Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 55
Found at i:5496700 original size:9 final size:9
Alignment explanation
Indices: 5496666--5496710 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
5496656 CATTTCAATT
5496666 TTCTTTTCTC
1 TTCTTTT-TC
* *
5496676 TTTTTTTTA
1 TTCTTTTTC
5496685 TTCCTTTTTC
1 TT-CTTTTTC
5496695 TTCTTTTTC
1 TTCTTTTTC
5496704 TTCTTTT
1 TTCTTTT
5496711 CATTTTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 17 0.57
10 13 0.43
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:5496739 original size:6 final size:6
Alignment explanation
Indices: 5496664--5496776 Score: 65
Period size: 6 Copynumber: 18.5 Consensus size: 6
5496654 CTCATTTCAA
* *
5496664 TTTTCT TTTCTCT TTTT-T TTATTCCT TTTTCT TCTTT-T TCTTC- TTTTCA
1 TTTTCT TTT-TCT TTTTCT TT-TT-CT TTTTCT T-TTTCT TTTTCT TTTTCT
* * *
5496713 TTTTCA TTTT-T ATTTCAT TTTTCT TTTCTCT TTCTT-T TTTTCT TTTTAT
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTT-TCT TT-TTCT TTTTCT TTTTCT
* *
5496762 TTTCCT TATTCT TTT
1 TTTTCT TTTTCT TTT
5496777 CTTCATTCTC
Statistics
Matches: 84, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
5 14 0.17
6 44 0.52
7 22 0.26
8 4 0.05
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTCT
Found at i:5496791 original size:37 final size:35
Alignment explanation
Indices: 5496699--5496793 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 35
5496689 TTTTTCTTCT
* *
5496699 TTTTCTTCTTTTCATTTTCATTTTTATTTCATTTTTC
1 TTTTCTTCTTCTC-TTTTC-TTTTTATTTCATTATTC
* *
5496736 TTTTC-TCTTTCTTTTTTTCTTTTTATTTTCCTTATTC
1 TTTTCTTC-TTC-TCTTTTCTTTTTA-TTTCATTATTC
5496773 TTTTCTTCATTCTCTTTTCTT
1 TTTTCTTC-TTCTCTTTTCTT
5496794 CGAGTGTAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
36 8 0.17
37 34 0.71
38 6 0.12
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (35 bp):
TTTTCTTCTTCTCTTTTCTTTTTATTTCATTATTC
Found at i:5498114 original size:50 final size:50
Alignment explanation
Indices: 5498050--5498178 Score: 240
Period size: 50 Copynumber: 2.6 Consensus size: 50
5498040 CACACTCCAA
*
5498050 TTTGCCTTTTCATTGTGACTAGGAGGGCTGGTTAGAGCCATATTATCGTG
1 TTTGCCTTTTCATTGCGACTAGGAGGGCTGGTTAGAGCCATATTATCGTG
*
5498100 TTTGTCTTTTCATTGCGACTAGGAGGGCTGGTTAGAGCCATATTATCGTG
1 TTTGCCTTTTCATTGCGACTAGGAGGGCTGGTTAGAGCCATATTATCGTG
5498150 TTTGCCTTTTCATTGCGACTAGGAGGGCT
1 TTTGCCTTTTCATTGCGACTAGGAGGGCT
5498179 AGATAGGACA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (50 bp):
TTTGCCTTTTCATTGCGACTAGGAGGGCTGGTTAGAGCCATATTATCGTG
Found at i:5498327 original size:22 final size:23
Alignment explanation
Indices: 5498302--5498344 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5498292 CAATTCCTTT
*
5498302 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATTCTTTACCTTGTTTTA
*
5498324 ATCTTATTTTTTACCTTGTTT
1 ATCTTATTCTTTACCTTGTTT
5498345 CCAATACCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (23 bp):
ATCTTATTCTTTACCTTGTTTTA
Found at i:5505484 original size:24 final size:23
Alignment explanation
Indices: 5505455--5505499 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
5505445 ACGATACAAA
*
5505455 GATGCGAATGTGAATACGAATGCG
1 GATGCGAATGCGAATAC-AATGCG
*
5505479 GATGCGGATGCGAATACAATG
1 GATGCGAATGCGAATACAATG
5505500 AGGCAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (23 bp):
GATGCGAATGCGAATACAATGCG
Found at i:5512143 original size:29 final size:29
Alignment explanation
Indices: 5512101--5512159 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5512091 ATTTTCACCT
5512101 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
5512130 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
5512159 A
1 A
5512160 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:5516833 original size:29 final size:29
Alignment explanation
Indices: 5516791--5516847 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5516781 TTTCACCTAA
5516791 CTAAATTGATGTAAGCAATGACATCAAAG
1 CTAAATTGATGTAAGCAATGACATCAAAG
*
5516820 CTAAATTGATGTAAGCAATGGCATCAAA
1 CTAAATTGATGTAAGCAATGACATCAAA
5516848 TTAATTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.25
Consensus pattern (29 bp):
CTAAATTGATGTAAGCAATGACATCAAAG
Found at i:5519582 original size:2 final size:2
Alignment explanation
Indices: 5519575--5519620 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5519565 TTTAATGCAT
5519575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5519616 TA TA T
1 TA TA T
5519621 TCAAGTTACT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5521732 original size:20 final size:20
Alignment explanation
Indices: 5521684--5521733 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5521674 TATTTATTTT
*
5521684 TTTTATTTTCTTTTTTTTTCC
1 TTTT-TTTTCTTTCTTTTTCC
* *
5521705 ATTTTTTTGTTTCTTTTTCC
1 TTTTTTTTCTTTCTTTTTCC
5521725 TTTTTTTTC
1 TTTTTTTTC
5521734 CAGGCAAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTTTCTTTCTTTTTCC
Found at i:5524935 original size:23 final size:23
Alignment explanation
Indices: 5524843--5524926 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
5524833 CTCGTATAAA
*
5524843 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
5524866 TGCACTGAAGTTCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
5524889 TGCACCGAAGTGTCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
5524912 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
5524927 TCTAAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:5526479 original size:64 final size:64
Alignment explanation
Indices: 5526391--5526552 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 64
5526381 TCTTTAACAT
** * * * *
5526391 GTGCATCGATACACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTAA-TTTTAAGGGG
1 GTGCATCGACGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCAATTTTTAA-GGG
* * * *
5526455 GTGCATCGACGCAC-TCCTTATGCATCGATGCACTAATTACATTCGATGTTTCAATTTTTAATGG
1 GTGCATCGACGCACTTCC-TATGCATCGATACACAAATCACATTCGATGTTTCAATTTTTAAGGG
* *
5526519 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGACGCACTTCCTATGCATCGATACACA
5526553 CTGGACAATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 2 0.02
64 70 0.86
65 9 0.11
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (64 bp):
GTGCATCGACGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCAATTTTTAAGGG
Found at i:5530049 original size:23 final size:23
Alignment explanation
Indices: 5530023--5530106 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
5530013 CTCGTATAAA
*
5530023 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
5530046 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
5530069 TACACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
5530092 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
5530107 TATAAAATGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:5532678 original size:13 final size:13
Alignment explanation
Indices: 5532660--5532686 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5532650 TGAAATATAG
5532660 TTATATTAATATT
1 TTATATTAATATT
5532673 TTATATTAATATT
1 TTATATTAATATT
5532686 T
1 T
5532687 AATTAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTAATATT
Found at i:5533209 original size:14 final size:14
Alignment explanation
Indices: 5533186--5533216 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5533176 ATCGATTAAC
*
5533186 TAATGTAAATTGCG
1 TAATGAAAATTGCG
5533200 TAATGAAAATTGCG
1 TAATGAAAATTGCG
5533214 TAA
1 TAA
5533217 AAGATCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (14 bp):
TAATGAAAATTGCG
Found at i:5536321 original size:2 final size:2
Alignment explanation
Indices: 5536314--5536375 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
5536304 TGCATCCATA
5536314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5536356 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
5536376 GCAACCACAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5539604 original size:17 final size:17
Alignment explanation
Indices: 5539568--5539609 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5539558 GTGTTTGTTG
* * *
5539568 CTCGAATGAGAGTTTTT
1 CTCGAAAGAGAATTTCT
5539585 CTCGAAAGAGAATTTCT
1 CTCGAAAGAGAATTTCT
5539602 CTC-AAAGA
1 CTCGAAAGA
5539610 AAGGGAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (17 bp):
CTCGAAAGAGAATTTCT
Found at i:5543478 original size:37 final size:36
Alignment explanation
Indices: 5543428--5543632 Score: 131
Period size: 37 Copynumber: 5.5 Consensus size: 36
5543418 AATATATAGT
* *
5543428 TTTTAAAACTATATAATATATAATTTTTTTAAAACA
1 TTTTAAAAATATATAATATATAATGTTTTTAAAACA
5543464 TTTTAGAAAATATATGTAATATATAA--TTTTTAAAATCA
1 TTTTA-AAAATATA--TAATATATAATGTTTTTAAAA-CA
*
5543502 TTTTCAAAACT-TAT-ATATAT-ATAGTTTTTGAAAACA
1 TTTT-AAAAATATATAATATATAAT-GTTTTT-AAAACA
* *
5543538 TTTTTAAAAACATAT-ATAT-T-ATAGTTTTGAAAACA
1 -TTTTAAAAATATATAATATATAAT-GTTTTTAAAACA
* * *
5543573 TTTTAAAAACAT-TTATATATTATATAGTTTTTAAAACGT
1 TTTTAAAAATATATAATATA-TA-AT-GTTTTTAAAAC-A
*
5543612 TTTTGAAAACTTATATAATAT
1 TTTT-AAAA-ATATATAATAT
5543633 TTTTGAAAAC
Statistics
Matches: 139, Mismatches: 10, Indels: 34
0.76 0.05 0.19
Matches are distributed among these distances:
33 2 0.01
34 22 0.16
35 7 0.05
36 26 0.19
37 33 0.24
38 23 0.17
39 15 0.11
40 4 0.03
41 2 0.01
42 5 0.04
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTTAAAAATATATAATATATAATGTTTTTAAAACA
Found at i:5543667 original size:41 final size:40
Alignment explanation
Indices: 5543622--5543709 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 40
5543612 TTTTGAAAAC
*
5543622 TTATATAATATTTTT-GAAAACATGTTGAAAACATTAGTATA
1 TTATATAATATTTTTAAAAAACATGTTGAAAA-ATTA-TATA
* * * *
5543663 TTATATAGTTTTTTTAAAAAAACATTTTGAAAATTTATATA
1 TTATATAATATTTTT-AAAAAACATGTTGAAAAATTATATA
5543704 TTATAT
1 TTATAT
5543710 GTTTTTGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 23 0.57
42 3 0.08
43 14 0.35
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (40 bp):
TTATATAATATTTTTAAAAAACATGTTGAAAAATTATATA
Found at i:5543677 original size:73 final size:72
Alignment explanation
Indices: 5543437--5543725 Score: 250
Period size: 71 Copynumber: 3.9 Consensus size: 72
5543427 TTTTTAAAAC
* * *
5543437 TATATAATATATAATTTTTTTAAAACATTTTAGAAAA-TATATGTAATATATAATTTTT-AAAAT
1 TATATATTATAT-AGTTTTTTAAAACATTTTTGAAAACTATA--T-ATA-AT-ATTTTTGAAAA-
*
5543500 CATTTTCAAAAC-T
59 CATTTTAAAAACAT
* * * *
5543513 TATATA-TATATAGTTTTTGAAAACATTTTTAAAAACATATATATTATAGTTTTGAAAACATTTT
1 TATATATTATATAGTTTTTTAAAACATTTTTGAAAAC-TATATATAATATTTTTGAAAACATTTT
5543577 AAAAACATT
65 AAAAACA-T
* * *
5543586 TATATATTATATAG-TTTTTAAAACGTTTTTGAAAACT-TATATAATATTTTTGAAAACATGTTG
1 TATATATTATATAGTTTTTTAAAACATTTTTGAAAACTATATATAATATTTTTGAAAACATTTTA
5543649 AAAACAT
66 AAAACAT
* *
5543656 TAGTATATTATATAGTTTTTTTAAAAAAACA-TTTTGAAAATTTATATATTATATGTTTTTGAAA
1 TA-TATATTATATAG-TTTTTT---AAAACATTTTTGAAAA-CTATATA-TA-ATATTTTTGAAA
*
5543720 ATATTT
58 ACATTT
5543726 ATGTATATAT
Statistics
Matches: 178, Mismatches: 19, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
70 3 0.02
71 56 0.31
72 7 0.04
73 33 0.19
74 28 0.16
75 14 0.08
76 16 0.09
77 4 0.02
78 2 0.01
79 15 0.08
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (72 bp):
TATATATTATATAGTTTTTTAAAACATTTTTGAAAACTATATATAATATTTTTGAAAACATTTTA
AAAACAT
Found at i:5543745 original size:9 final size:10
Alignment explanation
Indices: 5543720--5543768 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 10
5543710 GTTTTTGAAA
5543720 ATAT-TTATGT
1 ATATATTAT-T
5543730 ATATATATATT
1 ATATAT-TATT
5543741 ATATATTATT
1 ATATATTATT
5543751 AT-TATTATT
1 ATATATTATT
*
5543760 -TATTTTATT
1 ATATATTATT
5543769 TTATTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
8 1 0.03
9 13 0.37
10 10 0.29
11 8 0.23
12 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
ATATATTATT
Found at i:5543772 original size:20 final size:20
Alignment explanation
Indices: 5543739--5543790 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
5543729 TATATATATA
*
5543739 TTATATATTATTATTATTA-T
1 TTATTTATT-TTATTATTATT
*
5543759 TTATTTTATTTTATTTTTATT
1 TTA-TTTATTTTATTATTATT
5543780 TTATTTATTTT
1 TTATTTATTTT
5543791 TTTGGTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTATTTATTTTATTATTATT
Found at i:5543792 original size:16 final size:16
Alignment explanation
Indices: 5543752--5543792 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5543742 TATATTATTA
*
5543752 TTATTATTTATTTTAT
1 TTATTTTTTATTTTAT
5543768 TT-TATTTTTATTTTAT
1 TTAT-TTTTTATTTTAT
5543784 TTATTTTTT
1 TTATTTTTT
5543793 TGGTCTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATTTTTTATTTTAT
Found at i:5549992 original size:50 final size:50
Alignment explanation
Indices: 5549914--5550010 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
5549904 GTACGTCTTC
* * *
5549914 AGTTGGGTAGTGTGTGTAGGGATGAATTTGAGAATGCACCCGCGTAGACG
1 AGTTGGGTAGTGGGTGTAGGGATAAATTTAAGAATGCACCCGCGTAGACG
* * *
5549964 AGTTGGGTAGTGGGTGTAGGGATAAATTTAATAATGTATCCGCGTAG
1 AGTTGGGTAGTGGGTGTAGGGATAAATTTAAGAATGCACCCGCGTAG
5550011 GCAAGTGTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.26, C:0.09, G:0.36, T:0.29
Consensus pattern (50 bp):
AGTTGGGTAGTGGGTGTAGGGATAAATTTAAGAATGCACCCGCGTAGACG
Found at i:5554528 original size:15 final size:15
Alignment explanation
Indices: 5554505--5554556 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
5554495 TATATCATGA
5554505 TTTAAATATATATTT
1 TTTAAATATATATTT
*
5554520 TTTATATATATATTAT
1 TTTAAATATATATT-T
*
5554536 GTTAAA-A-ATATTAT
1 TTTAAATATATATT-T
5554550 TTTAAAT
1 TTTAAAT
5554557 CTTAATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.39
15 14 0.45
16 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTAAATATATATTT
Found at i:5562495 original size:14 final size:14
Alignment explanation
Indices: 5562476--5562516 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
5562466 TAAAGTACAA
5562476 TTTCTGATATCTGG
1 TTTCTGATATCTGG
5562490 TTTCTGAT-TACTGG
1 TTTCTGATAT-CTGG
*
5562504 CTTCTGATATCTG
1 TTTCTGATATCTG
5562517 ATTTTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.49
Consensus pattern (14 bp):
TTTCTGATATCTGG
Found at i:5562747 original size:60 final size:60
Alignment explanation
Indices: 5562628--5562803 Score: 252
Period size: 60 Copynumber: 3.0 Consensus size: 60
5562618 ATTTGTTCTG
* *
5562628 ATCTTCCATATTGGACTCCTAGATCTTAGT-G---AGGGTAAGTCCTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTATAGGATAAGTCCTTATGGATGCATGT
* *
5562684 ATCTTCCATGTTGGACTCCTATATCCTAGTGGTATAGGATAAGTCCTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTATAGGATAAGTCCTTATGGATGCATGT
* * * *
5562744 ATCTTCCATATTGGACTCCTAGATCCTATTGGTCTAGGGTAAGTCTTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTATAGGATAAGTCCTTATGGATGCATGT
5562804 TATAGGGTAT
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
56 27 0.25
57 1 0.01
60 78 0.74
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (60 bp):
ATCTTCCATATTGGACTCCTAGATCCTAGTGGTATAGGATAAGTCCTTATGGATGCATGT
Found at i:5564182 original size:22 final size:22
Alignment explanation
Indices: 5564155--5564204 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
5564145 AATTCAAACA
* *
5564155 ATTTTTAGGAATTATCTTTTGT
1 ATTTTTAGGAATTATCTTTAGC
5564177 ATTTTTAGGAATTATCTTTAGC
1 ATTTTTAGGAATTATCTTTAGC
5564199 ATTTTT
1 ATTTTT
5564205 TGGGCTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (22 bp):
ATTTTTAGGAATTATCTTTAGC
Found at i:5567661 original size:3 final size:3
Alignment explanation
Indices: 5567653--5567689 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
5567643 ACAAATAGAG
*
5567653 ATA ATA ATA ATA ATA ATA A-A AT- ATA ATG ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5567690 TGAAACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5568538 original size:41 final size:41
Alignment explanation
Indices: 5568488--5568589 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
5568478 ATGTCTTATG
*
5568488 GATGGCCCAAAGAACTTATCATCTTGCTCGAAAGACTTACA
1 GATGGCCCAAAGAACTTATCATCATGCTCGAAAGACTTACA
* * * * *
5568529 GATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCAAAGAACTT-ATCATCATGCTCGAAAGACTTACA
*
5568571 GATGGCCCGAAGAACTTAT
1 GATGGCCCAAAGAACTTAT
5568590 AAATTTTGGA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 15 0.31
42 34 0.69
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
GATGGCCCAAAGAACTTATCATCATGCTCGAAAGACTTACA
Found at i:5568601 original size:233 final size:233
Alignment explanation
Indices: 5567821--5569842 Score: 2719
Period size: 233 Copynumber: 8.7 Consensus size: 233
5567811 TGTCTGAAGT
* * * * * * * *
5567821 AAGACTGACAGATGACCTGAAGGATTTAAACATCACGTTCAAAAGTCTTACTGATGACCCGAAGG
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
** * * * * *
5567886 ACTTACCAACTTTGGAAATAGTTTACTATGTAAGAAACTTTTCTTACATTTCCAAAATTTCAATT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * * * * ** *
5567951 TTCATATTTAAATGAGAAATCTTTCTAATTTCTCGAGAGATGTGTGTAAACATCCTACCCAAAGG
131 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGG
* *
5568016 TCTTATGGATAGCCCAAAGGACTTATCATCTTGCTTGA
196 TCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
*
5568054 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGG
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
** * *
5568119 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTTTTACTTTTCAAAAATTTCGTAT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AAT
* * * ** * **
5568184 TTT-ATATTTAAATGAGAAGCCTTTCTCATTTATTTGA-A-ATCACGTGAAAACATTATGCCTTA
130 TTTCAGATTTAAATGAGAAACCTTTCTCATTT-TTTGAGAGA-CATGTGAAAACATCCTACCCAA
* * *
5568246 AGGTCGTAAGGATGGCCC-GAGGACTTATCATCTTGCTCGA
193 AGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
* *
5568286 AAGACTTACAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGA-TATATTGATGGCCCGAAG
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACT-TACTGATGGCCCGAAG
* *
5568350 GACTTATAAATTTTGGAAATAGTTTACTAGGTAGGAAACCTTTATTACTTTTCAAAAATTTCAAT
65 GACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
* ** ** * * * * *
5568415 TTTTAGATTTAAATGAGAAAATTTTCTCATTTTTCAAGACACATGTGAAAAGATCTTGCCCAAAT
130 TTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAG
*
5568480 GTCTTATGGATGGCCCAAAGAACTTATCATCTTGCTCGA
195 GTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
* *
5568519 AAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGA
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * **
5568584 ACTTATAAATTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTAACTTTTCAAATTTTTCAATT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * *
5568649 TTCAGAATTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGCGAGAACATCCTACCCAAAGG
131 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGG
* * *
5568714 TTTTATGGATGGCCCGAAGGACTTATCGTCTTGCTCGA
196 TCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
* * * * *
5568752 AAGACTCACAGATGATCCGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCAAAGG
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
5568817 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACC-TTCATTACTTTTCAAAAATTTCAAT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTC-TTACTTTTCAAAAATTTCAAT
* * * * * *
5568881 TTTTAGATTTAAATGAGAAATCTTTCTTATTTTTTGAGAGACATGTGAAAA-ATCATGCCCGAAG
130 TTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAG
* *
5568945 GTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGA
195 GTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
* * *
5568984 AAGACTTACAGATTACCCGAAGGATTTAAGAATCATGCTCGAAATACTTACTGATGGCCCGAAGG
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * *
5569049 ACTTATAAATTTTGGAAATAGTTTACTAAGTAAAAAACCTTTCTTACTTTTCAAAAATTTCAATA
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * * **
5569114 TTCAAATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACAT-TTTGCCAAAGG
131 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGG
* *
5569178 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGA
196 TCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
* * * * * *
5569216 AAGACTTACAGATGACACAAAGGATTTAAACATCATGCTCAAAAAACTTACTGATAGCCCGAAGG
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
** *
5569281 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAGAATTTCAATT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * * *
5569346 TTCAAATTTAGATGAGGAACCTTTCTCATTTTTTGAGAGACATGTGAAAACAACCTACCCAAAGG
131 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGG
** *
5569411 TCTTATGGATGGCCTGAATGACTTATCATCTTGCTCGA
196 TCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
* * * * * * *
5569449 AAGACTTAAAGATGATCTGAATGATTTAAACATCATGCTAGAAAGACTTACTAATGGCCCGAAGG
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
5569514 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * * * * * * *
5569579 TTAAAATTTGAATGAGAAACTTTTTTCATTTTATGAGAGACATATGAAAACATCCTACCCGAAGG
131 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGG
* * *
5569644 TCTTATGGATAGCCCGAAGGACTTATCATCTTGGTCGA
196 TCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
* * * * *
5569682 AAGACTCACAAATGACCTGAAGGATTTAAGTATCATGCTCAAAAGACTTACTGATGGCCCGAAGG
1 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
5569747 ACTTATAAATTTTGAAAATAATTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
*
5569812 TTTAGATTTAAATGAGAAACCTTTCTCATTT
131 TTCAGATTTAAATGAGAAACCTTTCTCATTT
5569843 CATTTTTTCT
Statistics
Matches: 1577, Mismatches: 199, Indels: 26
0.88 0.11 0.01
Matches are distributed among these distances:
231 9 0.01
232 613 0.39
233 946 0.60
234 9 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (233 bp):
AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
TTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGG
TCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
Found at i:5568726 original size:465 final size:463
Alignment explanation
Indices: 5567821--5569842 Score: 2730
Period size: 465 Copynumber: 4.3 Consensus size: 463
5567811 TGTCTGAAGT
* * * * * * * *
5567821 AAGACTGACAGATGACCTGAAGGATTTAAACATCACGTTCAAAAGTCTTACTGATGACCCGAAGG
1 AAGACTCACAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGG
** * * * * *
5567886 ACTTACCAACTTTGGAAATAGTTTACTATGTAAGAAACTTTTCTTACATTTCCAAAATTTCAATT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * * * ** *
5567951 TTCATATTTAAATGAGAAATCTTTCTAATTTCTCGAGAGATGTGTGTAAACATCCTACCCAAAGG
131 TTTAGATTTAAATGAGAAAT-TTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAGG
* *
5568016 TCTTATGGATAGCCCAAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGATTT
195 TCTTATGGATGGCCCAAA-GACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTT
* **
5568081 AAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACT
259 AAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACT
* * * * *
5568146 AGGTAAGAAACCTTTTTTACTTTTCAAAAATTTCGTATTTTATATTTAAATGAGAAGCCTTTCTC
324 AAGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AATTTTAAATTTAAATGAGAAACCTTTCTC
* ** * ** * *
5568211 ATTTATTTGA-A-ATCACGTGAAAACATTATGCCTTAAGGTCGTAAGGATGGCCCG-AGGACTTA
388 ATTT-TTTGAGAGA-CATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTA
5568273 TCATCTTGCTCGA
451 TCATCTTGCTCGA
* * *
5568286 AAGACTTACAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGA-TATATTGATGGCCCGAAG
1 AAGACTCACAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACT-TACTGATGGCCCGAAG
* *
5568350 GACTTATAAATTTTGGAAATAGTTTACTAGGTAGGAAACCTTTATTACTTTTCAAAAATTTCAAT
65 GACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
* * * * * *
5568415 TTTTAGATTTAAATGAGAAAATTTTCTCATTTTTCAAGACACATGTGAAAAGATCTTGCCCAAAT
130 TTTTAGATTTAAATGAG-AAATTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAG
*
5568480 GTCTTATGGATGGCCCAAAGAACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGGATT
194 GTCTTATGGATGGCCCAAAG-ACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATT
*
5568545 TAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGAACTTATAAATTTTGGAAATAGTTTAC
258 TAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTAC
* **
5568610 TAAGTAAGAAACCTTTCTAACTTTTCAAATTTTTCAATTTTCAGAA-TTAAATGAGAAACCTTTC
323 TAAGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTT-A-AATTTAAATGAGAAACCTTTC
* * *
5568674 TCATTTTTTGAGAGACATGCGAGAACATCCTACCCAAAGGTTTTATGGATGGCCCGAAGGACTTA
386 TCATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTA
*
5568739 TCGTCTTGCTCGA
451 TCATCTTGCTCGA
* * * *
5568752 AAGACTCACAGATGATCCGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCAAAGG
1 AAGACTCACAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGG
5568817 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACC-TTCATTACTTTTCAAAAATTTCAAT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTC-TTACTTTTCAAAAATTTCAAT
* * * * *
5568881 TTTTAGATTTAAATGAGAAATCTTTCTTATTTTTTGAGAGACATGTGAAAA-ATCATGCCCGAAG
130 TTTTAGATTTAAATGAGAAAT-TTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAG
* *
5568945 GTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATTACCCGAAGGATT
194 GTCTTATGGATGGCCC-AAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATT
* *
5569010 TAAGAATCATGCTCGAAATACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTAC
258 TAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTAC
* * *
5569075 TAAGTAAAAAACCTTTCTTACTTTTCAAAAATTTCAATATTCAAATTTGAATGAGAAACCTTTCT
323 TAAGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT-TTTAAATTTAAATGAGAAACCTTTCT
* **
5569140 CATTTTTTGAGAGACATGTGAAAACAT-TTTGCCAAAGGTCTTATGGATGGCCCGAAGGACTTAT
387 CATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTAT
*
5569204 CATCTTGCTTGA
452 CATCTTGCTCGA
* * * * *
5569216 AAGACTTACAGATGACAC-AAAGGATTTAAACATCATGCTCAAAAAACTTACTGATAGCCCGAAG
1 AAGACTCACAGATGACCCGAAA-GATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAG
** *
5569280 GACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAGAATTTCAAT
65 GACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
* * * ** * *
5569345 TTTCAAATTTAGATGAGGAACCTTTCTCATTTTTTGAGAGACATGTGAAAACAACCTACCCAAAG
130 TTTTAGATTTAAATGA-GAAATTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAG
* * * * * *
5569410 GTCTTATGGATGGCCTGAATGACTTATCATCTTGCTCGAAAGACTTAAAGATGATCTGAATGATT
194 GTCTTATGGATGGCC-CAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATT
* * *
5569475 TAAACATCATGCTAGAAAGACTTACTAATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTAC
258 TAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTAC
* * * *
5569540 TAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTAAAATTTGAATGAGAAACTTTTTT
323 TAAGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTT-AAATTTAAATGAGAAACCTTTCT
* * * *
5569605 CATTTTATGAGAGACATATGAAAACATCCTACCCGAAGGTCTTATGGATAGCCCGAAGGACTTAT
387 CATTTTTTGAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTAT
*
5569670 CATCTTGGTCGA
452 CATCTTGCTCGA
* * * *
5569682 AAGACTCACAAATGACCTGAAGGATTTAAGTATCATGCTCAAAAGACTTACTGATGGCCCGAAGG
1 AAGACTCACAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGG
* *
5569747 ACTTATAAATTTTGAAAATAATTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
66 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
*
5569812 TTTAGATTTAAATGAGAAACCTTTCTCATTT
131 TTTAGATTTAAATGAGAAA-TTTTCTCATTT
5569843 CATTTTTTCT
Statistics
Matches: 1376, Mismatches: 158, Indels: 45
0.87 0.10 0.03
Matches are distributed among these distances:
463 3 0.00
464 209 0.15
465 793 0.58
466 368 0.27
467 3 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (463 bp):
AAGACTCACAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGG
ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
TTTAGATTTAAATGAGAAATTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAGGT
CTTATGGATGGCCCAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAA
GCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAA
GTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTAAATTTAAATGAGAAACCTTTCTCATT
TTTTGAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATC
TTGCTCGA
Found at i:5571468 original size:2 final size:2
Alignment explanation
Indices: 5571463--5571505 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5571453 TGTGTGTGTG
5571463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5571504 TA
1 TA
5571506 ATCGTCTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5596084 original size:25 final size:25
Alignment explanation
Indices: 5596045--5596092 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
5596035 AGTCCATCCC
*
5596045 ATTTTTAATAATATAATATTTTATTT
1 ATTTTTAATAATAT-ATAATTTATTT
*
5596071 ATTTTT-ATATTATATAATTTAT
1 ATTTTTAATAATATATAATTTAT
5596093 ATCGCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 6 0.30
26 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTTAATAATATATAATTTATTT
Found at i:5597695 original size:33 final size:37
Alignment explanation
Indices: 5597649--5597724 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 37
5597639 TCAATTTTAT
*
5597649 AAATAAAAGTATTA-AGA-T-TATTAATT-TTTATTA
1 AAATAAAAGTATTATAAATTATATTAATTATTTATTA
*
5597682 AAATAAAATTATTATAAATTATATTAATTATTTATTA
1 AAATAAAAGTATTATAAATTATATTAATTATTTATTA
5597719 AAATAA
1 AAATAA
5597725 GAACTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 13 0.35
34 2 0.05
35 1 0.03
36 8 0.22
37 13 0.35
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (37 bp):
AAATAAAAGTATTATAAATTATATTAATTATTTATTA
Found at i:5597765 original size:17 final size:17
Alignment explanation
Indices: 5597732--5597789 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
5597722 TAAGAACTAT
5597732 ATATTAATTACTTATTAAA
1 ATATTAA-TA-TTATTAAA
5597751 ATATTAATATTATTAAA
1 ATATTAATATTATTAAA
*
5597768 ATATTAA-A-AATTAAA
1 ATATTAATATTATTAAA
5597783 ATATTAA
1 ATATTAA
5597790 AATAAGAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
15 13 0.34
16 1 0.03
17 15 0.39
18 2 0.05
19 7 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATTAATATTATTAAA
Found at i:5597782 original size:7 final size:8
Alignment explanation
Indices: 5597744--5597793 Score: 75
Period size: 8 Copynumber: 6.2 Consensus size: 8
5597734 ATTAATTACT
5597744 TATTAAAA
1 TATTAAAA
*
5597752 TATTAATAT
1 TATTAA-AA
5597761 TATTAAAA
1 TATTAAAA
5597769 TATTAAAA
1 TATTAAAA
5597777 -ATTAAAA
1 TATTAAAA
5597784 TATTAAAA
1 TATTAAAA
5597792 TA
1 TA
5597794 AGAATATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATTAAAA
Found at i:5597782 original size:15 final size:15
Alignment explanation
Indices: 5597745--5597791 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
5597735 TTAATTACTT
*
5597745 ATTAAAATATTAATATT
1 ATTAAAATATTAA-A-A
5597762 ATTAAAATATTAAAA
1 ATTAAAATATTAAAA
5597777 ATTAAAATATTAAAA
1 ATTAAAATATTAAAA
5597792 TAAGAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 15 0.52
16 1 0.03
17 13 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAATATTAAAA
Found at i:5597799 original size:14 final size:14
Alignment explanation
Indices: 5597745--5597802 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 14
5597735 TTAATTACTT
5597745 ATTAAAATATTAATA
1 ATTAAAATATTAA-A
5597760 TTATTAAAATATTAAAA
1 --ATTAAAATATT-AAA
5597777 ATTAAAATATTAAA
1 ATTAAAATATTAAA
5597791 A-TAAGAATATTA
1 ATTAA-AATATTA
5597803 TATTATATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.08
14 11 0.28
15 11 0.28
17 12 0.31
18 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATTAAAATATTAAA
Found at i:5597879 original size:23 final size:23
Alignment explanation
Indices: 5597853--5597896 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5597843 TAAAAATATT
*
5597853 TTTTATAAATAAT-TTATTATTAA
1 TTTT-TAAACAATATTATTATTAA
*
5597876 TTTTTTAACAATATTATTATT
1 TTTTTAAACAATATTATTATT
5597897 TTAATGAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTTAAACAATATTATTATTAA
Found at i:5597931 original size:23 final size:23
Alignment explanation
Indices: 5597885--5597931 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5597875 ATTTTTTAAC
* *
5597885 AATATTATTATTTTAATGAGTAT
1 AATATTATTATTATAATGAATAT
5597908 AATATTATATATTATAAT-AATAT
1 AATATTAT-TATTATAATGAATAT
5597931 A
1 A
5597932 GTTATAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AATATTATTATTATAATGAATAT
Found at i:5601137 original size:140 final size:140
Alignment explanation
Indices: 5600885--5601137 Score: 364
Period size: 140 Copynumber: 1.8 Consensus size: 140
5600875 TTAAATTAAT
* * **
5600885 GTTTTGATTTACTTGTCTAAAATGATTTGGACTTTTGATGATTTTGAATATTTTAATGGCATGAT
1 GTTTTGATTTACTTGTCTAAAATGATCTAGACTTTTGATGATACTGAATATTTTAATGGCATGAT
* * *
5600950 TTCTGATTTATTAGGTATCGTTGATTGAATTTATGACTTACTGTATATCACATAATCTTTGATAT
66 TTCTAATCTATTAGGTATCGTTGATTGAATTTATAACTTACTGTATATCACATAATCTTTGATAT
5601015 ATGTGTGTTC
131 ATGTGTGTTC
* * * *
5601025 GTTTTGATTTATTTTTCTGAATTGATCTAGACTTTTGATGATACTGAATATTTTAATGGCATGAT
1 GTTTTGATTTACTTGTCTAAAATGATCTAGACTTTTGATGATACTGAATATTTTAATGGCATGAT
* * *
5601090 TTCTAATCTATTATGTATCGTTGATT-AGATTTCTAATTTACTGTATAT
66 TTCTAATCTATTAGGTATCGTTGATTGA-ATTTATAACTTACTGTATAT
5601138 TGCTGGCATG
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
139 1 0.01
140 97 0.99
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (140 bp):
GTTTTGATTTACTTGTCTAAAATGATCTAGACTTTTGATGATACTGAATATTTTAATGGCATGAT
TTCTAATCTATTAGGTATCGTTGATTGAATTTATAACTTACTGTATATCACATAATCTTTGATAT
ATGTGTGTTC
Found at i:5602786 original size:24 final size:24
Alignment explanation
Indices: 5602761--5602870 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
5602751 AATCGGAGAT
*
5602761 ATCAGAAATCA-ACACAGAATTCAT
1 ATCAGAAATCAGA-ACAGAATTCAG
* * *
5602785 ATCATATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
5602809 ATCAGAAATCAGAACAGAATTTAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
5602833 ATCAGAAATCAGAAAAAAAATTCAA
1 ATCAGAAATCAG-AACAGAATTCAG
*
5602858 ATCGGAAATCAGA
1 ATCAGAAATCAGA
5602871 TAAAACATTC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
24 51 0.72
25 20 0.28
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:5602838 original size:12 final size:12
Alignment explanation
Indices: 5602761--5602845 Score: 57
Period size: 12 Copynumber: 7.1 Consensus size: 12
5602751 AATCGGAGAT
5602761 ATCAGAAATCA-
1 ATCAGAAATCAG
* * *
5602772 ACACAGAATTCAT
1 A-TCAGAAATCAG
* *
5602785 ATCATATATCAG
1 ATCAGAAATCAG
*
5602797 AACAG-AATCCAG
1 ATCAGAAAT-CAG
5602809 ATCAGAAATCAG
1 ATCAGAAATCAG
* * *
5602821 AACAGAATTTAG
1 ATCAGAAATCAG
5602833 ATCAGAAATCAG
1 ATCAGAAATCAG
5602845 A
1 A
5602846 AAAAAAATTC
Statistics
Matches: 53, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
11 3 0.06
12 46 0.87
13 4 0.08
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (12 bp):
ATCAGAAATCAG
Found at i:5605071 original size:6 final size:6
Alignment explanation
Indices: 5605060--5605088 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5605050 TGACTTTTTT
5605060 GTCAAA GTCAAA GTCAAA GTCAAA GTCAA
1 GTCAAA GTCAAA GTCAAA GTCAAA GTCAA
5605089 TGGGTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
GTCAAA
Found at i:5605227 original size:13 final size:13
Alignment explanation
Indices: 5605209--5605238 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5605199 ACTTTTTTGG
5605209 TCAAAGTCAACAA
1 TCAAAGTCAACAA
*
5605222 TCAAAGTCAACAG
1 TCAAAGTCAACAA
5605235 TCAA
1 TCAA
5605239 CAGGTCAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.17
Consensus pattern (13 bp):
TCAAAGTCAACAA
Found at i:5610993 original size:2 final size:2
Alignment explanation
Indices: 5610986--5611020 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5610976 TTGATGTTCT
5610986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5611021 GAGATAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5612856 original size:19 final size:19
Alignment explanation
Indices: 5612834--5612886 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
5612824 AATATAATAT
5612834 AATTAAATTTTTTATTTAA
1 AATTAAATTTTTTATTTAA
** *
5612853 AATTAAAATTGATT-TTTAT
1 AATT-AAATTTTTTATTTAA
*
5612872 AATTAAATATTTTAT
1 AATTAAATTTTTTAT
5612887 AATCTAATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 6 0.23
19 13 0.50
20 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTAAATTTTTTATTTAA
Found at i:5614754 original size:11 final size:11
Alignment explanation
Indices: 5614738--5614767 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5614728 GACTAACTCT
5614738 GAGTGTGAACA
1 GAGTGTGAACA
5614749 GAGTGTGAACA
1 GAGTGTGAACA
5614760 GAGTGTGA
1 GAGTGTGA
5614768 CAAGAAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.40, T:0.20
Consensus pattern (11 bp):
GAGTGTGAACA
Found at i:5616000 original size:30 final size:30
Alignment explanation
Indices: 5615964--5616053 Score: 171
Period size: 30 Copynumber: 3.0 Consensus size: 30
5615954 TAATAAGGTT
5615964 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
5615994 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
*
5616024 ATTTATTTTAAAATAAATTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
5616054 TGGATTGATT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:5616073 original size:52 final size:47
Alignment explanation
Indices: 5615941--5616230 Score: 200
Period size: 54 Copynumber: 5.9 Consensus size: 47
5615931 TATTAAAATA
*
5615941 ATTTTAAATAA-TT-T-AATAAGG-TT-ATTTATTTTAAAATAATTT
1 ATTTTAAATAATTTATAAATATGGATTGATTTATTTTAAAATAATTT
* * ** * * *
5615983 ATTATAAAATAATTTAT---TTTAAAATAATTTATTATAAAATAATTT
1 ATT-TTAAATAATTTATAAATATGGATTGATTTATTTTAAAATAATTT
5616028 ATTTTAAAATAAATTATTATAAAATATGGATTGATTTATTTTAAAATAATTT
1 ATTTT-AAAT-AA-T-TTAT-AAATATGGATTGATTTATTTTAAAATAATTT
* * * *
5616080 ATTTTTAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAGATTGATTT
1 ATTTTAAATAATTTATAAATATGGATTGATTTATTTT-AAA-AT--A---ATTT
* *
5616134 ATTTTAAATAATTTATTAATATGTATTGATTTATTTTAAAATATGGATTGATTT
1 ATTTTAAATAATTTATAAATATGGATTGATTTATTTT-AAA-AT--A---ATTT
* *
5616188 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 ATTTTAAATAATTTATAAATATGGATTGATTTATTTTAAAATA
5616231 TGGATTGATT
Statistics
Matches: 205, Mismatches: 23, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
42 3 0.01
43 8 0.04
44 4 0.02
45 26 0.13
46 2 0.01
47 19 0.09
48 11 0.05
49 3 0.01
50 3 0.01
51 4 0.02
52 29 0.14
53 3 0.01
54 90 0.44
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (47 bp):
ATTTTAAATAATTTATAAATATGGATTGATTTATTTTAAAATAATTT
Found at i:5616091 original size:14 final size:15
Alignment explanation
Indices: 5615964--5616096 Score: 151
Period size: 15 Copynumber: 8.5 Consensus size: 15
5615954 TAATAAGGTT
5615964 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
5615979 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
5615994 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
5616009 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
5616024 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
5616039 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
5616058 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
*
5616076 ATTTATTTT-TAATA
1 ATTTATTTTAAAATA
5616090 ATTTATT
1 ATTTATT
5616097 AGTATGTATT
Statistics
Matches: 102, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
14 11 0.11
15 71 0.70
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:5616114 original size:32 final size:31
Alignment explanation
Indices: 5616076--5616224 Score: 118
Period size: 32 Copynumber: 5.3 Consensus size: 31
5616066 TTTTAAAATA
5616076 ATTTATTTTTAATAATTTATTAGTATGTATTG
1 ATTTATTTTTAATAATTTATTAGTATG-ATTG
5616108 ATTTA-TTTT-A-AA---A-TA-TA-GATTG
1 ATTTATTTTTAATAATTTATTAGTATGATTG
* *
5616130 ATTTATTTTAAATAATTTATTAATATGTATTG
1 ATTTATTTTTAATAATTTATTAGTATG-ATTG
5616162 ATTTA-TTTTAA-AA--TA-T-G---GATTG
1 ATTTATTTTTAATAATTTATTAGTATGATTG
*
5616184 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTTAATAATTTATTAGTAT-GATTG
5616216 ATTTATTTT
1 ATTTATTTT
5616225 AAAATATGGA
Statistics
Matches: 93, Mismatches: 4, Indels: 40
0.68 0.03 0.29
Matches are distributed among these distances:
22 18 0.19
23 10 0.11
24 5 0.05
25 4 0.04
26 3 0.03
27 2 0.02
28 4 0.04
29 4 0.04
30 5 0.05
31 10 0.11
32 28 0.30
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (31 bp):
ATTTATTTTTAATAATTTATTAGTATGATTG
Found at i:5616144 original size:54 final size:55
Alignment explanation
Indices: 5616076--5617079 Score: 484
Period size: 54 Copynumber: 18.4 Consensus size: 55
5616066 TTTTAAAATA
* *
5616076 ATTTATTTTTAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAG-ATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
* * *
5616130 ATTTATTTTAAATAATTTATTAATATGTATTGATTTATTTTAAAATAT-GGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
*
5616184 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-GGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
* * * *
5616238 ATTTA--TT--AT--TGTAGTT-GTATGTATTGATTTCTTTTAAATACTTTATTAGTATGG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAA-A---TA-TAGTATTG
* * *
5616292 ATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTA-TG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-TAGTATTG
* * * * ** *
5616345 AATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGTATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TT-AAAATATA-GTATTG
* * * *
5616398 ATTTCTTTTAAATACTTTATTAGTATGTATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-TAGTATTG
* * * ** * *
5616458 A-TTAATTT--AT--TTTA-AAATATGGATTGATTTATTATTATAGTTGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TTA-AAATATA-GTATTG
*
5616510 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTG-ATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
* *
5616564 ATTTATTTTAAA-ATATTGATTAGTATGGATTGATTTATTTTAAAATAT-GGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
* *
5616618 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-TAGTATTG
* * * * *
5616672 ATTGA-TTT--AT--TTTA-AAATATAGATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-TAGTATTG
* * * *
5616726 ATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAAATAT-GGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
* ** * * * *
5616774 ATTTATTTTAAAATATGAATTTATT--TAT---TTTAAATAATTTATTAGTAT-GAATTG
1 ATTTATTTT--AA-AT-AATTTATTAGTATGGATTGATTTATTTTA-AAATATAGTATTG
*
5616828 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAGATAT-GTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
* * ** *
5616882 ATTTA--TT--AT--TGTATTTGTATAAATTAATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-TAG--T--ATTG
*
5616940 ATTTAGTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-TAG--T--ATTG
*
5617004 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTG-ATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
5617058 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
5617080 TTGTAGTTGT
Statistics
Matches: 778, Mismatches: 93, Indels: 158
0.76 0.09 0.15
Matches are distributed among these distances:
48 73 0.09
49 13 0.02
50 18 0.02
51 6 0.01
52 32 0.04
53 29 0.04
54 387 0.50
55 41 0.05
56 8 0.01
57 20 0.03
58 42 0.05
59 7 0.01
60 11 0.01
61 2 0.00
62 4 0.01
63 2 0.00
64 83 0.11
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (55 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTATTG
Found at i:5616169 original size:22 final size:22
Alignment explanation
Indices: 5616151--5616195 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5616141 ATAATTTATT
*
5616151 AATATGTATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAA
5616173 AATATGGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAA
5616195 A
1 A
5616196 TAATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (22 bp):
AATATGGATTGATTTATTTTAA
Found at i:5616221 original size:18 final size:18
Alignment explanation
Indices: 5616198--5616245 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
5616188 ATTTTAAATA
*
5616198 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
5616216 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
5616238 ATTTATTA
1 ATTTATTA
5616246 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:5616296 original size:32 final size:31
Alignment explanation
Indices: 5616254--5616361 Score: 108
Period size: 32 Copynumber: 3.7 Consensus size: 31
5616244 TATTGTAGTT
* *
5616254 GTATGTATTGATTTCTTTTAAATACTTTATTA
1 GTATGGATTGATTTATTTTAAATA-TTTATTA
5616286 GTATGGATTGATTTATTTT--A-A---A--A
1 GTATGGATTGATTTATTTTAAATATTTATTA
5616309 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAAT-ATTTATTA
*
5616340 GTATGAATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
5616362 ATATGGATTG
Statistics
Matches: 63, Mismatches: 3, Indels: 20
0.73 0.03 0.23
Matches are distributed among these distances:
22 18 0.29
23 1 0.02
24 1 0.02
25 1 0.02
26 1 0.02
29 2 0.03
30 1 0.02
31 1 0.02
32 37 0.59
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (31 bp):
GTATGGATTGATTTATTTTAAATATTTATTA
Found at i:5616312 original size:22 final size:22
Alignment explanation
Indices: 5616287--5616329 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5616277 ACTTTATTAG
5616287 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
5616309 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
5616330 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:5616429 original size:32 final size:32
Alignment explanation
Indices: 5616388--5616473 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
5616378 TATTGTAGTT
* *
5616388 GTATGTATTGATTTCTTTTAAATACTTTATTA
1 GTATGTATTGATTTATTTTAAATAATTTATTA
5616420 GTATGTATTGATTTATTTTAAATAATTTATTA
1 GTATGTATTGATTTATTTTAAATAATTTATTA
* *
5616452 GTATGGATTAATTTATTTTAAA
1 GTATGTATTGATTTATTTTAAA
5616474 ATATGGATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (32 bp):
GTATGTATTGATTTATTTTAAATAATTTATTA
Found at i:5616441 original size:112 final size:109
Alignment explanation
Indices: 5616309--5617015 Score: 568
Period size: 112 Copynumber: 6.5 Consensus size: 109
5616299 TATTTTAAAA
5616309 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAAATATGGATTGAT
* *
5616374 TTATTATTGTAGTTGTATGTATTGATTTCTTTTAAATACTTTATTAG
65 TTATTATT-TA-TTGTATGTATTGATTTATTTTAAATAATTTATTAG
* *
5616421 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGAT
*
5616486 TTATTATTATAGTTGTATGAATTGATTTATTTTAAATAATTTATTAG
65 TTATTATT-TA-TTGTATGTATTGATTTATTTTAAATAATTTATTAG
*
5616533 TATGGATTGATTTATTTT--A-AA---A-TA-T-TGATTGATTTATTTTAAAATATTGATTAGTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATT-G-A
** * ** * * *
5616589 TGGATTGATTTATTTTAAAATATGGATTGA-TTT--ATTATTGTAGTT-G
64 TTTATT-ATTTATTGT-ATGTATTGATTTATTTTAAATAATT-TA-TTAG
*
5616635 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGAT
* * * *
5616700 TTATT-TTAAATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAA
65 TTATTATT---T-ATTGTA-T-GTATTGATTTATTTTAAATAATTTATTAG
* *
5616743 TATGGATTGATTTATTTT-AA-AA--TA-T-G---GATTGATTTATTTTAAAATATGAATTTATT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATTGATT
*
5616799 TATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAG
66 TA---T---T-ATTTATT-GTATGTATTGATTTATTTTAAATAATTTATTAG
* * *
5616851 TATGGATTGATTTATTTTAAGAT-ATGTATT-G-ATTTATT-ATTGTATTTGTATAAAT-T-AAT
1 TATGGATTGATTTATTTTAA-ATAATTTATTAGTA-TGATTGATT-TATTT-TA-AAATATGGAT
* * * *
5616910 TTATTTTAAATAATTTATTAGTATGGATTGATTTAGTTTAAATAATTTATTAG
61 TGA-TTT--ATTATTTATT-GTATGTATTGATTTATTTTAAATAATTTATTAG
5616963 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAA
5617016 TAATTTATTA
Statistics
Matches: 496, Mismatches: 39, Indels: 120
0.76 0.06 0.18
Matches are distributed among these distances:
98 29 0.06
101 6 0.01
102 57 0.11
103 16 0.03
104 22 0.04
105 9 0.02
106 5 0.01
107 6 0.01
108 40 0.08
109 7 0.01
110 12 0.02
111 6 0.01
112 233 0.47
113 7 0.01
114 9 0.02
115 6 0.01
116 15 0.03
117 6 0.01
118 4 0.01
119 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (109 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATTGATT
TATTATTTATTGTATGTATTGATTTATTTTAAATAATTTATTAG
Found at i:5616469 original size:22 final size:22
Alignment explanation
Indices: 5616444--5616494 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
5616434 ATTTTAAATA
*
5616444 ATTTATTAGTATGGATTAATTT
1 ATTTATTAATATGGATTAATTT
* *
5616466 ATTT-TAAAATATGGATTGATTT
1 ATTTAT-TAATATGGATTAATTT
5616488 A-TTATTA
1 ATTTATTA
5616495 TAGTTGTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
ATTTATTAATATGGATTAATTT
Found at i:5616484 original size:134 final size:137
Alignment explanation
Indices: 5616125--5617015 Score: 734
Period size: 134 Copynumber: 6.6 Consensus size: 137
5616115 TTAAAATATA
* ** *
5616125 GATTGATTTATTTTAAATAATTTATTAATATGTATTGATTTATTTTAAA-ATATGGATT-G-ATT
1 GATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAATA-ATTTATTAGTATG
* * ** * * *
5616187 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTGATTTA-TT-AT-T
64 GA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTATAAATATGGATTGATTTATTTAATAT
*
5616248 GTAGTT-GTATG
127 TTA-TTAGTATG
* * * ** *
5616259 TATTGATTTCTTTTAAATACTTTATTAGTATGGATTGATTTATTTTAAA-ATATGGATT-G-ATT
1 GATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAATA-ATTTATTAGTATG
* * ** * * * *
5616321 TATTTTAAATAATTTATTAGTATGAATTGATTTATTTTA-AAATATGGATTGATTTA-TT-AT-T
64 GA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTATAAATATGGATTGATTTATTTAATAT
*
5616382 GTAGTT-GTATG
127 TTA-TTAGTATG
* * *
5616393 TATTGATTTCTTTTAAATACTTTATTAGTATGTATTGATTTATTTTAAATAATTTATTAGTATGG
1 GATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAATAATTTATTAGTATGG
* ** *
5616458 ATTAATTTATTTTAAAATATGGATTGATTTATTATTATAGTTGTATGAATTGATTTATTTTAAAT
65 ATTGATTTATTTTAAAATATGGATTGATTTATT-TTATA--AATATGGATTGATTTA-TTT-AAT
5616523 AATTTATTAGTATG
125 -ATTTATTAGTATG
*
5616537 GATTGATTTATTTT--A-AA---A-TA-T-TGATTGATTTATTTTAAA-ATATTGATTAGTATGG
1 GATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAATA-ATTTATTAGTATGG
* **
5616592 ATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAAT
65 ATTGATTTATTTTAAAATATGGATTGATTTATT-TTATA--AATATGGATTGATTTA-TTT-AAT
5616657 AATTTATTAGTATG
125 -ATTTATTAGTATG
5616671 GATTGATTTATTTT--A-AA---A-TA-TA-GATTGATTTATTTTAAATAATTTATTAGTATGGA
1 GATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAATAATTTATTAGTATGGA
5616727 TTGATTTATTTTAAAATATGGATTGATTTATTTTA-AAATATGGATTGATTTATTT--TA---A-
66 TTGATTTATTTTAAAATATGGATTGATTTATTTTATAAATATGGATTGATTTATTTAATATTTAT
*
5616785 -AATATG
131 TAGTATG
* *
5616791 AATTTATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGG
1 GATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAATAATTTATTAGTATGG
* * *** ** *
5616856 ATTGATTTATTTTAAGATATGTATTGATTTATTATTGTATTTGTATAAATTAATTTATTTTAAAT
65 ATTGATTTATTTTAAAATATGGATTGATTTA-T-TT-TATAAATATGGATTGATTTA-TTT-AAT
5616921 AATTTATTAGTATG
125 -ATTTATTAGTATG
* *
5616935 GATTGATTTAGTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGA
1 GATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAATAATTTATTAGTATGG
5617000 ATTGATTTATTTTAAA
65 ATTGATTTATTTTAAA
5617016 TAATTTATTA
Statistics
Matches: 665, Mismatches: 48, Indels: 78
0.84 0.06 0.10
Matches are distributed among these distances:
120 17 0.03
122 2 0.00
123 2 0.00
125 1 0.00
126 2 0.00
127 2 0.00
128 2 0.00
129 4 0.01
130 75 0.11
131 1 0.00
132 3 0.00
133 6 0.01
134 395 0.59
135 21 0.03
136 5 0.01
137 2 0.00
138 15 0.02
139 1 0.00
140 2 0.00
141 1 0.00
142 4 0.01
143 2 0.00
144 99 0.15
145 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (137 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAATAATTTATTAGTATGGA
TTGATTTATTTTAAAATATGGATTGATTTATTTTATAAATATGGATTGATTTATTTAATATTTAT
TAGTATG
Found at i:5616542 original size:32 final size:31
Alignment explanation
Indices: 5616500--5616607 Score: 110
Period size: 32 Copynumber: 3.7 Consensus size: 31
5616490 TATTATAGTT
*
5616500 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAA-TTATTA
5616532 GTATGGATTGATTTATTTT--A-AA--A-TA
1 GTATGGATTGATTTATTTTAAATAATTATTA
5616557 -T-T-GATTGATTTATTTTAAA-ATATTGATTA
1 GTATGGATTGATTTATTTTAAATA-ATT-ATTA
5616586 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
5616608 ATATGGATTG
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
22 14 0.22
23 1 0.02
24 3 0.05
25 3 0.05
26 1 0.02
28 1 0.02
29 4 0.06
30 2 0.03
31 1 0.02
32 35 0.54
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (31 bp):
GTATGGATTGATTTATTTTAAATAATTATTA
Found at i:5616562 original size:22 final size:22
Alignment explanation
Indices: 5616537--5616584 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
5616527 TATTAGTATG
5616537 GATTGATTTATTTTAAAATATT
1 GATTGATTTATTTTAAAATATT
5616559 GATTGATTTATTTTAAAATATT
1 GATTGATTTATTTTAAAATATT
5616581 GATT
1 GATT
5616585 AGTATGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATT
Found at i:5616602 original size:22 final size:21
Alignment explanation
Indices: 5616577--5616650 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 21
5616567 TATTTTAAAA
5616577 TATTGATTAGTATGGATTGATT
1 TATT-ATTAGTATGGATTGATT
*
5616599 TATT-TTAAAATATGGATTGATT
1 TATTATT--AGTATGGATTGATT
5616621 TATTATTGTAGTTGTATGGATTGATT
1 TATTA-T-TA---GTATGGATTGATT
5616647 TATT
1 TATT
5616651 TTAAATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
20 2 0.05
22 21 0.50
23 1 0.02
24 1 0.02
25 1 0.02
26 16 0.38
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (21 bp):
TATTATTAGTATGGATTGATT
Found at i:5616675 original size:32 final size:32
Alignment explanation
Indices: 5616634--5616741 Score: 146
Period size: 32 Copynumber: 3.7 Consensus size: 32
5616624 TATTGTAGTT
5616634 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
5616666 GTATGGATTGATTTATTTT--A-AA---A-TA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
5616691 -TA--GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
5616720 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
5616742 ATATGGATTG
Statistics
Matches: 66, Mismatches: 0, Indels: 20
0.77 0.00 0.23
Matches are distributed among these distances:
22 14 0.21
24 3 0.05
25 4 0.06
26 1 0.02
28 1 0.02
29 4 0.06
30 3 0.05
32 36 0.55
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:5616696 original size:22 final size:22
Alignment explanation
Indices: 5616671--5616807 Score: 132
Period size: 22 Copynumber: 5.8 Consensus size: 22
5616661 TATTAGTATG
5616671 GATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAAATATA
5616693 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTT-AA-AA--TA-TA
* *
5616720 GTATGGATTGATTTATTTTAAAATATG
1 G-ATTGA-T---TTATTTTAAAATATA
*
5616747 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATA
5616769 GATTGATTTATTTTAAAATAT-
1 GATTGATTTATTTTAAAATATA
*
5616790 GAATTTATTTATTTTAAA
1 G-ATTGATTTATTTTAAA
5616808 TAATTTATTA
Statistics
Matches: 100, Mismatches: 4, Indels: 22
0.79 0.03 0.17
Matches are distributed among these distances:
21 1 0.01
22 65 0.65
23 2 0.02
24 2 0.02
25 1 0.01
26 6 0.06
27 5 0.05
28 6 0.06
29 1 0.01
30 2 0.02
31 2 0.02
32 7 0.07
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:5616771 original size:44 final size:44
Alignment explanation
Indices: 5616721--5616807 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
5616711 AATTTATTAG
*
5616721 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAA
*
5616765 TATGGATTGATTTATTTTAAAATATGAATTTATTTATTTTAAA
1 TATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAA
5616808 TAATTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (44 bp):
TATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAA
Found at i:5616783 original size:98 final size:100
Alignment explanation
Indices: 5616667--5616953 Score: 346
Period size: 98 Copynumber: 2.8 Consensus size: 100
5616657 AATTTATTAG
*
5616667 TATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATAGATTAATTTATTTTAAATAATTTATTAGTATGGATTGAT
5616732 TTATTTTAAA-A-TATGGATTGATTTATTTTAAAA
66 TTATTTTAAATAGTATGGATTGATTTATTTTAAAA
* *
5616765 TATGGATTGATTTATTTTAAAATAT-GAATTTATTTATTTTAAATAATTTATTAGTATGAATTGA
1 TATGGATTGATTTATTTTAAAATATAG-ATTAATTTATTTTAAATAATTTATTAGTATGGATTGA
*
5616829 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAGA
65 TTTA-TTT---TAA---A-TAGTATGGATTGATTTATTTTAAAA
* *** *
5616873 TATGTATTGATTTATTATTGTATTTGTATAAATTAATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTA-T-TT-TA-AAATATAGATTAATTTATTTTAAATAATTTATTAGTATGGAT
*
5616938 TGATTTAGTTTAAATA
62 TGATTTATTTTAAATA
5616954 ATTTATTAGT
Statistics
Matches: 162, Mismatches: 11, Indels: 26
0.81 0.06 0.13
Matches are distributed among these distances:
97 1 0.01
98 64 0.40
99 3 0.02
102 3 0.02
104 2 0.01
105 2 0.01
107 1 0.01
108 37 0.23
109 1 0.01
110 2 0.01
111 4 0.02
112 42 0.26
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (100 bp):
TATGGATTGATTTATTTTAAAATATAGATTAATTTATTTTAAATAATTTATTAGTATGGATTGAT
TTATTTTAAATAGTATGGATTGATTTATTTTAAAA
Found at i:5616812 original size:18 final size:18
Alignment explanation
Indices: 5616791--5616848 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
5616781 TTAAAATATG
5616791 AATTTATTTATTTTAAAT
1 AATTTATTTATTTTAAAT
*
5616809 AATTTA-TTA--GT--AT
1 AATTTATTTATTTTAAAT
*
5616822 GAATTGATTTATTTTAAAT
1 -AATTTATTTATTTTAAAT
5616841 AATTTATT
1 AATTTATT
5616849 AGTATGGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
13 2 0.07
14 5 0.17
15 4 0.13
17 4 0.13
18 13 0.43
19 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
AATTTATTTATTTTAAAT
Found at i:5616813 original size:14 final size:14
Alignment explanation
Indices: 5616796--5616848 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
5616786 ATATGAATTT
5616796 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
5616810 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
5616828 ATTTATTTTAAATA
1 ATTTATTTTAAATA
5616842 ATTTATT
1 ATTTATT
5616849 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:5616832 original size:32 final size:32
Alignment explanation
Indices: 5616787--5616870 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
5616777 TATTTTAAAA
*
5616787 TATGAATTTATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
5616819 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
*
5616851 TATGGATTGATTTATTTTAA
1 TATGAATTGATTTATTTTAA
5616871 GATATGTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (32 bp):
TATGAATTGATTTATTTTAAATAATTTATTAG
Found at i:5616863 original size:18 final size:19
Alignment explanation
Indices: 5616842--5616889 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
5616832 ATTTTAAATA
5616842 ATTTATTAG-TATGGATTG
1 ATTTATTAGATATGGATTG
*
5616860 ATTTATTTTAAGATATGTATTG
1 ATTTA--TT-AGATATGGATTG
5616882 ATTTATTA
1 ATTTATTA
5616890 TTGTATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 5 0.20
19 1 0.04
20 4 0.16
21 2 0.08
22 13 0.52
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
ATTTATTAGATATGGATTG
Found at i:5616923 original size:14 final size:15
Alignment explanation
Indices: 5616901--5617024 Score: 58
Period size: 14 Copynumber: 7.9 Consensus size: 15
5616891 TGTATTTGTA
5616901 TAAATTAATTTATTT
1 TAAATTAATTTATTT
5616916 TAAA-TAATTTATTAGT
1 TAAATTAATTTATT--T
** * *
5616932 ATGGATTGATTTAGTT
1 -TAAATTAATTTATTT
5616948 TAAA-TAATTTATTAGT
1 TAAATTAATTTATT--T
** *
5616964 ATGGATTGATTTATTT
1 -TAAATTAATTTATTT
5616980 TAAA-TAATTTATTAGT
1 TAAATTAATTTATT--T
* *
5616996 ATGAATTGATTTATTT
1 -TAAATTAATTTATTT
5617012 TAAA-TAATTTATT
1 TAAATTAATTTATT
5617025 AGTATGGATT
Statistics
Matches: 79, Mismatches: 18, Indels: 25
0.65 0.15 0.20
Matches are distributed among these distances:
14 32 0.41
15 11 0.14
16 6 0.08
17 7 0.09
18 23 0.29
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (15 bp):
TAAATTAATTTATTT
Found at i:5616943 original size:18 final size:18
Alignment explanation
Indices: 5616922--5617042 Score: 70
Period size: 18 Copynumber: 7.4 Consensus size: 18
5616912 ATTTTAAATA
*
5616922 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
*
5616940 ATTTAGTT--TA--AA-TA
1 ATTTA-TTAGTATGAATTG
*
5616954 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
* *
5616972 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
5616986 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
5617004 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
5617018 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
5617036 ATTTATT
1 ATTTATT
5617043 TTAAAATATT
Statistics
Matches: 75, Mismatches: 14, Indels: 28
0.64 0.12 0.24
Matches are distributed among these distances:
13 2 0.03
14 25 0.33
15 5 0.07
16 4 0.05
17 5 0.07
18 32 0.43
19 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:5616950 original size:32 final size:32
Alignment explanation
Indices: 5616908--5617047 Score: 262
Period size: 32 Copynumber: 4.4 Consensus size: 32
5616898 GTATAAATTA
5616908 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
5616940 ATTTAGTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
5616972 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
5617004 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
5617036 ATTTATTTTAAA
1 ATTTATTTTAAA
5617048 ATATTGATTG
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 104 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:5617129 original size:31 final size:31
Alignment explanation
Indices: 5617094--5617153 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
5617084 AGTTGTATGG
* *
5617094 ATTATTTAAATTTCAGTATTGTAAAATTAAA
1 ATTATTTAAATCTCAGTATTGCAAAATTAAA
5617125 ATTATTTAAATCTCAGTATTGCAAAATTA
1 ATTATTTAAATCTCAGTATTGCAAAATTA
5617154 TTTTAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAATTAAA
Found at i:5618003 original size:2 final size:2
Alignment explanation
Indices: 5617996--5618027 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5617986 TTAATTTGTG
5617996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5618028 ATTAGATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5620591 original size:39 final size:39
Alignment explanation
Indices: 5620537--5620628 Score: 148
Period size: 39 Copynumber: 2.4 Consensus size: 39
5620527 TCTATGACTA
* *
5620537 CTAAGTCCTTACCGCATGCTCATCTGCTTTGTGCTCAGG
1 CTAAGACCTTACCGCAGGCTCATCTGCTTTGTGCTCAGG
*
5620576 CTAAGACCTTACCGCAGGCTCCTCTGCTTTGTGCTCAGG
1 CTAAGACCTTACCGCAGGCTCATCTGCTTTGTGCTCAGG
*
5620615 CTAAGATCTTACCG
1 CTAAGACCTTACCG
5620629 TAGATCCTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.17, C:0.32, G:0.21, T:0.30
Consensus pattern (39 bp):
CTAAGACCTTACCGCAGGCTCATCTGCTTTGTGCTCAGG
Found at i:5621441 original size:20 final size:20
Alignment explanation
Indices: 5621399--5621441 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5621389 CCAAATTCGA
*
5621399 AACGCGAATATGTAAATCGC
1 AACGCGAATATGTAAATCAC
* *
5621419 AACGCGAATTTGTAATTCAC
1 AACGCGAATATGTAAATCAC
5621439 AAC
1 AAC
5621442 ACATAAGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (20 bp):
AACGCGAATATGTAAATCAC
Found at i:5622085 original size:20 final size:20
Alignment explanation
Indices: 5622062--5622099 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5622052 ATTCGTAACA
5622062 CGAAAATGAAAATCACAACG
1 CGAAAATGAAAATCACAACG
*
5622082 CGAAAATGAAAATTACAA
1 CGAAAATGAAAATCACAA
5622100 TATGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (20 bp):
CGAAAATGAAAATCACAACG
Found at i:5622136 original size:20 final size:19
Alignment explanation
Indices: 5622102--5622154 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5622092 AATTACAATA
5622102 TGATTTTAGTTTCGCGTTG
1 TGATTTTAGTTTCGCGTTG
*
5622121 TGATTTTCATTTTCGCGTTG
1 TGATTTT-AGTTTCGCGTTG
* *
5622141 CGAATTTAAGTTTC
1 TG-ATTTTAGTTTC
5622155 AGAAACTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 7 0.25
20 17 0.61
21 4 0.14
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (19 bp):
TGATTTTAGTTTCGCGTTG
Found at i:5623574 original size:3 final size:3
Alignment explanation
Indices: 5623568--5623623 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
5623558 TTTTTATCCA
*
5623568 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5623616 TAT TAT TA
1 TAT TAT TA
5623624 AATATATTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5623663 original size:20 final size:19
Alignment explanation
Indices: 5623622--5623679 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
5623612 CTATTATTAT
* *
5623622 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
5623641 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
*
5623661 TAAATA-A-TAAAAAAAAA
1 TAAATATATTAAAAACAAA
5623678 TA
1 TA
5623680 TAATTACAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 11 0.32
18 1 0.03
19 6 0.18
20 16 0.47
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:5625059 original size:19 final size:19
Alignment explanation
Indices: 5625021--5625056 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5625011 AAATTTAGTC
5625021 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
5625040 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
5625057 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:5636501 original size:7 final size:7
Alignment explanation
Indices: 5636457--5636501 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
5636447 ATTATGTTTG
5636457 AAGAAAA
1 AAGAAAA
5636464 AA-AAAA
1 AAGAAAA
5636470 AAGGAAAA
1 AA-GAAAA
5636478 AAGAAAA
1 AAGAAAA
5636485 AAG-AAA
1 AAGAAAA
5636491 AAGAAAA
1 AAGAAAA
5636498 AAGA
1 AAGA
5636502 GGGTCAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.34
7 17 0.49
8 6 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:5636501 original size:13 final size:13
Alignment explanation
Indices: 5636457--5636501 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
5636447 ATTATGTTTG
*
5636457 AAGAAAAAAAAAA
1 AAGAAAAAGAAAA
5636470 AAGGAAAAAAGAAAA
1 AA-G-AAAAAGAAAA
5636485 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
5636498 AAGA
1 AAGA
5636502 GGGTCAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 16 0.55
14 2 0.07
15 11 0.38
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:5636862 original size:19 final size:20
Alignment explanation
Indices: 5636829--5636867 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5636819 TTCAAGTTCA
*
5636829 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
5636849 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
5636868 TTTCTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:5637737 original size:83 final size:81
Alignment explanation
Indices: 5637436--5638215 Score: 1204
Period size: 81 Copynumber: 9.5 Consensus size: 81
5637426 TTATATGGGT
* *
5637436 TCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAGCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
*
5637501 ATTTGGAAGATGAATG
66 ATTTAGAAGATGAATG
*
5637517 TCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
5637582 A-TTAGGAAGATGAATG
66 ATTTA-GAAGATGAATG
5637598 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
* *
5637663 ATATATAAGATGAATGG
66 ATTTAGAAGATGAAT-G
* * * *
5637680 CTCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATAAAACCAATCATTG
1 -TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTG
*
5637745 AATTTGGAAGATGAATG
65 AATTTAGAAGATGAATG
*
5637762 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
* *
5637827 ATATATAAGATGAATGG
66 ATTTAGAAGATGAAT-G
* * * *
5637844 CTCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATAAAACCAATCATTG
1 -TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTG
*
5637909 AATTTATAAGATGAATGG
65 AATTTAGAAGATGAAT-G
* *
5637927 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAAGCATTG
1 -TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTG
*
5637992 AATTTATAAGATGAATGG
65 AATTTAGAAGATGAAT-G
*
5638010 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTAGACAGAACCAATCATTG
1 -TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTG
5638075 AA-TTAGGAAGATGAATG
65 AATTTA-GAAGATGAATG
* * *
5638092 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATAAAACCAATCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
5638157 ATTTAGAAGATGAATG
66 ATTTAGAAGATGAATG
* *
5638173 TCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTG
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
5638216 ATTCAGTAGG
Statistics
Matches: 650, Mismatches: 41, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
80 2 0.00
81 335 0.52
82 12 0.02
83 301 0.46
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (81 bp):
TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
ATTTAGAAGATGAATG
Found at i:5637766 original size:164 final size:164
Alignment explanation
Indices: 5637436--5638215 Score: 1255
Period size: 164 Copynumber: 4.8 Consensus size: 164
5637426 TTATATGGGT
* *
5637436 TCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAGCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
** *
5637501 ATTTGGAAGATGAAT-G-TCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTA
66 ATTTATAAGATGAATGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTA
*
5637564 GACAGAACCAATCATTGAATTAGGAAGATGAATG
131 GACAAAACCAATCATTGAATTAGGAAGATGAATG
5637598 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
* * *
5637663 ATATATAAGATGAATGGCTCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
66 ATTTATAAGATGAATGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTA
* *
5637728 GATAAAACCAATCATTGAATTTGGAAGATGAATG
131 GACAAAACCAATCATTGAATTAGGAAGATGAATG
*
5637762 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
* * *
5637827 ATATATAAGATGAATGGCTCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
66 ATTTATAAGATGAATGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTA
* *
5637892 GATAAAACCAATCATTGAATTTA-TAAGATGAATGG
131 GACAAAACCAATCATTGAA-TTAGGAAGATGAAT-G
* *
5637927 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAAGCATTG
1 -TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTG
*
5637992 AATTTATAAGATGAATGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTT
65 AATTTATAAGATGAATGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
*
5638057 AGACAGAACCAATCATTGAATTAGGAAGATGAATG
130 AGACAAAACCAATCATTGAATTAGGAAGATGAATG
* * *
5638092 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATAAAACCAATCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
* * *
5638157 ATTTAGAAGATGAAT-G-TCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTG
66 ATTTATAAGATGAATGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
5638216 ATTCAGTAGG
Statistics
Matches: 580, Mismatches: 32, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
162 115 0.20
163 2 0.00
164 305 0.53
165 7 0.01
166 151 0.26
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (164 bp):
TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
ATTTATAAGATGAATGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTA
GACAAAACCAATCATTGAATTAGGAAGATGAATG
Found at i:5639146 original size:113 final size:113
Alignment explanation
Indices: 5638949--5639459 Score: 898
Period size: 113 Copynumber: 4.5 Consensus size: 113
5638939 CAAAGATTCA
* *
5638949 AATCCATCATTTGATGGATCAGCTTTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCCGAAG
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAG
*
5639013 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
5639062 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
5639127 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
5639175 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
5639240 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
5639288 AATTCATCACTTGATGGATCATTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
5639353 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
5639401 AATTCATCATTTGATGGATCATCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATC
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
5639460 AAGAGCTTAT
Statistics
Matches: 382, Mismatches: 15, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
113 380 0.99
114 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:5639710 original size:3 final size:3
Alignment explanation
Indices: 5639704--5639747 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
5639694 TTTTTATCCA
*
5639704 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5639748 AATATATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5639787 original size:20 final size:19
Alignment explanation
Indices: 5639746--5639790 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5639736 CTATTATTAT
* *
5639746 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
5639765 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
5639785 TAAATA
1 TAAATA
5639791 AAAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:5641978 original size:42 final size:42
Alignment explanation
Indices: 5641919--5642015 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
5641909 CCCCACTTCG
* * * *
5641919 AGAGCCATCACCTGATCGAGCCGATTCTACAGCTAGACACCC
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTACACAACC
* *
5641961 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACG
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTACACAACC
5642003 AGAGCCATCACCT
1 AGAGCCATCACCT
5642016 ATTCTATCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.16
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGAGCCGATTATACACCTACACAACC
Found at i:5642157 original size:21 final size:21
Alignment explanation
Indices: 5642130--5642179 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5642120 GTTAGGAGAG
* *
5642130 TTACGTGATGAGGTCAGTGCT
1 TTACGTGAGGAGGTCAGTACT
* *
5642151 TTGCGTGAGGAGGTCGGTACT
1 TTACGTGAGGAGGTCAGTACT
5642172 TTACGTGA
1 TTACGTGA
5642180 CAATAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAGTACT
Found at i:5642631 original size:21 final size:21
Alignment explanation
Indices: 5642605--5642698 Score: 152
Period size: 21 Copynumber: 4.5 Consensus size: 21
5642595 GGTCCCCTAT
*
5642605 CGTTCAATAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
5642626 CGTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
* * *
5642647 CGTTCAAGAGGCCCATCTCAT
1 CGTTCAAGAGGCCCCTCCCAC
5642668 CGTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
5642689 CGTTCAAGAG
1 CGTTCAAGAG
5642699 CCAATTCACA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.21, C:0.41, G:0.19, T:0.18
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:5644259 original size:20 final size:20
Alignment explanation
Indices: 5644234--5644279 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5644224 GCGTTGCGAT
*
5644234 TTTCGCGTTGCAAATTTTAC
1 TTTCGCGTTGCAAATTTGAC
* * *
5644254 TTTCGCTTTTCGAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
5644274 TTTCGC
1 TTTCGC
5644280 AACAATCGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTGAC
Found at i:5644298 original size:29 final size:29
Alignment explanation
Indices: 5644264--5644320 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
5644254 TTTCGCTTTT
5644264 CGAATTTGACTTTCGCAACAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
5644293 CGAATTTGACTTTCGCAACAATCGCAAC
1 CGAATTTGACTTTCGCAACAATCGCAAC
5644321 AAAAAATCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAACG
Found at i:5647072 original size:12 final size:12
Alignment explanation
Indices: 5647051--5647084 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5647041 GGTTGTGGGT
*
5647051 TTTGAGATTGTG
1 TTTGATATTGTG
5647063 TTTGATATTGTG
1 TTTGATATTGTG
*
5647075 TTTGGTATTG
1 TTTGATATTG
5647085 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:5647897 original size:20 final size:20
Alignment explanation
Indices: 5647849--5647900 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
5647839 TACCCAAAAC
5647849 ATTTGTGTTGCGAAAATAAA
1 ATTTGTGTTGCGAAAATAAA
** *
5647869 A--CCTGTTGCGAAATTAAA
1 ATTTGTGTTGCGAAAATAAA
5647887 ATTTGTGTTGCGAA
1 ATTTGTGTTGCGAA
5647901 TTCGAAAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 15 0.60
20 10 0.40
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (20 bp):
ATTTGTGTTGCGAAAATAAA
Found at i:5647916 original size:20 final size:19
Alignment explanation
Indices: 5647893--5647962 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
5647883 TAAAATTTGT
5647893 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTC-AAAATCGA
**
5647913 GTTGCGAAAACAAAATTCGCA
1 GTTGCGAATTCAAAA-TCG-A
*
5647934 -TTGCGAATTCAGAAATTGA
1 GTTGCGAATTCA-AAATCGA
*
5647953 GTTGTGAATT
1 GTTGCGAATT
5647963 TGAAATTCAG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 5 0.12
20 31 0.77
21 4 0.10
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (19 bp):
GTTGCGAATTCAAAATCGA
Found at i:5649592 original size:2 final size:2
Alignment explanation
Indices: 5649587--5649620 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5649577 ATTTTTTATC
5649587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5649621 TAATCTAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5653307 original size:24 final size:24
Alignment explanation
Indices: 5653279--5653329 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
5653269 TGCGAGAGAA
5653279 GAAGAGTAATCGAAGAAAATAGAG
1 GAAGAGTAATCGAAGAAAATAGAG
* *
5653303 GAAGAGTGATCGAATAAAATAGAG
1 GAAGAGTAATCGAAGAAAATAGAG
5653327 GAA
1 GAA
5653330 ATAAAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.29, T:0.14
Consensus pattern (24 bp):
GAAGAGTAATCGAAGAAAATAGAG
Found at i:5657163 original size:21 final size:21
Alignment explanation
Indices: 5657137--5657189 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
5657127 ATACCCACAG
5657137 CAGTATCGATACTAATTGCAT
1 CAGTATCGATACTAATTGCAT
5657158 CAGTATCGATACTAATTGCAT
1 CAGTATCGATACTAATTGCAT
5657179 CAGTATCGATA
1 CAGTATCGATA
5657190 TTGTTCCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (21 bp):
CAGTATCGATACTAATTGCAT
Found at i:5660813 original size:65 final size:64
Alignment explanation
Indices: 5660665--5660821 Score: 219
Period size: 65 Copynumber: 2.4 Consensus size: 64
5660655 ACTAAGCGTA
* * * * *
5660665 CATCGATGCATCAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTATGTG
1 CATCGATGCATCAAATGCATTCGATGTTTTCAAAAAGCCCGAGTGCATAGATGCATGGAAAGTG
*
5660729 CATCGATGCATCAAATGCATTCGATGTTTTCATTAAAA-CCCGAGTGCATAGATGTATGGAAAGT
1 CATCGATGCATCAAATGCATTCGATGTTTTCA--AAAAGCCCGAGTGCATAGATGCATGGAAAGT
5660793 G
64 G
5660794 CATCGATGCAT-AAACTGCATTCGATGTT
1 CATCGATGCATCAAA-TGCATTCGATGTT
5660822 CAATTTATTC
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
64 34 0.40
65 46 0.55
66 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (64 bp):
CATCGATGCATCAAATGCATTCGATGTTTTCAAAAAGCCCGAGTGCATAGATGCATGGAAAGTG
Found at i:5669565 original size:65 final size:64
Alignment explanation
Indices: 5669414--5669573 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 64
5669404 TGCACTAAGT
* * *
5669414 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAGCCCGAGTGCATCGATGCATGGTAA
*
5669478 GCGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAA-CCCGAGTGCATCGATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA--AAAAGCCCGAGTGCATCGATGCATGGTA
5669541 GA
64 -A
5669543 GTGCATCGATGCAT-AAACTGCATTCGATGTT
1 GTGCATCGATGCATCAAA-TGCATTCGATGTT
5669574 CAATTTATTC
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 37 0.43
65 46 0.53
66 4 0.05
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAGCCCGAGTGCATCGATGCATGGTAA
Found at i:5676271 original size:2 final size:2
Alignment explanation
Indices: 5676264--5676299 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5676254 TCCTAAAGAA
*
5676264 AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5676300 TAAGAATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5681114 original size:5 final size:5
Alignment explanation
Indices: 5681104--5681130 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5681094 GCAGACATAT
5681104 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AA
5681131 GTATTGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:5681552 original size:52 final size:52
Alignment explanation
Indices: 5681486--5681665 Score: 306
Period size: 52 Copynumber: 3.5 Consensus size: 52
5681476 TCTAGACAAA
* *
5681486 AGGCTATCTCTCGATGCTCTTACAATGCCCAAACATGTATTACCGAAACCCC
1 AGGCGATCTCTCGATGCTCTTACAATGCCCAAACATGTTTTACCGAAACCCC
* * *
5681538 AGACGATCTCTCGATGCTCTTACGATGCCCAAACATGTTTTACCAAAACCCC
1 AGGCGATCTCTCGATGCTCTTACAATGCCCAAACATGTTTTACCGAAACCCC
*
5681590 AGGCGATCTCTCGATCCTCTTACAATGCCCAAACATGTTTTACCGAAACCCC
1 AGGCGATCTCTCGATGCTCTTACAATGCCCAAACATGTTTTACCGAAACCCC
5681642 AGGCGATCTCTCGATGCTCTTACA
1 AGGCGATCTCTCGATGCTCTTACA
5681666 GTGTTAAGGT
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.26
Consensus pattern (52 bp):
AGGCGATCTCTCGATGCTCTTACAATGCCCAAACATGTTTTACCGAAACCCC
Found at i:5698462 original size:10 final size:9
Alignment explanation
Indices: 5698427--5698460 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
5698417 CCACATGTTC
5698427 AAAAAAATG
1 AAAAAAATG
5698436 AAAAAAATG
1 AAAAAAATG
5698445 AAAAAAATG
1 AAAAAAATG
5698454 AAAAAAA
1 AAAAAAA
5698461 ATTACGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:5701713 original size:51 final size:51
Alignment explanation
Indices: 5701651--5701751 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
5701641 TACATGTTTG
* * *
5701651 TTGATCCATTTATGGGTTATCAACATACGCTTCAGCATCCAGAAATAAAGT
1 TTGATCAATTTATGGGTTATCAACATACGCTTCAGCATCAAAAAATAAAGT
* *
5701702 TTGATCAATTTATGGGTTATCAGCATACGCTTCAGCGTCAAAAAATAAAG
1 TTGATCAATTTATGGGTTATCAACATACGCTTCAGCATCAAAAAATAAAG
5701752 GGTAATGAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (51 bp):
TTGATCAATTTATGGGTTATCAACATACGCTTCAGCATCAAAAAATAAAGT
Found at i:5703868 original size:24 final size:24
Alignment explanation
Indices: 5703836--5703888 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
5703826 CAATGGCGAT
5703836 GTCTAGACCTTGTTAGAATAAAGC
1 GTCTAGACCTTGTTAGAATAAAGC
*
5703860 GTCTAGACCTTGTTAGAATAAAGT
1 GTCTAGACCTTGTTAGAATAAAGC
5703884 GTCTA
1 GTCTA
5703889 ATACCTCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (24 bp):
GTCTAGACCTTGTTAGAATAAAGC
Found at i:5704581 original size:40 final size:38
Alignment explanation
Indices: 5704505--5704587 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 38
5704495 TATTTTAGGG
*
5704505 ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCT
1 ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCA
* * *
5704543 ACCAAAGATGAATTTTCTCATGTGTACAAGTTGGCCACCA
1 ACCAAAGATGAA-ATTCCCATGTGCA-AAGTTGGCCACCA
5704583 ACCAA
1 ACCAA
5704588 CTTGTTAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 12 0.31
39 10 0.26
40 17 0.44
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (38 bp):
ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCA
Found at i:5711541 original size:17 final size:16
Alignment explanation
Indices: 5711519--5711552 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5711509 TAAAAACAGT
5711519 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
5711536 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
5711552 A
1 A
5711553 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:5715377 original size:19 final size:20
Alignment explanation
Indices: 5715355--5715398 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5715345 GAGAAAAGGT
5715355 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
5715374 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
5715394 AAAAG
1 AAAAG
5715399 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:5721756 original size:17 final size:16
Alignment explanation
Indices: 5721734--5721767 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5721724 TAAAAACAGT
5721734 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
5721751 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
5721767 A
1 A
5721768 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:5730732 original size:20 final size:20
Alignment explanation
Indices: 5730707--5730799 Score: 83
Period size: 20 Copynumber: 5.0 Consensus size: 20
5730697 TTTGTTAGTT
5730707 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
5730727 ATTAGATAGAATCAGTTTT-
1 ATTAGATAGAATCAGTTTTA
** * *
5730746 -TTATTTTG--TTAG--TT-
1 ATTAGATAGAATCAGTTTTA
*
5730760 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
5730780 ATTAGATAGAATTAGTTTTA
1 ATTAGATAGAATCAGTTTTA
5730800 TTCTGTTGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
14 2 0.04
15 5 0.09
16 3 0.05
17 3 0.05
18 5 0.09
19 2 0.04
20 37 0.65
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.46
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:5730754 original size:53 final size:53
Alignment explanation
Indices: 5730691--5730798 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
5730681 TAACTAGATA
5730691 TTTTATTTTGTTAGTTATTAGATAGAATCAGTTTTAATTAGATAGAATCAGTT
1 TTTTATTTTGTTAGTTATTAGATAGAATCAGTTTTAATTAGATAGAATCAGTT
* *
5730744 TTTTATTTTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATTAGTT
1 TTTTATTTTGTTAGTTATTAGATAGAATCAGTTTTAATTAGATAGAATCAGTT
5730797 TT
1 TT
5730799 ATTCTGTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.51
Consensus pattern (53 bp):
TTTTATTTTGTTAGTTATTAGATAGAATCAGTTTTAATTAGATAGAATCAGTT
Found at i:5735345 original size:33 final size:33
Alignment explanation
Indices: 5735307--5735374 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
5735297 TAAATAGATA
*
5735307 TTTTATTTTGTTATTTATTAGATA-GAATCAGTT
1 TTTTATTTTGTTAGTTATTAGATATG-ATCAGTT
5735340 TTTTATTTTGTTAGTTATTAGATATGATCAGTT
1 TTTTATTTTGTTAGTTATTAGATATGATCAGTT
5735373 TT
1 TT
5735375 AATTAGATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.59
Consensus pattern (33 bp):
TTTTATTTTGTTAGTTATTAGATATGATCAGTT
Found at i:5737475 original size:5 final size:5
Alignment explanation
Indices: 5737465--5737496 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5737455 ATAAATTATC
5737465 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
5737497 TAACATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Done.