Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 26
Found at i:1748216 original size:20 final size:19
Alignment explanation
Indices: 1748154--1748217 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
1748144 TCAGTAGAGA
1748154 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
1748173 CATCTGATAAAGGAGAAGAA--
1 -GT-TCAT-AATGAGAAGAACT
1748193 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
1748213 GTTCA
1 GTTCA
1748218 ACCTTAGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 10 0.30
18 3 0.09
19 1 0.03
20 6 0.18
21 3 0.09
22 10 0.30
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:1752850 original size:3 final size:3
Alignment explanation
Indices: 1752838--1752872 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1752828 CATCTTTTAA
1752838 TAT T-T TAT TAT TAT TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
1752873 ATAATTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1752868 original size:13 final size:13
Alignment explanation
Indices: 1752842--1752878 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1752832 TTTTAATATT
1752842 TTATTATT-ATTA
1 TTATTATTAATTA
1752854 TTATTATTAATTA
1 TTATTATTAATTA
*
1752867 TTATTAATAATT
1 TTATTATTAATT
1752879 TACATGCAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:1754723 original size:2 final size:2
Alignment explanation
Indices: 1754718--1754770 Score: 67
Period size: 2 Copynumber: 27.5 Consensus size: 2
1754708 TTCCCTCACG
*
1754718 TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA TA TC TA TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
1754758 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1754771 TTAGTGTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
1 3 0.07
2 41 0.91
3 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1761504 original size:22 final size:22
Alignment explanation
Indices: 1761456--1761497 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1761446 GGGAAAAAGA
1761456 AAAAAAAAGAATAAGGAAGAAT
1 AAAAAAAAGAATAAGGAAGAAT
1761478 AAAAAAAAGAATAAGGAAGA
1 AAAAAAAAGAATAAGGAAGA
1761498 TTGAAAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (22 bp):
AAAAAAAAGAATAAGGAAGAAT
Found at i:1764172 original size:42 final size:42
Alignment explanation
Indices: 1764125--1764305 Score: 263
Period size: 42 Copynumber: 4.3 Consensus size: 42
1764115 CCAAAATTTA
1764125 TAAATCCTTCAGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTCAGGTCATCAGTAAGTCTTCCGAGCATGATGCT
*
1764167 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTCAGGTCATCAGTAAGTCTTCCGAGCATGATGCT
*
1764209 TAAATCCTTCAGGTCATCAGTAAGTATTCCGAGCATGATGCT
1 TAAATCCTTCAGGTCATCAGTAAGTCTTCCGAGCATGATGCT
* * ** * * *
1764251 TAAATACTTCGGGTCATCTTTAAGCCTTTCGAGCATGATGAT
1 TAAATCCTTCAGGTCATCAGTAAGTCTTCCGAGCATGATGCT
* *
1764293 TAAGTCCTCCAGG
1 TAAATCCTTCAGG
1764306 CAATCTAAAG
Statistics
Matches: 124, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 124 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (42 bp):
TAAATCCTTCAGGTCATCAGTAAGTCTTCCGAGCATGATGCT
Found at i:1764354 original size:37 final size:37
Alignment explanation
Indices: 1764306--1764379 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1764296 GTCCTCCAGG
**
1764306 CAATCTAAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 CAATCTAAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
*
1764343 CAATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
1 CAATCTAAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
1764380 TCAGATATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (37 bp):
CAATCTAAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
Found at i:1764586 original size:111 final size:110
Alignment explanation
Indices: 1764381--1764746 Score: 513
Period size: 111 Copynumber: 3.3 Consensus size: 110
1764371 GAAGCAAATT
* *
1764381 CAGATATGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTTTTTCAAGATTTGATATTTCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATA-TTCCTG
* * *
1764446 AGTGACAGCGGAACAAATCTCCCCCGATTCAATGGATCAACTCTCC
65 AGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTCTCC
*
1764492 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCGG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATT-CCTG
** *
1764557 AGTGACAATGGAACAAGTCTACCCTGATTCAATGGATCAACTTTCC
65 AGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTCTCC
* * ** *
1764603 TAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCAAATCTCTTTCAAGATTTGATATTACTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATC-CCTCTCTTTCAAGATTTGATATTCCTG
*
1764668 AGTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACATC-CC
65 AGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAAC-TCTCC
*
1764714 CAGATCTAATATTCCCT--GAGTGACAGCGGAACA
1 CAGATCTGATATTCCCTCAGAG-GA-AGCGGAACA
1764747 AATCTCTCAT
Statistics
Matches: 228, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
109 2 0.01
110 4 0.02
111 200 0.88
112 22 0.10
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (110 bp):
CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCTGA
GTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTCTCC
Found at i:1764902 original size:3 final size:3
Alignment explanation
Indices: 1764894--1764932 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1764884 TTAATATTTC
1764894 ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1764933 ATTTACATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1764911 original size:20 final size:20
Alignment explanation
Indices: 1764894--1764932 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1764884 TTAATATTTC
1764894 ATTATTATTATTATTATTAT
1 ATTATTATTATTATTATTAT
1764914 ATTATTATTATTATTATTA
1 ATTATTATTATTATTATTA
1764933 ATTTACATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTATTATTATTATTATTAT
Found at i:1764916 original size:17 final size:17
Alignment explanation
Indices: 1764896--1764930 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1764886 AATATTTCAT
1764896 TATTATTATTATTATTA
1 TATTATTATTATTATTA
1764913 TATTATTATTATTATTA
1 TATTATTATTATTATTA
1764930 T
1 T
1764931 TAATTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:1768136 original size:11 final size:11
Alignment explanation
Indices: 1768095--1768168 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 11
1768085 GTTTTTATTT
*
1768095 TAATATTTAAA
1 TAATATTTTAA
*
1768106 TAAAATCTTTAA
1 TAATAT-TTTAA
1768118 TTTAATATTTTAA
1 --TAATATTTTAA
1768131 TAATA-TTTAA
1 TAATATTTTAA
*
1768141 TAATGATTACTAA
1 TAAT-ATT-TTAA
1768154 TAATGA-TTTAA
1 TAAT-ATTTTAA
1768165 TAAT
1 TAAT
1768169 GATAATAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
10 9 0.17
11 18 0.35
12 6 0.12
13 14 0.27
14 5 0.10
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
TAATATTTTAA
Found at i:1768154 original size:13 final size:11
Alignment explanation
Indices: 1768126--1768187 Score: 76
Period size: 11 Copynumber: 5.7 Consensus size: 11
1768116 AATTTAATAT
1768126 TTTAATAAT-A
1 TTTAATAATGA
1768136 TTTAATAATGA
1 TTTAATAATGA
1768147 TTACTAATAATGA
1 TT--TAATAATGA
1768160 TTTAATAATGA
1 TTTAATAATGA
1768171 --TAATAATGA
1 TTTAATAATGA
*
1768180 TTTGATAA
1 TTTAATAA
1768188 CATTTTTGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 17 0.37
13 11 0.24
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTAATAATGA
Found at i:1768174 original size:20 final size:22
Alignment explanation
Indices: 1768128--1768187 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
1768118 TTTAATATTT
1768128 TAATAAT-ATTTAATAATGATTAC
1 TAATAATGATTTAATAATG--TAC
1768151 TAATAATGATTTAATAATG-A-
1 TAATAATGATTTAATAATGTAC
*
1768171 TAATAATGATTTGATAA
1 TAATAATGATTTAATAA
1768188 CATTTTTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
20 16 0.46
21 1 0.03
23 7 0.20
24 11 0.31
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (22 bp):
TAATAATGATTTAATAATGTAC
Found at i:1768446 original size:11 final size:11
Alignment explanation
Indices: 1768416--1768468 Score: 61
Period size: 11 Copynumber: 4.4 Consensus size: 11
1768406 TAAAAATATT
1768416 TAATGATTTCATA
1 TAATGATTT-A-A
1768429 CTAATGATTTAA
1 -TAATGATTTAA
1768441 TAATGATTACTAA
1 TAATGATT--TAA
1768454 TAATGATTTAA
1 TAATGATTTAA
1768465 TAAT
1 TAAT
1768469 AATTATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 15 0.41
12 1 0.03
13 12 0.32
14 9 0.24
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:1768461 original size:24 final size:24
Alignment explanation
Indices: 1768416--1768610 Score: 103
Period size: 24 Copynumber: 7.9 Consensus size: 24
1768406 TAAAAATATT
* *
1768416 TAATGATTTCATACTAATGATTTAA
1 TAATGATTAC-TAATAATGATTTAA
1768441 TAATGATTACTAATAATGATTTAA
1 TAATGATTACTAATAATGATTTAA
* * **
1768465 TAATAATTATTAATTTAA--AAATAA
1 TAATGATTACTAA--TAATGATTTAA
* *
1768489 GAAATGATTTGA-TACTAATGATTTAA
1 -TAATGA-TT-ACTAATAATGATTTAA
*
1768515 TAATGATTACTAATTATGATTTAA
1 TAATGATTACTAATAATGATTTAA
* * **
1768539 TAATTATTATTAATTTAA--AAATAA
1 TAATGATTACTAA--TAATGATTTAA
* * * *
1768563 GAAATGATTTAATACTAATGATTTAG
1 -TAATGA-TTACTAATAATGATTTAA
*
1768589 TAATGATTATTAATAATGATTT
1 TAATGATTACTAATAATGATTT
1768611 CGTTGTGGTC
Statistics
Matches: 127, Mismatches: 29, Indels: 29
0.69 0.16 0.16
Matches are distributed among these distances:
23 1 0.01
24 77 0.61
25 27 0.21
26 21 0.17
27 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (24 bp):
TAATGATTACTAATAATGATTTAA
Found at i:1768477 original size:13 final size:13
Alignment explanation
Indices: 1768416--1768609 Score: 60
Period size: 13 Copynumber: 15.6 Consensus size: 13
1768406 TAAAAATATT
* *
1768416 TAATGATTTCATAC
1 TAATGA-TTAATAA
1768430 TAATGATT--TAA
1 TAATGATTAATAA
*
1768441 TAATGATTACTAA
1 TAATGATTAATAA
1768454 TAATGATTTAATAA
1 TAATGA-TTAATAA
* *
1768468 TAATTATTAAT-T
1 TAATGATTAATAA
1768480 TAA--A--AATAA
1 TAATGATTAATAA
* * *
1768489 GAAATGATTTGATAC
1 -TAATGA-TTAATAA
1768504 TAATGATT--TAA
1 TAATGATTAATAA
*
1768515 TAATGATTACTAA
1 TAATGATTAATAA
*
1768528 TTATGATTTAATAA
1 TAATGA-TTAATAA
* * *
1768542 TTATTATTAAT-T
1 TAATGATTAATAA
1768554 TAA--A--AATAA
1 TAATGATTAATAA
* *
1768563 GAAATGATTTAATAC
1 -TAATGA-TTAATAA
*
1768578 TAATGATT--TAG
1 TAATGATTAATAA
*
1768589 TAATGATTATTAA
1 TAATGATTAATAA
1768602 TAATGATT
1 TAATGATT
1768610 TCGTTGTGGT
Statistics
Matches: 137, Mismatches: 21, Indels: 45
0.67 0.10 0.22
Matches are distributed among these distances:
8 6 0.04
10 6 0.04
11 30 0.22
12 7 0.05
13 43 0.31
14 38 0.28
15 7 0.05
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (13 bp):
TAATGATTAATAA
Found at i:1768495 original size:74 final size:74
Alignment explanation
Indices: 1768400--1768610 Score: 341
Period size: 74 Copynumber: 2.9 Consensus size: 74
1768390 ATTGAATTTT
*** *
1768400 TTAATTTAAAAATATTTAATGATTTCATACTAATGATTTAATAATGATTACTAATAATGATTTAA
1 TTAATTTAAAAATAAGAAATGATTTAATACTAATGATTTAATAATGATTACTAATAATGATTTAA
1768465 TAATAATTA
66 TAATAATTA
* *
1768474 TTAATTTAAAAATAAGAAATGATTTGATACTAATGATTTAATAATGATTACTAATTATGATTTAA
1 TTAATTTAAAAATAAGAAATGATTTAATACTAATGATTTAATAATGATTACTAATAATGATTTAA
*
1768539 TAATTATTA
66 TAATAATTA
* *
1768548 TTAATTTAAAAATAAGAAATGATTTAATACTAATGATTTAGTAATGATTATTAATAATGATTT
1 TTAATTTAAAAATAAGAAATGATTTAATACTAATGATTTAATAATGATTACTAATAATGATTT
1768611 CGTTGTGGTC
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 127 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (74 bp):
TTAATTTAAAAATAAGAAATGATTTAATACTAATGATTTAATAATGATTACTAATAATGATTTAA
TAATAATTA
Found at i:1768520 original size:11 final size:11
Alignment explanation
Indices: 1768504--1768542 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1768494 GATTTGATAC
1768504 TAATGATTTAA
1 TAATGATTTAA
1768515 TAATGATTACTAA
1 TAATGATT--TAA
*
1768528 TTATGATTTAA
1 TAATGATTTAA
1768539 TAAT
1 TAAT
1768543 TATTATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 14 0.58
13 10 0.42
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:1770072 original size:24 final size:24
Alignment explanation
Indices: 1770040--1770145 Score: 83
Period size: 24 Copynumber: 4.4 Consensus size: 24
1770030 GACCACAATG
1770040 AAATCATTATTAGTAATCATTACT
1 AAATCATTATTAGTAATCATTACT
* *
1770064 AAATCATTAGTA-TCAAATCATTTCT
1 AAATCATTATTAGT--AATCATTACT
* * * * *
1770089 -TA-CTTTAAATTAATAATAATTATT
1 AAATCATT--ATTAGTAATCATTACT
*
1770113 AAATCATTATTAGTAATCATTATT
1 AAATCATTATTAGTAATCATTACT
1770137 AAATCATTA
1 AAATCATTA
1770146 GTATCAAATC
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
23 4 0.06
24 42 0.67
25 13 0.21
26 4 0.06
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (24 bp):
AAATCATTATTAGTAATCATTACT
Found at i:1770123 original size:11 final size:11
Alignment explanation
Indices: 1770107--1770159 Score: 61
Period size: 11 Copynumber: 4.4 Consensus size: 11
1770097 ATTAATAATA
1770107 ATTATTAAATC
1 ATTATTAAATC
1770118 ATTATTAGTAATC
1 ATTATTA--AATC
1770131 ATTATTAAATC
1 ATTATTAAATC
1770142 ATTAGTATCAAATC
1 ATTA-T-T-AAATC
1770156 ATTA
1 ATTA
1770160 AATATTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 15 0.41
12 1 0.03
13 12 0.32
14 9 0.24
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:1770156 original size:38 final size:38
Alignment explanation
Indices: 1770040--1770159 Score: 126
Period size: 38 Copynumber: 3.2 Consensus size: 38
1770030 GACCACAATG
*
1770040 AAATCATTATTAGTAATCATTACTAAATCATTAGTATC
1 AAATCATTATTAGTAATCATTAATAAATCATTAGTATC
* * *
1770078 AAATCATTTCTTACTTTAA--ATTAAT-AATAATTA-T-T-
1 AAATCA-TTATTA--GTAATCATTAATAAATCATTAGTATC
*
1770113 AAATCATTATTAGTAATCATTATTAAATCATTAGTATC
1 AAATCATTATTAGTAATCATTAATAAATCATTAGTATC
1770151 AAATCATTA
1 AAATCATTA
1770160 AATATTTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
32 3 0.05
34 10 0.15
35 13 0.20
36 2 0.03
37 2 0.03
38 22 0.34
39 10 0.15
41 3 0.05
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.42
Consensus pattern (38 bp):
AAATCATTATTAGTAATCATTAATAAATCATTAGTATC
Found at i:1770372 original size:18 final size:18
Alignment explanation
Indices: 1770349--1770389 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1770339 AAGTAATCAT
1770349 TATTATCAAATCAATT-AA
1 TATTATCAAATC-ATTAAA
*
1770367 TATTATTAAATCATTAAA
1 TATTATCAAATCATTAAA
1770385 TATTA
1 TATTA
1770390 AAATTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTATCAAATCATTAAA
Found at i:1770408 original size:26 final size:26
Alignment explanation
Indices: 1770379--1770428 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1770369 TTATTAAATC
* *
1770379 ATTAAATATTAAAATTAAATCATTTT
1 ATTAAATATTAAAATAAAAACATTTT
1770405 ATTAAATATTAAAATAAAAACATT
1 ATTAAATATTAAAATAAAAACATT
1770429 GTTGAATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTAAATATTAAAATAAAAACATTTT
Found at i:1770877 original size:214 final size:214
Alignment explanation
Indices: 1770630--1771059 Score: 860
Period size: 214 Copynumber: 2.0 Consensus size: 214
1770620 CAAGGCATTC
1770630 ATGGGTTCACTGTAGATATCACCCCATTTGGAGAAATAATAAATAAAGTGTATTTTTTTGGGAAA
1 ATGGGTTCACTGTAGATATCACCCCATTTGGAGAAATAATAAATAAAGTGTATTTTTTTGGGAAA
1770695 TAATATACCTCATATGCATTATTTCAGCTATTTTGCTAATAATTTGGATGTGCTGTGTCGGGAGG
66 TAATATACCTCATATGCATTATTTCAGCTATTTTGCTAATAATTTGGATGTGCTGTGTCGGGAGG
1770760 GGTTTCGAAAGTGATGTTTTATAATAAATTCAAAAGTTAAAGGTAATTTGCAACTACTGCAGTGA
131 GGTTTCGAAAGTGATGTTTTATAATAAATTCAAAAGTTAAAGGTAATTTGCAACTACTGCAGTGA
1770825 GCCTCTAACTGAGGAGTTT
196 GCCTCTAACTGAGGAGTTT
1770844 ATGGGTTCACTGTAGATATCACCCCATTTGGAGAAATAATAAATAAAGTGTATTTTTTTGGGAAA
1 ATGGGTTCACTGTAGATATCACCCCATTTGGAGAAATAATAAATAAAGTGTATTTTTTTGGGAAA
1770909 TAATATACCTCATATGCATTATTTCAGCTATTTTGCTAATAATTTGGATGTGCTGTGTCGGGAGG
66 TAATATACCTCATATGCATTATTTCAGCTATTTTGCTAATAATTTGGATGTGCTGTGTCGGGAGG
1770974 GGTTTCGAAAGTGATGTTTTATAATAAATTCAAAAGTTAAAGGTAATTTGCAACTACTGCAGTGA
131 GGTTTCGAAAGTGATGTTTTATAATAAATTCAAAAGTTAAAGGTAATTTGCAACTACTGCAGTGA
1771039 GCCTCTAACTGAGGAGTTT
196 GCCTCTAACTGAGGAGTTT
1771058 AT
1 AT
1771060 TATTATTTCT
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 216 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (214 bp):
ATGGGTTCACTGTAGATATCACCCCATTTGGAGAAATAATAAATAAAGTGTATTTTTTTGGGAAA
TAATATACCTCATATGCATTATTTCAGCTATTTTGCTAATAATTTGGATGTGCTGTGTCGGGAGG
GGTTTCGAAAGTGATGTTTTATAATAAATTCAAAAGTTAAAGGTAATTTGCAACTACTGCAGTGA
GCCTCTAACTGAGGAGTTT
Found at i:1771453 original size:17 final size:17
Alignment explanation
Indices: 1771431--1771474 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1771421 TTTAGGTTGG
*
1771431 TTCGACTCGATTTTGAA
1 TTCGACTCGATTTCGAA
*
1771448 TTCGACTTGATTTCGAA
1 TTCGACTCGATTTCGAA
1771465 TTCGACTCGA
1 TTCGACTCGA
1771475 GACATTAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (17 bp):
TTCGACTCGATTTCGAA
Found at i:1771934 original size:16 final size:16
Alignment explanation
Indices: 1771901--1771957 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
1771891 GAAAGTGAGC
* **
1771901 AACGAGCATCGAGTTT
1 AACGAGCAACGAACTT
1771917 AACGAGCAACGAACTT
1 AACGAGCAACGAACTT
** *
1771933 AACGAATAATGAACTT
1 AACGAGCAACGAACTT
1771949 AACGAGCAA
1 AACGAGCAA
1771958 TAAATTTTCT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (16 bp):
AACGAGCAACGAACTT
Found at i:1771970 original size:19 final size:20
Alignment explanation
Indices: 1771948--1771995 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 20
1771938 ATAATGAACT
1771948 TAACGAGCAATAAA-TTTTC
1 TAACGAGCAATAAATTTTTC
1771967 TAACGAGCAATAAATTTTTC
1 TAACGAGCAATAAATTTTTC
1771987 TAACGAGCA
1 TAACGAGCA
1771996 CAAGTGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (20 bp):
TAACGAGCAATAAATTTTTC
Found at i:1772810 original size:21 final size:20
Alignment explanation
Indices: 1772725--1772881 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1772715 AAATGACCAA
**
1772725 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
***
1772744 -AAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1772763 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1772783 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1772804 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1772825 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1772845 CCAAAATTGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1772866 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1772882 ACACATAAAT
Statistics
Matches: 102, Mismatches: 29, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
18 15 0.15
19 1 0.01
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1772891 original size:20 final size:20
Alignment explanation
Indices: 1772868--1773038 Score: 202
Period size: 20 Copynumber: 8.5 Consensus size: 20
1772858 GCGAATATGA
* *
1772868 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
1772888 AAATCGTAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1772908 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1772928 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1772948 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1772968 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1772988 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1773008 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1773029 AAATCGCAAC
1 AAATCGCAAC
1773039 ACGATATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 108 0.85
21 17 0.13
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1772933 original size:60 final size:60
Alignment explanation
Indices: 1772868--1773038 Score: 234
Period size: 60 Copynumber: 2.8 Consensus size: 60
1772858 GCGAATATGA
* * *
1772868 AAATCGCAACGCGAACACATAAATCGTAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
1772928 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
**
1772988 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAAC
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAAC
1773039 ACGATATTTA
Statistics
Matches: 93, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 65 0.70
61 28 0.30
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:1773458 original size:33 final size:33
Alignment explanation
Indices: 1773419--1773489 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1773409 TTCACTTAGA
*
1773419 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1773452 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1773485 TTTCA
1 TTTCA
1773490 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1773592 original size:21 final size:20
Alignment explanation
Indices: 1773566--1773671 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
1773556 TGCAGAAGAG
1773566 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1773587 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1773607 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
1773628 TCGCAATGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1773642 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1773661 TCGCAACGAGA
1 TCGCAACGAGA
1773672 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1773623 original size:41 final size:38
Alignment explanation
Indices: 1773559--1773675 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
1773549 TTCAATTTGC
* *
1773559 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1773597 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAATGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1773638 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1773671 AGAAT
1 AGAAT
1773676 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.16, G:0.26, T:0.12
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1773655 original size:33 final size:33
Alignment explanation
Indices: 1773618--1773698 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1773608 CGCAACGAGA
*
1773618 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1773651 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1773684 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1773699 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1773678 original size:14 final size:14
Alignment explanation
Indices: 1773626--1773682 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1773616 GAGAAATGAA
*
1773626 AATCGCAATGAGAG
1 AATCGCAACGAGAG
*
1773640 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1773659 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1773673 AATCGCAACG
1 AATCGCAACG
1773683 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1773716 original size:19 final size:19
Alignment explanation
Indices: 1773694--1773821 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
1773684 GAAACCAAAA
*
1773694 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1773713 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1773727 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1773746 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1773760 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1773780 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1773800 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1773820 TC
1 TC
1773822 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1773735 original size:14 final size:14
Alignment explanation
Indices: 1773716--1773772 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1773706 TTTCATTTCG
1773716 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1773730 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1773749 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1773763 CGTTGCGATT
1 CGTTGCGATT
1773773 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1773741 original size:33 final size:33
Alignment explanation
Indices: 1773699--1773821 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1773689 CAAAATCGCA
1773699 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1773732 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1773765 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
1773806 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1773822 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1773783 original size:21 final size:21
Alignment explanation
Indices: 1773757--1773821 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1773747 CGCGTTGCGA
1773757 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1773778 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1773798 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1773819 TTC
1 TTC
1773822 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1775673 original size:93 final size:93
Alignment explanation
Indices: 1775514--1776165 Score: 1258
Period size: 93 Copynumber: 7.1 Consensus size: 93
1775504 TAGATTGCTT
*
1775514 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775579 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1775607 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775672 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1775700 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775764 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1775792 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775856 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1775884 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775949 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1775977 AGTAAATTTTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1776042 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1776070 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1776135 TTTGTCTTTGTTTTGTC-TTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1776161 AGTAA
1 AGTAA
1776166 TGCAATCCAT
Statistics
Matches: 554, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
91 6 0.01
92 192 0.35
93 356 0.64
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1775745 original size:185 final size:186
Alignment explanation
Indices: 1775514--1776165 Score: 1258
Period size: 185 Copynumber: 3.5 Consensus size: 186
1775504 TAGATTGCTT
*
1775514 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775579 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1775644 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1775700 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775764 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1775829 GTGTATTCTTTAACACTGTG-AATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1775884 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1775949 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTTTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1776014 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1776070 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1776135 TTTGTCTTTGTTTTGTC-TTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
1776166 TGCAATCCAT
Statistics
Matches: 462, Mismatches: 2, Indels: 6
0.98 0.00 0.01
Matches are distributed among these distances:
184 47 0.10
185 292 0.63
186 123 0.27
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1776016 original size:278 final size:278
Alignment explanation
Indices: 1775514--1776165 Score: 1256
Period size: 278 Copynumber: 2.4 Consensus size: 278
1775504 TAGATTGCTT
*
1775514 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775579 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1775644 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTG
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTG
1775709 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
1775774 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
1775792 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1775856 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1775921 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAA-TT
*
1775986 TTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
195 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
1776051 GTTTTGTCTTTTGGTTGAA
260 GTTTTGTCTTTTGGTTGAA
1776070 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1776135 TTTGTCTTTGTTTTGTC-TTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
1776166 TGCAATCCAT
Statistics
Matches: 370, Mismatches: 2, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
277 140 0.38
278 206 0.56
279 24 0.06
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTG
TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
TTTTGTCTTTTGGTTGAA
Found at i:1776292 original size:33 final size:32
Alignment explanation
Indices: 1776249--1776341 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1776239 CGCGAAACCA
**
1776249 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
1776281 AGAATCGCAACGCGAAACCAAAATCGCAGCGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1776314 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1776342 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.45, C:0.28, G:0.19, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1776339 original size:52 final size:52
Alignment explanation
Indices: 1776213--1776341 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
1776203 TAGTTTACTT
**
1776213 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * * *
1776265 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAGCGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1776318 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1776342 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1776347 original size:19 final size:19
Alignment explanation
Indices: 1776213--1776341 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1776203 TAGTTTACTT
* *
1776213 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1776233 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1776252 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1776271 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1776285 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1776304 TCGC-A-GCG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1776318 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1776337 TCGCA
1 TCGCA
1776342 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 17 0.19
15 3 0.03
16 5 0.06
17 5 0.06
18 3 0.03
19 44 0.49
20 13 0.14
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1776359 original size:19 final size:19
Alignment explanation
Indices: 1776337--1776508 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
1776327 GAAACCAAAA
*
1776337 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1776356 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1776372 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1776389 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1776405 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1776422 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1776441 TCGCGTTGCGA-TTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1776459 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
1776478 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1776498 TCGTGTTGCGA
1 TCGCGTTGCGA
1776509 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 15, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
18 17 0.13
19 60 0.48
20 12 0.10
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1776378 original size:14 final size:14
Alignment explanation
Indices: 1776359--1776415 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1776349 TTTCATTTCG
1776359 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1776373 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1776390 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1776406 CGTTGCGATT
1 CGTTGCGATT
1776416 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1776384 original size:33 final size:33
Alignment explanation
Indices: 1776342--1776434 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1776332 CAAAATCGCA
*
1776342 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1776375 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1776408 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1776435 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1776480 original size:37 final size:37
Alignment explanation
Indices: 1776337--1776491 Score: 132
Period size: 33 Copynumber: 4.4 Consensus size: 37
1776327 GAAACCAAAA
*
1776337 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGA-TTTCATTTCGCGTTGCGATTATCATT
* *
1776372 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGA-TTTCATTTCGCGTTGCGATTATCATT
* **
1776405 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGA-TTTCATTTCGCGTTGCGATTATCATT
** *
1776441 TCGCGTTGCGATTTGGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTCATTTCGCGTTGCGATTATCATT
1776478 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1776492 TAAGTTTCGT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
33 56 0.54
34 1 0.01
35 2 0.02
36 2 0.02
37 34 0.33
38 8 0.08
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (37 bp):
TCGCGTTGCGATTTCATTTCGCGTTGCGATTATCATT
Found at i:1778441 original size:14 final size:14
Alignment explanation
Indices: 1778422--1778457 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1778412 ATTGTTTAAT
1778422 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1778436 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1778450 TGATTTGT
1 TGATTTGT
1778458 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1778580 original size:19 final size:19
Alignment explanation
Indices: 1778564--1778661 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1778554 AAAAATGACT
1778564 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1778583 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1778602 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1778616 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1778635 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1778655 ATCGCAA
1 ATCGCAA
1778662 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1778693 original size:53 final size:53
Alignment explanation
Indices: 1778564--1778680 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1778554 AAAAATGACT
1778564 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1778616 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1778669 ATCGCAATGCGA
1 ATCGCAATGCGA
1778681 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1778698 original size:19 final size:19
Alignment explanation
Indices: 1778670--1778872 Score: 194
Period size: 19 Copynumber: 11.7 Consensus size: 19
1778660 AACGAGAGAA
* *
1778670 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1778689 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1778705 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1778722 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1778741 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1778757 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1778774 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1778793 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1778809 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1778826 TCCGCATTACGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1778844 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1778860 TCGCATTGCGATT
1 TCGCATTGCGATT
1778873 CTCTCGTTGC
Statistics
Matches: 151, Mismatches: 12, Indels: 42
0.74 0.06 0.20
Matches are distributed among these distances:
14 28 0.19
16 23 0.15
17 19 0.13
18 3 0.02
19 67 0.44
20 11 0.07
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1778733 original size:52 final size:52
Alignment explanation
Indices: 1778670--1778844 Score: 314
Period size: 52 Copynumber: 3.3 Consensus size: 52
1778660 AACGAGAGAA
* *
1778670 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1778722 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1778774 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1778826 TCCGCATTACGATTTTCAT
1 T-CGCATTGCGATTTTCAT
1778845 GTTGGGATTT
Statistics
Matches: 119, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 103 0.87
53 16 0.13
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1778894 original size:33 final size:33
Alignment explanation
Indices: 1778676--1778886 Score: 214
Period size: 33 Copynumber: 6.2 Consensus size: 33
1778666 AGAATCGCAA
*
1778676 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1778709 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
1778747 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
1778780 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
1778813 TGCGATTTTCATTTCCGCATTACGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
1778847 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1778880 TGCGATT
1 TGCGATT
1778887 GTAATTTCCG
Statistics
Matches: 145, Mismatches: 19, Indels: 28
0.76 0.10 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 70 0.48
34 28 0.19
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1781390 original size:24 final size:24
Alignment explanation
Indices: 1781356--1781402 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1781346 CTGAAACATC
1781356 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1781380 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1781403 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1782112 original size:20 final size:20
Alignment explanation
Indices: 1782084--1782313 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
1782074 AAATTTCAGT
* * *
1782084 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1782104 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1782124 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1782144 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1782164 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1782184 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1782204 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1782224 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1782244 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1782264 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1782284 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1782304 GTTGCGATTT
1 GTTGCGATTT
1782314 TGAAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1782330 original size:21 final size:21
Alignment explanation
Indices: 1782300--1782378 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 21
1782290 ATTTTCATAT
*
1782300 TCGCGTTGCGATTTTGAAAAA
1 TCGCATTGCGATTTTGAAAAA
* * * **
1782321 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGAAAAA
* * *
1782342 TCGCATTACGATTTTTAAGAA
1 TCGCATTGCGATTTTGAAAAA
*
1782363 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
1782379 GAAACTGATT
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTGAAAAA
Found at i:1783307 original size:20 final size:20
Alignment explanation
Indices: 1783284--1783367 Score: 55
Period size: 22 Copynumber: 4.0 Consensus size: 20
1783274 ATAATATTAT
1783284 TTATTAAAAAATTATTAATA
1 TTATTAAAAAATTATTAATA
** *
1783304 TTATTTTTTAAAATTTTATAATAA
1 TTA--TTAAAAAATTAT-TAAT-A
* *
1783328 TTTATT-TAACATTA-TAATA
1 -TTATTAAAAAATTATTAATA
1783347 TTATTCAAAAAATTATTAATA
1 TTATT-AAAAAATTATTAATA
1783368 AATATATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
18 5 0.10
19 1 0.02
20 13 0.27
21 5 0.10
22 15 0.31
23 6 0.12
24 1 0.02
25 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAAAAAATTATTAATA
Found at i:1783335 original size:22 final size:22
Alignment explanation
Indices: 1783282--1783394 Score: 69
Period size: 24 Copynumber: 5.2 Consensus size: 22
1783272 AAATAATATT
*
1783282 ATTTA-TTAAAAAATTATTAATA
1 ATTTATTTAAAATATTA-TAATA
*
1783304 TTATTT-TTTAAAATTTTATAATA
1 --ATTTATTTAAAATATTATAATA
*
1783327 ATTTATTT--AACATTATAAT-
1 ATTTATTTAAAATATTATAATA
* *
1783346 A-TTATTCAAAAAATTATTAATAA
1 ATTTATTTAAAATATTA-TAAT-A
* *
1783369 ATATATTTTAAATATT-TAATA
1 ATTTATTTAAAATATTATAATA
1783390 ATTTA
1 ATTTA
1783395 CTAATATTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
18 5 0.07
19 1 0.01
20 15 0.21
21 13 0.19
22 7 0.10
23 6 0.09
24 23 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTATTTAAAATATTATAATA
Found at i:1783456 original size:18 final size:20
Alignment explanation
Indices: 1783433--1783473 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
1783423 GAAATTAAGG
1783433 TATAATATCATAT-AT-TAT
1 TATAATATCATATCATATAT
1783451 TATAATATCATATCATATAT
1 TATAATATCATATCATATAT
1783471 TAT
1 TAT
1783474 TATAAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.62
19 2 0.10
20 6 0.29
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAATATCATATCATATAT
Found at i:1784212 original size:14 final size:14
Alignment explanation
Indices: 1784193--1784223 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1784183 TAATTGAATC
*
1784193 TTATTATTGCATCA
1 TTATTATTGCAACA
1784207 TTATTATTGCAACA
1 TTATTATTGCAACA
1784221 TTA
1 TTA
1784224 AATATTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (14 bp):
TTATTATTGCAACA
Found at i:1788211 original size:5 final size:5
Alignment explanation
Indices: 1788201--1788348 Score: 268
Period size: 5 Copynumber: 30.4 Consensus size: 5
1788191 GCCTAAAGAA
1788201 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-T-T
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1788249 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1788299 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-T-T ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1788347 AT
1 AT
1788349 CCGTTAATAA
Statistics
Matches: 139, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
3 4 0.03
4 4 0.03
5 131 0.94
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:1788682 original size:2 final size:2
Alignment explanation
Indices: 1788677--1788748 Score: 50
Period size: 2 Copynumber: 39.5 Consensus size: 2
1788667 TTTAAATTAA
* * * *
1788677 AT AT AT AA AT AT -T AT AT AT AT AT AT -T A- AT TT AA AT -T AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1788715 AT TT AT -T A- AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1788749 ATTATTATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
1 7 0.13
2 46 0.87
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1788711 original size:38 final size:38
Alignment explanation
Indices: 1788666--1788739 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
1788656 ATATGTATAT
1788666 ATTTAAATTAAATATATAAATATTATATATATATATTA
1 ATTTAAATTAAATATATAAATATTATATATATATATTA
* *
1788704 ATTTAAATTAAATTTATTAATATTATATATATATAT
1 ATTTAAATTAAATATATAAATATTATATATATATAT
1788740 ATATATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
ATTTAAATTAAATATATAAATATTATATATATATATTA
Found at i:1788722 original size:32 final size:35
Alignment explanation
Indices: 1788656--1788735 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 35
1788646 ATCGGGCCAG
1788656 ATATGTATATAT-TTAAATTAAATATATAAATATT-
1 ATAT-TATATATATTAAATTAAATATATAAATATTA
* *
1788690 ATA-TATATATATTAATTTAAAT-TA-AATTTATTA
1 ATATTATATATATTAAATTAAATATATAA-ATATTA
1788723 ATATTATATATAT
1 ATATTATATATAT
1788736 ATATATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 2 0.05
32 13 0.32
33 13 0.32
34 12 0.30
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (35 bp):
ATATTATATATATTAAATTAAATATATAAATATTA
Found at i:1790231 original size:2 final size:2
Alignment explanation
Indices: 1790226--1790429 Score: 87
Period size: 2 Copynumber: 99.5 Consensus size: 2
1790216 ATACACCAGA
* * * *
1790226 AT AT AT AT AT AT AT AT AT AT AT AT AA AC AGT AG GT AT AT -T AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T
* * *
1790269 GAA AT AT AT AT AT AT AT AT AT AGT AT AT AA AT AT AT AT AT AT AA
1 -AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * * *
1790313 AT A- AA AA AGC AGT AG GT AT AT AT AT AC A- AT A- AT AT AT AT AT
1 AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1790354 AT AA AC AGT AG GT AT AT -T AGT GAA AT AT AC AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT
*
1790396 AT AT AT AT AT GA- AA AT AGT AT AT AT AT AT AT AT A
1 AT AT AT AT AT -AT AT AT A-T AT AT AT AT AT AT AT A
1790430 AATACAAAAG
Statistics
Matches: 154, Mismatches: 32, Indels: 32
0.71 0.15 0.15
Matches are distributed among these distances:
1 6 0.04
2 134 0.87
3 12 0.08
4 2 0.01
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.38
Consensus pattern (2 bp):
AT
Found at i:1790334 original size:37 final size:37
Alignment explanation
Indices: 1790291--1790370 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
1790281 TATATATATA
*
1790291 GTATATAAATA-TATATATATAAATA-AAAAAGCAGTAG
1 GTATATAAATACAATA-ATATAAATATAAAAA-CAGTAG
* * *
1790328 GTATATATATACAATAATATATATATATAAACAGTAG
1 GTATATAAATACAATAATATAAATATAAAAACAGTAG
1790365 GTATAT
1 GTATAT
1790371 TAGTGAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 30 0.81
38 7 0.19
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.34
Consensus pattern (37 bp):
GTATATAAATACAATAATATAAATATAAAAACAGTAG
Found at i:1791263 original size:39 final size:39
Alignment explanation
Indices: 1791125--1791266 Score: 160
Period size: 39 Copynumber: 3.6 Consensus size: 39
1791115 CCTAATCCTC
* * * * * *
1791125 AAATTATTTCACTC-TAACATTTTAAATTCCTAATTTATA
1 AAATTATTTCAC-CATAACATTCTAAACTCTTAGTTTCTT
* * *
1791164 AAATTATTTTACCATAACATTTTAAATTCTTAGTTTCTT
1 AAATTATTTCACCATAACATTCTAAACTCTTAGTTTCTT
*
1791203 AAATTATTTCACCATAACATTCTAAACTCTTATTTTCTT
1 AAATTATTTCACCATAACATTCTAAACTCTTAGTTTCTT
* *
1791242 AAATTATTTCACCTTACCATTCTAA
1 AAATTATTTCACCATAACATTCTAA
1791267 TTTTTTTTAA
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
38 1 0.01
39 90 0.99
ACGTcount: A:0.35, C:0.18, G:0.01, T:0.46
Consensus pattern (39 bp):
AAATTATTTCACCATAACATTCTAAACTCTTAGTTTCTT
Found at i:1795404 original size:9 final size:9
Alignment explanation
Indices: 1795390--1795452 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
1795380 AGGGATTACC
1795390 TTTTTTTTA
1 TTTTTTTTA
1795399 TTTTTTGTTA
1 TTTTTT-TTA
* *
1795409 ATTTTGTTA
1 TTTTTTTTA
*
1795418 ATTTTTTTA
1 TTTTTTTTA
1795427 TTTATTATTTA
1 TTT-TT-TTTA
* *
1795438 TTATATTTA
1 TTTTTTTTA
1795447 TTTTTT
1 TTTTTT
1795453 GGGATAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
9 27 0.63
10 10 0.23
11 6 0.14
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1795449 original size:28 final size:28
Alignment explanation
Indices: 1795391--1795452 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
1795381 GGGATTACCT
* * * *
1795391 TTTTTTTATTTTTTGTTAATTTTGTTAA
1 TTTTTTTATTTATTATTAATTATATTAA
* *
1795419 TTTTTTTATTTATTATTTATTATATTTA
1 TTTTTTTATTTATTATTAATTATATTAA
1795447 TTTTTT
1 TTTTTT
1795453 GGGATAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (28 bp):
TTTTTTTATTTATTATTAATTATATTAA
Found at i:1795788 original size:42 final size:42
Alignment explanation
Indices: 1795737--1795891 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 42
1795727 TGACCCAAGG
* *
1795737 TGATGTTGATCCAACTCTTTATGTGATGGACGAGCGAAATGA
1 TGATGTTGATCCAACTCCTTATGTGATGGACGAGCAAAATGA
* *
1795779 TGATGTTGATCCAACTCCTTATGTGATGAACGAGTAAAATGA
1 TGATGTTGATCCAACTCCTTATGTGATGGACGAGCAAAATGA
* * * * * * * *
1795821 TTATGCTGATCCAACTCCTTATGCGATGGATGAAC-CAAGGT
1 TGATGTTGATCCAACTCCTTATGTGATGGACGAGCAAAATGA
* * *
1795862 TGGTGTTGTTCCAACTTCTTATGTGATGGA
1 TGATGTTGATCCAACTCCTTATGTGATGGA
1795892 AACGAGCTAG
Statistics
Matches: 93, Mismatches: 20, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
41 27 0.29
42 66 0.71
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (42 bp):
TGATGTTGATCCAACTCCTTATGTGATGGACGAGCAAAATGA
Found at i:1796184 original size:202 final size:201
Alignment explanation
Indices: 1795950--1796372 Score: 666
Period size: 202 Copynumber: 2.1 Consensus size: 201
1795940 TCATCGGATG
* * * *
1795950 AGTTCATCTCATTATGAACTCTCCACTGGAAATGTTGATCCACATCCTTCTGTGATGGAATCGAA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATATTGATCCACATCATTCTGTAATGGAATCGAA
* * * *
1796015 CAAAGTGATGATGCTGATCCAACTCCATATGCGATGGATGAGCCAAGTGTTTGATCAAGTTCTTC
66 CAAAGTGACGATGCTGATCCAACTCCATATGCGATGGATGAGCAAAGTGTTTGAACAAGTTATTC
* * * * *
1796080 TCATTATGAACTTCTTCATTGGAAATGTTGATCTAGCTTCTTCTGTGATGGATTCGAGCAAAGGT
131 TCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTCGAACAAAAGT
1796145 TGAACA
196 TGAACA
* * *
1796151 AGTTCTTCTCATTATGAACTCTCCTATTGGAAATATTGATCCACCTCATTTTGTAATGGAATCGA
1 AGTTCTTCTCATTATGAACTCTCC-ACTGGAAATATTGATCCACATCATTCTGTAATGGAATCGA
* *
1796216 ACAAAGTGACGATGCTGATCGAACTCCATATGTGATGGATGAGCAAAGTGTTTGAACAAGTTATT
65 ACAAAGTGACGATGCTGATCCAACTCCATATGCGATGGATGAGCAAAGTGTTTGAACAAGTTATT
*
1796281 CTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTTTGATGGATTCGAACAAAAG
130 CTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTCGAACAAAAG
1796346 TTGAACA
195 TTGAACA
1796353 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
1796373 TATTCTCCCT
Statistics
Matches: 202, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
201 23 0.11
202 179 0.89
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (201 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAATATTGATCCACATCATTCTGTAATGGAATCGAA
CAAAGTGACGATGCTGATCCAACTCCATATGCGATGGATGAGCAAAGTGTTTGAACAAGTTATTC
TCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTCGAACAAAAGT
TGAACA
Found at i:1796210 original size:79 final size:79
Alignment explanation
Indices: 1796065--1796221 Score: 201
Period size: 79 Copynumber: 2.0 Consensus size: 79
1796055 AGCCAAGTGT
* * * * * *
1796065 TTGATCAAGTTCTTCTCATTATGAACTTCTTCATTGGAAATGTTGATCTAGCTTCTTCTGTGATG
1 TTGAACAAGTTCTTCTCATTATGAACTTCCTCATTGGAAATATTGATCCAGCCTCTTCTGTAATG
* *
1796130 GATTCGAGCAAAGG
66 GAATCGAACAAAGG
*
1796144 TTGAACAAGTTCTTCTCATTATGAACTCTCCT-ATTGGAAATATTGATCCA-CCTCATTTTGTAA
1 TTGAACAAGTTCTTCTCATTATGAACT-TCCTCATTGGAAATATTGATCCAGCCTC-TTCTGTAA
1796207 TGGAATCGAACAAAG
64 TGGAATCGAACAAAG
1796222 TGACGATGCT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 3 0.04
79 61 0.91
80 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (79 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCCTCATTGGAAATATTGATCCAGCCTCTTCTGTAATG
GAATCGAACAAAGG
Found at i:1797998 original size:55 final size:54
Alignment explanation
Indices: 1797882--1798135 Score: 205
Period size: 54 Copynumber: 4.7 Consensus size: 54
1797872 ATTTACATTT
* * * * * *
1797882 ATCATCAAGAAACCCCTAAAAACTTAAGCTTCGATTCTTTAAAAATTCATTTGAAA
1 ATCATCAAGAAACCCCTAAAAA-TCAGGCTTAGCTTCTTTGAAAACTCATTT-AAA
* *
1797938 A-CATCAAAAAACCCCTAAAAATCAGGCTTAGCTTTTTTGAAAACTCATTTATAA
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTGAAAACTCATTTA-AA
* * ** * * *
1797992 ATCATCAAGAAA--CTTAAGAAAATTAAACTTAGTTTCTTTGAAAATTC-TTCTGAA
1 ATCATCAAGAAACCCCT-A-AAAATCAGGCTTAGCTTCTTTGAAAACTCATT-TAAA
* *
1798046 AT-ATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTAAAA
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTGAAAACTCATTT-AAA
* ** * *
1798100 AT-AACAAGAAACTTCTGAAAATCAGGCTTAGTTTCT
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCT
1798136 AAAAAAATCA
Statistics
Matches: 160, Mismatches: 29, Indels: 20
0.77 0.14 0.10
Matches are distributed among these distances:
53 38 0.24
54 67 0.42
55 54 0.34
56 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (54 bp):
ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTGAAAACTCATTTAAA
Found at i:1798069 original size:108 final size:108
Alignment explanation
Indices: 1797916--1798113 Score: 292
Period size: 108 Copynumber: 1.8 Consensus size: 108
1797906 TAAGCTTCGA
* *
1797916 TTCTTTAAAAATTCATTTGAAAACATCAAAAAACCCCTAAAAATCAGGCTTAGCTTTTTTGAAAA
1 TTCTTTAAAAATTCATTTGAAAACATCAAAAAACCCCTAAAAATCAGACTTAGCTTCTTTGAAAA
* *
1797981 CTCATTTATAAATCATCAAGAAACTTAAGAAAATTAAACTTAGT
66 CTCATTTAAAAAT-AACAAGAAACTTAAGAAAATTAAACTTAGT
* * * *
1798025 TTCTTTGAAAATTC-TTCTG-AAATATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTTGAAA
1 TTCTTTAAAAATTCATT-TGAAAACATCAAAAAACCCCTAAAAATCAGACTTAGCTTCTTTGAAA
1798088 ACTCATTTAAAAATAACAAGAAACTT
65 ACTCATTTAAAAATAACAAGAAACTT
1798114 CTGAAAATCA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 11 0.14
108 54 0.68
109 15 0.19
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (108 bp):
TTCTTTAAAAATTCATTTGAAAACATCAAAAAACCCCTAAAAATCAGACTTAGCTTCTTTGAAAA
CTCATTTAAAAATAACAAGAAACTTAAGAAAATTAAACTTAGT
Found at i:1800888 original size:55 final size:55
Alignment explanation
Indices: 1800804--1801076 Score: 370
Period size: 55 Copynumber: 4.9 Consensus size: 55
1800794 GTATTTGTTG
* * * * *
1800804 GAATTTCCGTATTGGCACTATGTGTGCAACCCCACTAAATTTATAGTGTGTTTAT
1 GAATTTCTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTAT
*
1800859 GAATTTCTATATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTAT
1 GAATTTCTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTAT
* *
1800914 GAATTT-TCGTGTTGGCACTATGTGTGCAACCCCCACGAAATTCATATTGAGTTTAT
1 GAATTTCT-GTATTGGCACTATGTGTGCAA-CCCCACGAAATTCATAATGAGTTTAT
* * * *
1800970 GAATTTCCGTATTGGCACTATGTGTTCAACCTCACGAAATTCATAATGAATTTAT
1 GAATTTCTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTAT
* * *
1801025 GAATTTTTATATTGGCACTATGTGTGCAACCCCAC-AGAATTTATAATGAGTT
1 GAATTTCTGTATTGGCACTATGTGTGCAACCCCACGA-AATTCATAATGAGTT
1801077 GAGATATTCA
Statistics
Matches: 192, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
54 2 0.01
55 140 0.73
56 50 0.26
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (55 bp):
GAATTTCTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTAT
Found at i:1801000 original size:111 final size:111
Alignment explanation
Indices: 1800804--1801057 Score: 384
Period size: 111 Copynumber: 2.3 Consensus size: 111
1800794 GTATTTGTTG
* * * * *
1800804 GAATTTCCGTATTGGCACTATGTGTGCAA-CCCCACTAAATTTATAGTGTGTTTATGAATTTCTA
1 GAATTTTCGTATTGGCACTATGTGTGCAACCCCCACGAAATTCATAGTGAGTTTATGAATTTCCA
*
1800868 TATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTAT
66 TATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAATTTAT
* * *
1800914 GAATTTTCGTGTTGGCACTATGTGTGCAACCCCCACGAAATTCATATTGAGTTTATGAATTTCCG
1 GAATTTTCGTATTGGCACTATGTGTGCAACCCCCACGAAATTCATAGTGAGTTTATGAATTTCCA
* *
1800979 TATTGGCACTATGTGTTCAACCTCACGAAATTCATAATGAATTTAT
66 TATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAATTTAT
**
1801025 GAATTTTTATATTGGCACTATGTGTGCAACCCC
1 GAATTTTCGTATTGGCACTATGTGTGCAACCCC
1801058 ACAGAATTTA
Statistics
Matches: 129, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
110 27 0.21
111 102 0.79
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (111 bp):
GAATTTTCGTATTGGCACTATGTGTGCAACCCCCACGAAATTCATAGTGAGTTTATGAATTTCCA
TATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAATTTAT
Found at i:1807653 original size:55 final size:55
Alignment explanation
Indices: 1807566--1807767 Score: 309
Period size: 55 Copynumber: 3.7 Consensus size: 55
1807556 TATGTGTGCA
* * *
1807566 GGCACTATGTGT--AACCTCATGAAATTTATAATGAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
* *
1807619 GGCATTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATATCTGTATT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
*
1807674 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTTTT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
* * *
1807729 GGCACTATGTGTGCAACCCCATGAAATTTATAATGAGTT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTT
1807768 GAAGTATTCA
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
53 11 0.08
55 125 0.92
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (55 bp):
GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
Found at i:1808662 original size:4 final size:4
Alignment explanation
Indices: 1808653--1808751 Score: 60
Period size: 4 Copynumber: 23.8 Consensus size: 4
1808643 GTATTTTATT
* *
1808653 TTTC TTTC TTTC TTTC TTT- TTGT- TTTCC ATTT- TTGC TTTC TTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TT-TC TTT-C -TTTC TTTC TTTC TTTC TTTC
* * * *
1808701 TCTC TCTC TTTC GTTTTC TTTGC TTTC TCTTC TTTA TTTC TTTC TCTC
1 TTTC TTTC TTTC --TTTC TTT-C TTTC T-TTC TTTC TTTC TTTC TTTC
1808749 TTT
1 TTT
1808752 TTTATGTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
3 5 0.07
4 56 0.74
5 8 0.11
6 7 0.09
ACGTcount: A:0.02, C:0.23, G:0.04, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:1808678 original size:24 final size:24
Alignment explanation
Indices: 1808646--1808697 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1808636 TCTTGAAGTA
* *
1808646 TTTTATTTTTC-TTTCTTTCTTTCT
1 TTTTATTTTCCATTT-TTGCTTTCT
*
1808670 TTTTGTTTTCCATTTTTGCTTTCT
1 TTTTATTTTCCATTTTTGCTTTCT
1808694 TTTT
1 TTTT
1808698 TTCTCTCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (24 bp):
TTTTATTTTCCATTTTTGCTTTCT
Found at i:1810171 original size:21 final size:22
Alignment explanation
Indices: 1810130--1810180 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1810120 ATGCACATGC
* *
1810130 AAATGCAAAGATGCAAAAATGG
1 AAATGCAAAAATACAAAAATGG
* *
1810152 GAATGCAAAAATAC-AAAATGT
1 AAATGCAAAAATACAAAAATGG
1810173 AAATGCAA
1 AAATGCAA
1810181 CAAAGGAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.16
Consensus pattern (22 bp):
AAATGCAAAAATACAAAAATGG
Found at i:1810606 original size:29 final size:30
Alignment explanation
Indices: 1810557--1810616 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1810547 AAAACACAAG
*
1810557 ACAAGACAAAATGAAATCAAGTTAGTAAAA
1 ACAAGAAAAAATGAAATCAAGTTAGTAAAA
*
1810587 ACAAGAAAAAAT-TAATCAAGTTAGTAAAA
1 ACAAGAAAAAATGAAATCAAGTTAGTAAAA
1810616 A
1 A
1810617 TGATTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.18
Consensus pattern (30 bp):
ACAAGAAAAAATGAAATCAAGTTAGTAAAA
Found at i:1814083 original size:9 final size:8
Alignment explanation
Indices: 1814033--1814080 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1814023 GAAAAAAGAA
1814033 ATTATTTT
1 ATTATTTT
*
1814041 ATTCATATT
1 ATT-ATTTT
1814050 ATTATTTT
1 ATTATTTT
1814058 ATATATTTT
1 AT-TATTTT
* *
1814067 ATAATATT
1 ATTATTTT
1814075 ATTATT
1 ATTATT
1814081 ATTTGGTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
8 17 0.53
9 15 0.47
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (8 bp):
ATTATTTT
Found at i:1815378 original size:46 final size:46
Alignment explanation
Indices: 1815277--1815388 Score: 109
Period size: 46 Copynumber: 2.4 Consensus size: 46
1815267 AGACTTATAT
* * * * * *
1815277 CATATTAAAACAATAATATTATCCAAATACATAATTAATAGTAGAC
1 CATATTAATACAATAATATTATCAAAATACATAATGAATACTACAA
* * * * *
1815323 CATAATAATACAATGATATTTTCAAAATACATAGTGAGTACTACAA
1 CATATTAATACAATAATATTATCAAAATACATAATGAATACTACAA
1815369 CATATTAATAC-ATCAATATT
1 CATATTAATACAAT-AATATT
1815389 GTTTAAGTGC
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
45 2 0.04
46 50 0.96
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.32
Consensus pattern (46 bp):
CATATTAATACAATAATATTATCAAAATACATAATGAATACTACAA
Found at i:1816413 original size:13 final size:13
Alignment explanation
Indices: 1816395--1816420 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1816385 CTCAAATTTC
1816395 GTAACAATTTAAT
1 GTAACAATTTAAT
1816408 GTAACAATTTAAT
1 GTAACAATTTAAT
1816421 ATAAAACTCA
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GTAACAATTTAAT
Found at i:1820251 original size:200 final size:200
Alignment explanation
Indices: 1819908--1820309 Score: 804
Period size: 200 Copynumber: 2.0 Consensus size: 200
1819898 TACGGGAGAG
1819908 TTTCATCGTGTACAATCACCAAGGAAATATGGGATAAACTACAAGTCACTCATGAAGGTATAAAC
1 TTTCATCGTGTACAATCACCAAGGAAATATGGGATAAACTACAAGTCACTCATGAAGGTATAAAC
1819973 GAGGTAAAAGAATCTAAAATTAGTATTCTAACTCATAGCAATGAAAATTCAGGATGAAAATAGAT
66 GAGGTAAAAGAATCTAAAATTAGTATTCTAACTCATAGCAATGAAAATTCAGGATGAAAATAGAT
1820038 GAAGATATCAAAGCTATGACGGATAGATTTTCCACGATTGTCAGTGGTCTCAAATCATTTAGAGA
131 GAAGATATCAAAGCTATGACGGATAGATTTTCCACGATTGTCAGTGGTCTCAAATCATTTAGAGA
1820103 GATCA
196 GATCA
1820108 TTTCATCGTGTACAATCACCAAGGAAATATGGGATAAACTACAAGTCACTCATGAAGGTATAAAC
1 TTTCATCGTGTACAATCACCAAGGAAATATGGGATAAACTACAAGTCACTCATGAAGGTATAAAC
1820173 GAGGTAAAAGAATCTAAAATTAGTATTCTAACTCATAGCAATGAAAATTCAGGATGAAAATAGAT
66 GAGGTAAAAGAATCTAAAATTAGTATTCTAACTCATAGCAATGAAAATTCAGGATGAAAATAGAT
1820238 GAAGATATCAAAGCTATGACGGATAGATTTTCCACGATTGTCAGTGGTCTCAAATCATTTAGAGA
131 GAAGATATCAAAGCTATGACGGATAGATTTTCCACGATTGTCAGTGGTCTCAAATCATTTAGAGA
1820303 GATCA
196 GATCA
1820308 TT
1 TT
1820310 CCAAATGAGA
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 202 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (200 bp):
TTTCATCGTGTACAATCACCAAGGAAATATGGGATAAACTACAAGTCACTCATGAAGGTATAAAC
GAGGTAAAAGAATCTAAAATTAGTATTCTAACTCATAGCAATGAAAATTCAGGATGAAAATAGAT
GAAGATATCAAAGCTATGACGGATAGATTTTCCACGATTGTCAGTGGTCTCAAATCATTTAGAGA
GATCA
Found at i:1824833 original size:23 final size:21
Alignment explanation
Indices: 1824793--1824864 Score: 92
Period size: 23 Copynumber: 3.3 Consensus size: 21
1824783 GCTAGGTATT
1824793 GATACCCCCTTGCATGGGTACC
1 GATACCCCCTTG-ATGGGTACC
*
1824815 GATACCCCCTTTGAGTGGGTACT
1 GATACCCCC-TTGA-TGGGTACC
1824838 GATACCCCCTTGA-GGGTACC
1 GATACCCCCTTGATGGGTACC
*
1824858 GCTACCC
1 GATACCC
1824865 TCCACGGGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.27
22 14 0.31
23 19 0.42
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (21 bp):
GATACCCCCTTGATGGGTACC
Found at i:1828734 original size:32 final size:32
Alignment explanation
Indices: 1828698--1828993 Score: 312
Period size: 32 Copynumber: 9.3 Consensus size: 32
1828688 GTTGTTACAC
* * *
1828698 TTAAAATATATTAATTTTAATATCCAACAAAA
1 TTAAAACATAATAATTTCAATATCCAACAAAA
* * *
1828730 TTAAAACATAATAATTTGAATATACAACAAAC
1 TTAAAACATAATAATTTCAATATCCAACAAAA
* * *
1828762 TTAAAACATAATAATTTTAGTATCCAAC-ACA
1 TTAAAACATAATAATTTCAATATCCAACAAAA
* * * *
1828793 CTAAAACATAATAACTTCAATATACAACAAAC
1 TTAAAACATAATAATTTCAATATCCAACAAAA
* * ** *
1828825 TTGAAACATAATAATTTGAATATAGAATAAAA
1 TTAAAACATAATAATTTCAATATCCAACAAAA
*
1828857 CTT-AGACATAATAATTTCAATATCCAACAAACA
1 -TTAAAACATAATAATTTCAATATCCAACAAA-A
* * *
1828890 -TAAAACATAATAATTTCAATACCCAACACAC
1 TTAAAACATAATAATTTCAATATCCAACAAAA
*
1828921 TTAAAACATAATAACTTCAATATCCAACAAACA
1 TTAAAACATAATAATTTCAATATCCAACAAA-A
* *
1828954 -TAAAACATAATAATTTTAATATCCAACAAAC
1 TTAAAACATAATAATTTCAATATCCAACAAAA
1828985 TTAAAACAT
1 TTAAAACAT
1828994 TACAAGTTCA
Statistics
Matches: 217, Mismatches: 40, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
31 25 0.12
32 189 0.87
33 3 0.01
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.28
Consensus pattern (32 bp):
TTAAAACATAATAATTTCAATATCCAACAAAA
Found at i:1828777 original size:64 final size:64
Alignment explanation
Indices: 1828696--1828993 Score: 366
Period size: 64 Copynumber: 4.7 Consensus size: 64
1828686 GGGTTGTTAC
* * * *
1828696 ACTTAAAATATATTAATTTTAATATCCAACAAAATTAAAACATAATAATTTGAATATACAACAA
1 ACTTAAAACATAATAATTTTAATATCCAACAAAATTAAAACATAATAACTTCAATATACAACAA
* * *
1828760 ACTTAAAACATAATAATTTTAGTATCCAAC-ACACTAAAACATAATAACTTCAATATACAACAA
1 ACTTAAAACATAATAATTTTAATATCCAACAAAATTAAAACATAATAACTTCAATATACAACAA
* * ** * * * *
1828823 ACTTGAAACATAATAATTTGAATATAGAATAAAACTT-AGACATAATAATTTCAATATCCAACAA
1 ACTTAAAACATAATAATTTTAATATCCAACAAAA-TTAAAACATAATAACTTCAATATACAACAA
* * * * * *
1828887 ACATAAAACATAATAATTTCAATACCCAACACACTTAAAACATAATAACTTCAATATCCAACAA
1 ACTTAAAACATAATAATTTTAATATCCAACAAAATTAAAACATAATAACTTCAATATACAACAA
* *
1828951 ACATAAAACATAATAATTTTAATATCCAACAAACTTAAAACAT
1 ACTTAAAACATAATAATTTTAATATCCAACAAAATTAAAACAT
1828994 TACAAGTTCA
Statistics
Matches: 199, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
63 55 0.28
64 143 0.72
65 1 0.01
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.28
Consensus pattern (64 bp):
ACTTAAAACATAATAATTTTAATATCCAACAAAATTAAAACATAATAACTTCAATATACAACAA
Found at i:1828928 original size:96 final size:94
Alignment explanation
Indices: 1828699--1828993 Score: 374
Period size: 96 Copynumber: 3.1 Consensus size: 94
1828689 TTGTTACACT
* * * *
1828699 TAAAATATATTAATTTTAATATCCAACAAAATTAAAACATAATAATTTGAATATACAACAAACTT
1 TAAAACATAATAATTTCAATATCCAACAAACTTAAAACATAATAATTTGAATATACAACAAACTT
* *
1828764 AAAACATAATAATTTTAGTATCCAACACAC
66 -AAACATAATAATTTTAATATCCAACAAAC
* * * * *
1828794 TAAAACATAATAACTTCAATATACAACAAACTTGAAACATAATAATTTGAATATAGAATAAAACT
1 TAAAACATAATAATTTCAATATCCAACAAACTTAAAACATAATAATTTGAATATACAA-CAAACT
* *
1828859 TAGACATAATAATTTCAATATCCAACAAAC
65 TAAACATAATAATTTTAATATCCAACAAAC
* * * * *
1828889 ATAAAACATAATAATTTCAATACCCAACACACTTAAAACATAATAACTTCAATATCCAACAAACA
1 -TAAAACATAATAATTTCAATATCCAACAAACTTAAAACATAATAATTTGAATATACAACAAAC-
*
1828954 TAAAACATAATAATTTTAATATCCAACAAAC
64 TTAAACATAATAATTTTAATATCCAACAAAC
1828985 TTAAAACAT
1 -TAAAACAT
1828994 TACAAGTTCA
Statistics
Matches: 170, Mismatches: 27, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
95 79 0.46
96 91 0.54
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (94 bp):
TAAAACATAATAATTTCAATATCCAACAAACTTAAAACATAATAATTTGAATATACAACAAACTT
AAACATAATAATTTTAATATCCAACAAAC
Found at i:1829145 original size:3 final size:3
Alignment explanation
Indices: 1829137--1829174 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1829127 GAAAATATAT
1829137 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1829175 ATTTTGGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1830434 original size:16 final size:16
Alignment explanation
Indices: 1830395--1830437 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1830385 TTTTTAGAAA
1830395 TTAATATTTTCTTCATT
1 TTAATATTTT-TTCATT
* *
1830412 TT-TTATTTTTTTATT
1 TTAATATTTTTTCATT
1830427 TTAATATTTTT
1 TTAATATTTTT
1830438 CTTAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 7 0.32
16 13 0.59
17 2 0.09
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (16 bp):
TTAATATTTTTTCATT
Found at i:1830631 original size:12 final size:13
Alignment explanation
Indices: 1830609--1830637 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1830599 CGAATTGAAT
1830609 TTTTAAATTTTAA
1 TTTTAAATTTTAA
1830622 TTTT-AATTTTAA
1 TTTTAAATTTTAA
1830634 TTTT
1 TTTT
1830638 CCTAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1830798 original size:16 final size:17
Alignment explanation
Indices: 1830761--1830798 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1830751 GCATACCAGT
1830761 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
1830778 ATTTT-TCTTAAAATTG
1 TTTTTGTCTTAAAAATG
1830794 TTTTT
1 TTTTT
1830799 AAAAGACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:1831692 original size:20 final size:20
Alignment explanation
Indices: 1831667--1831715 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1831657 AATGCTCCAA
1831667 TACAATCTTTAAGATATGGG
1 TACAATCTTTAAGATATGGG
1831687 TACAATCTTTAAGATATGGG
1 TACAATCTTTAAGATATGGG
*
1831707 TAAAATCTT
1 TACAATCTT
1831716 AGATTGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (20 bp):
TACAATCTTTAAGATATGGG
Found at i:1832705 original size:14 final size:13
Alignment explanation
Indices: 1832685--1832716 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1832675 AAAATAAATT
1832685 AATAAAAACATTA
1 AATAAAAACATTA
*
1832698 ATTAAAAACATTA
1 AATAAAAACATTA
1832711 AATAAA
1 AATAAA
1832717 TTAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (13 bp):
AATAAAAACATTA
Found at i:1837895 original size:26 final size:26
Alignment explanation
Indices: 1837866--1837919 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1837856 TGAACCCAAT
*
1837866 CCAAACTAAGTTGACTTTGACCTGAC
1 CCAAACTAAGTTGACTTTGACCCGAC
* *
1837892 CCAAATTGAGTTGACTTTGACCCGAC
1 CCAAACTAAGTTGACTTTGACCCGAC
1837918 CC
1 CC
1837920 TATCGTTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (26 bp):
CCAAACTAAGTTGACTTTGACCCGAC
Found at i:1841509 original size:39 final size:39
Alignment explanation
Indices: 1841446--1841537 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
1841436 ATATTTAAGG
** * *
1841446 GGGAATTGAAGAGTCCCTTGGGAGTTCGA-TATTTTTATT
1 GGGAATTGAAGAGTCCCTACGGAGTTAGAGT-GTTTTATT
*
1841485 GGGAATTGAAGAGTCTCTACGGAGTTAGAGTGTTTTATT
1 GGGAATTGAAGAGTCCCTACGGAGTTAGAGTGTTTTATT
* *
1841524 GTGAATTTAAGAGT
1 GGGAATTGAAGAGT
1841538 TCTTGGAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 44 0.98
40 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (39 bp):
GGGAATTGAAGAGTCCCTACGGAGTTAGAGTGTTTTATT
Found at i:1842392 original size:29 final size:29
Alignment explanation
Indices: 1842351--1842425 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
1842341 CCAGTGCTCA
1842351 ACTTTA-T-TTTGCCATAGAAATTCTTTG
1 ACTTTACTGTTTGCCATAGAAATTCTTTG
1842378 ACTTTACTGTTTGCCATAGAAATTCTTTG
1 ACTTTACTGTTTGCCATAGAAATTCTTTG
*
1842407 ACTTTACTGTTTTCCATAG
1 ACTTTACTGTTTGCCATAG
1842426 CATTTCATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 6 0.13
28 1 0.02
29 38 0.84
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (29 bp):
ACTTTACTGTTTGCCATAGAAATTCTTTG
Found at i:1845116 original size:90 final size:89
Alignment explanation
Indices: 1844960--1845136 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
1844950 CCTAACACAC
* *
1844960 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAATTACCCTAATCATATTAGGGTTATATTATTTCAAATTAATTAAATCTATA
* *
1845025 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
1845049 CCTTTTATATCCAAATTACCCTAATCATATTAGGGATTATATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAATTACCCTAATCATATTAGGG-TTATATTATTTCAAATTAATTAAATCTAT
1845114 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
1845137 TTTGAGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 33 0.40
90 49 0.60
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.44
Consensus pattern (89 bp):
CCTTTTATAGCCAAATTACCCTAATCATATTAGGGTTATATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:1845123 original size:20 final size:20
Alignment explanation
Indices: 1845098--1845167 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 20
1845088 TATTATTTCA
1845098 AATTAATTAAATCTATATTT
1 AATTAATTAAATCTATATTT
1845118 AATTAATTGAAAT-TAAATATTT
1 AATTAATT-AAATCT--ATATTT
*
1845140 GAGATT-ATTAAAACATATATTT
1 -A-ATTAATTAAATC-TATATTT
1845162 AATTAA
1 AATTAA
1845168 CTCTAGATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
20 12 0.29
21 6 0.15
22 15 0.37
23 4 0.10
24 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (20 bp):
AATTAATTAAATCTATATTT
Found at i:1848219 original size:5 final size:5
Alignment explanation
Indices: 1848211--1848255 Score: 67
Period size: 5 Copynumber: 9.4 Consensus size: 5
1848201 AAACAGTAAA
*
1848211 AAAAT AAAAT AATAT AAAAT --AAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1848256 GTACAAGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 3 0.08
5 33 0.92
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:1848228 original size:18 final size:18
Alignment explanation
Indices: 1848162--1848247 Score: 72
Period size: 18 Copynumber: 4.8 Consensus size: 18
1848152 TAAACTTAAT
*
1848162 TAAAATAAT-TAAAACAA
1 TAAAATAATATAAAAAAA
*
1848179 -CAAATAAATATATAAAAAA
1 TAAAAT-AATATA-AAAAAA
*
1848198 TAAAA-ACA-GTAAAAAAA
1 TAAAATA-ATATAAAAAAA
*
1848215 TAAAATAATATAAAATAA
1 TAAAATAATATAAAAAAA
*
1848233 TAAAATAAAATAAAA
1 TAAAATAATATAAAA
1848248 TAAAATAAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
16 4 0.07
17 15 0.27
18 27 0.49
19 6 0.11
20 3 0.05
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.21
Consensus pattern (18 bp):
TAAAATAATATAAAAAAA
Found at i:1848237 original size:23 final size:23
Alignment explanation
Indices: 1848194--1848255 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1848184 AAATATATAA
* * *
1848194 AAAATAAAA-ACAGTAAAAAAAT
1 AAAATAAAATAAAATAATAAAAT
*
1848216 AAAATAATATAAAATAATAAAAT
1 AAAATAAAATAAAATAATAAAAT
1848239 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
1848256 GTACAAGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 8 0.24
23 26 0.76
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (23 bp):
AAAATAAAATAAAATAATAAAAT
Found at i:1848250 original size:18 final size:18
Alignment explanation
Indices: 1848180--1848247 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
1848170 TTAAAACAAC
1848180 AAATAAATATATAAAAAATA
1 AAATAAA-ATA-AAAAAATA
* *
1848200 AAA-ACAGTAAAAAAATA
1 AAATAAAATAAAAAAATA
* *
1848217 AAATAATATAAAATAATA
1 AAATAAAATAAAAAAATA
1848235 AAATAAAATAAAA
1 AAATAAAATAAAA
1848248 TAAAATAAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 11 0.28
18 24 0.60
19 2 0.05
20 3 0.08
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (18 bp):
AAATAAAATAAAAAAATA
Found at i:1848446 original size:142 final size:138
Alignment explanation
Indices: 1848289--1848875 Score: 719
Period size: 134 Copynumber: 4.2 Consensus size: 138
1848279 TTACATTGAC
* * * * *
1848289 TAAAATGCAAGAAAATAAAA-TTCAGTAGTTAGCAGAGTTTGAACCATAATAATACGGATCATAC
1 TAAAGTGCAATAAAATAAAAGTT-AGTAGTTAGCAGAGTCTGAACCATAATAATGCGAATCATAC
*
1848353 CTCGGATCGGGTCACCACAAGGTCGAATCAAATATTAGAAATAATAAATAAATAAATTAACAAAT
65 CTCGGATCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAATAAATAAATAAA-T---AAAT
1848418 AAATAACAATGAT
126 AAATAACAATGAT
* *
1848431 TAAAGTGCAATAAAATAAAAGTTAGTAGTTTGCAGAGTCTGAACCATAATAATGTGAATCATACC
1 TAAAGTGCAATAAAATAAAAGTTAGTAGTTAGCAGAGTCTGAACCATAATAATGCGAATCATACC
* * *
1848496 -CTTGATCGGGTCACCACAAGGCTGAATCAAATATTAG--A-AA-CAATAAATAAATAAATAAAT
66 TC-GGATCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAATAAATAAATAAATAAATAAAT
*
1848556 AACAATTAT
130 AACAATGAT
* * * *
1848565 TAAAGTGTAATAAAATAAAAGTTAGTAGTTAGGAGAGTATGAACCATAATAATGTGAATCATACC
1 TAAAGTGCAATAAAATAAAAGTTAGTAGTTAGCAGAGTCTGAACCATAATAATGCGAATCATACC
* * *
1848630 CCGGATCGGGTCACCACAAGGCCGAATCGAATATTAGAAATAATAAGTAAATAAATAAAT--A-A
66 TCGGATCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAATAAATAAATAAATAAATAAATA
1848692 A-AATGAT
131 ACAATGAT
* *
1848699 TAAAGTGCAATAAAATTAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCGAATCATACC
1 TAAAGTGCAATAAAATAAAAGTTAGTAGTTAGCAGAGTCTGAACCATAATAATGCGAATCATACC
* * **
1848764 TCGGATCGGGTCACCGCAAGGCCAAATTGAATATTAGAATCAATAAGTAAATAAATAAATAAATA
66 TCGGATCGGGTCACCACAAGGCCGAATCAAATATTAG-A--AATAA-TAAATAAATAAATAAAT-
*
1848829 ACAAAATAAACAATGGT
126 ---AAAT-AACAATGAT
*
1848846 TAGAGTGCAA-AAAATAAAAGTTAGTAGTTA
1 TAAAGTGCAATAAAATAAAAGTTAGTAGTTA
1848876 ATTTGAAATA
Statistics
Matches: 389, Mismatches: 36, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
134 206 0.53
135 4 0.01
136 2 0.01
137 8 0.02
138 40 0.10
139 2 0.01
140 1 0.00
141 1 0.00
142 87 0.22
143 2 0.01
144 1 0.00
146 21 0.05
147 14 0.04
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (138 bp):
TAAAGTGCAATAAAATAAAAGTTAGTAGTTAGCAGAGTCTGAACCATAATAATGCGAATCATACC
TCGGATCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAATAAATAAATAAATAAATAAATA
ACAATGAT
Found at i:1848889 original size:28 final size:28
Alignment explanation
Indices: 1848857--1848918 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
1848847 AGAGTGCAAA
*
1848857 AAATAAAAGTTAGTAGTTAATTTGAAAT
1 AAATAAAAGTTAGTAGTTAATATGAAAT
* *
1848885 AAATAAAAGTTAGTGGTTAATATGCAAT
1 AAATAAAAGTTAGTAGTTAATATGAAAT
1848913 AAATAA
1 AAATAA
1848919 TATAGCAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.32
Consensus pattern (28 bp):
AAATAAAAGTTAGTAGTTAATATGAAAT
Found at i:1849527 original size:35 final size:35
Alignment explanation
Indices: 1849481--1849550 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
1849471 TCTCACCCCT
*
1849481 ATTCTTACATACTCACGTTCAAAGAAAGAATAAAA
1 ATTCTTACATACTCAAGTTCAAAGAAAGAATAAAA
1849516 ATTCTTACATACTCAAGTTCAAAGAAAGAATAAAA
1 ATTCTTACATACTCAAGTTCAAAGAAAGAATAAAA
1849551 CAAGGAGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.26
Consensus pattern (35 bp):
ATTCTTACATACTCAAGTTCAAAGAAAGAATAAAA
Found at i:1850352 original size:66 final size:66
Alignment explanation
Indices: 1850199--1850775 Score: 738
Period size: 66 Copynumber: 8.7 Consensus size: 66
1850189 GGGGATAATT
* * * * *
1850199 TGTTTCAAGAGAAACTGTCTTAAGAGAGATAAAATTTGTTTCAAGGGAAACA-ATCTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGAT-TCAAAG-AT
*
1850263 TTA
64 TTG
* *
1850266 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGATTG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
1850331 G
66 G
* *
1850332 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGATT
1850396 TG
65 TG
* * *
1850398 TTTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGA-TA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
*
1850462 A
66 G
* * * *
1850463 AGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGGGAAAC-GATCTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGATT
1850527 TG
65 TG
* * *
1850529 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGA-TA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
*
1850593 A
66 G
* * *
1850594 TGTTTCAAGAGAAATTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAAAATT-AAAGAC
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAAC-AGATTCAAAGA-
1850658 TTT-
63 TTTG
* * * * *
1850661 TGTTTCAAGAGAAATTTTCTCAAGAGAGA-TAACTTTGTTTCAAGGGAAACAGATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGA-TT
1850725 TG
65 TG
*
1850727 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGGGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGA
1850776 GACAAAATTT
Statistics
Matches: 447, Mismatches: 49, Indels: 27
0.85 0.09 0.05
Matches are distributed among these distances:
64 6 0.01
65 116 0.26
66 217 0.49
67 91 0.20
68 17 0.04
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
G
Found at i:1850522 original size:131 final size:132
Alignment explanation
Indices: 1850199--1850780 Score: 785
Period size: 131 Copynumber: 4.4 Consensus size: 132
1850189 GGGGATAATT
* * * *
1850199 TGTTTCAAGAGAAACTGTCTTAAGAGAGATAAAATTTGTTTCAAGGGAAACAATCTCAATGTTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG-ATT
* *
1850264 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGAT
65 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGAT
**
1850329 TGG
130 TAA
* *
1850332 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTT
* *
1850397 GTTTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGA-T
66 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATT
1850461 AA
131 AA
* * * *
1850463 AGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGGGAAACGATCTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTT
* *
1850528 GTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGA-T
66 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATT
1850592 AA
131 AA
* * * ** *
1850594 TGTTTCAAGAGAAATTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAAAATTAAAGACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAATCTCAAAGA-T
* * * * *
1850659 TT-TGTTTCAAGAGAAATTTTCTCAAGAGAGA-TAACTTTGTTTCAAGGGAAACAGATTCAAAGA
64 TTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGA
**
1850722 TTTTG
129 -TTAA
* * *
1850727 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGGGAGACAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAA
1850781 AATTTTGTTT
Statistics
Matches: 405, Mismatches: 40, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
131 184 0.45
132 111 0.27
133 110 0.27
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.29
Consensus pattern (132 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTT
GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATT
AA
Found at i:1850534 original size:197 final size:195
Alignment explanation
Indices: 1850199--1850775 Score: 768
Period size: 197 Copynumber: 2.9 Consensus size: 195
1850189 GGGGATAATT
* * * * *
1850199 TGTTTCAAGAGAAACTGTCTTAAGAGAGATAAAATTTGTTTCAAGGGAAAC-AATCTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAAT-TCAAAG--A
* *
1850263 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGA
63 TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA-CGATTCAAAGA
* * * *
1850328 TTGGTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA-CGATCTCAAA
127 TTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGAT-TCAAA
*
1850392 GAT-T
191 GATAA
1850396 TGTTTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGAT
1 TG--TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGAT
* * * *
1850461 AAAGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGGGAAACGATCTCAAAGAT
64 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGAT-TCAAAGAT
*
1850526 TTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGA
128 TTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGA
1850591 TAA
193 TAA
* *
1850594 TGTTTCAAGAGAAATTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAAAATT-AAAGAC
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAAC-AAATTCAAAGA-
* * * * *
1850658 TTTTGTTTCAAGAGAAATTTTCTCAAGAGAGA-TAACTTTGTTTCAAGGGAAACAGATTCAAAGA
63 TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-GATTCAAAGA
*
1850722 TTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGGGA
127 -TTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGA
1850776 GACAAAATTT
Statistics
Matches: 338, Mismatches: 30, Indels: 22
0.87 0.08 0.06
Matches are distributed among these distances:
196 33 0.10
197 162 0.48
198 75 0.22
199 65 0.19
200 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (195 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTA
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATTCAAAGATTTG
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGATAA
Found at i:1850774 original size:22 final size:22
Alignment explanation
Indices: 1850746--1850797 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1850736 AGAAACTGTC
*
1850746 TCAAGGGAGATAAAATTTTGTT
1 TCAAGGGAGACAAAATTTTGTT
1850768 TCAAGGGAGACAAAATTTTGTT
1 TCAAGGGAGACAAAATTTTGTT
*
1850790 TGAAGGGA
1 TCAAGGGA
1850798 AACAGACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (22 bp):
TCAAGGGAGACAAAATTTTGTT
Found at i:1852336 original size:4 final size:4
Alignment explanation
Indices: 1852329--1852504 Score: 235
Period size: 4 Copynumber: 44.0 Consensus size: 4
1852319 ATACATACAT
* *
1852329 ACAC ACAC ACAC ACAC ACAC ACAC ACAC AGAC ACAC AGAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * *
1852377 ACAC ACAC ACAC ACAC ACGC ACAC ACGC ACAC ACGC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * *
1852425 ACAC AAAC ACAC ACAC ACAC ACAC ACAC ACAC GCAC ACAC GCAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * *
1852473 ACAC AGAC GCAC GCAC GCAC ACAC GCAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1852505 GCACGCACGC
Statistics
Matches: 150, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 150 1.00
ACGTcount: A:0.45, C:0.48, G:0.07, T:0.00
Consensus pattern (4 bp):
ACAC
Found at i:1852505 original size:8 final size:8
Alignment explanation
Indices: 1852332--1852604 Score: 253
Period size: 8 Copynumber: 34.4 Consensus size: 8
1852322 CATACATACA
*
1852332 CACACACA
1 CACACACG
*
1852340 CACACACA
1 CACACACG
*
1852348 CACACACA
1 CACACACG
* *
1852356 CAGACACA
1 CACACACG
* *
1852364 CAGACACA
1 CACACACG
*
1852372 CACACACA
1 CACACACG
*
1852380 CACACACA
1 CACACACG
1852388 CACACACG
1 CACACACG
1852396 CACACACG
1 CACACACG
1852404 CACACACG
1 CACACACG
1852412 CACACA--
1 CACACACG
*
1852418 CACACACA
1 CACACACG
* *
1852426 CACAAACA
1 CACACACG
*
1852434 CACACACA
1 CACACACG
*
1852442 CACACACA
1 CACACACG
1852450 CACACACG
1 CACACACG
1852458 CACACACG
1 CACACACG
*
1852466 CACACACA
1 CACACACG
*
1852474 CACAGACG
1 CACACACG
*
1852482 CACGCACG
1 CACACACG
1852490 CACACACG
1 CACACACG
1852498 CACACACG
1 CACACACG
*
1852506 CACGCACG
1 CACACACG
* *
1852514 CACGCATG
1 CACACACG
*
1852522 CACGCACG
1 CACACACG
*
1852530 CACGCACG
1 CACACACG
*
1852538 CACGCACG
1 CACACACG
*
1852546 CACGCACG
1 CACACACG
*
1852554 CACGCACG
1 CACACACG
*
1852562 CACGCACG
1 CACACACG
**
1852570 CATGCACG
1 CACACACG
*
1852578 CACGCACG
1 CACACACG
*
1852586 CACGCACG
1 CACACACG
*
1852594 CACGCACG
1 CACACACG
1852602 CAC
1 CAC
1852605 GCACACACAT
Statistics
Matches: 246, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
6 6 0.02
8 240 0.98
ACGTcount: A:0.38, C:0.48, G:0.14, T:0.01
Consensus pattern (8 bp):
CACACACG
Found at i:1852509 original size:4 final size:4
Alignment explanation
Indices: 1852454--1852608 Score: 231
Period size: 4 Copynumber: 38.8 Consensus size: 4
1852444 CACACACACA
* * * * *
1852454 CACG CACA CACG CACA CACA CACAG -ACG CACG CACG CACA CACG CACA
1 CACG CACG CACG CACG CACG CAC-G CACG CACG CACG CACG CACG CACG
*
1852502 CACG CACG CACG CACG CATG CACG CACG CACG CACG CACG CACG CACG
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
*
1852550 CACG CACG CACG CACG CACG CATG CACG CACG CACG CACG CACG CACG
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
1852598 CACG CACG CAC
1 CACG CACG CAC
1852609 ACACATACAT
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
3 1 0.01
4 136 0.99
ACGTcount: A:0.29, C:0.48, G:0.21, T:0.01
Consensus pattern (4 bp):
CACG
Found at i:1855286 original size:31 final size:29
Alignment explanation
Indices: 1855243--1855305 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
1855233 AGATGCAATA
* *
1855243 AAACTAGACAAAATGAAATCAATGTTAGTAG
1 AAACAAGACAAAAAG-AATCAA-GTTAGTAG
*
1855274 AAACAAGACAAAAAGAATCAAGTTAGTTG
1 AAACAAGACAAAAAGAATCAAGTTAGTAG
1855303 AAA
1 AAA
1855306 TGATTAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.34
30 6 0.21
31 13 0.45
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.19
Consensus pattern (29 bp):
AAACAAGACAAAAAGAATCAAGTTAGTAG
Found at i:1857248 original size:16 final size:17
Alignment explanation
Indices: 1857227--1857262 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1857217 TTAAAACATC
*
1857227 AAATAAATATA-TAAAA
1 AAATAAAAATAGTAAAA
1857243 AAATAAAAATAGTAAAA
1 AAATAAAAATAGTAAAA
1857260 AAA
1 AAA
1857263 CAACATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
AAATAAAAATAGTAAAA
Found at i:1857260 original size:17 final size:16
Alignment explanation
Indices: 1857227--1857284 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
1857217 TTAAAACATC
*
1857227 AAATAAATATATAAAA
1 AAATAAAAATATAAAA
1857243 AAATAAAAATAGTAAAA
1 AAATAAAAATA-TAAAA
* *
1857260 AAACAACATAAAAT-AAA
1 AAATAA-A-AATATAAAA
1857277 AAATAAAA
1 AAATAAAA
1857285 TAAGTACAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.03
16 11 0.31
17 18 0.51
18 2 0.06
19 3 0.09
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (16 bp):
AAATAAAAATATAAAA
Done.