Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003701.1 Hibiscus syriacus cultivar Beakdansim tig00007915_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: 316188
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:189088 original size:15 final size:15
Alignment explanation
Indices: 189070--189149 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 15
189060 TCATACGGCC
189070 AGAGGACTTAATGCT
1 AGAGGACTTAATGCT
* * *
189085 AGAGGCCTTACTGCC
1 AGAGGACTTAATGCT
*
189100 AGAGGACTTGATGCT
1 AGAGGACTTAATGCT
* * * * *
189115 AGAAGCCATACTGCC
1 AGAGGACTTAATGCT
*
189130 AGATGACTTAATGCT
1 AGAGGACTTAATGCT
189145 AGAGG
1 AGAGG
189150 CCTTGGGTTT
Statistics
Matches: 46, Mismatches: 19, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (15 bp):
AGAGGACTTAATGCT
Found at i:190710 original size:31 final size:31
Alignment explanation
Indices: 190667--190730 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
190657 TGGTGACTAC
*
190667 ATCTTAAATAAATAAAAACGAAAATGATCAT
1 ATCTTAAATAAATAAAAACGAAAATGACCAT
* * *
190698 ATCTTAATTAAATAAAAATGAAAGTGACCAT
1 ATCTTAAATAAATAAAAACGAAAATGACCAT
190729 AT
1 AT
190731 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (31 bp):
ATCTTAAATAAATAAAAACGAAAATGACCAT
Found at i:194536 original size:120 final size:120
Alignment explanation
Indices: 194323--194563 Score: 446
Period size: 120 Copynumber: 2.0 Consensus size: 120
194313 GTTTGTCCTT
194323 CCCCAGAACTCTGCCCAAACTGATCAGGTCCAGGATTTGATCCTTGCCGAAAACTCTGTTCATTG
1 CCCCAGAACTCTGCCCAAACTGATCAGGTCCAGGATTTGATCCTTGCCGAAAACTCTGTTCATTG
**
194388 GCAGGATTTGCCCCTCGCTCAAAGTTCTGCCCATAGCTAGGATTCGGTCCCTGCC
66 GCAGGATTCACCCCTCGCTCAAAGTTCTGCCCATAGCTAGGATTCGGTCCCTGCC
*
194443 CCCCAGAACTCTGCCCAAACTGATCAGGTCCAGGATTTGATCCTTTCCGAAAACTCTGTTCATTG
1 CCCCAGAACTCTGCCCAAACTGATCAGGTCCAGGATTTGATCCTTGCCGAAAACTCTGTTCATTG
*
194508 GCAGGATTCACCTCTCGCTCAAAGTTCTGCCCATAGCTAGGATTCGGTCCCTGCC
66 GCAGGATTCACCCCTCGCTCAAAGTTCTGCCCATAGCTAGGATTCGGTCCCTGCC
194563 C
1 C
194564 ATATCCAGGA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 117 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (120 bp):
CCCCAGAACTCTGCCCAAACTGATCAGGTCCAGGATTTGATCCTTGCCGAAAACTCTGTTCATTG
GCAGGATTCACCCCTCGCTCAAAGTTCTGCCCATAGCTAGGATTCGGTCCCTGCC
Found at i:194566 original size:24 final size:24
Alignment explanation
Indices: 194534--194662 Score: 213
Period size: 24 Copynumber: 5.4 Consensus size: 24
194524 GCTCAAAGTT
* * * *
194534 CTGCCCATAGCTAGGATTCGGTCC
1 CTGCCCATATCCAGGATTTGGCCC
*
194558 CTGCCCATATCCAGGATTCGGCCC
1 CTGCCCATATCCAGGATTTGGCCC
194582 CTGCCCATATCCAGGATTTGGCCC
1 CTGCCCATATCCAGGATTTGGCCC
194606 CTGCCCATATCCAGGATTTGGCCC
1 CTGCCCATATCCAGGATTTGGCCC
194630 CTGCCCATATCCAGGATTTGGCCC
1 CTGCCCATATCCAGGATTTGGCCC
194654 CTGCCCATA
1 CTGCCCATA
194663 ATTCCCACTT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 101 1.00
ACGTcount: A:0.17, C:0.38, G:0.21, T:0.24
Consensus pattern (24 bp):
CTGCCCATATCCAGGATTTGGCCC
Found at i:194959 original size:105 final size:105
Alignment explanation
Indices: 194763--194974 Score: 307
Period size: 105 Copynumber: 2.0 Consensus size: 105
194753 GAAGTCCCTT
* * *
194763 TGTCGTCCCGGATTATAATTTCCCTGCCCTCCTTGATTGTAACTGCCCTGGTACGAAGGAACACC
1 TGTCGTCCAGAATTATAATTTCCCTGCCCTCCTTGATTGTAACCGCCCTGGTACGAAGGAACACC
* * *
194828 TCCTCTAGGAGCATAATCTCTGTTGTTAATTGGTGGCTGC
66 TCCTCTAGGAGCATAACCTCTATTGTTAATGGGTGGCTGC
* * * *
194868 TGTCGTCCAGAATTATAATTTCCCTGCCCTCCTTGGTTGTAGCCGCCCTGGTATGAAGGATCACC
1 TGTCGTCCAGAATTATAATTTCCCTGCCCTCCTTGATTGTAACCGCCCTGGTACGAAGGAACACC
* * *
194933 TCCTCTGGGAGGATAACCTCTATTGTTCATGGGTGGCTGC
66 TCCTCTAGGAGCATAACCTCTATTGTTAATGGGTGGCTGC
194973 TG
1 TG
194975 CCCGTAATTT
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
105 94 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (105 bp):
TGTCGTCCAGAATTATAATTTCCCTGCCCTCCTTGATTGTAACCGCCCTGGTACGAAGGAACACC
TCCTCTAGGAGCATAACCTCTATTGTTAATGGGTGGCTGC
Found at i:196916 original size:32 final size:32
Alignment explanation
Indices: 196861--196935 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
196851 TAATAGGACT
196861 TAATTGA-TTTTTTTAATCAAGTTCGAG-GATC
1 TAATTGATTTTTTTTAATCAAGTTCGAGAG-TC
* * **
196892 TGATTGATTTTTTTTAGTTGAGTTCGAGAGTC
1 TAATTGATTTTTTTTAATCAAGTTCGAGAGTC
196924 TAATT-ATTTTTT
1 TAATTGATTTTTT
196936 ATCAAAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 13 0.35
32 23 0.62
33 1 0.03
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (32 bp):
TAATTGATTTTTTTTAATCAAGTTCGAGAGTC
Found at i:197709 original size:13 final size:13
Alignment explanation
Indices: 197691--197724 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
197681 TCTTTATGCC
197691 TATATATTACATG
1 TATATATTACATG
*
197704 TATATATTATATG
1 TATATATTACATG
197717 TAATATAT
1 T-ATATAT
197725 GTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (13 bp):
TATATATTACATG
Found at i:201364 original size:15 final size:15
Alignment explanation
Indices: 201344--201374 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
201334 TCCAGTAAGC
201344 AAGATTAGTACTGAT
1 AAGATTAGTACTGAT
201359 AAGATTAGTACTGAT
1 AAGATTAGTACTGAT
201374 A
1 A
201375 CTCTTGGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
AAGATTAGTACTGAT
Found at i:201841 original size:27 final size:28
Alignment explanation
Indices: 201769--201851 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 28
201759 ACTTCTCGCT
201769 AAATGTTAGAGTGATTAAATTAAAAATAAATTA
1 AAAT-TTA-AGTGATTAAATT--AAA-AAATTA
201802 AAATTTAAGTGATTAAATTAAAAAATTA
1 AAATTTAAGTGATTAAATTAAAAAATTA
* * *
201830 AATTTTAA-TGATCAAAATAAAA
1 AAATTTAAGTGATTAAATTAAAA
201852 GTGAGCATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 3 0.06
31 12 0.26
32 3 0.06
33 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (28 bp):
AAATTTAAGTGATTAAATTAAAAAATTA
Found at i:210112 original size:24 final size:23
Alignment explanation
Indices: 210076--210147 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
210066 GTAAATGGAG
210076 ATATCAGAAATCAAAACAGAATTC
1 ATATCAG-AATCAAAACAGAATTC
* *
210100 ATATCAGATATCATAACAGAATCC
1 ATATCAGA-ATCAAAACAGAATTC
* *
210124 AGATCAGAATCAGAACAGAATTC
1 ATATCAGAATCAAAACAGAATTC
210147 A
1 A
210148 GGTAACGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (23 bp):
ATATCAGAATCAAAACAGAATTC
Found at i:210148 original size:12 final size:12
Alignment explanation
Indices: 210080--210171 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
210070 ATGGAGATAT
* *
210080 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
210092 CAGAATTCATAT
1 CAGAATTCAGAA
*
210104 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
210116 CAGAATCCAGAT
1 CAGAATTCAGAA
210128 CAGAA-TCAGAA
1 CAGAATTCAGAA
210139 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
210153 C-GTA-TCAGAA
1 CAGAATTCAGAA
210163 CAGAATTCA
1 CAGAATTCA
210172 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:210159 original size:47 final size:48
Alignment explanation
Indices: 210078--210168 Score: 116
Period size: 47 Copynumber: 1.9 Consensus size: 48
210068 AAATGGAGAT
* *
210078 ATCAGAAATCAAAACAGAATTCATATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
210126 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
210169 TCAATTCGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
47 29 0.76
48 6 0.16
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:215097 original size:24 final size:24
Alignment explanation
Indices: 215067--215176 Score: 93
Period size: 24 Copynumber: 4.6 Consensus size: 24
215057 GTAAACAGAG
*
215067 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
215091 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
* *
215115 AGATCAG-AATCAGAACAAAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
215138 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
215162 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
215177 TAAAATATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 15 0.22
24 49 0.72
25 2 0.03
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:215110 original size:12 final size:11
Alignment explanation
Indices: 215075--215159 Score: 55
Period size: 12 Copynumber: 7.3 Consensus size: 11
215065 AGATATCAGA
*
215075 AATCAAAACAG
1 AATCAGAACAG
* *
215086 AATTCATATCAG
1 AA-TCAGAACAG
215098 ATATCAGAACAG
1 A-ATCAGAACAG
*
215110 AATCCAGATCAG
1 AAT-CAGAACAG
*
215122 AATCAGAACAA
1 AATCAGAACAG
215133 AATTCAGGTAAC-G
1 AA-TCA-G-AACAG
*
215146 TATCAGAACAG
1 AATCAGAACAG
215157 AAT
1 AAT
215160 TCAATTCGGA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
10 3 0.05
11 16 0.28
12 32 0.56
13 3 0.05
14 3 0.05
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:215137 original size:47 final size:47
Alignment explanation
Indices: 215069--215159 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 47
215059 AAACAGAGAT
* *
215069 ATCAGAAATCAAAACAGAATTCA-TATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAAAATTCAGTAAC-G-TATCAGAACAGAATCCAG
*
215117 ATCAG-AATCAGAACAAAATTCAGGTAACGTATCAGAACAGAAT
1 ATCAGAAATCAAAACAAAATTCA-GTAACGTATCAGAACAGAAT
215160 TCAATTCGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
47 29 0.76
48 6 0.16
49 3 0.08
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAAAACAAAATTCAGTAACGTATCAGAACAGAATCCAG
Found at i:219646 original size:12 final size:12
Alignment explanation
Indices: 219629--219656 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
219619 ACGAGACAAT
219629 ATATGATTTGTG
1 ATATGATTTGTG
219641 ATATGATTTGTG
1 ATATGATTTGTG
219653 ATAT
1 ATAT
219657 TTTTATCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (12 bp):
ATATGATTTGTG
Found at i:221646 original size:3 final size:3
Alignment explanation
Indices: 221638--221718 Score: 112
Period size: 3 Copynumber: 27.0 Consensus size: 3
221628 ATTTATTTAT
* *
221638 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
221686 -TA TATA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
221719 AAAAAATAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 60 0.86
4 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:222813 original size:20 final size:21
Alignment explanation
Indices: 222767--222813 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
222757 CTGCTTTTAA
*
222767 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
222788 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
222807 ATATATT
1 ATATATT
222814 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:225301 original size:14 final size:14
Alignment explanation
Indices: 225282--225339 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
225272 TTTTAAATAA
225282 TTTACATTTACATT
1 TTTACATTTACATT
* *
225296 TTTACATTAACATA
1 TTTACATTTACATT
*
225310 TTTACATTTGCA-T
1 TTTACATTTACATT
* *
225323 TTTGCATTTGCATT
1 TTTACATTTACATT
225337 TTT
1 TTT
225340 TATGTCATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
13 11 0.30
14 26 0.70
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (14 bp):
TTTACATTTACATT
Found at i:225332 original size:13 final size:13
Alignment explanation
Indices: 225314--225338 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225304 AACATATTTA
225314 CATTTGCATTTTG
1 CATTTGCATTTTG
225327 CATTTGCATTTT
1 CATTTGCATTTT
225339 TTATGTCATA
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:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (13 bp):
CATTTGCATTTTG
Found at i:228593 original size:12 final size:12
Alignment explanation
Indices: 228555--228587 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
228545 TCCAGCAAAG
*
228555 AAAGAAGAAAAA
1 AAAGAAAAAAAA
228567 AAAGAAAAAAAA
1 AAAGAAAAAAAA
228579 AAAGAAAAA
1 AAAGAAAAA
228588 GGAAAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:231055 original size:114 final size:114
Alignment explanation
Indices: 230852--231079 Score: 384
Period size: 114 Copynumber: 2.0 Consensus size: 114
230842 AAGTGCCATG
*
230852 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTATTTGAGTTATCTGATC
* * * *
230917 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATAAATT
66 TGATTTGATATAAAACCCAAAACCAATCATTGGAATTAAAAGATAAATT
*
230966 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTATTTGAGTTATCTGATC
* *
231031 TGATTTGATATAAAACCCAGAACCAATCATTGGAATTAAAAGATGAATT
66 TGATTTGATATAAAACCCAAAACCAATCATTGGAATTAAAAGATAAATT
231080 GCATGATCGT
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTATTTGAGTTATCTGATC
TGATTTGATATAAAACCCAAAACCAATCATTGGAATTAAAAGATAAATT
Found at i:232368 original size:76 final size:76
Alignment explanation
Indices: 232219--232390 Score: 211
Period size: 76 Copynumber: 2.3 Consensus size: 76
232209 TAACAAGAAG
* * * *
232219 AAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCTGAATCAGGAATGTTGATGTATCCTGAATG
1 AAAATGTTGGAGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACG
* *
232284 TTTATATCAGC
66 TTCATATCAAC
* * * **
232295 AAAATGTTGGAGCATGCTGAAAGCCTTTTTCAATCAGAATGAAGAATGTTGATGTATTTTGAACG
1 AAAATGTTGGAGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACG
*
232360 TTCGTATCAAC
66 TTCATATCAAC
* *
232371 -AATTGTTGGCGCATGCTGAA
1 AAAATGTTGGAGCATGCTGAA
232391 GGCCCACATC
Statistics
Matches: 82, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 18 0.22
76 64 0.78
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (76 bp):
AAAATGTTGGAGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACG
TTCATATCAAC
Found at i:233626 original size:22 final size:22
Alignment explanation
Indices: 233595--233649 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
233585 CATCTACTTC
*
233595 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
233617 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
*
233639 TTCAAATATGA
1 TTCAAAGATGA
233650 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:234251 original size:115 final size:115
Alignment explanation
Indices: 234051--234371 Score: 573
Period size: 115 Copynumber: 2.8 Consensus size: 115
234041 CAAGGATTCA
* *
234051 AATTCATCACTCGATGGATCAACTTTTCCA--GAGAGGGTTCATAATGAGAAGAACTCATCTGAA
1 AATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAA
234114 GAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCG
66 GAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCG
*
234164 AATTCATCACTTGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAA
1 AATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAA
234229 GAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCG
66 GAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCG
234279 AATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCT---
1 AATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAA
234341 G-AAGAAGAAGAAGTTCATAATGAGAAGAACT
66 GAAAGAAGAAGAAGTTCATAATGAGAAGAACT
234372 CATCTGAAGA
Statistics
Matches: 202, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
111 30 0.15
112 1 0.00
113 29 0.14
115 142 0.70
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (115 bp):
AATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAA
GAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCG
Found at i:234338 original size:16 final size:16
Alignment explanation
Indices: 234319--234374 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
234309 GTGAAAGAGT
234319 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
*
234335 TCATCTGAA-GAAGAAGAAGT
1 TCA--T-AATG-AGAAGAA-C
234355 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
234371 TCAT
1 TCAT
234375 CTGAAGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (16 bp):
TCATAATGAGAAGAAC
Found at i:234356 original size:36 final size:38
Alignment explanation
Indices: 234316--234411 Score: 151
Period size: 40 Copynumber: 2.5 Consensus size: 38
234306 CCAGTGAAAG
234316 AGTTCATAATGAGAAGAACTCATCT-G-AAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTAGAAAGAAGAAGA
234352 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCT--AGAAAGAAGAAGA
*
234392 AGTTCATAATAAGAAGAACT
1 AGTTCATAATGAGAAGAACT
234412 TGTTCAACTT
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
36 25 0.45
39 1 0.02
40 29 0.53
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (38 bp):
AGTTCATAATGAGAAGAACTCATCTAGAAAGAAGAAGA
Found at i:234377 original size:151 final size:151
Alignment explanation
Indices: 234201--234524 Score: 571
Period size: 151 Copynumber: 2.1 Consensus size: 151
234191 CCAGTGAAAG
*
234201 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
234266 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAA
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCA--GAAAGAGTTCATAATGAGAA
234331 GAACTCATCT-G-AAGAAGAAGA
129 GAACTCATCTAGAAAGAAGAAGA
234352 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
*
234417 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGA
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAAAGAGTTCATAATGAGAAGA
234482 ACTCATCTGAAGAAAGAAGAAGA
131 ACTCATCT--AGAAAGAAGAAGA
*
234505 AGTTCATAATGAAAAGAACT
1 AGTTCATAATGAGAAGAACT
234525 TGTTCAACTT
Statistics
Matches: 166, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
149 29 0.17
151 107 0.64
152 1 0.01
153 29 0.17
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (151 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAAAGAGTTCATAATGAGAAGA
ACTCATCTAGAAAGAAGAAGA
Found at i:234386 original size:20 final size:19
Alignment explanation
Indices: 234327--234389 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 19
234317 GTTCATAATG
234327 AGAAGAACTCATCTGAAGA
1 AGAAGAACTCATCTGAAGA
*
234346 AGAAGAAGT--TCAT-AATG-
1 AGAAGAACTCATC-TGAA-GA
234363 AGAAGAACTCATCTGAAGAA
1 AGAAGAACTCATCTGAAG-A
234383 AGAAGAA
1 AGAAGAA
234390 GAAGTTCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 13
0.70 0.04 0.26
Matches are distributed among these distances:
17 12 0.34
18 4 0.11
19 12 0.34
20 7 0.20
ACGTcount: A:0.51, C:0.11, G:0.22, T:0.16
Consensus pattern (19 bp):
AGAAGAACTCATCTGAAGA
Found at i:234637 original size:115 final size:115
Alignment explanation
Indices: 234352--234750 Score: 720
Period size: 115 Copynumber: 3.5 Consensus size: 115
234342 AAGAAGAAGA
*
234352 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
234417 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCA--GAGAG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAG
*
234465 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAAAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
234530 AACTTTTCGCTCGAATTCATCACTTGATGGATCAACTTTTCCAGTGAAAG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAG
234580 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
234645 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAG
234695 AGTTCATAATGAGAAGAACTCATCT---G-AAGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACT
234751 CATCTGAAGA
Statistics
Matches: 278, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
111 30 0.11
112 1 0.00
113 105 0.38
115 142 0.51
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (115 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAG
Found at i:234717 original size:16 final size:16
Alignment explanation
Indices: 234698--234753 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
234688 GTGAAAGAGT
234698 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
*
234714 TCATCTGAA-GAAGAAGAAGT
1 TCA--T-AATG-AGAAGAA-C
234734 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
234750 TCAT
1 TCAT
234754 CTGAAGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (16 bp):
TCATAATGAGAAGAAC
Found at i:234735 original size:36 final size:38
Alignment explanation
Indices: 234695--234790 Score: 151
Period size: 40 Copynumber: 2.5 Consensus size: 38
234685 CCAGTGAAAG
234695 AGTTCATAATGAGAAGAACTCATCT-G-AAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTAGAAAGAAGAAGA
234731 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCT--AGAAAGAAGAAGA
*
234771 AGTTCATAATAAGAAGAACT
1 AGTTCATAATGAGAAGAACT
234791 TGTTCAACTT
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
36 25 0.45
39 1 0.02
40 29 0.53
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (38 bp):
AGTTCATAATGAGAAGAACTCATCTAGAAAGAAGAAGA
Found at i:234750 original size:379 final size:379
Alignment explanation
Indices: 234051--235128 Score: 2034
Period size: 379 Copynumber: 2.8 Consensus size: 379
234041 CAAGGATTCA
*
234051 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
234116 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTTGATGG
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTTGATGG
234181 ATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
131 ATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
234246 ATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGT
196 ATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGT
234311 GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATC
261 GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATC
*
234376 TGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTCGCTCG
326 TGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTCTCGCTCG
234430 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
234495 AAGAAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTTGATGG
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTTGATGG
234560 ATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
131 ATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
234625 ATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGT
196 ATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGT
234690 GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATC
261 GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATC
234755 TGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTCTCGCTCG
326 TGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTCTCGCTCG
234809 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
234874 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCACTCGATGG
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTTGATGG
*
234939 ATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTC
131 ATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
*
235004 ATAATAAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCA--
196 ATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGT
*
235067 GAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
261 GAAAGAGTTCATAATGAGAAGAACTCATCT---G-AAGAAGAAGAAGTTCATAATGAGAAGA
235129 GCTTGTTCGA
Statistics
Matches: 686, Mismatches: 9, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
377 29 0.04
379 629 0.92
380 1 0.00
381 27 0.04
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (379 bp):
AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTTGATGG
ATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGT
GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATC
TGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTCTCGCTCG
Found at i:234755 original size:151 final size:151
Alignment explanation
Indices: 234580--234903 Score: 571
Period size: 151 Copynumber: 2.1 Consensus size: 151
234570 CCAGTGAAAG
*
234580 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
*
234645 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAA
66 AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCA--GAAAGAGTTCATAATGAGAA
234710 GAACTCATCT-G-AAGAAGAAGA
129 GAACTCATCTAGAAAGAAGAAGA
234731 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
*
234796 AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGA
66 AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAAAGAGTTCATAATGAGAAGA
234861 ACTCATCTGAAGAAAGAAGAAGA
131 ACTCATCT--AGAAAGAAGAAGA
234884 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
234904 TGTTCAACTT
Statistics
Matches: 166, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
149 29 0.17
151 106 0.64
152 1 0.01
153 30 0.18
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (151 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAAAGAGTTCATAATGAGAAGA
ACTCATCTAGAAAGAAGAAGA
Found at i:234765 original size:20 final size:19
Alignment explanation
Indices: 234706--234768 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 19
234696 GTTCATAATG
234706 AGAAGAACTCATCTGAAGA
1 AGAAGAACTCATCTGAAGA
*
234725 AGAAGAAGT--TCAT-AATG-
1 AGAAGAACTCATC-TGAA-GA
234742 AGAAGAACTCATCTGAAGAA
1 AGAAGAACTCATCTGAAG-A
234762 AGAAGAA
1 AGAAGAA
234769 GAAGTTCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 13
0.70 0.04 0.26
Matches are distributed among these distances:
17 12 0.34
18 4 0.11
19 12 0.34
20 7 0.20
ACGTcount: A:0.51, C:0.11, G:0.22, T:0.16
Consensus pattern (19 bp):
AGAAGAACTCATCTGAAGA
Found at i:234946 original size:264 final size:265
Alignment explanation
Indices: 234201--235018 Score: 1053
Period size: 264 Copynumber: 3.1 Consensus size: 265
234191 CCAGTGAAAG
*
234201 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
234266 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAA
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAG-GAAAGAGTTCATAATGAGAA
** * ***** **
234331 GAACTCATCT---G-AAGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG-AAG
130 GAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT-TCAA-CTTTTAGCTCG
* * * * * *
234391 AAGTTCAT-AATAAGAAGAACTTGTTCAACTTTT-C-GCTCG--A-A-TTCATCACTCGATGGAT
193 AA-TTCATCACT----CG-A-TGGATCAACTTTTCCAG-T-GAAAGAGTTCAT-AAT-GA--GAA
* * **
234449 CAACT--TTTCCAG-AG-AG-
245 GAACTCATATGAAGAAGAAGA
234465 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAA-AAGAACTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAAT-AAGAAGAACTTGTT
*
234529 CAACTTTTCGCTCGAATTCATCACTTGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGA
65 CAACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAG-GAAAGAGTTCATAATGAGA
*
234594 AGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGA
129 AGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTAGCTCGA
*
234659 ATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAG
194 ATTCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATATGAAG
234724 AAGAAGA
259 AAGAAGA
234731 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
* *
234796 AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCA-GAGAGAGTTCATAATGAGAAG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGGAAAGAGTTCATAATGAGAAG
*
234860 AACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAAT
131 AACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTAGCTCGAAT
234925 TCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATATGAAGAA
196 TCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATAT---G-A
234990 AGAAGAAGA
257 AGAAGAAGA
*
234999 AGTTCATAATAAGAAGAACT
1 AGTTCATAATGAGAAGAACT
235019 TGTTCAACTT
Statistics
Matches: 502, Mismatches: 29, Indels: 42
0.88 0.05 0.07
Matches are distributed among these distances:
261 18 0.04
262 3 0.01
263 9 0.02
264 283 0.56
265 10 0.02
266 109 0.22
267 10 0.02
268 60 0.12
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (265 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGGAAAGAGTTCATAATGAGAAG
AACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTAGCTCGAAT
TCATCACTCGATGGATCAACTTTTCCAGTGAAAGAGTTCATAATGAGAAGAACTCATATGAAGAA
GAAGA
Found at i:235013 original size:228 final size:228
Alignment explanation
Indices: 234731--235146 Score: 787
Period size: 228 Copynumber: 1.8 Consensus size: 228
234721 AAGAAGAAGA
*
234731 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
234796 AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGA
66 AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGA
*
234861 ACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATT
131 ACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
234926 CATCACTCGATGGATCAACTTTTCCAGTGAAAG
196 CATCACTCGATGGATCAACTTTTCCAGTGAAAG
234959 AGTTCATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
*
235024 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGA
66 AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGA
* *
235089 ACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
131 ACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
235147 ATGACTCTAT
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
228 183 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (228 bp):
AGTTCATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGA
ACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
CATCACTCGATGGATCAACTTTTCCAGTGAAAG
Found at i:235014 original size:115 final size:113
Alignment explanation
Indices: 234731--235136 Score: 731
Period size: 113 Copynumber: 3.6 Consensus size: 113
234721 AAGAAGAAGA
234731 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
*
234796 AACTTCTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAG
*
234844 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
* *
234909 AACTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGTGAAAG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCA--GAGAG
*
234959 AGTTCATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
235024 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAG
* *
235072 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
235137 GACCTTTTGC
Statistics
Matches: 280, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
113 171 0.61
115 109 0.39
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
AACTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAG
Found at i:235248 original size:17 final size:17
Alignment explanation
Indices: 235190--235248 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
235180 CAAGATTTCC
235190 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
**
235207 AGAA-AAACTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
235225 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
235243 AGAAGA
1 AGAAGA
235249 GCTTGTGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 5 0.16
17 13 0.41
18 2 0.06
19 7 0.22
20 5 0.16
ACGTcount: A:0.51, C:0.12, G:0.22, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:235493 original size:9 final size:8
Alignment explanation
Indices: 235481--235559 Score: 54
Period size: 9 Copynumber: 9.4 Consensus size: 8
235471 TTTTTTACCC
235481 ATTTTATT
1 ATTTTATT
235489 -TATTTATT
1 AT-TTTATT
235497 ATTATTATT
1 ATT-TTATT
235506 ATTATTATT
1 ATT-TTATT
*
235515 ATTATAATT
1 ATT-TTATT
*
235524 ATTATA-T
1 ATTTTATT
*
235531 ATATTATT
1 ATTTTATT
*
235539 ATATATATT
1 AT-TTTATT
235548 ATTATTATT
1 ATT-TTATT
235557 ATT
1 ATT
235560 AAAAAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
7 6 0.11
8 12 0.21
9 39 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
ATTTTATT
Found at i:235500 original size:3 final size:3
Alignment explanation
Indices: 235492--235560 Score: 97
Period size: 3 Copynumber: 23.0 Consensus size: 3
235482 TTTTATTTAT
*
235492 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
235537 TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
235561 AAAAAATAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 4 0.07
3 50 0.83
4 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:236657 original size:20 final size:21
Alignment explanation
Indices: 236611--236657 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
236601 CTGCTTTTAA
*
236611 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
236632 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
236651 ATATATT
1 ATATATT
236658 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:241795 original size:17 final size:17
Alignment explanation
Indices: 241768--241804 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
241758 ATATAATTTA
241768 ATTTGAATTTATTTATGT
1 ATTTGAATTTATTTAT-T
241786 ATTT-AATTTATTTATT
1 ATTTGAATTTATTTATT
241802 ATT
1 ATT
241805 AATAAAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 11 0.58
18 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
ATTTGAATTTATTTATT
Found at i:243914 original size:17 final size:17
Alignment explanation
Indices: 243887--243923 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
243877 ATATAATTTA
243887 ATTTGAATTTATTTATGT
1 ATTTGAATTTATTTAT-T
243905 ATTT-AATTTATTTATT
1 ATTTGAATTTATTTATT
243921 ATT
1 ATT
243924 AATAAAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 11 0.58
18 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
ATTTGAATTTATTTATT
Found at i:251152 original size:29 final size:29
Alignment explanation
Indices: 251119--251179 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
251109 GAGCTATATG
251119 AGAATAAGTAATGTTCTTACATGATCACA
1 AGAATAAGTAATGTTCTTACATGATCACA
251148 AGAATAAGTAATGTTCTTACATGATCACA
1 AGAATAAGTAATGTTCTTACATGATCACA
251177 AGA
1 AGA
251180 TATGCGACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (29 bp):
AGAATAAGTAATGTTCTTACATGATCACA
Found at i:259245 original size:29 final size:29
Alignment explanation
Indices: 259190--259247 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
259180 GTTAACGGTA
*
259190 TAAAATACCATGTATGAAATCGGGAATTT
1 TAAAATACCATGTATGAAATCGAGAATTT
**
259219 TAAAATATTATGTATGAAA-CTGAGAATTT
1 TAAAATACCATGTATGAAATC-GAGAATTT
259248 GGTATACTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (29 bp):
TAAAATACCATGTATGAAATCGAGAATTT
Found at i:268037 original size:35 final size:36
Alignment explanation
Indices: 267998--268066 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
267988 TAGAAGTTAT
* *
267998 ATTATAAAT-ATAACATTTAAATTATATAAAATTAA
1 ATTATAAATGAAAACATTTAAATAATATAAAATTAA
* *
268033 ATTATTAATGAAAATATTTAAATAATATAAAATT
1 ATTATAAATGAAAACATTTAAATAATATAAAATT
268067 TTTAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 8 0.28
36 21 0.72
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (36 bp):
ATTATAAATGAAAACATTTAAATAATATAAAATTAA
Found at i:273323 original size:16 final size:16
Alignment explanation
Indices: 273274--273347 Score: 51
Period size: 19 Copynumber: 4.1 Consensus size: 16
273264 ATATAAACAT
273274 ATAAAATTAAAATATAA
1 ATAAAATTAAAA-ATAA
*
273291 ATAAACAATGACTAAAATAA
1 AT-AA-AATTA--AAAATAA
273311 ATAAAATTAAAAAGT-A
1 ATAAAATTAAAAA-TAA
273327 ATAAAACTTGTAAAAATAA
1 ATAAAA--T-TAAAAATAA
273346 AT
1 AT
273348 GAAAGTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
16 11 0.24
17 3 0.07
18 8 0.17
19 15 0.33
20 6 0.13
21 3 0.07
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:274789 original size:3 final size:3
Alignment explanation
Indices: 274783--274848 Score: 114
Period size: 3 Copynumber: 22.0 Consensus size: 3
274773 TAATTTTTAT
* *
274783 TAA TAA TAA TAA TAA TTA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
274831 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
274849 ATCAAATGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:275699 original size:113 final size:113
Alignment explanation
Indices: 275375--275702 Score: 455
Period size: 113 Copynumber: 2.9 Consensus size: 113
275365 AGAGTCATGC
* * *
275375 AAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTATTCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * **
275439 ATGAACTTTCTCTGGAAA-AGTTGATGCATCGAGTGATGAATTCGACCA
66 ATGAACTCTATCTGGAAATA-TTGATCCATCGAGTGATGAATTAAACCA
*
275487 AAAGGCTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * *
275552 ATGAACTCTACCTGGAAATGCTAATCCATCGAGTGATGAATTAAAGCA
66 ATGAACTCTATCTGGAAATATTGATCCATCGAGTGATGAATTAAACCA
* * *
275600 AAAGGTTAAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCCTCAGATGAGTTTTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
275665 ATGAACTCT-TCTGGAAATATTGATCCATTTGAGTGATG
66 ATGAACTCTATCTGGAAATATTGATCCA-TCGAGTGATG
275703 GATCCAAATC
Statistics
Matches: 190, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
112 51 0.27
113 139 0.73
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTATCTGGAAATATTGATCCATCGAGTGATGAATTAAACCA
Found at i:276107 original size:20 final size:20
Alignment explanation
Indices: 276082--276147 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
276072 CCTCTTTGAA
*
276082 AAGAGAATCTATCATCTTCG
1 AAGAGAATCTATCATCTTTG
**
276102 AAGAGAAAATATCATCTTTG
1 AAGAGAATCTATCATCTTTG
276122 AAGAGAATATCTATCATCTTTG
1 AAGAG-A-ATCTATCATCTTTG
276144 AAGA
1 AAGA
276148 ATGTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 22 0.56
21 1 0.03
22 16 0.41
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (20 bp):
AAGAGAATCTATCATCTTTG
Found at i:276146 original size:22 final size:21
Alignment explanation
Indices: 276064--276147 Score: 98
Period size: 22 Copynumber: 4.0 Consensus size: 21
276054 AAAATCCAAT
* * *
276064 AAATCTTTCCTCTTTGAAAAG
1 AAATCTATCATCTTTGAAGAG
*
276085 AGAATCTATCATCTTCGAAGAG
1 A-AATCTATCATCTTTGAAGAG
*
276107 AAA-ATATCATCTTTGAAGAG
1 AAATCTATCATCTTTGAAGAG
276127 AATATCTATCATCTTTGAAGA
1 AA-ATCTATCATCTTTGAAGA
276148 ATGTAAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
20 17 0.32
21 4 0.08
22 32 0.60
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (21 bp):
AAATCTATCATCTTTGAAGAG
Found at i:283754 original size:20 final size:20
Alignment explanation
Indices: 283726--283764 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
283716 GCAAAGATGC
* *
283726 AAATGCAAAAATGAAAATGT
1 AAATACAAAAATAAAAATGT
*
283746 AAATACAAACATAAAAATG
1 AAATACAAAAATAAAAATG
283765 CAAAAATGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (20 bp):
AAATACAAAAATAAAAATGT
Found at i:283881 original size:8 final size:7
Alignment explanation
Indices: 283861--283895 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
283851 ATAAAAGTAT
283861 AAATGCA
1 AAATGCA
283868 AAATGCA
1 AAATGCA
283875 AAGATGCA
1 AA-ATGCA
283883 AAATGC-
1 AAATGCA
283889 AAATGCA
1 AAATGCA
283896 TGTATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:283883 original size:15 final size:15
Alignment explanation
Indices: 283863--283891 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
283853 AAAAGTATAA
283863 ATGCAAAATGCAAAG
1 ATGCAAAATGCAAAG
283878 ATGCAAAATGCAAA
1 ATGCAAAATGCAAA
283892 TGCATGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAG
Found at i:284034 original size:43 final size:44
Alignment explanation
Indices: 283970--284056 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
283960 TCGTGCATCA
*
283970 AACAAAACTTTTACATGTAGGGGACAACTTTCAATCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCAATCCTAACTTC
* **
284014 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCAATCCTAACTTC
284057 TATAAGTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 31 0.79
44 8 0.21
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCAATCCTAACTTC
Found at i:284908 original size:46 final size:49
Alignment explanation
Indices: 284841--284931 Score: 125
Period size: 46 Copynumber: 1.9 Consensus size: 49
284831 TATAATATAT
* * * *
284841 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTT-GGAAAAATTAA
1 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAATTAA
284887 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAA
1 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAA
284932 ATGAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 20 0.53
47 5 0.13
48 6 0.16
49 7 0.18
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (49 bp):
CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAATTAA
Found at i:285433 original size:15 final size:15
Alignment explanation
Indices: 285415--285466 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
285405 ATAAAAACAT
285415 TAAAAAATAATATTA
1 TAAAAAATAATATTA
* *
285430 TAAAAAATATTATGA
1 TAAAAAATAATATTA
*
285445 -AAATAATAAGTATATA
1 TAAAAAATAA-TAT-TA
285461 TAAAAA
1 TAAAAA
285467 TTTTGAAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 7 0.25
15 16 0.57
16 1 0.04
17 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
TAAAAAATAATATTA
Found at i:285440 original size:12 final size:13
Alignment explanation
Indices: 285413--285452 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
285403 AAATAAAAAC
*
285413 ATTAAAAAATAAT
1 ATTATAAAATAAT
285426 ATTATAAAA-AAT
1 ATTATAAAATAAT
285438 ATTATGAAAATAAT
1 ATTAT-AAAATAAT
285452 A
1 A
285453 AGTATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 8 0.33
13 12 0.50
14 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
ATTATAAAATAAT
Found at i:286426 original size:16 final size:16
Alignment explanation
Indices: 286377--286450 Score: 51
Period size: 19 Copynumber: 4.1 Consensus size: 16
286367 ATATAAACAT
286377 ATAAAATTAAAATATAA
1 ATAAAATTAAAA-ATAA
*
286394 ATAAACAATGACTAAAATAA
1 AT-AA-AATTA--AAAATAA
286414 ATAAAATTAAAAAGT-A
1 ATAAAATTAAAAA-TAA
286430 ATAAAACTTGTAAAAATAA
1 ATAAAA--T-TAAAAATAA
286449 AT
1 AT
286451 GAAAGTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
16 11 0.24
17 3 0.07
18 8 0.17
19 15 0.33
20 6 0.13
21 3 0.07
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:287906 original size:3 final size:3
Alignment explanation
Indices: 287900--287950 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
287890 AATTTTTTAT
* * * *
287900 TAA TAA TAA TAA TTA TTA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
287948 TAA
1 TAA
287951 ATCAAGTGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:290976 original size:23 final size:22
Alignment explanation
Indices: 290945--290989 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
290935 ATATTCTTAG
*
290945 ACTTAGCTCGATTGAAGCTCAA
1 ACTTAGCTCGATTCAAGCTCAA
*
290967 ACTTGAGCTCGGTTCAAGCTCAA
1 ACTT-AGCTCGATTCAAGCTCAA
290990 TCTCGAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (22 bp):
ACTTAGCTCGATTCAAGCTCAA
Found at i:293975 original size:54 final size:53
Alignment explanation
Indices: 293866--293986 Score: 163
Period size: 54 Copynumber: 2.2 Consensus size: 53
293856 TACGAAGGGA
* * *
293866 TGTACCGATACACCCCCACTTCGAATATAATTTGGGAATCGATACACTCCTGTG
1 TGTACCGATACACCCCCACATAGAATATAATTTGGGAACCGATACAC-CCTGTG
* *
293920 TGTACCGATACACCCCCTACATAGAATGTATTTTGGGAACCGATACA-CCTAGTG
1 TGTACCGATACACCCCC-ACATAGAATATAATTTGGGAACCGATACACCCT-GTG
293974 TGTACCGATACAC
1 TGTACCGATACAC
293987 TCGGTCATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
53 3 0.05
54 33 0.55
55 24 0.40
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TGTACCGATACACCCCCACATAGAATATAATTTGGGAACCGATACACCCTGTG
Found at i:295282 original size:15 final size:17
Alignment explanation
Indices: 295262--295304 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
295252 ACTTTTTTTT
295262 TTCTTCTTCT-CA-TTC
1 TTCTTCTTCTACACTTC
295277 TTCTTCTTCTAACACTTC
1 TTCTTCTTCT-ACACTTC
295295 TTCTTCTTCT
1 TTCTTCTTCT
295305 TCAAACACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.40
17 2 0.08
18 13 0.52
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCTTCTTCTACACTTC
Found at i:295298 original size:21 final size:21
Alignment explanation
Indices: 295273--295322 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
295263 TCTTCTTCTC
*
295273 ATTCTTCTTCTTCTAACACTT
1 ATTCTTCTTCTTCAAACACTT
*
295294 CTTCTTCTTCTTCAAACACTT
1 ATTCTTCTTCTTCAAACACTT
295315 ATTCTTCT
1 ATTCTTCT
295323 CCTCCTCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.30, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTCTTCTTCTTCAAACACTT
Found at i:307018 original size:15 final size:15
Alignment explanation
Indices: 306994--307024 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
306984 TATCTAAAGA
306994 AGAATGAAATGAAAT
1 AGAATGAAATGAAAT
*
307009 AGAATTAAATGAAAT
1 AGAATGAAATGAAAT
307024 A
1 A
307025 ACTTATGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (15 bp):
AGAATGAAATGAAAT
Found at i:308663 original size:19 final size:19
Alignment explanation
Indices: 308631--308668 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
308621 TAATGATATA
*
308631 AATATTAAATTTCTTAAAT
1 AATATTAAATTTCTAAAAT
308650 AATATATAAA-TTCTAAAAT
1 AATAT-TAAATTTCTAAAAT
308669 TATTGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATTAAATTTCTAAAAT
Found at i:310059 original size:18 final size:20
Alignment explanation
Indices: 310032--310082 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
310022 TTAATTTTAC
*
310032 AAATATAAAAAAAT-C-AAA
1 AAATACAAAAAAATCCGAAA
*
310050 AAATACAAAACAATCCGAAA
1 AAATACAAAAAAATCCGAAA
*
310070 AATTACAAAAAAA
1 AAATACAAAAAAA
310083 AAATATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.44
19 1 0.04
20 14 0.52
ACGTcount: A:0.73, C:0.12, G:0.02, T:0.14
Consensus pattern (20 bp):
AAATACAAAAAAATCCGAAA
Found at i:311183 original size:24 final size:24
Alignment explanation
Indices: 311156--311207 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
311146 CGTTCATTTA
*
311156 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
311180 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
311204 CGTT
1 CGTT
311208 TATGTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:311194 original size:14 final size:14
Alignment explanation
Indices: 311166--311207 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
311156 CGTTCGTGAA
311166 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
311180 CG-T---TTATGTT
1 CGTTCGGTTATGTT
311190 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
311204 CGTT
1 CGTT
311208 TATGTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:311208 original size:24 final size:24
Alignment explanation
Indices: 311166--311214 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
311156 CGTTCGTGAA
311166 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
311190 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
311214 C
1 C
311215 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:311224 original size:24 final size:24
Alignment explanation
Indices: 311172--311227 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
311162 TGAACGTTCG
* *
311172 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
311196 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
311220 TTTATGTT
1 GTTATGTT
311228 TAACCCAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:312310 original size:16 final size:16
Alignment explanation
Indices: 312291--312363 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
312281 CCAACGTTTA
* *
312291 TGTTCGTTTATGTTTG
1 TGTTCATTTATGTTCG
312307 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
312323 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
312339 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
312355 T-TT-ATTTAT
1 TGTTCATTTAT
312364 TAAATTATTC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.09
15 2 0.04
16 46 0.87
ACGTcount: A:0.11, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Done.