Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1591247 original size:105 final size:105
Alignment explanation
Indices: 1590342--1591229 Score: 1496
Period size: 105 Copynumber: 8.5 Consensus size: 105
1590332 TGAAAGTTGT
* * * * *
1590342 GTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TT
* * * *
1590407 GTTGACAACCAGCTGTCCCTTCGTTGTAAAGTTGAACTTGT
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1590448 GTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1590513 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1590553 GTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---GTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
*
1590615 TTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
1590655 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1590720 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
1590760 ATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TT
*
1590825 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
1590866 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1590931 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1590971 GTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1591036 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
1591076 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
*
1591141 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGT
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
1591181 GTTGTCTCGAGTCCAA-ATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1591230 TGAAACTGAA
Statistics
Matches: 747, Mismatches: 31, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
102 98 0.13
104 32 0.04
105 458 0.61
106 159 0.21
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
Found at i:1596197 original size:5 final size:6
Alignment explanation
Indices: 1596172--1596230 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
1596162 AATAAGAGAT
1596172 AATATA AATATA AATATA AATA-A AATA-A AATA-A AATACT- AATA-A
1 AATATA AATATA AATATA AATATA AATATA AATATA AATA-TA AATATA
*
1596216 TAATATA TATATA AA
1 -AATATA AATATA AA
1596231 AAATTATATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
5 15 0.33
6 30 0.65
7 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:1596309 original size:70 final size:70
Alignment explanation
Indices: 1596227--1596398 Score: 215
Period size: 70 Copynumber: 2.4 Consensus size: 70
1596217 AATATATATA
* *
1596227 TAAAAAATTATATGTTATATGTTTTCAAACGTACTTTAAAAACTATATA-T-TAT-ATTGTCAAA
1 TAAAAAACTATAT-TTATATGTTTTCAAAAGTACTTTAAAAACTATATACTATATGATTGTCAAA
1596289 ACCGTTT
65 ACCG-TT
* * * *
1596296 TAAAAAAACTATATATTATACGTTTTCAAAATTACTTTAAAAACTATATACTATATGTTTTTCAA
1 T-AAAAAACTATAT-TTATATGTTTTCAAAAGTACTTTAAAAACTATATACTATATGATTGTCAA
*
1596361 AACTGTT
64 AACCGTT
*
1596368 TCAAAAACTATATTTATATGTTTTCAAAAGT
1 TAAAAAACTATATTTATATGTTTTCAAAAGT
1596399 TATATTTGAC
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
69 1 0.01
70 59 0.67
71 12 0.14
72 6 0.07
73 10 0.11
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (70 bp):
TAAAAAACTATATTTATATGTTTTCAAAAGTACTTTAAAAACTATATACTATATGATTGTCAAAA
CCGTT
Found at i:1596325 original size:37 final size:34
Alignment explanation
Indices: 1596229--1596396 Score: 155
Period size: 35 Copynumber: 4.8 Consensus size: 34
1596219 TATATATATA
* * *
1596229 AAAAATTATATGTTATATGTTTTC-AAACGTACTTT
1 AAAAACTATATATTATATGTTTTCAAAAC-T-GTTT
* *
1596264 AAAAACTATATATTATA--TTGTCAAAACCGTTTT
1 AAAAACTATATATTATATGTTTTCAAAACTG-TTT
* * *
1596297 AAAAAAACTATATATTATACGTTTTCAAAATTACTTT
1 --AAAAACTATATATTATATGTTTTCAAAACT-GTTT
*
1596334 AAAAACTATATACTATATGTTTTTCAAAACTGTTT
1 AAAAACTATATATTATATG-TTTTCAAAACTGTTT
1596369 CAAAAACTATAT-TTATATGTTTTCAAAA
1 -AAAAACTATATATTATATGTTTTCAAAA
1596397 GTTATATTTG
Statistics
Matches: 110, Mismatches: 14, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
33 7 0.06
34 13 0.12
35 58 0.53
36 21 0.19
37 11 0.10
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (34 bp):
AAAAACTATATATTATATGTTTTCAAAACTGTTT
Found at i:1597149 original size:36 final size:36
Alignment explanation
Indices: 1597100--1597331 Score: 152
Period size: 36 Copynumber: 6.7 Consensus size: 36
1597090 GGGTTTTTTG
1597100 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
* *
1597136 TGTTTCAAAAGAAACTGTCTCAAGA---A-AAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
* * * * *
1597168 AGTTTTAAAAGAAACTGTATCAAG-GGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGG-GACAAAATT
* * *
1597204 TGTTTCAAG-GAAA-AGATATTCAA-A-GG-----TTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGGGACAAAATT
* * * * *
1597233 TGTTTCAAGGGAAGCTATCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
* *
1597269 TGTTTCAAGGGAAACTGTCTCAAG-GGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGG-GACAA-AATT
*
1597306 TGTTTCAAGGGAAACTGTCTCAAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAG
1597332 AGAAAACTTG
Statistics
Matches: 151, Mismatches: 25, Indels: 38
0.71 0.12 0.18
Matches are distributed among these distances:
29 14 0.09
30 5 0.03
31 1 0.01
32 26 0.17
33 1 0.01
34 2 0.01
35 8 0.05
36 66 0.44
37 27 0.18
38 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
Found at i:1597317 original size:37 final size:36
Alignment explanation
Indices: 1597230--1597334 Score: 156
Period size: 37 Copynumber: 2.9 Consensus size: 36
1597220 TATTCAAAGG
* * *
1597230 TTTTGTTTCAAGGGAAGCTATCTTAAGAGAGACAAA
1 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
* *
1597266 ATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAGA
1 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA-A
1597303 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1597335 AAACTTGGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 30 0.49
37 31 0.51
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (36 bp):
TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
Found at i:1597946 original size:105 final size:105
Alignment explanation
Indices: 1597712--1598599 Score: 1487
Period size: 105 Copynumber: 8.5 Consensus size: 105
1597702 TGAAAGTTGT
* * * *
1597712 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TT
* * * *
1597777 GTTGACAACCAGCTGTCCCTTCGTTGTAAAGTTGAACTTGT
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
1597818 GTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
*
1597883 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
1597923 GTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---GTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
*
1597985 TTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1598025 GTTGTCTGGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1598090 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1598130 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TT
* *
1598195 ATTGACAACCAGCGGTCCCTTCGTCGTGAATTTGAACTTGC
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
1598236 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
*
1598301 TTGACAACCAGCGTTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1598341 GTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1598406 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
1598446 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTG
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1598511 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
1598551 GTTGTCTCGAGTCCAA-ATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1598600 TGAAACTGAA
Statistics
Matches: 740, Mismatches: 38, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
102 96 0.13
104 32 0.04
105 454 0.61
106 158 0.21
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (105 bp):
GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
Found at i:1598297 original size:211 final size:210
Alignment explanation
Indices: 1597712--1598599 Score: 1496
Period size: 211 Copynumber: 4.2 Consensus size: 210
1597702 TGAAAGTTGT
* *
1597712 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTT
1 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TT
* * * * *
1597777 GTTGACAACCAGCTGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTC
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
* * *
1597842 GTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTGTTGACAACCAGTGGTCCCTTCGTC
130 GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTC
1597907 GTGAAGTTGAACTTGC
195 GTGAAGTTGAACTTGC
*
1597923 GTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AA--GTTG
1 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTG
* *
1597985 TTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCTAATATCCTTCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
1598050 CTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCG
131 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCG
1598115 TGAAGTTGAACTTGC
196 TGAAGTTGAACTTGC
* *
1598130 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTT
1 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TT
* *
1598195 ATTGACAACCAGCGGTCCCTTCGTCGTGAATTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
*
1598260 GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGTTCCCTTCGTC
130 GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTC
1598325 GTGAAGTTGAACTTGC
195 GTGAAGTTGAACTTGC
* * * *
1598341 GTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTG
1 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTG
1598406 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
1598471 CTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCG
131 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCG
1598536 TGAAGTTGAACTTGC
196 TGAAGTTGAACTTGC
* *
1598551 GTTGTCTCGAGTCCAA-ATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA
1 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1598600 TGAAACTGAA
Statistics
Matches: 640, Mismatches: 33, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
207 191 0.30
208 3 0.00
209 31 0.05
210 162 0.25
211 253 0.40
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (210 bp):
GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTG
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCG
TGAAGTTGAACTTGC
Found at i:1598343 original size:418 final size:419
Alignment explanation
Indices: 1597712--1598599 Score: 1528
Period size: 418 Copynumber: 2.1 Consensus size: 419
1597702 TGAAAGTTGT
* *
1597712 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTT
1 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
* * * *
1597777 GTTGACAACCAGCTGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTC
66 ATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTC
* *
1597842 GTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTGTTGACAACCAGTGGTCCCTTCGTC
131 GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTGTTGACAACCAGCGGTCCCTTCGTC
* *
1597907 GTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
196 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGA
1597972 AATTGGGAA-GTTGTTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
261 AATTGGGAATGTTGTTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
1598036 TCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTGTTGACAACCAG
326 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTGTTGACAACCAG
1598101 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
391 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1598130 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTT
1 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
* * *
1598195 ATTGACAACCAGCGGTCCCTTCGTCGTGAATTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
66 ATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTC
* *
1598260 GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGTTCCCTTCGTC
131 GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTGTTGACAACCAGCGGTCCCTTCGTC
*
1598325 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGA
196 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGA
*
1598390 AATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
261 AATTGGGAA--TGTTGTTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1598455 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTGTTGACAACC
324 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTGTTGACAACC
1598520 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
389 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1598551 GTTGTCTCGAGTCCAA-ATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA
1 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1598600 TGAAACTGAA
Statistics
Matches: 442, Mismatches: 25, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
418 251 0.57
420 31 0.07
421 160 0.36
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (419 bp):
GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
ATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTC
GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTGTTGACAACCAGCGGTCCCTTCGTC
GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGA
AATTGGGAATGTTGTTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGC
Found at i:1608768 original size:10 final size:11
Alignment explanation
Indices: 1608755--1608823 Score: 67
Period size: 9 Copynumber: 6.5 Consensus size: 11
1608745 ACCTATTAAA
1608755 AATAAAATAA-
1 AATAAAATAAT
1608765 AAT-AAATAAT
1 AATAAAATAAT
*
1608775 AATATAACCTAAT
1 AATA-AA-ATAAT
1608788 ATATAAAATAAT
1 A-ATAAAATAAT
1608800 AAT-AAATAAT
1 AATAAAATAAT
1608810 -AT-AAATAAT
1 AATAAAATAAT
1608819 AATAA
1 AATAA
1608824 TAAAAAAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
9 15 0.30
10 15 0.30
11 3 0.06
12 7 0.14
13 7 0.14
14 3 0.06
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:1608777 original size:3 final size:3
Alignment explanation
Indices: 1608755--1608826 Score: 55
Period size: 3 Copynumber: 23.7 Consensus size: 3
1608745 ACCTATTAAA
1608755 AAT AA- AAT AA- AAT AAAT AAT AAT -AT AACCT AAT ATAT AA- AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA--T AAT A-AT AAT AAT AAT
1608800 AAT AAAT AAT -AT AAAT AAT AAT AAT AA
1 AAT -AAT AAT AAT -AAT AAT AAT AAT AA
1608827 AAAAAACTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 22
0.73 0.00 0.28
Matches are distributed among these distances:
2 10 0.17
3 34 0.59
4 11 0.19
5 3 0.05
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1608781 original size:22 final size:22
Alignment explanation
Indices: 1608756--1608832 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
1608746 CCTATTAAAA
1608756 ATAAAATAAAATAAATAATAAT
1 ATAAAATAAAATAAATAATAAT
** *
1608778 ATAACCTAATATATAA-AATAAT
1 ATAAAATAAAATA-AATAATAAT
*
1608800 A-ATAAATAATATAAATAATAAT
1 ATA-AAATAAAATAAATAATAAT
1608822 AATAAAA-AAAA
1 -ATAAAATAAAA
1608833 CTATATAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.07
22 34 0.77
23 6 0.14
24 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAAAATAAAATAAATAATAAT
Found at i:1608881 original size:22 final size:22
Alignment explanation
Indices: 1608842--1608890 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1608832 ACTATATAAC
*
1608842 ATATATTATATTTCCAAAAACT
1 ATATAATATATTTCCAAAAACT
* * *
1608864 ATATAATATGTTTTCAAAAATT
1 ATATAATATATTTCCAAAAACT
1608886 ATATA
1 ATATA
1608891 TGTTAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATAATATATTTCCAAAAACT
Found at i:1608966 original size:32 final size:33
Alignment explanation
Indices: 1608902--1609005 Score: 122
Period size: 33 Copynumber: 3.1 Consensus size: 33
1608892 GTTAATATAT
* *
1608902 TTTCATAAATCGTTTTCAAAAATCATATTATACG
1 TTTCAAAAATCGTTTTC-AAAACCATATTATACG
*
1608936 TTT-AAAAATCATTTTCAAAACCATATTATACG
1 TTTCAAAAATCGTTTTCAAAACCATATTATACG
*
1608968 TTTTCCAAAAT-GTTTTCAAAACCATATACTATACG
1 -TTTCAAAAATCGTTTTCAAAACCATAT--TATACG
1609003 TTT
1 TTT
1609006 TTAAAATTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
32 15 0.25
33 29 0.48
34 11 0.18
35 6 0.10
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (33 bp):
TTTCAAAAATCGTTTTCAAAACCATATTATACG
Found at i:1609017 original size:35 final size:35
Alignment explanation
Indices: 1608908--1609041 Score: 136
Period size: 35 Copynumber: 3.9 Consensus size: 35
1608898 ATATTTTCAT
1608908 AAATCGTTTTCAAAA--ATCATATTATACG-TTTAA
1 AAATCGTTTTCAAAACCAT-ATATTATACGTTTTAA
* *
1608941 AAATCATTTTCAAAACC--ATATTATACGTTTTCCA
1 AAATCGTTTTCAAAACCATATATTATACGTTTT-AA
* *
1608975 AAAT-GTTTTCAAAACCATATACTATACGTTTTTA
1 AAATCGTTTTCAAAACCATATATTATACGTTTTAA
* ** *
1609009 AAATTGTTTAAAAAAACATATATTATACGTTTT
1 AAATCGTTTTCAAAACCATATATTATACGTTTT
1609042 CGAAACCGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
32 10 0.12
33 28 0.33
34 10 0.12
35 37 0.44
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.40
Consensus pattern (35 bp):
AAATCGTTTTCAAAACCATATATTATACGTTTTAA
Found at i:1609127 original size:34 final size:35
Alignment explanation
Indices: 1609064--1609136 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 35
1609054 TATTAAACGT
1609064 TTTTCAAAATCATTTTTTAAAACTATATATTATAAG
1 TTTTCAAAATCATTTTTT-AAACTATATATTATAAG
*
1609100 TTTTCAAAATCATTTTTT-AACTATATATTATACG
1 TTTTCAAAATCATTTTTTAAACTATATATTATAAG
1609134 TTT
1 TTT
1609137 AAAAAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 18 0.50
36 18 0.50
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.51
Consensus pattern (35 bp):
TTTTCAAAATCATTTTTTAAACTATATATTATAAG
Found at i:1614865 original size:21 final size:21
Alignment explanation
Indices: 1614840--1614892 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1614830 GTGGTCATTC
1614840 GGATATATATGTAATCCTTTG
1 GGATATATATGTAATCCTTTG
1614861 GGATATATATGTAATCCTTTG
1 GGATATATATGTAATCCTTTG
* *
1614882 GAACATATATG
1 GGATATATATG
1614893 CTGTACTTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (21 bp):
GGATATATATGTAATCCTTTG
Found at i:1615242 original size:9 final size:9
Alignment explanation
Indices: 1615221--1615254 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1615211 TATATAAATA
*
1615221 AATGATAAG
1 AATGATAAT
*
1615230 AATGTTAAT
1 AATGATAAT
1615239 AATGATAAT
1 AATGATAAT
1615248 AATGATA
1 AATGATA
1615255 TGTGTGCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (9 bp):
AATGATAAT
Found at i:1619170 original size:28 final size:28
Alignment explanation
Indices: 1619138--1619205 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1619128 TGTTAAAGAG
*
1619138 TGGTCATTTGGGACATATGTGTTATATA
1 TGGTCATTCGGGACATATGTGTTATATA
* *
1619166 TGGTCCTTCGGGACATATGTGTTATATG
1 TGGTCATTCGGGACATATGTGTTATATA
*
1619194 TGGTCCTTCGGG
1 TGGTCATTCGGG
1619206 GAAAATCCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (28 bp):
TGGTCATTCGGGACATATGTGTTATATA
Found at i:1619459 original size:9 final size:9
Alignment explanation
Indices: 1619438--1619471 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1619428 TATATGAATA
*
1619438 AATGATAAG
1 AATGATAAT
*
1619447 AATGTTAAT
1 AATGATAAT
1619456 AATGATAAT
1 AATGATAAT
1619465 AATGATA
1 AATGATA
1619472 TGTGTGCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (9 bp):
AATGATAAT
Found at i:1626042 original size:21 final size:20
Alignment explanation
Indices: 1626012--1626091 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 20
1626002 AGAACCCCAA
*
1626012 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCT-TG
* *
1626033 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTT---G
*
1626056 GGGGGAATCGGTTCCCTCTTG
1 GGGGGAATCGATTCCC-CTTG
1626077 GGGGG-ATCGATTCCC
1 GGGGGAATCGATTCCC
1626092 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 10 0.20
21 21 0.42
23 16 0.32
24 3 0.06
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTTG
Found at i:1626094 original size:20 final size:19
Alignment explanation
Indices: 1626012--1626091 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 19
1626002 AGAACCCCAA
*
1626012 GGGGGTATCGATTCCCCTGT
1 GGGGGGATCGATTCCCCT-T
*
1626032 GGGGGGAATCGGTTCCCCTT
1 GGGGGG-ATCGATTCCCCTT
* *
1626052 CAAAGGGGGAATCGGTTCCCTCTT
1 ----GGGGGGATCGATTCCC-CTT
1626076 GGGGGGATCGATTCCC
1 GGGGGGATCGATTCCC
1626092 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 20 0.41
21 11 0.22
23 10 0.20
24 8 0.16
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (19 bp):
GGGGGGATCGATTCCCCTT
Found at i:1633745 original size:24 final size:24
Alignment explanation
Indices: 1633718--1633775 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
1633708 ACAGTCTGTA
*
1633718 CTTTTACAGTAGACGAGGCTTGTG
1 CTTTTGCAGTAGACGAGGCTTGTG
* *
1633742 CTTTTGCAGCAGACGAGGCTTTTG
1 CTTTTGCAGTAGACGAGGCTTGTG
1633766 CTTTTGCAGT
1 CTTTTGCAGT
1633776 GAATGAGTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (24 bp):
CTTTTGCAGTAGACGAGGCTTGTG
Found at i:1636429 original size:18 final size:19
Alignment explanation
Indices: 1636406--1636442 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1636396 AATGCGAATG
1636406 AAAAAT-AAAAGAAAACAA
1 AAAAATGAAAAGAAAACAA
*
1636424 AAAAATGAAAGGAAAACAA
1 AAAAATGAAAAGAAAACAA
1636443 GTTAGTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.05
Consensus pattern (19 bp):
AAAAATGAAAAGAAAACAA
Found at i:1641064 original size:10 final size:10
Alignment explanation
Indices: 1641023--1641082 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 10
1641013 AAATAAAATA
1641023 AATAAATAAT
1 AATAAATAAT
*
1641033 AATATAGCCTAAT
1 AATA-A--ATAAT
1641046 ATATAAAATAAT
1 A-AT-AAATAAT
1641058 AATAAATAAT
1 AATAAATAAT
1641068 -ATAAATAAT
1 AATAAATAAT
1641077 AATAAA
1 AATAAA
1641083 AACCTATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
10 16 0.38
11 3 0.07
12 5 0.12
13 5 0.12
14 3 0.07
15 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (10 bp):
AATAAATAAT
Found at i:1641093 original size:22 final size:20
Alignment explanation
Indices: 1641043--1641084 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1641033 AATATAGCCT
1641043 AATATATAAAATAATAATAAA
1 AATATAT-AAATAATAATAAA
*
1641064 TA-ATATAAATAATAATAAA
1 AATATATAAATAATAATAAA
1641083 AA
1 AA
1641085 CCTATATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 14 0.74
20 4 0.21
21 1 0.05
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATATATAAATAATAATAAA
Found at i:1641203 original size:33 final size:32
Alignment explanation
Indices: 1641154--1641292 Score: 127
Period size: 33 Copynumber: 4.1 Consensus size: 32
1641144 GTTAATATAT
1641154 TTTCAAAAATGATTTTCAAAAACCATATTATACG
1 TTTCAAAAATG-TTTTC-AAAACCATATTATACG
* *
1641188 -TTCAAAAATTGTTTTCAAAGCCATAATATACAG
1 TTTCAAAAA-TGTTTTCAAAACCATATTATAC-G
* * *
1641221 TTTCCAAAATGTTTTCAAAATCATATACTATATG
1 TTTCAAAAATGTTTTCAAAACCATAT--TATACG
**
1641255 TTTTCAAAAATGTTTAAAAAACCATATATTATACG
1 -TTTCAAAAATGTTTTCAAAACC--ATATTATACG
1641290 TTT
1 TTT
1641293 TCGAAACCGA
Statistics
Matches: 85, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
32 13 0.15
33 28 0.33
34 13 0.15
35 27 0.32
37 4 0.05
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (32 bp):
TTTCAAAAATGTTTTCAAAACCATATTATACG
Found at i:1641281 original size:35 final size:35
Alignment explanation
Indices: 1641153--1641294 Score: 109
Period size: 35 Copynumber: 4.1 Consensus size: 35
1641143 TGTTAATATA
*
1641153 TTTTCAAAAATGATTTTCAAAAACCATAT--TATACG
1 TTTTCAAAAATG--TTTAAAAAACCATATACTATACG
** *
1641188 --TTCAAAAATTGTTTTCAAAGCCATA-A-TATACAG
1 TTTTCAAAAA-TGTTTAAAAAACCATATACTATAC-G
* ** * *
1641221 -TTTCCAAAATGTTTTCAAAATCATATACTATATG
1 TTTTCAAAAATGTTTAAAAAACCATATACTATACG
*
1641255 TTTTCAAAAATGTTTAAAAAACCATATATTATACG
1 TTTTCAAAAATGTTTAAAAAACCATATACTATACG
1641290 TTTTC
1 TTTTC
1641295 GAAACCGATT
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
32 16 0.18
33 23 0.26
34 11 0.13
35 37 0.43
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (35 bp):
TTTTCAAAAATGTTTAAAAAACCATATACTATACG
Found at i:1641318 original size:36 final size:36
Alignment explanation
Indices: 1641272--1641400 Score: 129
Period size: 36 Copynumber: 3.6 Consensus size: 36
1641262 AAATGTTTAA
*
1641272 AAAACCATATATTATACGTTTTCG-AAACCGATTTTT
1 AAAACTATATATTATAC-TTTTCGAAAACCGATTTTT
* * *
1641308 AAAACTATATATTATACTTTTTGAAAACTGTTTTTT
1 AAAACTATATATTATACTTTTCGAAAACCGATTTTT
* ** *
1641344 AAAACTATATATTATACATTTAAAAAACACG-TTTTC
1 AAAACTATATATTATACTTTTCGAAAAC-CGATTTTT
1641380 AAAA-TATATACTATATACTTT
1 AAAACTATATA-T-TATACTTT
1641401 AAAAAATTAC
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
35 11 0.14
36 60 0.76
37 8 0.10
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (36 bp):
AAAACTATATATTATACTTTTCGAAAACCGATTTTT
Found at i:1641419 original size:35 final size:34
Alignment explanation
Indices: 1641304--1641428 Score: 96
Period size: 36 Copynumber: 3.6 Consensus size: 34
1641294 CGAAACCGAT
* ** *
1641304 TTTTAAAACTATATATTATACTTTTTGAAAAC-TG
1 TTTTAAAA-TATATATTATACATTTAAAAAACACG
1641338 TTTTTTAAAACTATATATTATACATTTAAAAAACACG
1 --TTTTAAAA-TATATATTATACATTTAAAAAACACG
*
1641375 TTTTCAAAATATATACTATATAC-TTTAAAAAATTAC-
1 TTTT-AAAATATATA-T-TATACATTTAAAAAA-CACG
*
1641411 TTTTAAAAT-TATTTTATA
1 TTTTAAAATATATATTATA
1641429 TATATTATAC
Statistics
Matches: 78, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
32 4 0.05
33 1 0.01
34 3 0.04
35 15 0.19
36 47 0.60
37 8 0.10
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (34 bp):
TTTTAAAATATATATTATACATTTAAAAAACACG
Found at i:1653080 original size:3 final size:3
Alignment explanation
Indices: 1653074--1653127 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
1653064 TTTATTTCAT
** *
1653074 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA ATA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1653119 TTTA TTA TT
1 -TTA TTA TT
1653128 TACAAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1653117 original size:15 final size:15
Alignment explanation
Indices: 1653075--1653127 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
1653065 TTATTTCATT
1653075 TATTATTATTATTAA
1 TATTATTATTATTAA
*
1653090 AATTATTATTATTAA
1 TATTATTATTATTAA
1653105 TATTA-TATATATT-A
1 TATTATTAT-TATTAA
1653119 T-TTATTATT
1 TATTATTATT
1653128 TACAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 4 0.12
14 8 0.24
15 22 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAA
Found at i:1654763 original size:9 final size:9
Alignment explanation
Indices: 1654749--1654781 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1654739 ATATCTTATG
1654749 TAATTAATT
1 TAATTAATT
1654758 TAATTAATT
1 TAATTAATT
*
1654767 TTA-TAATT
1 TAATTAATT
1654775 TAATTAA
1 TAATTAA
1654782 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:1657847 original size:8 final size:7
Alignment explanation
Indices: 1657821--1657908 Score: 58
Period size: 7 Copynumber: 12.4 Consensus size: 7
1657811 CATTTACATT
1657821 TTTTGCA
1 TTTTGCA
1657828 TTTTGCA
1 TTTTGCA
1657835 TTTTGCA
1 TTTTGCA
1657842 TCTTTGCA
1 T-TTTGCA
*
1657850 -TTTGTA
1 TTTTGCA
*
1657856 TTTT-TA
1 TTTTGCA
1657862 CTTTTGCA
1 -TTTTGCA
* *
1657870 TTGTACA
1 TTTTGCA
*
1657877 GTTTGCA
1 TTTTGCA
1657884 TTATT--A
1 TT-TTGCA
1657890 TTTTTGCA
1 -TTTTGCA
1657898 TTTTCGCA
1 TTTT-GCA
1657906 TTT
1 TTT
1657909 ACATTACATT
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
6 10 0.16
7 38 0.59
8 16 0.25
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (7 bp):
TTTTGCA
Found at i:1657892 original size:34 final size:35
Alignment explanation
Indices: 1657844--1657911 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
1657834 ATTTTGCATC
1657844 TTTGCATTTGTATTTTTAC-TTTT-GCATTGTACAG
1 TTTGCATTTGTATTTTTACATTTTCGCATT-TACAG
*
1657878 TTTGCATTAT-TATTTTTGCATTTTCGCATTTACA
1 TTTGCATT-TGTATTTTTACATTTTCGCATTTACA
1657912 TTACATTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 16 0.53
35 9 0.30
36 5 0.17
ACGTcount: A:0.19, C:0.13, G:0.12, T:0.56
Consensus pattern (35 bp):
TTTGCATTTGTATTTTTACATTTTCGCATTTACAG
Found at i:1663143 original size:75 final size:75
Alignment explanation
Indices: 1663011--1663246 Score: 343
Period size: 75 Copynumber: 3.2 Consensus size: 75
1663001 ACAAGAAGCA
* * ***
1663011 AATGATGGAGCATGCTGAAAGCTCATTTCAATCATG-ATCAGGAATATTGACACATTTTGAACGA
1 AATGTTGGGGCATGCTGAAAGCTCATTTCAATCA-GAATCAGGAATATTGATGTATTTTGAACGA
*
1663075 TTGAATTAGCT
65 TTGTATTAGCT
*
1663086 AATTTTGGGGCATGCTGAAAGCTCATTTCAATCAGAATCAGGAATATTGATGTATTTTGAACGAT
1 AATGTTGGGGCATGCTGAAAGCTCATTTCAATCAGAATCAGGAATATTGATGTATTTTGAACGAT
*
1663151 TGTATTAGTT
66 TGTATTAGCT
* * *
1663161 AATGTTGGGGGATGATGAAAGCTCATTTCAATCAGAATCAGGAATATTGATGT-TTTTGAATG-T
1 AATGTTGGGGCATGCTGAAAGCTCATTTCAATCAGAATCAGGAATATTGATGTATTTTGAACGAT
1663224 TGTATTAGCT
66 TGTATTAGCT
1663234 AATGTTGGGGCAT
1 AATGTTGGGGCAT
1663247 ATTGAAGGCC
Statistics
Matches: 146, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
73 22 0.15
74 9 0.06
75 115 0.79
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (75 bp):
AATGTTGGGGCATGCTGAAAGCTCATTTCAATCAGAATCAGGAATATTGATGTATTTTGAACGAT
TGTATTAGCT
Found at i:1664565 original size:20 final size:22
Alignment explanation
Indices: 1664519--1664582 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
1664509 TATATCTACA
1664519 CTCTTCAAAGATGACAGATTCT
1 CTCTTCAAAGATGACAGATTCT
*
1664541 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGACAGATTCT
* * *
1664563 CTTTTCAAAGAAGAAAGATT
1 CTCTTCAAAGATGACAGATT
1664583 TATTGAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (22 bp):
CTCTTCAAAGATGACAGATTCT
Found at i:1665346 original size:45 final size:45
Alignment explanation
Indices: 1665287--1665394 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
1665277 TTTTTGATAT
* *
1665287 TTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGG
1 TTTCAAAGCCTTCGGGTCATCTATAAGCCCTACAGTGCAGGATGG
* *
1665332 TTTCGAAA-CCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGT
1 TTTC-AAAGCCTTCGGGTCATCTATAAGCCCTACAGTGCAGGATGG
1665377 TTTCAAAAAGCCTTCGGG
1 TTTC--AAAGCCTTCGGG
1665395 AGCTTTCTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 41 0.75
46 6 0.11
47 8 0.15
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (45 bp):
TTTCAAAGCCTTCGGGTCATCTATAAGCCCTACAGTGCAGGATGG
Found at i:1665456 original size:45 final size:45
Alignment explanation
Indices: 1665402--1665595 Score: 253
Period size: 45 Copynumber: 4.3 Consensus size: 45
1665392 GGGAGCTTTC
* * * * *
1665402 TGATATTTTCAAAGCCTTCAGGTCATTTATAAGCCCTTCAGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
* * * *
1665447 TGTTGTTTTCAAAACGTTCGGGTCATCTGTAAGCCCTTCAGCGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
* *
1665492 TGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
* * *
1665537 TGATGCTTTCAAAACCTTCGGGTCATCCATAAGCCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
*
1665582 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
1665596 AGCCTTCAGG
Statistics
Matches: 129, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 129 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:1665467 original size:121 final size:121
Alignment explanation
Indices: 1665228--1666937 Score: 499
Period size: 135 Copynumber: 13.4 Consensus size: 121
1665218 CTATTTCCCA
* * * * *
1665228 CATCCGTAAGCTCTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTCTGATATTTTCAA
* *
1665293 AGCCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCGAAACCTTCGGGT
66 AGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACCTTCGGGT
1665349 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTCTGATATTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTCTGATATTTTCAA
* * * * *
1665414 AGCCTTCAGGTCATTTATAAGCCCTTCAGTGTATGTTGTTTTCAAAACGTTCGGGT
66 AGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACCTTCGGGT
* * * *
1665470 CATCTGTAAGCCCTTCAGCGCATGATGTTTTC-AAAA-CCTTCGGGTTATCTGTAAGCCCTTCAG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTC-GG------G--AG-CTTTC--
* * * * * *
1665533 TGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGCCCTACAGTGCAGGATGTTTTCAAAAAG
54 TG-AT-AT--TTTCAAAGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTC-AAAA-
* *
1665598 CCTTCAGGA
113 CCTTCGGGT
* * * *** * * ** *** * *
1665607 GATTTTTGACA-TTTTCAAAGCTTTC-GG--GTCATCTGTAAGCCCTTC---AG--TGCATGATG
1 CATCTGT-A-AGCCCT-ACAG--TGCAGGATGTTTTCAAAAAG-CCTTCGGGAGCTTTC-TGATA
* * * *
1665663 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
59 TTTTCAAAGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACCTTCGGGT
* * * * * ****
1665726 CATCTATAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG-TC-ATCTG-TAAGCCCTA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTCTGATATTTTC-A
* * ** * * * * **
1665786 CAG--TGCAGGATGTTTTCAAAAAG-CCATCGGGAGCTTTC-TGATATTTTCAAAGA-CTTCGGG
65 AAGCCTTCA-G--GTCATCTATAAGCCCTTC---AG--TGCATGATGGTTTCAAA-ACCTTCGGG
1665846 T
121 T
* * * *
1665847 CATCTATAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGTCATCTGTAAGCCCTTCAG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTC-GG------G--AG-CTTTC--
* * * * * * *
1665910 TGTATGATGTTTTCAAAACCTTCGGGCCATCTGTAAGACCTTCGGTGCATGATGTTTTCAAAACC
54 TG-AT-A--TTTTCAAAGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACC
1665975 TTCGGGT
115 TTCGGGT
* * * * * * *
1665982 CATCTATAAGCCCTACAGTGAAGGATGTTTTCAAAAAGCCTTCAGGAGATTTTTAATATTTTTAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTCTGATATTTTCAA
* * * *
1666047 AGCCTTC-GAGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAAACTTCGGGT
66 AGCCTTCAG-GTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACCTTCGGGT
* *
1666103 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGTCATCTGTAAGCCCTTTAG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTC-GG------G--AG--C-TT--
* * * * * *
1666166 TGCATGATGTTTTCAAA-CCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAGC
52 T-C-TGATATTTTCAAAGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAA-C
1666230 CTTCGGAG-
114 CTTCGG-GT
* * **** * * ** *** *
1666238 CTTTTTGATATTTTC-AAAGCCTTC-GG--GTCATCTGTAAGCCCTTC---AG--TGCATGATAT
1 C-ATCTG-TAAGCCCTACAG--TGCAGGATGTTTTCAAAAAG-CCTTCGGGAGCTTTC-TGATAT
* * * * * *
1666294 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAGCTTC-GAT
60 TTTCAAAGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACCTTCGGGT
* * *
1666355 CATCTGTAAGCTCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGTCATCTGTAAGCTCTTCAG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTC-GG------G--AG--CTT---
* * * *
1666418 TGCATGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACC
52 T-C-TGATATTTTCAAAGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACC
1666483 TTCGGGT
115 TTCGGGT
* * * * **
1666490 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACTTTCAGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAA-----A-GCCTTC-GGGAG--CTT---T-
* * * * *
1666555 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
53 C-TGATATTTTCAAAGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACCTT
1666620 CGGGT
117 CGGGT
* * *
1666625 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGTCATCTGTAAGCCCTTCAG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTC-GG------G--AG-CTTTC--
* * * *
1666688 TGCATAATGTTTTCAAAACCTTC-GAGCCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAC
54 TG-AT-A--TTTTCAAAGCCTTCAG-GTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAAC
1666752 CTTCGGGT
114 CTTCGGGT
* *
1666760 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGG------G--AG--CTT---T
* ** * * * * * *
1666823 GCATGATGTTTTCAAAATCTTCGGGTTATCTGTTAGCCCTTCAGTGCATGATGTTTTGAAAACCT
53 -C-TGATATTTTCAAAGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACCT
1666888 TCGGGT
116 TCGGGT
* *
1666894 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
1666938 TCATCTGTAA
Statistics
Matches: 1242, Mismatches: 195, Indels: 297
0.72 0.11 0.17
Matches are distributed among these distances:
114 7 0.01
115 14 0.01
116 11 0.01
117 19 0.02
118 32 0.03
119 64 0.05
120 18 0.01
121 327 0.26
122 5 0.00
123 2 0.00
124 4 0.00
125 3 0.00
126 8 0.01
127 6 0.00
128 8 0.01
129 7 0.01
130 3 0.00
131 7 0.01
132 5 0.00
133 5 0.00
134 227 0.18
135 366 0.29
136 21 0.02
137 22 0.02
138 23 0.02
139 12 0.01
140 3 0.00
141 9 0.01
143 4 0.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (121 bp):
CATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTCTGATATTTTCAA
AGCCTTCAGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCAAAACCTTCGGGT
Found at i:1665650 original size:211 final size:211
Alignment explanation
Indices: 1665281--1666986 Score: 2273
Period size: 211 Copynumber: 7.9 Consensus size: 211
1665271 GGGAGCTTTT
* * * * *
1665281 TGATATTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGGTTTCGAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
1665346 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTCTGATATTTT
66 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTT
* * * * * *
1665411 CAAAGCCTTCAGGTCATTTATAAGCCCTTCAGTGTATGTTGTTTTCAAAACGTTCGGGTCATCTG
131 CAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
*
1665476 TAAGCCCTTCAGCGCA
196 TAAGCCCTTCAGTGCA
* *
1665492 TGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
** * *
1665557 GGTCATCCATAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGATTTTTGACATTTT
66 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTT
*
1665622 CAAAGCTTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
131 CAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
1665687 TAAGCCCTTCAGTGCA
196 TAAGCCCTTCAGTGCA
*
1665703 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * *
1665768 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCATCGGGAGCTTTCTGATATTTT
66 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTT
* *
1665833 CAAAGACTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
131 CAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
*
1665898 TAAGCCCTTCAGTGTA
196 TAAGCCCTTCAGTGCA
* * *
1665914 TGATGTTTTCAAAACCTTCGGGCCATCTGTAAGACCTTCGGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * * *
1665979 GGTCATCTATAAGCCCTACAGTGAAGGATGTTTTCAAAAAGCCTTCAGGAGATTTTTAATATTTT
66 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTT
* * * *
1666044 TAAAGCCTTCGAGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAAACTTCGGGTCATCTG
131 CAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
1666109 TAAGCCCTTCAGTGCA
196 TAAGCCCTTCAGTGCA
*
1666125 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTC-AAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
*
1666189 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTC-AAAAGCCTTC-GGAGCTTTTTGATATTTT
66 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTT
*
1666252 CAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCGGGTCATCTG
131 CAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
1666317 TAAGCCCTTCAGTGCA
196 TAAGCCCTTCAGTGCA
* * *
1666333 TGATGTTTTCAAAAGCTTC-GATCATCTGTAAGCTCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * * *
1666397 GGTCATCTGTAAGCTCTTCAGTGCATGATATTTTC-AAAA-CCTTCGGGTCATCTGTAAGCCCTT
66 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG--A---G--A----TT
* * *
1666460 CAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
120 ---T--TTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
* *
1666525 ACTTTCAGGTCATCTGTAAGCCCTTCAGTGCA
180 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666557 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
1666622 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGTCATCTGTAAGCCCTT
66 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG--A---G--A----TT
** * * *
1666685 CAGTGCATAATGTTTTCAAAACCTTCGAGCCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
120 -TTTG-AT-A--TTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1666750 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
180 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1666782 TGATGTTTTCAAAACCTTC-GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * * * *
1666846 GGTTATCTGTTAGCCCTTCAGTGCATGATGTTTT-GAAAA-CCTTCGGGTCATCTGTAAGCCCTT
66 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG--A---G--A----TT
* * *
1666909 CAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
120 ---T--TTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1666974 ACCTTCGGGTCAT
180 ACCTTCGGGTCAT
1666987 TCATAAGACT
Statistics
Matches: 1365, Mismatches: 102, Indels: 43
0.90 0.07 0.03
Matches are distributed among these distances:
207 37 0.03
208 156 0.11
209 10 0.01
210 43 0.03
211 632 0.46
213 1 0.00
219 2 0.00
221 2 0.00
222 3 0.00
224 271 0.20
225 204 0.15
227 2 0.00
228 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (211 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTT
CAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
TAAGCCCTTCAGTGCA
Found at i:1665669 original size:45 final size:45
Alignment explanation
Indices: 1665618--1665806 Score: 333
Period size: 45 Copynumber: 4.2 Consensus size: 45
1665608 ATTTTTGACA
* *
1665618 TTTTCAAAGCTTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1665663 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
*
1665708 TTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
* *
1665753 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1665798 TTTTCAAAA
1 TTTTCAAAA
1665807 AGCCATCGGG
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 138 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
Found at i:1665880 original size:45 final size:45
Alignment explanation
Indices: 1665824--1666017 Score: 282
Period size: 45 Copynumber: 4.3 Consensus size: 45
1665814 GGGAGCTTTC
*
1665824 TGATATTTTCAAAGA-CTTCGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAA-ACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
* *
1665869 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
* * * *
1665914 TGATGTTTTCAAAACCTTCGGGCCATCTGTAAGACCTTCGGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
* *
1665959 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTACAGTGAA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
*
1666004 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
1666018 AGCCTTCAGG
Statistics
Matches: 134, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
44 1 0.01
45 133 0.99
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:1666199 original size:44 final size:45
Alignment explanation
Indices: 1666040--1666235 Score: 304
Period size: 45 Copynumber: 4.4 Consensus size: 45
1666030 ATTTTTAATA
* * * *
1666040 TTTTTAAAGCCTTCGAGTCATCTGTAAGCCCTTTAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
*
1666085 TTTTCAAAAACTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
*
1666130 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
* *
1666175 TTTTC-AAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1666219 TTTTCAAAAGCCTTCGG
1 TTTTCAAAA-CCTTCGG
1666236 AGCTTTTTGA
Statistics
Matches: 139, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
44 41 0.29
45 91 0.65
46 7 0.05
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (45 bp):
TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
Found at i:1666273 original size:74 final size:72
Alignment explanation
Indices: 1666170--1666308 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 72
1666160 CTTTAGTGCA
* *
1666170 TGATGTTTTCAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAGCCTTCG
1 TGATATTTTCAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTTTCAAAA-CCTTCG
1666235 GAGCTTTT
65 GAGCTTTT
* *
1666243 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCG
1 TGATATTTTCAAA-CCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTTTCAAAACCTTCG
1666308 G
65 G
1666309 GTCATCTGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 19 0.31
74 42 0.69
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (72 bp):
TGATATTTTCAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTTTCAAAACCTTCGG
AGCTTTT
Found at i:1666292 original size:45 final size:45
Alignment explanation
Indices: 1666243--1666986 Score: 1321
Period size: 45 Copynumber: 16.6 Consensus size: 45
1666233 CGGAGCTTTT
* *
1666243 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1666288 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1666333 TGATGTTTTCAAAAGCTTC-GATCATCTGTAAGCTCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1666377 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCTCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1666422 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666467 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1666512 TGATGTTTTCAAAACTTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666557 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666602 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666647 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1666692 TAATGTTTTCAAAACCTTCGAGCCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666737 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666782 TGATGTTTTCAAAACCTTC-GGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1666826 TGATGTTTTCAAAATCTTCGGGTTATCTGTTAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1666871 TGATGTTTTGAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666916 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1666961 TGATGTTTTCAAAACCTTCGGGTCAT
1 TGATGTTTTCAAAACCTTCGGGTCAT
1666987 TCATAAGACT
Statistics
Matches: 669, Mismatches: 28, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
44 84 0.13
45 585 0.87
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1666352 original size:118 final size:118
Alignment explanation
Indices: 1666125--1666352 Score: 386
Period size: 118 Copynumber: 1.9 Consensus size: 118
1666115 CTTCAGTGCA
* * *
1666125 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAACCTTCGG
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAACCTTCGG
1666190 GTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAGCCTTCGGAGCTTTT
66 GTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAGCCTTCGGAGCTTTT
*
1666243 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTC-AAACCTTCG
* *
1666308 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAG-CTTCG
65 GGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAGCCTTCG
1666353 ATCATCTGTA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
118 56 0.54
119 47 0.46
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (118 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAACCTTCGG
GTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAGCCTTCGGAGCTTTT
Found at i:1667151 original size:3 final size:3
Alignment explanation
Indices: 1667145--1667203 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
1667135 ATATTTCATT
** * *
1667145 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA ATA TGA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1667190 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
1667204 TAACAAATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.91
4 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1668858 original size:9 final size:9
Alignment explanation
Indices: 1668844--1668877 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1668834 ATATCTTATG
1668844 TTAATTAAT
1 TTAATTAAT
1668853 TTAATTAAT
1 TTAATTAAT
*
1668862 TTTA-TAAT
1 TTAATTAAT
1668870 TTAATTAA
1 TTAATTAA
1668878 AGAATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATTAAT
Found at i:1670650 original size:17 final size:16
Alignment explanation
Indices: 1670628--1670659 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1670618 GAGCATACTC
1670628 TTAATATTTATTTATTT
1 TTAATATTT-TTTATTT
1670645 TTAATATTTTTTATT
1 TTAATATTTTTTATT
1670660 AGAGACTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTAATATTTTTTATTT
Found at i:1671381 original size:17 final size:17
Alignment explanation
Indices: 1671359--1671392 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1671349 TTTAACATTT
1671359 AGTAAT-AATAATTAATA
1 AGTAATAAATAA-TAATA
1671376 AGTAATAAATAATAATA
1 AGTAATAAATAATAATA
1671393 CTAATAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
AGTAATAAATAATAATA
Found at i:1672229 original size:40 final size:41
Alignment explanation
Indices: 1672135--1672443 Score: 239
Period size: 40 Copynumber: 7.6 Consensus size: 41
1672125 TTAGCGGTGT
* * * * *
1672135 TTTTTGAACAAACGTCGATAAATACTCGTACTTTAGTGTCG
1 TTTTTGTACAAACGCCGCTAAATACTTGTACTTTAGTGGCG
* * *
1672176 TTTTTATATAAACGCCGCTAAATA-TTGTAGTTTAGTGGCG
1 TTTTTGTACAAACGCCGCTAAATACTTGTACTTTAGTGGCG
* * * *
1672216 TTTTTGTACAAACGCCACTAAAGACTCGTACTTTAGTGACG
1 TTTTTGTACAAACGCCGCTAAATACTTGTACTTTAGTGGCG
* * * * * ** *
1672257 CTTTTATATAAATGCTGCTAAATAC-TGTACTTTAACGGTG
1 TTTTTGTACAAACGCCGCTAAATACTTGTACTTTAGTGGCG
* * * ** *
1672297 TTTTAAGCACAAATGCCAATAAATACTTGTACTTTAGTGAC-
1 TTTT-TGTACAAACGCCGCTAAATACTTGTACTTTAGTGGCG
* * * *
1672338 TTTTTATACAAACGCCGATAAAGACTCGTACTTTAGTGGCG
1 TTTTTGTACAAACGCCGCTAAATACTTGTACTTTAGTGGCG
* * * * *
1672379 TTTTAAGCACAAACGCCGCTAAATAC-TATAGTTTAGTGGCA
1 TTTT-TGTACAAACGCCGCTAAATACTTGTACTTTAGTGGCG
* *
1672420 TTTGTGTACAAATGCCGCTAAATA
1 TTTTTGTACAAACGCCGCTAAATA
1672444 TTTAGTCTTT
Statistics
Matches: 203, Mismatches: 60, Indels: 11
0.74 0.22 0.04
Matches are distributed among these distances:
40 91 0.45
41 86 0.42
42 26 0.13
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTTTGTACAAACGCCGCTAAATACTTGTACTTTAGTGGCG
Found at i:1672262 original size:81 final size:82
Alignment explanation
Indices: 1672153--1672445 Score: 304
Period size: 81 Copynumber: 3.6 Consensus size: 82
1672143 CAAACGTCGA
* *
1672153 TAAATACTCGTACTTTAGTGTCGTTTTTATATAAACGCCGCTAAATATTGTAGTTTAGTGGCGTT
1 TAAATACTCGTACTTTAGTGACGTTTTTATATAAACGCCGCTAAATATTGTACTTTAGTGGCGTT
* *
1672218 TT-TGTACAAACGCCAC
66 TTAAGCACAAACGCCAC
* * * * * ** *
1672234 TAAAGACTCGTACTTTAGTGACGCTTTTATATAAATGCTGCTAAATACTGTACTTTAACGGTGTT
1 TAAATACTCGTACTTTAGTGACGTTTTTATATAAACGCCGCTAAATATTGTACTTTAGTGGCGTT
* *
1672299 TTAAGCACAAATGCCAA
66 TTAAGCACAAACGCCAC
* * * * *
1672316 TAAATACTTGTACTTTAGTGAC-TTTTTATACAAACGCCGATAAAGACTCGTACTTTAGTGGCGT
1 TAAATACTCGTACTTTAGTGACGTTTTTATATAAACGCCGCTAAATA-TTGTACTTTAGTGGCGT
*
1672380 TTTAAGCACAAACGCCGC
65 TTTAAGCACAAACGCCAC
* * * * * * * *
1672398 TAAATACT-ATAGTTTAGTGGCATTTGTGTACAAATGCCGCTAAATATT
1 TAAATACTCGTACTTTAGTGACGTTTTTATATAAACGCCGCTAAATATT
1672446 TAGTCTTTAA
Statistics
Matches: 170, Mismatches: 39, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
81 86 0.51
82 84 0.49
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (82 bp):
TAAATACTCGTACTTTAGTGACGTTTTTATATAAACGCCGCTAAATATTGTACTTTAGTGGCGTT
TTAAGCACAAACGCCAC
Found at i:1672431 original size:122 final size:121
Alignment explanation
Indices: 1672194--1672445 Score: 269
Period size: 122 Copynumber: 2.1 Consensus size: 121
1672184 TAAACGCCGC
* * *
1672194 TAAATATTGTAGTTTAGTGGCGTTTTTGTACAAACGCCACTAAAGACTCGTACTTTAGTGACGCT
1 TAAATATTGTACTTTAGTGACGTTTTTATACAAACGCCACTAAAGACTCGTACTTTAGTGACGCT
* * * * * **
1672259 TTTATATAAATGCTGCTAAATACTGTACTTTAACGGTGTTTTAAGCACAAATGCCAA
66 TTTACACAAACGCCGCTAAATACTATACTTTAACGGCATTTT-AGCACAAATGCCAA
*
1672316 TAAATACTTGTACTTTAGTGAC-TTTTTATACAAACGCCGA-TAAAGACTCGTACTTTAGTGGCG
1 TAAATA-TTGTACTTTAGTGACGTTTTTATACAAACGCC-ACTAAAGACTCGTACTTTAGTGACG
* ** * **
1672379 -TTTTAAGCACAAACGCCGCTAAATACTATAGTTTAGTGGCATTTGT-GTACAAATGCCGC
64 CTTTT-A-CACAAACGCCGCTAAATACTATACTTTAACGGCATTT-TAGCACAAATGCCAA
1672438 TAAATATT
1 TAAATATT
1672446 TAGTCTTTAA
Statistics
Matches: 108, Mismatches: 17, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
121 6 0.06
122 60 0.56
123 41 0.38
124 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (121 bp):
TAAATATTGTACTTTAGTGACGTTTTTATACAAACGCCACTAAAGACTCGTACTTTAGTGACGCT
TTTACACAAACGCCGCTAAATACTATACTTTAACGGCATTTTAGCACAAATGCCAA
Found at i:1677813 original size:41 final size:42
Alignment explanation
Indices: 1677707--1677815 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 42
1677697 AGTAAATAAT
* * * *
1677707 TTAAGTCCTTCGGGCCATCAGTAAGTCTCTCGAGCATGATGA
1 TTAAGTCCTTCGGGCCATCTGTAAGCCTCTAGAGCAAGATGA
* * *
1677749 TTAAAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA
1 TT--AAGTCCTTCGGGCCATCTGTAAGCCTCTAGAGCAAGATGA
1677793 -TAAGTCCTTCGGGCCATCTGTAA
1 TTAAGTCCTTCGGGCCATCTGTAA
1677816 AACCTTCGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 20 0.36
42 2 0.04
43 1 0.02
44 33 0.59
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (42 bp):
TTAAGTCCTTCGGGCCATCTGTAAGCCTCTAGAGCAAGATGA
Found at i:1678147 original size:41 final size:40
Alignment explanation
Indices: 1678020--1678148 Score: 150
Period size: 42 Copynumber: 3.1 Consensus size: 40
1678010 GAAGCAAATC
1678020 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTTGGGT
1 CATCAGT-AGTCTTTCGAGCATGATGAT-AAATCATTTGGGT
* *
1678062 CATCAGTACGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
1 CATCAGTA-GTCTTTCGAGCATGATGA-TAAATCATTTGGGT
** * * *
1678104 CATTTGTGAGTCTCTCGAGCAAGATGATAAATCTTTTGGGT
1 CATCAGT-AGTCTTTCGAGCATGATGATAAATCATTTGGGT
1678145 CATC
1 CATC
1678149 CATAAGACCT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
41 16 0.21
42 57 0.76
43 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (40 bp):
CATCAGTAGTCTTTCGAGCATGATGATAAATCATTTGGGT
Found at i:1678263 original size:53 final size:53
Alignment explanation
Indices: 1678183--1678351 Score: 241
Period size: 53 Copynumber: 3.2 Consensus size: 53
1678173 TTCACACTAT
* * *
1678183 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTATTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
* *
1678236 AAGATTATTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGACAG
1 AAGATTATTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
* * * *
1678289 AAGACTATTCGAGTTATACTCCCTAAAGCAAGAGGGAGGGAACCCGCTAGTCA-
1 AAGATTATTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGACAG
1678342 AAGATTATTC
1 AAGATTATTC
1678352 AAAGAAGAGG
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 99 0.95
54 5 0.05
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (53 bp):
AAGATTATTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
Found at i:1678552 original size:3 final size:3
Alignment explanation
Indices: 1678501--1678543 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1678491 TTTGTCCGGG
* * * *
1678501 ATT ATT ATT ATT ATT ATT TTT ATT TTT ATT TTT ATA ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1678544 AATATTATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1689296 original size:23 final size:22
Alignment explanation
Indices: 1689270--1689337 Score: 54
Period size: 23 Copynumber: 3.1 Consensus size: 22
1689260 ATCAGTAAGT
1689270 CTTTCGAGCATGATGATGAAATC
1 CTTTCGAGCATGATGAT-AAATC
* * *
1689293 CTTT-GGGTCATCA-G-TAAGT-
1 CTTTCGAG-CATGATGATAAATC
1689312 CTTTCGAGCATGATGATTAAATC
1 CTTTCGAGCATGATGA-TAAATC
1689335 CTT
1 CTT
1689338 CGGGTCATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
19 8 0.24
20 6 0.18
21 1 0.03
22 7 0.21
23 11 0.33
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (22 bp):
CTTTCGAGCATGATGATAAATC
Found at i:1689318 original size:42 final size:42
Alignment explanation
Indices: 1689259--1689388 Score: 179
Period size: 42 Copynumber: 3.1 Consensus size: 42
1689249 GAAGCAAATC
*
1689259 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTTGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATAAAATCCTTTGGGT
* *
1689301 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATAAAATCCTTTGGGT
** * * * *
1689343 CATTTGTGAGTCTCTCGAGCAAGATGATAAAATCTTTTGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATAAAATCCTTTGGGT
1689385 CATC
1 CATC
1689389 CATAAGACCT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATAAAATCCTTTGGGT
Found at i:1689503 original size:53 final size:53
Alignment explanation
Indices: 1689423--1689587 Score: 206
Period size: 53 Copynumber: 3.1 Consensus size: 53
1689413 TTCACACTAT
* * * **
1689423 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGGACTCGTAGGTAG
1 AAGATTGTTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
* * *
1689476 AAGATTATTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGACAG
1 AAGATTGTTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
* * * *
1689529 AAGACTGTTCGAGTTATACTCCCTAAAGCAAGAGGGAGGGAACCCGCTAGTCA-
1 AAGATTGTTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGACAG
1689582 AAGATT
1 AAGATT
1689588 ATTCAAAGAA
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 91 0.95
54 5 0.05
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
Found at i:1689763 original size:12 final size:12
Alignment explanation
Indices: 1689742--1689775 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1689732 TTGTCCGGGA
*
1689742 TTATTATTATTT
1 TTATTTTTATTT
1689754 TTATTTTTATTT
1 TTATTTTTATTT
1689766 TTATTTTTAT
1 TTATTTTTAT
1689776 AATTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:1689781 original size:18 final size:18
Alignment explanation
Indices: 1689741--1689783 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1689731 TTTGTCCGGG
*
1689741 ATTATTATTATTTTTATT
1 ATTATTATTATTTTTATA
* *
1689759 TTTATTTTTATTTTTATA
1 ATTATTATTATTTTTATA
1689777 ATTATTA
1 ATTATTA
1689784 AATATTAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTATTATTATTTTTATA
Found at i:1689789 original size:7 final size:7
Alignment explanation
Indices: 1689779--1689805 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1689769 TTTTTATAAT
1689779 TATTAAA
1 TATTAAA
1689786 TATTAAA
1 TATTAAA
1689793 TATTAAA
1 TATTAAA
1689800 TATTAA
1 TATTAA
1689806 TTAATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATTAAA
Found at i:1696046 original size:21 final size:21
Alignment explanation
Indices: 1696021--1696077 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1696011 TTATTTATTA
1696021 TTATGGATTTCAAGTGTCTTG
1 TTATGGATTTCAAGTGTCTTG
* * *
1696042 TTATGGATTTCAAATTTGTTG
1 TTATGGATTTCAAGTGTCTTG
*
1696063 TTATGGATGTCAAGT
1 TTATGGATTTCAAGT
1696078 TTATATGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (21 bp):
TTATGGATTTCAAGTGTCTTG
Found at i:1699695 original size:43 final size:42
Alignment explanation
Indices: 1699635--1699725 Score: 155
Period size: 43 Copynumber: 2.1 Consensus size: 42
1699625 ATTATACTTC
*
1699635 ATTATAATTTAAATTAGAGTAAACTATACCATTGACCACCCA
1 ATTATAATTTAAATTAGAGTAAACTATACCAGTGACCACCCA
1699677 ATTATAGATTTAAATTAGAGTAAACTATACCAGTGACCACCCA
1 ATTATA-ATTTAAATTAGAGTAAACTATACCAGTGACCACCCA
*
1699720 ACTATA
1 ATTATA
1699726 TTCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 6 0.13
43 40 0.87
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30
Consensus pattern (42 bp):
ATTATAATTTAAATTAGAGTAAACTATACCAGTGACCACCCA
Found at i:1701252 original size:30 final size:28
Alignment explanation
Indices: 1701203--1701277 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
1701193 ACATCTAAAC
1701203 ATTAAAAATATATTTTTATTATTACTCTTA
1 ATTAAAAATATA-TTTTATTATTA-TCTTA
* * *
1701233 ACTTTAAAATATATTTTATTCTTATTTTA
1 A-TTAAAAATATATTTTATTATTATCTTA
1701262 ATTAAAAATATATTTT
1 ATTAAAAATATATTTT
1701278 CTATATCTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 14 0.35
29 5 0.12
30 11 0.28
31 10 0.25
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (28 bp):
ATTAAAAATATATTTTATTATTATCTTA
Found at i:1701403 original size:29 final size:29
Alignment explanation
Indices: 1701326--1701404 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 29
1701316 ATATTCTATC
** *
1701326 AAAAATATATTTTATTTTTATTTTACCTT
1 AAAAATATATTTTATTTTTATCATAACTT
* *
1701355 -AAAATATATTTTAATCTTATCATAACTT
1 AAAAATATATTTTATTTTTATCATAACTT
1701383 AAAAATATATTTTATTTTTATC
1 AAAAATATATTTTATTTTTATC
1701405 TTCGCTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 23 0.55
29 19 0.45
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (29 bp):
AAAAATATATTTTATTTTTATCATAACTT
Found at i:1701484 original size:30 final size:30
Alignment explanation
Indices: 1701448--1701512 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1701438 GATTTTTTAC
*
1701448 ATATATTATATTCTTAACTTAAATTATTAA
1 ATATATTATAGTCTTAACTTAAATTATTAA
* *
1701478 ATATATTCTAGTCTTACCTTAAATTATTAA
1 ATATATTATAGTCTTAACTTAAATTATTAA
1701508 ATATA
1 ATATA
1701513 ATTTATCCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATATTATAGTCTTAACTTAAATTATTAA
Found at i:1701574 original size:31 final size:31
Alignment explanation
Indices: 1701508--1701590 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
1701498 AAATTATTAA
* *
1701508 ATATAATTTATCCTTA-TTTTAACATAAAAT
1 ATATATTTTATTCTTATTTTTAACATAAAAT
* *
1701538 ATATATTTTATTCTTATTTTTAACTTAATAT
1 ATATATTTTATTCTTATTTTTAACATAAAAT
* *
1701569 GTATATTTTATTTTTATTTTTA
1 ATATATTTTATTCTTATTTTTA
1701591 TTTAAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 14 0.30
31 32 0.70
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (31 bp):
ATATATTTTATTCTTATTTTTAACATAAAAT
Found at i:1701750 original size:57 final size:57
Alignment explanation
Indices: 1701662--1701790 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 57
1701652 ATATTATTAG
* ** * *
1701662 AATAAAATATAAATATTTAAGTTAAGGTAAGAATAAATTATTTTTTAAAGTTA-ATAAA
1 AATAAAATAT--ATTTTTAAGTTAAAATAAGAATAAAATATATTTTAAAGTTAGATAAA
*
1701720 AATTAAAATATATTTTTAAGTTAAAATAAGAATAAAATATATTTTAAAGTTAGGATAAG
1 AA-TAAAATATATTTTTAAGTTAAAATAAGAATAAAATATATTTTAAAGTTA-GATAAA
1701779 AATAAAATATAT
1 AATAAAATATAT
1701791 AATTTTAATG
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
57 36 0.58
58 12 0.19
59 14 0.23
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (57 bp):
AATAAAATATATTTTTAAGTTAAAATAAGAATAAAATATATTTTAAAGTTAGATAAA
Found at i:1701789 original size:29 final size:29
Alignment explanation
Indices: 1701660--1701790 Score: 135
Period size: 29 Copynumber: 4.5 Consensus size: 29
1701650 AAATATTATT
1701660 AGAATAAAATATAAATATTT-AAGTTAAGG-TA
1 AGAATAAAATAT--AT-TTTAAAGTT-AGGATA
* *
1701691 AGAATAAATTATTTTTTAAAGTTA--ATA
1 AGAATAAAATATATTTTAAAGTTAGGATA
* * **
1701718 AAAATTAAAATATATTTTTAAGTTAAAATA
1 AGAA-TAAAATATATTTTAAAGTTAGGATA
1701748 AGAATAAAATATATTTTAAAGTTAGGATA
1 AGAATAAAATATATTTTAAAGTTAGGATA
1701777 AGAATAAAATATAT
1 AGAATAAAATATAT
1701791 AATTTTAATG
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
27 5 0.06
28 21 0.25
29 42 0.49
30 6 0.07
31 11 0.13
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (29 bp):
AGAATAAAATATATTTTAAAGTTAGGATA
Found at i:1702872 original size:15 final size:15
Alignment explanation
Indices: 1702852--1702895 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1702842 AACATTAGAA
*
1702852 AATATTATTATTATT
1 AATATTACTATTATT
*
1702867 AATATTACTACTATT
1 AATATTACTATTATT
*
1702882 ATTATTACTATTAT
1 AATATTACTATTAT
1702896 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATTACTATTATT
Found at i:1703310 original size:8 final size:8
Alignment explanation
Indices: 1703297--1703455 Score: 140
Period size: 8 Copynumber: 18.8 Consensus size: 8
1703287 TAATTGTCTT
1703297 CTCTCTCC
1 CTCTCTCC
1703305 CTCTCTCC
1 CTCTCTCC
*
1703313 CTCCCTCTCT
1 CT--CTCTCC
*
1703323 CTCTCTCT
1 CTCTCTCC
1703331 CTCTCTCC
1 CTCTCTCC
*
1703339 CTCCCTCTCT
1 CT--CTCTCC
*
1703349 CTCTCTCT
1 CTCTCTCC
*
1703357 CTCCCTCC
1 CTCTCTCC
1703365 CTC-CTCC
1 CTCTCTCC
1703372 CTCTCTCTC
1 CTCTCTC-C
1703381 TCTCTCTCC
1 -CTCTCTCC
1703390 CTCTCCCTCC
1 CTCT--CTCC
*
1703400 CTCCCTCC
1 CTCTCTCC
*
1703408 CTCCCTCC
1 CTCTCTCC
*
1703416 CTCCCTCC
1 CTCTCTCC
*
1703424 CTCCCTCC
1 CTCTCTCC
1703432 CTCTCTCTC
1 CTCTCTC-C
1703441 TCTCTCTCC
1 -CTCTCTCC
1703450 CTCTCT
1 CTCTCT
1703456 ATTTCTCTCT
Statistics
Matches: 133, Mismatches: 7, Indels: 22
0.82 0.04 0.14
Matches are distributed among these distances:
7 7 0.05
8 87 0.65
9 4 0.03
10 35 0.26
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (8 bp):
CTCTCTCC
Found at i:1703316 original size:4 final size:4
Alignment explanation
Indices: 1703301--1703434 Score: 121
Period size: 4 Copynumber: 32.8 Consensus size: 4
1703291 TGTCTTCTCT
* * * * *
1703301 CTCC CTCT CTCC CTCC CTCTC TCTCT CTCT CTCT CTCC CTCC CTCTC TCTCT
1 CTCC CTCC CTCC CTCC CTC-C -CTCC CTCC CTCC CTCC CTCC CTC-C -CTCC
* * *
1703353 CTCT CTCC CTCC CT-C CTCC CTCTC TCTCT CTCT CTCC CT-- CTCC CTCC
1 CTCC CTCC CTCC CTCC CTCC CTC-C -CTCC CTCC CTCC CTCC CTCC CTCC
1703400 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC
1703435 TCTCTCTCTC
Statistics
Matches: 113, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.02
3 3 0.03
4 96 0.85
5 3 0.03
6 9 0.08
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (4 bp):
CTCC
Found at i:1703316 original size:12 final size:12
Alignment explanation
Indices: 1703296--1703455 Score: 166
Period size: 12 Copynumber: 13.2 Consensus size: 12
1703286 TTAATTGTCT
*
1703296 TCTCTCTCCCTC
1 TCTCCCTCCCTC
1703308 TCTCCCTCCCTC
1 TCTCCCTCCCTC
*
1703320 TCTCTCTCTCTCTC
1 TCTC-C-CTCCCTC
1703334 TCTCCCTCCCTC
1 TCTCCCTCCCTC
*
1703346 TCT--CTCTCTC
1 TCTCCCTCCCTC
1703356 TCTCCCTCCCTC
1 TCTCCCTCCCTC
*
1703368 -CTCCCTCTCTC
1 TCTCCCTCCCTC
*
1703379 TCTCTCTCTCC-C
1 TCTCCCTC-CCTC
1703391 TCTCCCTCCCTC
1 TCTCCCTCCCTC
*
1703403 CCTCCCTCCCTC
1 TCTCCCTCCCTC
*
1703415 CCTCCCTCCCTC
1 TCTCCCTCCCTC
*
1703427 CCTCCCTCTCTCTC
1 TCTCCCTC-C-CTC
*
1703441 TCTCTCTCCCTC
1 TCTCCCTCCCTC
1703453 TCT
1 TCT
1703456 ATTTCTCTCT
Statistics
Matches: 127, Mismatches: 12, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
10 9 0.07
11 12 0.09
12 82 0.65
13 5 0.04
14 19 0.15
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (12 bp):
TCTCCCTCCCTC
Found at i:1703462 original size:18 final size:18
Alignment explanation
Indices: 1703296--1703466 Score: 96
Period size: 18 Copynumber: 9.4 Consensus size: 18
1703286 TTAATTGTCT
*
1703296 TCTCTCTCCCTCTCTCCCTC
1 TCTCTCTCCCTCTCT--ATC
* * *
1703316 CCTCTCTCTCTCTCTCTC
1 TCTCTCTCCCTCTCTATC
* *
1703334 TCTCCCTCCCTCTCTCTC
1 TCTCTCTCCCTCTCTATC
* *
1703352 TCTCTCTCCCTCCCT-CC
1 TCTCTCTCCCTCTCTATC
* * *
1703369 TCCCTCTCTCTCTCTCTC
1 TCTCTCTCCCTCTCTATC
* *
1703387 TCCCTCTCCCTC-C-CTC
1 TCTCTCTCCCTCTCTATC
* * **
1703403 CCTCCCTCCCTCCCTCCCTC
1 TCTCTCTCCCT--CTCTATC
* * *
1703423 CCTCCCTCCCTCTCTCTC
1 TCTCTCTCCCTCTCTATC
*
1703441 TCTCTCTCCCTCTCTATT
1 TCTCTCTCCCTCTCTATC
1703459 TCTCTCTC
1 TCTCTCTC
1703467 TTCATTCTCC
Statistics
Matches: 125, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
16 11 0.09
17 14 0.11
18 72 0.58
19 1 0.01
20 27 0.22
ACGTcount: A:0.01, C:0.61, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTCTCTCCCTCTCTATC
Found at i:1710175 original size:2 final size:2
Alignment explanation
Indices: 1710170--1710199 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1710160 AAATCAAATA
1710170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1710200 CAATCAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1711364 original size:17 final size:17
Alignment explanation
Indices: 1711338--1711373 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1711328 TTGCATAATT
* *
1711338 TTTTCTTTTTTTGTTTA
1 TTTTCCTTTTATGTTTA
1711355 TTTTCCTTTTATGTTTA
1 TTTTCCTTTTATGTTTA
1711372 TT
1 TT
1711374 GTTTAGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTCCTTTTATGTTTA
Found at i:1715689 original size:18 final size:16
Alignment explanation
Indices: 1715655--1715693 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1715645 AATATATATC
1715655 AAAAATAAAAAACATA
1 AAAAATAAAAAACATA
*
1715671 AAAAATATAGAAAAGATA
1 AAAAATA-A-AAAACATA
1715689 AAAAA
1 AAAAA
1715694 AGAAGAGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (16 bp):
AAAAATAAAAAACATA
Found at i:1715724 original size:22 final size:22
Alignment explanation
Indices: 1715696--1715755 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1715686 ATAAAAAAAG
* *
1715696 AAGAGAGGGAAAAGTAAGCAAA
1 AAGAGAGAGAAAAGAAAGCAAA
*
1715718 AAGAGAGAGAAAGGAAAGCAAA
1 AAGAGAGAGAAAAGAAAGCAAA
1715740 AAG-GAGA-AAAAGAAAG
1 AAGAGAGAGAAAAGAAAG
1715756 AAAGAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.24
21 4 0.12
22 22 0.65
ACGTcount: A:0.63, C:0.03, G:0.32, T:0.02
Consensus pattern (22 bp):
AAGAGAGAGAAAAGAAAGCAAA
Found at i:1716532 original size:28 final size:28
Alignment explanation
Indices: 1716498--1716557 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1716488 TAGACCTTAA
*
1716498 CCAAATTAACCTTAAACACAT-TACCTCC
1 CCAAATTAACCTGAAACAC-TCTACCTCC
* *
1716526 CCAAATTAATCTGAAACACTCTACCTTC
1 CCAAATTAACCTGAAACACTCTACCTCC
1716554 CCAA
1 CCAA
1716558 GTCAACCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.38, C:0.35, G:0.02, T:0.25
Consensus pattern (28 bp):
CCAAATTAACCTGAAACACTCTACCTCC
Found at i:1720061 original size:18 final size:17
Alignment explanation
Indices: 1720040--1720073 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1720030 CAAAAGAAAT
1720040 AAAATATAGAATTAAAAG
1 AAAAT-TAGAATTAAAAG
*
1720058 AAAATTTGAATTAAAA
1 AAAATTAGAATTAAAA
1720074 TGACCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAATTAGAATTAAAAG
Found at i:1721283 original size:4 final size:4
Alignment explanation
Indices: 1721274--1721344 Score: 85
Period size: 4 Copynumber: 17.5 Consensus size: 4
1721264 CAAAAAATAA
1721274 AAAT AAAT AAAT AAAT AAAT AATAT AAAT AAAT -AAT AAAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT
1721321 -AAT AATAT AAAT AATAT ATAAT AA
1 AAAT AA-AT AAAT AA-AT A-AAT AA
1721345 GAACTATATA
Statistics
Matches: 60, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
3 9 0.15
4 36 0.60
5 14 0.23
6 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:1721327 original size:30 final size:30
Alignment explanation
Indices: 1721268--1721359 Score: 109
Period size: 30 Copynumber: 3.0 Consensus size: 30
1721258 TGTTAACAAA
1721268 AAATAAA-AATAAATAAATAAATAAATAATAT
1 AAATAAATAATAAAT-AATAAAT-AATAATAT
1721299 AAATAAATAATAAATAATAAATAATAATAT
1 AAATAAATAATAAATAATAAATAATAATAT
* *
1721329 AAAT-AAT-ATATAATAAGAACTATATAATAT
1 AAATAAATAATA-AATAATAAATA-ATAATAT
1721359 A
1 A
1721360 TATTAAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
28 3 0.05
29 12 0.21
30 20 0.36
31 14 0.25
32 7 0.12
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (30 bp):
AAATAAATAATAAATAATAAATAATAATAT
Found at i:1721331 original size:39 final size:39
Alignment explanation
Indices: 1721269--1721344 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 39
1721259 GTTAACAAAA
1721269 AATAAAAATAAATAAATAAATAAATAATATA-AATAAAT
1 AATAAAAATAAATAAATAAATAAATAATATATAATAAAT
1721307 AATAAATAATAAAT-AATAATATAAATAATATATAATAA
1 AATAAA-AATAAATAAATAA-ATAAATAATATATAATAA
1721345 GAACTATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
38 11 0.31
39 19 0.54
40 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (39 bp):
AATAAAAATAAATAAATAAATAAATAATATATAATAAAT
Found at i:1721361 original size:7 final size:7
Alignment explanation
Indices: 1721268--1721344 Score: 90
Period size: 7 Copynumber: 11.3 Consensus size: 7
1721258 TGTTAACAAA
1721268 AAATAA-
1 AAATAAT
1721274 AAATAAAT
1 AAAT-AAT
1721282 AAATAAAT
1 AAAT-AAT
1721290 AAATAAT
1 AAATAAT
*
1721297 ATA-AAT
1 AAATAAT
1721303 AAATAAT
1 AAATAAT
1721310 AAATAAT
1 AAATAAT
1721317 AAATAAT
1 AAATAAT
1721324 -AAT-AT
1 AAATAAT
1721329 AAATAAT
1 AAATAAT
*
1721336 ATATAAT
1 AAATAAT
1721343 AA
1 AA
1721345 GAACTATATA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
5 2 0.03
6 15 0.24
7 33 0.53
8 12 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATAAT
Found at i:1721387 original size:13 final size:13
Alignment explanation
Indices: 1721371--1721398 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1721361 ATTAAAAAAT
1721371 AATATGTTTTCAA
1 AATATGTTTTCAA
1721384 AATATGTTTTCAA
1 AATATGTTTTCAA
1721397 AA
1 AA
1721399 CTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
AATATGTTTTCAA
Found at i:1721429 original size:36 final size:34
Alignment explanation
Indices: 1721372--1721630 Score: 193
Period size: 36 Copynumber: 7.1 Consensus size: 34
1721362 TTAAAAAATA
*
1721372 ATAT-GTTTTCAAAATATGTTTTCAAAACTATATT
1 ATATAGTTTTCAAAA-ACGTTTTCAAAACTATATT
* *
1721406 ATATACGTTTTTAAAAACCGTTTTTAAAACTATATAT
1 ATATA-GTTTTCAAAAA-CGTTTTCAAAACTATAT-T
*
1721443 ATTATACGTTTTCAAAAGTACGTTTTCAAAACTATATA
1 A-TATA-GTTTTCAAAA--ACGTTTTCAAAACTATATT
* *
1721481 ATATATGTTTTCAAAAATGTGTTTTCAAAACCATATT
1 ATATA-GTTTTCAAAAA--CGTTTTCAAAACTATATT
* * *
1721518 AAATA-TTTTCAAAAACCGTTTTTTAAAAATTATATT
1 ATATAGTTTTCAAAAA-CG--TTTTCAAAACTATATT
*
1721554 ATAT-GCTTTCAAAAATCGTTTTCTAAAAACTATATATT
1 ATATAGTTTTCAAAAA-CGTTTTC--AAAAC--TATATT
**
1721592 ATATA-TTTTCAAAATATATTTTCAAAAACTATATT
1 ATATAGTTTTCAAAA-ACGTTTTC-AAAACTATATT
1721627 ATAT
1 ATAT
1721631 TATTATATAT
Statistics
Matches: 183, Mismatches: 24, Indels: 35
0.76 0.10 0.14
Matches are distributed among these distances:
34 9 0.05
35 22 0.12
36 55 0.30
37 41 0.22
38 38 0.21
39 17 0.09
40 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (34 bp):
ATATAGTTTTCAAAAACGTTTTCAAAACTATATT
Found at i:1721466 original size:14 final size:14
Alignment explanation
Indices: 1721447--1721473 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1721437 ATATATATTA
1721447 TACGTTTTCAAAAG
1 TACGTTTTCAAAAG
1721461 TACGTTTTCAAAA
1 TACGTTTTCAAAA
1721474 CTATATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
TACGTTTTCAAAAG
Found at i:1721491 original size:37 final size:36
Alignment explanation
Indices: 1721372--1721630 Score: 199
Period size: 37 Copynumber: 7.1 Consensus size: 36
1721362 TTAAAAAATA
* *
1721372 ATATGTTTTCAAAATATGTTTTCAAAACTATATTAT
1 ATATGTTTTCAAAATACGTTTTCAAAACTATATAAT
* * *
1721408 ATACGTTTTTAAAA-ACCGTTTTTAAAACTATATATATT
1 ATATGTTTTCAAAATA-CGTTTTCAAAACTATATA-A-T
*
1721446 ATACGTTTTCAAAAGTACGTTTTCAAAACTATATAAT
1 ATATGTTTTCAAAA-TACGTTTTCAAAACTATATAAT
** *
1721483 ATATGTTTTCAAAAATGTGTTTTCAAAACCATATTAA-
1 ATATGTTTTC-AAAATACGTTTTCAAAACTATA-TAAT
* * *
1721520 ATA--TTTTCAAAA-ACCGTTTTTTAAAAAT-TATATT
1 ATATGTTTTCAAAATA-CG-TTTTCAAAACTATATAAT
* *
1721554 ATATGCTTTCAAAA-ATCGTTTTCTAAAAACTATATATT
1 ATATGTTTTCAAAATA-CGTTTTC--AAAACTATATAAT
* ** *
1721592 ATATATTTTCAAAATATATTTTCAAAAACTATATTAT
1 ATATGTTTTCAAAATACGTTTTC-AAAACTATATAAT
1721629 AT
1 AT
1721631 TATTATATAT
Statistics
Matches: 180, Mismatches: 27, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
33 2 0.01
34 10 0.06
35 18 0.10
36 38 0.21
37 48 0.27
38 45 0.25
39 18 0.10
40 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (36 bp):
ATATGTTTTCAAAATACGTTTTCAAAACTATATAAT
Found at i:1721626 original size:15 final size:13
Alignment explanation
Indices: 1721592--1721618 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1721582 ACTATATATT
1721592 ATATATTTTCAAA
1 ATATATTTTCAAA
1721605 ATATATTTTCAAA
1 ATATATTTTCAAA
1721618 A
1 A
1721619 ACTATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATTTTCAAA
Found at i:1728188 original size:23 final size:22
Alignment explanation
Indices: 1728128--1728188 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
1728118 TTTGGTGCAG
1728128 AGGGAATCGATACCCCCTTGAT
1 AGGGAATCGATACCCCCTTGAT
*
1728150 AGGGAA-CTGATTCCCCCTTTGA-
1 AGGGAATC-GATACCCCC-TTGAT
1728172 AGGGGAATCGATACCCC
1 A-GGGAATCGATACCCC
1728189 AGGGTTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 1 0.03
22 15 0.45
23 16 0.48
24 1 0.03
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (22 bp):
AGGGAATCGATACCCCCTTGAT
Found at i:1731636 original size:3 final size:3
Alignment explanation
Indices: 1731628--1731659 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1731618 GTCTTATTTA
1731628 ATT ATT ATT ATT ATT ATT ATT ATT -TT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1731660 AATAATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1732306 original size:26 final size:26
Alignment explanation
Indices: 1732277--1732331 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1732267 CAGTTCGAAG
* *
1732277 AAAA-ACAAAAACAAAGAGGGAATAGAA
1 AAAACACAAAAA-AAA-AGAGAAAAGAA
1732304 AAAACACAAAAAAAAAGAGAAAAGAA
1 AAAACACAAAAAAAAAGAGAAAAGAA
1732330 AA
1 AA
1732332 TAGAGAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 7 0.28
28 7 0.28
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (26 bp):
AAAACACAAAAAAAAAGAGAAAAGAA
Found at i:1738214 original size:25 final size:25
Alignment explanation
Indices: 1738159--1738225 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
1738149 TGAAAAGGGC
*
1738159 AATATTTTTCAAAA-TTTTGATTTA
1 AATATTTTTCAAAATTTTTGAATTA
* *
1738183 AACATTTTTCAAAATTCTTTTAATT-
1 AATATTTTTCAAAATT-TTTGAATTA
1738208 AATATTTTTCAAAATTTT
1 AATATTTTTCAAAATTTT
1738226 GAAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.41
25 16 0.43
26 6 0.16
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (25 bp):
AATATTTTTCAAAATTTTTGAATTA
Found at i:1740125 original size:67 final size:66
Alignment explanation
Indices: 1739983--1740215 Score: 283
Period size: 67 Copynumber: 3.5 Consensus size: 66
1739973 CCCTAAAAAT
* * * *
1739983 AAATTTTATCTCGCTTGAGACAGTTTCTCTGGAAACACAAAACTTTGAGACA-GTTGCTCTTGAA
1 AAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGA-ATGTTTCTCTTGAA
1740047 AC
65 AC
* * *
1740049 AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAAACTTAGAGAATGTTTCTCTTAAA
1 AAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAT-AAAACTTTGAGAATGTTTCTCTTGAA
1740114 AC
65 AC
* * * * * *
1740116 AAATGTTGTCTCTCTTGAGACAGTTTCACTTAAAACAT-AAATTTTGAGATTGTTTC-CTTTGAA
1 AAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGAATGTTTCTC-TTGAA
1740179 AC
65 AC
* *
1740181 AATTTTTGTCTCGCTTGAGACAGTTTTTCTTGAAA
1 AAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1740216 TAATTTATCC
Statistics
Matches: 144, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
64 1 0.01
65 50 0.35
66 35 0.24
67 58 0.40
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (66 bp):
AAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGAATGTTTCTCTTGAAA
C
Found at i:1740433 original size:138 final size:139
Alignment explanation
Indices: 1740220--1740785 Score: 698
Period size: 139 Copynumber: 4.1 Consensus size: 139
1740210 TTGAAATAAT
* * * * *
1740220 TTATCCCTAAAGATGGCTAGACATCCTAATCACGTAGGAACAATGTCATCCACCGACCATATATA
1 TTATCCCTAAAGATGGCTAGACTTCCTCATCACGTAGGAACAATGTCATCCACCAACCAGATCTA
*
1740285 CTCATCACGTAGGA-CTAGTGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAACGTGT
66 CTCATCACGTAGGAGC-AGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAACGTGT
* *
1740349 TATCTCC-AT
130 TGTCTCCAAA
* * * * * *
1740358 TTATCCCTAAAGATGGCTAGACGTCTTCATCACATAGTAATAATGTCATCCACCAACCAGATCTC
1 TTATCCCTAAAGATGGCTAGACTTCCTCATCACGTAGGAACAATGTCATCCACCAACCAGATCTA
* *
1740423 CTCATCACGTAGGAGCAGTGTCATCATTAGATAACCAGACTTCCTCATCACGTA-GAAACCGTGT
66 CTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAA-CGTGT
1740487 TGTCTCCCAAA
130 TGTCT-CCAAA
1740498 TTATCCCTAAAGATGGCTAGACTTCCTCATCACGTAGGAACAAT-TCCATCCA-CAGACCAGATC
1 TTATCCCTAAAGATGGCTAGACTTCCTCATCACGTAGGAACAATGT-CATCCACCA-ACCAGATC
* * * *
1740561 TACTCATCACATAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATG
64 TACTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAACGTG
1740626 TTGTCTCCAAA
129 TTGTCTCCAAA
* * * * *
1740637 TTATCCCTAAAGATGGATAGACTTCCTCATCACGTAGAAATAATGTCATCCACCGACCATATC-A
1 TTATCCCTAAAGATGGCTAGACTTCCTCATCACGTAGGAACAATGTCATCCACCAACCAGATCTA
* * * * * * * * *
1740701 CCTCATCAAGTTGGAGAAGCCTCATCCTTAGATAATCAGACTTCATCATCATGTAGG-AACAATA
66 -CTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAAC-GTG
1740765 TTGTCTCCAAA
129 TTGTCTCCAAA
*
1740776 TT-TACCTAAA
1 TTATCCCTAAA
1740786 AATGACCAAA
Statistics
Matches: 375, Mismatches: 42, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
137 4 0.01
138 125 0.33
139 127 0.34
140 116 0.31
141 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (139 bp):
TTATCCCTAAAGATGGCTAGACTTCCTCATCACGTAGGAACAATGTCATCCACCAACCAGATCTA
CTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAACGTGTT
GTCTCCAAA
Found at i:1740777 original size:278 final size:278
Alignment explanation
Indices: 1740220--1740785 Score: 771
Period size: 278 Copynumber: 2.0 Consensus size: 278
1740210 TTGAAATAAT
* *
1740220 TTATCCCTAAAGATGGCTAGACATCCTAATCACGTAGGAACAATGTCATCCACCGACCATATATA
1 TTATCCCTAAAGATGGCTAGACATCCTAATCACGTAGGAACAATGTCATCCACAGACCAGATATA
* ** *
1740285 CTCATCACGTAGGACTAGTGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAACGTGTT
66 CTCATCACATAGGACTAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAACATGTT
* * * *
1740350 ATCTCCATTTATCCCTAAAGATGGCTAGACGTCTTCATCACATAGTAATAATGTCATCCACCAAC
131 ATCTCCAATTATCCCTAAAGATGGATAGACGTCCTCATCACATAGAAATAATGTCATCCACCAAC
* * * ** *
1740415 CAGATCTCCTCATCACGTAGGAGCAGTGTCATCATTAGATAACCAGACTTCCTCATCACGTAGAA
196 CAGATCACCTCATCAAGTAGGAGAAGCCTCATCATTAGATAACCAGACTTCATCATCACGTAGAA
** *
1740480 ACCGTGTTGTCTCCCAAA
261 ACAATATTGTCTCCCAAA
* * *
1740498 TTATCCCTAAAGATGGCTAGACTTCCTCATCACGTAGGAACAAT-TCCATCCACAGACCAGATCT
1 TTATCCCTAAAGATGGCTAGACATCCTAATCACGTAGGAACAATGT-CATCCACAGACCAGATAT
*
1740562 ACTCATCACATAGGAGC-AACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATG
65 ACTCATCACATAGGA-CTAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAACATG
* * *
1740626 TTGTCTCCAAATTATCCCTAAAGATGGATAGACTTCCTCATCACGTAGAAATAATGTCATCCACC
129 TTATCTCC-AATTATCCCTAAAGATGGATAGACGTCCTCATCACATAGAAATAATGTCATCCACC
* * * * * *
1740691 GACCATATCACCTCATCAAGTTGGAGAAGCCTCATCCTTAGATAATCAGACTTCATCATCATGTA
193 AACCAGATCACCTCATCAAGTAGGAGAAGCCTCATCATTAGATAACCAGACTTCATCATCACGTA
*
1740756 GGAACAATATTGTCT-CCAAA
258 GAAACAATATTGTCTCCCAAA
*
1740776 TT-TACCTAAA
1 TTATCCCTAAA
1740786 AATGACCAAA
Statistics
Matches: 251, Mismatches: 34, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
277 8 0.03
278 128 0.51
279 115 0.46
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (278 bp):
TTATCCCTAAAGATGGCTAGACATCCTAATCACGTAGGAACAATGTCATCCACAGACCAGATATA
CTCATCACATAGGACTAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAACATGTT
ATCTCCAATTATCCCTAAAGATGGATAGACGTCCTCATCACATAGAAATAATGTCATCCACCAAC
CAGATCACCTCATCAAGTAGGAGAAGCCTCATCATTAGATAACCAGACTTCATCATCACGTAGAA
ACAATATTGTCTCCCAAA
Found at i:1741099 original size:3 final size:3
Alignment explanation
Indices: 1741086--1741150 Score: 82
Period size: 3 Copynumber: 22.3 Consensus size: 3
1741076 GTCTTATTTA
* *
1741086 ATT ACT ATT ATT ATC A-T ATT CATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
1741131 ATT ATT ATT A-T ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
1741151 AATAATTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 46 0.85
4 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1741162 original size:24 final size:25
Alignment explanation
Indices: 1741093--1741173 Score: 85
Period size: 24 Copynumber: 3.2 Consensus size: 25
1741083 TTAATTACTA
*
1741093 TTATTATCAT-ATTCATTATTATTATT
1 TTATTATAATAATT-ATTATTA-TATT
* *
1741119 ATTATTATTATTATTATTATTATATT
1 -TTATTATAATAATTATTATTATATT
*
1741145 TTATTA-AATAATTTTTATTATATT
1 TTATTATAATAATTATTATTATATT
1741169 TTATT
1 TTATT
1741174 TTTAGACCCA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 20 0.41
25 6 0.12
26 4 0.08
27 16 0.33
28 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATTATAATAATTATTATTATATT
Found at i:1745764 original size:93 final size:95
Alignment explanation
Indices: 1745611--1745808 Score: 267
Period size: 93 Copynumber: 2.1 Consensus size: 95
1745601 TACTGATGGG
* * * * *
1745611 GTATCGATACTATGAGGAATGTATCGATACCATTGATTCCATAATGCAGAAATAGTATCGATACT
1 GTATCGATACTAGGAGGAAAGTATCGATACCATGGATTCCAGAATACAGAAATAGTATCGATACT
* * *
1745676 -ATAATGGAGTATCAGTACCATAGTATAGAA
66 GA-AAGGGAGTATCAGTACCACAATATAGAA
* * *
1745706 GTATCGGTACTAGGA-GAAAGTATCGATACCATGGA-TCCAGAATATAGAAATGGTATCGATACT
1 GTATCGATACTAGGAGGAAAGTATCGATACCATGGATTCCAGAATACAGAAATAGTATCGATACT
1745769 GAAAGGGAGTATCAGTACCACAATATAGAA
66 GAAAGGGAGTATCAGTACCACAATATAGAA
1745799 GTATCGATAC
1 GTATCGATAC
1745809 CATGGTAGGG
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
93 58 0.64
94 19 0.21
95 13 0.14
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (95 bp):
GTATCGATACTAGGAGGAAAGTATCGATACCATGGATTCCAGAATACAGAAATAGTATCGATACT
GAAAGGGAGTATCAGTACCACAATATAGAA
Found at i:1746527 original size:54 final size:54
Alignment explanation
Indices: 1746138--1746520 Score: 516
Period size: 54 Copynumber: 7.1 Consensus size: 54
1746128 TATGTATTGT
* * * *
1746138 AATTTTCGTATTGGCACTATGCGTGCAACTTAAGAAATTGATAATGAGTTTATA
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
** * *
1746192 AATTTTTGTATTGGCACTATGTGTGCAA-TCTAGGAAATTCGTAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACT-TAAGAAATTCATAATGAGTTTATG
* * *
1746246 AATTTCCATACTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * * * *
1746300 AATTTCCTTACTGGAACTATGTGTACAACCTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* *
1746354 AATTTCCGTATTGGGACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* *
1746408 AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * * * * *
1746462 AATTTCTGTATTGGCATTATGTGTACAACTTAAGTAATTCATATTAAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
1746516 AATTT
1 AATTT
1746521 TTGTATTAAC
Statistics
Matches: 297, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
53 1 0.00
54 296 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (54 bp):
AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
Found at i:1749820 original size:19 final size:19
Alignment explanation
Indices: 1749796--1749843 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1749786 TTTGGACGGA
1749796 GAAATGCTAAGAAAGTTTT
1 GAAATGCTAAGAAAGTTTT
1749815 GAAATGCTAAGAAAGTTTT
1 GAAATGCTAAGAAAGTTTT
1749834 GAAATGCTAA
1 GAAATGCTAA
1749844 AGAGAATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (19 bp):
GAAATGCTAAGAAAGTTTT
Found at i:1752676 original size:91 final size:93
Alignment explanation
Indices: 1752547--1752721 Score: 246
Period size: 91 Copynumber: 1.9 Consensus size: 93
1752537 TATAAGGAAG
* * * * *
1752547 ATATTGATACCATTGATTCCAGAATACAGAAATTGTATCGATACTGTAATGGAGTATCGGTACCA
1 ATATTGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTGAAAGGGAGAATCGGTACCA
* *
1752612 TAGTATAGAAGTATCGATACTAGAGAAA
66 CAATATAGAAGTATCGATACTAGAGAAA
**
1752640 ATATT-ATACCATGGA-TCCAGAATGTAGAAATGGTATCGATACTGAAAGGGAGAATCGGTACCA
1 ATATTGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTGAAAGGGAGAATCGGTACCA
*
1752703 CAATATATAAGTATCGATA
66 CAATATAGAAGTATCGATA
1752722 TCATAGTAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 58 0.81
92 9 0.12
93 5 0.07
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (93 bp):
ATATTGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTGAAAGGGAGAATCGGTACCA
CAATATAGAAGTATCGATACTAGAGAAA
Found at i:1753172 original size:54 final size:54
Alignment explanation
Indices: 1753047--1753433 Score: 546
Period size: 54 Copynumber: 7.2 Consensus size: 54
1753037 TATGTATTGT
* * *
1753047 AATTTTCGTATTAACACTATGTGTGCAACTTAATAAATTCAT-ATGAGTTTATG
1 AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
** * *
1753100 AATTTTTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
*
1753154 AATTTCCATATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * *
1753208 AATTTTCGTACTGACAGTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * *
1753262 AATTTCCTTATTGACACTATGTGTGCAACCTAAGAAATTTATAATGAGTTTATG
1 AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * * *
1753316 AATTTCTGTATTGGCACT-T-TATGTAACTTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * * * *
1753368 AATTTCCGTATAGGCACTATGTGTGCAATTTAATAAATTCATAATAAGTTTATG
1 AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
1753422 AATTTCCGTATT
1 AATTTCCGTATT
1753434 AGCACTGGGT
Statistics
Matches: 296, Mismatches: 35, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
52 45 0.15
53 39 0.13
54 212 0.72
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (54 bp):
AATTTCCGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
Found at i:1753420 original size:160 final size:162
Alignment explanation
Indices: 1753060--1753492 Score: 576
Period size: 160 Copynumber: 2.7 Consensus size: 162
1753050 TTTCGTATTA
* *
1753060 ACACTATGTGTGCAACTTAATAAATTCAT-ATGAGTTTATGAATTT-TTGTATTGGCACTATGTG
1 ACACTATGTGTGCAACTTAATAAATTCATAATGAGTTTATGAATTTCCT-TATTGACACTATGTG
* ** * *
1753123 TGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCATATTGACACTATGTGTGCAACTTAAG
65 TGCAACCTAAGAAATTTATAATGAGTTTATGAATTTCTGTATTGGCACTATGTATGCAACTTAAG
*
1753188 AAATTCATAATGAGTTTATGAATTTTCGTACTG
130 AAATTCATAATGAGTTTATGAATTTCCGTACTG
* *
1753221 ACAGTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCTTATTGACACTATGTGT
1 ACACTATGTGTGCAACTTAATAAATTCATAATGAGTTTATGAATTTCCTTATTGACACTATGTGT
*
1753286 GCAACCTAAGAAATTTATAATGAGTTTATGAATTTCTGTATTGGCACT-T-TATGTAACTTAAGA
66 GCAACCTAAGAAATTTATAATGAGTTTATGAATTTCTGTATTGGCACTATGTATGCAACTTAAGA
1753349 AATTCATAATGAGTTTATGAATTTCCGTA-TAG
131 AATTCATAATGAGTTTATGAATTTCCGTACT-G
* * * * **
1753381 GCACTATGTGTGCAATTTAATAAATTCATAATAAGTTTATGAATTTCCGTATT-AGCACTGGGTG
1 ACACTATGTGTGCAACTTAATAAATTCATAATGAGTTTATGAATTTCCTTATTGA-CACTATGTG
* * * * *
1753445 TGCAAAC-ACA-AAATTTATAGTAAGTTTGTGAATTACTGTATTGGCACT
65 TGCAACCTA-AGAAATTTATAATGAGTTTATGAATTTCTGTATTGGCACT
1753493 GCAGGTGCAA
Statistics
Matches: 243, Mismatches: 24, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
159 37 0.15
160 102 0.42
161 28 0.12
162 75 0.31
163 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (162 bp):
ACACTATGTGTGCAACTTAATAAATTCATAATGAGTTTATGAATTTCCTTATTGACACTATGTGT
GCAACCTAAGAAATTTATAATGAGTTTATGAATTTCTGTATTGGCACTATGTATGCAACTTAAGA
AATTCATAATGAGTTTATGAATTTCCGTACTG
Found at i:1753501 original size:53 final size:53
Alignment explanation
Indices: 1753348--1753504 Score: 142
Period size: 54 Copynumber: 2.9 Consensus size: 53
1753338 GTAACTTAAG
* * **
1753348 AAATTCATAATGAGTTTATGAATTTCCGTA-TAGGCACT-ATGTGTGCAATTTA-A
1 AAATTCATAATAAGTTTATGAATTACCGTATTA-GCACTGA-GTGTGCAA-ACACA
* *
1753401 TAAATTCATAATAAGTTTATGAATTTCCGTATTAGCACTGGGTGTGCAAACACA
1 -AAATTCATAATAAGTTTATGAATTACCGTATTAGCACTGAGTGTGCAAACACA
* * * * *
1753455 AAATTTATAGTAAGTTTGTGAATTACTGTATTGGCACTGCAG-GTGCAAAC
1 AAATTCATAATAAGTTTATGAATTACCGTATTAGCACTG-AGTGTGCAAAC
1753505 TATAGAGTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
53 42 0.48
54 44 0.50
55 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (53 bp):
AAATTCATAATAAGTTTATGAATTACCGTATTAGCACTGAGTGTGCAAACACA
Found at i:1757553 original size:65 final size:64
Alignment explanation
Indices: 1757481--1757779 Score: 281
Period size: 65 Copynumber: 4.7 Consensus size: 64
1757471 TGTTCCCTAA
* * * *
1757481 AAACAAATTTGTCTCGCTTGAGATAGTTTCTCTGGAAACACAAAACTTTGAGATTGTTTCTCTTG
1 AAACAAATTTGTCTCTCTTGAGACAATTTCTCTTGAAACA-AAAACTTTGAGATTGTTTCTCTTG
* * * *
1757546 AAACAAATTTTCTCTCTCTTGAGAC-A-TTCTATTGAAACATAAAAACTTTGAGACTATTTCTCT
1 AAACAAA-TTTGTCTCTCTTGAGACAATTTCTCTTGAAAC--AAAAACTTTGAGATTGTTTCTCT
1757609 TG
63 TG
* * * * * *
1757611 AAACATATGTTGTTTCTCTTGAGATAGTTTCT-TTGGAAACATAAAACCTTGATATTGTTTCTCT
1 AAACAAAT-TTGTCTCTCTTGAGACAATTTCTCTT-GAAACA-AAAACTTTGAGATTGTTTCTCT
1757675 TG
63 TG
* * *
1757677 AAAGAAATATGTCTCTCTTGAGACAATTTCTCTTGAAACATAAACTTT-A-A--GTTTC-CTTTG
1 AAACAAATTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAACTTTGAGATTGTTTCTC-TTG
* * *
1757737 AAATAAATTTTGTTTCGCTTGAGACAATTTCTCTTGAAACAAA
1 AAACAAA-TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAA
1757780 TTATCCCTAA
Statistics
Matches: 193, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
59 1 0.01
60 14 0.07
61 31 0.16
62 1 0.01
63 1 0.01
64 17 0.09
65 74 0.38
66 45 0.23
67 9 0.05
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (64 bp):
AAACAAATTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAACTTTGAGATTGTTTCTCTTG
Found at i:1758040 original size:136 final size:136
Alignment explanation
Indices: 1757778--1758438 Score: 710
Period size: 136 Copynumber: 4.8 Consensus size: 136
1757768 TCTTGAAACA
* **
1757778 AATTATCCCTAAAGATGGCTAGACATCCTCATCACAGGAACAATGTCATCCACATACCAGATCTC
1 AATTATCCCTAAAGATGGCTAGACGTCCTCATCACAGGAACAATGTCATCCACCGACCAGATCTC
* * * * *
1757843 CTCATCACCTAG-G-ATCAGTCATCCTTAGATAACCAGAATTTCTCATCACGTAAGAACCGTGTT
66 CTCATCACGTAGAGTAGCA-TCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTT
1757906 GTCTCCC
130 GTCTCCC
*
1757913 ATTTATCCCTAAAGATGGCTAGACGTCCTCATCACA-GAACAATGTCATCCACCGACCAGATCTC
1 AATTATCCCTAAAGATGGCTAGACGTCCTCATCACAGGAACAATGTCATCCACCGACCAGATCTC
* * * * *
1757977 CTTATCGCGTAAGAGTAGCATCATCCTTAGATAACTAGACTTTCTCATCACGTAGGAAACGTGTT
66 CTCATCACGT-AGAGTAGCATCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTT
*
1758042 ATCT-CC
130 GTCTCCC
* * * * * * *
1758048 ATTTATCCCTAAAGATAGCTAGACGTCTTCATCGTATAGGAAAAATTTCATCTACCGACCAGATC
1 AATTATCCCTAAAGATGGCTAGACGTCCTCATC--ACAGGAACAATGTCATCCACCGACCAGATC
* * * * ** * *
1758113 CCCTCATCACGCAGGAGCAACGCCATCATAAGATAACCAGACTTCCTCATCACGTAGGAACCGTG
64 TCCTCATCACGTA-GAGTAGCATCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGTG
1758178 TTGTCTCCC
128 TTGTCTCCC
* * * *
1758187 AAATTATCCCTAAATATGGCTAGACTTCCTCATCACGTAGGAATAATGCCATCCACCGACCAGAT
1 -AATTATCCCTAAAGATGGCTAGACGTCCTCATCAC--AGGAACAATGTCATCCACCGACCAGAT
* * *
1758252 ATACTCATCACGTAGTAGT-G--TCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCAT
63 CTCCTCATCACGTAG-AGTAGCATCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGT
*
1758314 GTTGTCTCCA
127 GTTGTCTCCC
* * ** *
1758324 AATTATCCCTAAAGATGGCTAGACGTCCTTATCACGTAGGAACAATGTCATCCACCTACCTTATA
1 AATTATCCCTAAAGATGGCTAGACGTCCTCATCAC--AGGAACAATGTCATCCACCGACCAGATC
* * **
1758389 TCCTCATCATGTAG-G-AACAAAGTCATCCTTAGATAACCATCCTTCCTCAT
64 TCCTCATCACGTAGAGTAGC--A-TCATCCTTAGATAACCAGACTTCCTCAT
1758439 TATATAGGAA
Statistics
Matches: 441, Mismatches: 67, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
134 34 0.08
135 69 0.16
136 114 0.26
137 53 0.12
138 79 0.18
139 29 0.07
140 63 0.14
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (136 bp):
AATTATCCCTAAAGATGGCTAGACGTCCTCATCACAGGAACAATGTCATCCACCGACCAGATCTC
CTCATCACGTAGAGTAGCATCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTTG
TCTCCC
Found at i:1758280 original size:275 final size:270
Alignment explanation
Indices: 1757776--1758378 Score: 748
Period size: 275 Copynumber: 2.2 Consensus size: 270
1757766 TCTCTTGAAA
* * *
1757776 CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACAGGAACAATGTCATCCACATACCAGATC
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACAGGAAAAATGTCATCCACAGACCAGATC
* * * * * *
1757841 TCCTCATCACCTAGGATCAGTCATCCTTAGATAACCAGAATTTCTCATCACGTAAGAACCGTGTT
66 CCCTCATCACCTAGGAGCAGCCATCATAAGATAACCAGAATTCCTCATCACGTAAGAACCGTGTT
* *
1757906 GTCTCCCATTTATCCCTAAAGATGGCTAGACGTCCTCATCACAGAACAATGTCATCCACCGACCA
131 GTCTCCCAATTATCCCTAAAGATGGCTAGACGTCCTCATCACAGAACAATGCCATCCACCGACCA
* * * * * *
1757971 GATCTCCTTATCGCGTAAGAGTAGCATCATCCTTAGATAACTAGACTTTCTCATCACGTAGGAAA
196 GATATACTCATCACGTAAGAGTAG-ATCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAA
*
1758036 CGTGTTATCTC
260 CATGTTATCTC
* * * * * * *
1758047 C-ATTTATCCCTAAAGATAGCTAGACGTCTTCATCGTATAGGAAAAATTTCATCTACCGACCAGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATC--ACAGGAAAAATGTCATCCACAGACCAGA
* *
1758111 TCCCCTCATCACGC-AGGAGCAACGCCATCATAAGATAACCAGACTTCCTCATCACGTAGGAACC
64 TCCCCTCATCAC-CTAGGAGC-A-GCCATCATAAGATAACCAGAATTCCTCATCACGTAAGAACC
* * *
1758175 GTGTTGTCTCCCAAATTATCCCTAAATATGGCTAGACTTCCTCATCACGTAGGAATAATGCCATC
126 GTGTTGTCTCCC-AATTATCCCTAAAGATGGCTAGACGTCCTCATCAC--A-GAACAATGCCATC
1758240 CACCGACCAGATATACTCATCACGT-AGTAGT-G-TCATCCTTAGATAACCAGACTTCCTCATCA
187 CACCGACCAGATATACTCATCACGTAAG-AGTAGATCATCCTTAGATAACCAGACTTCCTCATCA
* *
1758302 CGTAGGAACCATGTTGTCTC
251 CGTAGGAAACATGTTATCTC
* *
1758322 CAAATTATCCCTAAAGATGGCTAGACGTCCTTATCACGTAGGAACAATGTCATCCAC
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCAC--AGGAAAAATGTCATCCAC
1758379 CTACCTTATA
Statistics
Matches: 279, Mismatches: 40, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
270 29 0.10
271 1 0.00
272 38 0.14
273 2 0.01
274 48 0.17
275 78 0.28
276 44 0.16
277 4 0.01
278 35 0.13
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (270 bp):
CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACAGGAAAAATGTCATCCACAGACCAGATC
CCCTCATCACCTAGGAGCAGCCATCATAAGATAACCAGAATTCCTCATCACGTAAGAACCGTGTT
GTCTCCCAATTATCCCTAAAGATGGCTAGACGTCCTCATCACAGAACAATGCCATCCACCGACCA
GATATACTCATCACGTAAGAGTAGATCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAAAC
ATGTTATCTC
Found at i:1758793 original size:18 final size:19
Alignment explanation
Indices: 1758761--1758802 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1758751 TTTCAGGTCT
1758761 TATTTAATTACTATTACTA
1 TATTTAATTACTATTACTA
* *
1758780 TATTT-ATTATTATTATTA
1 TATTTAATTACTATTACTA
1758798 TATTT
1 TATTT
1758803 TATAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTAATTACTATTACTA
Found at i:1758804 original size:19 final size:19
Alignment explanation
Indices: 1758761--1758825 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1758751 TTTCAGGTCT
* * *
1758761 TATTTAATTACTATTACTA
1 TATTTTATTATTATTATTA
1758780 TA-TTTATTATTATTATTA
1 TATTTTATTATTATTATTA
* *
1758798 TATTTTATAATAATTATTA
1 TATTTTATTATTATTATTA
*
1758817 CATTTTATT
1 TATTTTATT
1758826 TCCAACCCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 15 0.39
19 23 0.61
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTATTATTATTATTA
Found at i:1759370 original size:21 final size:21
Alignment explanation
Indices: 1759346--1759391 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1759336 TCAAAAAACA
*
1759346 AAAAAAACAAAAAAAGAATAG
1 AAAAAAACAAAAAAAGAAAAG
* *
1759367 AAAACAACCAAAAAAGAAAAG
1 AAAAAAACAAAAAAAGAAAAG
1759388 AAAA
1 AAAA
1759392 GAGAGAAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.02
Consensus pattern (21 bp):
AAAAAAACAAAAAAAGAAAAG
Found at i:1769143 original size:31 final size:31
Alignment explanation
Indices: 1769108--1769175 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1769098 TCAGAAAACA
1769108 TAAGATAT-GACTACTTTCATTTTTATTTAAT
1 TAAGATATAG-CTACTTTCATTTTTATTTAAT
* *
1769139 TAAGATATAGTTACTTTCGTTTTTATTTAAT
1 TAAGATATAGCTACTTTCATTTTTATTTAAT
1769170 TAAGAT
1 TAAGAT
1769176 GTGGTCATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.51
Consensus pattern (31 bp):
TAAGATATAGCTACTTTCATTTTTATTTAAT
Found at i:1769346 original size:27 final size:27
Alignment explanation
Indices: 1769316--1769379 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
1769306 CATAAAATAT
*
1769316 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTTAAATCAAAATAAAAATAAA
** *
1769343 ATATTTTTAAATCAAGTTAATAATAAA
1 ATATTTTTAAATCAAAATAAAAATAAA
*
1769370 ATATATTTAA
1 ATATTTTTAA
1769380 TAAGTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (27 bp):
ATATTTTTAAATCAAAATAAAAATAAA
Found at i:1769388 original size:22 final size:22
Alignment explanation
Indices: 1769356--1769413 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 22
1769346 TTTTTAAATC
1769356 AAGTTAATAATAAAATATATTTAAT
1 AAGTTAAT-ATAAAA-ATATTT-AT
*
1769381 AAGTTAATATAAAAATATTTTT
1 AAGTTAATATAAAAATATTTAT
1769403 AAGTTAATATA
1 AAGTTAATATA
1769414 TATAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 12 0.38
23 6 0.19
24 6 0.19
25 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
AAGTTAATATAAAAATATTTAT
Found at i:1769395 original size:25 final size:25
Alignment explanation
Indices: 1769338--1769424 Score: 92
Period size: 25 Copynumber: 3.4 Consensus size: 25
1769328 GAAAATAAAA
1769338 ATAAAATATTTTTAAATCAAGTTAATA-
1 ATAAAATA-TTTT-AAT-AAGTTAATAT
1769365 ATAAAATATATTTAATAAGTTAATAT
1 ATAAAATAT-TTTAATAAGTTAATAT
1769391 A-AAAATATTTT--TAAGTTAATATAT
1 ATAAAATATTTTAATAAGTT-A-ATAT
1769415 ATAAAATATT
1 ATAAAATATT
1769425 ATGAATTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
22 6 0.11
23 1 0.02
24 8 0.15
25 24 0.44
26 5 0.09
27 11 0.20
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (25 bp):
ATAAAATATTTTAATAAGTTAATAT
Found at i:1769434 original size:25 final size:26
Alignment explanation
Indices: 1769387--1769443 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
1769377 TAATAAGTTA
* *
1769387 ATATA-AAAATATTTTTAAGTTAA-T
1 ATATATAAAATATTATGAAGTTAAGT
*
1769411 ATATATAAAATATTATGAATTTAAGT
1 ATATATAAAATATTATGAAGTTAAGT
*
1769437 ATTTATA
1 ATATATA
1769444 CACCAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 5 0.19
25 15 0.56
26 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATATAAAATATTATGAAGTTAAGT
Found at i:1771068 original size:16 final size:15
Alignment explanation
Indices: 1771049--1771172 Score: 50
Period size: 16 Copynumber: 7.7 Consensus size: 15
1771039 TCTCCCTTGC
*
1771049 TTTTTTTATTTATTT
1 TTTTTTTATTTTTTT
*
1771064 TTTTTATATTTTTTT
1 TTTTTTTATTTTTTT
** * *
1771079 TACTTTTGTTATTTT
1 TTTTTTTATTTTTTT
* *
1771094 TATTGTTATGTTTTTT
1 TTTTTTTAT-TTTTTT
* *
1771110 TCTCTTAATTTATTTAATAT
1 T-T-TT--TTTATTT-TTTT
*
1771130 TTTTATTATTTTATTT
1 TTTTTTTATTTT-TTT
* *
1771146 ATTTTTTATTTTATTC
1 TTTTTTTATTTT-TTT
*
1771162 TTTTTTGATTT
1 TTTTTTTATTT
1771173 ACTTTTTTTG
Statistics
Matches: 79, Mismatches: 23, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
15 29 0.37
16 36 0.46
18 4 0.05
19 3 0.04
20 7 0.09
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTTTATTTTTTT
Done.