Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 10 of 125
Found at i:1520090 original size:17 final size:18
Alignment explanation
Indices: 1520069--1520108 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1520059 TTTATTTTAA
1520069 ATAAAAAATTATTTAGAT
1 ATAAAAAATTATTTAGAT
*
1520087 -TAAAAATTTATTTAGAT
1 ATAAAAAATTATTTAGAT
1520104 ATAAA
1 ATAAA
1520109 TTAAAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
ATAAAAAATTATTTAGAT
Found at i:1520779 original size:2 final size:2
Alignment explanation
Indices: 1520772--1520796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1520762 AACCAAACCA
1520772 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1520797 TTTAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1520969 original size:18 final size:19
Alignment explanation
Indices: 1520948--1520983 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1520938 TTTTTATTTT
*
1520948 GATTTTATTT-TTTTTTCC
1 GATTTGATTTATTTTTTCC
1520966 GATTTGATTTATTTTTTC
1 GATTTGATTTATTTTTTC
1520984 TGCTGTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.69
Consensus pattern (19 bp):
GATTTGATTTATTTTTTCC
Found at i:1526469 original size:2 final size:2
Alignment explanation
Indices: 1526458--1526527 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
1526448 TTCCCAATTA
1526458 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1526499 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1526528 GTTTGTTCTA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1529002 original size:15 final size:15
Alignment explanation
Indices: 1528984--1529012 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1528974 CATTTGATAT
1528984 GGATGATATATTTGA
1 GGATGATATATTTGA
1528999 GGATGATATATTTG
1 GGATGATATATTTG
1529013 TGGTAGGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (15 bp):
GGATGATATATTTGA
Found at i:1532568 original size:27 final size:28
Alignment explanation
Indices: 1532514--1532565 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1532504 ACAATTTACT
* *
1532514 TTCAATATATTATATAATAAATAGAATA
1 TTCAATATATTACATAATAAATAAAATA
1532542 TTCAATA-ATTACATAA-AAATAAAA
1 TTCAATATATTACATAATAAATAAAA
1532566 ATAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (28 bp):
TTCAATATATTACATAATAAATAAAATA
Found at i:1532862 original size:8 final size:9
Alignment explanation
Indices: 1532841--1532878 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
1532831 TTTTATAAAA
1532841 AAAAATTTT
1 AAAAATTTT
1532850 AAAAATTTT
1 AAAAATTTT
1532859 AAAAA--TT
1 AAAAATTTT
1532866 ACAAAATTTT
1 A-AAAATTTT
1532876 AAA
1 AAA
1532879 TTTAGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.12
8 4 0.15
9 16 0.62
10 3 0.12
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:1532879 original size:24 final size:22
Alignment explanation
Indices: 1532827--1532881 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 22
1532817 ATCCTTTAAC
1532827 TAAATTTTATAAAAAAAAATTT
1 TAAATTTTATAAAAAAAAATTT
1532849 TAAAAATTTTA-AAAATTACAAAATTT
1 T--AAATTTTATAAAA--A-AAAATTT
1532875 TAAATTT
1 TAAATTT
1532882 AGATTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 1 0.04
23 4 0.14
24 14 0.50
25 1 0.04
26 8 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTTTATAAAAAAAAATTT
Found at i:1534969 original size:20 final size:20
Alignment explanation
Indices: 1534944--1534994 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1534934 TGTTATATGC
1534944 ATATTATTTATTAAATAAAA
1 ATATTATTTATTAAATAAAA
** **
1534964 ATATTAGATATTTTATAAAA
1 ATATTATTTATTAAATAAAA
*
1534984 ATTTTATTTAT
1 ATATTATTTAT
1534995 ATGTTATGTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATTATTTATTAAATAAAA
Found at i:1540214 original size:47 final size:47
Alignment explanation
Indices: 1540144--1540248 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 47
1540134 ATGATTGAAA
*** * *
1540144 GACCATTTGGATAGTGCTATAATGTTAACATTTTGTTCTCTATAATG
1 GACCATTTGGATAGCAATATAATGTGAACATTTTGTTCCCTATAATG
* *
1540191 GACCATTTGGATAGCAATTTAATGTGAATATTTTGTTCCCTATAATG
1 GACCATTTGGATAGCAATATAATGTGAACATTTTGTTCCCTATAATG
1540238 GACCATTTGGA
1 GACCATTTGGA
1540249 ATTGTTTGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (47 bp):
GACCATTTGGATAGCAATATAATGTGAACATTTTGTTCCCTATAATG
Found at i:1540995 original size:36 final size:36
Alignment explanation
Indices: 1540954--1541022 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
1540944 AACTATAGAA
* *
1540954 TGATGAAAATGCAAAAAGATGAAGATGAAGATATAG
1 TGATGAAAATACAAAAAGATGAAAATGAAGATATAG
* *
1540990 TGATGAAACTACAAAAAGATTAAAATGAAGATA
1 TGATGAAAATACAAAAAGATGAAAATGAAGATA
1541023 GAGCAAGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.20
Consensus pattern (36 bp):
TGATGAAAATACAAAAAGATGAAAATGAAGATATAG
Found at i:1541616 original size:30 final size:32
Alignment explanation
Indices: 1541548--1541617 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
1541538 TATATTTTGA
1541548 AAATTCAAGATGCAATTTATATATTTTTATTT
1 AAATTCAAGATGCAATTTATATATTTTTATTT
** * *
1541580 -TTTTCAATAT-CAATTTATTTATTTTT-TTT
1 AAATTCAAGATGCAATTTATATATTTTTATTT
1541609 AAATTCAAG
1 AAATTCAAG
1541618 TAATAAATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
29 3 0.10
30 20 0.67
31 7 0.23
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.54
Consensus pattern (32 bp):
AAATTCAAGATGCAATTTATATATTTTTATTT
Found at i:1542505 original size:12 final size:12
Alignment explanation
Indices: 1542488--1542515 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1542478 TTATTTTCTC
1542488 TAATTAGTAATT
1 TAATTAGTAATT
1542500 TAATTAGTAATT
1 TAATTAGTAATT
1542512 TAAT
1 TAAT
1542516 CAATCATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
TAATTAGTAATT
Found at i:1542998 original size:26 final size:26
Alignment explanation
Indices: 1542950--1542999 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1542940 AAAATAAAAA
* *
1542950 ATAATAATAATGATGAAATTAATACT
1 ATAATAATAATGATAAAACTAATACT
1542976 ATAATAATAAT-ATTAAAACTAATA
1 ATAATAATAATGA-TAAAACTAATA
1543000 ATAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (26 bp):
ATAATAATAATGATAAAACTAATACT
Found at i:1547199 original size:13 final size:13
Alignment explanation
Indices: 1547183--1547207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1547173 CGATATCACA
1547183 ATATAAAAATAAG
1 ATATAAAAATAAG
1547196 ATATAAAAATAA
1 ATATAAAAATAA
1547208 TACGATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
ATATAAAAATAAG
Found at i:1554740 original size:21 final size:20
Alignment explanation
Indices: 1554714--1554774 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1554704 GCCATTAACC
1554714 AAAAAATAAAAAATAATAAT
1 AAAAAATAAAAAATAATAAT
*
1554734 AACAAAATAAATAAA-AATTAT
1 AA-AAAATAAA-AAATAATAAT
* *
1554755 AAAATATAAAATATAA-AAT
1 AAAAAATAAAAAATAATAAT
1554774 A
1 A
1554775 TATATAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 5 0.15
20 11 0.32
21 15 0.44
22 3 0.09
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAAATAAAAAATAATAAT
Found at i:1554759 original size:14 final size:14
Alignment explanation
Indices: 1554742--1554816 Score: 64
Period size: 14 Copynumber: 5.0 Consensus size: 14
1554732 ATAACAAAAT
1554742 AAATA-AAAATTATA
1 AAATATAAAA-TATA
1554756 AAATATAAAATATA
1 AAATATAAAATATA
*
1554770 AAATATATATAA-GTA
1 AAATATA-A-AATATA
1554785 AAATATAAAAATATTTA
1 AAATAT-AAAATA--TA
1554802 AAATATTAAAATATA
1 AAATA-TAAAATATA
1554817 TATGATAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
14 18 0.35
15 16 0.31
16 3 0.06
17 13 0.25
18 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (14 bp):
AAATATAAAATATA
Found at i:1554766 original size:46 final size:47
Alignment explanation
Indices: 1554716--1554814 Score: 116
Period size: 46 Copynumber: 2.1 Consensus size: 47
1554706 CATTAACCAA
1554716 AAAATAAAAAATA-ATAATAA-CAAAATAAATAAAAAT-TATAAAATA-T
1 AAAATAAAAAATATAT-ATAAGCAAAAT--ATAAAAATATATAAAATATT
* * *
1554762 AAAATATAAAATATATATAAGTAAAATATAAAAATATTTAAAATATT
1 AAAATAAAAAATATATATAAGCAAAATATAAAAATATATAAAATATT
1554809 AAAATA
1 AAAATA
1554815 TATATGATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
45 8 0.17
46 24 0.52
47 14 0.30
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (47 bp):
AAAATAAAAAATATATATAAGCAAAATATAAAAATATATAAAATATT
Found at i:1554770 original size:23 final size:24
Alignment explanation
Indices: 1554744--1554816 Score: 89
Period size: 23 Copynumber: 3.1 Consensus size: 24
1554734 AACAAAATAA
1554744 ATAAAAAT-TATAAAATATAAAAT
1 ATAAAAATATATAAAATATAAAAT
* *
1554767 AT-AAAATATATATAA-GTAAAAT
1 ATAAAAATATATAAAATATAAAAT
*
1554789 ATAAAAATATTTAAAATATTAAAAT
1 ATAAAAATATATAAAATA-TAAAAT
1554814 ATA
1 ATA
1554817 TATGATAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 13 0.32
23 19 0.46
25 9 0.22
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (24 bp):
ATAAAAATATATAAAATATAAAAT
Found at i:1554805 original size:17 final size:17
Alignment explanation
Indices: 1554783--1554815 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1554773 TATATATAAG
1554783 TAAAATATAAAAATATT
1 TAAAATATAAAAATATT
*
1554800 TAAAATATTAAAATAT
1 TAAAATATAAAAATAT
1554816 ATATGATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATATAAAAATATT
Found at i:1554806 original size:9 final size:8
Alignment explanation
Indices: 1554754--1554815 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
1554744 ATAAAAATTA
1554754 TAAAATA-
1 TAAAATAT
1554761 TAAAATA-
1 TAAAATAT
1554768 TAAAATA-
1 TAAAATAT
* *
1554775 T-ATATAAG
1 TAAAAT-AT
1554783 TAAAATAT
1 TAAAATAT
*
1554791 AAAAATATT
1 TAAAATA-T
1554800 TAAAATAT
1 TAAAATAT
1554808 TAAAATAT
1 TAAAATAT
1554816 ATATGATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
6 3 0.07
7 16 0.35
8 17 0.37
9 10 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (8 bp):
TAAAATAT
Found at i:1557026 original size:23 final size:22
Alignment explanation
Indices: 1557000--1557046 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1556990 TAATAATAAT
*
1557000 AATAATAAATACATTTTTTAAAA
1 AATAATAAATA-ATTTTATAAAA
* *
1557023 AATAATTATTAATTTTATAAAA
1 AATAATAAATAATTTTATAAAA
1557045 AA
1 AA
1557047 AAAGAGAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATAAATAATTTTATAAAA
Found at i:1558509 original size:17 final size:17
Alignment explanation
Indices: 1558487--1558524 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1558477 CTAGGTTTCT
1558487 AAAACCCCATAAAATCC
1 AAAACCCCATAAAATCC
*
1558504 AAAACCCCTTAAAATCC
1 AAAACCCCATAAAATCC
1558521 AAAA
1 AAAA
1558525 TCCTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.32, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAACCCCATAAAATCC
Found at i:1558535 original size:16 final size:17
Alignment explanation
Indices: 1558487--1558535 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1558477 CTAGGTTTCT
1558487 AAAACCCC-ATAAAATCC
1 AAAACCCCTA-AAAATCC
*
1558504 AAAACCCCTTAAAATCC
1 AAAACCCCTAAAAATCC
*
1558521 AAAA-TCCTAAAAATC
1 AAAACCCCTAAAAATC
1558536 TTAAGGACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAACCCCTAAAAATCC
Found at i:1560212 original size:11 final size:11
Alignment explanation
Indices: 1560198--1560229 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1560188 AGCAAAAAAA
1560198 AAAAAAAAATG
1 AAAAAAAAATG
1560209 AAAAAAAAATG
1 AAAAAAAAATG
1560220 AAAAAAAAAT
1 AAAAAAAAAT
1560230 TAAAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.09
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:1564425 original size:1 final size:1
Alignment explanation
Indices: 1564414--1564474 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
1564404 TCAAGATTTC
* * * * * * * *
1564414 AAAAAATAAAAATAAAAAAAGAAAAAAAAAGAAAAAAGAAAAAAGAAAAAAGAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1564475 GTTTTATTTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (1 bp):
A
Found at i:1564431 original size:7 final size:7
Alignment explanation
Indices: 1564414--1564472 Score: 57
Period size: 7 Copynumber: 7.9 Consensus size: 7
1564404 TCAAGATTTC
*
1564414 AAAAAAT
1 AAAAAAG
1564421 AAAAATA-
1 AAAAA-AG
1564428 AAAAAAG
1 AAAAAAG
1564435 AAAAAAAAAG
1 --AAA-AAAG
1564445 AAAAAAG
1 AAAAAAG
1564452 AAAAAAG
1 AAAAAAG
1564459 AAAAAAG
1 AAAAAAG
1564466 AGAAAAA
1 A-AAAAA
1564473 AAGTTTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
6 1 0.02
7 29 0.63
8 9 0.20
9 3 0.07
10 4 0.09
ACGTcount: A:0.86, C:0.00, G:0.10, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:1564433 original size:14 final size:13
Alignment explanation
Indices: 1564414--1564474 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
1564404 TCAAGATTTC
* *
1564414 AAAAAATAAAAAT
1 AAAAAAAAAAAAG
*
1564427 AAAAAAAGAAAA-
1 AAAAAAAAAAAAG
*
1564439 AAAAAGAAAAAAG
1 AAAAAAAAAAAAG
1564452 AAAAAAGAAAAAAG
1 AAAAAA-AAAAAAG
1564466 AGAAAAAAA
1 A-AAAAAAA
1564475 GTTTTATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.25
13 15 0.38
14 10 0.25
15 5 0.12
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:1564456 original size:31 final size:31
Alignment explanation
Indices: 1564414--1564475 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1564404 TCAAGATTTC
*
1564414 AAAAAATAAAAATA-AAAAAAGAAAAAAAAAG
1 AAAAAAGAAAAA-AGAAAAAAGAAAAAAAAAG
*
1564445 AAAAAAGAAAAAAGAAAAAAGAGAAAAAAAG
1 AAAAAAGAAAAAAGAAAAAAGAAAAAAAAAG
1564476 TTTTATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.03
Consensus pattern (31 bp):
AAAAAAGAAAAAAGAAAAAAGAAAAAAAAAG
Found at i:1564475 original size:24 final size:24
Alignment explanation
Indices: 1564414--1564473 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
1564404 TCAAGATTTC
*
1564414 AAAAAATAAAAATA-AAAAAAGAAA
1 AAAAAAGAAAAA-AGAAAAAAGAAA
1564438 AAAAAAGAAAAAAGAAAAAAG-AA
1 AAAAAAGAAAAAAGAAAAAAGAAA
*
1564461 AAAAGAGAAAAAA
1 AAAAAAGAAAAAA
1564474 AGTTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (24 bp):
AAAAAAGAAAAAAGAAAAAAGAAA
Found at i:1566828 original size:41 final size:41
Alignment explanation
Indices: 1566768--1566860 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
1566758 AGTCTCTATG
*
1566768 TAAGAGTAACCATTCTCAATCAAGATTTCAAAGCCTCTGTT
1 TAAGAGGAACCATTCTCAATCAAGATTTCAAAGCCTCTGTT
**
1566809 TAAGAGGAACCAATT-TCAATCAAGATTTTGAAGCCTCTGTT
1 TAAGAGGAACC-ATTCTCAATCAAGATTTCAAAGCCTCTGTT
1566850 T-AGAGGGAACC
1 TAAGA-GGAACC
1566861 TTCATCAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
40 3 0.06
41 41 0.87
42 3 0.06
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (41 bp):
TAAGAGGAACCATTCTCAATCAAGATTTCAAAGCCTCTGTT
Found at i:1567470 original size:23 final size:23
Alignment explanation
Indices: 1567444--1567517 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 23
1567434 TATCCCAATC
*
1567444 GATTTTATAAAACCTCCAGGCAT
1 GATTTTATAAGACCTCCAGGCAT
* * * *
1567467 GATTCTGTAAGACCTTCAGGTAT
1 GATTTTATAAGACCTCCAGGCAT
* *
1567490 GA-TTTCTAAGACCTCCAAGCAT
1 GATTTTATAAGACCTCCAGGCAT
*
1567512 AATTTT
1 GATTTT
1567518 GATTAACGGT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (23 bp):
GATTTTATAAGACCTCCAGGCAT
Found at i:1567502 original size:22 final size:23
Alignment explanation
Indices: 1567455--1567511 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1567445 ATTTTATAAA
*
1567455 ACCTCCAGGCATGATTCTGTAAG
1 ACCTCCAGGCATGATTCTCTAAG
* *
1567478 ACCTTCAGGTATGATT-TCTAAG
1 ACCTCCAGGCATGATTCTCTAAG
*
1567500 ACCTCCAAGCAT
1 ACCTCCAGGCAT
1567512 AATTTTGATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (23 bp):
ACCTCCAGGCATGATTCTCTAAG
Found at i:1567631 original size:222 final size:222
Alignment explanation
Indices: 1567244--1567919 Score: 852
Period size: 222 Copynumber: 3.1 Consensus size: 222
1567234 TATCCTAGTC
* * **
1567244 GATTCTGTAAGATCTTCGGGTATGATTTCTAAGACCTCCGGGCATAATTTTGATTCGTGGTGTTA
1 GATTCTGTAAGACCTTCAGGTATGATTTCTAAGACCTCCGGGCATAATTTTGATTCACGGTGTTA
* * * * * *
1567309 TCCCGATCGATTTTTTTATTTTTTTGACTTACGATGTTATCACAGTCAATTTTGTAAGACCTTCG
66 TCCCGATCAATTTTTTTA-TTTTTTGACTTGCGATGTTATCACAGTCGATTCTGTAAGACCTCCA
* *
1567374 GGCATAATTTTGATTTACGATATTATCTCGATCGATTCCTTATTTTTTGACTTATGGTGTTATCC
130 GGCATAATTTTGATTTACGATGTTATCTCGATCGATTCCTTATTTTTTGACTTACGGTGTTATCC
*
1567439 CAATCGATTTTATAAAACCTCCAG-GCAT
195 CAATCGATTCTATAAAACCT-CAGAGCAT
** * *
1567467 GATTCTGTAAGACCTTCAGGTATGATTTCTAAGACCTCCAAGCATAATTTTGATTAACGGTATTA
1 GATTCTGTAAGACCTTCAGGTATGATTTCTAAGACCTCCGGGCATAATTTTGATTCACGGTGTTA
*
1567532 TCTCGATCAATTTTTTTATTTTTTGACTTGC-AGTGTTATCACAGTCGATTCTGTAAGACCTCCA
66 TCCCGATCAATTTTTTTATTTTTTGACTTGCGA-TGTTATCACAGTCGATTCTGTAAGACCTCCA
* * * * *
1567596 AGCATAATTTTAATTTACGATGTTATCTCGATCGATTCCTTATCTTTCGACTTACAGTGTTATCC
130 GGCATAATTTTGATTTACGATGTTATCTCGATCGATTCCTTATTTTTTGACTTACGGTGTTATCC
* * *
1567661 TAATCGATTCTATAAGACCTCTGAGCAT
195 CAATCGATTCTATAAAACCTCAGAGCAT
* * * *
1567689 GATTCTGTAAGACC-TCCGGATATGATTTCTAAGACCTTCGGGCATAATTTCGATTCACGATGTT
1 GATTCTGTAAGACCTTCAGG-TATGATTTCTAAGACCTCCGGGCATAATTTTGATTCACGGTGTT
* * * *
1567753 ATCCCGATCAA----TTT-TTTTTTAACTTGTGATGTTATAACAGTCGATTCTGTAAGACTTCCA
65 ATCCCGATCAATTTTTTTATTTTTTGACTTGCGATGTTATCACAGTCGATTCTGTAAGACCTCCA
* * *
1567813 GGCATAATTTTGATTTAC-AGTGTTATCCCTATCAATTCCTTATTTTTTGACTTACGGTGTTATC
130 GGCATAATTTTGATTTACGA-TGTTATCTCGATCGATTCCTTATTTTTTGACTTACGGTGTTATC
* * *
1567877 CCAATCGATTCTGTAAGACCTTC-GAGTAT
194 CCAATCGATTCTATAAAACC-TCAGAGCAT
*
1567906 GATT-TCTAAGACCT
1 GATTCTGTAAGACCT
1567920 CCAAGCATAA
Statistics
Matches: 395, Mismatches: 51, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
216 9 0.02
217 121 0.31
218 6 0.02
221 7 0.02
222 179 0.45
223 73 0.18
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (222 bp):
GATTCTGTAAGACCTTCAGGTATGATTTCTAAGACCTCCGGGCATAATTTTGATTCACGGTGTTA
TCCCGATCAATTTTTTTATTTTTTGACTTGCGATGTTATCACAGTCGATTCTGTAAGACCTCCAG
GCATAATTTTGATTTACGATGTTATCTCGATCGATTCCTTATTTTTTGACTTACGGTGTTATCCC
AATCGATTCTATAAAACCTCAGAGCAT
Found at i:1567688 original size:88 final size:89
Alignment explanation
Indices: 1567496--1567681 Score: 241
Period size: 88 Copynumber: 2.1 Consensus size: 89
1567486 GTATGATTTC
* * ** * *
1567496 TAAGACCTCCAAGCATAATTTTGATTAACGGTATTATCTCGATCAATTTTTTTATTTTTTGACTT
1 TAAGACCTCCAAGCATAATTTTAATTAACGATATTATCTCGATCAATTTCCTTATCTTTCGACTT
* * *
1567561 GCAGTGTTATCACAGTCGATTCTG
66 ACAGTGTTATCACAATCGATTCTA
* * *
1567585 TAAGACCTCCAAGCATAATTTTAATTTACGATGTTATCTCGATCGA-TTCCTTATCTTTCGACTT
1 TAAGACCTCCAAGCATAATTTTAATTAACGATATTATCTCGATCAATTTCCTTATCTTTCGACTT
1567649 ACAGTGTTATC-CTAATCGATTCTA
66 ACAGTGTTATCAC-AATCGATTCTA
1567673 TAAGACCTC
1 TAAGACCTC
1567682 TGAGCATGAT
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 1 0.01
88 42 0.50
89 41 0.49
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (89 bp):
TAAGACCTCCAAGCATAATTTTAATTAACGATATTATCTCGATCAATTTCCTTATCTTTCGACTT
ACAGTGTTATCACAATCGATTCTA
Found at i:1567997 original size:110 final size:110
Alignment explanation
Indices: 1567802--1568363 Score: 664
Period size: 110 Copynumber: 5.1 Consensus size: 110
1567792 GTCGATTCTG
* ** * * *
1567802 TAAGACTTCCAGGCATAATTTTGATTTACAGTGTTATCCCTATCAATTCCTTATTTTTTGACTTA
1 TAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTATCCCGATCGATTCTTTATTTTTTGACTTA
* * *
1567867 CGGTGTTATCCCAATCGATTCTGTAAGACCTTCGAGTATGATTTC
66 TGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGAGTATGATTTC
* * *
1567912 TAAGACCTCCAAGCATAATTTTGATTCGTAGTGTTATCCCGATCAATTCTTTATTTTTTGACTTA
1 TAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTATCCCGATCGATTCTTTATTTTTTGACTTA
* * * *
1567977 CGGTGTTATCTCAGTTGATTCTGTAAGACCTCCGAGAATGATTTC
66 TGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGAGTATGATTTC
* * * * * * * *
1568022 TAAGTCCTTCGGGCATAATTTTGATTCGCGGTGTTATCTCGATCGATTTTTTATCTTTTGACTTG
1 TAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTATCCCGATCGATTCTTTATTTTTTGACTTA
* *
1568087 TGGTGTTATCCCAGTCGATTCTGTAAGACCTCCG-GACATGATTTT
66 TGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGAG-TATGATTTC
* * * *
1568132 TAAGA-CTTCAGGACATAATTTTGATTCGCGGTGTTATCTCGATCGATTCCTTATTTTTTGACTT
1 TAAGACCTCCAGG-CATAATTTTGATTCGCAGTGTTATCCCGATCGATTCTTTATTTTTTGACTT
* *
1568196 ATGATGTTATCACAGTCGATTCTGTAAGACCTCC-AGGTATGATTTC
65 ATGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGA-GTATGATTTC
* * * *
1568242 TAAGACCTCC-GGACATAATTTTGATTCGTAATGTTATCCTGATCGATTCTTCATTTTTTGACTT
1 TAAGACCTCCAGG-CATAATTTTGATTCGCAGTGTTATCCCGATCGATTCTTTATTTTTTGACTT
* * * ** *
1568306 ATGGGGTTTATCCCAGTCGATTCTGTAAGATCTCTGAACATGATTCTG
65 ATGGTG-TTATCCCAGTCGATTCTGTAAGACCTCCGAGTATGATT-TC
1568354 TAAGACCTCC
1 TAAGACCTCC
1568364 GAGCATGATT
Statistics
Matches: 390, Mismatches: 54, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
109 7 0.02
110 336 0.86
111 35 0.09
112 12 0.03
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (110 bp):
TAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTATCCCGATCGATTCTTTATTTTTTGACTTA
TGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGAGTATGATTTC
Found at i:1568135 original size:22 final size:22
Alignment explanation
Indices: 1568110--1568153 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1568100 GTCGATTCTG
* *
1568110 TAAGACCTCCGGACATGATTTT
1 TAAGACCTCAGGACATAATTTT
*
1568132 TAAGACTTCAGGACATAATTTT
1 TAAGACCTCAGGACATAATTTT
1568154 GATTCGCGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (22 bp):
TAAGACCTCAGGACATAATTTT
Found at i:1568262 original size:22 final size:22
Alignment explanation
Indices: 1568220--1568262 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1568210 GTCGATTCTG
* *
1568220 TAAGACCTCCAGGTATGATTTC
1 TAAGACCTCCAGGCATAATTTC
1568242 TAAGACCTCC-GGACATAATTT
1 TAAGACCTCCAGG-CATAATTT
1568263 TGATTCGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (22 bp):
TAAGACCTCCAGGCATAATTTC
Found at i:1568354 original size:23 final size:23
Alignment explanation
Indices: 1568324--1568382 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1568314 TATCCCAGTC
*
1568324 GATTCTGTAAGATCTCTGAACAT
1 GATTCTGTAAGATCTCCGAACAT
* *
1568347 GATTCTGTAAGACCTCCGAGCAT
1 GATTCTGTAAGATCTCCGAACAT
*
1568370 GATT-TCTAAGATC
1 GATTCTGTAAGATC
1568383 ACCGGGCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (23 bp):
GATTCTGTAAGATCTCCGAACAT
Found at i:1568541 original size:109 final size:109
Alignment explanation
Indices: 1568346--1568587 Score: 308
Period size: 109 Copynumber: 2.2 Consensus size: 109
1568336 TCTCTGAACA
* * **
1568346 TGATTCTGTAAGACCTCCGAGCATGATTTCTAAGATCACCGGGCATAAATTTGATTCGCGGTATT
1 TGATTCTGTAAGACCTCCGAGCATGATTTCTAAAACCACCGGGCATAAATTCAATTCGCGGTATT
*
1568411 ATCCCGATCGATTCTTGATTTTTTGAC-TACGGTGTTGTCCAAGT
66 ATCCCGATCGATTCTTGA-TTTTTGACTTACGGTGTTATCCAAGT
** * * * * *
1568455 TGATTCTGTAAGACCTTTGGGCATGATTTTTAAAACCTCCGGGCATAAATTCAATTCGTGGTGTT
1 TGATTCTGTAAGACCTCCGAGCATGATTTCTAAAACCACCGGGCATAAATTCAATTCGCGGTATT
* * *
1568520 GTCCCGATTGATTCATT-ATTTTTGACTTACGGTGTTATCCTAGT
66 ATCCCGATCGATTC-TTGATTTTTGACTTACGGTGTTATCCAAGT
*
1568564 CGATTCTGTAAGACCTCCGAGCAT
1 TGATTCTGTAAGACCTCCGAGCAT
1568588 AAATTCGATT
Statistics
Matches: 112, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
108 8 0.07
109 102 0.91
110 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (109 bp):
TGATTCTGTAAGACCTCCGAGCATGATTTCTAAAACCACCGGGCATAAATTCAATTCGCGGTATT
ATCCCGATCGATTCTTGATTTTTGACTTACGGTGTTATCCAAGT
Found at i:1568793 original size:3 final size:3
Alignment explanation
Indices: 1568785--1568811 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1568775 TGTCTAGGTC
1568785 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1568812 ATATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1568829 original size:22 final size:22
Alignment explanation
Indices: 1568804--1568858 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1568794 TAATAATAAT
1568804 AATAATAAATATATTTT-TAAAA
1 AATAATAAATA-ATTTTATAAAA
* *
1568826 AATAATTATTAATTTTATAAAA
1 AATAATAAATAATTTTATAAAA
1568848 AATAA-AAATAA
1 AATAATAAATAA
1568859 GAGAAACAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAATAAATAATTTTATAAAA
Found at i:1568968 original size:45 final size:45
Alignment explanation
Indices: 1568904--1569013 Score: 166
Period size: 45 Copynumber: 2.4 Consensus size: 45
1568894 TGCCTTGCAC
**
1568904 CAGCCACCCTGCAGCCACCACTAGCTGCCCATGCTCACCAGCCTA
1 CAGCCACCCTGCAGCCACCACTAGCTGCCCACACTCACCAGCCTA
*
1568949 CAGCCACCCTGCAGCCACCACTAGTTGCCCACACTCACCAGCCTA
1 CAGCCACCCTGCAGCCACCACTAGCTGCCCACACTCACCAGCCTA
* * *
1568994 CAACCACCTTACAGCCACCA
1 CAGCCACCCTGCAGCCACCA
1569014 TATGTTCCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.25, C:0.49, G:0.13, T:0.13
Consensus pattern (45 bp):
CAGCCACCCTGCAGCCACCACTAGCTGCCCACACTCACCAGCCTA
Found at i:1572399 original size:15 final size:16
Alignment explanation
Indices: 1572379--1572411 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1572369 TGGGAATCCA
1572379 AACAATA-AAAAAATT
1 AACAATACAAAAAATT
*
1572394 AACAATACATAAAATT
1 AACAATACAAAAAATT
1572410 AA
1 AA
1572412 ACTTGCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (16 bp):
AACAATACAAAAAATT
Found at i:1572896 original size:115 final size:114
Alignment explanation
Indices: 1572694--1572908 Score: 351
Period size: 115 Copynumber: 1.9 Consensus size: 114
1572684 AAAATAAGTA
* *
1572694 TTTATTCACTACAAAATTCTAACTACAAAAAGGTTGTCAAGATTAATTTCTTTTAAGACAAACTA
1 TTTATTCACTACAAAATTCTAACCACAAAAAGATTGTCAAGATTAATTTCTTTTAAGACAAACTA
1572759 AAGAAAACCAAGGATATGGCCCCCACATTGGATTTTAGTGTTTAAAAAAT
66 AAGAAAACCAAGGATATGGCCCCCACATTGG-TTTTAGTGTTTAAAAAAT
* * * *
1572809 TTTATTCACTACAAAATTCTACCCACAAAAAGATTGTTAGGATCT-ATTTCTTTTAAGACAAATT
1 TTTATTCACTACAAAATTCTAACCACAAAAAGATTGTCAAGAT-TAATTTCTTTTAAGACAAACT
1572873 AAAGAAAACCAAGGATATGGCCCCCACATTGGTTTT
65 AAAGAAAACCAAGGATATGGCCCCCACATTGGTTTT
1572909 CATGCATAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 4 0.04
115 88 0.95
116 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (114 bp):
TTTATTCACTACAAAATTCTAACCACAAAAAGATTGTCAAGATTAATTTCTTTTAAGACAAACTA
AAGAAAACCAAGGATATGGCCCCCACATTGGTTTTAGTGTTTAAAAAAT
Found at i:1573822 original size:20 final size:21
Alignment explanation
Indices: 1573794--1573836 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1573784 TTGAAAATTA
* *
1573794 ACCAGGTTTTAT-CCATTTTG
1 ACCAAGTTTTATACAATTTTG
1573814 ACCAAGTTTTATACAATTTTG
1 ACCAAGTTTTATACAATTTTG
1573835 AC
1 AC
1573837 TTTGTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACCAAGTTTTATACAATTTTG
Found at i:1574694 original size:20 final size:20
Alignment explanation
Indices: 1574665--1574702 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1574655 AATAAAAGTG
*
1574665 AAACCTTAATGCGAAACCAA
1 AAACCCTAATGCGAAACCAA
*
1574685 AAACCCTAATGTGAAACC
1 AAACCCTAATGCGAAACC
1574703 CTTAAATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (20 bp):
AAACCCTAATGCGAAACCAA
Found at i:1574714 original size:33 final size:32
Alignment explanation
Indices: 1574677--1574741 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
1574667 ACCTTAATGC
1574677 GAAACCAAAAACCCTAATG-TGAAACCCTTAAAT
1 GAAACCAAAAACCCTAA-GATGAAACCC-TAAAT
** *
1574710 GAAACCCTAAACCCTTAGATGAAACCCTAAAT
1 GAAACCAAAAACCCTAAGATGAAACCCTAAAT
1574742 CCTTCATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.18
Consensus pattern (32 bp):
GAAACCAAAAACCCTAAGATGAAACCCTAAAT
Found at i:1574721 original size:20 final size:19
Alignment explanation
Indices: 1574702--1574784 Score: 87
Period size: 19 Copynumber: 4.3 Consensus size: 19
1574692 AATGTGAAAC
1574702 CCTTAAATGAAACCCTAAA
1 CCTTAAATGAAACCCTAAA
*
1574721 CCCTTAGATGAAACCCTAAA
1 -CCTTAAATGAAACCCTAAA
* *
1574741 TCCTT-CATGAAACCATAAA
1 -CCTTAAATGAAACCCTAAA
* **
1574760 CTTTAGGTGAAACCCTAAA
1 CCTTAAATGAAACCCTAAA
1574779 CCTTAA
1 CCTTAA
1574785 TTCACTCAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
18 3 0.06
19 27 0.52
20 22 0.42
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (19 bp):
CCTTAAATGAAACCCTAAA
Found at i:1574752 original size:19 final size:20
Alignment explanation
Indices: 1574698--1574780 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
1574688 CCCTAATGTG
*
1574698 AAACCCTTAAATGAAACCCT
1 AAACCCTTACATGAAACCCT
*
1574718 AAACCCTTAGATGAAACCCT
1 AAACCCTTACATGAAACCCT
* *
1574738 AAATCCTT-CATGAAACCAT
1 AAACCCTTACATGAAACCCT
* **
1574757 AAA-CTTTAGGTGAAACCCT
1 AAACCCTTACATGAAACCCT
1574776 AAACC
1 AAACC
1574781 TTAATTCACT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
18 3 0.06
19 23 0.43
20 27 0.51
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (20 bp):
AAACCCTTACATGAAACCCT
Found at i:1576785 original size:15 final size:16
Alignment explanation
Indices: 1576760--1576789 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1576750 GGGTTAGGAT
1576760 AATGAGAAAAAATAAA
1 AATGAGAAAAAATAAA
1576776 AATG-GAAAAAATAA
1 AATGAGAAAAAATAA
1576790 TTTCTATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
AATGAGAAAAAATAAA
Found at i:1577630 original size:13 final size:14
Alignment explanation
Indices: 1577608--1577641 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1577598 AGTTGAGTCA
1577608 TTTT-TTTTGTA-T
1 TTTTATTTTGTATT
1577620 TTTTATTTTGTATT
1 TTTTATTTTGTATT
1577634 TTTTATTT
1 TTTTATTT
1577642 CTATGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 7 0.35
14 9 0.45
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTATTTTGTATT
Found at i:1577707 original size:20 final size:19
Alignment explanation
Indices: 1577681--1577727 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
1577671 TTTACATGAT
1577681 TAAATTTAGAAAAAGAATAAA
1 TAAATTTA-AAAAAGAA-AAA
*
1577702 -AAATTTAAAAAATAAAAA
1 TAAATTTAAAAAAGAAAAA
1577720 TAAATTTA
1 TAAATTTA
1577728 TTAAGAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.12
19 14 0.58
20 7 0.29
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAATTTAAAAAAGAAAAA
Found at i:1577789 original size:25 final size:26
Alignment explanation
Indices: 1577759--1577815 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
1577749 CCAATGATGC
* *
1577759 AATTTTGA-AAAATT-TTAAATGATA
1 AATTTTTATAAAATTCTTAAATGAGA
**
1577783 AATTTTTATAAAATTCTTAGGTGAGA
1 AATTTTTATAAAATTCTTAAATGAGA
1577809 AATTTTT
1 AATTTTT
1577816 TCTAAATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 7 0.26
25 6 0.22
26 14 0.52
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (26 bp):
AATTTTTATAAAATTCTTAAATGAGA
Found at i:1581745 original size:18 final size:17
Alignment explanation
Indices: 1581724--1581759 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1581714 AAAATGTCTC
*
1581724 AAAGAAAGAAAAGCAAAA
1 AAAGAAAAAAAAG-AAAA
1581742 AAAGAAAAAAAAGAAAA
1 AAAGAAAAAAAAGAAAA
1581759 A
1 A
1581760 TGAATGTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAGAAAA
Found at i:1582140 original size:16 final size:16
Alignment explanation
Indices: 1582119--1582155 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1582109 AATGTATGGA
1582119 AAAAATGA-AAAGAAAG
1 AAAAATGAGAAA-AAAG
1582135 AAAAATGAGAAAAAAG
1 AAAAATGAGAAAAAAG
1582151 AAAAA
1 AAAAA
1582156 AAATGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:1582164 original size:16 final size:16
Alignment explanation
Indices: 1582118--1582164 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
1582108 TAATGTATGG
1582118 AAAAAATG-AAAAGAA
1 AAAAAATGAAAAAGAA
1582133 AGAAAAATGAGAAAAAAGAA
1 A-AAAAAT--G-AAAAAGAA
1582153 AAAAAATGAAAA
1 AAAAAATGAAAA
1582165 TGAGAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
15 1 0.04
16 10 0.37
17 1 0.04
18 1 0.04
19 6 0.22
20 8 0.30
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAAAATGAAAAAGAA
Found at i:1582194 original size:30 final size:25
Alignment explanation
Indices: 1582117--1582179 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 25
1582107 TTAATGTATG
*
1582117 GAAAAAATGAAAAGAAA-GAAAAATGA
1 GAAAAAA-GAAAAAAAATG-AAAATGA
1582143 GAAAAAAGAAAAAAAATGAAAATGA
1 GAAAAAAGAAAAAAAATGAAAATGA
1582168 GAGAAAAAGAAA
1 GA-AAAAAGAAA
1582180 GACTAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (25 bp):
GAAAAAAGAAAAAAAATGAAAATGA
Found at i:1583369 original size:21 final size:21
Alignment explanation
Indices: 1583325--1583618 Score: 146
Period size: 21 Copynumber: 13.1 Consensus size: 21
1583315 TTGATGAAGT
* * *
1583325 TTTGAATCTTCAAATAAAAATC
1 TTTGAGTCTT-AAATGAGAATC
*
1583347 TTTGAGTCTTAAACGAGAATC
1 TTTGAGTCTTAAATGAGAATC
* *
1583368 TTTAAGACATTTTCAAATGAGAATC
1 TTT--GA-GTCTT-AAATGAGAATC
*
1583393 TTTTAGTCTTAAATGAGAATC
1 TTTGAGTCTTAAATGAGAATC
* * * *
1583414 TTTAAAACGTTTTCAAATAAGAACC
1 TTT--GA-GTCTT-AAATGAGAATC
* *
1583439 CTTGAGTTTTAAATGAGAATC
1 TTTGAGTCTTAAATGAGAATC
* * * *
1583460 TTTAAGATGTTTTTGAATGAAAACC
1 TTT--GA-G-TCTTAAATGAGAATC
1583485 TTTGAGTCTTAAATGAGAATC
1 TTTGAGTCTTAAATGAGAATC
* * *
1583506 TTTAAGACATTTTCAAATGAGAACC
1 TTT--GA-GTCTT-AAATGAGAATC
* *
1583531 TTTGAATTTTAAATGAGAATC
1 TTTGAGTCTTAAATGAGAATC
1583552 TTTGAGT-TTCAAATGAGAATC
1 TTTGAGTCTT-AAATGAGAATC
*
1583573 TTTAAGAATCTT---TGAGAATC
1 TTT--GAGTCTTAAATGAGAATC
*
1583593 TTTGAGTTTTTTAAATGAGAATC
1 TTTGAG--TCTTAAATGAGAATC
1583616 TTT
1 TTT
1583619 AAGAAGAAAT
Statistics
Matches: 213, Mismatches: 34, Indels: 49
0.72 0.11 0.17
Matches are distributed among these distances:
18 2 0.01
20 16 0.08
21 80 0.38
22 23 0.11
23 27 0.13
24 13 0.06
25 52 0.24
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (21 bp):
TTTGAGTCTTAAATGAGAATC
Found at i:1583393 original size:46 final size:46
Alignment explanation
Indices: 1583346--1583554 Score: 283
Period size: 46 Copynumber: 4.5 Consensus size: 46
1583336 AAATAAAAAT
* *
1583346 CTTTGAGTCTTAAACGAGAATCTTTAAGACATTTTCAAATGAGAAT
1 CTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATGAGAAC
* * * *
1583392 CTTTTAGTCTTAAATGAGAATCTTTAAAACGTTTTCAAATAAGAAC
1 CTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATGAGAAC
* * ** ** *
1583438 CCTTGAGTTTTAAATGAGAATCTTTAAGATGTTTTTGAATGAAAAC
1 CTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATGAGAAC
1583484 CTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATGAGAAC
1 CTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATGAGAAC
* *
1583530 CTTTGAATTTTAAATGAGAATCTTT
1 CTTTGAGTCTTAAATGAGAATCTTT
1583555 GAGTTTCAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 139 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (46 bp):
CTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATGAGAAC
Found at i:1583596 original size:10 final size:10
Alignment explanation
Indices: 1583565--1583598 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1583555 GAGTTTCAAA
1583565 TGAGAATCTT
1 TGAGAATCTT
*
1583575 TAAGAATCTT
1 TGAGAATCTT
1583585 TGAGAATCTT
1 TGAGAATCTT
1583595 TGAG
1 TGAG
1583599 TTTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (10 bp):
TGAGAATCTT
Found at i:1583597 original size:41 final size:42
Alignment explanation
Indices: 1583544--1583623 Score: 135
Period size: 43 Copynumber: 1.9 Consensus size: 42
1583534 GAATTTTAAA
1583544 TGAGAATCTTTGAG-TTTCAAATGAGAATCTTTAAGAATCTT
1 TGAGAATCTTTGAGTTTTCAAATGAGAATCTTTAAGAATCTT
*
1583585 TGAGAATCTTTGAGTTTTTTAAATGAGAATCTTTAAGAA
1 TGAGAATCTTTGAG-TTTTCAAATGAGAATCTTTAAGAA
1583624 GAAATCAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 14 0.39
43 22 0.61
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (42 bp):
TGAGAATCTTTGAGTTTTCAAATGAGAATCTTTAAGAATCTT
Found at i:1583886 original size:107 final size:107
Alignment explanation
Indices: 1583667--1583874 Score: 256
Period size: 107 Copynumber: 2.0 Consensus size: 107
1583657 TGAAACTTTA
* * * * * * *
1583667 AAATTTATTAAATGTGAGCCTTTGAATTCAAATGAAAAGCTTTGAATTTTTGGATGTGAATCTCC
1 AAATTTGTTAAATATAAACCTTTGAACTCAAATGAAAAGCTTTAAACTTTTGGATGTGAATCTCC
** * * *
1583732 AAAATTTGAATGAAAAAGCTTGAACTTTTGGATGTGAACCCC
66 AAAATTAAAATGAAAAAGCTTGAAATGTTGGATGCGAACCCC
* *
1583774 AAATTTGTTAAATATAAACCTTTGAACTCGAATGAGAAGCTTTAAACTTTTGGATGTGAATCTCC
1 AAATTTGTTAAATATAAACCTTTGAACTCAAATGAAAAGCTTTAAACTTTTGGATGTGAATCTCC
* * *
1583839 AAAATTAAAATG-AGAATCTTTAAATGTTGGATGCGA
66 AAAATTAAAATGAAAAAGCTTGAAATGTTGGATGCGA
1583875 GTCTTGTAAT
Statistics
Matches: 84, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
106 18 0.21
107 66 0.79
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (107 bp):
AAATTTGTTAAATATAAACCTTTGAACTCAAATGAAAAGCTTTAAACTTTTGGATGTGAATCTCC
AAAATTAAAATGAAAAAGCTTGAAATGTTGGATGCGAACCCC
Found at i:1584331 original size:80 final size:79
Alignment explanation
Indices: 1584094--1584450 Score: 340
Period size: 81 Copynumber: 4.5 Consensus size: 79
1584084 TGTCGATGAC
* * *
1584094 CTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTACAAGAGCCTTCTATTTTCCAAAATTGTTGTG
1 CTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAAGAG-CTTTTATTTT-CAAAGTTGTTGTG
* * * *
1584159 TCTCTACCTAAAGGAG
64 CCTCTACTTAGAGAAG
* * * * * * * * * *
1584175 TTTTTATTTTTTAAAATTATTGTGCCTCTGTTTAAAGGTGCATTTTATTTACCAAAGTTATTGTA
1 CTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAAGAGC-TTTTATTT-TCAAAGTTGTTGTG
* *
1584240 CCTCTGCTTAGAGAAA
64 CCTCTACTTAGAGAAG
*
1584256 CCTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAAGAGCTTTTAATTTTCAAAGTTGTTGTGC
1 CTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAAGAGCTTTT-ATTTTCAAAGTTGTTGTGC
*
1584321 CTCTATTTAGAGAAG
65 CTCTACTTAGAGAAG
* * * * *
1584336 CTTTTATTTTCCAAAGTTGTTATGCCTCTGTTTAAAGGAGCTTTTA-TTTCTAAAGTTGTTGAGC
1 CTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAAGAGCTTTTATTTTC-AAAGTTGTTGTGC
* *
1584400 CTCTGA-TTAGAGGAT
65 CTCT-ACTTAGAGAAG
* * * **
1584415 CATTTATTTTTTAAAGTCGTTAAGCCTCTATTTAAA
1 CTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAA
1584451 GAAGTATTAT
Statistics
Matches: 224, Mismatches: 47, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
78 4 0.02
79 54 0.24
80 70 0.31
81 96 0.43
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (79 bp):
CTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAAGAGCTTTTATTTTCAAAGTTGTTGTGCC
TCTACTTAGAGAAG
Found at i:1584378 original size:40 final size:40
Alignment explanation
Indices: 1584094--1584451 Score: 301
Period size: 40 Copynumber: 8.9 Consensus size: 40
1584084 TGTCGATGAC
*
1584094 CTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTACAA-GAG
1 CTTTTATTTTCCAAAGTTGTTGTGCCTCTATTTA-AAGGAG
* * * **
1584134 CCTTCTATTTTCCAAAATTGTTGTGTCTCTACCTAAAGGAG
1 -CTTTTATTTTCCAAAGTTGTTGTGCCTCTATTTAAAGGAG
* ** * * * *
1584175 TTTTTATTTTTTAAAATTATTGTGCCTCTGTTTAAAGGTG
1 CTTTTATTTTCCAAAGTTGTTGTGCCTCTATTTAAAGGAG
* * * ** * * *
1584215 CATTTTATTTACCAAAGTTATTGTACCTCTGCTTAGAGAAA
1 C-TTTTATTTTCCAAAGTTGTTGTGCCTCTATTTAAAGGAG
* * *
1584256 CCTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAAGAG
1 CTTTTATTTTCCAAAGTTGTTGTGCCTCTATTTAAAGGAG
* *
1584296 CTTTTAATTTT-CAAAGTTGTTGTGCCTCTATTTAGAGAAG
1 CTTTT-ATTTTCCAAAGTTGTTGTGCCTCTATTTAAAGGAG
* *
1584336 CTTTTATTTTCCAAAGTTGTTATGCCTCTGTTTAAAGGAG
1 CTTTTATTTTCCAAAGTTGTTGTGCCTCTATTTAAAGGAG
* * * *
1584376 CTTTTA-TTTCTAAAGTTGTTGAGCCTCTGA-TTAGAGGAT
1 CTTTTATTTTCCAAAGTTGTTGTGCCTCT-ATTTAAAGGAG
* ** * **
1584415 CATTTATTTTTTAAAGTCGTTAAGCCTCTATTTAAAG
1 CTTTTATTTTCCAAAGTTGTTGTGCCTCTATTTAAAG
1584452 AAGTATTATT
Statistics
Matches: 253, Mismatches: 57, Indels: 15
0.78 0.18 0.05
Matches are distributed among these distances:
39 37 0.15
40 150 0.59
41 66 0.26
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (40 bp):
CTTTTATTTTCCAAAGTTGTTGTGCCTCTATTTAAAGGAG
Found at i:1584421 original size:79 final size:80
Alignment explanation
Indices: 1584096--1584494 Score: 292
Period size: 81 Copynumber: 4.9 Consensus size: 80
1584086 TCGATGACCT
* * * *
1584096 TTTATTTTTCAAAGTTGTTGTGCCTCTATTTACAA-GAGCCTTCTATTT-TCCAAAATTGTTGTG
1 TTTATTTTTCAAAGTTGTTATGCCTCTATTTA-AAGGAG-CTTTTATTTCT-CAAAGTTGTTGAG
* * * * ***
1584159 TCTCT-ACCTAAAGGAGTT
63 CCTCTGA-TTAGAGAAACA
* * * * * * *
1584177 TTTATTTTTTAAAATTATTGTGCCTCTGTTTAAAGGTGCATTTTATTTAC-CAAAGTTATTGTA-
1 TTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAGGAGC-TTTTATTT-CTCAAAGTTGTTG-AG
* *
1584240 CCTCTGCTTAGAGAAACC
63 CCTCTGATTAGAGAAACA
* * *
1584258 TTTATTTTTCAAAGTTGTTGTGCCTCTATTTAAAAGAGCTTTTAATTT-TCAAAGTTGTTGTGCC
1 TTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAGGAGCTTTT-ATTTCTCAAAGTTGTTGAGCC
* *
1584322 TCT-ATTTAGAGAAGCT
65 TCTGA-TTAGAGAAACA
* *
1584338 TTTATTTTCCAAAGTTGTTATGCCTCTGTTTAAAGGAGCTTTTATTTCT-AAAGTTGTTGAGCCT
1 TTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAGGAGCTTTTATTTCTCAAAGTTGTTGAGCCT
* *
1584402 CTGATTAGAGGATCA
66 CTGATTAGAGAAACA
* * * * * * * *
1584417 TTTATTTTTTAAAGTCGTTAAGCCTCTATTTAAAGAAGTATTATTTTTTTTTCAAAGTCGTTGAG
1 TTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAGGAG--CT-TTTATTTCTCAAAGTTGTTGAG
*
1584482 CCTCTGTTTAGAG
63 CCTCTGATTAGAG
1584495 GAGCCTTATT
Statistics
Matches: 255, Mismatches: 47, Indels: 30
0.77 0.14 0.09
Matches are distributed among these distances:
79 60 0.24
80 72 0.28
81 93 0.36
82 7 0.03
83 23 0.09
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (80 bp):
TTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAGGAGCTTTTATTTCTCAAAGTTGTTGAGCCT
CTGATTAGAGAAACA
Found at i:1584477 original size:43 final size:43
Alignment explanation
Indices: 1584416--1584519 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
1584406 TTAGAGGATC
*
1584416 ATTTATTTTTT-AAAGTCGTTAAGCCTCTATTTAAAGAAGTATT
1 ATTT-TTTTTTCAAAGTCGTTAAGCCTCTATTTAAAGAAGCATT
* * * * *
1584459 ATTTTTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTT
1 ATTTTTTTTTCAAAGTCGTTAAGCCTCTATTTAAAGAAGCATT
1584502 ATTTATTTTTTTCAAAGT
1 A-TT-TTTTTTTCAAAGT
1584520 TATGAGCCTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 6 0.12
43 31 0.60
44 2 0.04
45 13 0.25
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (43 bp):
ATTTTTTTTTCAAAGTCGTTAAGCCTCTATTTAAAGAAGCATT
Found at i:1584822 original size:15 final size:15
Alignment explanation
Indices: 1584789--1584843 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
1584779 AATTGCTTAT
1584789 TTTTA-GTTTTTTTGGA
1 TTTTATGTTTTTTT--A
1584805 TTTTAT-TTTATTTTA
1 TTTTATGTTT-TTTTA
*
1584820 TTTTATGTTTTTTTT
1 TTTTATGTTTTTTTA
1584835 TTTTA-GTTT
1 TTTTATGTTT
1584844 GATGCTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 4 0.11
15 16 0.46
16 11 0.31
17 4 0.11
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.78
Consensus pattern (15 bp):
TTTTATGTTTTTTTA
Found at i:1589424 original size:24 final size:26
Alignment explanation
Indices: 1589396--1589445 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 26
1589386 TTAATTTTAA
1589396 TATCTTCAAATA-AA-AAAAAATGCT
1 TATCTTCAAATATAATAAAAAATGCT
1589420 TATCTTCAAATATAATAAAAAATGCT
1 TATCTTCAAATATAATAAAAAATGCT
1589446 GTTGCTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 12 0.50
25 2 0.08
26 10 0.42
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (26 bp):
TATCTTCAAATATAATAAAAAATGCT
Found at i:1592047 original size:17 final size:17
Alignment explanation
Indices: 1592025--1592057 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1592015 CTTCTGATAC
1592025 ATGTAATGCAAGCATAA
1 ATGTAATGCAAGCATAA
1592042 ATGTAATGCAAGCATA
1 ATGTAATGCAAGCATA
1592058 TTCTGATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
ATGTAATGCAAGCATAA
Found at i:1595165 original size:13 final size:13
Alignment explanation
Indices: 1595147--1595178 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1595137 AGTTAATAGA
1595147 GGACCTCTGACTG
1 GGACCTCTGACTG
1595160 GGACCTCTGACTG
1 GGACCTCTGACTG
*
1595173 GTACCT
1 GGACCT
1595179 GGTTCAAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25
Consensus pattern (13 bp):
GGACCTCTGACTG
Found at i:1597502 original size:10 final size:11
Alignment explanation
Indices: 1597482--1597519 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
1597472 TATTAAAACT
1597482 TAAAA-ACTTA
1 TAAAATACTTA
*
1597492 TAAAATATTATA
1 TAAAATACT-TA
1597504 TAAAATACTTA
1 TAAAATACTTA
1597515 TAAAA
1 TAAAA
1597520 AATTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 5 0.21
11 9 0.38
12 10 0.42
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAATACTTA
Found at i:1597514 original size:23 final size:22
Alignment explanation
Indices: 1597482--1597525 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1597472 TATTAAAACT
*
1597482 TAAAAACTTATAAAATATTATA
1 TAAAAACTTATAAAAAATTATA
1597504 TAAAATACTTATAAAAAATTAT
1 TAAAA-ACTTATAAAAAATTAT
1597526 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAAACTTATAAAAAATTATA
Found at i:1600319 original size:6 final size:6
Alignment explanation
Indices: 1600299--1600337 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
1600289 AAGTTAAGCC
1600299 TGGC-G TGGACGG TGGCGG TGGCGG TGGCGG TGGCGG TGG
1 TGGCGG TGG-CGG TGGCGG TGGCGG TGGCGG TGGCGG TGG
1600338 TGGGGCTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 3 0.09
6 25 0.78
7 4 0.12
ACGTcount: A:0.03, C:0.15, G:0.64, T:0.18
Consensus pattern (6 bp):
TGGCGG
Found at i:1603175 original size:20 final size:20
Alignment explanation
Indices: 1603131--1603175 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1603121 TCAAATCAAA
*
1603131 TTATATATTTTTATTAATTT
1 TTATATATATTTATTAATTT
*
1603151 ATATATATATTT-TTAATTT
1 TTATATATATTTATTAATTT
1603170 TT-TATA
1 TTATATA
1603176 AAATAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATATATTTATTAATTT
Found at i:1605034 original size:19 final size:19
Alignment explanation
Indices: 1605002--1605048 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1604992 AATTTATTGG
*
1605002 TTTTAATTTGTAAACTTTTT
1 TTTTAATTTGTAAA-TTCTT
*
1605022 TTTTTATTT-TAAATTCTT
1 TTTTAATTTGTAAATTCTT
*
1605040 TTTTCATTT
1 TTTTAATTT
1605049 AACAAATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.50
19 4 0.17
20 8 0.33
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTAATTTGTAAATTCTT
Found at i:1605555 original size:21 final size:21
Alignment explanation
Indices: 1605529--1605577 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 21
1605519 GAAATTTCAG
1605529 TTAATCAAA-ATTTTGATTGAA
1 TTAATCAAATATTTTGATTG-A
1605550 TTAATCAAATTTATTTTGATTGA
1 TTAATCAAA--TATTTTGATTGA
1605573 TTAAT
1 TTAAT
1605578 TTTTTTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.36
23 6 0.24
24 10 0.40
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (21 bp):
TTAATCAAATATTTTGATTGA
Found at i:1607904 original size:89 final size:89
Alignment explanation
Indices: 1607777--1608347 Score: 507
Period size: 88 Copynumber: 6.4 Consensus size: 89
1607767 ATCCCAAACT
* * * * *
1607777 AAAATAAGGTGACCAAGA-CTGAATC-AAGGTCAAAAATAAATTATTAGGATAAAATCACGAATT
1 AAAATAAGGTGACCAAGATC-GAGTCGAA-GTCAAAAATAAATGATTAGGATGAAACCACGAATC
* * **
1607840 ATGTGATCGAGATGAAATCACTTGTC
64 ATGTGACCGAGATGAAACCACGAGTC
* *
1607866 AAAATAAGGTGACCAAGATCGAGTCGAAGTTAAAAATAAATGA-TCGAGATGAAACCACGAATCA
1 AAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAAATGATTAG-GATGAAACCACGAATCA
* * * *
1607930 TGTGATCGAAACGAAACCATGAGTC
65 TGTGACCGAGATGAAACCACGAGTC
* * * * * * * * *
1607955 AAAATAAGGTAACCAAAATTGAATCGATGTCAAAAAATAAATAATTAAGACGAAACCATGAATCA
1 AAAATAAGGTGACCAAGATCGAGTCGAAGTC-AAAAATAAATGATTAGGATGAAACCACGAATCA
*
1608020 TATGACCGAGATGAAACCACGAGTC
65 TGTGACCGAGATGAAACCACGAGTC
* * * * * *
1608045 AAAATAAGGTGACTAGGATCGAGTCAAAATCAAAAATAAATGATCAGGATGAAACCATGAATCAT
1 AAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAAATGATTAGGATGAAACCACGAATCAT
** * * * *
1608110 GCAACCGGGAT-AAACTATGGGTC
66 GTGACCGAGATGAAACCACGAGTC
** * * * * *
1608133 AAAATAAAATGACCAAGATCGAATCGAGGTAAAAAATAAATGA-TCGAGATGAAACCACGAACCA
1 AAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAAATGATTAG-GATGAAACCACGAATCA
1608197 TGTGACCG-GAATG-AACCACGAG-C
65 TGTGACCGAG-ATGAAACCACGAGTC
* * * * *
1608220 TAAAATAAGGTGACCAAGATCGAGTCGAGGTCAAAAATAAATGATCA-GATAAAATCATGAATCA
1 -AAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAAATGATTAGGATGAAACCACGAATCA
* * *
1608284 TGTGACCAAGACGAAATCACGAGTC
65 TGTGACCGAGATGAAACCACGAGTC
* *
1608309 AAAATAAAGTGACC-AGAATTGAGTCGAAGTC-AAAATAAA
1 AAAATAAGGTGACCAAG-ATCGAGTCGAAGTCAAAAATAAA
1608348 CAATCGAGAT
Statistics
Matches: 385, Mismatches: 83, Indels: 30
0.77 0.17 0.06
Matches are distributed among these distances:
87 35 0.09
88 147 0.38
89 131 0.34
90 71 0.18
91 1 0.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (89 bp):
AAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAAATGATTAGGATGAAACCACGAATCAT
GTGACCGAGATGAAACCACGAGTC
Found at i:1608052 original size:179 final size:176
Alignment explanation
Indices: 1607777--1608370 Score: 604
Period size: 179 Copynumber: 3.4 Consensus size: 176
1607767 ATCCCAAACT
* * * * * * * * * *
1607777 AAAATAAGGTGACCAAGACTGAATCAAGGTCAAAAATAAATTATTAGGATAAAATCACGAATTAT
1 AAAATAAAGTGACCAAAATTGAATCGAGGTCAAAAATAAATAATCAAGATGAAACCACGAATCAT
* * ** *
1607842 GTGATCGAGATGAAATCACTTGTCAAAATAAGGTGACCAAGATCGAGTCGAAGTTAAAAATAAAT
66 GTGACCGAGATGAAACCACGAGTCAAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAAAT
*
1607907 GATCGAGATGAAACCACGAATCATGTGATCGAAACGAAACCATGAGTC
131 GATC-AGATGAAACCATGAATCATGTGA-CGAAACGAAACCATGAGTC
* * * * * *
1607955 AAAATAAGGTAACCAAAATTGAATCGATGTCAAAAAATAAATAATTAAGACGAAACCATGAATCA
1 AAAATAAAGTGACCAAAATTGAATCGAGGTC-AAAAATAAATAATCAAGATGAAACCACGAATCA
* * * * *
1608020 TATGACCGAGATGAAACCACGAGTCAAAATAAGGTGACTAGGATCGAGTCAAAATCAAAAATAAA
65 TGTGACCGAGATGAAACCACGAGTCAAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAAA
** ** * * *
1608085 TGATCAGGATGAAACCATGAATCATGCAACCGGGA-TAAACTATGGGTC
130 TGATCA-GATGAAACCATGAATCATGTGA-CGAAACGAAACCATGAGTC
* * * * * * *
1608133 AAAATAAAATGACCAAGATCGAATCGAGGTAAAAAATAAATGATCGAGATGAAACCACGAACCAT
1 AAAATAAAGTGACCAAAATTGAATCGAGGTCAAAAATAAATAATCAAGATGAAACCACGAATCAT
*
1608198 GTGACCG-GAATG-AACCACGAG-CTAAAATAAGGTGACCAAGATCGAGTCGAGGTCAAAAATAA
66 GTGACCGAG-ATGAAACCACGAGTC-AAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAA
* * * * *
1608260 ATGATCAGATAAAATCATGAATCATGTGACCAAGACGAAATCACGAGTC
129 ATGATCAGATGAAACCATGAATCATGTGACGAA-ACGAAACCATGAGTC
* * * * * *
1608309 AAAATAAAGTGACCAGAATTGAGTCGAAGTC-AAAATAAACAATCGAGATGAAACCATGAATC
1 AAAATAAAGTGACCAAAATTGAATCGAGGTCAAAAATAAATAATCAAGATGAAACCACGAATC
1608371 TTAAAGAATG
Statistics
Matches: 337, Mismatches: 73, Indels: 15
0.79 0.17 0.04
Matches are distributed among these distances:
174 1 0.00
175 47 0.14
176 83 0.25
177 37 0.11
178 61 0.18
179 108 0.32
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (176 bp):
AAAATAAAGTGACCAAAATTGAATCGAGGTCAAAAATAAATAATCAAGATGAAACCACGAATCAT
GTGACCGAGATGAAACCACGAGTCAAAATAAGGTGACCAAGATCGAGTCGAAGTCAAAAATAAAT
GATCAGATGAAACCATGAATCATGTGACGAAACGAAACCATGAGTC
Found at i:1610098 original size:22 final size:20
Alignment explanation
Indices: 1610068--1610113 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1610058 TTCAAATTTT
1610068 AAAGATTCTCATCTAAAAGTTC
1 AAAGATTCTCAT-TAAAA-TTC
* *
1610090 AAAGCTTCTCATTCAAATTC
1 AAAGATTCTCATTAAAATTC
1610110 AAAG
1 AAAG
1610114 GTTCACCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 11 0.50
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (20 bp):
AAAGATTCTCATTAAAATTC
Found at i:1610274 original size:21 final size:20
Alignment explanation
Indices: 1610250--1610574 Score: 209
Period size: 21 Copynumber: 14.9 Consensus size: 20
1610240 GTTTTGCATA
*
1610250 TCAAATATTCTCATTTGAAAC
1 TCAAAGATTCTCATTT-AAAC
* *
1610271 TCAAAGATTCTCATTTACAT
1 TCAAAGATTCTCATTTAAAC
* * * * *
1610291 TTAACAAATTTTGAGTTTCACACC
1 TCAA-AGATTCTCA-TTT-A-AAC
*
1610315 TCAAAGATTCTCATTTAAAAT
1 TCAAAGATTCTCATTT-AAAC
* *
1610336 TCAAAAATTCTCATTTGAAAT
1 TCAAAGATTCTCATTT-AAAC
* *
1610357 TCAAAAATTCTCATTTAAGGAT
1 TCAAAGATTCTCATTTAA--AC
* *
1610379 TTAAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTT-AAAC
1610400 TCAAAGATTCTCATTTAAGAC
1 TCAAAGATTCTCATTTAA-AC
*
1610421 TCAAAGATTCCCATTTAACAC
1 TCAAAGATTCTCATTTAA-AC
* * *
1610442 TAAAAAATTCTCATTTAAAGAT
1 TCAAAGATTCTCATTT-AA-AC
1610464 TCAAAGATTCTCATTTGGAAAC
1 TCAAAGATTCTCATTT--AAAC
*
1610486 GTCTTAAAGATTTTCATTTAAGAC
1 -TC--AAAGATTCTCATTTAA-AC
1610510 TCAAAGATTCTCATTTGAAAATGTC
1 TCAAAGATTCTCATTT--AAA---C
* *
1610535 TAAAAGATTTTCATTTAAGAC
1 TCAAAGATTCTCATTTAA-AC
*
1610556 TCAAAGATTCTTATTTAAA
1 TCAAAGATTCTCATTTAAA
1610575 AATGTCTTAA
Statistics
Matches: 243, Mismatches: 41, Indels: 41
0.75 0.13 0.13
Matches are distributed among these distances:
20 10 0.04
21 136 0.56
22 42 0.17
23 21 0.09
24 6 0.02
25 28 0.12
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (20 bp):
TCAAAGATTCTCATTTAAAC
Found at i:1610502 original size:25 final size:23
Alignment explanation
Indices: 1610317--1610642 Score: 130
Period size: 21 Copynumber: 14.6 Consensus size: 23
1610307 TTCACACCTC
**
1610317 AAAGATTCTCATTT-AAAATTC-
1 AAAGATTCTCATTTGAAACGTCT
* *
1610338 AAAAATTCTCATTTGAAA-TTC-
1 AAAGATTCTCATTTGAAACGTCT
* * *
1610359 AAAAATTCTCATTT--AAGGATTT
1 AAAGATTCTCATTTGAAACG-TCT
*
1610381 AAAGATTCTCATTTGAAA-TTC-
1 AAAGATTCTCATTTGAAACGTCT
1610402 AAAGATTCTCATTT-AAGAC-TC-
1 AAAGATTCTCATTTGAA-ACGTCT
* *
1610423 AAAGATTCCCATTT-AACAC-T-A
1 AAAGATTCTCATTTGAA-ACGTCT
*
1610444 AAAAATTCTCATTT-AAA-GAT-T
1 AAAGATTCTCATTTGAAACG-TCT
1610465 CAAAGATTCTCATTTGGAAACGTCTT
1 -AAAGATTCTCATTT-GAAACGTC-T
*
1610491 AAAGATTTTCATTT-AAGAC-TC-
1 AAAGATTCTCATTTGAA-ACGTCT
*
1610512 AAAGATTCTCATTTGAAAATGTCT
1 AAAGATTCTCATTTG-AAACGTCT
*
1610536 AAAAGATTTTCATTT-AAGAC-TC-
1 -AAAGATTCTCATTTGAA-ACGTCT
* * *
1610558 AAAGATTCTTATTTAAAAATGTCTT
1 AAAGATTCTCATTT-GAAACGTC-T
1610583 AAAGATTCTCATTT--AA-GAT-T
1 AAAGATTCTCATTTGAAACG-TCT
* *
1610603 AAAAAATTCTCATTTGAAAATGTCT
1 -AAAGATTCTCATTTG-AAACGTCT
*
1610628 CAAAGATTTTCATTT
1 -AAAGATTCTCATTT
1610643 AAGACTCTCA
Statistics
Matches: 244, Mismatches: 25, Indels: 68
0.72 0.07 0.20
Matches are distributed among these distances:
19 2 0.01
20 4 0.02
21 120 0.49
22 35 0.14
23 16 0.07
24 12 0.05
25 54 0.22
26 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (23 bp):
AAAGATTCTCATTTGAAACGTCT
Found at i:1610517 original size:46 final size:46
Alignment explanation
Indices: 1610317--1610732 Score: 415
Period size: 46 Copynumber: 9.4 Consensus size: 46
1610307 TTCACACCTC
* * *
1610317 AAAGATTCTCATTTAAAATTCAAAAATTCTCATTTG-AAAT-TC--
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTT
* * *
1610359 AAAAATTCTCATTTAAGGATTTAAAGATTCTCATTTG-AAAT-TC--
1 AAAGATTCTCATTTAA-GACTCAAAGATTCTCATTTGAAAATGTCTT
* * *
1610402 AAAGATTCTCATTTAAGACTCAAAGATTCCCATTT-AACA---CTA
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTT
* * * *
1610444 AAAAATTCTCATTTAAAGATTCAAAGATTCTCATTTGGAAACGTCTT
1 AAAGATTCTCATTT-AAGACTCAAAGATTCTCATTTGAAAATGTCTT
* *
1610491 AAAGATTTTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTA
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTT
* * *
1610537 AAAGATTTTCATTTAAGACTCAAAGATTCTTATTTAAAAATGTCTT
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTT
* * * *
1610583 AAAGATTCTCATTTAAGATTAAAAAATTCTCATTTGAAAATGTCTC
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTT
* *
1610629 AAAGATTTTCATTTAAGA--C------TCTCATTT-AGAAACGTCTT
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGA-AAATGTCTT
* *
1610667 AAAGATTCTCATTTAAAACTCAAAGATTTTCATTTGAAAATGTCTT
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTT
*
1610713 AAAGATTTTCATTTAAGACT
1 AAAGATTCTCATTTAAGACT
1610733 TAAAACTTCA
Statistics
Matches: 314, Mismatches: 41, Indels: 34
0.81 0.11 0.09
Matches are distributed among these distances:
37 1 0.00
38 31 0.10
40 2 0.01
42 46 0.15
43 57 0.18
44 2 0.01
46 160 0.51
47 15 0.05
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (46 bp):
AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTT
Found at i:1610595 original size:92 final size:92
Alignment explanation
Indices: 1610317--1610732 Score: 458
Period size: 92 Copynumber: 4.7 Consensus size: 92
1610307 TTCACACCTC
* * * *
1610317 AAAGATTCTCATTTAAAATTCAAAAATTCTCATTTG-AAAT-TC-AAAA-ATTCTCATTTAAGGA
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTAAAAGATTTTCATTTAA-GA
* * *
1610378 TTTAAAGATTCTCATTT-GAAA--T-TC
65 CTCAAAGATTCTCATTTAGAAACGTCTT
* * * *
1610402 AAAGATTCTCATTTAAGACTCAAAGATTCCCATTT-AACA---CTAAAAAATTCTCATTTAAAGA
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTAAAAGATTTTCATTT-AAGA
* *
1610463 TTCAAAGATTCTCATTTGGAAACGTCTT
65 CTCAAAGATTCTCATTTAGAAACGTCTT
*
1610491 AAAGATTTTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTAAAAGATTTTCATTTAAGAC
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTAAAAGATTTTCATTTAAGAC
* * *
1610556 TCAAAGATTCTTATTTAAAAATGTCTT
66 TCAAAGATTCTCATTTAGAAACGTCTT
* * * *
1610583 AAAGATTCTCATTTAAGATTAAAAAATTCTCATTTGAAAATGTCTCAAAGATTTTCATTTAAGA-
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTAAAAGATTTTCATTTAAGAC
1610647 -C------TCTCATTTAGAAACGTCTT
66 TCAAAGATTCTCATTTAGAAACGTCTT
* * *
1610667 AAAGATTCTCATTTAAAACTCAAAGATTTTCATTTGAAAATGTCTTAAAGATTTTCATTTAAGAC
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTAAAAGATTTTCATTTAAGAC
1610732 T
66 T
1610733 TAAAACTTCA
Statistics
Matches: 286, Mismatches: 31, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
83 1 0.00
84 78 0.27
85 61 0.21
86 6 0.02
88 1 0.00
89 34 0.12
90 4 0.01
92 86 0.30
93 15 0.05
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (92 bp):
AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTAAAAGATTTTCATTTAAGAC
TCAAAGATTCTCATTTAGAAACGTCTT
Found at i:1610601 original size:38 final size:38
Alignment explanation
Indices: 1610559--1610682 Score: 113
Period size: 38 Copynumber: 3.1 Consensus size: 38
1610549 TTAAGACTCA
*
1610559 AAGATTCTTATTTAAAAATGTCTTAAAGATTCTCATTT
1 AAGATTCTCATTTAAAAATGTCTTAAAGATTCTCATTT
* * *
1610597 AAGATTAAAAAATTCTCATTTGAAAATGTCTCAAAGATTTTCATTT
1 AAG--------ATTCTCATTTAAAAATGTCTTAAAGATTCTCATTT
* * *
1610643 AAGACTCTCATTTAGAAACGTCTTAAAGATTCTCATTT
1 AAGATTCTCATTTAAAAATGTCTTAAAGATTCTCATTT
1610681 AA
1 AA
1610683 AACTCAAAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
38 34 0.50
46 34 0.50
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (38 bp):
AAGATTCTCATTTAAAAATGTCTTAAAGATTCTCATTT
Found at i:1610676 original size:25 final size:25
Alignment explanation
Indices: 1610643--1610727 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
1610633 ATTTTCATTT
*
1610643 AAGACTCTCATTTAGAAACGTCTTA
1 AAGATTCTCATTTAGAAACGTCTTA
1610668 AAGATTCTCATTTA-AAAC-TC--A
1 AAGATTCTCATTTAGAAACGTCTTA
* *
1610689 AAGATTTTCATTT-GAAAATGTCTTA
1 AAGATTCTCATTTAG-AAACGTCTTA
*
1610714 AAGATTTTCATTTA
1 AAGATTCTCATTTA
1610728 AGACTTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
21 13 0.25
22 3 0.06
23 4 0.08
24 4 0.08
25 27 0.53
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (25 bp):
AAGATTCTCATTTAGAAACGTCTTA
Found at i:1610676 original size:84 final size:84
Alignment explanation
Indices: 1610559--1610732 Score: 258
Period size: 84 Copynumber: 2.1 Consensus size: 84
1610549 TTAAGACTCA
* * * * *
1610559 AAGATTCTTATTTAAAAATGTCTTAAAGATTCTCATTTAAGATTAAAAAATTCTCATTTGAAAAT
1 AAGACTCTCATTTAAAAACGTCTTAAAGATTCTCATTTAAAACTAAAAAATTCTCATTTGAAAAT
1610624 GTCTCAAAGATTTTCATTT
66 GTCTCAAAGATTTTCATTT
* * * *
1610643 AAGACTCTCATTTAGAAACGTCTTAAAGATTCTCATTTAAAACTCAAAGATTTTCATTTGAAAAT
1 AAGACTCTCATTTAAAAACGTCTTAAAGATTCTCATTTAAAACTAAAAAATTCTCATTTGAAAAT
*
1610708 GTCTTAAAGATTTTCATTT
66 GTCTCAAAGATTTTCATTT
1610727 AAGACT
1 AAGACT
1610733 TAAAACTTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (84 bp):
AAGACTCTCATTTAAAAACGTCTTAAAGATTCTCATTTAAAACTAAAAAATTCTCATTTGAAAAT
GTCTCAAAGATTTTCATTT
Found at i:1610734 original size:21 final size:21
Alignment explanation
Indices: 1610664--1610736 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
1610654 TTAGAAACGT
* *
1610664 CTTAAAGATTCTCATTTAAAA
1 CTTAAAGATTTTCATTTAAGA
* *
1610685 CTCAAAGATTTTCATTTGAAAATGT
1 CTTAAAGATTTTCATTT---AA-GA
1610710 CTTAAAGATTTTCATTTAAGA
1 CTTAAAGATTTTCATTTAAGA
1610731 CTTAAA
1 CTTAAA
1610737 ACTTCATCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 22 0.52
22 2 0.05
24 2 0.05
25 16 0.38
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (21 bp):
CTTAAAGATTTTCATTTAAGA
Found at i:1612022 original size:19 final size:18
Alignment explanation
Indices: 1612000--1612044 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1611990 TCAATTTGAG
* *
1612000 TCTTTTTTTTCTTTTTTTC
1 TCTTTTTTTTC-ATTGTTC
1612019 TCTTATTTTTTCATTGTTC
1 TCTT-TTTTTTCATTGTTC
1612038 TCTTTTT
1 TCTTTTT
1612045 CCATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 13 0.57
20 7 0.30
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (18 bp):
TCTTTTTTTTCATTGTTC
Found at i:1612062 original size:13 final size:13
Alignment explanation
Indices: 1612044--1612068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1612034 GTTCTCTTTT
1612044 TCCATTTTTTTCA
1 TCCATTTTTTTCA
1612057 TCCATTTTTTTC
1 TCCATTTTTTTC
1612069 CTTTTCATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (13 bp):
TCCATTTTTTTCA
Found at i:1612492 original size:18 final size:19
Alignment explanation
Indices: 1612455--1612498 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1612445 TTTTCTCTTT
*
1612455 TTTCTTTGTTTTGCTTTTC
1 TTTCTTTCTTTTGCTTTTC
*
1612474 TTTCTTTCTTTT-TTTTTC
1 TTTCTTTCTTTTGCTTTTC
*
1612492 TATCTTT
1 TTTCTTT
1612499 AAGACCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTCTTTCTTTTGCTTTTC
Found at i:1616100 original size:116 final size:117
Alignment explanation
Indices: 1615965--1616176 Score: 288
Period size: 120 Copynumber: 1.8 Consensus size: 117
1615955 GCTTTTATAC
**
1615965 AAGAAAAATTGATACTTTCAACTTTTTCTT-AAA-GC-ATTTAGAGGTTTTT-ATTTCGAAAAAA
1 AAGAAAAATTGATACTTTCAAC-TTTTCTTAAAATGCTATTTAGAAATTTTTAATTT-GAAAAAA
*
1616026 ATTGATACTTTCAACTTTTTCTTAAAAATATTTTTCTTTGATAATTTTTATTTTT
64 ATTGATACTTTCAA-TTTTTCCTAAAAATATTTTTCTTTGATAATTTTTATTTTT
* * *
1616081 AAGAAAAATTGATACTTTCAACTTTTCTTCAAAATGCTTTTTTTGAAATTTTTAATTTTAAAAAA
1 AAGAAAAATTGATACTTTCAACTTTTCTT-AAAATGC-TATTTAGAAATTTTTAATTTGAAAAAA
*
1616146 ATTGATACTTTCAATTTTTCCTCAAAATATT
64 ATTGATACTTTCAATTTTTCCTAAAAATATT
1616177 GTTTGAAAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
115 7 0.08
116 22 0.27
117 3 0.04
118 2 0.02
119 15 0.18
120 30 0.36
121 4 0.05
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (117 bp):
AAGAAAAATTGATACTTTCAACTTTTCTTAAAATGCTATTTAGAAATTTTTAATTTGAAAAAAAT
TGATACTTTCAATTTTTCCTAAAAATATTTTTCTTTGATAATTTTTATTTTT
Found at i:1616171 original size:58 final size:57
Alignment explanation
Indices: 1616009--1616372 Score: 272
Period size: 61 Copynumber: 6.2 Consensus size: 57
1615999 CATTTAGAGG
** *
1616009 TTTTTATTTCGAAAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTCTTTGATAA
1 TTTTTATTTTTAAAAAAATTGATACTTTCAA-TTTTTCTTCAAAAT-TTTTT-TTTGA-AA
* *
1616070 TTTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCTTCAAAATGCTTTTTTTGAAA
1 TTTTTATTTTTAA-AAAAATTGATACTTTCAATTTTTCTTCAAAAT-TTTTTTTTGAAA
* * * *
1616129 TTTTTAATTTTAAAAAAATTGATACTTTCAATTTTTCCTCAAAA-TATTGTTTGAAAA
1 TTTTTATTTTTAAAAAAATTGATACTTTCAATTTTTCTTCAAAATTTTTTTTTG-AAA
* * * * *
1616186 TTCTTTA-TTTTAGGAAAACTT-ATACTTTTAATTTTTTTTAAAAAATATTTTTTTTAGAAA
1 TT-TTTATTTTTA-AAAAAATTGATACTTTCAATTTTTCTT-CAAAAT-TTTTTTTT-GAAA
** * ** * * * *
1616246 AATTTATTTTTAAGGAAAACGGTTATTTTCAACTTTT-TTCAAAAATATTTTTTT-AAA
1 TTTTTATTTTTAA-AAAAATTGATACTTTCAATTTTTCTTC-AAAATTTTTTTTTGAAA
* * * **
1616303 -TTTTATTTTTAAATAAAATTGATACTTTCAACTTTTCCTTAAAAATATGTTTCTTAAAAA
1 TTTTTATTTTTAAA-AAAATTGATACTTTCAA-TTTTTCTTCAAAAT-T-TTTTTTTGAAA
1616363 TTTTTATTTT
1 TTTTTATTTT
1616373 ATATTTTTTC
Statistics
Matches: 239, Mismatches: 45, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
56 30 0.13
57 36 0.15
58 45 0.19
59 30 0.13
60 32 0.13
61 48 0.20
62 18 0.08
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (57 bp):
TTTTTATTTTTAAAAAAATTGATACTTTCAATTTTTCTTCAAAATTTTTTTTTGAAA
Found at i:1616182 original size:116 final size:115
Alignment explanation
Indices: 1615965--1616348 Score: 315
Period size: 116 Copynumber: 3.3 Consensus size: 115
1615955 GCTTTTATAC
* * ** *
1615965 AAGAAAAATTGATACTTTCAACTTTTTCTT--AAA-GC--ATTTAGAGGTTTTT-ATTTCGAAAA
1 AAGAAAAATTGATACTTTCAAC-TTTTCTTAAAAATGCTTTTTTTGAAATTTTTAATTT-TAAAA
*
1616024 AAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTCTTTGATAATTTTTATTTTT
64 AAATTGATACTTTCAACTTTTTC-TCAAAATA---TT-TTTGATAATTTTTATTTTT
*
1616081 AAGAAAAATTGATACTTTCAACTTTTCTTCAAAATGCTTTTTTTGAAATTTTTAATTTTAAAAAA
1 AAGAAAAATTGATACTTTCAACTTTTCTTAAAAATGCTTTTTTTGAAATTTTTAATTTTAAAAAA
*
1616146 ATTGATACTTTCAA-TTTTTCCTCAAAATATTGTTTGAAAATTCTTTA-TTTT
66 ATTGATACTTTCAACTTTTT-CTCAAAATATT-TTTGATAATT-TTTATTTTT
* * * * * ** ** * *
1616197 AGGAAAACTT-ATACTTTTAATTTTTTTTAAAAAATATTTTTTTTAGAAAAATTTATTTTTAAGG
1 AAGAAAAATTGATACTTTCAACTTTTCTT-AAAAATGCTTTTTTT-GAAATTTTTAATTTTAA-A
** * * * *
1616261 AAAACGGTTATTTTCAACTTTTT-TCAAAAATATTTTT-TTAAATTTTATTTTT
63 AAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTGATAATTTTTATTTTT
1616313 AA-ATAAAATTGATACTTTCAACTTTTCCTTAAAAAT
1 AAGA-AAAATTGATACTTTCAACTTTT-CTTAAAAAT
1616349 ATGTTTCTTA
Statistics
Matches: 219, Mismatches: 32, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
115 27 0.12
116 70 0.32
117 45 0.21
118 25 0.11
119 17 0.08
120 31 0.14
121 4 0.02
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (115 bp):
AAGAAAAATTGATACTTTCAACTTTTCTTAAAAATGCTTTTTTTGAAATTTTTAATTTTAAAAAA
ATTGATACTTTCAACTTTTTCTCAAAATATTTTTGATAATTTTTATTTTT
Found at i:1616219 original size:57 final size:57
Alignment explanation
Indices: 1616022--1616221 Score: 183
Period size: 58 Copynumber: 3.4 Consensus size: 57
1616012 TTATTTCGAA
* * * *
1616022 AAAAATTGATACTTTCAACTTTTTCTTAAAAAT-ATTTTTCTTTGATAATTTTTATTTTTAAG
1 AAAAATTGATACTTTCAA-TTTTTCCTCAAAATCA---TTGTTTGAAAATTTTTA-TTTT-AG
* * * * *
1616084 AAAAATTGATACTTTCAACTTTTCTTCAAAATGCTTTTTTTG-AAATTTTTAATTTTAA
1 AAAAATTGATACTTTCAATTTTTCCTCAAAAT-CATTGTTTGAAAATTTTT-ATTTTAG
1616142 AAAAATTGATACTTTCAATTTTTCCTCAAAAT-ATTGTTTGAAAATTCTTTATTTTAGG
1 AAAAATTGATACTTTCAATTTTTCCTCAAAATCATTGTTTGAAAATT-TTTATTTTA-G
* *
1616200 AAAACTT-ATACTTTTAATTTTT
1 AAAAATTGATACTTTCAATTTTT
1616222 TTTAAAAAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
56 6 0.05
57 25 0.21
58 40 0.34
59 11 0.09
60 7 0.06
61 12 0.10
62 18 0.15
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.51
Consensus pattern (57 bp):
AAAAATTGATACTTTCAATTTTTCCTCAAAATCATTGTTTGAAAATTTTTATTTTAG
Found at i:1616237 original size:16 final size:16
Alignment explanation
Indices: 1616216--1616258 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
1616206 TATACTTTTA
1616216 ATTTTTTTTAAAAAAT
1 ATTTTTTTTAAAAAAT
1616232 ATTTTTTTTAGAAAAAT
1 ATTTTTTTTA-AAAAAT
*
1616249 -TTATTTTTAA
1 ATTTTTTTTAA
1616259 GGAAAACGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 18 0.72
17 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTTTTTTAAAAAAT
Found at i:1616347 original size:117 final size:115
Alignment explanation
Indices: 1616010--1616372 Score: 308
Period size: 117 Copynumber: 3.1 Consensus size: 115
1616000 ATTTAGAGGT
** ** *
1616010 TTTTATTTCGAAAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTCTTTGATAATTTTT
1 TTTTATTTTTAAAAAAACGGATACTTTCAACTTTTTCTCAAAAATA-TTTT-TTT-A-AA-TTTT
* ** *
1616075 ATTTTTAAGAAAAATTGATACTTTCAACTTTTCTTCAAAATGCTTTTTTT-GAAAT
61 ATTTTTAA-AAAAATTGATACTTTCAACTTTTCTTAAAAATATTTTTTTTAGAAAA
* ** **
1616130 TTTTAATTTTAAAAAAATTGATACTTTCAA-TTTTTCCTC-AAAATATTGTTTGAAAATTCTT-T
1 TTTTATTTTTAAAAAAACGGATACTTTCAACTTTTT-CTCAAAAATATT-TTTTTAAATT-TTAT
* * * * *
1616192 ATTTTAGGAAAACTT-ATACTTTTAATTTTTTTTAAAAAATATTTTTTTTAGAAAA
63 -TTTTA-AAAAAATTGATACTTTCAACTTTTCTT-AAAAATATTTTTTTTAGAAAA
* * * *
1616247 ATTTATTTTTAAGGAAAACGGTTATTTTCAACTTTTT-TCAAAAATATTTTTTTAAATTTTATTT
1 TTTTATTTTTAA-AAAAACGGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAATTTTATTT
* *
1616311 TTAAATAAAATTGATACTTTCAACTTTTCCTTAAAAATATGTTTCTTA-AAAA
65 TTAAA-AAAATTGATACTTTCAACTTTT-CTTAAAAATATTTTTTTTAGAAAA
1616363 TTTTTATTTT
1 -TTTTATTTT
1616373 ATATTTTTTC
Statistics
Matches: 196, Mismatches: 32, Indels: 33
0.75 0.12 0.13
Matches are distributed among these distances:
115 19 0.10
116 43 0.22
117 61 0.31
118 26 0.13
119 18 0.09
120 29 0.15
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (115 bp):
TTTTATTTTTAAAAAAACGGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAATTTTATTTT
TAAAAAAATTGATACTTTCAACTTTTCTTAAAAATATTTTTTTTAGAAAA
Found at i:1616466 original size:30 final size:30
Alignment explanation
Indices: 1616426--1616498 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1616416 AAATATTCTA
1616426 AAAAATACAAAAAAAACCAAAAAAATAAAAT
1 AAAAA-ACAAAAAAAACCAAAAAAATAAAAT
*
1616457 ACAAAACAAAAAAAACCAAAAAAATAAAAT
1 AAAAAACAAAAAAAACCAAAAAAATAAAAT
*
1616487 AAAAAATAAAAA
1 AAAAAACAAAAA
1616499 TATTAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 35 0.90
31 4 0.10
ACGTcount: A:0.82, C:0.10, G:0.00, T:0.08
Consensus pattern (30 bp):
AAAAAACAAAAAAAACCAAAAAAATAAAAT
Found at i:1616477 original size:9 final size:9
Alignment explanation
Indices: 1616425--1616490 Score: 53
Period size: 9 Copynumber: 6.9 Consensus size: 9
1616415 AAAATATTCT
*
1616425 AAAAAATAC
1 AAAAAAAAC
1616434 AAAAAAAACC
1 AAAAAAAA-C
1616444 AAAAAAATA-
1 AAAAAAA-AC
1616453 AAATACAAAAC
1 AAA-A-AAAAC
1616464 AAAAAAAAC
1 AAAAAAAAC
* *
1616473 CAAAAAAAT
1 AAAAAAAAC
1616482 AAAATAAAA
1 AAAA-AAAA
1616491 AATAAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
9 25 0.53
10 15 0.32
11 7 0.15
ACGTcount: A:0.82, C:0.11, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1617973 original size:12 final size:12
Alignment explanation
Indices: 1617956--1617985 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1617946 GGTGAGGGTT
1617956 TAGATGGCAATG
1 TAGATGGCAATG
1617968 TAGATGGCAATG
1 TAGATGGCAATG
*
1617980 TGGATG
1 TAGATG
1617986 TAACTGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.37, T:0.27
Consensus pattern (12 bp):
TAGATGGCAATG
Found at i:1618399 original size:13 final size:13
Alignment explanation
Indices: 1618383--1618412 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1618373 AAACAATGAT
1618383 AAATATGAAATAA
1 AAATATGAAATAA
1618396 AAATATGAAATAA
1 AAATATGAAATAA
1618409 AAAT
1 AAAT
1618413 GAATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
AAATATGAAATAA
Found at i:1618748 original size:20 final size:20
Alignment explanation
Indices: 1618725--1618763 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1618715 GGTAAAATAA
* *
1618725 ATAAAATGAAAATGAAAATC
1 ATAAAATAAAAAAGAAAATC
1618745 ATAAAATAAAAAAGAAAAT
1 ATAAAATAAAAAAGAAAAT
1618764 GAAAAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (20 bp):
ATAAAATAAAAAAGAAAATC
Found at i:1618770 original size:20 final size:20
Alignment explanation
Indices: 1618727--1618776 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1618717 TAAAATAAAT
* * *
1618727 AAAATGAAAATGAAAATCAT
1 AAAATAAAAAAGAAAATCAA
*
1618747 AAAATAAAAAAGAAAATGAA
1 AAAATAAAAAAGAAAATCAA
*
1618767 AAAAGAAAAA
1 AAAATAAAAA
1618777 CTTGCGATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (20 bp):
AAAATAAAAAAGAAAATCAA
Found at i:1618828 original size:20 final size:20
Alignment explanation
Indices: 1618803--1618841 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1618793 ATTGAAACGC
*
1618803 GGGTCAACGTGCGGATCCTT
1 GGGTCAACGCGCGGATCCTT
*
1618823 GGGTCAACGCGTGGATCCT
1 GGGTCAACGCGCGGATCCT
1618842 AGCTTAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (20 bp):
GGGTCAACGCGCGGATCCTT
Found at i:1619665 original size:3 final size:3
Alignment explanation
Indices: 1619657--1619703 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1619647 AGAAAAAGAA
1619657 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1619704 TAATAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1619708 original size:3 final size:3
Alignment explanation
Indices: 1619702--1619744 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1619692 CAACAACAAC
1619702 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1619745 CTTAATTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1621137 original size:21 final size:21
Alignment explanation
Indices: 1621100--1621140 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1621090 AACATTATTT
*
1621100 AAATCAAAAGTATAAAAAACC
1 AAATCAAAAATATAAAAAACC
*
1621121 AAATCAAGAAATAAAAAAAA
1 AAATCAA-AAATATAAAAAA
1621141 GAAAGATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.73, C:0.10, G:0.05, T:0.12
Consensus pattern (21 bp):
AAATCAAAAATATAAAAAACC
Found at i:1625011 original size:23 final size:23
Alignment explanation
Indices: 1624980--1625023 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1624970 GAAGGTCAAA
*
1624980 AAAACAAAAAACAAAACAAATCG
1 AAAACAAAAAACAAAAAAAATCG
* *
1625003 AAAATAAAAAGCAAAAAAAAT
1 AAAACAAAAAACAAAAAAAAT
1625024 TCACACACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.07
Consensus pattern (23 bp):
AAAACAAAAAACAAAAAAAATCG
Found at i:1627008 original size:20 final size:19
Alignment explanation
Indices: 1626971--1627009 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1626961 ACTTGTCAAG
* *
1626971 AAAAAATTAAAAGTGAAAA
1 AAAAAAATAAAAGAGAAAA
1626990 AAAAAAATAAGAAGAGAAAA
1 AAAAAAATAA-AAGAGAAAA
1627010 TTTGAGACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (19 bp):
AAAAAAATAAAAGAGAAAA
Found at i:1638632 original size:22 final size:22
Alignment explanation
Indices: 1638607--1638648 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1638597 ATCAACTTTC
*
1638607 CTTTTTTTTCTATCTTTTTTGG
1 CTTTTTTTTCTACCTTTTTTGG
*
1638629 CTTTTTTTTCTCCCTTTTTT
1 CTTTTTTTTCTACCTTTTTT
1638649 AATTTCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (22 bp):
CTTTTTTTTCTACCTTTTTTGG
Found at i:1641448 original size:20 final size:20
Alignment explanation
Indices: 1641423--1641468 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1641413 CGCTAAGCCG
*
1641423 TTTATTTTTTTTGGTATTTT
1 TTTATTTTTTTTGGGATTTT
1641443 TTTA-TTTTTTTGGGATTTT
1 TTTATTTTTTTTGGGATTTT
1641462 TTT-TTTT
1 TTTATTTT
1641469 ATGTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.09, C:0.00, G:0.11, T:0.80
Consensus pattern (20 bp):
TTTATTTTTTTTGGGATTTT
Found at i:1641464 original size:31 final size:31
Alignment explanation
Indices: 1641426--1641493 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1641416 TAAGCCGTTT
* * *
1641426 ATTTTTTTTGGTATTTTTTTATTTTTTTGGG
1 ATTTTTTTTGGTATGTCTTTATTTTTTTAGG
** *
1641457 ATTTTTTTTTTTATGTCTTTATTTTTTTAGT
1 ATTTTTTTTGGTATGTCTTTATTTTTTTAGG
1641488 ATTTTT
1 ATTTTT
1641494 GTATGATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.12, C:0.01, G:0.10, T:0.76
Consensus pattern (31 bp):
ATTTTTTTTGGTATGTCTTTATTTTTTTAGG
Found at i:1641627 original size:25 final size:24
Alignment explanation
Indices: 1641570--1641629 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 24
1641560 ATCCAATTAT
1641570 GAAA-TTTATAGAAATTTTAAATA
1 GAAATTTTATAGAAATTTTAAATA
*
1641593 GTAAATTTTTATA-AAATTCTTAAGTGA
1 G-AAA-TTTTATAGAAATT-TTAAAT-A
1641620 GAAATTTTAT
1 GAAATTTTAT
1641630 CTAAATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 11 0.35
26 14 0.45
27 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (24 bp):
GAAATTTTATAGAAATTTTAAATA
Found at i:1641981 original size:49 final size:50
Alignment explanation
Indices: 1641913--1642065 Score: 143
Period size: 49 Copynumber: 3.1 Consensus size: 50
1641903 AAAAAAAATA
1641913 AAAATAAAAGAATTTCTAAATAAG-CCCAAATGGTGAAAAATTTAGAAATTT
1 AAAA-AAAA-AATTTCTAAATAAGACCCAAATGGTGAAAAATTTAGAAATTT
** * * *
1641964 TGAAAAAAAATTTCTAAAT-TGACCCAAATGGTGAAAATTTTGGAAA--T
1 AAAAAAAAAATTTCTAAATAAGACCCAAATGGTGAAAAATTTAGAAATTT
* * * * * * *
1642011 AAAAAAAAGAATTTTTAAATAGGCCCCAAATGGTGGAGAATTTAAAAATTC
1 AAAAAAAA-AATTTCTAAATAAGACCCAAATGGTGAAAAATTTAGAAATTT
1642062 AAAA
1 AAAA
1642066 GAGAAAATAC
Statistics
Matches: 81, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
47 7 0.09
48 11 0.14
49 53 0.65
50 4 0.05
51 6 0.07
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (50 bp):
AAAAAAAAAATTTCTAAATAAGACCCAAATGGTGAAAAATTTAGAAATTT
Found at i:1646107 original size:8 final size:8
Alignment explanation
Indices: 1646103--1646177 Score: 93
Period size: 8 Copynumber: 9.6 Consensus size: 8
1646093 GAGAAAAGAA
1646103 AAAAAAT-
1 AAAAAATG
1646110 AAAAAATG
1 AAAAAATG
**
1646118 AAAAGGTG
1 AAAAAATG
1646126 AAAAAATG
1 AAAAAATG
1646134 AAAAAATG
1 AAAAAATG
1646142 -AAAAATG
1 AAAAAATG
1646149 AAAAAATG
1 AAAAAATG
*
1646157 AAAAAAAAG
1 -AAAAAATG
1646166 AAAAAAT-
1 AAAAAATG
1646173 AAAAA
1 AAAAA
1646178 GAAGGAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
7 19 0.32
8 33 0.56
9 7 0.12
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:1646115 original size:24 final size:24
Alignment explanation
Indices: 1646087--1646162 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 24
1646077 CTAATGGATG
1646087 AAAAATGAGAAAAGAAAAAAAAT-A
1 AAAAATGA-AAAAGAAAAAAAATGA
* **
1646111 AAAAATGAAAAGGTGAAAAAATGA
1 AAAAATGAAAAAGAAAAAAAATGA
1646135 AAAAATGAAAAATG--AAAAAATGA
1 AAAAATGAAAAA-GAAAAAAAATGA
1646158 AAAAA
1 AAAAA
1646163 AAGAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
23 25 0.54
24 20 0.43
25 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (24 bp):
AAAAATGAAAAAGAAAAAAAATGA
Found at i:1646119 original size:31 final size:29
Alignment explanation
Indices: 1646084--1646177 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 29
1646074 TCACTAATGG
1646084 ATGAAAAATGAGAAAAGAAAAAAAATAAAAA
1 ATGAAAAATGA-AAAA-AAAAAAAATAAAAA
* * *
1646115 ATGAAAAGGTGAAAAAATGAAAAAATGAAAA
1 ATGAAAA-ATGAAAAAA-AAAAAAATAAAAA
1646146 ATGAAAAAATGAAAAAAAAGAAAAAATAAAAA
1 ATG-AAAAATG-AAAAAAA-AAAAAATAAAAA
1646178 GAAGGAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 1 0.02
31 27 0.52
32 24 0.46
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (29 bp):
ATGAAAAATGAAAAAAAAAAAAATAAAAA
Found at i:1646129 original size:16 final size:16
Alignment explanation
Indices: 1646103--1646177 Score: 93
Period size: 15 Copynumber: 4.8 Consensus size: 16
1646093 GAGAAAAGAA
1646103 AAAAAAT-AAAAAATG
1 AAAAAATGAAAAAATG
**
1646118 AAAAGGTGAAAAAATG
1 AAAAAATGAAAAAATG
1646134 AAAAAATG-AAAAATG
1 AAAAAATGAAAAAATG
*
1646149 AAAAAATGAAAAAAAAG
1 AAAAAATG-AAAAAATG
1646166 AAAAAAT-AAAAA
1 AAAAAATGAAAAA
1646178 GAAGGAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
15 25 0.48
16 14 0.27
17 13 0.25
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (16 bp):
AAAAAATGAAAAAATG
Found at i:1646129 original size:23 final size:23
Alignment explanation
Indices: 1646103--1646162 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
1646093 GAGAAAAGAA
*
1646103 AAAAAAT-AAAAAATGAAAAGGTG
1 AAAAAATGAAAAAATGAAAA-ATG
1646126 AAAAAATGAAAAAATGAAAAATG
1 AAAAAATGAAAAAATGAAAAATG
1646149 AAAAAATGAAAAAA
1 AAAAAATGAAAAAA
1646163 AAGAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 23 0.66
24 12 0.34
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (23 bp):
AAAAAATGAAAAAATGAAAAATG
Found at i:1646137 original size:6 final size:7
Alignment explanation
Indices: 1646104--1646161 Score: 62
Period size: 7 Copynumber: 7.7 Consensus size: 7
1646094 AGAAAAGAAA
*
1646104 AAAAATA
1 AAAAATG
1646111 AAAAATG
1 AAAAATG
*
1646118 AAAAGGTG
1 AAAA-ATG
1646126 AAAAAATG
1 -AAAAATG
1646134 AAAAAATG
1 -AAAAATG
1646142 AAAAATG
1 AAAAATG
1646149 AAAAAATG
1 -AAAAATG
1646157 AAAAA
1 AAAAA
1646162 AAAGAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
7 22 0.49
8 19 0.42
9 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (7 bp):
AAAAATG
Done.