Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 19 of 207
Found at i:5645582 original size:18 final size:17
Alignment explanation
Indices: 5645561--5645616 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
5645551 ATATATAAAA
5645561 TATAAAAAAT-ATATATTT
1 TATAAAAAATCA-A-ATTT
*
5645579 TATAAAACATCAAATTT
1 TATAAAAAATCAAATTT
*
5645596 TATAAAATATCAAATATT
1 TATAAAAAATCAAAT-TT
5645614 TAT
1 TAT
5645617 GTATTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 18 0.53
18 15 0.44
19 1 0.03
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAAAAATCAAATTT
Found at i:5645595 original size:17 final size:17
Alignment explanation
Indices: 5645575--5645616 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
5645565 AAAAATATAT
5645575 ATTTTATAAAACATCAA
1 ATTTTATAAAACATCAA
*
5645592 ATTTTATAAAATATCAA
1 ATTTTATAAAACATCAA
5645609 ATATTTAT
1 AT-TTTAT
5645617 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTATAAAACATCAA
Found at i:5664268 original size:51 final size:50
Alignment explanation
Indices: 5664141--5664270 Score: 156
Period size: 50 Copynumber: 2.6 Consensus size: 50
5664131 TGATGGTCAG
* * * * *
5664141 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATGATAGGTCGC
1 GTGTGTAGTACTATGTGCAGGCTACTATGCGTACTCGAATGATAGATCCC
* *
5664191 ATGTGTAGTACTATGTGCAGGCTACTATGCGTAC-CGAATAGTTTCA-ATCCC
1 GTGTGTAGTACTATGTGCAGGCTACTATGCGTACTCGAAT-G-AT-AGATCCC
5664242 GTGTGTAGTACTATGTGCAGGCTACTATG
1 GTGTGTAGTACTATGTGCAGGCTACTATG
5664271 TGAAACGAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.06
50 32 0.46
51 32 0.46
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGCAGGCTACTATGCGTACTCGAATGATAGATCCC
Found at i:5664330 original size:45 final size:45
Alignment explanation
Indices: 5664279--5664366 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
5664269 TGTGAAACGA
* *
5664279 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
5664324 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
5664367 GAGTATCTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:5666734 original size:27 final size:27
Alignment explanation
Indices: 5666688--5666739 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5666678 GTATATATAT
5666688 ATTTAAGTCCATAATCTAACATTTTCC
1 ATTTAAGTCCATAATCTAACATTTTCC
* * *
5666715 ATTTAAGTCCTTAGTTTAACATTTT
1 ATTTAAGTCCATAATCTAACATTTT
5666740 TCTTGTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (27 bp):
ATTTAAGTCCATAATCTAACATTTTCC
Found at i:5668584 original size:21 final size:21
Alignment explanation
Indices: 5668558--5668605 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5668548 ATCTCTGAAT
*
5668558 AAATTGAATAAATTTTGAAGA
1 AAATTGAATAAATTCTGAAGA
* * *
5668579 ACATTGCATCAATTCTGAAGA
1 AAATTGAATAAATTCTGAAGA
5668600 AAATTG
1 AAATTG
5668606 TTCTTCAATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
AAATTGAATAAATTCTGAAGA
Found at i:5672942 original size:3 final size:3
Alignment explanation
Indices: 5672934--5672978 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
5672924 TTTTTGCATA
* * *
5672934 ATG ATG ATG GTG GTG GTG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
5672979 CCATTTGCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.27, C:0.00, G:0.40, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:5675781 original size:18 final size:17
Alignment explanation
Indices: 5675730--5675781 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
5675720 GCAACCCAAT
*
5675730 TTTATTTTATTTTCTTA
1 TTTATTTTATTTTTTTA
**
5675747 TTTATTTTAATAATTTTA
1 TTTATTTT-ATTTTTTTA
5675765 TTTATCTTTATTTTTTT
1 TTTAT-TTTATTTTTTT
5675782 TGTTCTAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 8 0.29
18 17 0.61
19 3 0.11
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTATTTTTTTA
Found at i:5689439 original size:15 final size:15
Alignment explanation
Indices: 5689419--5689447 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5689409 AAACAGGATA
5689419 TAAATGAGTAAATAG
1 TAAATGAGTAAATAG
5689434 TAAATGAGTAAATA
1 TAAATGAGTAAATA
5689448 ATAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (15 bp):
TAAATGAGTAAATAG
Found at i:5689452 original size:3 final size:3
Alignment explanation
Indices: 5689444--5689471 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5689434 TAAATGAGTA
5689444 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5689472 TAAGATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5690548 original size:16 final size:16
Alignment explanation
Indices: 5690527--5690557 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5690517 AGTAGGTGGC
*
5690527 GCGGCGTCAGAAGTCA
1 GCGGCGACAGAAGTCA
5690543 GCGGCGACAGAAGTC
1 GCGGCGACAGAAGTC
5690558 CAAAAGTCCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.26, G:0.39, T:0.10
Consensus pattern (16 bp):
GCGGCGACAGAAGTCA
Found at i:5691431 original size:50 final size:49
Alignment explanation
Indices: 5691355--5691538 Score: 215
Period size: 50 Copynumber: 3.7 Consensus size: 49
5691345 CTGTTCACTA
* * *
5691355 GGGAAGTAAGATTTGCTTTTGTAGCTTCAATCTATTTAACTGCAATGTC
1 GGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC
* ** ** *
5691404 GGGTAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
1 GGG-AAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC
* * *
5691454 AGAGAAGTAAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTC
1 -GGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC
* *
5691504 GGGGAAGCAAGACTCGTTGTTGTAGCTTCAATCTA
1 -GGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTA
5691539 AAATTTTTAT
Statistics
Matches: 109, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
49 3 0.03
50 104 0.95
51 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (49 bp):
GGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC
Found at i:5691530 original size:100 final size:100
Alignment explanation
Indices: 5691357--5691537 Score: 310
Period size: 100 Copynumber: 1.8 Consensus size: 100
5691347 GTTCACTAGG
* * *
5691357 GAAGTAAGATTTGCTTTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGTAAGCAAGATTCGCT
1 GAAGTAAGATTCGCTTTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGACTCGCT
5691422 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
*
5691457 GAAGTAAGATTCGCTGTTT-TAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGACTCGT
1 GAAGTAAGATTCGCT-TTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGACTCGC
5691521 TGTTGTAGCTTCAATCT
65 TGTTGTAGCTTCAATCT
5691538 AAAATTTTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
100 73 0.96
101 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (100 bp):
GAAGTAAGATTCGCTTTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGACTCGCT
GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
Found at i:5703180 original size:43 final size:44
Alignment explanation
Indices: 5703081--5703187 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 44
5703071 GTGGAATAGA
5703081 TTATCT-TCTTGAAGTTGCAGTGGAGTAGATTAAAGACAACAATC
1 TTATCTCTC-TGAAGTTGCAGTGGAGTAGATTAAAGACAACAATC
* * * ***
5703125 CTATCTCGCTGAAGTTGCAGTGG-GTGGATTAAA-ACCTTAGATC
1 TTATCTCTCTGAAGTTGCAGTGGAGTAGATTAAAGACAACA-ATC
5703168 TTATCTCTCTGAAGTTGCAG
1 TTATCTCTCTGAAGTTGCAG
5703188 AGAGCAGATC
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 3 0.06
43 30 0.57
44 19 0.36
45 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (44 bp):
TTATCTCTCTGAAGTTGCAGTGGAGTAGATTAAAGACAACAATC
Found at i:5704602 original size:29 final size:30
Alignment explanation
Indices: 5704544--5704613 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
5704534 TTACAGTTCA
**
5704544 AATTAG-TTTTTT-TTCTTTATTTTTAATT
1 AATTAGTTTTTTTATTCTTTATTCATAATT
*
5704572 AATTAGTTTTTTTATTCTTT-TTCATATTT
1 AATTAGTTTTTTTATTCTTTATTCATAATT
5704601 AATTA-TTTTTTTA
1 AATTAGTTTTTTTA
5704614 AAATATATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 14 0.38
29 17 0.46
30 6 0.16
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (30 bp):
AATTAGTTTTTTTATTCTTTATTCATAATT
Found at i:5715842 original size:26 final size:25
Alignment explanation
Indices: 5715788--5715842 Score: 58
Period size: 26 Copynumber: 2.1 Consensus size: 25
5715778 AGTTTTTCCC
* *
5715788 TTTTGAAATAGGGAAAATGTCATCCT
1 TTTTGAAATAAGGAAAATATCAT-CT
5715814 TTTTGAAACTAAGGAATAATATCAT-T
1 TTTTGAAA-TAAGGAA-AATATCATCT
5715840 TTT
1 TTT
5715843 GTTATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 12 0.48
27 6 0.24
28 7 0.28
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (25 bp):
TTTTGAAATAAGGAAAATATCATCT
Found at i:5720192 original size:100 final size:100
Alignment explanation
Indices: 5720019--5720226 Score: 407
Period size: 100 Copynumber: 2.1 Consensus size: 100
5720009 TTCAGTTTTC
*
5720019 ACAAATTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTGTA
1 ACAAACTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTGTA
5720084 GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
66 GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
5720119 ACAAACTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTGTA
1 ACAAACTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTGTA
5720184 GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
66 GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
5720219 ACAAACTT
1 ACAAACTT
5720227 ACAGCGAACA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 107 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (100 bp):
ACAAACTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTGTA
GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
Found at i:5722287 original size:25 final size:25
Alignment explanation
Indices: 5722259--5722318 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
5722249 GCTCGCAAGG
5722259 GCATCCCGTTAATTAGCTCTCATGA
1 GCATCCCGTTAATTAGCTCTCATGA
* * * * *
5722284 GCATTCTGTTATTTGGCTCTCTTGA
1 GCATCCCGTTAATTAGCTCTCATGA
*
5722309 GCTTCCCGTT
1 GCATCCCGTT
5722319 TATGGCTCGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (25 bp):
GCATCCCGTTAATTAGCTCTCATGA
Found at i:5722349 original size:49 final size:48
Alignment explanation
Indices: 5722274--5722511 Score: 162
Period size: 49 Copynumber: 4.8 Consensus size: 48
5722264 CCGTTAATTA
* * * * *
5722274 GCTCTCATGAGCATTCT-GTTATTTGGCTCTCTTGAGCTTCCCGTTTATG
1 GCTCT-ATGAGC-TTCTCGATAATTGGCTCTCATGAGCTTCCCGATAATG
***
5722323 GCTCGTATGAGCTTCTCGATAATTGGCTCTC-TGGAGCTTCTTAATAATTG
1 GCTC-TATGAGCTTCTCGATAATTGGCTCTCAT-GAGCTTCCCGATAA-TG
* * * *
5722373 GCTCTCATGAGCTT-TCTGATAATAGGATCTCGTGAGCTTCCTGATTAATG
1 GCTCT-ATGAGCTTCTC-GATAATTGGCTCTCATGAGCTTCCCGA-TAATG
* * * * * *
5722423 GCTCTCTGAAGCTTCCCAAT-ATTGGCTCGCATGAGCTTCTCGATTATG
1 GCTCTATG-AGCTTCTCGATAATTGGCTCTCATGAGCTTCCCGATAATG
* *
5722471 GCTCTTATGAGCTTCTCGTTACA-TGGCTCACATGAGCTTCC
1 GCTC-TATGAGCTTCTCGATA-ATTGGCTCTCATGAGCTTCC
5722512 TGTTATAAGG
Statistics
Matches: 149, Mismatches: 27, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
48 21 0.14
49 72 0.48
50 51 0.34
51 5 0.03
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (48 bp):
GCTCTATGAGCTTCTCGATAATTGGCTCTCATGAGCTTCCCGATAATG
Found at i:5722359 original size:25 final size:24
Alignment explanation
Indices: 5722268--5722510 Score: 133
Period size: 25 Copynumber: 9.8 Consensus size: 24
5722258 GGCATCCCGT
* *
5722268 TAATTAGCTCTCATGAGCATTCT-GT
1 TAATTGGCTCTC-TGAGC-TTCTCGA
* * *
5722293 TATTTGGCTCTCTTGAGCTTCCCGT
1 TAATTGGCTCTC-TGAGCTTCTCGA
* *
5722318 TTA-TGGCTCGTATGAGCTTCTCGA
1 TAATTGGCTC-TCTGAGCTTCTCGA
**
5722342 TAATTGGCTCTCTGGAGCTTCTTAA
1 TAATTGGCTCTCT-GAGCTTCTCGA
5722367 TAATTGGCTCTCATGAGCTT-TCTGA
1 TAATTGGCTCTC-TGAGCTTCTC-GA
* *
5722392 TAATAGGATCTCGTGAGCTTC-CTGA
1 TAATTGGCTCTC-TGAGCTTCTC-GA
* *
5722417 TTAA-TGGCTCTCTGAAGCTTCCCAA
1 -TAATTGGCTCTCTG-AGCTTCTCGA
*
5722442 T-ATTGGCTCGCATGAGCTTCTCGA
1 TAATTGGCTCTC-TGAGCTTCTCGA
* * *
5722466 TTA-TGGCTCTTATGAGCTTCTCGT
1 TAATTGGCTC-TCTGAGCTTCTCGA
*
5722490 TACA-TGGCTCACATGAGCTTC
1 TA-ATTGGCTCTC-TGAGCTTC
5722511 CTGTTATAAG
Statistics
Matches: 172, Mismatches: 30, Indels: 32
0.74 0.13 0.14
Matches are distributed among these distances:
23 1 0.01
24 61 0.35
25 105 0.61
26 5 0.03
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (24 bp):
TAATTGGCTCTCTGAGCTTCTCGA
Found at i:5722447 original size:99 final size:99
Alignment explanation
Indices: 5722268--5722484 Score: 226
Period size: 99 Copynumber: 2.2 Consensus size: 99
5722258 GGCATCCCGT
* * * * * * * *
5722268 TAATTAGCTCTCATGAGCATTCTGTTATTTGGCTCTCTTGAGCTTCCCGTTTATGGCTCGTATGA
1 TAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCCGTTAATGGCTCGTATGA
* * * *
5722333 GCTTCTCGATAATTGGCTCTC-TGGAGCTTCTTAA
66 GCTTCCCAATAATTGGCTCGCAT-GAGCTTCTCAA
* *
5722367 TAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCTGATTAATGGCTC-TCTG
1 TAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCCG-TTAATGGCTCGTATG
*
5722431 AAGCTTCCCAAT-ATTGGCTCGCATGAGCTTCTCGA
65 -AGCTTCCCAATAATTGGCTCGCATGAGCTTCTCAA
* *
5722466 TTA-TGGCTCTTATGAGCTT
1 TAATTGGCTCTCATGAGCTT
5722485 CTCGTTACAT
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
98 15 0.15
99 64 0.65
100 19 0.19
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (99 bp):
TAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCCGTTAATGGCTCGTATGA
GCTTCCCAATAATTGGCTCGCATGAGCTTCTCAA
Found at i:5722516 original size:25 final size:25
Alignment explanation
Indices: 5722445--5722559 Score: 85
Period size: 25 Copynumber: 4.6 Consensus size: 25
5722435 TTCCCAATAT
*
5722445 TGGCTCGCATGAGCTTCTCGATT--A
1 TGGCTCACATGAGCTTCTCG-TTACA
**
5722469 TGGCTCTTATGAGCTTCTCGTTACA
1 TGGCTCACATGAGCTTCTCGTTACA
*
5722494 TGGCTCACATGAGCTTC-CTGTTATA
1 TGGCTCACATGAGCTTCTC-GTTACA
* * * * * *
5722519 AGGCTCAAAAGAGATACTCGTTTATA
1 TGGCTCACATGAGCTTCTCG-TTACA
5722545 T-GCTCACATGAGCTT
1 TGGCTCACATGAGCTT
5722560 TCCTGAATAT
Statistics
Matches: 71, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
23 2 0.03
24 19 0.27
25 44 0.62
26 6 0.08
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCTCGTTACA
Found at i:5737054 original size:3 final size:3
Alignment explanation
Indices: 5737046--5737099 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
5737036 GTTCAGGTCA
5737046 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5737094 ATT ATT
1 ATT ATT
5737100 CAATAATTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5737403 original size:42 final size:42
Alignment explanation
Indices: 5737293--5737410 Score: 155
Period size: 42 Copynumber: 2.8 Consensus size: 42
5737283 GAAAAACGCT
* **
5737293 GCTAAAGAACATGATTTTTAGCGGCGCATTTTTCTAAGCACA
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCACA
* * * *
5737335 GCTAAAGAATATGATCTTTAGAGGCGTTTTTTTCTAAGCGCC
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCACA
*
5737377 GCTAAAGAACATGACCTTTAGCGGCGTTTATTTT
1 GCTAAAGAACATGATCTTTAGCGGCGTTT-TTTT
5737411 TGTAAACGCT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (42 bp):
GCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCACA
Found at i:5742579 original size:29 final size:28
Alignment explanation
Indices: 5742547--5742612 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
5742537 TTAAACCCAG
* *
5742547 ATTTTAAAATATGAAAATAGAAAAACTAA
1 ATTTTAAAA-ATAAAAATACAAAAACTAA
**
5742576 ATTTCTAAAAATAAAAATACAAGTACTAA
1 ATTT-TAAAAATAAAAATACAAAAACTAA
*
5742605 ATTCTAAA
1 ATTTTAAA
5742613 TTTTCGAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.13
29 22 0.71
30 5 0.16
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.29
Consensus pattern (28 bp):
ATTTTAAAAATAAAAATACAAAAACTAA
Found at i:5743387 original size:16 final size:15
Alignment explanation
Indices: 5743350--5743379 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5743340 GAAATAGTTT
5743350 CAAAA-AATAAACTC
1 CAAAACAATAAACTC
5743364 CAAAACAATAAACTC
1 CAAAACAATAAACTC
5743379 C
1 C
5743380 CTAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (15 bp):
CAAAACAATAAACTC
Found at i:5746507 original size:30 final size:30
Alignment explanation
Indices: 5746471--5746529 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
5746461 ATTTAAAGAG
*
5746471 ATTGCTTGCAAGTCAAGTTAAACAAAATAT
1 ATTGCTTACAAGTCAAGTTAAACAAAATAT
5746501 ATTGCTTACAAGTCAAGTTAAACAAAATA
1 ATTGCTTACAAGTCAAGTTAAACAAAATA
5746530 CATTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (30 bp):
ATTGCTTACAAGTCAAGTTAAACAAAATAT
Found at i:5755866 original size:21 final size:20
Alignment explanation
Indices: 5755841--5755888 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
5755831 TCTAGGTCAA
*
5755841 TTTAGGATCAAGGGTTAAGGG
1 TTTAGG-TCAAGGGTTAAAGG
**
5755862 TTTAGTGTTTAGGGTTAAAGG
1 TTTAG-GTCAAGGGTTAAAGG
5755883 TTTAGG
1 TTTAGG
5755889 GTTATACCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.35, T:0.38
Consensus pattern (20 bp):
TTTAGGTCAAGGGTTAAAGG
Found at i:5755972 original size:21 final size:21
Alignment explanation
Indices: 5755946--5755996 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
5755936 TACAATTTAA
5755946 GGTTTAGGGGATAAGGGTTGT
1 GGTTTAGGGGATAAGGGTTGT
5755967 GGTTTAGGGGATAAGGGTTGT
1 GGTTTAGGGGATAAGGGTTGT
5755988 GGTTTAGGG
1 GGTTTAGGG
5755997 TCTAGGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.33
Consensus pattern (21 bp):
GGTTTAGGGGATAAGGGTTGT
Found at i:5757445 original size:22 final size:22
Alignment explanation
Indices: 5757418--5757464 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5757408 GTCTTTCTAC
5757418 TTAGGTTTAATCAGTATAAAAT
1 TTAGGTTTAATCAGTATAAAAT
*
5757440 TTAGGTTTAATTAGTATAAAAT
1 TTAGGTTTAATCAGTATAAAAT
5757462 TTA
1 TTA
5757465 AGAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (22 bp):
TTAGGTTTAATCAGTATAAAAT
Found at i:5758710 original size:18 final size:18
Alignment explanation
Indices: 5758666--5758710 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5758656 AAATAAATTT
5758666 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
*
5758684 TAAAATATATAACTTACA
1 TAAATTATATAACTTACA
*
5758702 TAACTTATA
1 TAAATTATA
5758711 AATATTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATTATATAACTTACA
Found at i:5758752 original size:17 final size:18
Alignment explanation
Indices: 5758732--5758765 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5758722 ACATTTTTAA
5758732 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
5758749 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
5758766 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:5758936 original size:9 final size:9
Alignment explanation
Indices: 5758906--5759296 Score: 370
Period size: 9 Copynumber: 43.2 Consensus size: 9
5758896 TTTAAATTAT
5758906 ATAACTTAC
1 ATAACTTAC
* *
5758915 ATAAATTAT
1 ATAACTTAC
5758924 ATAACTTAC
1 ATAACTTAC
5758933 ATAACTTAC
1 ATAACTTAC
*
5758942 ATACCTTAC
1 ATAACTTAC
* *
5758951 ATAAATTAA
1 ATAACTTAC
5758960 ATAACTTAC
1 ATAACTTAC
5758969 ATAACTTAC
1 ATAACTTAC
*
5758978 ATAACTTAA
1 ATAACTTAC
5758987 ATAACTTAC
1 ATAACTTAC
5758996 ATAA--TAC
1 ATAACTTAC
*
5759003 ATAACCTAC
1 ATAACTTAC
* *
5759012 CTAACTTAA
1 ATAACTTAC
* *
5759021 ATTATTTAC
1 ATAACTTAC
5759030 ATAA--TAC
1 ATAACTTAC
5759037 ATAACTTAGTAC
1 ATAAC-T--TAC
*
5759049 ATAATTTAC
1 ATAACTTAC
5759058 ATAA--TAC
1 ATAACTTAC
5759065 ATAACTTATAC
1 ATAAC-T-TAC
5759076 ATAACTTAC
1 ATAACTTAC
** *
5759085 ATATTTTTTTC
1 ATA--ACTTAC
5759096 -TAAATTGCTTAC
1 AT-AA---CTTAC
* *
5759108 ATAAATTAT
1 ATAACTTAC
5759117 ATAACTTAC
1 ATAACTTAC
5759126 ATAACTTAC
1 ATAACTTAC
* *
5759135 ATAAATTAA
1 ATAACTTAC
5759144 ATAACTTAC
1 ATAACTTAC
5759153 ATAACTTAC
1 ATAACTTAC
*
5759162 ATAACATAC
1 ATAACTTAC
*
5759171 ATAACTTAA
1 ATAACTTAC
5759180 ATAACTTAC
1 ATAACTTAC
5759189 ATAACTTAC
1 ATAACTTAC
*
5759198 ATATCTTAC
1 ATAACTTAC
5759207 ATAACTTAC
1 ATAACTTAC
* *
5759216 ATAAATTAA
1 ATAACTTAC
5759225 ATAACTTAC
1 ATAACTTAC
5759234 ATAACTTAC
1 ATAACTTAC
*
5759243 ATAAATTAC
1 ATAACTTAC
5759252 ATAACTTAC
1 ATAACTTAC
5759261 ATAACTTAC
1 ATAACTTAC
5759270 ATAA--TAC
1 ATAACTTAC
5759277 ATAACCTT-C
1 ATAA-CTTAC
*
5759286 CTAACTTAC
1 ATAACTTAC
5759295 AT
1 AT
5759297 TATTGTCTAA
Statistics
Matches: 311, Mismatches: 49, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
7 28 0.09
8 3 0.01
9 251 0.81
10 3 0.01
11 13 0.04
12 12 0.04
13 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:5764983 original size:23 final size:23
Alignment explanation
Indices: 5764957--5765054 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
5764947 ATAAGTGCCA
5764957 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5764980 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5765003 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
5765025 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5765048 CACTGAT
1 CACTGAT
5765055 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5765022 original size:45 final size:45
Alignment explanation
Indices: 5764964--5765052 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
5764954 CCACACTGAT
* *
5764964 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
5765009 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
5765053 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:5767431 original size:21 final size:21
Alignment explanation
Indices: 5767405--5767452 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5767395 CAACAACTTA
*
5767405 AAGCAGAGG-CGGCAGCGAGTG
1 AAGCAGAGGTC-GCAGCGAGAG
5767426 AAGCAGAGGTCGCAGCGAGAG
1 AAGCAGAGGTCGCAGCGAGAG
5767447 AAGCAG
1 AAGCAG
5767453 CGATAGAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGTCGCAGCGAGAG
Found at i:5767916 original size:43 final size:42
Alignment explanation
Indices: 5767869--5767963 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
5767859 CATACCAAAC
* *
5767869 AGTGGCGTTTGTGAAATAAGCGCCGCTAAAGAACACTATTTTT
1 AGTGGCGTTTGTG-AACAAGCGCCGCTAAAGAACACTACTTTT
* * *
5767912 AGTGGCATTTTTGAACAAGCGCCGCTAAAGAACATTACTTTT
1 AGTGGCGTTTGTGAACAAGCGCCGCTAAAGAACACTACTTTT
*
5767954 AGAGGCGTTT
1 AGTGGCGTTT
5767964 TATTCCAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 34 0.76
43 11 0.24
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (42 bp):
AGTGGCGTTTGTGAACAAGCGCCGCTAAAGAACACTACTTTT
Found at i:5768007 original size:43 final size:43
Alignment explanation
Indices: 5767928--5768093 Score: 167
Period size: 43 Copynumber: 3.9 Consensus size: 43
5767918 ATTTTTGAAC
* * * * *
5767928 AAGCGCCGCTAAAGAACATTACTTTTAGAGGCGTTTTATTCCA
1 AAGCGCCGCTAAAGAACATGACATTTCGCGGCGTTTTATTCCT
* * * *
5767971 AAGCACCGCTAAAGAACATGAGATTTCGCGGTGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGACATTTCGCGGCGTTTTATTCCT
*
5768014 AAGCGTCGCTAAAGAACATGATC-TTTCGCGGCG-TTTATTTCCT
1 AAGCGCCGCTAAAGAACATGA-CATTTCGCGGCGTTTTA-TTCCT
* * *
5768057 TAGCGCGGCTAAAGAACATGATC-TTTAGCGGCGTTTT
1 AAGCGCCGCTAAAGAACATGA-CATTTCGCGGCGTTTT
5768094 TTTGTGTAAG
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
42 3 0.03
43 96 0.94
44 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGACATTTCGCGGCGTTTTATTCCT
Found at i:5768047 original size:86 final size:86
Alignment explanation
Indices: 5767928--5768096 Score: 198
Period size: 86 Copynumber: 2.0 Consensus size: 86
5767918 ATTTTTGAAC
*
5767928 AAGCGCCGCTAAAGAACATTACTTTTAGAGGCGTTT-TATTCCAAAGCACCGCTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGACTTTTAGAGGCGTTTAT-TTCCAAAGCACCGCTAAAGAACATGA
* *
5767992 GATTTCGCGGTGTTTTTTTCCT
65 GATTTAGCGGCGTTTTTTTCCT
* * * ** * *
5768014 AAGCGTCGCTAAAGAACATGA-TCTTTCGCGGCGTTTATTTCCTTAGCGCGGCTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGACT-TTTAGAGGCGTTTATTTCCAAAGCACCGCTAAAGAACATGA
**
5768078 TCTTTAGCGGCGTTTTTTT
65 GATTTAGCGGCGTTTTTTT
5768097 GTGTAAGAAC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 1 0.01
86 67 0.97
87 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (86 bp):
AAGCGCCGCTAAAGAACATGACTTTTAGAGGCGTTTATTTCCAAAGCACCGCTAAAGAACATGAG
ATTTAGCGGCGTTTTTTTCCT
Found at i:5770044 original size:17 final size:17
Alignment explanation
Indices: 5770024--5770059 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5770014 GATTGTATTG
5770024 ATTTACATGTTGTACGC
1 ATTTACATGTTGTACGC
*
5770041 ATTTACATGTTGTATGC
1 ATTTACATGTTGTACGC
5770058 AT
1 AT
5770060 CAAGCCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (17 bp):
ATTTACATGTTGTACGC
Found at i:5785080 original size:18 final size:18
Alignment explanation
Indices: 5785057--5785092 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5785047 TTTTTTATTC
*
5785057 TTTTTTTAAATAAAATTA
1 TTTTTTAAAATAAAATTA
*
5785075 TTTTTTAAAATGAAATTA
1 TTTTTTAAAATAAAATTA
5785093 GTGACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTTTAAAATAAAATTA
Found at i:5797832 original size:30 final size:31
Alignment explanation
Indices: 5797793--5797852 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5797783 GGAGGTGAGA
*
5797793 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
5797824 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
5797853 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:5798080 original size:9 final size:9
Alignment explanation
Indices: 5798066--5798102 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
5798056 TATAGTTTGA
5798066 TATTCGAAT
1 TATTCGAAT
5798075 TATTCGAAT
1 TATTCGAAT
5798084 TATTC-AAGT
1 TATTCGAA-T
5798093 TATTCGAAT
1 TATTCGAAT
5798102 T
1 T
5798103 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5802009 original size:21 final size:21
Alignment explanation
Indices: 5801946--5802011 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
5801936 CTCTGTTCTA
* *
5801946 CTTCTCTCGCTGCAGCCTCTA
1 CTTCCCTCGCTGCAGCCTCTG
*
5801967 CTTCCCTCGCTGCAGCCGCTG
1 CTTCCCTCGCTGCAGCCTCTG
*
5801988 CTTCCCTCGCTGCCGCCTCTG
1 CTTCCCTCGCTGCAGCCTCTG
5802009 CTT
1 CTT
5802012 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.05, C:0.47, G:0.18, T:0.30
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCTG
Found at i:5806241 original size:16 final size:16
Alignment explanation
Indices: 5806182--5806242 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
5806172 CGATTTTTCT
* *
5806182 GACGGAAGAGGAGTGC
1 GACGGTAGACGAGTGC
**
5806198 GACGGTAGA-GCCCTGC
1 GACGGTAGACG-AGTGC
**
5806214 GACGGTCCACGAGTGC
1 GACGGTAGACGAGTGC
5806230 GACGGTAGACGAG
1 GACGGTAGACGAG
5806243 CGCCAGCAGA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.43, T:0.10
Consensus pattern (16 bp):
GACGGTAGACGAGTGC
Found at i:5806788 original size:28 final size:28
Alignment explanation
Indices: 5806722--5806776 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5806712 AATATATAGT
* *
5806722 ACTAATAATTATAAATTTTAGTGTTTTC
1 ACTAATATTTTTAAATTTTAGTGTTTTC
5806750 ACTAATATTTTTAAATTTTAGTGTTTT
1 ACTAATATTTTTAAATTTTAGTGTTTT
5806777 TATTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (28 bp):
ACTAATATTTTTAAATTTTAGTGTTTTC
Found at i:5807900 original size:23 final size:23
Alignment explanation
Indices: 5807857--5807900 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5807847 CCTAAATTAT
* *
5807857 ACATATTTTACAATTACATAAGA
1 ACATATTTTAAAATTAAATAAGA
5807880 ACATA-TTTAAAATATAAATAA
1 ACATATTTTAAAAT-TAAATAA
5807901 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
ACATATTTTAAAATTAAATAAGA
Found at i:5808856 original size:113 final size:114
Alignment explanation
Indices: 5808603--5809061 Score: 594
Period size: 113 Copynumber: 4.1 Consensus size: 114
5808593 ATTAAGGTAA
*
5808603 AAGGCCATCGAAGGCCACTAAACGA---C---GTATTTTATTTTTTGCGGCGTTTTTCC-AGAAA
1 AAGGCCACCGAAGGCCACTAAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTTTTCCTA-AAA
* * *
5808661 ACGTCGCTAAAAA-AAAGACCATTAGCGGCGCTATACCAAAAACGCCACT
65 ACGCCGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACT
* ** * * * *
5808710 AGGGCCACTAAAGGCCCCTAAACGATGCTGTTGTATTTTATTTTTTGCGGCGTTTATCCTAAAAA
1 AAGGCCACCGAAGGCCACTAAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTTTTCCTAAAAA
* * *
5808775 TGCCGCTAAAAACACAGACCATTAGCGGCGCCAGACCAAAAATGCCACT
66 CGCCGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACT
* * *
5808824 AACGCCACCGTA-GCCACTAAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAA
1 AAGGCCACCGAAGGCCACTAAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTTTTCCTAAAAA
*
5808888 TGCCGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACT
66 CGCCGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACT
* * *
5808937 AAGGCCACCGAAGGCCACTAAACGACGCCATTGTATTTTATTTTTTGCGGCGTTTTTTTTTCTGA
1 AAGGCCACCGAAGGCCACTAAACGACGCCGTTGTATTTTATTTTTTGCGGCG---TTTTTCCTAA
* * * *
5809002 AAGCGCCGCTAAAAACACAGACCATTAGCGGCACAAGACAAAAAACGCCACT
63 AAACGCCGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACT
5809054 AAGGCCAC
1 AAGGCCAC
5809062 TAAACGACGC
Statistics
Matches: 304, Mismatches: 36, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
107 20 0.07
113 144 0.47
114 78 0.26
117 62 0.20
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (114 bp):
AAGGCCACCGAAGGCCACTAAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTTTTCCTAAAAA
CGCCGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACT
Found at i:5809319 original size:84 final size:84
Alignment explanation
Indices: 5809197--5809446 Score: 425
Period size: 84 Copynumber: 3.0 Consensus size: 84
5809187 TTAAAACGCC
*
5809197 GCTAAAAACACAGACCATTAGCGGTGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
1 GCTAAAAACACAGACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
5809262 AACGATGCCGTTGTATTTT
66 AACGATGCCGTTGTATTTT
*
5809281 GCTAAAAACAC-GAACCATTAGCGGCACTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACT
1 GCTAAAAACACAG-ACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACT
*
5809345 AAACAATGCCGTTGTATTTT
65 AAACGATGCCGTTGTATTTT
*
5809365 GCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCA-CGAA-GCCACTA
1 GCTAAAAACACAGACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
*
5809428 AACGACGCCGTTGTATTTT
66 AACGATGCCGTTGTATTTT
5809447 ATTTTTTGCG
Statistics
Matches: 157, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
82 24 0.15
83 5 0.03
84 127 0.81
85 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (84 bp):
GCTAAAAACACAGACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
AACGATGCCGTTGTATTTT
Found at i:5809321 original size:198 final size:191
Alignment explanation
Indices: 5808892--5809364 Score: 693
Period size: 198 Copynumber: 2.4 Consensus size: 191
5808882 TAAAAATGCC
5808892 GCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTA
1 GCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTA
* *
5808957 AACGACGCCATTGTATTTTATTTTTTGCGGCGTTTTTTTTTCTGAAAGCGCCGCTAAAAACACAG
66 AACGACGCCGTTGTATTTTATTTTTTGCGGCGTTTTTTTTTCTGAAAACGCCGCTAAAAACACAG
5809022 ACCATTAGCGGCACAAGACAAAAAACGCCACTAAGGCCACTAAACGACGCCGTTGTATTTT
131 ACCATTAGCGGCACAAGACAAAAAACGCCACTAAGGCCACTAAACGACGCCGTTGTATTTT
**
5809083 GCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGTTCACCGAAGGCCACTA
1 GCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTA
* *
5809148 AACGACGCCGTTGTATTTTATTTTTTGTGGTG-TTTTTTTT-T-AAAACGCCGCTAAAAACACAG
66 AACGACGCCGTTGTATTTTATTTTTTGCGGCGTTTTTTTTTCTGAAAACGCCGCTAAAAACACAG
** * *
5809210 ACCATTAGCGGTGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGATGCCGTTG
131 ACCATTAGCGGCACAAGACAAAAAACGCCACT----------AAGGCCACTAAACGACGCCGTTG
5809275 TATTTT
186 TATTTT
* *
5809281 GCTAAAAACAC-GAACCATTAGCGGCACTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACT
1 GCTAAAAACACAG-ACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACT
* *
5809345 AAACAATGCCGTTGTATTTT
65 AAACGACGCCGTTGTATTTT
5809365 GCTAAAAACA
Statistics
Matches: 255, Mismatches: 16, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
188 49 0.19
189 1 0.00
190 8 0.03
191 92 0.36
197 1 0.00
198 104 0.41
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (191 bp):
GCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTA
AACGACGCCGTTGTATTTTATTTTTTGCGGCGTTTTTTTTTCTGAAAACGCCGCTAAAAACACAG
ACCATTAGCGGCACAAGACAAAAAACGCCACTAAGGCCACTAAACGACGCCGTTGTATTTT
Found at i:5809489 original size:40 final size:39
Alignment explanation
Indices: 5809445--5809544 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
5809435 CCGTTGTATT
5809445 TTATTTTTTGCGGCGTTTTTCTTGGAAACGCCGCTAATGC
1 TTATTTTTTGCGGCGTTTTTCTT-GAAACGCCGCTAATGC
* * * * *
5809485 TTATTTTTTGCGGCGATTTCCTTTAAGCGTCGCTAATGC
1 TTATTTTTTGCGGCGTTTTTCTTGAAACGCCGCTAATGC
* **
5809524 TCGATTTTTACCGGCGTTTTT
1 T-TATTTTTTGCGGCGTTTTT
5809545 TGTATAAACG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
39 14 0.29
40 35 0.71
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (39 bp):
TTATTTTTTGCGGCGTTTTTCTTGAAACGCCGCTAATGC
Found at i:5811860 original size:12 final size:12
Alignment explanation
Indices: 5811845--5811880 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
5811835 GAAAAATAAT
5811845 AATATAAATTTA
1 AATATAAATTTA
5811857 AATATAAAATTTA
1 AATAT-AAATTTA
*
5811870 AATTTAAATTT
1 AATATAAATTT
5811881 TTTCATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATATAAATTTA
Found at i:5811868 original size:13 final size:13
Alignment explanation
Indices: 5811845--5811877 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5811835 GAAAAATAAT
5811845 AATAT-AAATTTA
1 AATATAAAATTTA
5811857 AATATAAAATTTA
1 AATATAAAATTTA
*
5811870 AATTTAAA
1 AATATAAA
5811878 TTTTTTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATATAAAATTTA
Found at i:5812025 original size:22 final size:22
Alignment explanation
Indices: 5811970--5812033 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
5811960 TTTTATATTT
*
5811970 ATTTAACCAAATATT-TTAATAA
1 ATTTAA-CAAATCTTATTAATAA
* *
5811992 A-TTAA-AATTCTTATTTATAA
1 ATTTAACAAATCTTATTAATAA
*
5812012 ATTTAACAAATCTTATGAATAA
1 ATTTAACAAATCTTATTAATAA
5812034 TAGAAATACG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 8 0.24
22 13 0.39
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTTAACAAATCTTATTAATAA
Found at i:5818034 original size:6 final size:6
Alignment explanation
Indices: 5818019--5818058 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
5818009 GGGCTTCACT
*
5818019 TCTTCG TCTTCC TCTTCC TCTTCC TCTTTCC -CTTCC TCTT
1 TCTTCC TCTTCC TCTTCC TCTTCC TC-TTCC TCTTCC TCTT
5818059 GTTCTACTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 4 0.13
6 23 0.74
7 4 0.13
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (6 bp):
TCTTCC
Found at i:5821090 original size:2 final size:2
Alignment explanation
Indices: 5821083--5821119 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5821073 GTAAACAGCC
5821083 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5821120 ATGAGTGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5829017 original size:17 final size:18
Alignment explanation
Indices: 5828984--5829019 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5828974 TTTATAAAAT
5828984 ATAAAATATATTAATTTA
1 ATAAAATATATTAATTTA
*
5829002 ATAAAA-ATATTTATTTA
1 ATAAAATATATTAATTTA
5829019 A
1 A
5829020 ATTAGTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAAATATATTAATTTA
Found at i:5830774 original size:40 final size:38
Alignment explanation
Indices: 5830728--5830863 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 38
5830718 CGTTTGAATT
*
5830728 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCG-TTTT-C
* * * *
5830768 AAAAACGCCGCTAAAGATCGAGCATTAGCGGTGAATTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCG--TTTTC
* * *
5830808 GAAAACGCCGCCAAAAAT-AAGCATTAGTGGCGTTTTCC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTT-C
*
5830846 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
5830864 CCTAAGTCCA
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
37 4 0.05
38 4 0.05
39 22 0.28
40 44 0.56
41 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTC
Found at i:5830964 original size:41 final size:42
Alignment explanation
Indices: 5830903--5831088 Score: 220
Period size: 41 Copynumber: 4.5 Consensus size: 42
5830893 TTTTAGGGCA
5830903 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTG-CC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTGACC
* * ** *
5830944 TTTAGCGGCTTTTTTAAAAAATTGCCGCTAATGCTTCTGACC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTGACC
* * * * *
5830986 TTTAGCGACGTTATTGATAAAGCGCCGGTAATGCTCGTG-CC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTGACC
* *
5831027 TTTAGTGGCGTTTCTGAAAAAAGCGCCGCTAATG---CTGACC
1 TTTAGCGGCGTTTTTG-AAAAAGCGCCGCTAATGCTCCTGACC
5831067 TTTAGCGGCGTTTTTGAAAAAG
1 TTTAGCGGCGTTTTTGAAAAAG
5831089 TGTTGCTAAT
Statistics
Matches: 118, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
39 8 0.07
40 16 0.14
41 48 0.41
42 46 0.39
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTGACC
Found at i:5831047 original size:83 final size:81
Alignment explanation
Indices: 5830903--5831088 Score: 239
Period size: 83 Copynumber: 2.3 Consensus size: 81
5830893 TTTTAGGGCA
* * **
5830903 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTGCCTTTAGCGGC-TTTTTTAAAAAATT
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTGCCTTTAGCGGCGTTTCTAAAAAAAGC
5830967 GCCGCTAATGCTTCTGACC
66 GCCGCTAATG---CTGACC
* * * * * * *
5830986 TTTAGCGACGTTATTGATAAAGCGCCGGTAATGCTCGTGCCTTTAGTGGCGTTTCTGAAAAAAGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTGCCTTTAGCGGCGTTTCTAAAAAAAGC
5831051 GCCGCTAATGCTGACC
66 GCCGCTAATGCTGACC
5831067 TTTAGCGGCGTTTTTGAAAAAG
1 TTTAGCGGCGTTTTTGAAAAAG
5831089 TGTTGCTAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 25 0.28
83 44 0.49
84 20 0.22
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (81 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCCTGCCTTTAGCGGCGTTTCTAAAAAAAGC
GCCGCTAATGCTGACC
Found at i:5832240 original size:10 final size:10
Alignment explanation
Indices: 5832225--5832252 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5832215 TAATGCTTTT
5832225 ATATTTAAAA
1 ATATTTAAAA
5832235 ATATTTAAAA
1 ATATTTAAAA
5832245 ATATTTAA
1 ATATTTAA
5832253 TCTAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATTTAAAA
Found at i:5838725 original size:86 final size:86
Alignment explanation
Indices: 5838575--5838908 Score: 390
Period size: 86 Copynumber: 3.9 Consensus size: 86
5838565 AAGTTATGTT
* * * * * * * *
5838575 TTTAACGGCGTTTCTGTGAGAAGCGCCGCCAAAGGT-TTGATCTATAGCGGCGTTTTTGACAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-ACAAAA
*
5838639 AGCGCCGCTAAAGGTCATGTTC
65 AGCGCCGCTAAAGGTCATGGTC
* *
5838661 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTATAAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTA-CAAAA
*
5838726 AGCGCCGCTAAAGGTCTTGGTC
65 AGCGCCGCTAAAGGTCATGGTC
* * * **
5838748 TTTAGCGGTGTTTG-AGGAAAAGCGCCACTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-CGGAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTACAAAAA
* * *
5838811 GCGCTGTTAAAGGTCTTGGTC
66 GCGCCGCTAAAGGTCATGGTC
* * *
5838832 TTTAGCGGCATTTGT-GGAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTGTTTCTAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTG-TAC-AAA
5838896 AA-CGCCGCTAAAG
64 AAGCGCCGCTAAAG
5838909 TTAGAGACAC
Statistics
Matches: 213, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
84 73 0.34
85 1 0.00
86 82 0.38
87 57 0.27
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTACAAAAA
GCGCCGCTAAAGGTCATGGTC
Found at i:5838782 original size:42 final size:43
Alignment explanation
Indices: 5838595--5838888 Score: 371
Period size: 42 Copynumber: 6.9 Consensus size: 43
5838585 TTTCTGTGAG
* * * * **
5838595 AAGCGCCGCCAAAGGT-TTGATCTATAGCGGCGTTTTTGACAAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-AGGAA
* * *
5838638 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTAGGAA
* **
5838681 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTATAAAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTA-GGAA
*
5838725 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGTGTTTG-AGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTAGGAA
* *
5838767 AAGCGCCACTAAAGGTCTTGGTCTTTAGCGGCGTTTGTCGG-A
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTAGGAA
* * *
5838809 AAGCGCTGTTAAAGGTCTTGGTCTTTAGCGGCATTTGT-GGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTAGGAA
*
5838851 AAGCGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTGT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT
5838889 TTCTAAAAAC
Statistics
Matches: 220, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
41 2 0.01
42 107 0.49
43 57 0.26
44 54 0.25
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTAGGAA
Found at i:5839008 original size:22 final size:22
Alignment explanation
Indices: 5838980--5839022 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5838970 TAGCGGCGCT
*
5838980 AAAAAGCGCCACTAAAGGCCTA
1 AAAAAGCGCCACTAAAAGCCTA
5839002 AAAAAGCGCCACTAAAAGCCT
1 AAAAAGCGCCACTAAAAGCCT
5839023 GTTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCACTAAAAGCCTA
Found at i:5841496 original size:21 final size:21
Alignment explanation
Indices: 5841471--5841514 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5841461 ATCTTCGAGG
5841471 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
5841492 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
5841513 AT
1 AT
5841515 GTAATCTTAG
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:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:5841520 original size:19 final size:19
Alignment explanation
Indices: 5841470--5841525 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
5841460 AATCTTCGAG
5841470 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5841489 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
5841510 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
5841526 AGATACGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5841756 original size:19 final size:21
Alignment explanation
Indices: 5841732--5841770 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5841722 GTTTTCTTTT
*
5841732 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
5841751 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
5841771 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:5845138 original size:24 final size:24
Alignment explanation
Indices: 5845111--5845158 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5845101 AATATAATAA
*
5845111 AAAATGAACTCAAAGTCATGAGTG
1 AAAATAAACTCAAAGTCATGAGTG
5845135 AAAATAAACTCAAAGTCATGAGTG
1 AAAATAAACTCAAAGTCATGAGTG
5845159 CCATGGCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (24 bp):
AAAATAAACTCAAAGTCATGAGTG
Found at i:5846824 original size:15 final size:15
Alignment explanation
Indices: 5846804--5846838 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
5846794 AATCGCCCGT
5846804 GAAGACTACACCGAA
1 GAAGACTACACCGAA
5846819 GAAGACTACACCGAA
1 GAAGACTACACCGAA
5846834 GAAGA
1 GAAGA
5846839 ATGGGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.23, G:0.23, T:0.06
Consensus pattern (15 bp):
GAAGACTACACCGAA
Found at i:5857130 original size:20 final size:19
Alignment explanation
Indices: 5857097--5857139 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5857087 TTATTAACAT
* *
5857097 AATAATATATATAAATATAA
1 AATAAGATAGATAAA-ATAA
5857117 AATAAGATAGATAAAATAA
1 AATAAGATAGATAAAATAA
5857136 AATA
1 AATA
5857140 CTCAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AATAAGATAGATAAAATAA
Found at i:5858512 original size:7 final size:7
Alignment explanation
Indices: 5858500--5858542 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
5858490 AGGTAAGGTA
*
5858500 CAAATTC
1 CAAACTC
*
5858507 CAAATTC
1 CAAACTC
5858514 CAAACTC
1 CAAACTC
5858521 CAAACTC
1 CAAACTC
5858528 CAAACTC
1 CAAACTC
5858535 CAAACTC
1 CAAACTC
5858542 C
1 C
5858543 CAACAGGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (7 bp):
CAAACTC
Found at i:5866799 original size:24 final size:24
Alignment explanation
Indices: 5866756--5866805 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5866746 TTTTTCTTCA
5866756 TTGCATTTGGAGTTCCAGAAGTGT
1 TTGCATTTGGAGTTCCAGAAGTGT
*
5866780 TTGCATTTAGGA-TTCTAGAAGTGT
1 TTGCATTT-GGAGTTCCAGAAGTGT
5866804 TT
1 TT
5866806 TTTTCTTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (24 bp):
TTGCATTTGGAGTTCCAGAAGTGT
Found at i:5867466 original size:123 final size:124
Alignment explanation
Indices: 5867231--5867471 Score: 360
Period size: 123 Copynumber: 2.0 Consensus size: 124
5867221 TTTTTTTAAG
** *
5867231 AACACTTTTTTATCGCAACAACAATGGAGAATTAGCCCTAAAAACTAGTAAAGTCCAAACCAAAG
1 AACACTTTTAAATCGCAACAACAATGGAGAATTAGCCCTAAAAACTAGTAAAGCCCAAACCAAAG
* **
5867296 TCCACAAATGGTAATCACACATGATGTGACTAGAAAACCTATGTATATCATTGCCCATA
66 TCCACAAATGGTAATCACAAATGATGTGACTAGAAAACCTACCTATATCATTGCCCATA
* *
5867355 AACACTTTTAAATC-CAACAACCATGGAGAATTAGCCCTAACAACTAGTAAAGCCCAAACCAAAG
1 AACACTTTTAAATCGCAACAACAATGGAGAATTAGCCCTAAAAACTAGTAAAGCCCAAACCAAAG
* * *
5867419 TCCACAGATGGTAATCACAAATGATGTGACTA-AGAGACTTACCTATATCATTG
66 TCCACAAATGGTAATCACAAATGATGTGACTAGA-AAACCTACCTATATCATTG
5867472 GTACTCAGGA
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
122 1 0.01
123 92 0.88
124 12 0.11
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.23
Consensus pattern (124 bp):
AACACTTTTAAATCGCAACAACAATGGAGAATTAGCCCTAAAAACTAGTAAAGCCCAAACCAAAG
TCCACAAATGGTAATCACAAATGATGTGACTAGAAAACCTACCTATATCATTGCCCATA
Found at i:5867862 original size:24 final size:24
Alignment explanation
Indices: 5867835--5867884 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5867825 AAAAGAATGA
5867835 GAAAAGACGAAAATTGTTATTTTG
1 GAAAAGACGAAAATTGTTATTTTG
5867859 GAAAAGACGAAAATTGTTATTTTG
1 GAAAAGACGAAAATTGTTATTTTG
5867883 GA
1 GA
5867885 TTTTTAGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (24 bp):
GAAAAGACGAAAATTGTTATTTTG
Found at i:5878547 original size:27 final size:27
Alignment explanation
Indices: 5878509--5878563 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5878499 AGGGGTTAAA
5878509 TGTCCAAATTTCATCACTTACAATAAC
1 TGTCCAAATTTCATCACTTACAATAAC
5878536 TGTCCAAATTTCATCACTTACAATAAC
1 TGTCCAAATTTCATCACTTACAATAAC
5878563 T
1 T
5878564 TTCTCATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (27 bp):
TGTCCAAATTTCATCACTTACAATAAC
Found at i:5879604 original size:185 final size:187
Alignment explanation
Indices: 5879246--5879642 Score: 576
Period size: 185 Copynumber: 2.2 Consensus size: 187
5879236 CATACTACTG
** *
5879246 CTGTAAAAGCTTTTAGTCTTTGAC---T--TTTAGAACTGGTAAACCTGTCTTTTATGTTCATCA
1 CTGTAAAAGCTTTTAGTCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATATTCATCA
* * *
5879306 TCTCTTGATAATATCAGATTTAGATCATCCTAGCAGTGTCATTGAACACCGCAAAAATCCCTAAG
66 TCTCATGATAATATCAGATTTAGATCATCCTACCAGTGACATTGAACACCGCAAAAATCCCTAAG
* *
5879371 CCTGTTATGCCACATTATTCATGTGCTATTAGGTCATCCTACCAGTGTCATTGAACA
131 CCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAACA
* * *
5879428 CTGTAAAAGCTTTTAGTCTTCGACTTTTAGTTTAGAACTGGTAGACCTACCTTTTATATTCATTA
1 CTGTAAAAGCTTTTAGTCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATATTCATCA
* *
5879493 TCTCATGATAATATCATATTTAGATCATCCTACCAGTGACATTG-A-A-CGCTAAAAATCCCTGA
66 TCTCATGATAATATCAGATTTAGATCATCCTACCAGTGACATTGAACACCGC-AAAAATCCCTAA
* * *
5879555 TCTTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAGCA
130 GCCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAACA
*
5879613 CTGTAAAAGCTTTTAGCCTTTGACTTTTAG
1 CTGTAAAAGCTTTTAGTCTTTGACTTTTAG
5879643 AAATGGTAAA
Statistics
Matches: 191, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
182 23 0.12
184 3 0.02
185 94 0.49
186 1 0.01
187 70 0.37
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (187 bp):
CTGTAAAAGCTTTTAGTCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATATTCATCA
TCTCATGATAATATCAGATTTAGATCATCCTACCAGTGACATTGAACACCGCAAAAATCCCTAAG
CCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAACA
Found at i:5884433 original size:94 final size:89
Alignment explanation
Indices: 5884291--5884583 Score: 246
Period size: 94 Copynumber: 3.3 Consensus size: 89
5884281 GACTTAAAAT
* * * *
5884291 GCTAGCAATGGCTCTGCTATTGACTTAGCTAGTAGTACCCTCGAAGGGTGTGTGTCGTTTTAACT
1 GCTAGCAATGGCCCTGCTATTGACTTAGCTAGCAATACCCTCGAAGGGTGTGTGT--TGTT---T
5884356 TAATGAAATTTGGCTAAGTGCCTTTGAAG
61 TAATGAAATTTGGCTAAGTGCCTTTGAAG
* *
5884385 GCTAGCAATGGCCCTGCTATTGACTTAGCTAGCAATATCCGT-GGAGGGTGTGTGTTGTTTTAAT
1 GCTAGCAATGGCCCTGCTATTGACTTAGCTAGCAATA-CCCTCGAAGGGTGTGTGTTGTTTTAAT
5884449 GAAATTTGGCTAAGTGCC-TT-ATA-
65 GAAATTTGGCTAAGTGCCTTTGA-AG
** * * ** *
5884472 G-TAG---TGGCTTTGCTATT-AGCTTAGCTAGCAGTGCCCTCGAAGGGTGCATG-TGTTTTAAC
1 GCTAGCAATGGCCCTGCTATTGA-CTTAGCTAGCAATACCCTCGAAGGGTGTGTGTTGTTTTAAT
* * **
5884531 GAAATTTGTCTAACTGCCTTAAAAG
65 GAAATTTGGCTAAGTGCCTTTGAAG
* * * * *
5884556 GATAGTATTGGCACTGCTATTAACTTAG
1 GCTAGCAATGGCCCTGCTATTGACTTAG
5884584 GCCACTTCTT
Statistics
Matches: 167, Mismatches: 20, Indels: 30
0.77 0.09 0.14
Matches are distributed among these distances:
82 28 0.17
83 34 0.20
84 2 0.01
85 3 0.02
86 3 0.02
87 2 0.01
88 19 0.11
89 24 0.14
92 3 0.02
94 46 0.28
95 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (89 bp):
GCTAGCAATGGCCCTGCTATTGACTTAGCTAGCAATACCCTCGAAGGGTGTGTGTTGTTTTAATG
AAATTTGGCTAAGTGCCTTTGAAG
Found at i:5884636 original size:13 final size:13
Alignment explanation
Indices: 5884597--5884649 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
5884587 ACTTCTTCAT
5884597 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
5884610 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
5884623 TGTTTTTGAGAAG
1 TGCTTTTGAAAAG
5884636 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
5884649 T
1 T
5884650 TTGATTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:5895171 original size:41 final size:41
Alignment explanation
Indices: 5895114--5895317 Score: 300
Period size: 41 Copynumber: 5.0 Consensus size: 41
5895104 GCATATTCGG
* *
5895114 ATCACCGGTACTTAGCCTGCTAGGTTTATAACCTGATTAAT
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
* * * *
5895155 ATCACCGGTACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
5895196 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
* * * * *
5895237 ATCATCGACACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
*
5895278 ATCACCGGCACTTAGCCTGCTAGGTGTATAACCTGATTCA
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCA
5895318 ATTCACCAAT
Statistics
Matches: 145, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 145 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (41 bp):
ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
Found at i:5895213 original size:82 final size:82
Alignment explanation
Indices: 5895108--5895324 Score: 355
Period size: 82 Copynumber: 2.6 Consensus size: 82
5895098 AATTTAGCAT
* * **
5895108 ATTCGGATCACCGGTACTTAGCCTGCTAGGTTTATAACCTGATTAATATCACCGGTACTTAGCCT
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTAATATCACCGACACTTAGCCT
5895173 GCTAGGCTTATAGCCTG
66 GCTAGGCTTATAGCCTG
* *
5895190 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCATATCATCGACACTTAGCCT
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTAATATCACCGACACTTAGCCT
5895255 GCTAGGCTTATAGCCTG
66 GCTAGGCTTATAGCCTG
*
5895272 ATTCAGATCACCGGCACTTAGCCTGCTAGGTGTATAACCTGATTCAAT-TCACC
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-AATATCACC
5895325 AATTCTAAAC
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
82 123 0.98
83 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.30
Consensus pattern (82 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTAATATCACCGACACTTAGCCT
GCTAGGCTTATAGCCTG
Found at i:5898021 original size:39 final size:39
Alignment explanation
Indices: 5897966--5898072 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 39
5897956 TTTTAGGTGA
* *
5897966 TCAATTATTTTCTAGAAGTGAATTGTAAGGTTCA-TCAGT
1 TCAATCATTTTCTAGAATTGAATTGTAAGGTTCATTCA-T
* * * *
5898005 TCAATCATTTTTTAGAATTGAATTAGGAAGGTTGATTTAT
1 TCAATCATTTTCTAGAATTGAATT-GTAAGGTTCATTCAT
5898045 TCAATCATTTTCTAGAATTGAATTGTAA
1 TCAATCATTTTCTAGAATTGAATTGTAA
5898073 AGTTGATCTA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 24 0.41
40 32 0.55
41 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (39 bp):
TCAATCATTTTCTAGAATTGAATTGTAAGGTTCATTCAT
Found at i:5900090 original size:19 final size:20
Alignment explanation
Indices: 5900068--5900115 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
5900058 AAACATAAAC
*
5900068 TTTTGAATTTTTATAAA-TA
1 TTTTGAATTTTTAAAAATTA
*
5900087 TTTTGAA-ATTTAAAAATTA
1 TTTTGAATTTTTAAAAATTA
5900106 TTTTGAATTT
1 TTTTGAATTT
5900116 CTTTTTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.29
19 16 0.67
20 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTGAATTTTTAAAAATTA
Found at i:5900097 original size:46 final size:43
Alignment explanation
Indices: 5900000--5900102 Score: 104
Period size: 46 Copynumber: 2.3 Consensus size: 43
5899990 AGTCCTCAAA
* *
5900000 ATTATTATTT-AAAAAAAATTAATTTAGAATTTTTTAAAAATT
1 ATTATAATTTAAAAAAAAATAAATTTAGAATTTTTTAAAAATT
* *
5900042 ATTATAATTTTAAAAAAAACATAAACTTTTGAATTTTTATAAATATT
1 ATTATAA-TTTAAAAAAAA-ATAAA-TTTAGAATTTTT-TAAAAATT
5900089 -TTGA-AATTTAAAAA
1 ATT-ATAATTTAAAAA
5900103 TTATTTTGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
42 6 0.12
43 3 0.06
44 7 0.14
45 12 0.24
46 15 0.29
47 8 0.16
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (43 bp):
ATTATAATTTAAAAAAAAATAAATTTAGAATTTTTTAAAAATT
Found at i:5909293 original size:23 final size:23
Alignment explanation
Indices: 5909261--5909304 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5909251 AAAATTCATT
* *
5909261 TATAATTTTTACAATAATAAAAA
1 TATAACTTTTAAAATAATAAAAA
*
5909284 TATAACTTTTAAAATATTAAA
1 TATAACTTTTAAAATAATAAA
5909305 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
TATAACTTTTAAAATAATAAAAA
Found at i:5909767 original size:12 final size:12
Alignment explanation
Indices: 5909750--5909774 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5909740 CGAGAATAAT
5909750 TTTTTAATATTA
1 TTTTTAATATTA
5909762 TTTTTAATATTA
1 TTTTTAATATTA
5909774 T
1 T
5909775 AAAAATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAATATTA
Found at i:5915033 original size:19 final size:20
Alignment explanation
Indices: 5914989--5915038 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
5914979 CTTATATATT
5914989 TTTTTATAATATTTTTACTGA
1 TTTTTATAATATTTTTA-TGA
* *
5915010 TTTTTATAGTATTTTT-TTA
1 TTTTTATAATATTTTTATGA
5915029 TTTTTATAAT
1 TTTTTATAAT
5915039 TTTGGAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 11 0.42
21 15 0.58
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (20 bp):
TTTTTATAATATTTTTATGA
Found at i:5917949 original size:31 final size:31
Alignment explanation
Indices: 5917914--5917975 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5917904 TGATCAATCA
5917914 TATGTTTTGTGTCATTAAGTTTTTCAAGTCT
1 TATGTTTTGTGTCATTAAGTTTTTCAAGTCT
*
5917945 TATGTTTTGTGTCATTAAGTTTTTCGAGTCT
1 TATGTTTTGTGTCATTAAGTTTTTCAAGTCT
5917976 ATTATGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.55
Consensus pattern (31 bp):
TATGTTTTGTGTCATTAAGTTTTTCAAGTCT
Found at i:5917966 original size:15 final size:15
Alignment explanation
Indices: 5917917--5917967 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
5917907 TCAATCATAT
5917917 GTTTTGTGTCATTAA
1 GTTTTGTGTCATTAA
*
5917932 GTTTT-TCAAGTC-TTAT
1 GTTTTGT---GTCATTAA
5917948 GTTTTGTGTCATTAA
1 GTTTTGTGTCATTAA
5917963 GTTTT
1 GTTTT
5917968 TCGAGTCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 4 0.14
15 13 0.45
16 8 0.28
17 4 0.14
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.57
Consensus pattern (15 bp):
GTTTTGTGTCATTAA
Found at i:5917968 original size:16 final size:16
Alignment explanation
Indices: 5917918--5917968 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
5917908 CAATCATATG
5917918 TTTTGTGTCATTAAGT
1 TTTTGTGTCATTAAGT
** *
5917934 TTTTCAAGTC-TTATG-
1 TTTT-GTGTCATTAAGT
5917949 TTTTGTGTCATTAAGT
1 TTTTGTGTCATTAAGT
5917965 TTTT
1 TTTT
5917969 CGAGTCTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
14 3 0.12
15 8 0.31
16 12 0.46
17 3 0.12
ACGTcount: A:0.18, C:0.08, G:0.16, T:0.59
Consensus pattern (16 bp):
TTTTGTGTCATTAAGT
Found at i:5922360 original size:21 final size:21
Alignment explanation
Indices: 5922326--5922366 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5922316 TCTGAAAAGA
5922326 CGAAATTATATTATTGTATTCT
1 CGAAATTATATTATT-TATTCT
5922348 CGAAATT-TATTATTTATTC
1 CGAAATTATATTATTTATTC
5922367 CAATAATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
22 7 0.37
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (21 bp):
CGAAATTATATTATTTATTCT
Found at i:5923520 original size:19 final size:19
Alignment explanation
Indices: 5923483--5923534 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
5923473 AATTAGTTGG
*
5923483 ATAAATTTTAAAATT-ATAT
1 ATAAATTTT-AATTTAATAT
5923502 ATAAATTTTAATTTAATAT
1 ATAAATTTTAATTTAATAT
* *
5923521 GT-AATTTGAATTTA
1 ATAAATTTTAATTTA
5923535 TGATTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
ATAAATTTTAATTTAATAT
Found at i:5929306 original size:114 final size:112
Alignment explanation
Indices: 5928809--5929462 Score: 736
Period size: 113 Copynumber: 5.8 Consensus size: 112
5928799 ATATAGCACA
* * * * * *
5928809 ATTAGCGGCGTTTAT-TTGTAAGCGCCGTAAAAAATGTTAACCAAAACGCATCGTTTGGTCTTGA
1 ATTAGCGGCGTTT-TGTAG-AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGA
* * * * * * * *
5928873 GGTATGTTAGTATTTGTGGTGTTTATGAAAAACACCGCTATAGCATATT
64 GGTATATTAGAATTAGTGGCGCTTACGAAAAACGCCGCTATAGCATAGT
* * * * *
5928922 ATCAGCGGCGTTTTGCACGAAACGCCGCAAAAAATGTTAACCAAAACGCATCGTTTGGTCTTGAG
1 ATTAGCGGCGTTTTGTA-GAAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAG
* * * * *
5928987 GTATATTAGAACTGGTGGCGCTAACTAAAAACGCCGCTATAGGATAGT
65 GTATATTAGAATTAGTGGCGCTTACGAAAAACGCCGCTATAGCATAGT
* * * *
5929035 ATTAGCGGCGTTTTGTACAAAACGTCGCAAAATATGTTAACCAAAACGTAGCGTTTGGTCTTGAG
1 ATTAGCGGCGTTTTGTA-GAAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAG
* * * * *
5929100 GTATATTAGATTTAGTGGCGCTTCCAAAAAAAGCCGCTATAGGATAGT
65 GTATATTAGAATTAGTGGCGCTTACGAAAAACGCCGCTATAGCATAGT
* *
5929148 ATTAGCGGCGTTTTGTACGAAACGCCGCAACATATCTTAACCAAAACGCAGCGTTTGGTCTTTAG
1 ATTAGCGGCGTTTTGTA-GAAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAG
* * *
5929213 GTATATTAGAGTTAGTGGCGCTTAGGGACAAACGCCGCTATAGCATAGT
65 GTATATTAGAATTAGTGGCGCTTA-CGAAAAACGCCGCTATAGCATAGT
* * * * *
5929262 ATTAGCGGCGCTTTATAGAAAACGCCGCAAAGTATCTTAACCAAAACGCAGCGTTTAGTCTTCAG
1 ATTAGCGGCGTTTTGTAG-AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAG
* * * *
5929327 GTATATTAGAATTAGTGGCGCTTATTGAAAAATGCCGCTAAAGCAGAGT
65 GTATATTAGAATTAGTGGCGCTTA-CGAAAAACGCCGCTATAGCATAGT
* *
5929376 ATTAGCGGCGCTGTGTAAGAAACGCCG-AAAAGTATCTTAACCAAAACGCAGCGTTTGGTCTTGA
1 ATTAGCGGCGTTTTGT-AGAAACGCCGCAAAA-TATCTTAACCAAAACGCAGCGTTTGGTCTTGA
* * *
5929440 TGTCTATTAGAATTAGTAGCGCT
64 GGTATATTAGAATTAGTGGCGCT
5929463 CATGTAAAAG
Statistics
Matches: 470, Mismatches: 65, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
112 1 0.00
113 276 0.59
114 191 0.41
115 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (112 bp):
ATTAGCGGCGTTTTGTAGAAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGG
TATATTAGAATTAGTGGCGCTTACGAAAAACGCCGCTATAGCATAGT
Found at i:5929817 original size:22 final size:21
Alignment explanation
Indices: 5929775--5929823 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5929765 TCTATGATGT
*
5929775 AGGTTTAGTGTTTTGGATTTA
1 AGGTTTAGAGTTTTGGATTTA
*
5929796 GGGTTTAGGAGTTTTAGG-TTTA
1 AGGTTTA-GAGTTTT-GGATTTA
5929818 AGGTTT
1 AGGTTT
5929824 GGGGTTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.26
22 15 0.65
23 2 0.09
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (21 bp):
AGGTTTAGAGTTTTGGATTTA
Found at i:5930472 original size:11 final size:11
Alignment explanation
Indices: 5930456--5930510 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
5930446 TAGAAGAATG
5930456 TATAAAAAATA
1 TATAAAAAATA
*
5930467 TATAAAAAATC
1 TATAAAAAATA
* *
5930478 TA-AATATTAATG
1 TATAA-A-AAATA
5930490 TATAAAAAATA
1 TATAAAAAATA
5930501 TATAAAAAAT
1 TATAAAAAAT
5930511 CTAAATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 2 0.06
11 26 0.72
12 6 0.17
13 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
TATAAAAAATA
Found at i:5930491 original size:34 final size:34
Alignment explanation
Indices: 5930452--5930520 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5930442 TGTCTAGAAG
5930452 AATGTATAAAAAATATATAAAAAATCTAAATATT
1 AATGTATAAAAAATATATAAAAAATCTAAATATT
5930486 AATGTATAAAAAATATATAAAAAATCTAAATATT
1 AATGTATAAAAAATATATAAAAAATCTAAATATT
5930520 A
1 A
5930521 GCGGCGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (34 bp):
AATGTATAAAAAATATATAAAAAATCTAAATATT
Found at i:5931868 original size:89 final size:89
Alignment explanation
Indices: 5931717--5931920 Score: 363
Period size: 89 Copynumber: 2.3 Consensus size: 89
5931707 ATTTTTAAAA
*
5931717 ACACATTACTTGGTATTCTGTTTTGGCACAACACTTACGCAAATGACTTTGTGGATTACTTGGTA
1 ACACATTACTTGGTATTCTGTTTTGGCACAACACTTAAGCAAATGACTTTGTGGATTACTTGGTA
5931782 TTCTGTTTTGGTAGGATTGTTTTG
66 TTCTGTTTTGGTAGGATTGTTTTG
* * *
5931806 ACACATTACTTGGTAATCTGTTTTGGCACAACAGTTAAGCAAATGGCTTTGTGGATTACTTGGTA
1 ACACATTACTTGGTATTCTGTTTTGGCACAACACTTAAGCAAATGACTTTGTGGATTACTTGGTA
5931871 TTCTGTTTTGGTAGGATTGTTTTG
66 TTCTGTTTTGGTAGGATTGTTTTG
*
5931895 GCACATTACTTGGTATTCTGTTTTGG
1 ACACATTACTTGGTATTCTGTTTTGG
5931921 TACTCTGTTT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 109 1.00
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.43
Consensus pattern (89 bp):
ACACATTACTTGGTATTCTGTTTTGGCACAACACTTAAGCAAATGACTTTGTGGATTACTTGGTA
TTCTGTTTTGGTAGGATTGTTTTG
Found at i:5931922 original size:13 final size:13
Alignment explanation
Indices: 5931904--5931934 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5931894 GGCACATTAC
*
5931904 TTGGTATTCTGTT
1 TTGGTACTCTGTT
5931917 TTGGTACTCTGTT
1 TTGGTACTCTGTT
5931930 TTGGT
1 TTGGT
5931935 CGGGTTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.10, G:0.26, T:0.58
Consensus pattern (13 bp):
TTGGTACTCTGTT
Found at i:5932144 original size:21 final size:21
Alignment explanation
Indices: 5932118--5932186 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
5932108 CTACAACTTA
*
5932118 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
5932139 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
* * *
5932160 AAGCAGAGGTTGCAGCAAGAA
1 AAGCAGAGGCTGCAGCGAGAG
5932181 AAGCAG
1 AAGCAG
5932187 CAAGAGAAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.38, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:5932193 original size:33 final size:33
Alignment explanation
Indices: 5932151--5932219 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
5932141 GCAGAGGCTA
* *
5932151 CAGCGAGAGAAGCAGAGGTTGCAGCAAGAAAAG
1 CAGCAAGAGAAGCAGAGGCTGCAGCAAGAAAAG
* *
5932184 CAGCAAGAGAAGCAGAGGCTGCAGCTAGAGAAG
1 CAGCAAGAGAAGCAGAGGCTGCAGCAAGAAAAG
5932217 CAG
1 CAG
5932220 AGGTTCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.36, T:0.06
Consensus pattern (33 bp):
CAGCAAGAGAAGCAGAGGCTGCAGCAAGAAAAG
Found at i:5932207 original size:21 final size:21
Alignment explanation
Indices: 5932183--5932222 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5932173 AGCAAGAAAA
5932183 GCAGCAAGAGAAGCAGAGGCT
1 GCAGCAAGAGAAGCAGAGGCT
*
5932204 GCAGCTAGAGAAGCAGAGG
1 GCAGCAAGAGAAGCAGAGG
5932223 TTCAAAAGAA
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:0.38, C:0.17, G:0.40, T:0.05
Consensus pattern (21 bp):
GCAGCAAGAGAAGCAGAGGCT
Found at i:5932755 original size:42 final size:42
Alignment explanation
Indices: 5932653--5932937 Score: 344
Period size: 42 Copynumber: 6.7 Consensus size: 42
5932643 TTTGTGAAAA
* * * ** *
5932653 AAGCGCCGCTAAAGAACAT-TTCTTTTCGCGACTTTTGTGAATC
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCTTTT-TTCATT
5932696 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTCATT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTCATT
*
5932738 AAGCGCCGCTAAAGAACATGATCTTTAGGGGCGTTTTTT-ATT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGC-TTTTTTCATT
* * *
5932780 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTGCATT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTCATT
* * * *
5932822 AAGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTCTCTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTCATT
*
5932864 AAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTT--TCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGC-T-TTTTTCAT-T
*
5932907 AAGCGCCGCTAAAGAACATGACCTTTAGCGG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGG
5932938 TGTTTTTTTT
Statistics
Matches: 214, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
41 4 0.02
42 138 0.64
43 66 0.31
44 6 0.03
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTCATT
Found at i:5932847 original size:126 final size:127
Alignment explanation
Indices: 5932696--5932943 Score: 392
Period size: 126 Copynumber: 2.0 Consensus size: 127
5932686 TTTGTGAATC
* * *
5932696 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTCATTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTCTCATTAAGCGCCGCTAAAGAACATGATC
* *
5932761 TTTAGGGGCGT-TTTTTAT-TAAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTGCATT
66 TTTAGCGGCGTCTTTTT-TCTAAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTTGCATT
* *
5932822 AAGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTCTCTTTAAGTGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTCTCATTAAGCGCCGCTAAAGAACATGATC
* *
5932887 TTTAGCGGCGTCTTTTTTCTAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGTTTT
66 TTTAGCGGCGTCTTTTTTCTAAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTT
5932944 TTTTGGTAAA
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
126 71 0.64
127 40 0.36
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (127 bp):
AAGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTCTCATTAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTCTTTTTTCTAAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTTGCATT
Found at i:5934909 original size:12 final size:12
Alignment explanation
Indices: 5934892--5934927 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
5934882 ATTTATTACA
5934892 TATAATAGTAAT
1 TATAATAGTAAT
5934904 TATAATAGTAAT
1 TATAATAGTAAT
5934916 TATAATAGTAAT
1 TATAATAGTAAT
5934928 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
TATAATAGTAAT
Found at i:5936124 original size:19 final size:18
Alignment explanation
Indices: 5936090--5936130 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5936080 AATGACAAAT
* *
5936090 ATGATAAATGAATATGAG
1 ATGAGAAATGAATATGAA
5936108 ATGAGAAATGAAATATGAA
1 ATGAGAAATG-AATATGAA
5936127 ATGA
1 ATGA
5936131 TGAATTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (18 bp):
ATGAGAAATGAATATGAA
Found at i:5937611 original size:49 final size:49
Alignment explanation
Indices: 5937539--5937632 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
5937529 TCGAGAGGGA
5937539 ATAAATAGTGATAAGAGTGTAGACAATGGAA-AACCAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAGAA-CAAGTTTAGCAATGT
*
5937588 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGAACAAGTTTAGCA
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAGAACAAGTTTAGCA
5937633 TTGCATAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
49 41 0.95
50 2 0.05
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.23
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAATGGAAGAACAAGTTTAGCAATGT
Found at i:5950004 original size:21 final size:21
Alignment explanation
Indices: 5949980--5950050 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
5949970 CATTGTTTCT
5949980 AATCTCACTGCTACAGTACCC
1 AATCTCACTGCTACAGTACCC
5950001 AATCTCACTGCTACAGTACCC
1 AATCTCACTGCTACAGTACCC
* * *
5950022 AATCTCACCGCTACAGTAACT
1 AATCTCACTGCTACAGTACCC
5950043 AATCTCAC
1 AATCTCAC
5950051 CGCCACCACT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.31, C:0.37, G:0.08, T:0.24
Consensus pattern (21 bp):
AATCTCACTGCTACAGTACCC
Found at i:5950547 original size:11 final size:11
Alignment explanation
Indices: 5950533--5950580 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
5950523 ATATCCAAAC
*
5950533 AATAACAACAA
1 AATAATAACAA
*
5950544 AATAATAGCAA
1 AATAATAACAA
*
5950555 TATAATAACAA
1 AATAATAACAA
* *
5950566 AATGATAGCAA
1 AATAATAACAA
5950577 AATA
1 AATA
5950581 GTAGCAGGGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (11 bp):
AATAATAACAA
Found at i:5950559 original size:22 final size:22
Alignment explanation
Indices: 5950534--5950576 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5950524 TATCCAAACA
5950534 ATAACAACAAAATAATAGCAAT
1 ATAACAACAAAATAATAGCAAT
* *
5950556 ATAATAACAAAATGATAGCAA
1 ATAACAACAAAATAATAGCAA
5950577 AATAGTAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAATAGCAAT
Found at i:5950585 original size:11 final size:11
Alignment explanation
Indices: 5950541--5950586 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
5950531 ACAATAACAA
5950541 CAAAATAATAG
1 CAAAATAATAG
* *
5950552 CAATATAATAA
1 CAAAATAATAG
*
5950563 CAAAATGATAG
1 CAAAATAATAG
*
5950574 CAAAATAGTAG
1 CAAAATAATAG
5950585 CA
1 CA
5950587 GGGAAAAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:5962857 original size:39 final size:39
Alignment explanation
Indices: 5962803--5962882 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
5962793 TACAATGTCA
5962803 TTGCTTCTTTTATTTCAGTGTTAAAACAGAGTATCTTCC
1 TTGCTTCTTTTATTTCAGTGTTAAAACAGAGTATCTTCC
*
5962842 TTGCTTCTTTTATTTCAGTGTTAAAATAGAGTATCTTCC
1 TTGCTTCTTTTATTTCAGTGTTAAAACAGAGTATCTTCC
5962881 TT
1 TT
5962883 ATTTGTGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (39 bp):
TTGCTTCTTTTATTTCAGTGTTAAAACAGAGTATCTTCC
Found at i:5967164 original size:28 final size:26
Alignment explanation
Indices: 5967111--5967164 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
5967101 TTAAGTAAAC
** *
5967111 ATATTATAATATATATGTTAACTTTA
1 ATATTATAATATATATAATAAATTTA
5967137 ATATTATAATATATATAAAATAAATTTA
1 ATATTATAATATATAT--AATAAATTTA
5967165 CACATGTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 16 0.70
28 7 0.30
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATTATAATATATATAATAAATTTA
Found at i:5969827 original size:19 final size:19
Alignment explanation
Indices: 5969779--5969827 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5969769 ATGCAATTCA
* *
5969779 AAAT-ATCATAAAAATTAT
1 AAATAATCATTAAAACTAT
* *
5969797 AAAAAATTATTAAAACTAT
1 AAATAATCATTAAAACTAT
5969816 AAATAATCATTA
1 AAATAATCATTA
5969828 TTAATAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATCATTAAAACTAT
Found at i:5969835 original size:25 final size:25
Alignment explanation
Indices: 5969802--5969851 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5969792 ATTATAAAAA
* *
5969802 ATTATTAAAACTATAAATAATCATT
1 ATTAATAAAACTATAAATAACCATT
*
5969827 ATTAATAAAATTATAAATAACCATT
1 ATTAATAAAACTATAAATAACCATT
5969852 TTTCTAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTAATAAAACTATAAATAACCATT
Found at i:5971980 original size:43 final size:43
Alignment explanation
Indices: 5971864--5972015 Score: 116
Period size: 43 Copynumber: 3.5 Consensus size: 43
5971854 TATGTAATAT
*
5971864 CATGTAAGACCACGTCTGGGAC-GTTGGCATCGATT-TGA-GATTTA
1 CATGTAAGACCACGTCTGGGACAG-AGGCATCG-TTAT-ATGA-TTA
** * * * * **
5971908 TGTGTAAGACCATGTTTGAGATATTGGCATCG-TATATGATTTA
1 CATGTAAGACCACGTCTGGGACAGAGGCATCGTTATATGA-TTA
* *
5971951 CGTGTAAGACC-CTGTCTGGGACAGAGGCATCGTTATTTGATTA
1 CATGTAAGACCAC-GTCTGGGACAGAGGCATCGTTATATGATTA
5971994 CATGTAAGACCACGTCTGGGAC
1 CATGTAAGACCACGTCTGGGAC
5972016 GCTGATATTG
Statistics
Matches: 86, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
42 2 0.02
43 53 0.62
44 31 0.36
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACAGAGGCATCGTTATATGATTA
Found at i:5974932 original size:7 final size:7
Alignment explanation
Indices: 5974920--5974944 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5974910 ATTTATATAA
5974920 ATGAAAT
1 ATGAAAT
5974927 ATGAAAT
1 ATGAAAT
5974934 ATGAAAT
1 ATGAAAT
5974941 ATGA
1 ATGA
5974945 TGATTGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
ATGAAAT
Found at i:5978787 original size:71 final size:71
Alignment explanation
Indices: 5978671--5978815 Score: 274
Period size: 71 Copynumber: 2.0 Consensus size: 71
5978661 GACATACACA
5978671 AATTGAGATGACCAATAATTTCTGTGATTATGGGCATTCTCACAAGTTGTTTCTTTTTAAATTAA
1 AATTGAGATGACCAATAATTTCTGTGATTATGGGCATTCTCACAAGTTGTTTCTTTTTAAATTAA
5978736 CCTGTT
66 CCTGTT
5978742 AATTGAGATG-CTCAATAATTTCTGTGATTATGGGCATTCTCACAAGTTGTTTCTTTTTAAATTA
1 AATTGAGATGAC-CAATAATTTCTGTGATTATGGGCATTCTCACAAGTTGTTTCTTTTTAAATTA
5978806 ACCTGTT
65 ACCTGTT
5978813 AAT
1 AAT
5978816 GAGGATTTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
70 1 0.01
71 72 0.99
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (71 bp):
AATTGAGATGACCAATAATTTCTGTGATTATGGGCATTCTCACAAGTTGTTTCTTTTTAAATTAA
CCTGTT
Found at i:5992665 original size:37 final size:37
Alignment explanation
Indices: 5992601--5992695 Score: 147
Period size: 37 Copynumber: 2.6 Consensus size: 37
5992591 AGTACACAAG
* *
5992601 TAATCCAACCGA-AACACGCCAACTGCTCATAAGAGT
1 TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
* *
5992637 TAATCCACCCGATAACACGTCAAATGCTCATAAGAGC
1 TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
5992674 TAATCCAACCGATAACACGCCA
1 TAATCCAACCGATAACACGCCA
5992696 CGACAGTAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 11 0.21
37 41 0.79
ACGTcount: A:0.39, C:0.32, G:0.13, T:0.17
Consensus pattern (37 bp):
TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
Found at i:5995135 original size:16 final size:16
Alignment explanation
Indices: 5995114--5995145 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5995104 TTATGTGTTT
*
5995114 AAATAATATAATATAA
1 AAATAACATAATATAA
5995130 AAATAACATAATATAA
1 AAATAACATAATATAA
5995146 TATACTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAACATAATATAA
Found at i:6001356 original size:25 final size:26
Alignment explanation
Indices: 6001305--6001368 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
6001295 GGACTCTCTG
* *
6001305 AAGCTAGTGTAAGCAGCATCGAACT-
1 AAGCTAGTGTTAGCAACATCGAACTA
* * *
6001330 AAGCTAGTGTTAGCAACCTTGATCTA
1 AAGCTAGTGTTAGCAACATCGAACTA
6001356 AAGCTAGTGTTAG
1 AAGCTAGTGTTAG
6001369 TAGCCCGGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 20 0.61
26 13 0.39
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (26 bp):
AAGCTAGTGTTAGCAACATCGAACTA
Found at i:6015847 original size:17 final size:18
Alignment explanation
Indices: 6015820--6015855 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
6015810 GTTGTTGATA
6015820 TATTATCTTATTTTATTT
1 TATTATCTTATTTTATTT
6015838 TATT-TCTTATTTTATTT
1 TATTATCTTATTTTATTT
6015855 T
1 T
6015856 CTATCTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (18 bp):
TATTATCTTATTTTATTT
Done.