Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_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: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1427921 original size:3 final size:3
Alignment explanation
Indices: 1427910--1427967 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
1427900 TGTTAAATAA
* * * * *
1427910 TAT TA- TAT TAT TAT TTT TAT CAT TAT TAA TAT CAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1427957 TAT TAT TAT TA
1 TAT TAT TAT TA
1427968 ATATAAGTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1427966 original size:12 final size:12
Alignment explanation
Indices: 1427907--1427971 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
1427897 TCATGTTAAA
1427907 TAATATTA-TAT
1 TAATATTATTAT
* *
1427918 TATTATTTTTAT
1 TAATATTATTAT
* * *
1427930 CATTATTAATAT
1 TAATATTATTAT
* *
1427942 CATTATTATTAT
1 TAATATTATTAT
1427954 TAATATTATTAT
1 TAATATTATTAT
1427966 TAATAT
1 TAATAT
1427972 AAGTACATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
11 6 0.13
12 39 0.87
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:1427966 original size:18 final size:18
Alignment explanation
Indices: 1427910--1427967 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
1427900 TGTTAAATAA
* *
1427910 TATTA-TATTATTATTTT
1 TATTATTATTAATATTAT
* *
1427927 TATCATTATTAATATCAT
1 TATTATTATTAATATTAT
1427945 TATTATTATTAATATTAT
1 TATTATTATTAATATTAT
1427963 TATTA
1 TATTA
1427968 ATATAAGTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 4 0.12
18 30 0.88
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATTATTAATATTAT
Found at i:1428167 original size:10 final size:10
Alignment explanation
Indices: 1428152--1428182 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1428142 TGCATAGCAT
1428152 TTTAGTTGCA
1 TTTAGTTGCA
1428162 TTTAGTTGCA
1 TTTAGTTGCA
1428172 TTTAGTTGCA
1 TTTAGTTGCA
1428182 T
1 T
1428183 ATAGGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:1438473 original size:22 final size:22
Alignment explanation
Indices: 1438448--1438489 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1438438 CAATTCATTT
1438448 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
1438470 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
1438490 CCAGCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1449888 original size:131 final size:131
Alignment explanation
Indices: 1449719--1450067 Score: 385
Period size: 131 Copynumber: 2.7 Consensus size: 131
1449709 CGATATTGAG
* ** * ** *
1449719 AATAGTAATATCTTTTCATTTCGGTCGGAGTAATAAATGACTGCTTTAATGCATGAGAGGTCATT
1 AATAGTAATATCTCTTCATTTCAATTGGAACAATAAATGATTGCTTTAATGCATGAGAGGTCATT
* * * * *
1449784 TATTCTCGATTAGAAATAATTTGATATTATCGTTTTC-TCTCGAATTAATATCGATTTTTAAGAT
66 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCAT-TCGAATCAATATCGAATTTTAAGAC
*
1449848 GG
130 GA
* * ** * * *
1449850 AATAGTGATGTCTCTTCATTTTGATTGGAACAATAAATGATTGCTTTAAGGTATAAGAGGTCATT
1 AATAGTAATATCTCTTCATTTCAATTGGAACAATAAATGATTGCTTTAATGCATGAGAGGTCATT
* * * *
1449915 TATTCTCGATTGGAAATCATTAGATATTATCGTTTTCATTTGAATCGATATTGAATTTTAAGACG
66 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCATTCGAATCAATATCGAATTTTAAGACG
1449980 A
131 A
* *** * * ** *
1449981 AATAGTAATATCTCTTTATTTCAATTGGGGTAATAAATAATTGTTTTAATGCGCGAAAGGTCATT
1 AATAGTAATATCTCTTCATTTCAATTGGAACAATAAATGATTGCTTTAATGCATGAGAGGTCATT
1450046 TATTCTCGATTGGAAATAATTA
66 TATTCTCGATTGGAAATAATTA
1450068 AATAATATTA
Statistics
Matches: 178, Mismatches: 39, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
131 177 0.99
132 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (131 bp):
AATAGTAATATCTCTTCATTTCAATTGGAACAATAAATGATTGCTTTAATGCATGAGAGGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCATTCGAATCAATATCGAATTTTAAGACG
A
Found at i:1450506 original size:131 final size:131
Alignment explanation
Indices: 1450256--1450572 Score: 357
Period size: 131 Copynumber: 2.4 Consensus size: 131
1450246 CAAAAATTCA
* * * *
1450256 AAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTTGATACTGTCGTTTTCTCTCGAATTA
1 AAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCA
* *** * *
1450321 ATATCGATTTTTAAGATGGAATAATGATATCTCTTCATTTCGATTGGAACAATAAATAACTGCTT
66 ATATCGAATTTTAAGACAAAATAATAATATCTCTTCATTTCAATTGGAACAATAAATAACTGCTT
1450386 T
131 T
* * * * *
1450387 AAGGTATGCGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATCGTTTT-TATTTGAATC
1 AAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCT-CTCGAATC
* * * * *** * * *
1450451 GATATTGAATTTTAAGACAAAATAGTAATATCTCTTTATTTCAATTGGGGTAATAAATTATTGTT
65 AATATCGAATTTTAAGACAAAATAATAATATCTCTTCATTTCAATTGGAACAATAAATAACTGCT
1450516 TT
130 TT
* * * *
1450518 CATGCAAGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
1 AAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
1450573 ACTTTTAAAA
Statistics
Matches: 152, Mismatches: 32, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
130 1 0.01
131 151 0.99
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (131 bp):
AAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCA
ATATCGAATTTTAAGACAAAATAATAATATCTCTTCATTTCAATTGGAACAATAAATAACTGCTT
T
Found at i:1464034 original size:13 final size:13
Alignment explanation
Indices: 1464018--1464077 Score: 77
Period size: 13 Copynumber: 4.6 Consensus size: 13
1464008 ACAATGAGCG
1464018 TCATAAATGCGCT
1 TCATAAATGCGCT
* *
1464031 TCATAAATGCACG
1 TCATAAATGCGCT
1464044 TCATAAATGCG-T
1 TCATAAATGCGCT
*
1464056 GTCATAAATGCGCA
1 -TCATAAATGCGCT
1464070 TCATAAAT
1 TCATAAAT
1464078 TCATGATGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (13 bp):
TCATAAATGCGCT
Found at i:1464039 original size:26 final size:26
Alignment explanation
Indices: 1464010--1464077 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 26
1464000 AATGACGCAC
1464010 AATGAGCGTCATAAATGCGCT-TCATA
1 AATGAGCGTCATAAATGCG-TGTCATA
1464036 AATGCA-CGTCATAAATGCGTGTCATA
1 AATG-AGCGTCATAAATGCGTGTCATA
* *
1464062 AATGCGCATCATAAAT
1 AATGAGCGTCATAAAT
1464078 TCATGATGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 1 0.03
26 35 0.95
27 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGTGTCATA
Found at i:1475256 original size:37 final size:37
Alignment explanation
Indices: 1475215--1475292 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
1475205 CTCGATGATA
*
1475215 TGGTATAAATAATCCTTGTTTGATATTCAATTAGATG
1 TGGTATAAATAAGCCTTGTTTGATATTCAATTAGATG
1475252 TGGTATAAATAAGCCTTGTTTGATATTCAATTAGATG
1 TGGTATAAATAAGCCTTGTTTGATATTCAATTAGATG
1475289 TGGT
1 TGGT
1475293 GACATGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (37 bp):
TGGTATAAATAAGCCTTGTTTGATATTCAATTAGATG
Found at i:1476066 original size:37 final size:37
Alignment explanation
Indices: 1476009--1476247 Score: 209
Period size: 37 Copynumber: 6.3 Consensus size: 37
1475999 GGGCAAGTCC
*
1476009 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
* *
1476046 ACCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
* * * * *
1476083 ATCAGTAAGCCTT-ACGGGCATGA-T-GATTAAGTC--CTCGGGAA
1 ATC-TTAAGCCTTCAC-CG-AAGAGTAG-TGAAG-CAAATC----A
* * *
1476124 ATCTTAAGCCTTTACCAAAGAGTAGTGAAGAAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
* * *
1476161 ATCTTAAGCCTCCACCAAAGAGTAGTAAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
*
1476198 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
*
1476235 ATCAGTAAGCCTT
1 ATC-TTAAGCCTT
1476248 TCGAGCATGA
Statistics
Matches: 161, Mismatches: 26, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
37 111 0.69
38 22 0.14
39 7 0.04
40 13 0.08
41 8 0.05
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
Found at i:1479030 original size:5 final size:5
Alignment explanation
Indices: 1479020--1479201 Score: 132
Period size: 5 Copynumber: 35.4 Consensus size: 5
1479010 ATAAAGAATA
1479020 AAAAG AAAAG AAAAG AATAA- AGAAAG -AAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AA-AAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAAAG
*
1479070 AAAAG AAAAG AAAAG AAAA- AAAGAG AAAAAG AAGAATG AAAA- AATAAC
1 AAAAG AAAAG AAAAG AAAAG AAA-AG -AAAAG AA-AA-G AAAAG AA-AAG
*
1479118 AAAAG -AATG AAAAG AGAAA- AAGAAG AAAAG AATGAATG AATGAA- AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AA-AAG AAAAG AA--AA-G AA--AAG AAAAG
*
1479167 AAAAG AAAAG AAAA- AAGA- AAAAG -AAAG ATAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AA
1479202 TAAAGAATAA
Statistics
Matches: 150, Mismatches: 5, Indels: 44
0.75 0.03 0.22
Matches are distributed among these distances:
4 25 0.17
5 87 0.58
6 23 0.15
7 8 0.05
8 7 0.05
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:1479046 original size:30 final size:29
Alignment explanation
Indices: 1479012--1479229 Score: 143
Period size: 30 Copynumber: 7.3 Consensus size: 29
1479002 AAATAAGAAT
1479012 AAAGAATAAAAAGAAAAGAAAAGAATAAAG
1 AAAGAA-AAAAAGAAAAGAAAAGAATAAAG
1479042 AAAGAAAGAAAAGAAAAGAAAAG-A-AAAG
1 AAAGAAA-AAAAGAAAAGAAAAGAATAAAG
1479070 AAAAGAAAAGAAAAGAAAA-AAAGAGAA-AAAG
1 -AAAG-AAA-AAAAGAAAAGAAA-AGAATAAAG
* *
1479101 -AAGAATGAAAAA-ATAACAAAAGAATGAAA-
1 AAAGAA--AAAAAGAAAAGAAAAGAAT-AAAG
* * *
1479130 AGAGAAAAAGAAGAAAAG-AATGAATGAATG
1 AAAGAAAAA-AAGAAAAGAAAAGAAT-AAAG
1479160 AAA-AAAGAAAAGAAAAGAAAAAAGAA-AAAG
1 AAAGAAA-AAAAGAAAAG--AAAAGAATAAAG
* *
1479190 AAAGATAAAGAA-TAAAGAATAAAGAATAAAG
1 AAAGA-AAAAAAGAAAAG-A-AAAGAATAAAG
1479221 AAAGAAAAA
1 AAAGAAAAA
1479230 GAATAAAGAA
Statistics
Matches: 154, Mismatches: 12, Indels: 44
0.73 0.06 0.21
Matches are distributed among these distances:
28 16 0.10
29 43 0.28
30 70 0.45
31 18 0.12
32 7 0.05
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (29 bp):
AAAGAAAAAAAGAAAAGAAAAGAATAAAG
Found at i:1479049 original size:25 final size:25
Alignment explanation
Indices: 1479006--1479239 Score: 133
Period size: 25 Copynumber: 9.5 Consensus size: 25
1478996 CCTAAAAAAT
*
1479006 AAGAATAAAGAATAAAAAGAAAAGAA
1 AAGAATAAAGAA-AGAAAGAAAAGAA
1479032 AAGAATAAAGAAAGAAAGAAAAGAA
1 AAGAATAAAGAAAGAAAGAAAAGAA
1479057 AAG-A-AAAGAAAAGAAAAGAAAAGAA
1 AAGAATAAAG-AAAG-AAAGAAAAGAA
*
1479082 AAGAAAAAAAGAGAA-AAAGAAGAATGAA
1 AAG-AATAAAGA-AAGAAAGAA-AA-GAA
*
1479110 AA-AATAACA-AAAGAATGAAAAGAGA
1 AAGAATAA-AGAAAGAAAGAAAAGA-A
* * *
1479135 AA-AA-GAAGAAAAGAATG-AATG-A
1 AAGAATAAAG-AAAGAAAGAAAAGAA
* *
1479157 ATGAA-AAA-AGA-AAAGAAAAGAA
1 AAGAATAAAGAAAGAAAGAAAAGAA
*
1479179 AA-AA-GAA-AAAGAAAGATAAAGAATA
1 AAGAATAAAGAAAGAAAGA-AAAG-A-A
*
1479204 AAGAATAAAG-AATAAAGAAAGA-AA
1 AAGAATAAAGAAAGAAAGAAA-AGAA
1479228 AAGAATAAAGAA
1 AAGAATAAAGAA
1479240 TAAACAAAAA
Statistics
Matches: 168, Mismatches: 15, Indels: 51
0.72 0.06 0.22
Matches are distributed among these distances:
20 3 0.02
21 11 0.07
22 9 0.05
23 13 0.08
24 23 0.14
25 51 0.30
26 32 0.19
27 15 0.09
28 11 0.07
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.06
Consensus pattern (25 bp):
AAGAATAAAGAAAGAAAGAAAAGAA
Found at i:1479232 original size:10 final size:10
Alignment explanation
Indices: 1479012--1479232 Score: 87
Period size: 10 Copynumber: 22.2 Consensus size: 10
1479002 AAATAAGAAT
*
1479012 AAAGAATAA-
1 AAAGAAAAAG
1479021 AAAG-AAAAG
1 AAAGAAAAAG
1479030 AAAAGAATAAAG
1 -AAAGAA-AAAG
*
1479042 AAAGAAAGA-
1 AAAGAAAAAG
1479051 AAAG-AAAAG
1 AAAGAAAAAG
1479060 AAA-AGAAAAG
1 AAAGA-AAAAG
1479070 AAA-AGAAAAG
1 AAAGA-AAAAG
1479080 AAAAGAAAAA-
1 -AAAGAAAAAG
1479090 AAGAGAAAAAG
1 AA-AGAAAAAG
1479101 AAGAATGAAAAA-
1 -A-AA-GAAAAAG
*
1479113 ATAA-CAAAAG
1 A-AAGAAAAAG
*
1479123 AATGAAAAGAG
1 AAAGAAAA-AG
*
1479134 AAA-AAGAAG
1 AAAGAAAAAG
* *
1479143 AAA-AGAATG
1 AAAGAAAAAG
*
1479152 AATGAATGAAA-
1 AAAGAA--AAAG
1479163 AAAG-AAAAG
1 AAAGAAAAAG
*
1479172 AAA-AGAAA-
1 AAAGAAAAAG
1479180 AAAGAAAAAG
1 AAAGAAAAAG
*
1479190 AAAGATAAAG
1 AAAGAAAAAG
* *
1479200 AATA-AAGAAT
1 AA-AGAAAAAG
1479210 AAAGAATAAAG
1 AAAGAA-AAAG
1479221 AAAGAAAAAG
1 AAAGAAAAAG
1479231 AA
1 AA
1479233 TAAAGAATAA
Statistics
Matches: 161, Mismatches: 24, Indels: 53
0.68 0.10 0.22
Matches are distributed among these distances:
8 12 0.07
9 39 0.24
10 61 0.38
11 33 0.20
12 9 0.06
13 7 0.04
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:1479237 original size:7 final size:7
Alignment explanation
Indices: 1479190--1479243 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
1479180 AAAGAAAAAG
1479190 AAAG-AT
1 AAAGAAT
1479196 AAAGAAT
1 AAAGAAT
1479203 AAAGAAT
1 AAAGAAT
1479210 AAAGAAT
1 AAAGAAT
1479217 AAAG---
1 AAAGAAT
1479221 AAAGAA-
1 AAAGAAT
1479227 AAAGAAT
1 AAAGAAT
1479234 AAAGAAT
1 AAAGAAT
1479241 AAA
1 AAA
1479244 CAAAAAGGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.09
6 10 0.23
7 30 0.68
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (7 bp):
AAAGAAT
Found at i:1480959 original size:3 final size:3
Alignment explanation
Indices: 1480949--1481000 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
1480939 TAAATAATAA
* * * * *
1480949 TAT T-T TAT TAT TAT TTT TAT CAT TAT TAG TAT CAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1480996 TAT TA
1 TAT TA
1481001 ATATAAGTAC
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1481028 original size:26 final size:26
Alignment explanation
Indices: 1480989--1481041 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1480979 ATCATTATTA
*
1480989 TTATTAATATTAATATAAGTACATTT
1 TTATTAATAATAATATAAGTACATTT
*
1481015 TTATTATTAATAATATAAGTACATTT
1 TTATTAATAATAATATAAGTACATTT
1481041 T
1 T
1481042 ATTTTCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
TTATTAATAATAATATAAGTACATTT
Found at i:1483472 original size:2 final size:2
Alignment explanation
Indices: 1483467--1483536 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
1483457 TGTTTCGACA
1483467 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
1483509 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
1483537 GCTTGAAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1485130 original size:21 final size:22
Alignment explanation
Indices: 1485106--1485156 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1485096 GAATTAATCA
*
1485106 ATAAAATAT-ATTAATACAATT
1 ATAAAATATAATCAATACAATT
*
1485127 AT-AAATATAATCAATACATTT
1 ATAAAATATAATCAATACAATT
1485148 ATACAAATA
1 ATA-AAATA
1485157 AGACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 14 0.56
23 5 0.20
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAAATATAATCAATACAATT
Found at i:1489363 original size:8 final size:8
Alignment explanation
Indices: 1489333--1489381 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
1489323 GAGCCCTTCA
1489333 AAAATTTT
1 AAAATTTT
1489341 AAAAATTTT
1 -AAAATTTT
1489350 --AA-TTT
1 AAAATTTT
*
1489355 AAAACTTT
1 AAAATTTT
1489363 AAAATTTT
1 AAAATTTT
*
1489371 GAAATTTT
1 AAAATTTT
1489379 AAA
1 AAA
1489382 TTGACCCCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 2 0.06
8 19 0.56
9 8 0.24
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (8 bp):
AAAATTTT
Found at i:1491963 original size:28 final size:28
Alignment explanation
Indices: 1491899--1491952 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1491889 ACATCGAGAT
*
1491899 AATGCTTGAAACACTATACCTTCGAGCC
1 AATGCTTGAAACACTATACCTTCAAGCC
* *
1491927 AATGCTTGACACATTATACCTTCAAG
1 AATGCTTGAAACACTATACCTTCAAG
1491953 TTAGTGCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (28 bp):
AATGCTTGAAACACTATACCTTCAAGCC
Found at i:1494075 original size:14 final size:14
Alignment explanation
Indices: 1494056--1494091 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1494046 TAAATTTTTA
1494056 TTTAATTAAGATAT
1 TTTAATTAAGATAT
1494070 TTTAATTAAGATAT
1 TTTAATTAAGATAT
1494084 TTTAATTA
1 TTTAATTA
1494092 GTGATGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
TTTAATTAAGATAT
Found at i:1500956 original size:8 final size:9
Alignment explanation
Indices: 1500922--1500959 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
1500912 TTTTTAATAA
1500922 AAAATATTT
1 AAAATATTT
*
1500931 AAAATATAT
1 AAAATATTT
1500940 AAAA-ATTT
1 AAAATATTT
1500948 AAAAT-TTT
1 AAAATATTT
1500956 AAAA
1 AAAA
1500960 AATTACGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 14 0.54
9 12 0.46
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAATATTT
Found at i:1500960 original size:17 final size:16
Alignment explanation
Indices: 1500917--1500963 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1500907 ATATATTTTT
1500917 AATA-AAAAATATTTAA
1 AATATAAAAA-ATTTAA
1500933 AATATATAAAAATTTAA
1 AATATA-AAAAATTTAA
*
1500950 AATTTTAAAAAATT
1 AA-TATAAAAAATT
1500964 ACGACTGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.15
17 16 0.59
18 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATAAAAAATTTAA
Found at i:1501047 original size:11 final size:10
Alignment explanation
Indices: 1501029--1501053 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1501019 CCCTGTGCCA
1501029 TCTTTTTTTT
1 TCTTTTTTTT
1501039 TCTTTTTTTT
1 TCTTTTTTTT
1501049 TCTTT
1 TCTTT
1501054 CATTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:1502865 original size:61 final size:59
Alignment explanation
Indices: 1502736--1502866 Score: 165
Period size: 61 Copynumber: 2.2 Consensus size: 59
1502726 AAAGAGGGTC
*
1502736 ATAGTTTAGGGATGAAATTAGAATGTTCAAAAGTTTAAGAAATAATTTAAAATGAGAATT
1 ATAGTTT-GGGATGAAATTAGAATATTCAAAAGTTTAAGAAATAATTTAAAATGAGAATT
* * * * *
1502796 ATATTTTGGAGATGAAATTAGAATATTCAAAAATTTTAA-AGACTAATTTAAAGTGAGGATT
1 ATAGTTTGG-GATGAAATTAGAATATTC-AAAAGTTTAAGA-AATAATTTAAAATGAGAATT
1502857 ATAGTTTGGG
1 ATAGTTTGGG
1502867 TACATATGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
59 2 0.03
60 25 0.41
61 34 0.56
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTAGAATATTCAAAAGTTTAAGAAATAATTTAAAATGAGAATT
Found at i:1503816 original size:12 final size:12
Alignment explanation
Indices: 1503791--1503848 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
1503781 ACGAAGATAT
* *
1503791 CAGAAATCAAAA
1 CAGAATTCAGAA
1503803 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
1503815 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1503827 CAGAAATCAGAA
1 CAGAATTCAGAA
1503839 CAGAATTCAG
1 CAGAATTCAG
1503849 GTCATTTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.52, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1503859 original size:24 final size:24
Alignment explanation
Indices: 1503803--1503871 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
1503793 GAAATCAAAA
* *
1503803 CAGAATTCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAT
*
1503827 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAT
*** *
1503851 CATTTATCAAAACAGAATTCA
1 CAGAAATCAGAACAGAATTCA
1503872 AGTCGAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.20
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAT
Found at i:1503883 original size:24 final size:24
Alignment explanation
Indices: 1503813--1503883 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 24
1503803 CAGAATTCAG
* * *
1503813 AACAGAA-TCCAGATCAGAAATCAG
1 AACAGAATTCAAG-TCATAAATCAA
* **
1503837 AACAGAATTCAGGTCATTTATCAA
1 AACAGAATTCAAGTCATAAATCAA
1503861 AACAGAATTCAAGTCGA-AAATCA
1 AACAGAATTCAAGTC-ATAAATCA
1503884 GATAAAATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
24 32 0.89
25 4 0.11
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (24 bp):
AACAGAATTCAAGTCATAAATCAA
Found at i:1506411 original size:8 final size:8
Alignment explanation
Indices: 1506371--1506417 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
1506361 TCAAAGTTTT
1506371 GGTCAACAG
1 GGTCAAC-G
1506380 TGGTCAACG
1 -GGTCAACG
1506389 TCGGTCAAC-
1 --GGTCAACG
1506398 GGTCAACG
1 GGTCAACG
1506406 GGTCAACG
1 GGTCAACG
1506414 GGTC
1 GGTC
1506418 GGGTCAACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 12 0.35
9 1 0.03
10 14 0.41
ACGTcount: A:0.23, C:0.26, G:0.34, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:1506411 original size:15 final size:16
Alignment explanation
Indices: 1506381--1506414 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1506371 GGTCAACAGT
1506381 GGTCAACGTCGGTCAAC
1 GGTCAACG-CGGTCAAC
1506398 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
1506413 GG
1 GG
1506415 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:1506418 original size:27 final size:28
Alignment explanation
Indices: 1506371--1506425 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
1506361 TCAAAGTTTT
1506371 GGTCAACAGTGGTCAACGTC-GGTCAAC
1 GGTCAACAGTGGTCAACGTCGGGTCAAC
1506398 GGTCAAC-G-GGTCAACGGGTCGGGTCAAC
1 GGTCAACAGTGGTCAAC--GTCGGGTCAAC
1506426 AAGTCGGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.28
26 1 0.04
27 10 0.40
28 7 0.28
ACGTcount: A:0.24, C:0.25, G:0.35, T:0.16
Consensus pattern (28 bp):
GGTCAACAGTGGTCAACGTCGGGTCAAC
Found at i:1506422 original size:13 final size:13
Alignment explanation
Indices: 1506404--1506453 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
1506394 CAACGGTCAA
1506404 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1506417 CGGGTCAACAAGTCGGGT
1 CGGGT---CAA--CGGGT
1506435 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1506448 CGGGTC
1 CGGGTC
1506454 GGGTCGGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 16 0.50
15 3 0.09
16 3 0.09
18 10 0.31
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1506435 original size:18 final size:18
Alignment explanation
Indices: 1506412--1506458 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1506402 AACGGGTCAA
1506412 CGGGTCGGGTCAACAAGT
1 CGGGTCGGGTCAACAAGT
**
1506430 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAAGT
1506448 CGGGTCGGGTC
1 CGGGTCGGGTC
1506459 GGGTTATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAAGT
Found at i:1508544 original size:24 final size:24
Alignment explanation
Indices: 1508517--1508604 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 24
1508507 GATATCATAA
* * *
1508517 ATCAAAACAGAATTCAGAACAGGT
1 ATCAGAACAGAATTCAGATCAGAT
* *
1508541 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATCAGAT
* **
1508565 ATCAGAACAGAATTCAGGTCATTT
1 ATCAGAACAGAATTCAGATCAGAT
1508589 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
1508605 AGTCGGAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAGAT
Found at i:1508581 original size:12 final size:12
Alignment explanation
Indices: 1508522--1508581 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
1508512 CATAAATCAA
1508522 AACAGAATTCAG
1 AACAGAATTCAG
*
1508534 AACAG-GTATCAG
1 AACAGAAT-TCAG
*
1508546 AACAGAATCCAG
1 AACAGAATTCAG
* *
1508558 ATCAGAAATCAG
1 AACAGAATTCAG
1508570 AACAGAATTCAG
1 AACAGAATTCAG
1508582 GTCATTTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.15
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:1508592 original size:48 final size:47
Alignment explanation
Indices: 1508510--1508618 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 47
1508500 AAACGAAGAT
* *
1508510 ATCATAAATCAAAACAGAATTCAGAACAGGTATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGGTATCAGAACAGAATCCA
** ** *
1508557 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGGTATCAGAACAGAATCCA
*
1508605 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1508619 TAAAATATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGGTATCAGAACAGAATCCA
Found at i:1508616 original size:24 final size:24
Alignment explanation
Indices: 1508515--1508618 Score: 86
Period size: 24 Copynumber: 4.3 Consensus size: 24
1508505 AAGATATCAT
* *
1508515 AAATCAAAACAGAATTC-AGAACAG
1 AAATCAGAACAGAATTCAAG-TCAG
** *
1508539 GTATCAGAACAGAA-TCCAGATCAG
1 AAATCAGAACAGAATTCAAG-TCAG
* *
1508563 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAGAACAGAATTCAAGTCAG
** *
1508587 TTATCAGAACAGAATTCAAGTCGG
1 AAATCAGAACAGAATTCAAGTCAG
1508611 AAATCAGA
1 AAATCAGA
1508619 TAAAATATTT
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 2 0.03
24 57 0.92
25 3 0.05
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.18
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAG
Found at i:1513172 original size:17 final size:17
Alignment explanation
Indices: 1513150--1513190 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1513140 TTTTTTTTAA
*
1513150 TTTAAACCTCTAAATTT
1 TTTAAAACTCTAAATTT
* *
1513167 TTTAAAATTTTAAATTT
1 TTTAAAACTCTAAATTT
1513184 TTTAAAA
1 TTTAAAA
1513191 TTTTAAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAAACTCTAAATTT
Found at i:1513191 original size:17 final size:17
Alignment explanation
Indices: 1513160--1513196 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1513150 TTTAAACCTC
1513160 TAAATTTTTTAAAATTT
1 TAAATTTTTTAAAATTT
1513177 TAAATTTTTTAAAATTT
1 TAAATTTTTTAAAATTT
1513194 TAA
1 TAA
1513197 GTTGACCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAATTTTTTAAAATTT
Found at i:1513723 original size:11 final size:11
Alignment explanation
Indices: 1513709--1513734 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1513699 TATATAAATT
1513709 AATTATAGTAG
1 AATTATAGTAG
1513720 AATTATAGTAG
1 AATTATAGTAG
1513731 AATT
1 AATT
1513735 CAACTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (11 bp):
AATTATAGTAG
Found at i:1513987 original size:23 final size:23
Alignment explanation
Indices: 1513960--1514006 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1513950 GGATTCACCC
1513960 GGGAATGGAATCCACATTTTCCT
1 GGGAATGGAATCCACATTTTCCT
1513983 GGGAATGGAATCCACATTTTCCT
1 GGGAATGGAATCCACATTTTCCT
1514006 G
1 G
1514007 TTTGATTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (23 bp):
GGGAATGGAATCCACATTTTCCT
Found at i:1515356 original size:31 final size:31
Alignment explanation
Indices: 1515321--1515406 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
1515311 AAATTACATA
* * *
1515321 TTTAATACATAAATTATGAATTTTAATCTGT
1 TTTAATACATAAATTATTAATTTTAATCCGG
***
1515352 TTTAATTTTTAAATTATTAATTTTAATCCGG
1 TTTAATACATAAATTATTAATTTTAATCCGG
*
1515383 TTTAATACATAAATTTTTAATTTT
1 TTTAATACATAAATTATTAATTTT
1515407 TTTAAATTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (31 bp):
TTTAATACATAAATTATTAATTTTAATCCGG
Found at i:1519455 original size:19 final size:19
Alignment explanation
Indices: 1519431--1519480 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1519421 ATGCATTTTC
*
1519431 AATTATTATATTAAAAATA
1 AATTATAATATTAAAAATA
*
1519450 AATTATAATATTAAAAATC
1 AATTATAATATTAAAAATA
1519469 AATTATAA-ATTA
1 AATTATAATATTA
1519481 TGATAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTATAATATTAAAAATA
Found at i:1524646 original size:15 final size:14
Alignment explanation
Indices: 1524595--1524647 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
1524585 AAGTCAACGG
* *
1524595 GTTGACTCGGATGA
1 GTTGACTCAGACGA
*
1524609 GTTGACTCAGACGG
1 GTTGACTCAGACGA
*
1524623 GTTGGCTCAGACCGA
1 GTTGACTCAGA-CGA
1524638 GTTGACTCAG
1 GTTGACTCAG
1524648 TGACTGGACT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:1528684 original size:4 final size:4
Alignment explanation
Indices: 1528675--1528700 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1528665 ATTTTGATAC
1528675 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
1528701 CTCACATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1529007 original size:19 final size:18
Alignment explanation
Indices: 1528980--1529018 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1528970 CAAGTATTTG
*
1528980 ATATGCATAATATATATAT
1 ATATACATAATAT-TATAT
1528999 ATATACATAATATTATAT
1 ATATACATAATATTATAT
1529017 AT
1 AT
1529019 TTAAATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATACATAATATTATAT
Found at i:1532887 original size:16 final size:14
Alignment explanation
Indices: 1532856--1532899 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
1532846 ACCAAAGAAT
1532856 TTTATTTTTGCTAC
1 TTTATTTTTGCTAC
1532870 TTTATTTTTAGTCTAC
1 TTTATTTTT-G-CTAC
1532886 TTGATATTTTTGCT
1 TT--TATTTTTGCT
1532900 TTATTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.35
15 1 0.04
16 8 0.31
17 1 0.04
18 7 0.27
ACGTcount: A:0.16, C:0.11, G:0.09, T:0.64
Consensus pattern (14 bp):
TTTATTTTTGCTAC
Found at i:1536918 original size:6 final size:6
Alignment explanation
Indices: 1536907--1536932 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1536897 TATTCTTTCA
1536907 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
1536933 GCTTTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:1545005 original size:3 final size:3
Alignment explanation
Indices: 1544997--1545048 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
1544987 TTATCTGGGT
*
1544997 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TG TTA TT- TT- TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1545041 TTT TTA TT
1 TTA TTA TT
1545049 TACAGAACCC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:1546229 original size:47 final size:47
Alignment explanation
Indices: 1546176--1546317 Score: 275
Period size: 47 Copynumber: 3.0 Consensus size: 47
1546166 AAACAATATT
1546176 ACCTTTGAAATTAAGAAAATAAGAATATAATGACAAATAATAAATGC
1 ACCTTTGAAATTAAGAAAATAAGAATATAATGACAAATAATAAATGC
*
1546223 ACCTTTGAAATTAAGAAAATAAAAATATAATGACAAATAATAAATGC
1 ACCTTTGAAATTAAGAAAATAAGAATATAATGACAAATAATAAATGC
1546270 ACCTTTGAAATTAAGAAAATAAGAATATAATGACAAATAATAAATGC
1 ACCTTTGAAATTAAGAAAATAAGAATATAATGACAAATAATAAATGC
1546317 A
1 A
1546318 ATGGATGCAA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 93 1.00
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.25
Consensus pattern (47 bp):
ACCTTTGAAATTAAGAAAATAAGAATATAATGACAAATAATAAATGC
Found at i:1546952 original size:2 final size:2
Alignment explanation
Indices: 1546945--1546974 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1546935 ATATTTTTAA
1546945 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1546975 ATAGTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1550157 original size:3 final size:3
Alignment explanation
Indices: 1550151--1550181 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1550141 AGCTGAAGTT
1550151 GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1550182 GATAAGGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1550843 original size:13 final size:13
Alignment explanation
Indices: 1550827--1550884 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
1550817 ATGATAAAAT
1550827 ATTAATTATGATA
1 ATTAATTATGATA
1550840 ATTAAATTA--ATA
1 ATT-AATTATGATA
* *
1550852 AATATATT-TAATA
1 ATTA-ATTATGATA
1550865 TATTAATTATGATA
1 -ATTAATTATGATA
1550879 ATTAAT
1 ATTAAT
1550885 ATACTTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
11 1 0.03
12 8 0.22
13 15 0.42
14 12 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
ATTAATTATGATA
Found at i:1550845 original size:21 final size:21
Alignment explanation
Indices: 1550821--1550883 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1550811 AATGTTATGA
1550821 TAAAATATTAATTATGATAAT
1 TAAAATATTAATTATGATAAT
* * *
1550842 TAAATTAATAA--AT-ATATT
1 TAAAATATTAATTATGATAAT
*
1550860 TAATATATTAATTATGATAAT
1 TAAAATATTAATTATGATAAT
1550881 TAA
1 TAA
1550884 TATACTTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
18 12 0.38
19 2 0.06
20 2 0.06
21 16 0.50
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TAAAATATTAATTATGATAAT
Found at i:1550904 original size:14 final size:14
Alignment explanation
Indices: 1550885--1551021 Score: 124
Period size: 14 Copynumber: 9.6 Consensus size: 14
1550875 GATAATTAAT
*
1550885 ATACTTTATAATTA
1 ATACTTTATATTTA
1550899 ATAC-TTATATTTA
1 ATACTTTATATTTA
1550912 TATACTTTAATATTTA
1 -ATACTTT-ATATTTA
*
1550928 ATA-TTTAATACTT-
1 ATACTTT-ATATTTA
1550941 ATA-TTATATAGTTTA
1 ATACTT-TATA-TTTA
1550956 ATACTTTATA-TTA
1 ATACTTTATATTTA
*
1550969 TATACTTTAGTACTTA
1 -ATACTTTA-TATTTA
1550985 TATACTTTATATTTA
1 -ATACTTTATATTTA
1551000 ATAC-TTATATTTA
1 ATACTTTATATTTA
1551013 TATACTTTA
1 -ATACTTTA
1551022 ATACTTATAT
Statistics
Matches: 107, Mismatches: 4, Indels: 23
0.80 0.03 0.17
Matches are distributed among these distances:
13 28 0.26
14 36 0.34
15 22 0.21
16 21 0.20
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (14 bp):
ATACTTTATATTTA
Found at i:1550982 original size:8 final size:7
Alignment explanation
Indices: 1550884--1551074 Score: 80
Period size: 7 Copynumber: 26.6 Consensus size: 7
1550874 TGATAATTAA
1550884 TATACTT
1 TATACTT
*
1550891 TATAATT
1 TATACTT
*
1550898 AATAC-T
1 TATACTT
*
1550904 TATATTT
1 TATACTT
1550911 ATATACTT
1 -TATACTT
1550919 TAATA-TT
1 T-ATACTT
1550926 TAATA-TT
1 T-ATACTT
1550933 TAATAC-T
1 T-ATACTT
1550940 TATA-TT
1 TATACTT
*
1550946 ATATAGTT
1 -TATACTT
1550954 TAATACTT
1 T-ATACTT
1550962 TATA-TT
1 TATACTT
1550968 ATATACTT
1 -TATACTT
1550976 TAGTACTT
1 TA-TACTT
1550984 ATATACTT
1 -TATACTT
1550992 TATA-TT
1 TATACTT
1550998 TAATAC-T
1 T-ATACTT
*
1551005 TATATTT
1 TATACTT
1551012 ATATACTT
1 -TATACTT
1551020 TAATAC-T
1 T-ATACTT
1551027 TATA-TT
1 TATACTT
* *
1551033 CAAACACTT
1 --TATACTT
1551042 TATTACTT
1 TA-TACTT
1551050 TATA-TT
1 TATACTT
* *
1551056 AAATATTT
1 -TATACTT
1551064 TATACTT
1 TATACTT
1551071 TATA
1 TATA
1551075 TATAAAGTGC
Statistics
Matches: 144, Mismatches: 16, Indels: 48
0.69 0.08 0.23
Matches are distributed among these distances:
6 22 0.15
7 69 0.48
8 49 0.34
9 4 0.03
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.53
Consensus pattern (7 bp):
TATACTT
Found at i:1551049 original size:44 final size:43
Alignment explanation
Indices: 1550883--1551034 Score: 154
Period size: 44 Copynumber: 3.5 Consensus size: 43
1550873 ATGATAATTA
* * *
1550883 ATATACTTT-ATAATTA-ATACTTATATTTATATACTTTAATATTT
1 ATATACTTTAATACTTATATTCATATATTTA-ATAC-TT-ATATTT
1550927 A-ATA-TTTAATACTTATATT-ATATAGTTTAATACTT-TATATT
1 ATATACTTTAATACTTATATTCATATA-TTTAATACTTATAT-TT
* * *
1550968 ATATACTTTAGTACTTATATACTTTATATTTAATACTTATATTT
1 ATATACTTTAATACTTATATTC-ATATATTTAATACTTATATTT
1551012 ATATACTTTAATACTTATATTCA
1 ATATACTTTAATACTTATATTCA
1551035 AACACTTTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
40 3 0.03
41 3 0.03
42 8 0.09
43 30 0.33
44 39 0.43
45 7 0.08
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (43 bp):
ATATACTTTAATACTTATATTCATATATTTAATACTTATATTT
Found at i:1551074 original size:44 final size:41
Alignment explanation
Indices: 1550904--1551078 Score: 158
Period size: 44 Copynumber: 4.1 Consensus size: 41
1550894 AATTAATACT
*
1550904 TATATTTATATACTTTAATATTTAATATTTAATACTTATATTA
1 TATATTTA-ATACTTT-ATATTAAATATTTAATACTTATATTA
* * *
1550947 TATAGTTTAATACTTTATATTATATACTTTAGTACTTATATACTT
1 TATA-TTTAATACTTTATATTAAATA-TTTAATACTTATAT--TA
*
1550992 TATATTTAATAC-TTATATTTATATACTTTAATACTTATATTCA
1 TATATTTAATACTTTATA-TTAAATA-TTTAATACTTATATT-A
* * * *
1551035 AACACTTTATTACTTTATATTAAATATTTTATACTT-TA-TA
1 TATA-TTTAATACTTTATATTAAATATTTAATACTTATATTA
1551075 TATA
1 TATA
1551079 AAGTGCCAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
40 3 0.03
41 1 0.01
42 11 0.10
43 40 0.36
44 46 0.41
45 10 0.09
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (41 bp):
TATATTTAATACTTTATATTAAATATTTAATACTTATATTA
Found at i:1551080 original size:22 final size:20
Alignment explanation
Indices: 1550905--1551080 Score: 127
Period size: 22 Copynumber: 8.1 Consensus size: 20
1550895 ATTAATACTT
*
1550905 ATATTTATATACTTTAATATTTA
1 ATATTTA-ATAC-TT-ATATTAA
*
1550928 ATATTTAATACTTATATTAT
1 ATATTTAATACTTATATTAA
*
1550948 ATAGTTTAATACTTTATATTAT
1 ATA-TTTAATAC-TTATATTAA
* **
1550970 ATACTTTAGTACTTATATACTTT
1 ATA-TTTAATACTTATAT--TAA
*
1550993 ATATTTAATACTTATATTTAT
1 ATATTTAATACTTATA-TTAA
1551014 ATACTTTAATACTTATATTCAA
1 ATA-TTTAATACTTATATT-AA
* *
1551036 ACACTTTATTACTTTATATTAA
1 ATA-TTTAATAC-TTATATTAA
*
1551058 ATATTTTATACTTTATATATAA
1 ATATTTAATAC-TTATAT-TAA
1551080 A
1 A
1551081 GTGCCAAATT
Statistics
Matches: 131, Mismatches: 13, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.06
21 36 0.27
22 67 0.51
23 20 0.15
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (20 bp):
ATATTTAATACTTATATTAA
Found at i:1552602 original size:8 final size:8
Alignment explanation
Indices: 1552589--1552639 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
1552579 ACATGCATCC
1552589 TATATACA
1 TATATACA
1552597 TATATACA
1 TATATACA
**
1552605 TGCAT-CA
1 TATATACA
*
1552612 TACATACA
1 TATATACA
1552620 TATATACA
1 TATATACA
*
1552628 TACATA-A
1 TATATACA
1552635 TATAT
1 TATAT
1552640 GAATATAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
7 11 0.31
8 25 0.69
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (8 bp):
TATATACA
Found at i:1552607 original size:23 final size:23
Alignment explanation
Indices: 1552577--1552628 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1552567 TAAAATTTTA
* *
1552577 ATACATGCATCCTATATACATAT
1 ATACATGCATCATACATACATAT
1552600 ATACATGCATCATACATACATAT
1 ATACATGCATCATACATACATAT
1552623 ATACAT
1 ATACAT
1552629 ACATAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (23 bp):
ATACATGCATCATACATACATAT
Found at i:1552619 original size:4 final size:4
Alignment explanation
Indices: 1552592--1552633 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
1552582 TGCATCCTAT
* * *
1552592 ATAC ATAT ATAC ATGC AT-C ATAC ATAC ATAT ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1552634 ATATATGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:1552646 original size:23 final size:23
Alignment explanation
Indices: 1552592--1552636 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1552582 TGCATCCTAT
* *
1552592 ATACATATATACATGCATCATAC
1 ATACATATATACATACATAATAC
1552615 ATACATATATACATACATAATA
1 ATACATATATACATACATAATA
1552637 TATGAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (23 bp):
ATACATATATACATACATAATAC
Found at i:1552907 original size:14 final size:14
Alignment explanation
Indices: 1552890--1552935 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1552880 TATATATTAG
1552890 GGTTTATAGTTTAT
1 GGTTTATAGTTTAT
1552904 GGTTTAGT-GTTTAT
1 GGTTTA-TAGTTTAT
* *
1552918 AGTTTAAAGTTTA-
1 GGTTTATAGTTTAT
1552931 GGTTT
1 GGTTT
1552936 TAAGGCTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.15
14 22 0.81
15 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (14 bp):
GGTTTATAGTTTAT
Found at i:1552929 original size:21 final size:20
Alignment explanation
Indices: 1552890--1552935 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1552880 TATATATTAG
**
1552890 GGTTTATAGTTTATGGTTTA
1 GGTTTATAGTTTAAAGTTTA
1552910 GTGTTTATAGTTTAAAGTTTA
1 G-GTTTATAGTTTAAAGTTTA
1552931 GGTTT
1 GGTTT
1552936 TAAGGCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (20 bp):
GGTTTATAGTTTAAAGTTTA
Found at i:1552937 original size:21 final size:21
Alignment explanation
Indices: 1552886--1552937 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1552876 AATATATATA
* **
1552886 TTAGGGTTTATAGTTTATGGT
1 TTAGGTTTTATAGTTTAAAGT
1552907 TTA-GTGTTTATAGTTTAAAGT
1 TTAGGT-TTTATAGTTTAAAGT
1552928 TTAGGTTTTA
1 TTAGGTTTTA
1552938 AGGCTTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (21 bp):
TTAGGTTTTATAGTTTAAAGT
Found at i:1553013 original size:17 final size:17
Alignment explanation
Indices: 1552991--1553039 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 17
1552981 TAATTTACTT
1552991 TATATAGTTTATATATA
1 TATATAGTTTATATATA
1553008 TATATAGGTTATATATATA
1 TATATA-GTT-TATATATA
1553027 TATATAGTTTATA
1 TATATAGTTTATA
1553040 AGAAATGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 14 0.47
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:1553039 original size:15 final size:17
Alignment explanation
Indices: 1552991--1553030 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1552981 TAATTTACTT
*
1552991 TATATAGTTTATATATA
1 TATATAGTGTATATATA
1553008 TATATAG-GTTATATATA
1 TATATAGTG-TATATATA
1553025 TATATA
1 TATATA
1553031 TAGTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
TATATAGTGTATATATA
Found at i:1553584 original size:15 final size:15
Alignment explanation
Indices: 1553564--1553600 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1553554 TAATTTACTT
1553564 TATATAGTTCATATA
1 TATATAGTTCATATA
*
1553579 TATATAGTTTATATA
1 TATATAGTTCATATA
1553594 TACTATA
1 TA-TATA
1553601 CATGGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (15 bp):
TATATAGTTCATATA
Found at i:1553702 original size:21 final size:21
Alignment explanation
Indices: 1553649--1553705 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1553639 AGTTAAGGGG
*
1553649 TTAGGGGTTAGGGTTAAAGAT
1 TTAGGGTTTAGGGTTAAAGAT
* * * * *
1553670 TAAAGGTATAGGGTTCATGAT
1 TTAGGGTTTAGGGTTAAAGAT
1553691 TTAGGGTTTAGGGTT
1 TTAGGGTTTAGGGTT
1553706 TTTATAAACT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.02, G:0.35, T:0.37
Consensus pattern (21 bp):
TTAGGGTTTAGGGTTAAAGAT
Found at i:1553767 original size:2 final size:2
Alignment explanation
Indices: 1553756--1553794 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1553746 ACAGTGTTTC
*
1553756 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1553795 GATTACTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1554160 original size:2 final size:2
Alignment explanation
Indices: 1554153--1554386 Score: 105
Period size: 2 Copynumber: 117.0 Consensus size: 2
1554143 ACTTTGAATA
*
1554153 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT -T A- AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * * * *
1554194 -T AT AGT TT AT AA ACT AT AT ACT TT TT AT AGT TT AT AC AT AT AT
1 AT AT A-T AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT
* * * * *
1554237 AGT TT AC AT AT AT AT AGT TT AC AT AT AT AGT TT AT AT AT AT AGT
1 A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T
* * * *
1554281 -T CAT AT AA AC AT A- AT TT AT AT AT AT AT AT CT -T AT A- AT A-
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1554319 AT -T TT AT AGT TT AT AT AT AA ACT -T AT AT -T AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
1554360 AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1554387 TTTTCAATTT
Statistics
Matches: 175, Mismatches: 33, Indels: 48
0.68 0.13 0.19
Matches are distributed among these distances:
1 12 0.07
2 151 0.86
3 12 0.07
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1554239 original size:15 final size:15
Alignment explanation
Indices: 1554219--1554281 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 15
1554209 ATATACTTTT
1554219 TATAGTTTATACATA
1 TATAGTTTATACATA
* *
1554234 TATAGTTTACATATA
1 TATAGTTTATACATA
1554249 TATAG-TT-TACATA
1 TATAGTTTATACATA
1554262 TATAGTTTAT--ATA
1 TATAGTTTATACATA
1554275 TATAGTT
1 TATAGTT
1554282 CATATAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
13 19 0.45
14 4 0.10
15 19 0.45
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:1554286 original size:13 final size:13
Alignment explanation
Indices: 1554231--1554287 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
1554221 TAGTTTATAC
1554231 ATATATAGTTTACAT
1 ATATATAG-TT-CAT
* *
1554246 ATATATAGTTTAC
1 ATATATAGTTCAT
*
1554259 ATATATAGTTTAT
1 ATATATAGTTCAT
1554272 ATATATAGTTCAT
1 ATATATAGTTCAT
1554285 ATA
1 ATA
1554288 AACATAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
13 28 0.74
14 2 0.05
15 8 0.21
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (13 bp):
ATATATAGTTCAT
Found at i:1554287 original size:11 final size:13
Alignment explanation
Indices: 1554228--1554281 Score: 81
Period size: 13 Copynumber: 4.0 Consensus size: 13
1554218 TTATAGTTTA
1554228 TACATATATAGTT
1 TACATATATAGTT
1554241 TACATATATATAGTT
1 TAC--ATATATAGTT
1554256 TACATATATAGTT
1 TACATATATAGTT
*
1554269 TATATATATAGTT
1 TACATATATAGTT
1554282 CATATAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
13 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (13 bp):
TACATATATAGTT
Found at i:1554287 original size:15 final size:15
Alignment explanation
Indices: 1554219--1554380 Score: 112
Period size: 15 Copynumber: 11.3 Consensus size: 15
1554209 ATATACTTTT
*
1554219 TATAGTTTATACATA
1 TATAGTTTATATATA
*
1554234 TATAGTTTACATATA
1 TATAGTTTATATATA
*
1554249 TATAG-TT-TACATA
1 TATAGTTTATATATA
1554262 TATAG-TT-TATATA
1 TATAGTTTATATATA
* *
1554275 TATAGTTCATATAAA
1 TATAGTTTATATATA
* *
1554290 CATAATTTATATATA
1 TATAGTTTATATATA
*
1554305 TATA-TCTTATAATAATTT
1 TATAGT-TTAT-AT-A-TA
1554323 TATAGTTTATATATA
1 TATAGTTTATATATA
*
1554338 -A-A-CTTATAT-TA
1 TATAGTTTATATATA
*
1554349 TATA-TATATATATA
1 TATAGTTTATATATA
*
1554363 TATA-TATATATATA
1 TATAGTTTATATATA
1554377 TATA
1 TATA
1554381 TTATATTTTT
Statistics
Matches: 120, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
11 2 0.02
12 7 0.06
13 28 0.23
14 25 0.21
15 42 0.35
16 3 0.03
17 3 0.03
18 9 0.08
19 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (15 bp):
TATAGTTTATATATA
Found at i:1554386 original size:50 final size:49
Alignment explanation
Indices: 1554244--1554386 Score: 121
Period size: 52 Copynumber: 2.8 Consensus size: 49
1554234 TATAGTTTAC
* * *
1554244 ATATATATAGTTTACATATATAGTTTATATATATAGTTCATATAAACATAATT
1 ATATATATA-TATATATATATA-TATATATATATA-TT-ATATAAACATAATT
* * * *
1554297 -TATATATATATATCT-TATA-ATAATTTTATAGTTTATATATAAACTTATATT
1 ATATATATATATATATATATATAT-A-TATATA-TAT-TATATAAACATA-ATT
1554348 ATATATATATATATATATATATATATATATATATTATAT
1 ATATATATATATATATATATATATATATATATATTATAT
1554387 TTTTCAATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 25 0.35
51 11 0.15
52 27 0.38
53 5 0.07
54 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (49 bp):
ATATATATATATATATATATATATATATATATATTATATAAACATAATT
Found at i:1556304 original size:11 final size:11
Alignment explanation
Indices: 1556288--1556350 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
1556278 GTATTATAGA
1556288 ATTTTTAATAT
1 ATTTTTAATAT
1556299 ATTTTTAA-A-
1 ATTTTTAATAT
1556308 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
1556319 ATCAATAATGT
1 ATTTTTAATAT
1556330 ATTTTTAATAT
1 ATTTTTAATAT
1556341 ATTTTTAATA
1 ATTTTTAATA
1556351 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:1562919 original size:21 final size:21
Alignment explanation
Indices: 1562895--1562955 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
1562885 GGCAACCAAC
1562895 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
1562916 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
1562931 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
1562952 TTTG
1 TTTG
1562956 GTAAAGTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
17 4 0.13
19 4 0.13
21 13 0.43
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:1562941 original size:36 final size:35
Alignment explanation
Indices: 1562894--1562964 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
1562884 TGGCAACCAA
1562894 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1562930 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1562965 GGTAGATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
Found at i:1564361 original size:31 final size:30
Alignment explanation
Indices: 1564294--1564363 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1564284 TTAACGGCTA
* ***
1564294 AGGGACTAAAATCTAACGGATCGGTAACGTT
1 AGGGACT-AAATCGAACGGATCAACAACGTT
*
1564325 AGGGACTAAATCGAACGGATCAACAATGTT
1 AGGGACTAAATCGAACGGATCAACAACGTT
1564355 AGGGGACTA
1 A-GGGACTA
1564364 TTCGCGTAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (30 bp):
AGGGACTAAATCGAACGGATCAACAACGTT
Found at i:1564675 original size:18 final size:17
Alignment explanation
Indices: 1564635--1564676 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1564625 TGATTAAGCG
*
1564635 CTGAATGATTCAAATGT
1 CTGAATGATTCAAAGGT
*
1564652 -TGAATGATTCAGAGGCT
1 CTGAATGATTCAAAGG-T
1564669 CTGAATGA
1 CTGAATGA
1564677 ATTAGCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (17 bp):
CTGAATGATTCAAAGGT
Found at i:1565512 original size:15 final size:15
Alignment explanation
Indices: 1565492--1565520 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1565482 CTTAATCATT
1565492 TGAATAACGAGGTTA
1 TGAATAACGAGGTTA
1565507 TGAATAACGAGGTT
1 TGAATAACGAGGTT
1565521 CAATGGGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (15 bp):
TGAATAACGAGGTTA
Found at i:1575490 original size:39 final size:39
Alignment explanation
Indices: 1575447--1575521 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
1575437 GGGCCTTAAC
*
1575447 GGGCTTGCTGGGTTAGG-TTTGCTTCGGTTGGGCTTTGTT
1 GGGCTTGCTGGGTCAGGCTTT-CTTCGGTTGGGCTTTGTT
1575486 GGGCTTGCTGGGTCAGGCTTTCTTCGGTTGGGCTTT
1 GGGCTTGCTGGGTCAGGCTTTCTTCGGTTGGGCTTT
1575522 ATTGTTGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 31 0.91
40 3 0.09
ACGTcount: A:0.03, C:0.16, G:0.40, T:0.41
Consensus pattern (39 bp):
GGGCTTGCTGGGTCAGGCTTTCTTCGGTTGGGCTTTGTT
Found at i:1575587 original size:3 final size:3
Alignment explanation
Indices: 1575573--1575628 Score: 51
Period size: 3 Copynumber: 17.3 Consensus size: 3
1575563 TAAAACCGAA
*
1575573 AAT AAT ATT AAT AAT AAT -AT AAT AAAT ATAT AAT AAT AAAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT -AAT AAT -AAT
1575621 ATAT AAT A
1 A-AT AAT A
1575629 TAAATATACT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
2 2 0.04
3 28 0.62
4 15 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1575653 original size:7 final size:7
Alignment explanation
Indices: 1575574--1575812 Score: 147
Period size: 7 Copynumber: 33.4 Consensus size: 7
1575564 AAAACCGAAA
1575574 ATAATAT
1 ATAATAT
1575581 -TAATA-
1 ATAATAT
1575586 ATAATAT
1 ATAATAT
1575593 AATAAATAT
1 -AT-AATAT
1575602 ATAATA-
1 ATAATAT
1575608 ATAA-AT
1 ATAATAT
1575614 AATAAATAT
1 -AT-AATAT
1575623 ATAATAT
1 ATAATAT
1575630 A-AATAT
1 ATAATAT
*
1575636 ACT-A-CT
1 A-TAATAT
1575642 ATAATAT
1 ATAATAT
1575649 ATAATA-
1 ATAATAT
*
1575655 AGTATATGCT
1 A-TA-AT-AT
1575665 ATAATAT
1 ATAATAT
1575672 ATAATAT
1 ATAATAT
*
1575679 AT-ACAT
1 ATAATAT
* *
1575685 GTGATAT
1 ATAATAT
1575692 ATAATAT
1 ATAATAT
1575699 ATAAATAT
1 AT-AATAT
*
1575707 ATATTAT
1 ATAATAT
*
1575714 AATAATAAG
1 -ATAAT-AT
*
1575723 ATAATGT
1 ATAATAT
*
1575730 ATAATGT
1 ATAATAT
1575737 ATAATAT
1 ATAATAT
1575744 ATAATAT
1 ATAATAT
*
1575751 ATACTAT
1 ATAATAT
1575758 ATATATAAT
1 ATA-AT-AT
1575767 ATTAAATAT
1 A-T-AATAT
*
1575776 ATTATAT
1 ATAATAT
*
1575783 ATACTAT
1 ATAATAT
*
1575790 AT-ATTT
1 ATAATAT
*
1575796 ATACTAT
1 ATAATAT
1575803 ATAATAT
1 ATAATAT
1575810 ATA
1 ATA
1575813 CTATCCCAGA
Statistics
Matches: 182, Mismatches: 25, Indels: 50
0.71 0.10 0.19
Matches are distributed among these distances:
5 2 0.01
6 32 0.18
7 97 0.53
8 30 0.16
9 16 0.09
10 4 0.02
11 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:1575680 original size:2 final size:2
Alignment explanation
Indices: 1575589--1575812 Score: 98
Period size: 2 Copynumber: 119.5 Consensus size: 2
1575579 ATTAATAATA
* * *
1575589 AT AT A- AT AA AT AT AT A- AT A- AT AA AT A- AT AA 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 AT
* *
1575626 AT AT AA AT AT ACT ACT AT A- AT AT AT A- AT A- AGT AT AT GCT AT
1 AT AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT A-T AT AT -AT AT
* * *
1575667 A- AT AT AT A- AT AT AT AC AT GT GAT AT AT A- AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
* * *
1575707 AT AT -T AT A- AT A- AT A- AG AT A- AT GT AT A- AT GT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1575742 AT AT A- AT AT AT ACT AT AT AT AT A- AT AT -T AA AT AT AT -T AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1575781 AT AT ACT AT AT AT TT AT ACT AT AT A- AT AT AT A
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT A
1575813 CTATCCCAGA
Statistics
Matches: 167, Mismatches: 25, Indels: 60
0.66 0.10 0.24
Matches are distributed among these distances:
1 23 0.14
2 130 0.78
3 14 0.08
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1575742 original size:65 final size:69
Alignment explanation
Indices: 1575619--1575776 Score: 200
Period size: 72 Copynumber: 2.3 Consensus size: 69
1575609 TAAATAATAA
1575619 ATATATAATATAAATATACTACTATAATATATAATAAGTATATGCTATAATATATAATATATACA
1 ATATATAATATAAATATACTACTATAATATATAATAAGTATATGCTATAATATATAATATATACA
1575684 TGTG
66 TGTG
*
1575688 ATATATAATATATAAATATA-TATTATAATA-ATAAGATAATGTATAATG-TATAATATATAATA
1 ATATAT-A-ATATAAATATACTACTATAATATAT-A-ATAA-GTAT-ATGCTATAATATATAATA
*
1575750 TATAC-TAT-
60 TATACATGTG
1575758 ATATATAATATTAAATATA
1 ATATATAATA-TAAATATA
1575777 TTATATATAC
Statistics
Matches: 80, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
68 3 0.04
69 17 0.21
70 17 0.21
71 17 0.21
72 23 0.29
73 3 0.04
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (69 bp):
ATATATAATATAAATATACTACTATAATATATAATAAGTATATGCTATAATATATAATATATACA
TGTG
Found at i:1585090 original size:43 final size:43
Alignment explanation
Indices: 1585043--1585262 Score: 183
Period size: 43 Copynumber: 5.1 Consensus size: 43
1585033 GATATAGCGA
*
1585043 CGTTTGTCCAAT-AATAGCCGTAATAGGTGTTAAGATTTAGTGG
1 CGTTTGTCCAATAAAT-GCCGCAATAGGTGTTAAGATTTAGTGG
* * **
1585086 CGTTTGTCCAATAAATGTCGCAATAGGTGTTGAGATTTAGCAG
1 CGTTTGTCCAATAAATGCCGCAATAGGTGTTAAGATTTAGTGG
* * * * * * * **
1585129 CTTTTTTCCCACAAACGCCTCAATAGGTGTTGAGATTTAGCAG
1 CGTTTGTCCAATAAATGCCGCAATAGGTGTTAAGATTTAGTGG
* * * * * *
1585172 TGTTTTTTCCCATAAATGCCGCAATTGGTGTTGAGATTTAGCGG
1 CG-TTTGTCCAATAAATGCCGCAATAGGTGTTAAGATTTAGTGG
* * * * *
1585216 CGTTT-TCCCACAAATGCCACAATAGGTGTTGAGATTTAGCGG
1 CGTTTGTCCAATAAATGCCGCAATAGGTGTTAAGATTTAGTGG
1585258 CGTTT
1 CGTTT
1585263 TTCCTGAAAC
Statistics
Matches: 152, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
42 39 0.26
43 73 0.48
44 40 0.26
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (43 bp):
CGTTTGTCCAATAAATGCCGCAATAGGTGTTAAGATTTAGTGG
Found at i:1585202 original size:44 final size:43
Alignment explanation
Indices: 1585098--1585264 Score: 219
Period size: 44 Copynumber: 3.9 Consensus size: 43
1585088 TTTGTCCAAT
* *
1585098 AAATGTCGCAATAGGTGTTGAGATTTAGCAGCTTTTTTCCCAC
1 AAATGCCGCAATAGGTGTTGAGATTTAGCAGGTTTTTTCCCAC
* * *
1585141 AAACGCCTCAATAGGTGTTGAGATTTAGCAGTGTTTTTTCCCAT
1 AAATGCCGCAATAGGTGTTGAGATTTAGCAG-GTTTTTTCCCAC
* **
1585185 AAATGCCGCAATTGGTGTTGAGATTTAGC-GGCGTTTTCCCAC
1 AAATGCCGCAATAGGTGTTGAGATTTAGCAGGTTTTTTCCCAC
* *
1585227 AAATGCCACAATAGGTGTTGAGATTTAGCGGCGTTTTT
1 AAATGCCGCAATAGGTGTTGAGATTTAGCAG-GTTTTT
1585265 CCTGAAACGC
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 36 0.34
43 30 0.28
44 40 0.38
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (43 bp):
AAATGCCGCAATAGGTGTTGAGATTTAGCAGGTTTTTTCCCAC
Found at i:1585263 original size:86 final size:87
Alignment explanation
Indices: 1585064--1585264 Score: 280
Period size: 86 Copynumber: 2.3 Consensus size: 87
1585054 TAATAGCCGT
* * * *
1585064 AATAGGTGTTAAGATTTAGTGGCG-TTTGTCCAATAAATGTCGCAATAGGTGTTGAGATTTAGCA
1 AATAGGTGTTGAGATTTAGCGGCGTTTTTTCCAATAAATGCCGCAATAGGTGTTGAGATTTAGCA
* *
1585128 GCTTTTTTCCCACAAACGCCTC
66 GCTGTTTTCCCACAAACGCCAC
* * * * *
1585150 AATAGGTGTTGAGATTTAGCAGTGTTTTTTCCCATAAATGCCGCAATTGGTGTTGAGATTTAGCG
1 AATAGGTGTTGAGATTTAGCGGCGTTTTTTCCAATAAATGCCGCAATAGGTGTTGAGATTTAGCA
*
1585215 GC-GTTTTCCCACAAATGCCAC
66 GCTGTTTTCCCACAAACGCCAC
1585236 AATAGGTGTTGAGATTTAGCGGCGTTTTT
1 AATAGGTGTTGAGATTTAGCGGCGTTTTT
1585265 CCTGAAACGC
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 63 0.63
87 37 0.37
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (87 bp):
AATAGGTGTTGAGATTTAGCGGCGTTTTTTCCAATAAATGCCGCAATAGGTGTTGAGATTTAGCA
GCTGTTTTCCCACAAACGCCAC
Found at i:1585406 original size:43 final size:43
Alignment explanation
Indices: 1585306--1585432 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
1585296 GCGATGATTT
* * * * * * *
1585306 TACAAACGCCTCAAAAGGTTAAGATATTTCGCGGCGTATTTCGGA
1 TACAAACACCGCAAAAGG-TATGATATATAGCGGCAT-TTTAGGA
* * * *
1585351 TACAAACGCCGCAAAAGGTCTGGTATATAGTGGCATTTTAGGA
1 TACAAACACCGCAAAAGGTATGATATATAGCGGCATTTTAGGA
*
1585394 TACAAACACCGCAAAAGGTATGATATATAGCGGCGTTTT
1 TACAAACACCGCAAAAGGTATGATATATAGCGGCATTTT
1585433 TTTACAAACG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
43 40 0.59
44 11 0.16
45 17 0.25
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (43 bp):
TACAAACACCGCAAAAGGTATGATATATAGCGGCATTTTAGGA
Found at i:1585783 original size:21 final size:21
Alignment explanation
Indices: 1585757--1585808 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1585747 TGCTGATATC
1585757 CTGCTTCTCTATATACTGCCG
1 CTGCTTCTCTATATACTGCCG
* * * *
1585778 CTGCTTTTCTCTATGCTGTCG
1 CTGCTTCTCTATATACTGCCG
*
1585799 CTACTTCTCT
1 CTGCTTCTCT
1585809 CTGTCTTTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.10, C:0.33, G:0.13, T:0.44
Consensus pattern (21 bp):
CTGCTTCTCTATATACTGCCG
Found at i:1595743 original size:21 final size:22
Alignment explanation
Indices: 1595701--1595749 Score: 82
Period size: 21 Copynumber: 2.2 Consensus size: 22
1595691 TCATGTTTTC
1595701 AAAAGCTATTATTTTCCTATTTG
1 AAAA-CTATTATTTTCCTATTTG
1595724 AAAACTATTATTTT-CTATTTG
1 AAAACTATTATTTTCCTATTTG
1595745 AAAAC
1 AAAAC
1595750 AGAAAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 12 0.46
22 10 0.38
23 4 0.15
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (22 bp):
AAAACTATTATTTTCCTATTTG
Found at i:1596895 original size:20 final size:20
Alignment explanation
Indices: 1596866--1596914 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1596856 TGATTGAATC
* *
1596866 AGTATTGATACCGAAGGGTG
1 AGTATCGATACCGAAGGGGG
*
1596886 AGTATCGATATCGAAGGGGG
1 AGTATCGATACCGAAGGGGG
1596906 AGTATCGAT
1 AGTATCGAT
1596915 TTAGGTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.35, T:0.24
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGGG
Found at i:1598789 original size:20 final size:20
Alignment explanation
Indices: 1598764--1598814 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1598754 ATTGAATCAA
* *
1598764 TATCGATACCGAAGGG-GGAG
1 TATCGATACCAAAGGGAAG-G
1598784 TATCGATACCAAAGGGAAGG
1 TATCGATACCAAAGGGAAGG
1598804 TATCGATACCA
1 TATCGATACCA
1598815 TTTTGAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (20 bp):
TATCGATACCAAAGGGAAGG
Found at i:1599344 original size:54 final size:54
Alignment explanation
Indices: 1599245--1599506 Score: 389
Period size: 54 Copynumber: 4.9 Consensus size: 54
1599235 ATAATTATGT
* ** *
1599245 ATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGC
1 ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTAC
* * * *
1599299 ATTTAACAGAATTCATCATATGTGGATGAATAACCATTTTGGCACTAAGTGTGC
1 ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTAC
*
1599353 ATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTAC
1 ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTAC
* * * * *
1599407 ATTTCACAGAATTCATCCTATGTGGATGAATAACTGTTTCGACACTATGTGTAT
1 ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTAC
*
1599461 ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTGACACT
1 ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTGGCACT
1599507 TTGTGTGTAA
Statistics
Matches: 189, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 189 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (54 bp):
ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTAC
Found at i:1599561 original size:162 final size:162
Alignment explanation
Indices: 1599245--1599561 Score: 386
Period size: 162 Copynumber: 2.0 Consensus size: 162
1599235 ATAATTATGT
* *
1599245 ATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTAACAGAA
1 ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTACATTTAACAGAA
* *** * **
1599310 TTCATCATATGTGGATGAATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
66 TTCATCATATGTGGATGAATAACCATTTTGACACTAAGTGTGCAAAACACAGAATTCATAATATG
* *
1599375 TGGATGAATAACCGTTTTGGCACTAAGTGTAC
131 TGGATGAATAACCGTATGGGCACTAAGTGTAC
* * * *
1599407 ATTTCACAGAATTCATCCTATGTGGATGAATAACTGTTTC-GACACTATGTGTATATTTCACAGA
1 ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCAG-CACTAAGTGTACATTTAACAGA
* * ** * *
1599471 ATTCATCCTATGTGGATGAATAACCGTTTTGACACTTTGTGTGTAAAACATAGAATTCATAATAT
65 ATTCATCATATGTGGATGAATAACCATTTTGACACTAAGTGTGCAAAACACAGAATTCATAATAT
* * *
1599536 G-GTTATGAATGATCGTATGGGCACTA
130 GTG-GATGAATAACCGTATGGGCACTA
1599562 CAGGTGCATT
Statistics
Matches: 129, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
161 2 0.02
162 127 0.98
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (162 bp):
ATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTACATTTAACAGAA
TTCATCATATGTGGATGAATAACCATTTTGACACTAAGTGTGCAAAACACAGAATTCATAATATG
TGGATGAATAACCGTATGGGCACTAAGTGTAC
Found at i:1603138 original size:23 final size:22
Alignment explanation
Indices: 1603106--1603148 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1603096 ATTGAATAAA
* *
1603106 ATAAATAAAAATTAAAGAAAAAT
1 ATAAAGAAAAAATAAA-AAAAAT
1603129 ATAAAGAAAAAATAAAAAAA
1 ATAAAGAAAAAATAAAAAAA
1603149 TTATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (22 bp):
ATAAAGAAAAAATAAAAAAAAT
Found at i:1603141 original size:13 final size:12
Alignment explanation
Indices: 1603106--1603148 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
1603096 ATTGAATAAA
*
1603106 ATAAATAAAAAT
1 ATAAAGAAAAAT
1603118 -TAAAGAAAAAT
1 ATAAAGAAAAAT
1603129 ATAAAGAAAAA-
1 ATAAAGAAAAAT
1603140 ATAAA-AAAA
1 ATAAAGAAAA
1603149 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 4 0.14
11 15 0.52
12 10 0.34
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (12 bp):
ATAAAGAAAAAT
Found at i:1604252 original size:39 final size:39
Alignment explanation
Indices: 1604208--1604291 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
1604198 GTAGACGGGC
* *
1604208 TTGGGCCTTACCGAGCTTGTTGGGTCAGCCTTGCTTTGG
1 TTGGGCCTTACAGAGCTTGCTGGGTCAGCCTTGCTTTGG
** * *
1604247 TTGGGCCTTGTAGGGCTTGCTGGGTCAGGCTTGCTTTGG
1 TTGGGCCTTACAGAGCTTGCTGGGTCAGCCTTGCTTTGG
1604286 TTGGGC
1 TTGGGC
1604292 TTCATTGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.06, C:0.20, G:0.38, T:0.36
Consensus pattern (39 bp):
TTGGGCCTTACAGAGCTTGCTGGGTCAGCCTTGCTTTGG
Found at i:1604392 original size:13 final size:11
Alignment explanation
Indices: 1604356--1604541 Score: 51
Period size: 11 Copynumber: 16.0 Consensus size: 11
1604346 AAATAATATT
1604356 AATA-ATAATA
1 AATATATAATA
*
1604366 CA-ATATAATA
1 AATATATAATA
1604376 AATATATAATA
1 AATATATAATA
*
1604387 GGAATATACTACTA
1 --AATATA-TAATA
1604401 TAATATATAATA
1 -AATATATAATA
* * **
1604413 AGTTTATGCTA
1 AATATATAATA
1604424 TAATATATAATA
1 -AATATATAATA
* * *
1604436 TATACAT-GT-
1 AATATATAATA
1604445 AATATATAATA
1 AATATATAATA
* *
1604456 TATAATTACTACTA
1 AAT-A-TA-TAATA
*
1604470 TAACATATAATA
1 -AATATATAATA
*
1604482 TATATAT-ATA
1 AATATATAATA
*
1604492 TATATAGTATATA
1 AATATA-TA-ATA
*
1604505 ATATTTATAATA
1 A-ATATATAATA
1604517 TTAATACTAT-ATA
1 --AATA-TATAATA
1604530 ATATATATAATA
1 A-ATATATAATA
1604542 TGTACTATAT
Statistics
Matches: 126, Mismatches: 29, Indels: 40
0.65 0.15 0.21
Matches are distributed among these distances:
9 6 0.05
10 19 0.15
11 32 0.25
12 25 0.20
13 26 0.21
14 17 0.13
15 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (11 bp):
AATATATAATA
Found at i:1604434 original size:7 final size:7
Alignment explanation
Indices: 1604422--1604552 Score: 93
Period size: 7 Copynumber: 19.6 Consensus size: 7
1604412 AAGTTTATGC
1604422 TATAATA
1 TATAATA
1604429 TATAATA
1 TATAATA
*
1604436 TAT-ACA
1 TATAATA
*
1604442 TGTAATA
1 TATAATA
1604449 TATAATA
1 TATAATA
1604456 TATAAT-
1 TATAATA
*
1604462 TACT-A-C
1 TA-TAATA
*
1604468 TATAACA
1 TATAATA
1604475 TATAATA
1 TATAATA
1604482 TAT-ATA
1 TATAATA
1604488 TAT-ATA
1 TATAATA
*
1604494 TATAGTA
1 TATAATA
1604501 TATAATA
1 TATAATA
1604508 TTTATAATA
1 --TATAATA
1604517 T-TAATA
1 TATAATA
1604523 CTAT-ATA
1 -TATAATA
1604530 -AT-ATA
1 TATAATA
1604535 TATAATA
1 TATAATA
* *
1604542 TGTACTA
1 TATAATA
1604549 TATA
1 TATA
1604553 TAACACAACA
Statistics
Matches: 101, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
5 6 0.06
6 29 0.29
7 58 0.57
8 1 0.01
9 7 0.07
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:1604436 original size:43 final size:44
Alignment explanation
Indices: 1604389--1604504 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 44
1604379 ATATAATAGG
* *
1604389 AATATACTACTATAATATATAATA-AGT-TTA-TGCTATAATATAT
1 AATATA-TACTATAATATATAATATA-TATTACTACTATAACATAT
*
1604432 AATATATACATGTAATATATAATATATAATTACTACTATAACATAT
1 AATATATAC-TATAATATATAATATAT-ATTACTACTATAACATAT
*
1604478 AATATATA-TATATATATATAGTATATA
1 AATATATACTATA-ATATATAATATATA
1604505 ATATTTATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
42 3 0.05
43 20 0.32
44 5 0.08
45 15 0.24
46 19 0.31
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (44 bp):
AATATATACTATAATATATAATATATATTACTACTATAACATAT
Found at i:1604438 original size:2 final size:2
Alignment explanation
Indices: 1604422--1604554 Score: 78
Period size: 2 Copynumber: 71.0 Consensus size: 2
1604412 AAGTTTATGC
* *
1604422 TA TA -A TA TA TA -A TA TA TA CA TG TA -A TA TA TA -A 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
*
1604460 -A T- TA CTA CTA TA -A CA TA TA -A TA TA TA TA TA TA TA TA TA GTA
1 TA TA TA -TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
1604501 TA TA -A TA TT TA TA -A TA T- TA -A TA CTA TA TA -A 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
*
1604539 -A TA TG TA CTA TA TA TA
1 TA TA TA TA -TA TA TA TA
1604555 ACACAACACA
Statistics
Matches: 104, Mismatches: 9, Indels: 36
0.70 0.06 0.24
Matches are distributed among these distances:
1 14 0.13
2 79 0.76
3 11 0.11
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1604454 original size:50 final size:45
Alignment explanation
Indices: 1604421--1604507 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
1604411 TAAGTTTATG
* * *
1604421 CTATAATATATAATATATACATGTAATATATAATATATAATTACTA
1 CTATAACATATAATATATACATAT-ATATATAATATATAATAACTA
* *
1604467 CTATAACATATAATATATATATATATATATAGTATATAATA
1 CTATAACATATAATATATACATATATATATAATATATAATA
1604508 TTTATAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 15 0.42
46 21 0.58
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (45 bp):
CTATAACATATAATATATACATATATATATAATATATAATAACTA
Found at i:1604458 original size:9 final size:9
Alignment explanation
Indices: 1604426--1604542 Score: 79
Period size: 9 Copynumber: 13.2 Consensus size: 9
1604416 TTATGCTATA
1604426 ATATATAAT
1 ATATATAAT
* *
1604435 ATATACATGT
1 ATATATA-AT
1604445 AATATATAAT
1 -ATATATAAT
*
1604455 ATATA-ATT
1 ATATATAAT
1604463 ACTACTAT-A-
1 A-TA-TATAAT
*
1604472 ACATATAAT
1 ATATATAAT
1604481 ATATAT-AT
1 ATATATAAT
1604489 ATATAT-AT
1 ATATATAAT
1604497 AGTATATAAT
1 A-TATATAAT
*
1604507 ATTTAT-A-
1 ATATATAAT
1604514 ATAT-TAAT
1 ATATATAAT
1604522 ACTATATAAT
1 A-TATATAAT
1604532 ATATATAAT
1 ATATATAAT
1604541 AT
1 AT
1604543 GTACTATATA
Statistics
Matches: 85, Mismatches: 10, Indels: 26
0.70 0.08 0.21
Matches are distributed among these distances:
6 1 0.01
7 7 0.08
8 18 0.21
9 41 0.48
10 12 0.14
11 6 0.07
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:1604564 original size:5 final size:5
Alignment explanation
Indices: 1604554--1604740 Score: 374
Period size: 5 Copynumber: 37.4 Consensus size: 5
1604544 TACTATATAT
1604554 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1604604 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1604654 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1604704 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AA
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AA
1604741 TATAATATAA
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 182 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAC
Found at i:1604747 original size:5 final size:5
Alignment explanation
Indices: 1604739--1604797 Score: 52
Period size: 5 Copynumber: 12.2 Consensus size: 5
1604729 AACACAACAC
** *
1604739 AATAT AATAT AATACT ACCAT AAAAT -ATAT AATAT -ATAT AATAT AATAT
1 AATAT AATAT AATA-T AATAT AATAT AATAT AATAT AATAT AATAT AATAT
*
1604788 -ATAT ACTAT A
1 AATAT AATAT A
1604798 TACTTATACC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 11 0.25
5 30 0.68
6 3 0.07
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:1604784 original size:14 final size:14
Alignment explanation
Indices: 1604765--1604797 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1604755 ACCATAAAAT
1604765 ATATAATATATATA
1 ATATAATATATATA
1604779 ATATAATATATATA
1 ATATAATATATATA
*
1604793 CTATA
1 ATATA
1604798 TACTTATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:1604784 original size:23 final size:24
Alignment explanation
Indices: 1604740--1604801 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
1604730 ACACAACACA
*
1604740 ATATAATATAATACTACCATAAAAT
1 ATATAATAT-ATACTAACATAAAAT
* *
1604765 ATATAATATATA-TAATATAATAT
1 ATATAATATATACTAACATAAAAT
*
1604788 ATATACTATATACT
1 ATATAATATATACT
1604802 TATACCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 19 0.59
24 4 0.12
25 9 0.28
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAATATATACTAACATAAAAT
Found at i:1608023 original size:3 final size:3
Alignment explanation
Indices: 1608003--1608050 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
1607993 TTTTAATTTC
*
1608003 ATT A-T ATT TTT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1608049 AT
1 AT
1608051 ATAATTATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1611795 original size:37 final size:36
Alignment explanation
Indices: 1611697--1611797 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
1611687 TTTCGTCCTA
1611697 CTAGGATTCAAACT-CTCAAAAATAGGATAGAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATAGGATAGAATTCTG
* *
1611734 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
** *
1611770 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAAAATAGGAT
1611798 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
36 26 0.46
37 30 0.54
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
Found at i:1612316 original size:15 final size:15
Alignment explanation
Indices: 1612274--1612316 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1612264 TTTTTTAAAG
1612274 TTATTATATATATATAT
1 TTATTAT-TAT-TATAT
* *
1612291 TTATAACTATTATAT
1 TTATTATTATTATAT
1612306 TTATTATTATT
1 TTATTATTATT
1612317 TTACTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:1612515 original size:16 final size:16
Alignment explanation
Indices: 1612494--1612527 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1612484 CATGTATTTA
1612494 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
1612510 TATTATTTTACTTTAT
1 TATTATATTACATTAT
1612526 TA
1 TA
1612528 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:1612532 original size:21 final size:22
Alignment explanation
Indices: 1612508--1612558 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1612498 ATATTACATT
*
1612508 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
1612529 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
1612551 TTTATTAT
1 ATTATTAT
1612559 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:1615914 original size:20 final size:20
Alignment explanation
Indices: 1615861--1615931 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
1615851 ACAAAAAGGG
*
1615861 AAAAAAGAAAAAAGAAAAGAAGC
1 AAAAAAG-AAAAA-ACAAGAA-C
1615884 AAAAAAGGAAAAAACAAGAAC
1 AAAAAA-GAAAAAACAAGAAC
* * *
1615905 AAAAAAGAAAGAACAAAAAT
1 AAAAAAGAAAAAACAAGAAC
1615925 AAAAAAG
1 AAAAAAG
1615932 GAACAAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 18 0.42
21 7 0.16
22 6 0.14
23 11 0.26
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAAGAAAAAACAAGAAC
Found at i:1617474 original size:36 final size:37
Alignment explanation
Indices: 1617427--1617531 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 37
1617417 GTGCTCACCA
1617427 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-CT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
*
1617463 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
* * *
1617500 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1617532 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 34 0.53
37 30 0.47
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
Done.