Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003744.1 Hibiscus syriacus cultivar Beakdansim tig00008013_pilon, whole genome shotgun sequence
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: 2457414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:1018319 original size:20 final size:20
Alignment explanation
Indices: 1018294--1018331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1018284 CATAAACTAC
*
1018294 TACAAAACTCAAAAATCAAT
1 TACAAAACCCAAAAATCAAT
*
1018314 TACAAAACCCTAAAATCA
1 TACAAAACCCAAAAATCA
1018332 CTTTAACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (20 bp):
TACAAAACCCAAAAATCAAT
Found at i:1025314 original size:25 final size:25
Alignment explanation
Indices: 1025269--1025324 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1025259 ATATCACAAA
*
1025269 TAAATATTTAAAGTATATTTTTATT
1 TAAATATTTAAAGTATATTTTAATT
* * *
1025294 TAAATATTTAATGTCTTTTTTAATT
1 TAAATATTTAAAGTATATTTTAATT
*
1025319 GAAATA
1 TAAATA
1025325 AATATCTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (25 bp):
TAAATATTTAAAGTATATTTTAATT
Found at i:1026451 original size:17 final size:18
Alignment explanation
Indices: 1026415--1026455 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1026405 ATATTATGTA
*
1026415 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
1026433 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
1026450 TTTACT
1 TTTACT
1026456 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:1032090 original size:12 final size:13
Alignment explanation
Indices: 1032073--1032101 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1032063 TATAATAAAA
1032073 AAAATTTATAAC-
1 AAAATTTATAACG
1032085 AAAATTTATAACG
1 AAAATTTATAACG
1032098 AAAA
1 AAAA
1032102 ATCGCACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAATTTATAACG
Found at i:1033199 original size:15 final size:15
Alignment explanation
Indices: 1033179--1033210 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1033169 AATTAAAAGA
*
1033179 TTATATTTATTTTAT
1 TTATATCTATTTTAT
1033194 TTATATCTATTTTAT
1 TTATATCTATTTTAT
1033209 TT
1 TT
1033211 TCAATTCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATATCTATTTTAT
Found at i:1035361 original size:29 final size:29
Alignment explanation
Indices: 1035321--1035384 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1035311 ATATACTCAG
1035321 GAGACTATTTTACAACTTTTAATAATCGA
1 GAGACTATTTTACAACTTTTAATAATCGA
* * *
1035350 GAGATTATTTTATAATTTTTAATAATCGA
1 GAGACTATTTTACAACTTTTAATAATCGA
*
1035379 AAGACT
1 GAGACT
1035385 CAACAAAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (29 bp):
GAGACTATTTTACAACTTTTAATAATCGA
Found at i:1035440 original size:2 final size:2
Alignment explanation
Indices: 1035433--1035457 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1035423 ACTTTACCCT
1035433 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1035458 GCTACCTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1035593 original size:18 final size:18
Alignment explanation
Indices: 1035567--1035603 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1035557 ATAATTATTC
*
1035567 TCAATTTGTTATTTTTAT
1 TCAAGTTGTTATTTTTAT
1035585 TCAAGTTGTTATTTTTAT
1 TCAAGTTGTTATTTTTAT
1035603 T
1 T
1035604 GGTATATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (18 bp):
TCAAGTTGTTATTTTTAT
Found at i:1036365 original size:43 final size:43
Alignment explanation
Indices: 1036282--1036365 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
1036272 TGCATAAGGA
* * *
1036282 ACTTCTCAAATTTAAAAATTCAAGAGAAAATAATATTCTCTGC
1 ACTTCTCAAATTCAAAAATTCAAGAGAAAATAACACTCTCTGC
* * * *
1036325 ACTTCTCAAATTCAAGACTTCAAGGGAAGATAACACTCTCT
1 ACTTCTCAAATTCAAAAATTCAAGAGAAAATAACACTCTCT
1036366 ACCGACGTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (43 bp):
ACTTCTCAAATTCAAAAATTCAAGAGAAAATAACACTCTCTGC
Found at i:1039926 original size:21 final size:21
Alignment explanation
Indices: 1039884--1039927 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1039874 CGTTACAATA
* * *
1039884 CTGATGTGGTGCTTCATGATG
1 CTGATGTGGTGATCCATAATG
1039905 CTGATGTGGTGATCCATAATG
1 CTGATGTGGTGATCCATAATG
1039926 CT
1 CT
1039928 AACATGGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (21 bp):
CTGATGTGGTGATCCATAATG
Found at i:1040079 original size:21 final size:20
Alignment explanation
Indices: 1040053--1040104 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1040043 TTTTAAATTC
1040053 AAAATTCAAAATAATAATACA
1 AAAATT-AAAATAATAATACA
* * *
1040074 AAAATTAAATTAAATTATTCA
1 AAAATTAAAAT-AATAATACA
1040095 AAAATTAAAA
1 AAAATTAAAA
1040105 ATATATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATTAAAATAATAATACA
Found at i:1041456 original size:22 final size:21
Alignment explanation
Indices: 1041382--1041456 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
1041372 ACTTGTAATA
* *
1041382 TATATTTTAATTATGTTTTTAAT
1 TATATTTTAA-TA-ATTTTTATT
* * *
1041405 TCTTTTTTAATAATTTAATTTTT
1 TATATTTTAATAATTT--TTATT
1041428 TAT-TTTTAATAATTTTGTATT
1 TATATTTTAATAATTTT-TATT
1041449 TATATTTT
1 TATATTTT
1041457 TTTGAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.02
21 9 0.22
22 18 0.44
23 13 0.32
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (21 bp):
TATATTTTAATAATTTTTATT
Found at i:1048290 original size:71 final size:68
Alignment explanation
Indices: 1048150--1048331 Score: 224
Period size: 71 Copynumber: 2.6 Consensus size: 68
1048140 TTAAAATTGG
* * * *
1048150 AAAGTATCAATATTTTTTCACAAAATATCGATACTTTCAAATTAAAAAAATGGAAAATTAGAAGG
1 AAAGTATCAATAGTTTTCCAC-AAATATCCATACTTTCAAATTAAAAAAATGGAAAATGAGAAGG
1048215 CTAC
65 CTAC
*
1048219 AAAGTATCAATA-TTTTCCACAAGTA-CCACTACTTTCAAATTTTAAAAAAACATGGAAAATGAG
1 AAAGTATCAATAGTTTTCCACAAATATCCA-TACTTTCAAA--TT-AAAAAA-ATGGAAAATGAG
1048282 AAGGCTAC
61 AAGGCTAC
* **
1048290 AAAGTATCGATAGTTTTCCACAAATATTGATACTTTCAAATT
1 AAAGTATCAATAGTTTTCCACAAATATCCATACTTTCAAATT
1048332 TTTTTATAGA
Statistics
Matches: 98, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
66 2 0.02
67 14 0.14
68 7 0.07
69 14 0.14
70 8 0.08
71 30 0.31
72 22 0.22
73 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (68 bp):
AAAGTATCAATAGTTTTCCACAAATATCCATACTTTCAAATTAAAAAAATGGAAAATGAGAAGGC
TAC
Found at i:1048962 original size:25 final size:25
Alignment explanation
Indices: 1048934--1048984 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1048924 GTTTGAAGAA
**
1048934 TGGGGTTGGTTTTTAATTTTAAGTG
1 TGGGGTTAATTTTTAATTTTAAGTG
1048959 TGGGGTTAATTTTTAATTTTAAGTG
1 TGGGGTTAATTTTTAATTTTAAGTG
1048984 T
1 T
1048985 TCTAGTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (25 bp):
TGGGGTTAATTTTTAATTTTAAGTG
Found at i:1049921 original size:15 final size:15
Alignment explanation
Indices: 1049903--1049980 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
1049893 TTATAGGAGT
1049903 ATATGTTATATGTGA
1 ATATGTTATATGTGA
* *
1049918 ATATGTTCTACGTGA
1 ATATGTTATATGTGA
* *
1049933 AAATGTTTTATGTGA
1 ATATGTTATATGTGA
* *
1049948 AAATGTTCA-ATATGA
1 ATATGTT-ATATGTGA
* *
1049963 ATGTGTTCTATGTGA
1 ATATGTTATATGTGA
1049978 ATA
1 ATA
1049981 AATGATACTT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.42
Consensus pattern (15 bp):
ATATGTTATATGTGA
Found at i:1050115 original size:23 final size:23
Alignment explanation
Indices: 1050085--1050151 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
1050075 GTAAAAGGTT
1050085 CTATGCGGTCCTTCGGGACAATC
1 CTATGCGGTCCTTCGGGACAATC
* * *
1050108 CTATGCGGTCATTCGGGATAATT
1 CTATGCGGTCCTTCGGGACAATC
* *
1050131 CTACGCGGTACTTCGGGACAA
1 CTATGCGGTCCTTCGGGACAA
1050152 ATTTATGTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
CTATGCGGTCCTTCGGGACAATC
Found at i:1050169 original size:46 final size:47
Alignment explanation
Indices: 1050083--1050201 Score: 113
Period size: 46 Copynumber: 2.6 Consensus size: 47
1050073 GAGTAAAAGG
* * *
1050083 TTCTATGCGGTCCTTCGGGAC-AATCCTATGCGGTCATTCGG-G-ATAA
1 TTCTACGCGGTACTTCGGGACAAAT-TTATGCGGTCATTCGGTGCAT-A
*
1050129 TTCTACGCGGTACTTCGGGACAAATTTATGTGGT-ACTTCGGTGCATA
1 TTCTACGCGGTACTTCGGGACAAATTTATGCGGTCA-TTCGGTGCATA
* *
1050176 TTCTACGTGGCACTTCGGTG-CAAATT
1 TTCTACGCGGTACTTCGG-GACAAATT
1050202 CTACGAGGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
45 1 0.02
46 31 0.50
47 27 0.44
48 3 0.05
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (47 bp):
TTCTACGCGGTACTTCGGGACAAATTTATGCGGTCATTCGGTGCATA
Found at i:1050190 original size:24 final size:24
Alignment explanation
Indices: 1050127--1050211 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 24
1050117 CATTCGGGAT
* *
1050127 AATTCTACGCGGTACTTCGG-GACA
1 AATTCTACGTGGCACTTCGGTG-CA
* *
1050151 AATT-TATGTGGTACTTCGGTGCA
1 AATTCTACGTGGCACTTCGGTGCA
*
1050174 TATTCTACGTGGCACTTCGGTGCA
1 AATTCTACGTGGCACTTCGGTGCA
*
1050198 AATTCTACGAGGCA
1 AATTCTACGTGGCA
1050212 GTTTCGACTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 18 0.35
24 34 0.65
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGTGCA
Found at i:1053268 original size:24 final size:24
Alignment explanation
Indices: 1053222--1053268 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1053212 TCGGTTTGAA
*
1053222 AGTTTTAATGTTTTTTTAAATTAC
1 AGTTTTAATGTTTTATTAAATTAC
*
1053246 AGTTTT-ATGTTTATATTACATTA
1 AGTTTTAATGTTT-TATTAAATTA
1053269 TGATATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (24 bp):
AGTTTTAATGTTTTATTAAATTAC
Found at i:1054415 original size:17 final size:18
Alignment explanation
Indices: 1054395--1054430 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1054385 TTTTTCTATT
1054395 TATTTATATT-TTTAATA
1 TATTTATATTATTTAATA
*
1054412 TATTTCTATTATTTAATA
1 TATTTATATTATTTAATA
1054430 T
1 T
1054431 CTTATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTATATTATTTAATA
Found at i:1058780 original size:21 final size:21
Alignment explanation
Indices: 1058751--1058803 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1058741 AAAAACTTCA
*
1058751 CTTCCCATTGCTATTCTTTCT
1 CTTCTCATTGCTATTCTTTCT
1058772 CTTCTCATTGCTATTCTTTCT
1 CTTCTCATTGCTATTCTTTCT
1058793 CTTCTCATTGC
1 CTTCTCATTGC
1058804 ATGCCTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.09, C:0.32, G:0.06, T:0.53
Consensus pattern (21 bp):
CTTCTCATTGCTATTCTTTCT
Found at i:1062641 original size:15 final size:14
Alignment explanation
Indices: 1062621--1062654 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1062611 GAAATACCCC
1062621 ACCGAACAGCCAATA
1 ACCGAA-AGCCAATA
1062636 ACCG-AAGCCAATA
1 ACCGAAAGCCAATA
1062649 ACCGAA
1 ACCGAA
1062655 GCCCAACCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.67
14 2 0.11
15 4 0.22
ACGTcount: A:0.47, C:0.32, G:0.15, T:0.06
Consensus pattern (14 bp):
ACCGAAAGCCAATA
Found at i:1062646 original size:13 final size:13
Alignment explanation
Indices: 1062628--1062657 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1062618 CCCACCGAAC
1062628 AGCCAATAACCGA
1 AGCCAATAACCGA
1062641 AGCCAATAACCGA
1 AGCCAATAACCGA
1062654 AGCC
1 AGCC
1062658 CAACCTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.33, G:0.17, T:0.07
Consensus pattern (13 bp):
AGCCAATAACCGA
Found at i:1063901 original size:26 final size:24
Alignment explanation
Indices: 1063839--1063901 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
1063829 TATTTCAATC
1063839 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
1063863 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
1063886 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
1063902 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:1063903 original size:22 final size:23
Alignment explanation
Indices: 1063873--1063919 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1063863 AAAATATATT
1063873 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
1063896 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
1063918 TA
1 TA
1063920 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:1063933 original size:32 final size:32
Alignment explanation
Indices: 1063867--1063946 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1063857 ATATTTAAAA
* *
1063867 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
1063899 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
1063931 TATATTATAATAATAT
1 TATATT-TATTAATAT
1063947 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:1064067 original size:27 final size:29
Alignment explanation
Indices: 1063978--1064089 Score: 83
Period size: 28 Copynumber: 4.0 Consensus size: 29
1063968 AATAATATAT
* * *
1063978 AATTAATTATTAATAAATTTATATTATTT-
1 AATTATTTAATAATAAA-TAATATTATTTA
* *
1064007 -ATTAATTTTAT-AGAAATAATATTA-TTA
1 AATT-ATTTAATAATAAATAATATTATTTA
*
1064034 AATTA-TTAATAATGAATAATATTATTTA
1 AATTATTTAATAATAAATAATATTATTTA
* *
1064062 TA-TATTTAATAATAATATAATAATATTT
1 AATTATTTAATAATAA-ATAATATTATTT
1064090 TAATAAAAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
26 6 0.09
27 21 0.32
28 23 0.35
29 15 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
AATTATTTAATAATAAATAATATTATTTA
Found at i:1064109 original size:23 final size:23
Alignment explanation
Indices: 1064048--1064133 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
1064038 ATTAATAATG
* *
1064048 AATAATATTATTT-ATATA-TTT
1 AATAATAATATTTAAAATATTTT
1064069 AATAATAATA--TAATAATATTTT
1 AATAATAATATTTAA-AATATTTT
* *
1064091 AATAAAAATATTTAAAATATATT
1 AATAATAATATTTAAAATATTTT
1064114 AATTAATAAT-TTTAAAATAT
1 AA-TAATAATATTTAAAATAT
1064134 AATATAACAC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 12 0.22
22 12 0.22
23 19 0.35
24 9 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATAATATTTAAAATATTTT
Found at i:1064112 original size:11 final size:12
Alignment explanation
Indices: 1064061--1064134 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 12
1064051 AATATTATTT
1064061 ATATATTTAATA
1 ATATATTTAATA
*
1064073 ATA-ATATAATA
1 ATATATTTAATA
1064084 ATAT-TTTAATAA
1 ATATATTTAAT-A
*
1064096 AAATATTTAA-A
1 ATATATTTAATA
1064107 ATATA-TTAATTA
1 ATATATTTAA-TA
1064119 ATA-ATTTTAA-A
1 ATATA-TTTAATA
1064130 ATATA
1 ATATA
1064135 ATATAACACT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
10 4 0.08
11 25 0.50
12 12 0.24
13 9 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATTTAATA
Found at i:1064267 original size:27 final size:26
Alignment explanation
Indices: 1064237--1064314 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 26
1064227 ATTATAAAAA
1064237 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATTT
* *
1064264 TAATATTT-TAA-AAAAAAATTATAT
1 TAATATTTATAATAAATAAATTATTT
*
1064288 TAAGT-TTTATGATAAATAATATTATTT
1 TAA-TATTTATAATAAATAA-ATTATTT
1064315 ATTGTATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 17 0.40
25 6 0.14
26 5 0.12
27 14 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATTT
Found at i:1064290 original size:24 final size:26
Alignment explanation
Indices: 1064204--1064312 Score: 71
Period size: 24 Copynumber: 4.1 Consensus size: 26
1064194 AAATATACCC
* * *
1064204 ATATTAATATTTTTATTAATAAAATT
1 ATATTAATATTTATAATAAAAAAATT
* *
1064230 ATAAAAATAATATTTAATAATAAATAAATT
1 AT---ATTAATATTT-ATAATAAAAAAATT
*
1064260 ATTTTAATATTT-TAA-AAAAAAATT
1 ATATTAATATTTATAATAAAAAAATT
* *
1064284 ATATTAAGT-TTTATGATAAATAATATT
1 ATATTAA-TATTTATAATAAA-AAAATT
1064311 AT
1 AT
1064313 TTATTGTATT
Statistics
Matches: 64, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
24 17 0.27
25 6 0.09
26 5 0.08
27 15 0.23
29 9 0.14
30 12 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATTAATATTTATAATAAAAAAATT
Found at i:1064442 original size:14 final size:14
Alignment explanation
Indices: 1064423--1064452 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1064413 CAGATAATGT
*
1064423 AATTCATTTTCCAG
1 AATTCAATTTCCAG
1064437 AATTCAATTTCCAG
1 AATTCAATTTCCAG
1064451 AA
1 AA
1064453 AACTAATTAC
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:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:1066270 original size:2 final size:2
Alignment explanation
Indices: 1066258--1066296 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1066248 TAATGTAACT
1066258 TA TA T- TA TA TA 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
1066297 ATTTACTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1067134 original size:12 final size:12
Alignment explanation
Indices: 1067117--1067150 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1067107 TAAAGATTTC
1067117 AAAGAAAATTAA
1 AAAGAAAATTAA
* *
1067129 AAAGAAAGTTTA
1 AAAGAAAATTAA
1067141 AAAGAAAATT
1 AAAGAAAATT
1067151 CAATTTGGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (12 bp):
AAAGAAAATTAA
Found at i:1068050 original size:27 final size:27
Alignment explanation
Indices: 1068012--1068075 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
1068002 TTAACTAGAT
1068012 CTTCTAGAAAACTGCTGCTGACTGAAC
1 CTTCTAGAAAACTGCTGCTGACTGAAC
* * *
1068039 CTTCTAGAAAACTGTTGTTGACTGGAC
1 CTTCTAGAAAACTGCTGCTGACTGAAC
1068066 CTTCTAGAAA
1 CTTCTAGAAA
1068076 CTACCATGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (27 bp):
CTTCTAGAAAACTGCTGCTGACTGAAC
Found at i:1069063 original size:26 final size:26
Alignment explanation
Indices: 1069034--1069083 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1069024 GATTATGATT
*
1069034 GTAATTTGGGATATTTCATATTTCGA
1 GTAATTTGAGATATTTCATATTTCGA
*
1069060 GTAATTTGAGATATTTCTTATTTC
1 GTAATTTGAGATATTTCATATTTC
1069084 AAATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (26 bp):
GTAATTTGAGATATTTCATATTTCGA
Found at i:1075743 original size:46 final size:47
Alignment explanation
Indices: 1075679--1075776 Score: 189
Period size: 46 Copynumber: 2.1 Consensus size: 47
1075669 GAAATAATTA
1075679 ATTATTAATCATTAATTGTTATTAATTGTTCGGTTACAAATTAATCT
1 ATTATTAATCATTAATTGTTATTAATTGTTCGGTTACAAATTAATCT
1075726 ATTATT-ATCATTAATTGTTATTAATTGTTCGGTTACAAATTAATCT
1 ATTATTAATCATTAATTGTTATTAATTGTTCGGTTACAAATTAATCT
1075772 ATTAT
1 ATTAT
1075777 AAATTTTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 45 0.88
47 6 0.12
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (47 bp):
ATTATTAATCATTAATTGTTATTAATTGTTCGGTTACAAATTAATCT
Found at i:1078264 original size:27 final size:29
Alignment explanation
Indices: 1078222--1078290 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
1078212 ATATGAGAAA
* *
1078222 ATATGAGAATAAGAAATAAG-TC-ATGTG-
1 ATATGTGAATATGAAA-AAGATCTATGTGT
*
1078249 ATATGTGAATATGAAAATGATCTATGTGT
1 ATATGTGAATATGAAAAAGATCTATGTGT
1078278 ATATGTGATATAT
1 ATATGTGA-ATAT
1078291 ATGATATATG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 16 0.46
28 5 0.14
29 8 0.23
30 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (29 bp):
ATATGTGAATATGAAAAAGATCTATGTGT
Found at i:1085525 original size:2 final size:2
Alignment explanation
Indices: 1085518--1085552 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1085508 TTTCCTTTTA
1085518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1085553 ACTTTTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1086480 original size:16 final size:17
Alignment explanation
Indices: 1086459--1086501 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1086449 TATGTAAAAT
1086459 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
1086475 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
1086492 AAATATTTAA
1 AAATATTTAA
1086502 TCAAGTAGTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:1086945 original size:135 final size:135
Alignment explanation
Indices: 1086702--1086948 Score: 374
Period size: 135 Copynumber: 1.8 Consensus size: 135
1086692 TTATGGACCA
1086702 CTAATTACCGAAGTAGGTAATCAATGTAACTTATGGGAAATCTAGGAAACCAATGCTTGAACGTT
1 CTAATTACCGAAGTAGGTAATCAATGTAACTTATGGGAAATCTAGGAAACCAATGCTTGAACGTT
** * * * *
1086767 TAGAAGGCCTGGCGACTTATGGAGGTCGTCCGGAGGACCTGGCGACCTATGGAGGTCTTCGAATA
66 TAGAAGGAATGGCGACTTATGGAGATCGCCCGGAAGACATGGCGACCTATGGAGGTCTTCGAATA
1086832 AAAGC
131 AAAGC
*
1086837 CTAATTACCGATA-TAGGTAAT-AACTGTAACTTATGGGAAATCTAGGAAACCAATGCTTGAGCG
1 CTAATTACCGA-AGTAGGTAATCAA-TGTAACTTATGGGAAATCTAGGAAACCAATGCTTGAACG
*
1086900 TTT-GGAGGAAATGGCGACTTATGGAGATCGCCCGGAAGACATGGCGACC
64 TTTAGAAGG-AATGGCGACTTATGGAGATCGCCCGGAAGACATGGCGACC
1086949 AACCCTCGAA
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
134 6 0.06
135 94 0.93
136 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.23
Consensus pattern (135 bp):
CTAATTACCGAAGTAGGTAATCAATGTAACTTATGGGAAATCTAGGAAACCAATGCTTGAACGTT
TAGAAGGAATGGCGACTTATGGAGATCGCCCGGAAGACATGGCGACCTATGGAGGTCTTCGAATA
AAAGC
Found at i:1094530 original size:20 final size:20
Alignment explanation
Indices: 1094505--1094542 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1094495 TAATTATTCC
1094505 ATCTTGAAAACATTTGCTCT
1 ATCTTGAAAACATTTGCTCT
*
1094525 ATCTTGCAAACATTTGCT
1 ATCTTGAAAACATTTGCT
1094543 GCAAATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (20 bp):
ATCTTGAAAACATTTGCTCT
Found at i:1097181 original size:35 final size:35
Alignment explanation
Indices: 1097135--1097203 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
1097125 TTTTTAAAAT
1097135 CGAATCGGACATTGAACCGGTAAAGGTACTGGTTC
1 CGAATCGGACATTGAACCGGTAAAGGTACTGGTTC
1097170 CGAATCGGACATTGAACCGGTAAAGGTACTGGTT
1 CGAATCGGACATTGAACCGGTAAAGGTACTGGTT
1097204 TACTGGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (35 bp):
CGAATCGGACATTGAACCGGTAAAGGTACTGGTTC
Found at i:1115197 original size:22 final size:22
Alignment explanation
Indices: 1115163--1115220 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
1115153 TAATATTAGT
*
1115163 GTTTGACAGTAACAAAATATCA
1 GTTTGACAATAACAAAATATCA
* *
1115185 GTTTGCCAATAACAAAATATAAA
1 GTTTGACAATAACAAAATAT-CA
1115208 GTTTGACTAATAA
1 GTTTGAC-AATAA
1115221 GTTCAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.60
23 7 0.23
24 5 0.17
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (22 bp):
GTTTGACAATAACAAAATATCA
Found at i:1121915 original size:30 final size:28
Alignment explanation
Indices: 1121879--1121941 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1121869 TGCTGATATT
*
1121879 TTGTTTTTAGTACCAATAAAGGTATCCGAC
1 TTGTTTTTAGTA--AAGAAAGGTATCCGAC
** *
1121909 TTGTTTTTTTTATAGAAAGGTATCCGAC
1 TTGTTTTTAGTAAAGAAAGGTATCCGAC
1121937 TTGTT
1 TTGTT
1121942 AATTATAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 19 0.66
30 10 0.34
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (28 bp):
TTGTTTTTAGTAAAGAAAGGTATCCGAC
Found at i:1132132 original size:16 final size:16
Alignment explanation
Indices: 1132111--1132143 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1132101 TAAAAAATAA
1132111 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1132127 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1132143 A
1 A
1132144 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1132237 original size:16 final size:16
Alignment explanation
Indices: 1132212--1132256 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1132202 TAATAAATAA
*
1132212 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
1132228 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1132244 ACGAACATAAACG
1 ACGAACATAAACG
1132257 TTGGAGACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1133358 original size:10 final size:10
Alignment explanation
Indices: 1133343--1133402 Score: 57
Period size: 10 Copynumber: 5.6 Consensus size: 10
1133333 ATAAATGAAT
1133343 GAACATAAAC
1 GAACATAAAC
1133353 GAACATAAAC
1 GAACATAAAC
*
1133363 GAATATAACTGAAC
1 GAACAT-A---AAC
*
1133377 GAACATTAAC
1 GAACATAAAC
*
1133387 GAACATAACC
1 GAACATAAAC
1133397 GAACAT
1 GAACAT
1133403 TCACGAACGT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 32 0.78
11 1 0.02
14 8 0.20
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.15
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1133366 original size:24 final size:24
Alignment explanation
Indices: 1133330--1133389 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1133320 GATTGGGTTA
*
1133330 AACATAAATGAAT-GAACATAAACG
1 AACATAAACGAATAGAAC-TAAACG
* *
1133354 AACATAAACGAATATAACTGAACG
1 AACATAAACGAATAGAACTAAACG
*
1133378 AACATTAACGAA
1 AACATAAACGAA
1133390 CATAACCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.57, C:0.15, G:0.12, T:0.17
Consensus pattern (24 bp):
AACATAAACGAATAGAACTAAACG
Found at i:1133394 original size:24 final size:24
Alignment explanation
Indices: 1133350--1133424 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
1133340 AATGAACATA
* *
1133350 AACGAACATAAACGAATATAACTG
1 AACGAACATTAACGAACATAACTG
1133374 AACGAACATTAACGAACATAAC--
1 AACGAACATTAACGAACATAACTG
* * *
1133396 --CGAACATTCACGAACGTAAATG
1 AACGAACATTAACGAACATAACTG
1133418 AACGAAC
1 AACGAAC
1133425 GAGACCTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 17 0.40
24 25 0.60
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (24 bp):
AACGAACATTAACGAACATAACTG
Found at i:1133411 original size:34 final size:34
Alignment explanation
Indices: 1133330--1133402 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
1133320 GATTGGGTTA
* *
1133330 AACATAAATGAATGAACATAAACGAACATAAACG
1 AACATAACTGAACGAACATAAACGAACATAAACG
* * *
1133364 AATATAACTGAACGAACATTAACGAACATAACCG
1 AACATAACTGAACGAACATAAACGAACATAAACG
1133398 AACAT
1 AACAT
1133403 TCACGAACGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (34 bp):
AACATAACTGAACGAACATAAACGAACATAAACG
Found at i:1133420 original size:20 final size:20
Alignment explanation
Indices: 1133343--1133420 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
1133333 ATAAATGAAT
*
1133343 GAACATAAACGAACATAAAC
1 GAACATAAACGAACATTAAC
*
1133363 GAATATAACTGAACGAACATTAAC
1 GAACAT-A---AACGAACATTAAC
* *
1133387 GAACATAACCGAACATTCAC
1 GAACATAAACGAACATTAAC
* *
1133407 GAACGTAAATGAAC
1 GAACATAAACGAAC
1133421 GAACGAGACC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 27 0.59
21 1 0.02
23 1 0.02
24 17 0.37
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
GAACATAAACGAACATTAAC
Found at i:1138216 original size:193 final size:196
Alignment explanation
Indices: 1137887--1138275 Score: 757
Period size: 193 Copynumber: 2.0 Consensus size: 196
1137877 TAATCAAAAC
1137887 CAGTTCCTTAAAGGCTTAAATGCAGAAAACAAGTTGATTTGTCTGTTTTGGGGTTCTTGGTAAAA
1 CAGTTCCTTAAAGGCTTAAATGCAGAAAACAAGTTGATTTGTCTGTTTTGGGGTTCTTGGTAAAA
1137952 ACGATTGAATTTTTTTTCCCTTGCTGTCTCCCTATTCCCCCAAAATTTGATTCGTAGGAGATGTT
66 ACGATTGAATTTTTTTTCCCTTGCTGTCTCCCTATTCCCCCAAAATTTGATTCGTAGGAGATGTT
1138017 TGGTTCAAGGAATATAAGA-TTTCATGTGAAT-AAATCCACGTTCTCATATTTGA-TGGTCGGCA
131 TGGTTCAAGGAATATAAGATTTTCATGTGAATAAAATCCACGTTCTCATATTTGATTGGTCGGCA
1138079 A
196 A
1138080 CAGTTCCTTAAAGGCTTAAATGCAGAAAACAAGTTGATTTGTCTGTTTTGGGGTTCTTGGTAAAA
1 CAGTTCCTTAAAGGCTTAAATGCAGAAAACAAGTTGATTTGTCTGTTTTGGGGTTCTTGGTAAAA
1138145 ACGATTGAATTTTTTTTCCCTTGCTGTCTCCCTATTCCCCCAAAATTTGATTCGTAGGAGATGTT
66 ACGATTGAATTTTTTTTCCCTTGCTGTCTCCCTATTCCCCCAAAATTTGATTCGTAGGAGATGTT
1138210 TGGTTCAAGGAATATAAGATTTTCATGTGAATAAAATCCACGTTCTCATATTTGATTGGTCGGCA
131 TGGTTCAAGGAATATAAGATTTTCATGTGAATAAAATCCACGTTCTCATATTTGATTGGTCGGCA
1138275 A
196 A
1138276 TCTTATTCCA
Statistics
Matches: 193, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
193 149 0.77
194 12 0.06
195 22 0.11
196 10 0.05
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (196 bp):
CAGTTCCTTAAAGGCTTAAATGCAGAAAACAAGTTGATTTGTCTGTTTTGGGGTTCTTGGTAAAA
ACGATTGAATTTTTTTTCCCTTGCTGTCTCCCTATTCCCCCAAAATTTGATTCGTAGGAGATGTT
TGGTTCAAGGAATATAAGATTTTCATGTGAATAAAATCCACGTTCTCATATTTGATTGGTCGGCA
A
Found at i:1145608 original size:112 final size:112
Alignment explanation
Indices: 1145411--1145638 Score: 447
Period size: 112 Copynumber: 2.0 Consensus size: 112
1145401 TTTTAAAATT
1145411 TCAAAAATTAATCTAACTTGAATTTAAACTGATAAAAATCTAAAATATTATTATATAATTTTTTA
1 TCAAAAATTAATCTAACTTGAATTTAAACTGATAAAAATCTAAAATATTATTATATAATTTTTTA
*
1145476 ACCCTTCAATTCTAGATAAAATATTGTAGGTCTTTTGTAAATCTAAA
66 ACCCTTCAATTCTAGATAAAATACTGTAGGTCTTTTGTAAATCTAAA
1145523 TCAAAAATTAATCTAACTTGAATTTAAACTGATAAAAATCTAAAATATTATTATATAATTTTTTA
1 TCAAAAATTAATCTAACTTGAATTTAAACTGATAAAAATCTAAAATATTATTATATAATTTTTTA
1145588 ACCCTTCAATTCTAGATAAAATACTGTAGGTCTTTTGTAAATCTAAA
66 ACCCTTCAATTCTAGATAAAATACTGTAGGTCTTTTGTAAATCTAAA
1145635 TCAA
1 TCAA
1145639 TTTAGGGACA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 115 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.39
Consensus pattern (112 bp):
TCAAAAATTAATCTAACTTGAATTTAAACTGATAAAAATCTAAAATATTATTATATAATTTTTTA
ACCCTTCAATTCTAGATAAAATACTGTAGGTCTTTTGTAAATCTAAA
Found at i:1147350 original size:26 final size:26
Alignment explanation
Indices: 1147321--1147370 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1147311 TTATTTTTAC
*
1147321 TGTTTTTATT-TTTCATATTTATTTGT
1 TGTTTTAATTATTTCAT-TTTATTTGT
*
1147347 TGTTTTAATTATTTTATTTTATTT
1 TGTTTTAATTATTTCATTTTATTT
1147371 ATTAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (26 bp):
TGTTTTAATTATTTCATTTTATTTGT
Found at i:1147362 original size:34 final size:32
Alignment explanation
Indices: 1147289--1147366 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 32
1147279 GTCCTTGTAC
* *
1147289 TTATTTTATTTTTCATTTTATGTTATTTTTAC
1 TTATTTTATTTTTCATTTTATGTTAGTTTTAA
1147321 TGT-TTTTATTTTTCATATTTATTTGTT-GTTTTAA
1 T-TATTTTATTTTTCAT-TTTA--TGTTAGTTTTAA
1147355 TTATTTTATTTT
1 TTATTTTATTTT
1147367 ATTTATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
32 14 0.36
33 6 0.15
34 15 0.38
35 4 0.10
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.73
Consensus pattern (32 bp):
TTATTTTATTTTTCATTTTATGTTAGTTTTAA
Found at i:1162064 original size:50 final size:48
Alignment explanation
Indices: 1161989--1162123 Score: 156
Period size: 45 Copynumber: 2.9 Consensus size: 48
1161979 TCCTACCCAA
**
1161989 CATGATATCTACCTC-CATGCTTTGTTATTCACAAAAATAAATCCTAACCG
1 CATGATATCTAATTCGCATGC-TTGTTATTCA-AAAAATAAA-CCTAACCG
1162039 CATGATATCTAATTCGCATGCTTG---TTCAAAAAATAAACCTAACCG
1 CATGATATCTAATTCGCATGCTTGTTATTCAAAAAATAAACCTAACCG
* *
1162084 CATGATATCTAGTTCGCATGCAT-TTATTCGAAAAAA-AAAC
1 CATGATATCTAATTCGCATGCTTGTTATTC-AAAAAATAAAC
1162124 GAAAATAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
45 29 0.38
46 9 0.12
47 11 0.14
48 6 0.08
50 16 0.21
51 5 0.07
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.30
Consensus pattern (48 bp):
CATGATATCTAATTCGCATGCTTGTTATTCAAAAAATAAACCTAACCG
Found at i:1163026 original size:17 final size:18
Alignment explanation
Indices: 1163006--1163039 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1162996 ATGCTTTCTC
1163006 ATTTTAAATAA-AAATTA
1 ATTTTAAATAACAAATTA
*
1163023 ATTTTAATTAACAAATT
1 ATTTTAAATAACAAATT
1163040 GAGGTCTGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTAAATAACAAATTA
Found at i:1172828 original size:45 final size:47
Alignment explanation
Indices: 1172760--1172848 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 47
1172750 TGCTTTGTTA
* *
1172760 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGTATGCTTG
1 TTCACAAAAATAAATCATAACCGCATGATATCTAATTCGCATGCTTG
*
1172807 TTCA-AAAAATAAA-CATAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAATAAATCATAACCGCATGATATCTAATTCGCATGC
1172849 ATTTATTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 26 0.67
46 9 0.23
47 4 0.10
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.29
Consensus pattern (47 bp):
TTCACAAAAATAAATCATAACCGCATGATATCTAATTCGCATGCTTG
Found at i:1181557 original size:117 final size:116
Alignment explanation
Indices: 1181394--1181756 Score: 546
Period size: 117 Copynumber: 3.1 Consensus size: 116
1181384 TGTCTTGTAA
** * *
1181394 TGAGGATGGTCCAGGTGTGGGATTTGATTCTACAATGCAGGCCTCAACAACCTCAGATGCCTGTG
1 TGAGGATGGTCCATCTGTGGGATTTGATTCTACATTGCAGGCCTCAACCACCTCAGATGCCTGTG
* * *
1181459 TAAGCTCTGGTTTATTATCAGGACGGGCAGATTCATCGGAAATAGCTTGTGC
66 TAAGCTCTGGTTTATTATCAGGATGGGCAGAATCATC-GAAACAGCTTGTGC
1181511 TGAGGATGGTCCATCTGTGGGATTTGATTCTACATTGCAGGCCTCAACCACCTCAGATGCCTGTG
1 TGAGGATGGTCCATCTGTGGGATTTGATTCTACATTGCAGGCCTCAACCACCTCAGATGCCTGTG
*
1181576 TAAGCTCTGGTTTATTATCAGGATGGGCAGACTCATCTGAAACAGCTTGTGC
66 TAAGCTCTGGTTTATTATCAGGATGGGCAGAATCATC-GAAACAGCTTGTGC
* *
1181628 TGAGGATGGTCCATCTGTGGGATTCGATTCTACATTGCAGGCGTCAACCACCTCAGATGCCTGTG
1 TGAGGATGGTCCATCTGTGGGATTTGATTCTACATTGCAGGCCTCAACCACCTCAGATGCCTGTG
* * * ** * *
1181693 TACGCTCCGGTTTTTTATCAGGATGGAAAGAATCATCAAAGACGGCTTGTGC
66 TAAGCTCTGGTTTATTATCAGGATGGGCAGAATCATCGAA-ACAGCTTGTGC
1181745 TGAGGATGGTCC
1 TGAGGATGGTCC
1181757 TCCTAAGGGG
Statistics
Matches: 227, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
116 2 0.01
117 225 0.99
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (116 bp):
TGAGGATGGTCCATCTGTGGGATTTGATTCTACATTGCAGGCCTCAACCACCTCAGATGCCTGTG
TAAGCTCTGGTTTATTATCAGGATGGGCAGAATCATCGAAACAGCTTGTGC
Found at i:1185215 original size:114 final size:114
Alignment explanation
Indices: 1185015--1185239 Score: 423
Period size: 114 Copynumber: 2.0 Consensus size: 114
1185005 TAGGGATGGT
* *
1185015 TTTACTCGCATCTGCTAAAGGAATTGATGTAGGCAAAGAATCTGTTGTAGTAATGGGAACTGAAG
1 TTTACTCACATCTGCTAAAGGAATTGATGTAGGCAAAGAATCTGTTGTAGTAATAGGAACTGAAG
1185080 GTTCAGTTTTCCCAATTGGAATAGTTGGATGCACTTTAGCTTCTGAGGA
66 GTTCAGTTTTCCCAATTGGAATAGTTGGATGCACTTTAGCTTCTGAGGA
*
1185129 TTTACTCACATCTGCTAAAGGAATTGATGTAGGCAAAGAATCTGTTGTTGTAATAGGAACTGAAG
1 TTTACTCACATCTGCTAAAGGAATTGATGTAGGCAAAGAATCTGTTGTAGTAATAGGAACTGAAG
1185194 GTTCAGTTTTCCCAATTGGAATAGTTGGATGCACTTTAGCTTCTGA
66 GTTCAGTTTTCCCAATTGGAATAGTTGGATGCACTTTAGCTTCTGA
1185240 AATTTGATTC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (114 bp):
TTTACTCACATCTGCTAAAGGAATTGATGTAGGCAAAGAATCTGTTGTAGTAATAGGAACTGAAG
GTTCAGTTTTCCCAATTGGAATAGTTGGATGCACTTTAGCTTCTGAGGA
Found at i:1221651 original size:22 final size:22
Alignment explanation
Indices: 1221625--1221667 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1221615 ATCCGAACAT
*
1221625 AAAATCTAAAAATTCAAAATAC
1 AAAATATAAAAATTCAAAATAC
* *
1221647 AAAATATAATAATTCATAATA
1 AAAATATAAAAATTCAAAATA
1221668 TAAATAATTC
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:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATATAAAAATTCAAAATAC
Found at i:1221675 original size:16 final size:15
Alignment explanation
Indices: 1221649--1221684 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1221639 CAAAATACAA
1221649 AATATAATAATTCAT
1 AATATAATAATTCAT
1221664 AATATAAATAATTCAT
1 AATAT-AATAATTCAT
*
1221680 TATAT
1 AATAT
1221685 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAATAATTCAT
Found at i:1223780 original size:24 final size:24
Alignment explanation
Indices: 1223753--1223802 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1223743 ATAAAGAACC
1223753 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
1223777 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
1223801 AA
1 AA
1223803 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:1226143 original size:15 final size:15
Alignment explanation
Indices: 1226107--1226149 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1226097 AAAATAATAT
* *
1226107 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
1226122 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
1226136 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
1226150 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:1229375 original size:24 final size:24
Alignment explanation
Indices: 1229348--1229397 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1229338 ATAAAGAACC
1229348 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
1229372 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
1229396 AA
1 AA
1229398 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:1230794 original size:18 final size:17
Alignment explanation
Indices: 1230745--1230798 Score: 74
Period size: 18 Copynumber: 3.2 Consensus size: 17
1230735 TATATCTGCA
*
1230745 AAAAAATTATAT-AATT
1 AAAATATTATATAAATT
*
1230761 AAAATATTAAATAAATT
1 AAAATATTATATAAATT
1230778 AAAATACTTATATAAATT
1 AAAATA-TTATATAAATT
1230796 AAA
1 AAA
1230799 TACAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 10 0.30
17 10 0.30
18 13 0.39
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATATTATATAAATT
Found at i:1234796 original size:21 final size:21
Alignment explanation
Indices: 1234770--1234809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1234760 CAGAACCCTA
*
1234770 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1234791 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1234810 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1234838 original size:20 final size:21
Alignment explanation
Indices: 1234792--1234852 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1234782 TTCCCCTGTG
1234792 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1234815 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1234835 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1234853 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1240691 original size:19 final size:19
Alignment explanation
Indices: 1240667--1240707 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1240657 GGTTATGAAA
1240667 CATACTGAAATTCTCCGAG
1 CATACTGAAATTCTCCGAG
*
1240686 CATACTGGAATTCTCCGAG
1 CATACTGAAATTCTCCGAG
1240705 CAT
1 CAT
1240708 GAGTTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (19 bp):
CATACTGAAATTCTCCGAG
Found at i:1243480 original size:27 final size:27
Alignment explanation
Indices: 1243442--1243509 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
1243432 TATCTAGAAA
*
1243442 TAACTTAAACCAAAAGCAACATAATTT
1 TAACTCAAACCAAAAGCAACATAATTT
1243469 TAACTCAAACCAAAAGCAACATAATTT
1 TAACTCAAACCAAAAGCAACATAATTT
*
1243496 TAACTGAAACCAAA
1 TAACTCAAACCAAA
1243510 GGATTGAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.53, C:0.21, G:0.04, T:0.22
Consensus pattern (27 bp):
TAACTCAAACCAAAAGCAACATAATTT
Found at i:1243690 original size:18 final size:18
Alignment explanation
Indices: 1243667--1243701 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1243657 ATCTCGACGC
*
1243667 GATGAGTTTGAATAAAAT
1 GATGAGTTTAAATAAAAT
1243685 GATGAGTTTAAATAAAA
1 GATGAGTTTAAATAAAA
1243702 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (18 bp):
GATGAGTTTAAATAAAAT
Found at i:1245022 original size:35 final size:35
Alignment explanation
Indices: 1244953--1245027 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
1244943 ATTGTTACTT
* **
1244953 GTTAAGCTCGTTAAAATTTTATTTAACTGTTTCTC
1 GTTAAGCTCGTTAAAATTTTACTTAACTCATTCTC
* * * *
1244988 TTTAAGCTCGTTAAAATTTTGCTTGATTCATTCTC
1 GTTAAGCTCGTTAAAATTTTACTTAACTCATTCTC
1245023 GTTAA
1 GTTAA
1245028 AAAAATTCGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (35 bp):
GTTAAGCTCGTTAAAATTTTACTTAACTCATTCTC
Found at i:1249895 original size:76 final size:76
Alignment explanation
Indices: 1249776--1249975 Score: 246
Period size: 76 Copynumber: 2.6 Consensus size: 76
1249766 CCGTTGTTCA
* * * *
1249776 AGGGGGAATCGGTACCCCCT-TGGGGGG-ATCGTTTCCCTCCGAGCA-TACTGGAATTCTCGGAG
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTA-TGGAAATCTCGGAG
**
1249838 -CAAAACTGTTT
65 CCAAAACCATTT
* *
1249849 AGGGGGGAATCGGTTCCTTCTATGGGGGGAATCGGTTCCCTCCGAGCATTATGGAAATCTCGGGG
1 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTATGGAAATCTCGGAG
1249914 CCAAAACCATTT
65 CCAAAACCATTT
*
1249926 AGGGGGAATCGGTTCCTCCTATGGGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGAATCGGTTCCTCCTAT---GGGGGGAATCGGTTCCCTCCGAGCA
1249976 ATCTGTAATT
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
73 1 0.01
74 16 0.15
75 7 0.06
76 49 0.45
77 12 0.11
79 24 0.22
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (76 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTATGGAAATCTCGGAGC
CAAAACCATTT
Found at i:1250581 original size:7 final size:7
Alignment explanation
Indices: 1250569--1250611 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
1250559 CACTATTCAT
1250569 AAATCCA
1 AAATCCA
1250576 AAATCCA
1 AAATCCA
1250583 ACAATCCACA
1 A-AAT-C-CA
1250593 AAATCCA
1 AAATCCA
1250600 ACAATCCA
1 A-AATCCA
1250608 AAAT
1 AAAT
1250612 ATCCAAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 14 0.44
8 11 0.34
9 4 0.12
10 3 0.09
ACGTcount: A:0.56, C:0.30, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATCCA
Found at i:1250596 original size:17 final size:17
Alignment explanation
Indices: 1250574--1250617 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1250564 TTCATAAATC
1250574 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
1250591 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
1250608 -AAATATCCAA
1 CAAA-ATCCAA
1250618 AATGTTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.55, C:0.32, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:1250620 original size:9 final size:8
Alignment explanation
Indices: 1250569--1250619 Score: 59
Period size: 8 Copynumber: 6.2 Consensus size: 8
1250559 CACTATTCAT
1250569 AAATCC-A
1 AAATCCAA
1250576 AAATCCAA
1 AAATCCAA
*
1250584 CAATCCACA
1 AAATCCA-A
1250593 AAATCCAA
1 AAATCCAA
*
1250601 CAATCCAA
1 AAATCCAA
1250609 AATATCCAA
1 AA-ATCCAA
1250618 AA
1 AA
1250620 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
7 6 0.16
8 16 0.43
9 15 0.41
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:1258499 original size:75 final size:76
Alignment explanation
Indices: 1258392--1258588 Score: 283
Period size: 75 Copynumber: 2.6 Consensus size: 76
1258382 GTTGTACAAG
* * * *
1258392 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCA-TACTGGAATTCTCGGAG-
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTA-TGGAAATCTCGGAGC
**
1258454 CAAAACTGTTTA
65 CAAAACCATTTA
*
1258466 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTATGGAAATCTCGGGGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTATGGAAATCTCGGAGCC
1258531 AAAACCATTTA
66 AAAACCATTTA
*
1258542 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
1258589 ATTTGTAATT
Statistics
Matches: 111, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
74 17 0.15
75 37 0.33
76 33 0.30
77 24 0.22
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTATGGAAATCTCGGAGCC
AAAACCATTTA
Found at i:1267870 original size:31 final size:31
Alignment explanation
Indices: 1267803--1267862 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1267793 CAATTTAAGG
*
1267803 CAAAATGGTTTTTGGACTTAAATTGAATTTA
1 CAAAATGGTATTTGGACTTAAATTGAATTTA
1267834 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTAAATTGAATTTA
1267863 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTAAATTGAATTTA
Found at i:1267954 original size:19 final size:19
Alignment explanation
Indices: 1267927--1267993 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1267917 AATATTTTTA
* *
1267927 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
1267946 TGAACAGTAACTTACTATT
1 TGAACAGTAAATTACTATT
* *
1267965 TGAATAGTAAATCACTATT
1 TGAACAGTAAATTACTATT
1267984 TGAACAGTAA
1 TGAACAGTAA
1267994 CCCGAGGCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1268134 original size:20 final size:21
Alignment explanation
Indices: 1268098--1268138 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1268088 ATTTGAATAT
*
1268098 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1268119 TATGAA-GGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1268139 CCTATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1268200 original size:21 final size:21
Alignment explanation
Indices: 1268167--1268206 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1268157 GTTTTGCAGA
*
1268167 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1268189 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1268207 AGATATGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1268489 original size:32 final size:34
Alignment explanation
Indices: 1268422--1268491 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
1268412 TTTTGTAAAG
1268422 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAACTA
*
1268456 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAACTA
1268488 GGGA
1 GGGA
1268492 GTTGTAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 12 0.34
33 1 0.03
34 22 0.63
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAACTA
Found at i:1281635 original size:16 final size:17
Alignment explanation
Indices: 1281599--1281633 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1281589 TGAAAGAATG
1281599 AAGAAAAAAATTTATAA
1 AAGAAAAAAATTTATAA
* *
1281616 AAGAAAAGAATTTGTAA
1 AAGAAAAAAATTTATAA
1281633 A
1 A
1281634 GAGATATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (17 bp):
AAGAAAAAAATTTATAA
Found at i:1297611 original size:5 final size:5
Alignment explanation
Indices: 1297597--1297630 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1297587 ATCACGACCA
*
1297597 CGAGC AGAGC CGAGC CGAGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
1297631 ATAGACGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.24, C:0.35, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:1298161 original size:31 final size:31
Alignment explanation
Indices: 1298123--1298202 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
1298113 AAAAAAGTTT
* *
1298123 TTGTTCATGTTCATTCATTAAGGAATATAGC
1 TTGTTCATATTCGTTCATTAAGGAATATAGC
*
1298154 TTGTTCATATTCGTTCATTAAGGAGTATAGC
1 TTGTTCATATTCGTTCATTAAGGAATATAGC
1298185 TTGTTCATATTCGTTCAT
1 TTGTTCATATTCGTTCAT
1298203 GTTCATTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (31 bp):
TTGTTCATATTCGTTCATTAAGGAATATAGC
Found at i:1298222 original size:20 final size:20
Alignment explanation
Indices: 1298199--1298236 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1298189 TCATATTCGT
1298199 TCATGTTCATTCATTTAAGA
1 TCATGTTCATTCATTTAAGA
*
1298219 TCATGTTCGTTCATTTAA
1 TCATGTTCATTCATTTAA
1298237 ATGATAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (20 bp):
TCATGTTCATTCATTTAAGA
Found at i:1298272 original size:14 final size:14
Alignment explanation
Indices: 1298253--1298292 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1298243 AACGAACATA
1298253 AACGAACACAAACG
1 AACGAACACAAACG
*
1298267 AACGAACATAAACG
1 AACGAACACAAACG
1298281 AAC-AACACAAAC
1 AACGAACACAAAC
1298293 ACACACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.60, C:0.28, G:0.10, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:1298284 original size:10 final size:10
Alignment explanation
Indices: 1298240--1298269 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1298230 CATTTAAATG
1298240 ATAAACGAAC
1 ATAAACGAAC
1298250 ATAAACGAAC
1 ATAAACGAAC
*
1298260 ACAAACGAAC
1 ATAAACGAAC
1298270 GAACATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1298564 original size:10 final size:10
Alignment explanation
Indices: 1298549--1298596 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 10
1298539 TCATCTGTTC
1298549 GAACATAAAT
1 GAACATAAAT
1298559 GAACATAAAT
1 GAACATAAAT
1298569 GAACGAACATAAAT
1 ----GAACATAAAT
1298583 GAACATAAAT
1 GAACATAAAT
1298593 GAAC
1 GAAC
1298597 GAACATAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 24 0.71
14 10 0.29
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.17
Consensus pattern (10 bp):
GAACATAAAT
Found at i:1298577 original size:24 final size:24
Alignment explanation
Indices: 1298548--1298648 Score: 132
Period size: 24 Copynumber: 4.2 Consensus size: 24
1298538 GTCATCTGTT
*
1298548 CGAACATAAATGAACATAAATGAA
1 CGAACATAAACGAACATAAATGAA
*
1298572 CGAACATAAATGAACATAAATGAA
1 CGAACATAAACGAACATAAATGAA
* *
1298596 CGAACATAAACGAACGA-ACATAAA
1 CGAACATAAACGAAC-ATAAATGAA
* *
1298620 CGAACATACACGAACGTAAATGAA
1 CGAACATAAACGAACATAAATGAA
1298644 CGAAC
1 CGAAC
1298649 GAACCATTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
24 67 0.99
25 1 0.01
ACGTcount: A:0.55, C:0.18, G:0.14, T:0.13
Consensus pattern (24 bp):
CGAACATAAACGAACATAAATGAA
Found at i:1298578 original size:14 final size:14
Alignment explanation
Indices: 1298559--1298624 Score: 86
Period size: 14 Copynumber: 5.0 Consensus size: 14
1298549 GAACATAAAT
1298559 GAACATAAATGAAC
1 GAACATAAATGAAC
1298573 GAACATAAAT----
1 GAACATAAATGAAC
1298583 GAACATAAATGAAC
1 GAACATAAATGAAC
*
1298597 GAACATAAACGAAC
1 GAACATAAATGAAC
*
1298611 GAACATAAACGAAC
1 GAACATAAATGAAC
1298625 ATACACGAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
10 10 0.21
14 37 0.79
ACGTcount: A:0.58, C:0.17, G:0.14, T:0.12
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:1298611 original size:38 final size:38
Alignment explanation
Indices: 1298559--1298652 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
1298549 GAACATAAAT
* * *
1298559 GAACATAAATGAACGAACATAAATGAACATAAATGAAC
1 GAACATAAACGAACGAACATAAACGAACATAAACGAAC
*
1298597 GAACATAAACGAACGAACATAAACGAACATACACGAAC
1 GAACATAAACGAACGAACATAAACGAACATAAACGAAC
*
1298635 GTAA-ATGAACGAACGAAC
1 G-AACATAAACGAACGAAC
1298653 CATTTGTTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
38 48 0.96
39 2 0.04
ACGTcount: A:0.55, C:0.18, G:0.15, T:0.12
Consensus pattern (38 bp):
GAACATAAACGAACGAACATAAACGAACATAAACGAAC
Found at i:1298635 original size:14 final size:13
Alignment explanation
Indices: 1298583--1298652 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 13
1298573 GAACATAAAT
*
1298583 GAACATAAATGAAC
1 GAACAT-AACGAAC
1298597 GAACATAAACGAAC
1 GAACAT-AACGAAC
1298611 GAACAT-A--AAC
1 GAACATAACGAAC
1298621 GAACATACACGAAC
1 GAACATA-ACGAAC
1298635 GTAA-ATGAACGAAC
1 G-AACAT-AACGAAC
1298649 GAAC
1 GAAC
1298653 CATTTGTTCG
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
10 9 0.19
12 2 0.04
13 2 0.04
14 32 0.67
15 3 0.06
ACGTcount: A:0.54, C:0.20, G:0.16, T:0.10
Consensus pattern (13 bp):
GAACATAACGAAC
Found at i:1298899 original size:24 final size:23
Alignment explanation
Indices: 1298868--1298920 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1298858 GGAAAGTTAT
*
1298868 ATTAAAAAT-TTAAGGGATATAAA
1 ATTAAAAATCTCAAGGG-TATAAA
*
1298891 ATTATAAAATCTCAATGGTATAAA
1 ATTA-AAAATCTCAAGGGTATAAA
1298915 ATTAAA
1 ATTAAA
1298921 TCATTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 6 0.23
24 15 0.58
25 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (23 bp):
ATTAAAAATCTCAAGGGTATAAA
Found at i:1300564 original size:39 final size:39
Alignment explanation
Indices: 1300521--1300618 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
1300511 TATAAAAACG
*
1300521 GATTGATGAGTACTCGTAATTTGGATCT-AAAAGTCAACA
1 GATTGATGAGTACTCATAATTTGGAT-TAAAAAGTCAACA
*
1300560 GATTGATGAATACTCATAATTTGGATTAAAAAGTCAACA
1 GATTGATGAGTACTCATAATTTGGATTAAAAAGTCAACA
* * *
1300599 CATTAATGCGTACTCATAAT
1 GATTGATGAGTACTCATAAT
1300619 CTAGATTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.02
39 51 0.98
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (39 bp):
GATTGATGAGTACTCATAATTTGGATTAAAAAGTCAACA
Found at i:1302520 original size:16 final size:14
Alignment explanation
Indices: 1302484--1302531 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 14
1302474 TATAATTTGG
1302484 TTCTTAATTTCATTGT
1 TTCTTAATTT-ATT-T
1302500 TTCTTTAATTTATTT
1 TTC-TTAATTTATTT
1302515 TGTCTTAAGTTTATTT
1 T-TCTTAA-TTTATTT
1302531 T
1 T
1302532 AGCTAAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.21
16 16 0.55
17 7 0.24
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (14 bp):
TTCTTAATTTATTT
Found at i:1305587 original size:30 final size:29
Alignment explanation
Indices: 1305553--1305612 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
1305543 ATGGATAACC
* *
1305553 TGAAAACTGCTTTATGTAAAATGAATTACA
1 TGAAAACTGCTTTACGT-AAATAAATTACA
*
1305583 TGAAAACTGTTTTACGTAAATAAATTACA
1 TGAAAACTGCTTTACGTAAATAAATTACA
1305612 T
1 T
1305613 TTTCTGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (29 bp):
TGAAAACTGCTTTACGTAAATAAATTACA
Found at i:1316379 original size:20 final size:20
Alignment explanation
Indices: 1316351--1316393 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1316341 CCATTTTCGT
1316351 AACGCGAATCTGTAAATCGC
1 AACGCGAATCTGTAAATCGC
* *
1316371 AACGTGAATTTGTAAATCGC
1 AACGCGAATCTGTAAATCGC
1316391 AAC
1 AAC
1316394 ACAGAAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
AACGCGAATCTGTAAATCGC
Found at i:1316410 original size:20 final size:19
Alignment explanation
Indices: 1316387--1316457 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
1316377 AATTTGTAAA
1316387 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
1316407 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* * *
1316427 TCACAAC-TGAATTTCAAAT
1 TCGCAACACGAA-GTCAAAT
1316446 TCGCAACACGAA
1 TCGCAACACGAA
1316458 TTTAGTTTCG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.02
19 16 0.38
20 25 0.60
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:1316645 original size:16 final size:15
Alignment explanation
Indices: 1316610--1316648 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1316600 TCCCCATCTC
*
1316610 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1316625 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1316641 TAATTTTT
1 TAATTTTT
1316649 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1319699 original size:18 final size:18
Alignment explanation
Indices: 1319666--1319701 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1319656 AAGCAAAAGG
**
1319666 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
1319684 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1319702 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1320065 original size:20 final size:20
Alignment explanation
Indices: 1320039--1320083 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1320029 CAAACCGAAA
1320039 ATCGCGTTGCAAATTTGACT
1 ATCGCGTTGCAAATTTGACT
* *
1320059 TTCGCGTTGCGAATTTGACT
1 ATCGCGTTGCAAATTTGACT
1320079 ATCGC
1 ATCGC
1320084 AACGCTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (20 bp):
ATCGCGTTGCAAATTTGACT
Found at i:1320096 original size:34 final size:34
Alignment explanation
Indices: 1320058--1320124 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
1320048 CAAATTTGAC
1320058 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
1 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
1320092 TTTCGCGTTGCGAATTTGACTATCGCAACGCTT
1 TTTCGCGTTGCGAATTTGACTATCGCAACGCTT
1320125 CAACAAGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (34 bp):
TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
Found at i:1320297 original size:61 final size:63
Alignment explanation
Indices: 1320175--1320297 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 63
1320165 TTTTAGAAAC
* *
1320175 AACATATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACACATCAAATT
1320240 A
63 A
* * *
1320241 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATCAA
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACACATCAA
1320298 TAATCAACTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
61 24 0.46
62 3 0.06
66 25 0.48
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACACATCAAATTA
Found at i:1321650 original size:21 final size:21
Alignment explanation
Indices: 1321609--1321706 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
1321599 GCGAGCGGGA
* *
1321609 CCTCTTAAACGAT-GAAGGGGG
1 CCTCTTGAACGATGGGA-GGGG
*
1321630 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGGGAGGGG
* * * *
1321651 CTTATTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGGGAGGGG
* **
1321672 CCTCTTGAACGATAGGAGACG
1 CCTCTTGAACGATGGGAGGGG
*
1321693 CCTCTTGAATGATG
1 CCTCTTGAACGATG
1321707 ATAGGTGCAT
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
20 1 0.02
21 53 0.93
22 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGGGAGGGG
Found at i:1323849 original size:19 final size:20
Alignment explanation
Indices: 1323769--1323855 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
1323759 AAACTTAAAT
**
1323769 TCGCAACGTAAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* * *
1323789 TCACAATGGGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1323809 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1323829 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
1323848 TCGCAACG
1 TCGCAACG
1323856 TGATTTTCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 12 0.20
20 47 0.80
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1324373 original size:20 final size:20
Alignment explanation
Indices: 1324348--1324476 Score: 136
Period size: 20 Copynumber: 6.5 Consensus size: 20
1324338 GCGTAAAAAT
1324348 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1324368 ATTTGACTTAT-GTGTTGCGA
1 ATTTGACTT-TCGCGTTGCGA
* * * *
1324388 TTTATAAATTT-GCGTCGCGA
1 ATT-TGACTTTCGCGTTGCGA
* *
1324408 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
1324428 ATTTGACTATCGCGTTGTGA
1 ATTTGACTTTCGCGTTGCGA
*
1324448 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
1324468 ATTTGACTT
1 ATTTGACTT
1324477 CTGTGTTGCG
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
19 5 0.06
20 79 0.89
21 5 0.06
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:1324425 original size:60 final size:60
Alignment explanation
Indices: 1324348--1324487 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 60
1324338 GCGTAAAAAT
* * * * *
1324348 ATTTGACTTTCGCGTTGCGAATTTGACTTAT-GTGTTGCGATTTATAAAT-TTGCGTCGCGA
1 ATTTGACTTTTGTGTTGCGAATTTGAC-TATCGCGTTGCGAATT-TAAATATCGCGTCGCGA
* * * *
1324408 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAAATATCGCGTCGCGA
*
1324468 ATTTGACTTCTGTGTTGCGA
1 ATTTGACTTTTGTGTTGCGA
1324488 TTTACAAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 6 0.09
60 62 0.91
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (60 bp):
ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAAATATCGCGTCGCGA
Found at i:1325104 original size:32 final size:34
Alignment explanation
Indices: 1325049--1325111 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 34
1325039 AATTATATAA
** *
1325049 TTTTTAAATTTGACACATTAAAATAACTTTTTTT
1 TTTTTAAATTTGACACACCAAAATAAATTTTTTT
1325083 TTTTTAAA-TTGACAC-CCAAAATAAATTTT
1 TTTTTAAATTTGACACACCAAAATAAATTTT
1325112 ATAGCCCAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 11 0.42
33 7 0.27
34 8 0.31
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (34 bp):
TTTTTAAATTTGACACACCAAAATAAATTTTTTT
Found at i:1328360 original size:31 final size:31
Alignment explanation
Indices: 1328322--1328380 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1328312 ATACAATCAA
*
1328322 TTTCGTTTTTATTTAATTAAGGTATGATTAT
1 TTTCGTTTTTATTTAATTAAGATATGATTAT
1328353 TTTCGTTTTTATTTAATTAAGATATGAT
1 TTTCGTTTTTATTTAATTAAGATATGAT
1328381 CACCACCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (31 bp):
TTTCGTTTTTATTTAATTAAGATATGATTAT
Found at i:1329555 original size:18 final size:19
Alignment explanation
Indices: 1329532--1329577 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
1329522 ATATATATTT
*
1329532 TTTCTTA-TTGAAAGCATG
1 TTTCTTATTTAAAAGCATG
1329550 TTTCTTAATTTTAAAAGCATG
1 TTTCTT-A-TTTAAAAGCATG
1329571 TTTCTTA
1 TTTCTTA
1329578 CTATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 1 0.04
20 1 0.04
21 16 0.67
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTCTTATTTAAAAGCATG
Found at i:1329568 original size:21 final size:21
Alignment explanation
Indices: 1329537--1329586 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1329527 TATTTTTTCT
*
1329537 TATTGAAAGCATGTTTCTTAA
1 TATTAAAAGCATGTTTCTTAA
* *
1329558 TTTTAAAAGCATGTTTCTTAC
1 TATTAAAAGCATGTTTCTTAA
1329579 TATTAAAA
1 TATTAAAA
1329587 TTTTTGTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
TATTAAAAGCATGTTTCTTAA
Found at i:1337999 original size:26 final size:26
Alignment explanation
Indices: 1337969--1338029 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
1337959 CCTGAGACAT
1337969 TACTTAAACGATATCAAGATGTTTAC
1 TACTTAAACGATATCAAGATGTTTAC
1337995 TACTTAAACGATATCAAGATGTTTAC
1 TACTTAAACGATATCAAGATGTTTAC
1338021 TACTTAAAC
1 TACTTAAAC
1338030 CAACCCGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (26 bp):
TACTTAAACGATATCAAGATGTTTAC
Found at i:1339368 original size:18 final size:18
Alignment explanation
Indices: 1339345--1339455 Score: 114
Period size: 18 Copynumber: 5.9 Consensus size: 18
1339335 GTTCAGTATT
*
1339345 TGTCCCGGAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1339363 TGTCCCGGAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1339382 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
1339401 TGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
* * *
1339421 TGTTCCGAAGAACCATTA
1 TGTCCCGAAGGACCACTA
1339439 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1339456 GTTCATCCCT
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
18 46 0.61
19 2 0.03
20 28 0.37
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1339457 original size:38 final size:38
Alignment explanation
Indices: 1339356--1339458 Score: 179
Period size: 38 Copynumber: 2.7 Consensus size: 38
1339346 GTCCCGGAGG
* *
1339356 ACCACTATGTCCCGGAGGACCACTGATTGTTCCGAAGA
1 ACCACTATGTCCCGAAGGACCACTGTTTGTTCCGAAGA
1339394 ACCACTATGTCCCGAAGGACCACTGTTTGTTCCGAAGA
1 ACCACTATGTCCCGAAGGACCACTGTTTGTTCCGAAGA
*
1339432 ACCATTATGTCCCGAAGGACCACTGTT
1 ACCACTATGTCCCGAAGGACCACTGTT
1339459 CATCCCTCGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (38 bp):
ACCACTATGTCCCGAAGGACCACTGTTTGTTCCGAAGA
Found at i:1344600 original size:19 final size:20
Alignment explanation
Indices: 1344576--1344618 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1344566 AGTCCGGAGG
1344576 ACCACTGATTG-TTCGAAGA
1 ACCACTGATTGTTTCGAAGA
*
1344595 ACCACTGTTTGTTTCGAAGA
1 ACCACTGATTGTTTCGAAGA
1344615 ACCA
1 ACCA
1344619 TTATGTCCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (20 bp):
ACCACTGATTGTTTCGAAGA
Found at i:1349687 original size:6 final size:6
Alignment explanation
Indices: 1349652--1349683 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1349642 TATGGAAGAA
*
1349652 GGAAAG GGAAAG GGAAAG GGAAAG GGGAAG GG
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GG
1349684 GAAGAGCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (6 bp):
GGAAAG
Found at i:1351335 original size:268 final size:273
Alignment explanation
Indices: 1351031--1351577 Score: 727
Period size: 277 Copynumber: 2.0 Consensus size: 273
1351021 GAAATATTTT
* * *
1351031 TTATAAAACAATATATTTTAATTAATTAGTAAAAACATTTTTTGTAATATTATATAATCAAA-T-
1 TTATAAAACAATATATTTTAATTAATTAATAAAAACA-TTATTATAATATTATATAATCAAACTA
*
1351094 TATTTTTATAC-ATGACCCTCAAACTCATAAAAAAA-T-AATATGATAC-CTTGATCAAC-TGTT
65 TATTTTTATACTATGACCCTCAAACTCAGAAAAAAACTCAATATGAT-CTCTTGATCAACAT-TT
* ** * * *
1351154 TCTATCATTAG-CATTACAATACCAACACAAC-ATTT-CATGATGCTGACTTGATGGTTCACGAT
128 TCTATCATTAGTCAATACAATACCAACACAACAATTTACA--ACACTAACGTGATGGTTCAAGAT
* * * *
1351216 AACTAATGACATATTTACATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAGTTTATA
191 AACTAATAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATA
*
1351281 ATTAATATACTTTTATTG
256 ATTAATACACTTTTATTG
1351299 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
1 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
* *
1351364 TTTTTTATACTTAATATGATCCTCAAACTCAGAAAAAAACTCAATATGATCTCTTGATCAACATT
66 ATTTTTATAC----TATGACCCTCAAACTCAGAAAAAAACTCAATATGATCTCTTGATCAACATT
* * ** * *
1351429 TTCTATCATTAGTCAATACAATATCAGCATGACAATTTACAACACTAACGTGATTGTTCAAGATG
127 TTCTATCATTAGTCAATACAATACCAACACAACAATTTACAACACTAACGTGATGGTTCAAGATA
*
1351494 ACTAATAACATATTCAAATTATCTTTTTAATTAATTAATAAAAACATATTCCCTTGAATTTATAA
192 ACTAATAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATAA
1351559 TTAATACACTTTTATTG
257 TTAATACACTTTTATTG
1351576 TT
1 TT
1351578 TTTCCTCTAC
Statistics
Matches: 241, Mismatches: 24, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
267 22 0.09
268 37 0.15
269 10 0.04
274 22 0.09
275 2 0.01
276 31 0.13
277 111 0.46
278 4 0.02
279 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (273 bp):
TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
ATTTTTATACTATGACCCTCAAACTCAGAAAAAAACTCAATATGATCTCTTGATCAACATTTTCT
ATCATTAGTCAATACAATACCAACACAACAATTTACAACACTAACGTGATGGTTCAAGATAACTA
ATAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATAATTAA
TACACTTTTATTG
Found at i:1355129 original size:14 final size:14
Alignment explanation
Indices: 1355089--1355131 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1355079 AAGGAATATC
*
1355089 AGATGAAAGAAAAA
1 AGATGAAAGATAAA
* *
1355103 AGGTGAAAAATAAA
1 AGATGAAAGATAAA
*
1355117 AGATTAAAGATAAA
1 AGATGAAAGATAAA
1355131 A
1 A
1355132 TAAATCAGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (14 bp):
AGATGAAAGATAAA
Done.