Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:966992 original size:30 final size:28
Alignment explanation
Indices: 966958--967031 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
966948 GATTTTCTTA
*
966958 ATATTGTTTATATGATATATGATTTACTGT
1 ATATT-TTTATATGATAT-TGAGTTACTGT
* *
966988 ATATTTCTGATATGATCTTGAGTTACTGT
1 ATATTT-TTATATGATATTGAGTTACTGT
*
967017 AT-TTCTGTATATGAT
1 ATATT-TTTATATGAT
967032 TTCTGAGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 9 0.24
29 14 0.38
30 14 0.38
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (28 bp):
ATATTTTTATATGATATTGAGTTACTGT
Found at i:967039 original size:29 final size:29
Alignment explanation
Indices: 966966--967031 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
966956 TAATATTGTT
*
966966 TATATGATATATGATTTACTGTATATTTCTG
1 TATATGATAT-TGAGTTACTG-ATATTTCTG
*
966997 -ATATGATCTTGAGTTACTG-TATTTCTG
1 TATATGATATTGAGTTACTGATATTTCTG
967024 TATATGAT
1 TATATGAT
967032 TTCTGAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 8 0.25
28 7 0.22
29 9 0.28
30 8 0.25
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (29 bp):
TATATGATATTGAGTTACTGATATTTCTG
Found at i:968363 original size:18 final size:18
Alignment explanation
Indices: 968314--968363 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
968304 AAGTCAACGA
*
968314 CGGTCAACAGTCAAAGGT
1 CGGTCAACGGTCAAAGGT
* *
968332 CGGTCAACGATCAATGGT
1 CGGTCAACGGTCAAAGGT
*
968350 CGGTCAATGGTCAA
1 CGGTCAACGGTCAA
968364 CGACTGTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (18 bp):
CGGTCAACGGTCAAAGGT
Found at i:968994 original size:31 final size:31
Alignment explanation
Indices: 968927--968995 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
968917 TTAGTTTGGA
*
968927 TCTGAATTTAATTAAAATTTTCACTATAGCC
1 TCTGAATTTAATTAAAATTTTCAATATAGCC
* * *
968958 CCTGAATTTAATTTAAA-TTTCAATTTAGTCC
1 TCTGAATTTAATTAAAATTTTCAATATAG-CC
968989 TCTGAAT
1 TCTGAAT
968996 AAATTTTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.43
Consensus pattern (31 bp):
TCTGAATTTAATTAAAATTTTCAATATAGCC
Found at i:973999 original size:19 final size:19
Alignment explanation
Indices: 973975--974013 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
973965 GATATTAGAA
*
973975 ATCAGAACAGAGATCAGAG
1 ATCAGAACAGAAATCAGAG
973994 ATCAGAACAGAAATCAGAG
1 ATCAGAACAGAAATCAGAG
974013 A
1 A
974014 AAATATTCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.23, T:0.10
Consensus pattern (19 bp):
ATCAGAACAGAAATCAGAG
Found at i:994515 original size:44 final size:44
Alignment explanation
Indices: 994412--994523 Score: 152
Period size: 44 Copynumber: 2.5 Consensus size: 44
994402 TCGGGTTTGA
* * *
994412 TTAAGTTCAGATGAAGAGAATATACTTCTCGAATTGGATCAAAT
1 TTAAGTACAGATGAAGAGAATATGCTTCTCGAATCGGATCAAAT
* *
994456 TTAAGTACAGATGAAGAAAATATGCTTCTTGAATCGGATCAAAT
1 TTAAGTACAGATGAAGAGAATATGCTTCTCGAATCGGATCAAAT
** *
994500 TTAAGTATTGGTGAAGAGAATATG
1 TTAAGTACAGATGAAGAGAATATG
994524 TATCCTTCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (44 bp):
TTAAGTACAGATGAAGAGAATATGCTTCTCGAATCGGATCAAAT
Found at i:1011345 original size:17 final size:16
Alignment explanation
Indices: 1011306--1011345 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1011296 ATAAATTCAA
1011306 ATATAAAAATATAGTT
1 ATATAAAAATATAGTT
*
1011322 ATAATAAAAATATATTTT
1 AT-ATAAAAATATA-GTT
1011340 ATATAA
1 ATATAA
1011346 CTCACTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 15 0.71
18 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
ATATAAAAATATAGTT
Found at i:1011444 original size:45 final size:44
Alignment explanation
Indices: 1011386--1011472 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
1011376 CGATTTTCTC
*
1011386 TTTTTTTAAATAATTA-AAATAAATTATT-AAAAAATAGTAAATTA
1 TTTTTTAAAATAA-TAGAAATAAATTATTAAAAAAATA-TAAATTA
* *
1011430 TTTTTTAAAGATAATAGTATTAAATTATTAAAAAAATATAAAT
1 TTTTTTAAA-ATAATAGAAATAAATTATTAAAAAAATATAAAT
1011473 ACATAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
44 10 0.27
45 19 0.51
46 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (44 bp):
TTTTTTAAAATAATAGAAATAAATTATTAAAAAAATATAAATTA
Found at i:1014115 original size:18 final size:18
Alignment explanation
Indices: 1014094--1014131 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1014084 CATATTTTTA
1014094 TTTAATAAAAATAATATT
1 TTTAATAAAAATAATATT
* *
1014112 TTTAATAAATATATTATT
1 TTTAATAAAAATAATATT
1014130 TT
1 TT
1014132 AGGTCGAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATAAAAATAATATT
Found at i:1015947 original size:91 final size:91
Alignment explanation
Indices: 1015792--1015973 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
1015782 TAAAATATTT
1015792 AAATACATGATAATTTGATATTTTTATGAGACAACTACCACAATCGCTCCTCTCTCGATCCATTT
1 AAATACATGATAATTTGATATTTTTATGAGACAACTACCACAATCGCTCCTCTCTCGATCCATTT
1015857 CTGAAAAAGAGTGTACCAATTAGATA
66 CTGAAAAAGAGTGTACCAATTAGATA
*
1015883 AAATACATGATAATTTGATATTTTTATGAGACAACTACCACAATCGCTCCTCTCTCGGTCCATTT
1 AAATACATGATAATTTGATATTTTTATGAGACAACTACCACAATCGCTCCTCTCTCGATCCATTT
*
1015948 CTGAACAAGAGTGTACCAATTAGATA
66 CTGAAAAAGAGTGTACCAATTAGATA
1015974 CTTATATTCA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (91 bp):
AAATACATGATAATTTGATATTTTTATGAGACAACTACCACAATCGCTCCTCTCTCGATCCATTT
CTGAAAAAGAGTGTACCAATTAGATA
Found at i:1019002 original size:31 final size:31
Alignment explanation
Indices: 1018967--1019025 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1018957 TAATTTAAAT
* *
1018967 TTAAATTTTAGATTAAATATTAAGTTGATTA
1 TTAAATTTTAGATAAAATACTAAGTTGATTA
*
1018998 TTAAATTTTAGATAAAATACTAATTTGA
1 TTAAATTTTAGATAAAATACTAAGTTGA
1019026 CCACTGGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (31 bp):
TTAAATTTTAGATAAAATACTAAGTTGATTA
Found at i:1021179 original size:114 final size:114
Alignment explanation
Indices: 1020979--1021208 Score: 460
Period size: 114 Copynumber: 2.0 Consensus size: 114
1020969 TGACGGTTTC
1020979 GGAGGAGACAAACTATCCATCATTTTATTTGGCATGGGATCGACAGCCGTGGTCGTAACAATCTA
1 GGAGGAGACAAACTATCCATCATTTTATTTGGCATGGGATCGACAGCCGTGGTCGTAACAATCTA
1021044 CCATTGTATCGCCACCGTTTGGTGGCATCGATACTCCAATAACCTCCTA
66 CCATTGTATCGCCACCGTTTGGTGGCATCGATACTCCAATAACCTCCTA
1021093 GGAGGAGACAAACTATCCATCATTTTATTTGGCATGGGATCGACAGCCGTGGTCGTAACAATCTA
1 GGAGGAGACAAACTATCCATCATTTTATTTGGCATGGGATCGACAGCCGTGGTCGTAACAATCTA
1021158 CCATTGTATCGCCACCGTTTGGTGGCATCGATACTCCAATAACCTCCTA
66 CCATTGTATCGCCACCGTTTGGTGGCATCGATACTCCAATAACCTCCTA
1021207 GG
1 GG
1021209 CCATATATCG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (114 bp):
GGAGGAGACAAACTATCCATCATTTTATTTGGCATGGGATCGACAGCCGTGGTCGTAACAATCTA
CCATTGTATCGCCACCGTTTGGTGGCATCGATACTCCAATAACCTCCTA
Found at i:1022277 original size:60 final size:60
Alignment explanation
Indices: 1022154--1022291 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 60
1022144 GAACATATAA
* * * * *
1022154 ATAGTCAGGTGACCATTTTGTAACTTTTAATAGTCGGATGTCTCAACAAAGTAATAGTTT
1 ATAGTCAGGCGACCATTTTATAACTTTTAATAGTCGGATATCTCAACAAAGCAATAGTCT
* *
1022214 ATAGTTAGGCGACCATTTTATAAGTTTTAATAGTTAC-GATAT-TCAACAAAGCAAT-GTCCT
1 ATAGTCAGGCGACCATTTTATAACTTTTAATAG-T-CGGATATCTCAACAAAGCAATAGT-CT
* *
1022274 ATAGTCATGAGACCATTT
1 ATAGTCAGGCGACCATTT
1022292 GTGGAGTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
59 2 0.03
60 57 0.88
61 5 0.08
62 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (60 bp):
ATAGTCAGGCGACCATTTTATAACTTTTAATAGTCGGATATCTCAACAAAGCAATAGTCT
Found at i:1028384 original size:6 final size:6
Alignment explanation
Indices: 1028373--1028407 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1028363 TTCAATCCCT
* *
1028373 ATGGTG ATGGTG ATGATG ATGGTG ATGATG ATGGT
1 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATGGT
1028408 TTGGGGCCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.34
Consensus pattern (6 bp):
ATGGTG
Found at i:1028394 original size:12 final size:12
Alignment explanation
Indices: 1028377--1028407 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1028367 ATCCCTATGG
1028377 TGATGGTGATGA
1 TGATGGTGATGA
1028389 TGATGGTGATGA
1 TGATGGTGATGA
1028401 TGATGGT
1 TGATGGT
1028408 TTGGGGCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (12 bp):
TGATGGTGATGA
Found at i:1030115 original size:25 final size:25
Alignment explanation
Indices: 1030055--1030117 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
1030045 TAATTTTAGA
*
1030055 TTTTTTAAAATTACATGATTTAAAAT
1 TTTTTTAAAA-TACATGAATTAAAAT
* * * * *
1030081 ATATTAAAAATACATTAATTATAAT
1 TTTTTTAAAATACATGAATTAAAAT
1030106 TTTTTTAAAATA
1 TTTTTTAAAATA
1030118 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (25 bp):
TTTTTTAAAATACATGAATTAAAAT
Found at i:1030877 original size:21 final size:19
Alignment explanation
Indices: 1030837--1030879 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1030827 TTTTAGCAAT
**
1030837 TTAAATTTTTAATATTAAA
1 TTAAATTTTTAATAAAAAA
1030856 TTAAATATTTTACATAAAAAA
1 TTAAAT-TTTTA-ATAAAAAA
1030877 TTA
1 TTA
1030880 TAAGATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAATTTTTAATAAAAAA
Found at i:1031679 original size:27 final size:27
Alignment explanation
Indices: 1031641--1031707 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
1031631 AAAACAGTGT
1031641 TGAATGATTCAGAATCAAAGTACATTC
1 TGAATGATTCAGAATCAAAGTACATTC
1031668 TGAATGATTCAGAATCAAAGTACATTC
1 TGAATGATTCAGAATCAAAGTACATTC
1031695 TGAATGATTCAGA
1 TGAATGATTCAGA
1031708 GCCATTATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (27 bp):
TGAATGATTCAGAATCAAAGTACATTC
Found at i:1035226 original size:115 final size:116
Alignment explanation
Indices: 1035043--1035273 Score: 439
Period size: 115 Copynumber: 2.0 Consensus size: 116
1035033 ATAGGCAGAG
1035043 ACGAACGTAAAAATTTATGTTAAAGGGTTTAAACTTAAAAAGTTATATTAAAATTTTAGGTGTGG
1 ACGAACGTAAAAATTTATGTTAAAGGGTTTAAACTTAAAAAGTTATATTAAAATTTTAGGTGTGG
1035108 CGAAATTTTATAATCAATTTATAAT-AAAAAAAACCTAAAATACAAGGGAA
66 CGAAATTTTATAATCAATTTATAATAAAAAAAAACCTAAAATACAAGGGAA
1035158 ACGAACGTAAAAATTTATGTTAAAGGGTTTAAACTTAAAAAGTTATATTAAAATTTTTAGGTGT-
1 ACGAACGTAAAAATTTATGTTAAAGGGTTTAAACTTAAAAAGTTATATTAAAA-TTTTAGGTGTG
1035222 GCGAAATTTTATAATCAATTTATAATAAAAAAAAACCTAAAATACAAGGGAA
65 GCGAAATTTTATAATCAATTTATAATAAAAAAAAACCTAAAATACAAGGGAA
1035274 TTTAAAGTTT
Statistics
Matches: 114, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
115 79 0.69
116 35 0.31
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (116 bp):
ACGAACGTAAAAATTTATGTTAAAGGGTTTAAACTTAAAAAGTTATATTAAAATTTTAGGTGTGG
CGAAATTTTATAATCAATTTATAATAAAAAAAAACCTAAAATACAAGGGAA
Found at i:1038545 original size:25 final size:26
Alignment explanation
Indices: 1038498--1038573 Score: 120
Period size: 25 Copynumber: 3.0 Consensus size: 26
1038488 CTACAATGAG
1038498 TGACAT-TCATAGAAATGCACCACTAA
1 TGACATGT-ATAGAAATGCACCACTAA
1038524 TGACATGTATAG-AATGCACCACTAA
1 TGACATGTATAGAAATGCACCACTAA
*
1038549 TGACATGTATTGAAATGCACCACTA
1 TGACATGTATAGAAATGCACCACTA
1038574 TATAAAATAG
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 24 0.51
26 22 0.47
27 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (26 bp):
TGACATGTATAGAAATGCACCACTAA
Found at i:1038975 original size:19 final size:20
Alignment explanation
Indices: 1038943--1038986 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1038933 CACAATTATT
*
1038943 TTATAACTGATTTATTAATTG
1 TTATAACT-ATTTATCAATTG
1038964 TTATAACT-TTTATCAATTG
1 TTATAACTATTTATCAATTG
1038983 TTAT
1 TTAT
1038987 CAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (20 bp):
TTATAACTATTTATCAATTG
Found at i:1039720 original size:32 final size:32
Alignment explanation
Indices: 1039697--1039784 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 32
1039687 AAAATTAACT
1039697 GATCCGATTTTGACTCGACCCGAAAACCAACC
1 GATCCGATTTTGACTCGACCCGAAAACCAACC
* *
1039729 GATTCGATTTTGACTCGACCCGAAACCCAACC
1 GATCCGATTTTGACTCGACCCGAAAACCAACC
** *
1039761 GATTTGATTTTGACCCGACCCGAA
1 GATCCGATTTTGACTCGACCCGAA
1039785 TTCCATAGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (32 bp):
GATCCGATTTTGACTCGACCCGAAAACCAACC
Found at i:1042121 original size:3 final size:3
Alignment explanation
Indices: 1042113--1042187 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
1042103 GTGCTTTCCG
1042113 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1042161 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1042188 GTTGAGGGAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1044996 original size:13 final size:13
Alignment explanation
Indices: 1044978--1045002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1044968 CCTTAGTTAT
1044978 AATGTATAATTAC
1 AATGTATAATTAC
1044991 AATGTATAATTA
1 AATGTATAATTA
1045003 TATATATATA
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:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AATGTATAATTAC
Found at i:1048392 original size:21 final size:21
Alignment explanation
Indices: 1048366--1048410 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1048356 CGATCTCATT
*
1048366 CTAAACGCTAAACCCTTAAA-C
1 CTAAACCCTAAA-CCTTAAATC
1048387 CTAAACCCTAAACCTTAAATC
1 CTAAACCCTAAACCTTAAATC
1048408 CTA
1 CTA
1048411 TAAAACGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.42, C:0.33, G:0.02, T:0.22
Consensus pattern (21 bp):
CTAAACCCTAAACCTTAAATC
Found at i:1048410 original size:14 final size:13
Alignment explanation
Indices: 1048366--1048401 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
1048356 CGATCTCATT
1048366 CTAAACGCTAAACC
1 CTAAAC-CTAAACC
1048380 CTTAAACCTAAACC
1 C-TAAACCTAAACC
1048394 CTAAACCT
1 CTAAACCT
1048402 TAAATCCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.33
14 9 0.43
15 5 0.24
ACGTcount: A:0.42, C:0.36, G:0.03, T:0.19
Consensus pattern (13 bp):
CTAAACCTAAACC
Found at i:1049308 original size:60 final size:60
Alignment explanation
Indices: 1049235--1049397 Score: 204
Period size: 60 Copynumber: 2.7 Consensus size: 60
1049225 CACATGTCCC
* * * *
1049235 TATTCTAAATTAGTTCTTAAACTTTTGAATATTACC-ATTTCATCCTCAAATTAT-GATCT
1 TATTCTAAATTAGTCCTTAAACTTTTAAATATT-CCAATTTCATCCTCAAACTATGGACCT
* *
1049294 TAATTCTAAATTAGTCCTTAAACTTTTAAATATTCCAATTTCATCCTTAAACTATGGCCCT
1 T-ATTCTAAATTAGTCCTTAAACTTTTAAATATTCCAATTTCATCCTCAAACTATGGACCT
* ** *
1049355 TATTCTAAATTAGTCCCTAAACTTTTAAACCTTCCGATTTCAT
1 TATTCTAAATTAGTCCTTAAACTTTTAAATATTCCAATTTCAT
1049398 TCCCAAATTC
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
59 3 0.03
60 84 0.92
61 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (60 bp):
TATTCTAAATTAGTCCTTAAACTTTTAAATATTCCAATTTCATCCTCAAACTATGGACCT
Found at i:1050554 original size:21 final size:20
Alignment explanation
Indices: 1050530--1050574 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1050520 TAATATTTTG
*
1050530 AAATTAATATGTATTA-TAATT
1 AAATTAA-AT-TATTATTAAAT
1050551 AAATTAAATTATTATTAAAT
1 AAATTAAATTATTATTAAAT
1050571 AAAT
1 AAAT
1050575 AATTCTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AAATTAAATTATTATTAAAT
Found at i:1051530 original size:20 final size:20
Alignment explanation
Indices: 1051505--1051574 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
1051495 GTATCAAAGG
1051505 GTATCCATACACCCTGCAGT
1 GTATCCATACACCCTGCAGT
1051525 GTATCCATACA--CTG--GT
1 GTATCCATACACCCTGCAGT
*
1051541 GTA-CCGATACCCCCTGCAGGT
1 GTATCC-ATACACCCTGCA-GT
*
1051562 GAATCCATACACC
1 GTATCCATACACC
1051575 TATGACTGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
15 2 0.05
16 9 0.22
18 6 0.15
20 11 0.28
21 10 0.25
22 2 0.05
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (20 bp):
GTATCCATACACCCTGCAGT
Found at i:1053596 original size:50 final size:50
Alignment explanation
Indices: 1053538--1053638 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
1053528 AGTATCAATT
*
1053538 TTTGTTTCTATTGAATTAATATTTAAGCTTAGATTATGTTAGTTGGATAC
1 TTTGTTTCTATTGAATTAATATTTAAGCTTAGATTATGTTAGTTAGATAC
1053588 TTTGTTTCTATTGAATTAATATTTAAGCTTAGATTATGTTAGTTAGATAC
1 TTTGTTTCTATTGAATTAATATTTAAGCTTAGATTATGTTAGTTAGATAC
1053638 T
1 T
1053639 AACATATAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (50 bp):
TTTGTTTCTATTGAATTAATATTTAAGCTTAGATTATGTTAGTTAGATAC
Found at i:1053832 original size:18 final size:18
Alignment explanation
Indices: 1053809--1053847 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1053799 TTTATGTTAT
1053809 CGAATAAACATTGGCTTG
1 CGAATAAACATTGGCTTG
1053827 CGAATAAACATTGGCTTG
1 CGAATAAACATTGGCTTG
1053845 CGA
1 CGA
1053848 TTATCCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (18 bp):
CGAATAAACATTGGCTTG
Found at i:1055022 original size:7 final size:7
Alignment explanation
Indices: 1055010--1055045 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1055000 AAATACTGTA
1055010 TGAATAG
1 TGAATAG
1055017 TGAATAG
1 TGAATAG
*
1055024 TGAATAA
1 TGAATAG
*
1055031 TGAACAG
1 TGAATAG
1055038 TGAATAG
1 TGAATAG
1055045 T
1 T
1055046 ACGATGTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (7 bp):
TGAATAG
Found at i:1056267 original size:14 final size:15
Alignment explanation
Indices: 1056240--1056268 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1056230 ATATCATATA
1056240 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
1056255 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
1056269 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:1059160 original size:30 final size:30
Alignment explanation
Indices: 1058964--1059180 Score: 213
Period size: 30 Copynumber: 7.2 Consensus size: 30
1058954 CTTCTTGCAA
* * * *
1058964 ATTGAAGTATTCTTC-CTTCCCTACTCTTCA
1 ATTGAAGTATTCTTCAC-CCCCTTCTCGTCG
* ** ** * *
1058994 ATTGGAGTATTCTTCTTCTTCTTCTCTTCA
1 ATTGAAGTATTCTTCACCCCCTTCTCGTCG
* ** *
1059024 ATTGAAGTGTTCTTCGTCCTCTTCTCGTCG
1 ATTGAAGTATTCTTCACCCCCTTCTCGTCG
* * *
1059054 ATTGAAGTATTCGTCACCTCCTTCTCTTCG
1 ATTGAAGTATTCTTCACCCCCTTCTCGTCG
*
1059084 ATTGAAGTGTTCTTCACCCCCTTCTCGTCG
1 ATTGAAGTATTCTTCACCCCCTTCTCGTCG
*
1059114 ATTGAAGTACTT-TTCACCCCTTTCTCGTCG
1 ATTGAAGTA-TTCTTCACCCCCTTCTCGTCG
*
1059144 ATTGAAGTATTCTTCACCCCCTTCTTGTCG
1 ATTGAAGTATTCTTCACCCCCTTCTCGTCG
1059174 ATTGAAG
1 ATTGAAG
1059181 GATTTTCCCT
Statistics
Matches: 157, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
29 2 0.01
30 153 0.97
31 2 0.01
ACGTcount: A:0.16, C:0.28, G:0.14, T:0.42
Consensus pattern (30 bp):
ATTGAAGTATTCTTCACCCCCTTCTCGTCG
Found at i:1059198 original size:30 final size:29
Alignment explanation
Indices: 1059013--1059202 Score: 170
Period size: 30 Copynumber: 6.3 Consensus size: 29
1059003 TTCTTCTTCT
* * * **
1059013 TCTTCTCTTCAATTGAAGTGTTCTTCGTCC
1 TCTTCTCGTCGATTGAAGTATT-TTCACCC
*
1059043 TCTTCTCGTCGATTGAAGTATTCGTCA-CC
1 TCTTCTCGTCGATTGAAGTATT-TTCACCC
* *
1059072 TCCTTCTCTTCGATTGAAGTGTTCTTCACCC
1 T-CTTCTCGTCGATTGAAGTATT-TTCACCC
*
1059103 CCTTCTCGTCGATTGAAGTACTTTTCACCC
1 TCTTCTCGTCGATTGAAGTA-TTTTCACCC
1059133 -CTTTCTCGTCGATTGAAGTATTCTTCACCC
1 TC-TTCTCGTCGATTGAAGTATT-TTCACCC
* * *
1059163 CCTTCTTGTCGATTGAAGGATTTTC-CCTC
1 TCTTCTCGTCGATTGAAGTATTTTCACC-C
1059192 ATCTTCTCGTC
1 -TCTTCTCGTC
1059203 AAATAGAGTA
Statistics
Matches: 137, Mismatches: 15, Indels: 16
0.82 0.09 0.10
Matches are distributed among these distances:
28 2 0.01
29 10 0.07
30 120 0.88
31 5 0.04
ACGTcount: A:0.15, C:0.30, G:0.14, T:0.41
Consensus pattern (29 bp):
TCTTCTCGTCGATTGAAGTATTTTCACCC
Found at i:1059199 original size:60 final size:60
Alignment explanation
Indices: 1059013--1059202 Score: 233
Period size: 60 Copynumber: 3.2 Consensus size: 60
1059003 TTCTTCTTCT
* * ** * *
1059013 TCTTCTCTTCAATTGAAGTGTTCTTCGTCCTCTTCTCGTCGATTGAAGTATTCGTCACCTC
1 TCTTCTCGTCGATTGAAGTGTTCTTCACCCCCTTCTCGTCGATTGAAGTATT-TTCACCTC
* *
1059074 -CTTCTCTTCGATTGAAGTGTTCTTCACCCCCTTCTCGTCGATTGAAGTACTTTTCACCCC
1 TCTTCTCGTCGATTGAAGTGTTCTTCACCCCCTTCTCGTCGATTGAAGTA-TTTTCACCTC
* * *
1059134 T-TTCTCGTCGATTGAAGTATTCTTCACCCCCTTCTTGTCGATTGAAGGATTTTC-CCTC
1 TCTTCTCGTCGATTGAAGTGTTCTTCACCCCCTTCTCGTCGATTGAAGTATTTTCACCTC
1059192 ATCTTCTCGTC
1 -TCTTCTCGTC
1059203 AAATAGAGTA
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
58 3 0.03
59 6 0.05
60 103 0.90
61 2 0.02
ACGTcount: A:0.15, C:0.30, G:0.14, T:0.41
Consensus pattern (60 bp):
TCTTCTCGTCGATTGAAGTGTTCTTCACCCCCTTCTCGTCGATTGAAGTATTTTCACCTC
Found at i:1071692 original size:20 final size:20
Alignment explanation
Indices: 1071650--1071692 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1071640 AATATGTCAT
***
1071650 ATTGTCATTGCAATTTTCGA
1 ATTGTCATTGCAATTTAAAA
*
1071670 ATTGTGATTGCAATTTAAAA
1 ATTGTCATTGCAATTTAAAA
1071690 ATT
1 ATT
1071693 TAAAAAGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (20 bp):
ATTGTCATTGCAATTTAAAA
Found at i:1073287 original size:73 final size:71
Alignment explanation
Indices: 1073157--1073297 Score: 174
Period size: 72 Copynumber: 2.0 Consensus size: 71
1073147 CGATTTCGGG
* *
1073157 GCAATAATAGTGGCGTTTTCTTGACAAACGACGCAATAAATCCATATATAATGGCGTTTTATTAA
1 GCAATAATAGTGGCGTTTTCTTGAAAAACGACGCAATAAATACATATATAATGGCGTTTT-TTAA
1073222 TAAAGCC
65 TAAAGCC
* * ** * * * *
1073229 GCAATAATAGTGGCGTTTTTTTGAAAAAACGTCGCAATAGGTATATCTATAGTGGCGTTTTTTAG
1 GCAATAATAGTGGCGTTTTCTTG-AAAAACGACGCAATAAATACATATATAATGGCGTTTTTTAA
1073294 TAAA
65 TAAA
1073298 ACGCCACTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 29 0.50
73 29 0.50
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (71 bp):
GCAATAATAGTGGCGTTTTCTTGAAAAACGACGCAATAAATACATATATAATGGCGTTTTTTAAT
AAAGCC
Found at i:1073887 original size:19 final size:19
Alignment explanation
Indices: 1073859--1073897 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1073849 CCTGGAGGCA
1073859 CTCTCGTTGCCTTATAATG
1 CTCTCGTTGCCTTATAATG
*
1073878 CTCTCTTTGCCTTATAATG
1 CTCTCGTTGCCTTATAATG
1073897 C
1 C
1073898 ATTAAGTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.28, G:0.13, T:0.44
Consensus pattern (19 bp):
CTCTCGTTGCCTTATAATG
Found at i:1082559 original size:20 final size:20
Alignment explanation
Indices: 1082517--1082559 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1082507 AATATGTCAT
***
1082517 ATTGTCATTGCAATTTTCGA
1 ATTGTCATTGCAATTTAAAA
*
1082537 ATTGTGATTGCAATTTAAAA
1 ATTGTCATTGCAATTTAAAA
1082557 ATT
1 ATT
1082560 TAAAAAGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (20 bp):
ATTGTCATTGCAATTTAAAA
Found at i:1084043 original size:49 final size:49
Alignment explanation
Indices: 1083989--1084083 Score: 190
Period size: 49 Copynumber: 1.9 Consensus size: 49
1083979 TGATAAATTA
1083989 TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGCTAG
1 TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGCTAG
1084038 TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGC
1 TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGC
1084084 GAGACTTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (49 bp):
TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGCTAG
Found at i:1098358 original size:20 final size:20
Alignment explanation
Indices: 1098316--1098358 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1098306 TGAATATGTC
***
1098316 ATTGTCATTGCAATTTTCGA
1 ATTGTCATTGCAATTTAAAA
*
1098336 ATTGTGATTGCAATTTAAAA
1 ATTGTCATTGCAATTTAAAA
1098356 ATT
1 ATT
1098359 TAAAAAGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (20 bp):
ATTGTCATTGCAATTTAAAA
Found at i:1099822 original size:49 final size:49
Alignment explanation
Indices: 1099768--1099862 Score: 190
Period size: 49 Copynumber: 1.9 Consensus size: 49
1099758 TGATAAATTA
1099768 TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGCTAG
1 TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGCTAG
1099817 TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGC
1 TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGC
1099863 GAGACTTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (49 bp):
TGCAGTTGAAGCATTTGGAAACAAATGATTAATTTTAAAGCTTAGCTAG
Found at i:1112895 original size:40 final size:41
Alignment explanation
Indices: 1112840--1112921 Score: 157
Period size: 40 Copynumber: 2.0 Consensus size: 41
1112830 GCTATAAAAG
1112840 GGGAAAGAAAACATTTCTGGG-ATTCTTTTGATTGGATACT
1 GGGAAAGAAAACATTTCTGGGAATTCTTTTGATTGGATACT
1112880 GGGAAAGAAAACATTTCTGGGAATTCTTTTGATTGGATACT
1 GGGAAAGAAAACATTTCTGGGAATTCTTTTGATTGGATACT
1112921 G
1 G
1112922 AGAATGGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 21 0.51
41 20 0.49
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (41 bp):
GGGAAAGAAAACATTTCTGGGAATTCTTTTGATTGGATACT
Found at i:1113816 original size:29 final size:27
Alignment explanation
Indices: 1113782--1113850 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 27
1113772 AATTGTGTTG
1113782 ATTTTAAAATATAAACATATAAATATTAT
1 ATTTTAAAATA-AAACAT-TAAATATTAT
* *
1113811 GA-TTTAAACCTAAAACATTAACTATTAT
1 -ATTTTAAA-ATAAAACATTAAATATTAT
1113839 ATTTTAAAATAA
1 ATTTTAAAATAA
1113851 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 4 0.12
28 15 0.44
29 12 0.35
30 3 0.09
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (27 bp):
ATTTTAAAATAAAACATTAAATATTAT
Found at i:1114228 original size:69 final size:69
Alignment explanation
Indices: 1114152--1114289 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
1114142 TTTTGTGTGT
1114152 GTTATTAGTACAATGTGTAATTTGTACAACAATTAAATTTATAATGACCTAAATTGTTATTAGAC
1 GTTATTAGTACAATGTGTAATTTGTACAACAATTAAATTTATAATGACCTAAATTGTTATTAGAC
1114217 TAAA
66 TAAA
1114221 GTTATTAGTACAATGTGTAATTTGTACAACAATTAAATTTATAATGACCTAAATTGTTATTAGAC
1 GTTATTAGTACAATGTGTAATTTGTACAACAATTAAATTTATAATGACCTAAATTGTTATTAGAC
1114286 TAAA
66 TAAA
1114290 AAATTGAGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.39
Consensus pattern (69 bp):
GTTATTAGTACAATGTGTAATTTGTACAACAATTAAATTTATAATGACCTAAATTGTTATTAGAC
TAAA
Found at i:1122333 original size:28 final size:28
Alignment explanation
Indices: 1122301--1122381 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
1122291 TATGACCCTC
*
1122301 ATTTTAAATTGGTCCCTAAACTTTAAAT
1 ATTTTAAATTAGTCCCTAAACTTTAAAT
* * *
1122329 ATTTTAATTTTA-TCCCTAAACTATGAAT
1 ATTTTAA-ATTAGTCCCTAAACTTTAAAT
1122357 ATGTTCTAAATTAGTCCAC-AAACTT
1 AT-TT-TAAATTAGTCC-CTAAACTT
1122382 CTAACATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
28 23 0.55
29 7 0.17
30 11 0.26
31 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (28 bp):
ATTTTAAATTAGTCCCTAAACTTTAAAT
Found at i:1126714 original size:2 final size:2
Alignment explanation
Indices: 1126707--1126735 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1126697 TTGGGCTAGT
1126707 TA TA 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 TA TA T
1126736 TATGGATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1127953 original size:32 final size:29
Alignment explanation
Indices: 1127928--1127986 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1127918 TTAACATGGA
*
1127928 AGAATAATTGTAAATTGTATCGTTAACAG
1 AGAATAATTGTAAACTGTATCGTTAACAG
* *
1127957 TGATTAATTGTAAACTGTATCGTTAACAG
1 AGAATAATTGTAAACTGTATCGTTAACAG
1127986 A
1 A
1127987 ATCAAGCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (29 bp):
AGAATAATTGTAAACTGTATCGTTAACAG
Found at i:1128167 original size:21 final size:18
Alignment explanation
Indices: 1128148--1128186 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1128138 TCACATCGTT
1128148 GTTAATTATTTAATGATC
1 GTTAATTATTTAATGATC
1128166 GTTAATTATTTAATGAT-
1 GTTAATTATTTAATGATC
1128183 GTTA
1 GTTA
1128187 TCATATAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (18 bp):
GTTAATTATTTAATGATC
Found at i:1132579 original size:2 final size:2
Alignment explanation
Indices: 1132515--1132568 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
1132505 AAAACATTAA
*
1132515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1132557 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
1132569 GTTTTATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1136227 original size:44 final size:45
Alignment explanation
Indices: 1136179--1136349 Score: 163
Period size: 44 Copynumber: 3.9 Consensus size: 45
1136169 GAGTGATATT
*
1136179 CCCATCTAAGTCAG-TCCAAATATAACTAAACGACAAGTGAAAAC
1 CCCATCTAAGGCAGATCCAAATATAACTAAACGACAAGTGAAAAC
* * * *
1136223 CCCATCTAAGGCA-ATCCAAATATAACTAAATGATAAGTGATATC
1 CCCATCTAAGGCAGATCCAAATATAACTAAACGACAAGTGAAAAC
** * * * *
1136267 TGCATCT-TGGCTGATCCAAATATAACTAAACGACAAGTG-ATAT
1 CCCATCTAAGGCAGATCCAAATATAACTAAACGACAAGTGAAAAC
* * * * *
1136310 CCCTTCTAA-GCCGATCCAAAAATAATTAAATGACAAGTGA
1 CCCATCTAAGGCAGATCCAAATATAACTAAACGACAAGTGA
1136350 TAGCCACTTT
Statistics
Matches: 100, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
43 33 0.33
44 67 0.67
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (45 bp):
CCCATCTAAGGCAGATCCAAATATAACTAAACGACAAGTGAAAAC
Found at i:1140567 original size:41 final size:40
Alignment explanation
Indices: 1140522--1140598 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
1140512 GGCGTTTGAA
*
1140522 TAAAAACGACACTAAAATACAAGTCTATAGCAGTGTTCGTG
1 TAAAAACGACACTAAAA-ACAACTCTATAGCAGTGTTCGTG
* * * *
1140563 TAAAAACGCCACTACAAACAACTCTCTAGCGGTGTT
1 TAAAAACGACACTAAAAACAACTCTATAGCAGTGTT
1140599 TTTATACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 16 0.52
41 15 0.48
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (40 bp):
TAAAAACGACACTAAAAACAACTCTATAGCAGTGTTCGTG
Found at i:1141078 original size:42 final size:43
Alignment explanation
Indices: 1140981--1141082 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 43
1140971 TGTCACTTAG
* *
1140981 GTACATGACTATTGCGACGTTTATTACAAAAAAGCCCAAGAAA
1 GTACATGACTATTGTGGCGTTTATTACAAAAAAGCCCAAGAAA
* * * * **
1141024 TTACATGA-TATTGTGGCGTTTATTATACAAACG-CCACTAAA
1 GTACATGACTATTGTGGCGTTTATTACAAAAAAGCCCAAGAAA
1141065 GTACATGACTATTGTGGC
1 GTACATGACTATTGTGGC
1141083 ATTTTGGAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
41 13 0.27
42 29 0.59
43 7 0.14
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (43 bp):
GTACATGACTATTGTGGCGTTTATTACAAAAAAGCCCAAGAAA
Found at i:1141143 original size:41 final size:41
Alignment explanation
Indices: 1141085--1141179 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
1141075 ATTGTGGCAT
* * * *
1141085 TTTGGAAA-AAACACCACTAAAGTA-TAATTCTATAGCGATG
1 TTTGTAAACAAACGCCACTAAAGTACGAATT-TATAGCGACG
* * *
1141125 TTTTTAAACAAACGCCACTAGAGTACGAGTTTATAGCGACG
1 TTTGTAAACAAACGCCACTAAAGTACGAATTTATAGCGACG
1141166 TTTGTAAACAAACG
1 TTTGTAAACAAACG
1141180 ACATGAAAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
40 6 0.13
41 36 0.80
42 3 0.07
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (41 bp):
TTTGTAAACAAACGCCACTAAAGTACGAATTTATAGCGACG
Found at i:1143467 original size:16 final size:16
Alignment explanation
Indices: 1143446--1143477 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1143436 TTATAAAATC
1143446 ACTATAAATTCTACAA
1 ACTATAAATTCTACAA
*
1143462 ACTATAAATTGTACAA
1 ACTATAAATTCTACAA
1143478 GAACGATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (16 bp):
ACTATAAATTCTACAA
Found at i:1145385 original size:15 final size:17
Alignment explanation
Indices: 1145363--1145400 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1145353 TGTGAAAGTT
*
1145363 ATGAAAAGTATAT-GAA
1 ATGAAAAGGATATCGAA
1145379 A-GAAAAGGATATCGAA
1 ATGAAAAGGATATCGAA
1145395 ATGAAA
1 ATGAAA
1145401 TGAATGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 5 0.26
17 4 0.21
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.18
Consensus pattern (17 bp):
ATGAAAAGGATATCGAA
Found at i:1148085 original size:63 final size:63
Alignment explanation
Indices: 1147979--1148102 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
1147969 ACCTAAAGGA
** * * *
1147979 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCC-TTGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCACAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGA-GCCTACCTAAGAAC
* *
1148042 ACATCTTAGGGCCACAGGGCCTACCCGAGA-ATGATCTCAGGGCCGTAGAGCCTACCTAAGA
1 ACATCTTAGGGCCACAGAGCCTACCCAAGATA-GATCTCAGGGCCGTAGAGCCTACCTAAGA
1148103 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (63 bp):
ACATCTTAGGGCCACAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
Found at i:1150971 original size:21 final size:21
Alignment explanation
Indices: 1150945--1151003 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 21
1150935 CGGTCAACGG
* * *
1150945 GTCGGGTCAATGGGTGGGGTC
1 GTCGGGTAAACGGGTCGGGTC
1150966 GTCGGGTAAACGGGTC-GG--
1 GTCGGGTAAACGGGTCGGGTC
1150984 GTCGGGTAAACGGGTCGGGT
1 GTCGGGTAAACGGGTCGGGT
1151004 TGGAACCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 16 0.48
19 2 0.06
20 2 0.06
21 13 0.39
ACGTcount: A:0.14, C:0.15, G:0.51, T:0.20
Consensus pattern (21 bp):
GTCGGGTAAACGGGTCGGGTC
Found at i:1150989 original size:18 final size:18
Alignment explanation
Indices: 1150966--1151003 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1150956 GGGTGGGGTC
1150966 GTCGGGTAAACGGGTCGG
1 GTCGGGTAAACGGGTCGG
1150984 GTCGGGTAAACGGGTCGG
1 GTCGGGTAAACGGGTCGG
1151002 GT
1 GT
1151004 TGGAACCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.18
Consensus pattern (18 bp):
GTCGGGTAAACGGGTCGG
Found at i:1153345 original size:22 final size:24
Alignment explanation
Indices: 1153307--1153350 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1153297 CAATTAATAA
1153307 AATAGTTTTAAAGTGG-ACAAAGG
1 AATAGTTTTAAAGTGGAACAAAGG
1153330 AATA-TTTTAGAA-TGGAACAAA
1 AATAGTTTTA-AAGTGGAACAAA
1153351 ATTTTAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (24 bp):
AATAGTTTTAAAGTGGAACAAAGG
Found at i:1158769 original size:453 final size:453
Alignment explanation
Indices: 1157923--1158832 Score: 1766
Period size: 453 Copynumber: 2.0 Consensus size: 453
1157913 GTAATACTGA
1157923 TCAACCATAAAAATTCCATTCCAACACCTTTGATCTTCAATTCAACTTCCAATAATTCCTCATAT
1 TCAACCATAAAAATTCCATTCCAACACCTTTGATCTTCAATTCAACTTCCAATAATTCCTCATAT
*
1157988 ACATATCAACATAAATTATTATATCAAAAACGGAGCTTAATTACGATAAACGGATCGAATCGGGT
66 ACATATCAACATAAATTATTATATCAAAAACGGAGCTTAATTACGATAAACGGATCGAATCAGGT
1158053 GATAAATCAGTGAAAAATAGCTTATCGAGTTTGAATTTAGCAAAACGGACTTCGGATTCGGATTC
131 GATAAATCAGTGAAAAATAGCTTATCGAGTTTGAATTTAGCAAAACGGACTTCGGATTCGGATTC
* *
1158118 AGGACGTCGAAAACATAAAATATGACTTTTCAGAAATTTGGAATTTTCGATCAAAATCAAAGTCA
196 AGAACGTCGAAAACATAAAATATGACTTTTCAAAAATTTGGAATTTTCGATCAAAATCAAAGTCA
*
1158183 ACGGGTTTGACTGGTAATTTCGAGGTCTTCGGGTTCGAATTTCAAAAAACAGACAGCGGAATCGG
261 ACGGGTTTGACTGGCAATTTCGAGGTCTTCGGGTTCGAATTTCAAAAAACAGACAGCGGAATCGG
1158248 ATTTGGAACGTTGAAAAATGTCAGGATAGGTATACTCGGTCAAAGTCAAAGGTCCTTTAATGCTC
326 ATTTGGAACGTTGAAAAATGTCAGGATAGGTATACTCGGTCAAAGTCAAAGGTCCTTTAATGCTC
1158313 GGTCAAAGCAGTCAAAGTTTTGGTCAACTTTGGTCAACACCGGTCAACGGTCAACGGGTCGGG
391 GGTCAAAGCAGTCAAAGTTTTGGTCAACTTTGGTCAACACCGGTCAACGGTCAACGGGTCGGG
1158376 TCAACCATAAAAATTCCATTCCAACACCTTTGATCTTCAATTCAACTTCCAATAATTCCTCATAT
1 TCAACCATAAAAATTCCATTCCAACACCTTTGATCTTCAATTCAACTTCCAATAATTCCTCATAT
1158441 ACATATCAACATAAATTATTATATCAAAAACGGAGCTTAATTACGATAAACGGATCGAATCAGGT
66 ACATATCAACATAAATTATTATATCAAAAACGGAGCTTAATTACGATAAACGGATCGAATCAGGT
* *
1158506 GATAAATCAGTGAAAAATAGCTTATCGGGTTTGAATTTAGCGAAACGGACTTCGGATTCGGATTC
131 GATAAATCAGTGAAAAATAGCTTATCGAGTTTGAATTTAGCAAAACGGACTTCGGATTCGGATTC
1158571 AGAACGTCGAAAACATAAAATATGACTTTTCAAAAATTTGGAATTTTCGATCAAAATCAAAGTCA
196 AGAACGTCGAAAACATAAAATATGACTTTTCAAAAATTTGGAATTTTCGATCAAAATCAAAGTCA
1158636 ACGGGTTTGACTGGCAATTTCGAGGTCTTCGGGTTCGAATTTCAAAAAACAGACAGCGGAATCGG
261 ACGGGTTTGACTGGCAATTTCGAGGTCTTCGGGTTCGAATTTCAAAAAACAGACAGCGGAATCGG
1158701 ATTTGGAACGTTGAAAAATGTCAGGATAGGTATACTCGGTCAAAGTCAAAGGTCCTTTAATGCTC
326 ATTTGGAACGTTGAAAAATGTCAGGATAGGTATACTCGGTCAAAGTCAAAGGTCCTTTAATGCTC
1158766 GGTCAAAGCAGTCAAAGTTTTGGTCAACTTTGGTCAACACCGGTCAACGGTCAACGGGTCGGG
391 GGTCAAAGCAGTCAAAGTTTTGGTCAACTTTGGTCAACACCGGTCAACGGTCAACGGGTCGGG
1158829 TCAA
1 TCAA
1158833 TGGGTGGGGT
Statistics
Matches: 451, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
453 451 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (453 bp):
TCAACCATAAAAATTCCATTCCAACACCTTTGATCTTCAATTCAACTTCCAATAATTCCTCATAT
ACATATCAACATAAATTATTATATCAAAAACGGAGCTTAATTACGATAAACGGATCGAATCAGGT
GATAAATCAGTGAAAAATAGCTTATCGAGTTTGAATTTAGCAAAACGGACTTCGGATTCGGATTC
AGAACGTCGAAAACATAAAATATGACTTTTCAAAAATTTGGAATTTTCGATCAAAATCAAAGTCA
ACGGGTTTGACTGGCAATTTCGAGGTCTTCGGGTTCGAATTTCAAAAAACAGACAGCGGAATCGG
ATTTGGAACGTTGAAAAATGTCAGGATAGGTATACTCGGTCAAAGTCAAAGGTCCTTTAATGCTC
GGTCAAAGCAGTCAAAGTTTTGGTCAACTTTGGTCAACACCGGTCAACGGTCAACGGGTCGGG
Found at i:1158844 original size:18 final size:18
Alignment explanation
Indices: 1158820--1158883 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
1158810 CAACGGTCAA
* *
1158820 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTAAACGGGT
*
1158838 GGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1158856 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1158874 CGGGTCGGGT
1 CGGGTCGGGT
1158884 TGGAACCGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.12, C:0.16, G:0.53, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1165636 original size:2 final size:2
Alignment explanation
Indices: 1165629--1165667 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1165619 GTGAAAACAT
1165629 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
1165668 GTAGGGTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1166320 original size:16 final size:16
Alignment explanation
Indices: 1166299--1166330 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1166289 TTATAAAATC
1166299 ACTATAAATTCTACAA
1 ACTATAAATTCTACAA
1166315 ACTATAAATTCTACAA
1 ACTATAAATTCTACAA
1166331 GAATGATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
ACTATAAATTCTACAA
Found at i:1167991 original size:52 final size:52
Alignment explanation
Indices: 1167879--1167991 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 52
1167869 CATACTACAA
* *
1167879 ATGATAAAAGGCATAAAAGGTGCCAAATTGATTATAGCACTATGGGGTGCAT
1 ATGATAAAAGGCATAAAAGGTGCCAAACTGATTATAACACTATGGGGTGCAT
*
1167931 ATGATAAAAGGCAT-AAAGGTGCCAAACTGATTATAACACTATGGGGTGGAT
1 ATGATAAAAGGCATAAAAGGTGCCAAACTGATTATAACACTATGGGGTGCAT
1167982 ATGATTAAAA
1 ATGA-TAAAA
1167992 AATGCATTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 38 0.67
52 19 0.33
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.25
Consensus pattern (52 bp):
ATGATAAAAGGCATAAAAGGTGCCAAACTGATTATAACACTATGGGGTGCAT
Found at i:1173950 original size:16 final size:16
Alignment explanation
Indices: 1173929--1173960 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1173919 TTATAAAATC
1173929 ACTATAAATTCTACAA
1 ACTATAAATTCTACAA
1173945 ACTATAAATTCTACAA
1 ACTATAAATTCTACAA
1173961 GAATGATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
ACTATAAATTCTACAA
Found at i:1175574 original size:16 final size:16
Alignment explanation
Indices: 1175553--1175585 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1175543 AAATGATAAA
1175553 AGGCATAAAAGGTGCC
1 AGGCATAAAAGGTGCC
1175569 AGGCATAAAAGGTGCC
1 AGGCATAAAAGGTGCC
1175585 A
1 A
1175586 AATTGATTAT
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:0.39, C:0.18, G:0.30, T:0.12
Consensus pattern (16 bp):
AGGCATAAAAGGTGCC
Found at i:1175639 original size:54 final size:55
Alignment explanation
Indices: 1175569--1175678 Score: 204
Period size: 54 Copynumber: 2.0 Consensus size: 55
1175559 AAAAGGTGCC
*
1175569 AGGCATAAAAGGTGCCAAATTGATTATATAGCACTATGGGGTGCATATGA-TAAA
1 AGGCATAAAAGGTGCCAAACTGATTATATAGCACTATGGGGTGCATATGATTAAA
1175623 AGGCATAAAAGGTGCCAAACTGATTATATAGCACTATGGGGTGCATATGATTAAA
1 AGGCATAAAAGGTGCCAAACTGATTATATAGCACTATGGGGTGCATATGATTAAA
1175678 A
1 A
1175679 AATGCACTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 49 0.91
55 5 0.09
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (55 bp):
AGGCATAAAAGGTGCCAAACTGATTATATAGCACTATGGGGTGCATATGATTAAA
Found at i:1175666 original size:29 final size:28
Alignment explanation
Indices: 1175579--1175675 Score: 78
Period size: 27 Copynumber: 3.5 Consensus size: 28
1175569 AGGCATAAAA
1175579 GGTGCCAAATTGATTATATAGCACTATGG
1 GGTGCCAAA-TGATTATATAGCACTATGG
* * ***
1175608 GGTG-CATATGA-TA-AAAGGCA-TAAAA
1 GGTGCCAAATGATTATATA-GCACTATGG
1175633 GGTGCCAAACTGATTATATAGCACTATGG
1 GGTGCCAAA-TGATTATATAGCACTATGG
*
1175662 GGTG-CATATGATTA
1 GGTGCCAAATGATTA
1175676 AAAAATGCAC
Statistics
Matches: 51, Mismatches: 11, Indels: 14
0.67 0.14 0.18
Matches are distributed among these distances:
25 8 0.16
26 8 0.16
27 12 0.24
28 11 0.22
29 12 0.24
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (28 bp):
GGTGCCAAATGATTATATAGCACTATGG
Found at i:1175674 original size:27 final size:27
Alignment explanation
Indices: 1175589--1175675 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
1175579 GGTGCCAAAT
1175589 TGATTATATAGCACTATGGGGTGCATA
1 TGATTATATAGCACTATGGGGTGCATA
* *** *
1175616 TGA-TA-AAAGGCA-TAAAAGGTGCCAAA
1 TGATTATATA-GCACTATGGGGTG-CATA
1175642 CTGATTATATAGCACTATGGGGTGCATA
1 -TGATTATATAGCACTATGGGGTGCATA
1175670 TGATTA
1 TGATTA
1175676 AAAAATGCAC
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
25 8 0.18
26 8 0.18
27 12 0.27
28 8 0.18
29 8 0.18
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (27 bp):
TGATTATATAGCACTATGGGGTGCATA
Found at i:1179824 original size:29 final size:29
Alignment explanation
Indices: 1179791--1179851 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
1179781 ATCACAGTAT
1179791 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTGGAGAACAAATTATGGCAAATTA
*
1179820 AAGATTGGAGAACAAATTATGTCAAATTA
1 AAGATTGGAGAACAAATTATGGCAAATTA
1179849 AAG
1 AAG
1179852 TTTAGAGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.25
Consensus pattern (29 bp):
AAGATTGGAGAACAAATTATGGCAAATTA
Found at i:1179865 original size:29 final size:29
Alignment explanation
Indices: 1179791--1179859 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
1179781 ATCACAGTAT
*
1179791 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTAGAGAACAAATTATGGCAAATTA
* *
1179820 AAGATTGGAGAACAAATTATGTCAAATTA
1 AAGATTAGAGAACAAATTATGGCAAATTA
*
1179849 AAGTTTAGAGA
1 AAGATTAGAGA
1179860 CTAAATATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (29 bp):
AAGATTAGAGAACAAATTATGGCAAATTA
Found at i:1182254 original size:32 final size:32
Alignment explanation
Indices: 1182203--1182310 Score: 110
Period size: 32 Copynumber: 3.4 Consensus size: 32
1182193 ATATTCAATT
* *
1182203 ATTATTTTGTAACAGTTTGATAGAATTTAATG
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* **
1182235 ATTATTTTATAATAATTTGATAGAATCCAATG
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* * * *
1182267 ATCATTTTAAAACAATTCGATA-AATTTAATA
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* *
1182298 ACTATTTTGTAAC
1 ATTATTTTATAAC
1182311 TTTTGAAAAT
Statistics
Matches: 60, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
31 15 0.25
32 45 0.75
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (32 bp):
ATTATTTTATAACAATTTGATAGAATTTAATG
Found at i:1182806 original size:29 final size:30
Alignment explanation
Indices: 1182757--1182819 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
1182747 TGATTCTATG
* *
1182757 TTAGGGGACTAAATTTGAACTTTTAAAATT
1 TTAGGGGACTAAATTTAAACTTATAAAATT
1182787 TTAGGGGA-TAAATTTAAACTTATAAAATT
1 TTAGGGGACTAAATTTAAACTTATAAAATT
1182816 TTAG
1 TTAG
1182820 AGGGTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (30 bp):
TTAGGGGACTAAATTTAAACTTATAAAATT
Found at i:1185643 original size:32 final size:32
Alignment explanation
Indices: 1185607--1185714 Score: 119
Period size: 32 Copynumber: 3.4 Consensus size: 32
1185597 ATATTCAATT
*
1185607 ATTATTTTGTAACAATTTGATAGAATTTAATG
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* **
1185639 ATTATTTTATAATAATTTGATAGAATCCAATG
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* * * *
1185671 ATCATTTTAAAACAATTCGATA-AATTTAATA
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* *
1185702 ACTATTTTGTAAC
1 ATTATTTTATAAC
1185715 TTTTGAAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
31 15 0.25
32 46 0.75
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (32 bp):
ATTATTTTATAACAATTTGATAGAATTTAATG
Found at i:1186335 original size:21 final size:21
Alignment explanation
Indices: 1186309--1186351 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1186299 CCTTCGAGAA
1186309 ACCAAATCACCACTCATGATC
1 ACCAAATCACCACTCATGATC
1186330 ACCAAATCACCACTCATGATC
1 ACCAAATCACCACTCATGATC
1186351 A
1 A
1186352 ACCCTTACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.37, G:0.05, T:0.19
Consensus pattern (21 bp):
ACCAAATCACCACTCATGATC
Found at i:1188129 original size:29 final size:30
Alignment explanation
Indices: 1188080--1188138 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1188070 TGATTCTATG
* *
1188080 TTAGGGGACTAAATTTGAACTTTTAAAATT
1 TTAGGGGACTAAATTTAAACTTATAAAATT
1188110 TTAGGGGA-TAAATTTAAACTTATAAAATT
1 TTAGGGGACTAAATTTAAACTTATAAAATT
1188139 CTAGAGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (30 bp):
TTAGGGGACTAAATTTAAACTTATAAAATT
Found at i:1192831 original size:29 final size:29
Alignment explanation
Indices: 1192798--1192858 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1192788 ATCACAGTAT
1192798 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTGGAGAACAAATTATGGCAAATTA
1192827 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTGGAGAACAAATTATGGCAAATTA
1192856 AAG
1 AAG
1192859 TTTAGAGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (29 bp):
AAGATTGGAGAACAAATTATGGCAAATTA
Found at i:1192872 original size:29 final size:29
Alignment explanation
Indices: 1192798--1192866 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
1192788 ATCACAGTAT
*
1192798 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTAGAGAACAAATTATGGCAAATTA
*
1192827 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTAGAGAACAAATTATGGCAAATTA
*
1192856 AAGTTTAGAGA
1 AAGATTAGAGA
1192867 CTAAATATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.25
Consensus pattern (29 bp):
AAGATTAGAGAACAAATTATGGCAAATTA
Found at i:1195301 original size:32 final size:32
Alignment explanation
Indices: 1195265--1195372 Score: 119
Period size: 32 Copynumber: 3.4 Consensus size: 32
1195255 ATATTCAATT
*
1195265 ATTATTTTGTAACAATTTGATAGAATTTAATG
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* **
1195297 ATTATTTTATAATAATTTGATAGAATCCAATG
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* * * *
1195329 ATCATTTTAAAACAATTCGATA-AATTTAATA
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* *
1195360 ACTATTTTGTAAC
1 ATTATTTTATAAC
1195373 TTTTGAAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
31 15 0.25
32 46 0.75
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (32 bp):
ATTATTTTATAACAATTTGATAGAATTTAATG
Found at i:1195994 original size:22 final size:22
Alignment explanation
Indices: 1195966--1196013 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1195956 ACCTTCGAGA
1195966 AACCAAATCACCACTCATGATC
1 AACCAAATCACCACTCATGATC
1195988 AACCAAATCACCACTCATGATC
1 AACCAAATCACCACTCATGATC
1196010 AACC
1 AACC
1196014 CTTACCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.38, G:0.04, T:0.17
Consensus pattern (22 bp):
AACCAAATCACCACTCATGATC
Found at i:1197790 original size:29 final size:30
Alignment explanation
Indices: 1197741--1197799 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1197731 TGATTCTATG
* *
1197741 TTAGGGGACTAAATTTGAACTTTTAAAATT
1 TTAGGGGACTAAATTTAAACTTATAAAATT
1197771 TTAGGGGA-TAAATTTAAACTTATAAAATT
1 TTAGGGGACTAAATTTAAACTTATAAAATT
1197800 CTAGAGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (30 bp):
TTAGGGGACTAAATTTAAACTTATAAAATT
Found at i:1202491 original size:29 final size:29
Alignment explanation
Indices: 1202458--1202518 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1202448 ATCACAGTAT
1202458 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTGGAGAACAAATTATGGCAAATTA
1202487 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTGGAGAACAAATTATGGCAAATTA
1202516 AAG
1 AAG
1202519 TTTAGAGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (29 bp):
AAGATTGGAGAACAAATTATGGCAAATTA
Found at i:1202532 original size:29 final size:29
Alignment explanation
Indices: 1202458--1202526 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
1202448 ATCACAGTAT
*
1202458 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTAGAGAACAAATTATGGCAAATTA
*
1202487 AAGATTGGAGAACAAATTATGGCAAATTA
1 AAGATTAGAGAACAAATTATGGCAAATTA
*
1202516 AAGTTTAGAGA
1 AAGATTAGAGA
1202527 CTAAATATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.25
Consensus pattern (29 bp):
AAGATTAGAGAACAAATTATGGCAAATTA
Found at i:1204963 original size:32 final size:32
Alignment explanation
Indices: 1204927--1205034 Score: 119
Period size: 32 Copynumber: 3.4 Consensus size: 32
1204917 ATATTCAATT
*
1204927 ATTATTTTGTAACAATTTGATAGAATTTAATG
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* **
1204959 ATTATTTTATAATAATTTGATAGAATCCAATG
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* * * *
1204991 ATCATTTTAAAACAATTCGATA-AATTTAATA
1 ATTATTTTATAACAATTTGATAGAATTTAATG
* *
1205022 ACTATTTTGTAAC
1 ATTATTTTATAAC
1205035 TTTTGAAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
31 15 0.25
32 46 0.75
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (32 bp):
ATTATTTTATAACAATTTGATAGAATTTAATG
Found at i:1205654 original size:22 final size:22
Alignment explanation
Indices: 1205626--1205673 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1205616 ACCTTCGAGA
1205626 AACCAAATCACCACTCATGATC
1 AACCAAATCACCACTCATGATC
1205648 AACCAAATCACCACTCATGATC
1 AACCAAATCACCACTCATGATC
1205670 AACC
1 AACC
1205674 CTTACCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.38, G:0.04, T:0.17
Consensus pattern (22 bp):
AACCAAATCACCACTCATGATC
Found at i:1207449 original size:29 final size:30
Alignment explanation
Indices: 1207400--1207458 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1207390 TGATTCTATG
* *
1207400 TTAGGGGACTAAATTTGAACTTTTAAAATT
1 TTAGGGGACTAAATTTAAACTTATAAAATT
1207430 TTAGGGGA-TAAATTTAAACTTATAAAATT
1 TTAGGGGACTAAATTTAAACTTATAAAATT
1207459 CTAGAGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (30 bp):
TTAGGGGACTAAATTTAAACTTATAAAATT
Found at i:1211262 original size:18 final size:18
Alignment explanation
Indices: 1211239--1211274 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1211229 CCTCGAGCGG
1211239 TAAAATTTAAAA-AAAAAT
1 TAAAA-TTAAAAGAAAAAT
1211257 TAAAATTAAAAGAAAAAT
1 TAAAATTAAAAGAAAAAT
1211275 GAATTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
TAAAATTAAAAGAAAAAT
Found at i:1216124 original size:2 final size:2
Alignment explanation
Indices: 1216112--1216170 Score: 109
Period size: 2 Copynumber: 29.0 Consensus size: 2
1216102 CTTGACCTAA
1216112 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1216155 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1216171 TAAAAATCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1216448 original size:17 final size:18
Alignment explanation
Indices: 1216416--1216449 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1216406 CAAAGAATAA
*
1216416 AATTTAAACGATTAAATG
1 AATTTAAACAATTAAATG
1216434 AATTTAAA-AATTAAAT
1 AATTTAAACAATTAAAT
1216450 TGATATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (18 bp):
AATTTAAACAATTAAATG
Found at i:1219079 original size:2 final size:2
Alignment explanation
Indices: 1219033--1219061 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1219023 TTTAATCCAA
1219033 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1219062 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1219514 original size:37 final size:37
Alignment explanation
Indices: 1219441--1219515 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
1219431 GTTGGAAAAT
* *
1219441 ATTTATATATTTTCTTATAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTATAAAAATTGAAAATCATAAA
*
1219478 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTATA-AAAATTGAAAATCATAAA
1219515 A
1 A
1219516 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 18 0.55
38 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTATAAAAATTGAAAATCATAAA
Found at i:1224614 original size:13 final size:13
Alignment explanation
Indices: 1224583--1224633 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
1224573 TAAATAAATA
*
1224583 TTTAAAATTTATA
1 TTTAAAATTTATT
**
1224596 AATAAAATTTATT
1 TTTAAAATTTATT
1224609 TTTAAAAATTTA-T
1 TTT-AAAATTTATT
*
1224622 TTTATAATTTAT
1 TTTAAAATTTAT
1224634 GTTCAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 7 0.23
13 15 0.50
14 8 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTAAAATTTATT
Found at i:1229209 original size:50 final size:50
Alignment explanation
Indices: 1229145--1229239 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
1229135 AAGAGAACGA
* * * *
1229145 GATAAATGAGCTTATAAACGAGCTTGTTCATTAACATAAATGAACGAGTC
1 GATAAATGAACTTATAAACGAGCTTCTTCATGAACATAAACGAACGAGTC
* * *
1229195 GATAAATGAACTTATTACCGAGCTTCTTCCTGAACATAAACGAAC
1 GATAAATGAACTTATAAACGAGCTTCTTCATGAACATAAACGAAC
1229240 CATGTTCATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (50 bp):
GATAAATGAACTTATAAACGAGCTTCTTCATGAACATAAACGAACGAGTC
Found at i:1232805 original size:31 final size:31
Alignment explanation
Indices: 1232770--1232846 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1232760 TAAATTCGTA
* * *
1232770 TTTAGTATCTAAATTATTAGTTT-TTATCCGT
1 TTTAGTATCTAAACTATCA-TTTCTTACCCGT
*
1232801 TTTAGTATCTAAACTATCATTTCTTGCCCGT
1 TTTAGTATCTAAACTATCATTTCTTACCCGT
1232832 TTTAGTATCTAAACT
1 TTTAGTATCTAAACT
1232847 TTCAATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTAGTATCTAAACTATCATTTCTTACCCGT
Found at i:1235610 original size:12 final size:12
Alignment explanation
Indices: 1235585--1235653 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
1235575 ACGGAGATAT
* *
1235585 CAGAAATCAAAA
1 CAGAATTCAGAA
1235597 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
1235609 CA-TATATCATAA
1 CAGAAT-TCAGAA
* *
1235621 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1235633 CAGAAATCAGAA
1 CAGAATTCAGAA
*
1235645 CATAATTCA
1 CAGAATTCA
1235654 AGTCGGAAAT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1235641 original size:24 final size:24
Alignment explanation
Indices: 1235583--1235646 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
1235573 AAACGGAGAT
*
1235583 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* * * *
1235607 AACATATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATCCAG
*
1235631 ATCAGAAATCAGAACA
1 ATCAGAAATCAAAACA
1235647 TAATTCAAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:1248429 original size:3 final size:3
Alignment explanation
Indices: 1248415--1248444 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1248405 GTTCATGAAA
*
1248415 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1248445 TTTATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1249694 original size:3 final size:3
Alignment explanation
Indices: 1249683--1249730 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
1249673 GTCCCTTTTT
* *
1249683 TTA TCA TTA TTA TTA TTTA TTA TTA TCA TTA TTTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA
1249731 AATAATGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 29 0.74
4 10 0.26
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1249704 original size:10 final size:10
Alignment explanation
Indices: 1249689--1249729 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1249679 TTTTTTATCA
1249689 TTATTATTAT
1 TTATTATTAT
1249699 TTATTATTA-
1 TTATTATTAT
*
1249708 TCATTATTTAT
1 TTATTA-TTAT
1249719 TTATTATTAT
1 TTATTATTAT
1249729 T
1 T
1249730 AAATAATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 5 0.19
10 17 0.63
11 5 0.19
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATTAT
Found at i:1249707 original size:16 final size:16
Alignment explanation
Indices: 1249682--1249730 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
1249672 TGTCCCTTTT
*
1249682 TTTATCATTATTATTA
1 TTTATTATTATTATTA
*
1249698 TTTATTATTATCATTA
1 TTTATTATTATTATTA
1249714 TTTATTTATTATTATTA
1 TTTA-TTATTATTATTA
1249731 AATAATGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:1250803 original size:19 final size:19
Alignment explanation
Indices: 1250775--1250813 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1250765 TTTTTGTGTC
*
1250775 TTTTAATTTAGTCTTATTA
1 TTTTAATTTAGTATTATTA
* *
1250794 TTTTATTTTATTATTATTA
1 TTTTAATTTAGTATTATTA
1250813 T
1 T
1250814 AGTCTTTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTAATTTAGTATTATTA
Found at i:1251115 original size:34 final size:32
Alignment explanation
Indices: 1251053--1251122 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1251043 ACCTTACAAC
* *
1251053 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
1251085 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
1251119 TCCC
1 TCCC
1251123 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:1251529 original size:21 final size:21
Alignment explanation
Indices: 1251485--1251552 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
1251475 TTGCAGCCTT
*
1251485 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
1251505 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
1251526 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
1251547 GATGCA
1 GATGCA
1251553 ATTGCATTCG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.19
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:1251677 original size:21 final size:21
Alignment explanation
Indices: 1251612--1251669 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1251602 CATTAGTGCA
1251612 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
1251633 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
1251654 GATGCATGGATGCACT
1 GATGCATGGATGCACT
1251670 TTTGGGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:1252354 original size:20 final size:21
Alignment explanation
Indices: 1252329--1252383 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1252319 TTGCAGCCTT
* *
1252329 GATGCATGGATGCATGAC-AG
1 GATGCATCGATGCATGACAAA
*
1252349 GATGCATCGATGCATGGCAAA
1 GATGCATCGATGCATGACAAA
1252370 GATGCATCGATGCA
1 GATGCATCGATGCA
1252384 CTAATTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGACAAA
Found at i:1252429 original size:20 final size:22
Alignment explanation
Indices: 1252404--1252459 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
1252394 TCGATGTTTG
*
1252404 GATGCATGGATGCATT-G-CCT
1 GATGCATGGATGCATTAGTCCA
* *
1252424 GATGCATCGATGCATTAGTGCA
1 GATGCATGGATGCATTAGTCCA
1252446 GATGCATGGATGCA
1 GATGCATGGATGCA
1252460 CTACAGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (22 bp):
GATGCATGGATGCATTAGTCCA
Found at i:1252596 original size:30 final size:30
Alignment explanation
Indices: 1252561--1252620 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1252551 AACTTTGAAT
*
1252561 AAATTCAATTCAAATCCAAAAATATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
* *
1252591 AAATTCAATTCCAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
1252621 CTTAAATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:1252791 original size:89 final size:89
Alignment explanation
Indices: 1252689--1252867 Score: 358
Period size: 89 Copynumber: 2.0 Consensus size: 89
1252679 CATTTGAAAA
1252689 ATTGGTTTTGGCAAAACTCCCCCTTAATAAATTGTTTAATGAAAAAGATATCAATTGTTACCAAT
1 ATTGGTTTTGGCAAAACTCCCCCTTAATAAATTGTTTAATGAAAAAGATATCAATTGTTACCAAT
1252754 TGTTGGAAAATATATGAAAATGTT
66 TGTTGGAAAATATATGAAAATGTT
1252778 ATTGGTTTTGGCAAAACTCCCCCTTAATAAATTGTTTAATGAAAAAGATATCAATTGTTACCAAT
1 ATTGGTTTTGGCAAAACTCCCCCTTAATAAATTGTTTAATGAAAAAGATATCAATTGTTACCAAT
1252843 TGTTGGAAAATATATGAAAATGTT
66 TGTTGGAAAATATATGAAAATGTT
1252867 A
1 A
1252868 AGCTCCTCCT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (89 bp):
ATTGGTTTTGGCAAAACTCCCCCTTAATAAATTGTTTAATGAAAAAGATATCAATTGTTACCAAT
TGTTGGAAAATATATGAAAATGTT
Found at i:1254023 original size:19 final size:20
Alignment explanation
Indices: 1253980--1254027 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1253970 TCTAAATCCT
*
1253980 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1254000 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1254019 TTTTCAAAA
1 TTTTCAAAA
1254028 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1254917 original size:32 final size:34
Alignment explanation
Indices: 1254881--1254950 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1254871 ACCTTACAAC
* *
1254881 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
*
1254913 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
1254947 TCCC
1 TCCC
1254951 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:1255359 original size:21 final size:21
Alignment explanation
Indices: 1255315--1255390 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
1255305 TTGCAGCCTT
* *
1255315 GATGCATGGATGCATGAC-AG
1 GATGCATCGATGCATGGCAAG
1255335 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
1255356 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
1255377 GATGCATCGATGCA
1 GATGCATCGATGCA
1255391 CTAATTGCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 16 0.30
21 37 0.70
ACGTcount: A:0.29, C:0.18, G:0.33, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:1255479 original size:21 final size:21
Alignment explanation
Indices: 1255410--1255510 Score: 116
Period size: 21 Copynumber: 4.8 Consensus size: 21
1255400 TTCGATGTTT
* *
1255410 GGATGCATGGATGCATTGC-C
1 GGATGCATGGATGCACTGCAG
* * * *
1255430 TGATGCATCGATGCATTAG-TG
1 GGATGCATGGATGCACT-GCAG
1255451 GAGATGCATGGATGCACTGCAG
1 G-GATGCATGGATGCACTGCAG
1255473 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCACTGCAG
1255494 GGATGCATGGATGCACT
1 GGATGCATGGATGCACT
1255511 TTGACACCCT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.21
21 39 0.56
22 16 0.23
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (21 bp):
GGATGCATGGATGCACTGCAG
Found at i:1255625 original size:30 final size:30
Alignment explanation
Indices: 1255591--1255650 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1255581 AACTTTGAAT
1255591 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
* *
1255621 AAATTCAATTCCAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
1255651 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:1257389 original size:12 final size:12
Alignment explanation
Indices: 1257372--1257422 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1257362 TTTAAAGAGG
1257372 TTTTATATTTAA
1 TTTTATATTTAA
1257384 TTTTATA-TTATA
1 TTTTATATTTA-A
*
1257396 TTTGAT-TTTAA
1 TTTTATATTTAA
1257407 TTTTA-ATATTAA
1 TTTTATAT-TTAA
1257419 TTTT
1 TTTT
1257423 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1257483 original size:64 final size:63
Alignment explanation
Indices: 1257384--1257540 Score: 248
Period size: 64 Copynumber: 2.5 Consensus size: 63
1257374 TTATATTTAA
*
1257384 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATAATAAAT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATAAT-AAT
*
1257445 TTTTAATATTATATTATAGATAATAATTTTAATATTAATTTTTTAAATAAATTAAATAATAAT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATAATAAT
1257508 TTTTCAATATTATATTATAGATATTTAATTTTA
1 TTTT-AATATTATATTATAGATA-TTAATTTTA
1257541 TATCATATAA
Statistics
Matches: 88, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
61 4 0.05
62 10 0.11
63 8 0.09
64 58 0.66
65 8 0.09
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (63 bp):
TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATAATAAT
Found at i:1257485 original size:12 final size:12
Alignment explanation
Indices: 1257380--1257486 Score: 60
Period size: 12 Copynumber: 8.7 Consensus size: 12
1257370 GGTTTTATAT
1257380 TTAATTTT-ATA
1 TTAATTTTAATA
* *
1257391 TT-ATATTTGATT
1 TTAAT-TTTAATA
1257403 TTAATTTTAATA
1 TTAATTTTAATA
1257415 TTAATTTTTTAA-A
1 TTAA--TTTTAATA
* *
1257428 -TAAATTAAATAA
1 TTAATTTTAAT-A
*
1257440 TAAATTTTTAATA
1 TTAA-TTTTAATA
*
1257453 TTATATTATAGATA
1 TTA-ATTTTA-ATA
*
1257467 ATAATTTTAATA
1 TTAATTTTAATA
1257479 TTAATTTT
1 TTAATTTT
1257487 TTAAATAAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
10 6 0.08
11 5 0.07
12 27 0.38
13 17 0.24
14 17 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:1257502 original size:24 final size:24
Alignment explanation
Indices: 1257466--1257511 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1257456 TATTATAGAT
* * *
1257466 AATAATTTTAATATTAATTTTTTA
1 AATAAATTAAATAATAATTTTTTA
1257490 AATAAATTAAATAATAATTTTT
1 AATAAATTAAATAATAATTTTT
1257512 CAATATTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATAAATTAAATAATAATTTTTTA
Found at i:1257595 original size:20 final size:19
Alignment explanation
Indices: 1257535--1257596 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1257525 TAGATATTTA
*
1257535 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1257554 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1257572 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1257592 ATTTT
1 ATTTT
1257597 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Done.