Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 139 of 205
Found at i:42240420 original size:38 final size:37
Alignment explanation
Indices: 42240378--42240630 Score: 122
Period size: 38 Copynumber: 6.7 Consensus size: 37
42240368 TTAAATTACT
42240378 TTTTTTATAATTTA-T-AATTTTTCAATAGTTTTTATAAA
1 TTTTTTATAATTTATTAAATTTTT--ATA-TTTTTATAAA
* *
42240416 TTTTTTATATTTTATTACAATTTTTATATTTTTATGAA
1 TTTTTTATAATTTATTA-AATTTTTATATTTTTATAAA
* * *
42240454 -TTTTTATAATCCTTATGAAA-TTTTA-A-ATATATCAAA
1 TTTTTTATAAT--TTATTAAATTTTTATATTTTTAT-AAA
* *
42240490 TATGTTTTATTAA-TT-TTATATTTTTATA-ATTTATAATAA
1 T-T-TTTTA-TAATTTATTAAATTTTTATATTTTTAT-A-AA
*
42240529 TTTTTTATAATTT-TTATAATTTTTATGACTTTTTTTTATAA
1 TTTTTTATAATTTATTA-AATTTTTAT-A--TTTTTATA-AA
* * *
42240570 TTTTATA-AATTT-TTAAAAATTTTAAATTTTTA-AAA
1 TTTTTTATAATTTATT-AAATTTTTATATTTTTATAAA
*
42240605 -TTTTTAAAATTT-TTAAAATTTTTATA
1 TTTTTTATAATTTATT-AAATTTTTATA
42240631 AATTCTTTTA
Statistics
Matches: 173, Mismatches: 21, Indels: 45
0.72 0.09 0.19
Matches are distributed among these distances:
34 5 0.03
35 23 0.13
36 10 0.06
37 36 0.21
38 41 0.24
39 19 0.11
40 17 0.10
41 18 0.10
42 4 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (37 bp):
TTTTTTATAATTTATTAAATTTTTATATTTTTATAAA
Found at i:42240469 original size:19 final size:18
Alignment explanation
Indices: 42240434--42240478 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
42240424 ATTTTATTAC
**
42240434 AATTTTTATATTTTTATG
1 AATTTTTATATCCTTATG
42240452 AATTTTTATAATCCTTATG
1 AATTTTTAT-ATCCTTATG
*
42240471 AAATTTTA
1 AATTTTTA
42240479 AATATATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
AATTTTTATATCCTTATG
Found at i:42240552 original size:9 final size:9
Alignment explanation
Indices: 42240379--42240631 Score: 144
Period size: 9 Copynumber: 27.0 Consensus size: 9
42240369 TAAATTACTT
42240379 TTTTTATAA
1 TTTTTATAA
42240388 --TTTATAA
1 TTTTTATAA
*
42240395 TTTTTCAATAG
1 TTTTT--ATAA
42240406 TTTTTATAAA
1 TTTTTAT-AA
*
42240416 TTTTTTATAT
1 -TTTTTATAA
*
42240426 TTTATTACAA
1 TTT-TTATAA
42240436 TTTTTAT-A
1 TTTTTATAA
42240444 TTTTTATGAA
1 TTTTTAT-AA
42240454 TTTTTATAA
1 TTTTTATAA
**
42240463 TCCTTATGAA
1 TTTTTAT-AA
*
42240473 ATTTTA-AA
1 TTTTTATAA
* * *
42240481 TATATCAAATA
1 T-TTTTATA-A
42240492 TGTTTTATTAA
1 T-TTTTA-TAA
42240503 -TTTTAT-A
1 TTTTTATAA
42240510 TTTTTATAA
1 TTTTTATAA
*
42240519 TTTATAATAA
1 TTT-TTATAA
42240529 TTTTTTATAA
1 -TTTTTATAA
42240539 TTTTTATAA
1 TTTTTATAA
*
42240548 TTTTTATGACTTT
1 TTTTTAT-A---A
42240561 TTTTTATAA
1 TTTTTATAA
42240570 -TTTTATAAA
1 TTTTTAT-AA
*
42240579 TTTTTAAAA
1 TTTTTATAA
*
42240588 ATTTTA-AA
1 TTTTTATAA
*
42240596 TTTTTAAAA
1 TTTTTATAA
*
42240605 TTTTTAAAA
1 TTTTTATAA
*
42240614 TTTTTAAAA
1 TTTTTATAA
42240623 TTTTTATAA
1 TTTTTATAA
42240632 ATTCTTTTAT
Statistics
Matches: 193, Mismatches: 26, Indels: 50
0.72 0.10 0.19
Matches are distributed among these distances:
7 8 0.04
8 30 0.16
9 83 0.43
10 39 0.20
11 24 0.12
12 2 0.01
13 7 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:42240583 original size:22 final size:22
Alignment explanation
Indices: 42240539--42240583 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
42240529 TTTTTTATAA
*
42240539 TTTTTATAATTTTTATGACTTT
1 TTTTTATAATTTTTATAACTTT
*
42240561 TTTTTATAA-TTTTATAAATTT
1 TTTTTATAATTTTTATAACTTT
42240582 TT
1 TT
42240584 AAAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTATAATTTTTATAACTTT
Found at i:42240870 original size:5 final size:5
Alignment explanation
Indices: 42240860--42240907 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
42240850 TTCATAAGGT
* * * *
42240860 ATATG ATATG ATATG ATATG ATATG ATATA ACATT ATATA ATATG ATA
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATA
42240908 GAAATGCTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (5 bp):
ATATG
Found at i:42241187 original size:6 final size:6
Alignment explanation
Indices: 42241176--42241217 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
42241166 TATGGCTTGA
42241176 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
42241218 AAGGTGGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
TGTATG
Found at i:42243351 original size:18 final size:19
Alignment explanation
Indices: 42243296--42243352 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
42243286 AATATGCTTT
42243296 TAGAGTTTAAGTCTTGTTTGA
1 TAGAGTTTAAGTC-T-TTTGA
* *
42243317 TAGACTTTTAA-TGTTTTGA
1 TAGA-GTTTAAGTCTTTTGA
42243336 TA-AGTTTAAGTCTTTTG
1 TAGAGTTTAAGTCTTTTG
42243353 GCCACTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 5 0.17
18 7 0.23
19 7 0.23
20 1 0.03
21 5 0.17
22 5 0.17
ACGTcount: A:0.25, C:0.05, G:0.19, T:0.51
Consensus pattern (19 bp):
TAGAGTTTAAGTCTTTTGA
Found at i:42249811 original size:94 final size:94
Alignment explanation
Indices: 42249707--42250008 Score: 293
Period size: 96 Copynumber: 3.2 Consensus size: 94
42249697 TAAATAAGGG
** ** * * * * *
42249707 ATTAGGGTTTAGGGTTTGTCAATTAAATTAATTATAAATTTTTCAAAATTGGATTAGGTTTCGTG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAATTAGATTAGGTTTAGAG
** * * *
42249772 TTTATTATTTTTTAA-TAAAAATCAATTAA
66 -TTAAGAGTTTTTAAGGAAAAATCAAATAA
* * *
42249801 ATTAGGGTTTAGGGTTACTTGAGTAATTTAATTATAAATTATTTAAAAATCAGATAAGGGTTTAG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATT-TTTAAAAATTAGATTA-GGTTTAG
*
42249866 AGTTAAGGGTTTTTAAGGAAAAATCAAATAA
64 AGTTAAGAGTTTTTAAGGAAAAATCAAATAA
* * *
42249897 ATTAGGGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTTATAAAATTTGATTAGGGGTTAG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTA-AAAATTAGATTA-GGTTTAG
* * * *
42249962 TGTTTAG-GGTTTTAAGTAAAAACTCAAATAA
64 AGTTAAGAGTTTTTAAGGAAAAA-TCAAATAA
* *
42249993 ATTAAGGTTTGGGGTT
1 ATTAGGGTTTAGGGTT
42250009 CAGGGTTACT
Statistics
Matches: 172, Mismatches: 31, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
94 34 0.20
95 39 0.23
96 99 0.58
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (94 bp):
ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAATTAGATTAGGTTTAGAG
TTAAGAGTTTTTAAGGAAAAATCAAATAA
Found at i:42249903 original size:96 final size:96
Alignment explanation
Indices: 42249780--42250008 Score: 311
Period size: 96 Copynumber: 2.4 Consensus size: 96
42249770 TGTTTATTAT
* *
42249780 TTTTTAA-TAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTATAAATTATT
1 TTTTTAAGTAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATT-TT
*
42249844 TA-AAAATCAGATAAGGGTTTAGAGTTAAGGG
65 TATAAAATCAGATAAGGGGTTAGAGTTAAGGG
* *
42249875 TTTTTAAGGAAAAATCAAATAAATTAGGGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTT
1 TTTTTAAGTAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTT
** * * *
42249940 ATAAAATTTGATTAGGGGTTAGTGTTTAGGG
66 ATAAAATCAGATAAGGGGTTAGAGTTAAGGG
* *
42249971 -TTTTAAGTAAAAACTCAAATAAATTAAGGTTTGGGGTT
1 TTTTTAAGTAAAAA-TCAAATAAATTAGGGTTTAGGGTT
42250009 CAGGGTTACT
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
95 23 0.20
96 94 0.80
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.39
Consensus pattern (96 bp):
TTTTTAAGTAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTT
ATAAAATCAGATAAGGGGTTAGAGTTAAGGG
Found at i:42250266 original size:126 final size:126
Alignment explanation
Indices: 42250041--42250583 Score: 818
Period size: 126 Copynumber: 4.3 Consensus size: 126
42250031 TTGTTAATTT
* * *
42250041 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCCTAAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* *
42250106 GTTTCTGAGCAAATAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTATTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* * * *
42250167 AAAGAAGCTCCCACGTGGATGCACTTTTGCTACAGTGGCTTCTGAAAAAATAATTTCGAGTAGAT
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
**
42250232 GTTTCTGAGCAAATAGTGTCAAAAACATTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* * * * *
42250293 AAAGAAGCTCTCACGTGGACACGCTTTTGCTACAGTAGCTCCTGAATAAATAATTTTGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* * * * * *
42250358 ATTTCTAAGCATATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTTAGTAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* * * *
42250419 AAAGAAGCTCCCAGGTGGACGCGCTTTTGCTACAGTGGCTTCTGAAAAAATAATTTTGAATAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* *
42250484 GTTTCTGAGCAAATAGCGT-AAAACACGCTTTAAGCAGAATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAA-ACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
42250545 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGC
42250584 GCATGTTTGG
Statistics
Matches: 372, Mismatches: 44, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
125 4 0.01
126 368 0.99
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:42256023 original size:11 final size:11
Alignment explanation
Indices: 42256009--42256037 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
42255999 TTTAAATAGA
42256009 AATTTGAGAGG
1 AATTTGAGAGG
42256020 AATTTGAGAGG
1 AATTTGAGAGG
42256031 AATTTGA
1 AATTTGA
42256038 AAGAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:42256057 original size:23 final size:22
Alignment explanation
Indices: 42256006--42256071 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
42255996 TCTTTTAAAT
*
42256006 AGAAATTTGAGAGGAATTTGAG
1 AGAAATTTGAGAAGAATTTGAG
*
42256028 AGGAATTTGA-AAGAATATTAGAG
1 AGAAATTTGAGAAGAAT-TT-GAG
*
42256051 AGAAATTGAGAGAAAGAATTT
1 AGAAATT-TGAG-AAGAATTT
42256072 AGTTGTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 5 0.14
22 11 0.31
23 9 0.26
24 2 0.06
25 2 0.06
26 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.26
Consensus pattern (22 bp):
AGAAATTTGAGAAGAATTTGAG
Found at i:42257324 original size:23 final size:23
Alignment explanation
Indices: 42257293--42257348 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
42257283 AAAAAATTAA
*
42257293 AATTTGAGTTAATT-GAATCAAGT
1 AATTCGAGTTAATTCGAAT-AAGT
* *
42257316 TATTCGAGTTGATTCGAATAAGT
1 AATTCGAGTTAATTCGAATAAGT
42257339 AATTCGAGTT
1 AATTCGAGTT
42257349 TCGAGTTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (23 bp):
AATTCGAGTTAATTCGAATAAGT
Found at i:42257353 original size:7 final size:7
Alignment explanation
Indices: 42257341--42257374 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
42257331 GAATAAGTAA
42257341 TTCGAGT
1 TTCGAGT
42257348 TTCGAGT
1 TTCGAGT
42257355 TTCGAGT
1 TTCGAGT
42257362 TTCGAGT
1 TTCGAGT
42257369 TT-GAGT
1 TTCGAGT
42257375 CGAGTTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (7 bp):
TTCGAGT
Found at i:42261479 original size:4 final size:4
Alignment explanation
Indices: 42261470--42261510 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
42261460 TATTAAAATG
* * *
42261470 ATAA ATAA ATAA ATAA ATAA GTAA ATCA ATAA AAAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
42261511 GATACTATGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:42278244 original size:21 final size:19
Alignment explanation
Indices: 42278224--42278282 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
42278214 TTTAAATAAT
42278224 TATAATTAGAATGAAATTAA
1 TATAATTAGAAT-AAATTAA
* *
42278244 TATAAAGTATAATCAAATTAA
1 TAT-AATTAGAAT-AAATTAA
*
42278265 TATATATTTGAATAAATT
1 TATA-ATTAGAATAAATT
42278283 TAAAATATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (19 bp):
TATAATTAGAATAAATTAA
Found at i:42283693 original size:44 final size:44
Alignment explanation
Indices: 42283597--42283838 Score: 203
Period size: 43 Copynumber: 5.6 Consensus size: 44
42283587 ATTACATGAT
* * * * *
42283597 TTCGTATAAGACCATAACTGGGCTA-TGACATTGATATATGTGA
1 TTCGTGTAAGACCATATCTGGGATATTGGCATCGATATATGTGA
** * *
42283640 CTTTTTGTAAGACCATATCTGGGATA-TGACATCGATATATGCGA
1 -TTCGTGTAAGACCATATCTGGGATATTGGCATCGATATATGTGA
* * *
42283684 TTACGTGTAAGACCATGTCTAGGACATTGGCATCG-T-TATGTGA
1 TT-CGTGTAAGACCATATCTGGGATATTGGCATCGATATATGTGA
* * *
42283727 TTTCGTGTAAGACCATGTTTGGGACATTGGCATCGATATA--TGA
1 -TTCGTGTAAGACCATATCTGGGATATTGGCATCGATATATGTGA
* * *
42283770 TTCGTGTAAGACCATAGCTGGGCTATTGGCATCG--ATATGTAA
1 TTCGTGTAAGACCATATCTGGGATATTGGCATCGATATATGTGA
* * *
42283812 TAACATGTAAGACCATATTTGGGATAT
1 T-TCGTGTAAGACCATATCTGGGATAT
42283839 AGCATTGTAT
Statistics
Matches: 163, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
40 3 0.02
42 32 0.20
43 61 0.37
44 58 0.36
45 9 0.06
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (44 bp):
TTCGTGTAAGACCATATCTGGGATATTGGCATCGATATATGTGA
Found at i:42283798 original size:42 final size:43
Alignment explanation
Indices: 42283592--42283807 Score: 178
Period size: 44 Copynumber: 5.0 Consensus size: 43
42283582 ATGGCATTAC
* * * *
42283592 ATGATTTCGTATAAGACCATAACTGGGCTA-TGACATTGATAT
1 ATGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
* * * *
42283634 ATGTGACTTT-TTGTAAGACCATATCTGGGATA-TGACATCGATAT
1 A--TGA-TTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
* * *
42283678 ATGCGATTACGTGTAAGACCAT-GTCTAGGAC-ATTGGCATCGTTAT
1 AT--GATTTCGTGTAAGACCATAG-CT-GGGCTATTGGCATCGATAT
* *
42283723 GTGATTTCGTGTAAGACCAT-GTTTGGGAC-ATTGGCATCGATAT
1 ATGATTTCGTGTAAGACCATAG-CTGGG-CTATTGGCATCGATAT
42283766 ATGA-TTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
1 ATGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
42283808 GTAATAACAT
Statistics
Matches: 143, Mismatches: 19, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
41 1 0.01
42 37 0.26
43 40 0.28
44 49 0.34
45 16 0.11
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
ATGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
Found at i:42283803 original size:85 final size:84
Alignment explanation
Indices: 42283592--42283835 Score: 235
Period size: 85 Copynumber: 2.8 Consensus size: 84
42283582 ATGGCATTAC
* * * * *
42283592 ATGATTTCGTATAAGACCATAACTGGGCTA-TGACATTGATATATGTGACTTT-TTGTAAGACCA
1 ATGA-TTCGTGTAAGACCATAGCTGGGCTATTGGCATCG-T-TATGTGA-TTTCATGTAAGACCA
* *
42283655 TATCTGGGATATGACATCGATAT
62 TATTTGGGACATGACATCGATAT
* *
42283678 ATGCGATTACGTGTAAGACCAT-GTCTAGGAC-ATTGGCATCGTTATGTGATTTCGTGTAAGACC
1 AT--GATT-CGTGTAAGACCATAG-CT-GGGCTATTGGCATCGTTATGTGATTTCATGTAAGACC
* *
42283741 ATGTTTGGGACATTGGCATCGATAT
61 ATATTTGGGACA-TGACATCGATAT
* * **
42283766 ATGATTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATATGTAATAACATGTAAGACCATATT
1 ATGATTCGTGTAAGACCATAGCTGGGCTATTGGCATCGTTATGTGATTTCATGTAAGACCATATT
42283831 TGGGA
66 TGGGA
42283836 TATAGCATTG
Statistics
Matches: 131, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
84 3 0.02
85 51 0.39
86 10 0.08
87 27 0.21
88 31 0.24
89 9 0.07
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (84 bp):
ATGATTCGTGTAAGACCATAGCTGGGCTATTGGCATCGTTATGTGATTTCATGTAAGACCATATT
TGGGACATGACATCGATAT
Found at i:42293876 original size:19 final size:20
Alignment explanation
Indices: 42293825--42293880 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
42293815 CAAGACACTA
42293825 ACCCAAACCTCAGCCC-AAT
1 ACCCAAACCTCAGCCCAAAT
* * *
42293844 AACC-TACCTGAGCCCAAAT
1 ACCCAAACCTCAGCCCAAAT
42293863 ACCCAAACCT-AGCCCAAA
1 ACCCAAACCTCAGCCCAAA
42293881 ACACCCCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.30
19 17 0.57
20 4 0.13
ACGTcount: A:0.39, C:0.43, G:0.07, T:0.11
Consensus pattern (20 bp):
ACCCAAACCTCAGCCCAAAT
Found at i:42293886 original size:20 final size:20
Alignment explanation
Indices: 42293849--42293891 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
42293839 CCAATAACCT
*
42293849 ACCTGAGCCCAAATACCCAA
1 ACCTGAGCCCAAACACCCAA
*
42293869 ACCT-AGCCCAAAACACCCCA
1 ACCTGAGCCC-AAACACCCAA
42293889 ACC
1 ACC
42293892 CATCTTCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.40, C:0.47, G:0.07, T:0.07
Consensus pattern (20 bp):
ACCTGAGCCCAAACACCCAA
Found at i:42296003 original size:22 final size:23
Alignment explanation
Indices: 42295962--42296004 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
42295952 AATTAGAAAA
42295962 AAATTTTAAAAATAAAAATTATT
1 AAATTTTAAAAATAAAAATTATT
*
42295985 AAATTTTAATAA-AAAAATTA
1 AAATTTTAAAAATAAAAATTA
42296005 AATTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATTTTAAAAATAAAAATTATT
Found at i:42296012 original size:18 final size:20
Alignment explanation
Indices: 42295972--42296018 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
42295962 AAATTTTAAA
*
42295972 AATAAAAATTATTAAATTTT
1 AATAAAAATAATTAAATTTT
42295992 AATAAAAA-AATTAAA-TTT
1 AATAAAAATAATTAAATTTT
42296010 AATAAAAAT
1 AATAAAAAT
42296019 TAGAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 11 0.44
19 6 0.24
20 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAAAAATAATTAAATTTT
Found at i:42296081 original size:19 final size:19
Alignment explanation
Indices: 42295973--42296082 Score: 64
Period size: 19 Copynumber: 5.8 Consensus size: 19
42295963 AATTTTAAAA
*
42295973 ATAAAAATTATTAAATTTT
1 ATAAAAATTATAAAATTTT
* * *
42295992 AATAAAAA-AATTAAATTTA
1 -ATAAAAATTATAAAATTTT
* **
42296011 ATAAAAATTAGAATTTTTT
1 ATAAAAATTATAAAATTTT
***
42296030 ATAAAAATCGTA-AAAAAAAT
1 ATAAAAAT--TATAAAATTTT
*
42296050 A-AAAAATTGTAAAATTTT
1 ATAAAAATTATAAAATTTT
*
42296068 ATAAAAATCATAAAA
1 ATAAAAATTATAAAA
42296083 AATTAACGAC
Statistics
Matches: 66, Mismatches: 19, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
17 1 0.02
18 13 0.20
19 39 0.59
20 11 0.17
21 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (19 bp):
ATAAAAATTATAAAATTTT
Found at i:42296250 original size:20 final size:19
Alignment explanation
Indices: 42296225--42296289 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
42296215 TATAATAATT
42296225 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTAC-AAA
* **
42296245 TTTAT-ATTTCTTTACATT
1 TTTATAATTTTTTTACAAA
* *
42296263 TTGTATAATTTTCTTACAAC
1 TT-TATAATTTTTTTACAAA
42296283 TTTATAA
1 TTTATAA
42296290 AAACTTATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 3 0.08
19 17 0.47
20 16 0.44
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTATAATTTTTTTACAAA
Found at i:42296356 original size:8 final size:8
Alignment explanation
Indices: 42296294--42296375 Score: 56
Period size: 8 Copynumber: 9.2 Consensus size: 8
42296284 TTATAAAAAC
*
42296294 TTATAATT
1 TTATATTT
42296302 TTATAATTTT
1 TTAT-A-TTT
42296312 TTATATTT
1 TTATATTT
42296320 CTATATATTT
1 -T-TATATTT
*
42296330 TATAATTTTT
1 T-T-ATATTT
*
42296340 TTACAATTT
1 TTA-TATTT
42296349 TTATATTT
1 TTATATTT
*
42296357 TTACGATTT
1 TTA-TATTT
42296366 TTATATTT
1 TTATATTT
42296374 TT
1 TT
42296376 TTTAAATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
8 21 0.35
9 20 0.33
10 19 0.32
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (8 bp):
TTATATTT
Found at i:42296359 original size:17 final size:17
Alignment explanation
Indices: 42296294--42296375 Score: 74
Period size: 17 Copynumber: 4.6 Consensus size: 17
42296284 TTATAAAAAC
* *
42296294 TTATAATTTTATAATTTT
1 TTATATTTTTACAA-TTT
* *
42296312 TTATATTTCTATATATTT
1 TTATATTTTTACA-ATTT
*
42296330 TATAATTTTTTTACAATTT
1 T-T-ATATTTTTACAATTT
*
42296349 TTATATTTTTACGATTT
1 TTATATTTTTACAATTT
42296366 TTATATTTTT
1 TTATATTTTT
42296376 TTTAAATTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
17 23 0.43
18 16 0.30
19 7 0.13
20 8 0.15
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (17 bp):
TTATATTTTTACAATTT
Found at i:42296377 original size:28 final size:28
Alignment explanation
Indices: 42296346--42296412 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
42296336 TTTTTTACAA
* *
42296346 TTTTTATATTTTTACGATTTTT-ATATTT
1 TTTTTAAATTTTTA-AATTTTTAATATTT
42296374 TTTTTAAATTTTTAAATTTTTAATATTT
1 TTTTTAAATTTTTAAATTTTTAATATTT
* *
42296402 TATTAAAATTT
1 TTTTTAAATTT
42296413 AATAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 6 0.18
28 28 0.82
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (28 bp):
TTTTTAAATTTTTAAATTTTTAATATTT
Found at i:42296385 original size:8 final size:8
Alignment explanation
Indices: 42296337--42296402 Score: 51
Period size: 8 Copynumber: 7.5 Consensus size: 8
42296327 TTTTATAATT
42296337 TTTTTACAA
1 TTTTTA-AA
*
42296346 TTTTTATA
1 TTTTTAAA
*
42296354 TTTTTACGA
1 TTTTTA-AA
*
42296363 TTTTTATATTT
1 TTTTTA-A--A
42296374 TTTTTAAA
1 TTTTTAAA
42296382 TTTTTAAA
1 TTTTTAAA
42296390 TTTTTAATA
1 TTTTTAA-A
42296399 TTTT
1 TTTT
42296403 ATTAAAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
8 22 0.47
9 18 0.38
10 1 0.02
11 6 0.13
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (8 bp):
TTTTTAAA
Found at i:42296393 original size:17 final size:17
Alignment explanation
Indices: 42296298--42296394 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
42296288 AAAAACTTAT
* *
42296298 AATTTTATAATTTTTTA
1 AATTTTTTAAATTTTTA
* * *
42296315 TATTTCTATATATTTTATA
1 AATTT-TTTAAATTTT-TA
*
42296334 ATTTTTTTACAATTTTTA
1 AATTTTTTA-AATTTTTA
* *
42296352 TA-TTTTTACGATTTTTA
1 AATTTTTTA-AATTTTTA
*
42296369 TATTTTTTTTAAATTTTTA
1 -A-ATTTTTTAAATTTTTA
42296388 AATTTTT
1 AATTTTT
42296395 AATATTTTAT
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
17 23 0.38
18 14 0.23
19 17 0.28
20 6 0.10
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (17 bp):
AATTTTTTAAATTTTTA
Found at i:42296407 original size:27 final size:28
Alignment explanation
Indices: 42296300--42296408 Score: 75
Period size: 28 Copynumber: 4.0 Consensus size: 28
42296290 AAACTTATAA
* *
42296300 TTTTATAATTTTTTATATTTCTA-TATAT
1 TTTTACAATTTTTTATATTT-TATTAAAT
* * * *
42296328 TTTATA-ATTTTTTTACAATTT-TTATAT
1 TTT-TACAATTTTTTATATTTTATTAAAT
* *
42296355 TTTTACGA-TTTTTATATTTTTTTTAAAT
1 TTTTACAATTTTTTATA-TTTTATTAAAT
*
42296383 TTTTA-AATTTTTAATATTTTATTAAA
1 TTTTACAATTTTTTATATTTTATTAAA
42296409 ATTTAATAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
26 9 0.14
27 22 0.34
28 31 0.48
29 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTTACAATTTTTTATATTTTATTAAAT
Found at i:42296457 original size:9 final size:9
Alignment explanation
Indices: 42296294--42296459 Score: 76
Period size: 9 Copynumber: 18.3 Consensus size: 9
42296284 TTATAAAAAC
42296294 TTATAA-TT
1 TTATAATTT
42296302 TTATAATTT
1 TTATAATTT
42296311 TT-TATATTT
1 TTATA-ATTT
*
42296320 CTAT-ATATT
1 TTATAAT-TT
42296329 TTATAATTTTT
1 TTATAA--TTT
*
42296340 TTACAATTT
1 TTATAATTT
42296349 TTAT-ATTT
1 TTATAATTT
**
42296357 TTACGATTT
1 TTATAATTT
*
42296366 TTATATTTT
1 TTATAATTT
*
42296375 TTTTAAATTT
1 TTAT-AATTT
42296385 TTA-AATTT
1 TTATAATTT
*
42296393 TTAATATTTT
1 TT-ATAATTT
*
42296403 ATTA-AAATT
1 -TTATAATTT
* *
42296412 TAATAATAT
1 TTATAATTT
**
42296421 TTATAGCTT
1 TTATAATTT
*
42296430 TTATTGA-TT
1 TTA-TAATTT
**
42296439 TTATTTTTT
1 TTATAATTT
42296448 TTATAATTT
1 TTATAATTT
42296457 TTA
1 TTA
42296460 ATAAAAACAG
Statistics
Matches: 116, Mismatches: 27, Indels: 29
0.67 0.16 0.17
Matches are distributed among these distances:
8 27 0.23
9 65 0.56
10 14 0.12
11 9 0.08
12 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTATAATTT
Found at i:42296678 original size:99 final size:99
Alignment explanation
Indices: 42296495--42296678 Score: 234
Period size: 99 Copynumber: 1.9 Consensus size: 99
42296485 TCTTGAAAAA
* * *
42296495 GTTTGAGGGTCTTTTGATGCATTTTGAAAGCTCAAGTACCCAATTGAATGCAAAAAAATAAAACA
1 GTTTGAGGGTCTTTTGATGCATTTTGAAAGCTCAAATACCCAAATGAATGCAAAAAAATAAAAAA
* *
42296560 GTAGGGGCTTAATTGTTTTTTTTTTTTTTGAAAG
66 GTAGGAGCATAATTGTTTTTTTTTTTTTTGAAAG
* *
42296594 GTTTGAGGG-CTTTTTTATGCATTTTGAAAG-TCCAAATACCCAAATGAGTGCAAAAAAA-AAAA
1 GTTTGAGGGTC-TTTTGATGCATTTTGAAAGCT-CAAATACCCAAATGAATGCAAAAAAATAAAA
**
42296656 AAG-A-GAGCATAATTACTTTTTTT
64 AAGTAGGAGCATAATTGTTTTTTTT
42296679 GAAAAAGCTT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
96 15 0.20
97 1 0.01
98 8 0.11
99 50 0.68
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (99 bp):
GTTTGAGGGTCTTTTGATGCATTTTGAAAGCTCAAATACCCAAATGAATGCAAAAAAATAAAAAA
GTAGGAGCATAATTGTTTTTTTTTTTTTTGAAAG
Found at i:42296821 original size:12 final size:12
Alignment explanation
Indices: 42296798--42296829 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
42296788 ATGAAATGAA
42296798 ATTATCATTTACC
1 ATTAT-ATTTACC
42296811 ATTATATTTACC
1 ATTATATTTACC
42296823 ATTATAT
1 ATTATAT
42296830 CACTCAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTATATTTACC
Found at i:42299749 original size:34 final size:33
Alignment explanation
Indices: 42299710--42299806 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 33
42299700 GGACTTAGAA
42299710 AATATAAAATATTTGAAATATTTTAATATAACTT
1 AATATAAAATATTT-AAATATTTTAATATAACTT
** *
42299744 AATATAAAATATTT-AAT-TTCAAAATATAATTT
1 AATATAAAATATTTAAATATT-TTAATATAACTT
* *
42299776 AAAATAAAATATTTTAAATAATTTAATATAA
1 AATATAAAATA-TTTAAATATTTTAATATAA
42299807 AAATAATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
31 2 0.04
32 22 0.42
33 3 0.06
34 24 0.46
35 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (33 bp):
AATATAAAATATTTAAATATTTTAATATAACTT
Found at i:42299859 original size:11 final size:11
Alignment explanation
Indices: 42299811--42299860 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
42299801 ATATAAAAAT
42299811 AATTA-TATTA
1 AATTATTATTA
* *
42299821 AAATATGATTA
1 AATTATTATTA
42299832 AATTATTTATT-
1 AATTA-TTATTA
*
42299843 ATTTATTATTA
1 AATTATTATTA
42299854 AATTATT
1 AATTATT
42299861 TGTAACACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
10 9 0.29
11 18 0.58
12 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
AATTATTATTA
Found at i:42300469 original size:13 final size:13
Alignment explanation
Indices: 42300445--42300488 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
42300435 TTAAGTCTTT
42300445 TACAGATACAGATA
1 TACAGA-ACAGATA
42300459 -ACAGAATCAGATA
1 TACAGAA-CAGATA
*
42300472 TGCAGAACAGATA
1 TACAGAACAGATA
42300485 TACA
1 TACA
42300489 AAATCCTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 1 0.04
13 20 0.77
14 5 0.19
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (13 bp):
TACAGAACAGATA
Found at i:42304938 original size:16 final size:16
Alignment explanation
Indices: 42304917--42304955 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42304907 TAAATTACTA
**
42304917 ATTACAGCTCTATTTC
1 ATTACAGCTCTATACC
*
42304933 ATTACAACTCTATACC
1 ATTACAGCTCTATACC
42304949 ATTACAG
1 ATTACAG
42304956 AGAGTTAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATACC
Found at i:42314349 original size:51 final size:50
Alignment explanation
Indices: 42314178--42314366 Score: 224
Period size: 51 Copynumber: 3.7 Consensus size: 50
42314168 AAAGTGAAAG
* *
42314178 TGATGGTCACATGTGTAGTACTATGTGCAAGCTACTACATGTACCAGA-A
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA
* * *
42314227 TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA
* *
42314278 -GAT--TCGATCATGTGTATAGTACTATATGCAGGCTACTACGTGTATCAGATA
1 TGATGGTC-A-CATGTG--TAGTACTATGTGCAGGCTACTACGTGTACCAGATA
*
42314329 GTGATGGTCCCATGTGTAGTACTATGTGCAGGCTACTA
1 -TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
42314367 TGTGAACCGG
Statistics
Matches: 118, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
47 2 0.02
49 10 0.08
50 42 0.36
51 53 0.45
53 9 0.08
55 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (50 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA
Found at i:42314615 original size:16 final size:16
Alignment explanation
Indices: 42314594--42314625 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42314584 TGATTGAAAG
*
42314594 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
42314610 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
42314626 GCAACAAAAT
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:42315697 original size:31 final size:31
Alignment explanation
Indices: 42315659--42315721 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
42315649 ATTTTGAGAT
42315659 TAATTTTCTAGTCAAATAAACGACAAATGAA
1 TAATTTTCTAGTCAAATAAACGACAAATGAA
*
42315690 TAATTTTCTAGTCAAATAAATGACAAATGAA
1 TAATTTTCTAGTCAAATAAACGACAAATGAA
42315721 T
1 T
42315722 TGATTACGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32
Consensus pattern (31 bp):
TAATTTTCTAGTCAAATAAACGACAAATGAA
Found at i:42320964 original size:18 final size:18
Alignment explanation
Indices: 42320941--42320975 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42320931 AGGGGTTTTT
*
42320941 TTTTTAACCTTATTTTCC
1 TTTTTAAACTTATTTTCC
*
42320959 TTTTTAAACTTTTTTTC
1 TTTTTAAACTTATTTTC
42320976 TTAATTTTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAAACTTATTTTCC
Found at i:42322360 original size:3 final size:3
Alignment explanation
Indices: 42322354--42322471 Score: 236
Period size: 3 Copynumber: 39.3 Consensus size: 3
42322344 TGTATTTCAA
42322354 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42322402 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42322450 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
42322472 GTACATTAGT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 115 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42322654 original size:117 final size:121
Alignment explanation
Indices: 42322450--42322670 Score: 292
Period size: 120 Copynumber: 1.9 Consensus size: 121
42322440 TTATTATTAT
* * * *
42322450 TATTATTATTATTATTATTATTGTACATTAGTGTATATCTTCATGTATGTATATATATATGTAGT
1 TATTATTATTATTATTATCATTGAACATTAGTATATATCTTCATGTATGTATATATATATATAGT
*
42322515 AATGTTTTTATTACTTTATTTTAATAT-TTTTATTATAATAGCTTTTGTATTTCAA
66 AATGTTTTTATGACTTTATTTTAATATATTTTATTATAATAGCTTTTGTATTTCAA
* * *
42322570 TATTATTATTATTATTATCATT-AACATTATTATATATTCTT-AT-TA-G-ATGTATATATATAT
1 TATTATTATTATTATTATCATTGAACATTAGTATATA-TCTTCATGTATGTATATATATATATAG
*
42322630 TACTGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
65 TAATGTTTTT-ATGACTTTATTTTAATAT-ATTTTATTATA
42322671 TTTACTTTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
116 20 0.23
117 18 0.20
118 2 0.02
119 23 0.26
120 25 0.28
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (121 bp):
TATTATTATTATTATTATCATTGAACATTAGTATATATCTTCATGTATGTATATATATATATAGT
AATGTTTTTATGACTTTATTTTAATATATTTTATTATAATAGCTTTTGTATTTCAA
Found at i:42322804 original size:22 final size:23
Alignment explanation
Indices: 42322776--42322857 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 23
42322766 AATTTTTTTA
42322776 ATATATATTATATGAATA-ATTT
1 ATATATATTATATGAATATATTT
* *
42322798 ATATATAATATTATGTATATATTT
1 ATATATATTA-TATGAATATATTT
* *
42322822 -TA-ATATTATCAGTTATATATCTTT
1 ATATATATTAT-A-TGA-ATATATTT
42322846 ATACTATATTAT
1 ATA-TATATTAT
42322858 TTCTAATACT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
21 1 0.02
22 15 0.33
23 10 0.22
24 11 0.24
25 2 0.04
27 7 0.15
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (23 bp):
ATATATATTATATGAATATATTT
Found at i:42323003 original size:22 final size:20
Alignment explanation
Indices: 42322971--42323011 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
42322961 TAAATATATG
*
42322971 TATATATTGTATGTATTTTA
1 TATATATTGTATATATTTTA
42322991 TATATATTATGTATATATTTT
1 TATATA-T-TGTATATATTTT
42323012 TAATATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
TATATATTGTATATATTTTA
Found at i:42323517 original size:3 final size:3
Alignment explanation
Indices: 42323466--42323535 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
42323456 TTTTCACATT
* * * *
42323466 TTA TT- TTA TTT TTA ATA TTA TTAA GTTA -TA TTT TTA -TA TTC TT-
1 TTA TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA
42323509 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
42323536 ATTTATATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
2 8 0.15
3 42 0.78
4 2 0.04
5 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42324587 original size:234 final size:226
Alignment explanation
Indices: 42324162--42324624 Score: 569
Period size: 234 Copynumber: 2.0 Consensus size: 226
42324152 GTGCTAATAT
* * *
42324162 CTTCCTCGCGCGTAACCGACTCCCGGACCCTACTTTGCTCTGATTTTAGCGTAGACCTAAACTCA
1 CTTCCTCGCGCGTAACCGACTCCCGAACCCTAATTTGCTCTGATTTGAGCGTAGACCTAAACTCA
* * * *
42324227 GCCTCCTTTTGTTTTAAAAATAAACTTATTAGGTGTCCGATCACACCTATAAAAAGGATCGGTGG
66 GCCTCATTTTGTTTTAAAAATAAAATTAATAGGTGTCCGATCACACCTATAAAAAAGATCGGTGG
* * *
42324292 CGACTCCTCTCTTTATTTTGAAATCAAACTTCAGTTTTCAAGTTTTCAATAAACAGCCACAATTA
131 CGACTCCTCTCTTTATTTTAAAATCAAACTTCAATTTCCAAGTTTTCAATAAACAGCCACAATTA
42324357 GCGACCGAAAGCAAATTTTTACGTCGCTACA-C
196 GCGACC--AAGCAAATTTTTACGTCGCTACATC
* *
42324389 CTTCCTGGCGCGTAACCGACTCCCGAACCCTAATTTGTCTCTGGAATTTGA-CGTGGACCTAAAC
1 CTTCCTCGCGCGTAACCGACTCCCGAACCCTAATTTG-CTCT-G-ATTTGAGCGTAGACCTAAAC
* * *
42324453 TTATCCTTCATTTTGTTTTAAAAATAAAGGAATCTAATGGGTGTCCGATCACACCCTA-AAAAAA
63 TCAGCC-TCATTTTGTTTTAAAAAT-AA--AAT-TAATAGGTGTCCGATCACA-CCTATAAAAAA
* * *
42324517 GATCGGTGGCGACTTC-CTGTTTATTTTAAAATC-AACTTTCAATTTCCAAGTTTCTTAATAAAT
122 GATCGGTGGCGACTCCTCTCTTTATTTTAAAATCAAAC-TTCAATTTCCAAGTTT-TCAATAAA-
** *
42324580 C-GCCACAATTAGCGGTCAAGTAAATTTTTACGTCGCTACATC
184 CAGCCACAATTAGCGACCAAGCAAATTTTTACGTCGCTACATC
42324622 CTT
1 CTT
42324625 TTCCAATGAG
Statistics
Matches: 202, Mismatches: 21, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
227 34 0.17
228 4 0.02
229 17 0.08
230 22 0.11
231 2 0.01
232 25 0.12
233 35 0.17
234 58 0.29
235 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (226 bp):
CTTCCTCGCGCGTAACCGACTCCCGAACCCTAATTTGCTCTGATTTGAGCGTAGACCTAAACTCA
GCCTCATTTTGTTTTAAAAATAAAATTAATAGGTGTCCGATCACACCTATAAAAAAGATCGGTGG
CGACTCCTCTCTTTATTTTAAAATCAAACTTCAATTTCCAAGTTTTCAATAAACAGCCACAATTA
GCGACCAAGCAAATTTTTACGTCGCTACATC
Found at i:42337306 original size:163 final size:163
Alignment explanation
Indices: 42337036--42337356 Score: 588
Period size: 163 Copynumber: 2.0 Consensus size: 163
42337026 AGTATTTGTT
* * *
42337036 GCATGATGCCTAGGAACCATTTTGGAATGAGCTAATTGTATATGTATTCTGTATTTTTATGCCCA
1 GCATGATGCCTAGGAACCATTTTGGAACGAGCTAATTGCAAATGTATTCTGTATTTTTATGCCCA
*
42337101 GTGGCAGAGGTATCAATATTTCGGGTTTAAGATTGATACTTCTGTGTTTCGAAATGTGTAGGAAG
66 GTGGCAGAGGTATCAATATTTCGAGTTTAAGATTGATACTTCTGTGTTTCGAAATGTGTAGGAAG
*
42337166 TCAGAATAGAGGTTTGGTATCGATACTCGGGAA
131 TCAGAATAGAGATTTGGTATCGATACTCGGGAA
42337199 GCATGATGCCTAGGAACCATTTTGGAACGAGCTAATTGCAAATGTATTCTGTATTTTTATGCCCA
1 GCATGATGCCTAGGAACCATTTTGGAACGAGCTAATTGCAAATGTATTCTGTATTTTTATGCCCA
*
42337264 GTGGTAGAGGTATCAATATTTCGAGTTTAAGATTGATACTTCTGTGTTTCGAAATGTGTAGGAAG
66 GTGGCAGAGGTATCAATATTTCGAGTTTAAGATTGATACTTCTGTGTTTCGAAATGTGTAGGAAG
42337329 TCAGAATAGAGATTTGGTATCGATACTC
131 TCAGAATAGAGATTTGGTATCGATACTC
42337357 TTTCCNNNNN
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
163 152 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.35
Consensus pattern (163 bp):
GCATGATGCCTAGGAACCATTTTGGAACGAGCTAATTGCAAATGTATTCTGTATTTTTATGCCCA
GTGGCAGAGGTATCAATATTTCGAGTTTAAGATTGATACTTCTGTGTTTCGAAATGTGTAGGAAG
TCAGAATAGAGATTTGGTATCGATACTCGGGAA
Found at i:42339392 original size:21 final size:21
Alignment explanation
Indices: 42339367--42339410 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
42339357 TCGAGTAGTC
42339367 AATCTATTTG-AAATCTTGCCA
1 AATCT-TTTGCAAATCTTGCCA
42339388 AATCTTTTGCAAATCTTGCCA
1 AATCTTTTGCAAATCTTGCCA
42339409 AA
1 AA
42339411 ACTTGATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (21 bp):
AATCTTTTGCAAATCTTGCCA
Found at i:42340005 original size:38 final size:38
Alignment explanation
Indices: 42339963--42340053 Score: 164
Period size: 38 Copynumber: 2.4 Consensus size: 38
42339953 CTCTATTGAG
* *
42339963 TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTAAA
1 TACATGTTAAGCATGTCTACTGCTACTGTTAAACTAAA
42340001 TACATGTTAAGCATGTCTACTGCTACTGTTAAACTAAA
1 TACATGTTAAGCATGTCTACTGCTACTGTTAAACTAAA
42340039 TACATGTTAAGCATG
1 TACATGTTAAGCATG
42340054 CTTATTGTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (38 bp):
TACATGTTAAGCATGTCTACTGCTACTGTTAAACTAAA
Found at i:42340459 original size:18 final size:18
Alignment explanation
Indices: 42340436--42340473 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42340426 TTTAAGAGAT
*
42340436 TTTTTTGTACAATTATGA
1 TTTTTTGTACAACTATGA
*
42340454 TTTTTTTTACAACTATGA
1 TTTTTTGTACAACTATGA
42340472 TT
1 TT
42340474 CAAACCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (18 bp):
TTTTTTGTACAACTATGA
Found at i:42345997 original size:12 final size:12
Alignment explanation
Indices: 42345980--42346005 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42345970 GATAATATGA
42345980 TTGATTGGTTGG
1 TTGATTGGTTGG
42345992 TTGATTGGTTGG
1 TTGATTGGTTGG
42346004 TT
1 TT
42346006 TGAGCAGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (12 bp):
TTGATTGGTTGG
Found at i:42351450 original size:20 final size:20
Alignment explanation
Indices: 42351425--42351467 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
42351415 TGGTTCAAAG
42351425 GGTAAGAAAATGAATGGAAT
1 GGTAAGAAAATGAATGGAAT
* *
42351445 GGTAAGTAAATTAATGGAAT
1 GGTAAGAAAATGAATGGAAT
42351465 GGT
1 GGT
42351468 TCATGATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (20 bp):
GGTAAGAAAATGAATGGAAT
Found at i:42352853 original size:18 final size:18
Alignment explanation
Indices: 42352816--42352851 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42352806 TTAATTTGGT
42352816 TAAAACGGGTTTTAAAAA
1 TAAAACGGGTTTTAAAAA
*
42352834 TAAAATCGGGTTTGAAAA
1 TAAAA-CGGGTTTTAAAA
42352852 TATTTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (18 bp):
TAAAACGGGTTTTAAAAA
Found at i:42357214 original size:43 final size:43
Alignment explanation
Indices: 42357133--42357214 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
42357123 ATTCGAAGAG
* * *
42357133 AGGGGAATGTGGTTGTTGATTGGATAGGTATAACTTGTCTGAA
1 AGGGGAATGTGGTTGTTAATTGGATAGCTAGAACTTGTCTGAA
*
42357176 AGGGGAATGTGGTTGTTAATTGGATAGCTAGAATTTGTC
1 AGGGGAATGTGGTTGTTAATTGGATAGCTAGAACTTGTC
42357215 CGAGAGGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.26, C:0.05, G:0.34, T:0.35
Consensus pattern (43 bp):
AGGGGAATGTGGTTGTTAATTGGATAGCTAGAACTTGTCTGAA
Found at i:42362009 original size:14 final size:14
Alignment explanation
Indices: 42361986--42362016 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42361976 AATGAGGAGG
42361986 AGCTCATCTGTTAC
1 AGCTCATCTGTTAC
*
42362000 AGCTCCTCTGTTAC
1 AGCTCATCTGTTAC
42362014 AGC
1 AGC
42362017 CCGTTTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (14 bp):
AGCTCATCTGTTAC
Found at i:42368877 original size:14 final size:14
Alignment explanation
Indices: 42368854--42368884 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42368844 AATGAGGAGG
42368854 AGCTCATCTGTTAC
1 AGCTCATCTGTTAC
*
42368868 AGCTCCTCTGTTAC
1 AGCTCATCTGTTAC
42368882 AGC
1 AGC
42368885 CCGTTTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (14 bp):
AGCTCATCTGTTAC
Found at i:42370960 original size:43 final size:43
Alignment explanation
Indices: 42370899--42371006 Score: 162
Period size: 43 Copynumber: 2.5 Consensus size: 43
42370889 ACTTTCAAGG
* *
42370899 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGTATCGATT
1 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
*
42370942 TGAGATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
* *
42370985 CGAGATTTCCATGTAAGACCAT
1 TGAGATTT-CGTGTAAGACCAT
42371007 GTCTAGGACA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 47 0.81
44 11 0.19
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
Found at i:42373265 original size:25 final size:25
Alignment explanation
Indices: 42373235--42373318 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 25
42373225 CAGCTCTTAT
*
42373235 GAGCTTACCGTTACTCAACTCGGAG
1 GAGCTTACCGTTATTCAACTCGGAG
* *
42373260 GAGCTTACCGTTATTCATCTCAGAG
1 GAGCTTACCGTTATTCAACTCGGAG
** * *
42373285 GAGCTTATAGTTATTCAGCTCGAAG
1 GAGCTTACCGTTATTCAACTCGGAG
42373310 GAGCTTACC
1 GAGCTTACC
42373319 ATCTACAACT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAACTCGGAG
Found at i:42379254 original size:17 final size:17
Alignment explanation
Indices: 42379229--42379263 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42379219 AATATTAATT
*
42379229 TATCAATAAACTAATAA
1 TATCAATAAAATAATAA
*
42379246 TATCGATAAAATAATAA
1 TATCAATAAAATAATAA
42379263 T
1 T
42379264 TTTTTTAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (17 bp):
TATCAATAAAATAATAA
Found at i:42393918 original size:12 final size:12
Alignment explanation
Indices: 42393890--42393932 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
42393880 AACCGTTTTC
*
42393890 AAAAAAAAAGAA
1 AAAAAAAAACAA
42393902 GAAAAAAAAACAA
1 -AAAAAAAAACAA
*
42393915 AAAAGAAAACAA
1 AAAAAAAAACAA
42393927 AGAAAA
1 A-AAAA
42393933 GGGGAATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:42393920 original size:17 final size:16
Alignment explanation
Indices: 42393890--42393923 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
42393880 AACCGTTTTC
*
42393890 AAAAAAAAAGAAGAAA
1 AAAAAAAAAAAAGAAA
42393906 AAAAAACAAAAAAGAAA
1 AAAAAA-AAAAAAGAAA
42393923 A
1 A
42393924 CAAAGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAA
Found at i:42398390 original size:15 final size:15
Alignment explanation
Indices: 42398366--42398399 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42398356 AACAATTACG
* *
42398366 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
42398381 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
42398396 ATAA
1 ATAA
42398400 CAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:42399419 original size:11 final size:11
Alignment explanation
Indices: 42399403--42399427 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42399393 TATAAACAAC
42399403 AAAAAACAAAA
1 AAAAAACAAAA
42399414 AAAAAACAAAA
1 AAAAAACAAAA
42399425 AAA
1 AAA
42399428 CGAAAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:42401535 original size:19 final size:18
Alignment explanation
Indices: 42401503--42401539 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
42401493 TTTTCTTATT
*
42401503 TTTAAAAATTAAAATAAA
1 TTTAAAAATAAAAATAAA
42401521 TTTAATAAATAAAAATAAA
1 TTTAA-AAATAAAAATAAA
42401540 AATATTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TTTAAAAATAAAAATAAA
Found at i:42404330 original size:37 final size:38
Alignment explanation
Indices: 42404258--42404344 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
42404248 CTTCGACCAA
* *
42404258 CCTGAACACCACATACGAGCTATATCAAGCCCATCCAC
1 CCTGCACACCACATACGAGCCATATCAAGCCCATCCAC
* *
42404296 CCTGCACACCACATAGGA-CCATGAT-AAGCCCATCCTC
1 CCTGCACACCACATACGAGCCAT-ATCAAGCCCATCCAC
*
42404333 CCTACACACCAC
1 CCTGCACACCAC
42404345 GATTGTGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 25 0.58
38 18 0.42
ACGTcount: A:0.32, C:0.43, G:0.10, T:0.15
Consensus pattern (38 bp):
CCTGCACACCACATACGAGCCATATCAAGCCCATCCAC
Found at i:42406541 original size:14 final size:14
Alignment explanation
Indices: 42406522--42406568 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
42406512 CAGTGTTGCG
42406522 AACCCCTATAGGCA
1 AACCCCTATAGGCA
* * *
42406536 AGCCCCTTTATGCA
1 AACCCCTATAGGCA
*
42406550 AACACCTATAGGCA
1 AACCCCTATAGGCA
42406564 AACCC
1 AACCC
42406569 ATATGTCAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.34, C:0.36, G:0.13, T:0.17
Consensus pattern (14 bp):
AACCCCTATAGGCA
Found at i:42408229 original size:88 final size:87
Alignment explanation
Indices: 42408132--42408676 Score: 519
Period size: 88 Copynumber: 6.2 Consensus size: 87
42408122 CTACTGCTAG
* * * * *
42408132 TACATGAAGACAATATTTGCTTTCTTCGATCCAC-TCCCTACCAATATAGGGAGACAGGA-CATG
1 TACATGAAGACAAGATCTGCTATCTTCGATCCACTTCCC-ACCAATATAGGAAGACAAGATC-TG
*
42408195 TTATCTTCGATCTACTTCACGCCAA
64 -CATCTTCGATCTACTTCACGCCAA
* * * * * *
42408220 TACATGAAGACAAGATCTGC-ATCTTGGATCCACTTCCTATCAATATAGGAAGATAAGACCAGCC
1 TACATGAAGACAAGATCTGCTATCTTCGATCCACTTCCCACCAATATAGGAAGACAAGATCTG-C
*
42408284 ATCCTCGATCTACTTCACGCCAA
65 ATCTTCGATCTACTTCACGCCAA
* * * * * *
42408307 TACGTGAAGATAAGATCTTCTTTCTTTGATCTACTTCGCCACCAATAT-GGAAAGACAAGATCTG
1 TACATGAAGACAAGATCTGCTATCTTCGATCCACTTC-CCACCAATATAGG-AAGACAAGATCTG
42408371 CATCTTCGATCTACTTCACGCCAA
64 CATCTTCGATCTACTTCACGCCAA
* * * *
42408395 TACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT-GGAAAGACAAGATCTG
1 TACATGAAGACAAGATCTGCTATCTTCGATCCACTTC-CCACCAATATAGG-AAGACAAGATCTG
* *
42408459 CATCTTCGATCCACTTC-CTACCAA
64 CATCTTCGATCTACTTCAC-GCCAA
* * * * * * * * *
42408483 TATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
1 TACATGAAGACAAGATCTGCTATCTTCGATCCACTTCCCACCAATATAGGAAGACAAGATCTGC-
* * * *
42408548 TTCTGCGATCTACTTCGCCACCAA
65 ATCTTCGATCTACTTC-ACGCCAA
*** * * * *
42408572 TATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTATCAATATAGGAAGATAGGATCTGCT
1 TACATGAAGACAAGATCTGCTATCTTCGATCCACTTCCCACCAATATAGGAAGACAAGATCTGC-
*
42408636 ACCTTCGATCTACTTCACGCCAA
65 ATCTTCGATCTACTTCACGCCAA
42408659 TACATGAAGACAAGATCT
1 TACATGAAGACAAGATCT
42408677 NTAAAATTAA
Statistics
Matches: 384, Mismatches: 63, Indels: 21
0.82 0.13 0.04
Matches are distributed among these distances:
87 109 0.28
88 234 0.61
89 40 0.10
90 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (87 bp):
TACATGAAGACAAGATCTGCTATCTTCGATCCACTTCCCACCAATATAGGAAGACAAGATCTGCA
TCTTCGATCTACTTCACGCCAA
Found at i:42408396 original size:132 final size:131
Alignment explanation
Indices: 42408132--42408676 Score: 552
Period size: 132 Copynumber: 4.1 Consensus size: 131
42408122 CTACTGCTAG
* * * * * * *
42408132 TACATGAAGACAATATTTGCTTTCTTCGATCCAC-TC-CCTACCAATATAGGGAGACAGGA-CAT
1 TACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCC-ACCAATAT-GGAAGACAAGATC-T
* * * * * * *
42408194 GTTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGC-ATCTTGGATCCACTTC-
63 G-CATCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
**
42408256 CTATCAA
126 C-GCCAA
* * * * * * * * * * *
42408263 TATAGGAAGATAAGACCAGCCATCCT-CGATCTACTTC-ACGCCAATACGTGAAGATAAGATCTT
1 TACATGAAGATAAGATCTG-CTTTCTGCGATCTACTTCGCCACCAATATG-GAAGACAAGATCTG
* * * *
42408326 CTTTCTTTGATCTACTTCGCCACCAATAT-GGAAAGACAAGATCTGC-ATCTTCGATCTACTTCA
64 C-ATCTTCGATCCACTTC-CTACCAATATAGG-AAGACAAGATCTGCTATCTTCGATCTACTTCA
42408389 CGCCAA
126 CGCCAA
42408395 TACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGAAAGACAAGATCTGC
1 TACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG-AAGACAAGATCTGC
* *
42408460 ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCC
65 ATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
42408525 AA
130 AA
*
42408527 TACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
1 TACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT-GGAAGACAAGATCTGC
* * * *
42408592 ATCTTCGATCCACTTCCTATCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCC
65 ATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
42408657 AA
130 AA
*
42408659 TACATGAAGACAAGATCT
1 TACATGAAGATAAGATCT
42408677 NTAAAATTAA
Statistics
Matches: 352, Mismatches: 48, Indels: 27
0.82 0.11 0.06
Matches are distributed among these distances:
130 1 0.00
131 74 0.21
132 254 0.72
133 23 0.07
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (131 bp):
TACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGAAGACAAGATCTGCA
TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA
A
Found at i:42408520 original size:220 final size:220
Alignment explanation
Indices: 42408226--42408651 Score: 638
Period size: 220 Copynumber: 1.9 Consensus size: 220
42408216 CCAATACATG
* *
42408226 AAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAAGACCAGCCATCCTCG
1 AAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGACCAGCCATCCTCG
* * * **
42408291 ATCTACTTCACGCCAATACGTGAAGATAAGATCTTCTTTCTTTGATCTACTTCGCCACCAATATG
66 ATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
* * * **
42408356 GAAAGACAAGATCTGCATCTTCGATCTACTTCAC-GCCAATACATGAAGATAAGATCTGCTTTCT
131 GAAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATACAGGAAGATAAGATCTGCTACCT
42408420 GCGATCTACTTCGCCACCAATATGGA
195 GCGATCTACTTCGCCACCAATATGGA
* * * * *
42408446 AAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCG
1 AAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGACCAGCCATCCTCG
42408511 ATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
66 ATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
* * * * *
42408576 GGAAGACAAGATCTGCATCTTCGATCCACTTCCTATCAATATAGGAAGATAGGATCTGCTACCTT
131 GAAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATACAGGAAGATAAGATCTGCTACCTG
42408641 CGATCTACTTC
196 CGATCTACTTC
42408652 ACGCCAATAC
Statistics
Matches: 183, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
219 1 0.01
220 182 0.99
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (220 bp):
AAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGACCAGCCATCCTCG
ATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
GAAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATACAGGAAGATAAGATCTGCTACCTG
CGATCTACTTCGCCACCAATATGGA
Found at i:42409199 original size:19 final size:18
Alignment explanation
Indices: 42409167--42409203 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
42409157 TTTTCTTATT
*
42409167 TTTAAAAATTAAAATAAA
1 TTTAAAAATAAAAATAAA
42409185 TTTAATAAATAAAAATAAA
1 TTTAA-AAATAAAAATAAA
42409204 AATATTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TTTAAAAATAAAAATAAA
Found at i:42411994 original size:37 final size:38
Alignment explanation
Indices: 42411922--42412008 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
42411912 CTTCGACCAA
* *
42411922 CCTGAACACCACATACGAGCTATATCAAGCCCATCCAC
1 CCTGCACACCACATACGAGCCATATCAAGCCCATCCAC
* *
42411960 CCTGCACACCACATAGGA-CCATGAT-AAGCCCATCCTC
1 CCTGCACACCACATACGAGCCAT-ATCAAGCCCATCCAC
*
42411997 CCTACACACCAC
1 CCTGCACACCAC
42412009 GATTGTGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 25 0.58
38 18 0.42
ACGTcount: A:0.32, C:0.43, G:0.10, T:0.15
Consensus pattern (38 bp):
CCTGCACACCACATACGAGCCATATCAAGCCCATCCAC
Found at i:42414205 original size:14 final size:14
Alignment explanation
Indices: 42414186--42414232 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
42414176 CAGTGTTGCG
42414186 AACCCCTATAGGCA
1 AACCCCTATAGGCA
* * *
42414200 AGCCCCTTTATGCA
1 AACCCCTATAGGCA
*
42414214 AACACCTATAGGCA
1 AACCCCTATAGGCA
42414228 AACCC
1 AACCC
42414233 ATATGTCAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.34, C:0.36, G:0.13, T:0.17
Consensus pattern (14 bp):
AACCCCTATAGGCA
Found at i:42418097 original size:44 final size:44
Alignment explanation
Indices: 42417715--42418236 Score: 178
Period size: 44 Copynumber: 11.7 Consensus size: 44
42417705 CGCAACGTCG
* * * *
42417715 GGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCA
1 GGGAGATAAGATTATCGGCTTCAATCTGCTCCACTGTAACTTCA
* ** ** * *
42417759 AGGAGATAAGATT-TGCTTCTTCGGTCTGCCCCACTGCAACTTCA
1 GGGAGATAAGATTAT-CGGCTTCAATCTGCTCCACTGTAACTTCA
* * *** * * * *
42417803 GGGGGATAAGACTTGTTTTC-TCAGTCTGCTCCGCTGCAACCTCA
1 GGGAGATAAGA-TTATCGGCTTCAATCTGCTCCACTGTAACTTCA
* *
42417847 GGGAGATAAGACCTAAT--GCAATTC-A-CT-CT--ACTGCAACTTCA
1 GGGAGATAAGA--TTATCGGC--TTCAATCTGCTCCACTGTAACTTCA
* ** * * *
42417888 GAGAGATAAGATATAT-TACTTTAATCCGTTCCACTGTAACTTCA
1 GGGAGATAAGAT-TATCGGCTTCAATCTGCTCCACTGTAACTTCA
* * * *
42417932 GGGAGATAGGA-TAGT-GTCTTCGATCTGCTCCGCTGTAA-TTCA
1 GGGAGATAAGATTA-TCGGCTTCAATCTGCTCCACTGTAACTTCA
* * * * * * * *
42417974 AGGAGATAAGA-TCTCTGTCTTCAATCGGATGCGATCTATTCT-GCTTGA
1 GGGAGATAAGATTATC-GGCTTCAATC---TGC--TCCACTGTAACTTCA
* * * ** * *
42418022 GAGAGATAAGGTCATTTG-TTTAATCCGCTCCACTGTAACTTCA
1 GGGAGATAAGATTATCGGCTTCAATCTGCTCCACTGTAACTTCA
*
42418065 GGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCA
1 GGGAGATAAGATTATCGGCTTCAATCTGCTCCACTGTAACTTCA
*
42418109 GGGAGATAAGATT-TCTGGCTTCAATCGGATGTAATATACTCTACTGTAACTTCA
1 GGGAGATAAGATTATC-GGCTTCAATC---TG-------CTCCACTGTAACTTCA
* ** ** * * *
42418163 GAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAACTTCA
1 GGGAGATAAGATTATCGGCTTCAATCTGCTCCACTGTAACTTCA
*
42418207 GGGAGATAGGATTATCGGCTTCAATCTGCT
1 GGGAGATAAGATTATCGGCTTCAATCTGCT
42418237 TCCTTACACT
Statistics
Matches: 350, Mismatches: 90, Indels: 76
0.68 0.17 0.15
Matches are distributed among these distances:
39 3 0.01
40 3 0.01
41 23 0.07
42 22 0.06
43 48 0.14
44 178 0.51
45 8 0.02
46 6 0.02
47 8 0.02
48 15 0.04
49 1 0.00
51 1 0.00
54 33 0.09
55 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (44 bp):
GGGAGATAAGATTATCGGCTTCAATCTGCTCCACTGTAACTTCA
Found at i:42420659 original size:6 final size:6
Alignment explanation
Indices: 42420648--42420676 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42420638 TGGCCTCTCC
42420648 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
42420677 ATTATGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:42428154 original size:27 final size:27
Alignment explanation
Indices: 42428124--42428214 Score: 128
Period size: 27 Copynumber: 3.4 Consensus size: 27
42428114 ATTAGAATTC
*
42428124 GCCACAAAGGTGATCCATTCAGAGTAT
1 GCCACAAAGGTGATCCATTCAAAGTAT
* * *
42428151 GCCACATAGGCGATCCATTCAAAGTAC
1 GCCACAAAGGTGATCCATTCAAAGTAT
* *
42428178 ACCATAAAGGTGATCCATTCAAAGTAT
1 GCCACAAAGGTGATCCATTCAAAGTAT
42428205 GCCACAAAGG
1 GCCACAAAGG
42428215 CTAACAGGAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (27 bp):
GCCACAAAGGTGATCCATTCAAAGTAT
Found at i:42438868 original size:13 final size:13
Alignment explanation
Indices: 42438835--42438876 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
42438825 AGGGGTAGGA
42438835 GTATATCTGTTCT
1 GTATATCTGTTCT
*
42438848 GTACATCTGATTCT
1 GTATATCTG-TTCT
42438862 G-ATATCTGTTTCT
1 GTATATCTG-TTCT
42438875 GT
1 GT
42438877 TATAAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (13 bp):
GTATATCTGTTCT
Found at i:42444748 original size:22 final size:22
Alignment explanation
Indices: 42444723--42444766 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
42444713 ATTAAGATAA
42444723 AGTTTTAATGTACTTTAAATTC
1 AGTTTTAATGTACTTTAAATTC
42444745 AGTTTTAATGTACTTTAAATTC
1 AGTTTTAATGTACTTTAAATTC
42444767 TAATAGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (22 bp):
AGTTTTAATGTACTTTAAATTC
Found at i:42445280 original size:30 final size:30
Alignment explanation
Indices: 42445191--42445280 Score: 85
Period size: 30 Copynumber: 2.9 Consensus size: 30
42445181 TGCTCAATAC
*
42445191 TTACATATTCTATCAATTTGA-TTCAAATT
1 TTACAAATTCTATCAATTTGACTTCAAATT
* * * *
42445220 TTAAATAATTCAATAAATTTAACCCTTCAAA-T
1 TTACA-AATTCTATCAATTTGA--CTTCAAATT
42445252 TTACAAATTCTATCAATTTGATCTTCAAA
1 TTACAAATTCTATCAATTTGA-CTTCAAA
42445281 GTTCCTAACC
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
29 4 0.09
30 19 0.40
31 13 0.28
32 5 0.11
33 6 0.13
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (30 bp):
TTACAAATTCTATCAATTTGACTTCAAATT
Found at i:42446049 original size:61 final size:61
Alignment explanation
Indices: 42445973--42446109 Score: 220
Period size: 61 Copynumber: 2.2 Consensus size: 61
42445963 GAAGTTTGAA
* *
42445973 GATCAAATTGATAGAATTTGTAAATATGAAGGGTTAAATTTATTGAATTATTTAGAATTAG
1 GATCAAATTGATAGAATTTGTAAATATGAAAGGTTAAATTTATTGAATTATTTAGAACTAG
* **
42446034 GATCAAATTGGTAGAATTTGTAAATATGAAAGGTTACGTTTATTGAATTATTTAGAACTAG
1 GATCAAATTGATAGAATTTGTAAATATGAAAGGTTAAATTTATTGAATTATTTAGAACTAG
*
42446095 AATCAAATTGATAGA
1 GATCAAATTGATAGA
42446110 TCATGTAAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (61 bp):
GATCAAATTGATAGAATTTGTAAATATGAAAGGTTAAATTTATTGAATTATTTAGAACTAG
Found at i:42447041 original size:28 final size:29
Alignment explanation
Indices: 42447017--42447071 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
42447007 ACTTAAAATC
42447017 ATTA-AAATAATA-GAAAATTTATAAAAAA
1 ATTACAAA-AATATGAAAATTTATAAAAAA
42447045 ATTACAAAAATATGAAAA-TTA-AAAAAA
1 ATTACAAAAATATGAAAATTTATAAAAAA
42447072 TATAGGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 6 0.24
28 11 0.44
29 8 0.32
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (29 bp):
ATTACAAAAATATGAAAATTTATAAAAAA
Found at i:42447064 original size:17 final size:17
Alignment explanation
Indices: 42447042--42447074 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42447032 AATTTATAAA
*
42447042 AAAATTACAAAAATATG
1 AAAATTAAAAAAATATG
42447059 AAAATTAAAAAAATAT
1 AAAATTAAAAAAATAT
42447075 AGGAAGGTAC
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:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAATTAAAAAAATATG
Found at i:42447414 original size:20 final size:20
Alignment explanation
Indices: 42447389--42447448 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
42447379 AATGGTTTCA
*
42447389 TAATTTTTTTCATATATTTT
1 TAATTTTTTTAATATATTTT
*
42447409 TAATTTTTTAAATA-ATTTT
1 TAATTTTTTTAATATATTTT
*
42447428 T-ATGTTTTTTTATAATATTTT
1 TAAT-TTTTTTAAT-ATATTTT
42447449 GTAAATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 2 0.06
19 13 0.39
20 13 0.39
21 5 0.15
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TAATTTTTTTAATATATTTT
Found at i:42447589 original size:17 final size:17
Alignment explanation
Indices: 42447569--42447625 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
42447559 TTCTTTTCAT
42447569 TTTTTATTTTTTATATA
1 TTTTTATTTTTTATATA
*
42447586 TTTTTATCTTTTATA-A
1 TTTTTATTTTTTATATA
*
42447602 TTTTCTATGTTTTTTTATA
1 TTTT-TAT-TTTTTATATA
42447621 TTTTT
1 TTTTT
42447626 TTGCACATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 5 0.15
17 17 0.50
18 7 0.21
19 5 0.15
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTTATATA
Found at i:42447589 original size:24 final size:24
Alignment explanation
Indices: 42447526--42447599 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
42447516 AATTTGTATA
**
42447526 ATTTTTTATA-ATTTAGATATTTTT
1 ATTTTTTATATATTTTCAT-TTTTT
* *
42447550 A-TTTTGATATTCTTTTCATTTTTT
1 ATTTTTTATA-TATTTTCATTTTTT
* *
42447574 ATTTTTTATATATTTTTATCTTTT
1 ATTTTTTATATATTTTCATTTTTT
42447598 AT
1 AT
42447600 AATTTTCTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
23 7 0.18
24 20 0.51
25 12 0.31
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (24 bp):
ATTTTTTATATATTTTCATTTTTT
Found at i:42448353 original size:3 final size:3
Alignment explanation
Indices: 42448345--42448388 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
42448335 CACCCTTTTA
42448345 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
42448389 ATTATTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:42448393 original size:3 final size:3
Alignment explanation
Indices: 42448387--42448418 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42448377 GTTGTTGTTG
42448387 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42448419 TGTTGTCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:42449298 original size:37 final size:36
Alignment explanation
Indices: 42449256--42449325 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
42449246 GTTACTAGTT
42449256 TACTGAATGCATGCTAAGCATACCACTGATATTGTTA
1 TACTGAATGCATGCTAAGCATACCACTG-TATTGTTA
* *
42449293 TACTGAATGCATGTTAAGCATGCCACTGTATTG
1 TACTGAATGCATGCTAAGCATACCACTGTATTG
42449326 AAAGTGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 5 0.16
37 26 0.84
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (36 bp):
TACTGAATGCATGCTAAGCATACCACTGTATTGTTA
Found at i:42451581 original size:15 final size:15
Alignment explanation
Indices: 42451558--42451593 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42451548 CACCACTATT
* *
42451558 AAAATATTATTTTAA
1 AAAAAATTAATTTAA
42451573 AAAAAATTAATTTAA
1 AAAAAATTAATTTAA
42451588 AAAAAA
1 AAAAAA
42451594 ATGGTGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAATTAATTTAA
Found at i:42457116 original size:73 final size:73
Alignment explanation
Indices: 42457026--42457172 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
42457016 ATGAAGGCAA
42457026 AGAAGGCTTGGAACACTGTTGTTTACAGCTAAATTACAAGTGAAATAACTATTTTCTCACAGTTC
1 AGAAGGCTTGGAACACTGTTGTTTACAGCTAAATTACAAGTGAAATAACTATTTTCTCACAGTTC
42457091 CCCATCTC
66 CCCATCTC
*
42457099 AGAAGGCTTGGAGCACTGTTGTTTACAGCTAAATTACAAGTGAAATAACTATTTTCTCACAGTTC
1 AGAAGGCTTGGAACACTGTTGTTTACAGCTAAATTACAAGTGAAATAACTATTTTCTCACAGTTC
42457164 CCCATCTC
66 CCCATCTC
42457172 A
1 A
42457173 CAACTTTGCA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (73 bp):
AGAAGGCTTGGAACACTGTTGTTTACAGCTAAATTACAAGTGAAATAACTATTTTCTCACAGTTC
CCCATCTC
Found at i:42459154 original size:9 final size:9
Alignment explanation
Indices: 42459137--42459262 Score: 191
Period size: 9 Copynumber: 14.1 Consensus size: 9
42459127 GTAGTGATTC
*
42459137 AATTTGGTT
1 AATTCGGTT
42459146 AATTCGGTT
1 AATTCGGTT
42459155 AATTCGG-T
1 AATTCGGTT
42459163 AATTCGGTT
1 AATTCGGTT
42459172 AATTCGGTT
1 AATTCGGTT
*
42459181 AATTCGGGT
1 AATTCGGTT
*
42459190 AATTCGGGT
1 AATTCGGTT
42459199 AATTCGGTT
1 AATTCGGTT
*
42459208 AATTCGGGT
1 AATTCGGTT
42459217 AATTCGGTT
1 AATTCGGTT
*
42459226 AATTCAGTT
1 AATTCGGTT
42459235 AATTCGGTT
1 AATTCGGTT
42459244 AATTCGGTT
1 AATTCGGTT
*
42459253 AATTTGGTT
1 AATTCGGTT
42459262 A
1 A
42459263 TTTTTAACCA
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
8 8 0.07
9 100 0.93
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:42464227 original size:37 final size:37
Alignment explanation
Indices: 42464184--42464272 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
42464174 ATCATAAATA
*
42464184 AATAAACTAATCAATGTTCAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
* *
42464221 ATTAAACTAATAAATGTTAAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
42464258 AATGAACTAATCAAT
1 AATAAACTAATCAAT
42464273 ATATTTATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (37 bp):
AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:42464352 original size:33 final size:33
Alignment explanation
Indices: 42464315--42464390 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
42464305 TTAAAACTTG
*
42464315 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
42464348 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
42464381 AATTATACAT
1 AATTATACAT
42464391 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:42467950 original size:16 final size:17
Alignment explanation
Indices: 42467929--42467960 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42467919 AAATATGCAA
42467929 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
42467945 TCACATAACTTCATAT
1 TCACATAACTTCATAT
42467961 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:42468220 original size:41 final size:42
Alignment explanation
Indices: 42468121--42468277 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 42
42468111 GACTCGTACA
* * * *
42468121 ATGCCAATGTCCCAGACGTGGTCTTATATGTAATCACATATTG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATA-CG
*
42468164 ATGCCACTGTCCCAGACAG-GGTCTTACACG-AATCAAATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAATCAAATACG
* *
42468205 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGT-CG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCA-AA-TACG
* *
42468248 ATGCCAACGTCCCAGACGTAGTCTTACACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG
42468278 ATAACATATA
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
41 28 0.29
42 12 0.12
43 56 0.57
44 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATACG
Found at i:42468262 original size:84 final size:84
Alignment explanation
Indices: 42468121--42468278 Score: 214
Period size: 84 Copynumber: 1.9 Consensus size: 84
42468111 GACTCGTACA
* * * * * *
42468121 ATGCCAATGTCCCAGACGTGGTCTTATATGTAATCACATATTGATGCCACTGTCCCAGACAG-GG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGAC-GTAG
42468185 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
42468205 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCC-ACTGTCCCAGACGTA
42468268 GTCTTACACGA
64 GTCTTACACGA
42468279 TAACATATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 2 0.03
84 61 0.94
85 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (84 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGACGTAGT
CTTACACGAATCAAATACG
Found at i:42471260 original size:16 final size:16
Alignment explanation
Indices: 42471239--42471272 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42471229 AATTTACTAT
42471239 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
42471255 TACACCTCTAATTCAA
1 TACACCTCTAATCCAA
42471271 TA
1 TA
42471273 GAGCGAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:42472198 original size:28 final size:28
Alignment explanation
Indices: 42472167--42472241 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
42472157 AAAAATAAAA
42472167 ATTTACCAAAATAT-TACAACTTTTTTTT
1 ATTTACCAAAATATATA-AACTTTTTTTT
42472195 ATTTACCAAAATATATAAACTTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTTT
*
42472223 ATTTACTAAAATATATAAA
1 ATTTACCAAAATATATAAA
42472242 AAAACCAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 43 0.96
29 2 0.04
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTACCAAAATATATAAACTTTTTTTT
Found at i:42472337 original size:27 final size:27
Alignment explanation
Indices: 42472298--42472373 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
42472288 TACTGGTCAC
*
42472298 GCCAATGGAATTGGCGGCACCAAAGGT
1 GCCAATGCAATTGGCGGCACCAAAGGT
* **
42472325 GCCAATGCCATTGGCGGCACCAATTGT
1 GCCAATGCAATTGGCGGCACCAAAGGT
*
42472352 GCC-ATACTAATTGGCGGCACCA
1 GCCAATGC-AATTGGCGGCACCA
42472374 CTCGTATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.07
27 39 0.93
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (27 bp):
GCCAATGCAATTGGCGGCACCAAAGGT
Found at i:42472468 original size:10 final size:10
Alignment explanation
Indices: 42472447--42472485 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
42472437 GAGTTGGCGC
42472447 GAAAAAGAAGA
1 GAAAAAG-AGA
42472458 GAAAAAGAGA
1 GAAAAAGAGA
42472468 GAAAAAGAGCA
1 GAAAAAGAG-A
42472479 GAAAAAG
1 GAAAAAG
42472486 GAGGTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 12 0.44
11 15 0.56
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (10 bp):
GAAAAAGAGA
Found at i:42472550 original size:19 final size:21
Alignment explanation
Indices: 42472512--42472550 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
42472502 AATAATTGAT
*
42472512 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
42472533 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
42472551 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:42472620 original size:3 final size:3
Alignment explanation
Indices: 42472614--42472654 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42472604 AGTATTATTA
42472614 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
42472655 AGTATGAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:42472864 original size:26 final size:26
Alignment explanation
Indices: 42472835--42472887 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
42472825 TTTTAGTGTG
*
42472835 TATTATT-TTGAGTATAAAATTATTAA
1 TATTATTCTT-AGTATAAAATTAATAA
42472861 TATTATTCTTAGTATAAAATTAATAA
1 TATTATTCTTAGTATAAAATTAATAA
42472887 T
1 T
42472888 TTTAGTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (26 bp):
TATTATTCTTAGTATAAAATTAATAA
Found at i:42472892 original size:62 final size:62
Alignment explanation
Indices: 42472801--42472975 Score: 318
Period size: 62 Copynumber: 2.9 Consensus size: 62
42472791 TATAGTTAGT
* *
42472801 TATTATTTTTAG--TAAAGTTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAA
1 TATTATTCTTAGTATAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAA
42472861 TATTATTCTTAGTATAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAA
1 TATTATTCTTAGTATAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAA
42472923 TATTATTCTTAGTATAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAA
1 TATTATTCTTAGTATAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAA
42472976 TTTTTTTTAA
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
60 11 0.10
62 100 0.90
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (62 bp):
TATTATTCTTAGTATAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAA
Found at i:42472911 original size:36 final size:35
Alignment explanation
Indices: 42472861--42472975 Score: 122
Period size: 36 Copynumber: 3.5 Consensus size: 35
42472851 AAATTATTAA
42472861 TATTATTCTTAGTATAAAATTAATAATTTTAGTGTG
1 TATTATT-TTAGTATAAAATTAATAATTTTAGTGTG
*
42472897 TATTATTTTGAGTATAAAATTATTAA---TA---T-
1 TATTATTTT-AGTATAAAATTAATAATTTTAGTGTG
*
42472926 TA-T-TCTTAGTATAAAATTAATAATTTTAGTGTG
1 TATTATTTTAGTATAAAATTAATAATTTTAGTGTG
42472959 TATTATTTTGAGTATAA
1 TATTATTTT-AGTATAA
42472976 TTTTTTTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
26 15 0.23
27 3 0.05
28 1 0.02
29 4 0.06
30 1 0.02
32 1 0.02
33 4 0.06
34 1 0.02
35 5 0.08
36 29 0.45
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.50
Consensus pattern (35 bp):
TATTATTTTAGTATAAAATTAATAATTTTAGTGTG
Found at i:42472926 original size:26 final size:26
Alignment explanation
Indices: 42472897--42472949 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
42472887 TTTTAGTGTG
*
42472897 TATTATT-TTGAGTATAAAATTATTAA
1 TATTATTCTT-AGTATAAAATTAATAA
42472923 TATTATTCTTAGTATAAAATTAATAA
1 TATTATTCTTAGTATAAAATTAATAA
42472949 T
1 T
42472950 TTTAGTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (26 bp):
TATTATTCTTAGTATAAAATTAATAA
Found at i:42473568 original size:18 final size:18
Alignment explanation
Indices: 42473525--42473569 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
42473515 TTGACATGGT
*
42473525 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
**
42473543 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
42473561 TGGTGGCGA
1 TGGTGGCGA
42473570 GCATTGGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.49, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:42479255 original size:19 final size:19
Alignment explanation
Indices: 42479220--42479257 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42479210 TTTAAACACA
42479220 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
42479239 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
42479258 ACCTTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:42479334 original size:4 final size:4
Alignment explanation
Indices: 42479317--42479418 Score: 68
Period size: 4 Copynumber: 24.5 Consensus size: 4
42479307 TCTCCTTTCC
*
42479317 CTTT CTTT CCTT CTTT CTTT CTTT -TTT CTTCT CTTCT CCTTT -TCTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T CTT-T -CTTT CT-TT
* * *
42479363 -TTT CTTT CTTT TTTT CTCTT C-TC CTTT CCCTCT CATTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CT-TT CTTT CTTT --CTTT C-TTT CTTT CTTT
42479409 CTTT CTTT CT
1 CTTT CTTT CT
42479419 ATCCCTCCTT
Statistics
Matches: 80, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
3 8 0.10
4 53 0.66
5 13 0.16
6 6 0.08
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:42479356 original size:44 final size:48
Alignment explanation
Indices: 42479264--42479370 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 48
42479254 AATTACCTTT
*
42479264 TTTCCCTTTTTTTTCCTTTCTTCCCTCTTCTATTTTTTTCTCTTCTCC
1 TTTCCCTTTTCTTTCCTTTCTTCCCTCTTCTATTTTTTTCTCTTCTCC
*
42479312 TTTCCC-TTTCTTTCC-TTCTT-TCT-TTCT-TTTTTCTTCTCTTCTCC
1 TTTCCCTTTTCTTTCCTTTCTTCCCTCTTCTATTTTT-TTCTCTTCTCC
* *
42479356 TTTTCTTTTTCTTTC
1 TTTCCCTTTTCTTTC
42479371 TTTTTTTCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
43 5 0.09
44 19 0.36
45 10 0.19
46 5 0.09
47 8 0.15
48 6 0.11
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (48 bp):
TTTCCCTTTTCTTTCCTTTCTTCCCTCTTCTATTTTTTTCTCTTCTCC
Found at i:42479380 original size:31 final size:34
Alignment explanation
Indices: 42479321--42479415 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 34
42479311 CTTTCCCTTT
42479321 CTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCTC
1 CTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCTC
*
42479355 CTTTTCTT-TTTCTTTC-TTTTT-TTCTCTTCTC
1 CTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCTC
42479386 CTTTCCCTCTCATTTCTTTCTTTCTTTCTT
1 CTTT-CCT-TC-TTTCTTTCTTT-TTTCTT
42479416 TCTATCCCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
31 14 0.27
32 7 0.13
33 9 0.17
34 7 0.13
35 8 0.15
36 2 0.04
37 3 0.06
38 2 0.04
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (34 bp):
CTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCTC
Found at i:42479384 original size:13 final size:12
Alignment explanation
Indices: 42479318--42479384 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 12
42479308 CTCCTTTCCC
* *
42479318 TTTCTTTCCTTC
1 TTTCTTTCTTTT
42479330 TTTCTTTC-TTT
1 TTTCTTTCTTTT
*
42479341 TTTC-TTCTCTT
1 TTTCTTTCTTTT
* * *
42479352 CTCCTTT-TCTT
1 TTTCTTTCTTTT
42479363 TTTCTTTCTTTT
1 TTTCTTTCTTTT
42479375 TTTCTCTTCT
1 TTTCT-TTCT
42479385 CCTTTCCCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
10 3 0.07
11 19 0.43
12 18 0.41
13 4 0.09
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTCTTTCTTTT
Found at i:42479418 original size:39 final size:38
Alignment explanation
Indices: 42479300--42479418 Score: 145
Period size: 39 Copynumber: 3.1 Consensus size: 38
42479290 CTTCTATTTT
*
42479300 TTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTCTTTC
1 TTTCTCTTCTCCTTTCCCTTTCTTTCTTTCTTTCTTTC
* * *
42479338 TTTTTTCTTCT-CTTCTCCTTTTC-TT-TTTCTTTCTTTT
1 -TTTCTCTTCTCCTT-TCCCTTTCTTTCTTTCTTTCTTTC
*
42479375 TTTCTCTTCTCCTTTCCCTCTCATTTCTTTCTTTCTTTC
1 TTTCTCTTCTCCTTTCCCTTTC-TTTCTTTCTTTCTTTC
42479414 TTTCT
1 TTTCT
42479419 ATCCCTCCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
36 15 0.22
37 13 0.19
38 7 0.10
39 32 0.48
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (38 bp):
TTTCTCTTCTCCTTTCCCTTTCTTTCTTTCTTTCTTTC
Found at i:42479424 original size:31 final size:31
Alignment explanation
Indices: 42479367--42479425 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
42479357 TTTCTTTTTC
* *
42479367 TTTCTTTTTTTCTCTTCTCCTTTCCCTCTCA
1 TTTCTTTCTTTCTCTTCTCCTATCCCTCTCA
*
42479398 TTTCTTTCTTTCT-TTCTTTCTATCCCTC
1 TTTCTTTCTTTCTCTTC-TCCTATCCCTC
42479426 CTTCTGCCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (31 bp):
TTTCTTTCTTTCTCTTCTCCTATCCCTCTCA
Found at i:42479500 original size:27 final size:27
Alignment explanation
Indices: 42479463--42479538 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
42479453 TAATACCAAC
*
42479463 TGGTGCTGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
42479490 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
42479517 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
42479539 GTGACCAGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:42479630 original size:26 final size:27
Alignment explanation
Indices: 42479594--42479665 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
42479584 TTTTGGTTTT
42479594 TTTATATATTTTGGTAAAT-AAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAG
42479620 TTTATATATTTTGGTAAATAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAG
*
42479647 TTGTA-ATATTTTGATAAAT
1 TT-TATATATTTTGGTAAAT
42479666 TTTTATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
26 19 0.44
27 22 0.51
28 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (27 bp):
TTTATATATTTTGGTAAATAAAAAAAG
Found at i:42480770 original size:20 final size:19
Alignment explanation
Indices: 42480727--42480770 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
42480717 ACTATTGTTT
*
42480727 TTATTTTTTTATCTTATAG
1 TTATTTTTTTATCTTATAA
*
42480746 TTATTTTTTTATCTTTTAA
1 TTATTTTTTTATCTTATAA
42480765 TATATT
1 T-TATT
42480771 GCAGTTATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (19 bp):
TTATTTTTTTATCTTATAA
Found at i:42489776 original size:62 final size:62
Alignment explanation
Indices: 42489642--42489919 Score: 452
Period size: 62 Copynumber: 4.5 Consensus size: 62
42489632 GGACGGGCAT
* * * * ** *
42489642 GTGTCCAGGCTGTGTAGCTCACTGTGTGGATTTTAGAGGT-ACA-ATGGCTCGGGACACAGGCGC
1 GTGTCTAGGCCGTGTAACTCACTGTTTGGATTTT-G-GGTCACACA-GGCTAAGGACACATGCGC
42489705 GTGTCTAGGCCGTGTAACTCACTGTTTGGATTTTGGGTCACACAGGCTAAGGACACATGCGC
1 GTGTCTAGGCCGTGTAACTCACTGTTTGGATTTTGGGTCACACAGGCTAAGGACACATGCGC
42489767 GTGTCTAGGCCGTGTAACTCACTGTTTGGATTTTGGGTCACACAGGCTAAGGACACATGCGC
1 GTGTCTAGGCCGTGTAACTCACTGTTTGGATTTTGGGTCACACAGGCTAAGGACACATGCGC
42489829 GTGTCTAGGCCGTGTAACTCACTGTTTGGATTTTGGGTCACACAGGCTAAGGACACATGCGC
1 GTGTCTAGGCCGTGTAACTCACTGTTTGGATTTTGGGTCACACAGGCTAAGGACACATGCGC
42489891 GTGTCTAGGCCGTGTAACTCACTGTTTGG
1 GTGTCTAGGCCGTGTAACTCACTGTTTGG
42489920 GATCCATGTG
Statistics
Matches: 206, Mismatches: 7, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
61 3 0.01
62 172 0.83
63 31 0.15
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.28
Consensus pattern (62 bp):
GTGTCTAGGCCGTGTAACTCACTGTTTGGATTTTGGGTCACACAGGCTAAGGACACATGCGC
Found at i:42491432 original size:19 final size:19
Alignment explanation
Indices: 42491408--42491445 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42491398 TTATAATTAT
*
42491408 TAATTAATAAATTTTTCTA
1 TAATTAATAAAATTTTCTA
42491427 TAATTAATAAAATTTTCTA
1 TAATTAATAAAATTTTCTA
42491446 ACTTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATTAATAAAATTTTCTA
Done.