Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, 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: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 44 of 93
Found at i:5461467 original size:9 final size:8
Alignment explanation
Indices: 5461443--5461483 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
5461433 AAAAAATAAT
5461443 AATTAAAA
1 AATTAAAA
5461451 AATTAAAA
1 AATTAAAA
5461459 AATTAAAA
1 AATTAAAA
*
5461467 AAATAAAA
1 AATTAAAA
5461475 AA-TAAAA
1 AATTAAAA
5461482 AA
1 AA
5461484 CAAAAAGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 7 0.22
8 25 0.78
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AATTAAAA
Found at i:5461474 original size:6 final size:7
Alignment explanation
Indices: 5461431--5461489 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
5461421 TATTAATTCT
5461431 ATAAAAA
1 ATAAAAA
*
5461438 ATAATAA
1 ATAAAAA
*
5461445 TTAAAAA
1 ATAAAAA
5461452 ATTAAAAA
1 A-TAAAAA
5461460 ATTAAAAAA
1 A-T-AAAAA
5461469 ATAAAAA
1 ATAAAAA
5461476 ATAAAAA
1 ATAAAAA
*
5461483 ACAAAAA
1 ATAAAAA
5461490 GTAGGGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
7 29 0.64
8 10 0.22
9 6 0.13
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.19
Consensus pattern (7 bp):
ATAAAAA
Found at i:5466006 original size:35 final size:35
Alignment explanation
Indices: 5465918--5466058 Score: 115
Period size: 35 Copynumber: 3.9 Consensus size: 35
5465908 CTAATGCGAT
* * *
5465918 GTGCATGAGATGTAATGTATGTATTATCTATTAAG
1 GTGCATGAGATGGAATGCATGTATTATCTATTAGG
* * * * *
5465953 ATGCCTGAAATATG-ATGCATGTACTATCTATTAGG
1 GTGCATGAGAT-GGAATGCATGTATTATCTATTAGG
* *
5465988 GTGCATGAGATGGAATGCATATATTATCTTATTATGAT
1 GTGCATGAGATGGAATGCATGTATTATC-TATTA-G-G
* *
5466026 GTGCATGAGATGG-GTACATGTATTATCGTATTA
1 GTGCATGAGATGGAATGCATGTATTATC-TATTA
5466059 CTTTTATTTT
Statistics
Matches: 82, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
34 1 0.01
35 46 0.56
36 5 0.06
37 17 0.21
38 13 0.16
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (35 bp):
GTGCATGAGATGGAATGCATGTATTATCTATTAGG
Found at i:5468717 original size:22 final size:24
Alignment explanation
Indices: 5468689--5468740 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
5468679 ACTAAAACTT
*
5468689 TTTTTCCTC-TT-TTTTTTTTTTC
1 TTTTTCCTCATTATTTTTCTTTTC
5468711 TTTTTCCTCATTCATTTTTCTTTTC
1 TTTTTCCTCATT-ATTTTTCTTTTC
5468736 TTTTT
1 TTTTT
5468741 TTTTCTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 2 0.08
25 15 0.58
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTCCTCATTATTTTTCTTTTC
Found at i:5469171 original size:3 final size:3
Alignment explanation
Indices: 5469156--5469214 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
5469146 TTGATTTTTG
*
5469156 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5469204 TTA TTA TTA TT
1 TTA TTA TTA TT
5469215 GTCATTGTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5469422 original size:21 final size:22
Alignment explanation
Indices: 5469373--5469423 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
5469363 AATTTGGATT
*
5469373 AAAGGGTTTAATTAATATAGTT
1 AAAGGGTTTAATTAATATAGTC
*
5469395 AAA-GGTTTAAATTCATA-A-TC
1 AAAGGGTTT-AATTAATATAGTC
5469415 AAAGGGTTT
1 AAAGGGTTT
5469424 TTGGATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (22 bp):
AAAGGGTTTAATTAATATAGTC
Found at i:5470116 original size:5 final size:5
Alignment explanation
Indices: 5470088--5470163 Score: 55
Period size: 6 Copynumber: 14.0 Consensus size: 5
5470078 GAATCGTAGG
* *
5470088 TTTT- TTTTT TTTCTA TTTTAA TTTTA TTTTT TATTTA TTTTATA TTTTGA
1 TTTTA TTTTA TTT-TA TTTT-A TTTTA TTTTA T-TTTA -TTT-TA TTTT-A
*
5470138 TTTTGA TTTTA ATTTA TTTTA TTTTA
1 TTTT-A TTTTA TTTTA TTTTA TTTTA
5470164 CTGGTTTCTA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.07
5 25 0.42
6 28 0.47
7 3 0.05
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:5470448 original size:20 final size:20
Alignment explanation
Indices: 5470395--5470448 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 20
5470385 GGAAAGTTTT
*
5470395 ATAAATAAATTTCAAAAAAATA
1 ATAAAT-AA-TTCAATAAAATA
*
5470417 AAAAATAA---AATAAAATA
1 ATAAATAATTCAATAAAATA
5470434 ATAAATAATTCAATA
1 ATAAATAATTCAATA
5470449 TTTCAAGCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
17 15 0.58
20 4 0.15
21 2 0.08
22 5 0.19
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAAATAATTCAATAAAATA
Found at i:5471087 original size:64 final size:63
Alignment explanation
Indices: 5470926--5471294 Score: 269
Period size: 64 Copynumber: 5.8 Consensus size: 63
5470916 TTTGTAGATA
* * * * * * * * ** *
5470926 GATTATTAAAGGTGTTTTTAGCCAAAACTACCTCCAATAATCCATTCCAAAA-TTTTTCAAGG
1 GATTATTAAAGGCGTTTTTTGTCAAAAATGCCTTCAATAATCCCTTCAAAAATTTTTTGTATG
* * * * *** *
5470988 GACTATTGAAGGCGTTTTTAGCCAAAAACATCTTTAATAATCCCTTCAATAAATTTTTATG-A-G
1 GATTATTAAAGGCGTTTTTTGTCAAAAATGCCTTCAATAATCCCTTCAA-AAATTTTT-TGTATG
* * * * *
5471051 AGATTATCAAAGGTGTTTTTTGTCGAAAATGCCTTTAATAATCCCCTTAATAAAATTTTTTGTAT
1 -GATTATTAAAGGCGTTTTTTGTCAAAAATGCCTTCAATAAT-CCCTTCA-AAAATTTTTTGTAT
5471116 G
63 G
* * * ** *
5471117 GATTATTAAAGGCG-CTTTTGTCCAAAAACGCATTCAATAATAACTTCTAAAATTTTTTGTATG
1 GATTATTAAAGGCGTTTTTTGT-CAAAAATGCCTTCAATAATCCCTTCAAAAATTTTTTGTATG
* * * * * * *
5471180 GATTATTGAAGGCATTTTTAGTCGAAAATACCTTCAATAATCCCTCTCCAAAATTTTTTGAATG
1 GATTATTAAAGGCGTTTTTTGTCAAAAATGCCTTCAATAATCCCT-TCAAAAATTTTTTGTATG
* * * *
5471244 GATTATTGAAGGTGTTTTTGGCCAAAAATGCCTTCAATAATCCCATTCAAA
1 GATTATTAAAGGCGTTTTTTGTCAAAAATGCCTTCAATAATCCC-TTCAAA
5471295 TTTTTGTAAG
Statistics
Matches: 243, Mismatches: 52, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
62 39 0.16
63 48 0.20
64 110 0.45
65 44 0.18
66 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (63 bp):
GATTATTAAAGGCGTTTTTTGTCAAAAATGCCTTCAATAATCCCTTCAAAAATTTTTTGTATG
Found at i:5476251 original size:15 final size:15
Alignment explanation
Indices: 5476212--5476252 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5476202 TTTCTCAATT
* *
5476212 CAATATCATAAGATG
1 CAATATCATGAGATA
*
5476227 CATTATCATGAGATA
1 CAATATCATGAGATA
5476242 CAATATCATGA
1 CAATATCATGA
5476253 CTACGATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (15 bp):
CAATATCATGAGATA
Found at i:5489417 original size:36 final size:36
Alignment explanation
Indices: 5489377--5489447 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
5489367 GTAAGATGTA
* * *
5489377 CATGAGATAGAATGCATGTAATACTATCAAGATATG
1 CATGAAATAGAATCCATGCAATACTATCAAGATATG
* *
5489413 CATGAAATGGAATCCATGCACTACTATCAAGATAT
1 CATGAAATAGAATCCATGCAATACTATCAAGATAT
5489448 ATATATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (36 bp):
CATGAAATAGAATCCATGCAATACTATCAAGATATG
Found at i:5491665 original size:41 final size:41
Alignment explanation
Indices: 5491620--5491706 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
5491610 AAAAAGTTTT
* *
5491620 TTAATAAATTATCAATTAAGGCATTTCAATGAA-GAAATGCC
1 TTAATAAATGATCAATTAAGGCATTT-AATGAACAAAATGCC
** * *
5491661 TTAATTGATGATCAATTAAGGCGTTTGATGAACAAAATGCC
1 TTAATAAATGATCAATTAAGGCATTTAATGAACAAAATGCC
5491702 TTAAT
1 TTAAT
5491707 TGATGCATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 5 0.13
41 34 0.87
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (41 bp):
TTAATAAATGATCAATTAAGGCATTTAATGAACAAAATGCC
Found at i:5491707 original size:41 final size:41
Alignment explanation
Indices: 5491630--5491815 Score: 142
Period size: 41 Copynumber: 4.4 Consensus size: 41
5491620 TTAATAAATT
* * *
5491630 ATCAATTAAGGCATTTCAATGAA-GAAATGCCTTAATTGATG
1 ATCAATTAAGGCATTT-GATGAACAAAATACCTTAATTGATG
* *
5491671 ATCAATTAAGGCGTTTGATGAACAAAATGCCTTAATTGATG
1 ATCAATTAAGGCATTTGATGAACAAAATACCTTAATTGATG
* * * ** * *
5491712 CATTCATCAATTTAAGACATTTCATGCATGAAACACCATAATTGATG
1 -----ATCAA-TTAAGGCATTTGATGAACAAAATACCTTAATTGATG
* * * *
5491759 ATTAATTAAGGCGTTTG-TGTACAAAAATACCTTAATTGATC
1 ATCAATTAAGGCATTTGATGAAC-AAAATACCTTAATTGATG
5491800 ATCAATTAAGGCATTT
1 ATCAATTAAGGCATTT
5491816 TTTCATGCCA
Statistics
Matches: 113, Mismatches: 24, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
40 8 0.07
41 69 0.61
42 4 0.04
46 5 0.04
47 27 0.24
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (41 bp):
ATCAATTAAGGCATTTGATGAACAAAATACCTTAATTGATG
Found at i:5493708 original size:145 final size:144
Alignment explanation
Indices: 5493546--5493866 Score: 332
Period size: 145 Copynumber: 2.2 Consensus size: 144
5493536 TGCGATCAAA
* * * * ****
5493546 GTTTTTAA-ATCACCAAAAATCATAAAATAAT-TTCACAACAAGATCTTGAGTGTTTTGTGAAAA
1 GTTTTTAATA-CATCAAAAATCATAAAATAATGTT-AAAACAAGATCTGGAGCGTTTCACAAAAA
*
5493609 GCCAACCTTAGGAAA-GGTCAAATTATGAAAATAC-CCATAAAA-GCTATTTTAGTAATTTCAT-
64 GCCAA-CTT-GGAAATGATCAAATTATGAAAATACTCC-TAAAAGGC-ATTTTAGTAATTT-ATC
*
5493670 ACATTTCAA-TGTACGACCAAG
124 ACATTCCAAGT-TACGACCAAG
* *
5493691 GTTTTTAATACATCAAAAATCATAAAATAATGTTAAAACATGATCTGGAGCGTTTCACAAAAAGT
1 GTTTTTAATACATCAAAAATCATAAAATAATGTTAAAACAAGATCTGGAGCGTTTCACAAAAAGC
** * * *
5493756 TGACTTTGAAATGATCAAATTATGAAAATACTCCTAAAATGGCATTTTAGTAATTTTTCACCTTC
66 CAACTTGGAAATGATCAAATTATGAAAATACTCCTAAAA-GGCATTTTAGTAATTTATCACATTC
*
5493821 CAAGTTACGATCAAG
130 CAAGTTACGACCAAG
* *
5493836 GTTTGTAATGCATCAAAAATCATAAAATAAT
1 GTTTTTAATACATCAAAAATCATAAAATAAT
5493867 ATTTAATCAT
Statistics
Matches: 148, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
143 4 0.03
144 27 0.18
145 111 0.75
146 6 0.04
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (144 bp):
GTTTTTAATACATCAAAAATCATAAAATAATGTTAAAACAAGATCTGGAGCGTTTCACAAAAAGC
CAACTTGGAAATGATCAAATTATGAAAATACTCCTAAAAGGCATTTTAGTAATTTATCACATTCC
AAGTTACGACCAAG
Found at i:5493892 original size:145 final size:145
Alignment explanation
Indices: 5493626--5493899 Score: 335
Period size: 145 Copynumber: 1.9 Consensus size: 145
5493616 TTAGGAAAGG
*
5493626 TCAAATTATGAAAATACCCATAAAAGCTATTTTAGTAATTTCATACATTTCAATGTACGACCAAG
1 TCAAATTATGAAAATACCCATAAAAGCTATTTTAGTAATTTCATACATTCCAATGTACGACCAAG
* * **
5493691 GTTTTTAATACATCAAAAATCATAAAATAATGTTAAAACATGATCTGGAGCGTTTCA-CAAAAAG
66 GTTTGTAATACATCAAAAATCATAAAATAATATTAAAACATGATCTAAAGCGTTTCACCAAAAAG
5493755 TTGACTTTGAAATGA
131 TTGACTTTGAAATGA
* *
5493770 TCAAATTATGAAAATACTCC-TAAAATGGC-ATTTTAGTAATTT-TTCACCTTCCAA-GTTACGA
1 TCAAATTATGAAAATAC-CCATAAAA--GCTATTTTAGTAATTTCAT-ACATTCCAATG-TACGA
* * * * * *
5493831 TCAAGGTTTGTAATGCATCAAAAATCATAAAATAATATTTAATCATGATTTAAAAG-TTTTCACC
61 CCAAGGTTTGTAATACATCAAAAATCATAAAATAATATTAAAACATGATCT-AAAGCGTTTCACC
5493895 AAAAA
125 AAAAA
5493900 CCAACTTCTA
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
144 24 0.22
145 76 0.69
146 10 0.09
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (145 bp):
TCAAATTATGAAAATACCCATAAAAGCTATTTTAGTAATTTCATACATTCCAATGTACGACCAAG
GTTTGTAATACATCAAAAATCATAAAATAATATTAAAACATGATCTAAAGCGTTTCACCAAAAAG
TTGACTTTGAAATGA
Found at i:5496324 original size:2 final size:2
Alignment explanation
Indices: 5496317--5496351 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5496307 TATGCTAATA
5496317 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5496352 GTGTGTGCCT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5502968 original size:12 final size:12
Alignment explanation
Indices: 5502953--5503090 Score: 51
Period size: 12 Copynumber: 11.3 Consensus size: 12
5502943 CTTTTGTATT
5502953 TTATTTATTTTA
1 TTATTTATTTTA
5502965 TTATTTATTATTA
1 TTATTTATT-TTA
*
5502978 TTATACGTATATTT-
1 TTAT--TTAT-TTTA
5502992 TTATTTA-TTTA
1 TTATTTATTTTA
5503003 TCTATTT-TTTT-
1 T-TATTTATTTTA
* * *
5503014 CTGTTAATATTTA
1 TTATTTAT-TTTA
*
5503027 -TATGTATTTTTA
1 TTATTTA-TTTTA
5503039 TATAGTTATATATTTA
1 T-TA-TT-TAT-TTTA
*
5503055 TTA-TTATATTA
1 TTATTTATTTTA
*
5503066 TAATTTA-TTTA
1 TTATTTATTTTA
5503077 TTA-TTATTTT-
1 TTATTTATTTTA
5503087 TTAT
1 TTAT
5503091 CTTGTAATAT
Statistics
Matches: 94, Mismatches: 13, Indels: 39
0.64 0.09 0.27
Matches are distributed among these distances:
10 12 0.13
11 15 0.16
12 35 0.37
13 9 0.10
14 6 0.06
15 9 0.10
16 8 0.09
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (12 bp):
TTATTTATTTTA
Found at i:5502977 original size:10 final size:10
Alignment explanation
Indices: 5502949--5503090 Score: 55
Period size: 10 Copynumber: 13.6 Consensus size: 10
5502939 TTTTCTTTTG
5502949 TATT-TTATT
1 TATTATTATT
5502958 TATTTTATTATT
1 TA--TTATTATT
5502970 TATTATTATT
1 TATTATTATT
*
5502980 ATACGTA-TATT
1 -TA-TTATTATT
5502991 T-TTATTTATT
1 TATTA-TTATT
*
5503001 TATCTATTTTTTT
1 TAT-TA--TTATT
* *
5503014 CTGTTAATATT
1 -TATTATTATT
5503025 TA-TATGTATT
1 TATTAT-TATT
*
5503035 T-TTATATAGT
1 TATTAT-TATT
5503045 TA-TA-TATT
1 TATTATTATT
5503053 TATTATTATAT
1 TATTATTAT-T
*
5503064 TATAATTTATT
1 TATTA-TTATT
5503075 TATTATTATT
1 TATTATTATT
*
5503085 TTTTAT
1 TATTAT
5503091 CTTGTAATAT
Statistics
Matches: 101, Mismatches: 14, Indels: 35
0.67 0.09 0.23
Matches are distributed among these distances:
8 7 0.07
9 6 0.06
10 42 0.42
11 22 0.22
12 15 0.15
13 7 0.07
14 2 0.02
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (10 bp):
TATTATTATT
Found at i:5502978 original size:22 final size:21
Alignment explanation
Indices: 5502939--5503162 Score: 68
Period size: 22 Copynumber: 10.2 Consensus size: 21
5502929 TTTTCTTTCT
*
5502939 TTTTCTTTTGTATT-TTATTTA
1 TTTTATTTT-TATTATTATTTA
5502960 TTTTATTATTTATTATTATTATA
1 TTTTATT-TTTATTATTATT-TA
* * *
5502983 CGTATATTTTTATTTATTTATCTA
1 -TTTTATTTTTA-TTA-TTATTTA
* * *
5503007 TTTT-TTTCTGTTAATATTTA
1 TTTTATTTTTATTATTATTTA
* *
5503027 TATGTATTTTTA-TA-TAGTTA
1 T-TTTATTTTTATTATTATTTA
*
5503047 -TATATTTATTATTA-TATTATA
1 TTTTATTT-TTATTATTATT-TA
* *
5503068 ATTTATTTATTATTATTTTTTA
1 TTTTATTT-TTATTATTATTTA
**
5503090 TCTTGTAATATTTT-TTA-GGTTTA
1 T-TT-T-AT-TTTTATTATTATTTA
* * * *
5503113 TCTTATTTTCATTATCTGTTAA
1 TTTTATTTTTATTAT-TATTTA
5503135 TTTTATTTTTATTCATTTATTTGA
1 TTTTATTTTTATT-A-TTATTT-A
5503159 TTTT
1 TTTT
5503163 TTCGATTATC
Statistics
Matches: 151, Mismatches: 29, Indels: 43
0.68 0.13 0.19
Matches are distributed among these distances:
18 6 0.04
19 6 0.04
20 21 0.14
21 20 0.13
22 46 0.30
23 22 0.15
24 20 0.13
25 8 0.05
26 2 0.01
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTATTATTATTTA
Found at i:5503066 original size:19 final size:20
Alignment explanation
Indices: 5503031--5503080 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
5503021 TATTTATATG
5503031 TATTT-TTA-TATAGTTATA
1 TATTTATTATTATAGTTATA
5503049 TATTTATTATTATA-TTATA
1 TATTTATTATTATAGTTATA
5503068 -ATTTATTTATTAT
1 TATTTA-TTATTAT
5503081 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.34
19 15 0.52
20 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTATTATTATAGTTATA
Found at i:5504084 original size:17 final size:16
Alignment explanation
Indices: 5504064--5504122 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
5504054 TTTATCTTAT
5504064 TTTTATTTTTGTTTTAC
1 TTTTATTTTT-TTTTAC
*
5504081 TTTTCTTTATTTTTTA-
1 TTTTATTT-TTTTTTAC
* *
5504097 TCTTTATTTATTTTCAC
1 T-TTTATTTTTTTTTAC
5504114 TTTTATTTT
1 TTTTATTTT
5504123 GTTCTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 13 0.38
17 19 0.56
18 2 0.06
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTATTTTTTTTTAC
Found at i:5504130 original size:22 final size:22
Alignment explanation
Indices: 5504092--5504133 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5504082 TTTCTTTATT
5504092 TTTTATCTTTATTTATTTTCAC
1 TTTTATCTTTATTTATTTTCAC
*
5504114 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTATT-TATTTTC
5504134 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTATTTATTTTCAC
Found at i:5504240 original size:59 final size:58
Alignment explanation
Indices: 5504140--5504614 Score: 614
Period size: 58 Copynumber: 8.0 Consensus size: 58
5504130 TTTCTTTAAA
5504140 TAAAAATCAAAGTTTCAAAAAAGAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAGTTTC-AAAAA-AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
** * *
5504201 TGGAAATCAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAATGTATCAATTTTTCT
1 TAAAAAT-AAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
5504260 TAAAAATAAA-TTTCAAAAAAA-AGGTTTTTGAGAAAAAGTTGAAAGTATCAATTCTCCT
1 TAAAAATAAAGTTTCAAAAAAATA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
** * *
5504318 TGGAAATCAAAGTTTCAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAAT-AAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
5504377 TAAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
5504435 TAAAAATAAATTTTCAAAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAAGTTTC-----AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
** * *
5504498 TGGAAATCAAAGTTTCAAAAAAATATATTTTTGAGGAAAGGTTGAAAGTATCAATTTTTCT
1 TAAAAAT-AAAGTTTC-AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
5504559 TAAAAATAAATTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TAAAAATAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
5504615 CCACACAAGA
Statistics
Matches: 366, Mismatches: 36, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
56 1 0.00
57 44 0.12
58 105 0.29
59 80 0.22
60 29 0.08
61 54 0.15
63 46 0.13
64 7 0.02
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.35
Consensus pattern (58 bp):
TAAAAATAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:5504367 original size:117 final size:119
Alignment explanation
Indices: 5504140--5504612 Score: 629
Period size: 117 Copynumber: 4.0 Consensus size: 119
5504130 TTTCTTTAAA
**
5504140 TAAAAATCAAAGTTTCAAAAAAGA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
1 TAAAAATCAAAGTTTCAAAAAA-ATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
*
5504204 AAATCAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAATGTATCAATTTTTCT
65 AAAT-AAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
** * * **
5504260 TAAAAAT-AAA-TTTCAAAAAAA-AGGTTTTTGAGAAAAAGTTGAAAGTATCAATTCTCCTTGGA
1 TAAAAATCAAAGTTTCAAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAA
*
5504322 AATCAAAGTTTCAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
66 AAT-AAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
* *
5504377 TAAAAAT-AAATTTTC-AAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAA
1 TAAAAATCAAAGTTTCAAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAA
* * *
5504439 AATAAATTTTCAAAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
66 AATAAAGTTTC-----AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
** * *
5504498 TGGAAATCAAAGTTTCAAAAAAATATATTTTTGAGGAAAGGTTGAAAGTATCAATTTTTCTTAAA
1 TAAAAATCAAAGTTTCAAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAA
* *
5504563 AATAAATTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
66 AATAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
5504613 CCCCACACAA
Statistics
Matches: 319, Mismatches: 25, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
116 7 0.02
117 144 0.45
118 51 0.16
119 3 0.01
120 7 0.02
121 45 0.14
122 7 0.02
123 6 0.02
124 49 0.15
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.35
Consensus pattern (119 bp):
TAAAAATCAAAGTTTCAAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAA
AATAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
Found at i:5508484 original size:7 final size:7
Alignment explanation
Indices: 5508474--5508537 Score: 51
Period size: 7 Copynumber: 9.0 Consensus size: 7
5508464 AAACGATGAT
5508474 GAAAAAA
1 GAAAAAA
*
5508481 GAAAGAA
1 GAAAAAA
5508488 GAAAAAA
1 GAAAAAA
*
5508495 -ACAAAA
1 GAAAAAA
5508501 -AAAAAA
1 GAAAAAA
* *
5508507 TAAAGAA
1 GAAAAAA
5508514 GAAAGAAA
1 GAAA-AAA
5508522 TGAAAAAA
1 -GAAAAAA
5508530 TGAAAAAA
1 -GAAAAAA
5508538 AGGAGATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
6 10 0.21
7 20 0.43
8 13 0.28
9 4 0.09
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (7 bp):
GAAAAAA
Found at i:5509829 original size:42 final size:42
Alignment explanation
Indices: 5509753--5510009 Score: 364
Period size: 42 Copynumber: 6.1 Consensus size: 42
5509743 ATGATTATCA
5509753 AGGAGCAATTTACTTTT-CAAAGTTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAG--TCGTGGTGCCTCTGTTTAG
* *
5509794 AGGAGTAATTTACTTTTCCAAAGTCATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
5509836 AGGAGCAATTTAC-TTTCTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-CAAAGTCGTGGTGCCTCTGTTTAG
5509878 AGGAGCAATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* *
5509919 AGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAA
1 AGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* * *
5509961 AGGAGCAATTTA-TGTTTCTCAAAGTCGTTGAGCCTTTGTTTAG
1 AGGAGCAATTTACT-TTTC-CAAAGTCGTGGTGCCTCTGTTTAG
5510004 AGGAGC
1 AGGAGC
5510010 TTTGGTCAAA
Statistics
Matches: 197, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
40 3 0.02
41 57 0.29
42 112 0.57
43 25 0.13
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (42 bp):
AGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:5509907 original size:83 final size:82
Alignment explanation
Indices: 5509753--5510009 Score: 383
Period size: 83 Copynumber: 3.1 Consensus size: 82
5509743 ATGATTATCA
*
5509753 AGGAGCAATTTACTTTTCAAAGTTTCGT--TGCCTCTGTTTAGAGGAGTAATTTACTTTTCCAAA
1 AGGAGCAATTTACTTTTCAAAG--TCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-TTTTCCAAA
*
5509816 GTCATGGTGCCTCTGTTTAG
63 GTCGTGGTGCCTCTGTTTAG
5509836 AGGAGCAATTTACTTTCTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGT
1 AGGAGCAATTTACTTT-TCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGT
5509901 CGTGGTGCCTCTGTTTAG
65 CGTGGTGCCTCTGTTTAG
*
5509919 AGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAAAGGAGCAATTTATGTTTCTCAAA
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAT-TTTC-CAAA
* * *
5509984 GTCGTTGAGCCTTTGTTTAG
63 GTCGTGGTGCCTCTGTTTAG
5510004 AGGAGC
1 AGGAGC
5510010 TTTGGTCAAA
Statistics
Matches: 162, Mismatches: 6, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
82 6 0.04
83 95 0.59
84 34 0.21
85 27 0.17
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (82 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTC
GTGGTGCCTCTGTTTAG
Found at i:5510037 original size:16 final size:15
Alignment explanation
Indices: 5510016--5510063 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
5510006 GAGCTTTGGT
5510016 CAAAAACAAAAAAAAA
1 CAAAAA-AAAAAAAAA
*
5510032 CAAAAAAAAGAAAACA
1 CAAAAAAAA-AAAAAA
5510048 CAAAAAAAAATAAAAA
1 CAAAAAAAAA-AAAAA
5510064 ATGAAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.02
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:5510045 original size:14 final size:14
Alignment explanation
Indices: 5510023--5510057 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5510013 GGTCAAAAAC
5510023 AAAAAAAAACA-AA
1 AAAAAAAAACACAA
5510036 AAAAAGAAAACACAA
1 AAAAA-AAAACACAA
5510051 AAAAAAA
1 AAAAAAA
5510058 TAAAAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 7 0.35
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACACAA
Found at i:5510052 original size:25 final size:24
Alignment explanation
Indices: 5510018--5510070 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
5510008 GCTTTGGTCA
5510018 AAAACAAAAAAAAACA-AAAAAAAG
1 AAAACAAAAAAAAA-ATAAAAAAAG
*
5510042 AAAACACAAAAAAAAATAAAAAATG
1 AAAACA-AAAAAAAAATAAAAAAAG
5510067 AAAA
1 AAAA
5510071 TGTTGAGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.85, C:0.08, G:0.04, T:0.04
Consensus pattern (24 bp):
AAAACAAAAAAAAAATAAAAAAAG
Found at i:5510245 original size:19 final size:18
Alignment explanation
Indices: 5510217--5510259 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5510207 CCCAATCCAA
*
5510217 TTTTTATCTTGTGTTATTT
1 TTTTTTTCTT-TGTTATTT
* *
5510236 TTTTTTTCTTTTTTCTTT
1 TTTTTTTCTTTGTTATTT
5510254 TTTTTT
1 TTTTTT
5510260 GTATTTTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTTTCTTTGTTATTT
Found at i:5510289 original size:10 final size:10
Alignment explanation
Indices: 5510274--5510402 Score: 72
Period size: 10 Copynumber: 12.4 Consensus size: 10
5510264 TTTATGTATT
5510274 TTATTATTTA
1 TTATTATTTA
5510284 TTATTATTATA
1 TTATTATT-TA
5510295 TGTA-TATTT-
1 T-TATTATTTA
5510304 TTATTTATTTA
1 TTA-TTATTTA
*
5510315 TCTATTTTTTTCTA
1 T-TA--TTATT-TA
*
5510329 TTAATATTTA
1 TTATTATTTA
5510339 -TATGTATTT-
1 TTAT-TATTTA
*
5510348 TTATATAGTTA
1 TTAT-TATTTA
5510359 -TA-TATTTA
1 TTATTATTTA
5510367 TTATTATATTA
1 TTATTAT-TTA
*
5510378 TAATTTATTTA
1 TTA-TTATTTA
*
5510389 TTATTATTTT
1 TTATTATTTA
5510399 TTAT
1 TTAT
5510403 CTTGTAATAT
Statistics
Matches: 94, Mismatches: 10, Indels: 30
0.70 0.07 0.22
Matches are distributed among these distances:
8 7 0.07
9 5 0.05
10 43 0.46
11 21 0.22
12 8 0.09
13 7 0.07
14 3 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATTATTTA
Found at i:5510305 original size:46 final size:45
Alignment explanation
Indices: 5510254--5510365 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 45
5510244 TTTTTTCTTT
* * * *
5510254 TTTTTTGTAT-TTTATGTATTTTATTATTTATTATTA-TTATATGTA
1 TTTTTTATATATTTATCTATTTT-TT-TCTATTAATATTTATATGTA
*
5510299 TATTTTTATTTATTTATCTATTTTTTTCTATTAATATTTATATGTA
1 T-TTTTTATATATTTATCTATTTTTTTCTATTAATATTTATATGTA
* *
5510345 -TTTTTATATAGTTATATATTT
1 TTTTTTATATATTTATCTATTT
5510366 ATTATTATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
44 18 0.32
45 9 0.16
46 18 0.32
47 11 0.20
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (45 bp):
TTTTTTATATATTTATCTATTTTTTTCTATTAATATTTATATGTA
Found at i:5510331 original size:39 final size:40
Alignment explanation
Indices: 5510263--5510373 Score: 93
Period size: 39 Copynumber: 2.7 Consensus size: 40
5510253 TTTTTTTGTA
5510263 TTTTATGTATTTTATTATTTATTATTATT-ATATGTATAT
1 TTTTATGTATTTTATTATTTATTATTATTAATATGTATAT
* * *
5510302 TTTTATTTA-TTTATCTATTT-TTTTCTATTAATATTTATAT
1 TTTTATGTATTTTAT-TATTTATTAT-TATTAATATGTATAT
* * *
5510342 GTATTTTTATATAGTTATATATTTATTATTAT
1 -T-TTTATGTAT-TTTAT-TATTTATTATTAT
5510374 ATTATAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
38 8 0.14
39 17 0.30
40 9 0.16
41 1 0.02
42 6 0.11
44 12 0.21
45 3 0.05
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (40 bp):
TTTTATGTATTTTATTATTTATTATTATTAATATGTATAT
Found at i:5510377 original size:46 final size:46
Alignment explanation
Indices: 5510273--5510385 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 46
5510263 TTTTATGTAT
* * * *
5510273 TTTATTATTTATTATTA-TTATATGTATATTTTTATTTATTTATCTA
1 TTTATTATTTATTAATATTTATATG-ATATTTTTATATAGTTATATA
5510319 TTT-TT-TTCTATTAATATTTATATG-TATTTTTATATAGTTATATA
1 TTTATTATT-TATTAATATTTATATGATATTTTTATATAGTTATATA
5510363 TTTATTATTATATT-ATAATTTAT
1 TTTATTATT-TATTAAT-ATTTAT
5510386 TTATTATTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
44 22 0.39
45 13 0.23
46 22 0.39
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (46 bp):
TTTATTATTTATTAATATTTATATGATATTTTTATATAGTTATATA
Found at i:5510483 original size:17 final size:18
Alignment explanation
Indices: 5510453--5510494 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
5510443 TTAATTTTAT
* *
5510453 TTTTATTCATTTATTTGA
1 TTTTATTCAATTATCTGA
5510471 TTTT-TTCAATTATCTGA
1 TTTTATTCAATTATCTGA
5510488 TTGTTAT
1 TT-TTAT
5510495 CATTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 13 0.65
18 6 0.30
19 1 0.05
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (18 bp):
TTTTATTCAATTATCTGA
Found at i:5510973 original size:11 final size:11
Alignment explanation
Indices: 5510945--5510975 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5510935 CCGGTAATCA
*
5510945 TCCGACCAACT
1 TCCGACGAACT
5510956 TCCGACGAACT
1 TCCGACGAACT
5510967 TCCGACGAA
1 TCCGACGAA
5510976 AAAACCCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.39, G:0.16, T:0.16
Consensus pattern (11 bp):
TCCGACGAACT
Found at i:5511001 original size:20 final size:20
Alignment explanation
Indices: 5510976--5511014 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5510966 TTCCGACGAA
* *
5510976 AAAACCCAGATTTCGGTGAT
1 AAAACCCAAAATTCGGTGAT
5510996 AAAACCCAAAATTCGGTGA
1 AAAACCCAAAATTCGGTGA
5511015 ATCTTCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAACCCAAAATTCGGTGAT
Found at i:5511431 original size:27 final size:27
Alignment explanation
Indices: 5511401--5511457 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
5511391 ATTAGGTTTA
5511401 TTTAATATT-TTTTATCTTTATC-TTATT
1 TTTAATATTGTTTTA-CTTT-TCTTTATT
* *
5511428 TTTATTTTTGTTTTACTTTTCTTTATT
1 TTTAATATTGTTTTACTTTTCTTTATT
5511455 TTT
1 TTT
5511458 TATCTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 19 0.73
28 5 0.19
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTAATATTGTTTTACTTTTCTTTATT
Found at i:5511447 original size:17 final size:16
Alignment explanation
Indices: 5511427--5511485 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
5511417 TTTATCTTAT
5511427 TTTTATTTTTGTTTTAC
1 TTTTATTTTT-TTTTAC
*
5511444 TTTTCTTTATTTTTTA-
1 TTTTATTT-TTTTTTAC
* *
5511460 TCTTTATTTATTTTCAC
1 T-TTTATTTTTTTTTAC
5511477 TTTTATTTT
1 TTTTATTTT
5511486 GTTCTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 13 0.38
17 19 0.56
18 2 0.06
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTATTTTTTTTTAC
Found at i:5511493 original size:22 final size:22
Alignment explanation
Indices: 5511455--5511496 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5511445 TTTCTTTATT
5511455 TTTTATCTTTATTTATTTTCAC
1 TTTTATCTTTATTTATTTTCAC
*
5511477 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTATT-TATTTTC
5511497 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTATTTATTTTCAC
Found at i:5511603 original size:59 final size:58
Alignment explanation
Indices: 5511503--5512091 Score: 731
Period size: 58 Copynumber: 9.9 Consensus size: 58
5511493 TTTCTTTAAA
*
5511503 TAAAAATCAAAGTTTCAAAAAAGAATATTTTTGAGGAAAAGTTGAAAGTATCAAGTTTT-CT
1 TAAAAAT-AAATTTTC-AAAAA-AATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCT
** * * * *
5511564 TGGAAATCAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAATGTATTAATTTTTCT
1 TAAAAAT-AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * * *
5511623 TAAAAATAAATTTCCAAAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTCTCCT
1 TAAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
5511681 TGAAAATCAAAGTTTCAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
*
5511740 TAAAAATAAATTTTC-AAAAAATA-TTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAATAAATTTTCAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCT
* *
5511796 TAAAAATAAATTTTCAAAAAAATGTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
5511854 TGAAAATCAAAATTTTCGAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT--AAATTTTCAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCT
*
5511914 TAAAAATAAATTTTCAAAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAATTTTC-----AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* ** * *
5511977 TGGAAACCAAAGTTTCAAAAAAATATATTTTTGAGGAAAGGTTGAAAGTATCAATTTTCCT
1 T-AAAAATAAATTTTC-AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
5512038 TAAAAATAAATTTTC-AAAAAATATTTTTGGGGAAAAATTGAAAGTATCAATTTT
1 TAAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
5512092 TCCCACACAA
Statistics
Matches: 464, Mismatches: 47, Indels: 38
0.85 0.09 0.07
Matches are distributed among these distances:
55 2 0.00
56 44 0.09
57 45 0.10
58 108 0.23
59 91 0.20
60 73 0.16
61 50 0.11
63 38 0.08
64 13 0.03
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (58 bp):
TAAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:5511666 original size:117 final size:115
Alignment explanation
Indices: 5511503--5512091 Score: 700
Period size: 117 Copynumber: 5.0 Consensus size: 115
5511493 TTTCTTTAAA
* * **
5511503 TAAAAATCAAAGTTTCAAAAAAGAATATTTTTGAGGAAAAGTTGAAAGTATCAAGTTTTCTTGGA
1 TAAAAAT-AAA-TTTCCAAAAA-AATATTTTTGAGAAAAAGTTGAAAGTATCAA-TTTTCTTAAA
* * * *
5511568 AATCAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAATGTATTAATTTTTCT
62 AAT-AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
5511623 TAAAAATAAATTTCCAAAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTCTCCTTGAAAAT
1 TAAAAATAAATTTCCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATT-TTCTTAAAAAT
* *
5511688 CAAAGTTTCAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
65 -AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
5511740 TAAAAATAAATTTTC-AAAAAATA-TTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
1 TAAAAATAAATTTCCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA-TTTTCTTAAAAAT
* *
5511803 AAATTTTCAAAAAAATGTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
65 AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
5511854 TGAAAATCAAAATTTTCGAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTTAAA
1 TAAAAAT--AAATTTCCAAAAAAATATTTTTGA-GAAAAAGTTGAAAGTATCAATTTT-CTTAAA
*
5511918 AATAAATTTTCAAAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
62 AATAAATTTTC-----AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* ** * * *
5511977 TGGAAACCAAAGTTTCAAAAAAATATATTTTTGAGGAAAGGTTGAAAGTATCAATTTTCCTTAAA
1 T-AAAAATAAA-TTTCCAAAAAA-ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-CTTAAA
* *
5512042 AATAAATTTTC-AAAAAATATTTTTGGGGAAAAATTGAAAGTATCAATTTT
62 AATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
5512092 TCCCACACAA
Statistics
Matches: 419, Mismatches: 33, Indels: 36
0.86 0.07 0.07
Matches are distributed among these distances:
114 53 0.13
115 34 0.08
116 19 0.05
117 112 0.27
118 86 0.21
119 3 0.01
120 7 0.02
122 3 0.01
123 49 0.12
124 52 0.12
125 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (115 bp):
TAAAAATAAATTTCCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTAAAAATA
AATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:5514544 original size:14 final size:16
Alignment explanation
Indices: 5514527--5514565 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
5514517 TGATCGTTAA
5514527 AAAATAAAAAC-AT-T
1 AAAATAAAAACTATAT
5514541 AAAATAAAAACTATAT
1 AAAATAAAAACTATAT
*
5514557 ATAATAAAA
1 AAAATAAAA
5514566 TTTTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 2 0.09
16 9 0.41
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAAAAACTATAT
Found at i:5524767 original size:19 final size:20
Alignment explanation
Indices: 5524743--5524780 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5524733 CAAAATTATT
5524743 TTTTTCACCTTTTA-AAAGA
1 TTTTTCACCTTTTATAAAGA
*
5524762 TTTTTCAGCTTTTATAAAG
1 TTTTTCACCTTTTATAAAG
5524781 CACCACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (20 bp):
TTTTTCACCTTTTATAAAGA
Found at i:5525502 original size:12 final size:12
Alignment explanation
Indices: 5525471--5525506 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
5525461 AGACAGAAAA
*
5525471 CACTGTAGCAGT
1 CACTGTAGTAGT
5525483 CAACTGTAGTAGT
1 C-ACTGTAGTAGT
5525496 CACTGTAGTAG
1 CACTGTAGTAG
5525507 AAGATAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (12 bp):
CACTGTAGTAGT
Found at i:5526290 original size:15 final size:15
Alignment explanation
Indices: 5526267--5526313 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
5526257 TAAGGTAATT
*
5526267 TCCAAATTTAATAGA
1 TCCAGATTTAATAGA
5526282 TCCAGATTTAATAGA
1 TCCAGATTTAATAGA
* *
5526297 TCCAGATATAATGGA
1 TCCAGATTTAATAGA
5526312 TC
1 TC
5526314 AACATCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (15 bp):
TCCAGATTTAATAGA
Found at i:5538498 original size:157 final size:158
Alignment explanation
Indices: 5538272--5538586 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 158
5538262 TATTACGTGA
5538272 TTTGATCTTGAATTTGATTCTTCACTTTTTTTTAAATTTAAAATATTTATCTTTTCATATTCTTT
1 TTTGATCTTGAATTTGATTCTTCACTTTTTTTTAAATTTAAAATATTTATCTTTTCATATTCTTT
*
5538337 AATTGGTTTTTTATTTAAATTTTAAAAATTTTAGATAATTTAATC-ATTTTGTAAATATATATTT
66 AATTGGTTTTTTATTTAAATTTTAAAAATTTTAGATAATTCAATCAATTTT-TAAATATATATTT
5538401 TTGATAAATAGTTTAAAATTAGTAAATAT
130 TTGATAAATAGTTTAAAATTAGTAAATAT
5538430 TTTGATCTTGAATTTGATTCTTCAC-TTTTTTTAAATTTAAAATATTTATCTTTTCATATTCTTT
1 TTTGATCTTGAATTTGATTCTTCACTTTTTTTTAAATTTAAAATATTTATCTTTTCATATTCTTT
5538494 AATTGGTTTTTTATTTAAATTTTAAAAATTTTAGATAATTCAATCAATTTTTAAATATATATTTT
66 AATTGGTTTTTTATTTAAATTTTAAAAATTTTAGATAATTCAATCAATTTTTAAATATATATTTT
*
5538559 TGATAAATAGTTTAAGATTAGTAAATAT
131 TGATAAATAGTTTAAAATTAGTAAATAT
5538587 CTTATATGTC
Statistics
Matches: 154, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
157 124 0.81
158 30 0.19
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.54
Consensus pattern (158 bp):
TTTGATCTTGAATTTGATTCTTCACTTTTTTTTAAATTTAAAATATTTATCTTTTCATATTCTTT
AATTGGTTTTTTATTTAAATTTTAAAAATTTTAGATAATTCAATCAATTTTTAAATATATATTTT
TGATAAATAGTTTAAAATTAGTAAATAT
Found at i:5539272 original size:29 final size:27
Alignment explanation
Indices: 5539224--5539298 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 27
5539214 TAAATTATAC
* *
5539224 TAAATTATTTAATATGATATCTGAACTT-
1 TAAATTTTTTAAT-TAATATCTGAA-TTA
*
5539252 TAAAATTTTTTAATGTAATATTTGAATTA
1 T-AAATTTTTTAAT-TAATATCTGAATTA
*
5539281 TAAATTTATTAATTAATA
1 TAAATTTTTTAATTAATA
5539299 AAGTATTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.12
28 14 0.35
29 21 0.52
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (27 bp):
TAAATTTTTTAATTAATATCTGAATTA
Found at i:5540927 original size:58 final size:58
Alignment explanation
Indices: 5540837--5541180 Score: 478
Period size: 58 Copynumber: 5.8 Consensus size: 58
5540827 TCTTGTGTAG
* * * *
5540837 GGAAAATTAATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAAGTCATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTGATTTTCAA
*
5540895 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAAA--TTGATTTTCAA
* * *
5540956 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTGATTTTCAA
5541014 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAA--TTGATTTTCAA
*** * *
5541074 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAA-CCCTTTTT-GAAATTTATTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGGAAATTGA-TTTTCAA
5541131 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAAATT
5541181 TTGATTTTTA
Statistics
Matches: 255, Mismatches: 20, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
56 3 0.01
57 35 0.14
58 95 0.37
59 24 0.09
60 55 0.22
61 43 0.17
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTGATTTTCAA
Found at i:5541091 original size:118 final size:119
Alignment explanation
Indices: 5540837--5541188 Score: 593
Period size: 119 Copynumber: 3.0 Consensus size: 119
5540827 TCTTGTGTAG
* * * *
5540837 GGAAAATTAATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAAGTCATTTTCAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAAGGAAAAT
*
5540902 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTGATTTTCAA
66 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTTCAA
5540956 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAAGGAAAAT
5541021 TGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAAATTTTGATTTTCAA
66 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTTCAA
* ***
5541074 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-CCCTTTTT-GAAATTTATTTTTTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTA-TTTTTAAGGAAAA
5541137 TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTT
65 TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTT
5541189 TATTTAAAGA
Statistics
Matches: 222, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
116 8 0.04
117 47 0.21
118 78 0.35
119 89 0.40
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.45
Consensus pattern (119 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAAGGAAAAT
TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTTCAA
Found at i:5541222 original size:6 final size:6
Alignment explanation
Indices: 5541205--5541280 Score: 50
Period size: 6 Copynumber: 12.3 Consensus size: 6
5541195 AAGAAAATAG
* * *
5541205 AATAATA AATAAA AAT--A AAGAAA AATAAAA AATAAA GAAAAGCAA AACAAA
1 AATAA-A AATAAA AATAAA AATAAA AAT-AAA AATAAA -AATA--AA AATAAA
*
5541256 AATAAA AAT-AA AATAAA GATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
5541281 GAATATTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
4 3 0.05
5 5 0.09
6 28 0.51
7 14 0.25
8 3 0.05
9 2 0.04
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (6 bp):
AATAAA
Found at i:5541235 original size:17 final size:17
Alignment explanation
Indices: 5541211--5541268 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
5541201 ATAGAATAAT
5541211 AAAT-AAAAATAAAGAA
1 AAATAAAAAATAAAGAA
5541227 AAATAAAAAATAAAGAA
1 AAATAAAAAATAAAGAA
** *
5541244 AAGCAAAACAA-AAATAA
1 AAATAAAA-AATAAAGAA
5541261 AAATAAAA
1 AAATAAAA
5541269 TAAAGATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 4 0.11
17 29 0.83
18 2 0.06
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.10
Consensus pattern (17 bp):
AAATAAAAAATAAAGAA
Found at i:5541238 original size:27 final size:27
Alignment explanation
Indices: 5541193--5541278 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 27
5541183 GATTTTTATT
*
5541193 TAAAG-AAAATAGAATAATAAATAAAAA
1 TAAAGAAAAATA-AAAAATAAATAAAAA
*
5541220 TAAAGAAAAATAAAAAATAAAGAAAAGCA
1 TAAAGAAAAATAAAAAATAAATAAAA--A
* *
5541249 -AAACAAAAAT-AAAAATAAAATAAAGA
1 TAAAGAAAAATAAAAAAT-AAATAAAAA
5541275 TAAA
1 TAAA
5541279 AAGAATATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
26 1 0.02
27 26 0.53
28 21 0.43
29 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (27 bp):
TAAAGAAAAATAAAAAATAAATAAAAA
Found at i:5541277 original size:17 final size:17
Alignment explanation
Indices: 5541206--5541280 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
5541196 AGAAAATAGA
5541206 ATAATAAATAAAAATAAAG
1 ATAA-AAAT-AAAATAAAG
*
5541225 A-AAAATAAAAAATAAAG
1 ATAAAA-ATAAAATAAAG
** * *
5541242 --AAAAGCAAAACAAAA
1 ATAAAAATAAAATAAAG
5541257 ATAAAAATAAAATAAAG
1 ATAAAAATAAAATAAAG
5541274 ATAAAAA
1 ATAAAAA
5541281 GAATATTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
15 7 0.16
16 4 0.09
17 29 0.66
18 3 0.07
19 1 0.02
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (17 bp):
ATAAAAATAAAATAAAG
Found at i:5541710 original size:19 final size:20
Alignment explanation
Indices: 5541686--5541724 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5541676 TTCATCAGAT
5541686 TCTGGGTTTGTT-GTCGGAA
1 TCTGGGTTTGTTCGTCGGAA
*
5541705 TCTGGGTTTTTTCGTCGGAA
1 TCTGGGTTTGTTCGTCGGAA
5541725 GTTCATCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.10, C:0.13, G:0.33, T:0.44
Consensus pattern (20 bp):
TCTGGGTTTGTTCGTCGGAA
Found at i:5542280 original size:22 final size:21
Alignment explanation
Indices: 5542229--5542285 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
5542219 AGATAATTAG
*
5542229 AACAGATAAATCAAAAAAAAT
1 AACAGATAAATAAAAAAAAAT
* *
5542250 TATAGGATAAATAAAAAAATAAT
1 AACA-GATAAATAAAAAAA-AAT
*
5542273 AACAGATATATAA
1 AACAGATAAATAA
5542286 TTAGATAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.07
22 21 0.75
23 5 0.18
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AACAGATAAATAAAAAAAAAT
Found at i:5542322 original size:7 final size:8
Alignment explanation
Indices: 5542305--5542362 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 8
5542295 TAAAAATACA
5542305 AAAATAAAT
1 AAAAT-AAT
5542314 AAAAT-AT
1 AAAATAAT
5542321 AAAATAAT
1 AAAATAAT
5542329 AATAATAAT
1 AA-AATAAT
5542338 -AAATAA-
1 AAAATAAT
**
5542344 ATTATAAT
1 AAAATAAT
*
5542352 ATAATAAT
1 AAAATAAT
5542360 AAA
1 AAA
5542363 TATATAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 16 0.39
8 14 0.34
9 11 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATAAT
Found at i:5542355 original size:25 final size:28
Alignment explanation
Indices: 5542307--5542361 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5542297 AAAATACAAA
5542307 AATAAATAAAATATAAAATAATAATAAT
1 AATAAATAAAATATAAAATAATAATAAT
* *
5542335 AATAAATAAATTATAATATAATAATAA
1 AATAAATAAAATATAAAATAATAATAA
5542362 ATATATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAAATAAAATATAAAATAATAATAAT
Found at i:5542374 original size:25 final size:23
Alignment explanation
Indices: 5542311--5542381 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
5542301 TACAAAAATA
*
5542311 AATAAAATATAAAATAATAATAAT
1 AATAAAATATAATATAAT-ATAAT
5542335 AAT-AAATA-AATTATAATATAAT
1 AATAAAATATAA-TATAATATAAT
5542357 AATAAATATATAACTAT-ATA-AAT
1 AATAAA-ATATAA-TATAATATAAT
5542380 AA
1 AA
5542382 AATACATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 10 0.24
23 17 0.41
24 9 0.22
25 5 0.12
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAAAATATAATATAATATAAT
Found at i:5542375 original size:22 final size:22
Alignment explanation
Indices: 5542333--5542377 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5542323 AATAATAATA
*
5542333 ATAATAAATAAATTATAATATA
1 ATAATAAATAAATAATAATATA
*
5542355 ATAATAAATATATAACT-ATATA
1 ATAATAAATAAATAA-TAATATA
5542377 A
1 A
5542378 ATAAAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATAAATAAATAATAATATA
Found at i:5542378 original size:38 final size:32
Alignment explanation
Indices: 5542306--5542385 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 32
5542296 AAAAATACAA
5542306 AAATAAATAAAATATAAAATAATAATAATAAT
1 AAATAAATAAAATATAAAATAATAATAATAAT
*
5542338 AAATAAATTATAATAT--AATAATAAATATATAACT
1 AAATAAA-TAAAATATAAAATAAT-AATA-ATAA-T
*
5542372 ATATAAATAAAATA
1 AAATAAATAAAATA
5542386 CATATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 6 0.15
32 11 0.27
33 17 0.41
34 7 0.17
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (32 bp):
AAATAAATAAAATATAAAATAATAATAATAAT
Found at i:5542380 original size:28 final size:27
Alignment explanation
Indices: 5542290--5542385 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 27
5542280 ATATAATTAG
* * *
5542290 ATAA-ATAAAAATACAAAAATAAATA-
1 ATAATATATAAATATAATAATAAATAT
*
5542315 A-AATATA-AAATAATAATAAT-AATAA
1 ATAATATATAAAT-ATAATAATAAATAT
5542340 ATAA-AT-TATAATATAATAATAAATAT
1 ATAATATATA-AATATAATAATAAATAT
*
5542366 ATAACTATATAAATAAAATA
1 ATAA-TATATAAATATAATA
5542386 CATATAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
24 10 0.18
25 22 0.39
26 13 0.23
28 10 0.18
29 2 0.04
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (27 bp):
ATAATATATAAATATAATAATAAATAT
Found at i:5542385 original size:25 final size:25
Alignment explanation
Indices: 5542307--5542396 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 25
5542297 AAAATACAAA
5542307 AATAAATA-A-AATATA-AAATAAT
1 AATAAATATATAATATATAAATAAT
*
5542329 AATAATAATAAATAA-ATTATAATATAAT
1 AAT-A-AATATATAATA-TATAA-ATAAT
5542357 AATAAATATATAACTATATAAATAA-
1 AATAAATATATAA-TATATAAATAAT
*
5542382 AATACATATA-AATAT
1 AATAAATATATAATAT
5542397 TAACAGAAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
22 3 0.05
23 4 0.07
24 6 0.11
25 11 0.19
26 16 0.28
27 8 0.14
28 9 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAAATATATAATATATAAATAAT
Found at i:5542685 original size:1 final size:1
Alignment explanation
Indices: 5542679--5542750 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
5542669 AACATTTTCA
* * * * * ** * * *
5542679 TTTTTTTTATTTTTTTTATATTTTTTGTTTTTTTTTTGTTTGCTTTTGTTTTTGTTTTTTTTATT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5542744 TTTTTTT
1 TTTTTTT
5542751 AACCAAAGCT
Statistics
Matches: 52, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.06, C:0.01, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:5542690 original size:9 final size:9
Alignment explanation
Indices: 5542673--5542749 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 9
5542663 CAACTCAACA
*
5542673 TTTTCATTT
1 TTTTTATTT
5542682 TTTTTATTT
1 TTTTTATTT
*
5542691 TTTTTATAT
1 TTTTTATTT
*
5542700 TTTTTGTTT
1 TTTTTATTT
5542709 TTTTT-TTGT
1 TTTTTATT-T
* *
5542718 TTGCTT-TTG
1 TT-TTTATTT
*
5542727 TTTTTGTTT
1 TTTTTATTT
5542736 TTTTTATTT
1 TTTTTATTT
5542745 TTTTT
1 TTTTT
5542750 TAACCAAAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
8 4 0.07
9 48 0.86
10 4 0.07
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (9 bp):
TTTTTATTT
Found at i:5542692 original size:10 final size:10
Alignment explanation
Indices: 5542679--5542751 Score: 67
Period size: 10 Copynumber: 6.9 Consensus size: 10
5542669 AACATTTTCA
5542679 TTTTTTTTAT
1 TTTTTTTTAT
5542689 TTTTTTTATAT
1 TTTTTTT-TAT
*
5542700 TTTTTGTTTTT
1 TTTTT-TTTAT
*
5542711 TTTTTGTTTGCT
1 TTTTT-TTT-AT
*
5542723 TTTGTTTTT-G
1 TTT-TTTTTAT
5542733 TTTTTTTTAT
1 TTTTTTTTAT
5542743 TTTTTTTTA
1 TTTTTTTTA
5542752 ACCAAAGCTC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
9 5 0.09
10 19 0.35
11 19 0.35
12 9 0.17
13 2 0.04
ACGTcount: A:0.07, C:0.01, G:0.07, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:5542695 original size:11 final size:11
Alignment explanation
Indices: 5542679--5542750 Score: 67
Period size: 11 Copynumber: 6.6 Consensus size: 11
5542669 AACATTTTCA
5542679 TTTTTTTTATT
1 TTTTTTTTATT
*
5542690 TTTTTTATATT
1 TTTTTTTTATT
5542701 TTTTGTTTT-TT
1 TTTT-TTTTATT
* **
5542712 TTTTGTTTGCT
1 TTTTTTTTATT
* *
5542723 TTTGTTTT-TG
1 TTTTTTTTATT
5542733 TTTTTTTTATT
1 TTTTTTTTATT
5542744 TTTTTTT
1 TTTTTTT
5542751 AACCAAAGCT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
10 10 0.21
11 35 0.73
12 3 0.06
ACGTcount: A:0.06, C:0.01, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:5542859 original size:41 final size:41
Alignment explanation
Indices: 5542758--5543222 Score: 589
Period size: 41 Copynumber: 11.1 Consensus size: 41
5542748 TTTAACCAAA
* * * *
5542758 GCTCCTCTAAACGGAGGCTCAAC-AATTTTGAGAAACATATAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTT--GAAA-ATA-AATT
* *
5542802 GCTCCTCTAAACAGAGGCACCATGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
* *
5542843 GCTCCTCTAAATAGAGGCACCACGACACCACGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGA-G------G-CACCACGACTTTTGAAAATAAATT
*
5542892 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
* * *
5542933 ACTCCTCTAAACAGAGGTACCACGAC-TTTAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
* *
5542973 GCTCCTCTAAATAGAGGCACCACGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
* *
5543014 ACTCCTCTAAACAAAGGCACCACGAC-TTTGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
*
5543054 GCTCCTCTAAACAAAGGCACCACGAC-TTTGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
* *
5543094 GCTTCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAA-TAAATT
* *
5543136 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
5543177 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
5543217 GCTCCT
1 GCTCCT
5543223 TAACAATCAT
Statistics
Matches: 377, Mismatches: 32, Indels: 28
0.86 0.07 0.06
Matches are distributed among these distances:
40 130 0.34
41 137 0.36
42 43 0.11
43 4 0.01
44 19 0.05
45 5 0.01
48 2 0.01
49 37 0.10
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
Found at i:5542891 original size:49 final size:49
Alignment explanation
Indices: 5542819--5542917 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
5542809 TAAACAGAGG
* *
5542819 CACCATGACTTTTGAAAGTAAATTGCTCCTCTAAATAGAGGCACCACGA
1 CACCACGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
5542868 CACCACGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
1 CACCACGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
5542917 C
1 C
5542918 TTTGGAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (49 bp):
CACCACGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
Found at i:5542978 original size:40 final size:40
Alignment explanation
Indices: 5542868--5543222 Score: 566
Period size: 40 Copynumber: 8.7 Consensus size: 40
5542858 GGCACCACGA
*
5542868 CACCACGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGG
1 CACCACGAC-TTTGAAAATAAATTGCTCCTCTAAACAGAGG
*
5542909 CACCACGACTTTGGAAAATAAATTACTCCTCTAAACAGAGG
1 CACCACGACTTT-GAAAATAAATTGCTCCTCTAAACAGAGG
* * *
5542950 TACCACGACTTTAAAAATAAATTGCTCCTCTAAATAGAGG
1 CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAGG
* *
5542990 CACCACGACTTTGGAAAATAAATTACTCCTCTAAACAAAGG
1 CACCACGACTTT-GAAAATAAATTGCTCCTCTAAACAGAGG
*
5543031 CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAAAGG
1 CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAGG
*
5543071 CACCACGACTTTGAAAATAAATTGCTTCTCTAAACAGAGG
1 CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAGG
5543111 CACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGG
1 CACCACGACTTT-GAAAA-TAAATTGCTCCTCTAAACAGAGG
*
5543153 CACCATGACTTTGGAAAATAAATTGCTCCTCTAAACAGAGG
1 CACCACGACTTT-GAAAATAAATTGCTCCTCTAAACAGAGG
5543194 CACCACGACTTTGAAAATAAATTGCTCCT
1 CACCACGACTTTGAAAATAAATTGCTCCT
5543223 TAACAATCAT
Statistics
Matches: 293, Mismatches: 17, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
40 133 0.45
41 121 0.41
42 39 0.13
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (40 bp):
CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAGG
Found at i:5542981 original size:81 final size:81
Alignment explanation
Indices: 5542868--5543222 Score: 586
Period size: 81 Copynumber: 4.4 Consensus size: 81
5542858 GGCACCACGA
*
5542868 CACCACGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
1 CACCACGAC-TTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
5542933 ACTCCTCTAAACAGAGG
65 ACTCCTCTAAACAGAGG
* * *
5542950 TACCACGACTTTAAAAATAAATTGCTCCTCTAAATAGAGGCACCACGACTTTGGAAAATAAATTA
1 CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTA
*
5543015 CTCCTCTAAACAAAGG
66 CTCCTCTAAACAGAGG
* *
5543031 CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAAAGGCACCACGACTTT-GAAAATAAATTG
1 CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTA
*
5543095 CTTCTCTAAACAGAGG
66 CTCCTCTAAACAGAGG
*
5543111 CACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATGACTTTGGAAAATAAAT
1 CACCACGACTTT-GAAAA-TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAAT
*
5543176 TGCTCCTCTAAACAGAGG
64 TACTCCTCTAAACAGAGG
5543194 CACCACGACTTTGAAAATAAATTGCTCCT
1 CACCACGACTTTGAAAATAAATTGCTCCT
5543223 TAACAATCAT
Statistics
Matches: 255, Mismatches: 15, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
80 37 0.15
81 133 0.52
82 46 0.18
83 39 0.15
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (81 bp):
CACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTA
CTCCTCTAAACAGAGG
Found at i:5544453 original size:11 final size:11
Alignment explanation
Indices: 5544433--5544469 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
5544423 ATCTTTCAGG
*
5544433 TTTTCATTTTT
1 TTTTCTTTTTT
5544444 TTTTCTTTTTT
1 TTTTCTTTTTT
5544455 TTTATCTTTTTT
1 TTT-TCTTTTTT
5544467 TTT
1 TTT
5544470 CTCATTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:5544477 original size:12 final size:11
Alignment explanation
Indices: 5544433--5544478 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
5544423 ATCTTTCAGG
5544433 TTTTCATTTTT
1 TTTTCATTTTT
*
5544444 TTTTCTTTTTT
1 TTTTCATTTTT
*
5544455 TTTATCTTTTTT
1 TTT-TCATTTTT
5544467 TTTCTCATTTTT
1 TTT-TCATTTTT
5544479 CATCTATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 13 0.42
12 18 0.58
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCATTTTT
Found at i:5544477 original size:22 final size:22
Alignment explanation
Indices: 5544439--5544483 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5544429 CAGGTTTTCA
** *
5544439 TTTTTTTTTCTTTTTTTTTATC
1 TTTTTTTTTCTCATTTTTCATC
5544461 TTTTTTTTTCTCATTTTTCATC
1 TTTTTTTTTCTCATTTTTCATC
5544483 T
1 T
5544484 ATTGTTGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTTTCTCATTTTTCATC
Found at i:5548408 original size:58 final size:57
Alignment explanation
Indices: 5548344--5548626 Score: 381
Period size: 58 Copynumber: 4.8 Consensus size: 57
5548334 TTGTGTAGGA
*
5548344 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGGAAATTCATTTTCAAGG
1 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTGGAAATTTATTTTCAAGG
*
5548402 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTGGAAATTTATTTTCAAGG
* *
5548460 AAAATTGATACTTTCAACTTTTCGCTAAAAATATTTTTTTGAAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTC-CCAAAAATATTTTTTTGGAAA-TTT-ATTTTCAAGG
* *** *
5548520 AAAATTAATACTTTCAACTTTTCCTCAAAAA-CCCTTTTT-GAAATTTATTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTGGAAATTTA-TTTTCAAGG
5548577 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTT
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATA--TTTTTTTGGAAATTT
5548627 TGATTTTTAT
Statistics
Matches: 198, Mismatches: 16, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
56 2 0.01
57 44 0.22
58 95 0.48
59 9 0.05
60 41 0.21
61 7 0.04
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGGAAATTTATTTTCAAGG
Found at i:5548605 original size:117 final size:118
Alignment explanation
Indices: 5548344--5548633 Score: 437
Period size: 117 Copynumber: 2.5 Consensus size: 118
5548334 TTGTGTAGGA
*
5548344 AAAATTGATACTTTCAACTTTTTCCC-AAAAATATTTTTTTGGAAA--TTCATTTTCAAGGAAAA
1 AAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTGGAAATTTTGATTTTCAAGGAAAA
* **
5548406 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAAGG
65 TTAATACTTTCAACTTTTCCCCAAAAATACCTTTTTGGAAATTTATTTTTAAGG
* *
5548460 AAAATTGATACTTTCAACTTTTCGCTAAAAATATTTTTTTGAAAATTTTGATTTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTTGATTTTCAAGGAAAAT
* *
5548525 TAATACTTTCAACTTTTCCTCAAAAA-CCCTTTTT-GAAATTTATTTTTTAAGG
66 TAATACTTTCAACTTTTCCCCAAAAATACCTTTTTGGAAATTTA-TTTTTAAGG
5548577 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTTGGAAATTTTGATTTT
5548634 TATTTAAAGA
Statistics
Matches: 158, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
115 6 0.04
116 44 0.28
117 46 0.29
118 41 0.26
119 21 0.13
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (118 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTTGATTTTCAAGGAAAAT
TAATACTTTCAACTTTTCCCCAAAAATACCTTTTTGGAAATTTATTTTTAAGG
Found at i:5548667 original size:6 final size:6
Alignment explanation
Indices: 5548656--5548715 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
5548646 ATAGAGTAAT
* *
5548656 AAATAA AAATAAA AAATAA AGAAAAGCA AAACAA AAATAA AAAT-A AAATAA
1 AAATAA AAAT-AA AAATAA A-AATA--A AAATAA AAATAA AAATAA AAATAA
*
5548707 AGATAA AAA
1 AAATAA AAA
5548716 GAATATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
5 5 0.11
6 25 0.57
7 9 0.20
8 3 0.07
9 2 0.05
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (6 bp):
AAATAA
Found at i:5548673 original size:17 final size:17
Alignment explanation
Indices: 5548653--5548788 Score: 77
Period size: 17 Copynumber: 8.1 Consensus size: 17
5548643 AAAATAGAGT
5548653 AATAAATAAAAATAAAA
1 AATAAATAAAAATAAAA
* **
5548670 AATAAAGAAAAGCAAAA
1 AATAAATAAAAATAAAA
5548687 CAA-AAATAAAAATAAAA
1 -AATAAATAAAAATAAAA
* * *
5548704 TAA-AGATAAAAA-GAAT
1 -AATAAATAAAAATAAAA
* ** ***
5548720 ATTAAATAAACCTATCT
1 AATAAATAAAAATAAAA
5548737 AATAAATAAAAATAAAA
1 AATAAATAAAAATAAAA
*
5548754 AAT-AA-ACAAATAAACA
1 AATAAATAAAAATAAA-A
5548770 AATAAATGAAAAA-AAAA
1 AATAAAT-AAAAATAAAA
5548787 AA
1 AA
5548789 ACCTGGAGCG
Statistics
Matches: 87, Mismatches: 25, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
15 9 0.10
16 14 0.16
17 55 0.63
18 5 0.06
19 4 0.05
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (17 bp):
AATAAATAAAAATAAAA
Found at i:5548697 original size:11 final size:11
Alignment explanation
Indices: 5548656--5548714 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
5548646 ATAGAGTAAT
5548656 AAATAAAAATA
1 AAATAAAAATA
*
5548667 AAA-AATAAAGA
1 AAATAA-AAATA
*
5548678 AAAGCAAAACA-A
1 AAA-TAAAA-ATA
5548690 AAATAAAAATA
1 AAATAAAAATA
*
5548701 AAATAAAGATA
1 AAATAAAAATA
5548712 AAA
1 AAA
5548715 AGAATATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.08
11 28 0.70
12 6 0.15
13 3 0.08
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:5548764 original size:8 final size:8
Alignment explanation
Indices: 5548746--5548775 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5548736 TAATAAATAA
5548746 AAATAAA-
1 AAATAAAC
5548753 AAATAAAC
1 AAATAAAC
5548761 AAATAAAC
1 AAATAAAC
5548769 AAATAAA
1 AAATAAA
5548776 TGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATAAAC
Found at i:5549084 original size:19 final size:19
Alignment explanation
Indices: 5549060--5549096 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5549050 GGTTGAAGAT
* *
5549060 TCACCGGATTCTGGGTTTG
1 TCACCGGAATCTAGGTTTG
5549079 TCACCGGAATCTAGGTTT
1 TCACCGGAATCTAGGTTT
5549097 TTTCATCGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (19 bp):
TCACCGGAATCTAGGTTTG
Found at i:5549694 original size:4 final size:4
Alignment explanation
Indices: 5549671--5549889 Score: 53
Period size: 4 Copynumber: 56.2 Consensus size: 4
5549661 ATATAATTAG
*
5549671 ATAA AT-A A-AA ATACA A-AA ATAA ATAA A-AT ATAA A-ATA AT-A AT-A
1 ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA
* * *
5549714 AT-A ATAA ATAA ATTATA ATATA AT-A ATAA ATAT ATAA CTAT ATAA ATAAA
1 ATAA ATAA ATAA A-TA-A ATA-A ATAA ATAA ATAA ATAA ATAA ATAA AT-AA
* * *
5549764 ATACA TATAA AT-A TTAA CAGAA AGAA A-AGA A-AA A-AA AT-A ATAA
1 ATA-A -ATAA ATAA ATAA -ATAA ATAA ATA-A ATAA ATAA ATAA ATAA
* * * * * *
5549807 ATAA ATAA ATAA AGAT ATAC ATAT ATTA ATAC ATAGTA AT-A ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA
* *
5549856 AT-A ATAAA ATAC ATAA A-AT ATAA A-AA A-AA ATAA A
1 ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
5549890 AATAATACAA
Statistics
Matches: 164, Mismatches: 25, Indels: 52
0.68 0.10 0.22
Matches are distributed among these distances:
3 46 0.28
4 90 0.55
5 21 0.13
6 7 0.04
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:5549703 original size:7 final size:8
Alignment explanation
Indices: 5549686--5549743 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 8
5549676 TAAAAATACA
5549686 AAAATAAAT
1 AAAAT-AAT
5549695 AAAAT-AT
1 AAAATAAT
5549702 AAAATAAT
1 AAAATAAT
5549710 AATAATAAT
1 AA-AATAAT
5549719 -AAATAA-
1 AAAATAAT
**
5549725 ATTATAAT
1 AAAATAAT
*
5549733 ATAATAAT
1 AAAATAAT
5549741 AAA
1 AAA
5549744 TATATAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 16 0.39
8 14 0.34
9 11 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATAAT
Found at i:5549736 original size:25 final size:28
Alignment explanation
Indices: 5549688--5549742 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5549678 AAAATACAAA
5549688 AATAAATAAAATATAAAATAATAATAAT
1 AATAAATAAAATATAAAATAATAATAAT
* *
5549716 AATAAATAAATTATAATATAATAATAA
1 AATAAATAAAATATAAAATAATAATAA
5549743 ATATATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAAATAAAATATAAAATAATAATAAT
Found at i:5549755 original size:25 final size:23
Alignment explanation
Indices: 5549692--5549762 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
5549682 TACAAAAATA
*
5549692 AATAAAATATAAAATAATAATAAT
1 AATAAAATATAATATAAT-ATAAT
5549716 AAT-AAATA-AATTATAATATAAT
1 AATAAAATATAA-TATAATATAAT
5549738 AATAAATATATAACTAT-ATA-AAT
1 AATAAA-ATATAA-TATAATATAAT
5549761 AA
1 AA
5549763 AATACATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 10 0.24
23 17 0.41
24 9 0.22
25 5 0.12
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAAAATATAATATAATATAAT
Found at i:5549759 original size:38 final size:32
Alignment explanation
Indices: 5549687--5549766 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 32
5549677 AAAAATACAA
5549687 AAATAAATAAAATATAAAATAATAATAATAAT
1 AAATAAATAAAATATAAAATAATAATAATAAT
*
5549719 AAATAAATTATAATAT--AATAATAAATATATAACT
1 AAATAAA-TAAAATATAAAATAAT-AATA-ATAA-T
*
5549753 ATATAAATAAAATA
1 AAATAAATAAAATA
5549767 CATATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 6 0.15
32 11 0.27
33 17 0.41
34 7 0.17
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (32 bp):
AAATAAATAAAATATAAAATAATAATAATAAT
Found at i:5549761 original size:28 final size:26
Alignment explanation
Indices: 5549698--5549766 Score: 61
Period size: 28 Copynumber: 2.5 Consensus size: 26
5549688 AATAAATAAA
5549698 ATATAAA-ATAATAAT-AATAATAAAT
1 ATATAAATATAATAATAAATAAT-AAT
*
5549723 AAATTATAATATAATAATAAATATATAACT
1 ATA-TA-AATATAATAATAAATA-ATAA-T
*
5549753 ATATAAATAAAATA
1 ATATAAATATAATA
5549767 CATATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
25 2 0.06
26 2 0.06
27 2 0.06
28 16 0.46
29 8 0.23
30 5 0.14
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (26 bp):
ATATAAATATAATAATAAATAATAAT
Found at i:5549766 original size:25 final size:25
Alignment explanation
Indices: 5549688--5549777 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 25
5549678 AAAATACAAA
5549688 AATAAATA-A-AATATA-AAATAAT
1 AATAAATATATAATATATAAATAAT
*
5549710 AATAATAATAAATAA-ATTATAATATAAT
1 AAT-A-AATATATAATA-TATAA-ATAAT
5549738 AATAAATATATAACTATATAAATAA-
1 AATAAATATATAA-TATATAAATAAT
*
5549763 AATACATATA-AATAT
1 AATAAATATATAATAT
5549778 TAACAGAAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
22 3 0.05
23 4 0.07
24 6 0.11
25 11 0.19
26 16 0.28
27 8 0.14
28 9 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAAATATATAATATATAAATAAT
Found at i:5549867 original size:29 final size:26
Alignment explanation
Indices: 5549834--5549890 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
5549824 TACATATATT
* *
5549834 AATACATAGTAATAATAAATAAATAATAA
1 AATACATA-AAAT-ATAAA-AAAAAATAA
5549863 AATACATAAAATATAAAAAAAAATAA
1 AATACATAAAATATAAAAAAAAATAA
5549889 AA
1 AA
5549891 ATAATACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 5 0.19
28 3 0.12
29 8 0.31
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (26 bp):
AATACATAAAATATAAAAAAAAATAA
Found at i:5549896 original size:21 final size:23
Alignment explanation
Indices: 5549847--5549901 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 23
5549837 ACATAGTAAT
*
5549847 AATAA-ATAAATAATAAAATACAT
1 AATAATATAAA-AATAAAATACAA
5549870 AA-AATATAAAAA-AAAATA-AA
1 AATAATATAAAAATAAAATACAA
*
5549890 AATAATACAAAA
1 AATAATATAAAA
5549902 TAAGAATCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 14 0.50
22 4 0.14
23 7 0.25
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (23 bp):
AATAATATAAAAATAAAATACAA
Found at i:5549901 original size:10 final size:9
Alignment explanation
Indices: 5549844--5549904 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 9
5549834 AATACATAGT
5549844 AATAATAAATA
1 AATAAT-AA-A
5549855 AATAAT-AA
1 AATAATAAA
5549863 AATACATAAA
1 AATA-ATAAA
5549873 ATATAA-AAA
1 A-ATAATAAA
5549882 AA-AATAAA
1 AATAATAAA
5549890 AATAATACAA
1 AATAATA-AA
5549900 AATAA
1 AATAA
5549905 GAATCGAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
7 2 0.05
8 11 0.25
9 11 0.25
10 11 0.25
11 9 0.20
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAATAAA
Found at i:5549901 original size:17 final size:17
Alignment explanation
Indices: 5549854--5549901 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
5549844 AATAATAAAT
5549854 AAATAATAAAATACATAA
1 AAATAATAAAA-ACATAA
*
5549872 AATATAA-AAAAAAATAA
1 AA-ATAATAAAAACATAA
5549889 AAATAATACAAAA
1 AAATAATA-AAAA
5549902 TAAGAATCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.15
17 8 0.31
18 10 0.38
19 4 0.15
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATAATAAAAACATAA
Found at i:5549904 original size:26 final size:26
Alignment explanation
Indices: 5549847--5549904 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
5549837 ACATAGTAAT
*
5549847 AATAAATAAATAATAAAATACATAAA
1 AATAAATAAAAAATAAAATACATAAA
5549873 ATATAAA-AAAAAATAAAAATA-ATACAA
1 A-ATAAATAAAAAAT-AAAATACATA-AA
5549900 AATAA
1 AATAA
5549905 GAATCGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (26 bp):
AATAAATAAAAAATAAAATACATAAA
Found at i:5553662 original size:234 final size:232
Alignment explanation
Indices: 5553259--5553698 Score: 571
Period size: 234 Copynumber: 1.9 Consensus size: 232
5553249 GATGAAAAAA
** *
5553259 TTTCATGTATTTTATAATTTGGACACAATTTATAGTAATGTGTGGTTATACATGAAATTTTGATT
1 TTTCATGTATTTTATAATTAAGACACAATTTATAGTAATGTGTGGTTATACATGAAATTTTGACT
* ** * *
5553324 ATTTTTAATGACATGAACTGTGATGAATATGGTTTTAGTGTCATGATCAAATAATTTTTAAGTAT
66 ATTTTTAATGACATGAACTGTGACGAATATGACTTTAATGTCATGATCAAATAATTTTTAAATAT
* * * ** * *
5553389 CTAAGAGTTGAAATAAAAATTTTAAAAGGAGATTATAAAAAACATAAGTTTTTTAATTTTAAGGG
131 CCAAGAGTTGAAATAAAAATCTCAAAAAAAGACTATAAAAAACATAAGTTTATTAATTTTAAGGG
5553454 TGATTATATTTAATTTTTTATTTGTTGAGTGAAAATT
196 TGATTATATTTAATTTTTTATTTGTTGAGTGAAAATT
*
5553491 TTTCATGTATTTTATAATTAAGACACAAATTTTATAGTATTGTGT-GTTATACATGAAATTTTGA
1 TTTCATGTATTTTATAATTAAGACAC-AA-TTTATAGTAATGTGTGGTTATACATGAAATTTTGA
* * *
5553555 CTGTTTTTAATGATATGAA-TGGTGACGGATATGACTTTAATGTCCATGATCAAATAATTTTTAA
64 CTATTTTTAATGACATGAACT-GTGACGAATATGACTTTAATGT-CATGATCAAATAATTTTTAA
* * ** * *
5553619 ATATCCAAGAGTT-AGAATGAAAGTCTCAAAAAAAGACTATAAAAAGTATTAGTTTATTAGTTTT
127 ATATCCAAGAGTTGA-AATAAAAATCTCAAAAAAAGACTATAAAAAACATAAGTTTATTAATTTT
* *
5553683 GAGGGTGGTTATATTT
191 AAGGGTGATTATATTT
5553699 GGTATCATAT
Statistics
Matches: 176, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
232 25 0.14
233 55 0.31
234 96 0.55
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (232 bp):
TTTCATGTATTTTATAATTAAGACACAATTTATAGTAATGTGTGGTTATACATGAAATTTTGACT
ATTTTTAATGACATGAACTGTGACGAATATGACTTTAATGTCATGATCAAATAATTTTTAAATAT
CCAAGAGTTGAAATAAAAATCTCAAAAAAAGACTATAAAAAACATAAGTTTATTAATTTTAAGGG
TGATTATATTTAATTTTTTATTTGTTGAGTGAAAATT
Found at i:5556083 original size:52 final size:52
Alignment explanation
Indices: 5556000--5556103 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
5555990 ATAAGCATAT
*
5556000 AAACTTGCCTATTAAGAATCTTTTTCCTCTTAAAATTCTTCTTCTGTAAGTC
1 AAACTTACCTATTAAGAATCTTTTTCCTCTTAAAATTCTTCTTCTGTAAGTC
* * * *
5556052 AAACTTACCTATTAAGAATCTCTTTT-TTCTTAGAATTTTTCTTTTGTAAGTC
1 AAACTTACCTATTAAGAATCT-TTTTCCTCTTAAAATTCTTCTTCTGTAAGTC
5556104 TTCTTATCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 42 0.91
53 4 0.09
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (52 bp):
AAACTTACCTATTAAGAATCTTTTTCCTCTTAAAATTCTTCTTCTGTAAGTC
Found at i:5557018 original size:52 final size:53
Alignment explanation
Indices: 5556899--5557003 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 53
5556889 ATAAGTATAT
* * * *
5556899 AAACTTGCTTATTAAAAAT-CCTTTTTCTCTTAGAATTTTTCTTCTGCAAGTC
1 AAACTTACCTATTAAAAATATCTTTTTCTCTTAGAATTCTTCTTCTGCAAGTC
* * *
5556951 AAACTTACCTATTAAAAATATCTTTTTCTTTTAGAATTCTTCTTTTGTAAGTC
1 AAACTTACCTATTAAAAATATCTTTTTCTCTTAGAATTCTTCTTCTGCAAGTC
5557004 TTCTTGTCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 17 0.38
53 28 0.62
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.48
Consensus pattern (53 bp):
AAACTTACCTATTAAAAATATCTTTTTCTCTTAGAATTCTTCTTCTGCAAGTC
Found at i:5566459 original size:51 final size:51
Alignment explanation
Indices: 5566399--5566530 Score: 169
Period size: 51 Copynumber: 2.6 Consensus size: 51
5566389 TCCTCAGTTG
**
5566399 TAGTTTATATGACTGCTATATCAAATATAC-ATTCAATGCTAGAAAGGTTAT
1 TAGTTTATATGACTGCTATATCAAATAT-CTATTCAATGCTAGAAAAATTAT
* * *
5566450 TAGTTTATATGACTGCTATATCAAATATCTATTCAATGTTGGAAAAATTGT
1 TAGTTTATATGACTGCTATATCAAATATCTATTCAATGCTAGAAAAATTAT
* *
5566501 TAGTTTATATGATTGGC-ATAGCAAATATCT
1 TAGTTTATATGACT-GCTATATCAAATATCT
5566531 TCTGAAAGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 1 0.01
51 69 0.96
52 2 0.03
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (51 bp):
TAGTTTATATGACTGCTATATCAAATATCTATTCAATGCTAGAAAAATTAT
Found at i:5567200 original size:30 final size:30
Alignment explanation
Indices: 5567102--5567207 Score: 94
Period size: 30 Copynumber: 3.5 Consensus size: 30
5567092 TATTTAAAAG
*
5567102 AAAAATTTAGAAAAAGTTTTTAAAA-ATTCTA
1 AAAAATTTATAAAAA-TTTTTAAAATATTC-A
* * * *
5567133 CAAAATCTAAAAAAAATTTTAAAAT-TAT-A
1 AAAAATTTATAAAAATTTTTAAAATAT-TCA
*
5567162 AAACAATTTCTAAAAATTTTTAAAATATTCA
1 AAA-AATTTATAAAAATTTTTAAAATATTCA
5567193 AAAAATTT-TAAAAAT
1 AAAAATTTATAAAAAT
5567208 GCTAAAAAAG
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
29 10 0.16
30 33 0.54
31 18 0.30
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAAATTTATAAAAATTTTTAAAATATTCA
Found at i:5567215 original size:20 final size:20
Alignment explanation
Indices: 5567173--5567216 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5567163 AACAATTTCT
* * *
5567173 AAAAATTTTTAAAATATTCA
1 AAAAATTTTAAAAATACTAA
*
5567193 AAAAATTTTAAAAATGCTAA
1 AAAAATTTTAAAAATACTAA
5567213 AAAA
1 AAAA
5567217 GCTAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAATTTTAAAAATACTAA
Found at i:5567272 original size:10 final size:10
Alignment explanation
Indices: 5567235--5567322 Score: 65
Period size: 10 Copynumber: 8.8 Consensus size: 10
5567225 TTTTTAAAAC
5567235 CTAAAAAATTT
1 CTAAAAAA-TT
*
5567246 CTAAAAAGTT
1 CTAAAAAATT
* * *
5567256 TTTAAAACTT
1 CTAAAAAATT
*
5567266 CAAAAAAAATT
1 C-TAAAAAATT
*
5567277 -TAAAAACTT
1 CTAAAAAATT
*
5567286 AT-AAAAATT
1 CTAAAAAATT
5567295 C-AAAATAATT
1 CTAAAA-AATT
5567305 CTAAAAAATT
1 CTAAAAAATT
5567315 CTAAAAAA
1 CTAAAAAA
5567323 ATGTTAAATT
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
9 16 0.27
10 27 0.45
11 17 0.28
ACGTcount: A:0.59, C:0.09, G:0.01, T:0.31
Consensus pattern (10 bp):
CTAAAAAATT
Found at i:5567309 original size:29 final size:30
Alignment explanation
Indices: 5567237--5567321 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 30
5567227 TTTAAAACCT
* * * *
5567237 AAAAAATTTCTAAAAAGTTTTTAAAACTTCA
1 AAAAAAATTCTAAAAA-ATTATAAAAATTCA
*
5567268 AAAAAAATT-TAAAAACTTATAAAAATTC-
1 AAAAAAATTCTAAAAAATTATAAAAATTCA
* *
5567296 AAAATAATTCTAAAAAATTCTAAAAA
1 AAAAAAATTCTAAAAAATTATAAAAA
5567322 AATGTTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 8 0.17
29 24 0.52
30 6 0.13
31 8 0.17
ACGTcount: A:0.60, C:0.08, G:0.01, T:0.31
Consensus pattern (30 bp):
AAAAAAATTCTAAAAAATTATAAAAATTCA
Found at i:5567414 original size:11 final size:11
Alignment explanation
Indices: 5567398--5567447 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
5567388 TTTAGTGAGC
5567398 AAAAATTTTTT
1 AAAAATTTTTT
* *
5567409 AAAAATTTCTC
1 AAAAATTTTTT
5567420 AAAAA---TTT
1 AAAAATTTTTT
5567428 AAAAATTTTTT
1 AAAAATTTTTT
5567439 AAAAATTTT
1 AAAAATTTT
5567448 AAGCAATTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
8 6 0.19
11 26 0.81
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAAATTTTTT
Found at i:5567430 original size:19 final size:19
Alignment explanation
Indices: 5567406--5567446 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
5567396 GCAAAAATTT
5567406 TTTAAAAATTTCTCAAAAA
1 TTTAAAAATTTCTCAAAAA
* *
5567425 TTTAAAAATTTTTTAAAAA
1 TTTAAAAATTTCTCAAAAA
5567444 TTT
1 TTT
5567447 TAAGCAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTAAAAATTTCTCAAAAA
Found at i:5567467 original size:10 final size:10
Alignment explanation
Indices: 5567398--5567470 Score: 55
Period size: 10 Copynumber: 7.3 Consensus size: 10
5567388 TTTAGTGAGC
*
5567398 AAAAATTTTTT
1 AAAAA-TTTCT
5567409 AAAAATTTCT
1 AAAAATTTCT
5567419 CAAAAA-TT-T
1 -AAAAATTTCT
*
5567428 AAAAATTTTTT
1 AAAAA-TTTCT
5567439 AAAAATTT-T
1 AAAAATTTCT
*
5567448 AAGCAA-TTCT
1 AA-AAATTTCT
5567458 AAAAATTTCT
1 AAAAATTTCT
5567468 AAA
1 AAA
5567471 TTTTTTGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
8 5 0.10
9 8 0.15
10 23 0.44
11 16 0.31
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (10 bp):
AAAAATTTCT
Found at i:5567500 original size:19 final size:19
Alignment explanation
Indices: 5567409--5567546 Score: 61
Period size: 19 Copynumber: 7.2 Consensus size: 19
5567399 AAAATTTTTT
5567409 AAAAATTTCTCAAAAATT-TA
1 AAAAATTT-T-AAAAATTATA
* *
5567429 AAAATTTTTTAAAAATTTTA
1 AAAA-ATTTTAAAAATTATA
** * *
5567449 AGCAATTCTAAAAATT-TCT
1 AAAAATTTTAAAAATTAT-A
**
5567468 AAATTTTTTGAAAAATTATA
1 AAAAATTTT-AAAAATTATA
*
5567488 AAAAATTTTAAAATTTATA
1 AAAAATTTTAAAAATTATA
*
5567507 TATAAA--TTAAAAA-TATA
1 -AAAAATTTTAAAAATTATA
* * *
5567524 AATTATTTTTATAAATTATA
1 AA-AAATTTTAAAAATTATA
5567544 AAA
1 AAA
5567547 TTATCATAAT
Statistics
Matches: 86, Mismatches: 22, Indels: 21
0.67 0.17 0.16
Matches are distributed among these distances:
16 1 0.01
17 5 0.06
18 7 0.08
19 36 0.42
20 33 0.38
21 4 0.05
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (19 bp):
AAAAATTTTAAAAATTATA
Found at i:5567766 original size:9 final size:10
Alignment explanation
Indices: 5567754--5567837 Score: 66
Period size: 10 Copynumber: 8.5 Consensus size: 10
5567744 TTTTCATAAT
5567754 TTTTTTAG-A
1 TTTTTTAGAA
*
5567763 TTTTTTTGAA
1 TTTTTTAGAA
5567773 TTTTTTA-ATA
1 TTTTTTAGA-A
* *
5567783 ATTTTTAAAA
1 TTTTTTAGAA
*
5567793 GTTTTTATGAA
1 TTTTTTA-GAA
* *
5567804 TTTTTGAAAA
1 TTTTTTAGAA
5567814 TTTTTT-GAA
1 TTTTTTAGAA
*
5567823 TTTTTTATAA
1 TTTTTTAGAA
5567833 TTTTT
1 TTTTT
5567838 AAAAACATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
9 16 0.27
10 35 0.59
11 8 0.14
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (10 bp):
TTTTTTAGAA
Found at i:5567834 original size:19 final size:19
Alignment explanation
Indices: 5567744--5567837 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 19
5567734 TGTTAAAATA
* *
5567744 TTTTCATAATTTTTTTAGAT
1 TTTTTATAATTTTTTGA-AT
5567764 TTTTT-TGAATTTTTT-AAT
1 TTTTTAT-AATTTTTTGAAT
*
5567782 AATTTTTAAAAGTTTTTATGAAT
1 --TTTTTATAA-TTTTT-TGAAT
* *
5567805 TTTTGAAAATTTTTTGAAT
1 TTTTTATAATTTTTTGAAT
5567824 TTTTTATAATTTTT
1 TTTTTATAATTTTT
5567838 AAAAACATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.03
19 19 0.31
20 24 0.39
21 13 0.21
22 1 0.02
23 3 0.05
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (19 bp):
TTTTTATAATTTTTTGAAT
Found at i:5567838 original size:9 final size:9
Alignment explanation
Indices: 5567727--5567838 Score: 64
Period size: 10 Copynumber: 11.3 Consensus size: 9
5567717 TTTAAATCTG
*
5567727 TTATAATTG
1 TTATAATTT
*
5567736 TTAAAATATT
1 TTATAAT-TT
5567746 TTCATAATTT
1 TT-ATAATTT
*
5567756 TTTTAGATTT
1 TTATA-ATTT
*
5567766 TTTTGAATTTT
1 TTAT-AA-TTT
5567777 TTAATAATTT
1 TT-ATAATTT
*
5567787 TTAAAAGTTT
1 TTATAA-TTT
5567797 TTATGAATTT
1 TTAT-AATTT
*
5567807 TTGAAAATTT
1 TT-ATAATTT
5567817 TT-TGAATTTT
1 TTAT-AA-TTT
5567827 TTATAATTT
1 TTATAATTT
5567836 TTA
1 TTA
5567839 AAAACATTTC
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
9 19 0.23
10 46 0.56
11 16 0.20
12 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (9 bp):
TTATAATTT
Found at i:5568811 original size:22 final size:20
Alignment explanation
Indices: 5568778--5568826 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
5568768 AGTTAAATTC
5568778 ATTAAAATTTGAATAAAAAT
1 ATTAAAATTTGAATAAAAAT
*
5568798 ATTAAAACTATTGAATTAAAAT
1 ATTAAAA-T-TTGAATAAAAAT
*
5568820 AATAAAA
1 ATTAAAA
5568827 GACTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 1 0.04
22 17 0.68
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
ATTAAAATTTGAATAAAAAT
Found at i:5570074 original size:17 final size:17
Alignment explanation
Indices: 5570052--5570086 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5570042 TAAAAAAATT
* *
5570052 TAATTTTTTATTTCATA
1 TAATTTTTAATTTAATA
5570069 TAATTTTTAATTTAATA
1 TAATTTTTAATTTAATA
5570086 T
1 T
5570087 TTTTAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TAATTTTTAATTTAATA
Found at i:5576311 original size:211 final size:211
Alignment explanation
Indices: 5575947--5576347 Score: 689
Period size: 211 Copynumber: 1.9 Consensus size: 211
5575937 ATAAATATGT
*
5575947 TTATCATAAAATTATATTTGATATCTAGATAATTAATTATATAAACAATAAATCCTAAATAATTA
1 TTATCATAAAATTATATTTGATATCTAGAGAATTAATTATATAAACAATAAATCCTAAATAATTA
* **
5576012 AGTAAACAATTATTATTTTATTAAGTTCAATATGTATAAGTATATTATTATCAATTGTTAATAAA
66 AGTAAACAATTATTATTTTATTAAGTTCAATACGTATAAACATATTATTATCAATTGTTAATAAA
* *
5576077 AGTATTATTTAATATAAAAATAATTTTAATAAATTTTAATTATTTATTTAATATATATAAACTTT
131 AGTATTATTTAATATAAAAATAATTTTAATAAAATTTAATTAATTATTTAATATATATAAACTTT
5576142 AATTTAATGTCATTTG
196 AATTTAATGTCATTTG
* *
5576158 TTATCATAAAATTATATTTGATATCTTGAGAATTAATTATATAAACAATACATCCTAAATAATCT
1 TTATCATAAAATTATATTTGATATCTAGAGAATTAATTATATAAACAATAAATCCTAAATAAT-T
5576223 -AGTAAACAATTATTATTTTATTAAGTCTCAATACGTATAAACATATTATTATCAATTGTTAATA
65 AAGTAAACAATTATTATTTTATTAAGT-TCAATACGTATAAACATATTATTATCAATTGTTAATA
*
5576287 AAAGTATTATTTAATAT-GAAATAATTTTAATAAAATTTAATTAATTATTTAATATATATAA
129 AAAGTATTATTTAATATAAAAATAATTTTAATAAAATTTAATTAATTATTTAATATATATAA
5576348 TGATTCCAAG
Statistics
Matches: 179, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
211 127 0.71
212 52 0.29
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (211 bp):
TTATCATAAAATTATATTTGATATCTAGAGAATTAATTATATAAACAATAAATCCTAAATAATTA
AGTAAACAATTATTATTTTATTAAGTTCAATACGTATAAACATATTATTATCAATTGTTAATAAA
AGTATTATTTAATATAAAAATAATTTTAATAAAATTTAATTAATTATTTAATATATATAAACTTT
AATTTAATGTCATTTG
Found at i:5579960 original size:19 final size:19
Alignment explanation
Indices: 5579936--5579974 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5579926 TAAAAAGTCA
*
5579936 TTATTTGAGGCGTTTTTAG
1 TTATTTAAGGCGTTTTTAG
5579955 TTATTTAAGGCGTTTTTAG
1 TTATTTAAGGCGTTTTTAG
5579974 T
1 T
5579975 CAAAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.05, G:0.23, T:0.54
Consensus pattern (19 bp):
TTATTTAAGGCGTTTTTAG
Found at i:5581738 original size:21 final size:21
Alignment explanation
Indices: 5581706--5581784 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 21
5581696 ATAAGTAAAA
5581706 AAAATCAT-AAAAAATAATTTT
1 AAAAT-ATAAAAAAATAATTTT
*
5581727 AAAATATAAAAAATAAAAGTTTT
1 AAAATATAAAAAA-ATAA-TTTT
* *
5581750 -AGATATTAAAAAAAT-ATTTC
1 AAAATA-TAAAAAAATAATTTT
* *
5581770 GAGATATAAAAAAAT
1 AAAATATAAAAAAAT
5581785 TGACAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 14 0.29
21 16 0.33
22 8 0.16
23 11 0.22
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAATATAAAAAAATAATTTT
Found at i:5583047 original size:22 final size:23
Alignment explanation
Indices: 5583003--5583049 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
5582993 TTTAACTTAT
*
5583003 TATAATAAATTTTAATTTGAAAA
1 TATAATAAATTTTAATATGAAAA
5583026 TATAA-AAATTTATAATAT-AAAA
1 TATAATAAATTT-TAATATGAAAA
5583048 TA
1 TA
5583050 ATTCAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TATAATAAATTTTAATATGAAAA
Found at i:5583172 original size:23 final size:23
Alignment explanation
Indices: 5583146--5583215 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
5583136 TAGTGATAAA
*
5583146 ATTTTTTTTATAAAAATTTCATC
1 ATTTTTTTAATAAAAATTTCATC
* *
5583169 A-TTTTTTAATAAAAATTTTATT
1 ATTTTTTTAATAAAAATTTCATC
* * *
5583191 ATTTTTTAAAATAATAATTTGATC
1 ATTTTTT-TAATAAAAATTTCATC
5583215 A
1 A
5583216 CTCTCAATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 19 0.50
23 6 0.16
24 13 0.34
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (23 bp):
ATTTTTTTAATAAAAATTTCATC
Found at i:5583173 original size:22 final size:22
Alignment explanation
Indices: 5583148--5583199 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
5583138 GTGATAAAAT
*
5583148 TTTTTTTATAAAAATTTCATCA
1 TTTTTTAATAAAAATTTCATCA
* *
5583170 TTTTTTAATAAAAATTTTATTA
1 TTTTTTAATAAAAATTTCATCA
5583192 TTTTTTAA
1 TTTTTTAA
5583200 AATAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTTAATAAAAATTTCATCA
Found at i:5588408 original size:1 final size:1
Alignment explanation
Indices: 5588402--5588441 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
5588392 GTAGAAAATG
5588402 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5588442 CTGTCATGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5589712 original size:1 final size:1
Alignment explanation
Indices: 5589706--5589736 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
5589696 AGTAATCTCA
*
5589706 TTTTTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5589737 ATGTTAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:5589931 original size:19 final size:19
Alignment explanation
Indices: 5589907--5589945 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5589897 TTTTTTTTAA
5589907 AATTATAATTATAA-ATTAC
1 AATTATAATTA-AATATTAC
5589926 AATTATAATTAAATATTAC
1 AATTATAATTAAATATTAC
5589945 A
1 A
5589946 TAATTGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTATAATTAAATATTAC
Done.