Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 38
Found at i:2778174 original size:37 final size:39
Alignment explanation
Indices: 2778110--2778189 Score: 130
Period size: 37 Copynumber: 2.1 Consensus size: 39
2778100 AATGTCACCT
2778110 GGTCAACGGTCAATGGTCGGTCGGTCAACGGTCGGGTCG
1 GGTCAACGGTCAATGGTCGGTCGGTCAACGGTCGGGTCG
2778149 GGTCAACGGTC-A-GGTCGGGT-GGTCAACGGTCGGGTCG
1 GGTCAACGGTCAATGGTC-GGTCGGTCAACGGTCGGGTCG
2778186 GGTC
1 GGTC
2778190 GGACCGGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
37 25 0.62
38 4 0.10
39 11 0.28
ACGTcount: A:0.14, C:0.23, G:0.44, T:0.20
Consensus pattern (39 bp):
GGTCAACGGTCAATGGTCGGTCGGTCAACGGTCGGGTCG
Found at i:2780734 original size:20 final size:20
Alignment explanation
Indices: 2780720--2780756 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2780710 ATTAAAATGT
2780720 TTTTAAAG-TATTTAAAAAG
1 TTTTAAAGCTATTTAAAAAG
*
2780739 TTTTAAAGCTTTTTAAAA
1 TTTTAAAGCTATTTAAAA
2780757 CATAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTTAAAGCTATTTAAAAAG
Found at i:2783110 original size:161 final size:161
Alignment explanation
Indices: 2782825--2783142 Score: 620
Period size: 161 Copynumber: 2.0 Consensus size: 161
2782815 TAGAAAATCC
2782825 TAGTGAGGAGCTAAGGTAGGGGATATAGACTTGGTTGAGAAGTCAAACCACTATAAATCATTGTG
1 TAGTGAGGAGCTAAGGTAGGGGATATAGACTTGGTTGAGAAGTCAAACCACTATAAATCATTGTG
2782890 CAAATTGTCTCATCTTTTTACTCCTACTCCCTGTACTCAAAAAGCCAGTTCACCCCCTCTTGGCA
66 CAAATTGTCTCATCTTTTTACTCCTACTCCCTGTACTCAAAAAGCCAGTTCACCCCCTCTTGGCA
2782955 AATTATTCGGTTGTTCATTTGAGCTTCTCCT
131 AATTATTCGGTTGTTCATTTGAGCTTCTCCT
2782986 TAGTGAGGAGCTAAGGTAGGGGATATAGACTTGGTTGAGAAGTCAAACCACTATAAATCATTGTG
1 TAGTGAGGAGCTAAGGTAGGGGATATAGACTTGGTTGAGAAGTCAAACCACTATAAATCATTGTG
2783051 CAAATTGTCTCATCTTTTTACTCCTTACTCCCTGTACTCAAAAAGCCAGTTCA-CCCCTCTTGGC
66 CAAATTGTCTCATCTTTTTACTCC-TACTCCCTGTACTCAAAAAGCCAGTTCACCCCCTCTTGGC
2783115 AAATTATTCGGTTGTTCATTTGAGCTTC
130 AAATTATTCGGTTGTTCATTTGAGCTTC
2783143 AATCGAAATA
Statistics
Matches: 156, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
161 128 0.82
162 28 0.18
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (161 bp):
TAGTGAGGAGCTAAGGTAGGGGATATAGACTTGGTTGAGAAGTCAAACCACTATAAATCATTGTG
CAAATTGTCTCATCTTTTTACTCCTACTCCCTGTACTCAAAAAGCCAGTTCACCCCCTCTTGGCA
AATTATTCGGTTGTTCATTTGAGCTTCTCCT
Found at i:2783810 original size:19 final size:21
Alignment explanation
Indices: 2783773--2783820 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2783763 AATGATTTTC
*
2783773 TTTTG-AAAGCAAAATTG-AA
1 TTTTGAAAAACAAAATTGAAA
2783792 TTTTGAAAAACAAAA-TGAAA
1 TTTTGAAAAACAAAATTGAAA
2783812 TTTT-AAAAA
1 TTTTGAAAAA
2783821 TTTATTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.31
Consensus pattern (21 bp):
TTTTGAAAAACAAAATTGAAA
Found at i:2785182 original size:24 final size:24
Alignment explanation
Indices: 2785155--2785232 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
2785145 TGTTCACGTG
2785155 GTATCGATACCAAAGGTAAGAGAA
1 GTATCGATACCAAAGGTAAGAGAA
* * *
2785179 GTATCAATACTC---GCT-AG-GTA
1 GTATCGATAC-CAAAGGTAAGAGAA
2785199 GTATCGATACCAAAGGTAAGAGAA
1 GTATCGATACCAAAGGTAAGAGAA
2785223 GTATCGATAC
1 GTATCGATAC
2785233 TTGCTAGGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 1 0.02
20 11 0.26
21 2 0.05
22 4 0.10
23 2 0.05
24 21 0.50
25 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (24 bp):
GTATCGATACCAAAGGTAAGAGAA
Found at i:2785203 original size:20 final size:20
Alignment explanation
Indices: 2785178--2785273 Score: 104
Period size: 20 Copynumber: 4.6 Consensus size: 20
2785168 AGGTAAGAGA
*
2785178 AGTATCAATACTCGCTAGGT
1 AGTATCGATACTCGCTAGGT
* *
2785198 AGTATCGATAC-CAAAGGTAAGAGA
1 AGTATCGATACTC---GCT-AG-GT
*
2785222 AGTATCGATACTTGCTAGGT
1 AGTATCGATACTCGCTAGGT
2785242 AGTATCGATACTCGCTAGGT
1 AGTATCGATACTCGCTAGGT
2785262 AGTATCGATACT
1 AGTATCGATACT
2785274 ACCATGTGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
19 1 0.02
20 42 0.67
21 2 0.03
22 4 0.06
23 2 0.03
24 12 0.19
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTCGCTAGGT
Found at i:2785218 original size:44 final size:44
Alignment explanation
Indices: 2785155--2785252 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
2785145 TGTTCACGTG
2785155 GTATCGATACCAAAGGTAAGAGAAGTATCAATACTCGCTAGGTA
1 GTATCGATACCAAAGGTAAGAGAAGTATCAATACTCGCTAGGTA
* *
2785199 GTATCGATACCAAAGGTAAGAGAAGTATCGATACTTGCTAGGTA
1 GTATCGATACCAAAGGTAAGAGAAGTATCAATACTCGCTAGGTA
2785243 GTATCGATAC
1 GTATCGATAC
2785253 TCGCTAGGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (44 bp):
GTATCGATACCAAAGGTAAGAGAAGTATCAATACTCGCTAGGTA
Found at i:2788857 original size:16 final size:16
Alignment explanation
Indices: 2788836--2788880 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2788826 TTCATGTAAA
2788836 AAAAATATTTAAATTT
1 AAAAATATTTAAATTT
**
2788852 AAAAATATAAAAATTT
1 AAAAATATTTAAATTT
*
2788868 ATTAAATATTTAA
1 A-AAAATATTTAA
2788881 TTAAGTAGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAATATTTAAATTT
Found at i:2788953 original size:15 final size:16
Alignment explanation
Indices: 2788933--2788962 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2788923 AATTTTGGTC
2788933 TAATTACAA-TTTAAG
1 TAATTACAAGTTTAAG
2788948 TAATTACAAGTTTAA
1 TAATTACAAGTTTAA
2788963 ATATTAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
TAATTACAAGTTTAAG
Found at i:2789111 original size:13 final size:13
Alignment explanation
Indices: 2789093--2789118 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2789083 AACTCGGGAC
2789093 CTCAAGGATAACA
1 CTCAAGGATAACA
2789106 CTCAAGGATAACA
1 CTCAAGGATAACA
2789119 ACAATCCCTT
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:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (13 bp):
CTCAAGGATAACA
Found at i:2791172 original size:19 final size:18
Alignment explanation
Indices: 2791122--2791164 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2791112 CAGTGACTAA
* *
2791122 ACAACTAAATATAATATC
1 ACAACCAAATATAATACC
2791140 ACAACCAAATTATAATACC
1 ACAACCAAA-TATAATACC
2791159 AGCAAC
1 A-CAAC
2791165 ATAATATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.21
Consensus pattern (18 bp):
ACAACCAAATATAATACC
Found at i:2792187 original size:3 final size:3
Alignment explanation
Indices: 2792174--2792222 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
2792164 TATATGTAAC
*
2792174 ATA ATTA ATA ATA ACA ATA A-A CA-A ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
2792219 ATA A
1 ATA A
2792223 AAAAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2792614 original size:133 final size:130
Alignment explanation
Indices: 2792447--2792796 Score: 393
Period size: 123 Copynumber: 2.7 Consensus size: 130
2792437 GAGACGGCTA
*
2792447 GTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGAGGGATGACACGTTCCTA
1 GTTATCTACGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCG-GGGATGACACGTTCCTA
* * *
2792512 CGTGTTGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAGCTCGGCTCCTACGTGATGAGGACGA
65 CGTGATGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAACACGGCTCCTAC-TGATGAGGACGA
2792577 CT
129 CT
* * * *
2792579 GGTTATCTA-GGGTGACTACAGCTCATACGTGATGAAGAGATC--GTCGGGGAATGACACGCTCA
1 -GTTATCTACGGGTGAC-ACGGCTCCTACGTGATGAAGAGATCTGGTCGGGG-ATGACACGTTCC
* * * *
2792641 T-CGTGATGAAGA-GTTCTGGCCATC--TA--A-AGGTGATAACACGGTTCCTACTGATGAGGAC
63 TACGTGATGAGGACG-GCTGGCCATCTTTAGGAGTGGTGATAACACGGCTCCTACTGATGAGGAC
*
2792699 GGCT
127 GACT
* * *
2792703 GTTATCTACGGTTGACACGGCTCCTACGTGAT---GATATCTGGTCTGGGATGACACAGTTCCTA
1 GTTATCTACGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGATGACAC-GTTCCTA
*
2792765 CATGATGAGGACGGCTGGCCATCTTTAGGAGT
65 CGTGATGAGGACGGCTGGCCATCTTTAGGAGT
2792797 TATTTTCAAG
Statistics
Matches: 180, Mismatches: 23, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
120 5 0.03
121 7 0.04
122 10 0.06
123 40 0.22
124 20 0.11
125 19 0.11
126 1 0.01
127 1 0.01
128 2 0.01
129 1 0.01
130 21 0.12
131 15 0.08
132 7 0.04
133 31 0.17
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (130 bp):
GTTATCTACGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGATGACACGTTCCTAC
GTGATGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAACACGGCTCCTACTGATGAGGACGACT
Found at i:2792858 original size:28 final size:28
Alignment explanation
Indices: 2792818--2792879 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
2792808 GAACCAAATT
2792818 AAAGATTTGTTTCAA-AAGAAACAAACCC
1 AAAGATTTGTTTCAAGAA-AAACAAACCC
* *
2792846 AAAGATTTGTTTCAAGAAAAATAAACTC
1 AAAGATTTGTTTCAAGAAAAACAAACCC
2792874 AAAGAT
1 AAAGAT
2792880 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAGAAAAACAAACCC
Found at i:2793115 original size:61 final size:59
Alignment explanation
Indices: 2793022--2793213 Score: 169
Period size: 61 Copynumber: 3.2 Consensus size: 59
2793012 CAAAGATGGT
* * *
2793022 AAAA-TTTGTTTCC-AAGAAACAAACTCAAGATTTTTCTCAAGA-ACTGTC-TCGAGAGAAAC
1 AAAATTTTGTTTCCAAAGAAA-AGATTCATGATTTTTCTCAAGACACTGTCAT--A-AGAAAC
* * * *
2793081 AAAATTTTGTTTCCAAAGAAAGAGATTCATGATTTTTTTTAAGACATTGTCATAAGAGAC
1 AAAATTTTGTTTCCAAAGAAA-AGATTCATGATTTTTCTCAAGACACTGTCATAAGAAAC
* * * *
2793141 AAAACTTTTTGTTTCCAAAG-AAAGATTCAATGATTTTTTTTAAGACATTGTCATAAGAGAC
1 AAAA--TTTTGTTTCCAAAGAAAAGATTC-ATGATTTTTCTCAAGACACTGTCATAAGAAAC
*
2793202 AAAACTTTGTTT
1 AAAATTTTGTTT
2793214 TTCAGAAATG
Statistics
Matches: 117, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
59 11 0.09
60 24 0.21
61 62 0.53
62 19 0.16
63 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (59 bp):
AAAATTTTGTTTCCAAAGAAAAGATTCATGATTTTTCTCAAGACACTGTCATAAGAAAC
Found at i:2793153 original size:62 final size:61
Alignment explanation
Indices: 2793085--2793209 Score: 225
Period size: 61 Copynumber: 2.0 Consensus size: 61
2793075 AGAAACAAAA
2793085 TTTTGTTTCCAAAGAAAGAGATTC-ATGATTTTTTTTAAGACATTGTCATAAGAGACAAAACT
1 TTTTGTTTCCAAAG-AA-AGATTCAATGATTTTTTTTAAGACATTGTCATAAGAGACAAAACT
2793147 TTTTGTTTCCAAAGAAAGATTCAATGATTTTTTTTAAGACATTGTCATAAGAGACAAAACT
1 TTTTGTTTCCAAAGAAAGATTCAATGATTTTTTTTAAGACATTGTCATAAGAGACAAAACT
2793208 TT
1 TT
2793210 GTTTTTCAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
60 6 0.10
61 42 0.68
62 14 0.23
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (61 bp):
TTTTGTTTCCAAAGAAAGATTCAATGATTTTTTTTAAGACATTGTCATAAGAGACAAAACT
Found at i:2793873 original size:67 final size:65
Alignment explanation
Indices: 2793718--2793946 Score: 340
Period size: 67 Copynumber: 3.5 Consensus size: 65
2793708 TCATTTTAAG
* * *
2793718 AGAAACAGATTCAAAGA--TTTATTTCAAAAGAAATTATCTT-A-AGAGACAAATTTTGTTTCCA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTGTTTCCA
*
2793779 AGAAACATACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTGTTTCCA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTGTTTCC-
2793844 AA
65 -A
*
2793846 AAAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA-TTTGTTTCC
2793911 A
65 A
* *
2793912 AGGAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
2793947 CAATCTCAAA
Statistics
Matches: 152, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
61 15 0.10
63 22 0.14
64 1 0.01
65 18 0.12
66 33 0.22
67 54 0.36
68 9 0.06
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (65 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTGTTTCCA
Found at i:2793936 original size:29 final size:30
Alignment explanation
Indices: 2793901--2793963 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
2793891 AGAGACAAAA
* *
2793901 TTTTGTTTC-CAAGGAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
2793930 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
2793960 TTTT
1 TTTT
2793964 TTCGCAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:2793972 original size:30 final size:30
Alignment explanation
Indices: 2793915--2793972 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2793905 GTTTCCAAGG
*
2793915 AACAAACTCAAAGATTTTTGTTTCAAAAGA
1 AACAAACTCAAAGATTTTTGTTGCAAAAGA
*
2793945 AACAATCTCAAAGATTTTT-TTCGCAAAA
1 AACAAACTCAAAGATTTTTGTT-GCAAAA
2793973 TTGTCTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.31
Consensus pattern (30 bp):
AACAAACTCAAAGATTTTTGTTGCAAAAGA
Found at i:2794337 original size:37 final size:37
Alignment explanation
Indices: 2794229--2794337 Score: 91
Period size: 37 Copynumber: 2.9 Consensus size: 37
2794219 AACAACCTTG
* *
2794229 AAATTTGTATTATGAGAGAAATGATGTCTC-AGCGAGA-CG
1 AAATTTGT-TT-TTAGAGAAAT--TGTCTCAAGCGAGACCA
* * * **
2794268 AAATTTG-CTTTA-AGATATAGTCTCAAATGAGACCA
1 AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACCA
2794303 AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGAC
1 AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGAC
2794338 AAAGTTTATT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
33 5 0.09
34 5 0.09
35 13 0.24
36 6 0.11
37 18 0.33
39 7 0.13
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (37 bp):
AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACCA
Found at i:2794524 original size:103 final size:100
Alignment explanation
Indices: 2794324--2794552 Score: 236
Period size: 104 Copynumber: 2.3 Consensus size: 100
2794314 TAGAGAAATT
* *
2794324 GTCTCAAGCGAGAC-AAAGTTTATTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACGAAA-TTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
*
2794388 TGTAAAATTCGAAATTTGGATCTCAGAGGG-AAAAG
65 TGTAAAATTCAAAATTTGGATCTCAGAGGGAAAAAG
* *
2794423 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
2794487 TAA-GTGAATCAAATTCAAAATTTGTATCTCA-A-GGAAAAAT
60 TAATGTG--TAAAATTCAAAATTTGGATCTCAGAGGGAAAAAG
* * *
2794527 GTCTCAAGTGAGATGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
2794553 AAAATTCTCA
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
99 22 0.20
100 3 0.03
101 2 0.02
102 4 0.04
103 25 0.23
104 33 0.30
105 20 0.18
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (100 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GTAAAATTCAAAATTTGGATCTCAGAGGGAAAAAG
Found at i:2794765 original size:30 final size:31
Alignment explanation
Indices: 2794731--2794804 Score: 78
Period size: 38 Copynumber: 2.2 Consensus size: 31
2794721 GATTCCTGCA
2794731 TGTTGAGGAA-ATGTCTTCAGAGGATCTGAT
1 TGTTGAGGAACATGTCTTCAGAGGATCTGAT
2794761 TGTTGACTTCAGGAAGCCATGTCTTCAGAGGATCTGAT
1 TGTTG-----AGGAA--CATGTCTTCAGAGGATCTGAT
2794799 TGTTGA
1 TGTTGA
2794805 CTTCAGGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
30 5 0.14
33 1 0.03
35 5 0.14
38 25 0.69
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (31 bp):
TGTTGAGGAACATGTCTTCAGAGGATCTGAT
Found at i:2794783 original size:38 final size:38
Alignment explanation
Indices: 2794741--2794817 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2794731 TGTTGAGGAA
2794741 ATGTCTTCAGAGGATCTGATTGTTGACTTCAGGAAGCC
1 ATGTCTTCAGAGGATCTGATTGTTGACTTCAGGAAGCC
2794779 ATGTCTTCAGAGGATCTGATTGTTGACTTCAGGAAGCC
1 ATGTCTTCAGAGGATCTGATTGTTGACTTCAGGAAGCC
2794817 A
1 A
2794818 AATATGTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (38 bp):
ATGTCTTCAGAGGATCTGATTGTTGACTTCAGGAAGCC
Found at i:2795049 original size:4 final size:4
Alignment explanation
Indices: 2795040--2795409 Score: 634
Period size: 4 Copynumber: 95.0 Consensus size: 4
2795030 TTTATGTATC
2795040 ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
2795086 CTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2795134 ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2795180 ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
2795226 ATGT ATGT AGGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2795274 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATG-
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
2795319 ATGT ATGT AGGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
2795367 ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATAT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2795410 TTTCTCGATC
Statistics
Matches: 348, Mismatches: 8, Indels: 20
0.93 0.02 0.05
Matches are distributed among these distances:
2 6 0.02
3 12 0.03
4 330 0.95
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:2797073 original size:19 final size:20
Alignment explanation
Indices: 2797049--2797096 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2797039 AAAAATACAG
*
2797049 TGTTTCAAGGT-GGAAAGAA
1 TGTTTCAAGGTCGAAAAGAA
2797068 TGTTTCAAGGTCGAAAAGAA
1 TGTTTCAAGGTCGAAAAGAA
*
2797088 TATTTCAAG
1 TGTTTCAAG
2797097 ATCTCAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (20 bp):
TGTTTCAAGGTCGAAAAGAA
Found at i:2802164 original size:3 final size:3
Alignment explanation
Indices: 2802151--2802201 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
2802141 TATATGTAAC
* *
2802151 ATA ATTA ATA ATA ACA ATA A-A CAAA ATA ATA ATA ATAA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA
2802198 ATA A
1 ATA A
2802202 ATAAAAAGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 1 0.02
3 33 0.80
4 7 0.17
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:2802192 original size:13 final size:13
Alignment explanation
Indices: 2802174--2802205 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2802164 ACAATAAACA
2802174 AAATAATAATAAT
1 AAATAATAATAAT
2802187 AAATAATAATAAT
1 AAATAATAATAAT
2802200 AAATAA
1 AAATAA
2802206 AAAGACCCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:2804743 original size:26 final size:27
Alignment explanation
Indices: 2804714--2804764 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2804704 GGCGAGAAAC
* *
2804714 AAAATTAATATAATAT-TAAAAATTAA
1 AAAATTAAAATAAAATGTAAAAATTAA
2804740 AAAATTAAAATAAAATGTAAAAATT
1 AAAATTAAAATAAAATGTAAAAATT
2804765 GAAGGTTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATTAAAATAAAATGTAAAAATTAA
Found at i:2807742 original size:8 final size:8
Alignment explanation
Indices: 2807729--2807797 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
2807719 TTTAAATTAT
2807729 AAATATAA
1 AAATATAA
*
2807737 AAATATTCA
1 AAATA-TAA
*
2807746 AAATAAAA
1 AAATATAA
**
2807754 AAATATTC
1 AAATATAA
2807762 AAATA-AA
1 AAATATAA
*
2807769 AAA-ATAT
1 AAATATAA
*
2807776 ACATATAA
1 AAATATAA
2807784 AAATACTAA
1 AAATA-TAA
2807793 AAATA
1 AAATA
2807798 CAAATTAAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
6 1 0.02
7 6 0.13
8 23 0.51
9 15 0.33
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (8 bp):
AAATATAA
Found at i:2807765 original size:16 final size:16
Alignment explanation
Indices: 2807729--2807786 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
2807719 TTTAAATTAT
*
2807729 AAATATAAAAATATTC
1 AAATAAAAAAATATTC
2807745 AAAATAAAAAAATATTC
1 -AAATAAAAAAATATTC
*
2807762 AAATAAAAAAATATAC
1 AAATAAAAAAATATTC
*
2807778 ATATAAAAA
1 AAATAAAAA
2807787 TACTAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
16 23 0.61
17 15 0.39
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAAAAATATTC
Found at i:2808936 original size:18 final size:18
Alignment explanation
Indices: 2808908--2808952 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
2808898 TTATCATTTC
* **
2808908 ATTATCCTTATTATTATT
1 ATTATCATTATTAGCATT
*
2808926 CTTATCATTATTAGCATT
1 ATTATCATTATTAGCATT
2808944 ATTATCATT
1 ATTATCATT
2808953 CATATCTCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATCATTATTAGCATT
Found at i:2809244 original size:28 final size:28
Alignment explanation
Indices: 2809208--2809261 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
2809198 GTCGTGAAAG
*
2809208 ACCATATATAACACATATGTCCCGAATA
1 ACCACATATAACACATATGTCCCGAATA
2809236 ACCACATATAACACATATGTCCCGAA
1 ACCACATATAACACATATGTCCCGAA
2809262 GGACCACTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (28 bp):
ACCACATATAACACATATGTCCCGAATA
Found at i:2809267 original size:28 final size:28
Alignment explanation
Indices: 2809207--2809268 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
2809197 TGTCGTGAAA
* *
2809207 GACCATATATAACACATATGTCCCGAAT
1 GACCACATATAACACATATGTCCCGAAG
*
2809235 AACCACATATAACACATATGTCCCGAAG
1 GACCACATATAACACATATGTCCCGAAG
2809263 GACCAC
1 GACCAC
2809269 TCTTTAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.19
Consensus pattern (28 bp):
GACCACATATAACACATATGTCCCGAAG
Found at i:2811180 original size:24 final size:24
Alignment explanation
Indices: 2811128--2811177 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
2811118 TGAATATTTG
*
2811128 AATAATTTTGTATTTAAAATTTAA
1 AATAATTTTGTATTTAAAAATTAA
2811152 AATAATTTT-TATCTTAAAAAATTAA
1 AATAATTTTGTAT-TT-AAAAATTAA
2811177 A
1 A
2811178 TAAGCCCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 11 0.48
25 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
AATAATTTTGTATTTAAAAATTAA
Found at i:2812895 original size:75 final size:76
Alignment explanation
Indices: 2812724--2812930 Score: 276
Period size: 74 Copynumber: 2.8 Consensus size: 76
2812714 GACCGTTGAA
* * * * *
2812724 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
**
2812788 ACAAAACTGTT
66 ACAAAACCATT
*
2812799 TA-GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
* *
2812862 GCCAAACCATT
66 ACAAAACCATT
* *
2812873 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 CAGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
2812931 TTTTTGGCTT
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
74 62 0.54
75 23 0.20
77 30 0.26
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
ACAAAACCATT
Found at i:2813559 original size:17 final size:17
Alignment explanation
Indices: 2813537--2813580 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2813527 TTCATAAATC
2813537 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
2813554 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
2813571 -AAATATCCAA
1 CAAA-ATCCAA
2813581 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:2813572 original size:9 final size:8
Alignment explanation
Indices: 2813532--2813582 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
2813522 CACCATTCAT
2813532 AAATCC-A
1 AAATCCAA
2813539 AAATCCAA
1 AAATCCAA
*
2813547 CAATCCACA
1 AAATCCA-A
2813556 AAAT-CAA
1 AAATCCAA
2813563 ACAATCCAA
1 A-AATCCAA
2813572 AATATCCAA
1 AA-ATCCAA
2813581 AA
1 AA
2813583 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:2815608 original size:21 final size:21
Alignment explanation
Indices: 2815554--2815616 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
2815544 ATTCCCCTGT
2815554 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
2815577 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
* *
2815598 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
2815617 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:2821489 original size:75 final size:76
Alignment explanation
Indices: 2821380--2821589 Score: 273
Period size: 75 Copynumber: 2.8 Consensus size: 76
2821370 GACCGTTGAA
* * *
2821380 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
**
2821444 ACAAAACTGTT
66 ACAAAACCATT
* * * *
2821455 TAGGGGGGAATCGGTTCCTCCTAT-GGGTGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
* *
2821519 GCCAAACCATT
66 ACAAAACCATT
*
2821530 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 CAGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
2821590 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
75 85 0.74
76 1 0.01
77 29 0.25
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
ACAAAACCATT
Found at i:2823285 original size:25 final size:25
Alignment explanation
Indices: 2823251--2823302 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2823241 TGTCTATTGG
2823251 AATAATAGGATGATGCTCTTCATTC
1 AATAATAGGATGATGCTCTTCATTC
2823276 AATAATAGGATGATGCTCTTCATTC
1 AATAATAGGATGATGCTCTTCATTC
2823301 AA
1 AA
2823303 GCCAACAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (25 bp):
AATAATAGGATGATGCTCTTCATTC
Found at i:2826758 original size:12 final size:13
Alignment explanation
Indices: 2826743--2826771 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2826733 TATTAATATT
2826743 TAATTTAAAAT-A
1 TAATTTAAAATAA
2826755 TAATTTAAAATAA
1 TAATTTAAAATAA
2826768 TAAT
1 TAAT
2826772 AATATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATTTAAAATAA
Found at i:2826778 original size:18 final size:18
Alignment explanation
Indices: 2826727--2826784 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
2826717 GACAAATCAG
*
2826727 AAAA-AATATTAATATTT
1 AAAATAATAATAATATTT
**
2826744 AATTTAA-AAT-ATAATTT
1 AAAATAATAATAAT-ATTT
2826761 AAAATAATAATAATATTT
1 AAAATAATAATAATATTT
2826779 AAAATA
1 AAAATA
2826785 CCTAAAACTC
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 2 0.06
17 13 0.41
18 15 0.47
19 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATAATAATAATATTT
Found at i:2828027 original size:14 final size:14
Alignment explanation
Indices: 2827992--2828030 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2827982 AACAAAGGTA
2827992 AATAAATAAAT-AC
1 AATAAATAAATAAC
2828005 -ATGAAATAAATAAC
1 AAT-AAATAAATAAC
2828019 AATAAATAAATA
1 AATAAATAAATA
2828031 TTTATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 8 0.35
14 11 0.48
15 2 0.09
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (14 bp):
AATAAATAAATAAC
Found at i:2831447 original size:15 final size:15
Alignment explanation
Indices: 2831427--2831477 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
2831417 ACCACAAATT
2831427 CCTCAATTTTCTGCA
1 CCTCAATTTTCTGCA
2831442 CCTCAATTTTCTGCA
1 CCTCAATTTTCTGCA
*
2831457 CAC-CAATTTTATGCA
1 C-CTCAATTTTCTGCA
2831472 CCTCAA
1 CCTCAA
2831478 ATTCCTCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
14 1 0.03
15 31 0.94
16 1 0.03
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.35
Consensus pattern (15 bp):
CCTCAATTTTCTGCA
Found at i:2833326 original size:21 final size:22
Alignment explanation
Indices: 2833300--2833352 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2833290 CCATTCAAAT
*
2833300 TCATCATCTTCTACACCA-TTA
1 TCATCATCTTCTACACCACATA
* *
2833321 TCATCATCATCTTCACCACATA
1 TCATCATCTTCTACACCACATA
2833343 T-ATCATCTTC
1 TCATCATCTTC
2833353 ATCTCAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (22 bp):
TCATCATCTTCTACACCACATA
Found at i:2833331 original size:24 final size:24
Alignment explanation
Indices: 2833300--2833356 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
2833290 CCATTCAAAT
2833300 TCATCATCTTCTA-CACCAT-TATCA
1 TCATCATCTTC-ACCA-CATATATCA
2833324 TCATCATCTTCACCACATATATCA
1 TCATCATCTTCACCACATATATCA
*
2833348 TCTTCATCT
1 TCATCATCT
2833357 CAACAATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.39
Consensus pattern (24 bp):
TCATCATCTTCACCACATATATCA
Found at i:2833474 original size:21 final size:20
Alignment explanation
Indices: 2833419--2833474 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
2833409 TACTACTTCA
*
2833419 TCACCATCACCACTTCCACC
1 TCACCATCACCACCTCCACC
* * *
2833439 TCTATCATTATCACCTCCACC
1 TC-ACCATCACCACCTCCACC
2833460 TTCACCATCACCACC
1 -TCACCATCACCACC
2833475 ACCATCTCCA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (20 bp):
TCACCATCACCACCTCCACC
Found at i:2838484 original size:31 final size:31
Alignment explanation
Indices: 2838449--2838515 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2838439 TAAAACTTGT
*
2838449 AATATAATCCCCCAATATTTAGTCCATTTGC
1 AATATAATCCCCCAAAATTTAGTCCATTTGC
** *
2838480 AATATGGTCCCTCAAAATTTAGTCCATTTGC
1 AATATAATCCCCCAAAATTTAGTCCATTTGC
2838511 AATAT
1 AATAT
2838516 GGTCCCTGAC
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:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (31 bp):
AATATAATCCCCCAAAATTTAGTCCATTTGC
Found at i:2838516 original size:31 final size:31
Alignment explanation
Indices: 2838456--2838522 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
2838446 TGTAATATAA
* *
2838456 TCCCCCAATATTTAGTCCATTTGCAATATGG
1 TCCCTCAAAATTTAGTCCATTTGCAATATGG
2838487 TCCCTCAAAATTTAGTCCATTTGCAATATGG
1 TCCCTCAAAATTTAGTCCATTTGCAATATGG
2838518 TCCCT
1 TCCCT
2838523 GACGTAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (31 bp):
TCCCTCAAAATTTAGTCCATTTGCAATATGG
Found at i:2842344 original size:17 final size:17
Alignment explanation
Indices: 2842312--2842343 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2842302 TCACTAACTA
2842312 TTTTCCTTTCATTTTTG
1 TTTTCCTTTCATTTTTG
2842329 TTTT-CTTTCATTTTT
1 TTTTCCTTTCATTTTT
2842344 TATCATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTCCTTTCATTTTTG
Found at i:2849287 original size:2 final size:2
Alignment explanation
Indices: 2849275--2849308 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
2849265 CTTTTATTAT
2849275 TA TA TA GTA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2849309 ATAATTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2849369 original size:36 final size:36
Alignment explanation
Indices: 2849317--2849435 Score: 113
Period size: 37 Copynumber: 3.2 Consensus size: 36
2849307 TAATAATTTC
*
2849317 AAACGTAATTTTTGAAAGTATATATTATAT-GTTCTGA
1 AAACGT-A-TTTTGAAAGTATATATTATATAGTTTTGA
2849354 AAACGTATTTATGAAAACGTATA-A-TATATAGTTTTGA
1 AAACGTATTT-TG-AAA-GTATATATTATATAGTTTTGA
*
2849391 AAA--TATTTTGAAAATATATATAATATATAGTTTTTGA
1 AAACGTATTTTGAAAGTATATAT--TATATAG-TTTTGA
2849428 AAACGTAT
1 AAACGTAT
2849436 ATAGTTTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 20
0.76 0.02 0.22
Matches are distributed among these distances:
32 4 0.06
33 4 0.06
34 2 0.03
35 8 0.12
36 15 0.22
37 28 0.41
38 5 0.07
39 3 0.04
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (36 bp):
AAACGTATTTTGAAAGTATATATTATATAGTTTTGA
Found at i:2849503 original size:38 final size:37
Alignment explanation
Indices: 2849432--2849526 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 37
2849422 TTTTGAAAAC
* **
2849432 GTATATAGTTTTTTAAAAAATGATTTTTGAAAAATATATA
1 GTATATAGTTTTTT--AAAATAATTTTAAAAAAATATA-A
2849472 GTATATAGTTTTTTAAAATAATTTTAAAAAAATATAA
1 GTATATAGTTTTTTAAAATAATTTTAAAAAAATATAA
2849509 -TATATAGTTTTTTTAAAA
1 GTATATAG-TTTTTTAAAA
2849527 AGTACAATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
36 7 0.14
37 11 0.22
38 19 0.37
40 14 0.27
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (37 bp):
GTATATAGTTTTTTAAAATAATTTTAAAAAAATATAA
Found at i:2849513 original size:36 final size:36
Alignment explanation
Indices: 2849433--2849621 Score: 118
Period size: 36 Copynumber: 5.4 Consensus size: 36
2849423 TTTGAAAACG
* * *
2849433 TATATAGTTTTTTAAAAAATGATTTTTGAAAAATATATAG
1 TATATAGTTTTTT--AAAAT-AATTTT-AAAAAAATATAA
2849473 TATATAGTTTTTTAAAATAATTTTAAAAAAATATAA
1 TATATAGTTTTTTAAAATAATTTTAAAAAAATATAA
* *
2849509 TATATAG----TT----T--TTTT-AAAAAGTACAA
1 TATATAGTTTTTTAAAATAATTTTAAAAAAATATAA
* * * *
2849534 TATATAGTTTTTTTAAAA-AGTTTTTGAAAACATATAG
1 TATATAG-TTTTTTAAAATA-ATTTTAAAAAAATATAA
*
2849571 TATATAG-TTTTTAAAATAATTTTAAAAAATGTATAA
1 TATATAGTTTTTTAAAATAATTTTAAAAAA-ATATAA
*
2849607 AATATA-TTTTTTAAA
1 TATATAGTTTTTTAAA
2849622 TATTTTGAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
25 16 0.14
26 4 0.03
28 1 0.01
30 2 0.02
32 2 0.02
35 17 0.14
36 39 0.33
37 19 0.16
38 5 0.04
40 13 0.11
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.46
Consensus pattern (36 bp):
TATATAGTTTTTTAAAATAATTTTAAAAAAATATAA
Found at i:2849553 original size:25 final size:25
Alignment explanation
Indices: 2849493--2849554 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
2849483 TTTAAAATAA
* * *
2849493 TTTTAAAAAAATATAATATATAGTT
1 TTTTTAAAAAGTACAATATATAGTT
2849518 TTTTTAAAAAGTACAATATATAGTT
1 TTTTTAAAAAGTACAATATATAGTT
2849543 TTTTTAAAAAGT
1 TTTTTAAAAAGT
2849555 TTTTGAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTTAAAAAGTACAATATATAGTT
Found at i:2849582 original size:97 final size:95
Alignment explanation
Indices: 2849360--2849618 Score: 296
Period size: 97 Copynumber: 2.7 Consensus size: 95
2849350 CTGAAAACGT
* * * * *
2849360 ATTTATGAAAACGTATAATATATAGTTTTGAAAAT-ATTTTGAAAATATATATAATATATAG--T
1 ATTTTTGAAAACATATAGTATATAGTTTTTAAAATAATTTT-AAAA-AAATATAATATATAGTTT
* *
2849422 TTTTGAAAACGTATATAGTTTTTTAAAAAATG
64 TTTTAAAAACATATATAGTTTTTTAAAAAATG
*
2849454 ATTTTTGAAAAATATATAGTATATAGTTTTTTAAAATAATTTTAAAAAAATATAATATATAGTTT
1 ATTTTTG-AAAACATATAGTATATAG-TTTTTAAAATAATTTTAAAAAAATATAATATATAGTTT
*
2849519 TTTTAAAAAGTACAATATATAGTTTTTTTAAAAA-G
64 TTTT-AAAA--AC-ATATATAGTTTTTTAAAAAATG
* *
2849554 -TTTTTGAAAACATATAGTATATAGTTTTTAAAATAATTTTAAAAAATGTATAAAATATA-TTTT
1 ATTTTTGAAAACATATAGTATATAGTTTTTAAAATAATTTTAAAAAA-ATATAATATATAGTTTT
2849617 TT
65 TT
2849619 AAATATTTTG
Statistics
Matches: 143, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
94 6 0.04
95 29 0.20
96 13 0.09
97 38 0.27
98 30 0.21
99 6 0.04
100 3 0.02
101 18 0.13
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.45
Consensus pattern (95 bp):
ATTTTTGAAAACATATAGTATATAGTTTTTAAAATAATTTTAAAAAAATATAATATATAGTTTTT
TTAAAAACATATATAGTTTTTTAAAAAATG
Found at i:2849641 original size:35 final size:36
Alignment explanation
Indices: 2849555--2849641 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 36
2849545 TTTAAAAAGT
**
2849555 TTTTGAAAAC-ATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACTATATAAAATATAGTTTTTAAAATAA
* * * *
2849590 TTTTAAAAAATGTATAAAATATA-TTTTTTAAAT-A
1 TTTTGAAAACTATATAAAATATAGTTTTTAAAATAA
2849624 TTTTGAAAACGTATATAA
1 TTTTGAAAAC-TATATAA
2849642 TTTTCTAAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
34 9 0.22
35 23 0.56
36 9 0.22
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (36 bp):
TTTTGAAAACTATATAAAATATAGTTTTTAAAATAA
Found at i:2849747 original size:20 final size:20
Alignment explanation
Indices: 2849711--2849748 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2849701 TATATTATTA
**
2849711 TTATTTATTTTCTTTTTTAT
1 TTATTTATTTTAATTTTTAT
2849731 TTATTTATTTTAATTTTT
1 TTATTTATTTTAATTTTT
2849749 GTTGTCAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (20 bp):
TTATTTATTTTAATTTTTAT
Found at i:2850777 original size:3 final size:3
Alignment explanation
Indices: 2850769--2850829 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
2850759 TATATATATA
*
2850769 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2850817 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
2850830 TTCTCCTTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2854852 original size:27 final size:27
Alignment explanation
Indices: 2854822--2854882 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
2854812 ATTTAAGTAA
2854822 GGAGTAAAATTGATATTTGAAAACTTT
1 GGAGTAAAATTGATATTTGAAAACTTT
2854849 GGAGTAAAATTGATATTTGAAAACTTT
1 GGAGTAAAATTGATATTTGAAAACTTT
2854876 GGAGTAA
1 GGAGTAA
2854883 TATTTGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (27 bp):
GGAGTAAAATTGATATTTGAAAACTTT
Found at i:2857307 original size:20 final size:20
Alignment explanation
Indices: 2857282--2857335 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2857272 TAAACCCGAT
*
2857282 AGGGGTATCGGTACCCCCCA
1 AGGGGTATCGATACCCCCCA
* *
2857302 AGGGGTATCGATACCCCTCG
1 AGGGGTATCGATACCCCCCA
2857322 AGGGGTATCGATAC
1 AGGGGTATCGATAC
2857336 ACATTCAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (20 bp):
AGGGGTATCGATACCCCCCA
Found at i:2862919 original size:20 final size:21
Alignment explanation
Indices: 2862877--2862919 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
2862867 ACTAAAATTG
* * *
2862877 ATATTTGAAAATTTTGGAGTA
1 ATATTTGAAAATATTCGAATA
2862898 ATATTTG-AAATATTCGAATA
1 ATATTTGAAAATATTCGAATA
2862918 AT
1 AT
2862920 GGAATCGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (21 bp):
ATATTTGAAAATATTCGAATA
Found at i:2862960 original size:19 final size:19
Alignment explanation
Indices: 2862922--2862961 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2862912 CGAATAATGG
* *
2862922 AATCGAATATAATATTTTA
1 AATCGAATATAAAATCTTA
2862941 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
2862960 AA
1 AA
2862962 ATTACTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:2866644 original size:16 final size:16
Alignment explanation
Indices: 2866623--2866653 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2866613 AAGAGCAAAA
*
2866623 CCTTAAACCCTTAAAT
1 CCTTAAACCATTAAAT
2866639 CCTTAAACCATTAAA
1 CCTTAAACCATTAAA
2866654 GACCTTAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (16 bp):
CCTTAAACCATTAAAT
Found at i:2878685 original size:113 final size:113
Alignment explanation
Indices: 2878478--2878704 Score: 296
Period size: 113 Copynumber: 2.0 Consensus size: 113
2878468 TGTTGTTTAA
* * * * *
2878478 TATTGTTCTAGACTTAATATTGTGGTTTGAGTCTTAAGATTTGACACTTTAATATTATGGTTTGT
1 TATTATTCTAGACTCAATATTGTGGTCTGAATCTTAAGATTTGACACTTTAATATTATGGATTGT
2878543 TTATAGATTTTATTATTTGACTTAATATTATGGTTTATTTATGGATTT
66 TTATAGATTTTATTATTTGACTTAATATTATGGTTTATTTATGGATTT
* * * * *
2878591 TATTATTCTAGAGTCAATATTGTGGTCTGAATCTTGAGATTTGATATTTTAATATTGTGGATTGT
1 TATTATTCTAGACTCAATATTGTGGTCTGAATCTTAAGATTTGACACTTTAATATTATGGATTGT
* * * *
2878656 TTATAGATTTTGTTGTTCTAGA-TT-TTATTATGGTTTGTTTATGGATTT
66 TTATAGATTTTATTATT-T-GACTTAATATTATGGTTTATTTATGGATTT
2878704 T
1 T
2878705 CTATAAAGTA
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
113 93 0.95
114 3 0.03
115 2 0.02
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.53
Consensus pattern (113 bp):
TATTATTCTAGACTCAATATTGTGGTCTGAATCTTAAGATTTGACACTTTAATATTATGGATTGT
TTATAGATTTTATTATTTGACTTAATATTATGGTTTATTTATGGATTT
Found at i:2878765 original size:19 final size:20
Alignment explanation
Indices: 2878717--2878769 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
2878707 ATAAAGTATT
*
2878717 AAATTTATTTATAATCATTTT
1 AAATTTATTTATAA-CATTTA
* *
2878738 ACATCTATTTATAA-ATTTA
1 AAATTTATTTATAACATTTA
2878757 AAATTTATTTATA
1 AAATTTATTTATA
2878770 TGTCATACCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTATTTATAACATTTA
Found at i:2879256 original size:77 final size:77
Alignment explanation
Indices: 2879171--2879324 Score: 254
Period size: 77 Copynumber: 2.0 Consensus size: 77
2879161 TATTTTTTAT
* * * * **
2879171 CTAACCATGTAGTGACTTTTGTCATAATCTAATTTGAGATTAAATTTATTTTAATTGAATTATAT
1 CTAACCATGTAGTGACATGTGCCACAATCTAATTAAAGATTAAATTTATTTTAATTGAATTATAT
2879236 TAACCAAATTGA
66 TAACCAAATTGA
2879248 CTAACCATGTAGTGACATGTGCCACAATCTAATTAAAGATTAAATTTATTTTAATTGAATTATAT
1 CTAACCATGTAGTGACATGTGCCACAATCTAATTAAAGATTAAATTTATTTTAATTGAATTATAT
2879313 TAACCAAATTGA
66 TAACCAAATTGA
2879325 TAGAATATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (77 bp):
CTAACCATGTAGTGACATGTGCCACAATCTAATTAAAGATTAAATTTATTTTAATTGAATTATAT
TAACCAAATTGA
Found at i:2880855 original size:30 final size:30
Alignment explanation
Indices: 2880795--2880855 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2880785 ATCGGTTTGG
* *
2880795 TCAAAATAGGTACATAAATTATATTTTTTT
1 TCAAAATAGGTACATAAAGTATATTATTTT
*
2880825 TCAAAATAGGTACCTAAAGTAT-TTAATTTT
1 TCAAAATAGGTACATAAAGTATATT-ATTTT
2880855 T
1 T
2880856 TTAACCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (30 bp):
TCAAAATAGGTACATAAAGTATATTATTTT
Found at i:2880966 original size:28 final size:26
Alignment explanation
Indices: 2880935--2881022 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 26
2880925 TAATTTACGC
2880935 ACCTATTTTGACATAAAATACTTTAGAT
1 ACCTATTTTGACA-AAAATACTTTAG-T
2880963 ACCTATTTTGACTAAAAAGATAACTTTAGT
1 ACCTATTTTGAC--AAAA-AT-ACTTTAGT
**
2880993 ATTTATTTTGACCAAAAATACTTTAAGT
1 ACCTATTTTGA-CAAAAATACTTT-AGT
2881021 AC
1 AC
2881023 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
27 5 0.10
28 18 0.35
29 7 0.14
30 13 0.25
31 8 0.16
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.39
Consensus pattern (26 bp):
ACCTATTTTGACAAAAATACTTTAGT
Found at i:2882090 original size:30 final size:29
Alignment explanation
Indices: 2881984--2882295 Score: 172
Period size: 30 Copynumber: 10.6 Consensus size: 29
2881974 TTAATTTTAC
** *
2881984 ATCTTAACATTACTAATATATTTTATTTTT
1 ATCTTAAC-TTAAAAATATATTTTATTCTT
* **
2882014 ATATTAACTTATTCAATATATTTTATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* *
2882044 GTCTTAA-TCTAAAAATATATTTTAGTCTTT
1 ATCTTAACT-TAAAAATATATTTTATTC-TT
* *
2882074 ATCTTAACTTAGAAATATATTTTATTCTC
1 ATCTTAACTTAAAAATATATTTTATTCTT
** * * *
2882103 ATCTTAACTTGTTACATAAATTATATTCTT
1 ATCTTAACTT-AAAAATATATTTTATTCTT
* * * * *
2882133 AACTT-ACATTATTAAATATATTCTATTATC
1 ATCTTAAC-TTA-AAAATATATTTTATTCTT
* * * *
2882163 ATATTAAATTATTAAACATGA--TTAGTTCTT
1 ATCTTAACTTA-AAAATAT-ATTTTA-TTCTT
* *
2882193 ATTTTAACTTAAAACATATCTTTTATTCTT
1 ATCTTAACTTAAAA-ATATATTTTATTCTT
2882223 ATCTTAACTTAAAAATATATTTTTATT-TT
1 ATCTTAACTTAAAAATATA-TTTTATTCTT
* * * *
2882252 AACTT--C-AAAAAATATATTATATTTTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* *
2882278 ATCTTAAATTTAAAATAT
1 ATCTTAACTTAAAAATAT
2882296 TATCAGAATA
Statistics
Matches: 217, Mismatches: 47, Indels: 37
0.72 0.16 0.12
Matches are distributed among these distances:
25 6 0.03
26 15 0.07
27 1 0.00
29 51 0.24
30 138 0.64
31 6 0.03
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTCTT
Found at i:2882108 original size:59 final size:59
Alignment explanation
Indices: 2881998--2882109 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
2881988 TAACATTACT
* ** **
2881998 AATATATTTTATTTTTATATTAACTTATTCAATATATTTTATTCTTGTCTTAATCTAAA
1 AATATATTTTATCTTTATATTAACTTATGAAATATATTTTATTCTCATCTTAATCTAAA
*
2882057 AATATATTTTAGTCTTTATCTTAACTTA-GAAATATATTTTATTCTCATCTTAA
1 AATATATTTTA-TCTTTATATTAACTTATGAAATATATTTTATTCTCATCTTAA
2882110 CTTGTTACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 32 0.70
60 14 0.30
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.54
Consensus pattern (59 bp):
AATATATTTTATCTTTATATTAACTTATGAAATATATTTTATTCTCATCTTAATCTAAA
Found at i:2882248 original size:24 final size:25
Alignment explanation
Indices: 2882216--2882269 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
2882206 ACATATCTTT
2882216 TATTCTTATCTTAACTT-AAAAATA
1 TATTCTTATCTTAACTTAAAAAATA
* *
2882240 TATTTTTATTTTAACTTCAAAAAATA
1 TATTCTTATCTTAACTT-AAAAAATA
2882266 TATT
1 TATT
2882270 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 15 0.58
26 11 0.42
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTCTTATCTTAACTTAAAAAATA
Found at i:2882277 original size:26 final size:24
Alignment explanation
Indices: 2882226--2882285 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
2882216 TATTCTTATC
*
2882226 TTAACTTAAAAATATATTTTTATT
1 TTAACTTAAAAATATATTTATATT
2882250 TTAACTTCAAAAA-ATATATTATATTT
1 TTAACTT-AAAAATATAT-TTATA-TT
*
2882276 TTATCTTAAA
1 TTAACTTAAA
2882286 TTTAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 11 0.35
25 12 0.39
26 8 0.26
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (24 bp):
TTAACTTAAAAATATATTTATATT
Found at i:2882293 original size:55 final size:54
Alignment explanation
Indices: 2882191--2882295 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 54
2882181 TGATTAGTTC
* * * *
2882191 TTATTTTAACTTAAAACATATCTTTTATTCTTATCTTAACTTAAAAATATATTT
1 TTATTTTAACTTAAAAAATATATTATATTCTTATCTTAAATTAAAAATATATTT
* *
2882245 TTATTTTAACTTCAAAAAATATATTATATTTTTATCTTAAATTTAAAATAT
1 TTATTTTAACTT-AAAAAATATATTATATTCTTATCTTAAATTAAAAATAT
2882296 TATCAGAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 12 0.27
55 32 0.73
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (54 bp):
TTATTTTAACTTAAAAAATATATTATATTCTTATCTTAAATTAAAAATATATTT
Found at i:2882452 original size:29 final size:29
Alignment explanation
Indices: 2882317--2882475 Score: 144
Period size: 30 Copynumber: 5.4 Consensus size: 29
2882307 CATATAAATA
* * *
2882317 TTTAAGTTAAGATAAGAGTAAATTGTATT
1 TTTAAGTTAAGATAAGAATAAAATATATT
* * *
2882346 TTTAAATTTAAGATAAGATTAAAACATATTT
1 TTT-AAGTTAAGATAAGAATAAAATATA-TT
* *
2882377 TTTAAATTAAAATAAGAATAAAATATATT
1 TTTAAGTTAAGATAAGAATAAAATATATT
* * * *
2882406 TTTAGGTTATGAAAAAAATAAAATATATT
1 TTTAAGTTAAGATAAGAATAAAATATATT
*
2882435 TAATAAGTTAAGATAA-AA-AAAATAT-TT
1 T-TTAAGTTAAGATAAGAATAAAATATATT
2882462 TTTAATGTTAAGAT
1 TTTAA-GTTAAGAT
2882476 GTAAAATTAA
Statistics
Matches: 106, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
26 3 0.03
27 11 0.10
28 7 0.07
29 31 0.29
30 49 0.46
31 5 0.05
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTAAGTTAAGATAAGAATAAAATATATT
Found at i:2882455 original size:27 final size:28
Alignment explanation
Indices: 2882425--2882492 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
2882415 TGAAAAAAAT
2882425 AAAATATATTTAATAA-GTTAAGATAAA
1 AAAATATATTTAATAATGTTAAGATAAA
** **
2882452 AAAA-ATATTTTTTAATGTTAAGATGTA
1 AAAATATATTTAATAATGTTAAGATAAA
*
2882479 AAATTA-ATTTAATA
1 AAAATATATTTAATA
2882493 TATGAATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
26 9 0.28
27 22 0.69
28 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (28 bp):
AAAATATATTTAATAATGTTAAGATAAA
Found at i:2882461 original size:26 final size:27
Alignment explanation
Indices: 2882425--2882475 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
2882415 TGAAAAAAAT
*
2882425 AAAATATATTTAATAA-GTTAAGATAA
1 AAAAAATATTTAATAATGTTAAGATAA
**
2882451 AAAAAATATTTTTTAATGTTAAGAT
1 AAAAAATATTTAATAATGTTAAGAT
2882476 GTAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (27 bp):
AAAAAATATTTAATAATGTTAAGATAA
Found at i:2884103 original size:10 final size:10
Alignment explanation
Indices: 2884088--2884112 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2884078 AGTTTTTCAT
2884088 TTTTCTTTTA
1 TTTTCTTTTA
2884098 TTTTCTTTTA
1 TTTTCTTTTA
2884108 TTTTC
1 TTTTC
2884113 AAGCTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:2884110 original size:21 final size:22
Alignment explanation
Indices: 2884059--2884111 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
2884049 TAAAGTTTTC
2884059 TCTTTTATTTTACTTTTCAAGT
1 TCTTTTATTTTACTTTTCAAGT
* * **
2884081 T-TTTCATTTTTCTTTT-ATTT
1 TCTTTTATTTTACTTTTCAAGT
2884101 TCTTTTATTTT
1 TCTTTTATTTT
2884112 CAAGCTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 3 0.12
21 21 0.84
22 1 0.04
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (22 bp):
TCTTTTATTTTACTTTTCAAGT
Found at i:2884292 original size:18 final size:19
Alignment explanation
Indices: 2884266--2884302 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2884256 TTGCGCTTAT
*
2884266 TTTTTAAAATCAAA-ATAG
1 TTTTCAAAATCAAAGATAG
2884284 TTTTCAAAATCAAAGATAG
1 TTTTCAAAATCAAAGATAG
2884303 ACTTTGGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (19 bp):
TTTTCAAAATCAAAGATAG
Found at i:2890052 original size:20 final size:20
Alignment explanation
Indices: 2889967--2890045 Score: 122
Period size: 20 Copynumber: 3.9 Consensus size: 20
2889957 AATCAGAATG
2889967 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATT-CCC
*
2889988 CCCAAGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
2890008 CCCAGGGGGTACTGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
2890028 CCCAGGGGGTACCGATTC
1 CCCAGGGGGTACAGATTC
2890046 TTCCCAGAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
20 38 0.70
21 16 0.30
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.16
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:2891422 original size:22 final size:22
Alignment explanation
Indices: 2891381--2891447 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
2891371 CTCGTATAAA
2891381 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
2891404 TGCACCAAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
2891426 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2891448 GATGTCCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 30 0.73
23 11 0.27
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2893165 original size:21 final size:21
Alignment explanation
Indices: 2893141--2893185 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2893131 TCTTGTTCGT
* *
2893141 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2893162 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2893183 TTG
1 TTG
2893186 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2896365 original size:22 final size:22
Alignment explanation
Indices: 2896324--2896390 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
2896314 CTCGTATAAA
2896324 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
2896347 TGCACCAAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
2896369 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2896391 GATGTCCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 30 0.73
23 11 0.27
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2898102 original size:21 final size:21
Alignment explanation
Indices: 2898078--2898122 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2898068 TCTTGTTCGT
* *
2898078 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2898099 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2898120 TTG
1 TTG
2898123 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2899982 original size:20 final size:20
Alignment explanation
Indices: 2899950--2899997 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2899940 ATAATTTGAT
*
2899950 TTTTG-AAAGCAAAA-GTTAA
1 TTTTGAAAAGCAAAATG-AAA
*
2899969 TTTTGAAAATCAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
2899989 TTTTGAAAA
1 TTTTGAAAA
2899998 ATAATTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 19 0.76
21 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:2901468 original size:22 final size:21
Alignment explanation
Indices: 2901426--2901469 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2901416 AATCAGATTG
*
2901426 CCCAGGGGATACAGATTCCCC
1 CCCAGGGGATACAGATCCCCC
*
2901447 CCCAGGGGGTACAGAATCCCCC
1 CCCAGGGGATACAG-ATCCCCC
2901469 C
1 C
2901470 AGTGGTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.23, C:0.41, G:0.25, T:0.11
Consensus pattern (21 bp):
CCCAGGGGATACAGATCCCCC
Found at i:2901469 original size:20 final size:20
Alignment explanation
Indices: 2901426--2901527 Score: 107
Period size: 20 Copynumber: 5.1 Consensus size: 20
2901416 AATCAGATTG
*
2901426 CCCAGGGGATACAGATTCCCC
1 CCCAGGGGGTACAGATT-CCC
*
2901447 CCCAGGGGGTACAGAATCCC
1 CCCAGGGGGTACAGATTCCC
* * * *
2901467 CCCAGTGGTTTC-GTTTCCC
1 CCCAGGGGGTACAGATTCCC
* *
2901486 CCCAGGGGGAACAGATCCCC
1 CCCAGGGGGTACAGATTCCC
*
2901506 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
2901526 CC
1 CC
2901528 TGTCTAACAG
Statistics
Matches: 64, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
19 13 0.20
20 36 0.56
21 15 0.23
ACGTcount: A:0.19, C:0.39, G:0.26, T:0.16
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:2902531 original size:20 final size:20
Alignment explanation
Indices: 2902502--2902544 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2902492 ATTCCACCAC
*
2902502 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2902522 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
2902542 ATG
1 ATG
2902545 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2907714 original size:20 final size:20
Alignment explanation
Indices: 2907685--2907727 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2907675 ATTCCACCAC
*
2907685 ATGCAACTATATGCTCATAA
1 ATGCAACTATATGATCATAA
* *
2907705 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCATAA
2907725 ATG
1 ATG
2907728 GGCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCATAA
Found at i:2909644 original size:6 final size:6
Alignment explanation
Indices: 2909633--2909672 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
2909623 ATTTTGTTAC
*
2909633 ATTTTT ATTTTT ATTTTT ATTTTT ACTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
2909673 CGATTAAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:2912684 original size:12 final size:12
Alignment explanation
Indices: 2912669--2912693 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2912659 GAAAAAAGAC
2912669 ATGGAAAACAAA
1 ATGGAAAACAAA
2912681 ATGGAAAACAAA
1 ATGGAAAACAAA
2912693 A
1 A
2912694 CAATAAAAAT
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:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (12 bp):
ATGGAAAACAAA
Found at i:2916782 original size:2 final size:2
Alignment explanation
Indices: 2916775--2916813 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2916765 GGGTGTTACA
2916775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2916814 ATTTTAAGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2917961 original size:29 final size:29
Alignment explanation
Indices: 2917896--2917961 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
2917886 AGGCCCCTAT
* * **
2917896 TTTTTTTATCTTTGTAATTAGGATCTTTG
1 TTTTTTTATCATTATAATTAGGATCTTAA
* *
2917925 TTTGTTTATCATTATAATTAGGCTCTTAA
1 TTTTTTTATCATTATAATTAGGATCTTAA
2917954 TTTTTTTA
1 TTTTTTTA
2917962 AATCTTATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.61
Consensus pattern (29 bp):
TTTTTTTATCATTATAATTAGGATCTTAA
Found at i:2917976 original size:43 final size:42
Alignment explanation
Indices: 2917929--2918116 Score: 161
Period size: 42 Copynumber: 4.4 Consensus size: 42
2917919 TCTTTGTTTG
*
2917929 TTTATCATTATAATT-AGGCTCTTAATTTTTTTAAATCTTATTT
1 TTTATCTTTATAATTGAGGCTCTTAA-TTTTTT-AATCTTATTT
* * *
2917972 TTTATCTTTATAACTGA-GATTTTAATTTTATTGAATCTTACTTT
1 TTTATCTTTATAATTGAGGCTCTTAATTTT-TT-AATCTTA-TTT
* * *
2918016 TTTATATTTATAATTGAAG-TCTCTAATTTTTTCAATC--CTTT
1 TTTATCTTTATAATTGAGGCTCT-TAATTTTTT-AATCTTATTT
* * * *
2918057 TTTACTTTTTATAATTGAGGCCCTTAATTTTTTAATCCTACTT
1 TTTA-TCTTTATAATTGAGGCTCTTAATTTTTTAATCTTATTT
*
2918100 TTTAACTTTATAATTGA
1 TTTATCTTTATAATTGA
2918117 TTCCCTTAAG
Statistics
Matches: 119, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
41 11 0.09
42 37 0.31
43 36 0.30
44 27 0.23
45 8 0.07
ACGTcount: A:0.27, C:0.11, G:0.06, T:0.56
Consensus pattern (42 bp):
TTTATCTTTATAATTGAGGCTCTTAATTTTTTAATCTTATTT
Found at i:2918123 original size:42 final size:43
Alignment explanation
Indices: 2917936--2918270 Score: 140
Period size: 45 Copynumber: 7.7 Consensus size: 43
2917926 TTGTTTATCA
* * * * * *
2917936 TTATAATT-AGGCTCTTAATTTTTTTAAATCTTATTTTTTATCT
1 TTATAATTGAGTCCCTTAA-TTTTTTCAATCCTACTTTTTAACT
* * * *
2917979 TTATAACTGAGAT--TTTAATTTTATTGAATCTTACTTTTTTATA-T
1 TTATAATTGAG-TCCCTTAATTTT-TTCAATCCTAC-TTTTTA-ACT
*
2918023 TTATAATTGAAGTCTC-TAATTTTTTCAATCCT--TTTTT-ACTTT
1 TTATAATTG-AGTCCCTTAATTTTTTCAATCCTACTTTTTAAC--T
*
2918065 TTATAATTGAGGCCCTTAATTTTTT-AATCCTACTTTTTAACT
1 TTATAATTGAGTCCCTTAATTTTTTCAATCCTACTTTTTAACT
* * * * *
2918107 TTATAATTGATTCCCTTAAGTTTTTCAAT-TTCACTTTCTACCT
1 TTATAATTGAGTCCCTTAATTTTTTCAATCCT-ACTTTTTAACT
* * * * * *
2918150 TTACAATTGAAG-CCCCTAAGTTTTCTT-AAT-CTCAATCTCTACCT
1 TTATAATTG-AGTCCCTTAA-TTTT-TTCAATCCT-ACTTTTTAACT
* * * * *
2918194 TTATAATTGAAGCCCCTTAAGTTGTTTCAAT-CTCAATTTCTACCT
1 TTATAATTG-AGTCCCTTAA-TTTTTTCAATCCT-ACTTTTTAACT
* *
2918239 TTATAATTGAATCCCCTTAAGTTGTTTCAATC
1 TTATAATTGAGT-CCCTTAA-TTTTTTCAATC
2918271 TCACTTTCTA
Statistics
Matches: 237, Mismatches: 31, Indels: 45
0.76 0.10 0.14
Matches are distributed among these distances:
39 1 0.00
41 15 0.06
42 47 0.20
43 51 0.22
44 59 0.25
45 64 0.27
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (43 bp):
TTATAATTGAGTCCCTTAATTTTTTCAATCCTACTTTTTAACT
Found at i:2918230 original size:45 final size:44
Alignment explanation
Indices: 2918022--2918281 Score: 239
Period size: 45 Copynumber: 6.0 Consensus size: 44
2918012 CTTTTTTATA
* * * * * *
2918022 TTTATAATTGAAGTCTC-TAATTTTTTCAATC-C-TTTTTTACTT
1 TTTATAATTGAAGCCCCTTAAGTTTTTCAATCTCAATTTCTAC-C
* * * * *
2918064 TTTATAATTG-AGGCCCTTAA-TTTTTTAATC-CTACTTTTTAAC
1 TTTATAATTGAAGCCCCTTAAGTTTTTCAATCTC-AATTTCTACC
** * *
2918106 TTTATAATTG-ATTCCCTTAAGTTTTTCAATTTCACTTTCTACC
1 TTTATAATTGAAGCCCCTTAAGTTTTTCAATCTCAATTTCTACC
* * *
2918149 TTTACAATTGAAGCCCC-TAAGTTTTCTTAATCTCAATCTCTACC
1 TTTATAATTGAAGCCCCTTAAGTTTT-TCAATCTCAATTTCTACC
2918193 TTTATAATTGAAGCCCCTTAAGTTGTTTCAATCTCAATTTCTACC
1 TTTATAATTGAAGCCCCTTAAGTT-TTTCAATCTCAATTTCTACC
* *
2918238 TTTATAATTGAATCCCCTTAAGTTGTTTCAATCTCACTTTCTAC
1 TTTATAATTGAAGCCCCTTAAGTT-TTTCAATCTCAATTTCTAC
2918282 ATTTTCTACC
Statistics
Matches: 185, Mismatches: 24, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
41 14 0.08
42 31 0.17
43 39 0.21
44 35 0.19
45 64 0.35
46 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (44 bp):
TTTATAATTGAAGCCCCTTAAGTTTTTCAATCTCAATTTCTACC
Found at i:2918933 original size:2 final size:2
Alignment explanation
Indices: 2918926--2918950 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2918916 AAATTTTTAA
2918926 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2918951 AATGTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2919535 original size:16 final size:17
Alignment explanation
Indices: 2919502--2919535 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2919492 TTAATTATTC
2919502 AACCAAAACTCTTTAAA
1 AACCAAAACTCTTTAAA
*
2919519 AACCCAAACTC-TTAAA
1 AACCAAAACTCTTTAAA
2919535 A
1 A
2919536 TCTCTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (17 bp):
AACCAAAACTCTTTAAA
Found at i:2921135 original size:125 final size:127
Alignment explanation
Indices: 2921000--2921258 Score: 450
Period size: 125 Copynumber: 2.0 Consensus size: 127
2920990 TATACTCATG
2921000 TAACATCGAATATAAGATTAATTATATTCGGGTGGTTCAAATGCCTTAAAATATTGTATGTTCTT
1 TAACATCGAATATAAGATTAATTATATTCGGGTGGTTCAAATGCCTTAAAATATTGTATGTTCTT
2921065 TTGTTTTAAATC-T-AGATAATGGGTAATTTTCATGTAATTTGTTTAATTATATATTTTTGT
66 TTGTTTTAAATCATGAGATAATGGGTAATTTTCATGTAATTTGTTTAATTATATATTTTTGT
2921125 TAACATCGAATATAAGATTAATTATATTCGGGTGGTTCAAATGCCTTAAAATATTGTATGTTCTT
1 TAACATCGAATATAAGATTAATTATATTCGGGTGGTTCAAATGCCTTAAAATATTGTATGTTCTT
2921190 TTGTTTTAAATCTAGATTATGAGATAATGGGTAATTTTCATGTAATTTGTTTAATTATATATTTT
66 TTGTTTTAAATC------ATGAGATAATGGGTAATTTTCATGTAATTTGTTTAATTATATATTTT
2921255 TGT
125 TGT
2921258 T
1 T
2921259 GTAGTAATTT
Statistics
Matches: 126, Mismatches: 0, Indels: 8
0.94 0.00 0.06
Matches are distributed among these distances:
125 77 0.61
132 1 0.01
133 48 0.38
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (127 bp):
TAACATCGAATATAAGATTAATTATATTCGGGTGGTTCAAATGCCTTAAAATATTGTATGTTCTT
TTGTTTTAAATCATGAGATAATGGGTAATTTTCATGTAATTTGTTTAATTATATATTTTTGT
Found at i:2922006 original size:159 final size:159
Alignment explanation
Indices: 2921717--2922034 Score: 636
Period size: 159 Copynumber: 2.0 Consensus size: 159
2921707 ATTTTAGAAG
2921717 AAAGATTTCTTGAAACGTATCTCCTCATGTCACGTCATGTCAATATTTCCCCAAAAAGCACGTTT
1 AAAGATTTCTTGAAACGTATCTCCTCATGTCACGTCATGTCAATATTTCCCCAAAAAGCACGTTT
2921782 TAAGGAATACGCCTCTTGTCCACCTAAATATAGGTACGTTTTACGTAATGTGTCTTATAAAAAAT
66 TAAGGAATACGCCTCTTGTCCACCTAAATATAGGTACGTTTTACGTAATGTGTCTTATAAAAAAT
2921847 GGTAATAAAATTTAGAAAAATGATATTGA
131 GGTAATAAAATTTAGAAAAATGATATTGA
2921876 AAAGATTTCTTGAAACGTATCTCCTCATGTCACGTCATGTCAATATTTCCCCAAAAAGCACGTTT
1 AAAGATTTCTTGAAACGTATCTCCTCATGTCACGTCATGTCAATATTTCCCCAAAAAGCACGTTT
2921941 TAAGGAATACGCCTCTTGTCCACCTAAATATAGGTACGTTTTACGTAATGTGTCTTATAAAAAAT
66 TAAGGAATACGCCTCTTGTCCACCTAAATATAGGTACGTTTTACGTAATGTGTCTTATAAAAAAT
2922006 GGTAATAAAATTTAGAAAAATGATATTGA
131 GGTAATAAAATTTAGAAAAATGATATTGA
2922035 CATGTAATAT
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 159 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (159 bp):
AAAGATTTCTTGAAACGTATCTCCTCATGTCACGTCATGTCAATATTTCCCCAAAAAGCACGTTT
TAAGGAATACGCCTCTTGTCCACCTAAATATAGGTACGTTTTACGTAATGTGTCTTATAAAAAAT
GGTAATAAAATTTAGAAAAATGATATTGA
Found at i:2923356 original size:12 final size:12
Alignment explanation
Indices: 2923319--2923356 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2923309 TTGTTAGTAA
2923319 TTAATTAATTA-T
1 TTAATT-ATTATT
2923331 TTAATTATTATT
1 TTAATTATTATT
*
2923343 TTATTTATTATT
1 TTAATTATTATT
2923355 TT
1 TT
2923357 TTTGCAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTAATTATTATT
Found at i:2923359 original size:15 final size:16
Alignment explanation
Indices: 2923327--2923358 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2923317 AATTAATTAA
2923327 TTATTTAATTATTATT
1 TTATTTAATTATTATT
2923343 TTATTT-ATTATT-TT
1 TTATTTAATTATTATT
2923357 TT
1 TT
2923359 TGCAGATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 6 0.38
16 6 0.38
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTATTTAATTATTATT
Found at i:2925674 original size:35 final size:34
Alignment explanation
Indices: 2925618--2925711 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 34
2925608 TCATTAAATA
*
2925618 CTTACTTTATTTTGTTAATTTTGTTGGA-TTTTT
1 CTTAATTTATTTTGTTAATTTTGTTGGACTTTTT
* *
2925651 TTTAAAATTTATTTTGTTTATTTTGTTGGACTTTTT
1 CTT--AATTTATTTTGTTAATTTTGTTGGACTTTTT
*
2925687 CTTAATTTATTTTGATAATTTTGTT
1 CTTAATTTATTTTGTTAATTTTGTT
2925712 TATTGTCATT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
33 2 0.04
34 20 0.38
35 23 0.44
36 7 0.13
ACGTcount: A:0.19, C:0.04, G:0.11, T:0.66
Consensus pattern (34 bp):
CTTAATTTATTTTGTTAATTTTGTTGGACTTTTT
Found at i:2926969 original size:23 final size:23
Alignment explanation
Indices: 2926943--2927006 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2926933 CAGCTCAAAT
2926943 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
2926966 AATTGCACCGGAGTGACGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
2926989 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
2927007 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:2927198 original size:98 final size:101
Alignment explanation
Indices: 2927017--2927234 Score: 379
Period size: 98 Copynumber: 2.2 Consensus size: 101
2927007 TATAATAATG
2927017 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCA-ATACA-ATACTAGAGATCAAGTATGTGTCT
2927082 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
64 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
* *
2927120 TCCCGAAGGACCGCATATCACTCCTTAAGAATC-ATAC-ATA-TAGGGATCAAGTATGTGTCTCA
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCAATACAATACTAGAGATCAAGTATGTGTCTCA
2927182 CCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CCAGACTTCACACATGTTCCAAAGAATACATATATA
2927218 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
2927235 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
98 73 0.65
99 3 0.03
101 4 0.04
103 32 0.29
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (101 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCAATACAATACTAGAGATCAAGTATGTGTCTCA
CCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:2928097 original size:64 final size:64
Alignment explanation
Indices: 2927984--2928212 Score: 225
Period size: 64 Copynumber: 3.5 Consensus size: 64
2927974 TAATGAAGGT
* * *
2927984 ATGCATCGATGCACTACTGACTGATGCATC-AGTGCATAAAATGTATTCGATGTTGT-ATTATTA
1 ATGCATCGATGCACTACT---T-ATGCATCGA-TGCACAAATTGCATTCGATGTT-TCATTATTA
*
2928047 CTGGG
60 ATGGG
* * *
2928052 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
* **
2928116 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCATTATTAATGGG
** *
2928179 AGTGCATCGATGCACTACCAATACATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
2928213 CTTCAAACAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
63 3 0.02
64 113 0.81
65 7 0.05
67 1 0.01
68 15 0.11
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:2933206 original size:20 final size:20
Alignment explanation
Indices: 2933073--2933209 Score: 127
Period size: 20 Copynumber: 6.8 Consensus size: 20
2933063 AAATGACCAA
*
2933073 CAAATTCGCAACGCGAATTTGT
1 CAAATTCGCAACGCG-A-TAGT
*
2933095 -AAATT-GCAACACAGA-AGT
1 CAAATTCGCAACGC-GATAGT
* *
2933113 CAAATTCGCAATGCGATAGC
1 CAAATTCGCAACGCGATAGT
* * *
2933133 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGT
* * *
2933153 CAAATTCGCAACACAAAAAGT
1 CAAATTCGCAACGC-GATAGT
2933174 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
2933194 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
2933210 AACACAATAT
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
18 2 0.02
19 7 0.07
20 63 0.65
21 25 0.26
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:2935416 original size:41 final size:40
Alignment explanation
Indices: 2935299--2935426 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 40
2935289 AATTTGTAAA
* * * *
2935299 TCGCAACACAGAAGTCAAATTCGCAATGCGATAGACAAAT
1 TCGCAACACAAAAGTCAAATTTGCAACGCGATAGTCAAAT
** * * * * * * *
2935339 TCGCAATGCGATAGACAAATTTGCATCACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTTGCAACGCGATAGTCAAAT
2935379 TCGCAACACAAAAAGTCAAATTTGCAACGCGATAGTCAAAT
1 TCGCAACAC-AAAAGTCAAATTTGCAACGCGATAGTCAAAT
2935420 TCGCAAC
1 TCGCAAC
2935427 GCGAAACACA
Statistics
Matches: 65, Mismatches: 22, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
40 34 0.52
41 31 0.48
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.20
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTTGCAACGCGATAGTCAAAT
Found at i:2935427 original size:20 final size:20
Alignment explanation
Indices: 2935311--2935430 Score: 114
Period size: 20 Copynumber: 6.0 Consensus size: 20
2935301 GCAACACAGA
*
2935311 AGTCAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
2935331 AGACAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
* * * * * *
2935351 AGACAAATTTGCATCACAAA
1 AGTCAAATTCGCAACGCGAT
* * *
2935371 AGTCAAATTCGCAACACAAAA
1 AGTCAAATTCGCAACGC-GAT
*
2935392 AGTCAAATTTGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
2935412 AGTCAAATTCGCAACGCGA
1 AGTCAAATTCGCAACGCGA
2935431 AACACAATAT
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 66 0.79
21 18 0.21
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:2938685 original size:18 final size:18
Alignment explanation
Indices: 2938662--2938698 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2938652 CGAAATTTAT
2938662 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2938680 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2938698 A
1 A
2938699 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2940883 original size:3 final size:3
Alignment explanation
Indices: 2940875--2940984 Score: 141
Period size: 3 Copynumber: 37.0 Consensus size: 3
2940865 TATATATATT
*
2940875 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
2940923 TAA TAA TAA TAA T-A TTA TTA TTA TAT TAA TAA TAA TAA TTA TTA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2940970 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
2940985 ATAAATCAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 95 0.98
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2941363 original size:123 final size:123
Alignment explanation
Indices: 2941144--2941428 Score: 439
Period size: 123 Copynumber: 2.3 Consensus size: 123
2941134 TTCTTTTCTT
** * * * *
2941144 TCTTCAGATGAGTTCTTCTCATTATGAACTTTC-C-GCTAGGGATGATGTTAACCTATTTCCTTC
1 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATCTCCTTA
*
2941207 TGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC
66 TGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC
* * *
2941265 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTGCTTA
1 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATCTCCTTA
*
2941330 TGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCC
66 TGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC
* *
2941388 TCTTCAGATAAGTTCTTCTTATTATGAACTTTCTCTGGAAA
1 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
2941429 TGTCAATCCA
Statistics
Matches: 149, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
121 33 0.22
122 1 0.01
123 115 0.77
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (123 bp):
TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATCTCCTTA
TGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC
Found at i:2941609 original size:196 final size:197
Alignment explanation
Indices: 2941275--2941688 Score: 728
Period size: 196 Copynumber: 2.1 Consensus size: 197
2941265 TCTTCAGATG
* * *
2941275 AGTTCTTCTCATTATGAACTT-TCTCTGGAAAGGTTGATGCTAATCTATCTGCTTATGTGATAGA
1 AGTTCTTCTCATTATGAACTTCTCTCTGGAAAGGCTAATGCTAATATATCTGCTTATGTGATAGA
2941339 ATTATGCAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCCTCTTCAGATAAGTTCT
66 ATTATGCAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCCTCTTCAGATAAGTTCT
*
2941404 TCTTATTATGAACTTTCTCTGGAAATGTCAATCCATCAAATGATGAATTT-AACCAAAAGGTTGA
131 TCTTATTATGAACTTTCTCTGGAAATGTCAATCCATCAAATGATGAATTTGAA-CAAAAGGTTAA
2941468 ACA
195 ACA
* *
2941471 AGTTCTTCTCATTGTGAACTTCT-TCTGGGAAA-GCTAATGCTAATATATCTGCTTCTGTGATAG
1 AGTTCTTCTCATTATGAACTTCTCTCT-GGAAAGGCTAATGCTAATATATCTGCTTATGTGATAG
2941534 AATTATGCAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCCTCTTCAGATAAGTTC
65 AATTATGCAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCCTCTTCAGATAAGTTC
2941599 TTCTTATTATGAACTTTCTCTGGAAATGTCAATCCATCAAATGATGAATTTGAACAAAAGGTTAA
130 TTCTTATTATGAACTTTCTCTGGAAATGTCAATCCATCAAATGATGAATTTGAACAAAAGGTTAA
2941664 ACA
195 ACA
2941667 AGTTCTTCTCATTATGAACTTC
1 AGTTCTTCTCATTATGAACTTC
2941689 GTCTTCCTTC
Statistics
Matches: 208, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
196 200 0.96
197 8 0.04
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (197 bp):
AGTTCTTCTCATTATGAACTTCTCTCTGGAAAGGCTAATGCTAATATATCTGCTTATGTGATAGA
ATTATGCAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCCTCTTCAGATAAGTTCT
TCTTATTATGAACTTTCTCTGGAAATGTCAATCCATCAAATGATGAATTTGAACAAAAGGTTAAA
CA
Found at i:2941747 original size:113 final size:112
Alignment explanation
Indices: 2941541--2941878 Score: 482
Period size: 113 Copynumber: 3.0 Consensus size: 112
2941531 TAGAATTATG
* * * * *
2941541 CAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCC-TCTTCAGAT-AAGTTCTTCTT
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTC
* * *
2941604 ATTATGAACTTTCTCTGGAAATGTCAATCCATCAAATGATGAATTTGAA
65 ATTATGAACTCTATCTGGAAATGT-GATCCATCAAATGATGAATTTGAA
*
2941653 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCGTCTTCCTTCTTCAGATGAATTCTTCTCA
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
* * * *
2941718 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAA
66 TTATGAACTCTATCTGGAAATG-TGATCCATCAAATGATGAATTTGAA
2941766 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
* * *
2941831 TTATGAACTCTATCTGGTAATGTTGATCCATCAATTGATGGATTTGAA
66 TTATGAACTCTATCTGGAAATG-TGATCCATCAAATGATGAATTTGAA
2941879 TCTTTGCTAA
Statistics
Matches: 202, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
112 38 0.19
113 161 0.80
114 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (112 bp):
CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
TTATGAACTCTATCTGGAAATGTGATCCATCAAATGATGAATTTGAA
Found at i:2941814 original size:319 final size:315
Alignment explanation
Indices: 2941203--2941805 Score: 834
Period size: 319 Copynumber: 1.9 Consensus size: 315
2941193 AACCTATTTC
*
2941203 CTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
1 CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
* * **
2941268 TCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTGCTTATGT
66 TCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA-G-TGATGCTAATCCA-CTGC-TAAAT
* * * *
2941333 GATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCCTCTTCAGATA
127 GATAGAATTATGCAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCGTCTTCCTCTTCAGATA
* **** *
2941398 AGTTCTTCTTATTATGAACTTTCTCTGGAAATGTCAATCCATCAAATGATGAATTTAACCAAAAG
192 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGTCAATCCATCAAATGATGAATTTAACCAAAAG
* *
2941463 GTTGAACAAGTTCTTCTCATTGTGAACTTCTTCTGGGAAAGCTAATGCTAATATATCTG
257 GTTAAACAAGTTCTTCTCATTATGAACTTCTTCTGGGAAAGCTAATGCTAATATATCTG
*
2941522 CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTCCTCT
1 CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
*
2941587 TCAGATAAGTTCTTCTTATTATGAACTTTCTCTGGAAA-TG-T-C-AATCCA-T-C-AAATGAT-
66 TCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTGATGCTAATCCACTGCTAAATGATA
*
2941644 GAATT-TGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCGTCTTCCTTCTTCAGATGA
131 GAATTATG--CAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCGTCTTCC-TCTTCAGAT-A
* *
2941708 A-TTCTTCTCATTATGAACTCGAACTGGAAAAG-CTGATCCATCAAGTGATGAATTTGAA-CAAA
192 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGTC-AATCCATCAAATGATGAATTT-AACCAAA
2941770 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCT
255 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCT
2941806 TCCTTCTTCA
Statistics
Matches: 256, Mismatches: 22, Indels: 22
0.85 0.07 0.07
Matches are distributed among these distances:
306 2 0.01
307 5 0.02
308 44 0.17
309 91 0.36
310 5 0.02
311 1 0.00
313 5 0.02
314 1 0.00
315 1 0.00
316 2 0.01
319 99 0.39
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (315 bp):
CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
TCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTGATGCTAATCCACTGCTAAATGATA
GAATTATGCAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCGTCTTCCTCTTCAGATAAGTT
CTTCTCATTATGAACTCGAACTGGAAAAGTCAATCCATCAAATGATGAATTTAACCAAAAGGTTA
AACAAGTTCTTCTCATTATGAACTTCTTCTGGGAAAGCTAATGCTAATATATCTG
Found at i:2942829 original size:93 final size:93
Alignment explanation
Indices: 2942667--2942866 Score: 346
Period size: 93 Copynumber: 2.2 Consensus size: 93
2942657 TTCTTATTTC
* * *
2942667 TACTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATT
1 TACTATGAGCACATTCATCTTCCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATC
2942732 AGATAACTCAAAGAACACTTCCAGAAGA
66 AGATAACTCAAAGAACACTTCCAGAAGA
2942760 TACTATGAGCACATTCATCTTCCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATC
1 TACTATGAGCACATTCATCTTCCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATC
*
2942825 AGATAACTCAAAGAACACTTCCAGGAGA
66 AGATAACTCAAAGAACACTTCCAGAAGA
* *
2942853 TGCTATTAGCACAT
1 TACTATGAGCACAT
2942867 GGTATTTGTT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 101 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (93 bp):
TACTATGAGCACATTCATCTTCCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATC
AGATAACTCAAAGAACACTTCCAGAAGA
Found at i:2943911 original size:16 final size:17
Alignment explanation
Indices: 2943858--2943912 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
2943848 TTCATAGAAG
*
2943858 AATAAATTGAATTTTCGAA
1 AATAAATTGAATCTT--AA
2943877 AATAAATTGAATCTT-A
1 AATAAATTGAATCTTAA
2943893 AATAAATTGAA-CTTAA
1 AATAAATTGAATCTTAA
2943909 AATA
1 AATA
2943913 GATAGAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 3 0.09
16 17 0.50
19 14 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (17 bp):
AATAAATTGAATCTTAA
Found at i:2944236 original size:1 final size:1
Alignment explanation
Indices: 2944232--2944293 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
2944222 CTTGACCCCC
* * * * * * * *
2944232 TTTTTTTTTCTTTTTCTTTTTTTTTTCTTTCTTTTTTTCTTTCTTTTTTTTCTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2944294 CTTCTCTTCA
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:2944251 original size:11 final size:11
Alignment explanation
Indices: 2944231--2944301 Score: 72
Period size: 11 Copynumber: 6.3 Consensus size: 11
2944221 TCTTGACCCC
2944231 CTTTTT-TTTT
1 CTTTTTCTTTT
2944241 CTTTTTCTTTT
1 CTTTTTCTTTT
*
2944252 TTTTTTCTTTCT
1 CTTTTTCTTT-T
*
2944264 TTTTTTCTTTCTT
1 CTTTTTC-TT-TT
*
2944277 TTTTTTCTTTT
1 CTTTTTCTTTT
*
2944288 CTTTTTCTTCT
1 CTTTTTCTTTT
2944299 CTT
1 CTT
2944302 CAAGCATAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
10 6 0.11
11 27 0.50
12 10 0.19
13 10 0.19
14 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTCTTTT
Done.