Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold3
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1336734
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 151046 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:865435 original size:25 final size:25
Alignment explanation
Indices: 865407--865493 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 25
865397 TACTGTCCTA
865407 GACAGTCATCAGTACTATTATACTT
1 GACAGTCATCAGTACTATTATACTT
*
865432 GACAGTCATCAGTAC--TTATCCTT
1 GACAGTCATCAGTACTATTATACTT
* *
865455 GCCTGGT-A-CA-T-CTTATTATACTT
1 GAC-AGTCATCAGTAC-TATTATACTT
865478 GACAGTCATCAGTACT
1 GACAGTCATCAGTACT
865494 TACCCTGGCC
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 4 0.08
23 20 0.42
24 4 0.08
25 17 0.35
26 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (25 bp):
GACAGTCATCAGTACTATTATACTT
Found at i:865482 original size:71 final size:71
Alignment explanation
Indices: 865362--865493 Score: 219
Period size: 71 Copynumber: 1.9 Consensus size: 71
865352 ATCATACTCA
* *
865362 ACAGTCATCAGTACTTACCCTTGCCTGGTACATCTTACTGTCCTAGACAGTCATCAGTACTATTA
1 ACAGTCATCAGTACTTACCCTTGCCTGGTACATCTTACTATACTAGACAGTCATCAGTACTATTA
865427 TACTTG
66 TACTTG
* * *
865433 ACAGTCATCAGTACTTATCCTTGCCTGGTACATCTTATTATACTTGACAGTCATCAGTACT
1 ACAGTCATCAGTACTTACCCTTGCCTGGTACATCTTACTATACTAGACAGTCATCAGTACT
865494 TACCCTGGCC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (71 bp):
ACAGTCATCAGTACTTACCCTTGCCTGGTACATCTTACTATACTAGACAGTCATCAGTACTATTA
TACTTG
Found at i:865489 original size:46 final size:46
Alignment explanation
Indices: 865422--865517 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
865412 TCATCAGTAC
* *
865422 TATTATACTTGACAGTCATCAGTACTTATCCTTGCCTGGTACATCT
1 TATTATACTTGACAGTCATCAGTACTTACCCTGGCCTGGTACATCT
*
865468 TATTATACTTGACAGTCATCAGTACTTACCCTGGCCTGGTACATTT
1 TATTATACTTGACAGTCATCAGTACTTACCCTGGCCTGGTACATCT
865514 TATT
1 TATT
865518 GCATGACTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
TATTATACTTGACAGTCATCAGTACTTACCCTGGCCTGGTACATCT
Found at i:866433 original size:161 final size:161
Alignment explanation
Indices: 866168--866894 Score: 1027
Period size: 161 Copynumber: 4.5 Consensus size: 161
866158 CTGGAATTTT
* * ***
866168 TCTGTCGAAAATTGCTTGATTGTACCCAAATTCAAACTTGACCTAGATATTATCATGATAATTTT
1 TCTGTCGAAAATTGCTTCAATGTACCCAAATTCAAACTTGACCTAGATATTATCATGATAAACCT
* * * *
866233 GTATACCACATTTCATTTCAATATGTTAATCCTCTGCGAAGAAAATGAGGGGAAACAGCAAATAA
66 GTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAAGAAAATGAGCGGAAACTGCAAATAA
* *
866298 CTGGAATTTTTCTATGTCAAAGGGCCATAAC
131 CTGGAATTTTTCTAAGTCCAAGGGCCATAAC
*
866329 TCTGTCGAAAATTGCTTGAATGTACCCAAATTCAAACTTGACCTAGATATTATCATGATAAACCT
1 TCTGTCGAAAATTGCTTCAATGTACCCAAATTCAAACTTGACCTAGATATTATCATGATAAACCT
* * *
866394 GTATACCACATTTCATTTCAATACGTTCATCCTCTGCGAAGAAAATGAGGGGAAACTGCAAATAA
66 GTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAAGAAAATGAGCGGAAACTGCAAATAA
* *
866459 ATGGAATTTTTCTAAGTCCAAGGGCTATAAC
131 CTGGAATTTTTCTAAGTCCAAGGGCCATAAC
* * *
866490 TCTATCGAAAATTG-TTCAATTGTACCC-AATATCGAACTTGATCTAGATATTATCATGATAAAC
1 TCTGTCGAAAATTGCTTCAA-TGTACCCAAAT-TCAAACTTGACCTAGATATTATCATGATAAAC
** * * *
866553 CTGTATATTAAAGTTCATTCCAATATGTTTATCCTCTGCGAAGAAAATGAGCGGAAACTGCAAAT
64 CTGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAAGAAAATGAGCGGAAACTGCAAAT
* *
866618 AACTGAAATTTTT-TAAAGCCCAAGGGCCATAAC
129 AACTGGAATTTTTCT-AAGTCCAAGGGCCATAAC
* * * * **
866651 TCTGTCGAAAACTGC-TCAATCATACCCAAAATCAAACTTGACCTAGATATTAACATGATAAATA
1 TCTGTCGAAAATTGCTTCAAT-GTACCCAAATTCAAACTTGACCTAGATATTATCATGATAAACC
*
866715 TGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAAGAAAATGAGCAGAAACTGCAAATA
65 TGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAAGAAAATGAGCGGAAACTGCAAATA
*
866780 ACTGGAATTTTTCTACGTCCAAGGGCCATAAC
130 ACTGGAATTTTTCTAAGTCCAAGGGCCATAAC
*
866812 TCTGTCGAAAATTGC-TCAATTGTACCC-AATATCGAACTTGACCTAGATATTATCATGATAAAC
1 TCTGTCGAAAATTGCTTCAA-TGTACCCAAAT-TCAAACTTGACCTAGATATTATCATGATAAAC
866875 CTGTATACCAAATTTC-TTTC
64 CTGTATACCAAATTTCATTTC
866895 CTCTGCGAAG
Statistics
Matches: 505, Mismatches: 52, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
160 15 0.03
161 486 0.96
162 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (161 bp):
TCTGTCGAAAATTGCTTCAATGTACCCAAATTCAAACTTGACCTAGATATTATCATGATAAACCT
GTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAAGAAAATGAGCGGAAACTGCAAATAA
CTGGAATTTTTCTAAGTCCAAGGGCCATAAC
Found at i:875928 original size:17 final size:17
Alignment explanation
Indices: 875889--875937 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
875879 GCAAATTTAC
*
875889 TCTTGATCTCTCGAA-C
1 TCTTGATCTCTCGAAGT
*
875905 TC-CGATCTCTCGAAGT
1 TCTTGATCTCTCGAAGT
875921 TCTTGATCTCTCGAAGT
1 TCTTGATCTCTCGAAGT
875938 AAAACCTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 13 0.46
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (17 bp):
TCTTGATCTCTCGAAGT
Found at i:878902 original size:17 final size:17
Alignment explanation
Indices: 878880--878916 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
878870 ACATAACGTG
878880 CGAGTACCCATTATTGC
1 CGAGTACCCATTATTGC
878897 CGAGTACCCATTATTGC
1 CGAGTACCCATTATTGC
878914 CGA
1 CGA
878917 TTGCTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (17 bp):
CGAGTACCCATTATTGC
Found at i:881573 original size:19 final size:19
Alignment explanation
Indices: 881528--881576 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
881518 GTCTTTTGAA
881528 GAAGAAAAAATCATAAAAT
1 GAAGAAAAAATCATAAAAT
* *
881547 GAATGAAAAATTGATAAAA-
1 GAA-GAAAAAATCATAAAAT
881566 GTAAGAAAAAA
1 G-AAGAAAAAA
881577 ATAATCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.16
Consensus pattern (19 bp):
GAAGAAAAAATCATAAAAT
Found at i:881683 original size:16 final size:16
Alignment explanation
Indices: 881664--881699 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
881654 CGAACAAGGT
*
881664 TTAGGGCGAACGATAA
1 TTAGGGCGAACGACAA
*
881680 TTAGGGCGAATGACAA
1 TTAGGGCGAACGACAA
881696 TTAG
1 TTAG
881700 AGTGAGCGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.22
Consensus pattern (16 bp):
TTAGGGCGAACGACAA
Found at i:889399 original size:18 final size:18
Alignment explanation
Indices: 889376--889410 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
889366 ATAACTGCTC
889376 AAATATGCACAAAATCTA
1 AAATATGCACAAAATCTA
889394 AAATATGCACAAAATCT
1 AAATATGCACAAAATCT
889411 TTATGTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATATGCACAAAATCTA
Found at i:890264 original size:30 final size:30
Alignment explanation
Indices: 890228--890290 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
890218 TGTCAACTTG
*
890228 AATGACTGTCAAAATCTACATACAAACTCA
1 AATGACTGTCAAAAACTACATACAAACTCA
* *
890258 AATGACTGTCAAAAACTACGTACAAACTTA
1 AATGACTGTCAAAAACTACATACAAACTCA
890288 AAT
1 AAT
890291 TATTGTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.24
Consensus pattern (30 bp):
AATGACTGTCAAAAACTACATACAAACTCA
Found at i:890578 original size:31 final size:31
Alignment explanation
Indices: 890543--890606 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
890533 ACGTACAATG
* *
890543 TCTACA-TACAAGTGTATAATAACTGTCGAAC
1 TCTACATTA-AAGTGTACAATAACTGTCAAAC
*
890574 TCTACATTTAAAGTGTACAATTACTGTCAAAC
1 TCTACA-TTAAAGTGTACAATAACTGTCAAAC
890606 T
1 T
890607 AAACGTACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 6 0.21
32 20 0.71
33 2 0.07
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (31 bp):
TCTACATTAAAGTGTACAATAACTGTCAAAC
Found at i:890683 original size:77 final size:77
Alignment explanation
Indices: 890432--891033 Score: 870
Period size: 77 Copynumber: 7.8 Consensus size: 77
890422 CTATACTAGT
* *
890432 AATTACTGTCAAACTATACGTACAATGTCCACATACAACAAGTATAATACAATGTAACTGTCGAA
1 AATTACTGTCAAACTATACGTACAATGTCTACATAC-A-AAGTGT-AT--AA--TAACTGTCGAA
*
890497 CTCTACATTCAAAGTGTAC
59 CTCTACATTTAAAGTGTAC
890516 AATTACTGTCAAACTATACGTACAATGTCTACATAC-AAGTGTATAATAACTGTCGAACTCTACA
1 AATTACTGTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACTCTACA
890580 TTTAAAGTGTAC
66 TTTAAAGTGTAC
* * * * *
890592 AATTACTGTCAAACTAAACGTACAGTGTCTACATACAGAGTGAATACTAACTGTCGAACTCTACA
1 AATTACTGTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACTCTACA
890657 TTTAAAGTGTAC
66 TTTAAAGTGTAC
*
890669 AATTACTCTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACTCTACA
1 AATTACTGTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACTCTACA
*
890734 TTTATAGTGTAC
66 TTTAAAGTGTAC
* *
890746 AATTACTGTCAAACTATAAGTACAATGTCTACATACAAAGTTTATAATAACTGTCGAACTCTACA
1 AATTACTGTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACTCTACA
*
890811 TTTAAATTGTAC
66 TTTAAAGTGTAC
* * * *
890823 AATTATTGTCCAACTATACGAACAGTGTCTACATACAAAGTG--T-ATAACTGTCGAACTCTACA
1 AATTACTGTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACTCTACA
890885 TTTAAAGTGTAC
66 TTTAAAGTGTAC
* * *
890897 AATTATTGTCAAACTATACTTACAATGTCTACATACAAAGTGTATAATAACTGTCTAACTCTACA
1 AATTACTGTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACTCTACA
*
890962 TTTAAAGTGTAT
66 TTTAAAGTGTAC
* * * * * *
890974 AATTACTGTCAAACTATACGTACAGTATCTACATATAGAGTGGAAAATAACTGTCGAACT
1 AATTACTGTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACT
891034 GGTACAATTA
Statistics
Matches: 472, Mismatches: 42, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
74 68 0.14
75 1 0.00
76 64 0.14
77 295 0.62
78 2 0.00
80 2 0.00
81 5 0.01
84 35 0.07
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (77 bp):
AATTACTGTCAAACTATACGTACAATGTCTACATACAAAGTGTATAATAACTGTCGAACTCTACA
TTTAAAGTGTAC
Found at i:890960 original size:32 final size:32
Alignment explanation
Indices: 890924--890997 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
890914 ACTTACAATG
*
890924 TCTACATACAAAGTGTATAATAACTGTCTAAC
1 TCTACATACAAAGTGTATAATAACTGTCAAAC
** *
890956 TCTACATTTAAAGTGTATAATTACTGTCAAAC
1 TCTACATACAAAGTGTATAATAACTGTCAAAC
* *
890988 TATACGTACA
1 TCTACATACA
890998 GTATCTACAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (32 bp):
TCTACATACAAAGTGTATAATAACTGTCAAAC
Found at i:891146 original size:139 final size:139
Alignment explanation
Indices: 890893--891267 Score: 633
Period size: 139 Copynumber: 2.7 Consensus size: 139
890883 CATTTAAAGT
* *
890893 GTACAATTATTGTCAAACTATACTTACAATGTCTACATACAAAGTGTATAATAACTGTCTAACTC
1 GTACAATTACTGTCAAACTATACTTACAATGTCTACATACAAAGTG--T-ATAACTGTCGAACTC
* *
890958 TACATTTAAAGTGTATAATTACTGTCAAACTATACGTACAGTATCTACATATAGAGTGGAAAATA
63 TACATTTAAAGTGTACAATTACTGTCAAACTATACGTACAGTATCTACATACAGAGTGGAAAATA
891023 ACTGTCGAACTG
128 ACTGTCGAACTG
* *
891035 GTACAATTACTGTCAAACTATACGTACAGTGTCTACATACAAAGTGTATAACTGTCGAACTCTAC
1 GTACAATTACTGTCAAACTATACTTACAATGTCTACATACAAAGTGTATAACTGTCGAACTCTAC
* *
891100 ATTTAAAGTGTACAATTGCTGTCAAACTATACGTACAGTGTCTACATACAGAGTGGAAAATAACT
66 ATTTAAAGTGTACAATTACTGTCAAACTATACGTACAGTATCTACATACAGAGTGGAAAATAACT
891165 GTCGAACTG
131 GTCGAACTG
*
891174 GTACAATTACTGTCAAACTATACTTACAATGTCTACATACTAAGTGTATAACTGTCGAACTCTAC
1 GTACAATTACTGTCAAACTATACTTACAATGTCTACATACAAAGTGTATAACTGTCGAACTCTAC
*
891239 ATTCAAAGTGTACAATTACTGTCAAACTA
66 ATTTAAAGTGTACAATTACTGTCAAACTA
891268 AGTACAAGCT
Statistics
Matches: 220, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
139 176 0.80
140 1 0.00
142 43 0.20
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (139 bp):
GTACAATTACTGTCAAACTATACTTACAATGTCTACATACAAAGTGTATAACTGTCGAACTCTAC
ATTTAAAGTGTACAATTACTGTCAAACTATACGTACAGTATCTACATACAGAGTGGAAAATAACT
GTCGAACTG
Found at i:891363 original size:32 final size:32
Alignment explanation
Indices: 891313--891391 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
891303 CTTAGTCCTA
* * *
891313 CAAACTATACATTA-AAAGTGTATAATTACTGT
1 CAAACTCTACA-TACAAAGTGTACAACTACTGT
891345 CGAAA-TCTACATACAAAGTGTACAACTACTGT
1 C-AAACTCTACATACAAAGTGTACAACTACTGT
*
891377 CAAACTCTACGTACA
1 CAAACTCTACATACA
891392 GGCTGTGATG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 5 0.12
32 32 0.80
33 3 0.08
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (32 bp):
CAAACTCTACATACAAAGTGTACAACTACTGT
Found at i:895268 original size:8 final size:7
Alignment explanation
Indices: 895253--895333 Score: 51
Period size: 8 Copynumber: 11.1 Consensus size: 7
895243 GTCGAGTGAG
895253 AGTGCGA
1 AGTGCGA
895260 AGTTGCGA
1 AG-TGCGA
895268 AG-GCGAA
1 AGTGCG-A
895275 AGTGCGA
1 AGTGCGA
895282 AGGTGCGA
1 A-GTGCGA
*
895290 CG-GCGA
1 AGTGCGA
*
895296 AGGAGCGA
1 A-GTGCGA
895304 AGATGCGA
1 AG-TGCGA
*
895312 CG-GCGA
1 AGTGCGA
*
895318 AGCGCGA
1 AGTGCGA
895325 AGATGCGA
1 AG-TGCGA
895333 A
1 A
895334 NNNNNNNNNN
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
6 12 0.20
7 16 0.27
8 31 0.53
ACGTcount: A:0.31, C:0.17, G:0.43, T:0.09
Consensus pattern (7 bp):
AGTGCGA
Found at i:895281 original size:22 final size:22
Alignment explanation
Indices: 895253--895333 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
895243 GTCGAGTGAG
*
895253 AGTGCGAAGTTGCGAAGGCGAA
1 AGTGCGAAGATGCGAAGGCGAA
* *
895275 AGTGCGAAGGTGCGACGGCGAA
1 AGTGCGAAGATGCGAAGGCGAA
* * *
895297 GGAGCGAAGATGCGACGGCG-A
1 AGTGCGAAGATGCGAAGGCGAA
*
895318 AGCGCGAAGATGCGAA
1 AGTGCGAAGATGCGAA
895334 NNNNNNNNNN
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 14 0.27
22 37 0.73
ACGTcount: A:0.31, C:0.17, G:0.43, T:0.09
Consensus pattern (22 bp):
AGTGCGAAGATGCGAAGGCGAA
Found at i:896364 original size:22 final size:22
Alignment explanation
Indices: 896336--896390 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
896326 TCAAAAAAAG
896336 GCGAAGGCGAAAGTGCGAAGTT
1 GCGAAGGCGAAAGTGCGAAGTT
*
896358 GCGAAGGCGAGAGTGCGAAGTT
1 GCGAAGGCGAAAGTGCGAAGTT
*
896380 GCGATGGCGAA
1 GCGAAGGCGAA
896391 GGAGCGATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.44, T:0.13
Consensus pattern (22 bp):
GCGAAGGCGAAAGTGCGAAGTT
Found at i:896397 original size:22 final size:22
Alignment explanation
Indices: 896336--896397 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
896326 TCAAAAAAAG
*
896336 GCGAAGGCGAAAGTGCGAAGTT
1 GCGAAGGCGAAGGTGCGAAGTT
896358 GCGAAGGCG-AGAGTGCGAAGTT
1 GCGAAGGCGAAG-GTGCGAAGTT
* *
896380 GCGATGGCGAAGGAGCGA
1 GCGAAGGCGAAGGTGCGA
896398 TAGTAGTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.29, C:0.15, G:0.45, T:0.11
Consensus pattern (22 bp):
GCGAAGGCGAAGGTGCGAAGTT
Found at i:896428 original size:8 final size:8
Alignment explanation
Indices: 896417--896538 Score: 50
Period size: 8 Copynumber: 16.4 Consensus size: 8
896407 CGCTCCTTCG
896417 CCTTCGCA
1 CCTTCGCA
896425 CCTTCGCA
1 CCTTCGCA
*
896433 CTTTCG--
1 CCTTCGCA
*
896439 CCATCGCA
1 CCTTCGCA
*
896447 TCTTCG--
1 CCTTCGCA
*
896453 CCGTCGCA
1 CCTTCGCA
*
896461 TCTTCGCA
1 CCTTCGCA
* *
896469 CTTTCGCT
1 CCTTCGCA
896477 CCTTCG--
1 CCTTCGCA
*
896483 CCGTCGCA
1 CCTTCGCA
896491 -CTCTCGCA
1 CCT-TCGCA
*
896499 CTTTCG--
1 CCTTCGCA
896505 CCTTCGCA
1 CCTTCGCA
*
896513 ACTTCGCA
1 CCTTCGCA
896521 -CTCTCGCA
1 CCT-TCGCA
*
896529 TCTTCG-A
1 CCTTCGCA
896536 CCT
1 CCT
896539 AAAGGCGAAT
Statistics
Matches: 83, Mismatches: 19, Indels: 25
0.65 0.15 0.20
Matches are distributed among these distances:
6 18 0.22
7 6 0.07
8 56 0.67
9 3 0.04
ACGTcount: A:0.11, C:0.44, G:0.15, T:0.30
Consensus pattern (8 bp):
CCTTCGCA
Found at i:896438 original size:22 final size:22
Alignment explanation
Indices: 896413--896527 Score: 101
Period size: 22 Copynumber: 5.2 Consensus size: 22
896403 GTATCGCTCC
896413 TTCGCCTTCGCACCTTCGCACT
1 TTCGCCTTCGCACCTTCGCACT
* *
896435 TTCGCCATCGCATCTTCGC-C-
1 TTCGCCTTCGCACCTTCGCACT
* * * *
896455 GTCGCATCTTCGCACTTTCGCTCC
1 TTCGC--CTTCGCACCTTCGCACT
*
896479 TTCGCCGTCGCA-CTCTCGCACT
1 TTCGCCTTCGCACCT-TCGCACT
*
896501 TTCGCCTTCGCAACTTCGCACT
1 TTCGCCTTCGCACCTTCGCACT
*
896523 CTCGC
1 TTCGC
896528 ATCTTCGACC
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
20 4 0.05
21 2 0.03
22 61 0.82
23 3 0.04
24 4 0.05
ACGTcount: A:0.10, C:0.44, G:0.16, T:0.30
Consensus pattern (22 bp):
TTCGCCTTCGCACCTTCGCACT
Found at i:896482 original size:30 final size:30
Alignment explanation
Indices: 896448--896528 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
896438 GCCATCGCAT
896448 CTTCGCCGTCGCA-TCTTCGCACTTTCGCTC
1 CTTCGCCGTCGCACTC-TCGCACTTTCGCTC
896478 CTTCGCCGTCGCACTCTCGCACTTTCG--C
1 CTTCGCCGTCGCACTCTCGCACTTTCGCTC
*
896506 CTTCGCAACTTCGCACTCTCGCA
1 CTTCGC--CGTCGCACTCTCGCA
896529 TCTTCGACCT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
28 7 0.15
30 38 0.81
31 2 0.04
ACGTcount: A:0.10, C:0.44, G:0.16, T:0.30
Consensus pattern (30 bp):
CTTCGCCGTCGCACTCTCGCACTTTCGCTC
Found at i:896497 original size:14 final size:15
Alignment explanation
Indices: 896428--896494 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 15
896418 CTTCGCACCT
*
896428 TCGCACT-TTCGCCA
1 TCGCACTCTTCGCCG
896442 TCGCA-TCTTCGCCG
1 TCGCACTCTTCGCCG
*
896456 TCGCA-TCTTCGCACTT
1 TCGCACTCTTCGC-C-G
*
896472 TCGCTC-CTTCGCCG
1 TCGCACTCTTCGCCG
896486 TCGCACTCT
1 TCGCACTCT
896495 CGCACTTTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 1 0.02
14 28 0.65
15 4 0.09
16 10 0.23
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.31
Consensus pattern (15 bp):
TCGCACTCTTCGCCG
Found at i:896518 original size:14 final size:16
Alignment explanation
Indices: 896486--896534 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
896476 TCCTTCGCCG
896486 TCGCACTCTCGC-ACTT
1 TCGCACTCTCGCAAC-T
896502 TCGC-CT-TCGCAACT
1 TCGCACTCTCGCAACT
*
896516 TCGCACTCTCGCATCT
1 TCGCACTCTCGCAACT
896532 TCG
1 TCG
896535 ACCTAAAGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 14 0.48
ACGTcount: A:0.12, C:0.43, G:0.14, T:0.31
Consensus pattern (16 bp):
TCGCACTCTCGCAACT
Found at i:910260 original size:21 final size:21
Alignment explanation
Indices: 910234--910276 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
910224 GTATACATTG
910234 AAGAATTTTAGGCAATTTCCA
1 AAGAATTTTAGGCAATTTCCA
*
910255 AAGAATTTTTGGCAATTTCCA
1 AAGAATTTTAGGCAATTTCCA
910276 A
1 A
910277 TTTTCACTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (21 bp):
AAGAATTTTAGGCAATTTCCA
Found at i:911698 original size:26 final size:26
Alignment explanation
Indices: 911669--911721 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
911659 ACAAGCACCT
911669 AGTGTGGAGTATGAACTACAAAGGGC
1 AGTGTGGAGTATGAACTACAAAGGGC
* *
911695 AGTGTGGGGTATGAACTATAAAGGGC
1 AGTGTGGAGTATGAACTACAAAGGGC
911721 A
1 A
911722 AACAGGAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.09, G:0.36, T:0.21
Consensus pattern (26 bp):
AGTGTGGAGTATGAACTACAAAGGGC
Found at i:912841 original size:27 final size:27
Alignment explanation
Indices: 912796--912847 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
912786 TGATCACATA
*
912796 ATACAATATCATAATATATAATATATG
1 ATACAATATCATAAAATATAATATATG
** *
912823 ATACAATATGGTAAAATATTATATA
1 ATACAATATCATAAAATATAATATA
912848 ATACTAAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (27 bp):
ATACAATATCATAAAATATAATATATG
Found at i:916815 original size:19 final size:18
Alignment explanation
Indices: 916779--916815 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
916769 ACGCCTGCCG
*
916779 ACGCCTGCCGGGGAAAAC
1 ACGCCTGCCGGAGAAAAC
916797 ACGCCTGCCGAGAGAAAAC
1 ACGCCTGCCG-GAGAAAAC
916816 CACACGCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.32, G:0.30, T:0.05
Consensus pattern (18 bp):
ACGCCTGCCGGAGAAAAC
Found at i:917307 original size:184 final size:183
Alignment explanation
Indices: 916966--917373 Score: 525
Period size: 184 Copynumber: 2.2 Consensus size: 183
916956 GTTGGAAAAG
* * *
916966 ATAGATAACTCTTACGTAGAATTCATACGCCTGCCGAGGAAATCTAGACGCCTGCCGTTTATTTG
1 ATAGATAACTCTTACGAAGAAATCATACGCCTGCCGAGAAAATCTAGACGCCTGCCGTTTATTTG
* * * *
917031 ATGGATTATTTTACTTTTTTCTTTGATATTTTATTTCTTTTAACTAAATAGATGATAATAGAAAT
66 ATGGATTATTTTAATTATTTCTTTGATATTTTATTTC-TTTAACTAAATAAACGATAATAGAAAT
* * * * *
917096 CAAAAGTTAATTTTATATTAATTAATTAACACAAAATAAGTAAAAATCGGGTAAG
130 AAAAACTTAACTTTAAATTAATTAATTAACACAAAATAAGTAAAAATC-GGTAAA
* * * * *
917151 CT-GATAGCTCTTACGAAGAAATCATACGCCTGCCAAGAAAATGTATACGCCTGCCGTTTATTTG
1 ATAGATAACTCTTACGAAGAAATCATACGCCTGCCGAGAAAATCTAGACGCCTGCCGTTTATTTG
* *
917215 ATGGATTATTTTAATTATTTCTTTGATATTTTAGTTTAC-TTAGCTTAATAAACGATAATAGAAA
66 ATGGATTATTTTAATTATTTCTTTGATATTTTA-TTT-CTTTAACTAAATAAACGATAATAGAAA
* ** *
917279 TAAAAACTTGACTTTAAATTCGTTAATTAACACAAAATTAGTAAAAATCGGTAAA
129 TAAAAACTTAACTTTAAATTAATTAATTAACACAAAATAAGTAAAAATCGGTAAA
* *
917334 ATAGATAACTCTTACGCAG-AATGCATACGCCCGCCGAGAA
1 ATAGATAACTCTTACGAAGAAAT-CATACGCCTGCCGAGAA
917374 GAGAACGGTA
Statistics
Matches: 191, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
183 9 0.05
184 177 0.93
185 4 0.02
186 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (183 bp):
ATAGATAACTCTTACGAAGAAATCATACGCCTGCCGAGAAAATCTAGACGCCTGCCGTTTATTTG
ATGGATTATTTTAATTATTTCTTTGATATTTTATTTCTTTAACTAAATAAACGATAATAGAAATA
AAAACTTAACTTTAAATTAATTAATTAACACAAAATAAGTAAAAATCGGTAAA
Found at i:919799 original size:2 final size:2
Alignment explanation
Indices: 919792--919816 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
919782 CACAAGCCAC
919792 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
919817 GTGAGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:922236 original size:185 final size:183
Alignment explanation
Indices: 921842--922285 Score: 500
Period size: 185 Copynumber: 2.4 Consensus size: 183
921832 CCAAGAAAAA
* * * * * * *
921842 AAAATTATCTATCAGATAACCGGCAGGCGTGTAC-TCTTCTCGGCAGGCGTATGCATTCTGCGTA
1 AAAATAATCCATCAAATAAACGGCAGGCGTATACATTTTCTCGGCAGGCGTATG-ATTCTACGTA
** * * * *
921906 AGAGTTATCTATTTTACCGATTTTTACTAATTTTGTGTTAATTAACGAATTTAAAGTCAAGTTTT
65 AGAGTTATCTAGCTTACCGATTTTTACTAATTTTATGTTAATTAACGAATTAAAAATCAACTTTT
* * *** * * * *
921971 TATTTCTGTTATCAATTATTAAGCTAGGTAAACTGAAATATCAAAGAAATAATT
130 GATTTCTATTATCAATTATTAAGCTAAAAAAAATAAAATATCAAAGAAAAAAGT
* *
922025 AAAATAATCCATCAAATAAACGGCAGGCGTATACATTTTCTTGGCAGGCGTATGATTTCTTCGTA
1 AAAATAATCCATCAAATAAACGGCAGGCGTATACATTTTCTCGGCAGGCGTATGA-TTCTACGTA
* * **
922090 AGAGCTATC-AGCTTACCCGATTTTTACTTATTTTATGTTAATTAATTAATATAAAAATCAACTT
65 AGAGTTATCTAGCTTA-CCGATTTTTACTAATTTTATGTTAATTAACGAAT-TAAAAATCAACTT
* *
922154 TTGATTTCTATTTTC-ATCTATTTAG-TAAAAAGAAATAAAATATCAAAGAAAAAAGT
128 TTGATTTCTATTATCAAT-TATTAAGCTAAAAA-AAATAAAATATCAAAGAAAAAAGT
* * *
922210 AAAATAATCCATCAAATAAACGGCAGGCGTCTAGATTTCCTCGGCAGGCGTATGAATTCTACGTA
1 AAAATAATCCATCAAATAAACGGCAGGCGTATACATTTTCTCGGCAGGCGTATG-ATTCTACGTA
922275 AGAGTTATCTA
65 AGAGTTATCTA
922286 TCTTTACCAA
Statistics
Matches: 218, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
183 34 0.16
184 68 0.31
185 114 0.52
186 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (183 bp):
AAAATAATCCATCAAATAAACGGCAGGCGTATACATTTTCTCGGCAGGCGTATGATTCTACGTAA
GAGTTATCTAGCTTACCGATTTTTACTAATTTTATGTTAATTAACGAATTAAAAATCAACTTTTG
ATTTCTATTATCAATTATTAAGCTAAAAAAAATAAAATATCAAAGAAAAAAGT
Found at i:924743 original size:11 final size:11
Alignment explanation
Indices: 924727--924756 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
924717 TGTATAAAAA
924727 TTGCATGATAT
1 TTGCATGATAT
924738 TTGCATGATAT
1 TTGCATGATAT
*
924749 TCGCATGA
1 TTGCATGA
924757 AACAACAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (11 bp):
TTGCATGATAT
Found at i:927211 original size:21 final size:21
Alignment explanation
Indices: 927185--927281 Score: 185
Period size: 21 Copynumber: 4.6 Consensus size: 21
927175 TGCGTCTTTT
927185 TACCCCAATGAACCCCAATGA
1 TACCCCAATGAACCCCAATGA
927206 TACCCCAATGAACCCCAATGA
1 TACCCCAATGAACCCCAATGA
927227 TACCCCAATGAACCCCAATGA
1 TACCCCAATGAACCCCAATGA
*
927248 TACCCCAATGAACCTCAATGA
1 TACCCCAATGAACCCCAATGA
927269 TACCCCAATGAAC
1 TACCCCAATGAAC
927282 TTTGAAATAC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.38, C:0.37, G:0.09, T:0.15
Consensus pattern (21 bp):
TACCCCAATGAACCCCAATGA
Found at i:927212 original size:11 final size:11
Alignment explanation
Indices: 927185--927279 Score: 153
Period size: 10 Copynumber: 9.0 Consensus size: 11
927175 TGCGTCTTTT
927185 TACCCCAATGA
1 TACCCCAATGA
927196 -ACCCCAATGA
1 TACCCCAATGA
927206 TACCCCAATGA
1 TACCCCAATGA
927217 -ACCCCAATGA
1 TACCCCAATGA
927227 TACCCCAATGA
1 TACCCCAATGA
927238 -ACCCCAATGA
1 TACCCCAATGA
927248 TACCCCAATGA
1 TACCCCAATGA
*
927259 -ACCTCAATGA
1 TACCCCAATGA
927269 TACCCCAATGA
1 TACCCCAATGA
927280 ACTTTGAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
10 39 0.50
11 39 0.50
ACGTcount: A:0.38, C:0.37, G:0.09, T:0.16
Consensus pattern (11 bp):
TACCCCAATGA
Found at i:929910 original size:11 final size:11
Alignment explanation
Indices: 929891--930063 Score: 211
Period size: 11 Copynumber: 16.5 Consensus size: 11
929881 AAGTTGATTA
929891 GGGTATCATTG
1 GGGTATCATTG
*
929902 GGATATCATT-
1 GGGTATCATTG
* *
929912 TGGTATCATAG
1 GGGTATCATTG
929923 GGGTATCATTAG
1 GGGTATCATT-G
*
929935 GTGTAT--TT-
1 GGGTATCATTG
929943 GGGTATCATTG
1 GGGTATCATTG
*
929954 GGGTAACATTG
1 GGGTATCATTG
*
929965 GGGTAACATTG
1 GGGTATCATTG
929976 GGGT-TCATTG
1 GGGTATCATTG
929986 GGGTATCATTG
1 GGGTATCATTG
929997 GGGT-TCATTG
1 GGGTATCATTG
930007 GGGTATCATTG
1 GGGTATCATTG
930018 GGGT-TCATTG
1 GGGTATCATTG
930028 GGGTATCATTG
1 GGGTATCATTG
*
930039 TGGT-TCATTG
1 GGGTATCATTG
930049 GGGT-TCATTG
1 GGGTATCATTG
930059 GGGTA
1 GGGTA
930064 AAAAGACGCA
Statistics
Matches: 141, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
8 5 0.04
10 59 0.42
11 71 0.50
12 6 0.04
ACGTcount: A:0.18, C:0.09, G:0.35, T:0.38
Consensus pattern (11 bp):
GGGTATCATTG
Found at i:929918 original size:21 final size:21
Alignment explanation
Indices: 929891--930062 Score: 208
Period size: 21 Copynumber: 8.2 Consensus size: 21
929881 AAGTTGATTA
*
929891 GGGTATCATTGGGATATCATT-
1 GGGT-TCATTGGGGTATCATTG
* *
929912 TGGTATCATAGGGGTATCATT-
1 GGGT-TCATTGGGGTATCATTG
* *
929933 AGGTGT-ATTTGGGTATCATTG
1 GGGT-TCATTGGGGTATCATTG
* *
929954 GGGTAACATTGGGGTAACATTG
1 GGGT-TCATTGGGGTATCATTG
929976 GGGTTCATTGGGGTATCATTG
1 GGGTTCATTGGGGTATCATTG
929997 GGGTTCATTGGGGTATCATTG
1 GGGTTCATTGGGGTATCATTG
930018 GGGTTCATTGGGGTATCATTG
1 GGGTTCATTGGGGTATCATTG
*
930039 TGGTTCATTGGGGT-TCATTG
1 GGGTTCATTGGGGTATCATTG
930059 GGGT
1 GGGT
930063 AAAAAGACGC
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
20 21 0.16
21 95 0.71
22 17 0.13
ACGTcount: A:0.18, C:0.09, G:0.35, T:0.38
Consensus pattern (21 bp):
GGGTTCATTGGGGTATCATTG
Found at i:933704 original size:20 final size:21
Alignment explanation
Indices: 933666--933704 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
933656 AAGATTACGT
*
933666 GAAAAACATATATCTTAAACC
1 GAAAAACATATATCATAAACC
*
933687 GAAAAACAT-TATGATAAA
1 GAAAAACATATATCATAAA
933705 TAAGAGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (21 bp):
GAAAAACATATATCATAAACC
Found at i:937592 original size:4 final size:4
Alignment explanation
Indices: 937583--937666 Score: 168
Period size: 4 Copynumber: 21.0 Consensus size: 4
937573 ATATGATGAG
937583 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
937631 TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC
937667 ACTGTCTCTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 80 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:937936 original size:14 final size:15
Alignment explanation
Indices: 937907--937936 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
937897 CCCCTTTGCT
937907 TTTATTCTATAAAAA
1 TTTATTCTATAAAAA
937922 TTTATTCTA-AAAAA
1 TTTATTCTATAAAAA
937936 T
1 T
937937 CTACACGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTATTCTATAAAAA
Found at i:951957 original size:4 final size:4
Alignment explanation
Indices: 951950--951975 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
951940 CCGTCCGTCC
951950 GTCT GTCT GTCT GTCT GTCT GTCT GT
1 GTCT GTCT GTCT GTCT GTCT GTCT GT
951976 GTCTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.27, T:0.50
Consensus pattern (4 bp):
GTCT
Found at i:963354 original size:17 final size:17
Alignment explanation
Indices: 963332--963364 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
963322 AACTAGTTGC
963332 AGTGAA-ATATTTACAAA
1 AGTGAACAT-TTTACAAA
963349 AGTGAACATTTTACAA
1 AGTGAACATTTTACAA
963365 TGACTCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (17 bp):
AGTGAACATTTTACAAA
Found at i:974356 original size:43 final size:43
Alignment explanation
Indices: 974295--974382 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
974285 ACATGTAGTA
* * * *
974295 ATCTTGGAACTTGATACCAAGTAAGCAGAAATCATTGGGATGG
1 ATCTTGGAACCTGATACCAAGTAAGCAAAAATCACTGAGATGG
974338 ATCTTGGAACCTGATACCAAGTAAGCAAAAATCACTGAGATGG
1 ATCTTGGAACCTGATACCAAGTAAGCAAAAATCACTGAGATGG
974381 AT
1 AT
974383 AGGAAGTAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.24
Consensus pattern (43 bp):
ATCTTGGAACCTGATACCAAGTAAGCAAAAATCACTGAGATGG
Found at i:978951 original size:16 final size:16
Alignment explanation
Indices: 978930--978960 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
978920 AAGACTTTTT
978930 GTTAACAAGCGTTACC
1 GTTAACAAGCGTTACC
978946 GTTAACAAGCGTTAC
1 GTTAACAAGCGTTAC
978961 TATTTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (16 bp):
GTTAACAAGCGTTACC
Found at i:988186 original size:436 final size:435
Alignment explanation
Indices: 987231--988206 Score: 1144
Period size: 436 Copynumber: 2.2 Consensus size: 435
987221 GGTTTTGATT
** * **
987231 AAAAGGGGCTGGCCCCTTTAATTAGGGGCCAGGAGGGCTCTAAAGTCTTTTAATTTTAACTCTTT
1 AAAAGGGGCTGGCCCCTCAAATTAGGGGCCAGGA-GGCTCTAAAGTCTTTTTATAATAACTCTTT
* * *
987296 ACTGAGCAATAATTTGTCATTAATTAT-GAAGCAAAAATGTTTATTGTACAGCTGTTTATCTACA
65 ACTGAGCAATAATTTGTTATTAATTATAGAAGCAAAAATGTTCATTGTACAGCTGTTCATCTACA
** ** * * *
987360 CAGTTCCTTATTTTAAACATTTGTTACCTAATTAGGGGTTTCAAGGGGCCAGAAGACCATAACTT
130 CAGGACC-TATACTAAACATATGTTACATAATTAGGGGTTTCAAGGGGCCAGAAGACCAAAACTT
* ** * *
987425 TGATCATTAATATCTTGAAAAGGAGAAATATTTTGAAAGGCAATGTTGAACAAAAGTTGCTTAAA
194 TGACCATTAATATCTTGAAAAGGAGAAATATTTTGAAAAACAATGTTGAACAAAAGTTGATGAAA
* * * * * * * * * *
987490 ATAATGTTCTTTAGAACATGGTTCTTTAAAATTTATGGTTTGTGGCCCTTGTAAGGAGTTTATGG
259 ATAATGTTCTTAACAACATGATACTCTAAAATTTATCGTTGGTGGCCCTAGTAAGGAGTTGAAGG
*
987555 GTCGGCCCCTAAAACACTGTTGTTCAGATATCTCCAAATCGGTCAACAATTTCTGAACACTTATT
324 GTCGGCCCCTAAAACACAGTTGTTCAGATATCTCCAAATCGGTCAACAATTTCTGAACACTTATT
* * * *
987620 AAACAAAATATGTTTATATTTATAAGATCTTTTATTTAATATGAAGA
389 AAACAAAATATGTTTATATTTACAAGACCTTTAATTTAATATCAAGA
* * * *
987667 AAAAGGGACTGGCCCCTCAAATTAGGGGCCAAGAGCGCTCTAAATTCTTTATATAATAACTCTTT
1 AAAAGGGGCTGGCCCCTCAAATTAGGGGCCAGGAG-GCTCTAAAGTCTTTTTATAATAACTCTTT
** *
987732 ACTGAAAAATAATTTGTTATTAATTATAGAAGCAAAAATGTTCATTGTACAGCTGTTCATCTATA
65 ACTGAGCAATAATTTGTTATTAATTATAGAAGCAAAAATGTTCATTGTACAGCTGTTCATCTACA
* * *
987797 CTGGACC-ATACTAAAGTCATATGTTACATAATTAGGGGTTTCAAGGGGCCAGAAGTCCAAAATT
130 CAGGACCTATACTAAA--CATATGTTACATAATTAGGGGTTTCAAGGGGCCAGAAGACCAAAACT
* * *
987861 TTGAACCA-TATTATCTTGAAAAGGAGAAATATTTTGAAAAACATTGTAT-AGCAAAAGTTGATG
193 TTG-ACCATTAATATCTTGAAAAGGAGAAATATTTTGAAAAACAATGT-TGAACAAAAGTTGATG
* ** *
987924 AAAATAATGTTGTTAACAATGTGATAC-CTAAAATTTTTCGTTGGTAGGCCC-AGTAAGGAGTTG
256 AAAATAATGTTCTTAACAACATGATACTCTAAAATTTATCGTTGGT-GGCCCTAGTAAGGAGTTG
* * *
987987 AAGGGTCGGCCCCTAAAACACAGTTGTTCCGATATCTCTATAA-CGGTTAACAA-TTCGTGAACA
320 AAGGGTCGGCCCCTAAAACACAGTTGTTCAGATATCTCCA-AATCGGTCAACAATTTC-TGAACA
* * * * *
988050 CTTGTTGAACAAAATATGTTTATATTTGCGAGACCTTTAATTTGATATCAAGA
383 CTTATTAAACAAAATATGTTTATATTTACAAGACCTTTAATTTAATATCAAGA
* *
988103 AAAAGGGGCTGACCCCTCAAATTAGGGGCCAGGATGGCTAC-AAAGTCTTTTTATAGTAAC-CTT
1 AAAAGGGGCTGGCCCCTCAAATTAGGGGCCAGGA-GGCT-CTAAAGTCTTTTTATAATAACTCTT
** * * * * *
988166 TTTTAGAGCGATATTTTGTTATTAATCATAAAAACAAAAAT
64 TACT-GAGCAATAATTTGTTATTAATTATAGAAGCAAAAAT
988207 AAAAGCTTAT
Statistics
Matches: 453, Mismatches: 75, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
435 15 0.03
436 276 0.61
437 158 0.35
438 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (435 bp):
AAAAGGGGCTGGCCCCTCAAATTAGGGGCCAGGAGGCTCTAAAGTCTTTTTATAATAACTCTTTA
CTGAGCAATAATTTGTTATTAATTATAGAAGCAAAAATGTTCATTGTACAGCTGTTCATCTACAC
AGGACCTATACTAAACATATGTTACATAATTAGGGGTTTCAAGGGGCCAGAAGACCAAAACTTTG
ACCATTAATATCTTGAAAAGGAGAAATATTTTGAAAAACAATGTTGAACAAAAGTTGATGAAAAT
AATGTTCTTAACAACATGATACTCTAAAATTTATCGTTGGTGGCCCTAGTAAGGAGTTGAAGGGT
CGGCCCCTAAAACACAGTTGTTCAGATATCTCCAAATCGGTCAACAATTTCTGAACACTTATTAA
ACAAAATATGTTTATATTTACAAGACCTTTAATTTAATATCAAGA
Found at i:997103 original size:53 final size:55
Alignment explanation
Indices: 997000--997160 Score: 159
Period size: 53 Copynumber: 2.9 Consensus size: 55
996990 CCTCACACTA
* * *
997000 ATTAGGGTTTTCCGTTTTCAAAGGAAGACCCTCTTGTTAATCTTCGGTTTC-ATT
1 ATTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTAATCTTCGGTTTCTATT
* * * * *
997054 -TTAGGGTCTTCCGTGTCCAACGAAAGACCCTCTTGTTATTCTAT-TGTTTCTTTTT
1 ATTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTAATCT-TCGGTTTC-TATT
* ** *
997109 ATTAAGGTCTTCCGTTTCCAACGGAAGACTTTCTTGTT-TTCGTTCGGTTTCT
1 ATTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTAATC-TTCGGTTTCT
997161 TTTTCTTCGC
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
53 41 0.47
54 1 0.01
55 7 0.08
56 38 0.44
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.44
Consensus pattern (55 bp):
ATTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTAATCTTCGGTTTCTATT
Found at i:997159 original size:56 final size:56
Alignment explanation
Indices: 997024--997164 Score: 141
Period size: 56 Copynumber: 2.6 Consensus size: 56
997014 TTTTCAAAGG
* * *
997024 AAGACCCTCTTGTTAATCT-TCGGTTTC--ATT-TTAGGGTCTTCCGTGTCCAACGA
1 AAGACCCTCTTGTTATTCTAT-GGTTTCTTTTTATTAAGGTCTTCCGTGTCCAACGA
* * *
997077 AAGACCCTCTTGTTATTCTATTGTTTCTTTTTATTAAGGTCTTCCGTTTCCAACGG
1 AAGACCCTCTTGTTATTCTATGGTTTCTTTTTATTAAGGTCTTCCGTGTCCAACGA
**
997133 AAGACTTTCTTGTT-TTCGT-TCGGTTTCTTTTT
1 AAGACCCTCTTGTTATTC-TAT-GGTTTCTTTTT
997165 CTTCGCTATT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
53 23 0.32
54 1 0.01
55 6 0.08
56 43 0.59
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (56 bp):
AAGACCCTCTTGTTATTCTATGGTTTCTTTTTATTAAGGTCTTCCGTGTCCAACGA
Found at i:1009372 original size:2 final size:2
Alignment explanation
Indices: 1009365--1009404 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1009355 GGACGAATCT
1009365 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1009405 ATTTATTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1009856 original size:2 final size:2
Alignment explanation
Indices: 1009849--1009889 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1009839 AAAAACATTA
1009849 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1009890 ACACACACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1009894 original size:2 final size:2
Alignment explanation
Indices: 1009889--1009930 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1009879 CTCTCTCTCT
1009889 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1009931 ATTCATGGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1019449 original size:2 final size:2
Alignment explanation
Indices: 1019442--1019486 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1019432 CCTTACAAAC
* *
1019442 GA GA GA GA GA GA GA GA GA GA GC GA GA GA GA GA GA GA GA AA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1019484 GA G
1 GA G
1019487 GCAGAGGGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1019532 original size:2 final size:2
Alignment explanation
Indices: 1019525--1019593 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
1019515 TAAGTTGTAA
1019525 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1019566 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1019594 TTGGCTTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1022562 original size:12 final size:12
Alignment explanation
Indices: 1022545--1022581 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1022535 NNATATTGTT
1022545 TGGTGGGGGGGG
1 TGGTGGGGGGGG
1022557 TGGTGGGGGGGG
1 TGGTGGGGGGGG
* *
1022569 GGGGGGGGGGGG
1 TGGTGGGGGGGG
1022581 T
1 T
1022582 AAACAATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (12 bp):
TGGTGGGGGGGG
Found at i:1023376 original size:13 final size:14
Alignment explanation
Indices: 1023352--1023380 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1023342 TACATGCTAA
1023352 TTTGGTTTTTTTTT
1 TTTGGTTTTTTTTT
1023366 TTTGGTTTTTTTTT
1 TTTGGTTTTTTTTT
1023380 T
1 T
1023381 GGGGGGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTGGTTTTTTTTT
Found at i:1028013 original size:1 final size:1
Alignment explanation
Indices: 1028009--1028036 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1027999 GCCCCCACCA
1028009 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1028037 AAAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1042217 original size:14 final size:14
Alignment explanation
Indices: 1042198--1042252 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
1042188 TTCAATTAAC
**
1042198 AGAGAGAGAGGCAG
1 AGAGAGAGAGAAAG
*
1042212 AGAGAGAGAAAAAG
1 AGAGAGAGAGAAAG
1042226 AGAGAGAGAGAAAG
1 AGAGAGAGAGAAAG
1042240 -GAAGAGAGAGAAA
1 AG-AGAGAGAGAAA
1042253 AAGAACCACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
13 1 0.03
14 35 0.97
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAGAAAG
Found at i:1042219 original size:16 final size:15
Alignment explanation
Indices: 1042198--1042252 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
1042188 TTCAATTAAC
*
1042198 AGAGAGAGAGGCAGAG
1 AGAGAGAAAGG-AGAG
*
1042214 AGAGAGAAAAAGAGAG
1 AGAGAG-AAAGGAGAG
1042230 AGAGAGAAAGGA-AG
1 AGAGAGAAAGGAGAG
1042244 AGAGAGAAA
1 AGAGAGAAA
1042253 AAGAACCACT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 11 0.31
15 5 0.14
16 16 0.46
17 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (15 bp):
AGAGAGAAAGGAGAG
Found at i:1050605 original size:40 final size:40
Alignment explanation
Indices: 1050507--1050841 Score: 468
Period size: 40 Copynumber: 8.5 Consensus size: 40
1050497 AGTCTAAAAA
* *
1050507 TTGATTGTTGTTTGATTTTAATA-G--G-TTGTTGTTTAT
1 TTGATTGTTGTTTGAATTGAATAGGTTGTTTGTTGTTTAT
* * *
1050543 TTGTTTGTTGTTTG-ATTAGAATAGGTTGTTTGATGTATAT
1 TTGATTGTTGTTTGAATT-GAATAGGTTGTTTGTTGTTTAT
* * *
1050583 TTGTTTGTTGTGTGAATTGAATATGTTGTTTGTTGTTTAT
1 TTGATTGTTGTTTGAATTGAATAGGTTGTTTGTTGTTTAT
* * *
1050623 TTGTTTGTTGTTTGATTTGAATAGGTTGTTTGATGTTTAT
1 TTGATTGTTGTTTGAATTGAATAGGTTGTTTGTTGTTTAT
*
1050663 TTGATTGTTGTGTGAATTGAATAGGTTGTTTGTTGTTTAT
1 TTGATTGTTGTTTGAATTGAATAGGTTGTTTGTTGTTTAT
1050703 TTGATTGTTGTTTGAATT-AATAGGTTGTTTGTTGTTTAT
1 TTGATTGTTGTTTGAATTGAATAGGTTGTTTGTTGTTTAT
* *
1050742 TTGATTGTTGTTTGATTTGAACAGGTTGTTTGTTGTTTAT
1 TTGATTGTTGTTTGAATTGAATAGGTTGTTTGTTGTTTAT
1050782 TTGATTGTTGTTTGAATT-AATAGGTTGTTTGTTGTTTAT
1 TTGATTGTTGTTTGAATTGAATAGGTTGTTTGTTGTTTAT
* *
1050821 TTTATTGTTGTTTGATTTGAA
1 TTGATTGTTGTTTGAATTGAA
1050842 GATCTGGGTT
Statistics
Matches: 267, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
35 2 0.01
36 17 0.06
37 1 0.00
39 75 0.28
40 169 0.63
41 3 0.01
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (40 bp):
TTGATTGTTGTTTGAATTGAATAGGTTGTTTGTTGTTTAT
Found at i:1050628 original size:15 final size:16
Alignment explanation
Indices: 1050608--1050641 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1050598 ATTGAATATG
1050608 TTGTTTGTTGTTT-AT
1 TTGTTTGTTGTTTGAT
1050623 TTGTTTGTTGTTTGAT
1 TTGTTTGTTGTTTGAT
1050639 TTG
1 TTG
1050642 AATAGGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.06, C:0.00, G:0.24, T:0.71
Consensus pattern (16 bp):
TTGTTTGTTGTTTGAT
Found at i:1050651 original size:25 final size:24
Alignment explanation
Indices: 1050623--1050785 Score: 79
Period size: 24 Copynumber: 7.8 Consensus size: 24
1050613 TGTTGTTTAT
1050623 TTGTTTGTTGTTTGATTTGAATAGG
1 TTGTTTGTTGTTT-ATTTGAATAGG
*
1050648 TTGTTTGATGTTTATTTG---A--
1 TTGTTTGTTGTTTATTTGAATAGG
* *
1050667 TTG-TTG-TG-TGAATTGAATAGG
1 TTGTTTGTTGTTTATTTGAATAGG
1050688 TTGTTTGTTGTTTATTTG---A--
1 TTGTTTGTTGTTTATTTGAATAGG
* *
1050707 TTG-TTG-T-TTGAATT-AATAGG
1 TTGTTTGTTGTTTATTTGAATAGG
1050727 TTGTTTGTTGTTTATTTG---A--
1 TTGTTTGTTGTTTATTTGAATAGG
* *
1050746 TTG-TTG-T-TTGATTTGAACAGG
1 TTGTTTGTTGTTTATTTGAATAGG
1050767 TTGTTTGTTGTTTATTTGA
1 TTGTTTGTTGTTTATTTGA
1050786 TTGTTGTTTG
Statistics
Matches: 102, Mismatches: 11, Indels: 51
0.62 0.07 0.31
Matches are distributed among these distances:
16 17 0.17
17 4 0.04
18 10 0.10
19 11 0.11
20 3 0.03
21 12 0.12
22 7 0.07
23 8 0.08
24 18 0.18
25 12 0.12
ACGTcount: A:0.17, C:0.01, G:0.25, T:0.58
Consensus pattern (24 bp):
TTGTTTGTTGTTTATTTGAATAGG
Found at i:1050751 original size:15 final size:16
Alignment explanation
Indices: 1050731--1050761 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1050721 AATAGGTTGT
1050731 TTGTTGTTT-ATTTGA
1 TTGTTGTTTGATTTGA
1050746 TTGTTGTTTGATTTGA
1 TTGTTGTTTGATTTGA
1050762 ACAGGTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.65
Consensus pattern (16 bp):
TTGTTGTTTGATTTGA
Found at i:1050768 original size:79 final size:80
Alignment explanation
Indices: 1050507--1050841 Score: 477
Period size: 79 Copynumber: 4.3 Consensus size: 80
1050497 AGTCTAAAAA
* *
1050507 TTGATTGTTGTTTGATTTTAATA-G--G-TTGTTGTTTATTTGTTTGTTGTTTG-ATTAGAATAG
1 TTGATTGTTGTTTGATTTGAATAGGTTGTTTGTTGTTTATTTGATTGTTGTTTGAATT-GAATAG
*
1050567 GTTGTTTGATGTATAT
65 GTTGTTTGATGTTTAT
* * * * * *
1050583 TTGTTTGTTGTGTGAATTGAATATGTTGTTTGTTGTTTATTTGTTTGTTGTTTGATTTGAATAGG
1 TTGATTGTTGTTTGATTTGAATAGGTTGTTTGTTGTTTATTTGATTGTTGTTTGAATTGAATAGG
1050648 TTGTTTGATGTTTAT
66 TTGTTTGATGTTTAT
* *
1050663 TTGATTGTTGTGTGAATTGAATAGGTTGTTTGTTGTTTATTTGATTGTTGTTTGAATT-AATAGG
1 TTGATTGTTGTTTGATTTGAATAGGTTGTTTGTTGTTTATTTGATTGTTGTTTGAATTGAATAGG
*
1050727 TTGTTTGTTGTTTAT
66 TTGTTTGATGTTTAT
*
1050742 TTGATTGTTGTTTGATTTGAACAGGTTGTTTGTTGTTTATTTGATTGTTGTTTGAATT-AATAGG
1 TTGATTGTTGTTTGATTTGAATAGGTTGTTTGTTGTTTATTTGATTGTTGTTTGAATTGAATAGG
*
1050806 TTGTTTGTTGTTTAT
66 TTGTTTGATGTTTAT
*
1050821 TTTATTGTTGTTTGATTTGAA
1 TTGATTGTTGTTTGATTTGAA
1050842 GATCTGGGTT
Statistics
Matches: 239, Mismatches: 15, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
76 19 0.08
77 1 0.00
79 117 0.49
80 100 0.42
81 2 0.01
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (80 bp):
TTGATTGTTGTTTGATTTGAATAGGTTGTTTGTTGTTTATTTGATTGTTGTTTGAATTGAATAGG
TTGTTTGATGTTTAT
Found at i:1056645 original size:172 final size:171
Alignment explanation
Indices: 1056142--1057024 Score: 1160
Period size: 172 Copynumber: 5.2 Consensus size: 171
1056132 GAATCATCTT
* *
1056142 GCTGATTAGTTTCTGAGAAGAAGAATCTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTA
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT-
* * *
1056207 ACACCCCCCCCCCA-TGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCT
65 ACACCCCCCCCCCATTGTGGCCCCACCCTACACCCGGGGATCATGATTTTCACAACTTTGAATCT
* **
1056271 ACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTTTTG
130 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* * *
1056313 GCTGATTAGTTTCTGAGGAGAAGATTTTTTAATATTTACTCTATATATTCCTATGTAAAAC-TT-
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTA
* * *
1056376 CGA----CCCCCCAGTGT-GCCCCACCCTAC-CTCCAGGGATAATGATTTTCACAACTTTGAATC
66 C-ACCCCCCCCCCATTGTGGCCCCACCCTACAC-CCGGGGATCATGATTTTCACAACTTTGAATC
*
1056435 TACACTGCCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
129 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
*
1056478 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACTTTA
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT-
* * * *
1056543 ACACCCCCCCCCCATTGTGGCCCCACCCTACACCCGGGGGTCGTGACTTTCACAACTATGAATCT
65 ACACCCCCCCCCCATTGTGGCCCCACCCTACACCCGGGGATCATGATTTTCACAACTTTGAATCT
* *
1056608 ACACTACCTGATGATGCTTTCACACAAGTTTCAGCTTTCCTG
130 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* * * *
1056650 GCTGATTAGTTTCTGAAAAGAACATTTTTAAAGATTTACTCTATATATTCCTTTGTAAAACTTCG
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT-T
* * *
1056715 ACCCCCCCCCCCCATTGTGGCCCCACCCTACCCCCGGGGATCATGATTTTCACAATTTTGAATCT
65 ACACCCCCCCCCCATTGTGGCCCCACCCTACACCCGGGGATCATGATTTTCACAACTTTGAATCT
*
1056780 ACACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTG
130 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* * *
1056822 GCCGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCATATGTTAAAA--TT
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATG-TAAAACTTT
* * * *
1056885 -CGA----CCCCCCATTGTGGCCCCACCCTACACCTGGGGGTCATGATTTTCATAA-TTT-AGTA
65 AC-ACCCCCCCCCCATTGTGGCCCCACCCTACACCCGGGGATCATGATTTTCACAACTTTGAAT-
1056943 CTTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
128 C-TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* *
1056988 G-T-CTTATGGTTCATGAGAAGAAGATTTTTGAAA-ATTT
1 GCTGATTA-GTTTC-TGAGAAGAAGATTTTT-AAAGATTT
1057025 CTCGAAATTT
Statistics
Matches: 634, Mismatches: 58, Indels: 45
0.86 0.08 0.06
Matches are distributed among these distances:
164 5 0.01
165 152 0.24
166 112 0.18
167 4 0.01
168 2 0.00
169 2 0.00
170 2 0.00
171 67 0.11
172 282 0.44
173 6 0.01
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (171 bp):
GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTA
CACCCCCCCCCCATTGTGGCCCCACCCTACACCCGGGGATCATGATTTTCACAACTTTGAATCTA
CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
Found at i:1057211 original size:20 final size:19
Alignment explanation
Indices: 1057186--1057231 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
1057176 TGAAAAGTTT
* *
1057186 ACAGACGGACAGACGGGCAG
1 ACAGACAGACAGACGGAC-G
1057206 ACAGACAGACAGACGGACG
1 ACAGACAGACAGACGGACG
1057225 ACAGACA
1 ACAGACA
1057232 AAATGTGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.41, C:0.26, G:0.33, T:0.00
Consensus pattern (19 bp):
ACAGACAGACAGACGGACG
Found at i:1086080 original size:2 final size:2
Alignment explanation
Indices: 1086073--1086102 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1086063 TAAGGCATAC
*
1086073 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1086103 AAACGTCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1086168 original size:17 final size:17
Alignment explanation
Indices: 1086146--1086180 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1086136 AGGTATAGGA
1086146 ATGTACATCAGTTATTT
1 ATGTACATCAGTTATTT
1086163 ATGTACATCAGTTATTT
1 ATGTACATCAGTTATTT
1086180 A
1 A
1086181 CATAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (17 bp):
ATGTACATCAGTTATTT
Found at i:1086351 original size:5 final size:5
Alignment explanation
Indices: 1086343--1086463 Score: 140
Period size: 5 Copynumber: 24.4 Consensus size: 5
1086333 GTTTAAATTC
* * *
1086343 CGTTT CGTTT CGATT --TTT GGTTT CGTTT CGTTT CGTTT GGTTT CGTTT
1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT
* * * *
1086391 CGATT GGTTT CGTTT CGTTT CGATT GGTTT CGTTT CGTTT CG-TT CGATTT
1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CG-TTT
1086441 CGTTT CGTTT CGATTT CGTTT CG
1 CGTTT CGTTT CG-TTT CGTTT CG
1086464 CACTTTACAG
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
3 2 0.02
4 4 0.04
5 83 0.85
6 9 0.09
ACGTcount: A:0.04, C:0.17, G:0.23, T:0.56
Consensus pattern (5 bp):
CGTTT
Found at i:1089790 original size:2 final size:2
Alignment explanation
Indices: 1089783--1089915 Score: 221
Period size: 2 Copynumber: 65.5 Consensus size: 2
1089773 GATCCATATA
1089783 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
1089825 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT GCT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT
**
1089868 CT CT CT CT GGG CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1089911 CT CT C
1 CT CT C
1089916 ATATTTCAAT
Statistics
Matches: 123, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
2 122 0.99
3 1 0.01
ACGTcount: A:0.00, C:0.48, G:0.04, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1091143 original size:2 final size:2
Alignment explanation
Indices: 1091136--1091162 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1091126 TCATGTATAN
1091136 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1091163 ATATTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1093598 original size:2 final size:2
Alignment explanation
Indices: 1093593--1093617 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1093583 CACACACACA
1093593 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1093618 AGGATGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1096235 original size:15 final size:15
Alignment explanation
Indices: 1096215--1096243 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1096205 GGACAGTGGT
1096215 AGTGGTAGTGGTAGA
1 AGTGGTAGTGGTAGA
1096230 AGTGGTAGTGGTAG
1 AGTGGTAGTGGTAG
1096244 TTAATGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.48, T:0.28
Consensus pattern (15 bp):
AGTGGTAGTGGTAGA
Found at i:1101673 original size:2 final size:2
Alignment explanation
Indices: 1101666--1101727 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1101656 CATATGCATG
1101666 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1101708 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
1101728 GGGCAGTTGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1103807 original size:166 final size:164
Alignment explanation
Indices: 1103561--1104029 Score: 586
Period size: 166 Copynumber: 2.8 Consensus size: 164
1103551 AACACCCCCC
* * * *
1103561 CCCCCCATTGTGGCCCCACCCTACACCCAGGGGTCATGATTTTCATAACTCTGAATCTTCACTAC
1 CCCCCCATTGTGGCCCCA-CCTACCCCCGGGGGTCATGATTTTCA-AACTTTGAATCTACACTAC
* * *
1103626 CTTAGGATGCTTCCACATAAGTTTC-GACTTTTCTGGTCAAATGGTTCTTGAGAAAAAGATTTTT
64 CTGAGGATGCTTCCACACAAGTTTCAG-CTTTCCTGGTCAAATGGTTCTTGAGAAAAAGATTTTT
*
1103690 AAAGATTTACTCTAAATATTCCTATGTATAA-ATTTGA
128 AAAGATTTACTCTAAATATTCCTATGTA-AATAGTTGA
1103727 CCCACCCATTGTGGCCCCACCTTACCCCCGGGGGTCATG-TTTTCACAACTTTGAATCTACACTA
1 CCC-CCCATTGTGGCCCCACC-TACCCCCGGGGGTCATGATTTTCA-AACTTTGAATCTACACTA
* * * ** * **
1103791 CCTGAGGATGCTTCCACACAAGTTTTAGCTTTCCTAGTCTAACAGTTTTTGAGAGGAAGATTTTT
63 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGTCAAATGGTTCTTGAGAAAAAGATTTTT
* *
1103856 AAAGATTCACTCTATATATTCCTATGTAAATAGTTGA
128 AAAGATTTACTCTAAATATTCCTATGTAAATAGTTGA
* * * *
1103893 CCCCCCATTGTGGCCCCATCCTACCCCAGGGGGTAATGACTTTCGAAACTTTGAATCTACACCAC
1 CCCCCCATTGTGGCCCCA-CCTACCCCCGGGGGTCATGATTTTC-AAACTTTGAATCTACACTAC
* * * *
1103958 CTGAGGATGCTTCCACAGAAGTGTCAGCTTTCCTGGCCAAATGGTTCTTGAGAAAATGATTTTTG
64 CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGTCAAATGGTTCTTGAGAAAAAGATTTTT-
1104023 AAA-ATTT
128 AAAGATTT
1104030 CTTGAAAATT
Statistics
Matches: 259, Mismatches: 36, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
165 32 0.12
166 192 0.74
167 35 0.14
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (164 bp):
CCCCCCATTGTGGCCCCACCTACCCCCGGGGGTCATGATTTTCAAACTTTGAATCTACACTACCT
GAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGTCAAATGGTTCTTGAGAAAAAGATTTTTAAA
GATTTACTCTAAATATTCCTATGTAAATAGTTGA
Found at i:1117127 original size:2 final size:2
Alignment explanation
Indices: 1117120--1117176 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1117110 TCATTTACAA
1117120 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1117162 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
1117177 AAATTGATCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1117789 original size:11 final size:11
Alignment explanation
Indices: 1117773--1117804 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1117763 TGAACATATT
1117773 TTTATGAAATA
1 TTTATGAAATA
1117784 TTTATGAAATA
1 TTTATGAAATA
1117795 --TATGAAATA
1 TTTATGAAATA
1117804 T
1 T
1117805 ATTTTTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (11 bp):
TTTATGAAATA
Found at i:1119670 original size:16 final size:16
Alignment explanation
Indices: 1119649--1119681 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1119639 CCTGTGCGTG
1119649 TGTACAGTGTAGTACA
1 TGTACAGTGTAGTACA
*
1119665 TGTACATTGTAGTACA
1 TGTACAGTGTAGTACA
1119681 T
1 T
1119682 ACATGTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (16 bp):
TGTACAGTGTAGTACA
Found at i:1124108 original size:15 final size:16
Alignment explanation
Indices: 1124087--1124123 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1124077 GAGCACTGCT
*
1124087 TAGTTCCATTACGTCA
1 TAGTTCCATCACGTCA
1124103 -AGTTCCATCACGTCA
1 TAGTTCCATCACGTCA
1124118 TAGTTC
1 TAGTTC
1124124 GCTGACGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (16 bp):
TAGTTCCATCACGTCA
Found at i:1137183 original size:19 final size:20
Alignment explanation
Indices: 1137119--1137185 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1137109 ATAGATAAAT
*
1137119 AGATATCAAAATTAATGGAG
1 AGATATCAAAATTAATGAAG
* *
1137139 AGATATCAGAATTAATGAAC
1 AGATATCAAAATTAATGAAG
1137159 AGATAT-AAAATTAATGAAG
1 AGATATCAAAATTAATGAAG
*
1137178 AAATATCA
1 AGATATCA
1137186 TTTTCCATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.40
20 24 0.60
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.25
Consensus pattern (20 bp):
AGATATCAAAATTAATGAAG
Found at i:1154012 original size:20 final size:20
Alignment explanation
Indices: 1153989--1154112 Score: 77
Period size: 20 Copynumber: 6.6 Consensus size: 20
1153979 TTGCAGATCT
1153989 TAAATAGACACTGTCATGCC
1 TAAATAGACACTGTCATGCC
** * *
1154009 TAAATAGATTCTGTGATGCT
1 TAAATAGACACTGTCATGCC
1154029 TAAATAGACACTG---T--C
1 TAAATAGACACTGTCATGCC
** *
1154044 --AAT--ATTCTGTCATGTC
1 TAAATAGACACTGTCATGCC
*
1154060 TAAATAGACACCGTCATGCC
1 TAAATAGACACTGTCATGCC
* * *
1154080 TAAATAGACATTGTGATGCT
1 TAAATAGACACTGTCATGCC
1154100 TAGAATAGACACT
1 TA-AATAGACACT
1154113 ACAGTCCTAA
Statistics
Matches: 76, Mismatches: 18, Indels: 19
0.67 0.16 0.17
Matches are distributed among these distances:
11 4 0.05
13 3 0.04
14 1 0.01
16 1 0.01
17 1 0.01
18 3 0.04
20 54 0.71
21 9 0.12
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (20 bp):
TAAATAGACACTGTCATGCC
Found at i:1154064 original size:31 final size:31
Alignment explanation
Indices: 1154016--1154075 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1154006 GCCTAAATAG
* *
1154016 ATTCTGTGATGCTTAAATAGACACTGTCAAT
1 ATTCTGTCATGCTTAAATAGACACCGTCAAT
1154047 ATTCTGTCATG-TCTAAATAGACACCGTCA
1 ATTCTGTCATGCT-TAAATAGACACCGTCA
1154076 TGCCTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (31 bp):
ATTCTGTCATGCTTAAATAGACACCGTCAAT
Found at i:1159658 original size:7 final size:7
Alignment explanation
Indices: 1159646--1159712 Score: 80
Period size: 7 Copynumber: 9.6 Consensus size: 7
1159636 GAGAAGGATC
1159646 ATTCGAG
1 ATTCGAG
1159653 ATTCGAG
1 ATTCGAG
* *
1159660 ATTCAAA
1 ATTCGAG
*
1159667 ATACGAG
1 ATTCGAG
*
1159674 ATTCGAA
1 ATTCGAG
*
1159681 ATACGAG
1 ATTCGAG
1159688 ATTCGAG
1 ATTCGAG
*
1159695 ATTCGAA
1 ATTCGAG
1159702 ATTCGAG
1 ATTCGAG
1159709 ATTC
1 ATTC
1159713 AATATCCAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:1159694 original size:21 final size:21
Alignment explanation
Indices: 1159646--1159712 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
1159636 GAGAAGGATC
* * *
1159646 ATTCGAGATTCGAGATTCAAA
1 ATTCGAGATTCGAAATTCGAG
* *
1159667 ATACGAGATTCGAAATACGAG
1 ATTCGAGATTCGAAATTCGAG
1159688 ATTCGAGATTCGAAATTCGAG
1 ATTCGAGATTCGAAATTCGAG
1159709 ATTC
1 ATTC
1159713 AATATCCAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (21 bp):
ATTCGAGATTCGAAATTCGAG
Found at i:1162292 original size:2 final size:2
Alignment explanation
Indices: 1162285--1162331 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1162275 GCTAGGTGAT
1162285 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1162327 GA GA G
1 GA GA G
1162332 TCGATGTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1162552 original size:8 final size:8
Alignment explanation
Indices: 1162521--1162570 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
1162511 TCTCTCTGTG
*
1162521 TCTGTCTG
1 TCTGTCTC
*
1162529 TCTGTCTG
1 TCTGTCTC
*
1162537 TTTGTCTC
1 TCTGTCTC
1162545 TCTGTCTC
1 TCTGTCTC
*
1162553 TCTCTCTC
1 TCTGTCTC
*
1162561 TCTCTCTC
1 TCTGTCTC
1162569 TC
1 TC
1162571 ATATCGACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.00, C:0.36, G:0.12, T:0.52
Consensus pattern (8 bp):
TCTGTCTC
Found at i:1162554 original size:2 final size:2
Alignment explanation
Indices: 1162541--1162570 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1162531 TGTCTGTTTG
*
1162541 TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1162571 ATATCGACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1162556 original size:12 final size:12
Alignment explanation
Indices: 1162521--1162570 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
1162511 TCTCTCTGTG
* *
1162521 TCTGTCTGTCTG
1 TCTGTCTCTCTC
* *
1162533 TCTGTTTGTCTC
1 TCTGTCTCTCTC
1162545 TCTGTCTCTCTC
1 TCTGTCTCTCTC
*
1162557 TCTCTCTCTCTC
1 TCTGTCTCTCTC
1162569 TC
1 TC
1162571 ATATCGACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.00, C:0.36, G:0.12, T:0.52
Consensus pattern (12 bp):
TCTGTCTCTCTC
Found at i:1163080 original size:7 final size:7
Alignment explanation
Indices: 1163065--1163131 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
1163055 TTTAGATATT
1163065 GAATCTC
1 GAATCTC
*
1163072 GAATTTC
1 GAATCTC
1163079 GAATCTC
1 GAATCTC
1163086 GAATCTC
1 GAATCTC
* *
1163093 GTATTTC
1 GAATCTC
1163100 GAATCTC
1 GAATCTC
* * *
1163107 GTATTTT
1 GAATCTC
1163114 GAATCTC
1 GAATCTC
*
1163121 GAATCTT
1 GAATCTC
1163128 GAAT
1 GAAT
1163132 GATCCTTCTC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (7 bp):
GAATCTC
Found at i:1163090 original size:21 final size:21
Alignment explanation
Indices: 1163065--1163131 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
1163055 TTTAGATATT
1163065 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
1163086 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * * * *
1163107 GTATTTTGAATCTCGAATCTT
1 GAATCTCGAATTTCGAATCTC
1163128 GAAT
1 GAAT
1163132 GATCCTTCTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:1170382 original size:2 final size:2
Alignment explanation
Indices: 1170375--1170403 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1170365 CGTAAAACAA
1170375 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1170404 GTAAAGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1170705 original size:2 final size:2
Alignment explanation
Indices: 1170698--1170724 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1170688 AGGTGTAAAG
1170698 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1170725 GACATCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1176549 original size:2 final size:2
Alignment explanation
Indices: 1176542--1176604 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1176532 AAGTCGGCCT
1176542 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
1176584 GG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
1176605 ATTGTATTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1176874 original size:22 final size:22
Alignment explanation
Indices: 1176847--1176888 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1176837 GTTAATAGCC
1176847 TAATTCAAGATGCCGCAGTTAA
1 TAATTCAAGATGCCGCAGTTAA
1176869 TAATTCAAGATGCCGCAGTT
1 TAATTCAAGATGCCGCAGTT
1176889 CTGTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (22 bp):
TAATTCAAGATGCCGCAGTTAA
Found at i:1184562 original size:16 final size:16
Alignment explanation
Indices: 1184541--1184571 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1184531 TCACCGAGAC
1184541 GAGGCATCAACTTTAT
1 GAGGCATCAACTTTAT
*
1184557 GAGGCATCACCTTTA
1 GAGGCATCAACTTTA
1184572 AAACCACCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (16 bp):
GAGGCATCAACTTTAT
Found at i:1185056 original size:22 final size:23
Alignment explanation
Indices: 1185013--1185056 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
1185003 GTATTGTATG
1185013 ATATTGTATCATATTTGATACACA
1 ATATTGTATCATA-TTGATACACA
1185037 ATATTGTATCATA-TGATACA
1 ATATTGTATCATATTGATACA
1185057 ATATAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (23 bp):
ATATTGTATCATATTGATACACA
Found at i:1185102 original size:15 final size:15
Alignment explanation
Indices: 1185043--1185155 Score: 65
Period size: 15 Copynumber: 7.5 Consensus size: 15
1185033 CACAATATTG
1185043 TATCATATGATACAA
1 TATCATATGATACAA
* *
1185058 TATAATTTGATA-AA
1 TATCATATGATACAA
* *
1185072 -A-CAT-TGTTTC-A
1 TATCATATGATACAA
1185083 TATCATATGATACAA
1 TATCATATGATACAA
*
1185098 TATCATCTGATACAGTACGA
1 TATCATATGATAC---A--A
* *
1185118 TATTATATAATACAA
1 TATCATATGATACAA
* *
1185133 TATCATTTTATACAA
1 TATCATATGATACAA
1185148 TATCATAT
1 TATCATAT
1185156 CATNNNNNNN
Statistics
Matches: 73, Mismatches: 15, Indels: 20
0.68 0.14 0.19
Matches are distributed among these distances:
11 4 0.05
12 3 0.04
13 4 0.05
14 6 0.08
15 43 0.59
17 1 0.01
18 1 0.01
20 11 0.15
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (15 bp):
TATCATATGATACAA
Found at i:1185593 original size:176 final size:177
Alignment explanation
Indices: 1185276--1186205 Score: 1370
Period size: 177 Copynumber: 5.3 Consensus size: 177
1185266 NNNNNNNNNN
1185276 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
* *
1185341 ATCATAAGACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
66 ATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAGAAATGGCT
1185406 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACC-T
131 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTT
* * **
1185452 AACTTCATCTAGCATCCGAAACCT-TCGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCAAAAG
1 AACCTCATCCAGCATCCGAAACCTAT-GGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAG
* * * * * **
1185516 TATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTAAGGACCAGTAGTAAGTAAGATAT-AA
65 TATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAGAAATGGC
* ** * *
1185580 TCATCAGAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTT
130 T-ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTT
1185629 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
* *
1185694 ATCATAAGACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
66 ATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAGAAATGGCT
1185759 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACC-T
131 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTT
* * **
1185805 AACTTCATCTAGCATCCGAAACCT-TCGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCAAAAG
1 AACCTCATCCAGCATCCGAAACCTAT-GGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAG
* * * * * **
1185869 TATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTAAGGACCAGTAGTAAGTAAGATAT-AA
65 TATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAGAAATGGC
* ** * *
1185933 TCATCAGAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTT
130 T-ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTT
1185982 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
*
1186047 ATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTTGGACCAGTAGTAACTTAGAAATGGCT
66 ATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAGAAATGGCT
* *
1186112 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAACACCTT
131 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTT
* * * * *
1186159 AACCTCCTCCAGCATCTGAAA-TTCATGGCCCAGATTCAGCATCCAAG
1 AACCTCATCCAGCATCCGAAACCT-ATGGCTCAGATTCAGCATTCAAG
1186206 TCTCTCAAGT
Statistics
Matches: 666, Mismatches: 77, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
175 4 0.01
176 308 0.46
177 350 0.53
178 4 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (177 bp):
AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
ATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAGAAATGGCT
ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTT
Found at i:1185623 original size:19 final size:19
Alignment explanation
Indices: 1185596--1185632 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1185586 GAGGGCACCT
*
1185596 GCTCCAAAAACTTTAACCA
1 GCTCCAAAAACCTTAACCA
*
1185615 GCTCTAAAAACCTTAACC
1 GCTCCAAAAACCTTAACC
1185633 TCATCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (19 bp):
GCTCCAAAAACCTTAACCA
Found at i:1185922 original size:353 final size:353
Alignment explanation
Indices: 1185276--1186205 Score: 1729
Period size: 353 Copynumber: 2.6 Consensus size: 353
1185266 NNNNNNNNNN
1185276 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1185341 ATCATAAGACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
66 ATCATAAGACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
1185406 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTAACTTCATCTAGCATCCGA
131 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTAACTTCATCTAGCATCCGA
1185471 AACCTTCGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCAAAAGTATCATAAGACACACCATCC
196 AACCTTCGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCAAAAGTATCATAAGACACACCATCC
1185536 ATGCAAGTTTGGTGAAGTAAGGACCAGTAGTAAGTAAGATATAATCATCAGAGGGCACCTGCTCC
261 ATGCAAGTTTGGTGAAGTAAGGACCAGTAGTAAGTAAGATATAATCATCAGAGGGCACCTGCTCC
1185601 AAAAACTTTAACCAGCTCTAAAAACCTT
326 AAAAACTTTAACCAGCTCTAAAAACCTT
1185629 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1185694 ATCATAAGACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
66 ATCATAAGACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
1185759 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTAACTTCATCTAGCATCCGA
131 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTAACTTCATCTAGCATCCGA
1185824 AACCTTCGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCAAAAGTATCATAAGACACACCATCC
196 AACCTTCGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCAAAAGTATCATAAGACACACCATCC
1185889 ATGCAAGTTTGGTGAAGTAAGGACCAGTAGTAAGTAAGATATAATCATCAGAGGGCACCTGCTCC
261 ATGCAAGTTTGGTGAAGTAAGGACCAGTAGTAAGTAAGATATAATCATCAGAGGGCACCTGCTCC
1185954 AAAAACTTTAACCAGCTCTAAAAACCTT
326 AAAAACTTTAACCAGCTCTAAAAACCTT
1185982 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
* *
1186047 ATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTTGGACCAGTAGTAACTTAGAAATGGCT
66 ATCATAAGACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
* * * * * *
1186112 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAACACCTTAACCTCCTCCAGCATCTG
131 ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACC-TAACTTCATCTAGCATCCG
* *
1186177 AAA--TTCATGGCCCAGATTCAGCATCCAAG
195 AAACCTTC--GGCTCAGATTCAGCATTCAAG
1186206 TCTCTCAAGT
Statistics
Matches: 564, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
352 3 0.01
353 524 0.93
354 37 0.07
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (353 bp):
AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
ATCATAAGACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
ATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACCTAACTTCATCTAGCATCCGA
AACCTTCGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCAAAAGTATCATAAGACACACCATCC
ATGCAAGTTTGGTGAAGTAAGGACCAGTAGTAAGTAAGATATAATCATCAGAGGGCACCTGCTCC
AAAAACTTTAACCAGCTCTAAAAACCTT
Found at i:1185976 original size:19 final size:19
Alignment explanation
Indices: 1185949--1185985 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1185939 GAGGGCACCT
*
1185949 GCTCCAAAAACTTTAACCA
1 GCTCCAAAAACCTTAACCA
*
1185968 GCTCTAAAAACCTTAACC
1 GCTCCAAAAACCTTAACC
1185986 TCATCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (19 bp):
GCTCCAAAAACCTTAACCA
Found at i:1186152 original size:19 final size:19
Alignment explanation
Indices: 1186130--1186169 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1186120 GCACCTGCAA
* *
1186130 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
*
1186149 CAAACACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
1186168 CA
1 CA
1186170 GCATCTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.40, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:1187310 original size:12 final size:12
Alignment explanation
Indices: 1187293--1187327 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1187283 TGACATGGAG
1187293 AGAGAGAGAGAA
1 AGAGAGAGAGAA
*
1187305 AGAGAGAGATAA
1 AGAGAGAGAGAA
*
1187317 AGGGAGAGAGA
1 AGAGAGAGAGA
1187328 TCACATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.43, T:0.03
Consensus pattern (12 bp):
AGAGAGAGAGAA
Found at i:1188020 original size:20 final size:20
Alignment explanation
Indices: 1187995--1188037 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1187985 GTGGCATGTC
*
1187995 AATCCTATAAAGATTGAAAT
1 AATCCTATAAAAATTGAAAT
1188015 AATCCTATAAAAATTGAAAT
1 AATCCTATAAAAATTGAAAT
1188035 AAT
1 AAT
1188038 GTTTAATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.30
Consensus pattern (20 bp):
AATCCTATAAAAATTGAAAT
Found at i:1198205 original size:168 final size:168
Alignment explanation
Indices: 1197867--1198973 Score: 1281
Period size: 168 Copynumber: 6.7 Consensus size: 168
1197857 CTTCATGTTT
* * * * * *
1197867 TGAACCCCTTACTCAGGGGCCATGAATTTCACAA-TTTAGGTCA-AGGAGATT-GTGGATATCAT
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTA-GT-AGAGG-GCTTCATGGACATCAT
* * * * * * * *
1197929 AACCATGTATTCATTTTTTTGCCCACATGTGTAGGAGT--AG-AGAAGATTTTTTAAGATTTAAA
63 AACCATGCATTTAGTTTTTTGCACACATGTATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
1197991 ACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
128 ACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
* ** * *
1198032 TGAACCCCTAACAAAGGGGTCATGAATTTCACAATTTTAGTAGAGGCCCTCATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATAAC
* * * * * ***
1198097 CATGTATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAATTTT
66 CATGCATTTAGTTTTTTGCACACATGTATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
1198162 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
131 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
* * *
1198200 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGACCTCATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATAAC
* * ** * * *
1198265 AATGCATTTAATTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
66 CATGCATTTAGTTTTTTGCACACATGTATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
*
1198330 TTTTTAC----T----AT-TT---CTCACCCTAGAGCC
131 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
* *
1198356 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAAT
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATAAC
** * * * *
1198421 CATGCATTTAGTTTTTAACAAATATATATGGGGGTAGAGAAGAAGA-TTTCTAAGATTTAATACA
66 CATGCATTTAGTTTTTTGCACACATGTATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
* *
1198485 TTTTTACTATTTGGCCATATTGGCCCAACCCTAGAGCC
131 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
* * *
1198523 TGAACCCCTGACCAAGGGGTCATGAACTTCACAA-TTTAGGTTGAGGGCTTCATGGACATCATAA
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTA-GTAGAGGGCTTCATGGACATCATAA
* * * * * ** *
1198587 TCATGCATTTAG-TTGTTGACAAATATATATGATAATAGAGAAGAAGATTTTCTAAGATTTAATA
65 CCATGCATTTAGTTTTTTG-CACACATGTATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
*
1198651 CATTTTTACTATATGGCCATATTGGCCCAACCCTAGAGCC
129 CATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
*
1198691 TGAACCCCTGACCCAGGGGTCATGAATTTCACAA-TTTAGGTTGAGGGCTTCATGGACATCATAA
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTA-GTAGAGGGCTTCATGGACATCATAA
* * * * *
1198755 TCATGCATTTAG-TTTTTG-ACAAATGTATATGGTAGTAGAGAAGAAGGTTTTCTAAGATTAAAT
65 CCATGCATTTAGTTTTTTGCACACATG--TATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
*
1198818 ACATTTTTACTATATGGCCACATTGGCCCCACCCTAGAGCC
128 ACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
* * * * * *
1198859 AGAACCCCGGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGCTTCATGGACAACATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATAAC
* * **
1198924 CATGCATTTAGTTTTTTCCTCACATGCGTGGGAGTAGAGAAGAAGATTTT
66 CATGCATTTAGTTTTTTGCACACATGTATGGGAGTAGAGAAGAAGATTTT
1198974 TGAAAATTTG
Statistics
Matches: 832, Mismatches: 84, Indels: 49
0.86 0.09 0.05
Matches are distributed among these distances:
155 25 0.03
156 118 0.14
159 3 0.00
160 2 0.00
163 2 0.00
164 5 0.01
165 79 0.09
166 14 0.02
167 106 0.13
168 465 0.56
169 8 0.01
170 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (168 bp):
TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATAAC
CATGCATTTAGTTTTTTGCACACATGTATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
Found at i:1198971 original size:336 final size:335
Alignment explanation
Indices: 1197867--1198973 Score: 1345
Period size: 323 Copynumber: 3.3 Consensus size: 335
1197857 CTTCATGTTT
* * * * *
1197867 TGAACCCCTTACTCAGGGGCCATGAATTTCACAATTTAGGTCA-AGGAGATT-GTGGATATCATA
1 TGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGT-AGAGG-GCTTCATGGACATCATA
* * * * ** * * * * *
1197930 ACCATGTATTCATTTTTTTGCCCACATGTGTAGGAGT--AG-AGAAGATTTTTTAAGATTTAAAA
64 ACCATGCATTTAGTTTTTTACAAACATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
* **
1197992 CATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTAACAAAGGGGTCATGA
129 CATTTTTACTATATGGCCATATTGG-CCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGA
* * * * * * *
1198057 ATTTCACAATTTTA-GTAGAGGCCCTCATGGACATCATAACCATGTATTCAGTTTTTTGCTCACA
193 ATTTCACAA-TTTAGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAG-TTTTTG-ACAAA
* * * ***
1198121 TG--TGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAATTTTTTTTTACTATATGGCCATATTG
255 TGTATATGGGAGTAGAGAAGAAGGTTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTG
1198184 GCCCCACCCTAGAGCC
320 GCCCCACCCTAGAGCC
* * * *
1198200 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGACCTCATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
* * * *
1198265 AATGCATTTAATTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
66 CATGCATTTAGTTTTTTACAAACATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
*
1198330 TTTTTAC----T----AT-TT--CTCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATT
131 TTTTTACTATATGGCCATATTGGCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATT
* * *
1198384 TCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATATATA
196 TCACAATTTAGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTGACAAATGTATA
* * * *
1198449 TGGGGGTAGAGAAGAA-GATTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCAA
261 TGGGAGTAGAGAAGAAGGTTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
1198513 CCCTAGAGCC
326 CCCTAGAGCC
* * * * *
1198523 TGAACCCCTGACCAAGGGGTCATGAACTTCACAATTTAGGTTGAGGGCTTCATGGACATCATAAT
1 TGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
* * * ** *
1198588 CATGCATTTAGTTGTTGACAAATATATATGATAATAGAGAAGAAGATTTTCTAAGATTTAATACA
66 CATGCATTTAGTTTTTTACAAACATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
1198653 TTTTTACTATATGGCCATATTGGCCCAACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAAT
131 TTTTTACTATATGGCCATATTGGCCC-ACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAAT
*
1198718 TTCACAATTTAGGTTGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTGACAAATGTAT
195 TTCACAATTTAGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTGACAAATGTAT
* * *
1198783 ATGGTAGTAGAGAAGAAGGTTTTCTAAGATTAAATACATTTTTACTATATGGCCACATTGGCCCC
260 ATGGGAGTAGAGAAGAAGGTTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC
1198848 ACCCTAGAGCC
325 ACCCTAGAGCC
* * * * *
1198859 AGAACCCCGGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGCTTCATGGACAACATAAC
1 TGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
* ** ***
1198924 CATGCATTTAGTTTTTTCCTCACATGCGTGGGAGTAGAGAAGAAGATTTT
66 CATGCATTTAGTTTTTTACAAACATATATGGGAGTAGAGAAGAAGATTTT
1198974 TGAAAATTTG
Statistics
Matches: 658, Mismatches: 95, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
322 4 0.01
323 181 0.28
324 92 0.14
327 3 0.00
328 2 0.00
331 2 0.00
332 5 0.01
333 75 0.11
334 2 0.00
335 116 0.18
336 176 0.27
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (335 bp):
TGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
CATGCATTTAGTTTTTTACAAACATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
TTTTTACTATATGGCCATATTGGCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATT
TCACAATTTAGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTGACAAATGTATA
TGGGAGTAGAGAAGAAGGTTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
CCCTAGAGCC
Found at i:1199153 original size:7 final size:7
Alignment explanation
Indices: 1199143--1199178 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
1199133 TAAAATTGTT
1199143 AACGCAC
1 AACGCAC
1199150 AACGCAC
1 AACGCAC
1199157 AGACGCAC
1 A-ACGCAC
*
1199165 GACGCAC
1 AACGCAC
1199172 AACGCAC
1 AACGCAC
1199179 GACGACGGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.39, C:0.42, G:0.19, T:0.00
Consensus pattern (7 bp):
AACGCAC
Found at i:1199164 original size:15 final size:14
Alignment explanation
Indices: 1199143--1199178 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1199133 TAAAATTGTT
1199143 AACGCACAACGCAC
1 AACGCACAACGCAC
*
1199157 AGACGCACGACGCAC
1 A-ACGCACAACGCAC
1199172 AACGCAC
1 AACGCAC
1199179 GACGACGGAC
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:0.39, C:0.42, G:0.19, T:0.00
Consensus pattern (14 bp):
AACGCACAACGCAC
Found at i:1201690 original size:18 final size:18
Alignment explanation
Indices: 1201667--1201706 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1201657 TCATGTGCTG
*
1201667 TAACAACGCG-AAATGTTA
1 TAACAACG-GAAAATGTAA
1201685 TAACAACGGAAAATGTAA
1 TAACAACGGAAAATGTAA
1201703 TAAC
1 TAAC
1201707 CATCATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (18 bp):
TAACAACGGAAAATGTAA
Found at i:1204287 original size:12 final size:12
Alignment explanation
Indices: 1204270--1204316 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
1204260 ACTAAATGCA
1204270 ATATATTAATAC
1 ATATATTAATAC
*
1204282 ATATATTAATAT
1 ATATATTAATAC
1204294 ATATA-T-ATA-
1 ATATATTAATAC
*
1204303 TTATATTAATAC
1 ATATATTAATAC
1204315 AT
1 AT
1204317 GTATATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.14
10 4 0.14
11 4 0.14
12 17 0.59
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATTAATAC
Found at i:1204303 original size:16 final size:16
Alignment explanation
Indices: 1204270--1204328 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
1204260 ACTAAATGCA
1204270 ATATATTAATACATAT
1 ATATATTAATACATAT
* *
1204286 AT-TAATATATATATAT
1 ATATATTA-ATACATAT
*
1204302 ATTATATTAATACATGT
1 A-TATATTAATACATAT
1204319 ATATATTAAT
1 ATATATTAAT
1204329 TGGTATCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.11
16 19 0.54
17 8 0.23
18 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATATTAATACATAT
Found at i:1204309 original size:21 final size:21
Alignment explanation
Indices: 1204283--1204326 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1204273 TATTAATACA
*
1204283 TATATTAATATATATATATAT
1 TATATTAATACATATATATAT
*
1204304 TATATTAATACATGTATATAT
1 TATATTAATACATATATATAT
1204325 TA
1 TA
1204327 ATTGGTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATTAATACATATATATAT
Found at i:1205832 original size:77 final size:77
Alignment explanation
Indices: 1205705--1205859 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
1205695 TATTGTAGTT
*
1205705 TATTTTGAGATTCTTTGATCATTCCAAATTTTACCCCCCAAAAAATAAAACCCTTTCCACTTGAT
1 TATTTTGAGATTCTTTGATCATTCCAAATTTTACCCCCAAAAAAATAAAACCCTTTCCACTTGAT
1205770 TTGCAGAAAACC
66 TTGCAGAAAACC
1205782 TATTTTGAGATTCTTTGATCATTCCAAATTTTACCCCCAAAAAAATAAAACCCTTTCCACTTGAT
1 TATTTTGAGATTCTTTGATCATTCCAAATTTTACCCCCAAAAAAATAAAACCCTTTCCACTTGAT
1205847 TTGCAGAAAACC
66 TTGCAGAAAACC
1205859 T
1 T
1205860 TTATTTTTAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (77 bp):
TATTTTGAGATTCTTTGATCATTCCAAATTTTACCCCCAAAAAAATAAAACCCTTTCCACTTGAT
TTGCAGAAAACC
Found at i:1218448 original size:11 final size:11
Alignment explanation
Indices: 1218432--1218456 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1218422 GGAAGACCGG
1218432 AATAATGGTAA
1 AATAATGGTAA
1218443 AATAATGGTAA
1 AATAATGGTAA
1218454 AAT
1 AAT
1218457 CGTAACTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (11 bp):
AATAATGGTAA
Found at i:1219028 original size:189 final size:192
Alignment explanation
Indices: 1218708--1219093 Score: 679
Period size: 189 Copynumber: 2.0 Consensus size: 192
1218698 CGAATGACAG
* * * *
1218708 CATCAACACATACTTTGGCTTACATACAGTTCATACATTAATATCATTGAAATTATGTGACAAAA
1 CATCAACACATACCTTGGCTTACATACAGTTCAGACATTAATATAATTGAAATTATGTGAAAAAA
* *
1218773 TGCTAATAATACAGTTACAAAGGTCTAAAAACGAAATCCGAATTTTCCGTGACCTAGAAGAAGTT
66 TGCTAATAATACAGTTACAAAGGTCAAAAAACGAAACCCGAATTTTCCGTGACCTAGAAGAAGTT
1218838 GTAGTTGACATTTCGAGTAGTCTCAC-TT-TATATATATTAATGAACAA-TTCTTTTTGGTT
131 GTAGTTGACATTTCGAGTAGTCTCACTTTATATATATATTAATGAACAATTTCTTTTTGGTT
*
1218897 CATCAACACATACCTTGGCTTACATACTGTTCAGACATTAATATAATTGAAATTATGTGAAAAAA
1 CATCAACACATACCTTGGCTTACATACAGTTCAGACATTAATATAATTGAAATTATGTGAAAAAA
1218962 TGCTAATAATACAGTTACAAAGGTCAAAAAACGAAACCCGAATTTTCCGTGACCTAGAAGAAGTT
66 TGCTAATAATACAGTTACAAAGGTCAAAAAACGAAACCCGAATTTTCCGTGACCTAGAAGAAGTT
*
1219027 GTAGTTGACATTTCGAGTAGTCTCACTTTATATATATATTAATGAACAATTTGTTTTTGGTT
131 GTAGTTGACATTTCGAGTAGTCTCACTTTATATATATATTAATGAACAATTTCTTTTTGGTT
1219089 CATCA
1 CATCA
1219094 GGTCTACCTC
Statistics
Matches: 186, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
189 149 0.80
190 2 0.01
191 19 0.10
192 16 0.09
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (192 bp):
CATCAACACATACCTTGGCTTACATACAGTTCAGACATTAATATAATTGAAATTATGTGAAAAAA
TGCTAATAATACAGTTACAAAGGTCAAAAAACGAAACCCGAATTTTCCGTGACCTAGAAGAAGTT
GTAGTTGACATTTCGAGTAGTCTCACTTTATATATATATTAATGAACAATTTCTTTTTGGTT
Found at i:1220048 original size:2 final size:2
Alignment explanation
Indices: 1220041--1220098 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1220031 CAAAGATGTT
1220041 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1220083 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
1220099 AATTTATTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1223331 original size:23 final size:22
Alignment explanation
Indices: 1223295--1223350 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
1223285 TTATTTTTGT
1223295 TTGATGTTTTAATTGGCCCAAG
1 TTGATGTTTTAATTGGCCCAAG
**
1223317 TTGATGTTTTTAATTGGTTCAAG
1 TTGATG-TTTTAATTGGCCCAAG
1223340 TTG-T-TTTTAAT
1 TTGATGTTTTAAT
1223351 AATTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 7 0.23
22 7 0.23
23 17 0.55
ACGTcount: A:0.21, C:0.07, G:0.20, T:0.52
Consensus pattern (22 bp):
TTGATGTTTTAATTGGCCCAAG
Found at i:1223881 original size:12 final size:12
Alignment explanation
Indices: 1223864--1223895 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1223854 ACTTTTATAA
1223864 ACACAATAATGT
1 ACACAATAATGT
1223876 ACACAATAATGT
1 ACACAATAATGT
*
1223888 ACAGAATA
1 ACACAATA
1223896 CATAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (12 bp):
ACACAATAATGT
Found at i:1226535 original size:21 final size:21
Alignment explanation
Indices: 1226511--1226552 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1226501 GGGTGGACTG
1226511 AGAAAAAATGAAAATAGGGCA
1 AGAAAAAATGAAAATAGGGCA
1226532 AGAAAAAATGAAAATAGGGCA
1 AGAAAAAATGAAAATAGGGCA
1226553 TGGAGTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.24, T:0.10
Consensus pattern (21 bp):
AGAAAAAATGAAAATAGGGCA
Found at i:1227377 original size:14 final size:14
Alignment explanation
Indices: 1227358--1227387 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1227348 ATTTAAATTG
*
1227358 TTTGTTTTTGTTGT
1 TTTGTTCTTGTTGT
1227372 TTTGTTCTTGTTGT
1 TTTGTTCTTGTTGT
1227386 TT
1 TT
1227388 CTGCTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.20, T:0.77
Consensus pattern (14 bp):
TTTGTTCTTGTTGT
Found at i:1227596 original size:31 final size:32
Alignment explanation
Indices: 1227543--1227602 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
1227533 AGGGTTGAAA
**
1227543 ATTGACCCGGGGGTCATTTTTCAACGTTGGAT
1 ATTGACCCGGGGGTCAACTTTCAACGTTGGAT
1227575 ATTGACCC-GGGGTCAACTTTCAACGTTG
1 ATTGACCCGGGGGTCAACTTTCAACGTTG
1227603 AAAATGGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (32 bp):
ATTGACCCGGGGGTCAACTTTCAACGTTGGAT
Found at i:1230787 original size:2 final size:2
Alignment explanation
Indices: 1230780--1230847 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1230770 NNNNNNNNNN
1230780 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1230822 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1230848 GGGAAGTGGG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1234571 original size:21 final size:21
Alignment explanation
Indices: 1234547--1234590 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1234537 GTGTTAAATA
1234547 GTTCGTATAACGTG-GGTGATC
1 GTTCGTATAACGTGCGG-GATC
*
1234568 GTTCGTGTAACGTGCGGGATC
1 GTTCGTATAACGTGCGGGATC
1234589 GT
1 GT
1234591 GCGTGTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.16, C:0.16, G:0.36, T:0.32
Consensus pattern (21 bp):
GTTCGTATAACGTGCGGGATC
Done.