Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009627.1 Hibiscus syriacus cultivar Beakdansim tig00117020_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: 344030
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:606 original size:2 final size:2
Alignment explanation
Indices: 556--589 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
546 ATTAATCCAC
556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
590 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:935 original size:21 final size:21
Alignment explanation
Indices: 911--964 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
901 CATACCCCAA
* *
911 GTATCGATATTCCTTGAAGAG
1 GTATCGATACTCCTCGAAGAG
932 GTATCGATACTCCTCGAAGAG
1 GTATCGATACTCCTCGAAGAG
953 GTATCGATACTC
1 GTATCGATACTC
965 ACCCTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (21 bp):
GTATCGATACTCCTCGAAGAG
Found at i:1480 original size:10 final size:10
Alignment explanation
Indices: 1465--1491 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1455 ACATGTTTCT
1465 AAACACTTAG
1 AAACACTTAG
1475 AAACACTTAG
1 AAACACTTAG
1485 AAACACT
1 AAACACT
1492 CTCACGTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.22, G:0.07, T:0.19
Consensus pattern (10 bp):
AAACACTTAG
Found at i:2318 original size:22 final size:22
Alignment explanation
Indices: 2275--2322 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2265 CATATAATTA
* *
2275 TAAATTAGTTGAAAATGTAAAGG
1 TAAATTAGTTGAAAAT-AAAAAG
*
2298 TAAATTA-TTTAAAATAAAAAG
1 TAAATTAGTTGAAAATAAAAAG
2319 TAAA
1 TAAA
2323 CTATATCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (22 bp):
TAAATTAGTTGAAAATAAAAAG
Found at i:3245 original size:29 final size:29
Alignment explanation
Indices: 3206--3261 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3196 ATCAAATATT
* *
3206 TTAACTATCACGTTAATTTTTCCATTATA
1 TTAACTATCACGTCAACTTTTCCATTATA
*
3235 TTAATTATCACGTCAACTTTTCCATTA
1 TTAACTATCACGTCAACTTTTCCATTA
3262 AATAGTCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (29 bp):
TTAACTATCACGTCAACTTTTCCATTATA
Found at i:3654 original size:3 final size:3
Alignment explanation
Indices: 3646--3675 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3636 TTTAATTAAA
3646 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3676 TGAAAACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4550 original size:22 final size:22
Alignment explanation
Indices: 4525--4569 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4515 GTCTTTAAAA
4525 ACCCAACAAATAGCTTTGCCCC
1 ACCCAACAAATAGCTTTGCCCC
4547 ACCCAACAAATAGCTTTGCCCC
1 ACCCAACAAATAGCTTTGCCCC
4569 A
1 A
4570 TATTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.09, T:0.18
Consensus pattern (22 bp):
ACCCAACAAATAGCTTTGCCCC
Found at i:14991 original size:31 final size:31
Alignment explanation
Indices: 14934--14992 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
14924 TTCAAGTTTT
*
14934 TTTGAGTTTAAGTCGAGCTTCAAATTTTGAC
1 TTTGAGTTTAAGTCGAGCTTAAAATTTTGAC
* *
14965 TTTGAGTTTGAGTTGA-CTTAACAATTTT
1 TTTGAGTTTAAGTCGAGCTTAA-AATTTT
14993 AAGTTTGCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (31 bp):
TTTGAGTTTAAGTCGAGCTTAAAATTTTGAC
Found at i:27052 original size:27 final size:27
Alignment explanation
Indices: 27012--27080 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
27002 GTGATCCTAC
* *
27012 ACTTGCCACAGCAACATCATTAACTCT
1 ACTTGCCTCGGCAACATCATTAACTCT
*
27039 ACTTGCCTCGGCAATATCATTAACTCT
1 ACTTGCCTCGGCAACATCATTAACTCT
27066 ACTTGCCTCGGCAAC
1 ACTTGCCTCGGCAAC
27081 TTCACTTGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.28
Consensus pattern (27 bp):
ACTTGCCTCGGCAACATCATTAACTCT
Found at i:27369 original size:37 final size:36
Alignment explanation
Indices: 27233--27374 Score: 250
Period size: 36 Copynumber: 3.9 Consensus size: 36
27223 ATTAATCTTC
27233 AATAAG-AAAATACCCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
*
27268 AATAAGAAAAATACTCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
*
27304 AATAAGAAAAATACTCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
27340 AATAAGAAAAGATACCCAAATTTCTTATGAAACCT
1 AATAAGAAAA-ATACCCAAATTTCTTATGAAACCT
27375 AAATTGGTGA
Statistics
Matches: 103, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
35 6 0.06
36 74 0.72
37 23 0.22
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.31
Consensus pattern (36 bp):
AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
Found at i:29678 original size:64 final size:63
Alignment explanation
Indices: 29600--29740 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
29590 TATTTAACAT
* * *
29600 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCAATGTTTCCAT-TTTAAGGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCAATGTTT-CATCTTTAAAGA
* * * * * *
29663 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCAATGTTTCATCTTTAAAGA
29727 GTGCATCGATGCAC
1 GTGCATCGATGCAC
29741 ATTAAATATG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 18 0.27
64 48 0.73
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCAATGTTTCATCTTTAAAGA
Found at i:33802 original size:24 final size:20
Alignment explanation
Indices: 33746--33803 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
33736 TTCCCCTTGA
33746 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
33766 AGTACATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
33789 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
33804 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:36093 original size:28 final size:28
Alignment explanation
Indices: 36062--36116 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
36052 GTATGCTTTT
36062 GAAAAATTTAAAGTTTAGATACTAAAAA
1 GAAAAATTTAAAGTTTAGATACTAAAAA
36090 GAAAAATTTAAAGTTTAGATACTAAAA
1 GAAAAATTTAAAGTTTAGATACTAAAA
36117 GACCAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (28 bp):
GAAAAATTTAAAGTTTAGATACTAAAAA
Found at i:38012 original size:14 final size:15
Alignment explanation
Indices: 37995--38028 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
37985 GATAAATATT
*
37995 TAAATATA-ATTTTC
1 TAAATATATATTTAC
38009 TAAATATATATTTAC
1 TAAATATATATTTAC
38024 TAAAT
1 TAAAT
38029 GATTGAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATATATATTTAC
Found at i:38651 original size:16 final size:16
Alignment explanation
Indices: 38630--38660 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38620 AAAAGAACAA
*
38630 TGTAATTCTATATCTC
1 TGTAATTATATATCTC
38646 TGTAATTATATATCT
1 TGTAATTATATATCT
38661 TTGTTTTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (16 bp):
TGTAATTATATATCTC
Found at i:44862 original size:31 final size:31
Alignment explanation
Indices: 44824--44948 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
44814 AGGGTCGAGG
44824 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
44855 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
44886 GTTTACCTATGTTCTTAGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
44917 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
44948 G
1 G
44949 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:48418 original size:19 final size:20
Alignment explanation
Indices: 48379--48418 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
48369 TCATGAGGGT
* *
48379 ATCGATACCCCCATTACGGA
1 ATCGATACCCCCATAAAGGA
48399 ATCGATACCCCC-TAAAGGA
1 ATCGATACCCCCATAAAGGA
48418 A
1 A
48419 AAATGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (20 bp):
ATCGATACCCCCATAAAGGA
Found at i:49066 original size:59 final size:58
Alignment explanation
Indices: 48973--49087 Score: 142
Period size: 59 Copynumber: 2.0 Consensus size: 58
48963 GATTACATGC
* * * * *
48973 AACATATGATATTAGATATATGTTTACACATACATGTGGTATGTGACAGAAGAGAAGG
1 AACATATGATATGAGATATATGATTACACATACATGTGATACGTGACAGAAAAGAAGG
* *
49031 AACATATGATTATGAGATCA-ATGATTACACGTACATGTGATACGTGACTGAAAAGAA
1 AACATATGA-TATGAGAT-ATATGATTACACATACATGTGATACGTGACAGAAAAGAA
49088 AAGATATGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 9 0.19
59 38 0.79
60 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (58 bp):
AACATATGATATGAGATATATGATTACACATACATGTGATACGTGACAGAAAAGAAGG
Found at i:49244 original size:31 final size:31
Alignment explanation
Indices: 49206--49330 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
49196 AGGGTCGAGG
49206 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
49237 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
49268 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
49299 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
49330 G
1 G
49331 GTCCTTCGGG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:49817 original size:21 final size:21
Alignment explanation
Indices: 49792--49834 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
49782 AAAGAATATA
49792 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
49813 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
49834 T
1 T
49835 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:58609 original size:12 final size:12
Alignment explanation
Indices: 58588--58620 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
58578 CGTCATCAAA
58588 AAAT-TATTTTT
1 AAATATATTTTT
58599 AAA-ATATTTTT
1 AAATATATTTTT
58610 AAATATATTTT
1 AAATATATTTT
58621 ATTAGTGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AAATATATTTTT
Found at i:58621 original size:11 final size:11
Alignment explanation
Indices: 58587--58620 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
58577 ACGTCATCAA
58587 AAAATTATTTTT
1 AAAA-TATTTTT
58599 AAAATATTTTT
1 AAAATATTTTT
58610 AAATATATTTT
1 AAA-ATATTTT
58621 ATTAGTGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:67511 original size:12 final size:12
Alignment explanation
Indices: 67494--67518 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67484 CTATATACCC
67494 TTAATAAAAAAT
1 TTAATAAAAAAT
67506 TTAATAAAAAAT
1 TTAATAAAAAAT
67518 T
1 T
67519 ATATATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAATAAAAAAT
Found at i:75288 original size:19 final size:20
Alignment explanation
Indices: 75261--75299 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
75251 ATGGTTATGG
75261 TTAGAGATTT-GAGTTTTTT
1 TTAGAGATTTGGAGTTTTTT
*
75280 TTAGTGATTTGGAGTTTTTT
1 TTAGAGATTTGGAGTTTTTT
75300 GTAATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.23, T:0.59
Consensus pattern (20 bp):
TTAGAGATTTGGAGTTTTTT
Found at i:78724 original size:32 final size:32
Alignment explanation
Indices: 78662--78724 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
78652 TTACGCCATC
* * * *
78662 ACTTTAGGTGACATGGCACGTGTCATGTCATT
1 ACTTTAGATGACATGACACGAGTCACGTCATT
*
78694 ACTTTAGATGACGTGACACGAGTCACGTCAT
1 ACTTTAGATGACATGACACGAGTCACGTCAT
78725 CAATTAAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (32 bp):
ACTTTAGATGACATGACACGAGTCACGTCATT
Found at i:82396 original size:19 final size:19
Alignment explanation
Indices: 82372--82408 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
82362 TGACTAAATT
82372 AGCCG-CCCATTAATGTTGA
1 AGCCGCCCCATT-ATGTTGA
82391 AGCCGCCCCATTATGTTG
1 AGCCGCCCCATTATGTTG
82409 CTTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (19 bp):
AGCCGCCCCATTATGTTGA
Found at i:83485 original size:64 final size:64
Alignment explanation
Indices: 83417--83637 Score: 218
Period size: 64 Copynumber: 3.5 Consensus size: 64
83407 TTGAAGGTGT
* ** * *
83417 ATCGATGCATTGGCAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAGGCAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATTAGTG
83480 C
64 C
* * *
83481 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGCAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
* * * * *
83545 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTA-TG
1 ATCGATGCAT-AGGCAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATTAGTG
83608 C
64 C
* * *
83609 ACCGATGCATCA-GTAGTACATCGATGCAT
1 ATCGATGCAT-AGGCAGTGCATCGATGCAT
83638 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 119 0.90
65 11 0.08
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAGGCAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
Found at i:84656 original size:29 final size:30
Alignment explanation
Indices: 84561--84653 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
84551 GTGGTCCTTA
84561 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
84591 TGGACAGTTACCGAGGATCTTTATGACATC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
84621 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
84650 TGGA
1 TGGA
84654 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 17 0.29
30 41 0.71
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:88137 original size:64 final size:64
Alignment explanation
Indices: 88069--88289 Score: 227
Period size: 64 Copynumber: 3.5 Consensus size: 64
88059 TTGAAGGTGT
* ** * *
88069 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATTAGTG
88132 C
64 C
* * *
88133 ATCGATGCATAAGTAGTGCATCGATGTATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
* * * * * *
88197 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTA-TG
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATTAGTG
88260 C
64 C
*
88261 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
88290 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 119 0.90
65 11 0.08
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
Found at i:89304 original size:29 final size:30
Alignment explanation
Indices: 89215--89306 Score: 150
Period size: 30 Copynumber: 3.1 Consensus size: 30
89205 GTGGTCTTTA
89215 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
89245 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
89275 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
89304 TGG
1 TGG
89307 GTAGGTCCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
29 17 0.29
30 42 0.71
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:94321 original size:19 final size:19
Alignment explanation
Indices: 94297--94333 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
94287 TAACTAAATT
94297 AGCCG-CCCATTAATGTTGA
1 AGCCGCCCCATT-ATGTTGA
94316 AGCCGCCCCATTATGTTG
1 AGCCGCCCCATTATGTTG
94334 CTTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (19 bp):
AGCCGCCCCATTATGTTGA
Found at i:96385 original size:21 final size:21
Alignment explanation
Indices: 96352--96399 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
96342 TTATTTATAT
96352 AAATATATATTTAATTA-TTA
1 AAATATATATTTAATTATTTA
96372 AAATATATTATTTAATTATTTA
1 AAATATA-TATTTAATTATTTA
96394 AAATAT
1 AAATAT
96400 TTTTTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.27
21 10 0.38
22 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATATATTTAATTATTTA
Found at i:97824 original size:27 final size:28
Alignment explanation
Indices: 97775--97831 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
97765 ATTTTTATTA
* * * *
97775 ATAATTTATTTTCATATCCTAAAATTTT
1 ATAATTTATATTCATAACATAAAAATTT
97803 ATAATTT-TATTCATAACATAAAAATTT
1 ATAATTTATATTCATAACATAAAAATTT
97830 AT
1 AT
97832 GTAGTCCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (28 bp):
ATAATTTATATTCATAACATAAAAATTT
Found at i:103902 original size:13 final size:13
Alignment explanation
Indices: 103861--103904 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
103851 TTATTTAAAA
103861 TAAATTATAATTT
1 TAAATTATAATTT
* *
103874 TAAAGTTTTTATTT
1 TAAA-TTATAATTT
*
103888 TAAATTAAAATTT
1 TAAATTATAATTT
103901 TAAA
1 TAAA
103905 ATTCTATAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TAAATTATAATTT
Found at i:104297 original size:14 final size:15
Alignment explanation
Indices: 104259--104298 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
104249 TTTTTTTCGG
104259 TTCGGTTCGAGTTTT
1 TTCGGTTCGAGTTTT
104274 TTAACGGTTCGAG-TTT
1 TT--CGGTTCGAGTTTT
104290 TTCGGTTCG
1 TTCGGTTCG
104299 GTTCGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.30
15 2 0.09
16 5 0.22
17 9 0.39
ACGTcount: A:0.10, C:0.15, G:0.28, T:0.47
Consensus pattern (15 bp):
TTCGGTTCGAGTTTT
Found at i:104468 original size:27 final size:25
Alignment explanation
Indices: 104424--104474 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
104414 CCGAATCAAA
*
104424 AAAATAAAACCTTTAAACCGAACCG
1 AAAATAAAACCTTTAAACCAAACCG
*
104449 AAAATCAAACCGTTTAAAACCAAACC
1 AAAATAAAACC-TTT-AAACCAAACC
104475 AAACCGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.53, C:0.25, G:0.06, T:0.16
Consensus pattern (25 bp):
AAAATAAAACCTTTAAACCAAACCG
Found at i:104782 original size:3 final size:3
Alignment explanation
Indices: 104774--104798 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
104764 AATCACTGAT
104774 CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG C
104799 ATTGCTAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:113129 original size:12 final size:12
Alignment explanation
Indices: 113105--113141 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
113095 TAAAGGGTGA
*
113105 CATACTAGGGCT
1 CATACTCGGGCT
*
113117 CATGCTCGGGCT
1 CATACTCGGGCT
113129 CATACTCGGGCT
1 CATACTCGGGCT
113141 C
1 C
113142 TCTTCCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.16, C:0.32, G:0.27, T:0.24
Consensus pattern (12 bp):
CATACTCGGGCT
Found at i:117440 original size:197 final size:194
Alignment explanation
Indices: 117108--117476 Score: 668
Period size: 197 Copynumber: 1.9 Consensus size: 194
117098 TGTTATATGT
*
117108 TCTTGCATATTTTTGTCTTCTTTTTTAATATTTTTCTTTAGATACAACTGTGTGTGATTATCTAG
1 TCTTGCATATTTTTGTCTTCTTTTTTAATATTTTTCTTCAGATACAACTGTGTGTGATTATCTAG
*
117173 AGAGTTGTAATACAAAGCTTATTTGGTGTCGGTTGTCTTATTCGTGTCGTTGCAAGTGAGTAAGA
66 AGAGTTGTAATACAAAGCTCATTTGGTGTCGGTTGTCTTATTCGTGTCGTTGCAAGTGAGTAAGA
*
117238 GCTGTTGATGAGTTCTTTGGTGTTCTAAGCACAAACCCATATCTAGAGAGTTGTAATACAAAGC
131 GCTGTTGATGAGTTCTTTGATGTTCTAAGCACAAACCCATATCTAGAGAGTTGTAATACAAAGC
117302 TCTTGCATATTTTTGTCTTCTTTTTT-ATATTTTTCTTCAGATACTTACAGCTGTGTGTGATTAT
1 TCTTGCATATTTTTGTCTTCTTTTTTAATATTTTTCTTCAGATAC--A-A-CTGTGTGTGATTAT
117366 CTAGAGAGTTGTAATACAAAGCTCATTTGGTGTCGGTTGTCTTATTCGTGTCGTTGCAAGTGAGT
62 CTAGAGAGTTGTAATACAAAGCTCATTTGGTGTCGGTTGTCTTATTCGTGTCGTTGCAAGTGAGT
117431 AAGAGCTGTTGATGAGTTCTTTGATGTTCTAAGCACAAACCCATAT
127 AAGAGCTGTTGATGAGTTCTTTGATGTTCTAAGCACAAACCCATAT
117477 GTAAAAGGAA
Statistics
Matches: 168, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
193 17 0.10
194 26 0.15
195 1 0.01
196 1 0.01
197 123 0.73
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (194 bp):
TCTTGCATATTTTTGTCTTCTTTTTTAATATTTTTCTTCAGATACAACTGTGTGTGATTATCTAG
AGAGTTGTAATACAAAGCTCATTTGGTGTCGGTTGTCTTATTCGTGTCGTTGCAAGTGAGTAAGA
GCTGTTGATGAGTTCTTTGATGTTCTAAGCACAAACCCATATCTAGAGAGTTGTAATACAAAGC
Found at i:122118 original size:12 final size:12
Alignment explanation
Indices: 122101--122131 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
122091 ATTTGAAAAG
122101 GATTTGCTTTTA
1 GATTTGCTTTTA
122113 GATTTGCTTTTA
1 GATTTGCTTTTA
122125 GAGTTTG
1 GA-TTTG
122132 TTGCCTGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.16, C:0.06, G:0.23, T:0.55
Consensus pattern (12 bp):
GATTTGCTTTTA
Found at i:133397 original size:30 final size:30
Alignment explanation
Indices: 133292--133460 Score: 176
Period size: 30 Copynumber: 5.6 Consensus size: 30
133282 AGACTGGAGG
* * *
133292 GTTGATGAAGGTACATGAGAAGTTTGGACT
1 GTTGATGAAGGTGCATTAGAAGATTGGACT
** * * *
133322 GCAGATGAAGGTGCATGAGAATATTGGACC
1 GTTGATGAAGGTGCATTAGAAGATTGGACT
** * *
133352 AATAATGAAGCTGCATTAGAAGATTGGACT
1 GTTGATGAAGGTGCATTAGAAGATTGGACT
* * *
133382 GTTGATGCAGGTGCATTAGAAGACTGAACT
1 GTTGATGAAGGTGCATTAGAAGATTGGACT
* *
133412 GTTGATGCAGGTGCATTAGAAGACTGGACT
1 GTTGATGAAGGTGCATTAGAAGATTGGACT
*
133442 GTTGATGCAGGTGCATTAG
1 GTTGATGAAGGTGCATTAG
133461 CTGTCAAAGA
Statistics
Matches: 117, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 117 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (30 bp):
GTTGATGAAGGTGCATTAGAAGATTGGACT
Found at i:135269 original size:71 final size:71
Alignment explanation
Indices: 135153--135294 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
135143 AAAACAGAAT
135153 GGAAGCCGTAATACACATTTAAACCGAATCATACACGTGAGGCTTTGGGGAAAAAGTTACACAAA
1 GGAAGCCGTAATACACATTTAAACCGAATCATACACGTGAGGCTTTGGGGAAAAAGTTACACAAA
135218 AGAAAG
66 AGAAAG
135224 GGAAGCCGTAATACACATTTAAACCGAATCATACACGTGAGGCTTTGGGGAAAAAGTTACACAAA
1 GGAAGCCGTAATACACATTTAAACCGAATCATACACGTGAGGCTTTGGGGAAAAAGTTACACAAA
135289 AGAAAG
66 AGAAAG
135295 TAAAGATACA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (71 bp):
GGAAGCCGTAATACACATTTAAACCGAATCATACACGTGAGGCTTTGGGGAAAAAGTTACACAAA
AGAAAG
Found at i:137021 original size:74 final size:74
Alignment explanation
Indices: 136781--137319 Score: 603
Period size: 74 Copynumber: 7.4 Consensus size: 74
136771 CTTAACCGGT
* * * * *
136781 TAAAATAAAATAGCCGCTACCTATTATATTAAAATACCTACCG--TTTTTTAAGGTTACTAATAA
1 TAAAAAAAAATAGGCGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
136844 TGTAAACGG
66 TGTAAACGG
*** * * *
136853 T--AAAAAAATAGGTACTACCTATTATATTAAAATACCAACCGATTTTTTTAAGGTTACTAATAA
1 TAAAAAAAAATAGGCGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
136916 TGTAAACGG
66 TGTAAACGG
* * * *
136925 T-AAAAAAAATAGGTGTTGCCTATTACATTAAACTACCTACAGATTTTTTTAAGGTTGCTAATAA
1 TAAAAAAAAATAGGCGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
*
136989 TATAAACGG
66 TGTAAACGG
* * **
136998 TAAAAAAAAATAGGTGTTACCTATTATATTAAAATACCTAATGATTTTTTTGAA--TATGCTAAT
1 TAAAAAAAAATAGGCGTTACCTATTACATTAAAATACCTACCGATTTTTTT-AAGGT-TGCTAAT
137061 AATGTAAACGG
64 AATGTAAACGG
* * *
137072 TAAAAAAAAATAGACGCTATCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
1 TAAAAAAAAATAGGCGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
*
137137 TATAAACGG
66 TGTAAACGG
* * * * * * *
137146 T--GAAAAAATATGCATTATCTATTACATTAAACTACCTACCGATTTTTTTGAATGTTGATAATA
1 TAAAAAAAAATAGGCGTTACCTATTACATTAAAATACCTACCGATTTTTTT-AAGGTTGCTAATA
*
137209 ATGTAAACGA
65 ATGTAAACGG
* * * * *
137219 TAAAATAAAATAGACGTTATCTATTACATTAAACTACCTACCGATTTTTTTGAAGGTTGATAATA
1 TAAAAAAAAATAGGCGTTACCTATTACATTAAAATACCTACCGATTTTTTT-AAGGTTGCTAATA
* *
137284 ATATAAACGA
65 ATGTAAACGG
*
137294 TAAAATAAAATAGGC-TCTACCTATTA
1 TAAAAAAAAATAGGCGT-TACCTATTA
137320 TTATTAAATT
Statistics
Matches: 408, Mismatches: 47, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
70 35 0.09
72 73 0.18
73 86 0.21
74 124 0.30
75 90 0.22
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (74 bp):
TAAAAAAAAATAGGCGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
TGTAAACGG
Found at i:137045 original size:147 final size:145
Alignment explanation
Indices: 136781--137327 Score: 649
Period size: 147 Copynumber: 3.7 Consensus size: 145
136771 CTTAACCGGT
* * * *
136781 TAAAATAAAATAGCCGCTACCTATTATATTAAAATACCTACCG--TTTTTTAAGGTTACTAATAA
1 TAAAA-AAAATAGACGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
*
136844 TGTAAACGGTAAAAAAATAGGTACTACCTATTATATTAAAATACC-AACCGATTTTTTT-AAGGT
65 TATAAACGGTAAAAAAATAGGTACTACCTATTATATTAAAATACCTAA-CGATTTTTTTGAA-GT
136907 TACTAATAATGTAAACGG
128 TACTAATAATGTAAACGG
** * * *
136925 TAAAAAAAATAGGTGTTGCCTATTACATTAAACTACCTACAGATTTTTTTAAGGTTGCTAATAAT
1 TAAAAAAAATAGACGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAAT
** *
136990 ATAAACGGTAAAAAAAAATAGGTGTTACCTATTATATTAAAATACCTAATGATTTTTTTGAA-TA
66 ATAAACGGT--AAAAAAATAGGTACTACCTATTATATTAAAATACCTAACGATTTTTTTGAAGT-
*
137054 TGCTAATAATGTAAACGG
128 TACTAATAATGTAAACGG
* *
137072 TAAAAAAAAATAGACGCTATCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
1 T-AAAAAAAATAGACGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAA
* * * * * * * *
137137 TATAAACGGTGAAAAAATATGCATTATCTATTACATTAAACTACCTACCGATTTTTTTGAATGTT
65 TATAAACGGTAAAAAAATAGGTACTACCTATTATATTAAAATACCTAACGATTTTTTTGAA-GTT
*
137202 GA-TAATAATGTAAACGA
129 -ACTAATAATGTAAACGG
* * *
137219 TAAAATAAAATAGACGTTATCTATTACATTAAACTACCTACCGATTTTTTTGAAGGTTGATAATA
1 TAAAA-AAAATAGACGTTACCTATTACATTAAAATACCTACCGATTTTTTT-AAGGTTGCTAATA
*
137284 ATATAAACGATAAAATAAAATAGGCT-CTACCTATTATTATTAAA
64 ATATAAACGGT-AAA-AAAATAGG-TACTACCTATTA-TATTAAA
137328 TTAAAAATAA
Statistics
Matches: 345, Mismatches: 41, Indels: 27
0.84 0.10 0.07
Matches are distributed among these distances:
143 30 0.09
144 5 0.01
145 28 0.08
146 47 0.14
147 119 0.34
148 93 0.27
149 2 0.01
150 15 0.04
151 6 0.02
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (145 bp):
TAAAAAAAATAGACGTTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAAT
ATAAACGGTAAAAAAATAGGTACTACCTATTATATTAAAATACCTAACGATTTTTTTGAAGTTAC
TAATAATGTAAACGG
Found at i:137210 original size:221 final size:221
Alignment explanation
Indices: 136781--137319 Score: 660
Period size: 221 Copynumber: 2.5 Consensus size: 221
136771 CTTAACCGGT
* * * *
136781 TAAAATAAAATAGCCGCTACCTATTATATTAAAATACCTACCG--TTTTTT-AAGGTTACTAATA
1 TAAAAAAAAATAGACGTTACCTATTATATTAAAATACCTACCGATTTTTTTGAA-GTTGCTAATA
** *
136843 ATGTAAACGGT--AAAAAAATAGGTACTACCTATTATATTAAAATACCAACCGATTTTTTTAAGG
65 ATGTAAACGGTAAAAAAAAATAGACACTACCTATTACATTAAAATACCAACCGATTTTTTTAAGG
* ** *
136906 TTACTAATAATGTAAACGGTAAAAAAAATAGGTGTTGCCTATTACATTAAACTACCTACAGATTT
130 TTACTAATAATATAAACGGTAAAAAAAATAGGCATTACCTATTACATTAAACTACCTACAGATTT
* *
136971 TTTTAAGGTTGCTAATAATATAAACGG
195 TTTTAAGGTTGATAATAATATAAACGA
** **
136998 TAAAAAAAAATAGGTGTTACCTATTATATTAAAATACCTAATGATTTTTTTGAA-TATGCTAATA
1 TAAAAAAAAATAGACGTTACCTATTATATTAAAATACCTACCGATTTTTTTGAAGT-TGCTAATA
* * *
137062 ATGTAAACGGTAAAAAAAAATAGACGCTATCTATTACATTAAAATACCTACCGATTTTTTTAAGG
65 ATGTAAACGGTAAAAAAAAATAGACACTACCTATTACATTAAAATACCAACCGATTTTTTTAAGG
* * * * *
137127 TTGCTAATAATATAAACGGT-GAAAAAATATGCATTATCTATTACATTAAACTACCTACCGATTT
130 TTACTAATAATATAAACGGTAAAAAAAATAGGCATTACCTATTACATTAAACTACCTACAGATTT
* *
137191 TTTTGAATGTTGATAATAATGTAAACGA
195 TTTT-AAGGTTGATAATAATATAAACGA
* * * * *
137219 TAAAATAAAATAGACGTTATCTATTACATTAAACTACCTACCGATTTTTTTGAAGGTTGATAATA
1 TAAAAAAAAATAGACGTTACCTATTATATTAAAATACCTACCGATTTTTTTGAA-GTTGCTAATA
* * * * *
137284 ATATAAACGATAAAATAAAATAGGCTCTACCTATTA
65 ATGTAAACGGTAAAAAAAAATAGACACTACCTATTA
137320 TTATTAAATT
Statistics
Matches: 272, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
217 37 0.14
218 1 0.00
219 24 0.09
220 43 0.16
221 129 0.47
222 37 0.14
223 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (221 bp):
TAAAAAAAAATAGACGTTACCTATTATATTAAAATACCTACCGATTTTTTTGAAGTTGCTAATAA
TGTAAACGGTAAAAAAAAATAGACACTACCTATTACATTAAAATACCAACCGATTTTTTTAAGGT
TACTAATAATATAAACGGTAAAAAAAATAGGCATTACCTATTACATTAAACTACCTACAGATTTT
TTTAAGGTTGATAATAATATAAACGA
Found at i:137724 original size:72 final size:73
Alignment explanation
Indices: 137644--137781 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 73
137634 CGGTTAAAAT
* * * *
137644 AAAATAGACGATACATGTTACATTAAAATACTTAGC-AATTTTTTGAAGGTAT-CTAATAATGTA
1 AAAATAGACGATACATATTACAATAAAATACCTACCGAATTTTTTGAAGGT-TGCTAATAATGTA
137707 AACGGTAAA
65 AACGGTAAA
* * * *
137716 AAAATAGACGCTACCTATTACAATAAAATACCTACCGATTTTTTTTAAGGTTGCTAATAATGTAA
1 AAAATAGACGATACATATTACAATAAAATACCTACCGAATTTTTTGAAGGTTGCTAATAATGTAA
137781 A
66 A
137782 TAATAAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 31 0.55
73 25 0.45
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (73 bp):
AAAATAGACGATACATATTACAATAAAATACCTACCGAATTTTTTGAAGGTTGCTAATAATGTAA
ACGGTAAA
Found at i:137790 original size:72 final size:72
Alignment explanation
Indices: 137644--137805 Score: 184
Period size: 73 Copynumber: 2.2 Consensus size: 72
137634 CGGTTAAAAT
* * * * * *
137644 AAAATAGACGATACATGTTACATTAAAATACTTAGCAATTTTTTGAAGGTATCTAATAATGTAAA
1 AAAATAGACGCTACCTATTACAATAAAATACCTACCAATTTTTTGAAGGTATCTAATAATGTAAA
**
137709 CGGTAAA
66 CAATAAA
* *
137716 AAAATAGACGCTACCTATTACAATAAAATACCTACCGATTTTTTTTAAGGT-TGCTAATAATGTA
1 AAAATAGACGCTACCTATTACAATAAAATACCTACC-AATTTTTTGAAGGTAT-CTAATAATGTA
*
137780 AATAATAAA
64 AACAATAAA
137789 AAAATATG-CGCTACCTA
1 AAAATA-GACGCTACCTA
137806 CAAGTTTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
72 31 0.41
73 44 0.58
74 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (72 bp):
AAAATAGACGCTACCTATTACAATAAAATACCTACCAATTTTTTGAAGGTATCTAATAATGTAAA
CAATAAA
Found at i:137829 original size:128 final size:127
Alignment explanation
Indices: 137682--137918 Score: 343
Period size: 128 Copynumber: 1.9 Consensus size: 127
137672 TACTTAGCAA
* *
137682 TTTTTTGAAGGTATCTAATAATGTAAACGGT-AAAAAAATAGACGCTACCTATTACAATAAAATA
1 TTTTTTGAAGGTATCTAATAATGTAAACGGTAAAAAAAATAGACACTAACTATTACAATAAAATA
* * *
137746 CCTACCGATTTTTTTTAAGGTTGCTAATAATGTAAATAATAAAAAAATATGCGCTACCTACAAG
66 CCTACCG-TTTTTTTAAAAGTTGCTAATAATGTAAACAA-AAAAAAATATGCGCTACCTACAAG
* * *
137810 TTTTTTTAAGGTTAT-TAATAATGTAAACGGTAAAAAAAATAGGCACTAACTATTACATTAAAAT
1 TTTTTTGAAGG-TATCTAATAATGTAAACGGTAAAAAAAATAGACACTAACTATTACAATAAAAT
* *
137874 ATCTACTGTTTTTTTAAAAGTTGCTAATAATGTAAACAAAAAAAA
65 ACCTACCGTTTTTTTAAAAGTTGCTAATAATGTAAACAAAAAAAA
137919 TAGGTGCTAC
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
127 6 0.06
128 54 0.56
129 37 0.38
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (127 bp):
TTTTTTGAAGGTATCTAATAATGTAAACGGTAAAAAAAATAGACACTAACTATTACAATAAAATA
CCTACCGTTTTTTTAAAAGTTGCTAATAATGTAAACAAAAAAAAATATGCGCTACCTACAAG
Found at i:138089 original size:75 final size:74
Alignment explanation
Indices: 137810--138394 Score: 725
Period size: 74 Copynumber: 7.9 Consensus size: 74
137800 TACCTACAAG
** * *
137810 TTTTTTTAAGGTTATTAATAATGTAAACGGTAAAA-AAAATAGGCACTAACTATTACATTAAAAT
1 TTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAAT
* *
137874 ATCTACTG-
66 ACCTACCGA
* * *
137882 TTTTTTTAAAAGTTGCTAATAATGTAAAC---AAAA-AAAATAGGTGCTACATATTACATTAAAA
1 TTTTTTT-AAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAA
* **
137943 TACTTATTGA
65 TACCTACCGA
* * *
137953 TTTTTCTTAAAGTTGCTAATAATGTAAACGGTAAAA-AAAATAGGCACTACCTATTACATTAAAC
1 TTTTT-TTAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAA
*
138017 TACCTACCGG
65 TACCTACCGA
* * * *
138027 TTTGTTTGAAGGTTGCTAATAAAGTAAACAGTAAAATAAAATAGGCTCTACCTATTACATTAAAA
1 TTT-TTTTAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAA
*
138092 TATCTACCGA
65 TACCTACCGA
* * * * *
138102 TTTGTTTAAAGATTACTAATAATGTAAACAGTAAAATAAAATAGGCGCTACCTATTACATTAAAT
1 TTT-TTTTAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAA
*
138167 TACCTACTGA
65 TACCTACCGA
* **
138177 TTTTTTTTAATGTTGCTAATAATGTAAACGACAAAATAAAATAGGCGCTACCTATTACATTAAAA
1 -TTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAA
*
138242 TATCTACCGA
65 TACCTACCGA
* * * * *
138252 TTTTTTCAAGATTACTAATAATGTAAACGGTAAAATAAAATAGGCGCCACCTATTACATTAAACT
1 TTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAAT
*
138317 ACCTATCGA
66 ACCTACCGA
* *
138326 TTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAGT
1 TTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAAT
138391 ACCT
66 ACCT
138395 CTCAGTTATT
Statistics
Matches: 445, Mismatches: 59, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
70 34 0.08
71 26 0.06
72 9 0.02
73 18 0.04
74 191 0.43
75 164 0.37
76 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (74 bp):
TTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAAT
ACCTACCGA
Found at i:138136 original size:149 final size:148
Alignment explanation
Indices: 137810--138388 Score: 771
Period size: 149 Copynumber: 3.9 Consensus size: 148
137800 TACCTACAAG
* * * * *
137810 TTTTTTTAAGGTTATTAATAATGTAAACGGTAAAA-AAAATAGGCACTAACTATTACATTAAAAT
1 TTTTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGGCACTACCTATTACATTAAACT
* * * * * *
137874 ATCTACTG-TTTTTTTAAAAGTTGCTAATAATGTAAAC--AAAA-AAAATAGGTGCTACATATTA
66 ACCTACCGATTTTTTTGAAGGTTGCTAATAATGTAAACGTAAAATAAAATAGGCGCTACCTATTA
**
137935 CATTAAAATA-CTTATTGA
131 CATTAAAATATC-TACCGA
*
137953 TTTTTCTTAAAG-TTGCTAATAATGTAAACGGTAAAA-AAAATAGGCACTACCTATTACATTAAA
1 -TTTT-TTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGGCACTACCTATTACATTAAA
* * * *
138016 CTACCTACCGGTTTGTTTGAAGGTTGCTAATAAAGTAAACAGTAAAATAAAATAGGCTCTACCTA
64 CTACCTACCGATTTTTTTGAAGGTTGCTAATAATGTAAAC-GTAAAATAAAATAGGCGCTACCTA
138081 TTACATTAAAATATCTACCGA
128 TTACATTAAAATATCTACCGA
* * *
138102 TTTGTTTAAAGATTACTAATAATGTAAACAGTAAAATAAAATAGGCGCTACCTATTACATTAAAT
1 TTT-TTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGGCACTACCTATTACATTAAAC
* * * *
138167 TACCTACTGATTTTTTTTAATGTTGCTAATAATGTAAACGACAAAATAAAATAGGCGCTACCTAT
65 TACCTACCGATTTTTTTGAAGGTTGCTAATAATGTAAACG-TAAAATAAAATAGGCGCTACCTAT
138232 TACATTAAAATATCTACCGA
129 TACATTAAAATATCTACCGA
* * *
138252 TTTTTTCAAGATTACTAATAATGTAAACGGTAAAATAAAATAGGCGCCACCTATTACATTAAACT
1 TTTTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGGCACTACCTATTACATTAAACT
*
138317 ACCTATCGA-TTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATT
66 ACCTACCGATTTTTTTGAAGGTTGCTAATAATGTAAAC-GTAAAATAAAATAGGCGCTACCTATT
138381 ACATTAAA
130 ACATTAAA
138389 GTACCTCTCA
Statistics
Matches: 386, Mismatches: 37, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
144 59 0.15
145 30 0.08
148 71 0.18
149 121 0.31
150 105 0.27
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (148 bp):
TTTTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGGCACTACCTATTACATTAAACT
ACCTACCGATTTTTTTGAAGGTTGCTAATAATGTAAACGTAAAATAAAATAGGCGCTACCTATTA
CATTAAAATATCTACCGA
Found at i:139439 original size:24 final size:24
Alignment explanation
Indices: 139412--139473 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
139402 CGTTCGTGAA
*
139412 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
139436 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
139460 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
139474 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:140972 original size:16 final size:16
Alignment explanation
Indices: 140951--141011 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
140941 GGGTCTCCAA
140951 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
140967 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
140983 CGTTTATGTTTGTGTT
1 CGTTTATGTTCGTGTT
140999 CGTTTATGTTCGT
1 CGTTTATGTTCGT
141012 TTATTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.07, C:0.11, G:0.25, T:0.57
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:141102 original size:16 final size:16
Alignment explanation
Indices: 141081--141111 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
141071 AAAAAAAATT
141081 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
141097 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
141112 ACTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:143244 original size:21 final size:20
Alignment explanation
Indices: 143219--143263 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
143209 TATAAAAAAA
*
143219 TTATTTAAAAAATTATTATTT
1 TTATTTAAAAAATCATT-TTT
*
143240 TTATTTAAAACATCATTTTT
1 TTATTTAAAAAATCATTTTT
143260 TTAT
1 TTAT
143264 ATTTCCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTTAAAAAATCATTTTT
Found at i:151361 original size:17 final size:17
Alignment explanation
Indices: 151339--151388 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
151329 AAATTCTTCT
151339 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
151356 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
151370 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
151387 AA
1 AA
151389 ATATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:152406 original size:2 final size:2
Alignment explanation
Indices: 152395--152424 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
152385 ATAATAATCT
152395 TA TA -A 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 T
152425 GGATGGATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:152442 original size:20 final size:20
Alignment explanation
Indices: 152419--152460 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
152409 ATATATATAT
*
152419 ATATATGGATGGATGGATGG
1 ATATATGAATGGATGGATGG
* *
152439 ATATATTAATGGGTGGATGG
1 ATATATGAATGGATGGATGG
152459 AT
1 AT
152461 GCTGCGGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (20 bp):
ATATATGAATGGATGGATGG
Found at i:152450 original size:24 final size:26
Alignment explanation
Indices: 152413--152461 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
152403 ATATATATAT
152413 ATATATATATATGGATGGATGGATGG
1 ATATATATATATGGATGGATGGATGG
*
152439 ATATAT-TA-ATGGGTGGATGGATG
1 ATATATATATATGGATGGATGGATG
152462 CTGCGGGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 2 0.09
26 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (26 bp):
ATATATATATATGGATGGATGGATGG
Found at i:168116 original size:47 final size:47
Alignment explanation
Indices: 168037--168162 Score: 175
Period size: 47 Copynumber: 2.7 Consensus size: 47
168027 TAAATGCTTA
168037 CGAATTAGATATCATGCGGTTAGGTTTA--TTTTTCGAACAAGCATG
1 CGAATTAGATATCATGCGGTTAGGTTTATTTTTTTCGAACAAGCATG
* * * *
168082 CGAACTAGATATCATGCAGTTAGGTTTATTTTTTTTGAATAAGCATG
1 CGAATTAGATATCATGCGGTTAGGTTTATTTTTTTCGAACAAGCATG
* *
168129 CGAATTAGATATTATGCGGTTAGGATTTCTTTTT
1 CGAATTAGATATCATGCGGTTAGG-TTTATTTTT
168163 GTGGATAACA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
45 26 0.37
47 36 0.51
48 8 0.11
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (47 bp):
CGAATTAGATATCATGCGGTTAGGTTTATTTTTTTCGAACAAGCATG
Found at i:174232 original size:8 final size:8
Alignment explanation
Indices: 174219--174246 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
174209 AGATCCTCCC
174219 ATATGTAT
1 ATATGTAT
174227 ATATGTAT
1 ATATGTAT
174235 ATATGTAT
1 ATATGTAT
174243 ATAT
1 ATAT
174247 ATCTTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:177754 original size:14 final size:15
Alignment explanation
Indices: 177732--177803 Score: 51
Period size: 18 Copynumber: 4.5 Consensus size: 15
177722 TTTTGCTTGA
*
177732 AGAAGAAAT-AAAAG
1 AGAAAAAATGAAAAG
177746 AGAAAAAATGAAAAAATG
1 AGAAAAAATG--AAAA-G
177764 AGAAAAAA-GAAAAATG
1 AGAAAAAATG-AAAA-G
177780 ATGGAAAAAATGAAAAG
1 A--GAAAAAATGAAAAG
177797 A-AAAAAA
1 AGAAAAAA
177804 AGAAGAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
14 14 0.28
16 8 0.16
17 7 0.14
18 20 0.40
19 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (15 bp):
AGAAAAAATGAAAAG
Found at i:177758 original size:8 final size:8
Alignment explanation
Indices: 177747--177864 Score: 55
Period size: 8 Copynumber: 13.9 Consensus size: 8
177737 AAATAAAAGA
177747 GAAAAAAT
1 GAAAAAAT
177755 GAAAAAAT
1 GAAAAAAT
*
177763 GAGAAAAAA
1 GA-AAAAAT
177772 GAAAAATGAT
1 GAAAAA--AT
177782 GGAAAAAAT
1 -GAAAAAAT
177791 GAAAAGAA-
1 GAAAA-AAT
* *
177799 AAAAAAGAA
1 GAAAAA-AT
*
177808 GAAAAAAGG
1 GAAAAAA-T
177817 GAAAAGGGAA-
1 GAAAA---AAT
*
177827 GGAAAAAT
1 GAAAAAAT
177835 G-AAAAAT
1 GAAAAAAT
*
177842 GGAAAAAAA
1 -GAAAAAAT
177851 G-AAAAAT
1 GAAAAAAT
177858 GAAAAAA
1 GAAAAAA
177865 AGAGAAATAA
Statistics
Matches: 87, Mismatches: 8, Indels: 30
0.70 0.06 0.24
Matches are distributed among these distances:
7 15 0.17
8 33 0.38
9 26 0.30
10 5 0.06
11 6 0.07
12 2 0.02
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (8 bp):
GAAAAAAT
Found at i:177768 original size:18 final size:18
Alignment explanation
Indices: 177741--177795 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
177731 AAGAAGAAAT
177741 AAAA-GAGAAAAAATGAA
1 AAAATGAGAAAAAATGAA
177758 AAAATGAGAAAAAA-G-A
1 AAAATGAGAAAAAATGAA
177774 AAAATGATGGAAAAAATGAA
1 AAAATGA--GAAAAAATGAA
177794 AA
1 AA
177796 GAAAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 8 0.24
17 5 0.15
18 16 0.48
19 1 0.03
20 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (18 bp):
AAAATGAGAAAAAATGAA
Found at i:179242 original size:36 final size:37
Alignment explanation
Indices: 179145--179254 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
179135 TCAAAACAGG
* * *
179145 TCAATCTTAAGCCTTCATGAAAGAGCAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
* * *
179182 TCAAACTTAAGCCTTAACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
179219 TC-ATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
179255 CTCGTTTGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
36 31 0.48
37 33 0.52
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
Found at i:179741 original size:55 final size:55
Alignment explanation
Indices: 179257--179740 Score: 519
Period size: 55 Copynumber: 8.9 Consensus size: 55
179247 GAAGCAAACT
* *
179257 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACT
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
179312 CATTT-TATGAAGATTGCTCGAGTTCTATACTCTCTGAAAGAATAGGGAGCGAACA
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
179367 CGTTTTGTTAAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CG-TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
179419 AGTTCGTTGAAGA---TT-GAG-TCTTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
179470 AGTTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
179525 CGTTT-TATGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACC
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
179580 CGTTTATTGAAGATT-TTCCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTT-CGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * ** *
179635 CGTTTTATTGAAGATTGTTCAAG-TCTTATACTCCCTGACTGAATAGGGAGCAGACA
1 CG-TTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACA
** * * *
179691 CGTTTGCCGAAGATTGTTTGAG-TCTTATACTCACTGAAAGAATAGGGAGC
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGC
179741 ATACCCGCCA
Statistics
Matches: 371, Mismatches: 43, Indels: 30
0.84 0.10 0.07
Matches are distributed among these distances:
50 1 0.00
51 57 0.15
52 34 0.09
53 1 0.00
54 6 0.02
55 216 0.58
56 53 0.14
57 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:181303 original size:2 final size:2
Alignment explanation
Indices: 181296--181324 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
181286 AAAAGTATGC
181296 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
181325 TTATTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:188200 original size:21 final size:22
Alignment explanation
Indices: 188170--188215 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
188160 GGTAAAAAAA
*
188170 TTACCGAAAATATT-ATTTTTT
1 TTACCGAAAATATTAATATTTT
*
188191 TTACCTAAAATATTAATATTTT
1 TTACCGAAAATATTAATATTTT
188213 TTA
1 TTA
188216 ATATTTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (22 bp):
TTACCGAAAATATTAATATTTT
Found at i:189675 original size:15 final size:15
Alignment explanation
Indices: 189655--189683 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
189645 TAGGAGGGAG
189655 AACTTCAACTTATAA
1 AACTTCAACTTATAA
189670 AACTTCAACTTATA
1 AACTTCAACTTATA
189684 TGATTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (15 bp):
AACTTCAACTTATAA
Found at i:212065 original size:31 final size:28
Alignment explanation
Indices: 212019--212101 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 28
212009 TTTGATAATA
212019 TAATAATTATTTTATAGAATTTAGATAAATT
1 TAATAA-TATTTTATA-AATTTA-ATAAATT
*
212050 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAA-A-TTTAATAAATT
212081 TAATAAGTATTTTATAAATTT
1 TAATAA-TATTTTATAAATTT
212102 TTAAACTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
29 3 0.07
30 3 0.07
31 35 0.76
32 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (28 bp):
TAATAATATTTTATAAATTTAATAAATT
Found at i:212076 original size:19 final size:21
Alignment explanation
Indices: 212019--212101 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 21
212009 TTTGATAATA
*
212019 TAATAATTATTTT-ATAGAATT
1 TAATAAGTATTTTAATA-AATT
*
212040 TAGATAAAT-TTATTAAT-AATT
1 TA-ATAAGTATT-TTAATAAATT
*
212061 TTATAA-TATTTTAATAAATT
1 TAATAAGTATTTTAATAAATT
212081 TAATAAGTATTTT-ATAAATT
1 TAATAAGTATTTTAATAAATT
212101 T
1 T
212102 TTAAACTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
19 6 0.11
20 23 0.43
21 15 0.28
22 7 0.13
23 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (21 bp):
TAATAAGTATTTTAATAAATT
Found at i:212102 original size:9 final size:9
Alignment explanation
Indices: 212057--212112 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 9
212047 ATTTATTAAT
212057 AATTTTATA
1 AATTTTATA
212066 ATATTTTAATA
1 A-ATTTT-ATA
*
212077 AATTTAATA
1 AATTTTATA
212086 AGTATTTTATA
1 A--ATTTTATA
212097 AATTTT-TA
1 AATTTTATA
*
212105 AACTTTAT
1 AATTTTAT
212113 TGACGAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 7 0.18
9 11 0.28
10 9 0.23
11 12 0.31
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (9 bp):
AATTTTATA
Found at i:212861 original size:31 final size:30
Alignment explanation
Indices: 212826--212905 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
212816 TCAATAAAGT
*
212826 TTAAAAACTTATAAAATACTTATTAAATTTA
1 TTAAAAACTTATAAAATA-TTAATAAATTTA
212857 TTAAAAGA-TTATAAAATTATTAATAAATTTA
1 TTAAAA-ACTTATAAAA-TATTAATAAATTTA
*
212888 TCTAAATAC-TATAAAATA
1 T-TAAAAACTTATAAAATA
212906 AATATTATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
30 2 0.05
31 34 0.79
32 7 0.16
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAAAACTTATAAAATATTAATAAATTTA
Found at i:213797 original size:22 final size:22
Alignment explanation
Indices: 213772--213826 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
213762 TTAATTTTTA
*
213772 AAATATTAGAT-TTT-AGTATCAT
1 AAATATTAAATATTTAAGTAT--T
213794 AAATATTAAATATTTAAGTATT
1 AAATATTAAATATTTAAGTATT
213816 AAATATTAAAT
1 AAATATTAAAT
213827 GATTAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 22 0.73
23 3 0.10
24 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
AAATATTAAATATTTAAGTATT
Found at i:213803 original size:7 final size:7
Alignment explanation
Indices: 213793--213838 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
213783 TTTAGTATCA
213793 TAAATAT
1 TAAATAT
213800 TAAATATT
1 TAAATA-T
*
213808 TAAGTAT
1 TAAATAT
213815 TAAATAT
1 TAAATAT
213822 TAAATGAT
1 TAAAT-AT
*
213830 TAAAAAT
1 TAAATAT
213837 TA
1 TA
213839 TATTTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 22 0.65
8 12 0.35
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (7 bp):
TAAATAT
Found at i:213831 original size:15 final size:15
Alignment explanation
Indices: 213793--213838 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
213783 TTTAGTATCA
213793 TAAAT-ATTAAATAT
1 TAAATGATTAAATAT
*
213807 TTAA-GTATTAAATAT
1 TAAATG-ATTAAATAT
*
213822 TAAATGATTAAAAAT
1 TAAATGATTAAATAT
213837 TA
1 TA
213839 TATTTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.12
15 22 0.85
16 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (15 bp):
TAAATGATTAAATAT
Found at i:213838 original size:22 final size:22
Alignment explanation
Indices: 213793--213838 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
213783 TTTAGTATCA
**
213793 TAAATATTAAATATTTAAGTAT
1 TAAATATTAAATATTTAAAAAT
213815 TAAATATTAAATGA-TTAAAAAT
1 TAAATATTAAAT-ATTTAAAAAT
213837 TA
1 TA
213839 TATTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
TAAATATTAAATATTTAAAAAT
Found at i:220319 original size:20 final size:21
Alignment explanation
Indices: 220282--220340 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
220272 CAACAATTGG
*
220282 TAACAATTGATATCATTTTGT
1 TAACAATTGGTATCATTTTGT
220303 TAACAATTGGT-TCATTTTGT
1 TAACAATTGGTATCATTTTGT
220323 TAACAATTGGTAT-ATTTT
1 TAACAATTGGTATCATTTT
220341 TCATTAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 25 0.69
21 11 0.31
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (21 bp):
TAACAATTGGTATCATTTTGT
Found at i:220415 original size:21 final size:21
Alignment explanation
Indices: 220376--220414 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
220366 CAACAATTGG
220376 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
220397 TAACAATTGGTAT-ATTTT
1 TAACAATTGATATCATTTT
220415 TCATTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:223582 original size:18 final size:16
Alignment explanation
Indices: 223559--223598 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
223549 TGATTATACG
223559 TATATGAATGACATGAAT
1 TATATGAATG-CATG-AT
*
223577 TATATGTATGCATGAT
1 TATATGAATGCATGAT
223593 TATATG
1 TATATG
223599 TGTTAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (16 bp):
TATATGAATGCATGAT
Found at i:223596 original size:16 final size:18
Alignment explanation
Indices: 223559--223599 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
223549 TGATTATACG
*
223559 TATATGAATGACATGAAT
1 TATATGTATGACATGAAT
223577 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
223593 TATATGT
1 TATATGT
223600 GTTAACATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:225314 original size:21 final size:21
Alignment explanation
Indices: 225288--225332 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
225278 GATTTCTGGG
* *
225288 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
225309 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
225330 CAA
1 CAA
225333 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:225799 original size:20 final size:22
Alignment explanation
Indices: 225759--225815 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
225749 TGAATGTGTG
*
225759 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
225781 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
225801 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
225816 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:226383 original size:31 final size:31
Alignment explanation
Indices: 226345--226438 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
226335 AGGGTCGAGG
226345 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
226376 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
226407 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
226438 G
1 G
226439 GTCCTTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:230179 original size:24 final size:26
Alignment explanation
Indices: 230152--230206 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
230142 AAAAACATTT
*
230152 TAATATTT-TTAA-TATTGATATAAA
1 TAATATTTCATAATTATTGATATAAA
* *
230176 TAATATTTCATAATTATTTATATCAA
1 TAATATTTCATAATTATTGATATAAA
230202 TAATA
1 TAATA
230207 CTCCTCAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 8 0.31
25 3 0.12
26 15 0.58
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (26 bp):
TAATATTTCATAATTATTGATATAAA
Found at i:231786 original size:20 final size:20
Alignment explanation
Indices: 231761--231813 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
231751 TATTCCCTAG
*
231761 TAATCTTTTATTCCTACTTA
1 TAATCTTTTATTCCTACTGA
231781 TAATCTTTTATTCCTACTGA
1 TAATCTTTTATTCCTACTGA
*
231801 TAATCTTATATTC
1 TAATCTTTTATTC
231814 TGTGAACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATCTTTTATTCCTACTGA
Found at i:237340 original size:24 final size:24
Alignment explanation
Indices: 237294--237340 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
237284 TTTCTATATA
**
237294 TAATAATATTACATATTTGATTAT
1 TAATAATATTACATATTAAATTAT
* *
237318 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
237341 AACTAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:246393 original size:6 final size:6
Alignment explanation
Indices: 246384--246421 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
246374 CCTCCTCCTC
*
246384 CACCTT CACCTT CACCTT CACCTT CACCGTC CACCTT C
1 CACCTT CACCTT CACCTT CACCTT CACC-TT CACCTT C
246422 CCATCCCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.16, C:0.53, G:0.03, T:0.29
Consensus pattern (6 bp):
CACCTT
Found at i:252958 original size:10 final size:11
Alignment explanation
Indices: 252944--252983 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
252934 TTTCCCCCTC
*
252944 TTTTTATATCA
1 TTTTAATATCA
252955 TTTTACATATCA
1 TTTTA-ATATCA
252967 TTTTACATATCA
1 TTTTA-ATATCA
252979 TTTTA
1 TTTTA
252984 CATAACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 4 0.15
12 23 0.85
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAATATCA
Found at i:252966 original size:12 final size:12
Alignment explanation
Indices: 252949--252987 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
252939 CCCTCTTTTT
252949 ATATCATTTTAC
1 ATATCATTTTAC
252961 ATATCATTTTAC
1 ATATCATTTTAC
252973 ATATCATTTTAC
1 ATATCATTTTAC
252985 ATA
1 ATA
252988 ACCAAACTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATCATTTTAC
Found at i:256992 original size:42 final size:43
Alignment explanation
Indices: 256919--257004 Score: 165
Period size: 42 Copynumber: 2.0 Consensus size: 43
256909 CTAGTAGCGA
256919 TGGTAGCGGCTGAAGCCAGCAGCTGTCCTCAACTTTGCTTAGG
1 TGGTAGCGGCTGAAGCCAGCAGCTGTCCTCAACTTTGCTTAGG
256962 TGGTAGCGGCTGAAG-CAGCAGCTGTCCTCAACTTTGCTTAGG
1 TGGTAGCGGCTGAAGCCAGCAGCTGTCCTCAACTTTGCTTAGG
257004 T
1 T
257005 TATAGGCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 28 0.65
43 15 0.35
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (43 bp):
TGGTAGCGGCTGAAGCCAGCAGCTGTCCTCAACTTTGCTTAGG
Found at i:257096 original size:15 final size:15
Alignment explanation
Indices: 257076--257107 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
257066 GGTGAAAATG
257076 TAAGATTATCAGAAA
1 TAAGATTATCAGAAA
*
257091 TAAGATTATTAGAAA
1 TAAGATTATCAGAAA
257106 TA
1 TA
257108 TTATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.31
Consensus pattern (15 bp):
TAAGATTATCAGAAA
Found at i:258173 original size:203 final size:200
Alignment explanation
Indices: 257779--258174 Score: 672
Period size: 203 Copynumber: 1.9 Consensus size: 200
257769 AAAATATTTT
257779 ATTAATTTAGTAGGCTATTAAAAATTGAAAAATAATTTATTGTTTATATGTATAGTTTTATTGGT
1 ATTAATTTAGTAGGCTATTAAAAATTGAAAAATAATTTATTGTTTATATGTATAGTTTTATTGGT
257844 GAGTATTTCATTAATTTAAAGTTATAAGTCATTCAATTTTATATCTTCTAAACCAGTCTTCTTTT
66 GAGTATTTCATTAATTTAAAGTTATAAGTCATTCAATTTTATATCTTCTAAACCAGTCTTCTTTT
*
257909 TTATTAAAATATTTATGATCTTTTGAGCAAGACGTTAACTTTGTTGATTGAATATAATATAATTT
131 TTATTAAAATATTTATGATCTTTTGAGCAAGACGTTAACTTTGTTGATTG---AGAATATAATTT
257974 GATCTACA
193 GATCTACA
257982 ATTAATTTAGTAGGCTATTAAAAATTGAAAAATAATTTATTGTTTATATGTATAGTTTTATTGGT
1 ATTAATTTAGTAGGCTATTAAAAATTGAAAAATAATTTATTGTTTATATGTATAGTTTTATTGGT
*
258047 GAGTATTTCATTAATTTAAAGTTATAAAGTAATCATTCAATTATTTATATCTTCTAAATCAGTCT
66 GAGTATTTCATTAATTTAAAGTTAT-AAG---TCATTCAA-T-TTTATATCTTCTAAACCAGTCT
258112 TC-TTTTTATTAAAATATTTATGATCTTTTGAGCAAGACGTTAA-TTTGTTGATTG-GAATATAA
125 TCTTTTTTATTAAAATATTTATGATCTTTTGAGCAAGACGTTAACTTTGTTGATTGAGAATATAA
258174 T
190 T
258175 ATAATTTGAT
Statistics
Matches: 185, Mismatches: 2, Indels: 12
0.93 0.01 0.06
Matches are distributed among these distances:
203 98 0.53
204 3 0.02
207 19 0.10
208 42 0.23
209 23 0.12
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (200 bp):
ATTAATTTAGTAGGCTATTAAAAATTGAAAAATAATTTATTGTTTATATGTATAGTTTTATTGGT
GAGTATTTCATTAATTTAAAGTTATAAGTCATTCAATTTTATATCTTCTAAACCAGTCTTCTTTT
TTATTAAAATATTTATGATCTTTTGAGCAAGACGTTAACTTTGTTGATTGAGAATATAATTTGAT
CTACA
Found at i:265765 original size:162 final size:162
Alignment explanation
Indices: 265462--265773 Score: 511
Period size: 162 Copynumber: 1.9 Consensus size: 162
265452 TCAATTTCAC
265462 ACACACATATACAAGATTGATCCTTAATTTATTTAAAGCATAATAACAAGATTGATCCTCATTGT
1 ACACACATATACAAGATTGATCCTTAATTTATTTAAAGCATAATAACAAGATTGATCCTCATTGT
* *
265527 TCCATCATTTTTCAGTTTCACCTAGGGGTGTTCAAAAGGTTAATCTGACCATCGACCGAATCGAA
66 TCCATCATTTTTCAGTTTCACCTAAGGGTGTTCAAAAGGTTAATCTGACCATCGACCGAACCGAA
*
265592 TTACTATTAACCGAATTAACTAATTTTTTTAT
131 TTACCATTAACCGAATTAACTAATTTTTTTAT
* * *
265624 ACACGCATGTACAAGATTGATCCTTAATTTATTTAAAGCATAATAACAAGATTGATCCTTATTGT
1 ACACACATATACAAGATTGATCCTTAATTTATTTAAAGCATAATAACAAGATTGATCCTCATTGT
* *
265689 TCCATTATTTTTCAGTTTCACCTAAGGGTGTTCAAAAGGTTAAT-TCGACCA-CTGATCGAACCG
66 TCCATCATTTTTCAGTTTCACCTAAGGGTGTTCAAAAGGTTAATCT-GACCATC-GACCGAACCG
*
265752 AGTTACCATTAACCGAATTAAC
129 AATTACCATTAACCGAATTAAC
265774 AAAACTTTTT
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
161 2 0.01
162 137 0.99
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (162 bp):
ACACACATATACAAGATTGATCCTTAATTTATTTAAAGCATAATAACAAGATTGATCCTCATTGT
TCCATCATTTTTCAGTTTCACCTAAGGGTGTTCAAAAGGTTAATCTGACCATCGACCGAACCGAA
TTACCATTAACCGAATTAACTAATTTTTTTAT
Found at i:265946 original size:16 final size:18
Alignment explanation
Indices: 265922--265962 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
265912 GGAATATTTT
*
265922 TTTATTTAGG-TTAA-AA
1 TTTAATTAGGATTAATAA
265938 TTTAATTAGGTATTAATAA
1 TTTAATTAGG-ATTAATAA
265957 TTTAAT
1 TTTAAT
265963 GAGTCTAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
18 4 0.19
19 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (18 bp):
TTTAATTAGGATTAATAA
Found at i:266835 original size:2 final size:2
Alignment explanation
Indices: 266830--266862 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
266820 AAGTTGAATA
266830 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 A
266863 GAAATTTGGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:270506 original size:6 final size:6
Alignment explanation
Indices: 270497--270526 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
270487 CATGGATCAC
*
270497 GGCAAC GGCAAG GGCAAG GGCAAG GGCAAG
1 GGCAAG GGCAAG GGCAAG GGCAAG GGCAAG
270527 ACAACGAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.47, T:0.00
Consensus pattern (6 bp):
GGCAAG
Found at i:271548 original size:20 final size:21
Alignment explanation
Indices: 271495--271549 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
271485 AAAAAAAGAC
271495 ATGTCACAAAGACAAAGATAAAT
1 ATGTCACAAAG--AAAGATAAAT
* * *
271518 GTGTCATAAAGAAAGA-GAAT
1 ATGTCACAAAGAAAGATAAAT
271538 ATGTCACAAAGA
1 ATGTCACAAAGA
271550 CATAATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 13 0.48
21 5 0.19
23 9 0.33
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (21 bp):
ATGTCACAAAGAAAGATAAAT
Found at i:271995 original size:17 final size:17
Alignment explanation
Indices: 271973--272011 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
271963 GTTTCAATTG
271973 AAAATACAAAAAAATCT
1 AAAATACAAAAAAATCT
* * *
271990 AAAATATATAAAAATTT
1 AAAATACAAAAAAATCT
272007 AAAAT
1 AAAAT
272012 TTGTAAACAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATACAAAAAAATCT
Found at i:272611 original size:37 final size:37
Alignment explanation
Indices: 272516--272683 Score: 113
Period size: 37 Copynumber: 4.7 Consensus size: 37
272506 TACATTTCGG
*
272516 TTTTAAAAAATTAATAGAATTGCTGA-AGCAATATTT
1 TTTTAAAAAATTAATAGAATTGTTGACAGCAATATTT
* *** *
272552 TTTT----AATTAATGGAACAATTGACA-TAATATTTT
1 TTTTAAAAAATTAATAGAATTGTTGACAGCAATA-TTT
* *
272585 TTTTAAAAAATTAATAGAATTGTTGAC-GCGATATAT
1 TTTTAAAAAATTAATAGAATTGTTGACAGCAATATTT
* * ** *
272621 TTTAAAAAATATTAATAGAACTACTGACA-C-ATGATAT
1 TTTTAAAAA-ATTAATAGAATTGTTGACAGCAAT-ATTT
*
272658 TTTT-AAAAATTAATAGAATCGTTGAC
1 TTTTAAAAAATTAATAGAATTGTTGAC
272684 CTGATATAAA
Statistics
Matches: 100, Mismatches: 22, Indels: 21
0.70 0.15 0.15
Matches are distributed among these distances:
32 17 0.17
33 8 0.08
35 14 0.14
36 20 0.20
37 41 0.41
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (37 bp):
TTTTAAAAAATTAATAGAATTGTTGACAGCAATATTT
Found at i:287164 original size:179 final size:179
Alignment explanation
Indices: 286856--287736 Score: 1491
Period size: 179 Copynumber: 4.9 Consensus size: 179
286846 GTGCATTTCG
* * *
286856 TAGCAAATACAACAACTACGTTTCCATGGTATCTTATTTGCTGAACTCTTTGCTTCCTCTTCAAC
1 TAGCAAATACAACAACTA-GTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAAC
286921 TGTATAATTATTTACTACCAAGTAAATAT-CCAATTAGATTATATGTGTGCCTGTAGGTATTTAA
65 TGTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAA
286985 GAGCATAAACATGATAATATAAAGGGTAAACTATATCAGTGATCACCTAA
130 GAGCATAAACATGATAATATAAAGGGTAAACTATATCAGTGATCACCTAA
* *
287035 TAACAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTACTGCCTCTTCAACT
1 TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
* * *
287100 GTATAATTATTTACTATCAAGTCAATATCCCAATTAGATTATATGTGTGCATGTAGGTATTTAAG
66 GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAAG
287165 AGCATAAACATGATAATATAAAGGGTAAACTATATCAGTGATCACCTAA
131 AGCATAAACATGATAATATAAAGGGTAAACTATATCAGTGATCACCTAA
287214 TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
1 TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
287279 GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAAG
66 GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAAG
*
287344 AGCATAAACATGATAATATAAAGGGTAAACTATATCAATGATCACCTAA
131 AGCATAAACATGATAATATAAAGGGTAAACTATATCAGTGATCACCTAA
* * * * *
287393 TAGCAAATACAACAACTAGTTTCCATGATTTCTTATCTGCTGAACTCTTTGCTTCCTCTTCAATT
1 TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
* *
287458 GTATAATTATTTACTACCAACTAAATATCCCAATTAGATTATATGTGTG-TTGTAGGTATTTAAG
66 GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAAG
** *
287522 AGCATAAACATGATAATATAAAATGTAAACTATATCAGTGACCACCTAA
131 AGCATAAACATGATAATATAAAGGGTAAACTATATCAGTGATCACCTAA
* * *
287571 TAGCAAATACAACAACTAATTTCCATGGTATCTTATCTGCTGAATTCTTTGTTGCCTCTTCAATT
1 TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
* *
287636 GTATAATTATTTACTACCAAGTCAATATCCCAATTAGATTATATGTGTGTCTGCT-GGTATTTAA
66 GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTG-TAGGTATTTAA
*
287700 GAGTATAAACATGATAATATAAA-GGTAAACTATATCA
130 GAGCATAAACATGATAATATAAAGGGTAAACTATATCA
287737 ATAACTACCT
Statistics
Matches: 663, Mismatches: 36, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
178 247 0.37
179 415 0.63
180 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (179 bp):
TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAAG
AGCATAAACATGATAATATAAAGGGTAAACTATATCAGTGATCACCTAA
Found at i:287554 original size:357 final size:358
Alignment explanation
Indices: 286856--287738 Score: 1504
Period size: 357 Copynumber: 2.5 Consensus size: 358
286846 GTGCATTTCG
* * *
286856 TAGCAAATACAACAACTACGTTTCCATGGTATCTTATTTGCTGAACTCTTTGCTTCCTCTTCAAC
1 TAGCAAATACAACAACTA-GTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAAC
286921 TGTATAATTATTTACTACCAAGTAAATAT-CCAATTAGATTATATGTGTGCCTGTAGGTATTTAA
65 TGTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAA
*
286985 GAGCATAAACATGATAATATAAAGGGTAAACTATATCAGTGATCACCTAATAACAAATACAACAA
130 GAGCATAAACATGATAATATAAAGGGTAAACTATATCAATGATCACCTAATAACAAATACAACAA
* *
287050 CTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTACTGCCTCTTCAACTGTATAATTATTTACT
195 CTAGTTTCCATGATATCTTATCTGCTGAACTCTTTACTGCCTCTTCAACTGTATAATTATTTACT
* * *
287115 ATCAAGTCAATATCCCAATTAGATTATATGTGTGCATGTAGGTATTTAAGAGCATAAACATGATA
260 ACCAACTAAATATCCCAATTAGATTATATGTGTGCATGTAGGTATTTAAGAGCATAAACATGATA
* *
287180 ATATAAAGGGTAAACTATATCAGTGATCACCTAA
325 ATATAAAAGGTAAACTATATCAGTGACCACCTAA
287214 TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
1 TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
287279 GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAAG
66 GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAAG
*
287344 AGCATAAACATGATAATATAAAGGGTAAACTATATCAATGATCACCTAATAGCAAATACAACAAC
131 AGCATAAACATGATAATATAAAGGGTAAACTATATCAATGATCACCTAATAACAAATACAACAAC
* * * *
287409 TAGTTTCCATGATTTCTTATCTGCTGAACTCTTTGCTTCCTCTTCAATTGTATAATTATTTACTA
196 TAGTTTCCATGATATCTTATCTGCTGAACTCTTTACTGCCTCTTCAACTGTATAATTATTTACTA
*
287474 CCAACTAAATATCCCAATTAGATTATATGTGTG-TTGTAGGTATTTAAGAGCATAAACATGATAA
261 CCAACTAAATATCCCAATTAGATTATATGTGTGCATGTAGGTATTTAAGAGCATAAACATGATAA
*
287538 TATAAAATGTAAACTATATCAGTGACCACCTAA
326 TATAAAAGGTAAACTATATCAGTGACCACCTAA
* * *
287571 TAGCAAATACAACAACTAATTTCCATGGTATCTTATCTGCTGAATTCTTTGTTGCCTCTTCAATT
1 TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
* *
287636 GTATAATTATTTACTACCAAGTCAATATCCCAATTAGATTATATGTGTGTCTGCT-GGTATTTAA
66 GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTG-TAGGTATTTAA
*
287700 GAGTATAAACATGATAATATAAA-GGTAAACTATATCAAT
130 GAGCATAAACATGATAATATAAAGGGTAAACTATATCAAT
287739 AACTACCTAA
Statistics
Matches: 499, Mismatches: 24, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
356 16 0.03
357 276 0.55
358 207 0.41
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (358 bp):
TAGCAAATACAACAACTAGTTTCCATGGTATCTTATCTGCTGAATTCTTTGCTGCCTCTTCAACT
GTATAATTATTTACTACCAAGTAAATATCCCAATTAGATTATATGTGTGCCTGTAGGTATTTAAG
AGCATAAACATGATAATATAAAGGGTAAACTATATCAATGATCACCTAATAACAAATACAACAAC
TAGTTTCCATGATATCTTATCTGCTGAACTCTTTACTGCCTCTTCAACTGTATAATTATTTACTA
CCAACTAAATATCCCAATTAGATTATATGTGTGCATGTAGGTATTTAAGAGCATAAACATGATAA
TATAAAAGGTAAACTATATCAGTGACCACCTAA
Found at i:288273 original size:31 final size:32
Alignment explanation
Indices: 288218--288292 Score: 118
Period size: 31 Copynumber: 2.4 Consensus size: 32
288208 TTCAATTTTT
288218 TCTTAACTTTAAAAAATATATTTTT-ATCATTA
1 TCTTAACTTTAAAAAATATATTTTTGA-CATTA
*
288250 TCTTAACTTTAAAAAATAT-TTTTTGACTTTA
1 TCTTAACTTTAAAAAATATATTTTTGACATTA
288281 TCTTAACTTTAA
1 TCTTAACTTTAA
288293 TTTTTTTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 21 0.51
32 20 0.49
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51
Consensus pattern (32 bp):
TCTTAACTTTAAAAAATATATTTTTGACATTA
Found at i:302535 original size:39 final size:39
Alignment explanation
Indices: 302481--302559 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 39
302471 TCCTGATTAC
*
302481 TATACATCTTTAGTATT-GGAAAAGCTAAAGATTTCAGGA
1 TATACATCTTTAGTATTGGGAAAA-CTAAAGACTTCAGGA
302520 TATACATCTTTAGTATTGGGAAAACTAAAGACTTCAGGA
1 TATACATCTTTAGTATTGGGAAAACTAAAGACTTCAGGA
302559 T
1 T
302560 TGCATTGAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 32 0.84
40 6 0.16
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (39 bp):
TATACATCTTTAGTATTGGGAAAACTAAAGACTTCAGGA
Found at i:315641 original size:16 final size:16
Alignment explanation
Indices: 315622--315658 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
315612 TTAAATTATT
315622 TTTAAATAATTTAATG
1 TTTAAATAATTTAATG
315638 TTTAAATAATTTAATG
1 TTTAAATAATTTAATG
315654 TTTAA
1 TTTAA
315659 TTTAATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
TTTAAATAATTTAATG
Found at i:319813 original size:3 final size:3
Alignment explanation
Indices: 319805--319838 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
319795 GAAGATGAGG
319805 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
319839 AGGGTCGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:321646 original size:18 final size:18
Alignment explanation
Indices: 321623--321657 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
321613 TATATGATTT
321623 ACAAA-TCAAACTACAATC
1 ACAAATTCAAACT-CAATC
321641 ACAAATTCAAACTCAAT
1 ACAAATTCAAACTCAAT
321658 TCTAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (18 bp):
ACAAATTCAAACTCAATC
Found at i:321957 original size:34 final size:34
Alignment explanation
Indices: 321919--321986 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
321909 TTTGTATTAT
*
321919 ATTAATATAAAAAATATAAAAAATTTTATATATA
1 ATTAATATAAAAAATATAAAAAATTATATATATA
*
321953 ATTAATATAAAAAATATAAAATATTATATATATA
1 ATTAATATAAAAAATATAAAAAATTATATATATA
321987 TATAATCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
ATTAATATAAAAAATATAAAAAATTATATATATA
Found at i:324803 original size:21 final size:21
Alignment explanation
Indices: 324770--324809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
324760 TTATTATTTT
324770 TTATCCATCTTTAAATTTTGA
1 TTATCCATCTTTAAATTTTGA
* *
324791 TTATTCATTTTTAAATTTT
1 TTATCCATCTTTAAATTTT
324810 ATCAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (21 bp):
TTATCCATCTTTAAATTTTGA
Found at i:330021 original size:30 final size:30
Alignment explanation
Indices: 329985--330046 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
329975 GATCAAATGT
329985 AACTCTTGGTTCTATGACGGGTGCATCTCG
1 AACTCTTGGTTCTATGACGGGTGCATCTCG
* * *
330015 AACTCTTGGTTCTTTGACGGGTTCATGTCG
1 AACTCTTGGTTCTATGACGGGTGCATCTCG
330045 AA
1 AA
330047 GTTCCAAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (30 bp):
AACTCTTGGTTCTATGACGGGTGCATCTCG
Found at i:330656 original size:85 final size:85
Alignment explanation
Indices: 330507--330666 Score: 284
Period size: 85 Copynumber: 1.9 Consensus size: 85
330497 ACAGTTTTAA
* *
330507 TGCCAATAAGCAACCAATTATCAGAATGGTCGATGAGAAAGCAAATGCACCCATCCTGATAAATT
1 TGCCAATAAGCAACCAATTATCAGAATGGTCGATGAGAAAGCAAATGCACCCACCCTGACAAATT
330572 TAGGAACTAACTGTTTTGAG
66 TAGGAACTAACTGTTTTGAG
* *
330592 TGCCGATAAGCAACCAATTATCAGAATGGTCGATGAGAAAGCAAATGCACCCACCCTGGCAAATT
1 TGCCAATAAGCAACCAATTATCAGAATGGTCGATGAGAAAGCAAATGCACCCACCCTGACAAATT
330657 TAGGAACTAA
66 TAGGAACTAA
330667 ATAAATATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (85 bp):
TGCCAATAAGCAACCAATTATCAGAATGGTCGATGAGAAAGCAAATGCACCCACCCTGACAAATT
TAGGAACTAACTGTTTTGAG
Found at i:333795 original size:28 final size:30
Alignment explanation
Indices: 333696--333824 Score: 203
Period size: 30 Copynumber: 4.4 Consensus size: 30
333686 GGTTCTTCGG
* *
333696 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
333726 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
333756 GACCTCTGGATAGTTACCGAGGAT-TTT-T
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
333784 GACCTCTGGATAGTTACCG-GG-TCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
333812 GACCTCTGGATAG
1 GACCTCTGGATAG
333825 GTCCTTCGGG
Statistics
Matches: 95, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
26 1 0.01
27 5 0.05
28 34 0.36
29 3 0.03
30 52 0.55
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:336643 original size:26 final size:26
Alignment explanation
Indices: 336608--336659 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
336598 AATGTTTTCA
336608 AAGAAGCAGCTTTTCTTTCATTTCTT
1 AAGAAGCAGCTTTTCTTTCATTTCTT
336634 AAGAAGCAGCTTTTCTTTCATTTCTT
1 AAGAAGCAGCTTTTCTTTCATTTCTT
336660 TTGCTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (26 bp):
AAGAAGCAGCTTTTCTTTCATTTCTT
Done.