Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_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: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1228914 original size:8 final size:8
Alignment explanation
Indices: 1228901--1228939 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1228891 GAACATTTCA
*
1228901 TGCATTCT
1 TGCATTTT
1228909 TGCA-TTT
1 TGCATTTT
1228916 TGCATTTT
1 TGCATTTT
*
1228924 TGCCTTTT
1 TGCATTTT
1228932 TGCATTTT
1 TGCATTTT
1228940 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:1230136 original size:11 final size:11
Alignment explanation
Indices: 1230122--1230167 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
1230112 AATAAAAAGG
1230122 GCAAAAAAAAA
1 GCAAAAAAAAA
1230133 GCAAAAAAAAA
1 GCAAAAAAAAA
1230144 GCAAAAAAAAGA
1 GCAAAAAAAA-A
*
1230156 ACAAAAAGAAAA
1 GCAAAAA-AAAA
1230168 AAGAAAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 21 0.66
12 8 0.25
13 3 0.09
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (11 bp):
GCAAAAAAAAA
Found at i:1230139 original size:12 final size:12
Alignment explanation
Indices: 1230124--1230168 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
1230114 TAAAAAGGGC
1230124 AAAAAAAAAGC-
1 AAAAAAAAAGCA
1230135 AAAAAAAAAGCA
1 AAAAAAAAAGCA
1230147 AAAAAAAGAA-CA
1 AAAAAAA-AAGCA
1230159 AAAAGAAAAA
1 AAAA-AAAAA
1230169 AGAAAAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.35
12 15 0.48
13 5 0.16
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGCA
Found at i:1230176 original size:9 final size:10
Alignment explanation
Indices: 1230125--1230169 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
1230115 AAAAAGGGCA
1230125 AAAAAAAAGC
1 AAAAAAAAGC
1230135 AAAAAAAAAGC
1 -AAAAAAAAGC
1230146 AAAAAAAAG-
1 AAAAAAAAGC
*
1230155 AACAAAAAG-
1 AAAAAAAAGC
1230164 AAAAAA
1 AAAAAA
1230170 GAAAAAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 13 0.41
10 9 0.28
11 10 0.31
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGC
Found at i:1230803 original size:22 final size:22
Alignment explanation
Indices: 1230775--1230818 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1230765 AGCTACCCCA
1230775 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
1230797 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
1230819 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:1231889 original size:36 final size:36
Alignment explanation
Indices: 1231781--1231904 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
1231771 ATTGAAAACA
* * *
1231781 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
1231817 TTTCCCTTGGAACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
1231854 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
1231890 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
1231905 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:1231998 original size:67 final size:68
Alignment explanation
Indices: 1231880--1232036 Score: 205
Period size: 68 Copynumber: 2.4 Consensus size: 68
1231870 TTTCGTCTAT
* **
1231880 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
1231941 CTCC
66 -TCC
* * *
1231945 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
1232010 TCC
66 TCC
* *
1232013 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
1232037 ACAGATATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:1232864 original size:105 final size:105
Alignment explanation
Indices: 1232686--1233403 Score: 1146
Period size: 105 Copynumber: 6.9 Consensus size: 105
1232676 GAGGCAACAT
* ** *
1232686 AAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAA
1232751 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
65 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
1232792 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
* *
1232857 TTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* *
1232897 AAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGAACCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
* *
1232959 TTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
*
1232999 AAGTTCAACTTCACGTCGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
*
1233064 TTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* **
1233104 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
*
1233169 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* * *
1233209 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCTAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
*
1233274 TTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* **
1233314 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAA-AA-TT-TC-A-TTCAGATTCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
* *
1233374 TTCAACTTCACGACGGAGGATATTGGACTC
66 TTCAACTTCACAACGAAGGATATTGGACTC
1233404 TGAACAATGC
Statistics
Matches: 578, Mismatches: 31, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 35 0.06
101 1 0.00
102 100 0.17
103 2 0.00
104 2 0.00
105 403 0.70
106 35 0.06
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
Found at i:1233045 original size:207 final size:207
Alignment explanation
Indices: 1232686--1233403 Score: 1118
Period size: 207 Copynumber: 3.4 Consensus size: 207
1232676 GAGGCAACAT
* ** *
1232686 AAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT---C-AACAACTTCTCAATTTCAGAGCCAA
1232751 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
62 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
*
1232816 CCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATT
127 CCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
1232881 GGACTTCAGACAACGC
192 GGACTTCAGACAACGC
* *
1232897 AAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACTTCTCAATTTCAGAACCAATTTC
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACTTCTCAATTTCAGAGCCAATTTC
* * *
1232962 AACTTCACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGTCGAAGGGACCGC
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1233027 TGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
131 TGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
1233092 TTCAGACAACGC
196 TTCAGACAACGC
* **
1233104 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT---CAACAACTTCTCAATTTCAGAGCCAAT
*
1233169 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGAC
63 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * * *
1233234 CGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCTAATTTCAACTTCACAACGAAGGATATTA
128 CGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
*
1233299 GACTCCAGACAACGC
193 GACTTCAGACAACGC
* * **
1233314 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAAAATT-TC-A-TTCAGATTCAATTT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACTTCTCAATTTCAGAGCCAATTT
* *
1233376 CAACTTCACGACGGAGGATATTGGACTC
65 CAACTTCACAACGAAGGATATTGGACTC
1233404 TGAACAATGC
Statistics
Matches: 470, Mismatches: 33, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
205 36 0.08
206 1 0.00
207 204 0.43
208 5 0.01
210 194 0.41
211 30 0.06
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (207 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACTTCTCAATTTCAGAGCCAATTTC
AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
TGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TTCAGACAACGC
Found at i:1234591 original size:18 final size:17
Alignment explanation
Indices: 1234552--1234594 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1234542 ATTTTATGGA
1234552 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1234568 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1234586 TATTATTAT
1 TATTATTAT
1234595 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1236715 original size:20 final size:20
Alignment explanation
Indices: 1236652--1236745 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
1236642 AAATAACCAA
**
1236652 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGATTTC
* * *
1236672 CAATTTTGCAACAC-AGTTTC
1 CAAATTCGCAACGCGA-TTTC
*
1236692 CAAATTCGCAACGCGATTTT
1 CAAATTCGCAACGCGATTTC
** * *
1236712 CAAATTTACAATGCGATTTT
1 CAAATTCGCAACGCGATTTC
*
1236732 CAAATTCACAACGC
1 CAAATTCGCAACGC
1236746 TAATTACCGA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
19 1 0.02
20 56 0.97
21 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:1249015 original size:14 final size:14
Alignment explanation
Indices: 1248996--1249023 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1248986 AAGACATCCA
1248996 TGCCCCAGCTTGAG
1 TGCCCCAGCTTGAG
1249010 TGCCCCAGCTTGAG
1 TGCCCCAGCTTGAG
1249024 GGGAGTGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.29, T:0.21
Consensus pattern (14 bp):
TGCCCCAGCTTGAG
Found at i:1255006 original size:16 final size:17
Alignment explanation
Indices: 1254967--1255008 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1254957 ATTGTGAAAT
*
1254967 CCTTTGCAGCACCGTCC
1 CCTTCGCAGCACCGTCC
*
1254984 TCTTCGCAGCACCG-CC
1 CCTTCGCAGCACCGTCC
1255000 CCTTCGCAG
1 CCTTCGCAG
1255009 TGCCGTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.12, C:0.48, G:0.19, T:0.21
Consensus pattern (17 bp):
CCTTCGCAGCACCGTCC
Found at i:1255154 original size:19 final size:19
Alignment explanation
Indices: 1255130--1255177 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
1255120 GACAACCCTT
1255130 CCTGTTCCGCTATTTGGTA
1 CCTGTTCCGCTATTTGGTA
*
1255149 CCTGTTCCGCCGCTGTTTGGTA
1 CCTGTT---CCGCTATTTGGTA
1255171 CCTGTTC
1 CCTGTTC
1255178 TACCGCTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 7 0.28
22 18 0.72
ACGTcount: A:0.06, C:0.31, G:0.23, T:0.40
Consensus pattern (19 bp):
CCTGTTCCGCTATTTGGTA
Found at i:1255167 original size:22 final size:22
Alignment explanation
Indices: 1255136--1255196 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1255126 CCTTCCTGTT
* *
1255136 CCGCTATTTGGTACCTGTTCCG
1 CCGCTGTTTGGTACCTGTTCCA
*
1255158 CCGCTGTTTGGTACCTGTTCTA
1 CCGCTGTTTGGTACCTGTTCCA
*
1255180 CCGCTG-TTGGTAACTGT
1 CCGCTGTTTGGTACCTGT
1255197 CCGGACAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 10 0.29
22 25 0.71
ACGTcount: A:0.10, C:0.28, G:0.25, T:0.38
Consensus pattern (22 bp):
CCGCTGTTTGGTACCTGTTCCA
Found at i:1263178 original size:23 final size:23
Alignment explanation
Indices: 1263152--1263195 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1263142 AAAATACTTT
*
1263152 CAAAGCCTGAAAACTCTGTTTAC
1 CAAAGCCGGAAAACTCTGTTTAC
1263175 CAAAGCCGGAAAACTCTGTTT
1 CAAAGCCGGAAAACTCTGTTT
1263196 CTACACTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (23 bp):
CAAAGCCGGAAAACTCTGTTTAC
Found at i:1274558 original size:61 final size:61
Alignment explanation
Indices: 1274466--1274584 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
1274456 TGCACTAAGC
* * *
1274466 TTACGCTCTAGTGCTAATCAGGATATGACACATAAGGTCGTGCCCACCACCTACACTAGGT
1 TTACACTCTAGTGCTAATCAGAATATAACACATAAGGTCGTGCCCACCACCTACACTAGGT
* * * *
1274527 TTACACTCTAGTGCTAATCCGAATATAACACATAAGGTTGTGCCCTCCACCTGCACTA
1 TTACACTCTAGTGCTAATCAGAATATAACACATAAGGTCGTGCCCACCACCTACACTA
1274585 AGTGTCCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (61 bp):
TTACACTCTAGTGCTAATCAGAATATAACACATAAGGTCGTGCCCACCACCTACACTAGGT
Found at i:1279770 original size:2 final size:2
Alignment explanation
Indices: 1279763--1279797 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1279753 TTCTCAGAAT
1279763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1279798 TTGCAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1280548 original size:44 final size:45
Alignment explanation
Indices: 1280449--1280549 Score: 177
Period size: 45 Copynumber: 2.3 Consensus size: 45
1280439 TTTTGACAAC
*
1280449 AAATATTCAAAAAGATTAAGTTGATTAAATAATAATTTTTTCAAT
1 AAATATTCAAAAAGATTAACTTGATTAAATAATAATTTTTTCAAT
*
1280494 AAATATTCAAAAAGATTAACTTGGTTAAATAATAA-TTTTTCAAT
1 AAATATTCAAAAAGATTAACTTGATTAAATAATAATTTTTTCAAT
1280538 AAATATTCAAAA
1 AAATATTCAAAA
1280550 GTAATAGTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
44 21 0.39
45 33 0.61
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (45 bp):
AAATATTCAAAAAGATTAACTTGATTAAATAATAATTTTTTCAAT
Found at i:1288173 original size:9 final size:9
Alignment explanation
Indices: 1288133--1288180 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
1288123 AATCATACTA
1288133 ATTTTTTTGT
1 ATTTTTTT-T
* *
1288143 AATTTTTCTG
1 -ATTTTTTTT
*
1288153 ATTTTTTAT
1 ATTTTTTTT
1288162 ATTTTTTTT
1 ATTTTTTTT
1288171 ATTTTTTTT
1 ATTTTTTTT
1288180 A
1 A
1288181 AATTTACAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
9 24 0.77
11 7 0.23
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:1289757 original size:27 final size:29
Alignment explanation
Indices: 1289727--1289783 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
1289717 AATTATGGTT
1289727 TTGA-AAAAA-AAAGTTTAGGTACTAAAC
1 TTGACAAAAACAAAGTTTAGGTACTAAAC
*
1289754 TTGACAAAAACTGATAGTTTAGGTACTAAA
1 TTGACAAAAAC--AAAGTTTAGGTACTAAA
1289784 TGTAAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.16
28 5 0.20
31 16 0.64
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (29 bp):
TTGACAAAAACAAAGTTTAGGTACTAAAC
Found at i:1290113 original size:42 final size:42
Alignment explanation
Indices: 1290053--1290132 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1290043 ACTGAATCAC
1290053 CACTATTTGATCAAATTGACACCCTTTAACTAGTCATTAAAA
1 CACTATTTGATCAAATTGACACCCTTTAACTAGTCATTAAAA
* *
1290095 CACTATTTGATCACATTGACACCCTTTGACTAGTCATT
1 CACTATTTGATCAAATTGACACCCTTTAACTAGTCATT
1290133 TTAATTCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (42 bp):
CACTATTTGATCAAATTGACACCCTTTAACTAGTCATTAAAA
Found at i:1292861 original size:41 final size:41
Alignment explanation
Indices: 1292804--1292888 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
1292794 ACGGACCTTA
1292804 CCTAGAATAATCATATGCCTTTCGTCTGGTTATATGTATTT
1 CCTAGAATAATCATATGCCTTTCGTCTGGTTATATGTATTT
*
1292845 CCTAGAATAATCATATGGCTTTCGTCTGGTTATATGTATTT
1 CCTAGAATAATCATATGCCTTTCGTCTGGTTATATGTATTT
1292886 CCT
1 CCT
1292889 GGGCATTGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (41 bp):
CCTAGAATAATCATATGCCTTTCGTCTGGTTATATGTATTT
Found at i:1303928 original size:18 final size:19
Alignment explanation
Indices: 1303893--1303932 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1303883 GCCTTTGTAT
* *
1303893 ATATATATATTTATTAATA
1 ATATATATATATAATAATA
1303912 ATATA-ATATATAATAATA
1 ATATATATATATAATAATA
1303930 ATA
1 ATA
1303933 ATAAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATATATATAATAATA
Found at i:1304214 original size:76 final size:76
Alignment explanation
Indices: 1304088--1305075 Score: 1813
Period size: 76 Copynumber: 13.0 Consensus size: 76
1304078 GGTCTTATGA
* *
1304088 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
1304152 AAGGGCTTACAG
65 AAGGACTTACAG
1304164 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304229 AGGACTTACAG
66 AGGACTTACAG
1304240 ATGACCCGAAGGATTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304304 AGGACTTACAG
66 AGGACTTACAG
*
1304315 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304380 AGGACTTACAG
66 AGGACTTACAG
1304391 ATGACCCGAAGGATTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304455 AGGACTTACAG
66 AGGACTTACAG
*
1304466 ATGACCCGAAGGATTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304531 AGGACTTACAG
66 AGGACTTACAG
*
1304542 ATGACTCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304607 AGGACTTACAG
66 AGGACTTACAG
*
1304618 ATGACTCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304683 AGGACTTACAG
66 AGGACTTACAG
* *
1304694 ATAACCCGAAGGATTTGAAAACATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304759 AGGACTTACAG
66 AGGACTTACAG
*
1304770 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304835 AGGACTTACAG
66 AGGACTTACAG
*
1304846 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304911 AGGACTTACAG
66 AGGACTTACAG
* * *
1304922 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGAAGGATTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1304987 AGGACTTACAG
66 AGGACTTACAG
1304998 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1305063 AGGAC-TACAG
66 AGGACTTACAG
1305073 ATG
1 ATG
1305076 TGAAATAGTT
Statistics
Matches: 890, Mismatches: 19, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
75 157 0.18
76 733 0.82
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:1310535 original size:21 final size:23
Alignment explanation
Indices: 1310496--1310549 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
1310486 TCTGATTTAA
*
1310496 TTTTTTTTCTATTTCTTTCCT-T
1 TTTTTTTTTTATTTCTTTCCTCT
*
1310518 TTTTTTTTTTCTTT-TTTCCTCT
1 TTTTTTTTTTATTTCTTTCCTCT
*
1310540 TTTTCTTTTT
1 TTTTTTTTTT
1310550 GCTGAGCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTTTTATTTCTTTCCTCT
Found at i:1315163 original size:26 final size:24
Alignment explanation
Indices: 1315126--1315182 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
1315116 TAATACTTGA
*
1315126 AAATAAATAATAATATAAAAATTATG
1 AAATAAATAATAATA-AAAAAAT-TG
1315152 AAAT-AATAAATAATAAAAAAATTG
1 AAATAAAT-AATAATAAAAAAATTG
1315176 AAATAAA
1 AAATAAA
1315183 AGAAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 6 0.21
25 11 0.39
26 11 0.39
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
AAATAAATAATAATAAAAAAATTG
Found at i:1315164 original size:7 final size:7
Alignment explanation
Indices: 1315127--1315168 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1315117 AATACTTGAA
1315127 AATAAAT
1 AATAAAT
1315134 AATAATAT
1 AATAA-AT
1315142 AA-AAAT
1 AATAAAT
*
1315148 TATGAAAT
1 AAT-AAAT
1315156 AATAAAT
1 AATAAAT
1315163 AATAAA
1 AATAAA
1315169 AAAATTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 3 0.10
7 17 0.57
8 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:1315179 original size:17 final size:17
Alignment explanation
Indices: 1315158--1315199 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1315148 TATGAAATAA
*
1315158 TAAATAATA-AAAAAAT
1 TAAATAAAAGAAAAAAT
1315174 TGAAATAAAAGAAAAAAT
1 T-AAATAAAAGAAAAAAT
1315192 TAAATAAA
1 TAAATAAA
1315200 TGATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAATAAAAGAAAAAAT
Found at i:1317249 original size:3 final size:3
Alignment explanation
Indices: 1317241--1317280 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
1317231 TATATTTATT
1317241 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1317281 GAAAAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1320292 original size:2 final size:2
Alignment explanation
Indices: 1320285--1320323 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1320275 TTGTACTTAT
1320285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1320324 TTTAACAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1321408 original size:26 final size:28
Alignment explanation
Indices: 1321347--1321409 Score: 67
Period size: 31 Copynumber: 2.2 Consensus size: 28
1321337 CGAGTATTGC
*
1321347 TGAGCTCGACTCGACTCAAAAACTTTGAAA
1 TGAGCTCGACTCGACTCAAAAACTTCG--A
*
1321377 TGGAGCTCGACTCGACTCGAAAAC-TCG-
1 T-GAGCTCGACTCGACTCAAAAACTTCGA
1321404 TGAGCT
1 TGAGCT
1321410 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 5 0.17
27 1 0.03
30 3 0.10
31 21 0.70
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCAAAAACTTCGA
Found at i:1321438 original size:6 final size:6
Alignment explanation
Indices: 1321421--1321451 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1321411 AAAATTTTTA
1321421 AACTCG -ACTCG AACTCG AACTCG AACTCG AA
1 AACTCG AACTCG AACTCG AACTCG AACTCG AA
1321452 ATCCTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
AACTCG
Found at i:1323419 original size:98 final size:98
Alignment explanation
Indices: 1323305--1323504 Score: 355
Period size: 98 Copynumber: 2.0 Consensus size: 98
1323295 TCAAATCGAT
* *
1323305 CCAACTTTGAAGAATTGTATGATAACCCCTTTCCTTCCCATCAAGTTGTCCTCACATTAAAAGTC
1 CCAACTTTGAAGAATTGTATGATAACCCCTTTCATTCCCATCAAGTTGTCCTCACAATAAAAGTC
1323370 TTCTCACTTCTAATCAAAAGGTTTTGATCTCTA
66 TTCTCACTTCTAATCAAAAGGTTTTGATCTCTA
* * *
1323403 CCAACTTTGAAGAATTGTATGATTACCTCTTTCATTCCCATCAAGTTGTCCTCACAATACAAGTC
1 CCAACTTTGAAGAATTGTATGATAACCCCTTTCATTCCCATCAAGTTGTCCTCACAATAAAAGTC
1323468 TTCTCACTTCTAATCAAAAGGTTTTGATCTCTA
66 TTCTCACTTCTAATCAAAAGGTTTTGATCTCTA
1323501 CCAA
1 CCAA
1323505 ATCCTTGTGT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (98 bp):
CCAACTTTGAAGAATTGTATGATAACCCCTTTCATTCCCATCAAGTTGTCCTCACAATAAAAGTC
TTCTCACTTCTAATCAAAAGGTTTTGATCTCTA
Found at i:1324905 original size:25 final size:25
Alignment explanation
Indices: 1324871--1324929 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
1324861 TCGAATGGGT
1324871 TTCGATGAGTTACGGTAAGAGGAAG
1 TTCGATGAGTTACGGTAAGAGGAAG
1324896 TTCGATGAGTTACGGTAAGAGGAAG
1 TTCGATGAGTTACGGTAAGAGGAAG
*
1324921 TGCGATGAG
1 TTCGATGAG
1324930 AAACATAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.08, G:0.37, T:0.24
Consensus pattern (25 bp):
TTCGATGAGTTACGGTAAGAGGAAG
Found at i:1330254 original size:13 final size:13
Alignment explanation
Indices: 1330236--1330272 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1330226 GTGGGTTTTG
1330236 ATTCCTTGGAAAC
1 ATTCCTTGGAAAC
1330249 ATTCCTTGGAAAC
1 ATTCCTTGGAAAC
1330262 ATTCCTTGGAA
1 ATTCCTTGGAA
1330273 GCCTCATCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (13 bp):
ATTCCTTGGAAAC
Found at i:1333889 original size:13 final size:13
Alignment explanation
Indices: 1333859--1333892 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1333849 TATTCCTTGA
1333859 TCTAC-ACAAAAT
1 TCTACAACAAAAT
1333871 TGCTACAACAAAAT
1 T-CTACAACAAAAT
1333885 TCTACAAC
1 TCTACAAC
1333893 TTCCTCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 11 0.55
14 8 0.40
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (13 bp):
TCTACAACAAAAT
Found at i:1337631 original size:60 final size:60
Alignment explanation
Indices: 1337519--1337631 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
1337509 ACACACACTA
* ** *
1337519 ATTTATGACTTGCAAAAAATGTGTGTCATAAAAAATGTCATGTTTTTTAAAATCTGAACG
1 ATTTATGACTTACAAAAAATGTGTGTCATAAAAAATGTCATAATTTTAAAAATCTGAACG
* ***
1337579 ATTTATGACTTAC-AATAATGTGTGTCATATTTAATAGTCATAATTTTAAAAAT
1 ATTTATGACTTACAAAAAATGTGTGTCATAAAAAAT-GTCATAATTTTAAAAAT
1337632 TTGCAAAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 18 0.41
60 26 0.59
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (60 bp):
ATTTATGACTTACAAAAAATGTGTGTCATAAAAAATGTCATAATTTTAAAAATCTGAACG
Found at i:1341642 original size:2 final size:2
Alignment explanation
Indices: 1341635--1341668 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
1341625 ATGGATTGCT
1341635 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
1341669 GTATTATGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1341726 original size:2 final size:2
Alignment explanation
Indices: 1341715--1341755 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1341705 TTTGTCAATC
1341715 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1341756 ATTTATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1341863 original size:45 final size:45
Alignment explanation
Indices: 1341775--1341867 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
1341765 ATACAATCAC
* * *
1341775 GACACACAAATGTCTGTCATCTTTTTTAATGACGTATGCTTCAAT
1 GACACACAAATGTCTGTCATCTTATTTAATGACGGAGGCTTCAAT
* * *
1341820 GACACACAAATGTGTGTCATCTTCATTT-ATGACGGGGGTTTCAAT
1 GACACACAAATGTCTGTCATCTT-ATTTAATGACGGAGGCTTCAAT
1341865 GAC
1 GAC
1341868 GCTCAATGCG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 38 0.93
46 3 0.07
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (45 bp):
GACACACAAATGTCTGTCATCTTATTTAATGACGGAGGCTTCAAT
Found at i:1343873 original size:17 final size:18
Alignment explanation
Indices: 1343835--1343880 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1343825 TAAAATAGGG
*
1343835 TTTTGTGCCCAAAATTCT
1 TTTTGTACCCAAAATTCT
1343853 TTTTGTACCCAAAATTCT
1 TTTTGTACCCAAAATTCT
*
1343871 TTTTTTACCC
1 TTTTGTACCC
1343881 TAAGGGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTTGTACCCAAAATTCT
Found at i:1346364 original size:18 final size:18
Alignment explanation
Indices: 1346343--1346377 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1346333 CGCCTTAAGC
*
1346343 TTGTTATGTATCAATGTA
1 TTGTTATGAATCAATGTA
*
1346361 TTGTTGTGAATCAATGT
1 TTGTTATGAATCAATGT
1346378 GCTTTCATCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.49
Consensus pattern (18 bp):
TTGTTATGAATCAATGTA
Found at i:1354528 original size:4 final size:4
Alignment explanation
Indices: 1354519--1354543 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1354509 TTTCTTTTAC
1354519 TGAG TGAG TGAG TGAG TGAG TGAG T
1 TGAG TGAG TGAG TGAG TGAG TGAG T
1354544 CAGCGAGCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.48, T:0.28
Consensus pattern (4 bp):
TGAG
Found at i:1354856 original size:28 final size:30
Alignment explanation
Indices: 1354792--1354856 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
1354782 GATTCTTCTA
* *
1354792 AATTATTTTATTATTATTTTCATATGAAATGG
1 AATT-TTTTATTATTATTTTAATATAAAAT-G
*
1354824 GATTTTTTATTATTA-TTTAATATAAAAT-
1 AATTTTTTATTATTATTTTAATATAAAATG
1354852 AATTT
1 AATTT
1354857 AAAATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 4 0.14
30 11 0.38
31 11 0.38
32 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (30 bp):
AATTTTTTATTATTATTTTAATATAAAATG
Found at i:1357176 original size:81 final size:81
Alignment explanation
Indices: 1357041--1357204 Score: 256
Period size: 81 Copynumber: 2.0 Consensus size: 81
1357031 CAGATTATTG
*
1357041 AGCAATTCAGTTAGAAAGAAAGAAACAACCAATATTACTCGAACTCGGGTGTGAGTATGAGATAT
1 AGCAATTCAGTTAGAAAGAAAGAAACAACCAATATTACTCGAACTCGGGTGTGAGTATCAGATAT
*
1357106 CGGTATGTGTCTGACA
66 CGGTAGGTGTCTGACA
* * * * *
1357122 AGCAATTTAGTTAGAAAGACAGAAACAACCAATGTTACTTGAATTCGGGTGTGAGTATCAGATAT
1 AGCAATTCAGTTAGAAAGAAAGAAACAACCAATATTACTCGAACTCGGGTGTGAGTATCAGATAT
*
1357187 CTGTAGGTGTCTGACA
66 CGGTAGGTGTCTGACA
1357203 AG
1 AG
1357205 TATGTTATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (81 bp):
AGCAATTCAGTTAGAAAGAAAGAAACAACCAATATTACTCGAACTCGGGTGTGAGTATCAGATAT
CGGTAGGTGTCTGACA
Found at i:1358874 original size:25 final size:25
Alignment explanation
Indices: 1358845--1358895 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1358835 GTAAAGAGCT
* *
1358845 ATCGGCATTGTTGAAATTTAAAAGA
1 ATCGGCACTGTAGAAATTTAAAAGA
* *
1358870 ATCGGTACTGTAGGAATTTAAAAGA
1 ATCGGCACTGTAGAAATTTAAAAGA
1358895 A
1 A
1358896 ATTTAAAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (25 bp):
ATCGGCACTGTAGAAATTTAAAAGA
Found at i:1358900 original size:11 final size:11
Alignment explanation
Indices: 1358884--1358908 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1358874 GTACTGTAGG
1358884 AATTTAAAAGA
1 AATTTAAAAGA
1358895 AATTTAAAAGA
1 AATTTAAAAGA
1358906 AAT
1 AAT
1358909 GAAAAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (11 bp):
AATTTAAAAGA
Found at i:1358932 original size:7 final size:8
Alignment explanation
Indices: 1358905--1358930 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1358895 AATTTAAAAG
1358905 AAATGAAA
1 AAATGAAA
1358913 AAATGAAA
1 AAATGAAA
1358921 AAATGAAA
1 AAATGAAA
1358929 AA
1 AA
1358931 TGTCTCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:1360337 original size:2 final size:2
Alignment explanation
Indices: 1360332--1360360 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1360322 ATATATCGAA
1360332 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1360361 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1360365 original size:2 final size:2
Alignment explanation
Indices: 1360360--1360418 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1360350 ACACACACAC
1360360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1360402 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1360419 CATACTTATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1361036 original size:226 final size:227
Alignment explanation
Indices: 1360542--1362354 Score: 2610
Period size: 226 Copynumber: 8.0 Consensus size: 227
1360532 CATTGATAAA
* *
1360542 GGTTGATAACAAATCAAGTGATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* *
1360607 TAAACTTTGGTAACATTTTCGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
66 TAAAATTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * * *
1360672 TATCATATTTT-TTATCTTCG-GGTTTCTAAGGCCTCATCAGCTTTAAAAAGGCACTACCTATTA
131 TAACCTATTTTGTTATCGTCGAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
1360735 CGTTACATAAGCGCTACCTAATATGTTATTAT
196 CGTTACATAAGCGCTACCTAATATGTTATTAT
* **
1360767 GGTTGATAACAAATCAAGTAATTAATCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCGGCT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * *
1360832 TAAACTTTGGTAACATTTTAGGTGTTACCTAATATGTTGATAATACTGGTAACAAATTAAGTAAT
66 TAAAATTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * ** * *
1360897 TTACCTATTTTATTATCGTCGA-ATTTCTAAAGGTTCCGTCAGC-TTAAAAAGGCGCTACTTATT
131 TAACCTATTTTGTTATCGTCGAGATTTCT-AAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATT
* *
1360960 ACGTTACATAAGTGCTACCTAATATGATATTAT
195 ACGTTACATAAGCGCTACCTAATATGTTATTAT
* * *
1360993 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGTTCTATCAGCT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * *
1361058 TAAAATTTGGTAACATTTTAGGTGTTACCTAATATGTTAATAATATTGATAACAAATTAAGTAAT
66 TAAAATTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * *
1361123 TAACCTATTTTGTTATCGTCG-GATTTCTAAGGTCCCATCAAC-TTAAAAATGCGCTACCTATTA
131 TAACCTATTTTGTTATCGTCGAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
* * *
1361186 CGTTATAGAAGTGCTACCTAATATGTTATTAT
196 CGTTACATAAGCGCTACCTAATATGTTATTAT
* * *
1361218 AGTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATCTCTAAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * *
1361283 TTAATTTTGGTAACATTTTCA-ACGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAA
66 TAAAATTTGGTAACATTTT-AGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAA
* * * * *
1361347 TTAACATATTTTGTTATCGTC-AGATTTCTAAAGCCCCATCAGTTTTAAAAATGCACTACCTATT
130 TTAACCTATTTTGTTATCGTCGAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATT
*
1361411 ACGTTACATAAGTGCTACCTAATATGTTATTAT
195 ACGTTACATAAGCGCTACCTAATATGTTATTAT
* * *
1361444 GATTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCAGATTTATAAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * * *
1361509 TAAATTTTGATAACATTTTAGGTGTTACCTAATATGTTGATAATACTGATAATAAATTAAGTAAT
66 TAAAATTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* *
1361574 TAACCTATTTTGTTATCGTC-AGATTTCTAAGACCCCATCAGCTTTAAAAAGGTGCTACCTATTA
131 TAACCTATTTTGTTATCGTCGAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
1361638 CGTTACATAAGCGCTACCTAATATGTTATTAT
196 CGTTACATAAGCGCTACCTAATATGTTATTAT
* * * * *
1361670 GTTTGATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCAGATTTATAAGGCTCCATCAGCT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* *
1361735 TAAATTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAATAAATTAAGTAAT
66 TAAAATTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
*
1361800 TAACCTATTTTGTTATCGTC-AGATTTCTAAGGCCCCATCAGCTTTAAAAAGGTGCTACCTATTA
131 TAACCTATTTTGTTATCGTCGAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
1361864 CGTTACATAAGCGCTACCTAATATGTTATTAT
196 CGTTACATAAGCGCTACCTAATATGTTATTAT
* * * * *
1361896 GTTTTATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGAATTTCTAAAGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * * *
1361961 TAAAATTTGATAACATTTTAAGCGTTACTTAATATATTGATAATACTGATAACAAATTAAGTAAT
66 TAAAATTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * *
1362026 TAACCTATTTTGTTATTGTCG-GATTTCTAAGGCCTCATCAAC-TCAAAAAGGCGCTACCTATGA
131 TAACCTATTTTGTTATCGTCGAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
*
1362089 CGTTACATAAGCGCTACCTAATATATTATTAT
196 CGTTACATAAGCGCTACCTAATATGTTATTAT
* * * * * *
1362121 GGTTGATAACAAATCAAGTAATTAACTGATTATGTTATCATTGGATTTTTAAGGCTCCATCAGCT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * *
1362186 TAAAATTTGGTAACATTTTAGGCATTATCTAATATGTTGATAATACTGATAACAAATTAAATAAT
66 TAAAATTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * ** * * *
1362251 TAACATATTTGGTTATCGT-TAGATTTCTAAGGGTCCATCAGCTTTAACAAGTCGTTACCTATTA
131 TAACCTATTTTGTTATCGTCGAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
** *
1362315 CGTTACATAAATGCTACCT-ATTTGTTATTAT
196 CGTTACATAAGCGCTACCTAATATGTTATTAT
1362346 GGTTGATAA
1 GGTTGATAA
1362355 TGTTTCCAAT
Statistics
Matches: 1439, Mismatches: 138, Indels: 22
0.90 0.09 0.01
Matches are distributed among these distances:
225 555 0.39
226 874 0.61
227 10 0.01
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (227 bp):
GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
TAAAATTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
TAACCTATTTTGTTATCGTCGAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
CGTTACATAAGCGCTACCTAATATGTTATTAT
Found at i:1361168 original size:108 final size:106
Alignment explanation
Indices: 1360975--1362282 Score: 920
Period size: 108 Copynumber: 11.7 Consensus size: 106
1360965 ACATAAGTGC
* * * * ** *
1360975 TACCTAATATGATATTATGGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATT
1 TACCTAATATGTTATAAT-ATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATT
* * * * *
1361040 TCTAAGGTTCTATCAGCTTAAAATTTGGTAACATTTTAGGTGT
65 TCTAAGG-CCCATCAACTTAAAATTTGGTAACATTTTAAGCGT
* *
1361083 TACCTAATATGTTAATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATT
1 TACCTAATATGTT-ATAATATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATT
* * *
1361148 TCTAAGGTCCCATCAACTTAAAA-ATGCGCTACCTATTACGTTATAGAAGT
65 TCTAAGG-CCCATCAACTTAAAATTTG-G-TAAC-ATT---TTA-AG-CGT
* * * *
1361198 GCTACCTAATATGTTATTATAGTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGA
1 --TACCTAATATGTTATAATA-TTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGA
* * *
1361263 TCTCTAAGGCTCCATCAACTTTAATTTTGGTAACATTTTCAA-CGT
63 TTTCTAAGGC-CCATCAACTTAAAATTTGGTAACATTTT-AAGCGT
* * *
1361308 TACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATT
1 TACCTAATATGTT-ATAATATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATT
* ** * * * * *
1361373 TCTAAAGCCCCATCAGTTTTAAAA-ATGCACTACCTATTACGTTACATAAGTGC
65 TCT-AAGGCCCATCA-ACTTAAAATTTG--GTAAC-A-T---TT---TAAGCGT
* * **
1361426 TACCTAATATGTTATTATGATTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCAGATT
1 TACCTAATATGTTATAAT-ATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATT
* * * * *
1361491 TATAAGGCTCCATCAACTTAAATTTTGATAACATTTTAGGTGT
65 TCTAAGGC-CCATCAACTTAAAATTTGGTAACATTTTAAGCGT
* * *
1361534 TACCTAATATGTTGATAATACTGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATT
1 TACCTAATATGTT-ATAATATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATT
* * ** * * *
1361599 TCTAAGACCCCATCAGCTTTAAAAAGGTGCTACCTATTACGTTACATAAGCGC
65 TCTAAG-GCCCATCAAC-TT-AAAATTTGGTAAC-A-T---TT---TAAGCGT
* * **
1361652 TACCTAATATGTTATTATGTTTGATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCAGATT
1 TACCTAATATGTTATAAT-ATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATT
* * * *
1361717 TATAAGGCTCCATCAGCTTAAATTTTGGTAACATTTTAGGCGT
65 TCTAAGGC-CCATCAACTTAAAATTTGGTAACATTTTAAGCGT
* * *
1361760 TACCTAATATGTTGATAATACTGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATT
1 TACCTAATATGTT-ATAATATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATT
* ** * * *
1361825 TCTAAGGCCCCATCAGCTTTAAAAAGGTGCTACCTATTACGTTACATAAGCGC
65 TCTAAGG-CCCATCAAC-TT-AAAATTTGGTAAC-A-T---TT---TAAGCGT
* * * **
1361878 TACCTAATATGTTATTATGTTTTATAACAAATTAAGTAATTAACCGGTTATGTTATCGTC-GAAT
1 TACCTAATATGTTATAAT-ATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAG-AT
* *
1361942 TTCTAAAGCTCCATCAACTTAAAATTTGATAACATTTTAAGCGT
64 TTCTAAGGC-CCATCAACTTAAAATTTGGTAACATTTTAAGCGT
* * * * * *
1361986 TACTTAATATATTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATTGTCGGATT
1 TACCTAATATGTT-ATAATATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATT
* ** * *
1362051 TCTAAGGCCTCATCAACTCAAAA-AGGCGCTACCTATGACGTTACATAAGCGC
65 TCTAAGGCC-CATCAACTTAAAATTTG-G-TAAC-AT----TT---TAAGCGT
* * * * * **
1362103 TACCTAATATATTATTATGGTTGATAACAAATCAAGTAATTAA-CTGATTATGTTATCATTGGAT
1 TACCTAATATGTTATAAT-ATTGATAACAAATTAAGTAATTAACCT-ATTATGTTATCGTCAGAT
* * * *
1362167 TTTTAAGGCTCCATCAGCTTAAAATTTGGTAACATTTTAGGCAT
64 TTCTAAGGC-CCATCAACTTAAAATTTGGTAACATTTTAAGCGT
* * * * *
1362211 TATCTAATATGTTGATAATACTGATAACAAATTAAATAATTAACATATT-TGGTTATCGTTAGAT
1 TACCTAATATGTT-ATAATATTGATAACAAATTAAGTAATTAACCTATTAT-GTTATCGTCAGAT
1362275 TTCTAAGG
64 TTCTAAGG
1362283 GTCCATCAGC
Statistics
Matches: 950, Mismatches: 169, Indels: 162
0.74 0.13 0.13
Matches are distributed among these distances:
107 5 0.01
108 407 0.43
109 47 0.05
110 26 0.03
111 11 0.01
112 6 0.01
113 4 0.00
114 6 0.01
115 16 0.02
116 38 0.04
117 177 0.19
118 207 0.22
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (106 bp):
TACCTAATATGTTATAATATTGATAACAAATTAAGTAATTAACCTATTATGTTATCGTCAGATTT
CTAAGGCCCATCAACTTAAAATTTGGTAACATTTTAAGCGT
Found at i:1361397 original size:451 final size:452
Alignment explanation
Indices: 1360542--1362354 Score: 2679
Period size: 451 Copynumber: 4.0 Consensus size: 452
1360532 CATTGATAAA
* *
1360542 GGTTGATAACAAATCAAGTGATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * *
1360607 TAAACTTTGGTAACATTTTCGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
66 TAAAATTTGATAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * * *
1360672 TATCATATTTT-TTATCTTCGGGTTTCTAAGGCCTCATCAGCTTTAAAAAGGCACTACCTATTAC
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCTCATCAACTTTAAAAAGGCGCTACCTATTAC
* *
1360736 GTTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAATCGGTTATG
196 GTTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGATTATG
* * *
1360801 TTATCGTCGGATTTCTAAGGCTCCATCGGCTTAAACTTTGGTAACATTTTAGGTGTTACCTAATA
261 TTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAATTTTGGTAACATTTTAGGCGTTACCTAATA
* * * *
1360866 TGTTGATAATACTGGTAACAAATTAAGTAATTTACCTATTTTATTATCGTC-GAATTTCTAAAGG
326 TGTTGATAATACTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAG-ATTTCTAAA-G
** * * *
1360930 TTCCGTCAGC-TTAAAAAGGCGCTACTTATTACGTTACATAAGTGCTACCTAATATGATATTAT
389 CCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTAT
* * *
1360993 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGTTCTATCAGCT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * * *
1361058 TAAAATTTGGTAACATTTTAGGTGTTACCTAATATGTTAATAATATTGATAACAAATTAAGTAAT
66 TAAAATTTGATAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
*
1361123 TAACCTATTTTGTTATCGTCGGATTTCTAAGGTCC-CATCAAC-TTAAAAATGCGCTACCTATTA
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGG-CCTCATCAACTTTAAAAAGGCGCTACCTATTA
* * * *
1361186 CGTTATAGAAGTGCTACCTAATATGTTATTATAGTTGATAACAAATCAAGTAATTAACCGATTAT
195 CGTTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGATTAT
* * * *
1361251 GTTATCGTCGGATCTCTAAGGCTCCATCAACTTTAATTTTGGTAACATTTTCA-ACGTTACCTAA
260 GTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAATTTTGGTAACATTTT-AGGCGTTACCTAA
1361315 TATGTTGATAATACTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTAAAG
324 TATGTTGATAATACTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTAAAG
* * *
1361380 CCCCATCAGTTTTAAAAATGCACTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTAT
389 CCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTAT
* * *
1361444 GATTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCAGATTTATAAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * *
1361509 TAAATTTTGATAACATTTTAGGTGTTACCTAATATGTTGATAATACTGATAATAAATTAAGTAAT
66 TAAAATTTGATAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * *
1361574 TAACCTATTTTGTTATCGTCAGATTTCTAAGACCCCATCAGCTTTAAAAAGGTGCTACCTATTAC
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCTCATCAACTTTAAAAAGGCGCTACCTATTAC
* * *
1361639 GTTACATAAGCGCTACCTAATATGTTATTATGTTTGATAACAAATTAAGTAATTAACCGGTTATG
196 GTTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGATTATG
* *
1361704 TTATCGTCAGATTTATAAGGCTCCATCAGCTTAAATTTTGGTAACATTTTAGGCGTTACCTAATA
261 TTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAATTTTGGTAACATTTTAGGCGTTACCTAATA
* * *
1361769 TGTTGATAATACTGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCC
326 TGTTGATAATACTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTAAAGCC
* *
1361834 CCATCAGCTTTAAAAAGGTGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTAT
391 CCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTAT
* * * * *
1361896 GTTTTATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGAATTTCTAAAGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * *
1361961 TAAAATTTGATAACATTTTAAGCGTTACTTAATATATTGATAATACTGATAACAAATTAAGTAAT
66 TAAAATTTGATAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * *
1362026 TAACCTATTTTGTTATTGTCGGATTTCTAAGGCCTCATCAAC-TCAAAAAGGCGCTACCTATGAC
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCTCATCAACTTTAAAAAGGCGCTACCTATTAC
* *
1362090 GTTACATAAGCGCTACCTAATATATTATTATGGTTGATAACAAATCAAGTAATTAACTGATTATG
196 GTTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGATTATG
* * * * * *
1362155 TTATCATTGGATTTTTAAGGCTCCATCAGCTTAAAATTTGGTAACATTTTAGGCATTATCTAATA
261 TTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAATTTTGGTAACATTTTAGGCGTTACCTAATA
* * * * **
1362220 TGTTGATAATACTGATAACAAATTAAATAATTAACATATTTGGTTATCGTTAGATTTCTAAGGGT
326 TGTTGATAATACTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTAAAGCC
* * * * *
1362285 CCATCAGCTTTAACAAGTCGTTACCTATTACGTTACATAAATGCTACCT-ATTTGTTATTAT
391 CCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTAT
1362346 GGTTGATAA
1 GGTTGATAA
1362355 TGTTTCCAAT
Statistics
Matches: 1226, Mismatches: 128, Indels: 17
0.89 0.09 0.01
Matches are distributed among these distances:
450 27 0.02
451 763 0.62
452 434 0.35
453 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (452 bp):
GGTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
TAAAATTTGATAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCTCATCAACTTTAAAAAGGCGCTACCTATTAC
GTTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGATTATG
TTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAATTTTGGTAACATTTTAGGCGTTACCTAATA
TGTTGATAATACTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTAAAGCC
CCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTAT
Found at i:1361839 original size:677 final size:677
Alignment explanation
Indices: 1360543--1362354 Score: 2713
Period size: 677 Copynumber: 2.7 Consensus size: 677
1360533 ATTGATAAAG
*
1360543 GTTGATAACAAATCAAGTGATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTT
1 GTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTT
* **
1360608 AAACTTTGGTAACATTTTCGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATT
66 AAAATTTGGTAACATTTTCAACGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATT
* * * *
1360673 ATCATATTTT-TTATCTTCGGGTTTCTAAGGCCTCATCAGCTTTAAAAAGGCACTACCTATTACG
131 AACATATTTTGTTATCGTCGGATTTCTAAGGCCTCATCAGATTTAAAAAGGCACTACCTATTACG
*
1360737 TTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAATCGGTTATGT
196 TTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGGTTATGT
* * *
1360802 TATCGTCGGATTTCTAAGGCTCCATCGGCTTAAACTTTGGTAACATTTTAGGTGTTACCTAATAT
261 TATCGTCGGATTTATAAGGCTCCATCAGCTTAAAATTTGGTAACATTTTAGGTGTTACCTAATAT
* * * *
1360867 GTTGATAATACTGGTAACAAATTAAGTAATTTACCTATTTTATTATCGTC-GAATTTCTAAAGGT
326 GTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAG-ATTTCT-AAGGC
* * * *
1360931 TCCGTCAGC-TTAAAAAGGCGCTACTTATTACGTTACATAAGTGCTACCTAATATGATATTATGG
389 TCCATCAGCTTTAAAAAGGTGCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTATGG
* * * *
1360995 TTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGTTCTATCAGCTTA
454 TTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCAGATTTATAAGGCTCCATCAGCTTA
* *
1361060 AAATTTGGTAACATTTTAGGTGTTACCTAATATGTTAATAATATTGATAACAAATTAAGTAATTA
519 AAATTTGGTAACATTTTAGGCGTTACCTAATATGTTAATAATACTGATAACAAATTAAGTAATTA
* * *
1361125 ACCTATTTTGTTATCGTCGGATTTCTAAGGTCCCATCAAC-TTAAAAATGCGCTACCTATTACGT
584 ACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAACTTTAAAAAGGCGCTACCTATTACGT
* *
1361189 TATAGAAGTGCTACCTAATATGTTATTAT
649 TACAGAAGCGCTACCTAATATGTTATTAT
*
1361218 AGTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATCTCTAAGGCTCCATCAACT
1 -GTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* *
1361283 TTAATTTTGGTAACATTTTCAACGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
65 TAAAATTTGGTAACATTTTCAACGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * *
1361348 TAACATATTTTGTTATCGTCAGATTTCTAAAGCCCCATCAGTTTTAAAAATGCACTACCTATTAC
130 TAACATATTTTGTTATCGTCGGATTTCTAAGGCCTCATCAGATTTAAAAAGGCACTACCTATTAC
* *
1361413 GTTACATAAGTGCTACCTAATATGTTATTATGATTGATAACAAATCAAGTAATTAACCGGTTATG
195 GTTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGGTTATG
* * * *
1361478 TTATCGTCAGATTTATAAGGCTCCATCAACTTAAATTTTGATAACATTTTAGGTGTTACCTAATA
260 TTATCGTCGGATTTATAAGGCTCCATCAGCTTAAAATTTGGTAACATTTTAGGTGTTACCTAATA
* * *
1361543 TGTTGATAATACTGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGACC
325 TGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCT
* *
1361608 CCATCAGCTTTAAAAAGGTGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGTT
390 CCATCAGCTTTAAAAAGGTGCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTATGGT
*
1361673 TGATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCAGATTTATAAGGCTCCATCAGCTTAA
455 TGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCAGATTTATAAGGCTCCATCAGCTTAA
* * *
1361738 ATTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAATAAATTAAGTAATTAA
520 AATTTGGTAACATTTTAGGCGTTACCTAATATGTTAATAATACTGATAACAAATTAAGTAATTAA
* *
1361803 CCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGTGCTACCTATTACGTT
585 CCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAACTTTAAAAAGGCGCTACCTATTACGTT
*
1361868 ACATAAGCGCTACCTAATATGTTATTAT
650 ACAGAAGCGCTACCTAATATGTTATTAT
* * * * *
1361896 GTTTTATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGAATTTCTAAAGCTCCATCAACT
1 G-TTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACT
* * *
1361961 TAAAATTTGATAACATTTT-AAGCGTTACTTAATATATTGATAATACTGATAACAAATTAAGTAA
65 TAAAATTTGGTAACATTTTCAA-CGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAA
* * * * * *
1362025 TTAACCTATTTTGTTATTGTCGGATTTCTAAGGCCTCATCA-ACTCAAAAAGGCGCTACCTATGA
129 TTAACATATTTTGTTATCGTCGGATTTCTAAGGCCTCATCAGATTTAAAAAGGCACTACCTATTA
* * *
1362089 CGTTACATAAGCGCTACCTAATATATTATTATGGTTGATAACAAATCAAGTAATTAACTGATTAT
194 CGTTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGGTTAT
* * * ** *
1362154 GTTATCATTGGATTTTTAAGGCTCCATCAGCTTAAAATTTGGTAACATTTTAGGCATTATCTAAT
259 GTTATCGTCGGATTTATAAGGCTCCATCAGCTTAAAATTTGGTAACATTTTAGGTGTTACCTAAT
* * * * *
1362219 ATGTTGATAATACTGATAACAAATTAAATAATTAACATATTTGGTTATCGTTAGATTTCTAAGGG
324 ATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGC
* * * *
1362284 TCCATCAGCTTTAACAA-GTCGTTACCTATTACGTTACATAAATGCTACCT-ATTTGTTATTATG
389 TCCATCAGCTTTAAAAAGGT-GCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTATG
1362347 GTTGATAA
453 GTTGATAA
1362355 TGTTTCCAAT
Statistics
Matches: 1024, Mismatches: 105, Indels: 14
0.90 0.09 0.01
Matches are distributed among these distances:
676 164 0.16
677 662 0.65
678 198 0.19
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (677 bp):
GTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTT
AAAATTTGGTAACATTTTCAACGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATT
AACATATTTTGTTATCGTCGGATTTCTAAGGCCTCATCAGATTTAAAAAGGCACTACCTATTACG
TTACATAAGCGCTACCTAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACCGGTTATGT
TATCGTCGGATTTATAAGGCTCCATCAGCTTAAAATTTGGTAACATTTTAGGTGTTACCTAATAT
GTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTC
CATCAGCTTTAAAAAGGTGCTACCTATTACGTTACATAAGTGCTACCTAATATGTTATTATGGTT
GATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCAGATTTATAAGGCTCCATCAGCTTAAA
ATTTGGTAACATTTTAGGCGTTACCTAATATGTTAATAATACTGATAACAAATTAAGTAATTAAC
CTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAACTTTAAAAAGGCGCTACCTATTACGTTA
CAGAAGCGCTACCTAATATGTTATTAT
Found at i:1368523 original size:3 final size:3
Alignment explanation
Indices: 1368509--1368560 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
1368499 ATATAAAATG
* * *
1368509 TAA TAT TAA TAA TAA T-A TAA TAA TAT TAA TGA -AA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1368554 TAA TAA T
1 TAA TAA T
1368561 TATTATTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 5 0.12
3 35 0.88
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1368532 original size:14 final size:14
Alignment explanation
Indices: 1368515--1368560 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
1368505 AATGTAATAT
1368515 TAATAATAATATAA
1 TAATAATAATATAA
*
1368529 TAATATTAATGA-AA
1 TAATAATAAT-ATAA
1368543 TAATAATAATATAA
1 TAATAATAATATAA
1368557 TAAT
1 TAAT
1368561 TATTATTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:1368985 original size:134 final size:134
Alignment explanation
Indices: 1368762--1369083 Score: 412
Period size: 134 Copynumber: 2.4 Consensus size: 134
1368752 GTTTGGGTCG
* * * *
1368762 TCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATATGGTCAGGGGATGACACGACTCATACGT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATATGGTCAGGGGATGACACGACTCATACGT
* * * *
1368827 GATGAAGAGTTCTGGCCATCTTTAGGAATGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTG
66 GATGAAGAGTTCTGGCCATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTG
1368892 ATTA
131 ATTA
* * * * *
1368896 TCTATGGTTGACATGGCTCCTACATGATGAAGAGATATGGTCAGGGGATGACACGGCTCATAC-T
1 TCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATATGGTCAGGGGATGACACGACTCATACGT
* * * ** *
1368960 AGATGAAGAGTTCTGGTCATTTTTAGAAAGGGCGATAACACGGTTCCTACGTGATGAGGGTGTCT
66 -GATGAAGAGTTCTGGCCATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCT
*
1369025 GGTTA
130 GATTA
* * * *
1369030 TCTAGGGGTAACACGACTCCTACGCGATGAAGAGATCTGGTCAGGGGATGACAC
1 TCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATATGGTCAGGGGATGACAC
1369084 TGGTCCTACG
Statistics
Matches: 160, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
133 1 0.01
134 159 0.99
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (134 bp):
TCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATATGGTCAGGGGATGACACGACTCATACGT
GATGAAGAGTTCTGGCCATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTG
ATTA
Found at i:1369110 original size:134 final size:133
Alignment explanation
Indices: 1368779--1369119 Score: 389
Period size: 134 Copynumber: 2.5 Consensus size: 133
1368769 GTGACACGGT
* * * *
1368779 TCCTACGTGATGAGGAAATATGGTCAGGGGATGACACGACTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATGAAGAGATATGGTCAGGGGATGACACG-GTCATACGTGATGAAGAGTTCTGGTC
* * * * * * *
1368844 ATCTTTAGGAATGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGATTATCTATGGTTGACA
65 ATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTAACA
* *
1368909 TGGC
130 CGAC
*
1368913 TCCTACATGATGAAGAGATATGGTCAGGGGATGACACGGCTCATAC-TAGATGAAGAGTTCTGGT
1 TCCTACGTGATGAAGAGATATGGTCAGGGGATGACACGG-TCATACGT-GATGAAGAGTTCTGGT
* * ** * *
1368977 CATTTTTAGAAAGGGCGATAACACGGTTCCTACGTGATGAGGGTGTCTGGTTATCTAGGGGTAAC
64 CATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTAAC
1369042 ACGAC
129 ACGAC
* * * * * *
1369047 TCCTACGCGATGAAGAGATCTGGTCAGGGGATGACACTGGTCCTACGTGATTAGGACG-GCTGGT
1 TCCTACGTGATGAAGAGATATGGTCAGGGGATGACAC-GGTCATACGTGATGAAGA-GTTCTGGT
1369111 CATCTTTAG
64 CATCTTTAG
1369120 TGATTATGGT
Statistics
Matches: 174, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
133 1 0.01
134 169 0.97
135 4 0.02
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (133 bp):
TCCTACGTGATGAAGAGATATGGTCAGGGGATGACACGGTCATACGTGATGAAGAGTTCTGGTCA
TCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTAACAC
GAC
Found at i:1369168 original size:28 final size:28
Alignment explanation
Indices: 1369144--1369207 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
1369134 AGGGAAACCA
1369144 ACTCAAAGATTTGTTTCAAAAGAAACAG
1 ACTCAAAGATTTGTTTCAAAAGAAACAG
* *
1369172 ACTCAAAGATTTGTTTCATGAA-AAACAT
1 ACTCAAAGATTTGTTTCA-AAAGAAACAG
1369200 ACTCAAAG
1 ACTCAAAG
1369208 GTGATGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (28 bp):
ACTCAAAGATTTGTTTCAAAAGAAACAG
Found at i:1370808 original size:21 final size:19
Alignment explanation
Indices: 1370782--1370881 Score: 56
Period size: 21 Copynumber: 4.5 Consensus size: 19
1370772 TCTTTGTCTT
1370782 TTTGCTTTTGTCTTCTTTTTC
1 TTTGCTTTT-TCTT-TTTTTC
1370803 TTTGCTTTTTCGTTTGCTATTTTTCC
1 TTTGCTTTTTC---T--T-TTTTT-C
* *
1370829 TTTGATTTTTCTTTGTTTCTT
1 TTTGCTTTTTCTTT-TTT-TC
1370850 TTTGCTATTTGTCTTTTTTTC
1 TTTGCT-TTT-TCTTTTTTTC
1370871 TTTGCTCTTTT
1 TTTGCT-TTTT
1370882 TCTCTTTGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
20 4 0.06
21 28 0.44
22 7 0.11
23 7 0.11
25 6 0.10
26 11 0.17
ACGTcount: A:0.03, C:0.16, G:0.10, T:0.71
Consensus pattern (19 bp):
TTTGCTTTTTCTTTTTTTC
Found at i:1370818 original size:12 final size:11
Alignment explanation
Indices: 1370782--1370881 Score: 61
Period size: 11 Copynumber: 8.9 Consensus size: 11
1370772 TCTTTGTCTT
1370782 TTTGCTTTTGTC
1 TTTGCTTTT-TC
1370794 -TT-CTTTTTC
1 TTTGCTTTTTC
1370803 TTTGCTTTTTC
1 TTTGCTTTTTC
1370814 GTTTGCTATTTTTCC
1 -TTTGC--TTTTT-C
*
1370829 TTTGATTTTTC
1 TTTGCTTTTTC
1370840 TTTG-TTTCTT-
1 TTTGCTTT-TTC
1370850 TTTGCTATTTGTC
1 TTTGCT-TTT-TC
1370863 -TT--TTTTTC
1 TTTGCTTTTTC
1370871 TTTGCTCTTTT
1 TTTGCT-TTTT
1370882 TCTCTTTGTT
Statistics
Matches: 72, Mismatches: 1, Indels: 30
0.70 0.01 0.29
Matches are distributed among these distances:
8 2 0.03
9 7 0.10
10 15 0.21
11 19 0.26
12 19 0.26
14 9 0.12
15 1 0.01
ACGTcount: A:0.03, C:0.16, G:0.10, T:0.71
Consensus pattern (11 bp):
TTTGCTTTTTC
Found at i:1370851 original size:26 final size:26
Alignment explanation
Indices: 1370788--1370852 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
1370778 TCTTTTTGCT
*
1370788 TTTGTCTTCTTTTTCTTTGCTTTTTCG
1 TTTGT-TTCTTTTTCTTTGATTTTTCG
* *
1370815 TTTGCTAT-TTTTCCTTTGATTTTTC-
1 TTTG-TTTCTTTTTCTTTGATTTTTCG
1370840 TTTGTTTCTTTTT
1 TTTGTTTCTTTTT
1370853 GCTATTTGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 2 0.06
25 8 0.26
26 15 0.48
27 5 0.16
28 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.09, T:0.72
Consensus pattern (26 bp):
TTTGTTTCTTTTTCTTTGATTTTTCG
Found at i:1370879 original size:15 final size:14
Alignment explanation
Indices: 1370771--1370890 Score: 81
Period size: 14 Copynumber: 8.6 Consensus size: 14
1370761 AGTCAAGGGA
1370771 CTCTTTGTCTTTTT
1 CTCTTTGTCTTTTT
1370785 GCT-TTTGTCTTCTTT
1 -CTCTTTGTCTT-TTT
*
1370800 TTCTTTG-CTTTTT
1 CTCTTTGTCTTTTT
* *
1370813 C-GTTTGCTATTTTT
1 CTCTTTG-TCTTTTT
*
1370827 C-CTTTG-ATTTTT
1 CTCTTTGTCTTTTT
*
1370839 CT-TTGTTTCTTTTT
1 CTCTT-TGTCTTTTT
*
1370853 GCTATTTGTCTTTTT
1 -CTCTTTGTCTTTTT
*
1370868 TTCTTTGCTCTTTTT
1 CTCTTTG-TCTTTTT
1370883 CTCTTTGT
1 CTCTTTGT
1370891 TTTGATTTGA
Statistics
Matches: 84, Mismatches: 11, Indels: 21
0.72 0.09 0.18
Matches are distributed among these distances:
12 13 0.15
13 4 0.05
14 33 0.39
15 32 0.38
16 2 0.02
ACGTcount: A:0.03, C:0.17, G:0.10, T:0.70
Consensus pattern (14 bp):
CTCTTTGTCTTTTT
Found at i:1372199 original size:21 final size:21
Alignment explanation
Indices: 1372157--1372199 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1372147 TTTCTGGGCT
* *
1372157 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
1372178 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1372199 A
1 A
1372200 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1372272 original size:23 final size:22
Alignment explanation
Indices: 1372228--1372272 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1372218 AATCTCATAG
*
1372228 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
1372250 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
1372273 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:1383313 original size:103 final size:103
Alignment explanation
Indices: 1383087--1383305 Score: 402
Period size: 103 Copynumber: 2.1 Consensus size: 103
1383077 AGTCGAGGGT
1383087 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATA
* *
1383152 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
66 CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATG
*
1383190 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATA
*
1383255 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATG
66 CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATG
1383293 ATATGTGGTCCTT
1 ATATGTGGTCCTT
1383306 ATGGACATTA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATA
CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATG
Found at i:1383357 original size:23 final size:23
Alignment explanation
Indices: 1383322--1383389 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1383312 ATTATTATAT
* *
1383322 GGCACTACAGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
1383345 GGCACTTTGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
1383368 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTGCAATTCTACG
1383390 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1386292 original size:2 final size:2
Alignment explanation
Indices: 1386280--1386320 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1386270 TTAACGTAAA
*
1386280 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1386321 AAATATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1388084 original size:20 final size:20
Alignment explanation
Indices: 1388059--1388193 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
1388049 AATTTGGAAA
* *
1388059 ATCGCAATGTGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1388079 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1388100 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1388120 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
1388140 TTCGCAACGTGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
1388160 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1388180 ATCGCAACGAGATA
1 ATCGCAACGCGATA
1388194 ATACAAAATC
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1388158 original size:40 final size:40
Alignment explanation
Indices: 1388100--1388193 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
1388090 ATAATACAAA
*
1388100 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
* * *
1388140 TTCGCAACGTGATTCTGACTTTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
*
1388180 ATCGCAACGAGATA
1 ATCGCAACGCGATA
1388194 ATACAAAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (40 bp):
ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
Found at i:1388430 original size:12 final size:12
Alignment explanation
Indices: 1388413--1388437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1388403 ATATAATCCT
1388413 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1388425 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1388437 G
1 G
1388438 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1388866 original size:20 final size:20
Alignment explanation
Indices: 1388838--1388893 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1388828 CAACGTGAAA
*
1388838 ATCGTAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1388858 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
1388878 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
1388894 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1390743 original size:44 final size:42
Alignment explanation
Indices: 1390695--1390789 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
1390685 CCTCTTCAAC
* * *
1390695 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGGGACTCTTGAGA
1 GATGACAGGGGCCTCTTGAACGAT--GGGAGGGGACTCTTGAGA
* * *
1390739 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGA
1390781 GATGACAGG
1 GATGACAGG
1390790 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 23 0.52
44 21 0.48
ACGTcount: A:0.21, C:0.15, G:0.43, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGA
Found at i:1391250 original size:20 final size:20
Alignment explanation
Indices: 1391227--1391274 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1391217 GCGATTTTGT
1391227 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATAGCCATTTCCG
* *
1391247 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGCCATTTCCG
1391267 CGTTGCGA
1 CGTTGCGA
1391275 AAGTAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTCCG
Found at i:1391285 original size:20 final size:20
Alignment explanation
Indices: 1391245--1391300 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1391235 TAGCCATTTC
* * *
1391245 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
1391265 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
1391285 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
1391301 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:1391849 original size:18 final size:18
Alignment explanation
Indices: 1391826--1391873 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1391816 CGGGTCGATC
1391826 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
* *
1391844 AGGTGATAGTTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1391862 AGGTGATGGCTC
1 AGGTGATGGCTC
1391874 CCGAAGAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.10, G:0.46, T:0.29
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1393196 original size:20 final size:20
Alignment explanation
Indices: 1393171--1393213 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1393161 AATAGTTTCT
1393171 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
1393191 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
1393211 GAA
1 GAA
1393214 TTTGTCGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1393714 original size:40 final size:40
Alignment explanation
Indices: 1393669--1393747 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
1393659 GTATTATCTC
1393669 GTTGCGAAAGTCAGTATCACGTTGCGAAAGTAAGTATCGT
1 GTTGCGAAAGTCAGTATCACGTTGCGAAAGTAAGTATCGT
* *
1393709 GTTGCGAAAGTCAGTATCGCGTTGCGATAGTAAGTATCG
1 GTTGCGAAAGTCAGTATCACGTTGCGAAAGTAAGTATCG
1393748 CATTGCGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (40 bp):
GTTGCGAAAGTCAGTATCACGTTGCGAAAGTAAGTATCGT
Found at i:1393756 original size:20 final size:20
Alignment explanation
Indices: 1393663--1393755 Score: 123
Period size: 20 Copynumber: 4.7 Consensus size: 20
1393653 GATTATGTAT
* *
1393663 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
*
1393683 TATCACGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
* *
1393703 TATCGTGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
*
1393723 TATCGCGTTGCGATAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
1393743 TATCGCATTGCGA
1 TATCGCGTTGCGA
1393756 TTTTCTCAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:1393789 original size:20 final size:21
Alignment explanation
Indices: 1393745--1393792 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1393735 ATAGTAAGTA
*
1393745 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACTCAAT
* *
1393766 TCGCGTTGCGATTTACT-TAT
1 TCGCATTGCGATTTACTCAAT
1393786 TCGCATT
1 TCGCATT
1393793 ACGAATTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (21 bp):
TCGCATTGCGATTTACTCAAT
Found at i:1393838 original size:21 final size:22
Alignment explanation
Indices: 1393786--1393838 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1393776 ATTTACTTAT
*
1393786 TCGCATTACG-AATTGAGAAAA
1 TCGCATTGCGAAATTGAGAAAA
**
1393807 TCGCAACGCGAAATTG-GAAAA
1 TCGCATTGCGAAATTGAGAAAA
1393828 TCGCATTGCGA
1 TCGCATTGCGA
1393839 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGAGAAAA
Found at i:1394624 original size:44 final size:44
Alignment explanation
Indices: 1394555--1394675 Score: 172
Period size: 44 Copynumber: 2.8 Consensus size: 44
1394545 ATCTCTCCAC
* * * *
1394555 TGTAATTGGTTCATGTCTAGCATTTGAGCTTATTGACTTGTTTA
1 TGTAATTGGTTTATGTCTAGAATTTGAGATTAATGACTTGTTTA
* *
1394599 TGTAATTGGTTTATGTCCAGAATTTGAGATTAATGATTTGTTTA
1 TGTAATTGGTTTATGTCTAGAATTTGAGATTAATGACTTGTTTA
*
1394643 TGTAATTGTTTTATGTCTAGAA-TTGAGATTAAT
1 TGTAATTGGTTTATGTCTAGAATTTGAGATTAAT
1394676 ACATGTTGCC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
43 11 0.16
44 58 0.84
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.48
Consensus pattern (44 bp):
TGTAATTGGTTTATGTCTAGAATTTGAGATTAATGACTTGTTTA
Found at i:1395030 original size:126 final size:126
Alignment explanation
Indices: 1394805--1395057 Score: 470
Period size: 126 Copynumber: 2.0 Consensus size: 126
1394795 TTGAATCGTT
*
1394805 ATTCTAGTTTTTCAACCAATGATGACTTAAAGAAAGGCCATGGGAAGACAATGTTGGCAAAAGAC
1 ATTCTAGTTTTTCAACCAATGATGACTTAAAGAAAGGCCATGAGAAGACAATGTTGGCAAAAGAC
1394870 TTGGCGATTCTTGTTGAGGAGTCGTCTCATAAAGATGAGAGGAAACCTAAGAGCAGAATGG
66 TTGGCGATTCTTGTTGAGGAGTCGTCTCATAAAGATGAGAGGAAACCTAAGAGCAGAATGG
*
1394931 ATTCTAGTTTTTCAACCAATGATGACTTAAAGAAAGGCCATGAGAAGATAATGTTGGCAAAAGAC
1 ATTCTAGTTTTTCAACCAATGATGACTTAAAGAAAGGCCATGAGAAGACAATGTTGGCAAAAGAC
* *
1394996 TTGGCGTTTCTTGTTGAGGAGTCGTCTCATAAAGATGAGAGGAAGCCTAAGAGCAGAATGG
66 TTGGCGATTCTTGTTGAGGAGTCGTCTCATAAAGATGAGAGGAAACCTAAGAGCAGAATGG
1395057 A
1 A
1395058 GCTTAAGAGG
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (126 bp):
ATTCTAGTTTTTCAACCAATGATGACTTAAAGAAAGGCCATGAGAAGACAATGTTGGCAAAAGAC
TTGGCGATTCTTGTTGAGGAGTCGTCTCATAAAGATGAGAGGAAACCTAAGAGCAGAATGG
Found at i:1398651 original size:15 final size:14
Alignment explanation
Indices: 1398630--1398671 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
1398620 TCTGAATATG
1398630 GTGATGATGCTGAT
1 GTGATGATGCTGAT
1398644 GCTGATGATGCT-AT
1 G-TGATGATGCTGAT
*
1398658 -TGTTGATGCTGAT
1 GTGATGATGCTGAT
1398671 G
1 G
1398672 AAGATAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
12 9 0.38
13 2 0.08
14 3 0.12
15 10 0.42
ACGTcount: A:0.19, C:0.10, G:0.33, T:0.38
Consensus pattern (14 bp):
GTGATGATGCTGAT
Found at i:1399243 original size:23 final size:24
Alignment explanation
Indices: 1399217--1399279 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
1399207 TTAGATGTTA
1399217 GTGAATGTTAAACGAACA-TGTCG
1 GTGAATGTTAAACGAACATTGTCG
* * *
1399240 GTGAATGTTAAA-TAAAATTGTTG
1 GTGAATGTTAAACGAACATTGTCG
1399263 GTGAATGTTAAACGAAC
1 GTGAATGTTAAACGAAC
1399280 GTAATCATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 3 0.09
23 28 0.85
24 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (24 bp):
GTGAATGTTAAACGAACATTGTCG
Found at i:1401147 original size:60 final size:60
Alignment explanation
Indices: 1401023--1401174 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
1401013 TTGACTCTGG
** * * * * *
1401023 TTTTTGTATTTA-TCGTTCAGTCCTTTAACTTTTTATTTTTGTTTTTTAGTTCTTTAAGT
1 TTTTTGTATTTATTATTTTAGTCCTTTAACTTTCTATTTTAGTATTTTAGTCCTTTAAGT
*
1401082 TTTTTGT-TTTTTCTATTTTAGTCCTTTAACTTTCTATTTTAGCTATTTTAGTCCTTTAAG-
1 TTTTTGTATTTAT-TATTTTAGTCCTTTAACTTTCTATTTTAG-TATTTTAGTCCTTTAAGT
* * *
1401142 TTTTTGTATTTATTATTTTGGTCCCTAAACTTT
1 TTTTTGTATTTATTATTTTAGTCCTTTAACTTT
1401175 ATTTATTTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
58 3 0.04
59 7 0.09
60 48 0.62
61 19 0.25
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.62
Consensus pattern (60 bp):
TTTTTGTATTTATTATTTTAGTCCTTTAACTTTCTATTTTAGTATTTTAGTCCTTTAAGT
Found at i:1401159 original size:30 final size:30
Alignment explanation
Indices: 1401023--1401188 Score: 117
Period size: 30 Copynumber: 5.6 Consensus size: 30
1401013 TTGACTCTGG
** *
1401023 TTTTTGTATTTA-TCGTTCAGTCCTTTAAC
1 TTTTTGTATTTATTATTTTAGTCCTTTAAC
* * * * *
1401052 TTTTTATTTTTGTT-TTTTAGTTCTTTAAGT
1 TTTTTGTATTTATTATTTTAGTCCTTTAA-C
*
1401082 TTTTTGT-TTTTTCTATTTTAGTCCTTTAAC
1 TTTTTGTATTTAT-TATTTTAGTCCTTTAAC
* * * *
1401112 TTTCTAT-TTTAGCTATTTTAGTCCTTTAAG
1 TTTTTGTATTTA-TTATTTTAGTCCTTTAAC
* * *
1401142 TTTTTGTATTTATTATTTTGGTCCCTAAAC
1 TTTTTGTATTTATTATTTTAGTCCTTTAAC
1401172 TTTATT-TATTTATTATT
1 TTT-TTGTATTTATTATT
1401189 CAGCCCTTTA
Statistics
Matches: 107, Mismatches: 23, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
29 24 0.22
30 64 0.60
31 19 0.18
ACGTcount: A:0.17, C:0.11, G:0.08, T:0.63
Consensus pattern (30 bp):
TTTTTGTATTTATTATTTTAGTCCTTTAAC
Found at i:1402760 original size:60 final size:60
Alignment explanation
Indices: 1402667--1402786 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
1402657 CATACCGAAC
1402667 CTCTGTCCATCATTAGGTGCCAAATTAGGTGTACACGAAGGAGGAATGACTCTAAACCTT
1 CTCTGTCCATCATTAGGTGCCAAATTAGGTGTACACGAAGGAGGAATGACTCTAAACCTT
1402727 CTCTGTCCATCATTAGGTGCCAAATTAGGTGTACACGAAGGAGGAATGACTCTAAACCTT
1 CTCTGTCCATCATTAGGTGCCAAATTAGGTGTACACGAAGGAGGAATGACTCTAAACCTT
1402787 TACCTTTTGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (60 bp):
CTCTGTCCATCATTAGGTGCCAAATTAGGTGTACACGAAGGAGGAATGACTCTAAACCTT
Found at i:1403045 original size:18 final size:18
Alignment explanation
Indices: 1403003--1403045 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1402993 AGTATATTGA
*
1403003 TTATCTTGTTTGTACTAAC
1 TTAT-TTGTTCGTACTAAC
* *
1403022 TAATTTGTTCGTACTACC
1 TTATTTGTTCGTACTAAC
1403040 TTATTT
1 TTATTT
1403046 ATTATATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.53
Consensus pattern (18 bp):
TTATTTGTTCGTACTAAC
Found at i:1403595 original size:12 final size:12
Alignment explanation
Indices: 1403578--1403604 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1403568 ATCAATAATT
1403578 TTTGCATCTGCA
1 TTTGCATCTGCA
1403590 TTTGCATCTGCA
1 TTTGCATCTGCA
1403602 TTT
1 TTT
1403605 TATAAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (12 bp):
TTTGCATCTGCA
Found at i:1403805 original size:16 final size:16
Alignment explanation
Indices: 1403784--1403814 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1403774 TCCTGAGGTT
1403784 TATGATGTTGATATCG
1 TATGATGTTGATATCG
1403800 TATGATGTTGATATC
1 TATGATGTTGATATC
1403815 ACATAGGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (16 bp):
TATGATGTTGATATCG
Found at i:1404873 original size:12 final size:11
Alignment explanation
Indices: 1404858--1404983 Score: 59
Period size: 12 Copynumber: 11.3 Consensus size: 11
1404848 AGATCAAATC
*
1404858 AAAGCAGAGAGA
1 AAAGCAAAGA-A
1404870 AAAGCAAAGAA
1 AAAGCAAAGAA
*
1404881 AAAGAAACAAAGAG
1 AAAG---CAAAGAA
1404895 AAA--AAAGAA
1 AAAGCAAAGAA
1404904 AAAG-AAAGAAA
1 AAAGCAAAG-AA
*
1404915 AAAACAAAGCAA
1 AAAGCAAAG-AA
*
1404927 AGAA-AAAAGCAA
1 A-AAGCAAAG-AA
*
1404939 AAAG-AAAAAA
1 AAAGCAAAGAA
1404949 AAAG-AAA-AA
1 AAAGCAAAGAA
*
1404958 AAATCAAAAGAA
1 AAAGC-AAAGAA
*
1404970 AAATCAAAGAA
1 AAAGCAAAGAA
1404981 AAA
1 AAA
1404984 AGGCAAGAAG
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
9 13 0.14
10 13 0.14
11 27 0.28
12 31 0.33
13 2 0.02
14 9 0.09
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAGCAAAGAA
Found at i:1404924 original size:50 final size:49
Alignment explanation
Indices: 1404869--1404983 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 49
1404859 AAGCAGAGAG
* *
1404869 AAAAGCAAAGAAAAAGAAACAAAG-AGAAAAAAGAAAAAGAAA-GAAAAAA
1 AAAAGCAAAGAAAAAGAAA-AAAGAAAAAAAAAGAAAAA-AAATCAAAAAA
* *
1404918 ACAAAGCAAAGAAAAAAGCAAAAAGAAAAAAAAAGAAAAAAAATCAAAAGA
1 A-AAAGCAAAG-AAAAAGAAAAAAGAAAAAAAAAGAAAAAAAATCAAAAAA
*
1404969 AAAATCAAAGAAAAA
1 AAAAGCAAAGAAAAA
1404984 AGGCAAGAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
49 6 0.11
50 24 0.42
51 27 0.47
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (49 bp):
AAAAGCAAAGAAAAAGAAAAAAGAAAAAAAAAGAAAAAAAATCAAAAAA
Found at i:1404966 original size:25 final size:27
Alignment explanation
Indices: 1404929--1404984 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
1404919 CAAAGCAAAG
1404929 AAAAAAGCAAAAAGAAAAA-AAAAGAA
1 AAAAAAGCAAAAAGAAAAATAAAAGAA
* *
1404955 AAAAAATC-AAAAGAAAAATCAAAGAA
1 AAAAAAGCAAAAAGAAAAATAAAAGAA
1404981 AAAA
1 AAAA
1404985 GGCAAGAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.82, C:0.05, G:0.09, T:0.04
Consensus pattern (27 bp):
AAAAAAGCAAAAAGAAAAATAAAAGAA
Found at i:1404983 original size:17 final size:16
Alignment explanation
Indices: 1404867--1404983 Score: 87
Period size: 17 Copynumber: 7.1 Consensus size: 16
1404857 CAAAGCAGAG
*
1404867 AGAAAAGCAAAGAAAA
1 AGAAAAACAAAGAAAA
*
1404883 AGAAACAA-AGAGAAAAA
1 AGAAA-AACAAAG-AAAA
*
1404900 AGAAAAAGAAAGAAAA
1 AGAAAAACAAAGAAAA
1404916 A-AACAAAGCAAAGAAAAA
1 AGAA-AAA-CAAAG-AAAA
* *
1404934 AGCAAAAAGAAAAAAAA
1 AG-AAAAACAAAGAAAA
**
1404951 AGAAAAA-AAATCAAA
1 AGAAAAACAAAGAAAA
1404966 AGAAAAATCAAAGAAAA
1 AGAAAAA-CAAAGAAAA
1404983 A
1 A
1404984 AGGCAAGAAG
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
15 15 0.19
16 23 0.28
17 30 0.37
18 8 0.10
19 3 0.04
20 2 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.02
Consensus pattern (16 bp):
AGAAAAACAAAGAAAA
Found at i:1404984 original size:26 final size:26
Alignment explanation
Indices: 1404869--1404984 Score: 82
Period size: 25 Copynumber: 4.4 Consensus size: 26
1404859 AAGCAGAGAG
* *
1404869 AAAAGCAAAGAAAAAGAAACAAAG-AGAA
1 AAAAG-AAA-AAAAAGCAA-AAAGAAAAA
1404897 AAAAGAAAAAGAAAG-AAAAA-AACAAA
1 AAAAGAAAAA-AAAGCAAAAAGAA-AAA
*
1404923 GCAAAG--AAAAAAGCAAAAAGAAAAA
1 -AAAAGAAAAAAAAGCAAAAAGAAAAA
*
1404948 AAAAGAAAAAAAATC-AAAAGAAAAA
1 AAAAGAAAAAAAAGCAAAAAGAAAAA
*
1404973 TCAAAGAAAAAA
1 -AAAAGAAAAAA
1404985 GGCAAGAAGC
Statistics
Matches: 74, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
24 8 0.11
25 25 0.34
26 25 0.34
27 11 0.15
28 5 0.07
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (26 bp):
AAAAGAAAAAAAAGCAAAAAGAAAAA
Found at i:1406683 original size:3 final size:3
Alignment explanation
Indices: 1406670--1406710 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1406660 CTACCAAAAA
1406670 TAT TA- TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1406711 CTAAGTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1406689 original size:14 final size:14
Alignment explanation
Indices: 1406670--1406710 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
1406660 CTACCAAAAA
1406670 TATTATATTATTAT
1 TATTATATTATTAT
1406684 TATTATATTATTAT
1 TATTATATTATTAT
1406698 TATTATTATTATT
1 TATTA-TATTATT
1406711 CTAAGTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:1408163 original size:55 final size:54
Alignment explanation
Indices: 1408104--1408209 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 54
1408094 TACCGTTCAG
* **
1408104 TCCTTTAACTTTCAATTTTTGCT-TTTTTGTCCTTTAAGTTTTTTTGCTATTTTAC
1 TCCTTTAACTTTCAATTTTAGCTATTTCAGTCCTTTAA-TTTTTTTG-TATTTTAC
*
1408159 TCCTTTAACTTTCTATTTTAGCTATTTCAGTCCTTTAATTTTTTTGTATTT
1 TCCTTTAACTTTCAATTTTAGCTATTTCAGTCCTTTAATTTTTTTGTATTT
1408210 GTTATTTTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
54 5 0.11
55 29 0.63
56 12 0.26
ACGTcount: A:0.16, C:0.16, G:0.07, T:0.61
Consensus pattern (54 bp):
TCCTTTAACTTTCAATTTTAGCTATTTCAGTCCTTTAATTTTTTTGTATTTTAC
Found at i:1408183 original size:30 final size:29
Alignment explanation
Indices: 1408102--1408231 Score: 106
Period size: 31 Copynumber: 4.5 Consensus size: 29
1408092 TTTACCGTTC
*
1408102 AGTCCTTTAACTTTCAATTTTTGCT-TTTT
1 AGTCCTTTAACTTTCTA-TTTTGCTATTTT
* *
1408131 TGTCCTTTAA-GTT-T-TTTTGCTATTTT
1 AGTCCTTTAACTTTCTATTTTGCTATTTT
* *
1408157 ACTCCTTTAACTTTCTATTTTAGCTATTTC
1 AGTCCTTTAACTTTCTATTTT-GCTATTTT
* * * *
1408187 AGTCCTTTAATTTTTTTGTATTTGTTATTTT
1 AGTCCTTTAA-CTTTCTAT-TTTGCTATTTT
*
1408218 GGTCCTTTAACTTT
1 AGTCCTTTAACTTT
1408232 ATGCATTTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
25 7 0.09
26 12 0.15
27 2 0.03
28 3 0.04
29 13 0.16
30 19 0.24
31 20 0.25
32 3 0.04
ACGTcount: A:0.16, C:0.15, G:0.08, T:0.60
Consensus pattern (29 bp):
AGTCCTTTAACTTTCTATTTTGCTATTTT
Found at i:1411875 original size:84 final size:83
Alignment explanation
Indices: 1411757--1411911 Score: 258
Period size: 84 Copynumber: 1.9 Consensus size: 83
1411747 TGTTAGTCGG
* * *
1411757 GACCATCTCCACCTAAGATGCGTTTAAAGTGAAAAAGAAAAAGTTC-ACAAAGAAGATTTGGTTG
1 GACCATCTCCACCTAACACGCGTTTAAAGTGAAAAAG-AAAAG-TCAACAAAGAAAATTTGGTTG
1411821 GATTTACCTGAGACATTACC
64 GATTTACCTGAGACATTACC
1411841 GACCATCTCCACCTAACACGCGTTTAAAGTGAAAAAGAAAAGTCAACAAAGAAAATTTGGTTGGA
1 GACCATCTCCACCTAACACGCGTTTAAAGTGAAAAAGAAAAGTCAACAAAGAAAATTTGGTTGGA
1411906 TTTACC
66 TTTACC
1411912 CCCATCCCTC
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
82 2 0.03
83 30 0.45
84 35 0.52
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (83 bp):
GACCATCTCCACCTAACACGCGTTTAAAGTGAAAAAGAAAAGTCAACAAAGAAAATTTGGTTGGA
TTTACCTGAGACATTACC
Found at i:1412691 original size:21 final size:21
Alignment explanation
Indices: 1412665--1412723 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
1412655 ATTTACCGTG
1412665 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
* *
1412686 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
1412707 ATTGCGGCCGTCGCGGG
1 ATTGCGGCCGTCGCGGG
1412724 TAACTCGGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.07, C:0.31, G:0.42, T:0.20
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:1413122 original size:75 final size:75
Alignment explanation
Indices: 1412957--1413231 Score: 418
Period size: 75 Copynumber: 3.7 Consensus size: 75
1412947 TCGGCGACTG
* *
1412957 TGTTCCCCTTTTACCCGATCCTTCTGGTTATGACTTTGGTACTTCTGCA----C--ATCCATTGA
1 TGTTCACCTTTTACCCGATCCTTCTGGTTATGACTTTGGTACTTATGCACCTCCATATCCATTGA
*
1413016 AAGGCAACCC
66 AGGGCAACCC
* * *
1413026 TGTTCACCTTTTACCCTATCCTTTTGGTTATGACTTTGGTACTTGTGCACCTCCATATCCATTGA
1 TGTTCACCTTTTACCCGATCCTTCTGGTTATGACTTTGGTACTTATGCACCTCCATATCCATTGA
1413091 AGGGCAACCC
66 AGGGCAACCC
* * *
1413101 TGTTCACCTTTTACCCGATCCTTCTAGTTGTGACTTTGGTACTTATGCGCCTCCATATCCATTGA
1 TGTTCACCTTTTACCCGATCCTTCTGGTTATGACTTTGGTACTTATGCACCTCCATATCCATTGA
1413166 AGGGCAACCC
66 AGGGCAACCC
*
1413176 TGTTCACCTTTTACCCGATCCTTCTGGTTATGACTTTGGTACTTATGCACATCCAT
1 TGTTCACCTTTTACCCGATCCTTCTGGTTATGACTTTGGTACTTATGCACCTCCAT
1413232 TGAAAGACAA
Statistics
Matches: 185, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
69 45 0.24
73 1 0.01
75 139 0.75
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.37
Consensus pattern (75 bp):
TGTTCACCTTTTACCCGATCCTTCTGGTTATGACTTTGGTACTTATGCACCTCCATATCCATTGA
AGGGCAACCC
Found at i:1413772 original size:36 final size:36
Alignment explanation
Indices: 1413725--1413815 Score: 173
Period size: 36 Copynumber: 2.5 Consensus size: 36
1413715 TTCATTCATC
1413725 TGGAGAATCTGCAAACGATCCACTTCCAAGACAATT
1 TGGAGAATCTGCAAACGATCCACTTCCAAGACAATT
1413761 TGGAGAATCTGCAAACGATCCACTTCCAAGACAATT
1 TGGAGAATCTGCAAACGATCCACTTCCAAGACAATT
*
1413797 TGGAGAAGCTGCAAACGAT
1 TGGAGAATCTGCAAACGAT
1413816 ACATTTCTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (36 bp):
TGGAGAATCTGCAAACGATCCACTTCCAAGACAATT
Found at i:1415080 original size:22 final size:22
Alignment explanation
Indices: 1415055--1415097 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1415045 TACGTTACGT
*
1415055 GACAAGTAACATTTTTTTTACC
1 GACAAGTAACATTATTTTTACC
1415077 GACAAGTAACATTATTTTTAC
1 GACAAGTAACATTATTTTTAC
1415098 AACAATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
GACAAGTAACATTATTTTTACC
Found at i:1415107 original size:24 final size:22
Alignment explanation
Indices: 1415056--1415102 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1415046 ACGTTACGTG
* *
1415056 ACAAGTAACATTTTTTTTACCG
1 ACAAGTAACATTATTTTTACCA
1415078 ACAAGTAACATTATTTTTA-CA
1 ACAAGTAACATTATTTTTACCA
1415099 ACAA
1 ACAA
1415103 TAAGTTGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (22 bp):
ACAAGTAACATTATTTTTACCA
Found at i:1418953 original size:23 final size:23
Alignment explanation
Indices: 1418927--1418985 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1418917 CACCACAGCT
*
1418927 CGTATAAATGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
* *
1418950 CGTATAATTGCATCGAAGTGCCG
1 CGTATAATTGCACCGAAGTGCCA
*
1418973 CGTAGAATTGCAC
1 CGTATAATTGCAC
1418986 TGTAGTTCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:1425919 original size:23 final size:23
Alignment explanation
Indices: 1425868--1425926 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
1425858 CTCGTATAAA
*
1425868 TGCACAGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1425891 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1425914 TGCACCGTAGTGC
1 TGCACCGAAGTGC
1425927 TATATTAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1429304 original size:38 final size:38
Alignment explanation
Indices: 1429239--1429343 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 38
1429229 ATCTCATTTT
* * *
1429239 TAAT-TTTCTTAAGACTTGTCT-CTTAGAAAACTTAATC
1 TAATCTTTCTTAAGA-TTGTTTCCCTAGAAAACTCAATC
*
1429276 TAATCTTTCTTAAGATTGTTTCCCTAGAAACCTCAATC
1 TAATCTTTCTTAAGATTGTTTCCCTAGAAAACTCAATC
* * * *
1429314 TCATCTCTCTTAAGATTGATTCTCTAGAAA
1 TAATCTTTCTTAAGATTGTTTCCCTAGAAA
1429344 CCAACTTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 9 0.16
38 49 0.84
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (38 bp):
TAATCTTTCTTAAGATTGTTTCCCTAGAAAACTCAATC
Found at i:1429495 original size:63 final size:63
Alignment explanation
Indices: 1429390--1429563 Score: 217
Period size: 62 Copynumber: 2.8 Consensus size: 63
1429380 TTCTAACCTA
* * *
1429390 TCATGAGGATTTTTTCCCAAATGTACGAATCGCATTACCGCATTCATTCGGACATTTTCACAT-T
1 TCATGAGGA-TTTTTCCCAAATGCATGAATTGCATTACCGCATTCATTCGGAC-TTTTCACATCT
* * * *
1429454 TCATGAGGATTTTTCCCAAATGCATGAATTACATTATCGCATTCATTCGGACTTTTTACCTCT
1 TCATGAGGATTTTTCCCAAATGCATGAATTGCATTACCGCATTCATTCGGACTTTTCACATCT
* * * *
1429517 T-ATGAGGACTTTTCCCAAATCCATGAATTGTATTACCACATTCATTC
1 TCATGAGGATTTTTCCCAAATGCATGAATTGCATTACCGCATTCATTC
1429564 AGAGTTTTAA
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
62 47 0.49
63 40 0.42
64 9 0.09
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (63 bp):
TCATGAGGATTTTTCCCAAATGCATGAATTGCATTACCGCATTCATTCGGACTTTTCACATCT
Found at i:1429542 original size:62 final size:62
Alignment explanation
Indices: 1429376--1429583 Score: 193
Period size: 62 Copynumber: 3.3 Consensus size: 62
1429366 ATTTCTTAAA
* * * ** * **
1429376 GACTTTCTAACCTATCATGAGGATTTTTTCCCAAATGTACGAATCGCATTACCGCATTCATTCG
1 GACTTT-TAACCTCTTATGAGGA-CTTTTCCCAAATCCATGAATTACATTACCGCATTCATTCG
* * * * *
1429440 GACATTTTCACAT-TTCATGAGGATTTTTCCCAAATGCATGAATTACATTATCGCATTCATTCG
1 GAC-TTTTAACCTCTT-ATGAGGACTTTTCCCAAATCCATGAATTACATTACCGCATTCATTCG
* ** * *
1429503 GACTTTTTACCTCTTATGAGGACTTTTCCCAAATCCATGAATTGTATTACCACATTCATTCA
1 GACTTTTAACCTCTTATGAGGACTTTTCCCAAATCCATGAATTACATTACCGCATTCATTCG
* *
1429565 GAGTTTTAACCTCTCATGA
1 GACTTTTAACCTCTTATGA
1429584 ATACTTTTTG
Statistics
Matches: 121, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
62 63 0.52
63 41 0.34
64 14 0.12
65 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (62 bp):
GACTTTTAACCTCTTATGAGGACTTTTCCCAAATCCATGAATTACATTACCGCATTCATTCG
Found at i:1429590 original size:62 final size:62
Alignment explanation
Indices: 1429375--1429735 Score: 174
Period size: 56 Copynumber: 6.0 Consensus size: 62
1429365 CATTTCTTAA
* * * ** * ** *
1429375 AGACTTTCTAACCTATCATGAGGATTTTTTCCCAAATGTACGAATCGCATTACCGCATTCATTC
1 AGACTTT-TAACCTCTCATGAAGA-CTTTTCCCAAATCCATGAATTACATTACCACATTCATTC
* * * * * * * * *
1429439 GGACATTTTCACATTTCATGAGGATTTTTCCCAAATGCATGAATTACATTATCGCATTCATTC
1 AGAC-TTTTAACCTCTCATGAAGACTTTTCCCAAATCCATGAATTACATTACCACATTCATTC
* * * * **
1429502 GGACTTTTTACCTCTTATGAGGACTTTTCCCAAATCCATGAATTGTATTACCACATTCATTC
1 AGACTTTTAACCTCTCATGAAGACTTTTCCCAAATCCATGAATTACATTACCACATTCATTC
* * * *** *
1429564 AGAGTTTTAACCTCTCATGAATACTTTT------TGCATGAATCGTATTACCGCATTCATTC
1 AGACTTTTAACCTCTCATGAAGACTTTTCCCAAATCCATGAATTACATTACCACATTCATTC
* * * * * * * *
1429620 AAACTTCTGACCTCTCATG-AGAACTTTT------TACATGAATCACATTATCACATTAATTT
1 AGACTTTTAACCTCTCATGAAG-ACTTTTCCCAAATCCATGAATTACATTACCACATTCATTC
* * * * * * *
1429676 TGACTTATGACCTCTCATGAGGACTTTTTCCAAATGCATGAA-TACATTATCACATTCATT
1 AGACTTTTAACCTCTCATGAAGACTTTTCCCAAATCCATGAATTACATTACCACATTCATT
1429736 TAGCCTTCTG
Statistics
Matches: 241, Mismatches: 47, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
55 1 0.00
56 89 0.37
57 1 0.00
61 16 0.07
62 77 0.32
63 38 0.16
64 16 0.07
65 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.37
Consensus pattern (62 bp):
AGACTTTTAACCTCTCATGAAGACTTTTCCCAAATCCATGAATTACATTACCACATTCATTC
Found at i:1429755 original size:61 final size:62
Alignment explanation
Indices: 1429650--1429765 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 62
1429640 GAACTTTTTA
* *
1429650 CATGAATCACATTATCACATTAATTTTGACTTATGACCTCTCATGAGGACTTTTTCCAAATG
1 CATGAATCACATTATCACATTAATTTAGACTTATGACCTCTCATGAGGACATTTTCCAAATG
* * * * *
1429712 CATGAAT-ACATTATCACATTCATTTAGCCTTCTGGCCTTTCATGAGGACATTTT
1 CATGAATCACATTATCACATTAATTTAGACTTATGACCTCTCATGAGGACATTTT
1429766 GCATGAATCA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
61 40 0.85
62 7 0.15
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (62 bp):
CATGAATCACATTATCACATTAATTTAGACTTATGACCTCTCATGAGGACATTTTCCAAATG
Found at i:1430368 original size:48 final size:48
Alignment explanation
Indices: 1430250--1430415 Score: 172
Period size: 48 Copynumber: 3.4 Consensus size: 48
1430240 TGATTTACAT
* *
1430250 ATCTGACCTACCCTGAAGAACAGCGGAGCAAATCCCATTTATTCTTTCCTA
1 ATCTGACCTACCCTGAAGAGCAGCGGAGCAAATCCC--TT-TCCTTTCCTA
* * * ** *
1430301 ATCTAACCTACCTTAAAGAGCAAAGGAGCAAATCCCTTTCCTTT-CTCG
1 ATCTGACCTACCCTGAAGAGCAGCGGAGCAAATCCCTTTCCTTTCCT-A
* * * *
1430349 ATCTGACCTACCCTGAAGAGCAGCGGAGCAGATCTCATTTCTTTTCCTT
1 ATCTGACCTACCCTGAAGAGCAGCGGAGCAAATC-CCTTTCCTTTCCTA
1430398 ATCTGACCTACCCTGAAG
1 ATCTGACCTACCCTGAAG
1430416 TTGCAGTAGA
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.02
48 33 0.35
49 28 0.29
50 2 0.02
51 30 0.32
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (48 bp):
ATCTGACCTACCCTGAAGAGCAGCGGAGCAAATCCCTTTCCTTTCCTA
Found at i:1432496 original size:38 final size:38
Alignment explanation
Indices: 1432437--1432537 Score: 132
Period size: 38 Copynumber: 2.7 Consensus size: 38
1432427 CCTCATTTTT
* *
1432437 TTTCTTAAGACTTGTCT-CCTAGAAAACTTAATCTAATC
1 TTTCTTAAGA-TTGTTTCCCTAGAAAACTCAATCTAATC
* *
1432475 TTTCTTAAGATTGTTTCCCTAGAAACCTCAATCTCATC
1 TTTCTTAAGATTGTTTCCCTAGAAAACTCAATCTAATC
* *
1432513 TTTCTTAAGATTGATTCTCTAGAAA
1 TTTCTTAAGATTGTTTCCCTAGAAA
1432538 CCAACTTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 5 0.09
38 51 0.91
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (38 bp):
TTTCTTAAGATTGTTTCCCTAGAAAACTCAATCTAATC
Found at i:1432745 original size:62 final size:61
Alignment explanation
Indices: 1432579--1432928 Score: 306
Period size: 56 Copynumber: 5.8 Consensus size: 61
1432569 AGACCTTCTA
* * * * * * *
1432579 ACCTATCATGAAGATTTTTCCCAAATGTATGAATCGCATTACTGCATTCATTCTGAAATTTTC
1 ACCTCTCATGAGGACTTTT-CCAAATGCATGAATCGCATTACCGCATTCATTCTG-ACTTTTG
* * * * * *
1432642 ACATTTCATGAGGATTTTTCCCAAACGCATGAATTGCATTACCGCATTCATTCTGACTTTTT
1 ACCTCTCATGAGGACTTTT-CCAAATGCATGAATCGCATTACCGCATTCATTCTGACTTTTG
* * * * * *
1432704 ACCTCTTATGAGGACTTTTCCCATATGCATGAATCGTATTACCACATTCATTCAGAGTTTTG
1 ACCTCTCATGAGGACTTTT-CCAAATGCATGAATCGCATTACCGCATTCATTCTGACTTTTG
** * ** *
1432766 ACCTCTCATGAATACTTTT-----TGCATTAATCGCATTACCGCATTCATTCAAACTTCTG
1 ACCTCTCATGAGGACTTTTCCAAATGCATGAATCGCATTACCGCATTCATTCTGACTTTTG
* * * * *
1432822 ATCTCTCATGAGGACTTTT-----TGCATGAATCACATTATCGCATTCATTTTGACTTATG
1 ACCTCTCATGAGGACTTTTCCAAATGCATGAATCGCATTACCGCATTCATTCTGACTTTTG
* *
1432878 ACCTCTCATGAGGACTTTTCCAAATGCATGAATCACATTATCGCATTCATT
1 ACCTCTCATGAGGACTTTTCCAAATGCATGAATCGCATTACCGCATTCATT
1432929 TAGCCTTCTG
Statistics
Matches: 241, Mismatches: 41, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
56 95 0.39
61 27 0.11
62 71 0.29
63 48 0.20
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (61 bp):
ACCTCTCATGAGGACTTTTCCAAATGCATGAATCGCATTACCGCATTCATTCTGACTTTTG
Found at i:1432801 original size:56 final size:56
Alignment explanation
Indices: 1432668--1432984 Score: 238
Period size: 56 Copynumber: 5.5 Consensus size: 56
1432658 TTTCCCAAAC
* * * * * *
1432668 GCATGAATTGCATTACCGCATTCATTCTGACTTTTTACCTCTTATGAGGACTTTTCCCATAT
1 GCATGAATCGCATTACCGCATTCATTCAGACTTATGACCTCTCATGAAGAC-TTT----T-T
* * * * *
1432730 GCATGAATCGTATTACCACATTCATTCAGAGTTTTGACCTCTCATGAATACTTTTT
1 GCATGAATCGCATTACCGCATTCATTCAGACTTATGACCTCTCATGAAGACTTTTT
* * * * *
1432786 GCATTAATCGCATTACCGCATTCATTCAAACTTCTGATCTCTCATGAGGACTTTTT
1 GCATGAATCGCATTACCGCATTCATTCAGACTTATGACCTCTCATGAAGACTTTTT
* * ** *
1432842 GCATGAATCACATTATCGCATTCATTTTGACTTATGACCTCTCATGAGGACTTTTCCAAAT
1 GCATGAATCGCATTACCGCATTCATTCAGACTTATGACCTCTCATGAAGACTTTT-----T
* * * * * * * * *
1432903 GCATGAATCACATTATCGCATTCATTTAGCCTTCTGGCCTTTCATGATGATTTTTT
1 GCATGAATCGCATTACCGCATTCATTCAGACTTATGACCTCTCATGAAGACTTTTT
* **
1432959 GCATGAATCACATTACAACATTCATT
1 GCATGAATCGCATTACCGCATTCATT
1432985 TAACCTCTCT
Statistics
Matches: 214, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
56 119 0.56
57 1 0.00
61 52 0.24
62 42 0.20
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (56 bp):
GCATGAATCGCATTACCGCATTCATTCAGACTTATGACCTCTCATGAAGACTTTTT
Found at i:1432983 original size:173 final size:174
Alignment explanation
Indices: 1432668--1432984 Score: 404
Period size: 173 Copynumber: 1.8 Consensus size: 174
1432658 TTTCCCAAAC
** * * * *
1432668 GCATGAATTGCATTACCGCATTCATTCTGACTTTTTACCTCTTATGAGGACTTTTCCCATATGCA
1 GCATGAATCACATTACCGCATTCATTCTGACTTATGACCTCTCATGAGGACTTTTCCCAAATGCA
** * * * *
1432733 TGAATCGTATTACCACATTCATTCAGAGTTTTGACCTCTCATGAATACTTTTTGCATTAATCGCA
66 TGAATCACATTACCACATTCATTCAGACTTCTGACCTCTCATGAATACTTTTTGCATGAATCACA
**
1432798 TTACCGCATTCATTCAAACTTCTGATCTCTCATGAGGACTTTTT
131 TTACAACATTCATTCAAACTTCTGATCTCTCATGAGGACTTTTT
* *
1432842 GCATGAATCACATTATCGCATTCATTTTGACTTATGACCTCTCATGAGGACTTTT-CCAAATGCA
1 GCATGAATCACATTACCGCATTCATTCTGACTTATGACCTCTCATGAGGACTTTTCCCAAATGCA
* * * * * * *
1432906 TGAATCACATTATCGCATTCATTTAGCCTTCTGGCCTTTCATG-ATGATTTTTTGCATGAATCAC
66 TGAATCACATTACCACATTCATTCAGACTTCTGACCTCTCATGAAT-ACTTTTTGCATGAATCAC
1432970 ATTACAACATTCATT
130 ATTACAACATTCATT
1432985 TAACCTCTCT
Statistics
Matches: 119, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
172 2 0.02
173 69 0.58
174 48 0.40
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (174 bp):
GCATGAATCACATTACCGCATTCATTCTGACTTATGACCTCTCATGAGGACTTTTCCCAAATGCA
TGAATCACATTACCACATTCATTCAGACTTCTGACCTCTCATGAATACTTTTTGCATGAATCACA
TTACAACATTCATTCAAACTTCTGATCTCTCATGAGGACTTTTT
Found at i:1433800 original size:17 final size:18
Alignment explanation
Indices: 1433763--1433802 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1433753 GCTATTTTGG
1433763 TTTTA-TTAGTTATTTCA
1 TTTTATTTAGTTATTTCA
*
1433780 -TTTATTTATTTATTT-A
1 TTTTATTTAGTTATTTCA
1433796 TTTTATT
1 TTTTATT
1433803 ATTAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTATTTAGTTATTTCA
Done.