Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 3 of 66
Found at i:967621 original size:23 final size:23
Alignment explanation
Indices: 967595--967640 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
967585 GATAAGGAAT
* *
967595 AAAATAGAAA-AACATGATAATAA
1 AAAATA-AAATAAAATGAAAATAA
967618 AAAATAAAATAAAATGAAAATAA
1 AAAATAAAATAAAATGAAAATAA
967641 CAATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (23 bp):
AAAATAAAATAAAATGAAAATAA
Found at i:968642 original size:14 final size:15
Alignment explanation
Indices: 968614--968643 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
968604 TTTTGTTTAG
968614 TGCATTTGTTTATTT
1 TGCATTTGTTTATTT
968629 TGCATTTG-TTATTT
1 TGCATTTGTTTATTT
968643 T
1 T
968644 ATTACTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
TGCATTTGTTTATTT
Found at i:977979 original size:38 final size:37
Alignment explanation
Indices: 977925--978211 Score: 355
Period size: 38 Copynumber: 7.6 Consensus size: 37
977915 TAATTTCAAG
* **
977925 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGCCAC
1 ATTTTTAAAGTTATGTTGCCTCAGCTTTGAGGAG-TTC
* *
977963 ATTTTTAAAGTTATGTTGCGTCAGCTTTGAAGAGTTTC
1 ATTTTTAAAGTTATGTTGCCTCAGCTTTGAGGAG-TTC
* *
978001 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCAC
1 ATTTTTAAAGTTATGTTGCCTCAGCTTTGAGGAGT-TC
*
978039 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTTC
1 ATTTTTAAAGTTATGTTGCCTCAGCTTTGAGGAGTTC
* *
978076 ATTTTTAAAGTTATGTTCCCTCAGCTTTGAAGAGTTC
1 ATTTTTAAAGTTATGTTGCCTCAGCTTTGAGGAGTTC
* *
978113 ATTTTTAAAAGTCT-CGTTGCCTTAGCTTTGAGGAGTTC
1 ATTTTT-AAAGT-TATGTTGCCTCAGCTTTGAGGAGTTC
978151 ATTTTTAAAGAAGTT-TCGTTGCCTCAGCTTTGAGGAGTTC
1 ATTTTT--A-AAGTTAT-GTTGCCTCAGCTTTGAGGAGTTC
978191 ATTTTTAAAGTT-TCGTTGCCT
1 ATTTTTAAAGTTAT-GTTGCCT
978212 NNNNNNNNNN
Statistics
Matches: 223, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
37 56 0.25
38 131 0.59
39 4 0.02
40 32 0.14
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (37 bp):
ATTTTTAAAGTTATGTTGCCTCAGCTTTGAGGAGTTC
Found at i:978124 original size:75 final size:74
Alignment explanation
Indices: 977925--978201 Score: 360
Period size: 75 Copynumber: 3.6 Consensus size: 74
977915 TAATTTCAAG
* * *
977925 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGCCACATTTTTAAAGTTATGTTGCGTCAGCTT
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAG-TACATTTTTAAAGTCATGTTGCCTCAGCTT
*
977990 TGAAGAGTTTC
65 TGAGGAG-TTC
978001 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCACATTTTTAAAGTCATGTTGCCTCAGCTT
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGT-ACATTTTTAAAGTCATGTTGCCTCAGCTT
978066 TGAGGAGTTC
65 TGAGGAGTTC
* * * * *
978076 ATTTTTAAAGTTATGTTCCCTCAGCTTTGAAGAGTTCATTTTTAAAAGTC-TCGTTGCCTTAGCT
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTACATTTTT-AAAGTCAT-GTTGCCTCAGCT
978140 TTGAGGAGTTC
64 TTGAGGAGTTC
* *
978151 ATTTTTAAAGAAGT-TTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAGT
1 ATTTTT--A-AAGTCAT-GTTGCCTCAGCTTTGAGGAGTACATTTTTAAAGT
978202 TTCGTTGCCT
Statistics
Matches: 182, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
74 8 0.04
75 69 0.38
76 67 0.37
77 7 0.04
78 31 0.17
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (74 bp):
ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTACATTTTTAAAGTCATGTTGCCTCAGCTTT
GAGGAGTTC
Found at i:982012 original size:16 final size:16
Alignment explanation
Indices: 981977--982041 Score: 76
Period size: 16 Copynumber: 3.8 Consensus size: 16
981967 ATTGCTTACG
981977 AAAAAATATAATAATAAT
1 AAAAAATATAA-AAT-AT
981995 AAAAAATATAAAATAT
1 AAAAAATATAAAATAT
* *
982011 AAAAAAAATAAAACAT
1 AAAAAATATAAAATAT
982027 AAAAGAATCATAAAA
1 AAAA-AAT-ATAAAA
982042 AAAATAAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
16 20 0.48
17 5 0.12
18 17 0.40
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAAAATATAAAATAT
Found at i:982148 original size:18 final size:19
Alignment explanation
Indices: 982125--982160 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
982115 ATCTAGAATT
*
982125 AAAATG-TAAGGTATAAAG
1 AAAATGATAAGGAATAAAG
982143 AAAATGATAAGGAATAAA
1 AAAATGATAAGGAATAAA
982161 AATAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (19 bp):
AAAATGATAAGGAATAAAG
Found at i:983576 original size:35 final size:35
Alignment explanation
Indices: 983514--983592 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
983504 ATTTTCTTCC
* *
983514 ACAAAAATATTAAAATTTAAATTTAAATAAGCAAAA
1 ACAAAAATATTAAAACTTAAAATTAAATAA-CAAAA
* *
983550 ACAAAAATCTT-AAACTTAAAATTAAATAACTAAA
1 ACAAAAATATTAAAACTTAAAATTAAATAACAAAA
983584 A-AAAAATAT
1 ACAAAAATAT
983593 ATGGGGAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
33 7 0.18
34 5 0.13
35 16 0.42
36 10 0.26
ACGTcount: A:0.65, C:0.08, G:0.01, T:0.27
Consensus pattern (35 bp):
ACAAAAATATTAAAACTTAAAATTAAATAACAAAA
Found at i:995457 original size:25 final size:26
Alignment explanation
Indices: 995429--995481 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
995419 GTTCCAACGG
* * *
995429 ATTTTCAACG-GAATTTTCGTTGAAA
1 ATTTTCAACGAAAAATTCCGTTGAAA
995454 ATTTTCAACGAAAAATTCCGTTGAAA
1 ATTTTCAACGAAAAATTCCGTTGAAA
995480 AT
1 AT
995482 CCGTTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (26 bp):
ATTTTCAACGAAAAATTCCGTTGAAA
Found at i:1008264 original size:14 final size:14
Alignment explanation
Indices: 1008245--1008271 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1008235 TGAAGTCAAC
1008245 GCCTTCCATAGCAT
1 GCCTTCCATAGCAT
1008259 GCCTTCCATAGCA
1 GCCTTCCATAGCA
1008272 CATTCAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (14 bp):
GCCTTCCATAGCAT
Found at i:1019090 original size:19 final size:19
Alignment explanation
Indices: 1019066--1019102 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1019056 GTACCCAATT
* *
1019066 TTCTCTTCCAAAACACAAC
1 TTCTCTTCAAAAAAACAAC
1019085 TTCTCTTCAAAAAAACAA
1 TTCTCTTCAAAAAAACAA
1019103 AAACAAAAAT
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:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
TTCTCTTCAAAAAAACAAC
Found at i:1023884 original size:24 final size:23
Alignment explanation
Indices: 1023840--1023885 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
1023830 AAATGAGAAA
*
1023840 AATAAATAAATATAAATAAAAGT
1 AATAAATAAATATAAAAAAAAGT
*
1023863 AATAATATAAATTAGAAAAAAAA
1 AATAA-ATAAA-TATAAAAAAAA
1023886 ATTAAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 5 0.26
25 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (23 bp):
AATAAATAAATATAAAAAAAAGT
Found at i:1027238 original size:16 final size:16
Alignment explanation
Indices: 1027217--1027250 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1027207 GAAGAATTAT
1027217 TTTTAATATTATTTAA
1 TTTTAATATTATTTAA
*
1027233 TTTTAATTTTATTTAA
1 TTTTAATATTATTTAA
1027249 TT
1 TT
1027251 AGTAGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATATTATTTAA
Found at i:1029415 original size:2 final size:2
Alignment explanation
Indices: 1029408--1029434 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1029398 TCATTATGCC
1029408 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
1029435 CAAATTTACA
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:1036440 original size:28 final size:28
Alignment explanation
Indices: 1036390--1036447 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
1036380 CTTATGGCTG
* * * *
1036390 CCCTTGACAAAGATTTGTTTTGTAAGAC
1 CCCTTGACAAAAATATCTCTTGTAAGAC
1036418 CCCTTGACAAAAATATCTCTTGTAAGAC
1 CCCTTGACAAAAATATCTCTTGTAAGAC
1036446 CC
1 CC
1036448 TTTTAAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (28 bp):
CCCTTGACAAAAATATCTCTTGTAAGAC
Found at i:1044915 original size:55 final size:55
Alignment explanation
Indices: 1044809--1044916 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 55
1044799 TTCACATACT
* * * * *
1044809 TTTATTGTGATTTGACATTTTTATAATTAATATTTTGTGATTAGGTATACTTTCA
1 TTTATTGTGATTTGACATTTTTACAATTAATACTTTATAATTAAGTATACTTTCA
* * *
1044864 TTTATTGTGATTTGATATTTTTACCATTAATACTTTATAATTAAGTTTACTTT
1 TTTATTGTGATTTGACATTTTTACAATTAATACTTTATAATTAAGTATACTTT
1044917 TATATACACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.28, C:0.06, G:0.10, T:0.56
Consensus pattern (55 bp):
TTTATTGTGATTTGACATTTTTACAATTAATACTTTATAATTAAGTATACTTTCA
Found at i:1045243 original size:2 final size:2
Alignment explanation
Indices: 1045236--1045268 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1045226 AATTTTTGTG
*
1045236 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1045269 CATAACTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1045716 original size:33 final size:33
Alignment explanation
Indices: 1045678--1045747 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1045668 TGTAACATAT
*
1045678 TAATATATCATAATTGATAATAATGTGATATGC
1 TAATATATCATAATTGATAATAATGTGATATAC
* *
1045711 TAATATATCATAATTGATGATGATGTGATATAC
1 TAATATATCATAATTGATAATAATGTGATATAC
1045744 TAAT
1 TAAT
1045748 TTAGTTTACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (33 bp):
TAATATATCATAATTGATAATAATGTGATATAC
Found at i:1048786 original size:17 final size:17
Alignment explanation
Indices: 1048740--1048786 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1048730 CCAATTATTT
* *
1048740 TTATTTTAAAATATTTA
1 TTATTTAAAAATAATTA
* *
1048757 -TATTTATATATAATTA
1 TTATTTAAAAATAATTA
1048773 TTATTTAAAAATAA
1 TTATTTAAAAATAA
1048787 AAAATAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTTAAAAATAATTA
Found at i:1053173 original size:12 final size:11
Alignment explanation
Indices: 1053152--1053213 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 11
1053142 ACACCCATTT
1053152 AAAAAA-ATAA
1 AAAAAATATAA
1053162 AAAAAATGAT-A
1 AAAAAAT-ATAA
*
1053173 AAAAAATA-AT
1 AAAAAATATAA
1053183 AAAAAATATAA
1 AAAAAATATAA
1053194 AATAAAATAATAA
1 AA-AAAAT-ATAA
1053207 GAAAAAA
1 -AAAAAA
1053214 GAGGAATGGC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
10 15 0.35
11 11 0.26
12 7 0.16
13 8 0.19
14 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (11 bp):
AAAAAATATAA
Found at i:1053176 original size:20 final size:20
Alignment explanation
Indices: 1053151--1053211 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 20
1053141 GACACCCATT
1053151 TAAAAAAATAA-AAAAAATGA
1 TAAAAAAATAATAAAAAAT-A
1053171 TAAAAAAATAATAAAAAATA
1 TAAAAAAATAATAAAAAATA
1053191 TAAAATAAAATAATAAGAAAA
1 T-AAA-AAAATAATAA-AAAA
1053212 AAGAGGAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.35
21 10 0.27
22 10 0.27
23 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (20 bp):
TAAAAAAATAATAAAAAATA
Found at i:1054492 original size:31 final size:31
Alignment explanation
Indices: 1054454--1054514 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1054444 ATTTTACTAC
*
1054454 ATAAAAAACTTAGTCAAA-AATAAAAAAATAT
1 ATAAAAAACTTA-TAAAATAATAAAAAAATAT
* *
1054485 ATAAAAAATTTATAAAATAATAAATAAATA
1 ATAAAAAACTTATAAAATAATAAAAAAATA
1054515 AATTTTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (31 bp):
ATAAAAAACTTATAAAATAATAAAAAAATAT
Found at i:1054506 original size:23 final size:24
Alignment explanation
Indices: 1054473--1054519 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1054463 TTAGTCAAAA
*
1054473 ATAAAAAAATATATAAA-AAATTT
1 ATAAAAAAATAAATAAATAAATTT
*
1054496 ATAAAATAATAAATAAATAAATTT
1 ATAAAAAAATAAATAAATAAATTT
1054520 TTGTTCACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAAAAAAATAAATAAATAAATTT
Found at i:1054655 original size:12 final size:12
Alignment explanation
Indices: 1054638--1054679 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
1054628 GAAACATAGA
1054638 ATAAAAAAAAAG
1 ATAAAAAAAAAG
1054650 ATAAAAAAATAA-
1 ATAAAAAAA-AAG
1054662 ATAACAAAAAAAG
1 ATAA-AAAAAAAG
1054675 ATAAA
1 ATAAA
1054680 TGAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (12 bp):
ATAAAAAAAAAG
Found at i:1054700 original size:15 final size:15
Alignment explanation
Indices: 1054650--1054716 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
1054640 AAAAAAAAAG
*
1054650 ATAAAAAAATAAATA
1 ATAAAAAAATATATA
* *
1054665 ACAAAAAAAGATA-A
1 ATAAAAAAATATATA
*
1054679 ATGAAAAATATATATA
1 AT-AAAAAAATATATA
*
1054695 AT-AAAAAATAATAAA
1 ATAAAAAAAT-ATATA
1054710 ATAAAAA
1 ATAAAAA
1054717 TAAGCTTCAC
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
14 8 0.20
15 25 0.62
16 7 0.17
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (15 bp):
ATAAAAAAATATATA
Found at i:1054701 original size:30 final size:26
Alignment explanation
Indices: 1054637--1054719 Score: 82
Period size: 30 Copynumber: 3.0 Consensus size: 26
1054627 AGAAACATAG
1054637 AATAAAAAAAAAGAT-AA-AAAAATA
1 AATAAAAAAAAAGATAAATAAAAATA
1054661 AATAACAAAAAAAGATAAATGAAAAATA
1 AATAA-AAAAAAAGATAAAT-AAAAATA
1054689 TATATAATAAAAAATA-ATAAAATAAAAATA
1 -A-ATAA-AAAAAA-AGAT-AAATAAAAATA
1054719 A
1 A
1054720 GCTTCACAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
24 5 0.10
25 10 0.20
26 2 0.04
28 7 0.14
29 2 0.04
30 19 0.38
31 5 0.10
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (26 bp):
AATAAAAAAAAAGATAAATAAAAATA
Found at i:1067273 original size:25 final size:25
Alignment explanation
Indices: 1067245--1067305 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1067235 TTTTATATCT
*
1067245 AATTTATATTTATTTA-TATTACAAA
1 AATTTATATTTATCTATTATTA-AAA
* *
1067270 AATTTACAATTATCTATTATTAAAA
1 AATTTATATTTATCTATTATTAAAA
1067295 ATATTTATATT
1 A-ATTTATATT
1067306 AATAATAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTTATATTTATCTATTATTAAAA
Found at i:1067307 original size:15 final size:16
Alignment explanation
Indices: 1067284--1067330 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
1067274 TACAATTATC
*
1067284 TATTATTAAAAATATT
1 TATTATTAAAAATAAT
*
1067300 TA-TATTAATAATAAT
1 TATTATTAAAAATAAT
1067315 TATTATTTAAAAATAA
1 TATTA-TTAAAAATAA
1067331 AGAATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 13 0.50
16 4 0.15
17 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTATTAAAAATAAT
Found at i:1075465 original size:32 final size:32
Alignment explanation
Indices: 1075424--1075485 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1075414 ATATATTTGG
*
1075424 TGAAGAAATAATGAAAAAAATTAACATAAATT
1 TGAAAAAATAATGAAAAAAATTAACATAAATT
* *
1075456 TGAAAAAATAATGAAGAAAGTTAACATAAA
1 TGAAAAAATAATGAAAAAAATTAACATAAA
1075486 ATCAAAAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.23
Consensus pattern (32 bp):
TGAAAAAATAATGAAAAAAATTAACATAAATT
Found at i:1090818 original size:37 final size:34
Alignment explanation
Indices: 1090777--1090851 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 34
1090767 AGCTCTTTTC
*
1090777 AACATATATATTTGGTGAAGAAATAATGAAGAAAATT
1 AACATATATA-TT--TGAAAAAATAATGAAGAAAATT
*
1090814 AAC--ATATATTTGAAAAAATAATGAAGAAAGTT
1 AACATATATATTTGAAAAAATAATGAAGAAAATT
1090846 AACATA
1 AACATA
1090852 AAGTCAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
32 23 0.68
34 3 0.09
35 5 0.15
37 3 0.09
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (34 bp):
AACATATATATTTGAAAAAATAATGAAGAAAATT
Found at i:1097423 original size:21 final size:21
Alignment explanation
Indices: 1097390--1097440 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1097380 TTCATTTTTC
*
1097390 TTATAATTT-TATATATGTATCA
1 TTAT-ATTTATATATATATAT-A
1097412 -TATATTTATATATATATATA
1 TTATATTTATATATATATATA
1097432 TTATATTTA
1 TTATATTTA
1097441 CAAGTATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTATATTTATATATATATATA
Found at i:1097916 original size:8 final size:7
Alignment explanation
Indices: 1097899--1097928 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1097889 TCCTTTCTCC
1097899 TTTTTCT
1 TTTTTCT
1097906 TTTTTCT
1 TTTTTCT
1097913 TTTTTCT
1 TTTTTCT
1097920 TTCTTTCT
1 TT-TTTCT
1097928 T
1 T
1097929 CCCTTTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.73
8 6 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:1097924 original size:4 final size:4
Alignment explanation
Indices: 1097901--1097976 Score: 63
Period size: 4 Copynumber: 19.2 Consensus size: 4
1097891 CTTTCTCCTT
*
1097901 TTTC TTT- TTTC TTT- TTTC TTTC TTTC TTCCC TTTCC TTTC --TC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC TTT-C TTTC TTTC TTTC
*
1097947 -TTC TTTC TTTCAC TTTC TTTT TTTC TTTC T
1 TTTC TTTC TTT--C TTTC TTTC TTTC TTTC T
1097977 CTCCTAGCCG
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
2 2 0.03
3 9 0.15
4 37 0.63
5 7 0.12
6 4 0.07
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:1097924 original size:18 final size:18
Alignment explanation
Indices: 1097901--1097974 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
1097891 CTTTCTCCTT
1097901 TTTCTTTTTTCTTTTTTC
1 TTTCTTTTTTCTTTTTTC
* ** *
1097919 TTTCTTTCTTCCCTTTCC
1 TTTCTTTTTTCTTTTTTC
1097937 TTTCTCTTTCTTCTTTCTTTCAC
1 TTTCT-TTT-TTCTTT-TTT--C
1097960 TTTCTTTTTTTCTTT
1 TTTC-TTTTTTCTTT
1097975 CTCTCCTAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
18 19 0.45
19 2 0.05
20 4 0.10
21 2 0.05
22 6 0.14
23 8 0.19
24 1 0.02
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCTTTTTTCTTTTTTC
Found at i:1097927 original size:31 final size:31
Alignment explanation
Indices: 1097891--1097976 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
1097881 CCCCCACCTC
*
1097891 CTTTCTCCTTTTTCTTTTTTCTTTTTTCTTT
1 CTTTCTCCTTTTTCTTTTTTCTTTCTTCTTT
* * *
1097922 CTTTCTTCC-CTTTCCTTTCTCTTTCTTCTTT
1 CTTTC-TCCTTTTTCTTTTTTCTTTCTTCTTT
* *
1097953 CTTTC-ACTTTCT-TTTTTTCTTTCT
1 CTTTCTCCTTTTTCTTTTTTCTTTCT
1097977 CTCCTAGCCG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
29 11 0.25
30 2 0.05
31 28 0.64
32 3 0.07
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (31 bp):
CTTTCTCCTTTTTCTTTTTTCTTTCTTCTTT
Found at i:1098021 original size:17 final size:18
Alignment explanation
Indices: 1097995--1098044 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 18
1097985 CGCTCCCCCC
*
1097995 TTCTTCTCTCTTTCTT-T
1 TTCTTTTCTCTTTCTTAT
1098012 TTCTTTTCTCTTTCTTAT
1 TTCTTTTCTCTTTCTTAT
1098030 TT-TTTTCTCTTTCTT
1 TTCTTTTCTCTTTCTT
1098045 CTCATTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 28 0.90
18 3 0.10
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCTTTTCTCTTTCTTAT
Found at i:1098046 original size:20 final size:22
Alignment explanation
Indices: 1098009--1098056 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
1097999 TCTCTCTTTC
* *
1098009 TTTTTCTTTTCTCTTTCTTATT
1 TTTTTCTCTTCTCTTTCTCATT
1098031 TTTTTCTCTT-TC-TTCTCATT
1 TTTTTCTCTTCTCTTTCTCATT
*
1098051 TCTTTC
1 TTTTTC
1098057 CCCCGCTGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 12 0.52
21 2 0.09
22 9 0.39
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTCTCTTCTCTTTCTCATT
Found at i:1098099 original size:14 final size:14
Alignment explanation
Indices: 1098072--1098119 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
1098062 CTGGCCTCTC
1098072 CTTTCTTT-TTCCT
1 CTTTCTTTCTTCCT
1098085 CTTTCTTTCTTCCT
1 CTTTCTTTCTTCCT
*
1098099 CCTTCTCTTTC-TCTT
1 -CTT-TCTTTCTTCCT
1098114 CTTTCT
1 CTTTCT
1098120 CCTTGCCGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 11 0.35
14 8 0.26
15 6 0.19
16 6 0.19
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
CTTTCTTTCTTCCT
Found at i:1098121 original size:21 final size:20
Alignment explanation
Indices: 1098083--1098123 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1098073 TTTCTTTTTC
1098083 CTCTTTCTTTCTTCCTCCTT
1 CTCTTTCTTTCTTCCTCCTT
*
1098103 CTCTTTCTCTTCTTTCTCCTT
1 CTCTTTCT-TTCTTCCTCCTT
1098124 GCCGACGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (20 bp):
CTCTTTCTTTCTTCCTCCTT
Found at i:1098511 original size:8 final size:8
Alignment explanation
Indices: 1098498--1098588 Score: 67
Period size: 8 Copynumber: 10.8 Consensus size: 8
1098488 TCTCTTCTTC
*
1098498 TTTTTTCT
1 TTTTTTAT
*
1098506 TTTTTTAA
1 TTTTTTAT
1098514 TTTTTTAT
1 TTTTTTAT
* *
1098522 TATTTTCT
1 TTTTTTAT
*
1098530 TTATTTAT
1 TTTTTTAT
1098538 TTTTTTAT
1 TTTTTTAT
1098546 ATTTTATT-T
1 -TTTT-TTAT
*
1098555 TATTTTAT
1 TTTTTTAT
1098563 TTTAATTTAT
1 TTT--TTTAT
1098573 ATTTTTTAT
1 -TTTTTTAT
1098582 TTATTTT
1 TT-TTTT
1098589 TTAGGTGTCT
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
7 2 0.03
8 39 0.60
9 14 0.22
10 7 0.11
11 3 0.05
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1098534 original size:12 final size:11
Alignment explanation
Indices: 1098505--1098590 Score: 61
Period size: 12 Copynumber: 7.4 Consensus size: 11
1098495 TTCTTTTTTC
*
1098505 TTTTT-TTAAT
1 TTTTTATTATT
1098515 TTTTTATTATT
1 TTTTTATTATT
1098526 TTCTTTATTTATT
1 TT-TTTA-TTATT
1098539 TTTTTA-TATTT
1 TTTTTATTA-TT
1098550 TATTTTATT-TT
1 T-TTTTATTATT
*
1098561 ATTTTAATTTATAT
1 -TTTTTA-TTAT-T
1098575 TTTTTATTTATT
1 TTTTTA-TTATT
1098587 TTTT
1 TTTT
1098591 AGGTGTCTAC
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
10 7 0.11
11 15 0.24
12 21 0.33
13 19 0.30
14 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:1098579 original size:29 final size:24
Alignment explanation
Indices: 1098500--1098590 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 24
1098490 TCTTCTTCTT
* *
1098500 TTTTCTTT-TTTTAATTTTTTATTA
1 TTTTATTTATTTTATTTTTTTA-TA
*
1098524 TTTTCTTTA-TTTATTTTTTTATA
1 TTTTATTTATTTTATTTTTTTATA
1098547 TTTTATTTTATTTTATTTTAATTTATA
1 TTTTA-TTTATTTTATTTT--TTTATA
1098574 -TTT-TTTA-TTTATTTTTT
1 TTTTATTTATTTTATTTTTT
1098591 AGGTGTCTAC
Statistics
Matches: 60, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.03
23 14 0.23
24 27 0.45
25 8 0.13
26 3 0.05
27 6 0.10
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTATTTATTTTATTTTTTTATA
Found at i:1098588 original size:10 final size:9
Alignment explanation
Indices: 1098498--1098589 Score: 69
Period size: 10 Copynumber: 9.7 Consensus size: 9
1098488 TCTCTTCTTC
*
1098498 TTTTTTCTT
1 TTTTTTATT
*
1098507 TTTTTAATT
1 TTTTTTATT
1098516 TTTTATTATT
1 TTTT-TTATT
*
1098526 TTCTTTATT
1 TTTTTTATT
1098535 TATTTTT-TT
1 T-TTTTTATT
*
1098544 ATATTTTATT
1 -TTTTTTATT
1098554 TTATTTTATT
1 TT-TTTTATT
* *
1098564 TTAATTTATA
1 TT-TTTTATT
1098574 TTTTTTATT
1 TTTTTTATT
1098583 TATTTTT
1 T-TTTTT
1098590 TAGGTGTCTA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
9 30 0.45
10 36 0.55
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTATT
Found at i:1106290 original size:24 final size:26
Alignment explanation
Indices: 1106263--1106312 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1106253 GTTAAGTTTG
1106263 AAATATTT-ATTTGATTTAAA-ATAA
1 AAATATTTAATTTGATTTAAATATAA
* *
1106287 AAATTTTTAATTTTATTTAAATATAA
1 AAATATTTAATTTGATTTAAATATAA
1106313 TAAAAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 11 0.50
26 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AAATATTTAATTTGATTTAAATATAA
Found at i:1106525 original size:3 final size:3
Alignment explanation
Indices: 1106517--1106554 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1106507 ACTCTTATCT
1106517 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1106555 TAAATACTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1117027 original size:15 final size:15
Alignment explanation
Indices: 1116988--1117031 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1116978 TAGATTTTTT
1116988 AAATATTAATAATCTA
1 AAATATTAATAAT-TA
1117004 AAA-A-T--TAATTA
1 AAATATTAATAATTA
1117015 AAATATTAATAATTA
1 AAATATTAATAATTA
1117030 AA
1 AA
1117032 TTNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
11 5 0.21
12 5 0.21
13 1 0.04
14 1 0.04
15 9 0.38
16 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATTAATAATTA
Found at i:1117557 original size:33 final size:31
Alignment explanation
Indices: 1117520--1117581 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
1117510 ATTTATCATT
1117520 TATTTTATTAATAATTGATAATATAAATATTAA
1 TATTTTATTAATAATT--TAATATAAATATTAA
* *
1117553 TATTTTATTTATAATTTAATATTAATATT
1 TATTTTATTAATAATTTAATATAAATATT
1117582 TTATTAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 12 0.44
33 15 0.56
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
TATTTTATTAATAATTTAATATAAATATTAA
Found at i:1118516 original size:38 final size:39
Alignment explanation
Indices: 1118435--1118517 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 39
1118425 CAGTTGTTTT
* * * *
1118435 CTTTCATAAAATAACTATTCAATAGTTGTATCTAATAAT
1 CTTTCATAAAATAACTATTCAAAAATTATATCTAATAAC
* *
1118474 CTTTCATGATATAACTATT-AAAAATTATATCTAATAAC
1 CTTTCATAAAATAACTATTCAAAAATTATATCTAATAAC
1118512 CTTTCA
1 CTTTCA
1118518 ATTAAAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
38 21 0.55
39 17 0.45
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (39 bp):
CTTTCATAAAATAACTATTCAAAAATTATATCTAATAAC
Found at i:1121038 original size:21 final size:21
Alignment explanation
Indices: 1121012--1121057 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1121002 TGTGACTAGC
*
1121012 TTTTAGGCATTACATGATTGG
1 TTTTAGGCATTACATGACTGG
*
1121033 TTTTAGGCATTACGTGACTGG
1 TTTTAGGCATTACATGACTGG
1121054 TTTT
1 TTTT
1121058 TAGACATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.46
Consensus pattern (21 bp):
TTTTAGGCATTACATGACTGG
Found at i:1121065 original size:22 final size:22
Alignment explanation
Indices: 1121003--1121081 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
1120993 TAATCACTGT
* *
1121003 GTGACTAGCTTTTAGGCATTAC
1 GTGACTGGTTTTTAGGCATTAC
* *
1121025 ATGATTGG-TTTTAGGCATTAC
1 GTGACTGGTTTTTAGGCATTAC
*
1121046 GTGACTGGTTTTTAGACATTGA-
1 GTGACTGGTTTTTAGGCATT-AC
*
1121068 GTGACTGATTTTTA
1 GTGACTGGTTTTTA
1121082 AGTAATGCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 19 0.40
22 28 0.58
23 1 0.02
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (22 bp):
GTGACTGGTTTTTAGGCATTAC
Found at i:1121118 original size:23 final size:23
Alignment explanation
Indices: 1121092--1121174 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
1121082 AGTAATGCCT
* *
1121092 AAGTCACACAATATCTTACTAAC
1 AAGTCACGCAATACCTTACTAAC
* *
1121115 AAGTCATGCAATCCCTTACTAAC
1 AAGTCACGCAATACCTTACTAAC
**
1121138 AAGTCACGCAATGTC-TA-TCAAC
1 AAGTCACGCAATACCTTACT-AAC
*
1121160 TAGTCACGCAATACC
1 AAGTCACGCAATACC
1121175 ATATCAACCA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 1 0.02
22 17 0.35
23 31 0.63
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (23 bp):
AAGTCACGCAATACCTTACTAAC
Found at i:1121189 original size:23 final size:23
Alignment explanation
Indices: 1121153--1121196 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1121143 ACGCAATGTC
* * *
1121153 TATCAACTAGTCACGCAATACCA
1 TATCAACCAATCACACAATACCA
1121176 TATCAACCAATCACACAATAC
1 TATCAACCAATCACACAATAC
1121197 ATAAAAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.32, G:0.05, T:0.20
Consensus pattern (23 bp):
TATCAACCAATCACACAATACCA
Found at i:1121229 original size:21 final size:21
Alignment explanation
Indices: 1121205--1121246 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1121195 ACATAAAAAC
*
1121205 TAGTCAAGCAATGCCCAAAGT
1 TAGTCAAGCAATACCCAAAGT
* *
1121226 TAGTCACGCAATATCCAAAGT
1 TAGTCAAGCAATACCCAAAGT
1121247 CAATTACGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
TAGTCAAGCAATACCCAAAGT
Found at i:1121453 original size:10 final size:10
Alignment explanation
Indices: 1121428--1121462 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1121418 TTCATATATA
1121428 AAAAATCACTT
1 AAAAAT-ACTT
*
1121439 CAAAATACTT
1 AAAAATACTT
1121449 AAAAATACTT
1 AAAAATACTT
1121459 AAAA
1 AAAA
1121463 TGCTCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATACTT
Found at i:1121471 original size:19 final size:21
Alignment explanation
Indices: 1121428--1121472 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1121418 TTCATATATA
*
1121428 AAAAATCACTTCAAAATACTT
1 AAAAATCACTTCAAAATACTC
*
1121449 AAAAAT-ACTT-AAAATGCTC
1 AAAAATCACTTCAAAATACTC
1121468 AAAAA
1 AAAAA
1121473 AAATTTTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 4 0.18
21 6 0.27
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAATCACTTCAAAATACTC
Found at i:1121472 original size:20 final size:21
Alignment explanation
Indices: 1121426--1121473 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
1121416 TCTTCATATA
1121426 TAAAAAATCACTTCAAAATAC
1 TAAAAAATCACTTCAAAATAC
* *
1121447 TTAAAAAT-ACTT-AAAATGC
1 TAAAAAATCACTTCAAAATAC
1121466 TCAAAAAA
1 T-AAAAAA
1121474 AATTTTCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.30
20 9 0.39
21 7 0.30
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (21 bp):
TAAAAAATCACTTCAAAATAC
Found at i:1127628 original size:24 final size:21
Alignment explanation
Indices: 1127603--1127643 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1127593 AAATAATTAA
*
1127603 AAAAATAATGATATTTGTCATG
1 AAAAA-AATTATATTTGTCATG
1127625 AAAAAAATTATATTTGTCA
1 AAAAAAATTATATTTGTCA
1127644 AACAGCTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (21 bp):
AAAAAAATTATATTTGTCATG
Found at i:1136437 original size:51 final size:51
Alignment explanation
Indices: 1136376--1136554 Score: 304
Period size: 51 Copynumber: 3.5 Consensus size: 51
1136366 ACAAACTTGA
*
1136376 ACTTAGTCTTGATCACGAACGTGCTTGATCTTCACGTCAAGGGTCTTCACG
1 ACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCACG
* *
1136427 ACTTAATCTTGATCACGAACGTACTTGATCTTCGCGTCAAGGGTCTTCACG
1 ACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCACG
* *
1136478 ACTTAGTCTTGATCACGAACTTGCTTGATCTTCGCATCAAGGGTCTTCACG
1 ACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCACG
*
1136529 ACTTAGTCTTGATCATGAACGTGCTT
1 ACTTAGTCTTGATCACGAACGTGCTT
1136555 CGCTTAATAT
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 119 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (51 bp):
ACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCACG
Found at i:1136580 original size:25 final size:25
Alignment explanation
Indices: 1136552--1136653 Score: 147
Period size: 25 Copynumber: 4.2 Consensus size: 25
1136542 CATGAACGTG
1136552 CTTCGCTTAATATCTTGATCACGAA
1 CTTCGCTTAATATCTTGATCACGAA
*
1136577 CTTCGCTTAATATCTTTATCACGAA
1 CTTCGCTTAATATCTTGATCACGAA
*
1136602 CTTCGTTTAATATCTTGATCACGAA
1 CTTCGCTTAATATCTTGATCACGAA
*
1136627 CTTCG-TT-GTCA-CTTGATCACGAA
1 CTTCGCTTAAT-ATCTTGATCACGAA
1136650 CTTC
1 CTTC
1136654 ATTGTTGCTT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
23 17 0.24
24 3 0.04
25 52 0.72
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (25 bp):
CTTCGCTTAATATCTTGATCACGAA
Found at i:1136754 original size:18 final size:18
Alignment explanation
Indices: 1136731--1136787 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
1136721 AAATGCTCCC
*
1136731 AATCTTCGAATGTCT-TCG
1 AATCTTCGAATGCCTCT-G
1136749 AATCTTCGAATGCCTCTG
1 AATCTTCGAATGCCTCTG
1136767 AATCTTCGAATGCCTCTG
1 AATCTTCGAATGCCTCTG
1136785 AAT
1 AAT
1136788 GAATGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
18 36 0.97
19 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (18 bp):
AATCTTCGAATGCCTCTG
Found at i:1137155 original size:80 final size:80
Alignment explanation
Indices: 1137034--1137288 Score: 331
Period size: 81 Copynumber: 3.2 Consensus size: 80
1137024 AATTTGAGTT
* * * * * *
1137034 TTATCTCTAAATTAATAT-AATTA-TTAGAGATAAATTAAATGACCAATGATTAAATTTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAAATTTTGATTG
1137097 GTCAAAATATAAATA
66 GTCAAAATATAAATA
1137112 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAAATTTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAAATTTTGATTG
*
1137177 GTCAAAAATATGAATA
66 GTC-AAAATATAAATA
* * *
1137193 TTATCTCTAAATTATCTTGATTTATTTAAAGATAAATTGAATGACCAATAACTAATTTTTTTGAT
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAA--ATTTTGAT
*
1137258 TGGTTC--AATTTAAATA
64 TGG-TCAAAATATAAATA
1137274 TTATCT-TCAAATTAT
1 TTATCTCT-AAATTAT
1137289 CTCAAGGGAT
Statistics
Matches: 158, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
78 16 0.10
79 4 0.03
80 41 0.26
81 85 0.54
83 10 0.06
84 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (80 bp):
TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAAATTTTGATTG
GTCAAAATATAAATA
Found at i:1137653 original size:28 final size:28
Alignment explanation
Indices: 1137621--1137755 Score: 126
Period size: 28 Copynumber: 4.6 Consensus size: 28
1137611 TATAATCTTG
* *
1137621 GAAGATGTATATTTCAATAAAACTACTT
1 GAAGAAGTATATTGCAATAAAACTACTT
* **
1137649 GAAGAAGTATATTGCAATAAAATTGTTT
1 GAAGAAGTATATTGCAATAAAACTACTT
* *
1137677 GAAGAAGTATATTGCAATAAAGCTATAATTTT
1 GAAGAAGTATATTGCAATAAAAC--T-A-CTT
* *
1137709 GAAAGAGGTATATTGCAATAAAACTATTT
1 G-AAGAAGTATATTGCAATAAAACTACTT
* *
1137738 AAAGAAATATATTGCAAT
1 GAAGAAGTATATTGCAAT
1137756 TAGGATTACA
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
28 59 0.66
29 3 0.03
30 2 0.02
31 1 0.01
32 4 0.04
33 20 0.22
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (28 bp):
GAAGAAGTATATTGCAATAAAACTACTT
Found at i:1138362 original size:293 final size:292
Alignment explanation
Indices: 1137835--1138417 Score: 1130
Period size: 293 Copynumber: 2.0 Consensus size: 292
1137825 TTTGCACATC
*
1137835 AAAATCAACTTGAGCATTACTGATATTCCATAAGCAAGCAAGACCGATTTTTTCATCTTCTCAAA
1 AAAATCAACTTGAGCATTACGGATATTCCATAAGCAAGCAAGACCGATTTTTTCATCTTCTCAAA
1137900 ATTATAAGGTATGCTGTCCTTTCTTTCTCTTCCCTTTATTAACATGGCAGTAGAATTCGCCTGCT
66 ATTATAAGGTATGCTGTCCTTTCTTTCTCTTCCCTTTATTAACATGGCAGTAGAATTCGCCTGCT
1137965 TATGGGCTTTTTTAATTATGCAACTCCCATTATTTTGCATGCTAAAATCTTGCAAGCTGCCATTT
131 TATGGGCTTTTTTAATTATGCAACTCCCATTATTTTGCATGCTAAAATCTTGCAAGCTGCCATTT
1138030 ATTCCAATTCCCAAACTACAAGCCGCCACTTGTTTTAATTCCCATGTTAAAAGCATGCAAGCCAC
196 ATTCCAATTCCCAAACTACAAGCCGCCACTTGTTTTAATTCCCATGTTAAAAGCATGCAAGCCAC
1138095 CATTTATCCAATTGCCATGATAAGCCACCATT
261 CATTTATCCAATTGCCATGATAAGCCACCATT
1138127 NAAAATCAACTTGAGCATTACGGATATTCCATAAGCAAGCAAGACCGATTTTTTCATCTTCTCAA
1 -AAAATCAACTTGAGCATTACGGATATTCCATAAGCAAGCAAGACCGATTTTTTCATCTTCTCAA
1138192 AATTATAAGGTATGCTGTCCTTTCTTTCTCTTCCCTTTATTAACATGGCAGTAGAATTCGCCTGC
65 AATTATAAGGTATGCTGTCCTTTCTTTCTCTTCCCTTTATTAACATGGCAGTAGAATTCGCCTGC
1138257 TTATGGGCTTTTTTAATTATGCAACTCCCATTATTTTGCATGCTAAAATCTTGCAAGCTGCCATT
130 TTATGGGCTTTTTTAATTATGCAACTCCCATTATTTTGCATGCTAAAATCTTGCAAGCTGCCATT
*
1138322 TATTCCAATTCCCAAGCTACAAGCCGCCACTTGTTTTAATTCCCATGTTAAAAGCATGCAAGCCA
195 TATTCCAATTCCCAAACTACAAGCCGCCACTTGTTTTAATTCCCATGTTAAAAGCATGCAAGCCA
*
1138387 CCATTTATCTAATTGCCATGATAAGCCACCA
260 CCATTTATCCAATTGCCATGATAAGCCACCA
1138418 CTTGCCACGT
Statistics
Matches: 287, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
293 287 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (292 bp):
AAAATCAACTTGAGCATTACGGATATTCCATAAGCAAGCAAGACCGATTTTTTCATCTTCTCAAA
ATTATAAGGTATGCTGTCCTTTCTTTCTCTTCCCTTTATTAACATGGCAGTAGAATTCGCCTGCT
TATGGGCTTTTTTAATTATGCAACTCCCATTATTTTGCATGCTAAAATCTTGCAAGCTGCCATTT
ATTCCAATTCCCAAACTACAAGCCGCCACTTGTTTTAATTCCCATGTTAAAAGCATGCAAGCCAC
CATTTATCCAATTGCCATGATAAGCCACCATT
Found at i:1139022 original size:40 final size:40
Alignment explanation
Indices: 1138967--1139301 Score: 286
Period size: 36 Copynumber: 8.8 Consensus size: 40
1138957 TTTAAAGTGA
* * * *
1138967 TGCTCTTTATAATAGCACACAATTTATTTTTCTCGGAGAG
1 TGCTCTTTATAATAGCACACAATTTATTATCCTTGGAGGG
* *
1139007 TGCTCTTTATCATAG--CAC---TTATTGATCCTTGGGGGG
1 TGCTCTTTATAATAGCACACAATTTATT-ATCCTTGGAGGG
*
1139043 TGCTCTTCATAATAGCACACAATTTATTATCCTTGGAGGG
1 TGCTCTTTATAATAGCACACAATTTATTATCCTTGGAGGG
1139083 TGCTCTTTATAATAG--CAC---TTATTGATCCTTGG-GAGG
1 TGCTCTTTATAATAGCACACAATTTATT-ATCCTTGGAG-GG
* *
1139119 TGCTCTTT-TAAACAGCACACAATTAATTATCCTTGGAGGG
1 TGCTCTTTAT-AATAGCACACAATTTATTATCCTTGGAGGG
*
1139159 TGCTCTTTATAATAG--CAC--TTGT-TGATCCTTGG-GAGG
1 TGCTCTTTATAATAGCACACAATT-TATTATCCTTGGAG-GG
** *
1139195 TGCTCTTTATTCTAGCACATAATTTATTATCCTTGGAGGG
1 TGCTCTTTATAATAGCACACAATTTATTATCCTTGGAGGG
* *
1139235 TGCTCTTTATAATAG--CAC--TTGT-TAATCTTTGG-GAGG
1 TGCTCTTTATAATAGCACACAATT-TATTATCCTTGGAG-GG
*
1139271 TGCTCTTTAAAATAGCACACAATTTATTATC
1 TGCTCTTTATAATAGCACACAATTTATTATC
1139302 ACCATGGTAT
Statistics
Matches: 238, Mismatches: 26, Indels: 62
0.73 0.08 0.19
Matches are distributed among these distances:
35 14 0.06
36 94 0.39
37 1 0.00
38 22 0.09
39 2 0.01
40 93 0.39
41 12 0.05
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (40 bp):
TGCTCTTTATAATAGCACACAATTTATTATCCTTGGAGGG
Found at i:1139098 original size:76 final size:76
Alignment explanation
Indices: 1138967--1139301 Score: 501
Period size: 76 Copynumber: 4.4 Consensus size: 76
1138957 TTTAAAGTGA
* * * * *
1138967 TGCTCTTTATAATAGCACACAATTTATTTTTCTCGGAGAGTGCTCTTTATCATAGCACTTATTGA
1 TGCTCTTTATAATAGCACACAATTTATTATCCTTGGAGGGTGCTCTTTATAATAGCACTTATTGA
*
1139032 TCCTTGGGGGG
66 TCCTTGGGAGG
*
1139043 TGCTCTTCATAATAGCACACAATTTATTATCCTTGGAGGGTGCTCTTTATAATAGCACTTATTGA
1 TGCTCTTTATAATAGCACACAATTTATTATCCTTGGAGGGTGCTCTTTATAATAGCACTTATTGA
1139108 TCCTTGGGAGG
66 TCCTTGGGAGG
* * *
1139119 TGCTCTTT-TAAACAGCACACAATTAATTATCCTTGGAGGGTGCTCTTTATAATAGCACTTGTTG
1 TGCTCTTTAT-AATAGCACACAATTTATTATCCTTGGAGGGTGCTCTTTATAATAGCACTTATTG
1139183 ATCCTTGGGAGG
65 ATCCTTGGGAGG
** * * *
1139195 TGCTCTTTATTCTAGCACATAATTTATTATCCTTGGAGGGTGCTCTTTATAATAGCACTTGTTAA
1 TGCTCTTTATAATAGCACACAATTTATTATCCTTGGAGGGTGCTCTTTATAATAGCACTTATTGA
*
1139260 TCTTTGGGAGG
66 TCCTTGGGAGG
*
1139271 TGCTCTTTAAAATAGCACACAATTTATTATC
1 TGCTCTTTATAATAGCACACAATTTATTATC
1139302 ACCATGGTAT
Statistics
Matches: 235, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
75 1 0.00
76 233 0.99
77 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (76 bp):
TGCTCTTTATAATAGCACACAATTTATTATCCTTGGAGGGTGCTCTTTATAATAGCACTTATTGA
TCCTTGGGAGG
Found at i:1139858 original size:65 final size:64
Alignment explanation
Indices: 1139655--1139859 Score: 302
Period size: 64 Copynumber: 3.2 Consensus size: 64
1139645 ACGTAGTTCA
* * * *
1139655 TTTTTTTTTTTGCCTTAACTTTTGCCTAAATTGTCCTATTAAGTATTTTCAACTTAGCAAGCTT
1 TTTTTTTTTTTGCCTTAACTTTTGCCTAAGTCGTCCTGTTAAGGATTTTCAACTTAGCAAGCTT
* * *
1139719 TTTTTTTTTTTGCCTTAACTTTTGCCTAAGTCGTCTTGTTAAGGATTTTCGACTTAGCAGGCTT
1 TTTTTTTTTTTGCCTTAACTTTTGCCTAAGTCGTCCTGTTAAGGATTTTCAACTTAGCAAGCTT
* * * *
1139783 TTTTTCTTTTTCGCCTTAACTTTTGTCTAAGTCGTCCTGTTAAGGATTTTCAACTTATCATGCTT
1 TTTTT-TTTTTTGCCTTAACTTTTGCCTAAGTCGTCCTGTTAAGGATTTTCAACTTAGCAAGCTT
1139848 TTTTTTTTTTTG
1 TTTTTTTTTTTG
1139860 AAGCAGTTTA
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
64 68 0.54
65 58 0.46
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (64 bp):
TTTTTTTTTTTGCCTTAACTTTTGCCTAAGTCGTCCTGTTAAGGATTTTCAACTTAGCAAGCTT
Found at i:1147047 original size:51 final size:51
Alignment explanation
Indices: 1146991--1147220 Score: 345
Period size: 51 Copynumber: 4.5 Consensus size: 51
1146981 CACAAACTTG
1146991 GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCAC
1 GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCAC
* * * *
1147042 GACTTAATCTTCAT-ACGGACGTACTTGATCTTCGCGTCAAGGGTCTTCAC
1 GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCAC
* ** * *
1147092 GGCTTAGTCTTGATCACGAATTTGCTTGATCTTCGTGTCAAGGGTATTCAC
1 GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCAC
* * *
1147143 GACTTAGTCTTGATCACGAACTTGCTTGATCTTCGCATCAAGGGTTTTCAC
1 GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCAC
1147194 GACTTAGTCTTGATCACGAACGTGCTT
1 GACTTAGTCTTGATCACGAACGTGCTT
1147221 CACTTAATAT
Statistics
Matches: 159, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
50 45 0.28
51 114 0.72
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (51 bp):
GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCAC
Found at i:1147118 original size:101 final size:102
Alignment explanation
Indices: 1146991--1147220 Score: 345
Period size: 101 Copynumber: 2.3 Consensus size: 102
1146981 CACAAACTTG
*
1146991 GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTCTTCACGACTTAATCTTCAT
1 GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTATTCACGACTTAATCTTCAT
* *
1147056 -ACGGACGTACTTGATCTTCGCGTCAAGGGTCTTCAC
66 CACGAACGTACTTGATCTTCGCATCAAGGGTCTTCAC
* ** * * *
1147092 GGCTTAGTCTTGATCACGAATTTGCTTGATCTTCGTGTCAAGGGTATTCACGACTTAGTCTTGAT
1 GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTATTCACGACTTAATCTTCAT
* * *
1147157 CACGAACTTGCTTGATCTTCGCATCAAGGGTTTTCAC
66 CACGAACGTACTTGATCTTCGCATCAAGGGTCTTCAC
1147194 GACTTAGTCTTGATCACGAACGTGCTT
1 GACTTAGTCTTGATCACGAACGTGCTT
1147221 CACTTAATAT
Statistics
Matches: 113, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
101 58 0.51
102 55 0.49
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (102 bp):
GACTTAGTCTTGATCACGAACGTGCTTGATCTTCGCGTCAAGGGTATTCACGACTTAATCTTCAT
CACGAACGTACTTGATCTTCGCATCAAGGGTCTTCAC
Found at i:1147311 original size:23 final size:25
Alignment explanation
Indices: 1147218--1147319 Score: 147
Period size: 25 Copynumber: 4.2 Consensus size: 25
1147208 CACGAACGTG
*
1147218 CTTCACTTAATATCTTGATCACGAA
1 CTTCGCTTAATATCTTGATCACGAA
*
1147243 CTTCGCTTAATATCTTTATCACGAA
1 CTTCGCTTAATATCTTGATCACGAA
1147268 CTTCGCTTAATATCTTGATCACGAA
1 CTTCGCTTAATATCTTGATCACGAA
*
1147293 CTTCG-TT-GT-TGCTTGATCACGAA
1 CTTCGCTTAATAT-CTTGATCACGAA
1147316 CTTC
1 CTTC
1147320 ATTGTTGCTT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
22 1 0.01
23 17 0.24
24 2 0.03
25 52 0.72
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (25 bp):
CTTCGCTTAATATCTTGATCACGAA
Found at i:1147324 original size:23 final size:23
Alignment explanation
Indices: 1147281--1147333 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1147271 CGCTTAATAT
*
1147281 CTTGATCACGAACTTCGTTGTTG
1 CTTGATCACGAACTTCATTGTTG
1147304 CTTGATCACGAACTTCATTGTTG
1 CTTGATCACGAACTTCATTGTTG
1147327 CTTGATC
1 CTTGATC
1147334 TTTACTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (23 bp):
CTTGATCACGAACTTCATTGTTG
Found at i:1147393 original size:17 final size:17
Alignment explanation
Indices: 1147371--1147427 Score: 87
Period size: 17 Copynumber: 3.3 Consensus size: 17
1147361 TGATCTCTAA
1147371 AATGCTCTCAATCTTCG
1 AATGCTCTCAATCTTCG
*
1147388 AATGCTCCCAATCTTCG
1 AATGCTCTCAATCTTCG
*
1147405 AATGCCTCTGAATCTTCG
1 AATG-CTCTCAATCTTCG
1147423 AATGC
1 AATGC
1147428 CCCTGAATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 21 0.58
18 15 0.42
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (17 bp):
AATGCTCTCAATCTTCG
Found at i:1147420 original size:18 final size:18
Alignment explanation
Indices: 1147371--1147524 Score: 125
Period size: 18 Copynumber: 8.5 Consensus size: 18
1147361 TGATCTCTAA
*
1147371 AATG-CTCTCAATCTTCG
1 AATGCCTCTGAATCTTCG
**
1147388 AATG-CTCCCAATCTTCG
1 AATGCCTCTGAATCTTCG
1147405 AATGCCTCTGAATCTTCG
1 AATGCCTCTGAATCTTCG
* *
1147423 AATGCCCCTGAATCTTTG
1 AATGCCTCTGAATCTTCG
**
1147441 AATGCCTCTGAATGAAT-G
1 AATGCCTCTGAAT-CTTCG
* ** ***
1147459 AAAATGGCTAGGGGGNCTTCG
1 --AATGCCT-CTGAATCTTCG
1147480 AATGCCTCTGAATCTTCG
1 AATGCCTCTGAATCTTCG
*
1147498 AATGCCTCTGAATCTTCA
1 AATGCCTCTGAATCTTCG
1147516 AATGCCTCT
1 AATGCCTCT
1147525 AAAATGAATG
Statistics
Matches: 108, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
17 20 0.19
18 72 0.67
19 7 0.06
20 7 0.06
21 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (18 bp):
AATGCCTCTGAATCTTCG
Found at i:1147488 original size:75 final size:75
Alignment explanation
Indices: 1147400--1147549 Score: 248
Period size: 75 Copynumber: 2.0 Consensus size: 75
1147390 TGCTCCCAAT
** *
1147400 CTTCGAATGCCTCTGAATCTTCGAATGCCCCTGAATCTTTGAATGCCTCT-GAATGAATGAAAAT
1 CTTCGAATGCCTCTGAATCTTCGAATGCCCCTGAATCTTCAAATGCCTCTAAAATGAATGAAAAT
1147464 GGCTAGGGGG
66 GGCTAGGGGG
*
1147474 NCTTCGAATGCCTCTGAATCTTCGAATGCCTCTGAATCTTCAAATGCCTCTAAAATGAATGAAAA
1 -CTTCGAATGCCTCTGAATCTTCGAATGCCCCTGAATCTTCAAATGCCTCTAAAATGAATGAAAA
1147539 TGGCTAGGGGG
65 TGGCTAGGGGG
1147550 AGCCCTCTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
75 47 0.67
76 23 0.33
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (75 bp):
CTTCGAATGCCTCTGAATCTTCGAATGCCCCTGAATCTTCAAATGCCTCTAAAATGAATGAAAAT
GGCTAGGGGG
Found at i:1147895 original size:80 final size:80
Alignment explanation
Indices: 1147774--1148016 Score: 339
Period size: 81 Copynumber: 3.0 Consensus size: 80
1147764 AATTTGAGTT
* * * * * *
1147774 TTATCTCTAAATTAATAT-AATTA-TTATAGATAAATTAAATGACCAATAATTAAATTTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAAATTTTGATTG
1147837 GTCAAAATATAAATA
66 GTCAAAATATAAATA
*
1147852 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACTAATAACTAAATTTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAAATTTTGATTG
*
1147917 GTCAAAAATATGAATA
66 GTC-AAAATATAAATA
* *
1147933 TTATCTCTAAATTATCTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAATTTTTTGATT
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAA-ATTTTGATT
* *
1147998 GGTC-CAATTTAAATA
65 GGTCAAAATATAAATA
1148013 TTAT
1 TTAT
1148017 TTTCAAATTA
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
78 16 0.11
79 4 0.03
80 51 0.35
81 64 0.44
82 12 0.08
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.42
Consensus pattern (80 bp):
TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGAATGACCAATAACTAAATTTTGATTG
GTCAAAATATAAATA
Found at i:1153633 original size:2 final size:2
Alignment explanation
Indices: 1153626--1153668 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
1153616 ATTCTCCTTT
*
1153626 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1153669 ATCCACTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1154212 original size:81 final size:79
Alignment explanation
Indices: 1154070--1154324 Score: 334
Period size: 81 Copynumber: 3.2 Consensus size: 79
1154060 ATCCATTGAG
* * * *
1154070 ATAATTTAAAAATAATATTTAAATTGGACCAATCAAAAAATTAGTTATTGGTCATCTAATTTATC
1 ATAATTTAGAGATAATATTTATATTTGACCAATC-AAAAATTAGTTATTGGTCATCTAATTTATC
1154135 TCTAAATAAATTAAA
65 TCTAAATAAATTAAA
* *
1154150 ATAATTTAGAGATAATATTTATACTTTTGACCAATCAAAAATTAGTTATTGGTTATCCAATTTAT
1 ATAATTTAGAGATAATATTTATA--TTTGACCAATCAAAAATTAGTTATTGGTCATCTAATTTAT
*
1154215 CTCTAAATAAATCAAA
64 CTCTAAATAAATTAAA
* * * *
1154231 ATAATTTAGAGATAGTATTCCTATATTTGACCAATCAAAATTTAATTATTGGTCATTTAATTTAT
1 ATAATTTAGAGATAATATT--TATATTTGACCAATCAAAAATTAGTTATTGGTCATCTAATTTAT
*
1154296 CTCT-AAT-AATTATA
64 CTCTAAATAAATTAAA
*
1154310 TTAATTTAGAGATAA
1 ATAATTTAGAGATAA
1154325 AATTGGATTG
Statistics
Matches: 154, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
79 18 0.12
80 23 0.15
81 99 0.64
82 10 0.06
83 4 0.03
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.40
Consensus pattern (79 bp):
ATAATTTAGAGATAATATTTATATTTGACCAATCAAAAATTAGTTATTGGTCATCTAATTTATCT
CTAAATAAATTAAA
Found at i:1154610 original size:17 final size:17
Alignment explanation
Indices: 1154571--1154627 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
1154561 TCATTTAGAG
* *
1154571 GCATTTGAAGATTCAGAA
1 GCATTCGAAGATTGAG-A
*
1154589 GCATTCGAAGATTGGGA
1 GCATTCGAAGATTGAGA
1154606 GCATTCGAAGATTGAGA
1 GCATTCGAAGATTGAGA
1154623 GCATT
1 GCATT
1154628 TCAGAGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
17 22 0.63
18 13 0.37
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.26
Consensus pattern (17 bp):
GCATTCGAAGATTGAGA
Found at i:1154778 original size:49 final size:49
Alignment explanation
Indices: 1154725--1154822 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
1154715 TCAAGATACT
* *
1154725 GTGTTCATGATCAAGATTAAGTCATCAAGACCCTTGAAGCGAAGATCAA
1 GTGTTCATAATCAAGATTAAGTCATCAAGACCCTTGAAGCAAAGATCAA
* *
1154774 GTGTTCGTAATCAAGATTAAGTCGTCAAGACCCTTGAAGCAAAGATCAA
1 GTGTTCATAATCAAGATTAAGTCATCAAGACCCTTGAAGCAAAGATCAA
1154823 ACAAATTCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (49 bp):
GTGTTCATAATCAAGATTAAGTCATCAAGACCCTTGAAGCAAAGATCAA
Found at i:1157717 original size:19 final size:17
Alignment explanation
Indices: 1157688--1157731 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
1157678 TAATATTTAA
1157688 AAAATTAAAATAAATAAAT
1 AAAA-TAAAATAAAT-AAT
1157707 AATAATAAAATAAATAAT
1 AA-AATAAAATAAATAAT
1157725 AAAATAA
1 AAAATAA
1157732 TTGAGAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.21
18 5 0.21
19 12 0.50
20 2 0.08
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATAAAATAAATAAT
Found at i:1157724 original size:12 final size:12
Alignment explanation
Indices: 1157703--1157731 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1157693 TAAAATAAAT
1157703 AAAT-AATAATA
1 AAATAAATAATA
1157714 AAATAAATAATA
1 AAATAAATAATA
1157726 AAATAA
1 AAATAA
1157732 TTGAGAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:1158524 original size:59 final size:59
Alignment explanation
Indices: 1158394--1158516 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 59
1158384 GCCGGGAACA
* * * * *
1158394 AAAGGAAAGAAAAAGAGAGAAGGGAGTTCGGCCAGACCAGGAGAGAAAAGAGAAGGAAG
1 AAAGGACAGAAAAAGAGAGAAGGAAGTTCGGCCAGACCAAGAAAGAAAAGAGAAGAAAG
*
1158453 AAAGGACAGAAAAAGAGAGATGGAAGTTCGGCC-GCACCAAAGAAAGAAAAGA-AAGAAAG
1 AAAGGACAGAAAAAGAGAGAAGGAAGTTCGGCCAG-ACC-AAGAAAGAAAAGAGAAGAAAG
1158512 AAAGG
1 AAAGG
1158517 GAGGAAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.02
59 44 0.79
60 11 0.20
ACGTcount: A:0.53, C:0.10, G:0.33, T:0.04
Consensus pattern (59 bp):
AAAGGACAGAAAAAGAGAGAAGGAAGTTCGGCCAGACCAAGAAAGAAAAGAGAAGAAAG
Found at i:1160583 original size:19 final size:19
Alignment explanation
Indices: 1160556--1160593 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1160546 CCATTTAACT
* *
1160556 TATTGGAGTATGATTTGAG
1 TATTAGAGTATAATTTGAG
1160575 TATTAGAGTATAATTTGAG
1 TATTAGAGTATAATTTGAG
1160594 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATAATTTGAG
Found at i:1161981 original size:13 final size:13
Alignment explanation
Indices: 1161963--1161987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1161953 GAAGAAATTG
1161963 TGATTTTATAAAA
1 TGATTTTATAAAA
1161976 TGATTTTATAAA
1 TGATTTTATAAA
1161988 TTTTCTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:1163749 original size:2 final size:2
Alignment explanation
Indices: 1163742--1163804 Score: 82
Period size: 2 Copynumber: 33.5 Consensus size: 2
1163732 TTCATATCCC
1163742 TA TA TA TA TA TA -A TA TA TA TA TA CTA -A TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
1163782 TA TA TA T- TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1163805 TAAAACTAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
1 5 0.09
2 48 0.87
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1182366 original size:2 final size:2
Alignment explanation
Indices: 1182354--1182387 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1182344 TAACCAATTT
* *
1182354 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1182388 ATCCACTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1186004 original size:19 final size:20
Alignment explanation
Indices: 1185971--1186017 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
1185961 GTTTGCTAAG
1185971 GATTTTGATTTTTTTTATGA
1 GATTTTGATTTTTTTTATGA
*
1185991 GATTTTGA-TTTTTTTATGG
1 GATTTTGATTTTTTTTATGA
1186010 GATTTTGA
1 GATTTTGA
1186018 GTTGAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (20 bp):
GATTTTGATTTTTTTTATGA
Found at i:1186299 original size:22 final size:22
Alignment explanation
Indices: 1186257--1186299 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1186247 TATTAAAATG
*
1186257 GTTTTTAAGTATTGCGAGACTA
1 GTTTTTAAGTATTACGAGACTA
* *
1186279 GTTTTTAGGTATTACGTGACT
1 GTTTTTAAGTATTACGAGACT
1186300 TAATCATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (22 bp):
GTTTTTAAGTATTACGAGACTA
Found at i:1186335 original size:22 final size:22
Alignment explanation
Indices: 1186310--1186378 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
1186300 TAATCATTGT
1186310 GTGACTAGTTTTTAGACATTAC
1 GTGACTAGTTTTTAGACATTAC
* * *
1186332 GTGA-TTGGTTTTAGGCATTAC
1 GTGACTAGTTTTTAGACATTAC
1186353 GTGACTAGTTTTTAGACATTAC
1 GTGACTAGTTTTTAGACATTAC
1186375 GTGA
1 GTGA
1186379 TTGATTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 18 0.45
22 22 0.55
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.41
Consensus pattern (22 bp):
GTGACTAGTTTTTAGACATTAC
Found at i:1186345 original size:21 final size:21
Alignment explanation
Indices: 1186319--1186386 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
1186309 TGTGACTAGT
*
1186319 TTTTAGACATTACGTGATTGG
1 TTTTAGACATTACGTGATTGA
* * *
1186340 TTTTAGGCATTACGTGACTAGT
1 TTTTAGACATTACGTGA-TTGA
1186362 TTTTAGACATTACGTGATTGA
1 TTTTAGACATTACGTGATTGA
1186383 TTTT
1 TTTT
1186387 TAAGCAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 22 0.55
22 18 0.45
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.46
Consensus pattern (21 bp):
TTTTAGACATTACGTGATTGA
Found at i:1186386 original size:22 final size:22
Alignment explanation
Indices: 1186318--1186388 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
1186308 GTGTGACTAG
1186318 TTTTTAGACATTACGTGATTG-
1 TTTTTAGACATTACGTGATTGA
* * *
1186339 GTTTTAGGCATTACGTGACT-A
1 TTTTTAGACATTACGTGATTGA
1186360 GTTTTTAGACATTACGTGATTGA
1 -TTTTTAGACATTACGTGATTGA
1186383 TTTTTA
1 TTTTTA
1186389 AGCAATATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
21 17 0.41
22 23 0.56
23 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (22 bp):
TTTTTAGACATTACGTGATTGA
Found at i:1186426 original size:23 final size:22
Alignment explanation
Indices: 1186400--1186478 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
1186390 GCAATATCTA
*
1186400 AGTCACACAATGCCTTACTAACT
1 AGTCACGCAATGCCTTA-TAACT
* *
1186423 AGTCACGCAATGCTTTATTAACA
1 AGTCACGCAATGCCTTA-TAACT
*
1186446 AGTCACGCCATGCC-TATCAACT
1 AGTCACGCAATGCCTTAT-AACT
1186468 AGTCACGCAAT
1 AGTCACGCAAT
1186479 ACCATATCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.02
22 15 0.32
23 31 0.66
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (22 bp):
AGTCACGCAATGCCTTATAACT
Found at i:1186474 original size:22 final size:22
Alignment explanation
Indices: 1186400--1186489 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 22
1186390 GCAATATCTA
*
1186400 AGTCACACAATGCCT-TACTAACT
1 AGTCACGCAATGCCTAT-C-AACT
* * *
1186423 AGTCACGCAATGCTTTATTAACA
1 AGTCACGCAATGC-CTATCAACT
*
1186446 AGTCACGCCATGCCTATCAACT
1 AGTCACGCAATGCCTATCAACT
*
1186468 AGTCACGCAATACCATATCAAC
1 AGTCACGCAATGCC-TATCAAC
1186490 CAATCACACA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 18 0.33
23 34 0.63
24 1 0.02
25 1 0.02
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.24
Consensus pattern (22 bp):
AGTCACGCAATGCCTATCAACT
Found at i:1186496 original size:23 final size:23
Alignment explanation
Indices: 1186460--1186503 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1186450 ACGCCATGCC
* * *
1186460 TATCAACTAGTCACGCAATACCA
1 TATCAACCAATCACACAATACCA
1186483 TATCAACCAATCACACAATAC
1 TATCAACCAATCACACAATAC
1186504 TTAAAAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.32, G:0.05, T:0.20
Consensus pattern (23 bp):
TATCAACCAATCACACAATACCA
Found at i:1186524 original size:22 final size:22
Alignment explanation
Indices: 1186497--1186566 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
1186487 AACCAATCAC
1186497 ACAATACTTAAAAACTAGTCAT
1 ACAATACTTAAAAACTAGTCAT
** ** *
1186519 ACAATACCCAAAGTC-AGTCAC
1 ACAATACTTAAAAACTAGTCAT
* *
1186540 GCAATACTTAAAAACTAGTTAT
1 ACAATACTTAAAAACTAGTCAT
1186562 ACAAT
1 ACAAT
1186567 GCCCAAAAAT
Statistics
Matches: 34, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.24
Consensus pattern (22 bp):
ACAATACTTAAAAACTAGTCAT
Found at i:1186757 original size:19 final size:21
Alignment explanation
Indices: 1186712--1186757 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
1186702 TCTTCATATA
*
1186712 TCAAAAATCACTCCAAAATAC
1 TCAAAAATCACTCCAAAACAC
*
1186733 TTAAAAAT-ACT-CAAAACAC
1 TCAAAAATCACTCCAAAACAC
1186752 TCAAAA
1 TCAAAA
1186758 GTTTTCTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 12 0.55
20 3 0.14
21 7 0.32
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.20
Consensus pattern (21 bp):
TCAAAAATCACTCCAAAACAC
Found at i:1192160 original size:3 final size:3
Alignment explanation
Indices: 1192152--1192191 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
1192142 AATCACATGT
* *
1192152 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1192192 CATCATCATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1192192 original size:6 final size:6
Alignment explanation
Indices: 1192169--1192219 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
1192159 TATTATTGTT
* * * *
1192169 ATTATT ATTATT ATTATC ATTATC ATCATC ATCATC ATTATC ATTATC
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC
1192217 ATT
1 ATT
1192220 TAAATAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTATC
Found at i:1192196 original size:9 final size:9
Alignment explanation
Indices: 1192178--1192212 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1192168 TATTATTATT
*
1192178 ATTATTATC
1 ATTATCATC
1192187 ATTATCATC
1 ATTATCATC
*
1192196 ATCATCATC
1 ATTATCATC
1192205 ATTATCAT
1 ATTATCAT
1192213 TATCATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (9 bp):
ATTATCATC
Found at i:1192996 original size:22 final size:23
Alignment explanation
Indices: 1192970--1193013 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1192960 TAAATTATAA
1192970 ATAAAATATTAAT-ATTTAAATT
1 ATAAAATATTAATGATTTAAATT
* *
1192992 ATAAATTATTAATGTTTTAAAT
1 ATAAAATATTAATGATTTAAAT
1193014 AGATTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATAAAATATTAATGATTTAAATT
Found at i:1193014 original size:42 final size:42
Alignment explanation
Indices: 1192918--1192997 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
1192908 TAATAACATT
* *
1192918 TAAATTATGAATAAAATATTAATATATTATAATTTTAATGAC
1 TAAATTATAAATAAAATATTAATATATTATAATTTAAATGAC
1192960 TAAATTATAAATAAAATATTAATAT-TTA-AATTATAAAT
1 TAAATTATAAATAAAATATTAATATATTATAATT-TAAAT
1192998 TATTAATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 4 0.11
41 7 0.20
42 24 0.69
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (42 bp):
TAAATTATAAATAAAATATTAATATATTATAATTTAAATGAC
Found at i:1193043 original size:17 final size:17
Alignment explanation
Indices: 1192990--1193044 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1192980 AATATTTAAA
*
1192990 TTATAAATTATTAATGT
1 TTATAAATTATTAATAT
*
1193007 TT-TAAATAGATT-A-A-
1 TTATAAAT-TATTAATAT
1193021 TTATAAATTATTAATAT
1 TTATAAATTATTAATAT
1193038 TTATAAA
1 TTATAAA
1193045 ATAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 7 0.23
17 12 0.40
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TTATAAATTATTAATAT
Found at i:1196495 original size:27 final size:27
Alignment explanation
Indices: 1196465--1196522 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
1196455 TACAAAAACA
*
1196465 TGTTACATACCATGGGTT-AAAAAAA-AT
1 TGTTACACACCAT--GTTGAAAAAAATAT
1196492 TGTTACACACCATGTTGAAAAAAATAT
1 TGTTACACACCATGTTGAAAAAAATAT
1196519 TGTT
1 TGTT
1196523 GTAACATGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 3 0.11
26 7 0.25
27 18 0.64
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (27 bp):
TGTTACACACCATGTTGAAAAAAATAT
Found at i:1196550 original size:54 final size:55
Alignment explanation
Indices: 1196492--1196610 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 55
1196482 TAAAAAAAAT
* *
1196492 TGTTACACACCATGTTG-AAAAAAATATTGTTGTAACA-TGCCATATATAAAAACA
1 TGTTACACACCATGTTGAAAAAAAATATTGTTATAACACT-CCATATACAAAAACA
*** * *
1196546 TGTTACATGTCATGTTGAAAAAAAAAATATTGTTATTACACTCCATGTACAAAAACA
1 TGTTACACACCATGTTG--AAAAAAAATATTGTTATAACACTCCATATACAAAAACA
1196603 TGTTACAC
1 TGTTACAC
1196611 GTCACTAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
54 14 0.26
57 38 0.72
58 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (55 bp):
TGTTACACACCATGTTGAAAAAAAATATTGTTATAACACTCCATATACAAAAACA
Found at i:1196624 original size:57 final size:57
Alignment explanation
Indices: 1196509--1196626 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 57
1196499 CACCATGTTG
* * * **
1196509 AAAAAAATATTGTTGTAACATGCCATATATAAAAACATGTTACATGTCATGTTGAAA
1 AAAAAAATATTGTTATAACATGCCATATACAAAAACATGTTACACGTCATAATGAAA
* *
1196566 AAAAAAATATTGTTATTACACT-CCATGTACAAAAACATGTTACACGTCACTAAT-AAA
1 AAAAAAATATTGTTATAACA-TGCCATATACAAAAACATGTTACACGTCA-TAATGAAA
1196623 AAAA
1 AAAA
1196627 GGTTGCTACA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 49 0.94
58 3 0.06
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (57 bp):
AAAAAAATATTGTTATAACATGCCATATACAAAAACATGTTACACGTCATAATGAAA
Found at i:1196687 original size:27 final size:28
Alignment explanation
Indices: 1196633--1196689 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1196623 AAAAGGTTGC
1196633 TACATGCCATATTAAAAAAAATTATTGT
1 TACATGCCATATTAAAAAAAATTATTGT
*
1196661 TACATGCCATATTCAAAAAAATT-TTGT
1 TACATGCCATATTAAAAAAAATTATTGT
1196688 TA
1 TA
1196690 TACTTTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (28 bp):
TACATGCCATATTAAAAAAAATTATTGT
Found at i:1197173 original size:70 final size:70
Alignment explanation
Indices: 1197060--1197200 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
1197050 CTCACCCCCA
1197060 AGAGCTGGTGAAGGATCGGTGGAGCCTCCTTTGATGCCAATCAGCCAATGTGCCTTGAATGGAAA
1 AGAGCTGGTGAAGGATCGGTGGAGCCTCCTTTGATGCCAATCAGCCAATGTGCCTTGAATGGAAA
1197125 CAATC
66 CAATC
1197130 AGAGCTGGTGAAGGATCGGTGGAGCCTCCTTTGATGCCAATCAGCCAATGTGCCTTGAATGGAAA
1 AGAGCTGGTGAAGGATCGGTGGAGCCTCCTTTGATGCCAATCAGCCAATGTGCCTTGAATGGAAA
1197195 CAATC
66 CAATC
1197200 A
1 A
1197201 AAGAGACTCA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (70 bp):
AGAGCTGGTGAAGGATCGGTGGAGCCTCCTTTGATGCCAATCAGCCAATGTGCCTTGAATGGAAA
CAATC
Found at i:1200063 original size:19 final size:19
Alignment explanation
Indices: 1200039--1200076 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1200029 ACTTCTAAAC
1200039 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
1200058 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
1200077 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:1203013 original size:14 final size:13
Alignment explanation
Indices: 1202994--1203019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1202984 CGTGGTAGAT
1202994 AAAAAAATTTTTG
1 AAAAAAATTTTTG
1203007 AAAAAAATTTTTG
1 AAAAAAATTTTTG
1203020 TGCCACATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAAAAATTTTTG
Found at i:1204231 original size:255 final size:254
Alignment explanation
Indices: 1203773--1204278 Score: 960
Period size: 255 Copynumber: 2.0 Consensus size: 254
1203763 ATTTTGTATT
* *
1203773 TACAAATTTTTTGTAGATCTAAATTAATAATCTAAATTTAAATTTAACAAAATTTGATTGTTTGA
1 TACAAAATTTTTGTAGATCTAAATTAATAATCTAAATTTAAATTTAACAAAATTTGATTATTTGA
1203838 ACTTAAATAAAATCGTTTTATAAGAACCTTTGAGTAAATTTAAATAAAAAGTAAATTAGGTAAGG
66 ACTTAAATAAAATCGTTTTATAAGAACCTTTGAGTAAATTTAAATAAAAAGTAAATTAGGTAAGG
1203903 GTTAAATAATTCCAAAAGAATGAATATTTGCAAATTGTGAAAGTTGCAATTAAATCAACCTATTT
131 GTTAAATAATTCCAAAAGAATGAATATTTGCAAATTGTGAAAGTTGCAATTAAATCAACCTATTT
*
1203968 TGCTTATTTGAGTTCAATTCAAGTTAAAAACTAAGTTAAATAAATTTTAAAATTACCTA
196 TGCTTATTTGAGTTCAATTCAAGTTAAAAACTAAGTTAAAAAAATTTTAAAATTACCTA
1204027 NTACAAAATTTTTGTAGATCTAAATTAATAATCTAAATTTAAATTTAACAAAATTTGATTATTTG
1 -TACAAAATTTTTGTAGATCTAAATTAATAATCTAAATTTAAATTTAACAAAATTTGATTATTTG
1204092 AACTTAAAT-AAATCGTTTTATAAGAACCTTTGAGTAAATTTAAATAAAAAGTAAATTAGGTAAG
65 AACTTAAATAAAATCGTTTTATAAGAACCTTTGAGTAAATTTAAATAAAAAGTAAATTAGGTAAG
1204156 GGTTAAATAATTCCAAAAGAATGAATATTTGCAAATTGTGAAAGTTGCAATTAAATCAACCTATT
130 GGTTAAATAATTCCAAAAGAATGAATATTTGCAAATTGTGAAAGTTGCAATTAAATCAACCTA-T
1204221 TTTGCTTATTTGAGTTCAATTCAAGTTAAAAACTAAGTTAAAAAAATTTTAAAATTAC
194 TTTGCTTATTTGAGTTCAATTCAAGTTAAAAACTAAGTTAAAAAAATTTTAAAATTAC
1204279 TATTATTATA
Statistics
Matches: 247, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
254 118 0.48
255 129 0.52
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (254 bp):
TACAAAATTTTTGTAGATCTAAATTAATAATCTAAATTTAAATTTAACAAAATTTGATTATTTGA
ACTTAAATAAAATCGTTTTATAAGAACCTTTGAGTAAATTTAAATAAAAAGTAAATTAGGTAAGG
GTTAAATAATTCCAAAAGAATGAATATTTGCAAATTGTGAAAGTTGCAATTAAATCAACCTATTT
TGCTTATTTGAGTTCAATTCAAGTTAAAAACTAAGTTAAAAAAATTTTAAAATTACCTA
Found at i:1204647 original size:31 final size:31
Alignment explanation
Indices: 1204612--1204690 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
1204602 AGCATCTCAA
*
1204612 TTTTGTTCAATTTAGTCCATGTACTATATAT
1 TTTTGTTCAATTTAATCCATGTACTATATAT
* *
1204643 TTTTGTTCAATTTAATTCATGTATTATATAT
1 TTTTGTTCAATTTAATCCATGTACTATATAT
*
1204674 TTTAGTTCAATTTAATC
1 TTTTGTTCAATTTAATC
1204691 TCTATGACGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (31 bp):
TTTTGTTCAATTTAATCCATGTACTATATAT
Found at i:1207864 original size:206 final size:201
Alignment explanation
Indices: 1207181--1207933 Score: 571
Period size: 203 Copynumber: 3.6 Consensus size: 201
1207171 GATATTTCTA
* * *
1207181 TGTAATAAAGAATATGTGATTTGATCATCTATTATTTTTTTTGTTCACAGTCAAAATAAGATAAT
1 TGTAATAAA-AATATATGATTAGATCATCTATTA--TTTCTT-TT---AGTCAAAATAAGATAAT
* * * * *
1207246 TTT-ATTAATATAAAAAA-TGATGCAATTGTTCAGATCTCGATATAATTAAGATATGTAAACAAA
59 TTTCATTAATATAAAAAATTGATACAATTGTTCATATCTCAATATAATTAAGATAAGTAAACAAT
* * * * **
1207309 TAAAAATTAGAGCCTCATTGGAAACATAAAAAATCAAGACAAATAAATAGT-TCTTAATTATTTA
124 TAAAAATTAGAGACTCATT-GAAATAT-AAAAATCAAGACAAATAAATACTATCATACGTATTTA
*
1207373 ACACTATCATTTTCTAT
187 ACATTATCATTTT-T-T
* * * * * *
1207390 TGCAATAAAAA-AAATGATTAGGTCATCTATTGTTTCTTTTAGTCAGAATAAAATAATTTT-ATT
1 TGTAATAAAAATATATGATTAGATCATCTATTATTTCTTTTAGTCAAAATAAGATAATTTTCATT
* * * * * *
1207453 CAGATCAAAAAATTGA-AGTAATAGCTT-ATATCTCAATATAATTGAGATAAATAAACAATTAAA
66 AATAT-AAAAAATTGATA-CAATTG-TTCATATCTCAATATAATTAAGATAAGTAAACAATTAAA
* * * * * * * *
1207516 AATCAGATATTTATTGATATATAAAGAATCAAAACAAATAAATAACTCTTATTCCATGCAGTCAG
128 AATTAGAGACTCATTGAAATATAAA-AATCAAGACAAATAAAT-A--C-TA-T-CATAC-GT-AT
* * * * * *
1207581 TAAACGTAAAACCTTTCTT
184 TTAACAT-TATCATTTTTT
* * *
1207600 TATAATAAAATATATATGATTGGATCATCTA-T-TTTCTTTTAGTCAAAACAAGATAATTTTAAT
1 TGTAATAAAA-ATATATGATTAGATCATCTATTATTTCTTTTAGTCAAAATAAGATAA-TTT--T
* * *
1207663 CATTAATATAAAAAATTGATACAATTGTTCATTTCTCAATGTAATTAAGGTAAGTAAACAATTAA
62 CATTAATATAAAAAATTGATACAATTGTTCATATCTCAATATAATTAAGATAAGTAAACAATTAA
*
1207728 AAATTAGAGACTCATTCGAAATATAAAAATTCAAGACAAATAAATA-TAT-AGCT-CGTATTTCA
127 AAATTAGAGACTCATT-GAAATATAAAAA-TCAAGACAAATAAATACTATCA--TACGTATTTAA
1207790 CATTATCATTTTTT
188 CATTATCATTTTTT
* * *
1207804 TGTAATAAAGAATATATGATTCGATCATCTATTATTTCTTTTCGTCAAAATAAGATAA-TTTGAT
1 TGTAATAAA-AATATATGATTAGATCATCTATTATTTCTTTTAGTCAAAATAAGATAATTTTCAT
** * * * * *
1207868 TAATATAAAAAAATTGATACAATTACTGATACCTCGATATAATTGAA-ATAAATAAATAATTAAA
65 TAATAT-AAAAAATTGATACAATTGTTCATATCTCAATATAATT-AAGATAAGTAAACAATTAAA
1207932 AA
128 AA
1207934 CACGTTTTTA
Statistics
Matches: 425, Mismatches: 87, Indels: 70
0.73 0.15 0.12
Matches are distributed among these distances:
201 27 0.06
202 36 0.08
203 94 0.22
204 42 0.10
205 12 0.03
206 26 0.06
207 17 0.04
208 5 0.01
209 12 0.03
210 31 0.07
211 11 0.03
212 22 0.05
213 60 0.14
214 30 0.07
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (201 bp):
TGTAATAAAAATATATGATTAGATCATCTATTATTTCTTTTAGTCAAAATAAGATAATTTTCATT
AATATAAAAAATTGATACAATTGTTCATATCTCAATATAATTAAGATAAGTAAACAATTAAAAAT
TAGAGACTCATTGAAATATAAAAATCAAGACAAATAAATACTATCATACGTATTTAACATTATCA
TTTTTT
Found at i:1212047 original size:18 final size:19
Alignment explanation
Indices: 1212019--1212054 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1212009 GGTAATAAAA
*
1212019 AATTAAAGAAGGAGAAGAT
1 AATTAAAGAAGAAGAAGAT
1212038 AATT-AAGAAGAAGAAGA
1 AATTAAAGAAGAAGAAGA
1212055 AGAAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (19 bp):
AATTAAAGAAGAAGAAGAT
Found at i:1217698 original size:84 final size:84
Alignment explanation
Indices: 1217601--1217853 Score: 434
Period size: 84 Copynumber: 3.0 Consensus size: 84
1217591 TCAGAGGAAT
*
1217601 AAAGAATCAATGTGGAGATAAAAATCTAAGGAGAGGTGGGTGAAAGAGAGAGATAGGAATATAAG
1 AAAGAATCAATGTGGAGATAGAAATCTAAGGAGAGGTGGGTGAAAGAGAGAGATAGGAATATAAG
1217666 ATATTTTCAGAGTAAGGCC
66 ATATTTTCAGAGTAAGGCC
* ** *
1217685 AAAGAATCAATGTGGAGATGGAAATCTCCGGAGAGGTGGGTGAAAAAGAGAGATAGGAATATAAG
1 AAAGAATCAATGTGGAGATAGAAATCTAAGGAGAGGTGGGTGAAAGAGAGAGATAGGAATATAAG
1217750 ATATTTTCAGAGTAAGGCC
66 ATATTTTCAGAGTAAGGCC
* * *
1217769 AAAGAATCGATGTGGAGATAGAAATCTAAGGAGACGTAGGTGAAAGAGAGAGATAGGAATATAAG
1 AAAGAATCAATGTGGAGATAGAAATCTAAGGAGAGGTGGGTGAAAGAGAGAGATAGGAATATAAG
1217834 ATATTTTCAGAGTAAGGCC
66 ATATTTTCAGAGTAAGGCC
1217853 A
1 A
1217854 GGGTGAGAAA
Statistics
Matches: 157, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 157 1.00
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (84 bp):
AAAGAATCAATGTGGAGATAGAAATCTAAGGAGAGGTGGGTGAAAGAGAGAGATAGGAATATAAG
ATATTTTCAGAGTAAGGCC
Found at i:1234060 original size:22 final size:21
Alignment explanation
Indices: 1234035--1234075 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1234025 ATATATGTAT
*
1234035 ATTTTTTAAACATCAAAAATTA
1 ATTTTCTAAACAT-AAAAATTA
*
1234057 ATTTTCTGAACATAAAAAT
1 ATTTTCTAAACATAAAAAT
1234076 AAAATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTTTCTAAACATAAAAATTA
Found at i:1243474 original size:21 final size:20
Alignment explanation
Indices: 1243448--1243490 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1243438 TGTTACTATA
1243448 TTTTCAAAAT-AAAAGATTATC
1 TTTTC-AAATGAAAAG-TTATC
*
1243469 TTTTCATATGAAAAGTTATC
1 TTTTCAAATGAAAAGTTATC
1243489 TT
1 TT
1243491 AGCTAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (20 bp):
TTTTCAAATGAAAAGTTATC
Found at i:1245257 original size:19 final size:18
Alignment explanation
Indices: 1245233--1245279 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1245223 CTTATCATTT
*
1245233 TTTAAATTATTGTCAAAAA
1 TTTAAATTAATG-CAAAAA
*
1245252 TTTAAATTAATGCATAAA
1 TTTAAATTAATGCAAAAA
*
1245270 TTGAAATTAA
1 TTTAAATTAA
1245280 ATAAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (18 bp):
TTTAAATTAATGCAAAAA
Found at i:1260754 original size:21 final size:22
Alignment explanation
Indices: 1260730--1260774 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1260720 AATAATAAAA
1260730 TATTA-ATTAAAAATAATAT-TT
1 TATTATATTAAAAA-AATATATT
*
1260751 TATTATTTTAAAAAAATATATT
1 TATTATATTAAAAAAATATATT
1260773 TA
1 TA
1260775 CATGAACGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTATATTAAAAAAATATATT
Found at i:1275230 original size:85 final size:86
Alignment explanation
Indices: 1275128--1275292 Score: 253
Period size: 85 Copynumber: 1.9 Consensus size: 86
1275118 TATAATTATC
* **
1275128 TTTCCTTAATTATCTTTTACCTTACTTGTATTTGAAG-AATGTTT-AGGTTAGGTTATTTTCTTA
1 TTTCCTTAATTATCTTTTACCTTACTTGTATTTCAAGAAAT-TTTAAAATTAGGTTATTTTCTTA
1275191 TCTATTTATGTATTTATTTAGG
65 TCTATTTATGTATTTATTTAGG
*
1275213 TTTCTTTAATTATCTTTTACCTTACTTGTATTTCAAGAAATTTTAAAATTAGGTTATTTTCTTAT
1 TTTCCTTAATTATCTTTTACCTTACTTGTATTTCAAGAAATTTTAAAATTAGGTTATTTTCTTAT
* *
1275278 TTATTTATTTATTTA
66 CTATTTATGTATTTA
1275293 GAAATTGTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
85 38 0.53
86 34 0.47
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (86 bp):
TTTCCTTAATTATCTTTTACCTTACTTGTATTTCAAGAAATTTTAAAATTAGGTTATTTTCTTAT
CTATTTATGTATTTATTTAGG
Found at i:1275570 original size:39 final size:39
Alignment explanation
Indices: 1275514--1275592 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
1275504 TTGACCATTA
* * *
1275514 TTCACCTTAGTGGAGTTTCTAACCTCACCAAGATTGGTG
1 TTCACCTTAATGAAGTTTCTAACCTCACCAAGATTAGTG
* *
1275553 TTCACCTTAATGAAGTTTCTAACCTTACCACGATTAGTG
1 TTCACCTTAATGAAGTTTCTAACCTCACCAAGATTAGTG
1275592 T
1 T
1275593 CTTCATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (39 bp):
TTCACCTTAATGAAGTTTCTAACCTCACCAAGATTAGTG
Found at i:1276047 original size:50 final size:50
Alignment explanation
Indices: 1275962--1276060 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
1275952 CTTAATAGTT
1275962 ATATAAAACTCTATTGAGTTAATAGATAGGCACATTCAA-ATTGAGAATAA
1 ATATAAAACTCTATTGAGTTAATAGATAGGCACATTCAAGA-TGAGAATAA
* * * * *
1276012 ATATAAAACTGTATTGAGTTAATTGTTAGGTACATTTAAGATGAGAATA
1 ATATAAAACTCTATTGAGTTAATAGATAGGCACATTCAAGATGAGAATA
1276061 TTTTGACTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 42 0.98
51 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.33
Consensus pattern (50 bp):
ATATAAAACTCTATTGAGTTAATAGATAGGCACATTCAAGATGAGAATAA
Found at i:1276166 original size:44 final size:44
Alignment explanation
Indices: 1276116--1276202 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
1276106 CTTAAAATGA
* *
1276116 TAAAATTTTCAAACTGTTAGATTTGTGCTCATTATTGTTTATGG
1 TAAAATTTTCAAACTATTACATTTGTGCTCATTATTGTTTATGG
*
1276160 TAAAATTTTCAAACTATTTCATTTGTGCTCATTATTGTTTATG
1 TAAAATTTTCAAACTATTACATTTGTGCTCATTATTGTTTATG
1276203 CATTGGGCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (44 bp):
TAAAATTTTCAAACTATTACATTTGTGCTCATTATTGTTTATGG
Done.