Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:452527 original size:21 final size:21
Alignment explanation
Indices: 452477--452517 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
452467 CTGTGCTGCC
452477 GCTGCTTCCGCTGCTGCTCTA
1 GCTGCTTCCGCTGCTGCTCTA
452498 GCTGCTTCCGCTGCTGCTCT
1 GCTGCTTCCGCTGCTGCTCT
452518 CTCTGTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.39, G:0.24, T:0.34
Consensus pattern (21 bp):
GCTGCTTCCGCTGCTGCTCTA
Found at i:462288 original size:41 final size:41
Alignment explanation
Indices: 462222--462382 Score: 213
Period size: 41 Copynumber: 4.0 Consensus size: 41
462212 CGTTTATACA
462222 AAAAAACGCCACTATTGATTA-CACTATT-CTGGCGTTTGTT
1 AAAAAACGCCACTATTGATTATCACTATTGC-GGCGTTTGTT
462262 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
* * * **
462302 CTAAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCT
1 -AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGT-T
*
462345 -AAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTG
462383 AGGAATAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 23 0.22
41 80 0.75
42 2 0.02
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (41 bp):
AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
Found at i:462340 original size:82 final size:81
Alignment explanation
Indices: 462223--462381 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 81
462213 GTTTATACAA
* *
462223 AAAAACGCCACTATTGATTACACTATTCTGGCGTTTGT-TAAAAAACGCCACTATTGATTATCAC
1 AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCT-AAAAACACCACTATTGATTATCAC
462287 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
*
462304 AAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1 AAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
462369 TATTGCGGCGTTT
65 TATTGCGGCGTTT
462382 GAGGAATAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 18 0.25
82 54 0.74
83 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCACT
ATTGCGGCGTTTTTCT
Found at i:462528 original size:41 final size:42
Alignment explanation
Indices: 462411--462610 Score: 156
Period size: 42 Copynumber: 4.8 Consensus size: 42
462401 ATGTGTAATA
* * * *
462411 TATTGCGGCGTTTGTGGTATAAACGCCACGAATTTACCACTC
1 TATTGCGGCGTTTGTAGTAAAAACGCCGCTAATTTACCACTC
* * * * *
462453 TATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACTC
1 TATTGCGGCGTTTGTAG-TAAAAACGCCGC-TAATTTACCACTC
* * *
462494 TATTGTGGCGTTTGTAGTATAAACGCCGCTAATTTACCACCC
1 TATTGCGGCGTTTGTAGTAAAAACGCCGCTAATTTACCACTC
* * * * * *
462536 TATTGTGGCATTTTTTGTAAAAACGCCGCTATATGT-CAACTC
1 TATTGCGGCGTTTGTAGTAAAAACGCCGCTA-ATTTACCACTC
* *
462578 TATTGCAGCGTTTGTACTAAAAAACGCCGCTAA
1 TATTGCGGCGTTTGTAGT-AAAAACGCCGCTAA
462611 AGTATCAATT
Statistics
Matches: 126, Mismatches: 25, Indels: 14
0.76 0.15 0.08
Matches are distributed among these distances:
41 33 0.26
42 77 0.61
43 16 0.13
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (42 bp):
TATTGCGGCGTTTGTAGTAAAAACGCCGCTAATTTACCACTC
Found at i:463354 original size:19 final size:19
Alignment explanation
Indices: 463327--463363 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
463317 ATGACCAACA
*
463327 AAATCGCAATGTGATCTCT
1 AAATCGCAACGTGATCTCT
*
463346 AAATTGCAACGTGATCTC
1 AAATCGCAACGTGATCTC
463364 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (19 bp):
AAATCGCAACGTGATCTCT
Found at i:463412 original size:20 final size:20
Alignment explanation
Indices: 463389--463542 Score: 143
Period size: 20 Copynumber: 7.6 Consensus size: 20
463379 GTTTCCAGAT
* *
463389 TCGCAATGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
463409 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
463429 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
*
463449 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
* *
463470 TCGCAACGTGATTCTGACTA
1 TCGCAACGCGATTATGACTA
*
463490 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
463511 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
463531 TCGCAACGCGAT
1 TCGCAACGCGAT
463543 AATACAAAAT
Statistics
Matches: 109, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
19 5 0.05
20 70 0.64
21 30 0.28
22 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:463483 original size:41 final size:41
Alignment explanation
Indices: 463389--463564 Score: 257
Period size: 41 Copynumber: 4.3 Consensus size: 41
463379 GTTTCCAGAT
* * * **
463389 TCGCAATGCGATTTTGACTATCGCAATGCG--AATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT-AA
463429 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
*
463470 TCGCAACGTGATTCTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
*
463511 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
*
463552 TCGCAATGCGATT
1 TCGCAACGCGATT
463565 TTCAAAGCGC
Statistics
Matches: 125, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
40 27 0.22
41 93 0.74
42 5 0.04
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
Found at i:463740 original size:22 final size:22
Alignment explanation
Indices: 463715--463757 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
463705 GATATTCGTC
463715 CCCATCTCCGACGAAATCCGTT
1 CCCATCTCCGACGAAATCCGTT
*
463737 CCCATCTCCGGCGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
463758 CTATCTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTT
Found at i:464240 original size:20 final size:20
Alignment explanation
Indices: 464133--464246 Score: 89
Period size: 20 Copynumber: 6.0 Consensus size: 20
464123 AAAATCGCAA
**
464133 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
*
464153 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
**
464173 CGATTTTCATTTT-GCGTTG
1 CGATAGTCATTTTCGCGTTG
*
464192 CGAT--T-A---TCTCGTTG
1 CGATAGTCATTTTCGCGTTG
**
464206 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
* *
464226 TGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
464246 C
1 C
464247 AATTTTAAGT
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
13 1 0.01
14 9 0.12
16 2 0.03
17 2 0.03
19 9 0.12
20 51 0.69
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTG
Found at i:464271 original size:73 final size:73
Alignment explanation
Indices: 464133--464271 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 73
464123 AAAATCGCAA
* * * ** ***
464133 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTGCGTTGCGATTA
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCAATTTTAAGTTTAAGAAACGATTA
464198 TCTCGTTG
66 TCTCGTTG
* *
464206 CGATAGTCAAATTCGCGTTGTGATAGTCATTTTCGTGTTGCAATTTTAAGTTTAAGAAACTATTA
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCAATTTTAAGTTTAAGAAACGATTA
464271 T
66 T
464272 TCTTCTGCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (73 bp):
CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCAATTTTAAGTTTAAGAAACGATTA
TCTCGTTG
Found at i:466178 original size:20 final size:20
Alignment explanation
Indices: 466155--466223 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
466145 CGAAACTTAA
466155 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
466175 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
466195 ATCGCAACGC-GAAGTTAACT
1 ATCGCAACGCGGAA-ATGACT
466215 ATCGCAACG
1 ATCGCAACG
466224 TGAAAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 3 0.07
20 43 0.93
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:466254 original size:20 final size:20
Alignment explanation
Indices: 466155--466261 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 20
466145 CGAAACTTAA
*
466155 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
*
466175 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
** *
466195 ATCGCAACGCGAAGTTAACT
1 ATCGCAACGCGAAAATGACT
*
466215 ATCGCAACGTG--AA--A--
1 ATCGCAACGCGAAAATGACT
*
466229 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
466249 ATCGCAACACGAA
1 ATCGCAACGCGAA
466262 TTTAGTTTCG
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
14 9 0.13
16 3 0.04
18 1 0.01
20 57 0.81
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:466348 original size:20 final size:20
Alignment explanation
Indices: 466319--466387 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
466309 GCGATTATCC
*
466319 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
466339 CGTTGTGATAGTC-ATTTCTG
1 CGTTGCGATAGTCAATTTC-G
*
466359 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
466379 CGTTGCGAT
1 CGTTGCGAT
466388 TTAAGTTTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.09
20 35 0.81
21 4 0.09
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:466402 original size:19 final size:20
Alignment explanation
Indices: 466374--466416 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
466364 CGATAGTCAT
466374 TTTCGCGTTGCGA-TTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
466393 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
466413 TTTC
1 TTTC
466417 AGAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:468386 original size:14 final size:14
Alignment explanation
Indices: 468367--468405 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
468357 TTGCTTGTTT
468367 AATTGATTTGTAAA
1 AATTGATTTGTAAA
468381 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
468395 AGTTGATTTGT
1 AATTGATTTGT
468406 TTAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:468552 original size:20 final size:20
Alignment explanation
Indices: 468527--468580 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
468517 AGGTACAGTT
*
468527 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
* *
468547 TCGCAATGCGAAAGCCAAAT
1 TCGCAACGCGAAAGCCAAAA
468567 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
468581 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.41, C:0.28, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:468616 original size:20 final size:20
Alignment explanation
Indices: 468574--468813 Score: 236
Period size: 20 Copynumber: 12.7 Consensus size: 20
468564 AATTCGCAAC
*
468574 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
468593 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
468613 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
468627 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
*
468647 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
468667 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
468687 GCAATAGTCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
* *
468707 GCGATAGTCATATTCGCGCT
1 GCGATAGTCAAATTCGCGTT
468727 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
468747 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
* *
468761 GCGATAATCAAATTTGCGTT
1 GCGATAGTCAAATTCGCGTT
468781 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
468801 GCGATATTCAAAT
1 GCGATAGTCAAAT
468814 GAATGTGTAA
Statistics
Matches: 182, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
14 21 0.12
16 2 0.01
18 2 0.01
19 8 0.04
20 149 0.82
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:469036 original size:140 final size:140
Alignment explanation
Indices: 468784--469066 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
468774 TTGCGTTGCG
468784 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
468849 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
468914 AATGCACATA
131 AATACACATA
* *
468924 ATAGTTAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
468989 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
469054 AATACACATA
131 AATACACATA
469064 ATA
1 ATA
469067 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:469147 original size:18 final size:18
Alignment explanation
Indices: 469124--469158 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
469114 AAGCCGGTTG
*
469124 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
469142 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
469159 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:470898 original size:14 final size:14
Alignment explanation
Indices: 470879--470915 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
470869 TCCCGTGGCA
470879 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
470893 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
470907 TTCTTCTTC
1 TT-TTCTTC
470916 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:471139 original size:24 final size:24
Alignment explanation
Indices: 471105--471158 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
471095 CTGAAACATC
471105 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
471129 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
471153 ATCAAA
1 ATCAAA
471159 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:471929 original size:20 final size:20
Alignment explanation
Indices: 471882--471989 Score: 94
Period size: 20 Copynumber: 5.3 Consensus size: 20
471872 TGAAATTAGT
*
471882 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
471902 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
471922 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
* * *
471943 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAGAATCGC
* * *
471963 ATTGCGATAGTCAAAATCAC
1 GTTGCGATAGTCAGAATCGC
471983 GTTGCGA
1 GTTGCGA
471990 ATTTGGAAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.01
20 52 0.73
21 16 0.23
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:472027 original size:20 final size:19
Alignment explanation
Indices: 472004--472049 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
471994 GGAAACTGAT
* *
472004 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
472024 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
472043 TTGCGAT
1 TTGCGAT
472050 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:472039 original size:19 final size:19
Alignment explanation
Indices: 472015--472051 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
472005 TGCGATACTG
*
472015 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
472034 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
472052 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:479074 original size:7 final size:7
Alignment explanation
Indices: 479064--479114 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
479054 GGAGTGTGGT
479064 GGCGGAC
1 GGCGGAC
479071 GGCGGAC
1 GGCGGAC
479078 GGCAGG-C
1 GGC-GGAC
479085 GGCGGAC
1 GGCGGAC
*
479092 GGCGGTC
1 GGCGGAC
*
479099 GACGGAC
1 GGCGGAC
479106 GGCGGAC
1 GGCGGAC
479113 GG
1 GG
479115 TGATGATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 2 0.05
7 34 0.89
8 2 0.05
ACGTcount: A:0.14, C:0.27, G:0.57, T:0.02
Consensus pattern (7 bp):
GGCGGAC
Found at i:481656 original size:17 final size:16
Alignment explanation
Indices: 481634--481665 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
481624 TTCCCCATTC
481634 TTCGTTTTCCGGTTCTG
1 TTCGTTTTCC-GTTCTG
481651 TTCGTTTTCCGTTCT
1 TTCGTTTTCCGTTCT
481666 TCGTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.25, G:0.19, T:0.56
Consensus pattern (16 bp):
TTCGTTTTCCGTTCTG
Found at i:482984 original size:28 final size:28
Alignment explanation
Indices: 482914--482984 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 28
482904 AAGGATAGTC
*
482914 AAAATAGAAATAAAATATAATGATATAT
1 AAAATAGAAATAAAATATAATAATATAT
* ** *
482942 AAGATTTAAAAAAAATA-AATAA-ATAATT
1 AAAATAGAAATAAAATATAATAATAT-A-T
482970 AAAATAGAAATAAAA
1 AAAATAGAAATAAAA
482985 CAATAGATGA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
26 2 0.06
27 5 0.16
28 25 0.78
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (28 bp):
AAAATAGAAATAAAATATAATAATATAT
Found at i:491446 original size:2 final size:2
Alignment explanation
Indices: 491439--491467 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
491429 ATGTTTAAAC
491439 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
491468 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:493390 original size:35 final size:35
Alignment explanation
Indices: 493344--493463 Score: 204
Period size: 35 Copynumber: 3.4 Consensus size: 35
493334 AAGAAAGCAT
493344 CACTTTCGATTCAAGTGAACGGAAGGAAGCATCGG
1 CACTTTCGATTCAAGTGAACGGAAGGAAGCATCGG
*
493379 CACTTTCGATTCAAGAAGAACGGAAGGAAGCATCGG
1 CACTTTCGATTCAAG-TGAACGGAAGGAAGCATCGG
*
493415 CACTTTCGATTCAAGTGAACGGAAGGAAGCATCAG
1 CACTTTCGATTCAAGTGAACGGAAGGAAGCATCGG
*
493450 CAGTTTCGATTCAA
1 CACTTTCGATTCAA
493464 TTGTTCATCT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 46 0.57
36 34 0.43
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (35 bp):
CACTTTCGATTCAAGTGAACGGAAGGAAGCATCGG
Found at i:493436 original size:71 final size:68
Alignment explanation
Indices: 493323--493463 Score: 219
Period size: 71 Copynumber: 2.0 Consensus size: 68
493313 GAAGGTGAAT
*
493323 AAGAAGAACGAAAGAAAGCATCACTTTCGATTCAAGTGAACGGAAGGAAGCATCGGCACTTTCGA
1 AAGAAGAACGAAAGAAAGCATCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTTCGA
493388 TTC
66 TTC
* * *
493391 AAGAAGAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCAGTTT
1 AAGAAGAACGAAAGAAAGCAT---CACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTT
493456 CGATTC
63 CGATTC
493462 AA
1 AA
493464 TTGTTCATCT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
68 19 0.29
71 47 0.71
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (68 bp):
AAGAAGAACGAAAGAAAGCATCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTTCGA
TTC
Found at i:494196 original size:2 final size:2
Alignment explanation
Indices: 494189--494216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
494179 AAAATGGCTA
494189 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
494217 TTCTGTGTGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:495677 original size:23 final size:23
Alignment explanation
Indices: 495634--495677 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
495624 CACACACCTT
*
495634 TGCTTTCTTTTTCTGTTCTTTTC
1 TGCTTTCTTTTTCTGTACTTTTC
495657 TGCTTTCTTTTT-TGTAACTTT
1 TGCTTTCTTTTTCTGT-ACTTT
495678 ATTTGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.05, C:0.18, G:0.09, T:0.68
Consensus pattern (23 bp):
TGCTTTCTTTTTCTGTACTTTTC
Found at i:502455 original size:2 final size:2
Alignment explanation
Indices: 502448--502531 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
502438 GAGAAACAGT
502448 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
502490 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
502532 AATTGATTTA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:508913 original size:47 final size:46
Alignment explanation
Indices: 508819--508917 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 46
508809 TCCGTTCAAG
* * * *
508819 TTTATTAATATATAATTTTAAAACATTTTAATTAATATAAATGTAT
1 TTTATTAAAATATAATTTTAAAACATTTTAATAAAAATAAATATAT
*
508865 TTATATTAAAATATAATTATT-AAA-ATTATTAATAAAAATAATTATAT
1 TT-TATTAAAATATAATT-TTAAAACATT-TTAATAAAAATAAATATAT
508912 TTTATT
1 TTTATT
508918 TTCAATACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
46 9 0.20
47 34 0.76
48 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (46 bp):
TTTATTAAAATATAATTTTAAAACATTTTAATAAAAATAAATATAT
Found at i:512293 original size:59 final size:61
Alignment explanation
Indices: 512229--512368 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 61
512219 ATTAGTTCTT
* * *
512229 AAACTTTTAAAGATTTCAATTTCAT-CCCAAAATATGAATCAT-ATTCTATATTGATCCCC-
1 AAACTTTTGAACATTTCAATTTAATCCCCAAAATATG-ATCATCATTCTATATTGATCCCCA
* * * * * *
512288 AAACTTTTGGACATTTCAAATTAATCCCCAAACTATGATCCTCATTTTATATTGGTCCCCA
1 AAACTTTTGAACATTTCAATTTAATCCCCAAAATATGATCATCATTCTATATTGATCCCCA
512349 AAACTTTTGAACATTTCAAT
1 AAACTTTTGAACATTTCAAT
512369 AAAGCCTCCG
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 24 0.36
60 25 0.37
61 18 0.27
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.37
Consensus pattern (61 bp):
AAACTTTTGAACATTTCAATTTAATCCCCAAAATATGATCATCATTCTATATTGATCCCCA
Found at i:512347 original size:60 final size:58
Alignment explanation
Indices: 512192--512367 Score: 172
Period size: 59 Copynumber: 2.9 Consensus size: 58
512182 TACACCATAC
* * * * ** * * *
512192 AATCCCAAACTATGACCCTAATTTTAAATTAGTTCTTAAACTTTTAAAGATTTCAATTT
1 AATCCCAAACTATGATCCT-ATTTTATATTGGTCCCCAAACTTTTGAACATTTCAAATT
* * * * * *
512251 CATCCCAAAATATGAATCATATTCTATATTGATCCCCAAACTTTTGGACATTTCAAATT
1 AATCCCAAACTATG-ATCCTATTTTATATTGGTCCCCAAACTTTTGAACATTTCAAATT
512310 AATCCCCAAACTATGATCCTCATTTTATATTGGTCCCCAAAACTTTTGAACATTTCAA
1 AAT-CCCAAACTATGATCCT-ATTTTATATTGGTCCCC-AAACTTTTGAACATTTCAA
512368 TAAAGCCTCC
Statistics
Matches: 92, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
59 46 0.50
60 28 0.30
61 18 0.20
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (58 bp):
AATCCCAAACTATGATCCTATTTTATATTGGTCCCCAAACTTTTGAACATTTCAAATT
Found at i:515595 original size:19 final size:19
Alignment explanation
Indices: 515546--515596 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
515536 TAGACTCTAC
*
515546 AGTCTTTGAAGACATAAAA
1 AGTCTTTGAAGCCATAAAA
515565 AGTCTTTGAAGCCATAAAA
1 AGTCTTTGAAGCCATAAAA
515584 AG-CATTTGAAGCC
1 AGTC-TTTGAAGCC
515597 TAGGTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 1 0.03
19 29 0.97
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (19 bp):
AGTCTTTGAAGCCATAAAA
Found at i:517094 original size:83 final size:83
Alignment explanation
Indices: 516950--517102 Score: 216
Period size: 83 Copynumber: 1.8 Consensus size: 83
516940 CTGTTGTGGG
* * * *
516950 GTTTTTTGAAAAAGCGCCACTATAGATAAACCCTATTGCAAAGTTTGTATAAAAACACCGCTAAA
1 GTTTGTTGAAAAAACGCAACTATAGATAAACCCTACTGCAAAGTTTGTATAAAAACACCGCTAAA
517015 GTACTACTCTATTGCGAC
66 GTACTACTCTATTGCGAC
* * * * * *
517033 GTTTGTTGAAAAAACGCAACTATAGATGAACTCTACTGCGACGTTTGTATAAAATCGCCGCTAAA
1 GTTTGTTGAAAAAACGCAACTATAGATAAACCCTACTGCAAAGTTTGTATAAAAACACCGCTAAA
517098 GTACT
66 GTACT
517103 CTTTATCGCA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 60 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (83 bp):
GTTTGTTGAAAAAACGCAACTATAGATAAACCCTACTGCAAAGTTTGTATAAAAACACCGCTAAA
GTACTACTCTATTGCGAC
Found at i:517128 original size:83 final size:83
Alignment explanation
Indices: 516958--517197 Score: 188
Period size: 83 Copynumber: 2.9 Consensus size: 83
516948 GGGTTTTTTG
* * *
516958 AAAAAGCGCCACTATAGATAAACCCTATTGCAAAGTTTGTATAAAAACACCGCTAAAGTACTACT
1 AAAAAACGCAACTATAGATAAACCCTACTGCAAAGTTTGTATAAAAACACCGCTAAAGTACTACT
* * * *
517023 CTATTGCGACGTTTGTTG
66 CTATCGCGACATCTGTTA
* * * * * *
517041 AAAAAACGCAACTATAGATGAACTCTACTGCGACGTTTGTATAAAATCGCCGCTAAAGTACT-CT
1 AAAAAACGCAACTATAGATAAACCCTACTGCAAAGTTTGTATAAAAACACCGCTAAAGTACTACT
* *
517105 TTATCGC-AGCATCTGTTC
66 CTATCGCGA-CATCTGTTA
* * * * * * *
517123 AAAAAATGCCACTA-AGA-ACGAACCCTATTACGACA-TTTGTA-AAAAA-ACAGCTAAATTACT
1 AAAAAACGCAACTATAGATA--AACCCTACTGC-AAAGTTTGTATAAAAACACCGCTAAAGTACT
*
517183 ACTCTATCACGACAT
63 ACTCTATCGCGACAT
517198 TTATTGGGAA
Statistics
Matches: 122, Mismatches: 29, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
80 11 0.09
81 18 0.15
82 40 0.33
83 53 0.43
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (83 bp):
AAAAAACGCAACTATAGATAAACCCTACTGCAAAGTTTGTATAAAAACACCGCTAAAGTACTACT
CTATCGCGACATCTGTTA
Found at i:518633 original size:2 final size:2
Alignment explanation
Indices: 518626--518651 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
518616 TTGTTCTACA
518626 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
518652 CATCCCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:519431 original size:45 final size:45
Alignment explanation
Indices: 519358--519683 Score: 402
Period size: 45 Copynumber: 7.2 Consensus size: 45
519348 ATGTACTTTA
* * * * *
519358 AACTATAACATATTTTTCTGTTGGTAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * *
519403 AATTATAGTATATTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * * *
519448 AACCATAGCATACTTTTATGTTAATAATGTACCCATAAACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * *
519493 AACTCTAGCATGCTCTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * * * *
519538 AACTATGGCACACTTTTCTGTTGATAATGCATCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* *
519583 AACTCTAGCACACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * * *
519628 AACTAAAGTATGA-TTTTTTGTTGATAATGTACCCATATAGATTTC
1 AACTATAGCAT-ACTTTTCTGTTGATAATGTACCCATATACATTTC
519673 AACTATAGCAT
1 AACTATAGCAT
519684 CATTTCATTA
Statistics
Matches: 239, Mismatches: 41, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
45 238 1.00
46 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (45 bp):
AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
Found at i:520115 original size:95 final size:96
Alignment explanation
Indices: 519969--520191 Score: 222
Period size: 95 Copynumber: 2.3 Consensus size: 96
519959 TGGCCCTTTA
* * * * *
519969 GTATCGATACCC-CTACTATGGTATCGATACTACCTTATTTTATTATCGATACCCCCTTTCAATA
1 GTATCGATACCCTC-ACCATGGTATCGATACCACCTTATTATAGTATCGATACCCCCCTTCAATA
* * *
520033 TTAATACCAAAATTAGCTTTGATATAAT-CTG
65 TCAATACCAAAATTAGATTCGATATAATCCTG
* **
520064 GTATCGATACCCTCACCATGGTATCGATACCA-C-TATGCTATAGTATTGATACCCCCCTTCGGT
1 GTATCGATACCCTCACCATGGTATCGATACCACCTTAT--TATAGTATCGATACCCCCCTTCAAT
* * **
520127 ATCGATACCAAAATTAGATTCGATGTTTTCCTG
64 ATCAATACCAAAATTAGATTCGATATAATCCTG
*
520160 GTATCTATACCCTC-CACATAGGTATCGATACC
1 GTATCGATACCCTCAC-CAT-GGTATCGATACC
520192 TCTTCCATAT
Statistics
Matches: 106, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
93 3 0.03
94 1 0.01
95 70 0.66
96 20 0.19
97 12 0.11
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (96 bp):
GTATCGATACCCTCACCATGGTATCGATACCACCTTATTATAGTATCGATACCCCCCTTCAATAT
CAATACCAAAATTAGATTCGATATAATCCTG
Found at i:520200 original size:21 final size:21
Alignment explanation
Indices: 520159--520234 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
520149 ATGTTTTCCT
* *
520159 GGTATCTATACC-CTCCACATA
1 GGTATCGATACCTCTTC-CATA
520180 GGTATCGATACCTCTTCCATA
1 GGTATCGATACCTCTTCCATA
*
520201 TGGTATCGATA-CTATT-CATACA
1 -GGTATCGATACCTCTTCCAT--A
520223 GGTATCGATACC
1 GGTATCGATACC
520235 CCATGAATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 3 0.06
21 29 0.62
22 15 0.32
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (21 bp):
GGTATCGATACCTCTTCCATA
Found at i:522221 original size:2 final size:2
Alignment explanation
Indices: 522214--522262 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
522204 ACCATAAAAG
522214 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
522256 AT AT AT A
1 AT AT AT A
522263 GATCTTTCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:522858 original size:14 final size:14
Alignment explanation
Indices: 522839--522872 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
522829 GTATTTACCG
522839 CTTACTACTTTCCT
1 CTTACTACTTTCCT
522853 CTTACTACTTTCCT
1 CTTACTACTTTCCT
522867 CTTACT
1 CTTACT
522873 CAAATTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (14 bp):
CTTACTACTTTCCT
Found at i:524496 original size:20 final size:19
Alignment explanation
Indices: 524454--524502 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
524444 AAAATGTTTT
** *
524454 TATGAATAGTATTGTACTG
1 TATGAATAGTACAGTACTA
524473 TATGAATAGTACCAGTACTA
1 TATGAATAGTA-CAGTACTA
524493 TATGAATAGT
1 TATGAATAGT
524503 GTTGATATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (19 bp):
TATGAATAGTACAGTACTA
Found at i:527031 original size:18 final size:18
Alignment explanation
Indices: 527008--527065 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
526998 CAACAATTGG
*
527008 TAACAATTGGTATCTTTT
1 TAACAATTGATATCTTTT
527026 TAACAATTGATATCCTTTT
1 TAACAATTGATAT-CTTTT
527045 GTAAACAATTGATATCTTTT
1 -T-AACAATTGATATCTTTT
527065 T
1 T
527066 CATTAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 12 0.33
19 6 0.17
20 6 0.17
21 12 0.33
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:527301 original size:19 final size:19
Alignment explanation
Indices: 527277--527325 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
527267 AAAATGTTTT
527277 TATGAATAGTATTGTACTG
1 TATGAATAGTATTGTACTG
*
527296 TATGAATAATATTGTACTG
1 TATGAATAGTATTGTACTG
527315 TATGAATAGTA
1 TATGAATAGTA
527326 CCGATATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (19 bp):
TATGAATAGTATTGTACTG
Found at i:527338 original size:20 final size:20
Alignment explanation
Indices: 527313--527368 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
527303 AATATTGTAC
527313 TGTATGAATAGTACCGATAT
1 TGTATGAATAGTACCGATAT
* *
527333 TGTATGAATAATACTGATAT
1 TGTATGAATAGTACCGATAT
* *
527353 TGTGTGAACAGTACCG
1 TGTATGAATAGTACCG
527369 CAGCTCAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
TGTATGAATAGTACCGATAT
Found at i:527343 original size:39 final size:39
Alignment explanation
Indices: 527277--527368 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
527267 AAAATGTTTT
** *
527277 TATGAATAGTATTGTACTGTATGAATAATATTG-TACTG
1 TATGAATAGTACCGTACTGTATGAATAATACTGATACTG
* *
527315 TATGAATAGTACCGATATTGTATGAATAATACTGATATTG
1 TATGAATAGTACCG-TACTGTATGAATAATACTGATACTG
* *
527355 TGTGAACAGTACCG
1 TATGAATAGTACCG
527369 CAGCTCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 12 0.27
39 17 0.38
40 16 0.36
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (39 bp):
TATGAATAGTACCGTACTGTATGAATAATACTGATACTG
Found at i:528689 original size:45 final size:45
Alignment explanation
Indices: 528624--528943 Score: 370
Period size: 45 Copynumber: 7.1 Consensus size: 45
528614 ATGTACTTTA
* * * *
528624 AACTATAACATATTTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCATA-CTTTTCTGTTGATAATGTACCCATATACATTTC
*
528670 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* ** *
528715 AACCATATTATACTTTTATGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * * * *
528760 AACTCTAGCATGCTCTTCTGTTGATAATGTAGCCATATACATTTG
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * * * * *
528805 AACTCTAGCACACTTTTCTGTTGATAATGCATCAATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * * *
528850 AACTCTAGCATGCTCTTCTGTTTATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * * * *
528895 AACTAAAGTATGCTTTTCTGTTGATAATGTACCGATATACATTTT
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
528940 AACT
1 AACT
528944 GTAACATCAT
Statistics
Matches: 234, Mismatches: 40, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
45 224 0.96
46 10 0.04
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.40
Consensus pattern (45 bp):
AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
Found at i:528967 original size:135 final size:134
Alignment explanation
Indices: 528733--528982 Score: 342
Period size: 135 Copynumber: 1.9 Consensus size: 134
528723 TATACTTTTA
**
528733 TGTTGATAATGTACCCATATACATTTCAACTCTAGCATGCTCTTCTGTTGATAATGTAGCCATAT
1 TGTTGATAATGTACCCATATACATTTCAACTAAAGCATGCTCTTCTGTTGATAATGTAGCCATAT
* * * *
528798 ACATTTGAACTCTAGCACACTTTTCTGTTGATAATGCATCAATATGCATTTCAACTCTAGCATGC
66 ACATTTGAACTCTA-CACACATTTCTGCTAATAATGCACCAATATGCATTTCAACTCTAGCATGC
528863 TCTTC
130 TCTTC
* * *
528868 TGTTTATAATGTACCCATATACATTTCAACTAAAGTATGCTTTTCTGTTGATAATGTA-CCGATA
1 TGTTGATAATGTACCCATATACATTTCAACTAAAGCATGCTCTTCTGTTGATAATGTAGCC-ATA
* * *
528932 TACATTTTAACTGTA-ACATCATTTCATGCTAATAATGCACCCATATGCATT
65 TACATTTGAACTCTACACA-CATTTC-TGCTAATAATGCACCAATATGCATT
528983 AGTATTTTCA
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
133 3 0.03
134 7 0.07
135 90 0.90
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (134 bp):
TGTTGATAATGTACCCATATACATTTCAACTAAAGCATGCTCTTCTGTTGATAATGTAGCCATAT
ACATTTGAACTCTACACACATTTCTGCTAATAATGCACCAATATGCATTTCAACTCTAGCATGCT
CTTC
Found at i:529384 original size:22 final size:20
Alignment explanation
Indices: 529340--529395 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
529330 TGGCCCTTTA
529340 GTATCGATACCCATACTATG
1 GTATCGATACCCATACTATG
* *
529360 GTATCGATACTACCCTATTATG
1 GTATCGATAC--CCATACTATG
529382 GTATCGATACCCAT
1 GTATCGATACCCAT
529396 TCTAGTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 13 0.42
22 18 0.58
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (20 bp):
GTATCGATACCCATACTATG
Found at i:529464 original size:72 final size:72
Alignment explanation
Indices: 529379--529538 Score: 198
Period size: 72 Copynumber: 2.2 Consensus size: 72
529369 CTACCCTATT
*
529379 ATGGTATCGATACCCATTCTAGTATCAATACCAAAATTAGCTTCGATATAGT-ATGGTATCGATA
1 ATGGTATCGATACCCATTC-AGTATCAATACCAAAATTAGATTCGATATAGTCATGGTATCGATA
529443 CCCT-CACC
65 CCCTCCA-C
* * * * **
529451 ATGGTATCGATACCCCATTCGGTATCGATACCAAAATTAGATTTGATGTTTTCATGGTATCGATA
1 ATGGTATCGATA-CCCATTCAGTATCAATACCAAAATTAGATTCGATATAGTCATGGTATCGATA
*
529516 CCCTCCAT
65 CCCTCCAC
529524 ATAGGTATCGATACC
1 AT-GGTATCGATACC
529539 TTTTCCATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
72 37 0.49
73 27 0.36
74 12 0.16
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (72 bp):
ATGGTATCGATACCCATTCAGTATCAATACCAAAATTAGATTCGATATAGTCATGGTATCGATAC
CCTCCAC
Found at i:529532 original size:21 final size:21
Alignment explanation
Indices: 529506--529582 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
529496 ATGTTTTCAT
529506 GGTATCGATACCCTCCATATA
1 GGTATCGATACCCTCCATATA
*
529527 GGTATCGATACCTTTTCCATAT-
1 GGTATCGATACC--CTCCATATA
** * *
529549 GGTATCGATACTGTTCATACA
1 GGTATCGATACCCTCCATATA
529570 GGTATCGATACCC
1 GGTATCGATACCC
529583 CATGAATCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.11
21 23 0.50
22 11 0.24
23 7 0.15
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (21 bp):
GGTATCGATACCCTCCATATA
Found at i:530635 original size:23 final size:23
Alignment explanation
Indices: 530574--530636 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
530564 GGAACCCTTG
* *
530574 ATTAAATTGAATAAATAGAATTTA
1 ATTAAATT-CATAAATAGAACTTA
530598 ATTAAATTC-TAAAATAGAACTTA
1 ATTAAATTCAT-AAATAGAACTTA
*
530621 A-TAATTTACATAAATA
1 ATTAAATT-CATAAATA
530637 TGGTCATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 6 0.18
23 18 0.55
24 9 0.27
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (23 bp):
ATTAAATTCATAAATAGAACTTA
Found at i:536776 original size:22 final size:21
Alignment explanation
Indices: 536758--536802 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
536748 CACCGAAGTG
536758 CCACATAGAATGTCTCGAAGGA
1 CCACATA-AATGTCTCGAAGGA
* *
536780 CCACATAAATGTCCCAAAGGA
1 CCACATAAATGTCTCGAAGGA
536801 CC
1 CC
536803 GTGTAGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.16
Consensus pattern (21 bp):
CCACATAAATGTCTCGAAGGA
Found at i:536792 original size:21 final size:22
Alignment explanation
Indices: 536758--536848 Score: 67
Period size: 23 Copynumber: 4.1 Consensus size: 22
536748 CACCGAAGTG
* *
536758 CCACATAGAATGTCTCGAAGGA
1 CCACATAGAATGTCCCAAAGGA
536780 CCACATA-AATGTCCCAAAGGA
1 CCACATAGAATGTCCCAAAGGA
*** * *
536801 CCGTGTAGAAATGTCCCGAATGA
1 CCACATAG-AATGTCCCAAAGGA
* * *
536824 CCACGTAGAATTATCCCGAAGGA
1 CCACATAGAA-TGTCCCAAAGGA
536847 CC
1 CC
536849 GCGTAGATCC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
21 16 0.29
22 9 0.16
23 30 0.55
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (22 bp):
CCACATAGAATGTCCCAAAGGA
Found at i:536814 original size:44 final size:46
Alignment explanation
Indices: 536766--536855 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 46
536756 TGCCACATAG
* * *
536766 AATGTCTCGAAGGACCACATA-AA-TGTCCCAAAGGACCGTGTAGA
1 AATGTCCCGAAGGACCACATAGAATTATCCCAAAGGACCGCGTAGA
* * *
536810 AATGTCCCGAATGACCACGTAGAATTATCCCGAAGGACCGCGTAGA
1 AATGTCCCGAAGGACCACATAGAATTATCCCAAAGGACCGCGTAGA
536856 TCCCTCAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 18 0.47
45 2 0.05
46 18 0.47
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.18
Consensus pattern (46 bp):
AATGTCCCGAAGGACCACATAGAATTATCCCAAAGGACCGCGTAGA
Found at i:536815 original size:23 final size:23
Alignment explanation
Indices: 536786--536855 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
536776 AGGACCACAT
* *
536786 AAATGTCCCAAAGGACCGTGTAG
1 AAATGTCCCGAAGGACCGCGTAG
* *
536809 AAATGTCCCGAATGACCACGTAG
1 AAATGTCCCGAAGGACCGCGTAG
* *
536832 AATTATCCCGAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCGCGTAG
536855 A
1 A
536856 TCCCTCAACT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
AAATGTCCCGAAGGACCGCGTAG
Found at i:536965 original size:16 final size:16
Alignment explanation
Indices: 536944--536992 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
536934 ACATAGCTTA
*
536944 TCACATTGACATTTAT
1 TCACATAGACATTTAT
*
536960 TCACATAGTTCATTT-T
1 TCACATAG-ACATTTAT
*
536976 CCACATAGACATTTAT
1 TCACATAGACATTTAT
536992 T
1 T
536993 ATATCTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (16 bp):
TCACATAGACATTTAT
Found at i:538918 original size:142 final size:145
Alignment explanation
Indices: 538590--538941 Score: 601
Period size: 142 Copynumber: 2.4 Consensus size: 145
538580 ATCTTTCCAG
538590 ATGTGT-TTTCACAGACTT--CACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAG
1 ATGTGTCTTTC-CAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAG
538652 AATTGCACCGTAGTGCCATATAAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCATATAC
65 AATTGCACCGTAGTGCCATATAAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA-ATA-
538717 ATATGCTAGGGATCAAGT
128 ATATGCTAGGGATCAAGT
538735 ATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGA
1 ATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGA
538800 A-TGCACCGTAGTGCCATA-ATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATC-AT-AT
66 ATTGCACCGTAGTGCCATATA-AATGTCCATAAGGACCACATAGAATTCTTTAAGAATCAATAAT
538861 ATGCTAGGGATCAAGT
130 ATGCTAGGGATCAAGT
* *
538877 ATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATACATATGTCTCGAAGAACCGCGTAGA
1 ATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGA
538942 CCCTCGACTC
Statistics
Matches: 201, Mismatches: 2, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
142 81 0.40
144 2 0.01
145 14 0.07
146 58 0.29
147 46 0.23
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (145 bp):
ATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGA
ATTGCACCGTAGTGCCATATAAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCAATAATA
TGCTAGGGATCAAGT
Found at i:539884 original size:23 final size:22
Alignment explanation
Indices: 539832--539885 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
539822 TAATTCAATT
539832 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAATCTTC
* *
539854 TCATATAACTTC-ATAATTTTC
1 TCATATAACTCCTATAATCTTC
539875 TATCATATAAC
1 --TCATATAAC
539886 CCATGTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.29
22 11 0.39
23 9 0.32
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (22 bp):
TCATATAACTCCTATAATCTTC
Found at i:539955 original size:18 final size:18
Alignment explanation
Indices: 539932--539966 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
539922 TCCCATCTAG
539932 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
539950 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
539967 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:543862 original size:23 final size:23
Alignment explanation
Indices: 543836--543880 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
543826 CACCACAGCT
*
543836 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
543859 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
543881 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:544118 original size:149 final size:149
Alignment explanation
Indices: 543859--544309 Score: 843
Period size: 149 Copynumber: 3.0 Consensus size: 149
543849 CGAAGTGCCC
* *
543859 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
543924 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
543989 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
*
544008 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCTATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
544073 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
544138 CATATGT-CCGAAGAACCG
131 CATATGTCCCGAAGAACCG
544156 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
544221 CATATACATATGCTAGGGATCAAGTATGTG-CTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
544285 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
544304 CGTAGA
1 CGTAGA
544310 CCCTCGACTC
Statistics
Matches: 295, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
147 40 0.14
148 121 0.41
149 134 0.45
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:545314 original size:18 final size:18
Alignment explanation
Indices: 545291--545325 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
545281 TCCCATCTAG
545291 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
545309 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
545326 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:556735 original size:33 final size:33
Alignment explanation
Indices: 556693--556758 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
556683 ATTGCATCAG
556693 AAAATAGATCAGTCCACTAGATCCTAGTGGCTT
1 AAAATAGATCAGTCCACTAGATCCTAGTGGCTT
556726 AAAATAGATCAGTCCACTAGATCCTAGTGGCTT
1 AAAATAGATCAGTCCACTAGATCCTAGTGGCTT
556759 CTCTTGTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (33 bp):
AAAATAGATCAGTCCACTAGATCCTAGTGGCTT
Found at i:557262 original size:24 final size:25
Alignment explanation
Indices: 557235--557286 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
557225 AAGGCTTTTT
* *
557235 TTTTTATCTT-TATATGTTTTCTCC
1 TTTTTATATTATATATATTTTCTCC
*
557259 TTTTTTTATTAATATATATTTTCTCC
1 TTTTTATATT-ATATATATTTTCTCC
557285 TT
1 TT
557287 GGATATTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
26 15 0.65
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTTATATTATATATATTTTCTCC
Found at i:561612 original size:23 final size:25
Alignment explanation
Indices: 561563--561613 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
561553 TTTTTTTACA
561563 AATTTATAAAATTATAAGGGGAGGTG
1 AATTTATAAAATTATAA-GGGAGGTG
*
561589 AATTTATAAAATT-TTA-GGAGGTG
1 AATTTATAAAATTATAAGGGAGGTG
561612 AA
1 AA
561614 AATAGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
25 2 0.08
26 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (25 bp):
AATTTATAAAATTATAAGGGAGGTG
Found at i:574881 original size:24 final size:23
Alignment explanation
Indices: 574853--574974 Score: 86
Period size: 24 Copynumber: 5.2 Consensus size: 23
574843 CATTTAAATG
574853 ATAAACGAACAAAAATGAATGAAC
1 ATAAACGAAC-AAAATGAATGAAC
** *
574877 ATAAACGAAC-GGATGCAAACGAAC
1 ATAAACGAACAAAATG--AATGAAC
* *
574901 ATAAACG-ACACAATAAATGAAC
1 ATAAACGAACAAAATGAATGAAC
* *
574923 GTAAACGAACACAAATGAACGAAC
1 ATAAACGAACA-AAATGAATGAAC
* * * *
574947 GTAAAAGAACACAATAAATGAAC
1 ATAAACGAACAAAATGAATGAAC
*
574970 GTAAA
1 ATAAA
574975 TGAAAATATA
Statistics
Matches: 78, Mismatches: 15, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
22 15 0.19
23 19 0.24
24 44 0.56
ACGTcount: A:0.57, C:0.16, G:0.15, T:0.11
Consensus pattern (23 bp):
ATAAACGAACAAAATGAATGAAC
Found at i:574906 original size:10 final size:10
Alignment explanation
Indices: 574873--574933 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 10
574863 AAAAATGAAT
574873 GAACATAAAC
1 GAACATAAAC
574883 GAACGGATGCAAAC
1 GAAC--AT--AAAC
574897 GAACATAAAC
1 GAACATAAAC
*
574907 GACACAATAAAT
1 GA-AC-ATAAAC
*
574919 GAACGTAAAC
1 GAACATAAAC
574929 GAACA
1 GAACA
574934 CAAATGAACG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 18 0.44
11 4 0.10
12 11 0.27
14 8 0.20
ACGTcount: A:0.54, C:0.20, G:0.16, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:575158 original size:14 final size:14
Alignment explanation
Indices: 575139--575189 Score: 93
Period size: 14 Copynumber: 3.6 Consensus size: 14
575129 GATTAGGTTA
*
575139 AACATAAATGAACG
1 AACATAAATAAACG
575153 AACATAAATAAACG
1 AACATAAATAAACG
575167 AACATAAATAAACG
1 AACATAAATAAACG
575181 AACATAAAT
1 AACATAAAT
575190 GAAATATTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.63, C:0.14, G:0.08, T:0.16
Consensus pattern (14 bp):
AACATAAATAAACG
Found at i:578174 original size:23 final size:23
Alignment explanation
Indices: 578094--578176 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
578084 TAAACGAATA
*
578094 TAAACGAACATAATAAATGAACG
1 TAAACGAACACAATAAATGAACG
* * **
578117 TAAACGAACTCAAATGAACAAACG
1 TAAACGAACAC-AATAAATGAACG
*
578141 TAAACAAACACAATAAATGAACG
1 TAAACGAACACAATAAATGAACG
*
578164 TAAATGAACACAA
1 TAAACGAACACAA
578177 ATGAAAATAG
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 29 0.62
24 18 0.38
ACGTcount: A:0.58, C:0.17, G:0.11, T:0.14
Consensus pattern (23 bp):
TAAACGAACACAATAAATGAACG
Found at i:583069 original size:20 final size:20
Alignment explanation
Indices: 583044--583097 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
583034 GACCAACAAA
583044 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
583064 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
583084 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
583098 ATGTTATTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:584086 original size:24 final size:24
Alignment explanation
Indices: 584059--584112 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
584049 GTATTCAAAA
*
584059 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGATCAATACCCGGAC
* *
584083 TTTGATCTTGATCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
584107 TTTGAT
1 TTTGAT
584113 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:585633 original size:23 final size:23
Alignment explanation
Indices: 585607--585670 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
585597 CAGCTCATAT
585607 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
585630 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
585653 AATTGCACTGTAGTGCCA
1 AATTGCACCGAAGTGCCA
585671 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:585859 original size:103 final size:103
Alignment explanation
Indices: 585686--585903 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
585676 TAATGTCCAT
* * *
585686 AAGGACCACATATCATTCCTTAAGAATCATATGCATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
585751 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
585789 AAGGACCACATATTATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
585854 TACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
585892 AAGGACCACATA
1 AAGGACCACATA
585904 GACCATCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:591193 original size:2 final size:2
Alignment explanation
Indices: 591181--591229 Score: 71
Period size: 2 Copynumber: 23.5 Consensus size: 2
591171 TCTTATGTCC
*
591181 AT AT CAT AT AT AT ACC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
591225 AT AT A
1 AT AT A
591230 AAACACGTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 40 0.93
3 3 0.07
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:591512 original size:23 final size:23
Alignment explanation
Indices: 591486--591549 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
591476 CAGCTCATAT
591486 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * **
591509 AATTGCACTGGAGTGCCGTGTAG
1 AATTGCACCGAAGTGCCACGTAG
591532 AATTGCACC-ATAGTGCCA
1 AATTGCACCGA-AGTGCCA
591550 TATAATAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:591764 original size:103 final size:102
Alignment explanation
Indices: 591557--591781 Score: 371
Period size: 103 Copynumber: 2.2 Consensus size: 102
591547 CCATATAATA
*
591557 ATGTCCAC-AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGATCAAGTATGTG
1 ATGTCC-CGAAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGGATCAAGTATGTG
*
591621 TCTCACCAAAATTCATACATGTTCCAAAGAATACAAAT
65 TCTCACCAAAATTCACACATGTTCCAAAGAATACAAAT
*
591659 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGGATCAAGTATGTG
* * *
591724 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
65 TCTCACCAAAATTCACACATGTTCCAAAGAATACAAAT
591762 ATGTCCCGAAGGACCACATA
1 ATGTCCCGAAGGACCACATA
591782 GACCCTCGAC
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 1 0.01
102 44 0.38
103 70 0.61
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (102 bp):
ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGGATCAAGTATGTGT
CTCACCAAAATTCACACATGTTCCAAAGAATACAAAT
Found at i:596096 original size:2 final size:2
Alignment explanation
Indices: 596089--596113 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
596079 TTGGTTATCT
596089 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
596114 GTCAATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:598254 original size:18 final size:18
Alignment explanation
Indices: 598231--598266 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
598221 ACGCAAAAGG
598231 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
598249 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
598267 CAACCGGCTT
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:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:598717 original size:25 final size:25
Alignment explanation
Indices: 598679--598728 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
598669 AAATCAATTA
*
598679 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
598704 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
598729 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:599157 original size:24 final size:24
Alignment explanation
Indices: 599106--599158 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
599096 TTTCATATGT
* * *
599106 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
599130 AATTTGAGTTTGAATTTTAATATA
1 AATTTGAGTTTGAATTTAAATATA
599154 AATTT
1 AATTT
599159 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:599462 original size:39 final size:39
Alignment explanation
Indices: 599419--599505 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
599409 TCCGATGCTC
*
599419 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATCGTGCCAAGCAAAAGGAA
*
599458 ATCAAAATCCAAATCTCATATCGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATCGTGCCAAGCAAAAGGAA
599497 ATCAAAATC
1 ATCAAAATC
599506 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATCGTGCCAAGCAAAAGGAA
Found at i:599739 original size:20 final size:20
Alignment explanation
Indices: 599707--599762 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
599697 CAACCGAAAA
*
599707 TCGCGTTGCGAATTTGACTT
1 TCGCATTGCGAATTTGACTT
*
599727 TCGCATTGTGAATTTGACTT
1 TCGCATTGCGAATTTGACTT
*
599747 TCGCGTTGCGAATTTG
1 TCGCATTGCGAATTTG
599763 TACCTTCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGAATTTGACTT
Found at i:599953 original size:62 final size:63
Alignment explanation
Indices: 599821--599962 Score: 180
Period size: 62 Copynumber: 2.2 Consensus size: 63
599811 TTTTAGAAAC
*
599821 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
599886 A
63 A
* * ** *
599887 AACAAATCAACTTTTACAAATCAATT-AATCAAAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
599949 AACAAATCAACTTT
1 AACAAATCAACTTT
599963 CAATGTAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
61 4 0.06
62 39 0.57
66 26 0.38
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:601338 original size:21 final size:21
Alignment explanation
Indices: 601314--601386 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
601304 GGCGGGACCA
601314 CTTGAACGATGACAGTGGCCT
1 CTTGAACGATGACAGTGGCCT
* * * *
601335 CTTGAACGGTGAGAGGGGCTT
1 CTTGAACGATGACAGTGGCCT
* *
601356 CTTCG-ATGATGATA-TGGGCCT
1 CTT-GAACGATGACAGT-GGCCT
601377 CTTGAACGAT
1 CTTGAACGAT
601387 AGGAGACGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (21 bp):
CTTGAACGATGACAGTGGCCT
Found at i:603616 original size:13 final size:13
Alignment explanation
Indices: 603598--603622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
603588 TTTTTTCAAC
603598 AAAAAGACAAAAT
1 AAAAAGACAAAAT
603611 AAAAAGACAAAA
1 AAAAAGACAAAA
603623 CAAAGACAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAGACAAAAT
Found at i:603868 original size:22 final size:22
Alignment explanation
Indices: 603840--603890 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
603830 GATGGAGATA
603840 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
603862 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
603884 GACGGAT
1 GACGGAT
603891 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:604043 original size:20 final size:20
Alignment explanation
Indices: 604018--604062 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
604008 GCGTAAAAAC
*
604018 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
604038 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
604058 ATTTG
1 ATTTG
604063 GAATATCGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:604071 original size:21 final size:21
Alignment explanation
Indices: 604027--604163 Score: 99
Period size: 20 Copynumber: 6.7 Consensus size: 21
604017 CATTTGACTT
*
604027 TCGCGTTGCGAATTT-GACTA
1 TCGCGTTGCGAATTTGGAATA
604047 TCGCGTTGCGAATTTGGAATA
1 TCGCGTTGCGAATTTGGAATA
*** *
604068 TCGCAACGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAATA
**
604089 TCGCAATGCG-ATTT--ACATA
1 TCGCGTTGCGAATTTGGA-ATA
* *
604108 TTCGCGTTGCGAAATTAGAA-A
1 -TCGCGTTGCGAATTTGGAATA
* *
604129 -CTGAGTTGCGAAATTGGAAT-
1 TC-GCGTTGCGAATTTGGAATA
604149 TCGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
604164 ATTGGTCATT
Statistics
Matches: 94, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 53 0.56
21 35 0.37
22 1 0.01
23 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAATA
Found at i:608780 original size:29 final size:29
Alignment explanation
Indices: 608726--609018 Score: 79
Period size: 30 Copynumber: 10.0 Consensus size: 29
608716 GCACAAATTT
* *
608726 AAACATAAAGGGA-AAAAATAATAAAAACAG
1 AAAC-TAAAGGGACTAAAAT-AGAAAAACAG
*
608756 AAACTAAAGGGACTAAAATAG-AAAA-AT
1 AAACTAAAGGGACTAAAATAGAAAAACAG
* * * *
608783 AAA-T-TAGGGGCTAAAATAATAAAAACAA
1 AAACTAAAGGGACTAAAAT-AGAAAAACAG
** * *
608811 AAAC-CCAGAGGACTAAAATGATAAAAAAAAG
1 AAACTAAAG-GGACTAAAAT-A-GAAAAACAG
* * * * * *
608842 AAATTTAA-GGACTGAAATACAAATATAG
1 AAACTAAAGGGACTAAAATAGAAAAACAG
* *
608870 AAGCTTAAAGGG-CTAAAATAGAAGAAACAT
1 AAAC-TAAAGGGACTAAAATAGAA-AAACAG
** *
608900 AAA-TTTAGGGA-TAAAAATA-AAGAAAGTAG
1 AAACTAAAGGGACT-AAAATAGAA-AAA-CAG
** * * *
608929 AAACTTTAGGGACCAAAATAGATGAAATAG
1 AAACTAAAGGGACTAAAATAGA-AAAACAG
* * *
608959 AAACTAAAGGGACTAAATTGGATAAAATAG
1 AAACTAAAGGGACTAAAATAGA-AAAACAG
* * *
608989 AAACTTAGGGGGCT-AAATAGAAAATACAG
1 AAACTAAAGGGACTAAAATAGAAAA-ACAG
609018 A
1 A
609019 CATTAGAAGG
Statistics
Matches: 196, Mismatches: 47, Indels: 41
0.69 0.17 0.14
Matches are distributed among these distances:
25 11 0.06
26 2 0.01
27 8 0.04
28 31 0.16
29 43 0.22
30 87 0.44
31 13 0.07
32 1 0.01
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.17
Consensus pattern (29 bp):
AAACTAAAGGGACTAAAATAGAAAAACAG
Found at i:608939 original size:30 final size:30
Alignment explanation
Indices: 608884--608998 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 30
608874 TTAAAGGGCT
* * *
608884 AAAATAGAAGAAACATAAA-TTTAGGGATA
1 AAAATAGAAGAAATAGAAACTTTAGGGACA
*
608913 AAAATA-AAGAAAGTAGAAACTTTAGGGACC
1 AAAATAGAAGAAA-TAGAAACTTTAGGGACA
* ** *
608943 AAAATAGATGAAATAGAAACTAAAGGGACT
1 AAAATAGAAGAAATAGAAACTTTAGGGACA
* *
608973 AAATTGGATA-AAATAGAAAC-TTAGGG
1 AAAATAGA-AGAAATAGAAACTTTAGGG
608999 GGCTAAATAG
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
28 6 0.09
29 14 0.20
30 44 0.64
31 5 0.07
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (30 bp):
AAAATAGAAGAAATAGAAACTTTAGGGACA
Found at i:611774 original size:149 final size:149
Alignment explanation
Indices: 611400--611780 Score: 566
Period size: 149 Copynumber: 2.6 Consensus size: 149
611390 GCGATACAAT
* * *
611400 ATTCACATATGTGACTGACACCATAATCGTAAATTAGTATTATGAATCAGATAACATTAAATTTG
1 ATTCACATATGTGACTGACACCGTAATCGTAATTTAGTATTATGAATCAGATAACATTGAATTTG
** * * *
611465 TACAAAAAATTTAAAAATAAATCACACTCGTAATGACCGTTACGCGTTATATAACTTCTGTAGTA
66 TACAAAATTTTTAGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACTTCTGTAGTA
611530 TCCACAACCGCGATACTGC
131 TCCACAACCGCGATACTGC
* *
611549 ATTCACATATGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTG
1 ATTCACATATGTGACTGACACCGTAATCGTAATTTAGTATTATGAATCAGATAACATTGAATTTG
*
611614 TACAAAATTTTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACGTT-TGTAGT
66 TACAAAATTTTTAGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAAC-TTCTGTAGT
* * *
611678 ATTCACAATCGTGATACTGC
130 ATCCACAACCGCGATACTGC
* * **
611698 ATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAACATTGAATTTG
1 ATTCACATATGTGACTGACACCGTAATCGTAATTTAGTATTATGAATCAGATAACATTGAATTTG
**
611763 TACAACCTTTTTAGAAAC
66 TACAAAATTTTTAGAAAC
611781 GATTGTTACG
Statistics
Matches: 208, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
149 206 0.99
150 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (149 bp):
ATTCACATATGTGACTGACACCGTAATCGTAATTTAGTATTATGAATCAGATAACATTGAATTTG
TACAAAATTTTTAGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACTTCTGTAGTA
TCCACAACCGCGATACTGC
Found at i:612203 original size:149 final size:149
Alignment explanation
Indices: 611857--612209 Score: 510
Period size: 149 Copynumber: 2.4 Consensus size: 149
611847 ATATCACAGT
* * ** * *
611857 GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTTAAAAATAAATCACACT
1 GTAATTTAGTATTATGAATCAGATAACATTGAATTTGTACAAAATTTTTAGAAACAAATCACACT
* *
611922 CGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATATTGCATTCACATA
66 AGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATACTGCATTCACATA
* *
611987 TGTGACTGACACCGTAATT
131 TGTGACTAACACCGTAATC
* *
612006 GTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATTTTTTGAAACAAATCACACT
1 GTAATTTAGTATTATGAATCAGATAACATTGAATTTGTACAAAATTTTTAGAAACAAATCACACT
* * *
612071 AGTAATGACCGTTACGCGTTATATAACGTT-TGTAGTATTCACAATCGTGATACTGCATTCACAT
66 AGTAATGACCGTTACGCGTTATATAAC-TTCTGTAGTATCCACAACCGCGATACTGCATTCACAT
*
612135 ATGTGACTAACGCCGTAATC
130 ATGTGACTAACACCGTAATC
** **
612155 GTAATTTAGTATTATGAATCCTATAACATTGAATTTGTACAACCTTTTTAGAAAC
1 GTAATTTAGTATTATGAATCAGATAACATTGAATTTGTACAAAATTTTTAGAAAC
612210 GATTGTTACG
Statistics
Matches: 181, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
149 179 0.99
150 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (149 bp):
GTAATTTAGTATTATGAATCAGATAACATTGAATTTGTACAAAATTTTTAGAAACAAATCACACT
AGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATACTGCATTCACATA
TGTGACTAACACCGTAATC
Found at i:612232 original size:429 final size:429
Alignment explanation
Indices: 611428--612757 Score: 2573
Period size: 429 Copynumber: 3.1 Consensus size: 429
611418 CACCATAATC
* * *
611428 GTAAATTAGTATTATGAATCAGATAACATTAAATTTGTACAAAAAATTTAAAAATAAATCACACT
1 GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTTAAAAATAAATCACACT
611493 CGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATACTGCATTCACATA
66 CGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATACTGCATTCACATA
611558 TGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATT
131 TGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATT
611623 TTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACGTTTGTAGTATTCACAATC
196 TTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACGTTTGTAGTATTCACAATC
611688 GTGATACTGCATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAAC
261 GTGATACTGCATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAAC
611753 ATTGAATTTGTACAACCTTTTTAGAAACGATTGTTACGTGTTATGTAACGTTGTAGTAATTGTAA
326 ATTGAATTTGTACAACCTTTTTAGAAACGATTGTTACGTGTTATGTAACGTTGTAGTAATTGTAA
611818 TCGTGATATTGCAATCACATCTACGACGGATATCACAGT
391 TCGTGATATTGCAATCACATCTACGACGGATATCACAGT
611857 GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTTAAAAATAAATCACACT
1 GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTTAAAAATAAATCACACT
*
611922 CGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATATTGCATTCACATA
66 CGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATACTGCATTCACATA
611987 TGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATT
131 TGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATT
612052 TTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACGTTTGTAGTATTCACAATC
196 TTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACGTTTGTAGTATTCACAATC
612117 GTGATACTGCATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAAC
261 GTGATACTGCATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAAC
612182 ATTGAATTTGTACAACCTTTTTAGAAACGATTGTTACGTGTTATGTAACGTTGTAGTAATTGTAA
326 ATTGAATTTGTACAACCTTTTTAGAAACGATTGTTACGTGTTATGTAACGTTGTAGTAATTGTAA
612247 TCGTGATATTGCAATCACATCTACGACGGATATCACAGT
391 TCGTGATATTGCAATCACATCTACGACGGATATCACAGT
612286 GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTT--AAA-AAATCACACT
1 GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTTAAAAATAAATCACACT
612348 CGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATACTGCATTCACATA
66 CGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATACTGCATTCACATA
612413 TGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATT
131 TGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATT
*
612478 TTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAATGTTTGTAGTATTCACAATC
196 TTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACGTTTGTAGTATTCACAATC
612543 GTGATACTGCATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAAC
261 GTGATACTGCATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAAC
612608 ATTGAATTTGTACAACCTTTTTAGAAACG---GTTACGTGTTATGTAACGTTGTAGTAATTGTAA
326 ATTGAATTTGTACAACCTTTTTAGAAACGATTGTTACGTGTTATGTAACGTTGTAGTAATTGTAA
612670 TCGTGATATTGCAATCACATCTACGACGGATATCACAGT
391 TCGTGATATTGCAATCACATCTACGACGGATATCACAGT
612709 GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTT
1 GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTT
612758 TTATACCCCT
Statistics
Matches: 895, Mismatches: 6, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
423 121 0.14
426 297 0.33
427 3 0.00
429 474 0.53
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (429 bp):
GTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAAAATTTAAAAATAAATCACACT
CGTAATGACCGTTACGCGTTATATAACTTCTGTAGTATCCACAACCGCGATACTGCATTCACATA
TGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATT
TTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACGTTTGTAGTATTCACAATC
GTGATACTGCATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAAC
ATTGAATTTGTACAACCTTTTTAGAAACGATTGTTACGTGTTATGTAACGTTGTAGTAATTGTAA
TCGTGATATTGCAATCACATCTACGACGGATATCACAGT
Found at i:612459 original size:146 final size:149
Alignment explanation
Indices: 612285--612622 Score: 504
Period size: 149 Copynumber: 2.3 Consensus size: 149
612275 GATATCACAG
* *
612285 TGTAATTTAGTATTATGAATAAGATAACATTCAATTTGTACAAAA-AATTT-AAA-AAATCACAC
1 TGTAATTTAGTATTATGAATCAGATAACATTGAATTTGTACAAAATAATTTGAAACAAATCACAC
*
612347 TCGTAATGACCGTTACGCGTTATATAACT-TCTGTAGTATCCACAACCGCGATACTGCATTCACA
66 TAGTAATGACCGTTACGCGTTATATAA-TGTCTGTAGTATCCACAACCGCGATACTGCATTCACA
*
612411 TATGTGACTGACACCGTAAT
130 TATGTGACTAACACCGTAAT
* **
612431 TGTAATTTAGTATTGTGAATCAGATAACATTGAATTTGTACAAAATTTTTTGAAACAAATCACAC
1 TGTAATTTAGTATTATGAATCAGATAACATTGAATTTGTACAAAATAATTTGAAACAAATCACAC
* * * *
612496 TAGTAATGACCGTTACGCGTTATATAATGTTTGTAGTATTCACAATCGTGATACTGCATTCACAT
66 TAGTAATGACCGTTACGCGTTATATAATGTCTGTAGTATCCACAACCGCGATACTGCATTCACAT
*
612561 ATGTGACTAACGCCGTAAT
131 ATGTGACTAACACCGTAAT
* **
612580 CGTAATTTAGTATTATGAATCCTATAACATTGAATTTGTACAA
1 TGTAATTTAGTATTATGAATCAGATAACATTGAATTTGTACAA
612623 CCTTTTTAGA
Statistics
Matches: 172, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
146 42 0.24
147 3 0.02
148 4 0.02
149 123 0.72
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (149 bp):
TGTAATTTAGTATTATGAATCAGATAACATTGAATTTGTACAAAATAATTTGAAACAAATCACAC
TAGTAATGACCGTTACGCGTTATATAATGTCTGTAGTATCCACAACCGCGATACTGCATTCACAT
ATGTGACTAACACCGTAAT
Found at i:613798 original size:42 final size:41
Alignment explanation
Indices: 613707--614034 Score: 451
Period size: 42 Copynumber: 7.8 Consensus size: 41
613697 CTATACACCA
* * *
613707 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
* * *
613751 GTAAGGTTTATCATTGCACACAGCAAAAGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
613793 GTAAGGCTTACTCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTAC-CTTGCACACAGCAAAGGGACCTGGGAAACT
613835 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
* *
613877 GTAAGGCTTACCCTTGCACACAGCAAAGGGGCCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
613919 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
* *
613961 ATAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
614003 GTAAGGCTTACCTTCGCACACAGCAAAGGGAC
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGAC
614035 ATGATAATAC
Statistics
Matches: 259, Mismatches: 17, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
41 12 0.05
42 211 0.81
43 23 0.09
44 13 0.05
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:613854 original size:84 final size:84
Alignment explanation
Indices: 613707--614034 Score: 516
Period size: 84 Copynumber: 3.9 Consensus size: 84
613697 CTATACACCA
* * * * * *
613707 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCATT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
*
613770 ACAGCAAAAGGACCTGGGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
*
613793 GTAAGGCTTACTCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
613858 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
613877 GTAAGGCTTACCCTTGCACACAGCAAAGGGGCCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
613942 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
613961 ATAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
614026 CAAAGGGAC
66 CAAAGGGAC
614035 ATGATAATAC
Statistics
Matches: 228, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
83 3 0.01
84 196 0.86
85 14 0.06
86 15 0.07
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:615006 original size:28 final size:28
Alignment explanation
Indices: 614965--615115 Score: 132
Period size: 29 Copynumber: 5.4 Consensus size: 28
614955 CATTTTACAC
*
614965 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCA-CCTTTTTAAATTAATTACCA
*
614994 AAATAGCACCTTTTTGAATTAATT-CCTA
1 AAATAGCACCTTTTTAAATTAATTACC-A
* *
615022 AAATAGCA-CTAATTTCAAATTAATTCCCA
1 AAATAGCACCT--TTTTAAATTAATTACCA
* *
615051 GAATATCA-CTTTTTGAAA--AATTACCA
1 AAATAGCACCTTTTT-AAATTAATTACCA
* * *
615077 AAATAGCACACATTTCAAATTAATTCCCA
1 AAATAGCAC-CTTTTTAAATTAATTACCA
615106 AAATAGCACC
1 AAATAGCACC
615116 AAAATCGAAT
Statistics
Matches: 100, Mismatches: 13, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
26 13 0.13
27 10 0.10
28 31 0.31
29 44 0.44
30 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (28 bp):
AAATAGCACCTTTTTAAATTAATTACCA
Found at i:615092 original size:55 final size:57
Alignment explanation
Indices: 614965--615115 Score: 184
Period size: 55 Copynumber: 2.7 Consensus size: 57
614955 CATTTTACAC
* * * * * *
614965 AAATAGCACCCTTTTTAAAATAATTACCAAAATAGCACCTTTTTGAATTAATTCCTA
1 AAATAGCACACATTTCAAATTAATTCCCAAAATAGCACCTTTTTGAATAAATTCCTA
* *
615022 AAATAGCACTA-ATTTCAAATTAATTCCCAGAATATCA-CTTTTTGAA-AAATTACC-A
1 AAATAGCAC-ACATTTCAAATTAATTCCCAAAATAGCACCTTTTTGAATAAATT-CCTA
615077 AAATAGCACACATTTCAAATTAATTCCCAAAATAGCACC
1 AAATAGCACACATTTCAAATTAATTCCCAAAATAGCACC
615116 AAAATCGAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
54 1 0.01
55 38 0.47
56 12 0.15
57 29 0.36
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (57 bp):
AAATAGCACACATTTCAAATTAATTCCCAAAATAGCACCTTTTTGAATAAATTCCTA
Found at i:615131 original size:84 final size:84
Alignment explanation
Indices: 614975--615131 Score: 208
Period size: 84 Copynumber: 1.9 Consensus size: 84
614965 AAATAGCACC
* ** * * **
614975 CTTTTTAAAATAATTACCAAAATAGCACCTTTTTGAATTAATTCCTAAAATAGCACTAATTTCAA
1 CTTTTTAAAATAATTACCAAAATAGCACCATTTCAAATTAATTCCCAAAATAGCACCAAAATCAA
*
615040 ATTAATTCCCAGAATATCA
66 ATAAATTCCCAGAATATCA
* *
615059 CTTTTTGAAA-AATTACCAAAATAGCACACATTTCAAATTAATTCCCAAAATAGCACCAAAATCG
1 CTTTTTAAAATAATTACCAAAATAGCAC-CATTTCAAATTAATTCCCAAAATAGCACCAAAATCA
615123 AATAAATTC
65 AATAAATTC
615132 TCAAAATAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
83 17 0.27
84 45 0.73
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (84 bp):
CTTTTTAAAATAATTACCAAAATAGCACCATTTCAAATTAATTCCCAAAATAGCACCAAAATCAA
ATAAATTCCCAGAATATCA
Found at i:621326 original size:42 final size:41
Alignment explanation
Indices: 621224--621554 Score: 430
Period size: 42 Copynumber: 7.8 Consensus size: 41
621214 CTATACACCA
* * *
621224 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
* * * *
621268 GTAAGGTTTATCCTTGCACACATCAAAGGGACTTGGGAAATT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* * *
621310 GTAAGGCTTACTCTTGCACACAGCAAAGAGACCTTGTAAACT
1 GTAAGGCTTAC-CTTGCACACAGCAAAGGGACCTGGGAAACT
621352 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
* * *
621394 GTAAGGCTTACCCTTGCACACAGTAAAGGGGCCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
621436 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
621478 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
621520 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
621555 ATAATACTTC
Statistics
Matches: 255, Mismatches: 24, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
41 12 0.05
42 208 0.82
43 21 0.08
44 14 0.05
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:621371 original size:84 final size:84
Alignment explanation
Indices: 621224--621554 Score: 495
Period size: 84 Copynumber: 3.9 Consensus size: 84
621214 CTATACACCA
* * * * *
621224 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
* * *
621287 ACATCAAAGGGACTTGGGAAATT
62 ACAGCAAAGGGACCTGGGAAACT
* * *
621310 GTAAGGCTTACTCTTGCACACAGCAAAGAGACCTTGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
621375 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
* *
621394 GTAAGGCTTACCCTTGCACACAGTAAAGGGGCCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
621459 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
621478 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
621543 CAAAGGGACCTG
66 CAAAGGGACCTG
621555 ATAATACTTC
Statistics
Matches: 225, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
83 4 0.02
84 193 0.86
85 14 0.06
86 14 0.06
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:622532 original size:29 final size:29
Alignment explanation
Indices: 622480--622570 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 29
622470 CACTTTACAC
* * * * *
622480 AAATAGCA-CCTTTTTAAAATAATTACTA
1 AAATAGCATCATTTTTGAATTAATTCCCA
*
622508 AAATAGCATTATTTTTGAATTAATTCCCA
1 AAATAGCATCATTTTTGAATTAATTCCCA
* *
622537 AAATAGCATCAATTTCGAATTAATTCCCA
1 AAATAGCATCATTTTTGAATTAATTCCCA
622566 AAATA
1 AAATA
622571 TCACTTTTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 8 0.15
29 45 0.85
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.35
Consensus pattern (29 bp):
AAATAGCATCATTTTTGAATTAATTCCCA
Found at i:622630 original size:29 final size:29
Alignment explanation
Indices: 622524--622635 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
622514 CATTATTTTT
*
622524 GAATTAATTCCCAAAATAGCATCAATTTC
1 GAATTAATTCCCAAAATAGCACCAATTTC
* ** *
622553 GAATTAATTCCCAAAATATCA-CTTTTTGA
1 GAATTAATTCCCAAAATAGCACCAATTT-C
** * *
622582 GAAAAAAATTTACCAAAATAGCACCCATTTC
1 G-AATTAA-TTCCCAAAATAGCACCAATTTC
*
622613 GATTTAATTCCCAAAATAGCACC
1 GAATTAATTCCCAAAATAGCACC
622636 TAAATCAAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
28 4 0.06
29 36 0.56
30 7 0.11
31 13 0.20
32 4 0.06
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (29 bp):
GAATTAATTCCCAAAATAGCACCAATTTC
Found at i:622715 original size:11 final size:11
Alignment explanation
Indices: 622699--622730 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
622689 GTCAAACCTG
622699 TCAAAACCGGT
1 TCAAAACCGGT
622710 TCAAAACCGGT
1 TCAAAACCGGT
622721 T--AAACCGGT
1 TCAAAACCGGT
622730 T
1 T
622731 TCCAGATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (11 bp):
TCAAAACCGGT
Found at i:635702 original size:21 final size:21
Alignment explanation
Indices: 635651--635703 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
635641 ATTATGACTA
635651 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
635672 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
635693 TCGCAATGCGA
1 TCGCAATGCGA
635704 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:635718 original size:20 final size:21
Alignment explanation
Indices: 635693--635744 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
635683 TTTTCCCAAT
*
635693 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
635713 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
635734 TCGCAATGCGA
1 TCGCAATGCGA
635745 TACTAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:635757 original size:41 final size:43
Alignment explanation
Indices: 635712--635805 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 43
635702 GAATAAGTAA
* **
635712 ATCGCAACGCGAAT-TTGGAAAATCGCAATGCGATACT-AATT
1 ATCGCAACGCGAATAATACAAAATCGCAATGCGATACTGAATT
* *
635753 ATCGCAACGTG-ATAATACAAAATCGCAATGCGATACTGACTT
1 ATCGCAACGCGAATAATACAAAATCGCAATGCGATACTGAATT
635795 -TCGCAACGCGA
1 ATCGCAACGCGA
635806 TACTGACTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
40 2 0.05
41 39 0.89
42 3 0.07
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (43 bp):
ATCGCAACGCGAATAATACAAAATCGCAATGCGATACTGAATT
Found at i:635758 original size:20 final size:21
Alignment explanation
Indices: 635733--635860 Score: 88
Period size: 20 Copynumber: 6.3 Consensus size: 21
635723 AATTTGGAAA
635733 ATCGCAATGCGATACT-AATT
1 ATCGCAATGCGATACTGAATT
* * * **
635753 ATCGCAACGTGATAAT-ACAAA
1 ATCGCAATGCGATACTGA-ATT
*
635774 ATCGCAATGCGATACTGACTT
1 ATCGCAATGCGATACTGAATT
* *
635795 -TCGCAACGCGATACTGACTT
1 ATCGCAATGCGATACTGAATT
* *
635815 -TCGCAATGCGATTCTGACTT
1 ATCGCAATGCGATACTGAATT
* * *
635835 -TCGCAACGCGATTCTGACTT
1 ATCGCAATGCGATACTGAATT
635855 -TCGCAA
1 ATCGCAA
635861 CGAGATTCTG
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
20 76 0.84
21 14 0.15
22 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (21 bp):
ATCGCAATGCGATACTGAATT
Found at i:635886 original size:20 final size:20
Alignment explanation
Indices: 635775--635882 Score: 155
Period size: 20 Copynumber: 5.4 Consensus size: 20
635765 TAATACAAAA
* *
635775 TCGCAATGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
635795 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
635815 TCGCAATGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
635835 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
635855 TCGCAACGAGATTCTGACTAT
1 TCGCAACGCGATTCTGACT-T
635876 T-GCAACG
1 TCGCAACG
635883 AGATAATACA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
20 80 0.98
21 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:636644 original size:24 final size:24
Alignment explanation
Indices: 636624--636670 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
636614 AAATTTGAAC
636624 TTGGTCAATACCCGGACTTTGATA
1 TTGGTCAATACCCGGACTTTGATA
* *
636648 TTGGTCAATACTCGGATTTTGAT
1 TTGGTCAATACCCGGACTTTGAT
636671 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACCCGGACTTTGATA
Found at i:636862 original size:12 final size:12
Alignment explanation
Indices: 636845--636869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
636835 ATATAATCCT
636845 GAAGAAGAAAAA
1 GAAGAAGAAAAA
636857 GAAGAAGAAAAA
1 GAAGAAGAAAAA
636869 G
1 G
636870 TCCCCGAAAA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:639175 original size:20 final size:20
Alignment explanation
Indices: 639150--639225 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
639140 CAACGGGGAA
*
639150 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
639170 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
639190 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* *
639210 ATCGTAACGAGAAAAT
1 ATCGCAACGCGAAAAT
639226 CGCAATGTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:639288 original size:19 final size:19
Alignment explanation
Indices: 639266--639308 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
639256 TTTCTCGTTG
639266 CGATTTTCATTTCGCATTA
1 CGATTTTCATTTCGCATTA
*
639285 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTA
639304 CGATT
1 CGATT
639309 CTCTCGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.47
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTA
Found at i:639485 original size:14 final size:14
Alignment explanation
Indices: 639448--639486 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
639438 CATCAATTAA
**
639448 ACAAATCAACATTT
1 ACAAATCAATTTTT
639462 ACAAATCAATTTTT
1 ACAAATCAATTTTT
639476 ACAAATCAATT
1 ACAAATCAATT
639487 AAACAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:640946 original size:40 final size:42
Alignment explanation
Indices: 640893--640983 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
640883 CCTCTTCAAC
*
640893 GATGACAGTGGCCTCTTGAACG-GT-GAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* * *
640933 GATGATAGGGGCCTCTTGAATGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
*
640975 GATAACAGG
1 GATGACAGG
640984 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 19 0.44
41 1 0.02
42 23 0.53
ACGTcount: A:0.23, C:0.14, G:0.40, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Done.