Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008208.1 Hibiscus syriacus cultivar Beakdansim tig00110830_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: 2533913
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1626779 original size:18 final size:20
Alignment explanation
Indices: 1626747--1626785 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
1626737 GGGTAATAAT
1626747 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
1626767 ATAAG-AATG-AAATAAATA
1 ATAAGTAATGAAAATAAATA
1626785 A
1 A
1626786 AGGATAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:1627235 original size:19 final size:20
Alignment explanation
Indices: 1627194--1627244 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1627184 GAAACCCCTT
*
1627194 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
1627214 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1627233 TGAAGATACATG
1 TGAAAATACATG
1627245 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1639034 original size:19 final size:21
Alignment explanation
Indices: 1638991--1639042 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1638981 GAAACCCCTT
1638991 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
1639012 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1639031 TGAAGATACATG
1 TGAAAATACATG
1639043 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:1641968 original size:17 final size:17
Alignment explanation
Indices: 1641940--1641989 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
1641930 GGTTAGGGTA
1641940 GAAAGAATAGAAGAAATG
1 GAAAG-ATAGAAGAAATG
1641958 GAAAGATAGAAGAAATG
1 GAAAGATAGAAGAAATG
*
1641975 AAAAGATAGAAGAAA
1 GAAAGATAGAAGAAA
1641990 GGATTTAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 26 0.84
18 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (17 bp):
GAAAGATAGAAGAAATG
Found at i:1642215 original size:11 final size:11
Alignment explanation
Indices: 1642199--1642251 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
1642189 TTTGAATTTC
*
1642199 TCTTTTTCTTT
1 TCTTTTTCTCT
*
1642210 TCTTTTCTTCTTT
1 TC-TTT-TTCTCT
1642223 TCTTCTTT-TCT
1 TCTT-TTTCTCT
1642234 TCTTTTTCTCT
1 TCTTTTTCTCT
1642245 TCTTTTT
1 TCTTTTT
1642252 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 3 0.08
11 18 0.49
12 7 0.19
13 9 0.24
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTTTTCTCT
Found at i:1642245 original size:16 final size:16
Alignment explanation
Indices: 1642209--1642239 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1642199 TCTTTTTCTT
1642209 TTCTTTTCTTCTTTTC
1 TTCTTTTCTTCTTTTC
1642225 TTCTTTTCTTCTTTT
1 TTCTTTTCTTCTTTT
1642240 TCTCTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTTCTTCTTTTC
Found at i:1643008 original size:19 final size:21
Alignment explanation
Indices: 1642965--1643016 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1642955 GAAACCCATT
1642965 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
1642986 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1643005 TGAAGATACATG
1 TGAAAATACATG
1643017 TTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:1653946 original size:4 final size:5
Alignment explanation
Indices: 1653918--1653943 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1653908 ACTCAAAAAG
1653918 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
1653944 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:1660423 original size:13 final size:13
Alignment explanation
Indices: 1660407--1660445 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1660397 CTTTTTGAAC
1660407 TTCTCTTTTTCTT
1 TTCTCTTTTTCTT
1660420 TTCT-TTTCTTCTT
1 TTCTCTTT-TTCTT
*
1660433 TTCTCCTTTTCTT
1 TTCTCTTTTTCTT
1660446 CTTTTTGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.13
13 18 0.78
14 2 0.09
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTCTCTTTTTCTT
Found at i:1660431 original size:8 final size:8
Alignment explanation
Indices: 1660420--1660461 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
1660410 TCTTTTTCTT
1660420 TTCTTTTC
1 TTCTTTTC
1660428 TTCTTTTC
1 TTCTTTTC
*
1660436 TCCTTTTC
1 TTCTTTTC
1660444 TTCTTTT-
1 TTCTTTTC
1660451 TGTCTTTTC
1 T-TCTTTTC
1660460 TT
1 TT
1660462 TATTTTTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 1 0.03
8 28 0.93
9 1 0.03
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (8 bp):
TTCTTTTC
Found at i:1661979 original size:2 final size:2
Alignment explanation
Indices: 1661968--1662007 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1661958 TAACTATAGG
1661968 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1662008 GAAAATAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1664943 original size:20 final size:19
Alignment explanation
Indices: 1664918--1664986 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1664908 TTTCCTCGGC
1664918 TTTCTTTTTTTTTGAATTTT
1 TTTCTTTTTTTTTG-ATTTT
* *
1664938 TTTCTTTTTCTTT--TTCT
1 TTTCTTTTTTTTTGATTTT
*
1664955 TTTCTTCTTTTTTGATTTT
1 TTTCTTTTTTTTTGATTTT
1664974 TCTTCTTCTTTTT
1 T-TTCTT-TTTTT
1664987 GTCTTTTCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 14 0.36
19 4 0.10
20 17 0.44
21 4 0.10
ACGTcount: A:0.04, C:0.13, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTCTTTTTTTTTGATTTT
Found at i:1664947 original size:6 final size:6
Alignment explanation
Indices: 1664936--1664997 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
1664926 TTTTTGAATT
* ** *
1664936 TTTTTC TTTTTC TTTTTC -TTTTC TTCTT- TTTTGA TTTTTC TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
1664982 TTTTTG TCTTTTC TTT
1 TTTTTC T-TTTTC TTT
1664998 CTTTTTGTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
5 8 0.18
6 31 0.70
7 5 0.11
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:1664959 original size:37 final size:36
Alignment explanation
Indices: 1664918--1665004 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
1664908 TTTCCTCGGC
* *
1664918 TTTCTTTTTTTTTGAATTTTT-TTCTTTTTCTTTTTCT
1 TTTCTTTTTTTTTG-ATTTTTCTTCTTCTT-TTTGTCT
*
1664955 TTTCTTCTTTTTTGATTTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTTTTTTGATTTTTCTTCTTCTTTTTGTCT
*
1664991 TTTCTTTCTTTTTG
1 TTTCTTTTTTTTTG
1665005 TACTCCAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 24 0.55
37 20 0.45
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (36 bp):
TTTCTTTTTTTTTGATTTTTCTTCTTCTTTTTGTCT
Found at i:1664966 original size:28 final size:28
Alignment explanation
Indices: 1664918--1665003 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
1664908 TTTCCTCGGC
**
1664918 TTTCTT-TT-TTTTTGAATTTTTTTCTT
1 TTTCTTCTTCTTTTTGTCTTTTTTTCTT
* **
1664944 TTTCTTTTTCTTTTCT-TCTTTTTTGATT
1 TTTCTTCTTCTTTT-TGTCTTTTTTTCTT
1664972 TTTCTTCTTCTTTTTGTCTTTTCTTTCTT
1 TTTCTTCTTCTTTTTGTCTTTT-TTTCTT
1665001 TTT
1 TTT
1665004 GTACTCCAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
26 6 0.12
27 3 0.06
28 31 0.65
29 8 0.17
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.79
Consensus pattern (28 bp):
TTTCTTCTTCTTTTTGTCTTTTTTTCTT
Found at i:1664993 original size:20 final size:19
Alignment explanation
Indices: 1664937--1665005 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 19
1664927 TTTTGAATTT
*
1664937 TTTTCTTTTTC-TTTT-TC
1 TTTTCTTCTTCTTTTTGTC
1664954 TTTTCTTC-T-TTTTTGAT-
1 TTTTCTTCTTCTTTTTG-TC
1664971 TTTTCTTCTTCTTTTTGTC
1 TTTTCTTCTTCTTTTTGTC
1664990 TTTTC-T-TTCTTTTTGT
1 TTTTCTTCTTCTTTTTGT
1665006 ACTCCAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
16 5 0.11
17 25 0.56
18 4 0.09
19 11 0.24
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTCTTCTTCTTTTTGTC
Found at i:1674693 original size:5 final size:5
Alignment explanation
Indices: 1674678--1674728 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
1674668 TTTGGAGTGT
*
1674678 AAGAGA AAGAA AAGAA AAGAA GAATCAA AAGCAA AA-AA AAGAA AAGAA
1 AAGA-A AAGAA AAGAA AAGAA -AA-GAA AAG-AA AAGAA AAGAA AAGAA
1674726 AAG
1 AAG
1674729 TGAAGCAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
4 4 0.10
5 21 0.54
6 12 0.31
7 2 0.05
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:1675948 original size:13 final size:15
Alignment explanation
Indices: 1675930--1675961 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1675920 ACGTAGGACC
1675930 TTTTTTCTT-TTT-G
1 TTTTTTCTTCTTTCG
1675943 TTTTTTCTTCTTTCG
1 TTTTTTCTTCTTTCG
1675958 TTTT
1 TTTT
1675962 GCTTTTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTCTTTCG
Found at i:1676198 original size:20 final size:21
Alignment explanation
Indices: 1676167--1676208 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1676157 ATTAAGGAAG
1676167 GAAATAGAAATGGAAAGAAAT
1 GAAATAGAAATGGAAAGAAAT
*
1676188 GAAAT-GAAATGGATAGAAAT
1 GAAATAGAAATGGAAAGAAAT
1676208 G
1 G
1676209 TTATCAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (21 bp):
GAAATAGAAATGGAAAGAAAT
Found at i:1699807 original size:15 final size:15
Alignment explanation
Indices: 1699772--1699800 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1699762 GTGCTTCAAC
1699772 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
1699786 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
1699801 CTTTTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:1700777 original size:33 final size:35
Alignment explanation
Indices: 1700739--1700855 Score: 159
Period size: 36 Copynumber: 3.3 Consensus size: 35
1700729 ATGGTGATGA
* * *
1700739 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGG-TGATGATATAGGCGTGAT
1700773 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
1700808 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGA-TATGGTGATGATATAGGCGTGAT
1700844 AATGGTGATGGA
1 AATGGTGATGGA
1700856 CAGATTGTAT
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
33 9 0.12
34 1 0.01
35 18 0.24
36 47 0.63
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:1700789 original size:13 final size:12
Alignment explanation
Indices: 1700770--1700855 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
1700760 TTATTGGCGT
1700770 GATATGGTGATG
1 GATATGGTGATG
1700782 GAATATGGTGAT-
1 G-ATATGGTGATG
*
1700794 GATATAGGCG-T-
1 GATAT-GGTGATG
1700805 GATAATGGTGATG
1 GAT-ATGGTGATG
1700818 GACTATGGTGAT-
1 GA-TATGGTGATG
*
1700830 GATATAGGCG-T-
1 GATAT-GGTGATG
1700841 GATAATGGTGATG
1 GAT-ATGGTGATG
1700854 GA
1 GA
1700856 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:1700825 original size:36 final size:36
Alignment explanation
Indices: 1700755--1700856 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
1700745 AATGGAAGGA
* * *
1700755 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1700790 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1700826 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
1700857 AGATTGTATC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 16 0.25
36 47 0.75
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:1706496 original size:33 final size:32
Alignment explanation
Indices: 1706432--1706496 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
1706422 CTTGTTGATG
*
1706432 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
1706464 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
1706497 GATGGAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:1706544 original size:36 final size:36
Alignment explanation
Indices: 1706485--1706575 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
1706475 GATGTTATTG
*
1706485 GCGTGAT-ATGGTGATGGAATATGGTGATGATATAA
1 GCGTGATAATGGTGATGGACTATGGTGATGATATAA
*
1706520 GCGTGATAATGGTGATGGACTATGGTGATGATATAG
1 GCGTGATAATGGTGATGGACTATGGTGATGATATAA
*
1706556 GTGTGATAATGGTGATGGAC
1 GCGTGATAATGGTGATGGAC
1706576 AGATTGTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 7 0.13
36 45 0.87
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
GCGTGATAATGGTGATGGACTATGGTGATGATATAA
Found at i:1711216 original size:3 final size:3
Alignment explanation
Indices: 1711203--1711242 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1711193 ATATATAAGC
1711203 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1711243 TACAATTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1711593 original size:43 final size:41
Alignment explanation
Indices: 1711446--1711774 Score: 184
Period size: 43 Copynumber: 7.7 Consensus size: 41
1711436 GGGTCGTCTA
* * * * *
1711446 AGGG-TGACATGGTTCCTACGTGATGAGGAAATCTGG-TCG
1 AGGGTTGACACGGCTCCTACGTGATGAGGAGAGCTGGATCT
* * * **
1711485 AGGGTTGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTT
1 AGGGTTGACACGGCTCCTACGTGATGAGGAGAGC-TGG--ATC-T
* * *
1711530 AAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT
1 -AGG-GTTGACACGGCTCCTACGTGATGAGGA-GAGCTGG--ATCT
* *
1711575 ATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGG-TCT
1 AGGGTTGACACGGCTCCTACGTGATGAGGAGAGCTGGATCT
* * * * **
1711615 GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT
1 AGGG-TTGACACGGCTCCTACGTGATGAGGAGAGCTGG--ATCT
* * *
1711659 AAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT
1 --AGG-GTTGACACGGCTCCTACGTGATGAGGA-GAGCTGG--ATCT
* *
1711705 ATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGG-TCT
1 AGGGTTGACACGGCTCCTACGTGATGAGGAGAGCTGGATCT
* * * *
1711745 GGGGATGACACGGTTCCTACATGATGAGGA
1 AGGGTTGACACGGCTCCTACGTGATGAGGA
1711775 CGGCTGGCCA
Statistics
Matches: 225, Mismatches: 46, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
39 4 0.02
40 55 0.24
41 32 0.14
42 2 0.01
43 56 0.25
44 9 0.04
45 1 0.00
46 41 0.18
47 24 0.11
48 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (41 bp):
AGGGTTGACACGGCTCCTACGTGATGAGGAGAGCTGGATCT
Found at i:1711654 original size:130 final size:130
Alignment explanation
Indices: 1711450--1711771 Score: 531
Period size: 130 Copynumber: 2.5 Consensus size: 130
1711440 CGTCTAAGGG
* * * * *
1711450 TGACATGGTTCCTACGTGATGAGGAAATCTGGTC-GAGGGTTGACACTGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTG-GGGATGACACGGCTCATACGTGATGAAG
*
1711514 AGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
65 AGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
1711579 T
130 T
1711580 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAG
1711645 AGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
65 AGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
1711709 T
130 T
* * *
1711710 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGA
1711772 GGACGGCTGG
Statistics
Matches: 181, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
129 20 0.11
130 132 0.73
131 29 0.16
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (130 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
GTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:1711840 original size:28 final size:28
Alignment explanation
Indices: 1711820--1711881 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1711810 AAACCAAATT
1711820 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
1711848 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
1711876 AAAGAT
1 AAAGAT
1711882 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:1712922 original size:29 final size:27
Alignment explanation
Indices: 1712890--1712980 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 27
1712880 ATGTTTTAAG
1712890 AGAAACATACTCAAAGATTTTTTCTCAAA
1 AGAAACA-ACTCAAAGATTTTTT-TCAAA
*
1712919 AGAAATAACTCAAAGATTTTTATTCAAA
1 AGAAACAACTCAAAGATTTTT-TTCAAA
*
1712947 ATG-AACAAACTCAAAGATTTGTTTCAAA
1 A-GAAAC-AACTCAAAGATTTTTTTCAAA
1712975 AGAAAC
1 AGAAAC
1712981 TGTCTCAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 32 0.58
29 22 0.40
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (27 bp):
AGAAACAACTCAAAGATTTTTTTCAAA
Found at i:1712999 original size:121 final size:119
Alignment explanation
Indices: 1712693--1713010 Score: 336
Period size: 120 Copynumber: 2.6 Consensus size: 119
1712683 TGAGACGAAT
* * * ** *
1712693 TTTTTTCCAAAGGAAACAATCTCAAAGGTTGGTTTTTCATTAGAAACTGTCTCAAGAGAGGCAAA
1 TTTTTTCAAAAGG-AACAAACTCAAA-GAT--TTTTTCAAAAGAAACTGTCTCAAGAGAGACAAA
* * * * **
1712758 ATTTGTTTTTAAAGAAATAAACTAAAAGATGATTTTGTTAGTAGAAACAAACTCAAAGA
62 ATATG-TTTTAAAGAAACAAACTAAAAGATGATTTTCTCAAAAGAAACAAACTCAAAGA
* * * *
1712817 TTTTTTCAAAAGGAATAGACTCCAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATAT
1 TTTTTTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATAT
* * * *
1712882 GTTTTAAGAGAAACATACTCAAAGAT-TTTTTCTCAAAAGAAA-TAACTCAAAGA
66 GTTTTAA-AGAAACAAACTAAAAGATGATTTTCTCAAAAGAAACAAACTCAAAGA
*
1712935 TTTTTATTCAAAATGAACAAACTCAAAGATTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
1 -TTTT-TTCAAAAGGAACAAACTCAAAGATTT-TTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
1713000 -ATCGTTTTAAA
63 TAT-GTTTTAAA
1713011 ATATTCAAAG
Statistics
Matches: 165, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
118 10 0.06
119 21 0.13
120 74 0.45
121 38 0.23
122 2 0.01
123 8 0.05
124 12 0.07
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (119 bp):
TTTTTTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATAT
GTTTTAAAGAAACAAACTAAAAGATGATTTTCTCAAAAGAAACAAACTCAAAGA
Found at i:1713255 original size:34 final size:35
Alignment explanation
Indices: 1713204--1713326 Score: 133
Period size: 36 Copynumber: 3.5 Consensus size: 35
1713194 CTCAAAGGAA
*
1713204 AAAT-GTCTCAAGCGAGACGAAGTTTGTTTTA-AG
1 AAATAGTCTCAAGCGAGACAAAGTTTGTTTTAGAG
* ** *
1713237 AGATAGTCTCAAATGAGACAAAATTTGTTTTTAGAG
1 AAATAGTCTCAAGCGAGACAAAGTTTG-TTTTAGAG
* *
1713273 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTTGAG
1 AAATAGTCTCAAGCGAGACAAAGTTTGTTTTAGAG
* *
1713308 AAAAAGATCTCAAGTGAGA
1 AAATAG-TCTCAAGCGAGA
1713327 TCAACTTTGT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
33 3 0.04
34 18 0.25
35 16 0.22
36 35 0.49
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (35 bp):
AAATAGTCTCAAGCGAGACAAAGTTTGTTTTAGAG
Found at i:1713457 original size:105 final size:101
Alignment explanation
Indices: 1713278--1713510 Score: 292
Period size: 105 Copynumber: 2.3 Consensus size: 101
1713268 TAGAGAAATT
1713278 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAAAGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAAAGATCTCAAGTGAGATCAACTTTGTTTAAT
* *
1713342 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
1713380 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAAGAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AGAAA-AAG-ATCTCAA-GTGAGATCAACTTTGTTT
* * * *
1713444 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AAT-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
1713485 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
1713511 AAAATTCTCA
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 8 0.07
104 6 0.05
105 78 0.68
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAAAGATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:1713597 original size:21 final size:21
Alignment explanation
Indices: 1713536--1713597 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
1713526 TGTGGAAAAA
*
1713536 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAGCGAGACAAAATT
* * * *
1713557 TGTTTTAA---AGA-GAAAGT
1 TGTCTCAAGCGAGACAAAATT
1713574 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGCGAGACAAAATT
1713595 TGT
1 TGT
1713598 TTTTAAGAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 8
0.62 0.20 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGCGAGACAAAATT
Found at i:1713614 original size:36 final size:36
Alignment explanation
Indices: 1713530--1713638 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 36
1713520 AAAATTTGTG
* *
1713530 GAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
*
1713566 GAGAAAGTTGTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAA
* * * * *
1713604 GAAAACTGTCTCTAGTGAGACGACACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
1713639 TTAATAAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
36 15 0.24
37 17 0.27
38 30 0.48
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
Found at i:1713972 original size:4 final size:4
Alignment explanation
Indices: 1713963--1714001 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
1713953 TTTATGTATC
1713963 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1714002 AGTTTTCTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 31 0.94
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:1717603 original size:32 final size:32
Alignment explanation
Indices: 1717567--1717628 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1717557 TGAAAAAAAG
* *
1717567 ACACAAACAACAGAAAATAAATAAGTTAGTGC
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGC
* *
1717599 ACACAAAGAAAAGAAAAGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
1717629 ACAGGTAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGC
Found at i:1721191 original size:3 final size:3
Alignment explanation
Indices: 1721178--1721226 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1721168 ATAAATAAGC
1721178 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1721225 AT
1 AT
1721227 TACAATTAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1722530 original size:13 final size:11
Alignment explanation
Indices: 1722489--1722573 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
1722479 ACAATCTGTC
1722489 CATCACCATTAT
1 CATCACCA-TAT
*
1722501 CA-CGCCTATAT
1 CATCACC-ATAT
1722512 CATCACCATAGT
1 CATCACCATA-T
1722524 CCATCACCATTAT
1 -CATCACCA-TAT
*
1722537 CA-CGCCTATAT
1 CATCACC-ATAT
1722548 CATCACCATATT
1 CATCACCATA-T
1722560 CCATCACCATAT
1 -CATCACCATAT
1722572 CA
1 CA
1722574 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1722533 original size:36 final size:36
Alignment explanation
Indices: 1722486--1722587 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
1722476 GATACAATCT
1722486 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
1722522 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1722558 TTCCATCACCA-TATCACGCCTATATTATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
1722588 ACAACTTATA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 18 0.28
36 46 0.72
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1725794 original size:29 final size:29
Alignment explanation
Indices: 1725761--1725818 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1725751 CAATGAGCTG
1725761 ACCTATAACTCATCTTCATGTAATTCATC
1 ACCTATAACTCATCTTCATGTAATTCATC
1725790 ACCTATAACTCATCTTCATGTAATTCATC
1 ACCTATAACTCATCTTCATGTAATTCATC
1725819 TATGGCCAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (29 bp):
ACCTATAACTCATCTTCATGTAATTCATC
Found at i:1725819 original size:15 final size:15
Alignment explanation
Indices: 1725770--1725819 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1725760 GACCTATAAC
1725770 TCATCTTCATGTAAT
1 TCATCTTCATGTAAT
* * * *
1725785 TCATC-ACCTATAAC
1 TCATCTTCATGTAAT
1725799 TCATCTTCATGTAAT
1 TCATCTTCATGTAAT
1725814 TCATCT
1 TCATCT
1725820 ATGGCCAGCT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.42
Consensus pattern (15 bp):
TCATCTTCATGTAAT
Found at i:1726684 original size:13 final size:11
Alignment explanation
Indices: 1726643--1726727 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
1726633 ACAATCTGTC
1726643 CATCACCATTAT
1 CATCACCA-TAT
*
1726655 CA-CGCCTATAT
1 CATCACC-ATAT
1726666 CATCACCATAGT
1 CATCACCATA-T
1726678 CCATCACCATTAT
1 -CATCACCA-TAT
*
1726691 CA-CGCCTATAT
1 CATCACC-ATAT
1726702 CATCACCATATT
1 CATCACCATA-T
1726714 CCATCACCATAT
1 -CATCACCATAT
1726726 CA
1 CA
1726728 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1726687 original size:36 final size:36
Alignment explanation
Indices: 1726640--1726736 Score: 178
Period size: 36 Copynumber: 2.7 Consensus size: 36
1726630 GATACAATCT
1726640 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
1726676 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1726712 TTCCATCACCA-TATCACGCCTATAT
1 GTCCATCACCATTATCACGCCTATAT
1726737 TATTACCAAC
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
35 14 0.23
36 46 0.77
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1728789 original size:24 final size:25
Alignment explanation
Indices: 1728754--1728808 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1728744 ACTTGGAGCC
*
1728754 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
1728778 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
1728802 TCAAGTG
1 TCAAGTG
1728809 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:1733486 original size:19 final size:20
Alignment explanation
Indices: 1733449--1733499 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1733439 TGAAGCCCTT
1733449 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
1733469 TGAAAATACATG-TTTTTAA
1 TGAAAATACATGATTTTTAA
*
1733488 TGAAGATACATG
1 TGAAAATACATG
1733500 CTCTTAGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1739014 original size:19 final size:20
Alignment explanation
Indices: 1738973--1739023 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1738963 GAAACCCCTT
*
1738973 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTCTAA
1738993 TGAAAATACATG-TTTCTAA
1 TGAAAATACATGATTTCTAA
*
1739012 TGAAGATACATG
1 TGAAAATACATG
1739024 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTCTAA
Found at i:1740282 original size:24 final size:24
Alignment explanation
Indices: 1740237--1740282 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1740227 GTTTCAGATA
* **
1740237 CAACATCACCACCATCTTCCATTT
1 CAACACCACCACCATCAACCATTT
*
1740261 CAACACCAGCACCATCAACCAT
1 CAACACCACCACCATCAACCAT
1740283 CTTCCATCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.43, G:0.02, T:0.20
Consensus pattern (24 bp):
CAACACCACCACCATCAACCATTT
Found at i:1743993 original size:23 final size:24
Alignment explanation
Indices: 1743962--1744065 Score: 67
Period size: 25 Copynumber: 4.4 Consensus size: 24
1743952 CACCATCTTC
*
1743962 CATCTCCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCCTATAT
*
1743985 CATCACCA-TAGTCCATCACC-ATTAT
1 CATCACCATTA-T-CATCGCCTA-TAT
* * *
1744010 CA-CGCCTTTATCATC-ACTATAGT
1 CATCACCATTATCATCGCCTATA-T
*
1744033 CCATCTCCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCGCCTATAT
1744057 CATCACCAT
1 CATCACCAT
1744066 ATTCCACCAC
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
22 5 0.08
23 22 0.35
24 11 0.18
25 24 0.39
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.32
Consensus pattern (24 bp):
CATCACCATTATCATCGCCTATAT
Found at i:1744000 original size:36 final size:36
Alignment explanation
Indices: 1743960--1744100 Score: 219
Period size: 36 Copynumber: 3.9 Consensus size: 36
1743950 AACACCATCT
*
1743960 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
1743996 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
1744032 TCCATCTCCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
1744068 TCCACCACCATTATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
1744101 ACTTATAAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1744077 original size:72 final size:72
Alignment explanation
Indices: 1743960--1744098 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
1743950 AACACCATCT
* *
1743960 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCATCACCATTATCACGCCTTTATCATC
1 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
1744025 ACTATAG
66 ACTATAG
* *
1744032 TCCATCTCCATTATCACGCCTATATCATCACCATATTCCACCACCATTATCACGCCTATATTATC
1 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
1744097 AC
66 AC
1744099 CAACTTATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (72 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
ACTATAG
Found at i:1746970 original size:13 final size:11
Alignment explanation
Indices: 1746929--1747013 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
1746919 ACAATCTGTC
1746929 CATCACCATTAT
1 CATCACCA-TAT
*
1746941 CA-CGCCTATAT
1 CATCACC-ATAT
1746952 CATCACCATAGT
1 CATCACCATA-T
1746964 CCATCACCATTAT
1 -CATCACCA-TAT
*
1746977 CA-CGCCTATAT
1 CATCACC-ATAT
1746988 CATCACCATATT
1 CATCACCATA-T
1747000 CCATCACCATAT
1 -CATCACCATAT
1747012 CA
1 CA
1747014 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1746973 original size:36 final size:36
Alignment explanation
Indices: 1746926--1747027 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
1746916 GATACAATCT
1746926 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
1746962 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
1746998 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
1747028 TCCTTCCATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 17 0.27
36 46 0.73
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1747042 original size:33 final size:34
Alignment explanation
Indices: 1746927--1747043 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 34
1746917 ATACAATCTG
* *
1746927 TCCATCACCATTATCACGCCTATATCATCACCAT
1 TCCATCACCATTATCACGCCAATAACATCACCAT
* *
1746961 AGTCCATCACCATTATCACGCCTATATCATCACCATAT
1 --TCCATCACCATTATCACGCCAATAACATCACC--AT
1746999 TCCATCACCA-TATCACGCCAATAACATCATCC-T
1 TCCATCACCATTATCACGCCAATAACATCA-CCAT
*
1747032 TCCATTACCATT
1 TCCATCACCATT
1747044 TCATCACCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 10 0.14
34 1 0.01
35 17 0.23
36 44 0.59
38 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCACCAT
Found at i:1747061 original size:33 final size:33
Alignment explanation
Indices: 1746927--1747066 Score: 88
Period size: 36 Copynumber: 4.1 Consensus size: 33
1746917 ATACAATCTG
* * *
1746927 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACACCAATAACATCATCC-T
* * *
1746961 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACACCAATAACATCATCC---T
*
1746999 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACACCAATAACATCATCCT
* * *
1747032 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CACCAATAACATCATCCT
1747065 TC
1 TC
1747067 ATTCATCAAC
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.07
35 17 0.18
36 44 0.47
38 2 0.02
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACACCAATAACATCATCCT
Found at i:1750327 original size:23 final size:24
Alignment explanation
Indices: 1750295--1750399 Score: 69
Period size: 25 Copynumber: 4.4 Consensus size: 24
1750285 ACACCATCTT
*
1750295 TCATCTCCATTATCA-CGCCTATA
1 TCATCACCATTATCATCGCCTATA
*
1750318 TCATCACCA-TAGTCCATCACC-ATTA
1 TCATCACCATTA-T-CATCGCCTA-TA
* * *
1750343 TCA-CGCCTTTATCATC-ACTATA
1 TCATCACCATTATCATCGCCTATA
*
1750365 GTCCATCTCCATTATCA-CGCCTATA
1 -T-CATCACCATTATCATCGCCTATA
1750390 TCATCACCAT
1 TCATCACCAT
1750400 ATTCCACCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
22 5 0.08
23 23 0.37
24 11 0.17
25 24 0.38
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (24 bp):
TCATCACCATTATCATCGCCTATA
Found at i:1750341 original size:36 final size:36
Alignment explanation
Indices: 1750296--1750434 Score: 215
Period size: 36 Copynumber: 3.9 Consensus size: 36
1750286 CACCATCTTT
*
1750296 CATCTCCATTATCACGCCTATATCATCACCATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
* *
1750332 CATCACCATTATCACGCCTTTATCATCACTATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
* *
1750368 CATCTCCATTATCACGCCTATATCATCACCATATTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
* *
1750404 CACCACCATTATCACGCCTATATTATCACCA
1 CATCACCATTATCACGCCTATATCATCACCA
1750435 ACTTATAAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATAGTC
Found at i:1750413 original size:72 final size:72
Alignment explanation
Indices: 1750296--1750432 Score: 238
Period size: 72 Copynumber: 1.9 Consensus size: 72
1750286 CACCATCTTT
* *
1750296 CATCTCCATTATCACGCCTATATCATCACCATAGTCCATCACCATTATCACGCCTTTATCATCAC
1 CATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATCAC
1750361 TATAGTC
66 TATAGTC
* *
1750368 CATCTCCATTATCACGCCTATATCATCACCATATTCCACCACCATTATCACGCCTATATTATCAC
1 CATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATCAC
1750433 CAACTTATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.31
Consensus pattern (72 bp):
CATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATCAC
TATAGTC
Found at i:1751911 original size:19 final size:20
Alignment explanation
Indices: 1751887--1751936 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1751877 CGGCCAAGAG
*
1751887 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
1751906 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
1751926 -ATGTATTTTCA
1 CATGTATTTTCA
1751937 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:1757183 original size:15 final size:15
Alignment explanation
Indices: 1757148--1757176 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1757138 GTGCTTTAAC
1757148 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
1757162 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
1757177 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:1761924 original size:35 final size:37
Alignment explanation
Indices: 1761855--1761934 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1761845 ATACTATTTC
*
1761855 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
1761892 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
1761927 CATCACCA
1 CATCACCA
1761935 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:1765508 original size:19 final size:20
Alignment explanation
Indices: 1765484--1765534 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1765474 CGGCCAAGAG
* *
1765484 CATGTATCTTCAT-TTAAAT
1 CATGTATTTTCATCATAAAT
1765503 CATGTATTTTCATCATAAAT
1 CATGTATTTTCATCATAAAT
1765523 CATGTATTTTCA
1 CATGTATTTTCA
1765535 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATCATAAAT
Found at i:1771621 original size:8 final size:8
Alignment explanation
Indices: 1771592--1771648 Score: 87
Period size: 8 Copynumber: 6.9 Consensus size: 8
1771582 TGGAGTGCAA
1771592 AAAAGAAAG
1 AAAAG-AAG
*
1771601 AAAAGACAA
1 AAAAGA-AG
1771610 AAAAGAAG
1 AAAAGAAG
1771618 AAAAGAAG
1 AAAAGAAG
1771626 AAAAGAAG
1 AAAAGAAG
1771634 AAAAGAAG
1 AAAAGAAG
1771642 AAAAGAA
1 AAAAGAA
1771649 AAGAAAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
8 33 0.73
9 12 0.27
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:1771623 original size:5 final size:5
Alignment explanation
Indices: 1771592--1771655 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
1771582 TGGAGTGCAA
*
1771592 AAAAG -AAAG AAAAG ACAA- AAAAG AAGAA- AAGAAG AAAAG AAGAA-
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AA-AAG AAAAG AA-AAG
1771636 AAGAAG AAAAG AAAAG AAAA
1 AA-AAG AAAAG AAAAG AAAA
1771656 AGAGAAGTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
4 7 0.14
5 36 0.71
6 8 0.16
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1771658 original size:16 final size:16
Alignment explanation
Indices: 1771591--1771658 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
1771581 TTGGAGTGCA
1771591 AAAAAG-AAAGAAAAG
1 AAAAAGAAAAGAAAAG
1771606 ACAAAA-AAGAAGAAAAG
1 A-AAAAGAA-AAGAAAAG
1771623 ---AAGAAAAGAAGAA-
1 AAAAAGAAAAGAA-AAG
*
1771636 AAGAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
1771652 AAAAAGA
1 AAAAAGA
1771659 GAAGTTCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 17
0.70 0.02 0.28
Matches are distributed among these distances:
13 7 0.16
14 4 0.09
15 3 0.07
16 21 0.49
17 8 0.19
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:1771669 original size:24 final size:20
Alignment explanation
Indices: 1771590--1771662 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 20
1771580 ATTGGAGTGC
1771590 AAAAAAGAAAGAAAAGACAAA-
1 AAAAAAG-AAGAAAAGA-AAAG
*
1771611 AAAGAAGAA-AAGAAGAAAAG
1 AAAAAAGAAGAA-AAGAAAAG
1771631 AAGAAAAGAAGAAAAGAAAAG
1 AA-AAAAGAAGAAAAGAAAAG
1771652 AAAAAGAGAAG
1 AAAAA-AGAAG
1771663 TTCAAAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 5 0.11
20 11 0.24
21 27 0.60
22 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAGAAAAGAAAAG
Found at i:1784727 original size:30 final size:29
Alignment explanation
Indices: 1784693--1784775 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
1784683 CAACTTGATA
1784693 AGCATTTGGAAGACACATACAGCTTGGTGG
1 AGCATTTGGAAGACACA-ACAGCTTGGTGG
* *
1784723 AGCATTTTGCAAGACA-AATAGCTTGGTGG
1 AGCA-TTTGGAAGACACAACAGCTTGGTGG
*
1784752 AGCATTTGGGAGACACAAACAGCT
1 AGCATTTGGAAGACAC-AACAGCT
1784776 CATAAAGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 9 0.20
29 15 0.33
30 11 0.24
31 10 0.22
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (29 bp):
AGCATTTGGAAGACACAACAGCTTGGTGG
Found at i:1785383 original size:12 final size:12
Alignment explanation
Indices: 1785363--1785393 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1785353 TAATTCCTTC
1785363 TTTTCTTTATCA
1 TTTTCTTTATCA
*
1785375 TTTTTTTTATCA
1 TTTTCTTTATCA
1785387 TTTTCTT
1 TTTTCTT
1785394 AGCCATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTTTATCA
Found at i:1791550 original size:22 final size:23
Alignment explanation
Indices: 1791498--1791556 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 23
1791488 TTGCTTTCTC
* * *
1791498 CTTTTCTTTTCTTTTCTTCTTTT
1 CTTTTTTTTTCTCTTCTTCTTGT
1791521 CTGATTTTTTTTCTCTTCTT-TTGT
1 CT--TTTTTTTTCTCTTCTTCTTGT
*
1791545 CTTTTTCTTTCT
1 CTTTTTTTTTCT
1791557 TTTTGCACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 9 0.30
23 2 0.07
24 5 0.17
25 14 0.47
ACGTcount: A:0.02, C:0.20, G:0.03, T:0.75
Consensus pattern (23 bp):
CTTTTTTTTTCTCTTCTTCTTGT
Found at i:1791557 original size:20 final size:21
Alignment explanation
Indices: 1791504--1791557 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1791494 TCTCCTTTTC
1791504 TTTTCTTTTCTTCTTTTCTGAT
1 TTTTC-TTTCTTCTTTTCTGAT
* * *
1791526 TTTTTTTCTCTTCTTTTGT-CT
1 TTTTCTT-TCTTCTTTTCTGAT
1791547 TTTTCTTTCTT
1 TTTTCTTTCTT
1791558 TTTGCACTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 14 0.52
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTCTTTCTTCTTTTCTGAT
Found at i:1796354 original size:13 final size:13
Alignment explanation
Indices: 1796336--1796361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1796326 CTAGGGAGCT
1796336 GTGTGGTGCAGCC
1 GTGTGGTGCAGCC
1796349 GTGTGGTGCAGCC
1 GTGTGGTGCAGCC
1796362 CTTAGCATGG
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:0.08, C:0.23, G:0.46, T:0.23
Consensus pattern (13 bp):
GTGTGGTGCAGCC
Found at i:1799054 original size:15 final size:15
Alignment explanation
Indices: 1799036--1799074 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1799026 TACTTCAGCC
*
1799036 TCTTCTTCTTCGATT
1 TCTTCTTCTTAGATT
1799051 TCTTCTTCTTAGATT
1 TCTTCTTCTTAGATT
1799066 TCTTCTTCT
1 TCTTCTTCT
1799075 ATTCTGGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.08, C:0.26, G:0.05, T:0.62
Consensus pattern (15 bp):
TCTTCTTCTTAGATT
Found at i:1799756 original size:24 final size:24
Alignment explanation
Indices: 1799710--1799758 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1799700 TTTTACTTCT
* * *
1799710 TTTTGAGTGCTGGATTTTTTTTTC
1 TTTTGAGTGCTGCACTTTGTTTTC
*
1799734 TTTTGAGTGCTTCACTTTGTTTTC
1 TTTTGAGTGCTGCACTTTGTTTTC
1799758 T
1 T
1799759 GATTTTTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.08, C:0.12, G:0.18, T:0.61
Consensus pattern (24 bp):
TTTTGAGTGCTGCACTTTGTTTTC
Found at i:1803058 original size:76 final size:72
Alignment explanation
Indices: 1802971--1803128 Score: 176
Period size: 74 Copynumber: 2.1 Consensus size: 72
1802961 TGAATAAATC
* **
1802971 TTCATGAATGTATCTTCATGGCTG-AATCCTTC-CTCCGGTGTGTGAACATGTTTGATTTGTCTT
1 TTCATGAATGTATC-T--TGGCTGAAATCCTTCTC-CCCGTGTGTGAACATGACT-ATTTGTCTT
* *
1803034 CTATGGATGAATG
61 CT-TGCATGAATA
* *
1803047 TTCATGAATGTATCTTGGCTGAAATTCTTCTCCCCTTGTGTGAACATGACTATTTGTCTTCTTGC
1 TTCATGAATGTATCTTGGCTGAAATCCTTCTCCCCGTGTGTGAACATGACTATTTGTCTTCTTGC
1803112 ATGAATA
66 ATGAATA
*
1803119 TGCATGAATG
1 TTCATGAATG
1803129 GATGAACTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
72 17 0.24
73 17 0.24
74 22 0.31
75 2 0.03
76 14 0.19
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (72 bp):
TTCATGAATGTATCTTGGCTGAAATCCTTCTCCCCGTGTGTGAACATGACTATTTGTCTTCTTGC
ATGAATA
Found at i:1804142 original size:19 final size:19
Alignment explanation
Indices: 1804118--1804156 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1804108 CATGGTTAGG
1804118 TTCATTGAATCTTCCCTTT
1 TTCATTGAATCTTCCCTTT
1804137 TTCATTGAATCTTCCCTTT
1 TTCATTGAATCTTCCCTTT
1804156 T
1 T
1804157 ATAAGGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.05, T:0.54
Consensus pattern (19 bp):
TTCATTGAATCTTCCCTTT
Found at i:1811613 original size:11 final size:12
Alignment explanation
Indices: 1811587--1811615 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1811577 CCAAAGATGA
1811587 AAAGGTATGTTG
1 AAAGGTATGTTG
1811599 AAAGGTATG-TG
1 AAAGGTATGTTG
1811610 AAAGGT
1 AAAGGT
1811616 GTTTAGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (12 bp):
AAAGGTATGTTG
Found at i:1814491 original size:8 final size:8
Alignment explanation
Indices: 1814463--1814510 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
1814453 TTGGAGTGCA
1814463 AAAAGAAAG
1 AAAAG-AAG
1814472 AAAAGACA-
1 AAAAGA-AG
1814480 AAAAGAAG
1 AAAAGAAG
1814488 AAAAGAAG
1 AAAAGAAG
1814496 AAAAGAAG
1 AAAAGAAG
1814504 AAAAGAA
1 AAAAGAA
1814511 AAGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 30 0.81
9 6 0.16
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:1814493 original size:5 final size:5
Alignment explanation
Indices: 1814463--1814517 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
1814453 TTGGAGTGCA
1814463 AAAAG -AAAG AAAAG ACAAA- AAGAAG AAAAG AAGAA- AAGAAG AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AA-AAG AAAAG AA-AAG AA-AAG AAAAG
1814509 AAAAG AAAA
1 AAAAG AAAA
1814518 AGAGAAGTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 5 0.11
5 30 0.68
6 9 0.20
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1814520 original size:16 final size:15
Alignment explanation
Indices: 1814462--1814520 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
1814452 ATTGGAGTGC
*
1814462 AAAAAGAAAGAAAAG
1 AAAAAAAAAGAAAAG
*
1814477 ACAAAAAGAAGAAAAG
1 A-AAAAAAAAGAAAAG
*
1814493 AAGAAAAGAAGAAAAG
1 AA-AAAAAAAGAAAAG
1814509 AAAAGAAAAAGA
1 AAAA-AAAAAGA
1814521 GAAGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
15 4 0.11
16 34 0.89
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:1827092 original size:110 final size:112
Alignment explanation
Indices: 1826899--1827120 Score: 430
Period size: 110 Copynumber: 2.0 Consensus size: 112
1826889 TGGTGCATAT
1826899 GGCGATCAAAATAGAAATGCAGCAACGTAGAAAATCTTCTTACCGAGGTAATACTCATTCTAAAG
1 GGCGATCAAAATAGAAATGCAGCAACGTAGAAAATCTTCTTACCGAGGTAATACTCATTCTAAAG
1826964 TTTTCTCTAATCCATTA-TTACTCCTAACAATG-CAGAAAGCAAGCA
66 TTTTCTCTAATCCATTATTTACTCCTAACAATGCCAGAAAGCAAGCA
1827009 GGCGATCAAAATAGAAATGCAGCAACGTAGAAAATCTTCTTACCGAGGTAATACTCATTCTAAAG
1 GGCGATCAAAATAGAAATGCAGCAACGTAGAAAATCTTCTTACCGAGGTAATACTCATTCTAAAG
1827074 TTTTCTCTAATCCATTATTTACTCCTAACAATGCCAGAAAGCAAGCA
66 TTTTCTCTAATCCATTATTTACTCCTAACAATGCCAGAAAGCAAGCA
1827121 CCACTTATGA
Statistics
Matches: 110, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
110 82 0.75
111 15 0.14
112 13 0.12
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (112 bp):
GGCGATCAAAATAGAAATGCAGCAACGTAGAAAATCTTCTTACCGAGGTAATACTCATTCTAAAG
TTTTCTCTAATCCATTATTTACTCCTAACAATGCCAGAAAGCAAGCA
Found at i:1829688 original size:99 final size:97
Alignment explanation
Indices: 1829528--1829706 Score: 261
Period size: 99 Copynumber: 1.8 Consensus size: 97
1829518 AGATAGTGGG
* ** *
1829528 TCAAAGTCCTATTTACCACCCCTTAGAACGGATTTGTAAGGGTGGGTCTTTTCTCTCTATAGCAC
1 TCAAAGTCCTATTTACCACCCCTTAGAACGAATTTGTAAGACTGGGTCTTTGCTCTCTATAGCAC
*
1829593 TGGTTCTTCCTTGGTCAATTCTAGGATACTAT
66 TCGTTCTTCCTTGGTCAATTCTAGGATACTAT
*
1829625 TCAAAGTCCTATTTACCATCATCCCTTAGAAC-AATTTGTAAGACTGGGTCTTTGCTCTTTATAG
1 TCAAAGTCCTATTTACCA-C--CCCTTAGAACGAATTTGTAAGACTGGGTCTTTGCTCTCTATAG
*
1829689 CACTCGTTCTTTCTTGGT
63 CACTCGTTCTTCCTTGGT
1829707 TATTCTAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
97 18 0.25
98 1 0.01
99 43 0.60
100 10 0.14
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.39
Consensus pattern (97 bp):
TCAAAGTCCTATTTACCACCCCTTAGAACGAATTTGTAAGACTGGGTCTTTGCTCTCTATAGCAC
TCGTTCTTCCTTGGTCAATTCTAGGATACTAT
Found at i:1831808 original size:20 final size:22
Alignment explanation
Indices: 1831773--1831812 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1831763 CATGCTTAGT
1831773 CATTCATTTGTTAGCTCATATG
1 CATTCATTTGTTAGCTCATATG
1831795 CATTCA-TT-TTAGCTCATA
1 CATTCATTTGTTAGCTCATA
1831813 GGTGATGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (22 bp):
CATTCATTTGTTAGCTCATATG
Found at i:1832618 original size:30 final size:29
Alignment explanation
Indices: 1832584--1832672 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
1832574 ACACGTTGGG
*
1832584 ACAGCTTGATGAAGCATTTGGAAGACACA
1 ACAGCTTGATGGAGCATTTGGAAGACACA
* *
1832613 TACAGCAT-AGTGGAGCATTTTGAAAGACA-A
1 -ACAGCTTGA-TGGAGCA-TTTGGAAGACACA
* *
1832643 ACAGCTTGGTGGAGCATTTGGGAGACACA
1 ACAGCTTGATGGAGCATTTGGAAGACACA
1832672 A
1 A
1832673 ACAACTCATA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 9 0.19
29 16 0.33
30 13 0.27
31 10 0.21
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (29 bp):
ACAGCTTGATGGAGCATTTGGAAGACACA
Found at i:1832675 original size:30 final size:30
Alignment explanation
Indices: 1832584--1832675 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
1832574 ACACGTTGGG
* * * *
1832584 ACAGCTTGATGAAGCATTTGGAAGACACAT
1 ACAGCTTGGTGGAGCATTTGGGAGACACAA
* * * * *
1832614 ACAGCATAGTGGAGCATTT-TGAAAGACAA
1 ACAGCTTGGTGGAGCATTTGGGAGACACAA
1832643 ACAGCTTGGTGGAGCATTTGGGAGACACAA
1 ACAGCTTGGTGGAGCATTTGGGAGACACAA
1832673 ACA
1 ACA
1832676 ACTCATAAAC
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 22 0.47
30 25 0.53
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (30 bp):
ACAGCTTGGTGGAGCATTTGGGAGACACAA
Found at i:1835299 original size:23 final size:23
Alignment explanation
Indices: 1835254--1835299 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1835244 TTATACCTAT
*
1835254 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
1835277 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
1835300 TATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:1836899 original size:22 final size:21
Alignment explanation
Indices: 1836874--1836934 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
1836864 AGAGTGTAAA
1836874 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAGAAAAAGA-AAAAGAAG
*
1836896 AGAAA-AAAAATCAGAAAAGAAG
1 AGAAAGAAAAA-GA-AAAAGAAG
1836918 A-AAAG-AAAAGAAAAAGA
1 AGAAAGAAAAAGAAAAAGA
1836935 GAAAGCAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 6 0.18
20 1 0.03
21 12 0.35
22 15 0.44
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (21 bp):
AGAAAGAAAAAGAAAAAGAAG
Found at i:1839814 original size:23 final size:23
Alignment explanation
Indices: 1839769--1839814 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1839759 TTATACCTAT
*
1839769 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
1839792 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
1839815 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:1841696 original size:25 final size:25
Alignment explanation
Indices: 1841664--1841719 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1841654 AAAAAATAGA
*
1841664 AAAG-AAATTGAAGCACTCCAAAAG
1 AAAGAAAATTGAAGCACTCAAAAAG
**
1841688 AAAGAAAATTTCAGCACTCAAAAAG
1 AAAGAAAATTGAAGCACTCAAAAAG
1841713 -AAGAAAA
1 AAAGAAAA
1841720 AAAAGCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.12
Consensus pattern (25 bp):
AAAGAAAATTGAAGCACTCAAAAAG
Found at i:1848508 original size:22 final size:22
Alignment explanation
Indices: 1848480--1848528 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1848470 TGCAAGGTAC
1848480 GTTCAAGACAATCCAGTGGACA
1 GTTCAAGACAATCCAGTGGACA
*
1848502 GTTCAAGGCAATCCAGTGGACA
1 GTTCAAGACAATCCAGTGGACA
1848524 GTTCA
1 GTTCA
1848529 CGTCACTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (22 bp):
GTTCAAGACAATCCAGTGGACA
Found at i:1852106 original size:30 final size:30
Alignment explanation
Indices: 1852070--1852148 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
1852060 TCAATGTCTC
*
1852070 CCAAATGCTCCACGAAGCTCTAAATATCTT
1 CCAAATGCTCCACCAAGCTCTAAATATCTT
* * * *
1852100 CCAAATGCTCCACTAAGCTGTATATGTCTT
1 CCAAATGCTCCACCAAGCTCTAAATATCTT
*
1852130 CCAAGTGCTCCACCAAGCT
1 CCAAATGCTCCACCAAGCT
1852149 ATCCCAACGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.27
Consensus pattern (30 bp):
CCAAATGCTCCACCAAGCTCTAAATATCTT
Found at i:1868950 original size:27 final size:24
Alignment explanation
Indices: 1868920--1868968 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 24
1868910 CAACAGAATC
1868920 AACAAAAAGAGAAAAAGAAAGAAGAAA
1 AACAAAAA-AG-AAAAGAAA-AAGAAA
1868947 AACAAAAAAGAAAAGAAAAAGA
1 AACAAAAAAGAAAAGAAAAAGA
1868969 CTCCTACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 8 0.36
26 2 0.09
27 8 0.36
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (24 bp):
AACAAAAAAGAAAAGAAAAAGAAA
Found at i:1875783 original size:35 final size:35
Alignment explanation
Indices: 1875742--1875821 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
1875732 ATGGTTAAGG
*
1875742 GATGGTGATGATATAGGCGTAAAATGGTGATGGAA
1 GATGGTGATGATATAGGCGTAAAATGGTAATGGAA
* *
1875777 GATGGTGATGATATAGGCGTGAAATTGTAATGGAA
1 GATGGTGATGATATAGGCGTAAAATGGTAATGGAA
1875812 GATGGTGATG
1 GATGGTGATG
1875822 CACAGATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.33, C:0.03, G:0.38, T:0.28
Consensus pattern (35 bp):
GATGGTGATGATATAGGCGTAAAATGGTAATGGAA
Found at i:1877009 original size:22 final size:21
Alignment explanation
Indices: 1876983--1877027 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1876973 TCATCATCAT
1876983 AGCTATAAAT-ATAATGTATGTA
1 AGCTAT-AATCATAATG-ATGTA
*
1877005 AGCTATTATCATAATGATGTA
1 AGCTATAATCATAATGATGTA
1877026 AG
1 AG
1877028 GCTAACCAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (21 bp):
AGCTATAATCATAATGATGTA
Found at i:1877357 original size:33 final size:33
Alignment explanation
Indices: 1877315--1877383 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1877305 GTTGATGAAT
*
1877315 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1877348 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1877381 GAA
1 GAA
1877384 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1877388 original size:13 final size:12
Alignment explanation
Indices: 1877369--1877454 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
1877359 TTATTGGCGT
1877369 GATATGGTGATG
1 GATATGGTGATG
1877381 GAATATGGTGAT-
1 G-ATATGGTGATG
*
1877393 GATATAGGCG-T-
1 GATAT-GGTGATG
1877404 GATAATGGTGATG
1 GAT-ATGGTGATG
1877417 GACTATGGTGAT-
1 GA-TATGGTGATG
*
1877429 GATATAGGCG-T-
1 GATAT-GGTGATG
1877440 GATAATGGTGATG
1 GAT-ATGGTGATG
1877453 GA
1 GA
1877455 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:1877424 original size:36 final size:36
Alignment explanation
Indices: 1877354--1877455 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
1877344 AATGGAAGGA
* * *
1877354 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1877389 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1877425 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
1877456 AGATTGTATC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 16 0.25
36 47 0.75
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:1882431 original size:23 final size:24
Alignment explanation
Indices: 1882388--1882436 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
1882378 AAAGGTTAAG
*
1882388 AAATATGATAAGGTAATGAAAAGA
1 AAATATGATAAGATAATGAAAAGA
*
1882412 AAATATGA-AAGAATAA-GAAATGA
1 AAATATGATAAG-ATAATGAAAAGA
1882435 AA
1 AA
1882437 TAGTAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.18, T:0.18
Consensus pattern (24 bp):
AAATATGATAAGATAATGAAAAGA
Found at i:1882619 original size:13 final size:15
Alignment explanation
Indices: 1882596--1882629 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1882586 TTTCTTTTTG
1882596 CTTTTGATTTTC-TT
1 CTTTTGATTTTCTTT
1882610 CTTTTG-TTTTCTTT
1 CTTTTGATTTTCTTT
1882624 CTTTTG
1 CTTTTG
1882630 CACTCCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.03, C:0.15, G:0.09, T:0.74
Consensus pattern (15 bp):
CTTTTGATTTTCTTT
Found at i:1883080 original size:33 final size:33
Alignment explanation
Indices: 1883038--1883106 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1883028 GTTGATGAAT
1883038 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGG-GATGAAATGGTAATG
* * * *
1883071 GAAGGATGATGTTATTGGGGTGATATGGTGATG
1 GAAGGATGATGTTAATGGGATGAAATGGTAATG
1883104 GAA
1 GAA
1883107 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGGATGAAATGGTAATG
Found at i:1883111 original size:13 final size:12
Alignment explanation
Indices: 1883092--1883156 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
1883082 TTATTGGGGT
1883092 GATATGGTGATG
1 GATATGGTGATG
1883104 GAATATGGTGAT-
1 G-ATATGGTGATG
*
1883116 GATATAGGCG-T-
1 GATAT-GGTGATG
1883127 GATAATGGTGATG
1 GAT-ATGGTGATG
1883140 GACTATGGTGAT-
1 GA-TATGGTGATG
1883152 GATAT
1 GATAT
1883157 AGGAGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:1883178 original size:36 final size:36
Alignment explanation
Indices: 1883090--1883178 Score: 144
Period size: 36 Copynumber: 2.5 Consensus size: 36
1883080 TGTTATTGGG
* *
1883090 GTGAT-ATGGTGATGGAATATGGTGATGATATAGGC
1 GTGATAATGGTGATGGACTATGGTGATGATATAGGA
1883125 GTGATAATGGTGATGGACTATGGTGATGATATAGGA
1 GTGATAATGGTGATGGACTATGGTGATGATATAGGA
*
1883161 GTGATAATTGTGATGGAC
1 GTGATAATGGTGATGGAC
1883179 AGATTGTATC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
35 5 0.10
36 45 0.90
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.31
Consensus pattern (36 bp):
GTGATAATGGTGATGGACTATGGTGATGATATAGGA
Found at i:1887429 original size:22 final size:21
Alignment explanation
Indices: 1887404--1887449 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1887394 TGCTGCAACA
* *
1887404 AAAGCAACAAAAAGAGAAAAAG
1 AAAG-AACAAAAAAACAAAAAG
*
1887426 AAAGAAGAAAAAAACAAAAAG
1 AAAGAACAAAAAAACAAAAAG
1887447 AAA
1 AAA
1887450 AGAAAAAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAGAACAAAAAAACAAAAAG
Found at i:1887437 original size:21 final size:19
Alignment explanation
Indices: 1887412--1887459 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
1887402 CAAAAGCAAC
*
1887412 AAAAAGAGAAAAAGAAAGAAG
1 AAAAAGACAAAAAG-AA-AAG
*
1887433 AAAAAAACAAAAAGAAAAG
1 AAAAAGACAAAAAGAAAAG
1887452 AAAAAGAC
1 AAAAAGAC
1887460 TCCTCCATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.42
20 2 0.08
21 12 0.50
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAGACAAAAAGAAAAG
Found at i:1887447 original size:14 final size:14
Alignment explanation
Indices: 1887409--1887450 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1887399 CAACAAAAGC
*
1887409 AACAAAAAGAGAAA
1 AACAAAAAGAAAAA
*
1887423 AAGAAAGAAGAAAAA
1 AACAAA-AAGAAAAA
1887438 AACAAAAAGAAAA
1 AACAAAAAGAAAA
1887451 GAAAAAGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (14 bp):
AACAAAAAGAAAAA
Found at i:1887455 original size:11 final size:11
Alignment explanation
Indices: 1887418--1887458 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1887408 CAACAAAAAG
1887418 AGAAAAAG-AA
1 AGAAAAAGAAA
1887428 AGAAGAAA-AAA
1 AGAA-AAAGAAA
*
1887439 ACAAAAAGAAA
1 AGAAAAAGAAA
1887450 AGAAAAAGA
1 AGAAAAAGA
1887459 CTCCTCCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:1891512 original size:35 final size:35
Alignment explanation
Indices: 1891411--1891516 Score: 122
Period size: 35 Copynumber: 3.0 Consensus size: 35
1891401 ATACTACATA
*
1891411 AACATCACCATCTTTCATCACCATTTTCACGCCTAC
1 AACATCACCATCTTTCATCACCA-TTTCACGCCTAT
* * * * *
1891447 AACATCACTATCTTCCATTACCACTGCACGCCTAT
1 AACATCACCATCTTTCATCACCATTTCACGCCTAT
* * *
1891482 ATCATTACCATCTTTTATCACCATTTCACGCCTAT
1 AACATCACCATCTTTCATCACCATTTCACGCCTAT
1891517 TATAACCACC
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
35 36 0.64
36 20 0.36
ACGTcount: A:0.27, C:0.36, G:0.04, T:0.33
Consensus pattern (35 bp):
AACATCACCATCTTTCATCACCATTTCACGCCTAT
Found at i:1892258 original size:30 final size:30
Alignment explanation
Indices: 1892222--1892300 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
1892212 TCAATGTCTC
*
1892222 CCAAATGCTCCACAAAGCTCTATATATTTT
1 CCAAATGCTCCACAAAGCTCTATATATCTT
* * * *
1892252 CCAAATGCTCCACTAAGTTGTATATGTCTT
1 CCAAATGCTCCACAAAGCTCTATATATCTT
* * *
1892282 CCAAGTGTTCCACCAAGCT
1 CCAAATGCTCCACAAAGCT
1892301 ATCCCAACGT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (30 bp):
CCAAATGCTCCACAAAGCTCTATATATCTT
Found at i:1895274 original size:19 final size:20
Alignment explanation
Indices: 1895252--1895308 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
1895242 AATTGGAGTG
1895252 CAAAAAGAAAAGAAAA-AGA
1 CAAAAAGAAAAGAAAACAGA
*
1895271 CAAAAAGAAGAAAAAAATCAGA
1 CAAAAAGAA-AAGAAAA-CAGA
1895293 -AAAGAAGAAAAGAAAA
1 CAAA-AAGAAAAGAAAA
1895309 GAAAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 9 0.28
20 6 0.19
21 9 0.28
22 8 0.25
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (20 bp):
CAAAAAGAAAAGAAAACAGA
Found at i:1895997 original size:309 final size:311
Alignment explanation
Indices: 1895436--1896057 Score: 1088
Period size: 309 Copynumber: 2.0 Consensus size: 311
1895426 AGTAAGTGTT
1895436 GTTTCTTGAATTGTAAGTCACCTCTTCCTTTTTTTTATCCTTTCATTTTCCTTGTCTTCAACCAT
1 GTTTCTTGAATTGTAAGTCACCTCTTCCTTTTTTTTATCCTTTCATTTTCCTTGTCTTCAACCAT
*
1895501 TTTTTTCTTTTAATACCTTTAAATCCTTTCTTCTACCTTTCCATTTCATCTATTCTTTCTACCCT
66 TTCTTTCTTTTAATACCTTTAAATCCTTTCTTCTACCTTTCCATTTCATCTATTCTTTCTACCCT
**
1895566 AACCTATCTGTAGCCGACGCACACAAGGAAAGAATTAACTTGTTATAATCTTGAGTAAGTTCCTC
131 AACCTATCTACAGCCGACGCACACAAGGAAAGAATTAACTTGTTATAATCTTGAGTAAGTTCCTC
1895631 AAAGGACTTAGCAAGAGAAATTAAGTGGAAAAAGGCTATTGAGAGAGTGAGATCAG-AAGTGGAA
196 AAAGGACTTAGCAAGAGAAATTAAGTGGAAAAAGGCTATTGAGAGAGTGAGATCAGAAAG-GGAA
* * *
1895695 TTGTTAAAAACGATAATTATA-T-CTGAGAGTAAACACGAGTGTTGAGTGGA
260 TTATTAAAAACCATAATTATATTCCCGAGAGTAAACACGAGTGTTGAGTGGA
1895745 GTTTCTTGAATTGTAAGTCACCTCTTCCTTTTTTTTATCCTTTCATTTTCCTTGTCTTCAACCAT
1 GTTTCTTGAATTGTAAGTCACCTCTTCCTTTTTTTTATCCTTTCATTTTCCTTGTCTTCAACCAT
* *
1895810 TTCTTTCTTTTAATACCTTTAAATCCTTTCTTCTATCTTTCCATTTCTTCTATTCTTTCTACCCT
66 TTCTTTCTTTTAATACCTTTAAATCCTTTCTTCTACCTTTCCATTTCATCTATTCTTTCTACCCT
* *
1895875 AACCTATTTACAGCCGACGCACACAAGGAAATAATTAACTTGTTATAATCTTGAGTAAGTTCCTC
131 AACCTATCTACAGCCGACGCACACAAGGAAAGAATTAACTTGTTATAATCTTGAGTAAGTTCCTC
* * *
1895940 AAAGGATTTAGCAAGAGAAATTGAGTGGAAAAAGGCTATTGAGAGAGTGATATCAGAAAGGGAAT
196 AAAGGACTTAGCAAGAGAAATTAAGTGGAAAAAGGCTATTGAGAGAGTGAGATCAGAAAGGGAAT
*
1896005 TATTAAAAGCCATAATTATATTCCCGAGAGTAAACACGAGTGTTGAGTGGA
261 TATTAAAAACCATAATTATATTCCCGAGAGTAAACACGAGTGTTGAGTGGA
1896056 GT
1 GT
1896058 GATCTTATCT
Statistics
Matches: 296, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
309 263 0.89
310 4 0.01
311 29 0.10
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (311 bp):
GTTTCTTGAATTGTAAGTCACCTCTTCCTTTTTTTTATCCTTTCATTTTCCTTGTCTTCAACCAT
TTCTTTCTTTTAATACCTTTAAATCCTTTCTTCTACCTTTCCATTTCATCTATTCTTTCTACCCT
AACCTATCTACAGCCGACGCACACAAGGAAAGAATTAACTTGTTATAATCTTGAGTAAGTTCCTC
AAAGGACTTAGCAAGAGAAATTAAGTGGAAAAAGGCTATTGAGAGAGTGAGATCAGAAAGGGAAT
TATTAAAAACCATAATTATATTCCCGAGAGTAAACACGAGTGTTGAGTGGA
Found at i:1910085 original size:19 final size:19
Alignment explanation
Indices: 1910023--1910082 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
1910013 TTGGAGTGCA
* *
1910023 AAAAGAAGACAAAAATCAG
1 AAAAGAAGAGAAAAATAAG
1910042 AAAAGAAGAGAAAAATAAG
1 AAAAGAAGAGAAAAATAAG
1910061 AAAAGAAGA-AAAGAA-AAG
1 AAAAGAAGAGAAA-AATAAG
1910079 AAAA
1 AAAA
1910083 AGAGAAGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 10 0.26
19 28 0.74
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAAGAAGAGAAAAATAAG
Found at i:1922616 original size:24 final size:21
Alignment explanation
Indices: 1922581--1922623 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
1922571 GGCACATTCT
*
1922581 TTTGAACTTCAAGAGGTACATCC
1 TTTGAAATTCAA-AGG-ACATCC
1922604 TTTGAAATGTCAAAGGACAT
1 TTTGAAAT-TCAAAGGACAT
1922624 GTCTTGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (21 bp):
TTTGAAATTCAAAGGACATCC
Found at i:1923846 original size:5 final size:5
Alignment explanation
Indices: 1923836--1923869 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1923826 TGCTTCAACT
1923836 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1923870 TGAGTGCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:1923915 original size:27 final size:26
Alignment explanation
Indices: 1923856--1923941 Score: 117
Period size: 27 Copynumber: 3.4 Consensus size: 26
1923846 TTTTCTTTTC
1923856 TTTTCTT-TTCTTTTTGAGTGCTTGAA
1 TTTTCTTCTTC-TTTTGAGTGCTTGAA
1923882 -TTT-TTCTTCTTTTGAGTGCTTGAA
1 TTTTCTTCTTCTTTTGAGTGCTTGAA
*
1923906 TTTGTCTTCTTCTTTTGAGTGCTTGCA
1 TTT-TCTTCTTCTTTTGAGTGCTTGAA
1923933 TTTT-TTCTT
1 TTTTCTTCTT
1923942 TGCTGAATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
24 17 0.31
25 13 0.24
26 2 0.04
27 23 0.42
ACGTcount: A:0.09, C:0.14, G:0.15, T:0.62
Consensus pattern (26 bp):
TTTTCTTCTTCTTTTGAGTGCTTGAA
Found at i:1934627 original size:24 final size:25
Alignment explanation
Indices: 1934574--1934632 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
1934564 GAATTGTTGA
* *
1934574 TGAGTGCTTCCAACTTTTTTTTTTT
1 TGAGTGCTTCCAACTTTCTTCTTTT
*
1934599 TGAGTGCTTTCAA-TTTCTTCTTTT
1 TGAGTGCTTCCAACTTTCTTCTTTT
1934623 TGAGTGCTTC
1 TGAGTGCTTC
1934633 TTTTCTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.56
Consensus pattern (25 bp):
TGAGTGCTTCCAACTTTCTTCTTTT
Found at i:1934644 original size:22 final size:24
Alignment explanation
Indices: 1934595--1934645 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1934585 AACTTTTTTT
**
1934595 TTTTTGAGTGCTTTCAATTTCTTC
1 TTTTTGAGTGCTTTCAATTTCTAA
*
1934619 TTTTTGAGTGC-TTC-TTTTCTAA
1 TTTTTGAGTGCTTTCAATTTCTAA
1934641 TTTTT
1 TTTTT
1934646 TTCTTGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.42
23 3 0.12
24 11 0.46
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.63
Consensus pattern (24 bp):
TTTTTGAGTGCTTTCAATTTCTAA
Found at i:1937832 original size:14 final size:15
Alignment explanation
Indices: 1937797--1937825 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1937787 AATTTGGAGT
1937797 GAAAAAGAAAGAAAA
1 GAAAAAGAAAGAAAA
1937812 GAAAAAG-AAGAAAA
1 GAAAAAGAAAGAAAA
1937826 TCAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAGAAAA
Found at i:1944528 original size:19 final size:20
Alignment explanation
Indices: 1944500--1944539 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1944490 GGATAATAAT
1944500 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
1944520 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
1944539 A
1 A
1944540 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:1944682 original size:35 final size:37
Alignment explanation
Indices: 1944606--1944682 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 37
1944596 GGAATGGCAA
*
1944606 TGGTGTTGGTTCGGTTAACTCTTCATGAAGGGGATAAGCT
1 TGGTGTTGGTTCGGTTAACTCTTCATGAAAGGG---AGCT
1944646 TGGTGTTGGTTCGGTTAACTCTTCAT-AAAGGG-GCT
1 TGGTGTTGGTTCGGTTAACTCTTCATGAAAGGGAGCT
1944681 TG
1 TG
1944683 ATGATTTGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
35 5 0.14
39 5 0.14
40 26 0.72
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.36
Consensus pattern (37 bp):
TGGTGTTGGTTCGGTTAACTCTTCATGAAAGGGAGCT
Found at i:1948398 original size:17 final size:18
Alignment explanation
Indices: 1948376--1948425 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
1948366 TTTTCTTTTC
1948376 TTTTCTTCTTTTCTG-ATT
1 TTTTCTTCTTTT-TGTATT
1948394 TTTCTCTTCTTTTTGTA-T
1 TTT-TCTTCTTTTTGTATT
1948412 TTTTCTTTCTTTTT
1 TTTTC-TTCTTTTT
1948426 TGCACTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.07
18 17 0.59
19 10 0.34
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCTTCTTTTTGTATT
Found at i:1948403 original size:19 final size:19
Alignment explanation
Indices: 1948379--1948425 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
1948369 TCTTTTCTTT
1948379 TCTTCTTTTCTG-ATTTTTC
1 TCTTCTTTT-TGTATTTTTC
1948398 TCTTCTTTTTGTATTTTTC
1 TCTTCTTTTTGTATTTTTC
1948417 T-TTCTTTTT
1 TCTTCTTTTT
1948426 TGCACTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (19 bp):
TCTTCTTTTTGTATTTTTC
Done.