Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 15 of 145
Found at i:5726724 original size:88 final size:88
Alignment explanation
Indices: 5726575--5727042 Score: 738
Period size: 88 Copynumber: 5.3 Consensus size: 88
5726565 AAGATCTGCT
* * * * *
5726575 AATGCACGAAGGCAAGATCTACTATCTCTGACCTGCTCTACTACAACCGAGGGAGACAAGGCTTG
1 AATGCAGGAAGGCAAGATCTGCTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
* *
5726640 TGTCTTCGATCTGCTTCACTGTC
66 TGTCTTTGATCTGCTTCGCTGTC
* *
5726663 AATGCAGGAAGGCAAAATCTACTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
1 AATGCAGGAAGGCAAGATCTGCTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
5726728 TGTCTTTGATCTGCTTCGCTGTC
66 TGTCTTTGATCTGCTTCGCTGTC
* * * *
5726751 AGTGCAAGAAGGCAAGATCTGCTATCTTGGACCTGCTCCACTACAACTGAGGGAGGCAAGGCTTG
1 AATGCAGGAAGGCAAGATCTGCTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
5726816 TGTCTTTGATCTGCTTCGCTGTC
66 TGTCTTTGATCTGCTTCGCTGTC
* *
5726839 AATGCAGGAACGTAAGATCTGCTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
1 AATGCAGGAAGGCAAGATCTGCTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
*
5726904 TGTCTTTGATCTTCTTCGCTGTC
66 TGTCTTTGATCTGCTTCGCTGTC
5726927 AATGCAGGAAGGCAAGATCTGCTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
1 AATGCAGGAAGGCAAGATCTGCTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
* * * *
5726992 CGTCTTCGATCTGCTTCGTTTTC
66 TGTCTTTGATCTGCTTCGCTGTC
* *
5727015 AATGCAAGAAGGGAAGATCTGCTATCTT
1 AATGCAGGAAGGCAAGATCTGCTATCTT
5727043 CATTGATCTG
Statistics
Matches: 351, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 351 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
AATGCAGGAAGGCAAGATCTGCTATCTTTGACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTG
TGTCTTTGATCTGCTTCGCTGTC
Found at i:5728275 original size:1 final size:1
Alignment explanation
Indices: 5728264--5728404 Score: 57
Period size: 1 Copynumber: 141.0 Consensus size: 1
5728254 TGGCCTCTCA
* * * * ** * * * * * *
5728264 TTTTCTTTTTTTCTTTTTCTTTTTCTTTTCCTTTCTTCTTTCTTTTCTTTTTTCTTTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * * *
5728329 TTTTCTTTTTTTTCTCTTTTTTCTCTTTTTTTTCTCTTTTTTTTCTTTTTTCTTCTTCTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
5728394 TTTGTTTTTTT
1 TTTTTTTTTTT
5728405 AATCTGAACT
Statistics
Matches: 92, Mismatches: 48, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 92 1.00
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.82
Consensus pattern (1 bp):
T
Found at i:5728300 original size:16 final size:14
Alignment explanation
Indices: 5728264--5728390 Score: 83
Period size: 13 Copynumber: 9.3 Consensus size: 14
5728254 TGGCCTCTCA
5728264 TTTTC-TTTTTTTC
1 TTTTCTTTTTTTTC
*
5728277 -TTT-TTCTTTTTC
1 TTTTCTTTTTTTTC
5728289 TTTTCCTTTCTTCTTTC
1 TTTT-CTTT-TT-TTTC
5728306 TTTTCTTTTTTCTT-
1 TTTTCTTTTTT-TTC
5728320 TTTT-TTCTTTTTTC
1 TTTTCTT-TTTTTTC
*
5728334 TTTT-TTTTCTCTT-
1 TTTTCTTTT-TTTTC
*
5728347 TTTTCTCTTTTTT-
1 TTTTCTTTTTTTTC
*
5728360 TTCTCTTTTTTTTC
1 TTTTCTTTTTTTTC
* *
5728374 TTTT-TTCTTCTTC
1 TTTTCTTTTTTTTC
5728387 TTTT
1 TTTT
5728391 TTGTTTGTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
12 10 0.11
13 38 0.41
14 24 0.26
15 6 0.07
16 6 0.07
17 8 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:5728307 original size:29 final size:28
Alignment explanation
Indices: 5728273--5728391 Score: 108
Period size: 29 Copynumber: 4.3 Consensus size: 28
5728263 ATTTTCTTTT
5728273 TTTCTTTTTCTTTTTCTTTTCCTTTCTTC
1 TTTCTTTTTCTTTTTCTTTT-CTTTCTTC
* *
5728302 TTTC-TTTTCTTTTTTCTTTTTTTTCTTT
1 TTTCTTTTTC-TTTTTCTTTTCTTTCTTC
*
5728330 TTTCTTTTT-TTTCTC-TTT-TTTC-TC
1 TTTCTTTTTCTTTTTCTTTTCTTTCTTC
*
5728354 TTT-TTTTTCTCTTTT-TTTTCTTTTTTC
1 TTTCTTTTTCT-TTTTCTTTTCTTTCTTC
5728381 TTCTTCTTTTT
1 -T-TTCTTTTT
5728392 TGTTTGTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
23 5 0.07
24 5 0.07
25 10 0.14
26 6 0.08
27 7 0.09
28 16 0.22
29 20 0.27
30 5 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTCTTTTTCTTTTTCTTTTCTTTCTTC
Found at i:5728313 original size:9 final size:8
Alignment explanation
Indices: 5728264--5728404 Score: 99
Period size: 9 Copynumber: 16.5 Consensus size: 8
5728254 TGGCCTCTCA
5728264 TTTTCTTT
1 TTTTCTTT
5728272 TTTTCTTT
1 TTTTCTTT
5728280 TTCTT-TTT
1 TT-TTCTTT
*
5728288 CTTTTCCTT
1 -TTTTCTTT
*
5728297 TCTTCTTT
1 TTTTCTTT
5728305 CTTTTC-TT
1 -TTTTCTTT
5728313 TTTTCTTTT
1 TTTTC-TTT
5728322 TTTTCTTT
1 TTTTCTTT
*
5728330 TTTCTTTTT
1 TTT-TCTTT
5728339 TTTCTCTTT
1 TTT-TCTTT
5728348 TTTCTCTTTT
1 TTT-TC-TTT
5728358 TTTTCTCTT
1 TTTTCT-TT
*
5728367 TTTTTTCTT
1 TTTTCT-TT
5728376 TTTTCTTCT
1 TTTTCTT-T
5728385 TCTTT-TTT
1 T-TTTCTTT
* *
5728393 GTTTGTTT
1 TTTTCTTT
5728401 TTTT
1 TTTT
5728405 AATCTGAACT
Statistics
Matches: 111, Mismatches: 10, Indels: 24
0.77 0.07 0.17
Matches are distributed among these distances:
7 8 0.07
8 38 0.34
9 56 0.50
10 9 0.08
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.82
Consensus pattern (8 bp):
TTTTCTTT
Found at i:5728372 original size:50 final size:48
Alignment explanation
Indices: 5728259--5728392 Score: 128
Period size: 50 Copynumber: 2.7 Consensus size: 48
5728249 CACCTTGGCC
5728259 TCTCATTTTCTTTTTTTC-TTTTTCTTTTTCTTTTCCTTTCTTCTTTCTTT
1 TCTC-TTTT-TTTTTTTCTTTTTTCTTTTT-TTTTCCTTTCTTCTTTCTTT
* * * *
5728309 TCTTTTTTCTTTTTTTTCTTTTTTCTTTTTTTTCTCTTTTTTCTCTTTTTTT
1 TC-TCTTT-TTTTTTTTCTTTTTTCTTTTTTTT-TCCTTTCT-TCTTTCTTT
* *
5728361 TCTCTTTTTTTTCTTT-TTTCTTCTTCTTTTTT
1 TCTCTTTTTTTT-TTTCTTTTTTCTTTTTTTTT
5728393 GTTTGTTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
49 1 0.01
50 34 0.48
51 26 0.37
52 10 0.14
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.81
Consensus pattern (48 bp):
TCTCTTTTTTTTTTTCTTTTTTCTTTTTTTTTCCTTTCTTCTTTCTTT
Found at i:5728373 original size:63 final size:67
Alignment explanation
Indices: 5728264--5728404 Score: 177
Period size: 63 Copynumber: 2.2 Consensus size: 67
5728254 TGGCCTCTCA
* *
5728264 TTTTC-TTTTTTTCTTTTTCTTTTTCTTTTCCTTTCTTCTTTCTTTTCTTTTTTCTT-TT-TTTT
1 TTTTCTTTTTTTTCTCTTTCTTTCTCTTTTCCTTTCTTCTTTCTTTTCTTTTTTCTTCTTCTTTT
5728326 CTT
66 -TT
* *
5728329 TTTTCTTTTTTTTCTCTTT-TTTCTCTTTT-TTTTC-TCTTTTTTTTCTTTTTTCTTCTTCTTTT
1 TTTTCTTTTTTTTCTCTTTCTTTCTCTTTTCCTTTCTTCTTTCTTTTCTTTTTTCTTCTTCTTTT
5728391 TT
66 TT
* *
5728393 GTTTGTTTTTTT
1 TTTTCTTTTTTT
5728405 AATCTGAACT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
63 19 0.28
64 18 0.27
65 18 0.27
66 12 0.18
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.82
Consensus pattern (67 bp):
TTTTCTTTTTTTTCTCTTTCTTTCTCTTTTCCTTTCTTCTTTCTTTTCTTTTTTCTTCTTCTTTT
TT
Found at i:5728379 original size:11 final size:11
Alignment explanation
Indices: 5728271--5728404 Score: 110
Period size: 11 Copynumber: 11.6 Consensus size: 11
5728261 TCATTTTCTT
5728271 TTTTTCTTTTTC
1 TTTTT-TTTTTC
*
5728283 TTTTTCTTTTCC
1 TTTTT-TTTTTC
* *
5728295 TTTCTTCTTTC
1 TTTTTTTTTTC
5728306 TTTTCTTTTTTC
1 TTTT-TTTTTTC
5728318 TTTTTTTTCTT-
1 TTTTTTTT-TTC
5728329 TTTTCTTTTTT-
1 TTTT-TTTTTTC
*
5728340 TTCTCTTTTTTC
1 TT-TTTTTTTTC
*
5728352 TCTTTTTTTTC
1 TTTTTTTTTTC
*
5728363 TCTTTTTTTTC
1 TTTTTTTTTTC
5728374 TTTTTTCTTCTTC
1 TTTTTT-TT-TTC
* *
5728387 TTTTTTGTTTG
1 TTTTTTTTTTC
5728398 TTTTTTT
1 TTTTTTT
5728405 AATCTGAACT
Statistics
Matches: 102, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
11 57 0.56
12 36 0.35
13 9 0.09
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:5731527 original size:3 final size:3
Alignment explanation
Indices: 5731514--5731581 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
5731504 CAATAACAAC
* * * *
5731514 AAT AAT GAT AAT AAAT AAAT AAA AAT AAT AA- AAT AAT AAT GAT AAC
1 AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5731560 AAT -AT AA- AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AA
5731582 AGATAAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
2 6 0.12
3 36 0.69
4 10 0.19
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:5731534 original size:17 final size:17
Alignment explanation
Indices: 5731514--5731600 Score: 61
Period size: 17 Copynumber: 4.9 Consensus size: 17
5731504 CAATAACAAC
*
5731514 AATAATGATAATAAATA
1 AATAATAATAATAAATA
*
5731531 AATAAAAATAATAAA-A
1 AATAATAATAATAAATA
* *
5731547 TAATAATGATAACAATATAA
1 -AATAATAATAATAA-AT-A
5731567 AATAATAAATAATAAAGATA
1 AATAAT-AATAAT-AA-ATA
*
5731587 AATAAAAAT-ATAAA
1 AATAATAATAATAAA
5731601 ACAATAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
16 2 0.04
17 26 0.47
18 3 0.05
19 9 0.16
20 11 0.20
21 4 0.07
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (17 bp):
AATAATAATAATAAATA
Found at i:5731546 original size:8 final size:8
Alignment explanation
Indices: 5731521--5731610 Score: 66
Period size: 8 Copynumber: 11.2 Consensus size: 8
5731511 AACAATAATG
5731521 ATAAT-AA
1 ATAATAAA
5731528 ATAAATAAAA
1 AT-AAT-AAA
5731538 ATAATAAA
1 ATAATAAA
5731546 ATAAT--A
1 ATAATAAA
*
5731552 ATGATAACA
1 ATAATAA-A
5731561 AT-ATAAA
1 ATAATAAA
5731568 ATAAT-AA
1 ATAATAAA
5731575 ATAATAAA
1 ATAATAAA
5731583 GATAAATAAA
1 -AT-AATAAA
5731593 A-ATATAAA
1 ATA-ATAAA
*
5731601 ACAATAAA
1 ATAATAAA
5731609 AT
1 AT
5731611 CCATGTATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 23
0.73 0.02 0.24
Matches are distributed among these distances:
6 5 0.07
7 13 0.19
8 31 0.45
9 10 0.14
10 10 0.14
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (8 bp):
ATAATAAA
Found at i:5731577 original size:29 final size:29
Alignment explanation
Indices: 5731531--5731608 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
5731521 ATAATAAATA
*
5731531 AATAAAAATAATAAAATAATAATGATAAC
1 AATAAAAATAATAAAATAATAAAGATAAC
5731560 AATATAAAATAAT-AAATAATAAAGAT-A-
1 AATA-AAAATAATAAAATAATAAAGATAAC
*
5731587 AATAAAAAT-ATAAAACAATAAA
1 AATAAAAATAATAAAATAATAAA
5731609 ATCCATGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 2 0.04
26 14 0.31
27 4 0.09
28 1 0.02
29 16 0.36
30 8 0.18
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (29 bp):
AATAAAAATAATAAAATAATAAAGATAAC
Found at i:5733857 original size:118 final size:118
Alignment explanation
Indices: 5733685--5733920 Score: 454
Period size: 118 Copynumber: 2.0 Consensus size: 118
5733675 ACATCGATGG
5733685 CCAAATTCTATTTACTATTATTGTTTTGGTATTTTTAATTTTTAATTTCAAAATATTTATTTTCT
1 CCAAATTCTATTTACTATTATTGTTTTGGTATTTTTAATTTTTAATTTCAAAATATTTATTTTCT
*
5733750 ATTATTCTATTTTACTAAAAAATGAAATAATTATAAATTCTTTTGAATACTAC
66 ATTATTCTATTTTACTAAAAAATGAAATAATTATAAATTCTTATGAATACTAC
5733803 CCAAATTCTATTTACTATTATTGTTTTGGTATTTTTAATTTTTAATTTCAAAATATTTATTTTCT
1 CCAAATTCTATTTACTATTATTGTTTTGGTATTTTTAATTTTTAATTTCAAAATATTTATTTTCT
*
5733868 ATTATTCTATTTTACTAAAAAATGAAATAATTATCAATTCTTATGAATACTAC
66 ATTATTCTATTTTACTAAAAAATGAAATAATTATAAATTCTTATGAATACTAC
5733921 ATACTCATTA
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (118 bp):
CCAAATTCTATTTACTATTATTGTTTTGGTATTTTTAATTTTTAATTTCAAAATATTTATTTTCT
ATTATTCTATTTTACTAAAAAATGAAATAATTATAAATTCTTATGAATACTAC
Found at i:5734471 original size:42 final size:42
Alignment explanation
Indices: 5734414--5734577 Score: 274
Period size: 42 Copynumber: 3.9 Consensus size: 42
5734404 GTTTACAAAC
*
5734414 AAAAACGCCGCTAAAGACCATGTTTTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * *
5734456 AAAAACGCCGCTAAAGATCATCTTCTTTAGCGGTGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
5734498 AAAAACGCCTCTAAAGACCATGTTCTTTAGGGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
5734540 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
5734578 TTATACAAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 111 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:5745679 original size:113 final size:114
Alignment explanation
Indices: 5745472--5745688 Score: 307
Period size: 113 Copynumber: 1.9 Consensus size: 114
5745462 NNNNNGGTTA
* *
5745472 TTTGTGGCGCTTTATCTAAAACGCCGCTAAAGCCCTGGATATTAGCGGCGCTTACTTGAAAAATG
1 TTTGTGGCGCTTTATCTAAAACGCCGCTAAAGCCCTGGATATTAGCGGCGCTTACTAGAAAAACG
5745537 CCGCTAAATCCCCGAAAGCTCGAAAACGGCATCGTTGGGCTCAGTTTTT
66 CCGCTAAATCCCCGAAAGCTCGAAAACGGCATCGTTGGGCTCAGTTTTT
* * * *
5745586 TTTGTGGCGCTTTGT-TGAAAACGCCGCTAAA-TCCTGGGTATTAGCGTCGCTT-C-AGAAAAAA
1 TTTGTGGCGCTTTATCT-AAAACGCCGCTAAAGCCCTGGATATTAGCGGCGCTTACTAG-AAAAA
* *
5745647 CGCCGCTAATTCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
64 CGCCGCTAAATCCCCGAAAGCTC-GAAAACGGCATCGTTGGG
5745689 ATTAGGTGTT
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
111 1 0.01
112 27 0.29
113 36 0.39
114 28 0.30
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (114 bp):
TTTGTGGCGCTTTATCTAAAACGCCGCTAAAGCCCTGGATATTAGCGGCGCTTACTAGAAAAACG
CCGCTAAATCCCCGAAAGCTCGAAAACGGCATCGTTGGGCTCAGTTTTT
Found at i:5745718 original size:112 final size:114
Alignment explanation
Indices: 5745489--5745727 Score: 288
Period size: 112 Copynumber: 2.1 Consensus size: 114
5745479 CGCTTTATCT
* *
5745489 AAAACGCCGCTAAAGCCCTGGATATTAGCGGCGCTTACTTGAAAAATGCCGCTAAATCCCCGAAA
1 AAAACGCCGCTAAAGCCCTGGATATTAGCGGCGCTTACTAGAAAAACGCCGCTAAATCCCCGAAA
* * * * * * *
5745554 GCTCGAAAACGGCATCGTTGGGCTCAGTTTTTTTTGTGGCGCTTTGTTG
66 GCTCGAAAACGGCATCGTTGGGATCAGTGTGTTTTGCGGCACTTTCTCG
* * * *
5745603 AAAACGCCGCTAAA-TCCTGGGTATTAGCGTCGCTT-C-AGAAAAAACGCCGCTAATTCCCCGAA
1 AAAACGCCGCTAAAGCCCTGGATATTAGCGGCGCTTACTAG-AAAAACGCCGCTAAATCCCCGAA
* *
5745665 AGCTCAGAAAACGGCGTCGTTGGGATTAG-GTGTTTTGCGGCACTTTCTCG
65 AGCTC-GAAAACGGCATCGTTGGGATCAGTGTGTTTTGCGGCACTTTCTCG
*
5745715 AAAATGCCGCTAA
1 AAAACGCCGCTAA
5745728 TGCTTATTTT
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
111 1 0.01
112 54 0.50
113 38 0.36
114 14 0.13
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.25
Consensus pattern (114 bp):
AAAACGCCGCTAAAGCCCTGGATATTAGCGGCGCTTACTAGAAAAACGCCGCTAAATCCCCGAAA
GCTCGAAAACGGCATCGTTGGGATCAGTGTGTTTTGCGGCACTTTCTCG
Found at i:5755435 original size:16 final size:16
Alignment explanation
Indices: 5755414--5755444 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5755404 TGTTAATACC
5755414 TAGAATTTATTACTTT
1 TAGAATTTATTACTTT
5755430 TAGAATTTATTACTT
1 TAGAATTTATTACTT
5755445 ATTTGAGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TAGAATTTATTACTTT
Found at i:5758766 original size:16 final size:16
Alignment explanation
Indices: 5758745--5758775 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5758735 TGTTAATACC
5758745 TAGAATTTATTACTTT
1 TAGAATTTATTACTTT
5758761 TAGAATTTATTACTT
1 TAGAATTTATTACTT
5758776 ATTTGAGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TAGAATTTATTACTTT
Found at i:5761568 original size:20 final size:20
Alignment explanation
Indices: 5761523--5761562 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5761513 AAAAACTGCA
*
5761523 ACTCCACAAAACACGGTTTT
1 ACTCTACAAAACACGGTTTT
5761543 ACTCTACAAAACACGGTTTT
1 ACTCTACAAAACACGGTTTT
5761563 TTTCTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (20 bp):
ACTCTACAAAACACGGTTTT
Found at i:5762495 original size:22 final size:21
Alignment explanation
Indices: 5762473--5762519 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
5762463 TAAGCTTAAT
5762473 AAATTCTTAATTTATTTTAAATA
1 AAATT-TT-ATTTATTTTAAATA
*
5762496 AAATTTTATTTA-TTTATATA
1 AAATTTTATTTATTTTAAATA
5762516 AAAT
1 AAAT
5762520 AAAATGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 5 0.22
22 2 0.09
23 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATTTTATTTATTTTAAATA
Found at i:5764231 original size:17 final size:17
Alignment explanation
Indices: 5764200--5764232 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5764190 AAAAATGATC
5764200 TTAACTAAAATATTATT
1 TTAACTAAAATATTATT
5764217 TTAA-TAAAATGATTAT
1 TTAACTAAAAT-ATTAT
5764233 ATTTCATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAACTAAAATATTATT
Found at i:5765513 original size:14 final size:13
Alignment explanation
Indices: 5765496--5765529 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5765486 AAACAGATAT
5765496 AAGAAAACAAAGAA
1 AAGAAAACAAA-AA
5765510 AAGAAAACAAAAA
1 AAGAAAACAAAAA
*
5765523 AATAAAA
1 AAGAAAA
5765530 TATGAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (13 bp):
AAGAAAACAAAAA
Found at i:5765847 original size:40 final size:40
Alignment explanation
Indices: 5765783--5765877 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
5765773 TGTTTATGAC
*
5765783 AAAAACGCCGCAAAAGGTCAAGCATTAGCGACACTTGTT-G
1 AAAAACGCCGCAAAAGATCAAGCATTAGCGACACTT-TTCG
* * * *
5765823 AAAAACGCCGCTATAGATCTAGCATTAGCGGCACTTTTCG
1 AAAAACGCCGCAAAAGATCAAGCATTAGCGACACTTTTCG
*
5765863 CAAAACGCCGCAAAA
1 AAAAACGCCGCAAAA
5765878 AAGTTGAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.04
40 44 0.96
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCAAAAGATCAAGCATTAGCGACACTTTTCG
Found at i:5765991 original size:14 final size:14
Alignment explanation
Indices: 5765968--5766014 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5765958 ATCATTTTAT
*
5765968 TTTAGGATTTAAGG
1 TTTAGTATTTAAGG
5765982 TTTAGTATTTAAGG
1 TTTAGTATTTAAGG
* * *
5765996 TTTAATATCTATGG
1 TTTAGTATTTAAGG
5766010 TTTAG
1 TTTAG
5766015 GGTTTTAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (14 bp):
TTTAGTATTTAAGG
Found at i:5766103 original size:21 final size:20
Alignment explanation
Indices: 5766061--5766105 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
5766051 GGATTAGAGT
*
5766061 TTTAAGTTTAGGGTTTATGG
1 TTTAAGTTTAGGGTTTAGGG
* *
5766081 TTTAGAGTTTATGGTTTGGGG
1 TTTA-AGTTTAGGGTTTAGGG
5766102 TTTA
1 TTTA
5766106 TTATTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (20 bp):
TTTAAGTTTAGGGTTTAGGG
Found at i:5766104 original size:14 final size:14
Alignment explanation
Indices: 5766066--5766106 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
5766056 AGAGTTTTAA
5766066 GTTTAGGGTTTATG
1 GTTTAGGGTTTATG
*
5766080 GTTTAGAGTTTATG
1 GTTTAGGGTTTATG
*
5766094 GTTTGGGGTTTAT
1 GTTTAGGGTTTAT
5766107 TATTTTATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:5766330 original size:14 final size:14
Alignment explanation
Indices: 5766289--5766427 Score: 77
Period size: 14 Copynumber: 9.8 Consensus size: 14
5766279 TTTAAGGTGT
*
5766289 AGGTTTATGGTTTGA
1 AGGTTTAGGGTTT-A
**
5766304 A-GTTTAGTTTTTA
1 AGGTTTAGGGTTTA
*
5766317 TGGTTTAGGGTTTA
1 AGGTTTAGGGTTTA
*
5766331 AGGTTTATGGTTTA
1 AGGTTTAGGGTTTA
* *
5766345 AGGGTTAGGG-GTA
1 AGGTTTAGGGTTTA
5766358 TAGAGTTTAGGGTTTA
1 -AG-GTTTAGGGTTTA
* * **
5766374 GGGGTTAGGGGCATA
1 AGGTTTA-GGGTTTA
* *
5766389 GGGTTTAGGGGTTA
1 AGGTTTAGGGTTTA
* *
5766403 AAGTTTATGGTTT-
1 AGGTTTAGGGTTTA
5766416 AGTGTTTAGGGT
1 AG-GTTTAGGGT
5766428 CTAATTTTAA
Statistics
Matches: 92, Mismatches: 26, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
13 4 0.04
14 66 0.72
15 20 0.22
16 2 0.02
ACGTcount: A:0.20, C:0.01, G:0.37, T:0.42
Consensus pattern (14 bp):
AGGTTTAGGGTTTA
Found at i:5766356 original size:7 final size:7
Alignment explanation
Indices: 5766346--5766402 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
5766336 TATGGTTTAA
5766346 GGGTTAG
1 GGGTTAG
5766353 GGGTATAG
1 GGGT-TAG
* *
5766361 AGTTTAG
1 GGGTTAG
*
5766368 GGTTTAG
1 GGGTTAG
5766375 GGGTTAG
1 GGGTTAG
*
5766382 GGGCATAG
1 GGG-TTAG
*
5766390 GGTTTAG
1 GGGTTAG
5766397 GGGTTA
1 GGGTTA
5766403 AAGTTTATGG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
7 30 0.75
8 10 0.25
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.32
Consensus pattern (7 bp):
GGGTTAG
Found at i:5766365 original size:29 final size:29
Alignment explanation
Indices: 5766333--5766403 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
5766323 AGGGTTTAAG
* *
5766333 GTTTATGGTTTAAGGGTTAGGGGTATAGA
1 GTTTAGGGTTTAAGGGTTAGGGGCATAGA
* *
5766362 GTTTAGGGTTTAGGGGTTAGGGGCATAGG
1 GTTTAGGGTTTAAGGGTTAGGGGCATAGA
*
5766391 GTTTAGGGGTTAA
1 GTTTAGGGTTTAA
5766404 AGTTTATGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.21, C:0.01, G:0.42, T:0.35
Consensus pattern (29 bp):
GTTTAGGGTTTAAGGGTTAGGGGCATAGA
Found at i:5766460 original size:44 final size:45
Alignment explanation
Indices: 5766398--5766486 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 45
5766388 AGGGTTTAGG
5766398 GGTTAAAGTTTATGGTTTAGTGTTTAGGGTCTAATTTTAAACAAA
1 GGTTAAAGTTTATGGTTTAGTGTTTAGGGTCTAATTTTAAACAAA
5766443 GGTTAAAG-TTATGGTTTAGTGTTTAGGGTCTAATTTTAAACAAA
1 GGTTAAAGTTTATGGTTTAGTGTTTAGGGTCTAATTTTAAACAAA
5766487 ACGGCACCGT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 36 0.82
45 8 0.18
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.42
Consensus pattern (45 bp):
GGTTAAAGTTTATGGTTTAGTGTTTAGGGTCTAATTTTAAACAAA
Found at i:5775149 original size:17 final size:17
Alignment explanation
Indices: 5775118--5775150 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5775108 AAAAATGATC
5775118 TTAACTAAAATATTATT
1 TTAACTAAAATATTATT
5775135 TTAA-TAAAATGATTAT
1 TTAACTAAAAT-ATTAT
5775151 ATTTCATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAACTAAAATATTATT
Found at i:5776431 original size:14 final size:13
Alignment explanation
Indices: 5776414--5776447 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5776404 AAACAGATAT
5776414 AAGAAAACAAAGAA
1 AAGAAAACAAA-AA
5776428 AAGAAAACAAAAA
1 AAGAAAACAAAAA
*
5776441 AATAAAA
1 AAGAAAA
5776448 TATGAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (13 bp):
AAGAAAACAAAAA
Found at i:5776765 original size:40 final size:40
Alignment explanation
Indices: 5776701--5776795 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
5776691 TGTTTATGAC
*
5776701 AAAAACGCCGCAAAAGGTCAAGCATTAGCGACACTTGTT-G
1 AAAAACGCCGCAAAAGATCAAGCATTAGCGACACTT-TTCG
* * * *
5776741 AAAAACGCCGCTATAGATCTAGCATTAGCGGCACTTTTCG
1 AAAAACGCCGCAAAAGATCAAGCATTAGCGACACTTTTCG
*
5776781 CAAAACGCCGCAAAA
1 AAAAACGCCGCAAAA
5776796 AAGTTGAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.04
40 44 0.96
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCAAAAGATCAAGCATTAGCGACACTTTTCG
Found at i:5776909 original size:14 final size:14
Alignment explanation
Indices: 5776886--5776932 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5776876 ATCATTTTAT
*
5776886 TTTAGGATTTAAGG
1 TTTAGTATTTAAGG
5776900 TTTAGTATTTAAGG
1 TTTAGTATTTAAGG
* * *
5776914 TTTAATATCTATGG
1 TTTAGTATTTAAGG
5776928 TTTAG
1 TTTAG
5776933 GGTTTTAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (14 bp):
TTTAGTATTTAAGG
Found at i:5777021 original size:21 final size:20
Alignment explanation
Indices: 5776979--5777023 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
5776969 GGATTAGAGT
*
5776979 TTTAAGTTTAGGGTTTATGG
1 TTTAAGTTTAGGGTTTAGGG
* *
5776999 TTTAGAGTTTATGGTTTGGGG
1 TTTA-AGTTTAGGGTTTAGGG
5777020 TTTA
1 TTTA
5777024 TTATTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (20 bp):
TTTAAGTTTAGGGTTTAGGG
Found at i:5777022 original size:14 final size:14
Alignment explanation
Indices: 5776984--5777024 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
5776974 AGAGTTTTAA
5776984 GTTTAGGGTTTATG
1 GTTTAGGGTTTATG
*
5776998 GTTTAGAGTTTATG
1 GTTTAGGGTTTATG
*
5777012 GTTTGGGGTTTAT
1 GTTTAGGGTTTAT
5777025 TATTTTATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:5777248 original size:14 final size:14
Alignment explanation
Indices: 5777207--5777345 Score: 77
Period size: 14 Copynumber: 9.8 Consensus size: 14
5777197 TTTAAGGTGT
*
5777207 AGGTTTATGGTTTGA
1 AGGTTTAGGGTTT-A
**
5777222 A-GTTTAGTTTTTA
1 AGGTTTAGGGTTTA
*
5777235 TGGTTTAGGGTTTA
1 AGGTTTAGGGTTTA
*
5777249 AGGTTTATGGTTTA
1 AGGTTTAGGGTTTA
* *
5777263 AGGGTTAGGG-GTA
1 AGGTTTAGGGTTTA
5777276 TAGAGTTTAGGGTTTA
1 -AG-GTTTAGGGTTTA
* * **
5777292 GGGGTTAGGGGCATA
1 AGGTTTA-GGGTTTA
* *
5777307 GGGTTTAGGGGTTA
1 AGGTTTAGGGTTTA
* *
5777321 AAGTTTATGGTTT-
1 AGGTTTAGGGTTTA
5777334 AGTGTTTAGGGT
1 AG-GTTTAGGGT
5777346 CTAATTTTAA
Statistics
Matches: 92, Mismatches: 26, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
13 4 0.04
14 66 0.72
15 20 0.22
16 2 0.02
ACGTcount: A:0.20, C:0.01, G:0.37, T:0.42
Consensus pattern (14 bp):
AGGTTTAGGGTTTA
Found at i:5777274 original size:7 final size:7
Alignment explanation
Indices: 5777264--5777320 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
5777254 TATGGTTTAA
5777264 GGGTTAG
1 GGGTTAG
5777271 GGGTATAG
1 GGGT-TAG
* *
5777279 AGTTTAG
1 GGGTTAG
*
5777286 GGTTTAG
1 GGGTTAG
5777293 GGGTTAG
1 GGGTTAG
*
5777300 GGGCATAG
1 GGG-TTAG
*
5777308 GGTTTAG
1 GGGTTAG
5777315 GGGTTA
1 GGGTTA
5777321 AAGTTTATGG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
7 30 0.75
8 10 0.25
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.32
Consensus pattern (7 bp):
GGGTTAG
Found at i:5777283 original size:29 final size:29
Alignment explanation
Indices: 5777251--5777321 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
5777241 AGGGTTTAAG
* *
5777251 GTTTATGGTTTAAGGGTTAGGGGTATAGA
1 GTTTAGGGTTTAAGGGTTAGGGGCATAGA
* *
5777280 GTTTAGGGTTTAGGGGTTAGGGGCATAGG
1 GTTTAGGGTTTAAGGGTTAGGGGCATAGA
*
5777309 GTTTAGGGGTTAA
1 GTTTAGGGTTTAA
5777322 AGTTTATGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.21, C:0.01, G:0.42, T:0.35
Consensus pattern (29 bp):
GTTTAGGGTTTAAGGGTTAGGGGCATAGA
Found at i:5780587 original size:43 final size:43
Alignment explanation
Indices: 5780531--5780789 Score: 177
Period size: 43 Copynumber: 6.0 Consensus size: 43
5780521 GAAGGGTACA
*
5780531 TTTAGCAGCGTTTGTGATAAAAGCGCCTCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCTCTAAAGATCATGTTC
* * * ** * *
5780574 TTTAACGGTGTTTGTGAAAAAAAAGTCGCTAAA-ATTCAT-TCTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCTCTAAAGA-TCATGT-TC
* * * * * * * *
5780617 TATAGCGACGTTTGTCATAAAACCGCCGCTAAAGCTTATGCTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCTCTAAAGATCATGTTC
* * *
5780660 TTTAGCGGCGCTTGTGATAAAAGC-TCTGCTAAAAATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCT-CTAAAGATCATGTTC
* * * * *
5780703 TTTAGCGGCGTTTGTGGGT-AAAGCACCACTAGAGGTCATGTTC
1 TTTAGCGGCGTTTGT-GATAAAAGCGCCTCTAAAGATCATGTTC
* * * * *
5780746 TTTAGCGGAGTTTTTTATAAAAGCGTCGT-TAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCG-CCTCTAAAGATCATGTTC
5780789 T
1 T
5780790 ATAATAGCGT
Statistics
Matches: 161, Mismatches: 46, Indels: 18
0.72 0.20 0.08
Matches are distributed among these distances:
42 4 0.02
43 153 0.95
44 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCTCTAAAGATCATGTTC
Found at i:5787803 original size:36 final size:36
Alignment explanation
Indices: 5787737--5787805 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
5787727 TGGGCACCCC
* * * * *
5787737 ATTTGTTGGTTATATCTACCAGTGCTGGGCACATCT
1 ATTTGTTGGTTATACCGACAAGCGCAGGGCACATCT
5787773 ATTTGTTGGTTATACCGACAAGCGCAGGGCACA
1 ATTTGTTGGTTATACCGACAAGCGCAGGGCACA
5787806 ACTTATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (36 bp):
ATTTGTTGGTTATACCGACAAGCGCAGGGCACATCT
Found at i:5790208 original size:39 final size:39
Alignment explanation
Indices: 5790161--5790327 Score: 183
Period size: 39 Copynumber: 4.3 Consensus size: 39
5790151 CAAAAGTGTT
* * * *
5790161 ATCAGGAGTATCGAAATATAACAGGGGCATGTAAGTGTG
1 ATCAGGAGTATCGAAGTACAACAGGGGCACGTAAGTGCG
* * *
5790200 TTCAGGAGTATTGAAGTACACCAGGGGCACGTAAGTGCG
1 ATCAGGAGTATCGAAGTACAACAGGGGCACGTAAGTGCG
* * * *
5790239 ATCAGGGGTACCTAAGTACAATAGGGGCACGTAAGTGCG
1 ATCAGGAGTATCGAAGTACAACAGGGGCACGTAAGTGCG
* * *
5790278 ATCAGGGGTA-CTGAAGTACAACAGGGGCATGTAAGTACG
1 ATCAGGAGTATC-GAAGTACAACAGGGGCACGTAAGTGCG
*
5790317 ATCAGGGGTAT
1 ATCAGGAGTAT
5790328 AATTATATAA
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
38 1 0.01
39 107 0.99
ACGTcount: A:0.32, C:0.15, G:0.33, T:0.20
Consensus pattern (39 bp):
ATCAGGAGTATCGAAGTACAACAGGGGCACGTAAGTGCG
Found at i:5790235 original size:19 final size:19
Alignment explanation
Indices: 5790213--5790315 Score: 82
Period size: 19 Copynumber: 5.3 Consensus size: 19
5790203 AGGAGTATTG
*
5790213 AAGTACACCAGGGGCACGT
1 AAGTACAACAGGGGCACGT
* * * *
5790232 AAGTGCGATCAGGGGTACCT
1 AAGTAC-AACAGGGGCACGT
*
5790252 AAGTACAATAGGGGCACGT
1 AAGTACAACAGGGGCACGT
* * *
5790271 AAGTGCGATCAGGGGTAC-T
1 AAGTAC-AACAGGGGCACGT
*
5790290 GAAGTACAACAGGGGCATGT
1 -AAGTACAACAGGGGCACGT
5790310 AAGTAC
1 AAGTAC
5790316 GATCAGGGGT
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
19 34 0.54
20 29 0.46
ACGTcount: A:0.32, C:0.18, G:0.33, T:0.17
Consensus pattern (19 bp):
AAGTACAACAGGGGCACGT
Found at i:5790246 original size:20 final size:20
Alignment explanation
Indices: 5790221--5790324 Score: 106
Period size: 20 Copynumber: 5.3 Consensus size: 20
5790211 TGAAGTACAC
*
5790221 CAGGGGCACGTAAGTGCGAT
1 CAGGGGCACGTAAGTACGAT
* * *
5790241 CAGGGGTACCTAAGTACAAT
1 CAGGGGCACGTAAGTACGAT
*
5790261 -AGGGGCACGTAAGTGCGAT
1 CAGGGGCACGTAAGTACGAT
* *
5790280 CAGGGGTAC-TGAAGTAC-AA
1 CAGGGGCACGT-AAGTACGAT
*
5790299 CAGGGGCATGTAAGTACGAT
1 CAGGGGCACGTAAGTACGAT
5790319 CAGGGG
1 CAGGGG
5790325 TATAATTATA
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
19 30 0.45
20 36 0.55
ACGTcount: A:0.30, C:0.17, G:0.37, T:0.16
Consensus pattern (20 bp):
CAGGGGCACGTAAGTACGAT
Found at i:5790283 original size:78 final size:78
Alignment explanation
Indices: 5790183--5790326 Score: 216
Period size: 78 Copynumber: 1.8 Consensus size: 78
5790173 GAAATATAAC
* * * * * *
5790183 AGGGGCATGTAAGTGTGTTCAGGAGTATTGAAGTACACCAGGGGCACGTAAGTGCGATCAGGGGT
1 AGGGGCACGTAAGTGCGATCAGGAGTACTGAAGTACAACAGGGGCACGTAAGTACGATCAGGGGT
5790248 ACCTAAGTACAAT
66 ACCTAAGTACAAT
* *
5790261 AGGGGCACGTAAGTGCGATCAGGGGTACTGAAGTACAACAGGGGCATGTAAGTACGATCAGGGGT
1 AGGGGCACGTAAGTGCGATCAGGAGTACTGAAGTACAACAGGGGCACGTAAGTACGATCAGGGGT
5790326 A
66 A
5790327 TAATTATATA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.19
Consensus pattern (78 bp):
AGGGGCACGTAAGTGCGATCAGGAGTACTGAAGTACAACAGGGGCACGTAAGTACGATCAGGGGT
ACCTAAGTACAAT
Found at i:5794698 original size:22 final size:22
Alignment explanation
Indices: 5794658--5794703 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5794648 TAATGCTCTC
*
5794658 TTTGGGTTTTTTTATTTTTAAT
1 TTTGGGTTTTTTTAGTTTTAAT
*
5794680 TTTGGGTTTTTATT-GTTTTGAT
1 TTTGGGTTTTT-TTAGTTTTAAT
5794702 TT
1 TT
5794704 ACAACTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.11, C:0.00, G:0.17, T:0.72
Consensus pattern (22 bp):
TTTGGGTTTTTTTAGTTTTAAT
Found at i:5801423 original size:17 final size:18
Alignment explanation
Indices: 5801401--5801435 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5801391 CAATTTGGGC
5801401 CATGTGGG-ACACACGAG
1 CATGTGGGCACACACGAG
*
5801418 CATGTGGGCCCACACGAG
1 CATGTGGGCACACACGAG
5801436 AAAACTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.29, G:0.34, T:0.11
Consensus pattern (18 bp):
CATGTGGGCACACACGAG
Found at i:5818936 original size:22 final size:23
Alignment explanation
Indices: 5818911--5818965 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5818901 GGCCTTGGCC
*
5818911 CATAATAGT-AACAGATATCAAT
1 CATAACAGTGAACAGATATCAAT
*
5818933 CAT-ACAGTGAATAGATATCAAT
1 CATAACAGTGAACAGATATCAAT
5818955 CAT-ACAGTGAA
1 CATAACAGTGAA
5818966 TAGTATGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (23 bp):
CATAACAGTGAACAGATATCAAT
Found at i:5818966 original size:22 final size:22
Alignment explanation
Indices: 5818923--5818968 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5818913 TAATAGTAAC
5818923 AGATATCAATCATACAGTGAAT
1 AGATATCAATCATACAGTGAAT
5818945 AGATATCAATCATACAGTGAAT
1 AGATATCAATCATACAGTGAAT
5818967 AG
1 AG
5818969 TATGTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (22 bp):
AGATATCAATCATACAGTGAAT
Found at i:5820173 original size:27 final size:26
Alignment explanation
Indices: 5819417--5820179 Score: 787
Period size: 27 Copynumber: 28.4 Consensus size: 26
5819407 GGTATAATAA
* *
5819417 TCATTTAACCCTATAGGGGTATTTCAG
1 TCATTTTACCCTAT-GGGGTATTTCGG
* * *
5819444 TCAGTCTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTAT-GGGGTATTTCGG
* * *
5819471 TCATTCTACCCTATAGGGTTATTTCGA
1 TCATTTTACCCTAT-GGGGTATTTCGG
** **
5819498 TCATTTTACCCTATAGGGGTATACCAA
1 TCATTTTACCCTAT-GGGGTATTTCGG
* * *
5819525 TCATTTTACCCTATGACGATATTTCAG
1 TCATTTTACCCTATG-GGGTATTTCGG
*
5819552 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTAT-GGGGTATTTCGG
*
5819579 TCATTTTACCC-AGTAGGGGTATTTCAG
1 TCATTTTACCCTA-T-GGGGTATTTCGG
* *
5819606 TCATTTTACCCTATAAGGGTATTTCGA
1 TCATTTTACCCTAT-GGGGTATTTCGG
* *
5819633 TCATTTTACCTTATCGGGTATTTCGG
1 TCATTTTACCCTATGGGGTATTTCGG
*
5819659 TCATTCTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTAT-GGGGTATTTCGG
* *
5819686 TCATTCTATCCTATGGGGATATTTCGG
1 TCATTTTACCCTATGGGG-TATTTCGG
* * * *
5819713 TCATTCTACCATATGGGGGCATTTCAG
1 TCATTTTACCCTAT-GGGGTATTTCGG
* *
5819740 TCATTCTACCCTATGGAGATACTTT-GG
1 TCATTTTACCCTATGG-GGTA-TTTCGG
*
5819767 TCATTTTACCTTATGGGGGTATTT-GG
1 TCATTTTACCCTAT-GGGGTATTTCGG
* *
5819793 TCATTTTATCATATGGGAGTATTTCGG
1 TCATTTTACCCTATGGG-GTATTTCGG
*
5819820 TGATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTAT-GGGGTATTTCGG
* * *
5819847 TCATTCTACCCTATGGGAGCATTTCAG
1 TCATTTTACCCTATGGG-GTATTTCGG
*
5819874 TTATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATG-GGGTATTTCGG
* *
5819901 TCATTTTACCATATGGGGTATTTCGA
1 TCATTTTACCCTATGGGGTATTTCGG
* *
5819927 TTATTTTACCCTATGAGGGTATTTCAG
1 TCATTTTACCCTATG-GGGTATTTCGG
5819954 TCATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATG-GGGTATTTCGG
*
5819981 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTAT-GGGGTATTTCGG
* *
5820008 TCATTTTACCTTATGAGGGTATTTCAG
1 TCATTTTACCCTATG-GGGTATTTCGG
*
5820035 TCATTCTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTAT-GGGGTATTTCGG
* *
5820062 TCATTCTACCTTATGGGGGTATTTCGG
1 TCATTTTACCCTAT-GGGGTATTTCGG
5820089 TCATTTTACCCTATGGAGGTATCTTC-G
1 TCATTTTACCCTATGG-GGTAT-TTCGG
*
5820116 TCATTTTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATG-GGGTATTTCGG
*
5820143 TCATTTTACCCTATAGGGGTATTTTGG
1 TCATTTTACCCTAT-GGGGTATTTCGG
5820170 TCATTTTACC
1 TCATTTTACC
5820180 TATTTTAGGG
Statistics
Matches: 630, Mismatches: 82, Indels: 48
0.83 0.11 0.06
Matches are distributed among these distances:
25 3 0.00
26 85 0.13
27 519 0.82
28 23 0.04
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (26 bp):
TCATTTTACCCTATGGGGTATTTCGG
Found at i:5823655 original size:12 final size:11
Alignment explanation
Indices: 5823633--5823670 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5823623 TAACATGTCG
5823633 ATTTTTAATTA
1 ATTTTTAATTA
5823644 ATTTTATAATTA
1 ATTTT-TAATTA
*
5823656 A-TTTTGATTA
1 ATTTTTAATTA
5823666 ATTTT
1 ATTTT
5823671 GATTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 6 0.25
11 11 0.46
12 7 0.29
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
ATTTTTAATTA
Found at i:5823665 original size:10 final size:10
Alignment explanation
Indices: 5823652--5823682 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5823642 TAATTTTATA
5823652 ATTAATTTTG
1 ATTAATTTTG
5823662 ATTAATTTTG
1 ATTAATTTTG
*
5823672 ATTATTTTTG
1 ATTAATTTTG
5823682 A
1 A
5823683 CAAATTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (10 bp):
ATTAATTTTG
Found at i:5824349 original size:43 final size:43
Alignment explanation
Indices: 5824302--5824569 Score: 199
Period size: 43 Copynumber: 6.2 Consensus size: 43
5824292 GCGCTTCCAT
* *
5824302 ATAAAACGCCGTTATAAGTC-TCGGCCTTTAGCGACGCTTTGCA
1 ATAAAACGCCGCTATAAGTCAT-GGCCTTTAGCGACGCTTTTCA
* * * *
5824345 ATAAAACGTCGCTATAAGTCATTGCCTTTAGCGGCGCTTTTCT
1 ATAAAACGCCGCTATAAGTCATGGCCTTTAGCGACGCTTTTCA
* * * *
5824388 ATAAAACGCCGCAATAACTCGTGGCCTTTAGCG--GCTCTTTAA
1 ATAAAACGCCGCTATAAGTCATGGCCTTTAGCGACGCT-TTTCA
* * * **
5824430 TATAAAACGCCACAATAAGTCATGGTCTTTAGC-AGCGCTTTTTT
1 -ATAAAACGCCGCTATAAGTCATGGCCTTTAGCGA-CGCTTTTCA
* * * *
5824474 ATAAAACGCCGCTATAAGTCACGGTCTTTAGTGGCACTCTTTT-A
1 ATAAAACGCCGCTATAAGTCATGGCCTTTAG-CG-ACGCTTTTCA
* * * * **
5824518 GA-AAAA-GCCGCTATAAGTCACGGTCTTTAGTGGCGCTTTTTT
1 -ATAAAACGCCGCTATAAGTCATGGCCTTTAGCGACGCTTTTCA
5824560 ATAAAACGCC
1 ATAAAACGCC
5824570 ACTAATTTAG
Statistics
Matches: 183, Mismatches: 29, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
41 10 0.05
42 8 0.04
43 146 0.80
44 8 0.04
45 10 0.05
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (43 bp):
ATAAAACGCCGCTATAAGTCATGGCCTTTAGCGACGCTTTTCA
Found at i:5824534 original size:86 final size:85
Alignment explanation
Indices: 5824301--5824569 Score: 254
Period size: 86 Copynumber: 3.1 Consensus size: 85
5824291 GGCGCTTCCA
** * * * * * * *
5824301 TATAAAACGCCGTTATAAGTCTCGGCCTTTAGCGACGCTTTGCA-ATAAAACGTCGCTATAAGTC
1 TATAAAACGCCGCAATAACTCACGGCCTTTAGCGGCTCTTT--ATAGAAAAAGCCGCTATAAGTC
* * *
5824365 ATTGCCTTTAGCGGCGCTTTTC
64 ATGGTCTTTAGCGGCGCTTTTT
** * * * *
5824387 TATAAAACGCCGCAATAACTCGTGGCCTTTAGCGGCTCTTTAATATAAAACGCCACAATAAGTCA
1 TATAAAACGCCGCAATAACTCACGGCCTTTAGCGGCTCTTT-ATAGAAAAAGCCGCTATAAGTCA
*
5824452 TGGTCTTTAGCAGCGCTTTTT
65 TGGTCTTTAGCGGCGCTTTTT
* * * *
5824473 TATAAAACGCCGCTATAAGTCACGGTCTTTAGTGGCACTCTTT-TAGAAAAAGCCGCTATAAGTC
1 TATAAAACGCCGCAATAACTCACGGCCTTTAGCGG--CTCTTTATAGAAAAAGCCGCTATAAGTC
* *
5824537 ACGGTCTTTAGTGGCGCTTTTT
64 ATGGTCTTTAGCGGCGCTTTTT
5824559 TATAAAACGCC
1 TATAAAACGCC
5824570 ACTAATTTAG
Statistics
Matches: 152, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
85 1 0.01
86 145 0.95
88 6 0.04
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (85 bp):
TATAAAACGCCGCAATAACTCACGGCCTTTAGCGGCTCTTTATAGAAAAAGCCGCTATAAGTCAT
GGTCTTTAGCGGCGCTTTTT
Found at i:5824698 original size:34 final size:33
Alignment explanation
Indices: 5824629--5824698 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
5824619 TTCCTACATG
** *
5824629 AAATCCAACAAAAAACAGCAAATATTTTTGCAA
1 AAATCCAACAAAAAACAGCAAATATAATTACAA
* * *
5824662 AAATCCAACCAAAAACAGCAAATCTAAATTATAA
1 AAATCCAACAAAAAACAGCAAATAT-AATTACAA
5824696 AAA
1 AAA
5824699 ATTATACGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.59, C:0.19, G:0.04, T:0.19
Consensus pattern (33 bp):
AAATCCAACAAAAAACAGCAAATATAATTACAA
Found at i:5827528 original size:23 final size:23
Alignment explanation
Indices: 5827502--5827552 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5827492 ATCCGTCCTT
5827502 TGTAATATCCC-AAAAATTACTAC
1 TGTAATA-CCCTAAAAATTACTAC
* *
5827525 TGTAGTACCCTGAAAATTACTAC
1 TGTAATACCCTAAAAATTACTAC
*
5827548 AGTAA
1 TGTAA
5827553 GAAAGTAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCTAAAAATTACTAC
Found at i:5838210 original size:43 final size:43
Alignment explanation
Indices: 5838157--5838438 Score: 352
Period size: 43 Copynumber: 6.6 Consensus size: 43
5838147 AAGTGCCATA
*
5838157 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGTCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGTCGC
* * * * *
5838200 TAAAGGTCATGTTCTTTAGCAGCGTTTGTGACACAAGAGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGTCGC
* * * *
5838243 AAAAGGTCATGTTCTTTAGTGGCTTTTGTGATTGAAGCG-CAGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGTC-GC
* * * * *
5838286 TAAAGGTCATATTGTTTAGCAGCATTTGTGATAGAAGCGTCAC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGTCGC
* * **
5838329 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGACACAAGCGAT-TT
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCG-TCGC
*
5838372 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGTCGC
5838415 TAAAGGTCATGTTCTTTAGCGGCG
1 TAAAGGTCATGTTCTTTAGCGGCG
5838439 CTTTTACAAC
Statistics
Matches: 201, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.00
43 198 0.99
44 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGTCGC
Found at i:5838326 original size:129 final size:129
Alignment explanation
Indices: 5838157--5838434 Score: 403
Period size: 129 Copynumber: 2.2 Consensus size: 129
5838147 AAGTGCCATA
* * *
5838157 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCAG
1 TAAAGGTCATGTTCTTTAGCAGCATTTGTGATAAAAGCGTCACTAAAGGTCATGTTCTTTAGCAG
* * * *
5838222 CGTTTGTGACACAAGAGCCGCAAAAGGTCATGTTCTTTAGTGGCTTTTGTGATTGAAGCGCAGC
66 CGTTTGTGACACAAGAGACGCAAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGCAGC
* * * *
5838286 TAAAGGTCATATTGTTTAGCAGCATTTGTGATAGAAGCGTCACTAAAGGTCATGTTCTTTAGCGG
1 TAAAGGTCATGTTCTTTAGCAGCATTTGTGATAAAAGCGTCACTAAAGGTCATGTTCTTTAGCAG
* **** *
5838351 CGTTTGTGACACAAGCGATTTTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGCCGC
66 CGTTTGTGACACAAGAGACGCAAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGCAGC
5838415 TAAAGGTCATGTTCTTTAGC
1 TAAAGGTCATGTTCTTTAGC
5838435 GGCGCTTTTA
Statistics
Matches: 130, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (129 bp):
TAAAGGTCATGTTCTTTAGCAGCATTTGTGATAAAAGCGTCACTAAAGGTCATGTTCTTTAGCAG
CGTTTGTGACACAAGAGACGCAAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAAGCGCAGC
Found at i:5846415 original size:17 final size:18
Alignment explanation
Indices: 5846393--5846427 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5846383 TACTCGCGTA
5846393 GGGCCCAC-AGGCCCATT
1 GGGCCCACTAGGCCCATT
*
5846410 GGGCCCACTCGGCCCATT
1 GGGCCCACTAGGCCCATT
5846428 CCAGTCCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (18 bp):
GGGCCCACTAGGCCCATT
Found at i:5847759 original size:22 final size:23
Alignment explanation
Indices: 5847706--5847761 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
5847696 CCTCTAACAT
*
5847706 CCTTACCACACCTGTGACGCCACC
1 CCTTGCCACACCTGTGACGCCA-C
*
5847730 TCCTTGCCACACCTGTGTCGCCA-
1 -CCTTGCCACACCTGTGACGCCAC
5847753 CCTTGCCAC
1 CCTTGCCAC
5847762 TATACCACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
25 20 0.69
ACGTcount: A:0.16, C:0.48, G:0.14, T:0.21
Consensus pattern (23 bp):
CCTTGCCACACCTGTGACGCCAC
Found at i:5847770 original size:30 final size:25
Alignment explanation
Indices: 5847705--5847755 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5847695 ACCTCTAACA
5847705 TCCTTACCACACCTGTGACGCCACC
1 TCCTTACCACACCTGTGACGCCACC
* *
5847730 TCCTTGCCACACCTGTGTCGCCACC
1 TCCTTACCACACCTGTGACGCCACC
5847755 T
1 T
5847756 TGCCACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.47, G:0.14, T:0.24
Consensus pattern (25 bp):
TCCTTACCACACCTGTGACGCCACC
Found at i:5852494 original size:25 final size:25
Alignment explanation
Indices: 5852443--5852496 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
5852433 TGAACCTCTA
*
5852443 ACCTCCTTACCACACCTGTGACACC
1 ACCTCCTTACCACACCTATGACACC
* * *
5852468 ACCTCCTTGCCACACCTATGTCCCC
1 ACCTCCTTACCACACCTATGACACC
5852493 ACCT
1 ACCT
5852497 TGCCACTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.50, G:0.07, T:0.22
Consensus pattern (25 bp):
ACCTCCTTACCACACCTATGACACC
Found at i:5856378 original size:39 final size:40
Alignment explanation
Indices: 5856335--5856493 Score: 182
Period size: 39 Copynumber: 4.1 Consensus size: 40
5856325 GCTATCAAGA
* * *
5856335 GTACCGAAATATAACAGGGGCATGTAAGTGC-ATCTAGGG
1 GTACCGAAGTACAACAGGGGCACGTAAGTGCGATCTAGGG
*
5856374 GTACCGAAGTACAACAGGGGCACGTAAGTGCGAT-TAGGT
1 GTACCGAAGTACAACAGGGGCACGTAAGTGCGATCTAGGG
* * * * *
5856413 GTGCCGAAGTATAGCAGGGGCACGTAATTGCTATC-AGGG
1 GTACCGAAGTACAACAGGGGCACGTAAGTGCGATCTAGGG
* **
5856452 GTACCGAAGTACAATAGGGGCACAAAAGTGCGATC-AGGG
1 GTACCGAAGTACAACAGGGGCACGTAAGTGCGATCTAGGG
5856491 GTA
1 GTA
5856494 TAATTTTATA
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 98 0.98
40 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.18
Consensus pattern (40 bp):
GTACCGAAGTACAACAGGGGCACGTAAGTGCGATCTAGGG
Found at i:5856402 original size:19 final size:19
Alignment explanation
Indices: 5856347--5856402 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
5856337 ACCGAAATAT
* *
5856347 AACAGGGGCATGTAAGTGC
1 AACAGGGGCACGTAAGTAC
* *
5856366 ATCTAGGGGTACCG-AAGTAC
1 AAC-AGGGGCA-CGTAAGTAC
5856386 AACAGGGGCACGTAAGT
1 AACAGGGGCACGTAAGT
5856403 GCGATTAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 13 0.46
21 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.34, T:0.16
Consensus pattern (19 bp):
AACAGGGGCACGTAAGTAC
Found at i:5856456 original size:78 final size:78
Alignment explanation
Indices: 5856338--5856485 Score: 217
Period size: 78 Copynumber: 1.9 Consensus size: 78
5856328 ATCAAGAGTA
* **
5856338 CCGAAATATAACAGGGGCATGTAAGTGCATCTAGGGGTACCGAAGTACAACAGGGGCACGTAAGT
1 CCGAAATATAACAGGGGCACGTAAGTGCATCTAGGGGTACCGAAGTACAACAGGGGCACAAAAGT
5856403 GCGATTAGGTGTG
66 GCGATTAGGTGTG
* * * *
5856416 CCGAAGTATAGCAGGGGCACGTAATTGCTATC-AGGGGTACCGAAGTACAATAGGGGCACAAAAG
1 CCGAAATATAACAGGGGCACGTAAGTGC-ATCTAGGGGTACCGAAGTACAACAGGGGCACAAAAG
5856480 TGCGAT
65 TGCGAT
5856486 CAGGGGTATA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 59 0.95
79 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (78 bp):
CCGAAATATAACAGGGGCACGTAAGTGCATCTAGGGGTACCGAAGTACAACAGGGGCACAAAAGT
GCGATTAGGTGTG
Found at i:5865754 original size:19 final size:18
Alignment explanation
Indices: 5865730--5865791 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
5865720 AAGCCCATAA
5865730 TTTTTAATAGTTTTAATAT
1 TTTTTAATAGTTTT-ATAT
*
5865749 TTTTTAATA-ATTTATATT
1 TTTTTAATAGTTTTATA-T
*
5865767 TATTTTAA-AGTTTTTTTAT
1 T-TTTTAATAG-TTTTATAT
5865786 TTTTTA
1 TTTTTA
5865792 GAATTAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.08
18 11 0.31
19 17 0.47
20 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTAATAGTTTTATAT
Found at i:5870111 original size:14 final size:14
Alignment explanation
Indices: 5870094--5870123 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5870084 TCCACAAGGT
*
5870094 TTTAAACATAAACA
1 TTTAAACACAAACA
5870108 TTTAAACACAAACA
1 TTTAAACACAAACA
5870122 TT
1 TT
5870124 CCTCCCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (14 bp):
TTTAAACACAAACA
Found at i:5872823 original size:138 final size:138
Alignment explanation
Indices: 5872565--5872838 Score: 433
Period size: 138 Copynumber: 2.0 Consensus size: 138
5872555 GACGCTACCG
* * *
5872565 ATGCTGATATCTCGTTAGAATTGTCTCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
1 ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
* * * * *
5872630 CGTAACAATCATTATAAACTGAATATCAATGAAGCCCTTACTTTGGCAACTACGAGTGATAATTT
66 CGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGTT
5872695 TACATCCA
131 TACATCCA
* * *
5872703 ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAATAAACCCC-CAGGGTTTGAAGTTGGTGA
1 ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAACAAACCCCAAAGGG-TTGAAGTCGGTGA
5872767 ACGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGT
65 ACGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGT
5872832 TTACATC
130 TTACATC
5872839 GAAGAAAAGA
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
137 4 0.03
138 120 0.97
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (138 bp):
ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
CGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGTT
TACATCCA
Found at i:5872881 original size:138 final size:137
Alignment explanation
Indices: 5872595--5872868 Score: 306
Period size: 138 Copynumber: 2.0 Consensus size: 137
5872585 TTGTCTCTTT
* * *
5872595 CAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATTATAAACTGAATATCAAT
1 CAATGAATAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAAT
* * * * * * * *
5872660 GAAGCCCTTACTTTGGCAACTACGAGTGATAATTTTACATCCAATGCCGATAGCTCGTTAGAATG
66 GAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATG-CAAAAGCACGTAACAATG
*** **
5872725 GTCTCTTT
130 GAAACTGA
* *
5872733 CAATGAATAAACCCC-CAGGGTTTGAAGTTGGTGAACGTAACAATCATCATAAACTGAAGATCAA
1 CAATGAATAAACCCCAAAGGG-TTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAA
*
5872797 TGAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCGAA-G-AAAAG-ACG-AACAATG
65 TGAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATGCAAAAGCACGTAACAAT-
5872858 GGGAAACTGA
129 -GGAAACTGA
5872868 C
1 C
5872869 GAATAGAAAT
Statistics
Matches: 114, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
133 4 0.04
134 2 0.02
135 8 0.07
137 5 0.04
138 95 0.83
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (137 bp):
CAATGAATAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAAT
GAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATGCAAAAGCACGTAACAATGG
AAACTGA
Found at i:5885873 original size:17 final size:17
Alignment explanation
Indices: 5885851--5885888 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
5885841 TAATAAACAA
5885851 ATGATTAGCAAATGATC
1 ATGATTAGCAAATGATC
5885868 ATGATTAGCAAATGATC
1 ATGATTAGCAAATGATC
5885885 ATGA
1 ATGA
5885889 AGCTTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (17 bp):
ATGATTAGCAAATGATC
Found at i:5895282 original size:21 final size:21
Alignment explanation
Indices: 5895258--5895301 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5895248 CATGTTTTGG
5895258 TTTCTGTATTAAGTTGATGTT
1 TTTCTGTATTAAGTTGATGTT
5895279 TTTCTGTATTAAGTTGATGTT
1 TTTCTGTATTAAGTTGATGTT
5895300 TT
1 TT
5895302 CCGTTTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.59
Consensus pattern (21 bp):
TTTCTGTATTAAGTTGATGTT
Found at i:5895359 original size:21 final size:21
Alignment explanation
Indices: 5895318--5895360 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5895308 GTGTTTATGG
*
5895318 ATTATATATAATTTTTATAGT
1 ATTATATATAATATTTATAGT
*
5895339 ATTATATATTATGATTT-TAGT
1 ATTATATATAAT-ATTTATAGT
5895360 A
1 A
5895361 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATATATAATATTTATAGT
Found at i:5895665 original size:44 final size:44
Alignment explanation
Indices: 5895577--5895668 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
5895567 ATTACAACAT
* *
5895577 CATTCCATTCAACCAAAGACAAGAATACTATTATAGTTCTATTC
1 CATTCCATTCAACCAAAGACAAGAATACTATTACAGCTCTATTC
*
5895621 CATTCCATTCAACC-AA-ACAATTGAATTGCTATTACAGCTC-ATTC
1 CATTCCATTCAACCAAAGACAA--GAA-TACTATTACAGCTCTATTC
5895665 CATT
1 CATT
5895669 ACAGCTCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
42 4 0.10
43 2 0.05
44 25 0.60
45 11 0.26
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAAGACAAGAATACTATTACAGCTCTATTC
Found at i:5895671 original size:15 final size:16
Alignment explanation
Indices: 5895651--5895689 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
5895641 TTGAATTGCT
5895651 ATTACAGCTC-ATTCC
1 ATTACAGCTCTATTCC
5895666 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
5895682 ATTACAGC
1 ATTACAGC
5895690 AAACCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:5895882 original size:23 final size:23
Alignment explanation
Indices: 5895828--5895895 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
5895818 ATTAACATTT
**
5895828 TTCGTGAACATGTTCAATTATATG
1 TTCGTGAACATGTTTGATTA-ATG
** *
5895852 TTTATGAACATGTTTGTTTAATG
1 TTCGTGAACATGTTTGATTAATG
5895875 TTCGTGAACATGTTTGATTAA
1 TTCGTGAACATGTTTGATTAA
5895896 GTTAAATGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.46
Consensus pattern (23 bp):
TTCGTGAACATGTTTGATTAATG
Found at i:5895905 original size:23 final size:23
Alignment explanation
Indices: 5895832--5895911 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
5895822 ACATTTTTCG
** *
5895832 TGAACATGTTCAATTATATGTTTA
1 TGAACATGTTTGATTA-ATGTTAA
* **
5895856 TGAACATGTTTGTTTAATGTTCG
1 TGAACATGTTTGATTAATGTTAA
5895879 TGAACATGTTTGATTAA-GTTAAA
1 TGAACATGTTTGATTAATGTT-AA
5895902 TGAACATGTT
1 TGAACATGTT
5895912 CGTGAATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.66
24 13 0.28
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.44
Consensus pattern (23 bp):
TGAACATGTTTGATTAATGTTAA
Found at i:5903658 original size:4 final size:4
Alignment explanation
Indices: 5903649--5903836 Score: 326
Period size: 4 Copynumber: 47.2 Consensus size: 4
5903639 AAATTTCATG
*
5903649 TACA TACA TACA TGCA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
5903697 CACA TACA TACA TACA CACA TACA TACA -ACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5903744 TACA TACA TACA TACA TACA TACA TACAA TACA T-CA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TAC-A TACA TACA TACA TACA TACA
5903792 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
5903837 TCAAGACCTT
Statistics
Matches: 175, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
3 6 0.03
4 165 0.94
5 4 0.02
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:5910086 original size:75 final size:76
Alignment explanation
Indices: 5909997--5910147 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 76
5909987 CAGATTGGCA
*
5909997 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAATGGGGAAATA-GGTGGCTGCAA
1 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
5910061 ATATCAAATAG
66 ATATCAAATAG
5910072 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
1 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
5910137 ATATCAAATAG
66 ATATCAAATAG
5910148 AGGAGTTTCA
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 52 0.70
76 22 0.30
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.26
Consensus pattern (76 bp):
TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
ATATCAAATAG
Found at i:5916398 original size:235 final size:236
Alignment explanation
Indices: 5915976--5916446 Score: 935
Period size: 235 Copynumber: 2.0 Consensus size: 236
5915966 AAATAATAAA
5915976 AAATTAATTTAATTTTTTAAAAATTATAAAAATATAGAGTATTAAAATAATAAAATTATATTTTT
1 AAATTAATTTAATTTTTTAAAAATTATAAAAATATAGAGTATTAAAATAATAAAATTATATTTTT
5916041 ACTATTGTAAAATATAAATTTGATTCTAACTTTCTCTCAAAAAAATTTCTGACTTCGTCATTGAG
66 ACTATTGTAAAATATAAATTTGATTCTAACTTTCTCTCAAAAAAATTTCTGACTTCGTCATTGAG
5916106 CATTGGAGTCGAGTCCTTAATTGTTGGTCAAACTGTATTATGTATGTAATGATTAATGTTGAAAA
131 CATTGGAGTCGAGTCCTTAATTGTTGGTCAAACTGTATTATGTATGTAATGATTAATGTTGAAAA
5916171 TATAATTCAAATTAACATGTTATTTTCCTACCTACGCATGC
196 TATAATTCAAATTAACATGTTATTTTCCTACCTACGCATGC
5916212 AAATTAATTT-ATTTTTTAAAAATTATAAAAATATAGAGTATTAAAATAATAAAATTATATTTTT
1 AAATTAATTTAATTTTTTAAAAATTATAAAAATATAGAGTATTAAAATAATAAAATTATATTTTT
5916276 ACTATTGTAAAATATAAATTTGATTCTAACTTTCTCTCAAAAAAATTTCTGACTTCGTCATTGAG
66 ACTATTGTAAAATATAAATTTGATTCTAACTTTCTCTCAAAAAAATTTCTGACTTCGTCATTGAG
5916341 CATTGGAGTCGAGTCCTTAATTGTTGGTCAAACTGTATTATGTATGTAATGATTAATGTTGAAAA
131 CATTGGAGTCGAGTCCTTAATTGTTGGTCAAACTGTATTATGTATGTAATGATTAATGTTGAAAA
5916406 TATAATTCAAATTAACATGTTATTTTCCTACCTACGCATGC
196 TATAATTCAAATTAACATGTTATTTTCCTACCTACGCATGC
5916447 TGCGCTCACC
Statistics
Matches: 235, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
235 225 0.96
236 10 0.04
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (236 bp):
AAATTAATTTAATTTTTTAAAAATTATAAAAATATAGAGTATTAAAATAATAAAATTATATTTTT
ACTATTGTAAAATATAAATTTGATTCTAACTTTCTCTCAAAAAAATTTCTGACTTCGTCATTGAG
CATTGGAGTCGAGTCCTTAATTGTTGGTCAAACTGTATTATGTATGTAATGATTAATGTTGAAAA
TATAATTCAAATTAACATGTTATTTTCCTACCTACGCATGC
Found at i:5918604 original size:28 final size:28
Alignment explanation
Indices: 5918573--5918633 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
5918563 ATATGGTCCA
5918573 GTTGAAACATTCTTAGATAATTG-TGGTT
1 GTTGAAACATTCTTAGATAATTGCT-GTT
5918601 GTTGAAACATTCTTAGATAATTGCTGTT
1 GTTGAAACATTCTTAGATAATTGCTGTT
5918629 GTTGA
1 GTTGA
5918634 TGAACTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (28 bp):
GTTGAAACATTCTTAGATAATTGCTGTT
Found at i:5928875 original size:51 final size:51
Alignment explanation
Indices: 5928812--5928946 Score: 146
Period size: 55 Copynumber: 2.5 Consensus size: 51
5928802 TGATAATCAT
*
5928812 TTATTTGAGCAAAGAATCCAC-CTTTTTTCAACTCGAGAGCAAGTTTTACAA
1 TTATTTGTGCAAA-AATCCACTCTTTTTTCAACTCGAGAGCAAGTTTTACAA
* * * * *
5928863 TTATTTGTGCAAAAATTCCACTTTTTTTTTTTCAATTTGAGAGCAAGTTTTCCAT
1 TTATTTGTGCAAAAA-TCCAC---TCTTTTTTCAACTCGAGAGCAAGTTTTACAA
*
5928918 TTATTTGTGCAAAAAATCCACTATTTTTT
1 TTATTTGTGC-AAAAATCCACTCTTTTTT
5928947 TTTTCAACAA
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
50 2 0.03
51 17 0.24
52 7 0.10
55 40 0.56
56 5 0.07
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (51 bp):
TTATTTGTGCAAAAATCCACTCTTTTTTCAACTCGAGAGCAAGTTTTACAA
Found at i:5928922 original size:55 final size:56
Alignment explanation
Indices: 5928834--5928954 Score: 190
Period size: 55 Copynumber: 2.2 Consensus size: 56
5928824 AGAATCCACC
*
5928834 TTTTTTCAACTCGAGAGCAAGTTTTACAATTATTTGTGCAAAAATTCCACT-TTTT
1 TTTTTTCAACTCGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTATTTT
* * * *
5928889 TTTTTTCAATTTGAGAGCAAGTTTTCCATTTATTTGTGCAAAAAATCCACTATTTT
1 TTTTTTCAACTCGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTATTTT
5928945 TTTTTTCAAC
1 TTTTTTCAAC
5928955 AAGGAAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 46 0.78
56 13 0.22
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (56 bp):
TTTTTTCAACTCGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTATTTT
Found at i:5932522 original size:13 final size:13
Alignment explanation
Indices: 5932506--5932530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5932496 AAACAATTAT
5932506 TTTATTTTTATAC
1 TTTATTTTTATAC
5932519 TTTATTTTTATA
1 TTTATTTTTATA
5932531 AAATTTAGGA
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTTATAC
Found at i:5944985 original size:6 final size:6
Alignment explanation
Indices: 5944974--5945016 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
5944964 TTCAAACCCA
* * *
5944974 TTTATT TTTATTT TTTATT TCTATT TTTATT TCTATT TCTATT
1 TTTATT TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT
5945017 CCAGTCTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:5945002 original size:12 final size:12
Alignment explanation
Indices: 5944974--5945016 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
5944964 TTCAAACCCA
*
5944974 TTTATTTTTATTT
1 TTTATTTCTA-TT
5944987 TTTATTTCTATT
1 TTTATTTCTATT
5944999 TTTATTTCTATT
1 TTTATTTCTATT
*
5945011 TCTATT
1 TTTATT
5945017 CCAGTCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTCTATT
Found at i:5945010 original size:18 final size:19
Alignment explanation
Indices: 5944976--5945016 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
5944966 CAAACCCATT
*
5944976 TATTTTTATTTTTTATTTC
1 TATTTTTATTTTCTATTTC
5944995 TATTTTTA-TTTCTATTTC
1 TATTTTTATTTTCTATTTC
5945013 TATT
1 TATT
5945017 CCAGTCTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTATTTTCTATTTC
Found at i:5946606 original size:7 final size:7
Alignment explanation
Indices: 5946594--5946619 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5946584 TACTAAAATC
5946594 ATTTTAA
1 ATTTTAA
5946601 ATTTTAA
1 ATTTTAA
5946608 ATTTTAA
1 ATTTTAA
5946615 ATTTT
1 ATTTT
5946620 CATTTTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:5946626 original size:14 final size:14
Alignment explanation
Indices: 5946595--5946639 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5946585 ACTAAAATCA
* *
5946595 TTTTAAATTTTAAA
1 TTTTAAATTTTCAT
5946609 TTTTAAATTTTCAT
1 TTTTAAATTTTCAT
5946623 TTTTACAAATTTTCAT
1 TTTT--AAATTTTCAT
5946639 T
1 T
5946640 ATAATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 16 0.59
16 11 0.41
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTAAATTTTCAT
Found at i:5947009 original size:21 final size:21
Alignment explanation
Indices: 5946983--5947038 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
5946973 AACAGCGGTG
*
5946983 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
5947004 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
5947025 GCGGTAAGATTAGA
1 GCGGTGAGATTAGA
5947039 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:5947850 original size:113 final size:113
Alignment explanation
Indices: 5947652--5947879 Score: 447
Period size: 113 Copynumber: 2.0 Consensus size: 113
5947642 AGACTATATC
*
5947652 CCCATACCTATTCCAAATATATGCCGAAAGATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
1 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
5947717 TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
66 TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
5947765 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
1 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
5947830 TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
66 TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
5947878 CC
1 CC
5947880 ATGATTGAAG
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (113 bp):
CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
Found at i:5951700 original size:2 final size:2
Alignment explanation
Indices: 5951688--5951722 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5951678 GGCACATGTC
5951688 AT AT A- AT AT AT AT -T 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 AT AT AT AT A
5951723 ACAAAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5952464 original size:17 final size:17
Alignment explanation
Indices: 5952442--5952474 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5952432 ATAGAAAGTC
*
5952442 AAAGATATTGGTATCAG
1 AAAGATATGGGTATCAG
5952459 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
5952475 AAATCTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:5955953 original size:17 final size:17
Alignment explanation
Indices: 5955931--5955963 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5955921 ATAGAAAGTC
5955931 AAAGATATGGATATCAG
1 AAAGATATGGATATCAG
*
5955948 AAAGATATGGGTATCA
1 AAAGATATGGATATCA
5955964 AAATTCTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAGATATGGATATCAG
Found at i:5957735 original size:28 final size:27
Alignment explanation
Indices: 5957699--5957753 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
5957689 AATTTTAAAA
*
5957699 TATATATTAAAAATATTTTTATATTTTTT
1 TATATATT-AAAATAGTTTT-TATTTTTT
*
5957728 TATA-ATTATAATAGTTTTTATTTTTT
1 TATATATTAAAATAGTTTTTATTTTTT
5957754 AAAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.33
27 9 0.38
28 3 0.12
29 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TATATATTAAAATAGTTTTTATTTTTT
Found at i:5957768 original size:23 final size:23
Alignment explanation
Indices: 5957742--5957785 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
5957732 ATTATAATAG
*
5957742 TTTTTATTTTTTAAAA-TAATTT
1 TTTTTAATTTTTAAAATTAATTT
5957764 TTTTTAATTTTTAAAATTAATT
1 TTTTTAATTTTTAAAATTAATT
5957786 AATTGATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTAATTTTTAAAATTAATTT
Found at i:5958142 original size:35 final size:35
Alignment explanation
Indices: 5958092--5958163 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
5958082 AAATACTCAC
5958092 AATCTTATATAGATCAAGAATAATGTATAAAAATG
1 AATCTTATATAGATCAAGAATAATGTATAAAAATG
*
5958127 AATCTTATATTGATCAAGAATAATGTATAAAAATG
1 AATCTTATATAGATCAAGAATAATGTATAAAAATG
5958162 AA
1 AA
5958164 GGTTTATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (35 bp):
AATCTTATATAGATCAAGAATAATGTATAAAAATG
Found at i:5959039 original size:2 final size:2
Alignment explanation
Indices: 5959034--5959061 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5959024 GCCACACACA
5959034 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
5959062 TTGAGCTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5961676 original size:24 final size:23
Alignment explanation
Indices: 5961649--5961694 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
5961639 TTTGGAGAAT
5961649 TTTGTGTTT-ACGTTTTGAGGGTTA
1 TTTGT-TTTGACGTTTTG-GGGTTA
*
5961673 TTTGTTTTGAGGTTTTGGGGTT
1 TTTGTTTTGACGTTTTGGGGTT
5961695 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.09, C:0.02, G:0.33, T:0.57
Consensus pattern (23 bp):
TTTGTTTTGACGTTTTGGGGTTA
Found at i:5962636 original size:42 final size:43
Alignment explanation
Indices: 5962580--5962700 Score: 147
Period size: 42 Copynumber: 2.8 Consensus size: 43
5962570 TTCCAATATG
*
5962580 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC-GTATA
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAGTATA
* * *
5962622 TGATTACGTGTAAGAGCC-TGTCTGGGACAGTGGCATCATTATT
1 TGATTACGTGTAAGA-CCATGTCTGGGACATTGGCATCAGTATA
* * **
5962665 TGATTACATGTAAGACCACGTCTGGGATGTTGGCAT
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
5962701 TATTCGAGCT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 34 0.51
43 33 0.49
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAGTATA
Found at i:5962699 original size:43 final size:42
Alignment explanation
Indices: 5962588--5962700 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 42
5962578 TGTGATTTCG
*
5962588 TGTAAGACCATGTCTGGGACA-TTGGCATCGTATATGATTACG
1 TGTAAGACCATGTCTGGGA-AGTTGGCATCGTATATGATTACA
* *
5962630 TGTAAGAGCC-TGTCTGGGACAG-TGGCATCATTATTTGATTACA
1 TGTAAGA-CCATGTCTGGGA-AGTTGGCATC-GTATATGATTACA
* *
5962673 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCATGTCTGGGAAGTTGGCAT
5962701 TATTCGAGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
42 28 0.46
43 33 0.54
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGAAGTTGGCATCGTATATGATTACA
Found at i:5970770 original size:20 final size:22
Alignment explanation
Indices: 5970746--5970787 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5970736 TTATGATTTT
5970746 AAAAAA-AATATATTGATTAAC
1 AAAAAATAATATATTGATTAAC
*
5970767 AAAAAATAATATTTTGATTAA
1 AAAAAATAATATATTGATTAA
5970788 TGGAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAAAATAATATATTGATTAAC
Found at i:5970844 original size:22 final size:19
Alignment explanation
Indices: 5970795--5970845 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
5970785 TAATGGAAAA
5970795 TAATTTTTTTAAAAATAAC
1 TAATTTTTTTAAAAATAAC
*
5970814 T-TTTCTTTTTAAAAAGCATAAC
1 TAATT-TTTTT-AAAA--ATAAC
5970836 TAATTTTTTT
1 TAATTTTTTT
5970846 TTTGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 4 0.16
22 11 0.44
23 2 0.08
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATTTTTTTAAAAATAAC
Found at i:5976607 original size:54 final size:54
Alignment explanation
Indices: 5976505--5976610 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
5976495 CTAAGTTGTC
* *
5976505 GGGCTTGGTGTGTGGAGGAGATGGGAAAGAGGTGGTTGCTGCCACGGGCGGCCG
1 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCACGGGCGGCCG
*
5976559 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGGTA-CACCGGGCGGC
1 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCA-CGGGCGGC
5976611 GGAGCTGGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 2 0.04
54 46 0.96
ACGTcount: A:0.17, C:0.13, G:0.51, T:0.19
Consensus pattern (54 bp):
GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCACGGGCGGCCG
Found at i:5980431 original size:4 final size:4
Alignment explanation
Indices: 5980422--5980456 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5980412 GAAGAAGAAG
5980422 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
5980457 GCATTAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:5989089 original size:12 final size:12
Alignment explanation
Indices: 5989072--5989101 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5989062 TTGAGAAAGG
*
5989072 GAAATGAAATGT
1 GAAATGAAATAT
5989084 GAAATGAAATAT
1 GAAATGAAATAT
5989096 GAAATG
1 GAAATG
5989102 GTGGATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (12 bp):
GAAATGAAATAT
Found at i:5991494 original size:23 final size:24
Alignment explanation
Indices: 5991458--5991505 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
5991448 TGATCCCCAT
5991458 ATTTTTTTCGTTTTAAGTAATTTA
1 ATTTTTTTCGTTTTAAGTAATTTA
* *
5991482 ATTTTTTTC-TTTTATGTTATTTA
1 ATTTTTTTCGTTTTAAGTAATTTA
5991505 A
1 A
5991506 ACTTTCTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (24 bp):
ATTTTTTTCGTTTTAAGTAATTTA
Found at i:5994016 original size:30 final size:30
Alignment explanation
Indices: 5993982--5994044 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
5993972 ACTTAACAAG
5993982 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
** * *
5994012 CAAATGTCTTTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
5994042 CAA
1 CAA
5994045 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:5997081 original size:11 final size:13
Alignment explanation
Indices: 5997050--5997074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5997040 TCTAAAGAAT
5997050 CCATATTTGACAA
1 CCATATTTGACAA
5997063 CCATATTTGACA
1 CCATATTTGACA
5997075 CATATTTAGA
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:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
CCATATTTGACAA
Found at i:5998769 original size:34 final size:34
Alignment explanation
Indices: 5998726--5998794 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
5998716 CTGCTTACTC
*
5998726 ATGGGGAAAATATGGAAAGGAAAAGGGAAAACAG
1 ATGGGGAAAAGATGGAAAGGAAAAGGGAAAACAG
5998760 ATGGGGAAAAGATGGAAAGGAAAAGGGAAAACAG
1 ATGGGGAAAAGATGGAAAGGAAAAGGGAAAACAG
5998794 A
1 A
5998795 GGATGGTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.54, C:0.03, G:0.36, T:0.07
Consensus pattern (34 bp):
ATGGGGAAAAGATGGAAAGGAAAAGGGAAAACAG
Found at i:6004827 original size:18 final size:17
Alignment explanation
Indices: 6004787--6004834 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
6004777 TATTATTAAG
*
6004787 TTTA-TATAAGATATTA
1 TTTATTATAAAATATTA
6004803 TTTATTATAAAATATTA
1 TTTATTATAAAATATTA
*
6004820 TCTTATTAAAAAATA
1 T-TTATTATAAAATA
6004835 AATTTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.14
17 12 0.43
18 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTATTATAAAATATTA
Found at i:6005062 original size:40 final size:40
Alignment explanation
Indices: 6005017--6005149 Score: 149
Period size: 40 Copynumber: 3.1 Consensus size: 40
6005007 AATAGTGAAG
6005017 AAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTTGA
1 AAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTTGA
*** **
6005057 AAAATATGTTTGACTAAAAATTTTAATTTTCTTAGAAAATAGTGAA
1 AAAATATGTTTGACTAAAAATTTTAA--AAATT---AAATTTTG-A
*
6005103 GAAAATATGTTTGACTAAAAATTTTAAAAATTAATTTTTGA
1 -AAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTTGA
6005144 AAAATA
1 AAAATA
6005150 AAAATATGTG
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
40 32 0.43
41 1 0.01
42 7 0.09
45 8 0.11
46 1 0.01
47 26 0.35
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (40 bp):
AAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTTGA
Found at i:6005092 original size:87 final size:87
Alignment explanation
Indices: 6004990--6005149 Score: 311
Period size: 87 Copynumber: 1.8 Consensus size: 87
6004980 GTTATTTTCG
6004990 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTT
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTT
6005055 GAAAAATATGTTTGACTAAAAA
66 GAAAAATATGTTTGACTAAAAA
*
6005077 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAATTTTT
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTT
6005142 GAAAAATA
66 GAAAAATA
6005150 AAAATATGTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (87 bp):
TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTT
GAAAAATATGTTTGACTAAAAA
Found at i:6005109 original size:47 final size:47
Alignment explanation
Indices: 6004990--6005129 Score: 186
Period size: 47 Copynumber: 3.1 Consensus size: 47
6004980 GTTATTTTCG
6004990 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
*** **
6005037 TTTTAA--AAATT---AAATTTTG-A-AAAATATGTTTGACTAAAAA
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
6005077 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
6005124 TTTTAA
1 TTTTAA
6005130 AAATTAATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
40 26 0.34
41 1 0.01
42 8 0.11
45 8 0.11
46 1 0.01
47 32 0.42
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.40
Consensus pattern (47 bp):
TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
Found at i:6005821 original size:31 final size:31
Alignment explanation
Indices: 6005769--6005867 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
6005759 TTAGGTAAAC
* * *
6005769 TACACTTTTAGTCACTAAACTATAGGAAAGTT
1 TACA-TTTTAGTCAGTTAACTATAAGAAAGTT
* *
6005801 TTCATTTTAGTCAGTTAACTA-AAAAAAG-T
1 TACATTTTAGTCAGTTAACTATAAGAAAGTT
* * **
6005830 TACAATTTAATCAGTTAACTATTCGAAAGTT
1 TACATTTTAGTCAGTTAACTATAAGAAAGTT
*
6005861 TCCATTT
1 TACATTT
6005868 AAGTGACAAT
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
29 19 0.37
30 9 0.17
31 21 0.40
32 3 0.06
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (31 bp):
TACATTTTAGTCAGTTAACTATAAGAAAGTT
Found at i:6017342 original size:18 final size:17
Alignment explanation
Indices: 6017309--6017429 Score: 84
Period size: 20 Copynumber: 6.5 Consensus size: 17
6017299 ATGAAAATTG
6017309 ATATAAAATTATAAAAT
1 ATATAAAATTATAAAAT
*
6017326 ATATAATATTAATAAAAT
1 ATATAAAATT-ATAAAAT
6017344 ATATTTAAAATTTTATAAAA-
1 ATA--TAAAA--TTATAAAAT
*
6017364 AGTATAAAATCATAAAAAT
1 A-TATAAAATTAT-AAAAT
*
6017383 AATATAAAAAGTATTAAAATT
1 -ATAT-AAAATTA-TAAAA-T
6017404 GATATAAAATTATAAAA-
1 -ATATAAAATTATAAAAT
6017421 ATTATAAAA
1 A-TATAAAA
6017430 AAAATCGTAA
Statistics
Matches: 84, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
16 1 0.01
17 19 0.23
18 14 0.17
19 13 0.15
20 21 0.25
21 14 0.17
22 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (17 bp):
ATATAAAATTATAAAAT
Found at i:6017352 original size:29 final size:30
Alignment explanation
Indices: 6017289--6017354 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
6017279 TTTTAAAAAA
6017289 ATTAAAATATATGAAAATTGATATAAAATT
1 ATTAAAATATATGAAAATTGATATAAAATT
*
6017319 A-TAAAATATAT-AATATT-A-ATAAAATAT
1 ATTAAAATATATGAAAATTGATATAAAAT-T
6017346 ATTTAAAAT
1 A-TTAAAAT
6017355 TTTATAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 7 0.22
27 3 0.09
28 5 0.16
29 16 0.50
30 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
ATTAAAATATATGAAAATTGATATAAAATT
Found at i:6017354 original size:48 final size:46
Alignment explanation
Indices: 6017282--6017430 Score: 151
Period size: 48 Copynumber: 3.1 Consensus size: 46
6017272 TAAAAAATTT
*
6017282 TAAAAA-AATTAAAATATATGAAAATTGATATAAAATTATAAAAT-A
1 TAAAAATAA-TAAAATATATTAAAATTGATATAAAATTATAAAATCA
* * *
6017327 TATAATATTAATAAAATATATTTAAAATT-TTATAAAAAGTATAAAATCA
1 TA-AA-AATAATAAAATATA-TTAAAATTGATAT-AAAATTATAAAATCA
* *
6017376 TAAAAATAATATAAAAAGTATTAAAATTGATATAAAATTATAAAAATTA
1 TAAAAATAATA-AAATA-TATTAAAATTGATATAAAATTAT-AAAATCA
6017425 TAAAAA
1 TAAAAA
6017431 AAATCGTAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
45 2 0.02
46 2 0.02
47 19 0.22
48 42 0.49
49 20 0.24
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (46 bp):
TAAAAATAATAAAATATATTAAAATTGATATAAAATTATAAAATCA
Found at i:6017371 original size:9 final size:9
Alignment explanation
Indices: 6017274--6017430 Score: 79
Period size: 9 Copynumber: 16.6 Consensus size: 9
6017264 GTTTTCCATA
*
6017274 AAAAATTTT
1 AAAAATTAT
*
6017283 AAAAA-AAT
1 AAAAATTAT
*
6017291 TAAAATATAT
1 AAAAAT-TAT
*
6017301 GAAAATTGAT
1 AAAAATT-AT
6017311 ATAAAATTAT
1 A-AAAATTAT
6017321 -AAAA-TAT
1 AAAAATTAT
*
6017328 ATAATATTAAT
1 A-AAAATT-AT
*
6017339 AAAATATATTT
1 AAAA-AT-TAT
*
6017350 AAAATTTTAT
1 AAAA-ATTAT
*
6017360 AAAAAGTAT
1 AAAAATTAT
*
6017369 -AAAATCAT
1 AAAAATTAT
6017377 AAAAATAATAT
1 AAAAAT--TAT
*
6017388 AAAAAGTAT
1 AAAAATTAT
*
6017397 TAAAATTGAT
1 AAAAATT-AT
6017407 ATAAAATTAT
1 A-AAAATTAT
6017417 AAAAATTAT
1 AAAAATTAT
6017426 AAAAA
1 AAAAA
6017431 AAATCGTAAT
Statistics
Matches: 113, Mismatches: 20, Indels: 30
0.69 0.12 0.18
Matches are distributed among these distances:
7 3 0.03
8 15 0.13
9 38 0.34
10 25 0.22
11 31 0.27
12 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6017390 original size:28 final size:28
Alignment explanation
Indices: 6017356--6017429 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
6017346 ATTTAAAATT
6017356 TTATAAAAAGTATAAAA-TCATA-AAAA
1 TTATAAAAAGTATAAAATTCATATAAAA
*
6017382 TAATATAAAAAGTATTAAAATTGATATAAAA
1 T--TATAAAAAGTA-TAAAATTCATATAAAA
*
6017413 TTATAAAAATTATAAAA
1 TTATAAAAAGTATAAAA
6017430 AAAATCGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 1 0.02
28 16 0.39
29 15 0.37
30 4 0.10
31 5 0.12
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
TTATAAAAAGTATAAAATTCATATAAAA
Found at i:6017411 original size:11 final size:10
Alignment explanation
Indices: 6017291--6017430 Score: 95
Period size: 9 Copynumber: 14.5 Consensus size: 10
6017281 TTAAAAAAAT
6017291 TAAAA-TATA
1 TAAAATTATA
6017300 TGAAAATTGATA
1 T-AAAATT-ATA
6017312 TAAAA-T-TA
1 TAAAATTATA
6017320 TAAAA-TATA
1 TAAAATTATA
*
6017329 TAATATTA-A
1 TAAAATTATA
*
6017338 TAAAATATATT
1 TAAAAT-TATA
*
6017349 TAAAATTTTA
1 TAAAATTATA
6017359 TAAAA--AGTA
1 TAAAATTA-TA
*
6017368 TAAAATCATA
1 TAAAATTATA
*
6017378 -AAAATAATA
1 TAAAATTATA
*
6017387 TAAAAAGTAT-
1 T-AAAATTATA
6017397 TAAAATTGATA
1 TAAAATT-ATA
6017408 TAAAATTATA
1 TAAAATTATA
6017418 -AAAATTATA
1 TAAAATTATA
6017427 -AAAA
1 TAAAA
6017431 AAATCGTAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
8 8 0.07
9 46 0.43
10 24 0.22
11 25 0.23
12 4 0.04
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (10 bp):
TAAAATTATA
Done.