TTTTGTTTCAAAAGAAACA-ATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGA-CTCAAAGAT
739431 TTTT
1 TTTT
739435 TTCACAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
28 7 0.09
29 2 0.02
30 44 0.54
31 2 0.02
33 2 0.02
34 2 0.02
36 2 0.02
37 13 0.16
38 1 0.01
39 7 0.09
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:739360 original size:67 final size:67
Alignment explanation
Indices: 739248--739417 Score: 304
Period size: 67 Copynumber: 2.5 Consensus size: 67
739238 TCATTTTAAG
* *
739248 AGAAACAGATTCAAAGATTTTTTTTTTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTC
1 AGAAACAGACTCAAAGA-TTTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTC
739313 CAA
65 CAA
*
739316 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTCC
739381 AA
66 AA
739383 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
739418 CAATCTCAAA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 83 0.84
68 16 0.16
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:739443 original size:30 final size:29
Alignment explanation
Indices: 739366--739443 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
739356 TTAAGAGAGA
739366 CAAA-ATTTTGTTTCC-AAAGAAACAGACT
1 CAAAGATTTT-TTTCCAAAAGAAACAGACT
*
739394 CAAAGATTTTTGTTTCAAAAGAAACA-ATCT
1 CAAAGATTTTT-TTCCAAAAGAAACAGA-CT
739424 CAAAGATTTTTTTCACAAAA
1 CAAAGATTTTTTTC-CAAAA
739444 TTGTCTCAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 5 0.12
29 11 0.26
30 27 0.63
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (29 bp):
CAAAGATTTTTTTCCAAAAGAAACAGACT
Found at i:739608 original size:27 final size:26
Alignment explanation
Indices: 739520--739615 Score: 86
Period size: 27 Copynumber: 3.5 Consensus size: 26
739510 AAAACTTTGT
* *
739520 TTCAAAAGAAATAGACTCAAAGATATTTGT
1 TTCAAAAGAAACA-ACTCAAAG--ATTT-A
739550 TTCAAAAGAAACAACTCAAAGATTTTA
1 TTCAAAAGAAACAACTCAAAGA-TTTA
*
739577 TTCAAAAGGAACAGACTCAAAGA-TTA
1 TTCAAAAGAAACA-ACTCAAAGATTTA
*
739603 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
739616 TGTCTCAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 4 0.07
27 22 0.38
28 12 0.21
29 8 0.14
30 12 0.21
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (26 bp):
TTCAAAAGAAACAACTCAAAGATTTA
Found at i:739937 original size:36 final size:35
Alignment explanation
Indices: 739831--739956 Score: 128
Period size: 36 Copynumber: 3.5 Consensus size: 35
739821 AACAACCTTG
* *
739831 AAATTTGTATTATGAGAAATGATGTCTCAAGCAAGACA
1 AAATTTGTTTTA-GAGAAAT--TGTCTCAAGCGAGACA
* * * **
739869 AAATTTGCTTTA-AGATATAGTCTCAAATGAGACA
1 AAATTTGTTTTAGAGAAATTGTCTCAAGCGAGACA
739903 AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACA
1 AAATTTG-TTTTAGAGAAATTGTCTCAAGCGAGACA
* *
739939 AAGTTTGTTTTTGAGAAA
1 AAATTTGTTTTAGAGAAA
739957 ACGATCTCAA
Statistics
Matches: 72, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
34 19 0.26
35 14 0.19
36 29 0.40
38 10 0.14
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (35 bp):
AAATTTGTTTTAGAGAAATTGTCTCAAGCGAGACA
Found at i:739984 original size:36 final size:36
Alignment explanation
Indices: 739854--739972 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
739844 GAGAAATGAT
** * *
739854 GTCTCAAGCAAGACAAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
739888 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
739924 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
739959 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
739973 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:740036 original size:102 final size:103
Alignment explanation
Indices: 739924--740155 Score: 294
Period size: 104 Copynumber: 2.3 Consensus size: 103
739914 TAGAGAAATT
* *
739924 GTCTCAAGCGAGACAAAGTTTGTTTTTG-AG-AA-AACGATCTCAA-GTGAGATCAACTTTG-TT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAAGAAACAACAATCT-AAGGTGAGATCAA-TTTGTTT
* *
739984 TAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
63 TAA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
740026 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTGTTTTA
1 GTCTCAAGCGAGACAAAATTTGTTTTG-AAGAAACAACAATCTAAGGTGAGATCAATTTGTTTTA
* * *
740091 AGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
65 AGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
740130 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
740156 AAAATTCTCA
Statistics
Matches: 114, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
101 5 0.04
102 21 0.18
103 2 0.02
104 65 0.57
105 21 0.18
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (103 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAGAAACAACAATCTAAGGTGAGATCAATTTGTTTTAA
GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:740285 original size:156 final size:156
Alignment explanation
Indices: 740021--740311 Score: 417
Period size: 156 Copynumber: 1.9 Consensus size: 156
740011 TCTCAAAGGG
* *
740021 AAAAGGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTG
1 AAAAGGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGATGAGATCAATTTG
* * *
740086 TTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGCAATTT
66 TTTTAAGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAACGAGACGAAATTT
740151 GTTTTAAAATTCTCAAAATTTGTGGA
131 GTTTTAAAATTCTCAAAATTTGTGGA
* * * * *
740177 AAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAATAAA-TACGATCTCAA-ATGAGATCAACTT
1 AAAAGGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGATGAGATCAA-TT
* * *
740240 TG-TTTAATGTGAAACAAATTCAAATTTTGTATCTTAAAGGAAAAATGTCTCAAATGAGACGAAA
64 TGTTTTAA-GTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAACGAGACGAAA
740304 TTTGTTTT
128 TTTGTTTT
740312 GAAAGAAATT
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
155 19 0.16
156 100 0.84
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (156 bp):
AAAAGGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGATGAGATCAATTTG
TTTTAAGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAACGAGACGAAATTT
GTTTTAAAATTCTCAAAATTTGTGGA
Done.