Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_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: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:2666783 original size:26 final size:25
Alignment explanation
Indices: 2666741--2666805 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 25
2666731 AATTAAGCTA
*
2666741 ATAATAAAATATATTTAATAAGTTAAT
1 ATAATAAAATAT-TTTTA-AAGTTAAT
2666768 ATAA-AAAATATTTTTAAAGTTAAT
1 ATAATAAAATATTTTTAAAGTTAAT
2666792 ATATATAAAATATT
1 ATA-ATAAAATATT
2666806 ATGAATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 11 0.31
25 5 0.14
26 15 0.43
27 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
ATAATAAAATATTTTTAAAGTTAAT
Found at i:2678372 original size:203 final size:203
Alignment explanation
Indices: 2677942--2678338 Score: 523
Period size: 203 Copynumber: 2.0 Consensus size: 203
2677932 GCAAATGCTT
* * *
2677942 TTGCGGCGTTTGTATAACAAGCGCCACTATTGATGAACGCTATTGTGGCGTTTTTCTAAAAACAA
1 TTGCAGCGTTTGTATAACAAACGCCACTATTGATGAACGCTATTGTGGCGTTTGTCTAAAAACAA
* * *
2678007 CGCTAAGATATTCTTTATTGCGGCGTTTGTTGGAAAAACGGCACAATAAACAACACTATTGCGGC
66 CGCTAAGATATTCTTTATTGCGGCGTTTGTTGGAAAAACGCCACAATAAACAACACTATTACGAC
* * * *
2678072 GTTTGTGCTAAAAATGGCGCTAATTACTACTCTATACCGGCGTTTTTAAAAACACGCCACTATAG
131 ATTTGTGCTAAAAA-GACGCTAATTACTACTCTATAACGGCGTTTTGAAAAACACGCCACTATAG
**
2678137 CACATGTTC
195 CACAAATTC
* * * *
2678146 TTGCGGCTTTTGTATAACAAACGCCACTATTTATGAACGCTATTGTGGCGTTTGTCT-AAAATAA
1 TTGCAGCGTTTGTATAACAAACGCCACTATTGATGAACGCTATTGTGGCGTTTGTCTAAAAACAA
* * *
2678210 CGCTAA-AGTATTCTTTATTGCGGCGTTTGTTGGCAAAATGCCACAATAAACAACCCTATTACGA
66 CGCTAAGA-TATTCTTTATTGCGGCGTTTGTTGGAAAAACGCCACAATAAACAACACTATTACGA
* * *
2678274 CATTTGTGCTAAAAA-ACTCTAACTTACTCCTCTATAACGGCGTTTGTGAAAGAA-ACGCCGCTA
130 CATTTGTGCTAAAAAGACGCTAA-TTACTACTCTATAACGGCGTTT-TGAAA-AACACGCCACTA
2678337 TA
192 TA
2678339 TGTTTAAATT
Statistics
Matches: 171, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
201 5 0.03
202 21 0.12
203 90 0.53
204 55 0.32
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (203 bp):
TTGCAGCGTTTGTATAACAAACGCCACTATTGATGAACGCTATTGTGGCGTTTGTCTAAAAACAA
CGCTAAGATATTCTTTATTGCGGCGTTTGTTGGAAAAACGCCACAATAAACAACACTATTACGAC
ATTTGTGCTAAAAAGACGCTAATTACTACTCTATAACGGCGTTTTGAAAAACACGCCACTATAGC
ACAAATTC
Found at i:2679855 original size:24 final size:24
Alignment explanation
Indices: 2679823--2679876 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
2679813 TGTCGGATTG
*
2679823 CAAGCACTCATCAGTCTCTAGCTT
1 CAAGCACTCATCAGTCTCTAACTT
2679847 CAAGCACTCATCAGTCTCTAACTT
1 CAAGCACTCATCAGTCTCTAACTT
2679871 CAAGCA
1 CAAGCA
2679877 TTTAGTACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.33, G:0.11, T:0.26
Consensus pattern (24 bp):
CAAGCACTCATCAGTCTCTAACTT
Found at i:2685824 original size:3 final size:3
Alignment explanation
Indices: 2685816--2685873 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
2685806 GCAAAAATGT
*
2685816 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2685864 ATTA ATA ATA
1 A-TA ATA ATA
2685874 TTTGTAAGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2690437 original size:3 final size:3
Alignment explanation
Indices: 2690429--2690492 Score: 105
Period size: 3 Copynumber: 21.7 Consensus size: 3
2690419 TGCATGATAT
2690429 TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTAC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC
2690474 TTC TTC -TC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TT
2690493 AGATTGTGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:2690471 original size:27 final size:26
Alignment explanation
Indices: 2690429--2690492 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 26
2690419 TGCATGATAT
2690429 TTCTTCTTCTTCTTCTTCTTCTTCTC
1 TTCTTCTTCTTCTTCTTCTTCTTCTC
2690455 TTCTTCTTACTTCTTCTTCTTCTTCTC
1 TTCTTCTT-CTTCTTCTTCTTCTTCTC
2690482 TTCTTCTTCTT
1 TTCTTCTTCTT
2690493 AGATTGTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 11 0.30
27 26 0.70
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66
Consensus pattern (26 bp):
TTCTTCTTCTTCTTCTTCTTCTTCTC
Found at i:2690529 original size:116 final size:116
Alignment explanation
Indices: 2690377--2690604 Score: 415
Period size: 116 Copynumber: 2.0 Consensus size: 116
2690367 TTTGGTGATG
*
2690377 AGATTGTGAAATGTAAGGGACTGCAACATATATACATAAGTATGCATGATATTTCTTCTTCTTCT
1 AGATTGTGAAATGTAAGGGACTGCAACATATATACATAAGTATGCATGAT-CTTCTTCTTCTTCT
2690442 TCTTCTTCTTC-TCTTCTTCTTACTTCTTCTTCTTCTTC-TCTTCTTCTTCTT
65 TCTTCTTCTTCTTCTTCTTCTT-CTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
2690493 AGATTGTGAAATGTAAGGGACTGCAACATATATACATAAGTATGCATGATCTTCTTCTTCTTCTT
1 AGATTGTGAAATGTAAGGGACTGCAACATATATACATAAGTATGCATGATCTTCTTCTTCTTCTT
2690558 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
66 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
2690605 CTTCTTCTCT
Statistics
Matches: 109, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
115 40 0.37
116 69 0.63
ACGTcount: A:0.18, C:0.23, G:0.10, T:0.49
Consensus pattern (116 bp):
AGATTGTGAAATGTAAGGGACTGCAACATATATACATAAGTATGCATGATCTTCTTCTTCTTCTT
CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
Found at i:2690550 original size:3 final size:3
Alignment explanation
Indices: 2690542--2690772 Score: 366
Period size: 3 Copynumber: 77.3 Consensus size: 3
2690532 GTATGCATGA
2690542 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2690590 TCT TCT TCT TCT TC- TCT TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2690636 TCT TCT TCT TCT TCT TCT TCTT TCT TCT TCT TCT TC- TCT TCTT TCT
1 TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TC-T TCT
*
2690682 TCT TCTT TCT TCT TCT T-T CTCT TCT TAT TCT TCT TCT TCT TCTT TCT
1 TCT TC-T TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TC-T TCT
2690729 TCT TCT TCT TCT TC- TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2690773 AAAAAAAAAA
Statistics
Matches: 215, Mismatches: 2, Indels: 22
0.90 0.01 0.09
Matches are distributed among these distances:
2 11 0.05
3 191 0.89
4 13 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2692402 original size:20 final size:20
Alignment explanation
Indices: 2692369--2692408 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2692359 ATTCGATTCA
2692369 ATGCAGTCACGATTAATATG
1 ATGCAGTCACGATTAATATG
* *
2692389 ATGCATTCATGATTAATATG
1 ATGCAGTCACGATTAATATG
2692409 TTAATATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (20 bp):
ATGCAGTCACGATTAATATG
Found at i:2699472 original size:25 final size:25
Alignment explanation
Indices: 2699438--2699486 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
2699428 AGGTTGGATT
2699438 AATGGAAGGCTTGAATGAATGTGTG
1 AATGGAAGGCTTGAATGAATGTGTG
2699463 AATGGAAGGCTTGAATGAATGTGT
1 AATGGAAGGCTTGAATGAATGTGT
2699487 CAAAGGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.29
Consensus pattern (25 bp):
AATGGAAGGCTTGAATGAATGTGTG
Found at i:2699479 original size:13 final size:13
Alignment explanation
Indices: 2699438--2699479 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2699428 AGGTTGGATT
2699438 AATGGAAGGCTTG
1 AATGGAAGGCTTG
*
2699451 AAT-GAATG-TGTG
1 AATGGAAGGCT-TG
2699463 AATGGAAGGCTTG
1 AATGGAAGGCTTG
2699476 AATG
1 AATG
2699480 AATGTGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 13 0.54
14 1 0.04
ACGTcount: A:0.33, C:0.05, G:0.36, T:0.26
Consensus pattern (13 bp):
AATGGAAGGCTTG
Found at i:2699494 original size:25 final size:25
Alignment explanation
Indices: 2699441--2699494 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
2699431 TTGGATTAAT
* *
2699441 GGAAGGCTTGAATGAATGTGTGAAT
1 GGAAGGCTTGAATGAATGTGTCAAA
2699466 GGAAGGCTTGAATGAATGTGTCAAA
1 GGAAGGCTTGAATGAATGTGTCAAA
2699491 GGAA
1 GGAA
2699495 ATAATTCAAG
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:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (25 bp):
GGAAGGCTTGAATGAATGTGTCAAA
Found at i:2709169 original size:34 final size:35
Alignment explanation
Indices: 2709091--2709170 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 35
2709081 AATACCTTTG
* * *
2709091 ATACATTTGCATATTTGCATTCTCATCTTTTCATT
1 ATACATTTGCATATTTGCATTCACATCTCTACATT
*
2709126 -TGCATTTGCAT-TTGTGCATTCACATCTCTACATT
1 ATACATTTGCATATT-TGCATTCACATCTCTACATT
2709160 ATACA-TTGCAT
1 ATACATTTGCAT
2709171 GCTAATTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
33 2 0.05
34 33 0.87
35 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (35 bp):
ATACATTTGCATATTTGCATTCACATCTCTACATT
Found at i:2711731 original size:41 final size:41
Alignment explanation
Indices: 2711627--2711732 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
2711617 AAAGAGCGAG
* * *
2711627 TAAGTCTTTCGGGTCATCAGTAAGTTTTCGAGCATGATGAT
1 TAAGTCATTCGGGTCATCTGTAAGTTTTCGAGCAGGATGAT
* * * *
2711668 TAAATCATTTGTGTCATTTGTAAGTTTTTCGATG-AGGATGA-
1 TAAGTCATTCGGGTCATCTGTAAG-TTTTCGA-GCAGGATGAT
*
2711709 TAAGTCATTCGGGCCATCTGTAAG
1 TAAGTCATTCGGGTCATCTGTAAG
2711733 ACCTTCAGAC
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 37 0.73
42 13 0.25
43 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (41 bp):
TAAGTCATTCGGGTCATCTGTAAGTTTTCGAGCAGGATGAT
Found at i:2712068 original size:15 final size:15
Alignment explanation
Indices: 2712038--2712066 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2712028 AGAATTCAAG
2712038 ACCTTCAGGTCATTT
1 ACCTTCAGGTCATTT
2712053 ACCTTCAGGT-ATTT
1 ACCTTCAGGTCATTT
2712067 TAAATTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (15 bp):
ACCTTCAGGTCATTT
Found at i:2712331 original size:44 final size:44
Alignment explanation
Indices: 2712225--2712431 Score: 245
Period size: 44 Copynumber: 4.7 Consensus size: 44
2712215 CCTTGGCTCA
*** **
2712225 TCCATCACATAAGGAGTTGGATCAGTTTCACTTTCTTCGCTCGAT
1 TCCATCACATAAGGAGTTGGATCAACATCACCAT-TTCGCTCGAT
* * * *
2712270 TCCATCAAATAAAGAGTTGGATCAGCATCACCATTTCGCTCGTT
1 TCCATCACATAAGGAGTTGGATCAACATCACCATTTCGCTCGAT
* * *
2712314 TCCATCACATAAGGAGTTGGAGCAACATCGACC-TTTTGCTAGAT
1 TCCATCACATAAGGAGTTGGATCAACATC-ACCATTTCGCTCGAT
* * *
2712358 TCCATCACATAAGGAGTTGGATCAACATCACAATTTCGCTTGTT
1 TCCATCACATAAGGAGTTGGATCAACATCACCATTTCGCTCGAT
*
2712402 TCCATCACATAAGGAGTTGGAACAACATCA
1 TCCATCACATAAGGAGTTGGATCAACATCA
2712432 ATATTATTTT
Statistics
Matches: 140, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.01
44 107 0.76
45 31 0.22
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (44 bp):
TCCATCACATAAGGAGTTGGATCAACATCACCATTTCGCTCGAT
Found at i:2712381 original size:88 final size:89
Alignment explanation
Indices: 2712225--2712431 Score: 283
Period size: 88 Copynumber: 2.3 Consensus size: 89
2712215 CCTTGGCTCA
* *** * *
2712225 TCCATCACATAAGGAGTTGGATCAGTTTCACTTTCTTCGCTCGATTCCATCAAATAAAGAGTTGG
1 TCCATCACATAAGGAGTTGGAACAACATCACCTTCTTCGCTAGATTCCATCAAATAAAGAGTTGG
* *
2712290 ATCAGCATCACCATTTCGCTCGTT
66 ATCAACATCACAATTTCGCTCGTT
* * *
2712314 TCCATCACATAAGGAGTTGGAGCAACATCGACCTT-TT-GCTAGATTCCATCACATAAGGAGTTG
1 TCCATCACATAAGGAGTTGGAACAACATC-ACCTTCTTCGCTAGATTCCATCAAATAAAGAGTTG
*
2712377 GATCAACATCACAATTTCGCTTGTT
65 GATCAACATCACAATTTCGCTCGTT
2712402 TCCATCACATAAGGAGTTGGAACAACATCA
1 TCCATCACATAAGGAGTTGGAACAACATCA
2712432 ATATTATTTT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
87 1 0.01
88 73 0.70
89 27 0.26
90 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (89 bp):
TCCATCACATAAGGAGTTGGAACAACATCACCTTCTTCGCTAGATTCCATCAAATAAAGAGTTGG
ATCAACATCACAATTTCGCTCGTT
Found at i:2713337 original size:15 final size:15
Alignment explanation
Indices: 2713317--2713372 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2713307 TAACCGGTTT
2713317 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2713332 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
2713349 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2713364 CGATTTTAA
1 CGGTTTTAA
2713373 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:2713345 original size:17 final size:17
Alignment explanation
Indices: 2713320--2713370 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2713310 CCGGTTTCGG
2713320 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
2713337 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
2713352 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
2713369 TT
1 TT
2713371 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:2713567 original size:21 final size:21
Alignment explanation
Indices: 2713538--2713594 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2713528 TTTTACACTT
*
2713538 AGGGAACCGATTCCCTATGAG
1 AGGGTACCGATTCCCTATGAG
2713559 AGGGTACCGATTCCCTATGAG
1 AGGGTACCGATTCCCTATGAG
2713580 AGGGTACCGATTCCC
1 AGGGTACCGATTCCC
2713595 CCACGCTCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (21 bp):
AGGGTACCGATTCCCTATGAG
Found at i:2713811 original size:13 final size:13
Alignment explanation
Indices: 2713790--2713844 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2713780 AAGTTCGATA
*
2713790 AATTCAAATACTT
1 AATTGAAATACTT
2713803 AATTGAAATACTT
1 AATTGAAATACTT
* *
2713816 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
2713830 AATTGAAATACTT
1 AATTGAAATACTT
2713843 AA
1 AA
2713845 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2713926 original size:32 final size:33
Alignment explanation
Indices: 2713830--2713928 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2713820 AACTCAACAT
* * *
2713830 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2713863 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2713896 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2713928 A
1 A
2713929 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2713947 original size:21 final size:21
Alignment explanation
Indices: 2713923--2713962 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2713913 ACTTCAAGTT
2713923 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2713944 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
2713963 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2719539 original size:21 final size:21
Alignment explanation
Indices: 2719515--2719557 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2719505 AATGGACCGA
*
2719515 TATAAAATGAATTTAGAAAAT
1 TATAAAATAAATTTAGAAAAT
* * *
2719536 TATAGAGTAAATTTATAAAAT
1 TATAAAATAAATTTAGAAAAT
2719557 T
1 T
2719558 TTAAGAAACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (21 bp):
TATAAAATAAATTTAGAAAAT
Found at i:2721119 original size:5 final size:5
Alignment explanation
Indices: 2721111--2721136 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2721101 TTTTATTATT
2721111 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
2721137 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:2721768 original size:11 final size:11
Alignment explanation
Indices: 2721752--2721779 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2721742 TAAGGTTATA
2721752 CTCTTTAGTTT
1 CTCTTTAGTTT
2721763 CTCTTTAGTTT
1 CTCTTTAGTTT
2721774 CTCTTT
1 CTCTTT
2721780 TGATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.64
Consensus pattern (11 bp):
CTCTTTAGTTT
Found at i:2724052 original size:23 final size:20
Alignment explanation
Indices: 2723997--2724052 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 20
2723987 GATTATCTAA
2723997 GAATATGAAATAAGAGATAT
1 GAATATGAAATAAGAGATAT
* *
2724017 G-ATAAGGACATAAGGAATGATAT
1 GAAT-ATGAAATAA-G-A-GATAT
2724040 GAATATGAAATAA
1 GAATATGAAATAA
2724053 TATGAAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
19 2 0.07
20 8 0.30
21 1 0.04
22 1 0.04
23 13 0.48
24 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.21, T:0.23
Consensus pattern (20 bp):
GAATATGAAATAAGAGATAT
Found at i:2726955 original size:32 final size:33
Alignment explanation
Indices: 2726911--2726980 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
2726901 ACCTTACAAC
* * *
2726911 TCCCTAG-TTTTTACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTAACGGGATAAACTAGAACATT
*
2726943 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAGCTTTTA-ACGGGATAAACTAGAACATT
2726977 TCCC
1 TCCC
2726981 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (33 bp):
TCCCTAGCTTTTAACGGGATAAACTAGAACATT
Found at i:2729713 original size:32 final size:33
Alignment explanation
Indices: 2729669--2729738 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
2729659 ACCTTACAAC
* *
2729669 TCCCTAG-TTTTTACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
*
2729701 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTA-ACGGGATAAACTAGAACCTT
2729735 TCCC
1 TCCC
2729739 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (33 bp):
TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
Found at i:2730122 original size:20 final size:20
Alignment explanation
Indices: 2730086--2730162 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
2730076 CCGTTAGACA
*
2730086 GGGGGAATCGGTATCCCCTGG
1 GGGGGAATCTGT-TCCCCTGG
*
2730107 GGGGGAATATGTTCCCTCT--
1 GGGGGAATCTGTTCCC-CTGG
* *
2730126 GGGGGAATCGGTCCCCCTGG
1 GGGGGAATCTGTTCCCCTGG
2730146 GGGGGAATCTGTTCCCC
1 GGGGGAATCTGTTCCCC
2730163 CTGGACAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
18 2 0.04
19 13 0.28
20 19 0.41
21 12 0.26
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.22
Consensus pattern (20 bp):
GGGGGAATCTGTTCCCCTGG
Found at i:2730123 original size:19 final size:19
Alignment explanation
Indices: 2730086--2730161 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
2730076 CCGTTAGACA
*
2730086 GGGGGAATCGGTATCCCCTGG
1 GGGGGAATCTGT-T-CCCTGG
* **
2730107 GGGGGAATATGTTCCCTCT
1 GGGGGAATCTGTTCCCTGG
* *
2730126 GGGGGAATCGGTCCCCCTGG
1 GGGGGAATCTGT-TCCCTGG
2730146 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
2730162 CCTGGACAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 17 0.40
20 16 0.37
21 10 0.23
ACGTcount: A:0.13, C:0.25, G:0.39, T:0.22
Consensus pattern (19 bp):
GGGGGAATCTGTTCCCTGG
Found at i:2730159 original size:39 final size:40
Alignment explanation
Indices: 2730086--2730166 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
2730076 CCGTTAGACA
* *
2730086 GGGGGAATCGGTATCCCCTGGGGGGGAATATGTTCCCTCT
1 GGGGGAATCGGTACCCCCTGGGGGGGAATATGTTCCCCCT
*
2730126 GGGGGAATCGGT-CCCCCTGGGGGGGAATCTGTTCCCCCT
1 GGGGGAATCGGTACCCCCTGGGGGGGAATATGTTCCCCCT
2730165 GG
1 GG
2730167 ACAATCTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 26 0.68
40 12 0.32
ACGTcount: A:0.12, C:0.26, G:0.40, T:0.22
Consensus pattern (40 bp):
GGGGGAATCGGTACCCCCTGGGGGGGAATATGTTCCCCCT
Found at i:2730163 original size:21 final size:21
Alignment explanation
Indices: 2730086--2730166 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
2730076 CCGTTAGACA
*
2730086 GGGGGAATCGGTAT-CCCCTGG
1 GGGGGAATCTGT-TCCCCCTGG
* *
2730107 GGGGGAATATGTTCCCTCT--
1 GGGGGAATCTGTTCCCCCTGG
*
2730126 GGGGGAATC-GGTCCCCCTGG
1 GGGGGAATCTGTTCCCCCTGG
2730146 GGGGGAATCTGTTCCCCCTGG
1 GGGGGAATCTGTTCCCCCTGG
2730167 ACAATCTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
18 7 0.14
19 8 0.16
20 10 0.20
21 24 0.49
ACGTcount: A:0.12, C:0.26, G:0.40, T:0.22
Consensus pattern (21 bp):
GGGGGAATCTGTTCCCCCTGG
Found at i:2732204 original size:20 final size:20
Alignment explanation
Indices: 2732179--2732233 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
2732169 GATGGTTTAT
* *
2732179 AGGTCATTCAGGATATATAG
1 AGGTCATTCAGGACATACAG
*
2732199 AGGTCATTCGGGACATACAG
1 AGGTCATTCAGGACATACAG
* *
2732219 AGGTCCTTCGGGACA
1 AGGTCATTCAGGACA
2732234 AATTTCACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (20 bp):
AGGTCATTCAGGACATACAG
Found at i:2733116 original size:32 final size:33
Alignment explanation
Indices: 2733061--2733126 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
2733051 TAGTATAAGA
2733061 TAGTTATGAGAATGGTCGAAGTGAATCGAGAGG
1 TAGTTATGAGAATGGTCGAAGTGAATCGAGAGG
*
2733094 TAGTTATGAGAAT-GTCGAAGTGAATTGAGAGG
1 TAGTTATGAGAATGGTCGAAGTGAATCGAGAGG
2733126 T
1 T
2733127 GATAAACCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.33, C:0.05, G:0.35, T:0.27
Consensus pattern (33 bp):
TAGTTATGAGAATGGTCGAAGTGAATCGAGAGG
Found at i:2736140 original size:42 final size:41
Alignment explanation
Indices: 2736040--2736523 Score: 328
Period size: 42 Copynumber: 11.9 Consensus size: 41
2736030 AGAAAATAAT
* * * **
2736040 GTACTTTAGTGGCATTTTTATACAAACGCCGCTAA--AGGTC
1 GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTA-CAC
*
2736080 GTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTCATTACAC
1 GTACTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACAC
* * *
2736122 GTATTTTAGTGGCATTTTATGCACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACAC
* * * * * * * *
2736164 GCACTATAGTGGCGTTTTTATATAAACGCC-ATAAATAC-T
1 GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACAC
* * * **
2736203 GTAC-TTAATGGGCGTTTTTATACAAACGCCGCTAA--AGGC
1 GTACTTTAGT-GGCGTTTTAACACAAACGCCGCTAATTACAC
* * * *
2736242 GTACTTTAGTGGTGTTTTAAGCAAAAACGCCACTAATTACAT
1 GTACTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACAC
* *
2736284 GTTCTTTAGTGGCATTTTATACACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACAC
* * * * * * * ** *
2736326 ATACTCTAGTTGCATTTTTATATAAACGCCGAGAAATACTA-
1 GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTAC-AC
* * ***
2736367 -TACTTTAGTGGCGTTTTTATACAAACGCCGCTAA-TGGTC
1 GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACAC
** *
2736406 GTACTTTAGTGGCGTTGCAAGCACAAACGCCACTAATTACAC
1 GTACTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACAC
** *
2736448 GTACTTTTA-TGGTATTTTATGCACAAACGCCGCTAATTACAC
1 GTAC-TTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACAC
*
2736490 GTACTTTAGTGGCATTTTTAA-A-AAACGCCGCTAA
1 GTACTTTAGTGGC-GTTTTAACACAAACGCCGCTAA
2736524 AGGTCATCTT
Statistics
Matches: 344, Mismatches: 79, Indels: 42
0.74 0.17 0.09
Matches are distributed among these distances:
38 4 0.01
39 35 0.10
40 99 0.29
41 54 0.16
42 141 0.41
43 11 0.03
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (41 bp):
GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACAC
Found at i:2736396 original size:40 final size:40
Alignment explanation
Indices: 2736023--2736421 Score: 222
Period size: 40 Copynumber: 9.8 Consensus size: 40
2736013 TTTTATGAGA
* *
2736023 AAACGCCAGA-AAATAATGTACTTTAGTGGCATTTTTATAC
1 AAACGCC-GATAAATACTGTACTTTAGTGGCGTTTTTATAC
* * *
2736063 AAACGCCGCTAAAGGT-C-GTACTTTAGTGGCGTTTTAAGCAC
1 AAACGCCGATAAA--TACTGTACTTTAGTGGCGTTTTTA-TAC
* * * * * *
2736104 AAACGCCGCTCATTACACGTATTTTAGTGGC-ATTTTATGCAC
1 AAACGCCGATAAATAC-TGTACTTTAGTGGCGTTTTTAT--AC
* * * * * *
2736146 AAACGCCGCTAATTACACGCACTATAGTGGCGTTTTTATAT
1 AAACGCCGATAAATAC-TGTACTTTAGTGGCGTTTTTATAC
*
2736187 AAACGCC-ATAAATACTGTAC-TTAATGGGCGTTTTTATAC
1 AAACGCCGATAAATACTGTACTTTAGT-GGCGTTTTTATAC
* ** * * * *
2736226 AAACGCCGCTAAAGGC-GTACTTTAGTGGTGTTTTAAGCAA
1 AAACGCCGATAAATACTGTACTTTAGTGGCGTTTTTA-TAC
* * * *
2736266 AAACGCC-ACTAATTACATGTTCTTTAGTGGCATTTTATACAC
1 AAACGCCGA-TAAATAC-TGTACTTTAGTGGCGTTTT-TATAC
* * ** * * * *
2736308 AAACGCCGCTAATTACACATACTCTAGTTGCATTTTTATAT
1 AAACGCCGATAAATAC-TGTACTTTAGTGGCGTTTTTATAC
* *
2736349 AAACGCCGAGAAATACTATACTTTAGTGGCGTTTTTATAC
1 AAACGCCGATAAATACTGTACTTTAGTGGCGTTTTTATAC
* **
2736389 AAACGCCGCT-AATGGTCGTACTTTAGTGGCGTT
1 AAACGCCGATAAATACT-GTACTTTAGTGGCGTT
2736422 GCAAGCACAA
Statistics
Matches: 277, Mismatches: 62, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
38 3 0.01
39 40 0.14
40 98 0.35
41 41 0.15
42 88 0.32
43 7 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (40 bp):
AAACGCCGATAAATACTGTACTTTAGTGGCGTTTTTATAC
Found at i:2736467 original size:164 final size:164
Alignment explanation
Indices: 2736023--2736518 Score: 716
Period size: 162 Copynumber: 3.0 Consensus size: 164
2736013 TTTTATGAGA
* *
2736023 AAACGCCAGAAAATAATGTACTTTAGTGGCATTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
1 AAACGCCAG-AAATACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
* *
2736088 GTGGCGTTTTAAGCACAAACGCCGCTCATTACACGTA-TTTTAGTGGCATTTTATGCACAAACGC
65 GTGGCGTTTTAAGCACAAACGCCACTAATTACACGTACTTTTAGTGGCATTTTATGCACAAACGC
* *
2736152 CGCTAATTACACGCACTATAGTGGCGTTTTTATAT
130 CGCTAATTACACGTACTATAGTGGCATTTTTATAT
* *
2736187 AAACGCCATAAATACTGTAC-TTAATGGGCGTTTTTATACAAACGCCGCTAAAGG-CGTACTTTA
1 AAACGCCAGAAATACTGTACTTTAGT-GGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
* * * * *
2736250 GTGGTGTTTTAAGCAAAAACGCCACTAATTACATGTTC-TTTAGTGGCATTTTATACACAAACGC
65 GTGGCGTTTTAAGCACAAACGCCACTAATTACACGTACTTTTAGTGGCATTTTATGCACAAACGC
* * *
2736314 CGCTAATTACACATACTCTAGTTGCATTTTTATAT
130 CGCTAATTACACGTACTATAGTGGCATTTTTATAT
* *
2736349 AAACGCCGAGAAATACTATACTTTAGTGGCGTTTTTATACAAACGCCGCTAATGGTCGTACTTTA
1 AAACGCC-AGAAATACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
** *
2736414 GTGGCGTTGCAAGCACAAACGCCACTAATTACACGTACTTTTA-TGGTATTTTATGCACAAACGC
65 GTGGCGTTTTAAGCACAAACGCCACTAATTACACGTACTTTTAGTGGCATTTTATGCACAAACGC
* *
2736478 CGCTAATTACACGTACTTTAGTGGCATTTTTA-AA
130 CGCTAATTACACGTACTATAGTGGCATTTTTATAT
2736512 AAACGCC
1 AAACGCC
2736519 GCTAAAGGTC
Statistics
Matches: 294, Mismatches: 32, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
162 106 0.36
163 83 0.28
164 101 0.34
165 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (164 bp):
AAACGCCAGAAATACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTAG
TGGCGTTTTAAGCACAAACGCCACTAATTACACGTACTTTTAGTGGCATTTTATGCACAAACGCC
GCTAATTACACGTACTATAGTGGCATTTTTATAT
Found at i:2738013 original size:27 final size:29
Alignment explanation
Indices: 2737947--2738013 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
2737937 TAACATTAGT
* *
2737947 TATAAAGGAGTTAACACTGGTACTTTCAAAA
1 TATAAAGGAGTTAACACTAGTA-TAT-AAAA
2737978 TATAAAGGAGTTAACACTAGT-TAT-AAA
1 TATAAAGGAGTTAACACTAGTATATAAAA
2738005 TATAAAGGA
1 TATAAAGGA
2738014 CTTCCATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 12 0.35
29 2 0.06
31 20 0.59
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.28
Consensus pattern (29 bp):
TATAAAGGAGTTAACACTAGTATATAAAA
Found at i:2741773 original size:43 final size:43
Alignment explanation
Indices: 2741723--2742075 Score: 539
Period size: 43 Copynumber: 8.2 Consensus size: 43
2741713 ACGGTCATTA
* * * *
2741723 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-AACCTTTT
1 GCGGCGTTTGT-CCCAAAAACGCCGCTATAGATCTCGACCTATT
* * ** *
2741766 GTGGCGTTTGTTCCAAAAATACCGCTATAAATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
* * *
2741809 ACGGCGTTTGTTCCAAAAACGTCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
*
2741852 GCGGCGTTTGTCCCAAAAACACCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
* *
2741895 GCGGCGTTTGTCCCAAAAACGCTGCTATAGATCTAGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
2741938 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
2741981 GCGGCGTTTG-CCCAAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCC-AAAAACGCCGCTATAGATCTCGACCTATT
2742024 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
2742067 GCGGCGTTT
1 GCGGCGTTT
2742076 TTTGTTCACA
Statistics
Matches: 285, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
42 22 0.08
43 260 0.91
44 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
Found at i:2742613 original size:20 final size:20
Alignment explanation
Indices: 2742588--2742625 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2742578 GTCGAGGGTC
2742588 CATAGGTTC-TTCGGGACATA
1 CATAGG-TCGTTCGGGACATA
2742608 CATAGGTCGTTCGGGACA
1 CATAGGTCGTTCGGGACA
2742626 AATTTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
CATAGGTCGTTCGGGACATA
Found at i:2748948 original size:18 final size:19
Alignment explanation
Indices: 2748913--2748948 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2748903 AAATGAAAGT
2748913 TTTCAAAGTTTTGGGTTTA
1 TTTCAAAGTTTTGGGTTTA
*
2748932 TTTCAAA-TTTTGTGTTT
1 TTTCAAAGTTTTGGGTTT
2748949 TCTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (19 bp):
TTTCAAAGTTTTGGGTTTA
Found at i:2750433 original size:17 final size:17
Alignment explanation
Indices: 2750411--2750445 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2750401 GCATTTTGCC
2750411 CCTAAAATGTCGCTAAT
1 CCTAAAATGTCGCTAAT
2750428 CCTAAAATGTCGCTAAT
1 CCTAAAATGTCGCTAAT
2750445 C
1 C
2750446 AAAACTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (17 bp):
CCTAAAATGTCGCTAAT
Found at i:2750761 original size:12 final size:12
Alignment explanation
Indices: 2750744--2750800 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
2750734 TTTCTGAAAT
2750744 GCTGCTTCTCTC
1 GCTGCTTCTCTC
2750756 GCTGC-TCTCT-
1 GCTGCTTCTCTC
2750766 -CTG-TT-TCTC
1 GCTGCTTCTCTC
*
2750775 TC-GCTTCTCTC
1 GCTGCTTCTCTC
*
2750786 TCTGCTTCTCTC
1 GCTGCTTCTCTC
2750798 GCT
1 GCT
2750801 TCAACTTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
8 3 0.08
9 5 0.13
10 3 0.08
11 11 0.29
12 16 0.42
ACGTcount: A:0.00, C:0.40, G:0.14, T:0.46
Consensus pattern (12 bp):
GCTGCTTCTCTC
Found at i:2750801 original size:21 final size:21
Alignment explanation
Indices: 2750745--2750802 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
2750735 TTCTGAAATG
*
2750745 CTGCTTCTCTCGCTGCTCTCT
1 CTGCTTCTCTCGCTTCTCTCT
*
2750766 CTGTTTCTCTCGCTTCTCTCT
1 CTGCTTCTCTCGCTTCTCTCT
2750787 CTGCTTCTCTCGCTTC
1 CTGCTTCTCTCGCTTC
2750803 AACTTTGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.00, C:0.41, G:0.12, T:0.47
Consensus pattern (21 bp):
CTGCTTCTCTCGCTTCTCTCT
Found at i:2752047 original size:23 final size:23
Alignment explanation
Indices: 2751989--2752048 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
2751979 TATATTTATA
* * *
2751989 AATAATATAATAATGAAAGTAAT
1 AATAAAATAATATTAAAAGTAAT
* *
2752012 AATTTACAT-ATATTAAAAGTAAT
1 AA-TAAAATAATATTAAAAGTAAT
2752035 AATAAAATAATATT
1 AATAAAATAATATT
2752049 GCAAATAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 4 0.14
23 21 0.72
24 4 0.14
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (23 bp):
AATAAAATAATATTAAAAGTAAT
Found at i:2752439 original size:64 final size:64
Alignment explanation
Indices: 2752370--2752558 Score: 170
Period size: 64 Copynumber: 3.1 Consensus size: 64
2752360 TTACGAGACT
2752370 AAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAAAATTTAAATAAC
1 AAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAAAATTTAAATAAC
*** * ** * ** * * *
2752434 AAATTAAAAGGCATAAAAGTCAATT-TCAGTGACTAAA--A-GA-AATTAC--GA---GACT---
1 AAATTAAAATATATGAAAGTTTATTGT-AGTGACTAAATTATAATAAACACAAAATTTAAATAAC
2752486 AAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAAAATTTAAATAAC
1 AAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAAAATTTAAATAAC
2752550 AAATTAAAA
1 AAATTAAAA
2752559 GGCATAAAAG
Statistics
Matches: 87, Mismatches: 24, Indels: 28
0.63 0.17 0.20
Matches are distributed among these distances:
52 29 0.33
53 1 0.01
54 1 0.01
55 3 0.03
56 4 0.05
58 2 0.02
60 4 0.05
61 3 0.03
62 1 0.01
63 1 0.01
64 38 0.44
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (64 bp):
AAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAAAATTTAAATAAC
Found at i:2752561 original size:116 final size:116
Alignment explanation
Indices: 2752357--2752589 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
2752347 ATATAAAATA
2752357 AAATTACGAGACTAAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAA
1 AAATTACGAGACTAAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAA
2752422 AATTTAAATAACAAATTAAAAGGCATAAAAGTCAATTTCAGTGACTAAAAG
66 AATTTAAATAACAAATTAAAAGGCATAAAAGTCAATTTCAGTGACTAAAAG
2752473 AAATTACGAGACTAAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAA
1 AAATTACGAGACTAAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAA
2752538 AATTTAAATAACAAATTAAAAGGCATAAAAGTCAATTTCAGTGACTAAAAG
66 AATTTAAATAACAAATTAAAAGGCATAAAAGTCAATTTCAGTGACTAAAAG
2752589 A
1 A
2752590 GTTTCCTTCA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (116 bp):
AAATTACGAGACTAAATTAAAATATATGAAAGTTTATTGTAGTGACTAAATTATAATAAACACAA
AATTTAAATAACAAATTAAAAGGCATAAAAGTCAATTTCAGTGACTAAAAG
Found at i:2753389 original size:3 final size:3
Alignment explanation
Indices: 2753383--2753452 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
2753373 AATAATTATT
* *
2753383 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
2753426 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2753453 ATGAAAAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2753428 original size:18 final size:18
Alignment explanation
Indices: 2753371--2753452 Score: 96
Period size: 18 Copynumber: 4.4 Consensus size: 18
2753361 ATCTGGACTT
2753371 ATAATAATTATTTAATAATA
1 ATAATAA-TATTT-ATAATA
*
2753391 AT-ATAATATATATAATATA
1 ATAATAATATTTAT-A-ATA
2753410 ATAATAATATTTATAATA
1 ATAATAATATTTATAATA
2753428 ATAATAATAATTT-TAATA
1 ATAATAAT-ATTTATAATA
2753446 ATAATAA
1 ATAATAA
2753453 ATGAAAAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.04
18 28 0.50
19 14 0.25
20 12 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATAATATTTATAATA
Found at i:2754948 original size:18 final size:18
Alignment explanation
Indices: 2754925--2754960 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2754915 TAACAACATC
2754925 TATCTATAAGTATTACTA
1 TATCTATAAGTATTACTA
2754943 TATCTATAAGTATTACTA
1 TATCTATAAGTATTACTA
2754961 ATGAGCTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
TATCTATAAGTATTACTA
Found at i:2756025 original size:42 final size:42
Alignment explanation
Indices: 2755979--2756179 Score: 141
Period size: 42 Copynumber: 4.8 Consensus size: 42
2755969 ATGTTTTTTG
* *
2755979 AAAAAATGCCAATATAAATGAACCCTATTACGACTTTTGCAT
1 AAAAAATGCCACTATAAATGAACCCTATTACGACTTTTGTAT
* * * *
2756021 -AAAAATAGCCACTA-AAGT-ACTACTCTATTGCGA-TGTTTGTAG
1 AAAAAAT-GCCACTATAAATGA--ACCCTATTACGACT-TTTGTAT
*
2756063 AAAAAATGCCACTATAAATGAACCCTATTACGACATTTGTAT
1 AAAAAATGCCACTATAAATGAACCCTATTACGACTTTTGTAT
* * * * * *
2756105 -AAAAACGCCGCTA-AAGTAT-TACTCTATTGC-AGTGTTTGT-T
1 AAAAAATGCCACTATAA--ATGAACCCTATTACGACT-TTTGTAT
*
2756145 GAAAAAATGCCACTATAGATGAACCCTATTACGAC
1 -AAAAAATGCCACTATAAATGAACCCTATTACGAC
2756180 ATATCTATAA
Statistics
Matches: 118, Mismatches: 25, Indels: 31
0.68 0.14 0.18
Matches are distributed among these distances:
40 5 0.04
41 36 0.31
42 65 0.55
43 11 0.09
44 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (42 bp):
AAAAAATGCCACTATAAATGAACCCTATTACGACTTTTGTAT
Found at i:2756036 original size:84 final size:83
Alignment explanation
Indices: 2755938--2756181 Score: 346
Period size: 84 Copynumber: 2.9 Consensus size: 83
2755928 GCGTTTGTAA
* * ** * *
2755938 AAAAATGCCCCTAAAGTACGACTCTGCTGCGATGTTTTTTGAAAAAATGCCAATATAAATGAACC
1 AAAAATGCCACTAAAGTACTACTCTATTGCGATGTTTGTTGAAAAAATGCCACTATAAATGAACC
*
2756003 CTATTACGACTTTTGCAT
66 CTATTACGACATTTGCAT
*
2756021 AAAAATAGCCACTAAAGTACTACTCTATTGCGATGTTTGTAGAAAAAATGCCACTATAAATGAAC
1 AAAAAT-GCCACTAAAGTACTACTCTATTGCGATGTTTGTTGAAAAAATGCCACTATAAATGAAC
*
2756086 CCTATTACGACATTTGTAT
65 CCTATTACGACATTTGCAT
* * * *
2756105 AAAAACGCCGCTAAAGTATTACTCTATTGC-AGTGTTTGTTGAAAAAATGCCACTATAGATGAAC
1 AAAAATGCCACTAAAGTACTACTCTATTGCGA-TGTTTGTTGAAAAAATGCCACTATAAATGAAC
2756169 CCTATTACGACAT
65 CCTATTACGACAT
2756182 ATCTATAAAA
Statistics
Matches: 145, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
82 1 0.01
83 71 0.49
84 73 0.50
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (83 bp):
AAAAATGCCACTAAAGTACTACTCTATTGCGATGTTTGTTGAAAAAATGCCACTATAAATGAACC
CTATTACGACATTTGCAT
Found at i:2756142 original size:83 final size:83
Alignment explanation
Indices: 2755931--2756204 Score: 352
Period size: 83 Copynumber: 3.3 Consensus size: 83
2755921 TATTGCAGCG
* * * * ** * * *
2755931 TTTGTAAAAAAATGCCCCTAAAGTACGACTCTGCTGCGATGTTTTTTGAAAAAATGCCAATATAA
1 TTTGTATAAAAACGCCGCTAAAGTACTACTCTATTGCGATGTTTGTAGAAAAAATGCCACTATAA
*
2755996 ATGAACCCTATTACGACT
66 ATGAACCCTATTACGACA
* * *
2756014 TTTGCATAAAAATAGCCACTAAAGTACTACTCTATTGCGATGTTTGTAGAAAAAATGCCACTATA
1 TTTGTATAAAAA-CGCCGCTAAAGTACTACTCTATTGCGATGTTTGTAGAAAAAATGCCACTATA
2756079 AATGAACCCTATTACGACA
65 AATGAACCCTATTACGACA
* *
2756098 TTTGTATAAAAACGCCGCTAAAGTATTACTCTATTGC-AGTGTTTGTTGAAAAAATGCCACTATA
1 TTTGTATAAAAACGCCGCTAAAGTACTACTCTATTGCGA-TGTTTGTAGAAAAAATGCCACTATA
*
2756162 GATGAACCCTATTACGACA
65 AATGAACCCTATTACGACA
* * *
2756181 TATCTATAAAAACACCGCTAAAGT
1 TTTGTATAAAAACGCCGCTAAAGT
2756205 TACCATTTTA
Statistics
Matches: 169, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
82 1 0.01
83 95 0.56
84 73 0.43
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30
Consensus pattern (83 bp):
TTTGTATAAAAACGCCGCTAAAGTACTACTCTATTGCGATGTTTGTAGAAAAAATGCCACTATAA
ATGAACCCTATTACGACA
Found at i:2756245 original size:14 final size:14
Alignment explanation
Indices: 2756226--2756255 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2756216 GGCATTTGGA
2756226 ATGTAAAGGCCGTT
1 ATGTAAAGGCCGTT
2756240 ATGTAAAGGCCGTT
1 ATGTAAAGGCCGTT
2756254 AT
1 AT
2756256 ATGTTTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (14 bp):
ATGTAAAGGCCGTT
Found at i:2756461 original size:30 final size:30
Alignment explanation
Indices: 2756425--2756490 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2756415 GTTCATGGAC
*
2756425 GGTTAACCGTACCGTTTAGTCTAAATGGTT
1 GGTTAACCGTACCGTTTAGTCTAAACGGTT
* **
2756455 GGTTAACTGTATTGTTTAGTCTAAACGGTT
1 GGTTAACCGTACCGTTTAGTCTAAACGGTT
2756485 -GTTAAC
1 GGTTAAC
2756491 TTCTAACGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (30 bp):
GGTTAACCGTACCGTTTAGTCTAAACGGTT
Found at i:2756522 original size:22 final size:22
Alignment explanation
Indices: 2756497--2756542 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2756487 TAACTTCTAA
*
2756497 CGGTTAACCGTTATTAATAGTT
1 CGGTTAACCGTTATTAAAAGTT
*
2756519 CGGTTAACTGTTATTAAAAGTT
1 CGGTTAACCGTTATTAAAAGTT
2756541 CG
1 CG
2756543 ATTACAGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (22 bp):
CGGTTAACCGTTATTAAAAGTT
Found at i:2767182 original size:45 final size:45
Alignment explanation
Indices: 2767121--2767248 Score: 238
Period size: 45 Copynumber: 2.8 Consensus size: 45
2767111 TATCGTTTCC
*
2767121 GAGAAGATCAATTGTGTCTAAGTTGTATATCTAATATTCAAACGA
1 GAGAAGATCGATTGTGTCTAAGTTGTATATCTAATATTCAAACGA
*
2767166 GATAAGATCGATTGTGTCTAAGTTGTATATCTAATATTCAAACGA
1 GAGAAGATCGATTGTGTCTAAGTTGTATATCTAATATTCAAACGA
2767211 GAGAAGATCGATTGTGTCTAAGTTGTATATCTAATATT
1 GAGAAGATCGATTGTGTCTAAGTTGTATATCTAATATT
2767249 TTTCTATTCA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (45 bp):
GAGAAGATCGATTGTGTCTAAGTTGTATATCTAATATTCAAACGA
Found at i:2768886 original size:21 final size:21
Alignment explanation
Indices: 2768860--2768899 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2768850 GTTTCCAGAT
2768860 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
2768881 TCGCAACGCGAACTTCGAC
1 TCGCAACGCGAACATCGAC
2768900 CACGACCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.35, G:0.20, T:0.15
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:2768907 original size:6 final size:6
Alignment explanation
Indices: 2768896--2768928 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2768886 ACGCGAACTT
2768896 CGACCA CGACCA CGACCA CGACCA CGACCA CGA
1 CGACCA CGACCA CGACCA CGACCA CGACCA CGA
2768929 GACGAGACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:2769093 original size:39 final size:39
Alignment explanation
Indices: 2769039--2769138 Score: 200
Period size: 39 Copynumber: 2.6 Consensus size: 39
2769029 AATAGTATTT
2769039 CCAATACTATGTGGGATTGAGCATTACCAACACTTGTTC
1 CCAATACTATGTGGGATTGAGCATTACCAACACTTGTTC
2769078 CCAATACTATGTGGGATTGAGCATTACCAACACTTGTTC
1 CCAATACTATGTGGGATTGAGCATTACCAACACTTGTTC
2769117 CCAATACTATGTGGGATTGAGC
1 CCAATACTATGTGGGATTGAGC
2769139 CTTAAATAGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (39 bp):
CCAATACTATGTGGGATTGAGCATTACCAACACTTGTTC
Found at i:2769600 original size:5 final size:5
Alignment explanation
Indices: 2769586--2769616 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2769576 CGCGCGCCGC
2769586 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
2769617 GGTCGTGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:2769717 original size:21 final size:21
Alignment explanation
Indices: 2769667--2769747 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 21
2769657 TCTTGCGATT
* *
2769667 TTGGACTGTCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
2769686 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
2769707 TTTGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
2769728 TTGGACTATCACAATGCGAA
1 TTGGACTATCGCAACGCGAA
2769748 TATGTAAATC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.22
21 39 0.78
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:2771862 original size:12 final size:12
Alignment explanation
Indices: 2771841--2771887 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
2771831 TTCATGAACA
*
2771841 AGCTCGTTTATG
1 AGCTCATTTATG
*
2771853 TGCTCATTTATG
1 AGCTCATTTATG
* *
2771865 AGCTCGTTTATC
1 AGCTCATTTATG
2771877 AGCTCATTTAT
1 AGCTCATTTAT
2771888 TTATATTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (12 bp):
AGCTCATTTATG
Found at i:2771868 original size:24 final size:24
Alignment explanation
Indices: 2771841--2771887 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2771831 TTCATGAACA
**
2771841 AGCTCGTTTATGTGCTCATTTATG
1 AGCTCGTTTATCAGCTCATTTATG
2771865 AGCTCGTTTATCAGCTCATTTAT
1 AGCTCGTTTATCAGCTCATTTAT
2771888 TTATATTCAT
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:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (24 bp):
AGCTCGTTTATCAGCTCATTTATG
Found at i:2772128 original size:33 final size:34
Alignment explanation
Indices: 2772091--2772165 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
2772081 ATCAAATATA
2772091 TAAACGAACTA-TAAACAAACACTAAAACAACGC
1 TAAACGAACTATTAAACAAACACTAAAACAACGC
* **
2772124 TAAACGAA-TATTAAACGAACACTAAATGAACGC
1 TAAACGAACTATTAAACAAACACTAAAACAACGC
2772157 TAAACGAAC
1 TAAACGAAC
2772166 ATGTTCATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.15
Consensus pattern (34 bp):
TAAACGAACTATTAAACAAACACTAAAACAACGC
Found at i:2772154 original size:11 final size:11
Alignment explanation
Indices: 2772091--2772166 Score: 66
Period size: 11 Copynumber: 6.9 Consensus size: 11
2772081 ATCAAATATA
2772091 TAAACGAACTA-
1 TAAACGAAC-AC
*
2772102 TAAACAAACAC
1 TAAACGAACAC
*
2772113 TAAAAC-AACGC
1 T-AAACGAACAC
* *
2772124 TAAACGAATAT
1 TAAACGAACAC
2772135 TAAACGAACAC
1 TAAACGAACAC
* *
2772146 TAAATGAACGC
1 TAAACGAACAC
2772157 TAAACGAACA
1 TAAACGAACA
2772167 TGTTCATGAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
10 5 0.10
11 42 0.82
12 4 0.08
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.14
Consensus pattern (11 bp):
TAAACGAACAC
Found at i:2772208 original size:25 final size:23
Alignment explanation
Indices: 2772175--2772224 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
2772165 CATGTTCATG
*
2772175 AACACGTTCGTGAACATATAAAACA
1 AACACGTTCGCGAACAT-T-AAACA
*
2772200 AACATGTTCGCGAACATTAAACA
1 AACACGTTCGCGAACATTAAACA
2772223 AA
1 AA
2772225 TGTTAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
24 1 0.04
25 15 0.65
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (23 bp):
AACACGTTCGCGAACATTAAACA
Found at i:2772265 original size:71 final size:70
Alignment explanation
Indices: 2772157--2772290 Score: 205
Period size: 71 Copynumber: 1.9 Consensus size: 70
2772147 AAATGAACGC
* *
2772157 TAAACGAACATGTTCATGAACACGTTCGTGAACATATAAAACAAACATGTTCGCGAACATTAAAC
1 TAAACGAACATGTTCATGAACACGTTCATGAACATAT-AAACAAACACGTTCGCGAACATTAAAC
2772222 AAATGT
65 AAATGT
* * * *
2772228 TAAACTAACATGTTCATGATCACGTTCATGAATATATAAACGAACACGTTCGCGAACATTAAA
1 TAAACGAACATGTTCATGAACACGTTCATGAACATATAAACAAACACGTTCGCGAACATTAAA
2772291 TGAACATGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
70 24 0.42
71 33 0.58
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (70 bp):
TAAACGAACATGTTCATGAACACGTTCATGAACATATAAACAAACACGTTCGCGAACATTAAACA
AATGT
Found at i:2772295 original size:23 final size:23
Alignment explanation
Indices: 2772264--2772308 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2772254 CATGAATATA
2772264 TAAACGAACACGTTCGCGAACAT
1 TAAACGAACACGTTCGCGAACAT
* * *
2772287 TAAATGAACATGTTCGTGAACA
1 TAAACGAACACGTTCGCGAACA
2772309 AAAAATAAAT
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:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (23 bp):
TAAACGAACACGTTCGCGAACAT
Found at i:2772314 original size:23 final size:23
Alignment explanation
Indices: 2772269--2772314 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2772259 ATATATAAAC
**
2772269 GAACACGTTCGCGAACATTAAAT
1 GAACACGTTCGCGAACAAAAAAT
* *
2772292 GAACATGTTCGTGAACAAAAAAT
1 GAACACGTTCGCGAACAAAAAAT
2772315 AAATGAACAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (23 bp):
GAACACGTTCGCGAACAAAAAAT
Found at i:2775078 original size:66 final size:66
Alignment explanation
Indices: 2774991--2775126 Score: 236
Period size: 66 Copynumber: 2.1 Consensus size: 66
2774981 TACATTATAT
*
2774991 ATGTCCCTACAAATATGGATTTTAACTCAACAATCTCTCACTAGGACAACATATGTTTCCTGAAA
1 ATGTCCCTACAAATATGGATTTTAACCCAACAATCTCTCACTAGGACAACATATGTTTCCTGAAA
2775056 A
66 A
* * *
2775057 ATGTGCCTACAAATATGGATTTTAACCCAACAATCTCTCACTAGGGCAACATATGTTTCCTGACA
1 ATGTCCCTACAAATATGGATTTTAACCCAACAATCTCTCACTAGGACAACATATGTTTCCTGAAA
2775122 A
66 A
2775123 ATGT
1 ATGT
2775127 ACAACCTTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (66 bp):
ATGTCCCTACAAATATGGATTTTAACCCAACAATCTCTCACTAGGACAACATATGTTTCCTGAAA
A
Found at i:2782665 original size:57 final size:57
Alignment explanation
Indices: 2782601--2782709 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
2782591 ATACAACCCC
* *
2782601 CGTCACGAACAGTAAGGCTCTCAGCACAAAGTCGAGGAACCTGCAAGTATTCAACCT
1 CGTCACGAACAATAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATTCAACCT
2782658 CGTCACGAACAATAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATTC
1 CGTCACGAACAATAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATTC
2782710 TTCCTCCAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (57 bp):
CGTCACGAACAATAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATTCAACCT
Found at i:2784461 original size:36 final size:36
Alignment explanation
Indices: 2784410--2784482 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
2784400 GATTAATTAT
*
2784410 AATCTACATATCCATGGCCGATTCTTTTATCACTTA
1 AATCTACATAACCATGGCCGATTCTTTTATCACTTA
* *
2784446 AATCTACATAACCATGGCTGCTTCTTTTATCACTTA
1 AATCTACATAACCATGGCCGATTCTTTTATCACTTA
2784482 A
1 A
2784483 TTCCAGAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (36 bp):
AATCTACATAACCATGGCCGATTCTTTTATCACTTA
Found at i:2786971 original size:23 final size:24
Alignment explanation
Indices: 2786931--2786975 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2786921 AACTCAAAAA
2786931 AAAATTAGAAGCTCGATTGAAGCT
1 AAAATTAGAAGCTCGATTGAAGCT
* *
2786955 AAAATTCG-AGCTTGATTGAAG
1 AAAATTAGAAGCTCGATTGAAG
2786976 TGAAAGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAATTAGAAGCTCGATTGAAGCT
Found at i:2789627 original size:17 final size:18
Alignment explanation
Indices: 2789607--2789648 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2789597 CAACCTTTTG
2789607 TTTTTTTAACTATTT-AC
1 TTTTTTTAACTATTTGAC
* *
2789624 TTTTTTAAACTTTTTGAC
1 TTTTTTTAACTATTTGAC
2789642 TTTTTTT
1 TTTTTTT
2789649 CCTTTTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTTTAACTATTTGAC
Found at i:2789927 original size:12 final size:13
Alignment explanation
Indices: 2789905--2789933 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2789895 GAATCGAGTT
2789905 TTTTAAATTTCAA
1 TTTTAAATTTCAA
2789918 TTTT-AATTTCAA
1 TTTTAAATTTCAA
2789930 TTTT
1 TTTT
2789934 TTGTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAAATTTCAA
Found at i:2790824 original size:16 final size:16
Alignment explanation
Indices: 2790803--2790846 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
2790793 GAATACTAAG
2790803 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
2790819 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
*
2790835 CATGTGGTGTAG
1 CATGTGGGGTAG
2790847 GACTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.23, C:0.07, G:0.39, T:0.32
Consensus pattern (16 bp):
CATGTGGGGTAGATAT
Found at i:2793972 original size:93 final size:92
Alignment explanation
Indices: 2793811--2794048 Score: 312
Period size: 93 Copynumber: 2.7 Consensus size: 92
2793801 TATTATATGT
* * *
2793811 ATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATGAGA
1 ATACAATAAAGC-TGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAAA
2793876 TTCAACTAACCTGATAAAGGTGATTATA
65 TTCAACTAACCTGATAAAGGTGATTATA
* *
2793904 ATACAATAAAGCGTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAAA
1 ATACAATAAAGC-TGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAAA
* * * *
2793969 TTCAGCTAGCTTGATATAGGTGATTATA
65 TTCAACTAACCTGATAAAGGTGATTATA
*
2793997 AT---AT-----TGAGTTGTCCCTCTAAAGCAATTGGTTAAACGGCCCGGCTTTATGGAT
1 ATACAATAAAGCTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGAT
2794049 TCAGCTAGCC
Statistics
Matches: 132, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
84 45 0.34
90 2 0.02
93 85 0.64
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (92 bp):
ATACAATAAAGCTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAAAT
TCAACTAACCTGATAAAGGTGATTATA
Found at i:2795333 original size:86 final size:85
Alignment explanation
Indices: 2795162--2795485 Score: 371
Period size: 86 Copynumber: 3.8 Consensus size: 85
2795152 CCCAACCCAG
* * * * *
2795162 TACAGCATAACTCAAGGAGAGAAGGGTTATCTGTTATCAAAGACCTTCGAGTTCGATTATATTCA
1 TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCA
* *
2795227 GCTCAAAGGCACATCAAATT
66 GCTTAAAGGCATATCAAATT
* * * *
2795247 TACAGCATAGCTCAAGGCGAGAAGGGTTATATGTTAACAAAATACCTTCAAGTTCGATTACATTC
1 TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAA-ACCTTCGAGTTCGATTACATTC
*
2795312 AGCTTAAAGGCATATCCAATT
65 AGCTTAAAGGCATATCAAATT
* * * *
2795333 TATAACATAACTCAAGGCGAGAAGGGTTATCTGTCAGCAAAAACCTTCTAGTTCGATTACATTCA
1 TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCA
* *
2795398 GC-TCAAGGCATGTCAAATT
66 GCTTAAAGGCATATCAAATT
* * * * * ** * * * *
2795417 CACAGAATAGCTTAAGTCGAGAAAAGCTATCTGTCAACAAAAACTTTCGAGTTAGATTTCATTCA
1 TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCA
2795482 GCTT
66 GCTT
2795486 GATGACACAT
Statistics
Matches: 202, Mismatches: 35, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
84 66 0.33
85 62 0.31
86 74 0.37
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (85 bp):
TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCA
GCTTAAAGGCATATCAAATT
Found at i:2801509 original size:22 final size:22
Alignment explanation
Indices: 2801483--2801564 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
2801473 TTGGTGCAGA
2801483 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* *
2801505 GGGAA-CTGATTCCCCCTTTGCAG
1 GGGAATC-GATACCCCC-TTGAAG
* * * *
2801528 GGGAACCAATTCCCCCTTGTAG
1 GGGAATCGATACCCCCTTGAAG
2801550 GGGAATCGATACCCC
1 GGGAATCGATACCCC
2801565 TAGGGTTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
21 1 0.02
22 30 0.60
23 18 0.36
24 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:2801529 original size:23 final size:22
Alignment explanation
Indices: 2801477--2801554 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
2801467 GCATTTTTGG
*
2801477 TGCAGAGGGAA-TCGATACCCCCT
1 TGCAG-GGGAACT-GATTCCCCCT
*
2801500 TGAAGGGGAACTGATTCCCCCTT
1 TGCAGGGGAACTGATTCCCCC-T
**
2801523 TGCAGGGGAACCAATTCCCCCT
1 TGCAGGGGAACTGATTCCCCCT
*
2801545 TGTAGGGGAA
1 TGCAGGGGAA
2801555 TCGATACCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
22 23 0.49
23 24 0.51
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.21
Consensus pattern (22 bp):
TGCAGGGGAACTGATTCCCCCT
Found at i:2803180 original size:18 final size:18
Alignment explanation
Indices: 2803143--2803181 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2803133 AGAACAACAC
* *
2803143 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
2803161 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
2803179 GAG
1 GAG
2803182 TATCAAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.31, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:2805255 original size:19 final size:19
Alignment explanation
Indices: 2805231--2805267 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2805221 AACACCGAAG
2805231 TCTTCATGACAAGTTTCGA
1 TCTTCATGACAAGTTTCGA
*
2805250 TCTTCATGATAAGTTTCG
1 TCTTCATGACAAGTTTCG
2805268 GGCTTCACGA
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:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (19 bp):
TCTTCATGACAAGTTTCGA
Found at i:2805273 original size:19 final size:19
Alignment explanation
Indices: 2805232--2805274 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2805222 ACACCGAAGT
*
2805232 CTTCATGACAAGTTTCGAT
1 CTTCATGACAAGTTTCGAG
* *
2805251 CTTCATGATAAGTTTCGGG
1 CTTCATGACAAGTTTCGAG
2805270 CTTCA
1 CTTCA
2805275 CGACGAAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (19 bp):
CTTCATGACAAGTTTCGAG
Found at i:2806813 original size:2 final size:2
Alignment explanation
Indices: 2806808--2806876 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
2806798 TTGTTTACTT
2806808 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
2806850 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2806877 CATTTTCTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2807098 original size:35 final size:35
Alignment explanation
Indices: 2807054--2807134 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
2807044 TTTTTCTAAA
* * * *
2807054 TGTTTTTTTTTTCAATTTTTTAACTTTTTCCACTT
1 TGTTCTTTTTTTCAACTTTTCAACCTTTTCCACTT
*
2807089 TGTTCTTTTTTTCAACTTTTCAACCTTTTCGACTT
1 TGTTCTTTTTTTCAACTTTTCAACCTTTTCCACTT
* *
2807124 TTTTCCTTTTT
1 TGTTCTTTTTT
2807135 GAATATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.12, C:0.19, G:0.04, T:0.65
Consensus pattern (35 bp):
TGTTCTTTTTTTCAACTTTTCAACCTTTTCCACTT
Found at i:2813382 original size:23 final size:23
Alignment explanation
Indices: 2813350--2813418 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 23
2813340 ACATTTTCTT
*
2813350 TTAATATTTTAAATTAAAATATA
1 TTAATTTTTTAAATTAAAATATA
2813373 TTAATTTTTTAATTTAAATTAAAATATA
1 TTAA---TTT--TTTAAATTAAAATATA
*
2813401 TTAATTTTTTAATTTAAA
1 TTAATTTTTTAAATTAAA
2813419 TATTAGTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 14 0.36
25 3 0.08
26 2 0.05
28 20 0.51
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATTTTTTAAATTAAAATATA
Found at i:2813392 original size:28 final size:28
Alignment explanation
Indices: 2813357--2813419 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
2813347 CTTTTAATAT
2813357 TTTAAATTAAAATATATTAATTTTTTAA
1 TTTAAATTAAAATATATTAATTTTTTAA
2813385 TTTAAATTAAAATATATTAATTTTTTAA
1 TTTAAATTAAAATATATTAATTTTTTAA
2813413 TTTAAAT
1 TTTAAAT
2813420 ATTAGTAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTAAATTAAAATATATTAATTTTTTAA
Found at i:2813620 original size:34 final size:35
Alignment explanation
Indices: 2813541--2813632 Score: 86
Period size: 34 Copynumber: 2.7 Consensus size: 35
2813531 TTTTTTTGAG
2813541 TTTGAATATTAAAATG-TATT-TATATCTTTTGAATA
1 TTTGAATATTAAAA-GATATTAT-TATCTTTTGAATA
* *
2813576 TCTCAA-ATTAAAAGATATTATTATCTATTT-AA-A
1 TTTGAATATTAAAAGATATTATTATCT-TTTGAATA
*
2813609 TTTGAATATTAAAATATATCTATT
1 TTTGAATATTAAAAGATAT-TATT
2813633 TTAAGTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
33 6 0.13
34 29 0.62
35 12 0.26
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (35 bp):
TTTGAATATTAAAAGATATTATTATCTTTTGAATA
Found at i:2816388 original size:30 final size:30
Alignment explanation
Indices: 2816345--2816404 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2816335 AAGAAGAAGA
2816345 AAAAAATTATGTGTGGTTTCCTGGTTTGTG
1 AAAAAATTATGTGTGGTTTCCTGGTTTGTG
* *
2816375 AAAAATTTGTGTGTGGTTTCCTGGTTTGTG
1 AAAAAATTATGTGTGGTTTCCTGGTTTGTG
2816405 CTAAGTTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.45
Consensus pattern (30 bp):
AAAAAATTATGTGTGGTTTCCTGGTTTGTG
Found at i:2818665 original size:42 final size:42
Alignment explanation
Indices: 2818524--2818753 Score: 259
Period size: 41 Copynumber: 5.5 Consensus size: 42
2818514 AAAAATGTCA
* * * *
2818524 CTAAATGTTTGAACCTATTGTAGTGTTTGTAAGAAAAACGCTG
1 CTAAATGTATGAACCTATTGTGGCGTTTGTAA-AAAAACGTTG
* * * * * **
2818567 TTAAATGTATGAACCTATTGCGGTGTTTGT-AAAAATCATCA
1 CTAAATGTATGAACCTATTGTGGCGTTTGTAAAAAAACGTTG
*
2818608 CTAAATGTAT-AACCTATTGTGGCATTTGTAAAAAAACGTTG
1 CTAAATGTATGAACCTATTGTGGCGTTTGTAAAAAAACGTTG
* *
2818649 CTAAATGTATGAACCTATTGTGG-GTTTGTAAAAAAACATTA
1 CTAAATGTATGAACCTATTGTGGCGTTTGTAAAAAAACGTTG
* * **
2818690 CTAAATGTATGAACCTATTGCGGCCTTTGTAAAAAAACGCCG
1 CTAAATGTATGAACCTATTGTGGCGTTTGTAAAAAAACGTTG
*
2818732 CTAAATGTCTGAACCTATTGTG
1 CTAAATGTATGAACCTATTGTG
2818754 ACATTTTTTA
Statistics
Matches: 156, Mismatches: 28, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
40 16 0.10
41 68 0.44
42 46 0.29
43 26 0.17
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (42 bp):
CTAAATGTATGAACCTATTGTGGCGTTTGTAAAAAAACGTTG
Found at i:2818752 original size:83 final size:83
Alignment explanation
Indices: 2818521--2818753 Score: 317
Period size: 83 Copynumber: 2.8 Consensus size: 83
2818511 AAGAAAAATG
* * ** *
2818521 TCACTAAATGTTTGAACCTATTGTAGTGTTTGTAAGAAAAACGCTGTTAAATGTATGAACCTATT
1 TCACTAAATGTATGAACCTATTGTGGCATTTGTAA-AAAAACGCTGCTAAATGTATGAACCTATT
* *
2818586 GCGGTGTTTGTAAAAATCA
65 GTGGTGTTTGTAAAAAACA
*
2818605 TCACTAAATGTAT-AACCTATTGTGGCATTTGTAAAAAAACGTTGCTAAATGTATGAACCTATTG
1 TCACTAAATGTATGAACCTATTGTGGCATTTGTAAAAAAACGCTGCTAAATGTATGAACCTATTG
2818669 TGG-GTTTGTAAAAAAACA
66 TGGTGTTTGT-AAAAAACA
* * * * *
2818687 TTACTAAATGTATGAACCTATTGCGGCCTTTGTAAAAAAACGCCGCTAAATGTCTGAACCTATTG
1 TCACTAAATGTATGAACCTATTGTGGCATTTGTAAAAAAACGCTGCTAAATGTATGAACCTATTG
2818752 TG
66 TG
2818754 ACATTTTTTA
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
81 6 0.05
82 49 0.37
83 66 0.50
84 12 0.09
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (83 bp):
TCACTAAATGTATGAACCTATTGTGGCATTTGTAAAAAAACGCTGCTAAATGTATGAACCTATTG
TGGTGTTTGTAAAAAACA
Found at i:2821794 original size:25 final size:25
Alignment explanation
Indices: 2821728--2821795 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
2821718 TTTTCCTCAC
*
2821728 TATCTCTTCATTCTTCATTTTCTTT
1 TATCTCTTCATTCTTCCTTTTCTTT
* *
2821753 CATCTATTCATTCTTCCTTTTCTTT
1 TATCTCTTCATTCTTCCTTTTCTTT
2821778 TATCTCTTCATTCTTCCT
1 TATCTCTTCATTCTTCCT
2821796 CTCCAAGAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (25 bp):
TATCTCTTCATTCTTCCTTTTCTTT
Found at i:2823210 original size:90 final size:89
Alignment explanation
Indices: 2823097--2823271 Score: 271
Period size: 90 Copynumber: 2.0 Consensus size: 89
2823087 TCCCGAATAT
* * * *
2823097 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAATCCCTGATATGA-TTA
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAAACCCTAATATGACTGA
2823161 GGGTAACTTGGATATAAAAGGATTA
66 -GGTAACTTGGATATAAAAGGATTA
*
2823186 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAAACCCTAATATGACTG
*
2823251 AGGTAACTTGGCTATAAAAGG
65 AGGTAACTTGGATATAAAAGG
2823272 GTGTGGTAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 7 0.09
90 69 0.88
91 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAAACCCTAATATGACTGA
GGTAACTTGGATATAAAAGGATTA
Found at i:2830073 original size:89 final size:89
Alignment explanation
Indices: 2829966--2830130 Score: 287
Period size: 89 Copynumber: 1.9 Consensus size: 89
2829956 ATTTAATTTT
* *
2829966 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTGATATGA-TTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCTAATATGACTTA-GGTAACTT
2830030 GGATATAAAAGGATTATTAAATTCC
65 GGATATAAAAGGATTATTAAATTCC
2830055 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCTAATATGACTTAGGTAACTTG
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCTAATATGACTTAGGTAACTTG
*
2830120 GCTATAAAAGG
66 GATATAAAAGG
2830131 GTGTGTTAGG
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
89 69 0.96
90 3 0.04
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCTAATATGACTTAGGTAACTTG
GATATAAAAGGATTATTAAATTCC
Found at i:2841836 original size:18 final size:18
Alignment explanation
Indices: 2841809--2841845 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2841799 AAATTATCTT
*
2841809 CTATTAAATCTCTTTTTA
1 CTATTAAATCTCATTTTA
*
2841827 CTATTTAATCTCATTTTA
1 CTATTAAATCTCATTTTA
2841845 C
1 C
2841846 CAAAACCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (18 bp):
CTATTAAATCTCATTTTA
Found at i:2843895 original size:15 final size:15
Alignment explanation
Indices: 2843872--2843914 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2843862 TTCTATTTTT
2843872 TATTT-TTTATTT-C
1 TATTTATTTATTTAC
*
2843885 TATTTGATTTATTTAG
1 TATTT-ATTTATTTAC
2843901 TATTTATTTATTTA
1 TATTTATTTATTTA
2843915 TTTATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.19
15 16 0.62
16 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (15 bp):
TATTTATTTATTTAC
Found at i:2843908 original size:4 final size:4
Alignment explanation
Indices: 2843852--2843925 Score: 59
Period size: 4 Copynumber: 19.0 Consensus size: 4
2843842 GGAACGCTTC
*
2843852 ATTT A-TT ATTT -TCT ATTT -TTT ATTT -TTT ATTTCT ATTT GATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TT-T ATTT -ATTT ATTT
* *
2843899 A-GT ATTT ATTT ATTT ATTT ATTA ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2843926 TGTCTAATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
3 13 0.23
4 33 0.59
5 8 0.14
6 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:2843925 original size:8 final size:8
Alignment explanation
Indices: 2843852--2843925 Score: 59
Period size: 7 Copynumber: 9.5 Consensus size: 8
2843842 GGAACGCTTC
2843852 ATTTA-TT
1 ATTTATTT
*
2843859 ATTT-TCT
1 ATTTATTT
2843866 ATTT-TTT
1 ATTTATTT
2843873 ATTT-TTT
1 ATTTATTT
2843880 ATTTCTATTT
1 A-TT-TATTT
2843890 GATTTATTT
1 -ATTTATTT
*
2843899 A-GTATTT
1 ATTTATTT
2843906 ATTTATTT
1 ATTTATTT
*
2843914 ATTTATTA
1 ATTTATTT
2843922 ATTT
1 ATTT
2843926 TGTCTAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
7 25 0.45
8 19 0.34
9 6 0.11
10 5 0.09
11 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (8 bp):
ATTTATTT
Found at i:2848375 original size:106 final size:105
Alignment explanation
Indices: 2848127--2849095 Score: 1400
Period size: 106 Copynumber: 9.4 Consensus size: 105
2848117 ATATCGTGCC
* * * *
2848127 ACTCGAGACAACACAAGTTCAACTTCACGACGGAGGGACCGCTGGTTGTC-AATA-AA-----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCA
2848185 ATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2848221 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAACTTCTC
2848286 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2848327 ACTCCAGACAACGCAAGTTCAACTTCTCGACGAAGGGACCGCTGGTTGTCAATAAACAACATC-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAACTTCTC
* * **
2848391 AAATTTCAGAGCCAATTCCAACTTCATAGTGAAGGATATTGG
65 -AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2848433 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC-CTGGTTGTCAAAAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCA
2848497 ATTT-AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
2848536 ACTCCAGA-AACGCAAGTTCAACTTCACAACGAAGGGACTGCTGGTTATC-ACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCA
*
2848599 ATTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2848638 ACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAACTTCTC
**
2848703 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2848744 ACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAACTTCTC
*
2848809 AATTTCAGGGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2848850 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG-T-TC---AACAAATTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCA
2848910 ATTTCAGAG-CAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2848949 ACTCCAGACAACGCAAGTTCAACTTCACGACGAA-GGACCGCTGGTTGTCAATAA-AATTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCA
* * *
2849012 ATTTCAGAGTCAATTTCAATTTCAC-GCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2849051 ACTCAAGACAACACAAGTTC-ACTTCACGACGAAAGGA-CGCTGGTT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
2849096 CATAACAACT
Statistics
Matches: 804, Mismatches: 45, Indels: 45
0.90 0.05 0.05
Matches are distributed among these distances:
94 46 0.06
95 1 0.00
96 2 0.00
97 2 0.00
98 10 0.01
99 65 0.08
100 20 0.02
101 21 0.03
102 144 0.18
103 100 0.12
104 17 0.02
105 29 0.04
106 347 0.43
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2848644 original size:311 final size:311
Alignment explanation
Indices: 2848127--2849095 Score: 1435
Period size: 311 Copynumber: 3.2 Consensus size: 311
2848117 ATATCGTGCC
* * *
2848127 ACTCGAGACAACACAAGTTCAACTTCACGACGGAGGGACCGCTGGTTGTCAATAAACAA-TT-TC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
2848190 --------CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTC
66 AATTTAGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
*
2848247 ACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC
131 ACGACGAAGGGACCGCTGGTT-TC-A-CAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC
*
2848312 AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCTCGACGAAGGGACCGCTGGTTGTC
193 AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
* *
2848377 AATAAACAACATCCAAATTTCAGAGCCAATTCCAACTTCATAGTGAAGGATATTGG
258 AATAAACAACTTCC-AATTTCAGAGCCAATTTCAACTTCA-AGTGAAGGATATTGG
*
2848433 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC-CTGGTTGTCAA-AAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
2848496 AATTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA-AACGCAAGTTCAACTT
66 AATTTAG-GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* * *
2848560 CACAACGAAGGGACTGCTGGTTATCACAACAACTTCCCAATTT-AGAGCCAATTTCAACTTCACA
130 CACGACGAAGGGACCGCTGGTT-TCACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
2848624 GCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
194 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
2848689 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
259 ATAAACAACTTC-CAATTTCAGAGCCAATTTCAACTTCA-AGTGAAGGATATTGG
* * *
2848744 ACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
2848809 AATTTCAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTT-A-GGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
2848874 TCACGACGAAGGGACCGCTGG-TT--CAACAAATTCTCAATTTCAGAG-CAATTTCAACTTCACA
129 TCACGACGAAGGGACCGCTGGTTTCACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
2848935 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA-GGACCGCTGGTTGTCA
194 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * * * *
2848999 AT-AA-AATTTCCCAATTTCAGAGTCAATTTCAATTTCACGCGAAGGATATTGG
259 ATAAACAACTT-CCAATTTCAGAGCCAATTTCAACTTCAAGTGAAGGATATTGG
* *
2849051 ACTCAAGACAACACAAGTTC-ACTTCACGACGAAAGGA-CGCTGGTT
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
2849096 CATAACAACT
Statistics
Matches: 610, Mismatches: 34, Indels: 39
0.89 0.05 0.06
Matches are distributed among these distances:
304 6 0.01
305 21 0.03
306 55 0.09
307 30 0.05
308 28 0.05
309 3 0.00
310 17 0.03
311 248 0.41
312 31 0.05
313 18 0.03
314 79 0.13
315 74 0.12
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (311 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTAGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
ACGACGAAGGGACCGCTGGTTTCACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
AAACAACTTCCAATTTCAGAGCCAATTTCAACTTCAAGTGAAGGATATTGG
Found at i:2850714 original size:20 final size:19
Alignment explanation
Indices: 2850684--2850734 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
2850674 TTTTTCTATT
2850684 TTTATTT-TTTTATTTCTA
1 TTTATTTATTTTATTTCTA
*
2850702 TTTGATTTATTTTA---GTA
1 TTT-ATTTATTTTATTTCTA
2850719 TTTATTTATTTTATTT
1 TTTATTTATTTTATTT
2850735 TGTCTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
16 10 0.37
17 5 0.19
18 3 0.11
19 4 0.15
20 5 0.19
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTATTTATTTTATTTCTA
Found at i:2850727 original size:16 final size:17
Alignment explanation
Indices: 2850700--2850731 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2850690 TTTTTATTTC
2850700 TATTTGATTTATTTTAG
1 TATTTGATTTATTTTAG
2850717 TATTT-ATTTATTTTA
1 TATTTGATTTATTTTA
2850732 TTTTGTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
TATTTGATTTATTTTAG
Found at i:2851814 original size:24 final size:24
Alignment explanation
Indices: 2851787--2851838 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2851777 GATGTACTGT
2851787 TTTTGGTTTTTA-TTGTCTTTGGGC
1 TTTTGGTTTTTATTTG-CTTTGGGC
*
2851811 TTTTGGTTTTTATTTGCTTTGGGT
1 TTTTGGTTTTTATTTGCTTTGGGC
2851835 TTTT
1 TTTT
2851839 AGTTCTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.04, C:0.06, G:0.23, T:0.67
Consensus pattern (24 bp):
TTTTGGTTTTTATTTGCTTTGGGC
Found at i:2856195 original size:63 final size:64
Alignment explanation
Indices: 2855984--2856204 Score: 215
Period size: 65 Copynumber: 3.4 Consensus size: 64
2855974 ATTCATATCC
* * **
2855984 CTTTTGAATATTTCAAATTAAAAGATATTTATATCTTTA-ATTTGAATATTAGTAGG-ATA-ATT
1 CTTTTGAATATTTCAAATT-AAA-ATATATATATATTTAGATTTGAATATTAAAAGGTATATA-T
2856046 ATT
63 A-T
* *
2856049 CTTTTAAATATTTCAAATTAAAATATATTTATTATTTACTTGACTTTGAATATTAAAA-GT-TAT
1 CTTTTGAATATTTCAAATTAAAATATATATA-TATTTA---GA-TTTGAATATTAAAAGGTATAT
2856112 -T-T
61 ATAT
* *
2856114 CTGTTGAATATTTCAAATTAAAATA-ATATATATTTAGGTTTGAATATTAAAAGGTATATATAT
1 CTTTTGAATATTTCAAATTAAAATATATATATATTTAGATTTGAATATTAAAAGGTATATATAT
* *
2856177 CTTTTGAATATTTTAAATTAAAAGATAT
1 CTTTTGAATATTTCAAATTAAAATATAT
2856205 TATTATCTAT
Statistics
Matches: 130, Mismatches: 13, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
59 14 0.11
60 3 0.02
61 3 0.02
62 1 0.01
63 36 0.28
64 14 0.11
65 42 0.32
67 1 0.01
68 4 0.03
69 12 0.09
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (64 bp):
CTTTTGAATATTTCAAATTAAAATATATATATATTTAGATTTGAATATTAAAAGGTATATATAT
Found at i:2858604 original size:32 final size:32
Alignment explanation
Indices: 2858566--2858630 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2858556 AACTAAAACC
2858566 ACCAAAAGAGACACTCAAGATGAAGTGCAAAA
1 ACCAAAAGAGACACTCAAGATGAAGTGCAAAA
2858598 ACCAAAAGAGACACTCAAGATGAAGTGCAAAA
1 ACCAAAAGAGACACTCAAGATGAAGTGCAAAA
2858630 A
1 A
2858631 GGAAGAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.54, C:0.18, G:0.18, T:0.09
Consensus pattern (32 bp):
ACCAAAAGAGACACTCAAGATGAAGTGCAAAA
Found at i:2859029 original size:15 final size:17
Alignment explanation
Indices: 2858999--2859030 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2858989 CGTTCGTGAA
2858999 CGTTCGATTATATGTTC
1 CGTTCGATTATATGTTC
2859016 CGTTC-ATT-TATGTTC
1 CGTTCGATTATATGTTC
2859031 GAATAGAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (17 bp):
CGTTCGATTATATGTTC
Found at i:2870146 original size:14 final size:14
Alignment explanation
Indices: 2870119--2870158 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
2870109 CGAAGGCTCT
*
2870119 GGCGACGAACAGTTC
1 GGCG-CGAAGAGTTC
2870134 GGCGCGAAGAGTTC
1 GGCGCGAAGAGTTC
2870148 GGCGCGAAGAG
1 GGCGCGAAGAG
2870159 GGATCGTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.25, C:0.23, G:0.42, T:0.10
Consensus pattern (14 bp):
GGCGCGAAGAGTTC
Found at i:2875880 original size:29 final size:29
Alignment explanation
Indices: 2875838--2875896 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2875828 ATTTTCACCT
**
2875838 AACTAAATTGATGTAAGCAATGGCATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
2875867 AACTAAATTGATGTAAGCAATAACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
2875896 A
1 A
2875897 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATAACATCAA
Found at i:2877246 original size:18 final size:18
Alignment explanation
Indices: 2877223--2877268 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2877213 AACATTCTCA
*
2877223 GTAATCTTATTCCCGCCG
1 GTAATCTTATTCCCACCG
* *
2877241 GTAATCATATTCCCACTG
1 GTAATCTTATTCCCACCG
2877259 GTAATCTTAT
1 GTAATCTTAT
2877269 ATTCCGTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (18 bp):
GTAATCTTATTCCCACCG
Found at i:2880308 original size:29 final size:29
Alignment explanation
Indices: 2880266--2880321 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
2880256 TAAAAATCTT
2880266 TTTGATTATTGATAATATATATATATATA
1 TTTGATTATTGATAATATATATATATATA
2880295 TTTGATTATTGATAATATATATATATA
1 TTTGATTATTGATAATATATATATATA
2880322 AATGTAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (29 bp):
TTTGATTATTGATAATATATATATATATA
Found at i:2880881 original size:17 final size:17
Alignment explanation
Indices: 2880859--2880894 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2880849 TTATTTTTTA
2880859 AACAAGGTGGAGATACT
1 AACAAGGTGGAGATACT
2880876 AACAAGGTGGAGATACT
1 AACAAGGTGGAGATACT
2880893 AA
1 AA
2880895 AATTCATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (17 bp):
AACAAGGTGGAGATACT
Found at i:2881852 original size:3 final size:3
Alignment explanation
Indices: 2881846--2881929 Score: 80
Period size: 3 Copynumber: 27.0 Consensus size: 3
2881836 ATTATATATG
* * *
2881846 TTA TTA TTA TCA -TA TTA TTA TTA TTA TTA TTA TTAA TTA CATG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA
* *
2881892 TTA TTA TTA CATA TATA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA
2881930 AATAATATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
2 1 0.02
3 56 0.85
4 9 0.14
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:2881878 original size:29 final size:29
Alignment explanation
Indices: 2881859--2881939 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
2881849 TTATTATCAT
*
2881859 ATTATTATTATTA-TTATTATTAATTACAT
1 ATTATTATTATTACATATTATT-ATTACAT
*
2881888 GTTATTATTATTACATATATATTATTA-AT
1 ATTATTATTATTACATAT-TATTATTACAT
* *
2881917 ATTATTATTATTAAATAATATTA
1 ATTATTATTATTACATATTATTA
2881940 CAAAGCCCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.11
29 29 0.64
30 7 0.16
31 4 0.09
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (29 bp):
ATTATTATTATTACATATTATTATTACAT
Found at i:2890667 original size:42 final size:42
Alignment explanation
Indices: 2890606--2890687 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
2890596 CACAAATTTG
*
2890606 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGTT
1 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGTT
* *
2890648 TAAATCCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATG
1 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG
2890688 ATAAGTCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGTT
Found at i:2890911 original size:3 final size:3
Alignment explanation
Indices: 2890903--2891002 Score: 60
Period size: 3 Copynumber: 31.0 Consensus size: 3
2890893 TTATCCATTT
*
2890903 TTA TTA TTAA TTA TATA TGCTA TTA TTA TCA -TA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA T-TA T--TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
2890951 TTAA TTA CATG TTA TTA -TA TATA TATA TATA TTA TTA ATA ATA TTA
1 TT-A TTA -TTA TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA
2890997 TTA TTA
1 TTA TTA
2891003 AATAATATTA
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
2 3 0.04
3 53 0.66
4 21 0.26
5 3 0.04
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:2890942 original size:26 final size:27
Alignment explanation
Indices: 2890923--2891002 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 27
2890913 TTATATATGC
2890923 TATT-ATTATCATATTATTAT-TATTAT
1 TATTAATTA-CATATTATTATATATTAT
*
2890949 TATTAATTACATGTTATTATATATATAT
1 TATTAATTACATATTATTATATAT-TAT
* *
2890977 ATATATTATTA-ATAATATTAT-TATTA
1 -TAT-TAATTACATATTATTATATATTA
2891003 AATAATATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
26 14 0.31
27 9 0.20
28 6 0.13
29 11 0.24
30 5 0.11
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (27 bp):
TATTAATTACATATTATTATATATTAT
Found at i:2890948 original size:20 final size:19
Alignment explanation
Indices: 2890904--2891002 Score: 69
Period size: 20 Copynumber: 4.9 Consensus size: 19
2890894 TATCCATTTT
2890904 TATTATTAATTATATATGCTAT
1 TATTATT-ATTATATAT--TAT
2890926 TATTATCATATTAT-TATTAT
1 TATTAT--TATTATATATTAT
* *
2890946 TATTATTAATTACATGTTAT
1 TATTATT-ATTATATATTAT
2890966 TA-TATATATATATATATTAT
1 TATTAT-TAT-TATATATTAT
* *
2890986 TAATAATATTAT-TATTA
1 TATTATTATTATATATTA
2891003 AATAATATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
18 6 0.09
19 12 0.18
20 30 0.46
21 2 0.03
22 9 0.14
23 5 0.08
24 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTATTATTATATATTAT
Found at i:2892792 original size:3 final size:3
Alignment explanation
Indices: 2892784--2892839 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
2892774 TAAGCTACCA
2892784 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2892831 AAT AAT AAT
1 AAT AAT AAT
2892840 TAAATACATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.