Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001349.1 Hibiscus syriacus cultivar Beakdansim tig00002627_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 85988
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3494 original size:21 final size:22
Alignment explanation
Indices: 3465--3522 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
3455 TTGTGCTTAA
3465 TGCATCGAT-ACACCATGAAGG
1 TGCATCGATCACACCATGAAGG
* * *
3486 TGCACCGATGCACACCTTGAATG
1 TGCATCGAT-CACACCATGAAGG
3509 TGCATCGATGCACA
1 TGCATCGAT-CACA
3523 AGGCCATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 8 0.26
23 23 0.74
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (22 bp):
TGCATCGATCACACCATGAAGG
Found at i:3506 original size:23 final size:23
Alignment explanation
Indices: 3474--3522 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3464 ATGCATCGAT
3474 ACACCATGAAGGTGCACCGATGC
1 ACACCATGAAGGTGCACCGATGC
* * *
3497 ACACCTTGAATGTGCATCGATGC
1 ACACCATGAAGGTGCACCGATGC
3520 ACA
1 ACA
3523 AGGCCATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (23 bp):
ACACCATGAAGGTGCACCGATGC
Found at i:6256 original size:64 final size:62
Alignment explanation
Indices: 6178--6367 Score: 197
Period size: 64 Copynumber: 3.0 Consensus size: 62
6168 ATTCACCAAT
* *
6178 CCATGCATCGATGCACCATGAATCAAATTG-AACATCGAATGCATTTCATGCATCGATGCACATA
1 CCATGCATCGATGCACC-TGAAT-ATATTGAAACATCGAATGCATTTGATGCATCGATGCACA-A
* *
6242 CCATGCATCAATGCA-CTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCACC
1 CCATGCATCGATGCACCTGA--ATATAT-TG-AAACATCGAATGCATTTGATGCATCGATGCA-C
*
6305 AG
61 AA
** * *
6307 CCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1 CCATGCATCGATGCAC-CTGAATATATTGAAACATCGAATGCATTTGATGCATCGATGCAC
6368 TTTTAGTGCA
Statistics
Matches: 108, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
62 4 0.04
63 4 0.04
64 46 0.43
65 46 0.43
66 5 0.05
67 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (62 bp):
CCATGCATCGATGCACCTGAATATATTGAAACATCGAATGCATTTGATGCATCGATGCACAA
Found at i:6287 original size:65 final size:63
Alignment explanation
Indices: 6208--6367 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
6198 AATCAAATTG
* *
6208 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCAATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCAATGCACTCAGGATATTT-TG-
6272 A
63 A
* * * *
6273 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCAATGCACTCAGGATATTTTGA
*
6337 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
6368 TTTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 50 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCAATGCACTCAGGATATTTTGA
Found at i:7479 original size:2 final size:2
Alignment explanation
Indices: 7472--7510 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7462 AAAATATTAA
7472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7511 ATTTTAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8615 original size:2 final size:2
Alignment explanation
Indices: 8608--8637 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8598 GAGCTCCTTT
8608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8638 AAAATATACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14627 original size:27 final size:27
Alignment explanation
Indices: 14589--14651 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
14579 ATGGAGTTAC
14589 AGAGAGTCCAAAATCTCCATTTTGAAA
1 AGAGAGTCCAAAATCTCCATTTTGAAA
14616 AGAGAGTCCAAAATCTCCATTTTGAAA
1 AGAGAGTCCAAAATCTCCATTTTGAAA
14643 AGAGAGTCC
1 AGAGAGTCC
14652 TTACTCTGCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (27 bp):
AGAGAGTCCAAAATCTCCATTTTGAAA
Found at i:17736 original size:2 final size:2
Alignment explanation
Indices: 17729--17761 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17719 GGTGGTTAAC
17729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17762 GCAAAACGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18324 original size:4 final size:4
Alignment explanation
Indices: 18315--18972 Score: 1288
Period size: 4 Copynumber: 165.5 Consensus size: 4
18305 TGTAATTTTG
18315 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18363 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18411 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18459 GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18505 GTAT GTAT GTAT GTAT GTA- -TAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18551 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18599 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18647 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18695 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18743 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18791 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18839 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18887 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18935 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
18973 TATAAGCCTT
Statistics
Matches: 650, Mismatches: 0, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
2 4 0.01
4 646 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:20598 original size:16 final size:16
Alignment explanation
Indices: 20577--20614 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
20567 CGAATAAAAG
20577 CATGCGAACTAGATAC
1 CATGCGAACTAGATAC
20593 CATGCGAACTAGATAC
1 CATGCGAACTAGATAC
20609 CATGCG
1 CATGCG
20615 GTTAAGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (16 bp):
CATGCGAACTAGATAC
Found at i:20659 original size:16 final size:17
Alignment explanation
Indices: 20638--20670 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20628 TCTTGAAAAT
*
20638 AAATCAT-TTTGGGTAG
1 AAATCATGTTCGGGTAG
20654 AAATCATGTTCGGGTAG
1 AAATCATGTTCGGGTAG
20671 GATTACTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (17 bp):
AAATCATGTTCGGGTAG
Found at i:26773 original size:16 final size:17
Alignment explanation
Indices: 26740--26773 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
26730 CCATCCATTT
*
26740 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
26757 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
26773 T
1 T
26774 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:27969 original size:27 final size:27
Alignment explanation
Indices: 27936--28023 Score: 176
Period size: 27 Copynumber: 3.3 Consensus size: 27
27926 TTCTTTTAAG
27936 GATGAAATTAGATAAGATTAGGTTTAT
1 GATGAAATTAGATAAGATTAGGTTTAT
27963 GATGAAATTAGATAAGATTAGGTTTAT
1 GATGAAATTAGATAAGATTAGGTTTAT
27990 GATGAAATTAGATAAGATTAGGTTTAT
1 GATGAAATTAGATAAGATTAGGTTTAT
28017 GATGAAA
1 GATGAAA
28024 AAAACTTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (27 bp):
GATGAAATTAGATAAGATTAGGTTTAT
Found at i:29165 original size:42 final size:42
Alignment explanation
Indices: 29105--29220 Score: 205
Period size: 42 Copynumber: 2.8 Consensus size: 42
29095 CCCGAAATCT
*
29105 CGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
*
29147 CGTGTTTGTGTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
*
29189 CGTGTTTGTTTCACGTAATTCATTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
29221 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
Found at i:29433 original size:21 final size:23
Alignment explanation
Indices: 29390--29440 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
29380 ATCATTCATC
29390 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
29414 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
*
29435 ATAATA
1 AAAATA
29441 ATATAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
23 8 0.31
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:29454 original size:22 final size:23
Alignment explanation
Indices: 29407--29501 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 23
29397 TATTTATTAA
* *
29407 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
29428 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
29451 -ATATTTTTAATATTATATAAAATAATC
1 AATATTTATAATA--ATAT--AAT-ATT
29478 AATTATATTATAATAATATAATAT
1 AA-TAT-TTATAATAATATAATAT
29502 AAGATATTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
21 11 0.19
22 15 0.25
23 4 0.07
24 4 0.07
25 2 0.03
26 6 0.10
27 2 0.03
28 5 0.08
29 3 0.05
30 7 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:29464 original size:31 final size:30
Alignment explanation
Indices: 29418--29571 Score: 121
Period size: 31 Copynumber: 5.1 Consensus size: 30
29408 ATATTTAAAA
29418 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTT-TTAATATTTATAAT-ATATAATAT
29450 TATATTTTTAATATTATATAA-A-ATAATCAAT
1 TATATTTTTAATATT-TATAATATATAAT--AT
* *
29481 TATA-TTATAATA-ATATAATATA-AGATAT
1 TATATTTTTAATATTTATAATATATA-ATAT
29509 TATATTTTT-AT-TTTAATAATATATAATAAT
1 TATATTTTTAATATTT-ATAATATATAAT-AT
29539 T-T-TTTTTATATATTTAATAATGA-ATAATAT
1 TATATTTTTA-ATATTT-ATAAT-ATATAATAT
29569 TAT
1 TAT
29572 TTATATTTAA
Statistics
Matches: 102, Mismatches: 4, Indels: 33
0.73 0.03 0.24
Matches are distributed among these distances:
28 19 0.19
29 21 0.21
30 20 0.20
31 29 0.28
32 13 0.13
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (30 bp):
TATATTTTTAATATTTATAATATATAATAT
Found at i:29474 original size:64 final size:64
Alignment explanation
Indices: 29400--29639 Score: 166
Period size: 59 Copynumber: 3.8 Consensus size: 64
29390 AAAATATTAT
*
29400 TTAT-TAAAATATTTAAAATATATTTATTAATATTTATAATAATATAATATTATATTTTTAATA
1 TTATATAAAATATATAAAATATATTTATTAATATTTATAATAATATAATATTATATTTTTAATA
* * *
29463 TTATATAAAATA-ATCAATTATA-TTA-TAATA-ATATAAT-ATA-AGATATTATATTTTT-AT-
1 TTATATAAAATATATAAAATATATTTATTAATATTTATAATAATATA-ATATTATATTTTTAATA
* * *
29520 TT-TA-ATAATATATAATAAT-T-TTTTTTATATATTTAATAATGAATAATATTATTTATATTTA
1 TTATATAAAATATATAA-AATATATTTATTA-ATATTT-ATAAT-AAT-ATAATA-TTATATTT-
*
29581 AATAATA
59 -TTAATA
* * * * *
29588 TTTTAGTAAAGATATTTAAAATATACTAATTAATATTTTTAA-AATATAATAT
1 TTATA-TAAA-ATATATAAAATATATTTATTAATATTTATAATAATATAATAT
29640 AACACTATTA
Statistics
Matches: 135, Mismatches: 18, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
55 5 0.04
56 8 0.06
57 6 0.04
58 6 0.04
59 17 0.13
60 11 0.08
61 5 0.04
62 5 0.04
63 14 0.10
64 16 0.12
66 1 0.01
67 3 0.02
68 7 0.05
69 5 0.04
71 8 0.06
72 14 0.10
73 4 0.03
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (64 bp):
TTATATAAAATATATAAAATATATTTATTAATATTTATAATAATATAATATTATATTTTTAATA
Found at i:29532 original size:24 final size:23
Alignment explanation
Indices: 29500--29546 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
29490 ATAATATAAT
* *
29500 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
29524 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
29547 TATATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:29752 original size:90 final size:85
Alignment explanation
Indices: 29604--29772 Score: 189
Period size: 90 Copynumber: 1.9 Consensus size: 85
29594 TAAAGATATT
* * * * * *
29604 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAA-A
29669 TAATTTATAATATTTTATTTCAC
65 TAA-TTA-AATATTTTATTTCAC
*
29692 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATA-TTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
*
29755 AAATTATTAAATATTTTA
62 AAATAATTAAATATTTTA
29773 AAATAATAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
87 9 0.13
88 12 0.17
89 5 0.07
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (85 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAAAT
AATTAAATATTTTATTTCAC
Found at i:29767 original size:26 final size:26
Alignment explanation
Indices: 29738--29810 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 26
29728 TTATAAAAAT
29738 AATATTTAATAATAAATAAATTATTA
1 AATATTTAATAATAAATAAATTATTA
29764 AATATTTTAA-AAT-AAT-AA-TATTA
1 AATA-TTTAATAATAAATAAATTATTA
* *
29787 AGT-TTT-ATGATAAATAATATTATT
1 AATATTTAATAATAAATAA-ATTATT
29811 TATTATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
20 1 0.03
21 5 0.13
22 3 0.08
23 8 0.21
24 3 0.08
25 7 0.18
26 7 0.18
27 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
AATATTTAATAATAAATAAATTATTA
Found at i:29961 original size:29 final size:30
Alignment explanation
Indices: 29928--29992 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
29918 TTCCAGAAAT
* *
29928 GTAATTCATTTTTC-ATAATTCAAATTTCA
1 GTAATTCATTTTCCAATAATTCAAATTCCA
29957 GTAATTCATTTTCCAATAATTCAAATTCCA
1 GTAATTCATTTTCCAATAATTCAAATTCCA
29987 GTAATT
1 GTAATT
29993 TAAATTGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (30 bp):
GTAATTCATTTTCCAATAATTCAAATTCCA
Found at i:29963 original size:15 final size:15
Alignment explanation
Indices: 29928--30009 Score: 78
Period size: 15 Copynumber: 5.5 Consensus size: 15
29918 TTCCAGAAAT
**
29928 GTAATTCATTTTTCA
1 GTAATTCAAATTTCA
29943 -TAATTCAAATTTCA
1 GTAATTCAAATTTCA
*
29957 GTAATTC-ATTTTCCA
1 GTAATTCAAATTT-CA
* *
29972 ATAATTCAAATTCCA
1 GTAATTCAAATTTCA
* *
29987 GTAATTTAAATTGCA
1 GTAATTCAAATTTCA
30002 GTAATTCA
1 GTAATTCA
30010 TTTTTCGGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
14 16 0.30
15 35 0.65
16 3 0.06
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (15 bp):
GTAATTCAAATTTCA
Found at i:30404 original size:35 final size:35
Alignment explanation
Indices: 30358--30425 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
30348 GACTGGTTGA
30358 TTCTTCTTCTTCTTATGGTCACCACTAGCTACCGC
1 TTCTTCTTCTTCTTATGGTCACCACTAGCTACCGC
30393 TTCTTCTTCTTCTTATGGTCACCACTAGCTACC
1 TTCTTCTTCTTCTTATGGTCACCACTAGCTACC
30426 ACATTCTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.15, C:0.34, G:0.10, T:0.41
Consensus pattern (35 bp):
TTCTTCTTCTTCTTATGGTCACCACTAGCTACCGC
Found at i:33468 original size:31 final size:31
Alignment explanation
Indices: 33415--33495 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
33405 TATGATTTTA
* * *
33415 AAAAATGAAAGTTGAGGTACTAAATCGGAAC
1 AAAAGTGATAGTTTAGGTACTAAATCGGAAC
*
33446 AAAAGTGATAGTTTGGGTACTAAATCGGAAC
1 AAAAGTGATAGTTTAGGTACTAAATCGGAAC
33477 AAAAGTGATAGTTTAGGTA
1 AAAAGTGATAGTTTAGGTA
33496 TTGAACATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGATAGTTTAGGTACTAAATCGGAAC
Found at i:34362 original size:15 final size:17
Alignment explanation
Indices: 34331--34362 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
34321 ATGTATTTTT
34331 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
34348 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
34363 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:34488 original size:9 final size:9
Alignment explanation
Indices: 34461--34501 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
34451 AAAGAAAAAG
34461 AAAATAACA
1 AAAATAACA
34470 AAAAT--CA
1 AAAATAACA
34477 AAAATCAA-A
1 AAAAT-AACA
34486 AAAATAACA
1 AAAATAACA
34495 AAAATAA
1 AAAATAA
34502 TAATATGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.25
8 2 0.07
9 19 0.68
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAACA
Found at i:35742 original size:58 final size:58
Alignment explanation
Indices: 35666--35787 Score: 237
Period size: 58 Copynumber: 2.1 Consensus size: 58
35656 AATATTCTTT
35666 TATTTA-TTTTTTCAATGATGACCTAACATCAACGTCACCGTTAAGATGTTAGAACAA
1 TATTTAGTTTTTTCAATGATGACCTAACATCAACGTCACCGTTAAGATGTTAGAACAA
35723 TATTTAGTTTTTTCAATGATGACCTAACATCAACGTCACCGTTAAGATGTTAGAACAA
1 TATTTAGTTTTTTCAATGATGACCTAACATCAACGTCACCGTTAAGATGTTAGAACAA
35781 TATTTAG
1 TATTTAG
35788 ATTAAGCTCC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 6 0.09
58 58 0.91
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (58 bp):
TATTTAGTTTTTTCAATGATGACCTAACATCAACGTCACCGTTAAGATGTTAGAACAA
Found at i:38900 original size:22 final size:22
Alignment explanation
Indices: 38869--38952 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 22
38859 TATAAACACG
*
38869 TTTCTTCTTCTTCCATAAATAT
1 TTTCTACTTCTTCCATAAATAT
*
38891 TTTCTACTTCTTTCATAAACTCA-
1 TTTCTACTTCTTCCATAAA-T-AT
* * *
38914 TTGCTTCTTCTTCTATAAAT-T
1 TTTCTACTTCTTCCATAAATAT
**
38935 CAT-TACTTCTTCCATAAA
1 TTTCTACTTCTTCCATAAA
38953 CTCGTTTCTT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 13 0.27
22 18 0.38
23 16 0.33
24 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.01, T:0.50
Consensus pattern (22 bp):
TTTCTACTTCTTCCATAAATAT
Found at i:38922 original size:20 final size:20
Alignment explanation
Indices: 38895--38965 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
38885 AAATATTTTC
38895 TACTTCTTTCATAAACTCAT
1 TACTTCTTTCATAAACTCAT
* *
38915 TGCTTCTTCTTCTATAAATTCAT
1 TACTTC-T-TTC-ATAAACTCAT
* *
38938 TACTTCTTCCATAAACTCGT
1 TACTTCTTTCATAAACTCAT
*
38958 TTCTTCTT
1 TACTTCTT
38966 CTTCTTCTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 20 0.49
21 3 0.07
22 4 0.10
23 14 0.34
ACGTcount: A:0.23, C:0.25, G:0.03, T:0.49
Consensus pattern (20 bp):
TACTTCTTTCATAAACTCAT
Found at i:38925 original size:23 final size:23
Alignment explanation
Indices: 38847--38968 Score: 87
Period size: 23 Copynumber: 5.5 Consensus size: 23
38837 TGAACCATTC
* * *
38847 TTCTTATTC-TTCTATAAACACGT
1 TTCTTCTTCTTTC-ATAAACTCAT
*
38870 TTCTTCTTCTTCCATAAA-T-ATT
1 TTCTTCTTCTTTCATAAACTCA-T
*
38892 TTCTACTTCTTTCATAAACTCAT
1 TTCTTCTTCTTTCATAAACTCAT
* *
38915 TGCTTCTTC-TTCTATAAATTCAT
1 TTCTTCTTCTTTC-ATAAACTCAT
* *
38938 TACTTCTTC---CATAAACTCGT
1 TTCTTCTTCTTTCATAAACTCAT
38958 TTCTTCTTCTT
1 TTCTTCTTCTT
38969 CTTCTTCTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
20 16 0.20
21 1 0.01
22 20 0.25
23 39 0.49
24 3 0.04
ACGTcount: A:0.22, C:0.25, G:0.02, T:0.51
Consensus pattern (23 bp):
TTCTTCTTCTTTCATAAACTCAT
Found at i:38955 original size:43 final size:45
Alignment explanation
Indices: 38853--38970 Score: 150
Period size: 43 Copynumber: 2.7 Consensus size: 45
38843 ATTCTTCTTA
* * * **
38853 TTCTTCTATAAACACGTTTCTTCTTCTTCCATAAATATTTTCTAC
1 TTCTTCCATAAACTCGTTTCTTCTTCTTCTATAAATATCATCTAC
* * *
38898 TTCTTTCATAAACTCATTGCTTCTTCTTCTATAAAT-TCAT-TAC
1 TTCTTCCATAAACTCGTTTCTTCTTCTTCTATAAATATCATCTAC
38941 TTCTTCCATAAACTCGTTTCTTCTTCTTCT
1 TTCTTCCATAAACTCGTTTCTTCTTCTTCT
38971 TCTTCTTCTT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
43 30 0.48
44 2 0.03
45 30 0.48
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (45 bp):
TTCTTCCATAAACTCGTTTCTTCTTCTTCTATAAATATCATCTAC
Found at i:38966 original size:20 final size:20
Alignment explanation
Indices: 38897--39070 Score: 72
Period size: 23 Copynumber: 8.3 Consensus size: 20
38887 ATATTTTCTA
*
38897 CTTCTTTCATAAACTCATTGCTT
1 CTTCTTCCATAAACTCA-T--TT
* * *
38920 CTTCTTCTATAAATTCATTA
1 CTTCTTCCATAAACTCATTT
*
38940 CTTCTTCCATAAACTCGTTT
1 CTTCTTCCATAAACTCATTT
*
38960 CTTCTT-C-T----TCTTCTT
1 CTTCTTCCATAAACTCAT-TT
* *
38975 CTTCTTCCATAAACCCCTTTATT
1 CTTCTTCCATAAA-CTC-AT-TT
* * *
38998 CTCCTTCCTTAAACACATTT
1 CTTCTTCCATAAACTCATTT
*
39018 CTTTTTCTTCCATAAACCCATTTTTT
1 C---TTCTTCCATAAACTCA---TTT
*
39044 CTTCTTCCATAAACCCATTT
1 CTTCTTCCATAAACTCATTT
39064 CTTCTTC
1 CTTCTTC
39071 TTCCATAAAC
Statistics
Matches: 118, Mismatches: 18, Indels: 33
0.70 0.11 0.20
Matches are distributed among these distances:
14 3 0.03
15 8 0.07
16 1 0.01
17 1 0.01
18 1 0.01
19 1 0.01
20 36 0.31
21 1 0.01
22 4 0.03
23 58 0.49
26 4 0.03
ACGTcount: A:0.20, C:0.30, G:0.01, T:0.48
Consensus pattern (20 bp):
CTTCTTCCATAAACTCATTT
Found at i:39088 original size:23 final size:23
Alignment explanation
Indices: 38970--39080 Score: 159
Period size: 23 Copynumber: 4.8 Consensus size: 23
38960 CTTCTTCTTC
*
38970 TTCTTCTTCTTCCATAAACCCCT
1 TTCTTCTTCTTCCATAAACCCAT
* * * *
38993 TTATTCTCCTTCCTTAAACACAT
1 TTCTTCTTCTTCCATAAACCCAT
*
39016 TTCTTTTTCTTCCATAAACCCAT
1 TTCTTCTTCTTCCATAAACCCAT
*
39039 TTTTTCTTCTTCCATAAACCCAT
1 TTCTTCTTCTTCCATAAACCCAT
39062 TTCTTCTTCTTCCATAAAC
1 TTCTTCTTCTTCCATAAAC
39081 ATATTTCTCT
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (23 bp):
TTCTTCTTCTTCCATAAACCCAT
Found at i:40691 original size:15 final size:15
Alignment explanation
Indices: 40673--40724 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
40663 ATGTTATATG
40673 TGTGAATGTGTTTTA
1 TGTGAATGTGTTTTA
** *
40688 TGTGAAAATGCTTTA
1 TGTGAATGTGTTTTA
* *
40703 TATGAATGTGTTCTA
1 TGTGAATGTGTTTTA
40718 TGTGAAT
1 TGTGAAT
40725 AGAAGATACC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (15 bp):
TGTGAATGTGTTTTA
Found at i:40873 original size:25 final size:25
Alignment explanation
Indices: 40845--40900 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
40835 GGTCATTTGA
** *
40845 GACAAATTTCTACGTGGTTCTTCAG
1 GACAAATTTCTACGCCGTCCTTCAG
*
40870 GACAAA-TTCTACGCCGTCCTTCGG
1 GACAAATTTCTACGCCGTCCTTCAG
40894 GACAAAT
1 GACAAAT
40901 CCATGTTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (25 bp):
GACAAATTTCTACGCCGTCCTTCAG
Found at i:41441 original size:20 final size:20
Alignment explanation
Indices: 41402--41441 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41392 ATATTATCAA
* * *
41402 ATATTTATTTTCATTTTTAT
1 ATATTAATTTTCAATATTAT
41422 ATATTAATTTTCAATATTAT
1 ATATTAATTTTCAATATTAT
41442 TTTTTTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTAATTTTCAATATTAT
Found at i:42774 original size:644 final size:644
Alignment explanation
Indices: 41546--42832 Score: 2403
Period size: 644 Copynumber: 2.0 Consensus size: 644
41536 CACCTCATAT
*
41546 TCGTATCCGAGTCTGGTACAGGTTGGGGTGTTACATTTATTGGTATCAGAGCTACGGTTTAACTT
1 TCGTATCCGAGTCGGGTACAGGTTGGGGTGTTACATTTATTGGTATCAGAGCTACGGTTTAACTT
* *
41611 ATTTTAAGTTTGAAATAAAGCTAATTATGTTTTAAAAAGTGTACATGCCAACGAAATGTTAAAAA
66 ATTTTAAGTTCGAAATAAAGCTAATTATGTTTTAAAAAATGTACATGCCAACGAAATGTTAAAAA
41676 TTTATGATCTGATAAAGGAAATTGTATGTTATCCTTGCTAATAGAGTTAGTAATTATATCTTAAT
131 TTTATGATCTGATAAAGGAAATTGTATGTTATCCTTGCTAATAGAGTTAGTAATTATATCTTAAT
41741 AGATGTTGGACTACGAGAGCTCCTGAAGTGAAGCGGGAGATGGACATGAGGGAAGTAGAAATTCA
196 AGATGTTGGACTACGAGAGCTCCTGAAGTGAAGCGGGAGATGGACATGAGGGAAGTAGAAATTCA
41806 CCTGCCCAAGTTAGATAAGGTGAAGAGCAGGTGCCTCAAGGAGTGCTTGTGCAAGATTAGTGAGT
261 CCTGCCCAAGTTAGATAAGGTGAAGAGCAGGTGCCTCAAGGAGTGCTTGTGCAAGATTAGTGAGT
* * *
41871 ATTTTTCAAGACGTTGGATGTGATTTTGACGCGTTTCAAACCGTCTACTCCCCCATCTCCTAAGT
326 ATTTTTCAAGACGTTGGACGTGATTTTGACACGTTTCAAACCGTCTACTCCCCCAGCTCCTAAGT
*
41936 TAAATATTGCAAAGGAGTTAAAGAGTTTAGGAGTACTTGAGATTAGGGGAAAAGCTGAAGAAGGT
391 TAAATATTGCAAAGGAGTTAAAGAGTTTAGGAGTACTTGAGATTAGAGGAAAAGCTGAAGAAGGT
*
42001 TTTGTTTCTGTAGATCTTTGGCTCAACGATATAAAGATTATGCTTGAGGGTCTTTATTTTTCTAA
456 TTTGTTTCTGTAGATCTTTGGCTCAACGATATAAAGATTATGCTTGAGGGTCTTCATTTTTCTAA
*
42066 AATGGAGAAGCTGGATGGAGTAGTCTCATTGCTACGAGGTCAAGTGCGTATATGGTGGACTAATG
521 AATGGAGAAGATGGATGGAGTAGTCTCATTGCTACGAGGTCAAGTGCGTATATGGTGGACTAATG
42131 TGATGTGAGAGCTCATAGGGACCAAGTAACATGGTCGCTCTTTTTAGAAGAGTTCAAGC
586 TGATGTGAGAGCTCATAGGGACCAAGTAACATGGTCGCTCTTTTTAGAAGAGTTCAAGC
*
42190 TCGTATCCGAGTCGGGTACAGGTTGGGGTGTTATATTTATTGGTATCAGAGCTACGGTTTAACTT
1 TCGTATCCGAGTCGGGTACAGGTTGGGGTGTTACATTTATTGGTATCAGAGCTACGGTTTAACTT
42255 ATTTTAAGTTCGAAATAAAGCTAATTATGTTTTAAAAAATGTACATGCCAACGAAATGTTAAAAA
66 ATTTTAAGTTCGAAATAAAGCTAATTATGTTTTAAAAAATGTACATGCCAACGAAATGTTAAAAA
* *
42320 TTTATGATCTGATAAAGTAAATTGTATGTTATCCTTGTTAATAGAGTTAGTAATTATATCTTAAT
131 TTTATGATCTGATAAAGGAAATTGTATGTTATCCTTGCTAATAGAGTTAGTAATTATATCTTAAT
*
42385 AGATGTTGGACTACGAGGGCTCCTGAAGTGAAGCGGGAGATGGACATGAGGGAAGTAGAAATTCA
196 AGATGTTGGACTACGAGAGCTCCTGAAGTGAAGCGGGAGATGGACATGAGGGAAGTAGAAATTCA
42450 CCTGCCCAAGTTAGATAAGGTGAAGAGCAGGTGCCTCAAGGAGTGCTTGTGCAAGATTAGTGAGT
261 CCTGCCCAAGTTAGATAAGGTGAAGAGCAGGTGCCTCAAGGAGTGCTTGTGCAAGATTAGTGAGT
* * * *
42515 CTTTTTCAGGATGTTGGACGTGATTTTGACACGTTTCAAACCGTCTGCTCCCCCAGCTCCTAAGT
326 ATTTTTCAAGACGTTGGACGTGATTTTGACACGTTTCAAACCGTCTACTCCCCCAGCTCCTAAGT
*
42580 TAAATATTGCAAAGGAGTTAAAGAGTTTAGGAGTACTTGAGATTAGAGGAAAAGCTTAAGAAGGT
391 TAAATATTGCAAAGGAGTTAAAGAGTTTAGGAGTACTTGAGATTAGAGGAAAAGCTGAAGAAGGT
*
42645 TTTGTTTCTGTAGATCTTTGGCTCAACGATATAAAGATTATGCTTGAGGGTCTTCATTTTTCTGA
456 TTTGTTTCTGTAGATCTTTGGCTCAACGATATAAAGATTATGCTTGAGGGTCTTCATTTTTCTAA
42710 AATGGAGAAGATGGATGGAGTAGTCTCATTGCTACGAGGTCAAGTGCGTATATGGTGGACTAATG
521 AATGGAGAAGATGGATGGAGTAGTCTCATTGCTACGAGGTCAAGTGCGTATATGGTGGACTAATG
42775 TGATGTGAGAGCTCATAGGGACCAAGTAACATGGTCGCTCTTTTTAGAAGAGTTCAAG
586 TGATGTGAGAGCTCATAGGGACCAAGTAACATGGTCGCTCTTTTTAGAAGAGTTCAAG
42833 AACAAGTATA
Statistics
Matches: 624, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
644 624 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (644 bp):
TCGTATCCGAGTCGGGTACAGGTTGGGGTGTTACATTTATTGGTATCAGAGCTACGGTTTAACTT
ATTTTAAGTTCGAAATAAAGCTAATTATGTTTTAAAAAATGTACATGCCAACGAAATGTTAAAAA
TTTATGATCTGATAAAGGAAATTGTATGTTATCCTTGCTAATAGAGTTAGTAATTATATCTTAAT
AGATGTTGGACTACGAGAGCTCCTGAAGTGAAGCGGGAGATGGACATGAGGGAAGTAGAAATTCA
CCTGCCCAAGTTAGATAAGGTGAAGAGCAGGTGCCTCAAGGAGTGCTTGTGCAAGATTAGTGAGT
ATTTTTCAAGACGTTGGACGTGATTTTGACACGTTTCAAACCGTCTACTCCCCCAGCTCCTAAGT
TAAATATTGCAAAGGAGTTAAAGAGTTTAGGAGTACTTGAGATTAGAGGAAAAGCTGAAGAAGGT
TTTGTTTCTGTAGATCTTTGGCTCAACGATATAAAGATTATGCTTGAGGGTCTTCATTTTTCTAA
AATGGAGAAGATGGATGGAGTAGTCTCATTGCTACGAGGTCAAGTGCGTATATGGTGGACTAATG
TGATGTGAGAGCTCATAGGGACCAAGTAACATGGTCGCTCTTTTTAGAAGAGTTCAAGC
Found at i:49077 original size:16 final size:17
Alignment explanation
Indices: 49046--49080 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
49036 AAATTTTCAA
49046 AAAGTTTTCAAAAAGTC
1 AAAGTTTTCAAAAAGTC
*
49063 AAAGTTTT-GAAAAGTC
1 AAAGTTTTCAAAAAGTC
49079 AA
1 AA
49081 TGTGACACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (17 bp):
AAAGTTTTCAAAAAGTC
Found at i:52662 original size:21 final size:21
Alignment explanation
Indices: 52636--52677 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52626 TTGTATTATA
* *
52636 TTTAGGGTTTATATTTTAAAT
1 TTTAGGGTTTAGAATTTAAAT
52657 TTTAGGGTTTAGAATTTAAAT
1 TTTAGGGTTTAGAATTTAAAT
52678 AGATAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTAGGGTTTAGAATTTAAAT
Found at i:53796 original size:24 final size:22
Alignment explanation
Indices: 53769--53813 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
53759 TATCAAAATC
53769 ATGATTCA-GTAGTATATTGTAAAA
1 ATGA-TCATGTAGT-TATT-TAAAA
53793 ATGATCATGTAGTTATTTAAA
1 ATGATCATGTAGTTATTTAAA
53814 TCACATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 9 0.45
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (22 bp):
ATGATCATGTAGTTATTTAAAA
Found at i:57087 original size:2 final size:2
Alignment explanation
Indices: 57080--57106 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57070 CTAAACCTAA
57080 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
57107 AAAGAACAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57885 original size:18 final size:17
Alignment explanation
Indices: 57843--57885 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
57833 TTTATAAAAT
57843 TTAAAA-AAAAAATAAA
1 TTAAAATAAAAAATAAA
*
57859 TTATCAATAAAAAATATAA
1 TTA-AAATAAAAAATA-AA
57878 TTAAAATA
1 TTAAAATA
57886 TCTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.14
17 2 0.09
18 12 0.55
19 5 0.23
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
TTAAAATAAAAAATAAA
Found at i:59833 original size:2 final size:2
Alignment explanation
Indices: 59826--59924 Score: 89
Period size: 2 Copynumber: 50.5 Consensus size: 2
59816 TCATATACAT
* * * *
59826 TA TA TA TA -A TA TCA TA CA TA CA TA CA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
59868 TA TA TA TA TA TA TA TA TA TA TA TA T- TGA -A GA GA T- TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
59908 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
59925 TGAAGAGATT
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
1 4 0.05
2 74 0.93
3 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:59939 original size:32 final size:32
Alignment explanation
Indices: 59870--59941 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
59860 TATATATATA
*
59870 TATATATATATATATATATATATTGAAGAGAT
1 TATATGTATATATATATATATATTGAAGAGAT
59902 TATATGTATATATATATATATATTGAAGAGAT
1 TATATGTATATATATATATATATTGAAGAGAT
59934 TATATGTA
1 TATATGTA
59942 ACACCCTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (32 bp):
TATATGTATATATATATATATATTGAAGAGAT
Found at i:60870 original size:20 final size:20
Alignment explanation
Indices: 60841--60889 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
60831 TCGAAAAGTT
60841 TGAGTCAACTCAGATCGAAA
1 TGAGTCAACTCAGATCGAAA
* * * *
60861 TGAGTTAACTCGGATTGAAC
1 TGAGTCAACTCAGATCGAAA
60881 TGAGTCAAC
1 TGAGTCAAC
60890 CCGAACTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (20 bp):
TGAGTCAACTCAGATCGAAA
Found at i:60979 original size:16 final size:17
Alignment explanation
Indices: 60954--60987 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
60944 CCGAGGTGTC
60954 ACATTAACTTTT-CAAA
1 ACATTAACTTTTACAAA
*
60970 ACATTTACTTTTACAAA
1 ACATTAACTTTTACAAA
60987 A
1 A
60988 GAAAGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATTAACTTTTACAAA
Found at i:61404 original size:18 final size:18
Alignment explanation
Indices: 61378--61412 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61368 ATCATTTACA
* *
61378 TTATCATTATTAATCTTC
1 TTATAATTATCAATCTTC
61396 TTATAATTATCAATCTT
1 TTATAATTATCAATCTT
61413 ATTCTGATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAATTATCAATCTTC
Found at i:62331 original size:23 final size:24
Alignment explanation
Indices: 62287--62331 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
62277 ATTAGGGCAC
* *
62287 GTAGAAATTGTCCCGAATGACCGT
1 GTAGAAATTCTCCCGAAGGACCGT
62311 GTAGAAA-TCTCCCGAAGGACC
1 GTAGAAATTCTCCCGAAGGACC
62332 ACATATAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (24 bp):
GTAGAAATTCTCCCGAAGGACCGT
Found at i:66267 original size:16 final size:17
Alignment explanation
Indices: 66242--66275 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
66232 CTGAGGTATC
66242 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
66258 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
66275 A
1 A
66276 GAAAGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:66694 original size:18 final size:18
Alignment explanation
Indices: 66668--66702 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
66658 ATCATTTACA
* *
66668 TTATCATTATTAATCTTC
1 TTATAATTATCAATCTTC
66686 TTATAATTATCAATCTT
1 TTATAATTATCAATCTT
66703 ATTCTGATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAATTATCAATCTTC
Found at i:69460 original size:65 final size:63
Alignment explanation
Indices: 69306--69463 Score: 169
Period size: 65 Copynumber: 2.4 Consensus size: 63
69296 GTGCACTAAG
* *
69306 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATACATTCGATG-TTTCATAAAAT-CTC
* * ** *
69371 AGTGCATCGGTGCATGGTAT-GTGCATCGATGCATGAAATACATTCGATG-TTCAATTTAAT-TT
1 AGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAAATACATTCGATGTTTC-ATAAAATCTC
69433 ATGGTGCATCGATGCATGGATTGGTGCATCG
1 A--GTGCATCGATGCATGG-TTGGTGCATCG
69464 GTGTATCACT
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
62 2 0.03
63 3 0.04
64 21 0.27
65 52 0.66
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATACATTCGATGTTTCATAAAATCTC
Found at i:75980 original size:22 final size:21
Alignment explanation
Indices: 75938--75977 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
75928 GAGTTTATTC
*
75938 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
75959 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
75978 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:77921 original size:19 final size:19
Alignment explanation
Indices: 77897--77953 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
77887 TTGAACCCTT
77897 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
77916 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
* * *
77935 GGTGCATCGATGCATTAAG
1 AGTGCATCGGTGCACTAAG
77954 TGCATTCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:78069 original size:65 final size:65
Alignment explanation
Indices: 77935--78095 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 65
77925 GTGCACTAAG
* * * *
77935 GGTGCATCGATGCATTAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATACATGGCT
* * * *
77999 GGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAA-ATCCTCAGTGCATCGGTACATGG-
1 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATACATGGC
78062 T
65 T
* * *
78063 ATGTGCATCGATGCATGAAATGTATTCGATGTT
1 -GGTGCATCGATGCATCAAATGCATTCGATGTT
78096 CAATTTAATT
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 28 0.34
65 51 0.62
66 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (65 bp):
GGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATACATGGCT
Found at i:78134 original size:65 final size:63
Alignment explanation
Indices: 77935--78136 Score: 180
Period size: 65 Copynumber: 3.1 Consensus size: 63
77925 GTGCACTAAG
* * * *
77935 GGTGCATCGATGCATTAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGC
1 GGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGT
77998 T
63 T
* * *
77999 GGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAATCCTCAGTGCATCGGTACATGGTA
1 GGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-
78064 T
63 T
* * **
78065 -GTGCATCGATGCATGAAATGTATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGA
1 GGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-
78127 TT
62 TT
78129 GGTGCATC
1 GGTGCATC
78137 ACTCTGAAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 19
0.78 0.10 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 47 0.41
65 55 0.48
66 5 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (63 bp):
GGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTT
Found at i:79178 original size:136 final size:142
Alignment explanation
Indices: 78859--79212 Score: 466
Period size: 136 Copynumber: 2.5 Consensus size: 142
78849 AAATAAGGTA
* * * ** *
78859 TTATTTA-TT-AAAATATCA-AAAAGAAATCTAGTTACTTTAAGA-GTCCTTTCTTTAATATT-A
1 TTATTTATTTAAAAATATAAGAAAAGACATCTAGTTACCTTAAGACAACCCTT-TTTAATATTAA
78919 AAAATAAATAAATATTAATAAGAATATGATAATTTTCCTAAAAAATATAATTTAAATAAAACTAA
65 AAAATAAATAAATATTAATAAGAATATGATAATTTTCCT-AAAAATATAATTTAAATAAAACTAA
78984 ATTAAATATAGTATT
129 ATT-AATATAGTATT
* *
78999 TTATTTATTTAAAAATATCAGAAAAGATATCTAGTTACCTTAAGACAACCCCTTTTTAATATTAA
1 TTATTTATTTAAAAATATAAGAAAAGACATCTAGTTACCTTAAGACAA-CCCTTTTTAATATTAA
79064 AAAAT-AATAAATATTAATAAG-A-AT-ATAATTTTCCT-AAAATATAATTTAAATAAAACTAAA
65 AAAATAAATAAATATTAATAAGAATATGATAATTTTCCTAAAAATATAATTTAAATAAAACTAAA
79124 TT-A-ATAGTATT
130 TTAATATAGTATT
* *
79135 TTATTTATTTAAAAATATAAGTAAAGGGCATCTAG-TACCTTAAGACAACCCTTTCTTAATA-TA
1 TTATTTATTTAAAAATATAAG-AAAAGACATCTAGTTACCTTAAGACAACCCTTT-TTAATATTA
79198 AAAAATAAATAAATA
64 AAAAATAAATAAATA
79213 CTATTATTTA
Statistics
Matches: 196, Mismatches: 9, Indels: 22
0.86 0.04 0.10
Matches are distributed among these distances:
135 14 0.07
136 55 0.28
137 11 0.06
139 27 0.14
140 7 0.04
141 13 0.07
142 11 0.06
143 23 0.12
144 25 0.13
145 10 0.05
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.37
Consensus pattern (142 bp):
TTATTTATTTAAAAATATAAGAAAAGACATCTAGTTACCTTAAGACAACCCTTTTTAATATTAAA
AAATAAATAAATATTAATAAGAATATGATAATTTTCCTAAAAATATAATTTAAATAAAACTAAAT
TAATATAGTATT
Found at i:80399 original size:15 final size:15
Alignment explanation
Indices: 80369--80410 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
80359 TTTATTTATT
80369 ATAAT-ATAAT-AT-
1 ATAATAATAATAATG
*
80381 ATAATAATGATAATG
1 ATAATAATAATAATG
80396 ATAATAATAATAATG
1 ATAATAATAATAATG
80411 GACAAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.20
13 4 0.16
14 2 0.08
15 14 0.56
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (15 bp):
ATAATAATAATAATG
Found at i:84444 original size:143 final size:142
Alignment explanation
Indices: 84214--84588 Score: 512
Period size: 142 Copynumber: 2.6 Consensus size: 142
84204 TTAGGATTTT
* ** *
84214 ATAAATA-AGGTA-TTATTTATTAAAAAATATCAGAAAATGGTATCTAGTTACTTTAAGACAAAC
1 ATAAATATA-GTATTTATTTATTTAAAAATATCA-AAAATGACATCTAGTTACCTTAAGAC-AAC
* * * *
84277 CATTTATTTAATATT--AAAAAATAAATAATAATAATAATATGATAATTTTTCATAAAAAATATA
63 CCTTT-CTTAATATTAAAAAAAATAAATAATAATAAGAATATGATAATTTTTCAT-AAAAACATA
84340 ATTTAAATAAAAC-AAA
126 ATTTAAATAAAACTAAA
84356 AT-AATATAGTATTTTATTTATTTAAAAATATCAAAAATGACATCTAGTTACCTTAAGACAACCC
1 ATAAATATAGTA-TTTATTTATTTAAAAATATCAAAAATGACATCTAGTTACCTTAAGACAACCC
* *
84420 TTTCTTAATATTAAAAAATAATAAATATTAATAAGAATATGATAATTTTTCCTAAAAACATAATT
65 TTTCTTAATATTAAAAAA-AATAAATAATAATAAGAATATGATAATTTTTCATAAAAACATAATT
84485 TAAATAAAACTAAA
129 TAAATAAAACTAAA
* * *
84499 TTAAATATAGTATTT-TTTATTTAAAAATATCAGAAATGACATCTATTTACCTTAAGACAACCTC
1 ATAAATATAGTATTTATTTATTTAAAAATATCAAAAATGACATCTAGTTACCTTAAGACAACC-C
84563 TTTCTTAATATTAAAAAAAATAAATA
65 TTTCTTAATATTAAAAAAAATAAATA
84589 CTATTATTTA
Statistics
Matches: 211, Mismatches: 13, Indels: 18
0.87 0.05 0.07
Matches are distributed among these distances:
140 8 0.04
141 14 0.07
142 104 0.49
143 76 0.36
144 9 0.04
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.37
Consensus pattern (142 bp):
ATAAATATAGTATTTATTTATTTAAAAATATCAAAAATGACATCTAGTTACCTTAAGACAACCCT
TTCTTAATATTAAAAAAAATAAATAATAATAAGAATATGATAATTTTTCATAAAAACATAATTTA
AATAAAACTAAA
Found at i:85850 original size:3 final size:3
Alignment explanation
Indices: 85844--85890 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
85834 TTTATTATTT
*
85844 ATA ATA ATA ATA ATA A-A ATA ATG AT- ATA ATA A-A A-A ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
85887 ATA A
1 ATA A
85891 AAACGGGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 10 0.26
3 29 0.74
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:85865 original size:8 final size:8
Alignment explanation
Indices: 85844--85890 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
85834 TTTATTATTT
85844 ATAATAATA
1 ATAATAA-A
85853 ATAATAAA
1 ATAATAAA
85861 ATAATGATATA
1 ATAAT-A-A-A
85872 ATAA-AAA
1 ATAATAAA
85879 ATAATAAA
1 ATAATAAA
85887 ATAA
1 ATAA
85891 AAACGGGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
7 5 0.15
8 14 0.41
9 9 0.26
10 1 0.03
11 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (8 bp):
ATAATAAA
Done.