Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 43
Found at i:5498069 original size:21 final size:21
Alignment explanation
Indices: 5498047--5498085 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5498037 ATGCCATATA
5498047 AAAGATAG-GATT-TTGAGTTT
1 AAAGA-AGTGATTATTGAGTTT
5498067 AAAGAAGTGATTATTGAGT
1 AAAGAAGTGATTATTGAGT
5498086 AGAAACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (21 bp):
AAAGAAGTGATTATTGAGTTT
Found at i:5498164 original size:19 final size:20
Alignment explanation
Indices: 5498129--5498166 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5498119 GAATATAAAA
*
5498129 TGAGGTGAAATATGAAGTGT
1 TGAGCTGAAATATGAAGTGT
5498149 TGAGCTGAAA-ATGAAGTG
1 TGAGCTGAAATATGAAGTG
5498167 ATTTTCGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAAATATGAAGTGT
Found at i:5498371 original size:63 final size:63
Alignment explanation
Indices: 5498249--5498371 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 63
5498239 AAACGAAATA
*
5498249 AAAACATCGAATGCAATAAGTGCATCGATGCATAGGGAGTGCATCAATACACCCCTTAAGACG
1 AAAACATCGAATGCAATAAGTGCATCGATGCATAGGGAGTGCATCAATACACACCTTAAGACG
* ** * * * *
5498312 AAAACATCGAATGTAATTTGTGTATCGATGCATAGGTAGTGCATCGATACACACGTTAAG
1 AAAACATCGAATGCAATAAGTGCATCGATGCATAGGGAGTGCATCAATACACACCTTAAG
5498372 GGATGCATCG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (63 bp):
AAAACATCGAATGCAATAAGTGCATCGATGCATAGGGAGTGCATCAATACACACCTTAAGACG
Found at i:5498964 original size:18 final size:18
Alignment explanation
Indices: 5498940--5498992 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
5498930 AGGGATTATC
*
5498940 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
5498958 TGTGGTCATTCGGGATAT
1 AGTGGTCCTTCGGGACAT
*
5498976 AGTGGTCCTTCAGGACA
1 AGTGGTCCTTCGGGACA
5498993 AATATTTAGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:5501088 original size:3 final size:3
Alignment explanation
Indices: 5501080--5501132 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
5501070 TTTTTTATCG
** *
5501080 TTA TTA TTA TTA TTA TTA TTA TCG TTA -TA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5501127 TTA TTA
1 TTA TTA
5501133 ATTTACAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5508532 original size:4 final size:4
Alignment explanation
Indices: 5508523--5508568 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
5508513 GATCGAGAAA
*
5508523 ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT A-AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
5508568 A
1 A
5508569 AAATTTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:5508554 original size:18 final size:17
Alignment explanation
Indices: 5508531--5508566 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
5508521 AAACATACAT
5508531 ACATACATACATATATAC
1 ACATACATACATA-ATAC
5508549 ACATACATACATAATAC
1 ACATACATACATAATAC
5508566 A
1 A
5508567 TAAAATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (17 bp):
ACATACATACATAATAC
Found at i:5509161 original size:102 final size:102
Alignment explanation
Indices: 5508972--5509162 Score: 255
Period size: 103 Copynumber: 1.9 Consensus size: 102
5508962 TTGAGACAAA
* *
5508972 TTCTTTTAAAACAAACTTCGTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTGAATTTGATT
1 TTCTTTCAAAACAAACTTCGTCGCTTGAGACACTTTTCCTTTGAGATACAAATTTGAATTTGATT
*
5509037 CACTTAAAACAGAATTAATCTCACCTTAGATTGTTGT
66 CACTTAAAACAGAAGTAATCTCACCTTAGATTGTTGT
* *
5509074 TTCTTTCAAAACAAATTTCGTCTCGCTTGAGAC-CTTTTCCTTTGAGATCCAAATTTCGAATTTG
1 TTCTTTCAAAACAAACTTCG--TCGCTTGAGACACTTTTCCTTTGAGATACAAATTT-GAATTTG
* *
5509138 -TTCA-TATTAAACA-AAGTGATCTCAC
63 ATTCACT-TAAAACAGAAGTAATCTCAC
5509163 TTGGGATCGT
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
102 29 0.37
103 31 0.40
104 18 0.23
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (102 bp):
TTCTTTCAAAACAAACTTCGTCGCTTGAGACACTTTTCCTTTGAGATACAAATTTGAATTTGATT
CACTTAAAACAGAAGTAATCTCACCTTAGATTGTTGT
Found at i:5509253 original size:27 final size:28
Alignment explanation
Indices: 5509213--5509390 Score: 228
Period size: 27 Copynumber: 6.5 Consensus size: 28
5509203 ATAATTCTCT
5509213 TAAAAATCTTTGAGTTTGTTCCTTTTAA
1 TAAAAATCTTTGAGTTTGTTCCTTTTAA
5509241 TAAAAATC-TTGAGTTT-TTCCTTTTAAA
1 TAAAAATCTTTGAGTTTGTTCCTTTT-AA
*
5509268 TAAAAATCTTTGAGTTTGTTCCTTTAAA
1 TAAAAATCTTTGAGTTTGTTCCTTTTAA
5509296 T-AAAATCTTTGAGTTTGTTCCTTTTAA
1 TAAAAATCTTTGAGTTTGTTCCTTTTAA
*
5509323 -ATAAAATCTTGGAG-TTGTTCCTTTTGAA
1 TA-AAAATCTTTGAGTTTGTTCCTTTT-AA
* *
5509351 TAAATATCTTTGAG-TTGTTTCTTTT--
1 TAAAAATCTTTGAGTTTGTTCCTTTTAA
*
5509376 GAAAAATCTTTGAGT
1 TAAAAATCTTTGAGT
5509391 CTATTTTTTT
Statistics
Matches: 134, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
25 12 0.09
26 8 0.06
27 54 0.40
28 52 0.39
29 8 0.06
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (28 bp):
TAAAAATCTTTGAGTTTGTTCCTTTTAA
Found at i:5509278 original size:55 final size:56
Alignment explanation
Indices: 5509213--5509390 Score: 237
Period size: 55 Copynumber: 3.3 Consensus size: 56
5509203 ATAATTCTCT
5509213 TAAAAATCTTTGAGTTTGTTCCTTTTAATAAAAATC-TTGAGTTTTTCCTTTTAAA
1 TAAAAATCTTTGAGTTTGTTCCTTTTAATAAAAATCTTTGAGTTTTTCCTTTTAAA
*
5509268 TAAAAATCTTTGAGTTTGTTCCTTTAAAT-AAAATCTTTGAGTTTGTTCCTTTTAAA
1 TAAAAATCTTTGAGTTTGTTCCTTTTAATAAAAATCTTTGAGTTT-TTCCTTTTAAA
* *
5509324 T-AAAATCTTGGAG-TTGTTCCTTTTGAATAAATATCTTTGAGTTGTTT-CTTTT---
1 TAAAAATCTTTGAGTTTGTTCCTTTT-AATAAAAATCTTTGAGTT-TTTCCTTTTAAA
*
5509376 GAAAAATCTTTGAGT
1 TAAAAATCTTTGAGT
5509391 CTATTTTTTT
Statistics
Matches: 110, Mismatches: 6, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
53 11 0.10
54 16 0.15
55 55 0.50
56 27 0.25
57 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (56 bp):
TAAAAATCTTTGAGTTTGTTCCTTTTAATAAAAATCTTTGAGTTTTTCCTTTTAAA
Found at i:5509530 original size:29 final size:28
Alignment explanation
Indices: 5509489--5509617 Score: 107
Period size: 29 Copynumber: 4.3 Consensus size: 28
5509479 AATTTGTGAA
5509489 AAAAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAAAATCTTTGAG-TTGTTTCTTTTG
*
5509518 AAAAAAAATCTTTGAGTTGTTTCTTTGG
1 AAAAAAAATCTTTGAGTTGTTTCTTTTG
** * * *
5509546 AAACAAATTTTGTCTCTTAAGATAGTTTCTTTTA
1 AAA-AAA---AATCT-TTGAG-TTGTTTCTTTTG
5509580 AAACAAAAATCTTTGAGTATGTTTC-TTTG
1 AAA-AAAAATCTTTGAGT-TGTTTCTTTTG
*
5509609 AAACAAAAT
1 AAAAAAAAT
5509618 TTTATCTATT
Statistics
Matches: 80, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
28 19 0.24
29 26 0.32
30 9 0.11
31 3 0.04
32 3 0.04
33 4 0.05
34 16 0.20
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (28 bp):
AAAAAAAATCTTTGAGTTGTTTCTTTTG
Found at i:5509707 original size:63 final size:62
Alignment explanation
Indices: 5509509--5509710 Score: 239
Period size: 63 Copynumber: 3.2 Consensus size: 62
5509499 TTTGAGATTG
* * *
5509509 TTTCTTTTGAAAAAAAATCTTTGAG-TTGTTTCTTTGGAAAC-AAATTTTGTCTCTTAAGATAG
1 TTTCTTTTG-AAAAAAATCTTTGAGTTTGTTTCTTT-GAAACAAAATTTTGTCTCTAAAGACAA
* * * *
5509571 TTTCTTTTAAAACAAAAATCTTTGAGTATGTTTCTTTGAAACAAAATTTTATCTATTAAAGACAA
1 TTTCTTTT-GAA-AAAAATCTTTGAGTTTGTTTCTTTGAAACAAAATTTTGTCT-CTAAAGACAA
**
5509636 TTTC-TTTGAAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAA
1 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTT-CTTTGAAACAAAATTTTGTCTCTAAAGACAA
*
5509698 CTTCTTTTGAAAA
1 TTTCTTTTGAAAA
5509711 TACCACCTTT
Statistics
Matches: 119, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
62 39 0.33
63 48 0.40
64 22 0.18
65 10 0.08
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (62 bp):
TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGAAACAAAATTTTGTCTCTAAAGACAA
Found at i:5509897 original size:14 final size:15
Alignment explanation
Indices: 5509863--5509905 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
5509853 TTTTGAGTCG
*
5509863 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
5509878 TTTCTCTTGAAACA-
1 TTTCTCTTGAAACAT
*
5509892 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
5509906 AGATCATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.42
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:5510514 original size:43 final size:43
Alignment explanation
Indices: 5510330--5510519 Score: 123
Period size: 43 Copynumber: 4.6 Consensus size: 43
5510320 TCATCCCCAG
* * * * *
5510330 ACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTCTCACCCTTAGATA
* * * *
5510373 ACCAG-CCGT-C-C-TCACGTAGGAACCGTGTTATCACCTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTCTCA-C-CCTTAGATA
* * * * *
5510415 GCCAGAACTCTTCATCACGTATGAGCCGTCATCA-GC-T-G---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTC-TCACCCTTAGATA
*
5510453 ACCAGATCTCCTCATCACGTAGGAGCCGTCTCACCCTTAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTCTCACCCTTAGATA
5510496 ACCAG-CCGTCCTCATCACGTAGGA
1 ACCAGACC-TCCTCATCACGTAGGA
5510520 ACTGTGTTAT
Statistics
Matches: 111, Mismatches: 21, Indels: 30
0.69 0.13 0.19
Matches are distributed among these distances:
37 3 0.03
38 27 0.24
39 1 0.01
40 18 0.16
41 2 0.02
42 15 0.14
43 29 0.26
44 1 0.01
45 13 0.12
46 2 0.02
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (43 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTCTCACCCTTAGATA
Found at i:5510779 original size:3 final size:3
Alignment explanation
Indices: 5510771--5510811 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
5510761 TTTATCGTTA
*
5510771 TAT TAT TAT TAT TAT T-T ATAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
5510812 ATTTACAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5510791 original size:18 final size:18
Alignment explanation
Indices: 5510768--5510804 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5510758 TTTTTTATCG
*
5510768 TTATATTATTATTATTAT
1 TTATATTATTATTACTAT
5510786 TTATATTATTATTACTAT
1 TTATATTATTATTACTAT
5510804 T
1 T
5510805 ATTATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATATTATTATTACTAT
Found at i:5515210 original size:54 final size:54
Alignment explanation
Indices: 5515152--5515512 Score: 443
Period size: 54 Copynumber: 6.8 Consensus size: 54
5515142 CCATACGGTC
* * ** ** *
5515152 ATTCATAAACATATTATGAATTATGTGGGTTGCACACATAGTGCCGAAAC-GATT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAG-TT
* ** **
5515206 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAATGTTGAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* * * *
5515260 ATTCAACAACATATGATGGATTCTGTGAATTGAACACTTAGTGCCGAAACAGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* * * *
5515314 ATTCATCAACATATAATGAATTCGGTGAATTGCACACTTAGTGTCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* * *
5515368 ATTAATCAACATATGATGGATTCGGTGAATTGCACACTTA--GCCGAAACAGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
5515420 ATTCATCAACATATGATG-ATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
5515473 ATTCATCAAC--ATGATGAATTCCG-GAATTG--CACTTAGTGCC
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC
5515513 TATTTGGTAA
Statistics
Matches: 269, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
49 11 0.04
51 32 0.12
52 33 0.12
53 22 0.08
54 170 0.63
55 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
Found at i:5515822 original size:20 final size:20
Alignment explanation
Indices: 5515797--5515864 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
5515787 TGTTATCATA
5515797 TATCGATACCTTCCTTACAG
1 TATCGATACCTTCCTTACAG
* * *
5515817 TATCGATACC-CCCTTTCGG
1 TATCGATACCTTCCTTACAG
5515836 TATCGATA-CTT-CTTGAACAG
1 TATCGATACCTTCCTT--ACAG
5515856 TATCGATAC
1 TATCGATAC
5515865 TACTAGTTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 4 0.11
19 14 0.37
20 20 0.53
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (20 bp):
TATCGATACCTTCCTTACAG
Found at i:5515838 original size:19 final size:20
Alignment explanation
Indices: 5515797--5515844 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5515787 TGTTATCATA
*
5515797 TATCGATACCTTCCTTACAG
1 TATCGATACCTCCCTTACAG
* *
5515817 TATCGATACC-CCCTTTCGG
1 TATCGATACCTCCCTTACAG
5515836 TATCGATAC
1 TATCGATAC
5515845 TTCTTGAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.33
Consensus pattern (20 bp):
TATCGATACCTCCCTTACAG
Found at i:5517225 original size:43 final size:42
Alignment explanation
Indices: 5517156--5517331 Score: 118
Period size: 41 Copynumber: 4.2 Consensus size: 42
5517146 TAAATCTTAT
* **
5517156 TTTTTACCTT-ATAATTGATTTC-CTAATTTTATTCAATCACAC
1 TTTTTATCTTAATAATTGAAGTCTCTAATTTT-TTCAATC-CAC
* **
5517198 TTTTTATCTTAATTATT-AAGTCTCTAATTTTTTTCAAT-CTT
1 TTTTTATCTTAATAATTGAAGTCTCTAA-TTTTTTCAATCCAC
* *
5517239 TTTTTATCTTTATAATTGAGGTCTCTAATTTTTT-AATCCCAC
1 TTTTTATCTTAATAATTGAAGTCTCTAATTTTTTCAAT-CCAC
* * * *
5517281 -TTTTAACTTTATAATTGAGGAC-CTTAATTTTTT-AATCC-C
1 TTTTTATCTTAATAATTGAAGTCTC-TAATTTTTTCAATCCAC
5517320 ATTTTCTATCTT
1 -TTTT-TATCTT
5517332 TTCTACATAT
Statistics
Matches: 110, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
39 1 0.01
40 6 0.05
41 57 0.52
42 27 0.25
43 15 0.14
44 4 0.04
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.54
Consensus pattern (42 bp):
TTTTTATCTTAATAATTGAAGTCTCTAATTTTTTCAATCCAC
Found at i:5517271 original size:41 final size:39
Alignment explanation
Indices: 5517136--5517317 Score: 116
Period size: 41 Copynumber: 4.4 Consensus size: 39
5517126 TTTATAAACA
* * **
5517136 TCCTAATTTTTAAATCTTATTTTT-TACCTTATAATTGATT
1 TCCTAATTTTTTAATCTT-TTTTTAT-CTTTATAATTGAGG
** * * *
5517176 TCCTAATTTTATTCAATCACACTTTTTATCTTAATTATT-AAG
1 TCCTAATTTT-TT-AAT--CTTTTTTTATCTTTATAATTGAGG
5517218 TCTCTAATTTTTTTCAATCTTTTTTTATCTTTATAATTGAGG
1 TC-CTAA-TTTTTT-AATCTTTTTTTATCTTTATAATTGAGG
*** *
5517260 TCTCTAATTTTTTAATCCCACTTTTAACTTTATAATTGAGG
1 TC-CTAATTTTTTAAT-CTTTTTTTATCTTTATAATTGAGG
*
5517301 ACCTTAATTTTTTAATC
1 TCC-TAATTTTTTAATC
5517318 CCATTTTCTA
Statistics
Matches: 114, Mismatches: 18, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
40 15 0.13
41 56 0.49
42 15 0.13
43 22 0.19
44 6 0.05
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (39 bp):
TCCTAATTTTTTAATCTTTTTTTATCTTTATAATTGAGG
Found at i:5517318 original size:41 final size:41
Alignment explanation
Indices: 5517240--5517617 Score: 231
Period size: 41 Copynumber: 9.0 Consensus size: 41
5517230 TTCAATCTTT
* * *
5517240 TTTTATCTTTATAATTGAGG-TCTCTAATTTTTTAATCCCAC
1 TTTTAACTTTATAATTGAGGACCT-TAATTTTTTAATCTCAC
* *
5517281 TTTTAACTTTATAATTGAGGACCTTAATTTTTTAATCCCAT
1 TTTTAACTTTATAATTGAGGACCTTAATTTTTTAATCTCAC
* * *
5517322 TTTCTATCTTTTCTACATATAATTGAGG-CTCCTAATTTTTTAATCCCAC
1 TTT-TAAC---T-T---TATAATTGAGGAC-CTTAATTTTTTAATCTCAC
* * *
5517371 -TTTAAATTTATAA--GAGGCCCTTAAGTTTTTTAATCTCGC
1 TTTTAACTTTATAATTGAGGACCTTAA-TTTTTTAATCTCAC
* * * * *
5517410 TTTCTACCTTTACAATTGA-GTCCCTAAGTTTTTTCAATCTCAA
1 TTT-TAACTTTATAATTGAGGACCTTAA-TTTTTT-AATCTCAC
*
5517453 TTTCTACCTTTATAATTGA-GACCCTT-ATTTTTT-ATCTCACC
1 TTT-TAACTTTATAATTGAGGA-CCTTAATTTTTTAATCTCA-C
* * * *
5517494 TTTTAACTTTATAATTGAGGCCCTTGCATTTTTCAATATCAC
1 TTTTAACTTTATAATTGAGGACCTT-AATTTTTTAATCTCAC
* * * *
5517536 TTCTACCTTT-TAATTGA-GACCCCTAAGTTTTTTCAATCTCAA
1 TTTTAACTTTATAATTGAGGA-CCTTAA-TTTTTT-AATCTCAC
* *
5517578 TTAT-ACTTTATAATTGAGGCCCTTAATTTTTTCAATCTCA
1 TTTTAACTTTATAATTGAGGACCTTAATTTTTT-AATCTCA
5517618 ATTTCTACAT
Statistics
Matches: 271, Mismatches: 38, Indels: 56
0.74 0.10 0.15
Matches are distributed among these distances:
38 8 0.03
39 13 0.05
40 33 0.12
41 83 0.31
42 60 0.22
43 35 0.13
44 4 0.01
45 1 0.00
46 1 0.00
47 2 0.01
48 3 0.01
49 28 0.10
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.47
Consensus pattern (41 bp):
TTTTAACTTTATAATTGAGGACCTTAATTTTTTAATCTCAC
Found at i:5517504 original size:83 final size:84
Alignment explanation
Indices: 5517339--5517632 Score: 254
Period size: 83 Copynumber: 3.6 Consensus size: 84
5517329 CTTTTCTACA
* * ** * *
5517339 TATAATTGAGGCTCCTAA-TTTTTT-AATC-CCACTT-TAAATTTATAA--GAGGCCCTTAAGTT
1 TATAATTGAGGC-CCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACCCCTAAGTT
** *
5517398 TTTTAATCTCGCTTTCTACCTT
65 TTTTAATCTC-AATTATA-CTT
* * *
5517420 TACAATTGAGTCCCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGA-CCCTTA-TTT
1 TATAATTGAGGCCCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACCCCTAAGTTT
* *
5517483 TTT-ATCTCACCTTTTAACTT
66 TTTAATCTCA-ATTAT-ACTT
* * * *
5517503 TATAATTGAGGCCCT-TGCATTTTTCAATATC-ACTTCTACCTTT-TAATTGAGACCCCTAAGTT
1 TATAATTGAGGCCCTAAG-TTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACCCCTAAGTT
5517565 TTTTCAATCTCAATTATACTT
65 TTTT-AATCTCAATTATACTT
*
5517586 TATAATTGAGGCCCTTAA-TTTTTTCAATCTCAATTTCTACATTTATA
1 TATAATTGAGGCCC-TAAGTTTTTTCAATCTCAATTTCTACCTTTATA
5517633 TTAAGGCCTC
Statistics
Matches: 170, Mismatches: 26, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
80 5 0.03
81 25 0.15
82 21 0.12
83 74 0.44
84 30 0.18
85 12 0.07
86 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (84 bp):
TATAATTGAGGCCCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACCCCTAAGTTT
TTTAATCTCAATTATACTT
Found at i:5517620 original size:41 final size:42
Alignment explanation
Indices: 5517339--5517640 Score: 245
Period size: 42 Copynumber: 7.3 Consensus size: 42
5517329 CTTTTCTACA
* * **
5517339 TATAATTGAGGCTCC-TAATTTTTT-AATCCCACTT-TAAATT
1 TATAATTGAGGC-CCTTAATTTTTTCAATCTCAATTCTACCTT
**
5517379 TATAA--GAGGCCCTTAAGTTTTTT-AATCTCGCTTTCTACCTT
1 TATAATTGAGGCCCTTAA-TTTTTTCAATCTC-AATTCTACCTT
* *
5517420 TACAATTGAGTCCC-TAAGTTTTTTCAATCTCAATTTCTACCTT
1 TATAATTGAGGCCCTTAA-TTTTTTCAATCTCAA-TTCTACCTT
* * * *
5517463 TATAATTGAGACCCTT-ATTTTTT--ATCTCACCTTTTAACTT
1 TATAATTGAGGCCCTTAATTTTTTCAATCTCA-ATTCTACCTT
* * *
5517503 TATAATTGAGGCCCTTGCA-TTTTTCAATATCACTTCTACCTT
1 TATAATTGAGGCCCTT-AATTTTTTCAATCTCAATTCTACCTT
* * *
5517545 T-TAATTGAGACCCCTAAGTTTTTTCAATCTCAATTATA-CTT
1 TATAATTGAGGCCCTTAA-TTTTTTCAATCTCAATTCTACCTT
*
5517586 TATAATTGAGGCCCTTAATTTTTTCAATCTCAATTTCTACATT
1 TATAATTGAGGCCCTTAATTTTTTCAATCTCAA-TTCTACCTT
*
5517629 TAT-ATTAAGGCC
1 TATAATTGAGGCC
5517641 TCTATTTTTT
Statistics
Matches: 214, Mismatches: 29, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
37 2 0.01
38 8 0.04
39 11 0.05
40 36 0.17
41 44 0.21
42 68 0.32
43 44 0.21
44 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (42 bp):
TATAATTGAGGCCCTTAATTTTTTCAATCTCAATTCTACCTT
Found at i:5517640 original size:125 final size:125
Alignment explanation
Indices: 5517411--5517640 Score: 310
Period size: 125 Copynumber: 1.8 Consensus size: 125
5517401 TAATCTCGCT
* *
5517411 TTCTACCTTTACAATTGAGTCCCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACC
1 TTCTACCTTTACAATTGAGCCCCTAAGTTTTTTCAATCTCAATTTATACCTTTATAATTGAGACC
* *
5517476 CTTATTTTTTATCTCACCTTTTAACTTTATAATTGAGGCCCTTGCATTTTTCAATATCAC
66 CTTATTTTTTATCTCACATTTTAACTTTATAATTAAGGCCCTTGCATTTTTCAATATCAC
* *
5517536 TTCTACCTTT-TAATTGAGACCCCTAAGTTTTTTCAATCTCAA-TTATA-CTTTATAATTGAGGC
1 TTCTACCTTTACAATTGAG-CCCCTAAGTTTTTTCAATCTCAATTTATACCTTTATAATTGAGAC
5517598 CCTTAATTTTTTCAATCTCA-ATTTCT-ACATTTAT-ATTAAGGCC
65 CCTT-ATTTTTT--ATCTCACATTT-TAAC-TTTATAATTAAGGCC
5517641 TCTATTTTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
123 18 0.19
124 18 0.19
125 45 0.48
126 12 0.13
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (125 bp):
TTCTACCTTTACAATTGAGCCCCTAAGTTTTTTCAATCTCAATTTATACCTTTATAATTGAGACC
CTTATTTTTTATCTCACATTTTAACTTTATAATTAAGGCCCTTGCATTTTTCAATATCAC
Found at i:5518189 original size:21 final size:19
Alignment explanation
Indices: 5518163--5518260 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 19
5518153 CATATTCGCA
5518163 TTGCGATAGTCCAAGTTTGCG
1 TTGCGATAGTCCAAG-TT-CG
*
5518184 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
5518205 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
5518226 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
5518247 TTGCGATAATCCAA
1 TTGCGATAGTCCAA
5518261 AATCGCAACG
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
19 16 0.25
21 30 0.46
22 2 0.03
23 17 0.26
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:5518201 original size:23 final size:21
Alignment explanation
Indices: 5518172--5518253 Score: 96
Period size: 21 Copynumber: 3.8 Consensus size: 21
5518162 ATTGCGATAG
5518172 TCCAAGTTTGCGTTGCGATTTAT
1 TCCAAG-TT-CGTTGCGATTTAT
*
5518195 TCCAAGTTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATTTAT
*
5518214 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
5518237 TCCAAGTTCGTTGCGAT
1 TCCAAGTTCGTTGCGAT
5518254 AATCCAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
19 9 0.18
21 25 0.49
22 2 0.04
23 15 0.29
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (21 bp):
TCCAAGTTCGTTGCGATTTAT
Found at i:5518214 original size:42 final size:42
Alignment explanation
Indices: 5518163--5518260 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
5518153 CATATTCGCA
*
5518163 TTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
5518205 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
5518247 TTGCGATAATCCAA
1 TTGCGATAGTCCAA
5518261 AATCGCAACG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:5518434 original size:21 final size:21
Alignment explanation
Indices: 5518408--5518474 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
5518398 GCGACGGCGC
5518408 GCGATAGTCCAAGTTCGCATT
1 GCGATAGTCCAAGTTCGCATT
5518429 GCGATAGTCCAAGTTCGCATT
1 GCGATAGTCCAAGTTCGCATT
* *
5518450 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCCAAGTTCGCATT
5518471 GCGA
1 GCGA
5518475 ATCTAGAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (21 bp):
GCGATAGTCCAAGTTCGCATT
Found at i:5519699 original size:2 final size:2
Alignment explanation
Indices: 5519624--5519680 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
5519614 CTAGCCCACC
5519624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5519665 AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
5519681 AAGCTTTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5520126 original size:6 final size:6
Alignment explanation
Indices: 5520115--5520143 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5520105 AGAACGCACT
5520115 ACTTCA ACTTCA ACTTCA ACTTCA ACTTC
1 ACTTCA ACTTCA ACTTCA ACTTCA ACTTC
5520144 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
ACTTCA
Found at i:5521387 original size:8 final size:8
Alignment explanation
Indices: 5521370--5521437 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
5521360 AAAACTATAT
5521370 AAATAAAA
1 AAATAAAA
*
5521378 AAAT-ACA
1 AAATAAAA
5521385 AAATAAAA
1 AAATAAAA
*
5521393 ATAAGTAGAA
1 A-AA-TAAAA
*
5521403 AAA-AATA
1 AAATAAAA
5521410 AAATAAAA
1 AAATAAAA
* *
5521418 GAATAAAT
1 AAATAAAA
*
5521426 AAATAAAT
1 AAATAAAA
5521434 AAAT
1 AAAT
5521438 GAATATATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
7 11 0.23
8 27 0.57
9 4 0.09
10 5 0.11
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (8 bp):
AAATAAAA
Found at i:5521396 original size:25 final size:27
Alignment explanation
Indices: 5521368--5521434 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
5521358 GAAAAACTAT
5521368 ATAAATAAAAAAATACAAAAT-AAA-A
1 ATAAATAAAAAAATACAAAATAAAAGA
* *
5521393 ATAAGTAGAAAAAA-ATAAAATAAAAGA
1 ATAAATA-AAAAAATACAAAATAAAAGA
*
5521420 ATAAATAAATAAATA
1 ATAAATAAAAAAATA
5521435 AATGAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 12 0.35
26 14 0.41
27 8 0.24
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (27 bp):
ATAAATAAAAAAATACAAAATAAAAGA
Found at i:5521447 original size:2 final size:2
Alignment explanation
Indices: 5521440--5521466 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5521430 AAATAAATGA
5521440 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 A
5521467 AAAAATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5521795 original size:3 final size:3
Alignment explanation
Indices: 5521783--5521816 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
5521773 AAATATATAT
5521783 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5521817 TATACGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:5523522 original size:105 final size:105
Alignment explanation
Indices: 5523046--5523772 Score: 1207
Period size: 105 Copynumber: 6.9 Consensus size: 105
5523036 CTGGAACTGG
*
5523046 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT--GTATGTTCTGGAGT
1 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT-TG-TCTGGAGT
5523109 CCAATATCCTTCGTTGTG-AGTTGAAATTGGCTCTGAAATTGA
63 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* * *
5523151 GAAGTTGTTTGTTGACAACCAGC-GTCCCTTCGTCGTAAAGTTGAACTTACGTTGTCTGGAGTCC
1 GAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
5523215 -ATATCATTCGTTGTGAAGTTGAAATTGGCTC-GAAA-TGA
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
5523253 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCC
1 GAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
5523318 AATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGG
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
5523359 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCC
1 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
5523424 AATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
5523465 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
5523530 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
5523570 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
5523635 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
5523675 GAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
5523740 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
5523773 TTAAAACCTG
Statistics
Matches: 587, Mismatches: 26, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
102 26 0.04
103 56 0.10
104 77 0.13
105 323 0.55
106 105 0.18
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
Found at i:5524504 original size:78 final size:75
Alignment explanation
Indices: 5524376--5524529 Score: 281
Period size: 78 Copynumber: 2.0 Consensus size: 75
5524366 AATCGCCCTT
5524376 TCCGGGTTTTCAACTTGGACCCTCATTGGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAACC
1 TCCGGGTTTTCAACTTGGACCCTCATTGGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAA--
5524441 CCCTTATTTCTC
64 CCCTTATTTCTC
5524453 TCCGGGTTTTCAACTTGGACCCATCATTGGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAAC
1 TCCGGGTTTTCAACTTGGACCC-TCATTGGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAAC
5524518 CCTTATTTCTC
65 CCTTATTTCTC
5524529 T
1 T
5524530 TCTTTTGTTC
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
76 13 0.17
77 22 0.29
78 41 0.54
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.37
Consensus pattern (75 bp):
TCCGGGTTTTCAACTTGGACCCTCATTGGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAACC
CTTATTTCTC
Found at i:5524548 original size:22 final size:22
Alignment explanation
Indices: 5524523--5524567 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5524513 TGAACCCTTA
5524523 TTTCTCTTCTT-TTGTTCTTTTT
1 TTTCTCTT-TTCTTGTTCTTTTT
*
5524545 TTTCTCTTTTCTTTTTCTTTTT
1 TTTCTCTTTTCTTGTTCTTTTT
5524567 T
1 T
5524568 CAATTTAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTCTCTTTTCTTGTTCTTTTT
Found at i:5524554 original size:19 final size:20
Alignment explanation
Indices: 5524530--5524568 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5524520 TTATTTCTCT
*
5524530 TCTTTTGTTCTT-TTTTTTC
1 TCTTTTCTTCTTCTTTTTTC
*
5524549 TCTTTTCTTTTTCTTTTTTC
1 TCTTTTCTTCTTCTTTTTTC
5524569 AATTTAGGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (20 bp):
TCTTTTCTTCTTCTTTTTTC
Found at i:5524615 original size:85 final size:87
Alignment explanation
Indices: 5524491--5524653 Score: 194
Period size: 85 Copynumber: 1.9 Consensus size: 87
5524481 GGTTGCAAGA
* * *
5524491 CGCCCTTTGCGGGTTTTCATCTTGAACCCTTATTTCTCTTCTT-TTGTTCTT-TTTTTT-CTCTT
1 CGCCCTTTGCGGGTTTTCACCCTGAAACCTTATTTCTCTT-TTGTT-TT-TTGTTTTTTGCTCTT
5524553 TTCTTTTTCTT-TTTTCAATTTAGGG
63 TTCTTTTT-TTGTTTTCAATTTAGGG
* * *
5524578 CGCCCTTT-CGGGTTTTCACCCT-AAACGTTTTTTCTCTTTTGTTTTTTGTTTTTTGCTCTTTTG
1 CGCCCTTTGCGGGTTTTCACCCTGAAACCTTATTTCTCTTTTGTTTTTTGTTTTTTGCTCTTTTC
5524641 TTTTTTTGTTTTC
66 TTTTTTTGTTTTC
5524654 TTGTTTTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
83 2 0.03
84 12 0.18
85 32 0.48
86 12 0.18
87 8 0.12
ACGTcount: A:0.07, C:0.21, G:0.12, T:0.60
Consensus pattern (87 bp):
CGCCCTTTGCGGGTTTTCACCCTGAAACCTTATTTCTCTTTTGTTTTTTGTTTTTTGCTCTTTTC
TTTTTTTGTTTTCAATTTAGGG
Found at i:5524623 original size:15 final size:15
Alignment explanation
Indices: 5524621--5524663 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
5524611 CTCTTTTGTT
*
5524621 TTTTGTTTTTTGCTC
1 TTTTGTTTTTTTCTC
* *
5524636 TTTTGTTTTTTTGTT
1 TTTTGTTTTTTTCTC
5524651 TTCTTGTTTTTTT
1 TT-TTGTTTTTTT
5524664 TTCCAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (15 bp):
TTTTGTTTTTTTCTC
Found at i:5524624 original size:7 final size:7
Alignment explanation
Indices: 5524604--5524662 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
5524594 CACCCTAAAC
5524604 GTTTTTT
1 GTTTTTT
* *
5524611 CTCTTTT
1 GTTTTTT
5524618 GTTTTTT
1 GTTTTTT
5524625 GTTTTTT
1 GTTTTTT
*
5524632 GCTCTTTT
1 G-TTTTTT
5524640 GTTTTTTT
1 G-TTTTTT
5524648 GTTTTCTT
1 GTTTT-TT
5524656 GTTTTTT
1 GTTTTTT
5524663 TTTCCAACTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
7 24 0.56
8 19 0.44
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (7 bp):
GTTTTTT
Found at i:5524630 original size:8 final size:8
Alignment explanation
Indices: 5524614--5524663 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
5524604 GTTTTTTCTC
5524614 TTTTG-TT
1 TTTTGTTT
5524621 TTTTG-TT
1 TTTTGTTT
* *
5524628 TTTTGCTC
1 TTTTGTTT
5524636 TTTTGTTT
1 TTTTGTTT
5524644 TTTTGTTT
1 TTTTGTTT
*
5524652 TCTTGTTT
1 TTTTGTTT
5524660 TTTT
1 TTTT
5524664 TTCCAACTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
7 12 0.32
8 25 0.68
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (8 bp):
TTTTGTTT
Found at i:5531220 original size:39 final size:39
Alignment explanation
Indices: 5531153--5531230 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
5531143 TTCACAGCAG
* *
5531153 GTGCAACTTTCGCTTTGGTAACGAATGAGTCCTCGGGTA
1 GTGCAACTTTCCCTTTAGTAACGAATGAGTCCTCGGGTA
* * *
5531192 GTGCAGCTTTCCCTTTAGTAGCGGATGAGTCCTCGGGTA
1 GTGCAACTTTCCCTTTAGTAACGAATGAGTCCTCGGGTA
5531231 ATACTCCGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (39 bp):
GTGCAACTTTCCCTTTAGTAACGAATGAGTCCTCGGGTA
Found at i:5531597 original size:22 final size:21
Alignment explanation
Indices: 5531573--5531615 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 21
5531563 ATACGAATGT
5531573 AAAAACATGGAGAATAAAAAATAA
1 AAAAACAT-GA-AATAAAAAAT-A
5531597 AAAAACATGAAATAAAAAA
1 AAAAACATGAAATAAAAAA
5531616 ATACAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (21 bp):
AAAAACATGAAATAAAAAATA
Found at i:5534886 original size:8 final size:8
Alignment explanation
Indices: 5534861--5534904 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
5534851 ATAAAAGGAA
*
5534861 AAATAAAT
1 AAATATAT
*
5534869 AAATAAAT
1 AAATATAT
5534877 AAATATAT
1 AAATATAT
5534885 AATATATAT
1 AA-ATATAT
*
5534894 ATATATAT
1 AAATATAT
5534902 AAA
1 AAA
5534905 AATGTAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATATAT
Found at i:5535112 original size:2 final size:2
Alignment explanation
Indices: 5535107--5535177 Score: 62
Period size: 2 Copynumber: 37.5 Consensus size: 2
5535097 GAAAATACAC
* * * *
5535107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AA AA AA AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
5535149 AT AT AT A- AT A- AT AT AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5535178 AAATAATAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
1 5 0.08
2 56 0.90
3 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:5535178 original size:12 final size:12
Alignment explanation
Indices: 5535146--5535277 Score: 59
Period size: 12 Copynumber: 11.2 Consensus size: 12
5535136 TGAAAAAAAA
5535146 AATATATATAAT
1 AATATATATAAT
5535158 -A-ATATATAAT
1 AATATATATAAT
5535168 AATATATATAA-
1 AATATATATAAT
*
5535179 AATA-ATAAAACT
1 AATATATATAA-T
* *
5535191 AA-AAATA-AAGG
1 AATATATATAA-T
* *
5535202 AATATAGAAAAT
1 AATATATATAAT
*
5535214 AA-A-ATAGAA-
1 AATATATATAAT
*
5535223 AATATAATCAAATAT
1 AATAT-AT-ATA-AT
5535238 ATATATATATAAT
1 A-ATATATATAAT
5535251 AATA-ATAATAAT
1 AATATAT-ATAAT
*
5535263 AAAATATATAAT
1 AATATATATAAT
5535275 AAT
1 AAT
5535278 GAAACGTAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 32
0.68 0.09 0.24
Matches are distributed among these distances:
9 2 0.02
10 19 0.21
11 14 0.15
12 38 0.41
13 9 0.10
14 3 0.03
15 3 0.03
16 4 0.04
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (12 bp):
AATATATATAAT
Found at i:5542639 original size:26 final size:26
Alignment explanation
Indices: 5542610--5542674 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
5542600 TATCAAATAT
5542610 ATATTTATTATTAA-CTTAATTTAAAA
1 ATATTTATT-TTAATCTTAATTTAAAA
*
5542636 ATATTATATTTTAATTTTAATTTAAAA
1 ATATT-TATTTTAATCTTAATTTAAAA
*
5542663 ATATATATTTTA
1 ATATTTATTTTA
5542675 TTTTTATCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 16 0.46
27 19 0.54
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATTTATTTTAATCTTAATTTAAAA
Found at i:5542671 original size:31 final size:30
Alignment explanation
Indices: 5542604--5542706 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
5542594 TTAACTTATC
5542604 AAATATATATT-TATTATTAA-CTTAATTT-
1 AAATATATATTATATT-TTAATCTTAATTTA
*
5542632 AAA-A-ATATTATATTTTAATTTTAATTTAA
1 AAATATATATTATATTTTAATCTTAATTT-A
* * *
5542661 AAATATATATTTTATTTTTATCTAAACTTTTA
1 AAATATATATTATATTTTAATCTTAA--TTTA
*
5542693 AAATATATTTTATA
1 AAATATATATTATA
5542707 ATTATTTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
26 9 0.15
27 12 0.20
28 3 0.05
29 3 0.05
30 1 0.02
31 16 0.27
32 13 0.22
33 3 0.05
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (30 bp):
AAATATATATTATATTTTAATCTTAATTTA
Found at i:5542679 original size:26 final size:27
Alignment explanation
Indices: 5542625--5542680 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
5542615 TATTATTAAC
5542625 TTAATTTAAAAATATTATATTTTAATT
1 TTAATTTAAAAATATTATATTTTAATT
*
5542652 TTAATTTAAAAATA-TATATTTTATTT
1 TTAATTTAAAAATATTATATTTTAATT
5542678 TTA
1 TTA
5542681 TCTAAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTAATTTAAAAATATTATATTTTAATT
Found at i:5542686 original size:25 final size:27
Alignment explanation
Indices: 5542625--5542686 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
5542615 TATTATTAAC
*
5542625 TTAATTTAAAAATATTATATTTTAATT
1 TTAATCTAAAAATATTATATTTTAATT
*
5542652 TTAATTTAAAAATA-TATATTTT-ATT
1 TTAATCTAAAAATATTATATTTTAATT
*
5542677 TTTATCTAAA
1 TTAATCTAAA
5542687 CTTTTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 11 0.33
26 8 0.24
27 14 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
TTAATCTAAAAATATTATATTTTAATT
Found at i:5543034 original size:30 final size:31
Alignment explanation
Indices: 5542978--5543054 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
5542968 CTTTTCAAAG
*
5542978 TATATATATT-ATCTTAATTTACTAAATATAT
1 TATAT-TATTAATCTTAAATTACTAAATATAT
*
5543009 TATATTATTAAT-TTAAATTATTAAATATAT
1 TATATTATTAATCTTAAATTACTAAATATAT
*
5543039 TTTATTATT-ATCTTAA
1 TATATTATTAATCTTAA
5543055 TTTTAAAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.05
30 32 0.78
31 7 0.17
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (31 bp):
TATATTATTAATCTTAAATTACTAAATATAT
Found at i:5543115 original size:26 final size:25
Alignment explanation
Indices: 5543075--5543145 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 25
5543065 ATTTTAACAT
*
5543075 AAAATATATATATTTAAATTAAAATA
1 AAAATA-AAATATTTAAATTAAAATA
*
5543101 GAAAATAAAATATTTTGAAATTAATATA
1 -AAAATAAAATA-TTT-AAATTAAAATA
5543129 ATAAA-AAATATATTTAA
1 A-AAATAAA-ATATTTAA
5543146 TCAATTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 6 0.16
27 16 0.42
28 16 0.42
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
AAAATAAAATATTTAAATTAAAATA
Found at i:5543141 original size:28 final size:28
Alignment explanation
Indices: 5543073--5543143 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
5543063 GTATTTTAAC
*
5543073 ATAAAATATATATATTTAAATTAAAATAG
1 ATAAAAAATATAT-TTTAAATTAAAATAG
*
5543102 A-AAATAAA-ATATTTTGAAATTAATATA-
1 ATAAA-AAATATATTTT-AAATTAAAATAG
5543129 ATAAAAAATATATTT
1 ATAAAAAATATATTT
5543144 AATCAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 7 0.19
28 26 0.72
29 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (28 bp):
ATAAAAAATATATTTTAAATTAAAATAG
Found at i:5543185 original size:29 final size:25
Alignment explanation
Indices: 5543122--5543186 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 25
5543112 ATTTTGAAAT
5543122 TAATATA-ATAAAAAATATATTTAA
1 TAATATATATAAAAAATATATTTAA
5543146 TCAAT-TAATATAAAAAATATATGTTAAAA
1 T-AATAT-ATATAAAAAATATAT-TT--AA
5543175 GTAATATATATA
1 -TAATATATATA
5543187 TATATACACG
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
24 2 0.06
25 4 0.12
26 13 0.39
27 2 0.06
29 10 0.30
30 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (25 bp):
TAATATATATAAAAAATATATTTAA
Found at i:5543694 original size:31 final size:31
Alignment explanation
Indices: 5543659--5543725 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
5543649 AATGAGAAAA
*
5543659 ATGTACAAAACACAAACATAAATGATCAATC
1 ATGTACAAAACACAAACATAAACGATCAATC
5543690 ATGTACAAAACACAAACATAAACGATCAATC
1 ATGTACAAAACACAAACATAAACGATCAATC
5543721 ATGTA
1 ATGTA
5543726 GGAAAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.19
Consensus pattern (31 bp):
ATGTACAAAACACAAACATAAACGATCAATC
Found at i:5544659 original size:65 final size:64
Alignment explanation
Indices: 5544569--5544703 Score: 173
Period size: 65 Copynumber: 2.1 Consensus size: 64
5544559 TACTAATTAC
* * * * *
5544569 ATTCGATGTTTCAAAAGAGCTAGGAGTGTATCGATGCATTATATGTGCATCGGTACATAAAATGA
1 ATTCGATGTTTCAAAAAAGCTAGGAGTGCATCGATGCATGA-ATGTGCATCAGTACACAAAATGA
* * *
5544634 ATTCGATGTTTCAATAAAATC-AGGAGTGCATCGATGCATGACTGTGCATCAGTACACAAAATGC
1 ATTCGATGTTTCAA-AAAAGCTAGGAGTGCATCGATGCATGAATGTGCATCAGTACACAAAATGA
5544698 ATTCGA
1 ATTCGA
5544704 ATTAGGGTGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 25 0.41
65 32 0.52
66 4 0.07
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (64 bp):
ATTCGATGTTTCAAAAAAGCTAGGAGTGCATCGATGCATGAATGTGCATCAGTACACAAAATGA
Found at i:5545023 original size:45 final size:47
Alignment explanation
Indices: 5544973--5545089 Score: 125
Period size: 54 Copynumber: 2.4 Consensus size: 47
5544963 TGTTATATCG
5544973 AAACATTAAAAT-G-TTTTC-AACAATCTCCCCCTTTTTGATATAACA
1 AAACATTAAAATAGATTTTCTAA-AATCTCCCCCTTTTTGATATAACA
5545018 AAACATTTAAATAATTTTAAGATTTTCTAAAATCTCCCCCTTTTTGATATAACA
1 AAACA-TT-AA-AA---T-AGATTTTCTAAAATCTCCCCCTTTTTGATATAACA
*
5545072 AAACATTTAAATA-ATTTT
1 AAACATTAAAATAGATTTT
5545090 AAGATTTTCT
Statistics
Matches: 61, Mismatches: 1, Indels: 19
0.75 0.01 0.23
Matches are distributed among these distances:
45 5 0.08
46 7 0.11
47 3 0.05
48 3 0.05
51 3 0.05
52 1 0.02
53 3 0.05
54 34 0.56
55 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.39
Consensus pattern (47 bp):
AAACATTAAAATAGATTTTCTAAAATCTCCCCCTTTTTGATATAACA
Found at i:5545053 original size:54 final size:55
Alignment explanation
Indices: 5544986--5545099 Score: 214
Period size: 54 Copynumber: 2.1 Consensus size: 55
5544976 CATTAAAATG
5544986 TTTTC-AACAATCTCCCCCTTTTTGATATAACAAAACATTTAAATAATTTTAAGA
1 TTTTCTAACAATCTCCCCCTTTTTGATATAACAAAACATTTAAATAATTTTAAGA
5545040 TTTTCTAA-AATCTCCCCCTTTTTGATATAACAAAACATTTAAATAATTTTAAGA
1 TTTTCTAACAATCTCCCCCTTTTTGATATAACAAAACATTTAAATAATTTTAAGA
5545094 TTTTCT
1 TTTTCT
5545100 TTGAAAATCA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
54 57 0.97
55 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.42
Consensus pattern (55 bp):
TTTTCTAACAATCTCCCCCTTTTTGATATAACAAAACATTTAAATAATTTTAAGA
Found at i:5545442 original size:14 final size:15
Alignment explanation
Indices: 5545423--5545456 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5545413 TTCAAACATC
5545423 CATATC-ATCCAAAA
1 CATATCAATCCAAAA
5545437 CATATCAATCCAAAA
1 CATATCAATCCAAAA
5545452 -ATATC
1 CATATC
5545457 CAAAATGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (15 bp):
CATATCAATCCAAAA
Found at i:5547404 original size:44 final size:44
Alignment explanation
Indices: 5547355--5547452 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
5547345 ACCTTAGTGT
* **
5547355 TCGATGCACATTTAAGGAATGCATCGGTGTA-TCTTCATAGCGTA
1 TCGATGCACATTCAAGGAATGCATCGGTACACT-TTCATAGCGTA
* *
5547399 TCGATGCACATTCAGGGAATGCATCGGTACACTTTCATAGTGTA
1 TCGATGCACATTCAAGGAATGCATCGGTACACTTTCATAGCGTA
5547443 TCGATGCACA
1 TCGATGCACA
5547453 GTGCACAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 47 0.98
45 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (44 bp):
TCGATGCACATTCAAGGAATGCATCGGTACACTTTCATAGCGTA
Found at i:5547824 original size:17 final size:17
Alignment explanation
Indices: 5547802--5547834 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5547792 CTAATTGATG
5547802 CAAAGTATCAACATATT
1 CAAAGTATCAACATATT
5547819 CAAAGTATCAACATAT
1 CAAAGTATCAACATAT
5547835 ACTAGTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (17 bp):
CAAAGTATCAACATATT
Found at i:5559385 original size:16 final size:19
Alignment explanation
Indices: 5559345--5559389 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 19
5559335 AAAAGGACAA
5559345 TATCGATACCGAATGAGTAG
1 TATCGATACCGAATGAG-AG
5559365 TATCGATACC-AA-GAG-G
1 TATCGATACCGAATGAGAG
5559381 TATCGATAC
1 TATCGATAC
5559390 TAATGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.40
18 3 0.12
19 2 0.08
20 10 0.40
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (19 bp):
TATCGATACCGAATGAGAG
Found at i:5560220 original size:24 final size:24
Alignment explanation
Indices: 5560186--5560231 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5560176 GACATTTTAT
*
5560186 GCACTTCGGTGTAATTTCTACGTG
1 GCACTTCGGTGCAATTTCTACGTG
*
5560210 GCACTTTGGTGCAATTTCTACG
1 GCACTTCGGTGCAATTTCTACG
5560232 AGCTGTGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (24 bp):
GCACTTCGGTGCAATTTCTACGTG
Found at i:5560411 original size:348 final size:349
Alignment explanation
Indices: 5559892--5560563 Score: 1214
Period size: 348 Copynumber: 1.9 Consensus size: 349
5559882 ATTTCATCCT
5559892 ATGTGATTACATGAAATGTGAGGTAAACTATGTAGCATTTATTTATGTGATTACATAAAAATATG
1 ATGTGATTACATGAAATGTGAGGTAAACTATGTAGCATTTATTTATGTGATTACATAAAAATATG
5559957 ATATAAGCTATGTGAAAATGATATGTGATTATATGTCTAATATGTAATACAAGCTATGTGAAGTG
66 ATATAAGCTATGTGAAAATGATATGTGATTATATG-CTAATATGTAATACAAGCTATGTGAAGTG
*
5560022 TGTAAATGGTAAAGCCCATAAGTATGTGATATGATGCTAAAGCTATAATTGGCATGCCTAGAGTC
130 TGTAAATGGTAAAGCCCATAAGTATGTGATATGAAGCTAAAGCTATAATTGGCATGCCTAGAGTC
5560087 GAGGGTTCTGCGCGGGTCCTTCTAGCAA-TT-CGTAGTCCTTCAGGACATTTCTACGC-GGTCCT
195 GAGGGTTCTGCGCGGGT-CTTCTAG-AATTTACGTAGTCCTTCAGGACA-TTCTACGCGGGTCCT
5560149 TAGGTACAATACTATGTGGTCCTTCGGGACA-TTTTAT-GCACTTCGGTGTAATTTCTACGTGGC
257 TAGGTACAATACTATGTGGTCCTTCGGGACATTTTTATGGCACTTCGGTGTAATTTCTACGTGGC
5560212 ACTTTGGTGCAATTTCTACGAGCTGTGG
322 ACTTTGGTGCAATTTCTACGAGCTGTGG
5560240 ATGTGATTACATGAAATGTGAGGTAAACTATGTAGCATTTATTTATGTGATTACATAAAAATATG
1 ATGTGATTACATGAAATGTGAGGTAAACTATGTAGCATTTATTTATGTGATTACATAAAAATATG
5560305 ATATAAGCTATGTGAAAATGATATATGTGATTATATG-T-ATATGTAATACAAGCTATGTGAAGT
66 ATATAAGCTATGTGAAAATG--ATATGTGATTATATGCTAATATGTAATACAAGCTATGTGAAGT
5560368 GTGTAAATGGTAAAGCCCATAAGTATGTGATATGAAAGCTAAAGCTATAATTGGCATGCCTAGAG
129 GTGTAAATGGTAAAGCCCATAAGTATGTGATATG-AAGCTAAAGCTATAATTGGCATGCCTAGAG
5560433 TCGAGGGTTCTGCGCGGGTCTTCTAGAATTTACGTAGTCCTTCAGGACATTCTACGCGGGTCCTT
193 TCGAGGGTTCTGCGCGGGTCTTCTAGAATTTACGTAGTCCTTCAGGACATTCTACGCGGGTCCTT
*
5560498 AGGTACAATACTATGTGGTCCTTCGGGACATTTTTGTGGCACTTCGGTGTAATTTCTACGTGGCA
258 AGGTACAATACTATGTGGTCCTTCGGGACATTTTTATGGCACTTCGGTGTAATTTCTACGTGGCA
5560563 C
323 C
5560564 GGTCCTTAGG
Statistics
Matches: 314, Mismatches: 2, Indels: 14
0.95 0.01 0.04
Matches are distributed among these distances:
346 2 0.01
347 76 0.24
348 188 0.60
349 5 0.02
350 43 0.14
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (349 bp):
ATGTGATTACATGAAATGTGAGGTAAACTATGTAGCATTTATTTATGTGATTACATAAAAATATG
ATATAAGCTATGTGAAAATGATATGTGATTATATGCTAATATGTAATACAAGCTATGTGAAGTGT
GTAAATGGTAAAGCCCATAAGTATGTGATATGAAGCTAAAGCTATAATTGGCATGCCTAGAGTCG
AGGGTTCTGCGCGGGTCTTCTAGAATTTACGTAGTCCTTCAGGACATTCTACGCGGGTCCTTAGG
TACAATACTATGTGGTCCTTCGGGACATTTTTATGGCACTTCGGTGTAATTTCTACGTGGCACTT
TGGTGCAATTTCTACGAGCTGTGG
Found at i:5560562 original size:24 final size:24
Alignment explanation
Indices: 5560533--5560656 Score: 83
Period size: 24 Copynumber: 5.0 Consensus size: 24
5560523 GGACATTTTT
5560533 GTGGCACTTCGGTGTAATTTCTAC
1 GTGGCACTTCGGTGTAATTTCTAC
* ** * * *
5560557 GTGGCACGGTCCTTAGGTACAATACTAT
1 GTGGCAC-TTCGGT--GTA-ATTTCTAC
* *
5560585 GTGGTC-CTTCGG-G-ACATTTTTAT
1 GTGG-CACTTCGGTGTA-ATTTCTAC
5560608 GTGGCACTTCGGTGTAATTTCTAC
1 GTGGCACTTCGGTGTAATTTCTAC
* *
5560632 GTGGCACTTTGGTGCAATTTCTAC
1 GTGGCACTTCGGTGTAATTTCTAC
5560656 G
1 G
5560657 AGCTGTGGTG
Statistics
Matches: 76, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 17 0.22
24 38 0.50
25 4 0.05
27 5 0.07
28 10 0.13
29 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (24 bp):
GTGGCACTTCGGTGTAATTTCTAC
Found at i:5560882 original size:11 final size:11
Alignment explanation
Indices: 5560866--5560891 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5560856 TTTATATGAT
5560866 TTTATAAAATG
1 TTTATAAAATG
5560877 TTTATAAAATG
1 TTTATAAAATG
5560888 TTTA
1 TTTA
5560892 AGTGTTTTAA
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:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTATAAAATG
Found at i:5574662 original size:76 final size:76
Alignment explanation
Indices: 5574569--5574830 Score: 425
Period size: 76 Copynumber: 3.4 Consensus size: 76
5574559 GGATGAAATA
* * * * **
5574569 TTGAAATCATCATGCACTGAAGGGCTTACAGATGACCCAAAGATTTTGAAAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
* *
5574634 CCCAAGGCATT
66 CCGAAGGCTTT
5574645 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
5574710 CCGAAGGCTTT
66 CCGAAGGCTTT
* *
5574721 TTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTATGGCTTTGAAAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
5574786 CCGAAGGCTTT
66 CCGAAGGCTTT
*
5574797 TTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCATGCACTGCAGGACTTACAGATG
5574831 TGGGAAATAG
Statistics
Matches: 176, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 176 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
CCGAAGGCTTT
Found at i:5575699 original size:22 final size:22
Alignment explanation
Indices: 5575674--5575750 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
5575664 AATAAAGCTT
*
5575674 TCATCTTTGAAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
5575696 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
5575718 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
5575740 TCATCTTTGAA
1 TCATCTTTGAA
5575751 GAGTGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5577246 original size:13 final size:13
Alignment explanation
Indices: 5577228--5577253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5577218 ATACATCAAC
5577228 ATTCCTGATTCTG
1 ATTCCTGATTCTG
5577241 ATTCCTGATTCTG
1 ATTCCTGATTCTG
5577254 GAATAAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTCCTGATTCTG
Found at i:5578230 original size:31 final size:31
Alignment explanation
Indices: 5578195--5578257 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
5578185 AGAGGTGTGG
*
5578195 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTACAGAGTTGACAGAT
5578226 TCTGAATTCATCAATTACAGAGTTGACAGAT
1 TCTGAATTCATCAATTACAGAGTTGACAGAT
5578257 T
1 T
5578258 TTATATGTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (31 bp):
TCTGAATTCATCAATTACAGAGTTGACAGAT
Found at i:5580720 original size:4 final size:4
Alignment explanation
Indices: 5580695--5580765 Score: 60
Period size: 4 Copynumber: 17.8 Consensus size: 4
5580685 TTCTCCCCTT
* *
5580695 TTTC TTT- TTCC TTT- TTTT TTTC TTTC TTTC TTTC TTTC TTTGC TGGATT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C T---TTC
5580744 TTTC TTT- TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTT
5580766 GCTGGATGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 10 0.18
4 41 0.73
5 2 0.04
6 1 0.02
8 2 0.04
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:5580755 original size:30 final size:31
Alignment explanation
Indices: 5580711--5580772 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
5580701 TTTCCTTTTT
5580711 TTTTTCTTTCTTTCTTTCTTTCTTTGCTGGA
1 TTTTTCTTTCTTTCTTTCTTTCTTTGCTGGA
5580742 TTTTTCTTT-TTTCTTTCTTTCTTTGCTGGA
1 TTTTTCTTTCTTTCTTTCTTTCTTTGCTGGA
5580772 T
1 T
5580773 GAGTATAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.03, C:0.18, G:0.10, T:0.69
Consensus pattern (31 bp):
TTTTTCTTTCTTTCTTTCTTTCTTTGCTGGA
Found at i:5588370 original size:2 final size:2
Alignment explanation
Indices: 5588363--5588433 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
5588353 GGGCTTGTAG
5588363 TA TA TA 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
5588405 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5588434 ATAAAAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5591493 original size:10 final size:10
Alignment explanation
Indices: 5591476--5591523 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
5591466 AACACGCTGG
5591476 GCATCCGAGA
1 GCATCCGAGA
*
5591486 GTATCCGAG-
1 GCATCCGAGA
5591495 GCCATCCGAGA
1 G-CATCCGAGA
5591506 GCATCCGAG-
1 GCATCCGAGA
5591515 GCCATCCGA
1 G-CATCCGA
5591524 CCGAGGCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 30 0.91
11 1 0.03
ACGTcount: A:0.25, C:0.33, G:0.29, T:0.12
Consensus pattern (10 bp):
GCATCCGAGA
Found at i:5591502 original size:20 final size:20
Alignment explanation
Indices: 5591477--5591523 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
5591467 ACACGCTGGG
*
5591477 CATCCGAGAGTATCCGAGGC
1 CATCCGAGAGCATCCGAGGC
5591497 CATCCGAGAGCATCCGAGGC
1 CATCCGAGAGCATCCGAGGC
5591517 CATCCGA
1 CATCCGA
5591524 CCGAGGCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.34, G:0.28, T:0.13
Consensus pattern (20 bp):
CATCCGAGAGCATCCGAGGC
Found at i:5591529 original size:14 final size:14
Alignment explanation
Indices: 5591510--5591542 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5591500 CCGAGAGCAT
5591510 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
5591524 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
5591538 ACGAG
1 CCGAG
5591543 CTATGCGAGG
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:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:5591537 original size:10 final size:10
Alignment explanation
Indices: 5591488--5591523 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5591478 ATCCGAGAGT
5591488 ATCCGAGGCC
1 ATCCGAGGCC
5591498 ATCCGAGAG-C
1 ATCCGAG-GCC
5591508 ATCCGAGGCC
1 ATCCGAGGCC
5591518 ATCCGA
1 ATCCGA
5591524 CCGAGGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 22 0.92
11 1 0.04
ACGTcount: A:0.25, C:0.36, G:0.28, T:0.11
Consensus pattern (10 bp):
ATCCGAGGCC
Found at i:5591576 original size:33 final size:33
Alignment explanation
Indices: 5591524--5591596 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
5591514 GGCCATCCGA
* * *
5591524 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAACGAGCTATGCGAGGGAAT
*
5591557 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAACGAGCTATGCGAGGGAAT
*
5591590 CCAAGGG
1 CCGAGGG
5591597 AAGCCAAGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.27, G:0.37, T:0.10
Consensus pattern (33 bp):
CCGAGGGCAACCGAACGAGCTATGCGAGGGAAT
Found at i:5591607 original size:33 final size:33
Alignment explanation
Indices: 5591539--5591608 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
5591529 GCCATCCGAA
* * *
5591539 CGAGCTATGCGAGGGCATCCGAGGGCAACCGAG
1 CGAGCTATGCGAGGGAATCCAAGGGCAACCAAG
5591572 CGAGCTATGCGAGGGAATCCAAGGG-AAGCCAAG
1 CGAGCTATGCGAGGGAATCCAAGGGCAA-CCAAG
5591605 CGAG
1 CGAG
5591609 GGTAGGTCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.29, C:0.24, G:0.39, T:0.09
Consensus pattern (33 bp):
CGAGCTATGCGAGGGAATCCAAGGGCAACCAAG
Found at i:5591748 original size:29 final size:29
Alignment explanation
Indices: 5591697--5591753 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
5591687 GAGCAAGGGT
*
5591697 AGGTCGCCCGGAGTACATAGCGACCTACA
1 AGGTCGCCCGGAATACATAGCGACCTACA
* *
5591726 AGGTCGCCCGGAATGCATGGCGACCTAC
1 AGGTCGCCCGGAATACATAGCGACCTAC
5591754 GGCACCCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.32, G:0.30, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAATACATAGCGACCTACA
Found at i:5592829 original size:3 final size:3
Alignment explanation
Indices: 5592821--5592845 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5592811 TATCTTTTCG
5592821 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5592846 ATAAGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5593988 original size:15 final size:15
Alignment explanation
Indices: 5593950--5594057 Score: 157
Period size: 15 Copynumber: 7.3 Consensus size: 15
5593940 AAATAATTTT
5593950 AAATAATTTA--ATA
1 AAATAATTTATTATA
* * *
5593963 AGATTATTTATTTTA
1 AAATAATTTATTATA
5593978 AAATAATTTATTATA
1 AAATAATTTATTATA
5593993 AAATAATTTATTATA
1 AAATAATTTATTATA
5594008 AAATAATTTATTATA
1 AAATAATTTATTATA
*
5594023 AAATAATTTATTTTA
1 AAATAATTTATTATA
*
5594038 AAATAAATTATTATA
1 AAATAATTTATTATA
5594053 AAATA
1 AAATA
5594058 TGGATTGATT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
13 8 0.10
15 76 0.90
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (15 bp):
AAATAATTTATTATA
Found at i:5594120 original size:32 final size:31
Alignment explanation
Indices: 5594082--5594209 Score: 103
Period size: 22 Copynumber: 4.6 Consensus size: 31
5594072 TTAAAAAAAA
5594082 TTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAATAATTTATTAGTATG-ATTGAT
5594114 TTATTTT-AA-AA--TA-T-G---GATTGAT
1 TTATTTTAAATAATTTATTAGTATGATTGAT
*
5594136 TGATTTTAAATAATTTATTAGTATTGATTGAT
1 TTATTTTAAATAATTTATTAGTA-TGATTGAT
5594168 TTATTTT--A-AA---A-TA-TA-GATTGAT
1 TTATTTTAAATAATTTATTAGTATGATTGAT
5594190 TTATTTTAAATAATTTATTA
1 TTATTTTAAATAATTTATTA
5594210 TTGTAGTTGT
Statistics
Matches: 77, Mismatches: 2, Indels: 37
0.66 0.02 0.32
Matches are distributed among these distances:
22 26 0.34
23 3 0.04
24 5 0.06
25 4 0.05
26 4 0.05
27 2 0.03
28 4 0.05
29 4 0.05
30 3 0.04
31 2 0.03
32 20 0.26
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (31 bp):
TTATTTTAAATAATTTATTAGTATGATTGAT
Found at i:5594147 original size:54 final size:54
Alignment explanation
Indices: 5594084--5594209 Score: 218
Period size: 54 Copynumber: 2.3 Consensus size: 54
5594074 AAAAAAAATT
*
5594084 ATTTTAAATAATTTATTAGTA-TGAATTGATTTATTTTAAAATATGGATTGATTG
1 ATTTTAAATAATTTATTAGTATTG-ATTGATTTATTTTAAAATATAGATTGATTG
*
5594138 ATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATAGATTGATTT
1 ATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATAGATTGATTG
5594192 ATTTTAAATAATTTATTA
1 ATTTTAAATAATTTATTA
5594210 TTGTAGTTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
54 67 0.97
55 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (54 bp):
ATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATAGATTGATTG
Found at i:5597589 original size:21 final size:21
Alignment explanation
Indices: 5597565--5597610 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5597555 AATTTACGCA
5597565 TTTAGTA-TCTAAA-TTATTAAT
1 TTTAGTACT-TAAACTT-TTAAT
5597586 TTTAGTACTTAAACTTTTAAT
1 TTTAGTACTTAAACTTTTAAT
5597607 TTTA
1 TTTA
5597611 TGTTGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTAGTACTTAAACTTTTAAT
Found at i:5597704 original size:21 final size:22
Alignment explanation
Indices: 5597673--5597717 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
5597663 AAAAATTCGG
*
5597673 ATTCGGATCCGGATATTCGGAT
1 ATTCGGATCCGAATATTCGGAT
*
5597695 ATTC-GATCCGAATTTTCGGAT
1 ATTCGGATCCGAATATTCGGAT
5597716 AT
1 AT
5597718 CCGAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (22 bp):
ATTCGGATCCGAATATTCGGAT
Found at i:5597721 original size:16 final size:17
Alignment explanation
Indices: 5597700--5597732 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5597690 CGGATATTCG
5597700 ATCCGAA-TTTTCGGAT
1 ATCCGAATTTTTCGGAT
5597716 ATCCGAATTTTTCGGAT
1 ATCCGAATTTTTCGGAT
5597733 CGGATACAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (17 bp):
ATCCGAATTTTTCGGAT
Found at i:5599134 original size:19 final size:18
Alignment explanation
Indices: 5599086--5599173 Score: 83
Period size: 19 Copynumber: 4.8 Consensus size: 18
5599076 AGGGTGTCAA
*
5599086 AGTGCATCCATGCACCCCG
1 AGTGCATCCATGCA-CCTG
*
5599105 TAGTCCATCCATGCACCTG
1 -AGTGCATCCATGCACCTG
5599124 CAGTGCATCCATGCA-CT-
1 -AGTGCATCCATGCACCTG
* *
5599141 -GTGCATCGATGCAACTTG
1 AGTGCATCCATGC-ACCTG
5599159 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
5599174 TCCATTTCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
15 11 0.19
16 1 0.02
17 1 0.02
18 4 0.07
19 27 0.47
20 13 0.23
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (18 bp):
AGTGCATCCATGCACCTG
Found at i:5601047 original size:29 final size:29
Alignment explanation
Indices: 5600992--5601050 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5600982 AATTCATTAT
* * * *
5600992 TCTTTTATTCAACAGTGTTTTACCGTTCA
1 TCTTTTACTCAACAATATTTAACCGTTCA
*
5601021 TCTTTTACTCAACAATATTTAATCGTTCA
1 TCTTTTACTCAACAATATTTAACCGTTCA
5601050 T
1 T
5601051 TTAACTGGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (29 bp):
TCTTTTACTCAACAATATTTAACCGTTCA
Found at i:5601228 original size:68 final size:68
Alignment explanation
Indices: 5601119--5601286 Score: 230
Period size: 68 Copynumber: 2.5 Consensus size: 68
5601109 ACCCAACGGT
* * * * *
5601119 ACTTAACCGTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCCTCAAA
1 ACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATACACAGCTAGGCCTCAAA
*
5601184 GGC
66 GAC
* * * *
5601187 ACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTTAAA
1 ACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATACACAGCTAGGCCTCAAA
5601252 GAC
66 GAC
*
5601255 ACTTAGCCTTTCATCTAACTGGCAT-AATGACA
1 ACTTAGCCTTTCATCTAACTAGCATAAATGACA
5601287 TAAATGACAC
Statistics
Matches: 89, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 7 0.08
68 82 0.92
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30
Consensus pattern (68 bp):
ACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATACACAGCTAGGCCTCAAA
GAC
Found at i:5601486 original size:225 final size:225
Alignment explanation
Indices: 5601092--5601506 Score: 690
Period size: 225 Copynumber: 1.8 Consensus size: 225
5601082 AATGCACCGC
*
5601092 TAGGCCATTATTCTTTTACCCAACGGTACTTAACCGTTCATCTAACTTGCATAATTGACACCTTT
1 TAGGCCATTATTCTTTTACCCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
* * * *
5601157 CTGTCAAATACACAGCTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAAATGACACA
66 CTGTCAAATACACAGCTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTAGAAAAAATAACACA
5601222 TTTCTGTCATATGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAATGACA
131 TTTCTGTCATATGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAATGACA
5601287 TAAATGACACATTTCTTTCATCTGCACAGT
196 TAAATGACACATTTCTTTCATCTGCACAGT
* *
5601317 TAGGCCATTATTGTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
1 TAGGCCATTATTCTTTTACCCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
* * * *
5601382 CTGTCAAATGCACAGCTAGGCTTCAAAGGCATTTAATCTTTCATCTAA-TAGGAAAAAATAACAC
66 CTGTCAAATACACAGCTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTA-GAAAAAATAACAC
*
5601446 CTTTCTGTCATATGCACAGTTAGGCCTTAAAGGA-ACTTAGCCTTTCATCTAACTGGCATAA
130 ATTTCTGTCATATGCACAGTTAGGCCTTAAA-GACACTTAGCCTTTCATCTAACTGGCATAA
5601507 ATAACACCTT
Statistics
Matches: 176, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
224 2 0.01
225 172 0.98
226 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (225 bp):
TAGGCCATTATTCTTTTACCCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
CTGTCAAATACACAGCTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTAGAAAAAATAACACA
TTTCTGTCATATGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAATGACA
TAAATGACACATTTCTTTCATCTGCACAGT
Found at i:5601533 original size:68 final size:68
Alignment explanation
Indices: 5601344--5601536 Score: 255
Period size: 68 Copynumber: 2.8 Consensus size: 68
5601334 ACTCAACGGT
* * * * *
5601344 ACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCTTCAAA
1 ACTTAACCTTTCATCTAACTGGCATAAATAACACCTTTCTGTCATATGCACAGTTAGGCTTCAAA
*
5601409 GGC
66 GGA
* * * *
5601412 ATTTAATCTTTCATCTAA-TAGGAAAAAATAACACCTTTCTGTCATATGCACAGTTAGGCCTT-A
1 ACTTAACCTTTCATCTAACT-GGCATAAATAACACCTTTCTGTCATATGCACAGTTAGG-CTTCA
5601475 AAGGA
64 AAGGA
*
5601480 ACTTAGCCTTTCATCTAACTGGCATAAATAACACCTTTCTGTCATATGCACAGTTAG
1 ACTTAACCTTTCATCTAACTGGCATAAATAACACCTTTCTGTCATATGCACAGTTAG
5601537 TCCATTATTC
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
67 1 0.01
68 102 0.95
69 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (68 bp):
ACTTAACCTTTCATCTAACTGGCATAAATAACACCTTTCTGTCATATGCACAGTTAGGCTTCAAA
GGA
Found at i:5601889 original size:59 final size:59
Alignment explanation
Indices: 5601825--5601986 Score: 234
Period size: 59 Copynumber: 2.7 Consensus size: 59
5601815 TTCCCCTATG
* * * * *
5601825 GAAATTCATACATTTAGTATAAATCTCTTATCATTTTAGCACACAAGGTGCCCAATACA
1 GAAATTCATACATTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCAATACA
* * *
5601884 GAAATTCATACACTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCTATACG
1 GAAATTCATACATTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCAATACA
* *
5601943 GTAATTCATACATTGAGTATGAATTTCCTAACATTTTAGCACAC
1 GAAATTCATACATTTAGTATGAATTTCCTAACATTTTAGCACAC
5601987 TTAGTGCCAT
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 92 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (59 bp):
GAAATTCATACATTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCAATACA
Found at i:5602437 original size:94 final size:96
Alignment explanation
Indices: 5602275--5602497 Score: 265
Period size: 94 Copynumber: 2.4 Consensus size: 96
5602265 TCCAGTTCAA
* * * * * * * *
5602275 TAGTATCGATACTAC-TACCCTGGTACCGATACT-TCTATACTATGGTATCGATACTCCTTTATG
1 TAGTATCGATAC-CCTTACCATGGTATCGATACTATCTATACTATGATACCGATACCCCCTTACG
* *
5602338 GTATCGATATCAATTTTAGGTTTGAAGTTGCC
65 GTATCGATATCAATTTTAGATTCGAAGTTGCC
* * *
5602370 TAGTATTGATA-CCTTATCATGGTATCGATACTATC-ATACTATGATACCGATACCCCCTTCCGG
1 TAGTATCGATACCCTTACCATGGTATCGATACTATCTATACTATGATACCGATACCCCCTTACGG
* *
5602433 TATCGATATCAATTTTAGATTCGATGTTGCT
66 TATCGATATCAATTTTAGATTCGAAGTTGCC
*
5602464 TGGTATCGATACCCTTACCATGGTATCGATACTA
1 TAGTATCGATACCCTTACCATGGTATCGATACTA
5602498 CCTCGTTGGA
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
93 1 0.01
94 73 0.68
95 33 0.31
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (96 bp):
TAGTATCGATACCCTTACCATGGTATCGATACTATCTATACTATGATACCGATACCCCCTTACGG
TATCGATATCAATTTTAGATTCGAAGTTGCC
Found at i:5606254 original size:2 final size:2
Alignment explanation
Indices: 5606207--5606241 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5606197 TGTTGAACAT
5606207 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
5606242 CATCCCTATA
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:5606492 original size:110 final size:110
Alignment explanation
Indices: 5606322--5606521 Score: 256
Period size: 110 Copynumber: 1.8 Consensus size: 110
5606312 GGTATTTAGC
* * * * * * **
5606322 CTTTCATCTAACTTGCATATTTGACACTTTTCTGTCAAATGTATAGCTAATTCATTATTCTTTTA
1 CTTTCATCTAACTGGCATAATTAACACTTTTCTATCAAATGCACAGCTAAGCCATTATTCTTTTA
* ** *
5606387 TTCAACAGTGTTTTACCGTTCATCTTTTACTCAACAATATTTAAT
66 CTCAACAGTACTTAACCGTTCATCTTTTACTCAACAATATTTAAT
* * *
5606432 CTTTCATTTAACTGGCATAATTAACACTTTTCTATCAAATGCACCGCTAGGCCATTATTCTTTTA
1 CTTTCATCTAACTGGCATAATTAACACTTTTCTATCAAATGCACAGCTAAGCCATTATTCTTTTA
*
5606497 CTCAACGGTACTTAACCGTTCATCT
66 CTCAACAGTACTTAACCGTTCATCT
5606522 AATTGGCATA
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
110 74 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (110 bp):
CTTTCATCTAACTGGCATAATTAACACTTTTCTATCAAATGCACAGCTAAGCCATTATTCTTTTA
CTCAACAGTACTTAACCGTTCATCTTTTACTCAACAATATTTAAT
Found at i:5606545 original size:81 final size:81
Alignment explanation
Indices: 5606409--5606565 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
5606399 TTACCGTTCA
* * * * *
5606409 TCTTTTACTCAACAATATTTAATCTTTCATTTAACTGGCATAATTAACACTTTTCTATCAAATGC
1 TCTTTTACTCAACAATACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGC
*
5606474 ACCGCTAGGCCATTAT
66 ACAGCTAGGCCATTAT
** * * *
5606490 TCTTTTACTCAACGGTACTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTTTCAAATGC
1 TCTTTTACTCAACAATACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGC
5606555 ACAGCTAGGCC
66 ACAGCTAGGCC
5606566 TCAAAGGCAC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAACAATACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGC
ACAGCTAGGCCATTAT
Found at i:5606606 original size:68 final size:68
Alignment explanation
Indices: 5606497--5606623 Score: 164
Period size: 68 Copynumber: 1.9 Consensus size: 68
5606487 TATTCTTTTA
* * * * * *
5606497 CTCAACGGTACTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTTTCAAATGCACAGCTA
1 CTCAAAGGCACTTAACCGTTCATCGAACTGGCATAAATGACACATTTCTTTCAAATGCACAGCTA
5606562 GGC
66 GGC
* * * *
5606565 CTCAAAGGCACTTAGCCTTTCATCGAACTGGCATAAATGACACATTTTTTTCATATGCA
1 CTCAAAGGCACTTAACCGTTCATCGAACTGGCATAAATGACACATTTCTTTCAAATGCA
5606624 TAGTTAGTCC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 49 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAACCGTTCATCGAACTGGCATAAATGACACATTTCTTTCAAATGCACAGCTA
GGC
Found at i:5607002 original size:59 final size:60
Alignment explanation
Indices: 5606933--5607093 Score: 202
Period size: 59 Copynumber: 2.7 Consensus size: 60
5606923 TCCCCTATGG
* * *
5606933 AAATTCATACATTTAGTATGAATCTCTTATCATTTTAGCACACAAGGTGCCCAATA-AAT
1 AAATTCATACATTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACAAT
* * * * **
5606992 AAATTTATACACTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCTATACGGT
1 AAATTCATACATTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACAAT
*
5607052 -AATTCATACATTGAGTATGAATTTCTTAACATATTT-GCACAC
1 AAATTCATACATTTAGTATGAATTTCTTAACAT-TTTAGCACAC
5607094 TTAGTGCCAT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 83 0.95
60 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (60 bp):
AAATTCATACATTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACAAT
Found at i:5607544 original size:94 final size:96
Alignment explanation
Indices: 5607382--5607604 Score: 256
Period size: 94 Copynumber: 2.4 Consensus size: 96
5607372 TCCAGTTCAA
* * * * * * * *
5607382 TAGTATCGATACTAC-TACCCTGGTACCGATACT-TCTATACTATGGTATCGATACTCCTTTATG
1 TAGTATCGATAC-CCTTACCATGGTATCGATACTATCTATACTATGATACCGATACCCCCTTACG
* * *
5607445 GTATCGATCTCAATTTTAGGTTTGAAGTTGCC
65 GTATCGATATCAATTTTAGATTCGAAGTTGCC
* * *
5607477 TAGTATTGATA-CCTTATCATGGTATCGATACTATC-ATACTATGATACCGATACCCCCTTCCGG
1 TAGTATCGATACCCTTACCATGGTATCGATACTATCTATACTATGATACCGATACCCCCTTACGG
* *
5607540 TATCGATATCAATTTTAGATTCGATGTTGCT
66 TATCGATATCAATTTTAGATTCGAAGTTGCC
*
5607571 TGGTATCGATACCCTTACCATGGTATCGATACTA
1 TAGTATCGATACCCTTACCATGGTATCGATACTA
5607605 CCTCGTTGGA
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
93 1 0.01
94 72 0.68
95 33 0.31
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (96 bp):
TAGTATCGATACCCTTACCATGGTATCGATACTATCTATACTATGATACCGATACCCCCTTACGG
TATCGATATCAATTTTAGATTCGAAGTTGCC
Found at i:5607700 original size:20 final size:20
Alignment explanation
Indices: 5607671--5607716 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5607661 CCATTTTAGC
5607671 CTAT-AGTATCAGTAATGTT
1 CTATCAGTATCAGTAATGTT
* *
5607690 CTATCAGTATCGGTACTGTT
1 CTATCAGTATCAGTAATGTT
5607710 CTATCAG
1 CTATCAG
5607717 AATCGATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
CTATCAGTATCAGTAATGTT
Found at i:5608200 original size:3 final size:3
Alignment explanation
Indices: 5608192--5608226 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5608182 CTACTCACGT
5608192 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5608227 GAAATGCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5608895 original size:31 final size:31
Alignment explanation
Indices: 5608853--5608911 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5608843 TCGGGGTGTT
5608853 TTTCTTGTTATTGT-TTTCAATCTTAATTATA
1 TTTCTTGTTATTGTATTTCAAT-TTAATTATA
* *
5608884 TTTCTTTTTATTTTATTTCAATTTAATT
1 TTTCTTGTTATTGTATTTCAATTTAATT
5608912 CTTTATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.66
Consensus pattern (31 bp):
TTTCTTGTTATTGTATTTCAATTTAATTATA
Found at i:5613007 original size:63 final size:63
Alignment explanation
Indices: 5612888--5613031 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 63
5612878 ATGCACATGA
* ** * *
5612888 AGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATCAGTGTATCGATGCACAAG-T
1 AGTGCATCGATGCAC-CCCCTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCA-AAGTT
* * * * *
5612952 GGTGCATCGATGCACCCCCTAAAATACAAACATCGAATGAGATTTA-TGTACCGATGCATAGTT
1 AGTGCATCGATGCACCCCCTAAAATAAAAACATCGAATGACA-TCAGTGTACCGATGCAAAGTT
5613015 AGTGCATCGATGCACCC
1 AGTGCATCGATGCACCC
5613032 GTTAAGGGAT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.03
63 50 0.75
64 15 0.22
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (63 bp):
AGTGCATCGATGCACCCCCTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCAAAGTT
Found at i:5613625 original size:18 final size:20
Alignment explanation
Indices: 5613602--5613654 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 20
5613592 AGGGATTATC
5613602 AGTGGTCCTTCGGGAC-A-T
1 AGTGGTCCTTCGGGACAATT
* *
5613620 AGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGGACAATT
*
5613640 AGTGGTCATTCGGGA
1 AGTGGTCCTTCGGGA
5613655 TAAATTTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 13 0.46
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAATT
Found at i:5619941 original size:63 final size:63
Alignment explanation
Indices: 5619822--5619965 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 63
5619812 ATGCACATAA
** * *
5619822 AGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATCAGTGTATCGATGCACAAG-T
1 AGTGCATCGATGCAC-CCCCTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCA-AAGTT
* * * * *
5619886 GGTGCATCGATGCACCCCCTAAAATACAAACATCGAATGAGATTTA-TGTACCGATGCATAGTT
1 AGTGCATCGATGCACCCCCTAAAATAAAAACATCGAATGACA-TCAGTGTACCGATGCAAAGTT
*
5619949 AGTGCATCAATGCACCC
1 AGTGCATCGATGCACCC
5619966 GTTAAGGGAT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.03
63 49 0.73
64 16 0.24
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (63 bp):
AGTGCATCGATGCACCCCCTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCAAAGTT
Found at i:5620557 original size:18 final size:18
Alignment explanation
Indices: 5620534--5620607 Score: 76
Period size: 18 Copynumber: 4.0 Consensus size: 18
5620524 GAGGGATTAT
*
5620534 TAGTGGTCCTTCAGGACA
1 TAGTGGTCCTTCGGGACA
* *
5620552 TAGTGGTTCTTCGGAACAA
1 TAGTGGTCCTTCGGGAC-A
*
5620571 TCAGTGGTCCTTCGGGATA
1 T-AGTGGTCCTTCGGGACA
* *
5620590 TAATGGTCATTCGGGACA
1 TAGTGGTCCTTCGGGACA
5620608 AATTTTCAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
18 28 0.62
19 4 0.09
20 13 0.29
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:5623749 original size:29 final size:31
Alignment explanation
Indices: 5623693--5623756 Score: 114
Period size: 29 Copynumber: 2.1 Consensus size: 31
5623683 AACTATGGAG
5623693 CAATGGAATTTCAAAAGAGCAATGCTTAATT
1 CAATGGAATTTCAAAAGAGCAATGCTTAATT
5623724 CAAT-GAATTTCAAAA-AGCAATGCTTAATT
1 CAATGGAATTTCAAAAGAGCAATGCTTAATT
5623753 CAAT
1 CAAT
5623757 AGAGCAACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 18 0.55
30 11 0.33
31 4 0.12
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (31 bp):
CAATGGAATTTCAAAAGAGCAATGCTTAATT
Found at i:5630012 original size:19 final size:19
Alignment explanation
Indices: 5629985--5630021 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5629975 CTAAATGGAA
5629985 CTTACGCAATAACGAAGAG
1 CTTACGCAATAACGAAGAG
*
5630004 CTTATGCAATAACGAAGA
1 CTTACGCAATAACGAAGA
5630022 CTACATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
CTTACGCAATAACGAAGAG
Found at i:5642396 original size:17 final size:18
Alignment explanation
Indices: 5642353--5642393 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5642343 GAATTATATT
5642353 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
5642370 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
5642388 ATTAAA
1 AGTAAA
5642394 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:5642450 original size:10 final size:10
Alignment explanation
Indices: 5642435--5642485 Score: 93
Period size: 10 Copynumber: 5.1 Consensus size: 10
5642425 CTTAAACAGA
5642435 GAGAGAATTT
1 GAGAGAATTT
*
5642445 GAGAGAAATT
1 GAGAGAATTT
5642455 GAGAGAATTT
1 GAGAGAATTT
5642465 GAGAGAATTT
1 GAGAGAATTT
5642475 GAGAGAATTT
1 GAGAGAATTT
5642485 G
1 G
5642486 GTGTGATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.27
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:5651356 original size:32 final size:32
Alignment explanation
Indices: 5651320--5651423 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
5651310 TTTGTATTTA
5651320 CATATTTTGGAGACTGATGTTGGGAGCACCAT
1 CATATTTTGGAGACTGATGTTGGGAGCACCAT
*** * * * * *
5651352 CATATTTCAAATACTTACAT-TTGGTA-AACATAT
1 CATATTTTGGAGAC-T-GATGTTGGGAGCAC-CAT
*
5651385 TATATTTTGGAGACTGATGTTGGGAGCACCAT
1 CATATTTTGGAGACTGATGTTGGGAGCACCAT
5651417 CATATTT
1 CATATTT
5651424 CAAATACTTA
Statistics
Matches: 49, Mismatches: 18, Indels: 10
0.64 0.23 0.13
Matches are distributed among these distances:
31 2 0.04
32 26 0.53
33 19 0.39
34 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (32 bp):
CATATTTTGGAGACTGATGTTGGGAGCACCAT
Found at i:5651402 original size:65 final size:65
Alignment explanation
Indices: 5651321--5651459 Score: 278
Period size: 65 Copynumber: 2.1 Consensus size: 65
5651311 TTGTATTTAC
5651321 ATATTTTGGAGACTGATGTTGGGAGCACCATCATATTTCAAATACTTACATTTGGTAAACATATT
1 ATATTTTGGAGACTGATGTTGGGAGCACCATCATATTTCAAATACTTACATTTGGTAAACATATT
5651386 ATATTTTGGAGACTGATGTTGGGAGCACCATCATATTTCAAATACTTACATTTGGTAAACATATT
1 ATATTTTGGAGACTGATGTTGGGAGCACCATCATATTTCAAATACTTACATTTGGTAAACATATT
5651451 ATATTTTGG
1 ATATTTTGG
5651460 TTTTATGTCA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 74 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (65 bp):
ATATTTTGGAGACTGATGTTGGGAGCACCATCATATTTCAAATACTTACATTTGGTAAACATATT
Found at i:5651456 original size:33 final size:33
Alignment explanation
Indices: 5651353--5651456 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 33
5651343 GAGCACCATC
5651353 ATATTTCAAATACTTACATTTGGTAAACATATT
1 ATATTTCAAATACTTACATTTGGTAAACATATT
*** * * * * * *
5651386 ATATTTTGGAGAC-T-GATGTTGG-GAGCACCATC
1 ATATTTCAAATACTTACAT-TTGGTAAACA-TATT
5651418 ATATTTCAAATACTTACATTTGGTAAACATATT
1 ATATTTCAAATACTTACATTTGGTAAACATATT
5651451 ATATTT
1 ATATTT
5651457 TGGTTTTATG
Statistics
Matches: 48, Mismatches: 18, Indels: 10
0.63 0.24 0.13
Matches are distributed among these distances:
31 5 0.10
32 16 0.33
33 22 0.46
34 5 0.10
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (33 bp):
ATATTTCAAATACTTACATTTGGTAAACATATT
Found at i:5654569 original size:31 final size:32
Alignment explanation
Indices: 5654534--5654595 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
5654524 GGTATCCGAG
5654534 TACCCGACATA-CGGGTA-CCGCAAAATCCGGT
1 TACCCGA-ATATCGGGTACCCGCAAAATCCGGT
* *
5654565 TACCCGATTATCGGGTACCCGCAACATCCGG
1 TACCCGAATATCGGGTACCCGCAAAATCCGG
5654596 GTCGGGCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 2 0.07
31 13 0.48
32 12 0.44
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.18
Consensus pattern (32 bp):
TACCCGAATATCGGGTACCCGCAAAATCCGGT
Found at i:5656545 original size:30 final size:30
Alignment explanation
Indices: 5656509--5656570 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
5656499 AACGACGTTT
5656509 TTGAAAAATTACTCCCCCTTACTTTAACAC
1 TTGAAAAATTACTCCCCCTTACTTTAACAC
* *
5656539 TTGAAAAATTACTCTCCCTTATTTTAACAC
1 TTGAAAAATTACTCCCCCTTACTTTAACAC
5656569 TT
1 TT
5656571 CTCCCATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (30 bp):
TTGAAAAATTACTCCCCCTTACTTTAACAC
Found at i:5662813 original size:20 final size:20
Alignment explanation
Indices: 5662771--5662813 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5662761 TATTTTAATT
* *
5662771 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
5662791 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
5662811 TTT
1 TTT
5662814 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:5665211 original size:3 final size:3
Alignment explanation
Indices: 5665205--5665281 Score: 138
Period size: 3 Copynumber: 25.7 Consensus size: 3
5665195 AAAATAGATG
5665205 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
5665250 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5665282 GCATATATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 67 0.93
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.