Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009598.1 Hibiscus syriacus cultivar Beakdansim tig00116978_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: 236377
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:130459 original size:21 final size:21
Alignment explanation
Indices: 130378--130464 Score: 113
Period size: 21 Copynumber: 4.1 Consensus size: 21
130368 GAACGGTGGG
*
130378 AGGGACCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* *
130399 AGGGGCCTCTTGAACGGT-AGG
1 AGGGGCCTCTTGAACGATGA-C
* *
130420 AGGGGCCTCTTGAAGGATGAT
1 AGGGGCCTCTTGAACGATGAC
130441 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
130462 AGG
1 AGG
130465 TGCTTCGGGC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.20
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:130623 original size:12 final size:12
Alignment explanation
Indices: 130604--130645 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
130594 GGGCCTCTAA
*
130604 AAATAAATTAAT
1 AAATAAATCAAT
*
130616 ACATAAATCAAT
1 AAATAAATCAAT
130628 AAATAAA-CAAAT
1 AAATAAATC-AAT
130640 AAATAA
1 AAATAA
130646 TGCCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:130781 original size:21 final size:21
Alignment explanation
Indices: 130756--130814 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
130746 GTTGAGCGGC
*
130756 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
130777 TACCTCACCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
*
130798 TACTTCACCACGTAAAG
1 TACCTCACCACGTAAAG
130815 CACCATTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:130898 original size:21 final size:21
Alignment explanation
Indices: 130868--130914 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
130858 ACCATTGTCT
* * *
130868 TCACGTAAAGTACTTACCTCC
1 TCACGCAAAGCACTTACCTCA
*
130889 TCACGCAAAGCATTTACCTCA
1 TCACGCAAAGCACTTACCTCA
130910 TCACG
1 TCACG
130915 TAACTCCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.26
Consensus pattern (21 bp):
TCACGCAAAGCACTTACCTCA
Found at i:132421 original size:43 final size:43
Alignment explanation
Indices: 132368--132673 Score: 479
Period size: 43 Copynumber: 7.1 Consensus size: 43
132358 AACAAAAAAT
132368 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
1 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
132411 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
1 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
** *
132454 GCCTTAATAGGTCGAGATCTATAGCGGCATTTTTGGGACAAAC
1 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
*
132497 GCCGCAATAGATCGAGATCTATAGCGGCGTTTTTGGGACAAAC
1 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
*
132540 GCTGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
1 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
* * *
132583 GCCTCAATAGGTCGAGATTTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
* * * **
132626 GCCACAAAAGGT-TAGATCTATAGCGGCGTTTTTTGATACAAAC
1 GCCGCAATAGGTCGAGATCTATAGCGGCG-TTTTTGGGACAAAC
132669 GCCGC
1 GCCGC
132674 TAATGACCGT
Statistics
Matches: 242, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
42 14 0.06
43 228 0.94
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (43 bp):
GCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGACAAAC
Found at i:135967 original size:82 final size:82
Alignment explanation
Indices: 135726--135995 Score: 328
Period size: 82 Copynumber: 3.3 Consensus size: 82
135716 TTAGCGGCGT
* * * *
135726 TATATATTCGGATATTGCGGCATTTTTTACATAAATGCCACTAAAGTACGCGTTTTTAGCGGCGT
1 TATATATTCGGATATCGCGGCGTTTTTTACATAAATGCCACTAAAGTACACATTTTTAGCGGCGT
* *
135791 TTACACAAAAACGCCAT
66 TTTCACAAAAACGCCAC
* * * * * ** *
135808 TATATATTTGGATATCGCGGCG-TTTGTCCAAAAATACCACTAAAGTACGTGA-TTTTAGCGGCA
1 TATATATTCGGATATCGCGGCGTTTTTTACATAAATGCCACTAAAGTAC-ACATTTTTAGCGGCG
**** *
135871 TTTTTGTGAAAACGCCGC
65 TTTTCACAAAAACGCCAC
*
135889 TATATATTCGGATATTGCGGCGTTTTTTACATAAATGCCACTAAAGTACACATTTTTAGCGGCGT
1 TATATATTCGGATATCGCGGCGTTTTTTACATAAATGCCACTAAAGTACACATTTTTAGCGGCGT
135954 TTTCACAAAAACGCCAC
66 TTTCACAAAAACGCCAC
*
135971 TATATATTTGGATATCGCGGCGTTT
1 TATATATTCGGATATCGCGGCGTTT
135996 GTAAAAAAAC
Statistics
Matches: 151, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
81 64 0.42
82 87 0.58
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (82 bp):
TATATATTCGGATATCGCGGCGTTTTTTACATAAATGCCACTAAAGTACACATTTTTAGCGGCGT
TTTCACAAAAACGCCAC
Found at i:136305 original size:19 final size:19
Alignment explanation
Indices: 136254--136307 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
136244 AATAGTTTCT
*
136254 GAAACTTAAAATCGCAACGC
1 GAAAC-TAAAATCGCAAAGC
*
136274 GAAAATGAAAATCGCAAAGC
1 GAAACT-AAAATCGCAAAGC
136294 GAAACTAAAATCGC
1 GAAACTAAAATCGC
136308 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.50, C:0.20, G:0.17, T:0.13
Consensus pattern (19 bp):
GAAACTAAAATCGCAAAGC
Found at i:136700 original size:22 final size:22
Alignment explanation
Indices: 136672--136729 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
136662 GATGGTGATA
136672 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
136694 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
136716 GACGGGTGTCGCCG
1 GACGGATTTCGCCG
136730 TAGAGAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.17
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:136855 original size:19 final size:20
Alignment explanation
Indices: 136833--136870 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
136823 AATATTGTGT
136833 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
136852 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
136871 CACACTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:136920 original size:20 final size:20
Alignment explanation
Indices: 136897--136945 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
136887 GACTTCTGTA
136897 TTGCGAATTACAGATTCGCG
1 TTGCGAATTACAGATTCGCG
*
136917 TTGCGATTTACAGATTCGCG
1 TTGCGAATTACAGATTCGCG
136937 TTGCGAATT
1 TTGCGAATT
136946 TGTTGGTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TTGCGAATTACAGATTCGCG
Found at i:137195 original size:20 final size:19
Alignment explanation
Indices: 137170--137207 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
137160 AATTTATAAA
137170 ATTTTTAAAAATAAAAATAG
1 ATTTTTAAAAA-AAAAATAG
*
137190 ATTTTTAATAAAAAAATA
1 ATTTTTAAAAAAAAAATA
137208 TATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
ATTTTTAAAAAAAAAATAG
Found at i:138907 original size:29 final size:29
Alignment explanation
Indices: 138874--138947 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
138864 AAAAAATTAG
138874 TTAATTCGGTTCGATGAATAATTTTCAAA
1 TTAATTCGGTTCGATGAATAATTTTCAAA
* * * *
138903 TTAATTCAGTTTGGTTAATAATTTTCAAA
1 TTAATTCGGTTCGATGAATAATTTTCAAA
* *
138932 TAAATTTTGGTTCGAT
1 TTAA-TTCGGTTCGAT
138948 TAACGAACAG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 28 0.80
30 7 0.20
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (29 bp):
TTAATTCGGTTCGATGAATAATTTTCAAA
Found at i:139029 original size:135 final size:135
Alignment explanation
Indices: 138864--139120 Score: 381
Period size: 135 Copynumber: 1.9 Consensus size: 135
138854 AGTTAAAGGA
* * * * *
138864 AAAAAATTAGTTAATTCGGTTCGATGAATAATTTTCAAATTAATTCAGTTTGGTTAATAATTTTC
1 AAAAAATCAGTCAATTCGGTGCGATGAATAATGTTCAAATTAATTCAGTTCGGTTAATAATTTTC
* *
138929 AAATAAATTTTGGTTCGATTAA-CGAACAGAATTAACCGAATTTTTGCTTCGATTAATTCGATTA
66 AAATAAATTTTGGTTCGATTAACCGAAC-CAATTAACCGAAGTTTTGCTTCGATTAATTCGATTA
138993 ATAATT
130 ATAATT
* * **
138999 AAAAAATCAGTCAATTCGGTGCGGTTAATAATGTTCAAATTAATTTTGTTCGGTTAATAATTTTC
1 AAAAAATCAGTCAATTCGGTGCGATGAATAATGTTCAAATTAATTCAGTTCGGTTAATAATTTTC
* *
139064 AAATAAATTTTGGTTCGATTAACCGAGCCAATTAATCGAAGTTTTGCTTCGATTAAT
66 AAATAAATTTTGGTTCGATTAACCGAACCAATTAACCGAAGTTTTGCTTCGATTAAT
139121 AATTAAAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
135 104 0.96
136 4 0.04
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (135 bp):
AAAAAATCAGTCAATTCGGTGCGATGAATAATGTTCAAATTAATTCAGTTCGGTTAATAATTTTC
AAATAAATTTTGGTTCGATTAACCGAACCAATTAACCGAAGTTTTGCTTCGATTAATTCGATTAA
TAATT
Found at i:139053 original size:29 final size:30
Alignment explanation
Indices: 139020--139085 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
139010 CAATTCGGTG
*
139020 CGGTTAATAATGTTCAAATTAATTTT-GTT
1 CGGTTAATAATGTTCAAATAAATTTTGGTT
*
139049 CGGTTAATAATTTTCAAATAAATTTTGGTT
1 CGGTTAATAATGTTCAAATAAATTTTGGTT
*
139079 CGATTAA
1 CGGTTAA
139086 CCGAGCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 24 0.73
30 9 0.27
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (30 bp):
CGGTTAATAATGTTCAAATAAATTTTGGTT
Found at i:139152 original size:28 final size:29
Alignment explanation
Indices: 139121--139177 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
139111 TTCGATTAAT
139121 AATTAA-AAAAATCGGTTAATAATTTTCA
1 AATTAATAAAAATCGGTTAATAATTTTCA
** **
139149 AATTAATTTAGTTCGGTTAATAATTTTCA
1 AATTAATAAAAATCGGTTAATAATTTTCA
139178 TACAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (29 bp):
AATTAATAAAAATCGGTTAATAATTTTCA
Found at i:139275 original size:29 final size:29
Alignment explanation
Indices: 139230--139307 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
139220 TTTGCTTCGG
**
139230 TTAATTCGGTTCAGTTAATAATTTTCAAA
1 TTAATTCGGTTTGGTTAATAATTTTCAAA
139259 TTAATTCGGTTTGGTTAATAATTTTCAAA
1 TTAATTCGGTTTGGTTAATAATTTTCAAA
* * *
139288 TAAATTTTGGTTTGATTAAT
1 TTAA-TTCGGTTTGGTTAAT
139308 CGAACCGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 30 0.70
30 13 0.30
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (29 bp):
TTAATTCGGTTTGGTTAATAATTTTCAAA
Found at i:139293 original size:108 final size:110
Alignment explanation
Indices: 139011--139330 Score: 394
Period size: 108 Copynumber: 2.9 Consensus size: 110
139001 AAAATCAGTC
* * *
139011 AATTCGGTGCGGTTAATAATGTTCAAATTAATTTTGTTCGGTTAATAATTTTCAAATAAATTTTG
1 AATTCGGTTCGGTTAATAATTTTCAAATTAATTTAGTTCGGTTAATAATTTTCAAATAAATTTTG
* * *
139076 GTTCGATTAACCGAGCC-AATTAATCGAAGTTTTGCTTCGATTAAT
66 GTTCGATTAACCGAACCGAATTAATCGAATTTTTGCTTCGAGT-AT
**** * *
139121 AATTAAAAAAATCGGTTAATAATTTTCAAATTAATTTAGTTCGGTTAATAATTTTCATACAAATT
1 AATT---CGGTTCGGTTAATAATTTTCAAATTAATTTAGTTCGGTTAATAATTTTCAAATAAATT
*
139186 TTGGTTCGATTAACCAAACCGAATTAATCGAATTTTTGCTTCG-GT-T
63 TTGGTTCGATTAACCGAACCGAATTAATCGAATTTTTGCTTCGAGTAT
* ** *
139232 AATTCGGTTCAGTTAATAATTTTCAAATTAATTCGGTTTGGTTAATAATTTTCAAATAAATTTTG
1 AATTCGGTTCGGTTAATAATTTTCAAATTAATTTAGTTCGGTTAATAATTTTCAAATAAATTTTG
* * * *
139297 GTTTGATTAATCGAACCGAATTAACCAAATTTTT
66 GTTCGATTAACCGAACCGAATTAATCGAATTTTT
139331 TTCTTTAACG
Statistics
Matches: 178, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
108 80 0.45
110 4 0.02
111 5 0.03
113 68 0.38
114 21 0.12
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (110 bp):
AATTCGGTTCGGTTAATAATTTTCAAATTAATTTAGTTCGGTTAATAATTTTCAAATAAATTTTG
GTTCGATTAACCGAACCGAATTAATCGAATTTTTGCTTCGAGTAT
Found at i:139783 original size:30 final size:30
Alignment explanation
Indices: 139749--139837 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
139739 ATACTATGTA
*
139749 AATATTAAGGACTATATATAAAATTATGCC
1 AATATTAAGGACCATATATAAAATTATGCC
139779 AATATTAAGGACCATATATAAAATTATGCC
1 AATATTAAGGACCATATATAAAATTATGCC
* * *
139809 AATACTAAGGACCAAATATATAATTATGC
1 AATATTAAGGACCATATATAAAATTATGC
139838 AAATTTATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (30 bp):
AATATTAAGGACCATATATAAAATTATGCC
Found at i:146636 original size:24 final size:24
Alignment explanation
Indices: 146609--146699 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
146599 TCAAATTTGA
* * *
146609 ATTCTGTTATGATACCTGACGTGG
1 ATTCTGATATGATACTTGACATGG
*
146633 ATTCTGATATGATA-TTAACATGG
1 ATTCTGATATGATACTTGACATGG
* * *
146656 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACATGG
146680 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
146700 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.34
24 37 0.66
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:148816 original size:18 final size:18
Alignment explanation
Indices: 148793--148853 Score: 104
Period size: 18 Copynumber: 3.3 Consensus size: 18
148783 TGACCGGTCA
*
148793 TAACCCGACCCGACTCGT
1 TAACCCGACCCGACCCGT
148811 TAACCCGACCCGACCCGT
1 TAACCCGACCCGACCCGT
148829 TAACCCGACCCGACCCCGT
1 TAACCCGACCCGA-CCCGT
148848 TAACCC
1 TAACCC
148854 ATTGACCGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
18 30 0.73
19 11 0.27
ACGTcount: A:0.23, C:0.49, G:0.15, T:0.13
Consensus pattern (18 bp):
TAACCCGACCCGACCCGT
Found at i:151386 original size:47 final size:48
Alignment explanation
Indices: 151328--151452 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 48
151318 TCAAATTTGA
* * * *
151328 ATTCTGTTATGATACCTGACCTGGATTATGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTATGATATGATACATGACATGG
* * * *
151375 ATTCTGATATGATACATTACCTGGATTCTGATATGTTACATGACCTGG
1 ATTCTGATATGATACATGACCTGGATTATGATATGATACATGACATGG
* * * *
151423 ATTGTGATATGATACTTGACTTGAATTATG
1 ATTCTGATATGATACATGACCTGGATTATG
151453 TTTTGATTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
47 32 0.51
48 31 0.49
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTATGATATGATACATGACATGG
Found at i:151404 original size:24 final size:24
Alignment explanation
Indices: 151328--151442 Score: 133
Period size: 24 Copynumber: 4.8 Consensus size: 24
151318 TCAAATTTGA
* *
151328 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACATGACCTGG
* * * *
151352 ATTATGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGG
*
151375 ATTCTGATATGATACATTACCTGG
1 ATTCTGATATGATACATGACCTGG
*
151399 ATTCTGATATGTTACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
151423 ATTGTGATATGATACTTGAC
1 ATTCTGATATGATACATGAC
151443 TTGAATTATG
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
23 19 0.25
24 56 0.75
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:152933 original size:179 final size:180
Alignment explanation
Indices: 152633--152994 Score: 654
Period size: 179 Copynumber: 2.0 Consensus size: 180
152623 GGGTGTAATT
* *
152633 GGTTGTTCAAGGTTAAGAGGAAATCGAATGAGTCTGTTGATCGGTTTAAAGTTTGGTTGGTTGCC
1 GGTTGTTAAAGGTTAAGAGGAAATCGAATGAGTCTGTTGATCGGTTTAAAGTTTAGTTGGTTGCC
* *
152698 AAGGGCTATTCTCAGATAGCCAGTAATGATTTTCGTGAAACATTTAGTCCAGTTGTTCTATCCAC
66 AAGGGCTATTCTCAGATAACCAGTAATGATTTTCATGAAACATTTAGTCCAGTTGTTCTATCCAC
152763 CATCATAAGAACTA-TTTTGACACTTCGGTTCTTCAGGGATGGACGAGAC
131 CATCATAAGAACTATTTTTGACACTTCGGTTCTTCAGGGATGGACGAGAC
* *
152812 GGTTGTTAAAGGTTAAGAGGAAATCGAATGGGTTTGTTGATCGGTTTAAAGTTTAGTTGGTTGCC
1 GGTTGTTAAAGGTTAAGAGGAAATCGAATGAGTCTGTTGATCGGTTTAAAGTTTAGTTGGTTGCC
152877 AAGGGCTATTCTCAGATAACCAGTAATGATTTTCATGAAACATTTAGTCCAGTTGTTCTATCCAC
66 AAGGGCTATTCTCAGATAACCAGTAATGATTTTCATGAAACATTTAGTCCAGTTGTTCTATCCAC
*
152942 CATCATAAGAACTATTTTTGACATTTCGGTTCTTCAGGGATGGACGAGAC
131 CATCATAAGAACTATTTTTGACACTTCGGTTCTTCAGGGATGGACGAGAC
152992 GGT
1 GGT
152995 AGATCGACAT
Statistics
Matches: 175, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
179 138 0.79
180 37 0.21
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (180 bp):
GGTTGTTAAAGGTTAAGAGGAAATCGAATGAGTCTGTTGATCGGTTTAAAGTTTAGTTGGTTGCC
AAGGGCTATTCTCAGATAACCAGTAATGATTTTCATGAAACATTTAGTCCAGTTGTTCTATCCAC
CATCATAAGAACTATTTTTGACACTTCGGTTCTTCAGGGATGGACGAGAC
Found at i:157634 original size:51 final size:51
Alignment explanation
Indices: 157551--157647 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
157541 AGTAAGGCGC
* * *
157551 GCCCCCTACAGCGCGTTTTACGCTGATTTGGCACCACGTGGGGTATGGCAA
1 GCCCCCTACAGCGCGCTTTACGCTAATATGGCACCACGTGGGGTATGGCAA
* *
157602 GCCCCCTGCAGCGCGCTTTACGCTAATATGGCATCACGTGGGGTAT
1 GCCCCCTACAGCGCGCTTTACGCTAATATGGCACCACGTGGGGTAT
157648 AGCGCGGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.18, C:0.30, G:0.29, T:0.24
Consensus pattern (51 bp):
GCCCCCTACAGCGCGCTTTACGCTAATATGGCACCACGTGGGGTATGGCAA
Found at i:157903 original size:17 final size:16
Alignment explanation
Indices: 157881--157929 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
157871 ATATTTTGTT
157881 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAA-TA
*
157898 TTTAATTTTTTTTAATA
1 TTTAA-TTTATTTAATA
* *
157915 TTTTATTTAATTAAT
1 TTTAATTTATTTAAT
157930 TTTTTTTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTAATTTATTTAATA
Found at i:157906 original size:24 final size:23
Alignment explanation
Indices: 157857--157926 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
157847 TTAAGGTATA
**
157857 TTTTATTATATTTAATATTTTGT
1 TTTTATTATATTTAATATTTAAT
157880 TTTTAATT-TATTTAAGTATTTAAT
1 TTTT-ATTATATTTAA-TATTTAAT
*
157904 TTTTTTTAATATTT--TATTTAAT
1 TTTTATT-ATATTTAATATTTAAT
157926 T
1 T
157927 AATTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 9 0.22
23 13 0.32
24 13 0.32
25 5 0.12
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (23 bp):
TTTTATTATATTTAATATTTAAT
Found at i:157917 original size:12 final size:14
Alignment explanation
Indices: 157899--157936 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
157889 ATTTAAGTAT
157899 TTAATTTTTTTTAA
1 TTAATTTTTTTTAA
*
157913 -T-ATTTTATTTAA
1 TTAATTTTTTTTAA
157925 TTAATTTTTTTT
1 TTAATTTTTTTT
157937 TGCAGATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
12 10 0.50
13 2 0.10
14 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTAATTTTTTTTAA
Found at i:157919 original size:18 final size:18
Alignment explanation
Indices: 157880--157928 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
157870 AATATTTTGT
157880 TTTTAATTTATTTAAGTA
1 TTTTAATTTATTTAAGTA
*
157898 -TTTAATTTTTTTTAA-TA
1 TTTTAA-TTTATTTAAGTA
*
157915 TTTT-ATTTAATTAA
1 TTTTAATTTATTTAA
157929 TTTTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.27
17 8 0.31
18 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTAATTTATTTAAGTA
Found at i:157919 original size:26 final size:27
Alignment explanation
Indices: 157879--157936 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
157869 TAATATTTTG
* *
157879 TTTTTAATTTATTTAAGTATTTAATTT
1 TTTTTAATATATTTAAGTAATTAATTT
**
157906 TTTTTAATAT-TTTATTTAATTAATTT
1 TTTTTAATATATTTAAGTAATTAATTT
157932 TTTTT
1 TTTTT
157937 TGCAGATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTAATATATTTAAGTAATTAATTT
Found at i:162275 original size:17 final size:17
Alignment explanation
Indices: 162250--162291 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
162240 AATAATAATT
*
162250 AAATAAAATA-TTAAAA
1 AAATTAAATACTTAAAA
*
162266 AAATGTAAATACTTAAAT
1 AAAT-TAAATACTTAAAA
162284 AAATTAAA
1 AAATTAAA
162292 AACAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
AAATTAAATACTTAAAA
Found at i:162299 original size:30 final size:30
Alignment explanation
Indices: 162243--162319 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 30
162233 CAAAAAAAAT
*
162243 AATAATTAAATAAAATATTAAAAAAATGTA
1 AATAATTAAATAAAATATAAAAAAAATGTA
* * *
162273 AATACTTAAATAAATTA-AAAACAAAATATTA
1 AATAATTAAATAAAATATAAAA-AAAAT-GTA
162304 AAT-A-T-AATAAAATATA
1 AATAATTAAATAAAATATA
162320 CCTTAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
28 8 0.21
29 5 0.13
30 20 0.53
31 5 0.13
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (30 bp):
AATAATTAAATAAAATATAAAAAAAATGTA
Found at i:163615 original size:22 final size:22
Alignment explanation
Indices: 163535--163625 Score: 80
Period size: 23 Copynumber: 4.1 Consensus size: 22
163525 GAAAGAAATC
*
163535 ATAAAAAAAATAAAATAATAAT-A
1 ATAAATAAAA-AAAATAA-AATAA
*
163558 ATACATCAAAAAAAATAAAATAA
1 ATAAAT-AAAAAAAATAAAATAA
*
163581 ATAAATAATAAAAAAT-AGATAA
1 ATAAATAA-AAAAAATAAAATAA
* *
163603 ATCAATGAAAAAAATAAAA-AA
1 ATAAATAAAAAAAATAAAATAA
163624 AT
1 AT
163626 GTTAAATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
21 11 0.19
22 18 0.32
23 24 0.42
24 4 0.07
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (22 bp):
ATAAATAAAAAAAATAAAATAA
Found at i:164921 original size:23 final size:21
Alignment explanation
Indices: 164886--164939 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
164876 GAAAAGGAAA
*
164886 AAAACAAAAGAAAGAATTAAAAT
1 AAAA-AAAAGAAA-AATAAAAAT
*
164909 AAATAAAACGAAAAATAAATAAT
1 AAA-AAAAAGAAAAATAAA-AAT
164932 AAAAAAAA
1 AAAAAAAA
164940 ACAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 9 0.35
23 16 0.62
24 1 0.04
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.13
Consensus pattern (21 bp):
AAAAAAAAGAAAAATAAAAAT
Found at i:164938 original size:16 final size:16
Alignment explanation
Indices: 164904--164946 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
164894 AGAAAGAATT
*
164904 AAAATAAATAAAACGA
1 AAAATAAATAAAACAA
*
164920 AAAATAAATAATAAAAA
1 AAAATAAATAA-AACAA
*
164937 AAAACAAATA
1 AAAATAAATA
164947 TATATTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAATAAATAAAACAA
Found at i:165046 original size:36 final size:36
Alignment explanation
Indices: 164997--165181 Score: 158
Period size: 36 Copynumber: 4.8 Consensus size: 36
164987 TAAGAAAACA
* *
164997 TTTTCAAAACTATATAT-TATATATATTAAAAAATG
1 TTTTAAAAACTATATATATATATATATTACAAAATG
*
165032 TTTTCAAAAACTATATAATATATATATATATTTTTTCAAAATG
1 TTTT-AAAAAC--TAT-ATATATATATATA---TTACAAAATG
165075 TTTTAAAAACTATATAATATATATATATATATGTTTTCAAAATG
1 TTTTAAAAACTATAT-ATATATATATAT-TA------CAAAATG
* * *
165119 TTTTAAAAACTATATAT-TATATATGTTTTCAAAATA
1 TTTTAAAAACTATATATATATATAT-ATTACAAAATG
165155 TTTTAAAAACTATATATATATATATAT
1 TTTTAAAAACTATATATATATATATAT
165182 ATATATATAT
Statistics
Matches: 124, Mismatches: 8, Indels: 35
0.74 0.05 0.21
Matches are distributed among these distances:
35 4 0.03
36 29 0.23
37 8 0.06
38 4 0.03
39 6 0.05
40 22 0.18
42 14 0.11
43 15 0.12
44 22 0.18
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTTAAAAACTATATATATATATATATTACAAAATG
Found at i:165099 original size:44 final size:44
Alignment explanation
Indices: 165026--165305 Score: 255
Period size: 42 Copynumber: 6.8 Consensus size: 44
165016 TATATATTAA
165026 AAAATGTTTTCAAAAACTATATAATATATATATATAT-T-TTTTC
1 AAAATGTTTT-AAAAACTATATAATATATATATATATATGTTTTC
165069 AAAATGTTTTAAAAACTATATAATATATATATATATATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATATATATGTTTTC
165113 AAAATGTTTTAAAAAC-------TATATAT-TATATATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATATATATGTTTTC
* * *
165149 AAAATATTTTAAAAACTATAT-ATATATATATATATAT-ATAT-
1 AAAATGTTTTAAAAACTATATAATATATATATATATATGTTTTC
* * * * * * *
165190 ATATATGTTTTCAAAATTTTTTAA-AAACTATATAATATGTGTTTTC
1 A-AAATGTTTTAAAAACTATATAATATA-TATAT-ATATATGTTTTC
*
165236 AAAATGTTTT-AAAA-T-TAT-ATAT-TAT-T-TATA--TATTC
1 AAAATGTTTTAAAAACTATATAATATATATATATATATGTTTTC
165271 AAAATGTTTTAAAAAGCTATATAATATATATATAT
1 AAAATGTTTTAAAAA-CTATATAATATATATATAT
165306 TCAAAAACCA
Statistics
Matches: 195, Mismatches: 18, Indels: 48
0.75 0.07 0.18
Matches are distributed among these distances:
35 14 0.07
36 32 0.16
37 10 0.05
38 1 0.01
39 4 0.02
40 7 0.04
41 5 0.03
42 55 0.28
43 26 0.13
44 30 0.15
45 10 0.05
46 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (44 bp):
AAAATGTTTTAAAAACTATATAATATATATATATATATGTTTTC
Found at i:165133 original size:122 final size:121
Alignment explanation
Indices: 164997--165305 Score: 367
Period size: 122 Copynumber: 2.5 Consensus size: 121
164987 TAAGAAAACA
*
164997 TTTTCAAAACTATATATTATATATATTAAAAAATGTTTTCAAAAACTATATAATATATATATATA
1 TTTT-AAAACTATATATTATATATATT-CAAAATGTTTT-AAAAACTATATAATATATATATATA
* * *
165062 T-TTTTTCA-AAATGTTTTAAAAACTATAT-AATA-TATATATATATATGTTTTCAAAATG
63 TATATAT-ATAAATGTTTTAAAAACTATATAAAAACTATATA-ATATATGTTTTCAAAATG
* *
165119 TTTTAAAAACTATATATTATATATGTTTTCAAAATATTTTAAAAACTATAT-ATATATATATATA
1 TTTT-AAAACTATATATTATATA--TATTCAAAATGTTTTAAAAACTATATAATATATATATATA
* * * * * *
165183 TATATATATATATGTTTTCAAAATTTTTTAAAAACTATATAATATGTGTTTTCAAAATG
63 TATATATATAAATGTTTTAAAAACTATATAAAAACTATATAATATATGTTTTCAAAATG
*
165242 TTTTAAAATTATATATTATTTATATATTCAAAATGTTTTAAAAAGCTATATAATATATATATAT
1 TTTTAAAACTATATATTA--TATATATTCAAAATGTTTTAAAAA-CTATATAATATATATATAT
165306 TCAAAAACCA
Statistics
Matches: 161, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
121 15 0.09
122 82 0.51
123 39 0.24
124 25 0.16
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (121 bp):
TTTTAAAACTATATATTATATATATTCAAAATGTTTTAAAAACTATATAATATATATATATATAT
ATATATAAATGTTTTAAAAACTATATAAAAACTATATAATATATGTTTTCAAAATG
Found at i:165172 original size:2 final size:2
Alignment explanation
Indices: 165165--165195 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
165155 TTTTAAAAAC
165165 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 T
165196 GTTTTCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:165193 original size:53 final size:51
Alignment explanation
Indices: 165129--165227 Score: 171
Period size: 53 Copynumber: 1.9 Consensus size: 51
165119 TTTTAAAAAC
165129 TATATATTATATATGTTTTCAAAATATTTTAAAAACTATATATATATATATA
1 TATATATTATATATGTTTTCAAAATATTTTAAAAACTATATA-ATATATATA
*
165181 TATATATATATATATGTTTTCAAAATTTTTTAAAAACTATATAATAT
1 TATATAT-TATATATGTTTTCAAAATATTTTAAAAACTATATAATAT
165228 GTGTTTTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 11 0.24
53 34 0.76
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.48
Consensus pattern (51 bp):
TATATATTATATATGTTTTCAAAATATTTTAAAAACTATATAATATATATA
Found at i:165205 original size:89 final size:85
Alignment explanation
Indices: 165085--165268 Score: 280
Period size: 89 Copynumber: 2.1 Consensus size: 85
165075 TTTTAAAAAC
165085 TATATA-ATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATGTTTTC
1 TATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATA--ATATATGTTTTC
165149 AAAATATTTTAAAAACTATATAT
64 AAAATATTTT-AAAACTATATAT
* *
165172 ATATATATATATATATATATATATGTTTTCAAAATTTTTTAAAAACTATATAATATGTGTTTTCA
1 -TATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATGTTTTCA
* *
165237 AAATGTTTTAAAATTATATAT
65 AAATATTTTAAAACTATATAT
*
165258 TATTTATATAT
1 TATATATATAT
165269 TCAAAATGTT
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
85 10 0.11
86 11 0.12
87 20 0.22
88 6 0.07
89 43 0.48
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (85 bp):
TATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATGTTTTCAA
AATATTTTAAAACTATATAT
Found at i:165301 original size:35 final size:34
Alignment explanation
Indices: 165183--165303 Score: 127
Period size: 35 Copynumber: 3.5 Consensus size: 34
165173 TATATATATA
* * *
165183 TATATATATATATGTTTTCAAAATTTTTTAAAAAC
1 TATATA-ATATATATATTCAAAATGTTTTAAAAAC
* * *
165218 TATATAATATGTGTTTTCAAAATGTTTTAAAATTA-
1 TATATAATATATATATTCAAAATGTTTTAAAA--AC
* *
165253 TATATTATTTATATATTCAAAATGTTTTAAAAAGC
1 TATATAATATATATATTCAAAATGTTTTAAAAA-C
165288 TATATAATATATATAT
1 TATATAATATATATAT
165304 ATTCAAAAAC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
33 1 0.01
34 24 0.33
35 47 0.64
36 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (34 bp):
TATATAATATATATATTCAAAATGTTTTAAAAAC
Found at i:165303 original size:37 final size:36
Alignment explanation
Indices: 165181--165311 Score: 151
Period size: 37 Copynumber: 3.7 Consensus size: 36
165171 TATATATATA
* * *
165181 TATATATATATATATGTTTTCAAAATTTTTTAAAAAC
1 TATATA-ATATATATATATTCAAAATGTTTTAAAAAC
* * *
165218 TATATAATATGTGT-T-TTCAAAATGTTTT-AAAAT
1 TATATAATATATATATATTCAAAATGTTTTAAAAAC
* *
165251 TATATATTATTTATATATTCAAAATGTTTTAAAAAGC
1 TATATAATATATATATATTCAAAATGTTTTAAAAA-C
165288 TATATAATATATATATATTCAAAA
1 TATATAATATATATATATTCAAAA
165312 ACCAATTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
33 15 0.19
34 13 0.16
35 14 0.17
36 10 0.12
37 28 0.35
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATAATATATATATATTCAAAATGTTTTAAAAAC
Found at i:165581 original size:2 final size:2
Alignment explanation
Indices: 165574--165612 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
165564 CAATCTTTCT
165574 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
165613 TGGATAATCC
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:167158 original size:2 final size:2
Alignment explanation
Indices: 167151--167176 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
167141 ATCCTAACTC
167151 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
167177 GTTCTGGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:171259 original size:2 final size:2
Alignment explanation
Indices: 171252--171282 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
171242 TCAATACATG
171252 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 T
171283 GTTAGATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:181125 original size:14 final size:14
Alignment explanation
Indices: 181108--181144 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
181098 ATATGTTCGC
*
181108 TTATATTCGTTCAT
1 TTATGTTCGTTCAT
*
181122 TTATGTTCGTTTAT
1 TTATGTTCGTTCAT
181136 TTATGTTCG
1 TTATGTTCG
181145 AACAGAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (14 bp):
TTATGTTCGTTCAT
Found at i:181423 original size:10 final size:10
Alignment explanation
Indices: 181408--181487 Score: 80
Period size: 10 Copynumber: 8.1 Consensus size: 10
181398 GTGTTTGTGT
181408 TGTTCGTTTA
1 TGTTCGTTTA
181418 TGTTCGTTTA
1 TGTTCGTTTA
181428 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
181441 TGTTCGTTTA
1 TGTTCGTTTA
181451 T-TT--TTGT-
1 TGTTCGTT-TA
181458 T-TTCGTTTA
1 TGTTCGTTTA
*
181467 CGTTCGTTTA
1 TGTTCGTTTA
181477 TGTTCGTTTA
1 TGTTCGTTTA
181487 T
1 T
181488 CATTTAAATG
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 4 0.07
10 39 0.65
13 10 0.17
ACGTcount: A:0.09, C:0.10, G:0.19, T:0.62
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:181426 original size:23 final size:23
Alignment explanation
Indices: 181408--181477 Score: 95
Period size: 23 Copynumber: 2.9 Consensus size: 23
181398 GTGTTTGTGT
181408 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCGTTTATTG
181431 TGTTCGTTTATGTTCGTTTATTTTTG
1 TGTTCGTTTATGTTCGTTTA---TTG
* *
181457 TTTTCGTTTACGTTCGTTTAT
1 TGTTCGTTTATGTTCGTTTAT
181478 GTTCGTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 21 0.50
26 21 0.50
ACGTcount: A:0.09, C:0.10, G:0.19, T:0.63
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTTATTG
Found at i:181485 original size:26 final size:24
Alignment explanation
Indices: 181405--181477 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 24
181395 TTTGTGTTTG
181405 TGTTGTTCGTTTATGTTCGTTTA-T
1 TGTT-TTCGTTTATGTTCGTTTATT
*
181429 TGTGTTCGTTTATGTTCGTTTATTTT
1 TGTTTTCGTTTATGTTCGTTTA--TT
*
181455 TGTTTTCGTTTACGTTCGTTTAT
1 TGTTTTCGTTTATGTTCGTTTAT
181478 GTTCGTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
23 18 0.42
24 4 0.09
26 21 0.49
ACGTcount: A:0.08, C:0.10, G:0.19, T:0.63
Consensus pattern (24 bp):
TGTTTTCGTTTATGTTCGTTTATT
Found at i:182956 original size:7 final size:7
Alignment explanation
Indices: 182944--182976 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
182934 GTTCGAATCG
182944 AATTTTT
1 AATTTTT
182951 AATTTTT
1 AATTTTT
*
182958 AA-TTTA
1 AATTTTT
182964 AATTTTT
1 AATTTTT
182971 AATTTT
1 AATTTT
182977 CGCATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
AATTTTT
Found at i:182969 original size:13 final size:13
Alignment explanation
Indices: 182951--182975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
182941 TCGAATTTTT
182951 AATTTTTAATTTA
1 AATTTTTAATTTA
182964 AATTTTTAATTT
1 AATTTTTAATTT
182976 TCGCATTTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTAATTTA
Found at i:183428 original size:28 final size:29
Alignment explanation
Indices: 183388--183442 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
183378 ATATATAATA
*
183388 TTTAAAACATAAATTTAATATTTTTATAT
1 TTTAAAACATAAATTTAACATTTTTATAT
*
183417 TTTAAAA-TTAAATTTAACATTTTTAT
1 TTTAAAACATAAATTTAACATTTTTAT
183443 TTTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAAAACATAAATTTAACATTTTTATAT
Found at i:184733 original size:14 final size:14
Alignment explanation
Indices: 184714--184741 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
184704 TCTGTTCCAG
184714 GGCGGCATGTACGT
1 GGCGGCATGTACGT
184728 GGCGGCATGTACGT
1 GGCGGCATGTACGT
184742 CGAGGACGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.43, T:0.21
Consensus pattern (14 bp):
GGCGGCATGTACGT
Found at i:185632 original size:13 final size:13
Alignment explanation
Indices: 185588--185631 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
185578 GAACCGGTCT
185588 GACCCGACCGACC
1 GACCCGACCGACC
*
185601 GACCCGACCCGATC
1 GACCCGA-CCGACC
185615 GA-CCGACCGACCC
1 GACCCGACCGA-CC
185628 GACC
1 GACC
185632 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.15
13 14 0.54
14 8 0.31
ACGTcount: A:0.23, C:0.52, G:0.23, T:0.02
Consensus pattern (13 bp):
GACCCGACCGACC
Found at i:192883 original size:18 final size:18
Alignment explanation
Indices: 192841--192884 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
192831 TTTGACCGGT
*
192841 CTGACCCGACCCGACCCGG
1 CTGA-CCGACCCGACCCGA
*
192860 CCGACCGACCCGACCCGA
1 CTGACCGACCCGACCCGA
192878 CTGACCG
1 CTGACCG
192885 TTGACTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.18, C:0.52, G:0.25, T:0.05
Consensus pattern (18 bp):
CTGACCGACCCGACCCGA
Found at i:203963 original size:2 final size:2
Alignment explanation
Indices: 203956--204012 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
203946 ATTTCGAATA
203956 AT AT AT 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
*
203998 AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT A
204013 AATTAACAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:205539 original size:10 final size:11
Alignment explanation
Indices: 205524--205575 Score: 70
Period size: 11 Copynumber: 4.6 Consensus size: 11
205514 TAGGAAATAG
205524 AAATAATT-AA
1 AAATAATTAAA
205534 AAATAATTAAA
1 AAATAATTAAA
*
205545 AACATAAAATAAA
1 AA-AT-AATTAAA
205558 AAATAATTAAA
1 AAATAATTAAA
205569 AAATAAT
1 AAATAAT
205576 GAAGATTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 8 0.22
11 17 0.46
12 4 0.11
13 8 0.22
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAATTAAA
Found at i:205749 original size:39 final size:38
Alignment explanation
Indices: 205638--205788 Score: 113
Period size: 36 Copynumber: 4.1 Consensus size: 38
205628 TGTTATATTG
* *
205638 ATAA-AAAAAACAGAAAACAATAATAAAATAACAATAA
1 ATAACAAAAAACAGAAAACAATAACAAACTAACAATAA
* *
205675 A-AAC-AAAAACA-AAAA-TA-AACAATACTTAA-GA-AA
1 ATAACAAAAAACAGAAAACAATAACAA-AC-TAACAATAA
205708 ATAACAAAAAACAGAAAACAATAACAAACTAACATATAA
1 ATAACAAAAAACAGAAAACAATAACAAACTAACA-ATAA
* *** * *
205747 ATAATAAAATAACACTTAAGAATCACAAAC-AACAATAA
1 ATAACAAAA-AACAGAAAACAATAACAAACTAACAATAA
205785 ATAA
1 ATAA
205789 AACAGTAAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
33 7 0.08
34 6 0.07
35 14 0.16
36 16 0.18
37 4 0.04
38 14 0.16
39 14 0.16
40 15 0.17
ACGTcount: A:0.70, C:0.13, G:0.03, T:0.15
Consensus pattern (38 bp):
ATAACAAAAAACAGAAAACAATAACAAACTAACAATAA
Found at i:205797 original size:12 final size:12
Alignment explanation
Indices: 205777--205835 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
205767 AATCACAAAC
205777 AACAATAAATAA
1 AACAATAAATAA
*
205789 AACAGTAAAT--
1 AACAATAAATAA
* *
205799 AACAA-ATAGAA
1 AACAATAAATAA
205810 AACAATAAATAA
1 AACAATAAATAA
205822 AACAGA-AAATAA
1 AACA-ATAAATAA
205834 AA
1 AA
205836 TATAACATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
9 2 0.05
10 4 0.11
11 5 0.14
12 25 0.68
13 1 0.03
ACGTcount: A:0.73, C:0.08, G:0.05, T:0.14
Consensus pattern (12 bp):
AACAATAAATAA
Found at i:205920 original size:9 final size:9
Alignment explanation
Indices: 205908--205984 Score: 56
Period size: 9 Copynumber: 8.8 Consensus size: 9
205898 ACAAAAAAAC
205908 AAAAACAAT
1 AAAAACAAT
*
205917 AAAAATAA-
1 AAAAACAAT
205925 AAAAAC-AT
1 AAAAACAAT
*
205933 AATAAC-AT
1 AAAAACAAT
205941 -AAAACAAT
1 AAAAACAAT
*
205949 AAAAATAAAT
1 AAAAA-CAAT
205959 AAAATA-AAT
1 AAAA-ACAAT
*
205968 AAAATAAAAT
1 AAAA-ACAAT
205978 AAAAACA
1 AAAAACA
205985 GGAAAAAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
7 5 0.09
8 14 0.25
9 22 0.39
10 14 0.25
11 1 0.02
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAACAAT
Found at i:205948 original size:32 final size:32
Alignment explanation
Indices: 205862--205976 Score: 105
Period size: 32 Copynumber: 3.6 Consensus size: 32
205852 TAAAACACAC
205862 AAAACAT-ATAA-ATAACATACAAATAAAAA-AAGA
1 AAAACATAATAACATAA-A-AC-AATAAAAATAA-A
* * *
205895 ATAACAAAAAAACA-AAAACAATAAAAATAAA
1 AAAACATAATAACATAAAACAATAAAAATAAA
205926 AAAACATAATAACATAAAACAATAAAAATAAA
1 AAAACATAATAACATAAAACAATAAAAATAAA
* *
205958 TAAA-ATAAATAAAATAAAA
1 AAAACAT-AATAACATAAAA
205977 TAAAAACAGG
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
31 22 0.32
32 35 0.51
33 6 0.09
34 5 0.07
35 1 0.01
ACGTcount: A:0.77, C:0.08, G:0.01, T:0.15
Consensus pattern (32 bp):
AAAACATAATAACATAAAACAATAAAAATAAA
Found at i:205960 original size:4 final size:5
Alignment explanation
Indices: 205950--205981 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
205940 TAAAACAATA
205950 AAAAT -AAAT AAAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
205982 ACAGGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.32
5 17 0.68
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:206229 original size:21 final size:21
Alignment explanation
Indices: 206203--206282 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
206193 AAAAAATGTA
*
206203 AGGAGTCAAGAATAGTAGATG
1 AGGAGTCAAGAACAGTAGATG
* * *
206224 AGGAGTTAAAAACAGTAGTTG
1 AGGAGTCAAGAACAGTAGATG
* * *
206245 AGGAGTCACGTACAATAGATG
1 AGGAGTCAAGAACAGTAGATG
* * *
206266 ATGAGTCACGAATAGTA
1 AGGAGTCAAGAACAGTA
206283 AATCGAGAAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.41, C:0.09, G:0.29, T:0.21
Consensus pattern (21 bp):
AGGAGTCAAGAACAGTAGATG
Found at i:206452 original size:26 final size:26
Alignment explanation
Indices: 206416--206487 Score: 135
Period size: 26 Copynumber: 2.8 Consensus size: 26
206406 GAAGGTTAGG
206416 GTTTGATTTGAAAAACAAAACAAAAA
1 GTTTGATTTGAAAAACAAAACAAAAA
206442 GTTTGATTTGAAAAACAAAACAAAAA
1 GTTTGATTTGAAAAACAAAACAAAAA
*
206468 GTTTGTTTTGAAAAACAAAA
1 GTTTGATTTGAAAAACAAAA
206488 AGAACAAAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.26
Consensus pattern (26 bp):
GTTTGATTTGAAAAACAAAACAAAAA
Found at i:206586 original size:93 final size:94
Alignment explanation
Indices: 206487--206656 Score: 222
Period size: 93 Copynumber: 1.8 Consensus size: 94
206477 GAAAAACAAA
* *
206487 AAGAACAAAGGAAGAACAATA-GATGAAAGTTTGGGTTTGAAC-CAAAAAA-AGAAGAAATTTTT
1 AAGAACAAAGGAAGAACAA-AGGATAAAAGTTAGGGTTTGAACTCAAAAAATA-AAG-AATTTTT
206549 ATGTTA-TTTGGATCTAGGAAAGAGATGTATG
63 ATGTTATTTTGGATCTAGGAAAGAGATGTATG
** * * *
206580 AAGAACAAATTAAGAATAAAGGATAAAAGTTAGGGTTTGATCTTAAAAAATAAAGAATTTTTATG
1 AAGAACAAAGGAAGAACAAAGGATAAAAGTTAGGGTTTGAACTCAAAAAATAAAGAATTTTTATG
206645 TTATTTTGGATC
66 TTATTTTGGATC
206657 GAAGAAATAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
92 1 0.02
93 47 0.71
94 17 0.26
95 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (94 bp):
AAGAACAAAGGAAGAACAAAGGATAAAAGTTAGGGTTTGAACTCAAAAAATAAAGAATTTTTATG
TTATTTTGGATCTAGGAAAGAGATGTATG
Found at i:207239 original size:2 final size:2
Alignment explanation
Indices: 207232--207916 Score: 180
Period size: 2 Copynumber: 344.0 Consensus size: 2
207222 ATACATACTT
* * *
207232 TA TA TA TA TA GTT TA TA CTT TA TA TA TA -A TT TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
207275 TA TA TA TA GT- TCA TA T- TT TA CT- TA TA T- TA TA TA TA TA TA
1 TA TA TA TA -TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
207314 TA TA TA CTC TA TA CTT TA TA TA TA CTT TA TA GA TA TA AA CTA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * * * * *
207358 TGG TA TA T- TA TA TA TA AA TA TA AA CTA TA TA GTT TG TA CA AA
1 T-A TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * *
207400 TA GTA TA TA -A TA GA TA TA GTA TA -A TG TA TG TA -A TT TCA TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA
* * *
207440 TA CTT TA TA TA TA TA TA TA TA TA TA TC TA TA T- TA -A TA AA CT-
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * ** * *
207481 TA CCA TA TC TA GC T- TT TA TA TA TA TA TA TA TA TA TA TA TA CA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
207523 TA CA TA GTA TA CA TA -A T- TT TA TA TA TA GT- TT TA TA TA AA T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
207563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
207604 CA TA GTA TA TA AA CA TA TA GTT TA TA TA T- TG TA TA TGA -A TA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA
* ** *
207645 TA GA CTA TA TA GC T- TA TA TA TA GT- TCA TA TA TA GTT TA -A CTA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA -TA TA TA -TA
* * ** * * *
207687 TA TA GTT TA TA T- TA AA GC TA TA TA GTA TG TA TG TA TG TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
207730 TA TA TA TA TA TA T- TA TA TA TA GTA TA -A CTA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA
*
207771 CT- TA TA -A GTA TA -A TA TA TA TT TA TA T- TA TA TA CT- TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * * *
207809 -A GTA TA -A TG TA TA TT TA CA AA AA TA TA T- TA TA -A TG TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
207848 CT- TA TA T- TA TA TA TA TA -A T- TA TA TA T- TA TA TA -A T- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
207884 TA TA T- TA TA TA -A GTA TA TCA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA -TA TA T-A TA TA TA T-A TA TA
207917 ATACATTGTA
Statistics
Matches: 498, Mismatches: 100, Indels: 170
0.65 0.13 0.22
Matches are distributed among these distances:
1 44 0.09
2 405 0.81
3 49 0.10
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:207248 original size:11 final size:10
Alignment explanation
Indices: 207219--207349 Score: 59
Period size: 11 Copynumber: 12.1 Consensus size: 10
207209 TATTTTTTAC
*
207219 TTTATACATA
1 TTTATATATA
207229 CTTTATATATA
1 -TTTATATATA
*
207240 TAGTT-TATA-C
1 T--TTATATATA
207250 TTTATATATAA
1 TTTATATAT-A
207261 TTTATATATA
1 TTTATATATA
207271 TATATATATATA
1 T-T-TATATATA
* *
207283 GTTCATATTTTA
1 -TTTATA-TATA
*
207295 CTTATATTATA
1 TTTATA-TATA
*
207306 TATATATATA
1 TTTATATATA
* *
207316 TATACTCTATA
1 TTTA-TATATA
207327 CTTTATATATA
1 -TTTATATATA
*
207338 CTTTATAGATA
1 -TTTATATATA
207349 T
1 T
207350 AAACTATATG
Statistics
Matches: 95, Mismatches: 14, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
8 2 0.02
9 4 0.04
10 13 0.14
11 58 0.61
12 17 0.18
13 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (10 bp):
TTTATATATA
Found at i:207251 original size:31 final size:31
Alignment explanation
Indices: 207206--207272 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
207196 ATGTAATTTC
* * *
207206 ATATATTTTTTACTTTATACATACTTTATAT
1 ATATAGTTTATACTTTATACATAATTTATAT
*
207237 ATATAGTTTATACTTTATATATAATTTATAT
1 ATATAGTTTATACTTTATACATAATTTATAT
207268 ATATA
1 ATATA
207273 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.55
Consensus pattern (31 bp):
ATATAGTTTATACTTTATACATAATTTATAT
Found at i:207278 original size:37 final size:38
Alignment explanation
Indices: 207232--207350 Score: 127
Period size: 37 Copynumber: 3.1 Consensus size: 38
207222 ATACATACTT
207232 TATATATATAGTTTATACTTTATATATAATTTATATATATA
1 TATATATATAGTTTATACTTTATATATAA--T-TATATATA
* *
207273 TATATATATAGTTCATATTTTACT-TAT-ATTATATATA
1 TATATATATAGTTTATACTTTA-TATATAATTATATATA
* * * *
207310 TATATATATACTCTATACTTTATATATACTT-TATAGA
1 TATATATATAGTTTATACTTTATATATAATTATATATA
207347 TATA
1 TATA
207351 AACTATATGG
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
36 1 0.01
37 38 0.57
38 3 0.04
40 1 0.01
41 23 0.34
42 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (38 bp):
TATATATATAGTTTATACTTTATATATAATTATATATA
Found at i:207688 original size:13 final size:12
Alignment explanation
Indices: 207650--207695 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
207640 GAATATAGAC
*
207650 TATATAGCTT-A
1 TATATAGTTTAA
*
207661 TATATAG-TTCA
1 TATATAGTTTAA
207672 TATATAGTTTAA
1 TATATAGTTTAA
207684 CTATATAGTTTA
1 -TATATAGTTTA
207696 TATTAAAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 2 0.06
11 15 0.48
12 3 0.10
13 11 0.35
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (12 bp):
TATATAGTTTAA
Found at i:207748 original size:13 final size:13
Alignment explanation
Indices: 207705--207993 Score: 111
Period size: 13 Copynumber: 21.4 Consensus size: 13
207695 ATATTAAAGC
*
207705 TATATAGTATGTATG
1 TATATA-TAT-TATA
*
207720 TATGTATATATATA
1 TATATATAT-TATA
207734 TATATATATTATA
1 TATATATATTATA
*
207747 TATAGTATAACTATA
1 TATA-TAT-ATTATA
207762 TAGTATATACTTATA
1 TA-TATATA-TTATA
207777 -AGTATA-A-TATA
1 TA-TATATATTATA
*
207788 TATTTATATTATA
1 TATATATATTATA
*
207801 TACT-TATAAGTATA
1 TA-TATAT-ATTATA
* *
207815 -ATGTATATTTACA
1 TATATATA-TTATA
* *
207828 AAAATATATTATA
1 TATATATATTATA
*
207841 -ATGTATACTTATA
1 TATATATA-TTATA
207854 T-TATATA-TATA
1 TATATATATTATA
207865 -ATTATATATTATA
1 TA-TATATATTATA
207878 TAATTATATATTATA
1 T-A-TATATATTATA
*
207893 TA-AGTATATCATA
1 TATA-TATATTATA
*
207906 TATATCATATAATA
1 TATAT-ATATTATA
* *
207920 CAT-TGTACTTATA
1 TATATATA-TTATA
*
207933 GTATAGATAATTATA
1 -TATATAT-ATTATA
*
207948 -ATGTATACTTATA
1 TATATATA-TTATA
207961 T-TATATACTTATA
1 TATATATA-TTATA
207974 TAGGTATATACTTATA
1 TA--TATATA-TTATA
207990 -ATAT
1 TATAT
207994 GCATAAGTAT
Statistics
Matches: 216, Mismatches: 27, Indels: 64
0.70 0.09 0.21
Matches are distributed among these distances:
11 11 0.05
12 19 0.09
13 83 0.38
14 48 0.22
15 40 0.19
16 15 0.07
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (13 bp):
TATATATATTATA
Found at i:207776 original size:21 final size:19
Alignment explanation
Indices: 207752--207821 Score: 53
Period size: 19 Copynumber: 3.9 Consensus size: 19
207742 TTATATATAG
207752 TATAACTATATAGTATATACT
1 TATAACTATA-A-TATATACT
*
207773 TATAAGTATAATATATA-T
1 TATAACTATAATATATACT
207791 T-T-A-TAT--TATATACT
1 TATAACTATAATATATACT
* *
207805 TATAAGTATAATGTATA
1 TATAACTATAATATATA
207822 TTTACAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 6 0.15
14 2 0.05
15 4 0.10
16 2 0.05
17 4 0.10
18 2 0.05
19 11 0.27
20 1 0.02
21 9 0.22
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (19 bp):
TATAACTATAATATATACT
Found at i:208585 original size:16 final size:16
Alignment explanation
Indices: 208564--208604 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
208554 TTATGTGACC
208564 CGATCTGAACGAGATT
1 CGATCTGAACGAGATT
*
208580 CGATCTGAACGAGCTT
1 CGATCTGAACGAGATT
*
208596 CAATCTGAA
1 CGATCTGAA
208605 GTTCATCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (16 bp):
CGATCTGAACGAGATT
Found at i:214397 original size:20 final size:20
Alignment explanation
Indices: 214374--214416 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
214364 AACGCGATCC
214374 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
214394 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
214414 CCA
1 CCA
214417 AAAGCGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:214424 original size:20 final size:20
Alignment explanation
Indices: 214381--214425 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
214371 TCCCCAGAAT
* *
214381 CGCAAATCAGTTTCCAGAAT
1 CGCAAATCAGTTTCCAAAAG
214401 CGCAAATCAGTTTCCAAAAG
1 CGCAAATCAGTTTCCAAAAG
214421 CGCAA
1 CGCAA
214426 CGCGATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.20
Consensus pattern (20 bp):
CGCAAATCAGTTTCCAAAAG
Found at i:214493 original size:21 final size:21
Alignment explanation
Indices: 214411--214493 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
214401 CGCAAATCAG
*
214411 TTTCCAAAAGCGCAACGCGAT
1 TTTCCAAAATCGCAACGCGAT
* *
214432 TCTT-GAAAATCGCAATGCGAT
1 T-TTCCAAAATCGCAACGCGAT
** * * **
214453 AGTACAAATTCGCATTGCGAT
1 TTTCCAAAATCGCAACGCGAT
214474 TTTCCAAAATCGCAACGCGA
1 TTTCCAAAATCGCAACGCGA
214494 AATCGCAACG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (21 bp):
TTTCCAAAATCGCAACGCGAT
Found at i:214498 original size:13 final size:13
Alignment explanation
Indices: 214480--214505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
214470 CGATTTTCCA
214480 AAATCGCAACGCG
1 AAATCGCAACGCG
214493 AAATCGCAACGCG
1 AAATCGCAACGCG
214506 TATGGGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.23, T:0.08
Consensus pattern (13 bp):
AAATCGCAACGCG
Found at i:214518 original size:20 final size:20
Alignment explanation
Indices: 214493--214605 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
214483 TCGCAACGCG
**
214493 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
214513 AAATCGCAATGCGTTATCCGT
1 AAATCGCAACGCG-TATCCGT
*
214534 ATATCGCAACGCGTAT-CGT
1 AAATCGCAACGCGTATCCGT
* * *
214553 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
214573 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
214593 AAATCGCAACGCG
1 AAATCGCAACGCG
214606 ATATTTAAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
18 1 0.01
19 15 0.19
20 45 0.58
21 17 0.22
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:215022 original size:33 final size:33
Alignment explanation
Indices: 214983--215053 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
214973 TTCACTTAGA
*
214983 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
215016 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
215049 TTTCA
1 TTTCA
215054 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:215193 original size:14 final size:14
Alignment explanation
Indices: 215174--215228 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
215164 AGAATGACTG
215174 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
215188 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
215207 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
215221 TCGCAACG
1 TCGCAACG
215229 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:215266 original size:19 final size:18
Alignment explanation
Indices: 215239--215356 Score: 80
Period size: 14 Copynumber: 7.1 Consensus size: 18
215229 CGAAACCAAA
*
215239 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
215258 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
215272 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
215291 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
215305 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
215323 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
215338 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
215356 T
1 T
215357 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.39
16 8 0.10
17 8 0.10
18 1 0.01
19 30 0.39
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:215280 original size:14 final size:14
Alignment explanation
Indices: 215261--215350 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
215251 TTTCATTTCG
215261 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
215275 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
215294 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
215308 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
215325 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
215341 CGTTGCGATT
1 CGTTGCGATT
215351 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:215286 original size:33 final size:33
Alignment explanation
Indices: 215244--215358 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
215234 CCAAATCGCA
215244 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
215277 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
215310 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
215343 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
215359 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:217683 original size:11 final size:11
Alignment explanation
Indices: 217661--217694 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
217651 GTTTTCAATA
217661 GTTTAATTGATT
1 GTTT-ATTGATT
*
217673 GTTTTTTGATT
1 GTTTATTGATT
217684 GTTTATTGATT
1 GTTTATTGATT
217695 TGTAAAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (11 bp):
GTTTATTGATT
Found at i:217781 original size:14 final size:14
Alignment explanation
Indices: 217762--217797 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
217752 ATTGTTTAAT
217762 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
217776 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
217790 TGATTTGT
1 TGATTTGT
217798 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:217927 original size:18 final size:18
Alignment explanation
Indices: 217904--218003 Score: 136
Period size: 18 Copynumber: 5.6 Consensus size: 18
217894 AAAAATGACT
217904 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
217922 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
217941 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
217955 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
217973 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
217993 ATCGCAATGCG
1 ATCGCAATGCG
218004 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 8 0.11
16 5 0.07
17 5 0.07
18 27 0.37
19 16 0.22
20 12 0.16
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:217996 original size:38 final size:38
Alignment explanation
Indices: 217904--218003 Score: 133
Period size: 33 Copynumber: 2.8 Consensus size: 38
217894 AAAAATGACT
217904 ATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
*
217941 ATCGCAA--CG--A-GAGAATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
217973 ATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGC-GAAATGAAAATCGCAATGCG
218004 TTTATAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
32 10 0.19
33 18 0.33
34 1 0.02
35 3 0.06
37 8 0.15
38 14 0.26
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (38 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
Found at i:218052 original size:33 final size:33
Alignment explanation
Indices: 218010--218336 Score: 208
Period size: 33 Copynumber: 9.5 Consensus size: 33
218000 TGCGTTTATA
218010 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
218043 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
218079 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
218114 ATTTCGCATTGCGATTTTCATTTCGTATTGCGA-TTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
218151 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
218184 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
218224 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
218255 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* * *
218288 ATTTCGCGTTGCGATTTTCAT-GTTGGGATTTTC
1 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
*
218321 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
218337 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 20, Indels: 50
0.78 0.06 0.16
Matches are distributed among these distances:
31 9 0.04
32 8 0.03
33 124 0.50
34 5 0.02
35 18 0.07
36 17 0.07
37 21 0.08
38 35 0.14
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:218056 original size:19 final size:19
Alignment explanation
Indices: 218032--218336 Score: 347
Period size: 19 Copynumber: 17.4 Consensus size: 19
218022 GATTATCTCG
218032 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
218051 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
218070 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
218084 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
218103 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
218122 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
218141 TTGCGA-TTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
218159 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
218174 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
218192 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
218211 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
218225 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
218244 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
218263 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
218277 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
218296 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
218310 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
218329 TTGCGATT
1 TTGCGATT
218337 GTATTTTCCG
Statistics
Matches: 248, Mismatches: 13, Indels: 50
0.80 0.04 0.16
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.12
17 31 0.12
18 18 0.07
19 134 0.54
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:218271 original size:52 final size:52
Alignment explanation
Indices: 218032--218308 Score: 343
Period size: 52 Copynumber: 5.2 Consensus size: 52
218022 GATTATCTCG
*
218032 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
218084 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
218141 TTGCGA-TTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
218192 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
218244 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
218296 TTGCGATTTTCAT
1 TTGCGATTTTCAT
218309 GTTGGGATTT
Statistics
Matches: 209, Mismatches: 8, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
51 24 0.11
52 148 0.71
53 3 0.01
54 6 0.03
55 5 0.02
56 17 0.08
57 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:220626 original size:12 final size:12
Alignment explanation
Indices: 220609--220633 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
220599 TCTTCGGGGA
220609 CTTTTTCTTCTT
1 CTTTTTCTTCTT
220621 CTTTTTCTTCTT
1 CTTTTTCTTCTT
220633 C
1 C
220634 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:220846 original size:24 final size:23
Alignment explanation
Indices: 220807--220852 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
220797 CTGAAACATC
*
220807 ATCAAATCCGTGTATTTACCAAT
1 ATCAAATCCGTGTATTGACCAAT
220830 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
220853 GACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Found at i:221552 original size:20 final size:20
Alignment explanation
Indices: 221543--221892 Score: 456
Period size: 20 Copynumber: 17.5 Consensus size: 20
221533 TACAGATTAT
*
221543 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
* * *
221563 CGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGATACG
*
221583 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
221603 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
221623 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
221643 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
221663 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
221683 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
221703 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
*
221723 CGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATACG
221743 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
221763 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
221783 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
221803 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
221823 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
221843 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
221863 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
221883 CGTTGCGATT
1 CGTTGCGATT
221893 ATGGAAAATC
Statistics
Matches: 294, Mismatches: 29, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 285 0.97
21 4 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:222551 original size:113 final size:112
Alignment explanation
Indices: 222345--222919 Score: 864
Period size: 110 Copynumber: 5.1 Consensus size: 112
222335 TTGTCGGTTT
* * *
222345 GTGTTGATACTTTATAAAAATATAT-TAATCCATAACAATATAACAAGT-AAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATGTATCT-ATCCATAACAATATAACAGGTAAAAAAAATGACAAAA
222408 CCGGTCTATAAATGACAAAACAGGTTAAGCGCTACCAGATATATTGAAA
65 CCGGTCTATAAATGACAAAACAGG-TAAGCGCTACCAGATATATTGAAA
*
222457 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACATGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
*
222522 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 CGGTCTATAAATGACAAAACAGGT-AAGCGCTACCAGATATATTGAAA
222570 GTGTCGATACTTTATAAAAATGTAT-TGATCCATAACAATATAAC-GGTAAAAAAAAAAATGACA
1 GTGTCGATACTTTATAAAAATGTATCT-ATCCATAACAATATAACAGGT---AAAAAAAATGACA
222633 AAACCGGTCTATAAATGACAAAACAGGTAAGCGCTACCAGATATATTGAAA
62 AAACCGGTCTATAAATGACAAAACAGGTAAGCGCTACCAGATATATTGAAA
*
222684 GTGTCGATACTTTAT-AAAATGTATCGATCC--AACAATATAACAGGTAAAAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGT-AAAAAAAATGACAAAA
* *
222746 CCGGTCTATAAATGACAAAACAGGTAAGCGCTACCAGATATGTTGATA
65 CCGGTCTATAAATGACAAAACAGGTAAGCGCTACCAGATATATTGAAA
* *
222794 GTGTCGATACTTTAT-AAAATGTATCGATCCATAACAATAAAACAGGT-AAAAAAATGACAAAAA
1 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAAAATGAC-AAAA
* * *
222857 CCGGTCTAT-AATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
65 CCGGTCTATAAATGACAAAACAGGT-AAGCGCTACCAGATATATTGAAA
*
222905 GTGTCAATACTTTAT
1 GTGTCGATACTTTAT
222920 TATAAGTTTC
Statistics
Matches: 438, Mismatches: 12, Indels: 27
0.92 0.03 0.06
Matches are distributed among these distances:
110 119 0.27
111 60 0.14
112 64 0.15
113 117 0.27
114 37 0.08
115 41 0.09
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
CGGTCTATAAATGACAAAACAGGTAAGCGCTACCAGATATATTGAAA
Found at i:223116 original size:182 final size:181
Alignment explanation
Indices: 222793--223161 Score: 555
Period size: 182 Copynumber: 2.0 Consensus size: 181
222783 ATATGTTGAT
222793 AGTGTCGATACTTTATAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAAAC
1 AGTGTCGATACTTTATAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAAAC
* * *
222858 CGGTCTATAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCAATACTTTATTAT
66 CGGTCGATAATAACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCAATACTTTATTAT
* * *
222923 AAGTTTCGACACTTTT-GAAATTTAAAAGATAAGAAGTTATAGCGCTAATAA
131 AAGTATCGACACTTTTAG-AATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
* * * *
222974 AGTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC-AAAA
1 AGTGTCGATACTTTAT-AAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAAA
* *
223038 CCGGTTTCGA-AATAACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
65 CCGG--TCGATAATAACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCAATACTTTAT
*
223102 TATCAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
128 TATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
*
223156 AATGTC
1 AGTGTC
223162 TGTAGACACC
Statistics
Matches: 169, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
181 23 0.14
182 142 0.84
183 4 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (181 bp):
AGTGTCGATACTTTATAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAAAC
CGGTCGATAATAACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCAATACTTTATTAT
AAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
Found at i:223209 original size:3 final size:3
Alignment explanation
Indices: 223196--223259 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
223186 TCTTTTATAT
223196 TTA TT- TTA TTA TTA TTA GTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
223241 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
223260 ACAATATATA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:229539 original size:227 final size:228
Alignment explanation
Indices: 229138--229596 Score: 895
Period size: 227 Copynumber: 2.0 Consensus size: 228
229128 GGTTTCTGAA
229138 TATACAAGGGAGATCATCGCCATTATGAATGAAATTGTAGAGCTGAGTCTGAGGGCTAGGCCTTA
1 TATACAAGGGAGATCATCGCCATTATGAATGAAATTGTAGAGCTGAGTCTGAGGGCTAGGCCTTA
229203 TATGTAATAGAACTCCTTTGTAATGAGTGAAACTTTTTATCCAATGAAAGTATTTCCGAATGGTT
66 TATGTAATAGAACTCCTTTGTAATGAGTGAAACTTTTTATCCAATGAAAGTATTTCCGAATGGTT
229268 ACTGCTTGGGTCAACGCCTTTTTGCATTTCATACTTGCATCATTCATTA-GCATAAGTAAATTCA
131 ACTGCTTGGGTCAACGCCTTTTTGCATTTCATACTTGCATCATTCATTATGCATAAGT-AATTCA
229332 TCATTTATAATGCATCACCAATAAATGTATCATT
195 TCATTTATAATGCATCACCAATAAATGTATCATT
229366 TATAC-AGGGAGATCATCGCCATTATGAATGAAATTGTAGAGCTGAGTCTGAGGGCTAGGCCTTA
1 TATACAAGGGAGATCATCGCCATTATGAATGAAATTGTAGAGCTGAGTCTGAGGGCTAGGCCTTA
229430 TATGTAATAGAACTCCTTTGTAATGAGTGAAACTTTTTATCCAATGAAAGTATTTCCGAATGGTT
66 TATGTAATAGAACTCCTTTGTAATGAGTGAAACTTTTTATCCAATGAAAGTATTTCCGAATGGTT
229495 ACTGCTTGGGTCAACGCCTTTTTGCATTTCATACTTGCATCATTCATTATGCATAAGTAATTCAT
131 ACTGCTTGGGTCAACGCCTTTTTGCATTTCATACTTGCATCATTCATTATGCATAAGTAATTCAT
229560 CATTTATAATGCATCACCAATAAATGTATCATT
196 CATTTATAATGCATCACCAATAAATGTATCATT
229593 TATA
1 TATA
229597 GCACATTACC
Statistics
Matches: 230, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
227 217 0.94
228 13 0.06
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (228 bp):
TATACAAGGGAGATCATCGCCATTATGAATGAAATTGTAGAGCTGAGTCTGAGGGCTAGGCCTTA
TATGTAATAGAACTCCTTTGTAATGAGTGAAACTTTTTATCCAATGAAAGTATTTCCGAATGGTT
ACTGCTTGGGTCAACGCCTTTTTGCATTTCATACTTGCATCATTCATTATGCATAAGTAATTCAT
CATTTATAATGCATCACCAATAAATGTATCATT
Done.