Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 40 of 222
Found at i:11927251 original size:24 final size:21
Alignment explanation
Indices: 11927235--11927275 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11927225 TATATGTAGG
11927235 TATAATAATAATAATATATAA
1 TATAATAATAATAATATATAA
11927256 TATAATAATAATAATA-ATAA
1 TATAATAATAATAATATATAA
11927276 CAAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TATAATAATAATAATATATAA
Found at i:11927285 original size:24 final size:24
Alignment explanation
Indices: 11927236--11927291 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
11927226 ATATGTAGGT
* *
11927236 ATAATAATAATAATATATAATATA
1 ATAATAATAATAATACAAAATATA
11927260 ATAATAATAATAATAACAAAAT-TA
1 ATAATAATAATAAT-ACAAAATATA
11927284 ATAA-AATA
1 ATAATAATA
11927292 GACTAAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 4 0.14
24 20 0.69
25 5 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAATAATAATAATACAAAATATA
Found at i:11927770 original size:21 final size:19
Alignment explanation
Indices: 11927734--11927808 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
11927724 AATCATATCT
11927734 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
11927753 TCCAAGATTGCACATATCATA
1 TCTAAGATTG--CATATCATA
11927774 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
11927793 TCTAAGGTTGCATATC
1 TCTAAGATTGCATATC
11927809 CTTGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:11927782 original size:40 final size:38
Alignment explanation
Indices: 11927727--11927804 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 38
11927717 ATTACAAAAT
11927727 CATATCTTCTAAGATTGCATATCATATCCAAGATTGCA
1 CATATCTTCTAAGATTGCATATCATATCCAAGATTGCA
* *
11927765 CATATCATATCTAAGATTGCATATCATATCTAAGGTTGCA
1 CATATC-T-TCTAAGATTGCATATCATATCCAAGATTGCA
11927805 TATCCTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 6 0.17
39 1 0.03
40 29 0.81
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (38 bp):
CATATCTTCTAAGATTGCATATCATATCCAAGATTGCA
Found at i:11937960 original size:28 final size:27
Alignment explanation
Indices: 11937928--11937987 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
11937918 ACAAAAATTC
* *
11937928 ATTATGATTCAAATATTAATATTAATA
1 ATTATAATTCAAATAATAATATTAATA
* *
11937955 TATTATAATTTAAATAATATTATTAATA
1 -ATTATAATTCAAATAATAATATTAATA
11937983 ATTAT
1 ATTAT
11937988 TACAAGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTATAATTCAAATAATAATATTAATA
Found at i:11939103 original size:17 final size:17
Alignment explanation
Indices: 11939081--11939114 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11939071 ATATTTTGTA
11939081 ATTTTATATTTATCCTT
1 ATTTTATATTTATCCTT
11939098 ATTTTATATTTATCCTT
1 ATTTTATATTTATCCTT
11939115 GCTATACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATATTTATCCTT
Found at i:11939356 original size:13 final size:13
Alignment explanation
Indices: 11939326--11939350 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11939316 TAACTTTTAA
11939326 AAAAATTAAAAAG
1 AAAAATTAAAAAG
11939339 AAAAATTAAAAA
1 AAAAATTAAAAA
11939351 TTAAAAGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATTAAAAAG
Found at i:11948911 original size:15 final size:14
Alignment explanation
Indices: 11948890--11948925 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
11948880 ATAATCGTTA
*
11948890 ATAATTATCTTAAT
1 ATAATTATCCTAAT
11948904 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
11948919 ATAATTA
1 ATAATTA
11948926 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:11949487 original size:14 final size:14
Alignment explanation
Indices: 11949468--11949494 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11949458 CTAAATTATA
11949468 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
11949482 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
11949495 TATTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:11949504 original size:16 final size:14
Alignment explanation
Indices: 11949466--11949504 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
11949456 CCCTAAATTA
11949466 TATTTTTTTCTTTT
1 TATTTTTTTCTTTT
*
11949480 TCTTTTTTTCTTTTT
1 TATTTTTTTC-TTTT
11949495 TATTTATTTT
1 TATTT-TTTT
11949505 GATTTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.43
15 8 0.38
16 4 0.19
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (14 bp):
TATTTTTTTCTTTT
Found at i:11950922 original size:5 final size:5
Alignment explanation
Indices: 11950912--11950963 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
11950902 GTTGTAAAAT
* *
11950912 AATAA AATAA AATAA AGTAATA AATAA AGT-A AATAA AATAA AAT-A AATAA
1 AATAA AATAA AATAA AAT-A-A AATAA AATAA AATAA AATAA AATAA AATAA
11950962 AA
1 AA
11950964 ATTGGGTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 7 0.18
5 27 0.69
6 2 0.05
7 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:11950963 original size:9 final size:9
Alignment explanation
Indices: 11950906--11950963 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
11950896 AAATAAGTTG
11950906 TAAAAT-AA
1 TAAAATAAA
11950914 TAAAATAAAA
1 TAAAAT-AAA
*
11950924 TAAAGT-AA
1 TAAAATAAA
11950932 T-AAATAAA
1 TAAAATAAA
11950940 GT-AAATAAAA
1 -TAAAAT-AAA
11950950 TAAAATAAA
1 TAAAATAAA
11950959 TAAAA
1 TAAAA
11950964 ATTGGGTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
7 3 0.07
8 11 0.26
9 14 0.33
10 14 0.33
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
TAAAATAAA
Found at i:11956279 original size:28 final size:28
Alignment explanation
Indices: 11956235--11956306 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
11956225 ATAAAAAATT
* *
11956235 AGCACTAAGTGTACGAGTTTAATTGTGA
1 AGCACTAAGTGTGCGAGTTTAATTATGA
* *
11956263 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTAATTATGA
11956291 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
11956307 ACTTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTAATTATGA
Found at i:11964786 original size:18 final size:18
Alignment explanation
Indices: 11964757--11964801 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
11964747 AATTATAAAA
11964757 TATAAAATATATATATGAAT
1 TATAAAATATATATAT--AT
*
11964777 TATAAAATATGTATATAT
1 TATAAAATATATATATAT
11964795 TATAAAA
1 TATAAAA
11964802 AAACGTATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TATAAAATATATATATAT
Found at i:11965913 original size:25 final size:22
Alignment explanation
Indices: 11965865--11965907 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11965855 GTAGGCAGGG
11965865 GTTAGGTGCGACGATGACAGAA
1 GTTAGGTGCGACGATGACAGAA
* *
11965887 GTTAGGTGCGGCGATGGCAGA
1 GTTAGGTGCGACGATGACAGA
11965908 GCAAGTGGCG
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:0.26, C:0.14, G:0.42, T:0.19
Consensus pattern (22 bp):
GTTAGGTGCGACGATGACAGAA
Found at i:11966401 original size:44 final size:43
Alignment explanation
Indices: 11966350--11966458 Score: 121
Period size: 45 Copynumber: 2.5 Consensus size: 43
11966340 CCACTTAACG
*
11966350 TCAGGGAGATAAGACTTGTTGCTTCAACT-TGCTCCACTGCAGCT
1 TCAGGGAGATAAGACTTGTT-CTTC-ACTCTGCTCCACTGCAACT
** * *
11966394 TCAGGGAGATAAGGTTTGATATCTTCAGTCTGCTTCACTGCAACT
1 TCAGGGAGATAAGACTTG-T-TCTTCACTCTGCTCCACTGCAACT
*
11966439 TTAGGGAGATAAGACTTGTT
1 TCAGGGAGATAAGACTTGTT
11966459 TGGTGTGATC
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.02
44 19 0.35
45 33 0.61
46 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
TCAGGGAGATAAGACTTGTTCTTCACTCTGCTCCACTGCAACT
Found at i:11966724 original size:44 final size:43
Alignment explanation
Indices: 11966618--11966809 Score: 117
Period size: 44 Copynumber: 4.4 Consensus size: 43
11966608 GTCTGATGCG
* * **
11966618 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATT-TT-A
1 ATCTGCTCCACTGCAACTTCAG-GAGATAGGATTGAT--TTCTTCA
* * **
11966662 ATCCGCTTCACTATAACTTCAGGAAGATAGGATTGATTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGG-AGATAGGATTGATTTCTTCA
* * *
11966706 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGA----TGCG
1 ATCTGCTCCACTGCAACTTCA-GGAGATAGGATT-GATTTCTTCA
* * * **
11966747 ATCTGCTCTACTGCAATTTCAAGGAGATAGGATTGGTTTCTTTT
1 ATCTGCTCCACTGCAACTTC-AGGAGATAGGATTGATTTCTTCA
* *
11966791 GTCTACTCCACTGCAACTT
1 ATCTGCTCCACTGCAACTT
11966810 TAGGGGATGA
Statistics
Matches: 112, Mismatches: 26, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
40 1 0.01
41 31 0.28
42 3 0.03
43 3 0.03
44 70 0.62
45 4 0.04
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGAGATAGGATTGATTTCTTCA
Found at i:11967015 original size:99 final size:100
Alignment explanation
Indices: 11966898--11967244 Score: 450
Period size: 99 Copynumber: 3.5 Consensus size: 100
11966888 TGATTAACTA
* ** * * *
11966898 CAATGTCAGGGAAACAAGATTCGTCGTTGTA-CTTCAATCTATTCTATTGCACCGCTAGAGAAGT
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGT
*
11966962 AAGATTCGCTATTGTGGCTTCAATCTTTTTAATTG
66 AAGATTCGCTGTTGTGGCTTCAATCTTTTTAATTG
* * * *
11966997 CAATGTCGGGGAAGCAAGATTCACCGTT-TAGCTTCAATATATTCCACTGCACTGCCAGGGAAGT
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGT
*
11967061 AAGATTCG-TCGTTGTGGCTTCAATATTTTTAATTG
66 AAGATTCGCT-GTTGTGGCTTCAATCTTTTTAATTG
* * * * * *
11967096 CAATGTCGGGGAAGCAAGATTCATCGTTGTAGCTTTAATCTGTTCCACTGCATC-ATCAGGGAAG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCT-AGGGAAG
* *
11967160 TAAGATTTGCTGTTATGGCTTCAATCTTTTTAATTG
65 TAAGATTCGCTGTTGTGGCTTCAATCTTTTTAATTG
* *
11967196 CAAAGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTACTCCACT
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTATTCCACT
11967245 ACACTGCCAG
Statistics
Matches: 214, Mismatches: 29, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
98 3 0.01
99 109 0.51
100 101 0.47
101 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (100 bp):
CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGT
AAGATTCGCTGTTGTGGCTTCAATCTTTTTAATTG
Found at i:11967016 original size:50 final size:50
Alignment explanation
Indices: 11966898--11967236 Score: 244
Period size: 50 Copynumber: 6.8 Consensus size: 50
11966888 TGATTAACTA
* *
11966898 CAATGTCAGGGAAACAAGATTCG-TCGTTGTA-CTTCAATCTATTCT-ATTG
1 CAATGTCAGGGAAGCAAGATTCGCT-GTTGTAGCTTCAATCT-TTTTAATTG
** * * * *
11966947 CACCG-CTAGAGAAGTAAGATTCGCTATTGTGGCTTCAATCTTTTTAATTG
1 CAATGTC-AGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTTTTTAATTG
* * * * * ** *
11966997 CAATGTCGGGGAAGCAAGATTCACCGTT-TAGCTTCAATATATTCCACTG
1 CAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTTTTTAATTG
* * * * *
11967046 CACTGCCAGGGAAGTAAGATTCG-TCGTTGTGGCTTCAATATTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCGCT-GTTGTAGCTTCAATCTTTTTAATTG
* * * * ** *
11967096 CAATGTCGGGGAAGCAAGATTC-ATCGTTGTAGCTTTAATCTGTTCCACTG
1 CAATGTCAGGGAAGCAAGATTCGCT-GTTGTAGCTTCAATCTTTTTAATTG
* * * * *
11967146 C-ATCATCAGGGAAGTAAGATTTGCTGTTATGGCTTCAATCTTTTTAATTG
1 CAAT-GTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTTTTTAATTG
* * *
11967196 CAAAGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCT
1 CAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCT
11967237 ACTCCACTAC
Statistics
Matches: 215, Mismatches: 64, Indels: 21
0.72 0.21 0.07
Matches are distributed among these distances:
48 1 0.00
49 61 0.28
50 150 0.70
51 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (50 bp):
CAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTTTTTAATTG
Found at i:11968500 original size:19 final size:18
Alignment explanation
Indices: 11968478--11968528 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
11968468 TTGGCCTCTC
11968478 CTTTTGACTTTTTCATTCT
1 CTTTT-ACTTTTTCATTCT
* *
11968497 CTTTTTTCTTTTTC-TTTT
1 C-TTTTACTTTTTCATTCT
11968515 CTTTTA-TTTTTCAT
1 CTTTTACTTTTTCAT
11968529 CATCTTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 6 0.22
17 5 0.19
18 4 0.15
19 8 0.30
20 4 0.15
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.73
Consensus pattern (18 bp):
CTTTTACTTTTTCATTCT
Found at i:11972666 original size:18 final size:19
Alignment explanation
Indices: 11972621--11972671 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
11972611 ATATAGAAAT
*
11972621 TATAAATATAAAATATATA
1 TATAATTATAAAATATATA
*
11972640 TATGAATTATAAAATATGTA
1 TAT-AATTATAAAATATATA
11972660 TAT-ATTATAAAA
1 TATAATTATAAAA
11972672 AGAAACGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.31
19 3 0.10
20 17 0.59
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (19 bp):
TATAATTATAAAATATATA
Found at i:11973766 original size:22 final size:22
Alignment explanation
Indices: 11973740--11973782 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11973730 GTGGGAAGGG
*
11973740 GTTAGGTACGGCGATGACAGAA
1 GTTAGGTACGACGATGACAGAA
* *
11973762 GTTAGGTCCGACGATGGCAGA
1 GTTAGGTACGACGATGACAGA
11973783 GCAAGTGGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.37, T:0.19
Consensus pattern (22 bp):
GTTAGGTACGACGATGACAGAA
Found at i:11976340 original size:26 final size:23
Alignment explanation
Indices: 11976291--11976346 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 23
11976281 ACTTCAAATC
* *
11976291 TTTTTTAATAATAATATCTCATA
1 TTTTTTAATAATAATATATAATA
11976314 TTTTTTATATATATAAATATATAATA
1 TTTTTTA-ATA-AT-AATATATAATA
11976340 TATTTTT
1 T-TTTTT
11976347 TTAGTATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
24 3 0.11
25 2 0.07
26 10 0.37
27 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTTAATAATAATATATAATA
Found at i:11978413 original size:14 final size:13
Alignment explanation
Indices: 11978387--11978412 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11978377 TAAAACATAT
11978387 GAAACAAAAAAAA
1 GAAACAAAAAAAA
11978400 GAAACAAAAAAAA
1 GAAACAAAAAAAA
11978413 ACTATACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
GAAACAAAAAAAA
Found at i:11978553 original size:3 final size:3
Alignment explanation
Indices: 11978545--11978599 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
11978535 ATACATGTTG
11978545 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11978593 ATA ATA A
1 ATA ATA A
11978600 CAGAATGACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11980589 original size:263 final size:263
Alignment explanation
Indices: 11980123--11980677 Score: 986
Period size: 263 Copynumber: 2.1 Consensus size: 263
11980113 CTTCGATATA
*
11980123 CTTCACGCCAATACATGAAGACAAGATCTGCTTTTTCAATCGATTCCACTGCCGACCGGGGAGGT
1 CTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCAATCGATTCCACTGCCGACCGGGGAGGT
*
11980188 AGAATTGCTGGCTTCAATATACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTCGATCT
66 AGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTCGATCT
* *
11980253 GCTCCACTACTGCTTAGGGAGGCAAGATCTGTAATCTTCAATCTACTTCGCTGTCGGTATGGGAA
131 GCTCCACTACTGCTTAGGGAGGCAAGATCTGTAATCTTCAATCTACTTCGCCGCCGGTATGGGAA
* *
11980318 GATAAAATATGTATTTTTGATCCACTTCGCTACCAATACAGGAAGACAGGACCTACTATCTTTGA
196 GATAAAATATGTATATTCGATCCACTTCGCTACCAATACAGGAAGACA-GACCTACTATCTTTGA
11980383 TCTC
260 TCTC
* **
11980387 CTTCACACCAGTACATGAAGACGGGATCTGCTTTTTCAATCGATTCCACTGCCGACCGGGGAGGT
1 CTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCAATCGATTCCACTGCCGACCGGGGAGGT
11980452 AGAATTACTGGCTTCAATATACTCCACTGCAACTTCA-GGAGGTAAAATCCGCCATCTTCGATCT
66 AGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTCGATCT
11980516 GCTCCACTACTGCTTAGGGAGGCAAGATCTGTAATCTTCAATCTACTTCGCCGCCGGTATGGGAA
131 GCTCCACTACTGCTTAGGGAGGCAAGATCTGTAATCTTCAATCTACTTCGCCGCCGGTATGGGAA
*
11980581 GATAAAATATGTATATTCGATCCACTTCGCTACCAATATAGGAAGACAGACCTACTATCTTTGAT
196 GATAAAATATGTATATTCGATCCACTTCGCTACCAATACAGGAAGACAGACCTACTATCTTTGAT
11980646 CTC
261 CTC
* *
11980649 TTTCACGCCAGTACATGAAGACACGATCT
1 CTTCACGCCAGTACATGAAGACAAGATCT
11980678 TTTTCTTCAA
Statistics
Matches: 277, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
262 45 0.16
263 135 0.49
264 97 0.35
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (263 bp):
CTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCAATCGATTCCACTGCCGACCGGGGAGGT
AGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTCGATCT
GCTCCACTACTGCTTAGGGAGGCAAGATCTGTAATCTTCAATCTACTTCGCCGCCGGTATGGGAA
GATAAAATATGTATATTCGATCCACTTCGCTACCAATACAGGAAGACAGACCTACTATCTTTGAT
CTC
Found at i:11980805 original size:45 final size:43
Alignment explanation
Indices: 11980665--11981093 Score: 265
Period size: 45 Copynumber: 9.7 Consensus size: 43
11980655 GCCAGTACAT
* * ** * *
11980665 GAAGACACGATCTTTTTCTTCAACCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGTTTCTTTGATCTACTTC-CCACCAGTATGG
* * * ***
11980709 GGAGACAAGATCTGTTTCTTTGATCTA-TTCACGCCAGTACAT
1 GAAGACAAGATCTGTTTCTTTGATCTACTTCCCACCAGTATGG
* *
11980751 GAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCT-GTTTCTTTGATCTACTTC-CCACCAGTATGG
* * * ***
11980796 GAAGACAAGATCTGTTGACTTTGATCTACTTCACGCC-GATACAT
1 GAAGACAAGATCTGTT-TCTTTGATCTACTTCCCACCAG-TATGG
* * *
11980840 GAAGACAAGATTTGCTTTCTTTTATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTG-TTTCTTTGATCTACTTC-CCACCAGTATGG
* * * ***
11980885 GGAGACAAGATCTGTTGACTTTGATCTACTT--CACGCTGATACAT
1 GAAGACAAGATCTGTT-TCTTTGATCTACTTCCCAC-CAG-TATGG
* * *
11980929 GAAGACAATATCTACTTTCTTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCT-GTTTCTTT-GATCTACTTC-CCACCAGTATGG
* * * * * ***
11980975 GAATG-CGAGATCTGTATATTTGATCTACTTCACGCCAGTACAT
1 GAA-GACAAGATCTGTTTCTTTGATCTACTTCCCACCAGTATGG
* * *
11981018 GAAGACAAGATCTGTATTCCTTCGATCTGCTTCCCACCAGCATGG
1 GAAGACAAGATCTGT-TT-CTTTGATCTACTTCCCACCAGTATGG
* *
11981063 GAAGGCGAGATCTGTTATCTTTGATCTACTT
1 GAAGACAAGATCTGTT-TCTTTGATCTACTT
11981094 TACGCCAGTA
Statistics
Matches: 283, Mismatches: 81, Indels: 42
0.70 0.20 0.10
Matches are distributed among these distances:
42 23 0.08
43 36 0.13
44 97 0.34
45 109 0.39
46 12 0.04
47 3 0.01
48 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
GAAGACAAGATCTGTTTCTTTGATCTACTTCCCACCAGTATGG
Found at i:11980858 original size:89 final size:88
Alignment explanation
Indices: 11980639--11981118 Score: 557
Period size: 89 Copynumber: 5.4 Consensus size: 88
11980629 GACCTACTAT
* * ** * * * *
11980639 CTTTGATCT-CTTTCACGCCAGTACATGAAGACACGATCT-TTTTCTTCAACCTACTCCACCACC
1 CTTTGATCTAC-TTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACC
* *
11980702 AGTATGGGGAGACAAGATCTGTTT
65 AGTATGGGAAGACAAGATCTGTTA
11980726 CTTTGATCTA-TTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCA
11980790 GTATGGGAAGACAAGATCTGTTGA
66 GTATGGGAAGACAAGATCTGTT-A
* * * * * *
11980814 CTTTGATCTACTTCACGCC-GATACATGAAGACAAGATTTGCTTTCTTTTATCTACTCCACCACC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACC
*
11980878 AGTATGGGGAGACAAGATCTGTTGA
65 AGTATGGGAAGACAAGATCTGTT-A
* *
11980903 CTTTGATCTACTTCACG-CTGATACATGAAGACAATATCTACTTTCTTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTACTTTCTTT-GATCTGCTTCGCCAC
*
11980967 CAGTATGGGAATG-CGAGATCTGTATA
64 CAGTATGGGAA-GACAAGATCTGT-TA
* *
11980993 -TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTA-TTCCTTCGATCTGCTTC-CCAC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATC--TACTTTCTTTGATCTGCTTCGCCAC
* * *
11981055 CAGCATGGGAAGGCGAGATCTGTTA
64 CAGTATGGGAAGACAAGATCTGTTA
*
11981080 TCTTTGATCTACTTTACGCCAGTACATGAAGACAA-ATCT
1 -CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
11981119 GCTGCTTTTC
Statistics
Matches: 346, Mismatches: 32, Indels: 31
0.85 0.08 0.08
Matches are distributed among these distances:
86 28 0.08
87 51 0.15
88 39 0.11
89 186 0.54
90 38 0.11
91 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (88 bp):
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCA
GTATGGGAAGACAAGATCTGTTA
Found at i:11980867 original size:44 final size:44
Alignment explanation
Indices: 11980638--11981119 Score: 289
Period size: 44 Copynumber: 11.0 Consensus size: 44
11980628 AGACCTACTA
* *
11980638 TCTTTGATCT-CTTTCACG-CCAGTACATGAAGACACGATCTTTT
1 TCTTTGATCTAC-TTCACGCCCAGTACATGAAGACAAGATCTGTT
** * * *** *
11980681 TCTTCAACCTACTCCAC-CACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCACGC-CCAGTACATGAAGACAAGATCTGTT
*
11980725 TCTTTGATCTA-TTCACG-CCAGTACATGAAGACAAGATCTACTT
1 TCTTTGATCTACTTCACGCCCAGTACATGAAGACAAGATCT-GTT
* * ***
11980768 TCTTTGATCTGCTTCGC-CACCAGTATGGGAAGACAAGATCTGTT
1 TCTTTGATCTACTTCACGC-CCAGTACATGAAGACAAGATCTGTT
* * *
11980812 GACTTTGATCTACTTCACGCCGA-TACATGAAGACAAGATTTGCTT
1 -TCTTTGATCTACTTCACGCCCAGTACATGAAGACAAGATCTG-TT
* * *** *
11980857 TCTTTTATCTACTCCAC-CACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCACGC-CCAGTACATGAAGACAAGATCTGTT
* ** * *
11980901 GACTTTGATCTACTTCACGCTGA-TACATGAAGACAATATCTACTT
1 -TCTTTGATCTACTTCACGCCCAGTACATGAAGACAAGATCT-GTT
* * *** * *
11980946 TCTTTCGATCTGCTTCGC-CACCAGTATGGGAATG-CGAGATCTGTA
1 TCTTT-GATCTACTTCACGC-CCAGTACATGAA-GACAAGATCTGTT
*
11980991 TATTTGATCTACTTCACG-CCAGTACATGAAGACAAGATCTGTAT
1 TCTTTGATCTACTTCACGCCCAGTACATGAAGACAAGATCTGT-T
* * * *
11981035 TCCTTCGATCTGCTTC-C-CACCAG--CATGGGAAGGCGAGATCTGTT
1 T-CTTTGATCTACTTCACGC-CCAGTACAT--GAAGACAAGATCTGTT
*
11981079 ATCTTTGATCTACTTTACG-CCAGTACATGAAGACAA-ATCTG
1 -TCTTTGATCTACTTCACGCCCAGTACATGAAGACAAGATCTG
11981120 CTGCTTTTCA
Statistics
Matches: 323, Mismatches: 83, Indels: 66
0.68 0.18 0.14
Matches are distributed among these distances:
42 19 0.06
43 54 0.17
44 119 0.37
45 114 0.35
46 16 0.05
47 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
TCTTTGATCTACTTCACGCCCAGTACATGAAGACAAGATCTGTT
Found at i:11980999 original size:178 final size:175
Alignment explanation
Indices: 11980639--11981118 Score: 627
Period size: 178 Copynumber: 2.7 Consensus size: 175
11980629 GACCTACTAT
* *
11980639 CTTTGATCT-CTTTCACGCCAGTACATGAAGACACGATCTT-TTTCTTCAACCTACTCCACCACC
1 CTTTGATCTAC-TTCACGCCAGTACATGAAGACAAGAT-TTGTTTCTTCAATCTACTCCACCACC
*
11980702 AGTATGGGGAGACAAGATCTGTTTCTTTGATCTA-TTCACGCCAGTACATGAAGACAAGATCTAC
64 AGTATGGGGAGACAAGATCTGTTACTTTGATCTACTTCACGCCAGTACATGAAGACAA-ATCTAC
11980766 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTGA
128 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTGA
**
11980814 CTTTGATCTACTTCACGCC-GATACATGAAGACAAGATTTGCTTTCTTTTATCTACTCCACCACC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATTTG-TTTCTTCAATCTACTCCACCACC
*
11980878 AGTATGGGGAGACAAGATCTGTTGACTTTGATCTACTTCACG-CTGATACATGAAGACAATATCT
64 AGTATGGGGAGACAAGATCTGTT-ACTTTGATCTACTTCACGCCAG-TACATGAAGACAA-ATCT
*
11980942 ACTTTCTTTCGATCTGCTTCGCCACCAGTATGGGAATG-CGAGATCTGTAT-A
126 ACTTTCTTT-GATCTGCTTCGCCACCAGTATGGGAA-GACAAGATCTGT-TGA
* * * *
11980993 -TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTATTCCTTCGATCTGCTTC-CCACC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATTTGT-TT-CTTCAATCTACTCCACCACC
* * * * *
11981056 AGCATGGGAAGGCGAGATCTGTTATCTTTGATCTACTTTACGCCAGTACATGAAGACAAATCT
64 AGTATGGGGAGACAAGATCTGTTA-CTTTGATCTACTTCACGCCAGTACATGAAGACAAATCT
11981119 GCTGCTTTTC
Statistics
Matches: 271, Mismatches: 19, Indels: 28
0.85 0.06 0.09
Matches are distributed among these distances:
174 3 0.01
175 32 0.12
176 44 0.16
177 18 0.07
178 123 0.45
179 49 0.18
180 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (175 bp):
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATTTGTTTCTTCAATCTACTCCACCACCAG
TATGGGGAGACAAGATCTGTTACTTTGATCTACTTCACGCCAGTACATGAAGACAAATCTACTTT
CTTTGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTGA
Found at i:11982476 original size:46 final size:46
Alignment explanation
Indices: 11982403--11982493 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
11982393 TTAACCTCTC
* * * * *
11982403 CTTTTTTTTTACTCAAGGCTCCTTTTGTAGGGTTTCACCCTGGTCT
1 CTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCT
*
11982449 CTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTC
1 CTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTC
11982494 CCACCTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (46 bp):
CTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCT
Found at i:11982503 original size:47 final size:46
Alignment explanation
Indices: 11982406--11982504 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 46
11982396 ACCTCTCCTT
* * * * * * **
11982406 TTTTTTTACTCAAGGCTCCTTTTGTAGGGTTTCACCCTGGTCTCTT
1 TTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCCC
*
11982452 TTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACC
1 TTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCC-CC
11982499 TTTTTT
1 TTTTTT
11982505 AAGCAGAGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
46 37 0.86
47 6 0.14
ACGTcount: A:0.12, C:0.26, G:0.16, T:0.45
Consensus pattern (46 bp):
TTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCCC
Found at i:11986793 original size:14 final size:13
Alignment explanation
Indices: 11986767--11986792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11986757 TAAAACATAT
11986767 GAAACAAAAAAAA
1 GAAACAAAAAAAA
11986780 GAAACAAAAAAAA
1 GAAACAAAAAAAA
11986793 ACTATACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
GAAACAAAAAAAA
Found at i:11986933 original size:3 final size:3
Alignment explanation
Indices: 11986925--11986952 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11986915 ATACATGTTG
11986925 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11986953 CAGAATGACT
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):
ATA
Found at i:11994048 original size:40 final size:40
Alignment explanation
Indices: 11993993--11994074 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
11993983 TTAATTTCAG
*
11993993 CTTTCGTAGTTTACTGATTTTCAGGTTTCTCGTTACCCAC
1 CTTTCATAGTTTACTGATTTTCAGGTTTCTCGTTACCCAC
*
11994033 CTTTCATAGTTTACTGATTTTTAGGTTTCTCGTTACCCAC
1 CTTTCATAGTTTACTGATTTTCAGGTTTCTCGTTACCCAC
11994073 CT
1 CT
11994075 GGTTCGGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.13, T:0.46
Consensus pattern (40 bp):
CTTTCATAGTTTACTGATTTTCAGGTTTCTCGTTACCCAC
Found at i:11998982 original size:47 final size:48
Alignment explanation
Indices: 11998890--11998992 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 48
11998880 AAAATATGAT
* *
11998890 TATGTGATTTCCGTGTAAGACTATATCTGGATATGGCATC-A-GTGTGA
1 TATGTG-TTTCCGTGTAAGACCATAGCTGGATATGGCATCGATGTGTGA
* * *
11998937 TATGTGTTTCCGTGTAAGACCATAGCTGGGCTATGGCTTCGGTGTGTGA
1 TATGTGTTTCCGTGTAAGACCATAGCT-GGATATGGCATCGATGTGTGA
11998986 TATGTGT
1 TATGTGT
11998993 AATGTGCAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 19 0.40
47 16 0.33
49 13 0.27
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.37
Consensus pattern (48 bp):
TATGTGTTTCCGTGTAAGACCATAGCTGGATATGGCATCGATGTGTGA
Found at i:12016179 original size:14 final size:13
Alignment explanation
Indices: 12016144--12016169 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12016134 TAAAACATAT
12016144 GAAACAAAAAAAA
1 GAAACAAAAAAAA
12016157 GAAACAAAAAAAA
1 GAAACAAAAAAAA
12016170 CTATACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
GAAACAAAAAAAA
Found at i:12016308 original size:3 final size:3
Alignment explanation
Indices: 12016300--12016342 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
12016290 ATACATGTTG
12016300 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12016343 CAGAATGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12023976 original size:40 final size:40
Alignment explanation
Indices: 12023921--12024002 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
12023911 TCAATTTCAG
12023921 CTTTCGTAGTTTACTGATTTTCAGGTTTCTCGTTACCCAC
1 CTTTCGTAGTTTACTGATTTTCAGGTTTCTCGTTACCCAC
*
12023961 CTTTCGTAGTTTACTGATTTTTAGGTTTCTCGTTACCCAC
1 CTTTCGTAGTTTACTGATTTTCAGGTTTCTCGTTACCCAC
12024001 CT
1 CT
12024003 GGTTCGGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.46
Consensus pattern (40 bp):
CTTTCGTAGTTTACTGATTTTCAGGTTTCTCGTTACCCAC
Found at i:12024630 original size:18 final size:19
Alignment explanation
Indices: 12024600--12024636 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12024590 ATTAGTTTTT
*
12024600 CTTTTATTATTTATTTTAA
1 CTTTTATTATTTATATTAA
12024619 CTTTTATT-TTTATATTAA
1 CTTTTATTATTTATATTAA
12024637 AAGGTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTTATTATTTATATTAA
Found at i:12028926 original size:47 final size:49
Alignment explanation
Indices: 12028834--12028936 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 49
12028824 AAAATATGAT
* *
12028834 TATGTGATTTCCGTGTAAGACTATATCTGGATATGGCATC-A-GTGTGA
1 TATGTGATTTCCGTGTAAGACCATAGCTGGATATGGCATCGATGTGTGA
* * *
12028881 TATGTG-TTTCCGTGTAAGACCATAGCTGGGCTATGGCTTCGGTGTGTGA
1 TATGTGATTTCCGTGTAAGACCATAGCT-GGATATGGCATCGATGTGTGA
12028930 TATGTGA
1 TATGTGA
12028937 CAATGTGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
46 19 0.40
47 16 0.34
49 12 0.26
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (49 bp):
TATGTGATTTCCGTGTAAGACCATAGCTGGATATGGCATCGATGTGTGA
Found at i:12035824 original size:56 final size:52
Alignment explanation
Indices: 12035736--12035976 Score: 262
Period size: 50 Copynumber: 4.7 Consensus size: 52
12035726 AAAGAGATCT
* * * *
12035736 CATGTAAGACCATGTTTGAGACATGACATTGGCATCCTTGAGATCATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC--GAGA-CATGAGAGGTCC
*
12035792 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGAC--GAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACATGAGAGGTCC
*
12035842 CATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAG--ATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACATGAGAGGTCC
* * * **
12035892 CCTGTAAGACCATGTCTGGGACATGGC-ATGAGCA-C-TGACATGAGAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTG-GCACCGAGACATGAG-AGGTCC
* *
12035943 CATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCA
12035977 TGTTATTATT
Statistics
Matches: 164, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
48 1 0.01
49 3 0.02
50 88 0.54
51 32 0.20
52 3 0.02
53 4 0.02
55 2 0.01
56 31 0.19
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (52 bp):
CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACATGAGAGGTCC
Found at i:12054864 original size:25 final size:25
Alignment explanation
Indices: 12054824--12054893 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
12054814 AGGAAGTGCT
* **
12054824 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACAA
* *
12054849 AAAAGGGCTTTTCCCCAGTTTATAA
1 AAAAGGGCTTTGCCCCAGTTTACAA
12054874 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
12054894 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACAA
Found at i:12055182 original size:29 final size:28
Alignment explanation
Indices: 12055148--12055202 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
12055138 AGACTGAATT
* *
12055148 AGGGCTTAGGCCCATACTGCTACTGTTTA
1 AGGGCTAAGGCCCAGACTG-TACTGTTTA
12055177 AGGGCTAAGGCCCAGACTGTACTGTT
1 AGGGCTAAGGCCCAGACTGTACTGTT
12055203 ACTGAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (28 bp):
AGGGCTAAGGCCCAGACTGTACTGTTTA
Found at i:12057046 original size:28 final size:28
Alignment explanation
Indices: 12057006--12057215 Score: 368
Period size: 28 Copynumber: 7.5 Consensus size: 28
12056996 TAAATTGTAC
12057006 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
12057034 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
12057062 AGCACTAAGTGTGCGTGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
12057090 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
12057118 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
12057146 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
12057174 AGCACTAAGTGTGCGAG-TTGATTGTAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
12057201 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12057216 GACTTAATAT
Statistics
Matches: 177, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
27 23 0.13
28 154 0.87
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:12057123 original size:84 final size:84
Alignment explanation
Indices: 12056981--12057215 Score: 373
Period size: 84 Copynumber: 2.8 Consensus size: 84
12056971 GAGATTGGCG
* * * *
12056981 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGT
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGT
12057046 GCGAGTTTGATTATGTAGCA
65 GCGAGTTTGATTATGTAGCA
* *
12057066 CTAAGTGTGCGTGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTG
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTG
12057131 CGAGTTTGATTATGTAGCA
66 CGAGTTTGATTATGTAGCA
* * *
12057150 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTGTATAGCACTGAGTGTG
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTG
12057214 CG
66 CG
12057216 GACTTAATAT
Statistics
Matches: 140, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
83 22 0.16
84 103 0.74
85 15 0.11
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (84 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTG
CGAGTTTGATTATGTAGCA
Found at i:12065233 original size:27 final size:28
Alignment explanation
Indices: 12065190--12065358 Score: 178
Period size: 26 Copynumber: 6.7 Consensus size: 28
12065180 CGGGTTAAAT
12065190 TGTACGCACTAAGTGTGCGAGTTTGATTA
1 TGTA-GCACTAAGTGTGCGAGTTTGATTA
12065219 TGTAGCACTAA-TGTGCGAGTTTG-TTA
1 TGTAGCACTAAGTGTGCGAGTTTGATTA
12065245 TGTAGCACTAAGTGTGCGAG-TTGATT-
1 TGTAGCACTAAGTGTGCGAGTTTGATTA
12065271 TGTA-CACT-A-TGT-C-AGTTTG-TTA
1 TGTAGCACTAAGTGTGCGAGTTTGATTA
12065293 T-TAG--CTAAGT-TGCGAGTTTGATTA
1 TGTAGCACTAAGTGTGCGAGTTTGATTA
*
12065317 TATA-CACTAAGTGTGCGAG-TTGA-TA
1 TGTAGCACTAAGTGTGCGAGTTTGATTA
*
12065342 --TAGCACTGAGTGTGCGA
1 TGTAGCACTAAGTGTGCGA
12065359 CTTATATACT
Statistics
Matches: 124, Mismatches: 1, Indels: 35
0.77 0.01 0.22
Matches are distributed among these distances:
20 2 0.02
21 8 0.06
22 7 0.06
23 11 0.09
24 18 0.15
25 8 0.06
26 31 0.25
27 28 0.23
28 7 0.06
29 4 0.03
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (28 bp):
TGTAGCACTAAGTGTGCGAGTTTGATTA
Found at i:12065340 original size:26 final size:27
Alignment explanation
Indices: 12065196--12065337 Score: 164
Period size: 27 Copynumber: 5.6 Consensus size: 27
12065186 AAATTGTACG
12065196 CACTAAGTGTGCGAGTTTGATTATGTA
1 CACTAAGTGTGCGAGTTTGATTATGTA
12065223 GCACTAA-TGTGCGAGTTTG-TTATGTA
1 -CACTAAGTGTGCGAGTTTGATTATGTA
12065249 GCACTAAGTGTGCGAG-TTGATT-TGTA
1 -CACTAAGTGTGCGAGTTTGATTATGTA
12065275 CACT-A-TGT-C-AGTTTG-TTAT-TA
1 CACTAAGTGTGCGAGTTTGATTATGTA
* *
12065296 -GCTAAGT-TGCGAGTTTGATTATATA
1 CACTAAGTGTGCGAGTTTGATTATGTA
12065321 CACTAAGTGTGCGAGTT
1 CACTAAGTGTGCGAGTT
12065338 GATATAGCAC
Statistics
Matches: 100, Mismatches: 2, Indels: 25
0.79 0.02 0.20
Matches are distributed among these distances:
20 2 0.02
21 8 0.08
22 7 0.07
23 9 0.09
24 5 0.05
25 6 0.06
26 27 0.27
27 30 0.30
28 6 0.06
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (27 bp):
CACTAAGTGTGCGAGTTTGATTATGTA
Found at i:12065365 original size:23 final size:22
Alignment explanation
Indices: 12065314--12065367 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 22
12065304 GCGAGTTTGA
*
12065314 TTATATACACTAAGTGTGCGAG
1 TTATATACACTAAGTGTGCGAC
*
12065336 TTGATATAGCACTGAGTGTGCGAC
1 TT-ATATA-CACTAAGTGTGCGAC
12065360 TTATATAC
1 TTATATAC
12065368 TTTGAATCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 15 0.54
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (22 bp):
TTATATACACTAAGTGTGCGAC
Found at i:12073376 original size:28 final size:28
Alignment explanation
Indices: 12073336--12073488 Score: 265
Period size: 28 Copynumber: 5.5 Consensus size: 28
12073326 TAAATTGTAC
12073336 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
12073364 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
12073392 AGCACTAA-TGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
12073419 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
12073447 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
12073474 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12073489 GACTTAATAT
Statistics
Matches: 122, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
27 51 0.42
28 71 0.58
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:12073410 original size:55 final size:56
Alignment explanation
Indices: 12073311--12073488 Score: 270
Period size: 55 Copynumber: 3.2 Consensus size: 56
12073301 GAGATTGGCG
* * * *
12073311 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
12073368 CTAAGTGTGCGAGTTTGATTATGTAGCACTAA-TGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
12073423 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
12073478 CTGAGTGTGCG
1 CTAAGTGTGCG
12073489 GACTTAATAT
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
55 77 0.69
56 20 0.18
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:12073487 original size:83 final size:83
Alignment explanation
Indices: 12073336--12073488 Score: 263
Period size: 83 Copynumber: 1.8 Consensus size: 83
12073326 TAAATTGTAC
* *
12073336 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAT
12073401 GTGCGAGTTTGATTATGT
66 GTGCGAGTTTGATTATGT
*
12073419 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCACTGAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACT-AA
12073483 TGTGCG
65 TGTGCG
12073489 GACTTAATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
82 15 0.23
83 51 0.77
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (83 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAT
GTGCGAGTTTGATTATGT
Found at i:12075803 original size:28 final size:28
Alignment explanation
Indices: 12075771--12075842 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
12075761 TTTAATAAGT
*
12075771 TCGCACACTTAGTGCTTAATAATCAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
12075799 TCGCACACTTAGTGCTTCACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
*
12075827 TCGTACACTTAGTGCT
1 TCGCACACTTAGTGCT
12075843 AATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:12081121 original size:9 final size:9
Alignment explanation
Indices: 12081107--12081164 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
12081097 GCAACCCAAT
12081107 TTTTATTTA
1 TTTTATTTA
12081116 TTTTATTT-
1 TTTTATTTA
12081124 TATTTACTTTA
1 T-TTTA-TTTA
12081135 -TTTA-TTA
1 TTTTATTTA
*
12081142 CTTTATTTTA
1 TTTTA-TTTA
12081152 TTTTA-TTA
1 TTTTATTTA
12081160 TTTTA
1 TTTTA
12081165 CAACTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
7 3 0.07
8 13 0.31
9 16 0.38
10 10 0.24
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:12081122 original size:5 final size:5
Alignment explanation
Indices: 12081107--12081158 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
12081097 GCAACCCAAT
* *
12081107 TTTTA -TTTA TTTTA TTTTA -TTTA CTTTA TTTATTA CTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA
12081157 TT
1 TT
12081159 ATTTTACAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 8 0.20
5 27 0.68
6 2 0.05
7 3 0.08
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:12083154 original size:15 final size:15
Alignment explanation
Indices: 12083129--12083163 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12083119 GACTCTATTT
*
12083129 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
12083143 TAATTAATATTAAGA
1 TAATTAATATTAAGA
12083158 TAATTA
1 TAATTA
12083164 TTAACGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:12086013 original size:35 final size:35
Alignment explanation
Indices: 12085974--12086043 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
12085964 TAGATGGTAT
12085974 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
1 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
12086009 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
1 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
12086044 CATCTATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (35 bp):
ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
Found at i:12086961 original size:33 final size:33
Alignment explanation
Indices: 12086919--12086987 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
12086909 TTAACATGTG
*
12086919 TTTCAATTGTACTAAATTGTAACAAATTAATAA
1 TTTCAATTGTACTAAATTGTAACAAACTAATAA
*
12086952 TTTCAATTGTACTAAATTGTAATAAACTAATAA
1 TTTCAATTGTACTAAATTGTAACAAACTAATAA
12086985 TTT
1 TTT
12086988 TACTATCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (33 bp):
TTTCAATTGTACTAAATTGTAACAAACTAATAA
Found at i:12087974 original size:42 final size:44
Alignment explanation
Indices: 12087902--12088007 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 44
12087892 CATCATGAAC
*
12087902 ATGGTTTCTTCCACGTTGCATTGTCTTGTCA-AGTCATTGATTTA
1 ATGGTTGCTTCCACGTTGCATTGTCTTGTCACA-TCATTGATTTA
*
12087946 ATGGTTGCTTCCAC-TT-CATTGTCTTGTCACATTATTGATTTA
1 ATGGTTGCTTCCACGTTGCATTGTCTTGTCACATCATTGATTTA
* * *
12087988 ATGTTTGTTTCCACATTGCA
1 ATGGTTGCTTCCACGTTGCA
12088008 ATCTCTTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 35 0.64
43 5 0.09
44 15 0.27
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (44 bp):
ATGGTTGCTTCCACGTTGCATTGTCTTGTCACATCATTGATTTA
Found at i:12094254 original size:20 final size:18
Alignment explanation
Indices: 12094204--12094256 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
12094194 GTTCTTCATA
12094204 AAAATTTAAAAAATTATT
1 AAAATTTAAAAAATTATT
* *
12094222 AAAA-TTATTAAAATTTTGAT
1 AAAATTTA-AAAAATTAT--T
12094242 AAAATTTAAAAAATT
1 AAAATTTAAAAAATT
12094257 CAATAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
20 11 0.39
21 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATTTAAAAAATTATT
Found at i:12101110 original size:18 final size:18
Alignment explanation
Indices: 12101087--12101179 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
12101077 CCCAACTACT
*
12101087 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
12101105 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
12101123 GTATATGTGAATAGTATC
1 GTATACGTGAATAGTACC
**
12101141 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
*
12101159 GTATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
12101177 GTA
1 GTA
12101180 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:12101144 original size:36 final size:36
Alignment explanation
Indices: 12101087--12101179 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
12101077 CCCAACTACT
* *
12101087 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATATGTGAATAGTACCGTATACGTGAATAGTGCC
* *
12101123 GTATATGTGAATAGTATCGTATACGTGAATAGTGTC
1 GTATATGTGAATAGTACCGTATACGTGAATAGTGCC
12101159 GTATATGTGAATAGTACCGTA
1 GTATATGTGAATAGTACCGTA
12101180 AACGGTCGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (36 bp):
GTATATGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:12104694 original size:19 final size:19
Alignment explanation
Indices: 12104661--12104713 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
12104651 CACCAATTTC
*
12104661 TTTTAAAAA-ATAAAAATA
1 TTTTAAAAATAAAAAAATA
*
12104679 TTTTAAAAATAAAAAAGTA
1 TTTTAAAAATAAAAAAATA
12104698 TTTTAAAAATAAAAAA
1 TTTTAAAAATAAAAAA
12104714 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 9 0.28
19 23 0.72
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TTTTAAAAATAAAAAAATA
Found at i:12104712 original size:7 final size:7
Alignment explanation
Indices: 12104702--12104726 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12104692 AAAGTATTTT
12104702 AAAAATA
1 AAAAATA
12104709 AAAAATA
1 AAAAATA
12104716 AAAAATA
1 AAAAATA
12104723 AAAA
1 AAAA
12104727 TATATATTTA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:12115841 original size:24 final size:24
Alignment explanation
Indices: 12115814--12115859 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12115804 AGAACAATCC
* *
12115814 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
12115838 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
12115860 AAAATATGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:12123834 original size:89 final size:88
Alignment explanation
Indices: 12123683--12124014 Score: 286
Period size: 89 Copynumber: 3.8 Consensus size: 88
12123673 ACAGATCGAG
* * * *
12123683 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AAGTAGGCAAGTCTTATC-CACCTGAAGTTG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGT-GGTAA-TCCTATCTC-GCTGAAGTTG
*
12123746 CAGTGAGGCAGACTGAAGGTGGCAAA
63 CAGTGAGGCAGACTGAAGATGGCAAA
12123772 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAG-TGGTAATCCTATCTCGCTGAAGTTGCA
* * * **** *
12123837 GTGA-GCGGA-TTAAAACCTTAGA
65 GTGAGGCAGACTGAAGATGGCAAA
* * ** * * * * * *
12123859 TCTTATCTCTCTGAAGTTGCA-AAGAACAGATCACA-T-CTAGTCTTATCCTC-CTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTGGTAATCCTAT-CTCGCTGAAGTTGCA
12123920 GTGAGGCAGACTGAAGATGGCAAA
65 GTGAGGCAGACTGAAGATGGCAAA
* ** * * *
12123944 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAG-TGGTAATCCTATCTCGCTGAAGTTGCA
12124009 GT-AGGC
65 GTGAGGC
12124015 GGATTAAAAC
Statistics
Matches: 187, Mismatches: 45, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
83 22 0.12
84 8 0.04
85 24 0.13
86 18 0.10
87 24 0.13
88 10 0.05
89 72 0.39
90 8 0.04
91 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTGGTAATCCTATCTCGCTGAAGTTGCAG
TGAGGCAGACTGAAGATGGCAAA
Found at i:12123973 original size:172 final size:172
Alignment explanation
Indices: 12123725--12124094 Score: 591
Period size: 172 Copynumber: 2.2 Consensus size: 172
12123715 TAAGTAGGCA
* *
12123725 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGGTGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* *
12123790 ACAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCAGT-GAGCGGATTAAAACC
66 ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAG-GCGGATTAAAACC
12123854 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
130 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
*
12123897 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
** *
12123962 GTAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGTAGTAGGCGGATTAAAACCT
66 ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCT
* * * * *
12124027 TATATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCT
131 TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
12124069 AGTCTTAT-CTCCCTGAAGTTGCAGTG
1 AGTCTTATCCT-CCTGAAGTTGCAGTG
12124095 GAACGGACTA
Statistics
Matches: 183, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 2 0.01
172 180 0.98
173 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (172 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCT
TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
Found at i:12124121 original size:216 final size:216
Alignment explanation
Indices: 12123899--12124307 Score: 728
Period size: 216 Copynumber: 1.9 Consensus size: 216
12123889 TCACATCTAG
* *
12123899 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGT
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGT
*
12123964 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGTAGTAGGCGGATTAAAACCTTA
66 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCTTA
* *
12124029 TATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
131 GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
12124094 GGAACGGACTAAGTAAGCAAA
196 GGAACGGACTAAGTAAGCAAA
* *
12124115 TCTTATCTTCCTGAATTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGT
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGT
*
12124180 AGTGGAGCAGATTAAAGTCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCTTA
66 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCTTA
* *
12124245 GATCTTATCTCTCTGAAGTTGCAGAGAGCGGATCGCATTTAGTCTTATCTCCCTGAAGTTGCA
131 GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCA
12124308 CCAGGAGCAA
Statistics
Matches: 183, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
216 183 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (216 bp):
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGT
AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCTTA
GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
GGAACGGACTAAGTAAGCAAA
Found at i:12124176 original size:172 final size:172
Alignment explanation
Indices: 12123725--12124195 Score: 582
Period size: 172 Copynumber: 2.7 Consensus size: 172
12123715 TAAGTAGGCA
*
12123725 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGGT-GGCAAATCTTATCTCCCTGAAGT
1 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAA-GTAGGCAAATCTTATCTTCCTGAAGT
* * *
12123789 TACAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCAGTGAGCGGATTAAAACC
65 TGCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCCCTGAAGTTGTAGTGAGCGGATTAAAACC
12123854 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
130 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
*
12123897 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAG-ATGGCAAATCTTATC-TCCTTGAAG
1 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGTA-GGCAAATCTTATCTTCC-TGAAG
* *
12123960 TTGTAGTGGAGCAGATTAAAGCCGGTAATCCTATC-CCGCTGAAGTTGTAGT-AGGCGGATTAAA
64 TTGCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCC-CTGAAGTTGTAGTGA-GCGGATTAAA
* * * * *
12124023 ACCTTATATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCT
127 ACCTTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
* * * *
12124069 AGTCTTATCTC-CCTGAAGTTGCAGTG-GAACGGACT-AAGTAAGCAAATCTTATCTTCCTGAAT
1 AGTCTTATC-CACCTGAAGTTGCAGTGAG-GCAGACTGAAGTAGGCAAATCTTATCTTCCTGAAG
* * * * * * *
12124131 TTGCAGT-GAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGTAGTGGAGCAGATTAA
64 TTGCAGTGGA-GCAGATTAAAGCTGG-TAATCCTATCTCCCTGAAGTTGTAGT-GAGCGGATTAA
12124195 A
126 A
12124196 GTCGGTAATC
Statistics
Matches: 260, Mismatches: 25, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
170 2 0.01
171 42 0.16
172 203 0.78
173 12 0.05
174 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (172 bp):
AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGTAGGCAAATCTTATCTTCCTGAAGTT
GCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCCCTGAAGTTGTAGTGAGCGGATTAAAACCT
TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
Found at i:12124190 original size:45 final size:44
Alignment explanation
Indices: 12123683--12124190 Score: 186
Period size: 44 Copynumber: 11.7 Consensus size: 44
12123673 ACAGATCGAG
* * *
12123683 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAGGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
*
12123727 TCTTATC-CACCTGAAGTTGCAGT-GAGGCAGACTGAAGGT-GGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AA-GTAAGCAAA
* * **
12123772 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCT--GGTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAA
* * * * * *
12123816 TCCTATCTCGCTGAAGTTGCAGT-GAGCGGATTAA--AACCTTAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC--AAA
* ** * * * * * *
12123859 TCTTATCTCTCTGAAGTTGCA-AAGAACAGA-TCA--CATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
*
12123899 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAG-ATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAA
* * * ** **
12123944 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAG-CCGGTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAAA
* * * * * * *
12123988 TCCTATC-CCGCTGAAGTTGTAGTAG-GCGGATTAA--AACCTTATA
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTAAGTAAGC--AAA
** * * * * * *
12124031 TCTTATCTCTTTGAAGTTGCAG-AGAGCAGA-T-CG-CATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
* *
12124071 TCTTATCTCCCTGAAGTTGCAGTGGAACGGACTAAGTAAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
* * *
12124115 TCTTATCTTCCTGAATTTGCAGT-GAGGCAGACTGAAG-ATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAA
* *
12124160 TCTTATCTCCCTGAAGTGGTAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
12124191 TTAAAGTCGG
Statistics
Matches: 346, Mismatches: 83, Indels: 69
0.69 0.17 0.14
Matches are distributed among these distances:
39 1 0.00
40 40 0.12
41 9 0.03
42 15 0.04
43 69 0.20
44 104 0.30
45 98 0.28
46 10 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
Found at i:12125700 original size:19 final size:20
Alignment explanation
Indices: 12125659--12125700 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
12125649 GTTTCTATGT
* *
12125659 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
12125679 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
12125698 CAT
1 CAT
12125701 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Found at i:12127920 original size:21 final size:21
Alignment explanation
Indices: 12127876--12127913 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12127866 TAACTTGTAA
12127876 TAAATTATTAATAATATTATT
1 TAAATTATTAATAATATTATT
12127897 TAAATTA-TAAT-ATATTA
1 TAAATTATTAATAATATTA
12127914 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATTAATAATATTATT
Found at i:12127935 original size:28 final size:28
Alignment explanation
Indices: 12127881--12127935 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
12127871 TGTAATAAAT
* *
12127881 TATTAATAATATTATTTAAATTATAATA
1 TATTAATAATAATATTTAAATCATAATA
* *
12127909 TATTAATATTAATATTTGAATCATAAT
1 TATTAATAATAATATTTAAATCATAAT
12127936 GAGTTTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TATTAATAATAATATTTAAATCATAATA
Found at i:12129933 original size:19 final size:19
Alignment explanation
Indices: 12129909--12129946 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12129899 GATTGTACTA
12129909 GTCAAAATGCATCAGACAT
1 GTCAAAATGCATCAGACAT
*
12129928 GTCAAAATGTATCAGACAT
1 GTCAAAATGCATCAGACAT
12129947 AAGTGGATGA
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:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (19 bp):
GTCAAAATGCATCAGACAT
Found at i:12132002 original size:13 final size:13
Alignment explanation
Indices: 12131986--12132037 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
12131976 TTTAAATCAA
12131986 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
12131999 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
*
12132012 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
12132025 GCTTTTCAAAAGC
1 ACTTTTCAAAAGC
12132038 TTTACCAAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
12 4 0.13
13 22 0.73
14 4 0.13
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:12133168 original size:20 final size:20
Alignment explanation
Indices: 12133145--12133191 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
12133135 CTTAAAATAC
12133145 GTAATAAATATAAAAAATTA
1 GTAATAAATATAAAAAATTA
*
12133165 GTAATAAATATAAAAAATTC
1 GTAATAAATATAAAAAATTA
12133185 GTAATAA
1 GTAATAA
12133192 TAAAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (20 bp):
GTAATAAATATAAAAAATTA
Found at i:12133204 original size:23 final size:22
Alignment explanation
Indices: 12133146--12133204 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
12133136 TTAAAATACG
12133146 TAATAAATATAAAAAATTAGTAA
1 TAATAAA-ATAAAAAATTAGTAA
* *
12133169 T-A-AATATAAAAAATTCGTAA
1 TAATAAAATAAAAAATTAGTAA
12133189 TAATAAAATAATAAAA
1 TAATAAAATAA-AAAA
12133205 GATGATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 15 0.50
21 3 0.10
22 7 0.23
23 5 0.17
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (22 bp):
TAATAAAATAAAAAATTAGTAA
Found at i:12135100 original size:98 final size:98
Alignment explanation
Indices: 12134931--12135123 Score: 341
Period size: 98 Copynumber: 2.0 Consensus size: 98
12134921 ACAATAAAAC
* *
12134931 TTTAAAGGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCC
12134996 TTTAGAATCCCAAACTCGGAATATTTCCTTTAT
66 TTTAGAATCCCAAACTCGGAATATTTCCTTTAT
* *
12135029 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCC
*
12135094 TTTAGAATCTCAAACTCGGAATATTTCCTT
66 TTTAGAATCCCAAACTCGGAATATTTCCTT
12135124 CAGGATTTTT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.28
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCC
TTTAGAATCCCAAACTCGGAATATTTCCTTTAT
Found at i:12136210 original size:25 final size:25
Alignment explanation
Indices: 12136182--12136233 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
12136172 GAGGGGCTGG
12136182 AAGGGAAATTTTCTCTTCTTCTCTA
1 AAGGGAAATTTTCTCTTCTTCTCTA
12136207 AAGGGAAATTTTCTCTTCTTCTCTA
1 AAGGGAAATTTTCTCTTCTTCTCTA
12136232 AA
1 AA
12136234 ACGACGCCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (25 bp):
AAGGGAAATTTTCTCTTCTTCTCTA
Found at i:12136653 original size:19 final size:19
Alignment explanation
Indices: 12136629--12136700 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
12136619 AATTATATCT
12136629 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
12136648 TCTAAGATTATACATCATA
1 TCTAAGATTGCATATCATA
12136667 TCTAAGATTGCATAT-ATA
1 TCTAAGATTGCATATCATA
*
12136685 TCTAGGATTGCATATC
1 TCTAAGATTGCATATC
12136701 CTCAAAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 17 0.38
19 28 0.62
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12140345 original size:20 final size:19
Alignment explanation
Indices: 12140312--12140367 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
12140302 TCCAGCTTCA
*
12140312 TTTAGTTTTTAAAAAT-AT
1 TTTAATTTTTAAAAATAAT
*
12140330 TTTCTATTTTTAAAAAATAAT
1 TTT-AATTTTT-AAAAATAAT
12140351 TTTAATTTTTTAAAAAT
1 TTTAA-TTTTTAAAAAT
12140368 TAAAAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.10
19 5 0.16
20 13 0.42
21 10 0.32
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTAATTTTTAAAAATAAT
Found at i:12149230 original size:32 final size:34
Alignment explanation
Indices: 12149166--12149231 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
12149156 AACACCAATT
*
12149166 TTTTAAAAAAATAAAAAAAGTTTTTTTTAAAATA
1 TTTTAAAAAAATAAAAAAAGTTTTTTTAAAAATA
*
12149200 TTTTAAAAATA-AAAAAAAG-TTTTTTAAAAATA
1 TTTTAAAAAAATAAAAAAAGTTTTTTTAAAAATA
12149232 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.40
33 8 0.27
34 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (34 bp):
TTTTAAAAAAATAAAAAAAGTTTTTTTAAAAATA
Found at i:12151171 original size:21 final size:21
Alignment explanation
Indices: 12151127--12151164 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12151117 TAACTTGTAA
12151127 TAAATTATTAATAATATTATT
1 TAAATTATTAATAATATTATT
12151148 TAAATTA-TAAT-ATATTA
1 TAAATTATTAATAATATTA
12151165 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATTAATAATATTATT
Found at i:12151186 original size:28 final size:28
Alignment explanation
Indices: 12151132--12151186 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
12151122 TGTAATAAAT
* *
12151132 TATTAATAATATTATTTAAATTATAATA
1 TATTAATAATAATATTTAAATCATAATA
* *
12151160 TATTAATATTAATATTTGAATCATAAT
1 TATTAATAATAATATTTAAATCATAAT
12151187 GAATTTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TATTAATAATAATATTTAAATCATAATA
Found at i:12153187 original size:19 final size:19
Alignment explanation
Indices: 12153163--12153200 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12153153 GATTGTACTA
12153163 GTCAAAATGCATCAGACAT
1 GTCAAAATGCATCAGACAT
*
12153182 GTCAAAATGTATCAGACAT
1 GTCAAAATGCATCAGACAT
12153201 AAGTGGATGA
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:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (19 bp):
GTCAAAATGCATCAGACAT
Found at i:12155316 original size:13 final size:13
Alignment explanation
Indices: 12155300--12155365 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
12155290 TTTAAACCAA
12155300 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
12155313 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
*
12155326 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
12155339 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
12155352 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
12155365 A
1 A
12155366 TTACCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 4 0.09
13 37 0.82
14 4 0.09
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:12156044 original size:17 final size:18
Alignment explanation
Indices: 12156018--12156051 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12156008 AAATTAGAGA
12156018 ATAAAAAAATAA-AAATC
1 ATAAAAAAATAAGAAATC
*
12156035 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
12156052 AAAAAGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATC
Found at i:12156489 original size:19 final size:20
Alignment explanation
Indices: 12156454--12156492 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12156444 TAAATAACTT
12156454 AAAATACGTAATAAATATAA
1 AAAATACGTAATAAATATAA
*
12156474 AAAATTCGTAAT-AATATAA
1 AAAATACGTAATAAATATAA
12156493 TAATAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATACGTAATAAATATAA
Found at i:12158065 original size:13 final size:13
Alignment explanation
Indices: 12158047--12158071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12158037 CAATAACTCC
12158047 AAAAATATTTAAT
1 AAAAATATTTAAT
12158060 AAAAATATTTAA
1 AAAAATATTTAA
12158072 AGGTTCGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATATTTAAT
Found at i:12162724 original size:17 final size:17
Alignment explanation
Indices: 12162702--12162735 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12162692 ATCCACTAAT
*
12162702 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
12162719 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
12162736 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:12167363 original size:17 final size:17
Alignment explanation
Indices: 12167341--12167374 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12167331 ATCCACTAAT
*
12167341 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
12167358 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
12167375 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:12189733 original size:75 final size:76
Alignment explanation
Indices: 12189605--12189828 Score: 423
Period size: 75 Copynumber: 3.0 Consensus size: 76
12189595 TCAGTAACAT
12189605 GATTCATTCGACTTGCTACAAAATTAAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
1 GATTCATTCGACTTGCTACAAAATTAAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
12189670 CACAAGTTGGG
66 CACAAGTTGGG
12189681 GATTCATTCGACTTGCTACAAAATT-AAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
1 GATTCATTCGACTTGCTACAAAATTAAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
12189745 CACAAGTTGGG
66 CACAAGTTGGG
* *
12189756 GATTCATTCGAGTTGCTACAAAATTAAAAGCCAAGTAAGTCTACCTTCTCCATCAATCCCCATTC
1 GATTCATTCGACTTGCTACAAAATTAAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
12189821 CACAAGTT
66 CACAAGTT
12189829 CGGGTCATCC
Statistics
Matches: 145, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
75 74 0.51
76 71 0.49
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (76 bp):
GATTCATTCGACTTGCTACAAAATTAAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
CACAAGTTGGG
Found at i:12190636 original size:22 final size:22
Alignment explanation
Indices: 12190582--12190638 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
12190572 ATAAAACAAA
* * *
12190582 AACAGCAAAATAGTAGCAATAT
1 AACAACAAAATAGTAGCAAAAC
* * *
12190604 AATAACGAAATGGTAGCAAAAC
1 AACAACAAAATAGTAGCAAAAC
12190626 AACAACAAAATAG
1 AACAACAAAATAG
12190639 CAGTGAAATG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
AACAACAAAATAGTAGCAAAAC
Found at i:12197496 original size:6 final size:6
Alignment explanation
Indices: 12197475--12197519 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
12197465 TCGAAATGGT
* *
12197475 TCAAAA T-AAAA -AAAAA TCAAAA TCAAAA TCAAAA TTAAAA T-AAAA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA
12197520 AAAAAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 12 0.34
6 23 0.66
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (6 bp):
TCAAAA
Found at i:12197496 original size:16 final size:16
Alignment explanation
Indices: 12197475--12197537 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
12197465 TCGAAATGGT
12197475 TCAAAATAAAAAAAAA
1 TCAAAATAAAAAAAAA
*
12197491 TCAAAATCAAAATCAAAA
1 TCAAAAT-AAAA-AAAAA
*
12197509 TTAAAATAAAAAAAAA
1 TCAAAATAAAAAAAAA
**
12197525 GAAAAATAAAAAA
1 TCAAAATAAAAAA
12197538 TAAAAGTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 22 0.55
17 8 0.20
18 10 0.25
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (16 bp):
TCAAAATAAAAAAAAA
Found at i:12197504 original size:12 final size:11
Alignment explanation
Indices: 12197477--12197535 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
12197467 GAAATGGTTC
*
12197477 AAAAT-AAAAA
1 AAAATCAAAAT
12197487 AAAATCAAAAT
1 AAAATCAAAAT
12197498 CAAAATCAAAATT
1 -AAAATCAAAA-T
*
12197511 AAAAT-AAAAA
1 AAAATCAAAAT
**
12197521 AAAAGAAAAAT
1 AAAATCAAAAT
12197532 AAAA
1 AAAA
12197536 AATAAAAGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 9 0.22
11 16 0.39
12 15 0.37
13 1 0.02
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAATCAAAAT
Found at i:12197520 original size:6 final size:6
Alignment explanation
Indices: 12197477--12197542 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
12197467 GAAATGGTTC
* * * *
12197477 AAAAT- AAAA-A AAAATC AAAATC AAAATC AAAATT AAAAT- AAAA-A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
12197521 AAAAGA AAAATAA AAAATA AAA
1 AAAATA AAAAT-A AAAATA AAA
12197543 GTCAAAAGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
5 16 0.30
6 31 0.58
7 6 0.11
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:12197524 original size:28 final size:27
Alignment explanation
Indices: 12197475--12197542 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
12197465 TCGAAATGGT
**
12197475 TCAAAATAAAAAAAAATCAAAATCAAAA
1 TCAAAATAAAAAAAAA-CAAAAGAAAAA
12197503 TCAAAATTAAAATAAAAA-AAAAGAAAAA
1 TCAAAA-TAAAA-AAAAACAAAAGAAAAA
*
12197531 TAAAAAATAAAA
1 T-CAAAATAAAA
12197543 GTCAAAAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 20 0.59
29 9 0.26
30 5 0.15
ACGTcount: A:0.78, C:0.06, G:0.01, T:0.15
Consensus pattern (27 bp):
TCAAAATAAAAAAAAACAAAAGAAAAA
Found at i:12197549 original size:28 final size:28
Alignment explanation
Indices: 12197517--12197582 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
12197507 AATTAAAATA
* *
12197517 AAAAAAAAGAAAAATAAAAAATAAAAGTC
1 AAAAGAAA-AAAAAGAAAAAATAAAAGTC
* * *
12197546 AAAAGCAAAAAGAGAAAAAATCAAAGTC
1 AAAAGAAAAAAAAGAAAAAATAAAAGTC
*
12197574 AAAACAAAA
1 AAAAGAAAA
12197583 TATGAAAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.76, C:0.08, G:0.09, T:0.08
Consensus pattern (28 bp):
AAAAGAAAAAAAAGAAAAAATAAAAGTC
Found at i:12197986 original size:12 final size:12
Alignment explanation
Indices: 12197957--12197997 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
12197947 ATGAAGTTCA
12197957 AAAAAAAAAGATG
1 AAAAAAAAA-ATG
*
12197970 AAAAATGAAAATG
1 AAAAA-AAAAATG
12197983 AAAAAAAAAATG
1 AAAAAAAAAATG
12197995 AAA
1 AAA
12197998 GAGTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.36
13 13 0.52
14 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (12 bp):
AAAAAAAAAATG
Found at i:12198217 original size:87 final size:87
Alignment explanation
Indices: 12198071--12198619 Score: 746
Period size: 87 Copynumber: 6.3 Consensus size: 87
12198061 AGTTGAAAAC
* *
12198071 CCTGCATTAACAGCGAAGTAGATCA-AAAACGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
1 CCTGCATTAACAGCGAAGCAGAT-AGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
*
12198135 TTAAAGATAGCATATTTTGCCTT
65 TTAAAGATAGCAGATTTTGCCTT
* *
12198158 CCTGCATTAACAGCGAAGCAAATAGAAAATGAAGTCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
1 CCTGCATTAACAGCGAAGCAGATAGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
* * *
12198223 TAAAGATTGCAGATCTTACCTT
66 TAAAGATAGCAGATTTTGCCTT
* * * *
12198245 CCTACATTAATAGTGAAGCAGATCGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
1 CCTGCATTAACAGCGAAGCAGATAGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
*
12198310 TAAAGATAGCATATTTTGCCTT
66 TAAAGATAGCAGATTTTGCCTT
* * *
12198332 CCTACATTAACAGCGAAGCAGATCA-AAAATGAAGTCTTGCCTCCATCGGTTGCAATGGAGCTGG
1 CCTGCATTAACAGCGAAGCAGAT-AGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
* *
12198396 TTAAAAATAGTAGATTTTGCCTT
65 TTAAAGATAGCAGATTTTGCCTT
* **
12198419 CCTGTATTAACAGTAAAGCAGATAGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT-GT
1 CCTGCATTAACAGCGAAGCAGATAGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
* *
12198483 TAAAG-GAGTAGATTTTGCCTT
66 TAAAGATAGCAGATTTTGCCTT
* * * ** *
12198504 CCTGCGTTAACAGCGAAGCAGTTTGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGT
1 CCTGCATTAACAGCGAAGCAGATAGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
*
12198569 TAAAGATAGCAGATATTGCCTT
66 TAAAGATAGCAGATTTTGCCTT
* * * *
12198591 CCTGCATTGACAGTGGAGCAGATCGAAAA
1 CCTGCATTAACAGCGAAGCAGATAGAAAA
12198620 CGGTGAATCT
Statistics
Matches: 405, Mismatches: 52, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
85 68 0.17
86 15 0.04
87 322 0.80
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (87 bp):
CCTGCATTAACAGCGAAGCAGATAGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
TAAAGATAGCAGATTTTGCCTT
Found at i:12198673 original size:43 final size:43
Alignment explanation
Indices: 12198624--12198835 Score: 264
Period size: 43 Copynumber: 4.9 Consensus size: 43
12198614 CGAAAACGGT
* *
12198624 GAATCTTATCTTCCCCAGGAGTAGGGAAATAGATCTAAGTGGC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGC
* * *
12198667 GGATCTTATCTTCCCTAGGAGTAGGGAAACAGATCT-AGACGAC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG-CGGC
* * *
12198710 AAATCTAATCTTCTCCAGGAGTAGGGAAACAGATCTAAGCGGC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGC
* * * *
12198753 GGATCTTATCTGCCCCAAGAGTAGGGAAACAGATCTAAGCGGT
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGC
* * * *
12198796 GAATCTTATTTTCCCCATGAGTAGGGAAACAAATTTAAGC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGC
12198836 CACTAGTCCT
Statistics
Matches: 143, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
42 2 0.01
43 139 0.97
44 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (43 bp):
GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGC
Found at i:12204805 original size:3 final size:3
Alignment explanation
Indices: 12204797--12204830 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12204787 TGTTATGACA
12204797 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12204831 TCTTAAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12206994 original size:21 final size:21
Alignment explanation
Indices: 12206970--12207012 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12206960 TAAAATGTAG
12206970 TTTTTTA-TTTA-ATTTCTATA
1 TTTTTTATTTTATATTT-TATA
12206990 TTTTTTATTTTATATTTTATA
1 TTTTTTATTTTATATTTTATA
12207011 TT
1 TT
12207013 ATTAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 10 0.48
22 4 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTATTTTATATTTTATA
Found at i:12212128 original size:28 final size:28
Alignment explanation
Indices: 12212096--12212167 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
12212086 TTTAATAAGT
*
12212096 TCGCACACTTAGTGCTTAATAATCAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
12212124 TCGCACACTTAGTGCTTCACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
*
12212152 TCGCACATTTAGTGCT
1 TCGCACACTTAGTGCT
12212168 AATCTCTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:12217464 original size:5 final size:5
Alignment explanation
Indices: 12217454--12217521 Score: 68
Period size: 5 Copynumber: 13.4 Consensus size: 5
12217444 GCAACCCAAT
* *
12217454 TTTTA TTTTA TTATT- TATTA TTTTA TTTTA TTTTA -TTTA CTTTA TTTATTA
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA
*
12217505 CTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
12217522 ATTTATTACT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 6 0.11
5 40 0.75
6 4 0.08
7 3 0.06
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:12217487 original size:31 final size:30
Alignment explanation
Indices: 12217454--12217535 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 30
12217444 GCAACCCAAT
*
12217454 TTTTATTTTATTATTTATTATTTTATTTTA
1 TTTTATTTTATTATTTATTACTTTATTTTA
12217484 TTTTA-TTTACTTTATTTATTACTTTATTTTA
1 TTTTATTTTA--TTATTTATTACTTTATTTTA
*
12217515 TTTTATTATTTATTACTTATT
1 TTTTA-T-TTTATTATTTATT
12217536 TGGATATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 4 0.09
30 5 0.11
31 24 0.53
32 8 0.18
34 4 0.09
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTTATTTTATTATTTATTACTTTATTTTA
Found at i:12218958 original size:101 final size:102
Alignment explanation
Indices: 12218716--12218977 Score: 463
Period size: 102 Copynumber: 2.6 Consensus size: 102
12218706 TTTAACATGT
* *
12218716 TGGGCTGAGTAACCGGGGTAGGGTGCTTGGCTATTATCTCTCTTCGTGTCAAAACGTTCGATGTG
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
12218781 TTCTTAAGAAAAAATTATAAAAAAATTAAGAGTCTGC
66 TTCTTAAGAAAAAATTATAAAAAAATTAAGAGTCTGC
* * *
12218818 TGGGCTGAGTAACTGGGGTGGGGTGTTTGGTTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
12218883 TTCTTAAGAAAAAATTAT-AAAAAATTAAGAGTCTGC
66 TTCTTAAGAAAAAATTATAAAAAAATTAAGAGTCTGC
*
12218919 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAAGGTTC
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTC
12218978 AGTATATTCC
Statistics
Matches: 151, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
101 73 0.48
102 78 0.52
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (102 bp):
TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
TTCTTAAGAAAAAATTATAAAAAAATTAAGAGTCTGC
Found at i:12219052 original size:12 final size:13
Alignment explanation
Indices: 12219028--12219062 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
12219018 AAATCAAAAT
*
12219028 AAATAAAACAGAA
1 AAATAAAAAAGAA
12219041 AAA-AAAAAAGAA
1 AAATAAAAAAGAA
12219053 AAATAAAAAA
1 AAATAAAAAA
12219063 ATATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.86, C:0.03, G:0.06, T:0.06
Consensus pattern (13 bp):
AAATAAAAAAGAA
Found at i:12219643 original size:15 final size:15
Alignment explanation
Indices: 12219618--12219652 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12219608 GACTCTATTT
*
12219618 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
12219632 TAATTAATATTAAGA
1 TAATTAATATTAAGA
12219647 TAATTA
1 TAATTA
12219653 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:12221303 original size:14 final size:14
Alignment explanation
Indices: 12221281--12221315 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12221271 GTACCTCGTT
*
12221281 AAAATCTTATTAAG
1 AAAAACTTATTAAG
12221295 AAAAACTTATTAAG
1 AAAAACTTATTAAG
12221309 AAAAACT
1 AAAAACT
12221316 CTATGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (14 bp):
AAAAACTTATTAAG
Found at i:12230069 original size:21 final size:21
Alignment explanation
Indices: 12230027--12230069 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12230017 CTGGGGTAAA
*
12230027 TAATTAATATATAACAATGTT
1 TAATTAATATATAACAAGGTT
* *
12230048 TAATTAATTTATAATAAGGTT
1 TAATTAATATATAACAAGGTT
12230069 T
1 T
12230070 TGTTTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TAATTAATATATAACAAGGTT
Found at i:12231881 original size:17 final size:18
Alignment explanation
Indices: 12231855--12231888 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12231845 AAATTTGAGA
12231855 ATAAAAAAATAA-AAATC
1 ATAAAAAAATAAGAAATC
*
12231872 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
12231889 AGAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATC
Found at i:12233065 original size:14 final size:15
Alignment explanation
Indices: 12233046--12233079 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12233036 CCAAATACAA
*
12233046 CCCAAAAC-CCGAAG
1 CCCAAAACACCCAAG
12233060 CCCAAAACACCCAAG
1 CCCAAAACACCCAAG
12233075 CCCAA
1 CCCAA
12233080 TTTCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.44, C:0.47, G:0.09, T:0.00
Consensus pattern (15 bp):
CCCAAAACACCCAAG
Found at i:12234198 original size:3 final size:3
Alignment explanation
Indices: 12234192--12234252 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
12234182 TTTTAGTGTC
* * * **
12234192 ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATC ATT ACT GCT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12234240 ATT AATT ATT ATT
1 ATT -ATT ATT ATT
12234253 GGCTTTATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:12247848 original size:394 final size:390
Alignment explanation
Indices: 12247054--12248330 Score: 1598
Period size: 394 Copynumber: 3.3 Consensus size: 390
12247044 GTAACCATAG
* * *
12247054 ATTGCAATTAAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGTATCGAAACAGA
1 ATTGCAATTAAAAAGATCGAAGCCACAACGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
*
12247119 TTGAAGCTACAACGGCGAGTCTCACTTCCC---CATTGCAATTTAAAAGATCGAAGCCACAACGG
66 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACATTGCAATTTAAAAGATCGAAGCCACAACGG
* *
12247181 CAAATCTTACTTTCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTT-CCC
131 CGAATCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * ** * *
12247245 -CATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGAAATGCAGCAGAACA
196 ACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAGTCTTAC-TTCAGGCGATGCAACGGAACA
12247309 GATTGAAGCTACAATGGC-GAGTCTCACTTCCC--CATTGCAATTTAAAAGATCGAAGCCACAAC
260 GATTGAAGCTACAATGGCGGA-TCTCACTTCCCTACATTGCAATTTAAAAGATCGAAGCCACAAC
* * * * *
12247371 GGTGAATCTTACTTCCAGGCGATGCAACGGAACAAATTGAAGCTACAACGACGAGTCTCACTTCC
324 GGCGAGTCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCC
12247436 CC
389 CC
* * *
12247438 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTAAAAAGATCGAAGCCACAACGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
* *
12247503 TTGAAGCTACAACGGCGAGTCTCACTTCCCTAACATTGCAATTTAAAAGATCGAAGCCACAACGG
66 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACATTGCAATTTAAAAGATCGAAGCCACAACGG
* * *
12247568 CGAATCTTACTTCCAGGCGATGCAACGGAACATATTGAAGCTACAACAGCGAGTCTCACTTCCCC
131 CGAATCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * ** * *
12247633 AACATTGC-AGTCAAATAGATTGAAGCTACAATAGCGAGTCTCACATCATTGGCGATGCAACGGA
196 -ACATTGCAATTTAAA-AGATTGAAGCCACAACGGCGAGTCTTACTTCA--GGCGATGCAACGGA
* * *
12247697 ACAGATTGAAGCTACAATAGCGGATCTTACTTCCCTAACATTGCAATTAAAAAGATCGAAGCCAC
257 ACAGATTGAAGCTACAATGGCGGATCTCACTTCCCT-ACATTGCAATTTAAAAGATCGAAGCCAC
* *
12247762 AATGGCGAGTCTTACTTTCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACT
321 AACGGCGAGTCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACT
12247827 TCCCC
386 TCCCC
* *
12247832 ATTACAATTAAAAAGATCGAAGCCACAATGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
1 ATTGCAATTAAAAAGATCGAAGCCACAACGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
* * * *
12247897 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATTGAGGCCACGACGG
66 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACATTGCAATTTAAAAGATCGAAGCCACAACGG
* * * * *
12247962 CGGATCTTACTTACTTA-GCAATGCAGCGAAACAGATTGAAGCTACAACGGCGAATCTCACTTCC
131 CGAATCTTACTT-C-CAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCC
* * *
12248026 CCGACATTGCAATTTAAAAGATTGAGGCCACGACGGCG-GATCTTACTTCCAAGCGAT-CTAGA-
194 CC-ACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAG-TCTTACTT-CAGGCGATGC-A-AC
* * *
12248088 GGAACAGATTGAAGCTACAATGGCGGATCTCAC-TCCCTCGACATTGTAATTTAAAAGATTGAGG
254 GGAACAGATTGAAGCTACAATGGCGGATCTCACTTCCCT--ACATTGCAATTTAAAAGATCGAAG
* * ** * *
12248152 CCACGACGGC-AGATCTTACTTCCAAGTAATGCAGCGGAACAGATTGAAGCTACAATGGCGAATC
317 CCACAACGGCGAG-TCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTC
*
12248216 TCACTCCCCTGAC
381 TCACTTCCC---C
* * * * * * *
12248229 ATTGCAATT-AAAAGATTGAGGCCACAACGGCAAATCTTA-TTTCTAAGCAGGTACAGTGGAACA
1 ATTGCAATTAAAAAGATCGAAGCCACAACGGCAAATCTTACTTTC-AGGC-GATGCAGCGAAACA
* * *
12248292 GATTGAAGCTACAATGACGAATCTCGCTTCCCTGACATT
64 GATTGAAGCTACAACGGCGAATCTCACTTCCCTGACATT
12248331 TTAAACAGAT
Statistics
Matches: 775, Mismatches: 91, Indels: 41
0.85 0.10 0.05
Matches are distributed among these distances:
384 91 0.12
387 88 0.11
388 3 0.00
389 8 0.01
390 28 0.04
391 40 0.05
392 2 0.00
393 8 0.01
394 338 0.44
395 77 0.10
396 38 0.05
397 54 0.07
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (390 bp):
ATTGCAATTAAAAAGATCGAAGCCACAACGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
TTGAAGCTACAACGGCGAATCTCACTTCCCTGACATTGCAATTTAAAAGATCGAAGCCACAACGG
CGAATCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCC
ACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCAGGCGATGCAACGGAACAG
ATTGAAGCTACAATGGCGGATCTCACTTCCCTACATTGCAATTTAAAAGATCGAAGCCACAACGG
CGAGTCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCC
Found at i:12248074 original size:50 final size:50
Alignment explanation
Indices: 12247116--12248259 Score: 313
Period size: 49 Copynumber: 23.4 Consensus size: 50
12247106 GTATCGAAAC
*
12247116 AGATTGAAGCTACAACGGC-GAGTCTCACTT-CCC--CATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGACATTGCAATTTAAA
* ** * * * * **** *
12247163 AGATCGAAGCCACAACGGCAAATCTTACTT-TCAGGCGA-TGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGAC-ATTGCAATTTAAA
*
12247212 AGATTGAAGCTACAACGGC-GAGTCTCACTT-CCC--CATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGACATTGCAATTTAAA
* * * * ** * **** *
12247259 AGATCGAAGCCACAACGGCGAATCTTACTTTCAGGA-AATGCAGCAGAAC
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGACATTGCAATTTAAA
* *
12247308 AGATTGAAGCTACAATGGC-GAGTCTCACTT-CCC--CATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGACATTGCAATTTAAA
* * * * * * ***
12247355 AGATCGAAGCCACAACGGTGAATCTTACTT-CCAGGCGA-TGCAACGGAACA
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGAC-ATTGCAATTTAA-A
* *
12247405 A-ATTGAAGCTACAACGAC-GAGTCTCACTT-CCC--CATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGACATTGCAATTTAAA
* * * * * * **** *
12247451 AGATCGAAGCCACAACGGCGAATCTTACTT-TCAGGCGA-TGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGAC-ATTGCAATTTAAA
* **
12247500 AGATTGAAGCTACAACGGC-GAGTCTCACTTCCCTAACATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGACATTGCAATTTAAA
* * * * * *** *
12247550 AGATCGAAGCCACAACGGCGAATCTTACTT-CCAGGCGA-TGCAACGGAAC
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGAC-ATTGCAATTTAAA
* * * * * *
12247599 ATATTGAAGCTACAACAGC-GAGTCTCACTTCCCCAACATTGC-AGTCAAA
1 AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGACATTGCAATTTAAA
* ** * *** * *** *
12247648 TAGATTGAAGCTACAATAGC-GAGTCTCACATCATTGGCGA-TGCAACGGAAC
1 -AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGAC-ATTGCAATTTAAA
* ** * ** *
12247699 AGATTGAAGCTACAATAGCGGATCTTACTTCCCTAACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGACATTGCAATTTAAA
* * * * * * **** *
12247749 AGATCGAAGCCACAATGGC-GAGTCTTACTT-TCAGGCGA-TGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGAC-ATTGCAATTTAAA
* * *
12247798 AGATTGAAGCTACAACGGC-GAGTCTCACTT-CCC--CATTACAATTAAAA
1 AGATTGAAGCCACAACGGCGGA-TCTCACTTCCCCGACATTGCAATTTAAA
* * ** * * * * ***
12247845 AGATCGAAGCCACAATGGCAAATCTTACTT-TCAGGCGA-TGC-AGCGAAA
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGAC-ATTGCAATTTAAA
* *
12247893 CAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAA
1 -AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGACATTGCAATTTAAA
* * * * ** * ***
12247944 AGATTGAGGCCACGACGGCGGATCTTACTT-ACTTAGCAATGC-AGCGAAA
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGA-CATTGCAATTTAAA
* *
12247993 CAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAA
1 -AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGACATTGCAATTTAAA
* * * ** ** *
12248044 AGATTGAGGCCACGACGGCGGATCTTACTTCCAAG-CGA-T-CTAGA-GGAAC
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGAC-ATTGC-A-ATTTAAA
* * *
12248093 AGATTGAAGCTACAATGGCGGATCTCAC-TCCCTCGACATTGTAATTTAAA
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCC-CGACATTGCAATTTAAA
* * * * ** **** *
12248143 AGATTGAGGCCACGACGGCAGATCTTACTTCCAAGTA-A-TGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCCG-ACATTGCAATTTAAA
* * *
12248192 AGATTGAAGCTACAATGGCGAATCTCAC-TCCCCTGACATTGCAA-TTAAA
1 AGATTGAAGCCACAACGGCGGATCTCACTTCCCC-GACATTGCAATTTAAA
*
12248241 AGATTGAGGCCACAACGGC
1 AGATTGAAGCCACAACGGC
12248260 AAATCTTATT
Statistics
Matches: 773, Mismatches: 259, Indels: 128
0.67 0.22 0.11
Matches are distributed among these distances:
46 5 0.01
47 147 0.19
48 24 0.03
49 310 0.40
50 266 0.34
51 21 0.03
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTCACTTCCCCGACATTGCAATTTAAA
Found at i:12248330 original size:99 final size:97
Alignment explanation
Indices: 12247054--12248323 Score: 1506
Period size: 96 Copynumber: 13.0 Consensus size: 97
12247044 GTAACCATAG
* * * *
12247054 ATTGCAATTAAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGTATCGAAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
12247119 TTGAAGCTACAACGGCGAGTCTCACTTCCC-C
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCAC
*
12247150 ATTGCAATTTAAAAGATCGAAGCCACAACGGCAAATCTTACTTTCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
12247215 TTGAAGCTACAACGGCGAGTCTCACTTCCC-C
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCAC
** *
12247246 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGAAATGCAGCAGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
12247311 TTGAAGCTACAATGGCGAGTCTCACTTCCC-C
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCAC
* * * *
12247342 ATTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCGATGCAACGGAACAAA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
12247407 TTGAAGCTACAACGACGAGTCTCACTTCCC-C
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCAC
12247438 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
12247503 TTGAAGCTACAACGGCGAGTCTCACTTCCCTAAC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCC--AC
* * *
12247537 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAACGGAACATA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
12247602 TTGAAGCTACAACAGCGAGTCTCACTTCCCCAAC
66 TTGAAGCTACAACGGCGAGTCTCACTT-CCC-AC
* * * * ** * * * *
12247636 ATTGC-AGTCAAATAGATTGAAGCTACAATAGCGAGTCTCAC-ATCATTGGCGATGCAACGGAAC
1 ATTGCAATTTAAA-AGATCGAAGCCACAACGGCGAATCTTACTTTCA--GGCGATGCAGCGGAAC
** *
12247699 AGATTGAAGCTACAATAGCG-GATCTTACTTCCCTAAC
63 AGATTGAAGCTACAACGGCGAG-TCTCACTTCCC--AC
* * *
12247736 ATTGCAATTAAAAAGATCGAAGCCACAATGGCGAGTCTTACTTTCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
12247801 TTGAAGCTACAACGGCGAGTCTCACTTCCC-C
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCAC
* * * * *
12247832 ATTACAATTAAAAAGATCGAAGCCACAATGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
12247897 TTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
66 TTGAAGCTACAACGGCGAGTCTCACTT-CCC-AC
* * * * * * *
12247931 ATTGCAATTTAAAAGATTGAGGCCACGACGGCGGATCTTACTTACTTA-GCAATGCAGCGAAACA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT--TCAGGCGATGCAGCGGAACA
*
12247995 GATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
64 GATTGAAGCTACAACGGCGAGTCTCACTT-CCC-AC
* * * * * * *
12248031 ATTGCAATTTAAAAGATTGAGGCCACGACGGCGGATCTTACTTCCAAGCGAT-CTAGAGGAACAG
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGC-AGCGGAACAG
* *
12248095 ATTGAAGCTACAATGGCG-GATCTCACTCCCTCGAC
65 ATTGAAGCTACAACGGCGAG-TCTCACTTCC-C-AC
* * * * * * **
12248130 ATTGTAATTTAAAAGATTGAGGCCACGACGGC-AGATCTTACTTCCAAGTAATGCAGCGGAACAG
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGA-ATCTTACTTTCAGGCGATGCAGCGGAACAG
* * *
12248194 ATTGAAGCTACAATGGCGAATCTCACTCCCCTGAC
65 ATTGAAGCTACAACGGCGAGTCTCACTTCCC--AC
* * * * * * *
12248229 ATTGCAA-TTAAAAGATTGAGGCCACAACGGCAAATCTTA-TTTCTAAGCAGGTACAGTGGAACA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTC-AGGC-GATGCAGCGGAACA
* * * *
12248292 GATTGAAGCTACAATGACGAATCTCGCTTCCC
64 GATTGAAGCTACAACGGCGAGTCTCACTTCCC
12248324 TGACATTTTA
Statistics
Matches: 1054, Mismatches: 92, Indels: 53
0.88 0.08 0.04
Matches are distributed among these distances:
96 447 0.42
97 6 0.01
98 44 0.04
99 375 0.36
100 172 0.16
101 10 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (97 bp):
ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
TTGAAGCTACAACGGCGAGTCTCACTTCCCAC
Found at i:12248744 original size:14 final size:15
Alignment explanation
Indices: 12248725--12248760 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
12248715 ACCCAAATAC
*
12248725 AGCCCAAAAC-CCGA
1 AGCCCAAAACACCCA
12248739 AGCCCAAAACACCCA
1 AGCCCAAAACACCCA
12248754 AGCCCAA
1 AGCCCAA
12248761 TTTCATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.44, C:0.44, G:0.11, T:0.00
Consensus pattern (15 bp):
AGCCCAAAACACCCA
Found at i:12249877 original size:3 final size:3
Alignment explanation
Indices: 12249871--12249928 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
12249861 TTTTAGTGTC
* * * **
12249871 ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATC ATT ACT GCT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12249919 AATT ATT ATT
1 -ATT ATT ATT
12249929 GGCTTTATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Done.