Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008248.1 Kokia drynarioides strain JFW-HI SEQ_122913, 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: 319511
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 30 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:6897 original size:18 final size:18
Alignment explanation
Indices: 6876--6921 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
6866 GTGGAACCTA
6876 AGGAGAAGAAGGAA-AATG
1 AGGAGAAGAAGGAATAA-G
6894 AGGA-AGAGAAGGAATAAG
1 AGGAGA-AGAAGGAATAAG
6912 AGGAGAAGAA
1 AGGAGAAGAA
6922 TGAAGAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 21 0.84
19 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.39, T:0.04
Consensus pattern (18 bp):
AGGAGAAGAAGGAATAAG
Found at i:12751 original size:24 final size:24
Alignment explanation
Indices: 12704--12761 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
12694 AAAAACCTTA
12704 AAAATCTTTAAACATTACAAAATAT
1 AAAAT-TTTAAACATTACAAAATAT
*
12729 ATAATATTTAAA-ATTA-AATAATAT
1 AAAAT-TTTAAACATTACAA-AATAT
12753 AAAATTTTA
1 AAAATTTTA
12762 TAAGTTACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 6 0.21
24 13 0.45
25 10 0.34
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAATTTTAAACATTACAAAATAT
Found at i:13772 original size:2 final size:2
Alignment explanation
Indices: 13765--13796 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13755 TAGCTGTTTT
13765 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
13797 AAAGAAGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:19553 original size:75 final size:75
Alignment explanation
Indices: 19361--19541 Score: 317
Period size: 75 Copynumber: 2.4 Consensus size: 75
19351 AATCTCGTAT
*
19361 CTCCTCAACCTACTACTGCTTCTCTCTCTCCTATCTCTCTCCCGCTCCCTCTCTAGCTCACGATC
1 CTCCTCGACCTACTACTGCTTCTCTCTCTCCTATCTCTCTCCCGCTCCCTCTCTAGCTCACGATC
19426 ACTCTCGTGC
66 ACTCTCGTGC
* * *
19436 CTCCTCGACCTACTACTGCTCCTCTCTCTCCTATCTCTCTCCCGTTCCCTCTCTATCTCACGATC
1 CTCCTCGACCTACTACTGCTTCTCTCTCTCCTATCTCTCTCCCGCTCCCTCTCTAGCTCACGATC
*
19501 ACTTTCGTGC
66 ACTCTCGTGC
19511 CTCCTCGACCTACTACTGCTTCTCTCTCTCC
1 CTCCTCGACCTACTACTGCTTCTCTCTCTCC
19542 GGTCTATCTC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 100 1.00
ACGTcount: A:0.11, C:0.46, G:0.08, T:0.35
Consensus pattern (75 bp):
CTCCTCGACCTACTACTGCTTCTCTCTCTCCTATCTCTCTCCCGCTCCCTCTCTAGCTCACGATC
ACTCTCGTGC
Found at i:19590 original size:33 final size:35
Alignment explanation
Indices: 19550--19669 Score: 104
Period size: 33 Copynumber: 3.4 Consensus size: 35
19540 CCGGTCTATC
*
19550 TCCCTCTCTTTCTCCTTTTCCTTCTCTCTTTCC-C
1 TCCCTCTCTTTCTCCTTTTCCTTCTCTCTTTCCTA
* * *
19584 T-CCTCTCTCTCT-CTTTT-TTTCTCTCTCTCCTA
1 TCCCTCTCTTTCTCCTTTTCCTTCTCTCTTTCCTA
* *
19616 TCCCTCTCTTTCTCCTTATCTCTATCTCTTCTTTCTCTC
1 TCCCTCTCTTTCTCCTTTTC-CT-TCTC-TCTTTC-CTA
* *
19655 TCCCTTTCCTTCTCC
1 TCCCTCTCTTTCTCC
19670 CTCTCCCCGC
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
31 11 0.16
32 6 0.09
33 20 0.30
34 5 0.07
36 1 0.01
37 4 0.06
38 5 0.07
39 15 0.22
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (35 bp):
TCCCTCTCTTTCTCCTTTTCCTTCTCTCTTTCCTA
Found at i:20506 original size:18 final size:18
Alignment explanation
Indices: 20485--20519 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20475 TATTTCGAGC
20485 AAAAATTTAATTTTTTAA
1 AAAAATTTAATTTTTTAA
20503 AAAAATTTAATTTTTTA
1 AAAAATTTAATTTTTTA
20520 TCTCTCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAAATTTAATTTTTTAA
Found at i:21032 original size:11 final size:11
Alignment explanation
Indices: 21016--21058 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
21006 TTGTTCCTGC
*
21016 CTTATTTTTAT
1 CTTATTTATAT
21027 CTTATTTATAT
1 CTTATTTATAT
* *
21038 TTTATTTATTT
1 CTTATTTATAT
21049 CTTTATTTAT
1 C-TTATTTAT
21059 TTATCCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTATTTATAT
Found at i:21697 original size:24 final size:24
Alignment explanation
Indices: 21639--21697 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
21629 ATAAATGATT
* *
21639 TTAA-ATTTTAAATAATATTTTTA
1 TTAATATTTTAAAAAATATTTATA
*
21662 AT-ATATTATTAAAAAATATTTATA
1 TTAATATT-TTAAAAAATATTTATA
21686 TTAATATTTTAA
1 TTAATATTTTAA
21698 TTATAAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 1 0.03
23 4 0.14
24 19 0.66
25 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAATATTTTAAAAAATATTTATA
Found at i:21775 original size:23 final size:22
Alignment explanation
Indices: 21733--21776 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
21723 AATATTTAAC
*
21733 AATAATAAAATATTAATATTTT
1 AATAATAAAATATGAATATTTT
*
21755 AATAATATAAATATGAGTATTT
1 AATAATA-AAATATGAATATTT
21777 GTTTAACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
AATAATAAAATATGAATATTTT
Found at i:22092 original size:29 final size:30
Alignment explanation
Indices: 22036--22092 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
22026 ATTCATAAAT
* *
22036 AAATTTTAATTTTATACAATTTTATACATA
1 AAATTTTAATTTAATACAATTCTATACATA
22066 AAATTTTAATTTAAT-CTAATTCT-TACA
1 AAATTTTAATTTAATAC-AATTCTATACA
22093 AATTACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (30 bp):
AAATTTTAATTTAATACAATTCTATACATA
Found at i:22324 original size:22 final size:23
Alignment explanation
Indices: 22298--22353 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 23
22288 GGCGCTCTCT
*
22298 TATTTTTTTC-ATTTAATTTGTA
1 TATTTTTTTCGAATTAATTTGTA
22320 TATTTTTTTCGGTGAATTAATTTGTA
1 TATTTTTTTC---GAATTAATTTGTA
22346 TATTTTTT
1 TATTTTTT
22354 AAAACATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 10 0.34
26 19 0.66
ACGTcount: A:0.21, C:0.04, G:0.09, T:0.66
Consensus pattern (23 bp):
TATTTTTTTCGAATTAATTTGTA
Found at i:22470 original size:21 final size:22
Alignment explanation
Indices: 22444--22485 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
22434 TTGGTAATTA
22444 TTTTTTCA-ACAG-TTTAAAAAG
1 TTTTTTCACA-AGCTTTAAAAAG
22465 TTTTTTCACAAGCTTTAAAAA
1 TTTTTTCACAAGCTTTAAAAA
22486 ACATCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
TTTTTTCACAAGCTTTAAAAAG
Found at i:27328 original size:20 final size:20
Alignment explanation
Indices: 27305--27431 Score: 220
Period size: 20 Copynumber: 6.3 Consensus size: 20
27295 TTTGTAGTTT
27305 GGTGCCCTTGCTTGCACTTC
1 GGTGCCCTTGCTTGCACTTC
27325 GGTGCCCTTGCTTGCACTTC
1 GGTGCCCTTGCTTGCACTTC
27345 GGTGCCCTTGCTTGCACTTC
1 GGTGCCCTTGCTTGCACTTC
27365 GGTGCCCTTGCTTGCACTTC
1 GGTGCCCTTGCTTGCACTTC
27385 GGTGCCCTTGCTTGCACTTC
1 GGTGCCCTTGCTTGCACTTC
* *
27405 GATGCCATTG-TCTGCACTTC
1 GGTGCCCTTGCT-TGCACTTC
27425 GGTGCCC
1 GGTGCCC
27432 CTGTATGCAC
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
19 1 0.01
20 101 0.99
ACGTcount: A:0.06, C:0.35, G:0.25, T:0.34
Consensus pattern (20 bp):
GGTGCCCTTGCTTGCACTTC
Found at i:27450 original size:20 final size:20
Alignment explanation
Indices: 27427--27520 Score: 95
Period size: 20 Copynumber: 4.7 Consensus size: 20
27417 TGCACTTCGG
* **
27427 TGCCCCTGTATGCACTTTTA
1 TGCCCCTATATGCACACTTA
*
27447 TGCCCCTAAATGCACACTTA
1 TGCCCCTATATGCACACTTA
27467 TGCCCCTATATG--CACTTCA
1 TGCCCCTATATGCACACTT-A
*
27486 GTGCCCCTGA-ATGCACACTTG
1 -TGCCCCT-ATATGCACACTTA
27507 TGCCCCTATATGCA
1 TGCCCCTATATGCA
27521 ATCCGATGCC
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.08
19 2 0.03
20 49 0.79
21 1 0.02
22 5 0.08
ACGTcount: A:0.21, C:0.34, G:0.15, T:0.30
Consensus pattern (20 bp):
TGCCCCTATATGCACACTTA
Found at i:27471 original size:40 final size:40
Alignment explanation
Indices: 27427--27520 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
27417 TGCACTTCGG
* *
27427 TGCCCCTGTATGCACTTTTA-TGCCCCTAAATGCACACTTA
1 TGCCCCTATATGCAC-TTCAGTGCCCCTAAATGCACACTTA
* *
27467 TGCCCCTATATGCACTTCAGTGCCCCTGAATGCACACTTG
1 TGCCCCTATATGCACTTCAGTGCCCCTAAATGCACACTTA
27507 TGCCCCTATATGCA
1 TGCCCCTATATGCA
27521 ATCCGATGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.06
40 46 0.94
ACGTcount: A:0.21, C:0.34, G:0.15, T:0.30
Consensus pattern (40 bp):
TGCCCCTATATGCACTTCAGTGCCCCTAAATGCACACTTA
Found at i:27530 original size:60 final size:60
Alignment explanation
Indices: 27417--27534 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
27407 TGCCATTGTC
* * ** **
27417 TGCACTTCGGTGCCCCTGTATGCACTTTTATGCCCCTAAATGCACACTTATGCCCCTATA
1 TGCACTTCAGTGCCCCTGAATGCACACTTATGCCCCTAAATGCACACCGATGCCCCTATA
* *
27477 TGCACTTCAGTGCCCCTGAATGCACACTTGTGCCCCTATATGCA-ATCCGATGCCCCTA
1 TGCACTTCAGTGCCCCTGAATGCACACTTATGCCCCTAAATGCACA-CCGATGCCCCTA
27535 ATGGTATAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (60 bp):
TGCACTTCAGTGCCCCTGAATGCACACTTATGCCCCTAAATGCACACCGATGCCCCTATA
Found at i:27531 original size:40 final size:38
Alignment explanation
Indices: 27446--27537 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 38
27436 ATGCACTTTT
* *
27446 ATGCCCCTAAATGCACACTTATGCCCCTATATGCACTTC
1 ATGCCCCT-AATGCACACTTATGCCCCTATATGCAATCC
*
27485 AGTGCCCCTGAATGCACACTTGTGCCCCTATATGCAATCC
1 A-TGCCCCT-AATGCACACTTATGCCCCTATATGCAATCC
27525 GATGCCCCTAATG
1 -ATGCCCCTAATG
27538 GTATAGTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 5 0.11
40 41 0.87
41 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (38 bp):
ATGCCCCTAATGCACACTTATGCCCCTATATGCAATCC
Found at i:31441 original size:21 final size:21
Alignment explanation
Indices: 31394--31442 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31384 AATAGTGCAG
31394 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* *
31415 AGTTCTACCGATACAAGTGTC
1 ACTTCTACCGATACAAGTGAC
*
31436 TCTTCTA
1 ACTTCTA
31443 TTGAAACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:42718 original size:131 final size:131
Alignment explanation
Indices: 42484--42746 Score: 402
Period size: 131 Copynumber: 2.0 Consensus size: 131
42474 GAATTTGGGA
* *
42484 ATTACATGTTATATGGGTGTTAGTCTTAGATGTCCTACCGATGGCTGAGATCGACATATGTTGCG
1 ATTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCAATGGCTGAGATCGACATATGTTGCG
* * * * *
42549 GATTCTCCACAACTTGTGTGAGCAGCATCGTGTAGCTTAATATCTCGACCCACAGCTCGTGTGAG
66 AATTCTCCACAACTCGTGTGAACAGCATCGTGTAGCTTAACATATCGACCCACAGCTCGTGTGAG
42614 C
131 C
* *
42615 ATTACATGTTATATGGGTGCTGGTCTTAGATGTCCTA-CAATGGCTGAGATCCGGCATATGTTGC
1 ATTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCAATGGCTGAGAT-CGACATATGTTGC
* * *
42679 GAATTCTTCATAGCTCGTGTGAACAGCATCGTGTAGCTTAACATATCGACCCACAGCTCGTGTGA
65 GAATTCTCCACAACTCGTGTGAACAGCATCGTGTAGCTTAACATATCGACCCACAGCTCGTGTGA
42744 GC
130 GC
42746 A
1 A
42747 GTCCCATTTC
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
130 12 0.10
131 107 0.90
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (131 bp):
ATTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCAATGGCTGAGATCGACATATGTTGCG
AATTCTCCACAACTCGTGTGAACAGCATCGTGTAGCTTAACATATCGACCCACAGCTCGTGTGAG
C
Found at i:46897 original size:84 final size:84
Alignment explanation
Indices: 46794--47037 Score: 303
Period size: 84 Copynumber: 2.9 Consensus size: 84
46784 AATGCTGTTC
* * ** *
46794 CAAGCCAGAATACAAAGTAACGCTCCTTCGAGTCGGAATACAGAGTAATGCTCTTTCGAGCTAGA
1 CAAGCCAGAATACAAAGTAATGCTCTTTCGAGTCAAAATACAGAGTAATGCTCTTTCGAGCCAGA
46859 ATACAGAGTAACGCTCCTT
66 ATACAGAGTAACGCTCCTT
* * * *
46878 CAAGCCAAAATATATAGTAATGCTCTTTCAAGTCAAAATACAGAGTAATGCTCTTTCGAGCCAGA
1 CAAGCCAGAATACAAAGTAATGCTCTTTCGAGTCAAAATACAGAGTAATGCTCTTTCGAGCCAGA
* * *
46943 ATACATA-TCAATGCTCTTT
66 ATACAGAGT-AACGCTCCTT
* * * * *
46962 CAAGTCAGAATACAGAGTAATGCTCTTTCGAGCCAAAATACAGAGTAATACTCCTTT-GAGCCAA
1 CAAGCCAGAATACAAAGTAATGCTCTTTCGAGTCAAAATACAGAGTAATGCT-CTTTCGAGCCAG
47026 AATACAGAGTAA
65 AATACAGAGTAA
47038 TTCTGAAGCT
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
83 1 0.01
84 130 0.96
85 5 0.04
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (84 bp):
CAAGCCAGAATACAAAGTAATGCTCTTTCGAGTCAAAATACAGAGTAATGCTCTTTCGAGCCAGA
ATACAGAGTAACGCTCCTT
Found at i:47038 original size:28 final size:28
Alignment explanation
Indices: 46796--47038 Score: 256
Period size: 28 Copynumber: 8.7 Consensus size: 28
46786 TGCTGTTCCA
* * * *
46796 AGCCAGAATACAAAGTAACGCTCCTTCG
1 AGCCAAAATACAGAGTAATGCTCTTTCG
* **
46824 AGTCGGAATACAGAGTAATGCTCTTTCG
1 AGCCAAAATACAGAGTAATGCTCTTTCG
* * * * *
46852 AGCTAGAATACAGAGTAACGCTCCTTCA
1 AGCCAAAATACAGAGTAATGCTCTTTCG
* * *
46880 AGCCAAAATATATAGTAATGCTCTTTCA
1 AGCCAAAATACAGAGTAATGCTCTTTCG
*
46908 AGTCAAAATACAGAGTAATGCTCTTTCG
1 AGCCAAAATACAGAGTAATGCTCTTTCG
* * *
46936 AGCCAGAATACATA-TCAATGCTCTTTCA
1 AGCCAAAATACAGAGT-AATGCTCTTTCG
* *
46964 AGTCAGAATACAGAGTAATGCTCTTTCG
1 AGCCAAAATACAGAGTAATGCTCTTTCG
*
46992 AGCCAAAATACAGAGTAATACTCCTTT-G
1 AGCCAAAATACAGAGTAATGCT-CTTTCG
47020 AGCCAAAATACAGAGTAAT
1 AGCCAAAATACAGAGTAAT
47039 TCTGAAGCTT
Statistics
Matches: 181, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
27 1 0.01
28 175 0.97
29 5 0.03
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (28 bp):
AGCCAAAATACAGAGTAATGCTCTTTCG
Found at i:47038 original size:56 final size:56
Alignment explanation
Indices: 46766--47038 Score: 273
Period size: 56 Copynumber: 4.9 Consensus size: 56
46756 TATTGCTCAA
* * * * * * *
46766 TCGAGCC-AGATACAAAATAATGCTGTTCCAAGCCAGAATACAAAGTAACGCTCCT
1 TCGAGCCAAAATACAGAGTAATGCTCTTTCAAGCCAGAATACAGAGTAATGCTCCT
* ** * * *
46821 TCGAGTCGGAATACAGAGTAATGCTCTTTCGAGCTAGAATACAGAGTAACGCTCCT
1 TCGAGCCAAAATACAGAGTAATGCTCTTTCAAGCCAGAATACAGAGTAATGCTCCT
* * * * * *
46877 TCAAGCCAAAATATATAGTAATGCTCTTTCAAGTCAAAATACAGAGTAATGCTCTT
1 TCGAGCCAAAATACAGAGTAATGCTCTTTCAAGCCAGAATACAGAGTAATGCTCCT
* * * *
46933 TCGAGCCAGAATACATA-TCAATGCTCTTTCAAGTCAGAATACAGAGTAATGCTCTT
1 TCGAGCCAAAATACAGAGT-AATGCTCTTTCAAGCCAGAATACAGAGTAATGCTCCT
* * *
46989 TCGAGCCAAAATACAGAGTAATACTCCTTT-GAGCCAAAATACAGAGTAAT
1 TCGAGCCAAAATACAGAGTAATGCT-CTTTCAAGCCAGAATACAGAGTAAT
47039 TCTGAAGCTT
Statistics
Matches: 182, Mismatches: 32, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
55 7 0.04
56 170 0.93
57 5 0.03
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (56 bp):
TCGAGCCAAAATACAGAGTAATGCTCTTTCAAGCCAGAATACAGAGTAATGCTCCT
Found at i:49938 original size:21 final size:21
Alignment explanation
Indices: 49896--49949 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
49886 TGCGAATTTA
*
49896 TACCGATACAAGTGACAATTC
1 TACCGATACAAGAGACAATTC
* **
49917 TACTGATACAAGAGACTCTTC
1 TACCGATACAAGAGACAATTC
*
49938 TACCGAAACAAG
1 TACCGATACAAG
49950 TCATGCTTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (21 bp):
TACCGATACAAGAGACAATTC
Found at i:54444 original size:3 final size:3
Alignment explanation
Indices: 54436--54473 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
54426 TTAGGGATTT
*
54436 AAG AAG AAG AAG AAG AAG AAG AAG -AG ACG ATAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AA
54474 TTGAGGGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:55738 original size:51 final size:51
Alignment explanation
Indices: 55673--55853 Score: 272
Period size: 51 Copynumber: 3.5 Consensus size: 51
55663 GAATCCATAA
55673 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
* * **
55724 ATTCACGATGACACTTAGTCATCAGACCCCTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
** * *
55775 ACTCACGATGACACTTAGTTGTCGGAACTTTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
* *
55826 ACTCACGATGACACTTAATCACCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
55854 CTTTCGTTAT
Statistics
Matches: 114, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 114 1.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
Found at i:57215 original size:195 final size:196
Alignment explanation
Indices: 56883--57269 Score: 722
Period size: 195 Copynumber: 2.0 Consensus size: 196
56873 TATTTAAAAC
* * * *
56883 AAATAATTTTACGACTCGACTTGTTGGAGTTTTGGTCCTGAAACCACTATTTTCGACACCACTAA
1 AAATAATTTTACGACTCGACTTGTTAGAGTTGTGGTCCCGAAACCACAATTTTCGACACCACTAA
*
56948 AAATAGGGCTGTTACACCATTTACGTCACATGTCACAACATTATTCTACCACGTGTCTTAGACTT
66 AAATAGGGCTGTTACACCATTTACGTCACATGTCACAACATTATTCTACCACGTGTCTCAGACTT
57013 AACGGTATTAGACTCAGGTACCAAATCAGTGGAC-AAAAAAACTACCAATTTGGGAAAAAAATAA
131 AACGGTATTAGACTCAGGTACCAAATCAGTGGACAAAAAAAACTACCAATTTGGGAAAAAAATAA
57077 T
196 T
57078 AAATAATTTTACGACTCGACTTGTTAGAGTTGTGGTCCCGAAACCACAATTTTCGACACCACTAA
1 AAATAATTTTACGACTCGACTTGTTAGAGTTGTGGTCCCGAAACCACAATTTTCGACACCACTAA
57143 AAATAGGGCTGTTACACCATTTACGTCACATGTCACAACATTATTCTACCACGTGTCTCAGACTT
66 AAATAGGGCTGTTACACCATTTACGTCACATGTCACAACATTATTCTACCACGTGTCTCAGACTT
57208 AACGGTATTAGACTCAGGTACCAAATCAGTGGACAAAAAAAACTACCAATTTGGGAAAAAAA
131 AACGGTATTAGACTCAGGTACCAAATCAGTGGACAAAAAAAACTACCAATTTGGGAAAAAAA
57270 ACTTTAGGCG
Statistics
Matches: 186, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
195 159 0.85
196 27 0.15
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (196 bp):
AAATAATTTTACGACTCGACTTGTTAGAGTTGTGGTCCCGAAACCACAATTTTCGACACCACTAA
AAATAGGGCTGTTACACCATTTACGTCACATGTCACAACATTATTCTACCACGTGTCTCAGACTT
AACGGTATTAGACTCAGGTACCAAATCAGTGGACAAAAAAAACTACCAATTTGGGAAAAAAATAA
T
Found at i:60395 original size:3 final size:3
Alignment explanation
Indices: 60389--60448 Score: 54
Period size: 3 Copynumber: 20.0 Consensus size: 3
60379 TGTGGGTGGT
*
60389 GAA GAA G-A GAA GGAA GAA G-A GAA GAAA GAA GAA GCAA G-A GAA AAA
1 GAA GAA GAA GAA -GAA GAA GAA GAA G-AA GAA GAA G-AA GAA GAA GAA
*
60434 GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
60449 TTTGTAGCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
2 6 0.13
3 32 0.68
4 9 0.19
ACGTcount: A:0.67, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:60435 original size:27 final size:27
Alignment explanation
Indices: 60389--60448 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 27
60379 TGTGGGTGGT
60389 GAAGAAGAGAAGGAAGAAGAGAAGAAAGAA
1 GAAGAAGAG-AGGAA-AA-AGAAGAAAGAA
*
60419 GAAGCA-AGA-GAAAAAGAA-AAAGAA
1 GAAGAAGAGAGGAAAAAGAAGAAAGAA
60443 GAAGAA
1 GAAGAA
60449 TTTGTAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
24 11 0.39
25 4 0.14
26 2 0.07
27 3 0.11
28 1 0.04
29 2 0.07
30 5 0.18
ACGTcount: A:0.67, C:0.02, G:0.32, T:0.00
Consensus pattern (27 bp):
GAAGAAGAGAGGAAAAAGAAGAAAGAA
Found at i:63183 original size:22 final size:22
Alignment explanation
Indices: 63123--63184 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
63113 TGATCTGAGA
*
63123 AAAAATAAAAG-AAACAAAATT
1 AAAAATAAAAGAAAACAGAATT
63144 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
*
63166 AAAAGA-AATAGAAAACAGA
1 AAAA-ATAAAAGAAAACAGA
63185 GGTGTTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.30
22 25 0.68
23 1 0.03
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.11
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:64020 original size:31 final size:30
Alignment explanation
Indices: 63984--64049 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
63974 TAAACATAAA
**
63984 TTAAATACGAATTTTAATAATAAATAATATC
1 TTAAATACGAATCCTAATAA-AAATAATATC
** *
64015 TTAAATATTAATCCTAATAAAAATAATATT
1 TTAAATACGAATCCTAATAAAAATAATATC
64045 TTAAA
1 TTAAA
64050 ATAAAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (30 bp):
TTAAATACGAATCCTAATAAAAATAATATC
Found at i:67889 original size:16 final size:16
Alignment explanation
Indices: 67868--67926 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 16
67858 TAAATAACGC
*
67868 GAATAATTATACGAAT
1 GAATAAATATACGAAT
67884 GAATAAATATACGAA-
1 GAATAAATATACGAAT
** *
67899 -AATAAGCATAAGAAT
1 GAATAAATATACGAAT
67914 G-ATAAA-ATACGAA
1 GAATAAATATACGAA
67927 ATAAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 17 0.49
15 4 0.11
16 14 0.40
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.22
Consensus pattern (16 bp):
GAATAAATATACGAAT
Found at i:68074 original size:28 final size:30
Alignment explanation
Indices: 68043--68098 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
68033 GAGAAATGAA
68043 ATTTT-AGAAAATTTGAGGTT-AAAATGCG
1 ATTTTGAGAAAATTTGAGGTTCAAAATGCG
* * *
68071 ATTTTGGGAAAGTTTGGGGTTCAAAATG
1 ATTTTGAGAAAATTTGAGGTTCAAAATG
68099 TGTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 12 0.52
30 6 0.26
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (30 bp):
ATTTTGAGAAAATTTGAGGTTCAAAATGCG
Found at i:68114 original size:30 final size:30
Alignment explanation
Indices: 68091--68293 Score: 191
Period size: 30 Copynumber: 6.9 Consensus size: 30
68081 AGTTTGGGGT
*
68091 TCAAAATGTGTTTTTTAAGAAGTTCG-GGG
1 TCAAAATGTGATTTTTAAGAAGTTCGAGGG
* *
68120 GCTAAAATGTGATTTTTAAGGAGTTCGAGGG
1 TC-AAAATGTGATTTTTAAGAAGTTCGAGGG
* * *
68151 TAAAAATGTGATTTTTATGAAGTTCGAGAG
1 TCAAAATGTGATTTTTAAGAAGTTCGAGGG
* * *
68181 CCAAAATGTGATTTTTACGAAGTTTGAGGG
1 TCAAAATGTGATTTTTAAGAAGTTCGAGGG
* * *
68211 TCAAAATGT-ATTTTTACGAAATTCGA-GA
1 TCAAAATGTGATTTTTAAGAAGTTCGAGGG
* * *
68239 T-AAAATATAATTTTTACA-AAGTTCAAGGG
1 TCAAAATGTGATTTTTA-AGAAGTTCGAGGG
* * *
68268 TCAAAATGTAAGTTTTACGAAGTTCG
1 TCAAAATGTGATTTTTAAGAAGTTCG
68294 GGGGGCTCTT
Statistics
Matches: 141, Mismatches: 26, Indels: 13
0.78 0.14 0.07
Matches are distributed among these distances:
27 6 0.04
28 15 0.11
29 18 0.13
30 99 0.70
31 3 0.02
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (30 bp):
TCAAAATGTGATTTTTAAGAAGTTCGAGGG
Found at i:68134 original size:60 final size:58
Alignment explanation
Indices: 68062--68238 Score: 160
Period size: 60 Copynumber: 3.0 Consensus size: 58
68052 AATTTGAGGT
* * *
68062 TAAAATGCGATTTTGGGAAAGTTTG-GGGTTCAAAATGTGTTTTTTAAGAAGTTCGGGGGC
1 TAAAATGTGATTTT--GAAAGTTTGAGGG-TCAAAATGTGTTTTTTAAGAAGTTCGAGAGC
* * * * *
68122 TAAAATGTGATTTTTAAGGAGTTCGAGGGTAAAAATGTGATTTTTATGAAGTTCGAGAGC
1 TAAAATGTGATTTTGAA--AGTTTGAGGGTCAAAATGTGTTTTTTAAGAAGTTCGAGAGC
* * * * *
68182 CAAAATGTGATTTTTACGAAGTTTGAGGGTCAAAATGT-ATTTTTACGAAATTCGAGA
1 TAAAATGTGATTTTGA--AAGTTTGAGGGTCAAAATGTGTTTTTTAAGAAGTTCGAGA
68239 TAAAATATAA
Statistics
Matches: 99, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.02
59 17 0.17
60 76 0.77
61 3 0.03
62 1 0.01
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.35
Consensus pattern (58 bp):
TAAAATGTGATTTTGAAAGTTTGAGGGTCAAAATGTGTTTTTTAAGAAGTTCGAGAGC
Found at i:68261 original size:57 final size:59
Alignment explanation
Indices: 68141--68293 Score: 184
Period size: 57 Copynumber: 2.6 Consensus size: 59
68131 ATTTTTAAGG
* * * * * *
68141 AGTTCGAGGGTAAAAATGTGATTTTTATGAAGTTCGAGAGCCAAAATGTGATTTTTACGA
1 AGTTCGAGGGTCAAAATGTAATTTTTACGAAGTTCGAGA-CCAAAATATAATTTTTACAA
* * *
68201 AGTTTGAGGGTCAAAATGT-ATTTTTACGAAATTCGAGA-TAAAATATAATTTTTACAA
1 AGTTCGAGGGTCAAAATGTAATTTTTACGAAGTTCGAGACCAAAATATAATTTTTACAA
* *
68258 AGTTCAAGGGTCAAAATGTAAGTTTTACGAAGTTCG
1 AGTTCGAGGGTCAAAATGTAATTTTTACGAAGTTCG
68294 GGGGGCTCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
57 32 0.40
58 14 0.17
59 17 0.21
60 17 0.21
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (59 bp):
AGTTCGAGGGTCAAAATGTAATTTTTACGAAGTTCGAGACCAAAATATAATTTTTACAA
Found at i:68917 original size:20 final size:20
Alignment explanation
Indices: 68891--68938 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
68881 CCGTTGTCGG
68891 CCACCACCGACCGTCACCAT
1 CCACCACCGACCGTCACCAT
* * *
68911 CCGCCACTGACCGTCACCGT
1 CCACCACCGACCGTCACCAT
68931 CCACCACC
1 CCACCACC
68939 ATACACGACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.56, G:0.12, T:0.10
Consensus pattern (20 bp):
CCACCACCGACCGTCACCAT
Found at i:70098 original size:85 final size:85
Alignment explanation
Indices: 69955--70149 Score: 300
Period size: 85 Copynumber: 2.3 Consensus size: 85
69945 CTCTTGGTCT
* * *
69955 ACTTCTCTGTATCTCATCAAGAAGACGGATTTTGTTCACTTCTCTACATCTCGTCAAGAAGATAA
1 ACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTACATCTCGTCAAGAAGATAA
* * * *
70020 TCATTTTATTGCTTTGACCC
66 CCACTTTATTACTTCGACCC
* * *
70040 ACTTCTCTATATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCGTCAAGAAGATGA
1 ACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTACATCTCGTCAAGAAGATAA
70105 CCACTTTATTACTTCGACCC
66 CCACTTTATTACTTCGACCC
70125 ACTTCTCTGTATCTCATCAGGAAGA
1 ACTTCTCTGTATCTCATCAGGAAGA
70150 TGGGGTTTGA
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 99 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (85 bp):
ACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTACATCTCGTCAAGAAGATAA
CCACTTTATTACTTCGACCC
Found at i:70470 original size:209 final size:207
Alignment explanation
Indices: 70038--70587 Score: 821
Period size: 209 Copynumber: 2.6 Consensus size: 207
70028 TTGCTTTGAC
* * *
70038 CCACTTCTCTATATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCGTCAAGAAGAT
1 CCACTTCTCTGTATCTCATCAAGAAGACG-ATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGAT
* *
70103 GACCACTTTATTACTTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCAC
65 GACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCAC
* * * *
70168 TCGCATTAAGTTTCACTTCATTGAATTGGTATACTTCTTTGTATCTCATTAGGAAGATGACCGCT
130 TCACATTAAGCTTCACTTCATTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCT
70233 TCATTGTTTTAAT
195 TCATTGTTTTAAT
* * *
70246 CCACTTCTCTGTATCTCATCAAGAAAACAGATTTGGTTCGCTTCTCTGCATCTCATCAGGAAGAT
1 CCACTTCTCTGTATCTCATCAAGAAGAC-GATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGAT
* * * * *
70311 GACCACTTTATTGCTTCAACCCATTTCTTTGTATCTCATTAAGAAGATGGGATTTGGAAGTTTCA
65 GACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTT-GAAGTTTCA
* * * *
70376 CTCACATTGAGCTTCGCTTCATTGAATTGGTCTACTTCTCTGTATCTCATCAGGAATATGACCGC
129 CTCACATTAAGCTTCACTTCATTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGC
70441 TTCATTGTTTTAAT
194 TTCATTGTTTTAAT
* * *
70455 CCACTTCTTTGTATCTCATCAAGAAGATGGATTTTGTTCACTTCTCTGCATCTCGTCAGGAAGAT
1 CCACTTCTCTGTATCTCATCAAGAAGA-CGATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGAT
* *
70520 GACCACTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTTGAATTTTCA
65 GACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATGGGG-TTTGAAGTTTCA
70585 CTC
129 CTC
70588 TTCCTTATGA
Statistics
Matches: 304, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
208 105 0.35
209 196 0.64
210 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (207 bp):
CCACTTCTCTGTATCTCATCAAGAAGACGATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGATG
ACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACT
CACATTAAGCTTCACTTCATTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCTT
CATTGTTTTAAT
Found at i:70553 original size:85 final size:85
Alignment explanation
Indices: 70409--70569 Score: 241
Period size: 85 Copynumber: 1.9 Consensus size: 85
70399 GAATTGGTCT
* * * * * *
70409 ACTTCTCTGTATCTCATCAGGAATATGACCGCTTCATTGTTTTAATCCACTTCTTTGTATCTCAT
1 ACTTCTCTGCATCTCATCAGGAAGATGACCACTTCATTGCTTTAACCCACTTCTCTGTATCTCAT
70474 CAAGAAGATGGATTTTGTTC
66 CAAGAAGATGGATTTTGTTC
* * *
70494 ACTTCTCTGCATCTCGTCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCTCAT
1 ACTTCTCTGCATCTCATCAGGAAGATGACCACTTCATTGCTTTAACCCACTTCTCTGTATCTCAT
70559 CAAGAAGATGG
66 CAAGAAGATGG
70570 GGTTTTGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (85 bp):
ACTTCTCTGCATCTCATCAGGAAGATGACCACTTCATTGCTTTAACCCACTTCTCTGTATCTCAT
CAAGAAGATGGATTTTGTTC
Found at i:70783 original size:39 final size:39
Alignment explanation
Indices: 70740--71101 Score: 280
Period size: 39 Copynumber: 9.3 Consensus size: 39
70730 TGATCGAGGC
* **
70740 AAAAGATCGAATGGTTGTAATCTGCCCCAGGCTCGGGGT
1 AAAAGATCGGATGACTGTAATCTGCCCCAGGCTCGGGGT
* * * *
70779 AAAAGATTGGCTGA-TGGTGATCTGCCCCAAGCTCGGGGT
1 AAAAGATCGGATGACT-GTAATCTGCCCCAGGCTCGGGGT
* * ** ** *
70818 AAAAGATCTGATGGCTACAATCTGCCTTAGGCTCGAGGT
1 AAAAGATCGGATGACTGTAATCTGCCCCAGGCTCGGGGT
* * * *
70857 AAAAGATCTGATAACTGCAATCTGCCCCAGGCTTGGGGT
1 AAAAGATCGGATGACTGTAATCTGCCCCAGGCTCGGGGT
* * * ** * *
70896 AAGAGATTGGCTGA-TGGTGTTTTGCCCTAGGCTCGGGGT
1 AAAAGATCGGATGACT-GTAATCTGCCCCAGGCTCGGGGT
* * **
70935 AAAAGATTGGATGACTGCAATCTGCCCCAGGCTCAAGGT
1 AAAAGATCGGATGACTGTAATCTGCCCCAGGCTCGGGGT
* ** * * *
70974 AAAAGATCGGATGGCTAAAATTTACCCCAGGCTCAGGGT
1 AAAAGATCGGATGACTGTAATCTGCCCCAGGCTCGGGGT
* * * *
71013 AAGAGATTGGTTGA-TGGTGATCTGCCCCAGGCTCGGGGT
1 AAAAGATCGGATGACT-GTAATCTGCCCCAGGCTCGGGGT
* * * *
71052 AAAAGATCGGATGACTGTGATCTGCCCCATGATTGGGGT
1 AAAAGATCGGATGACTGTAATCTGCCCCAGGCTCGGGGT
*
71091 AAGAGATCGGA
1 AAAAGATCGGA
71102 ATCTTCAATC
Statistics
Matches: 249, Mismatches: 68, Indels: 12
0.76 0.21 0.04
Matches are distributed among these distances:
38 3 0.01
39 243 0.98
40 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
AAAAGATCGGATGACTGTAATCTGCCCCAGGCTCGGGGT
Found at i:71097 original size:78 final size:78
Alignment explanation
Indices: 70695--71080 Score: 325
Period size: 78 Copynumber: 4.9 Consensus size: 78
70685 GCCCCTATCG
* * ** * * * * * *
70695 CGGGGTAAGAGATTGGTTGATGGTGATCTGCTTCATGATCGAGGCAAAAGATCGAATGGTTGTAA
1 CGGGGTAAAAGATTGGATGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGGCTGTAA
70760 TCTGCCCCAGGCT
66 TCTGCCCCAGGCT
* * * **
70773 CGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCTGATGGCTACAA
1 CGGGGTAAAAGATTGGATGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGGCTGTAA
**
70838 TCTGCCTTAGGCT
66 TCTGCCCCAGGCT
* * ** * * *
70851 CGAGGTAAAAGATCT-GATAACT-GCAATCTGCCCCAGGCTTGGGGTAAGAGATTGGCTGATGG-
1 CGGGGTAAAAGAT-TGGATGA-TGGTGATCTGCCCCAGGCTCGGGGTAAAAGA-T--CGGATGGC
* *
70913 TGT--TTTGCCCTAGGCT
61 TGTAATCTGCCCCAGGCT
** ** **
70929 CGGGGTAAAAGATTGGATGACT-GCAATCTGCCCCAGGCTCAAGGTAAAAGATCGGATGGCTAAA
1 CGGGGTAAAAGATTGGATGA-TGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGGCTGTA
* *
70993 ATTTACCCCAGGCT
65 ATCTGCCCCAGGCT
* * * * *
71007 CAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGACTGTGA
1 CGGGGTAAAAGATTGGATGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGGCTGTAA
71072 TCTGCCCCA
66 TCTGCCCCA
71081 TGATTGGGGT
Statistics
Matches: 247, Mismatches: 51, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
75 6 0.02
76 1 0.00
77 3 0.01
78 226 0.91
79 3 0.01
80 1 0.00
81 7 0.03
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (78 bp):
CGGGGTAAAAGATTGGATGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGGCTGTAA
TCTGCCCCAGGCT
Found at i:71101 original size:117 final size:117
Alignment explanation
Indices: 70758--71080 Score: 421
Period size: 117 Copynumber: 2.8 Consensus size: 117
70748 GAATGGTTGT
* * *
70758 AATCTGCCCCAGGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAG
1 AATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAG
* * * ** * **
70823 ATCTGATGGCTACAATCTGCCTTAGGCTCGAGGTAAAAGATCTGATAACTGC
66 ATCGGATGACTGCAATCTGCCCCAGGCTCGAGGTAAAAGATCGGATAACTAA
* * * * *
70875 AATCTGCCCCAGGCTTGGGGTAAGAGATTGGCTGATGGTGTTTTGCCCTAGGCTCGGGGTAAAAG
1 AATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAG
* * **
70940 ATTGGATGACTGCAATCTGCCCCAGGCTCAAGGTAAAAGATCGGATGGCTAA
66 ATCGGATGACTGCAATCTGCCCCAGGCTCGAGGTAAAAGATCGGATAACTAA
* * *
70992 AATTTACCCCAGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAG
1 AATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAG
**
71057 ATCGGATGACTGTGATCTGCCCCA
66 ATCGGATGACTGCAATCTGCCCCA
71081 TGATTGGGGT
Statistics
Matches: 177, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
117 177 1.00
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (117 bp):
AATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAG
ATCGGATGACTGCAATCTGCCCCAGGCTCGAGGTAAAAGATCGGATAACTAA
Found at i:71472 original size:50 final size:50
Alignment explanation
Indices: 71344--71472 Score: 125
Period size: 50 Copynumber: 2.6 Consensus size: 50
71334 AGACTCGTCG
* * * ** * * **
71344 TTGTGGCTTCAATCTTTCCCGTCATGT-TTTTAAGGTATCGGGTTCGCTG
1 TTGTGGCCTCAACCTTTCCCATCAAATCTTTTAAGATATCGAGTTCGCCA
** * *
71393 TTGCAGCCTCAACCTTTCTCATCACATCTTTTAAGATATCGAGTTCGCCA
1 TTGTGGCCTCAACCTTTCCCATCAAATCTTTTAAGATATCGAGTTCGCCA
*
71443 TTGTGGCCTCAACCTTTCCCTTCAAATCTT
1 TTGTGGCCTCAACCTTTCCCATCAAATCTT
71473 CATGGTATCG
Statistics
Matches: 62, Mismatches: 17, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
49 19 0.31
50 43 0.69
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (50 bp):
TTGTGGCCTCAACCTTTCCCATCAAATCTTTTAAGATATCGAGTTCGCCA
Found at i:82984 original size:16 final size:16
Alignment explanation
Indices: 82963--83021 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 16
82953 ATGTGAAGAA
*
82963 GAATAATTATACGAAT
1 GAATAAATATACGAAT
82979 GAATAAATATACGAA-
1 GAATAAATATACGAAT
** *
82994 -AATAAGCATAAGAAT
1 GAATAAATATACGAAT
83009 G-ATAAA-ATACGAA
1 GAATAAATATACGAA
83022 ATAAAAAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 17 0.49
15 4 0.11
16 14 0.40
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.22
Consensus pattern (16 bp):
GAATAAATATACGAAT
Found at i:83192 original size:30 final size:30
Alignment explanation
Indices: 83156--83290 Score: 114
Period size: 30 Copynumber: 4.5 Consensus size: 30
83146 AATTGGGGTT
83156 AAAATGTGATTTTTAAGAAGTTC-AGAGGCC
1 AAAATGTGATTTTTAAGAAGTTCGAG-GGCC
*
83186 AAAATGTGATTTTTTACGAAGTTCGAGGGCC
1 AAAATGTGA-TTTTTAAGAAGTTCGAGGGCC
* * **
83217 AAAATGTGATTTTGT-TGAAGTTCAAGGGTT
1 AAAATGTGATTTT-TAAGAAGTTCGAGGGCC
* * * * * *
83247 AAAATGTAAGTTATACGAAGTTCG-GCGTC
1 AAAATGTGATTTTTAAGAAGTTCGAGGGCC
*
83276 AAAATGTAATTTTTA
1 AAAATGTGATTTTTA
83291 TGTAGTTTGG
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
29 17 0.20
30 41 0.47
31 27 0.31
32 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (30 bp):
AAAATGTGATTTTTAAGAAGTTCGAGGGCC
Found at i:83207 original size:31 final size:31
Alignment explanation
Indices: 83156--83229 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
83146 AATTGGGGTT
83156 AAAATGTGA-TTTTTAAGAAGTTC-AGAGGCC
1 AAAATGTGATTTTTTAAGAAGTTCGAG-GGCC
*
83186 AAAATGTGATTTTTTACGAAGTTCGAGGGCC
1 AAAATGTGATTTTTTAAGAAGTTCGAGGGCC
83217 AAAATGTGATTTT
1 AAAATGTGATTTT
83230 GTTGAAGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 9 0.22
31 30 0.73
32 2 0.05
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (31 bp):
AAAATGTGATTTTTTAAGAAGTTCGAGGGCC
Found at i:83251 original size:61 final size:59
Alignment explanation
Indices: 83156--83290 Score: 139
Period size: 61 Copynumber: 2.3 Consensus size: 59
83146 AATTGGGGTT
** * *
83156 AAAATGTGATTTTTAAGAAGTTCAGAGGCCAAAATGTGATTTTTTACGAAGTTCGAGGGCC
1 AAAATGTGATTTTTAAGAAGTTCAGAGGCCAAAATGT-AAGTTATACGAAGTTCG-GCGCC
* ** *
83217 AAAATGTGATTTTGT-TGAAGTTCA-AGGGTTAAAATGTAAGTTATACGAAGTTCGGCGTC
1 AAAATGTGATTTT-TAAGAAGTTCAGA-GGCCAAAATGTAAGTTATACGAAGTTCGGCGCC
*
83276 AAAATGTAATTTTTA
1 AAAATGTGATTTTTA
83291 TGTAGTTTGG
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
58 1 0.02
59 15 0.24
60 15 0.24
61 30 0.48
62 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAATGTGATTTTTAAGAAGTTCAGAGGCCAAAATGTAAGTTATACGAAGTTCGGCGCC
Found at i:91575 original size:27 final size:27
Alignment explanation
Indices: 91535--91612 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
91525 GAGTAATCTA
** *
91535 ATTTTGGCTTGAAAGAGCGTTATTCTG
1 ATTTTGGCACGAAAGAGCGATATTCTG
91562 ATTTTGGCACGAAAGAGCGATATTCT-
1 ATTTTGGCACGAAAGAGCGATATTCTG
* * *
91588 A--TTGGCTCGTAAGAGTGATATTCTG
1 ATTTTGGCACGAAAGAGCGATATTCTG
91613 TCTGGCTTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
24 20 0.45
26 1 0.02
27 23 0.52
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (27 bp):
ATTTTGGCACGAAAGAGCGATATTCTG
Found at i:91624 original size:25 final size:24
Alignment explanation
Indices: 91538--91652 Score: 97
Period size: 25 Copynumber: 4.6 Consensus size: 24
91528 TAATCTAATT
* * *
91538 TTGGCTTGAAAGAGCGTTATTCTG
1 TTGGCTCGTAAGAGCGATATTCTG
* * *
91562 ATTTTGGCACGAAAGAGCGATATTCTA
1 ---TTGGCTCGTAAGAGCGATATTCTG
*
91589 TTGGCTCGTAAGAGTGATATTCTG
1 TTGGCTCGTAAGAGCGATATTCTG
*
91613 TCTGGCTTGTAAGAGCGATATT-TG
1 T-TGGCTCGTAAGAGCGATATTCTG
91637 TTTGGGCTCGTAAGAG
1 -TT-GGCTCGTAAGAG
91653 ATAAACTCTA
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
24 24 0.32
25 30 0.41
27 20 0.27
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.35
Consensus pattern (24 bp):
TTGGCTCGTAAGAGCGATATTCTG
Found at i:97026 original size:20 final size:20
Alignment explanation
Indices: 96964--97082 Score: 89
Period size: 20 Copynumber: 6.0 Consensus size: 20
96954 TCGGTGTTCT
* * * *
96964 TGAATGCACATTAGAGCTCT
1 TGAATGCACATTCGTGCCCC
* * * *
96984 TGAATGAATATTAGTGCCTC
1 TGAATGCACATTCGTGCCCC
* *
97004 TGAATGCACATTTGTTCCCC
1 TGAATGCACATTCGTGCCCC
* *
97024 TGATTGCACATTCATGCCCC
1 TGAATGCACATTCGTGCCCC
*
97044 T-AATTGCACATTCGTGCCCT
1 TGAA-TGCACATTCGTGCCCC
97064 TGAATGCAC-TTCGATGCCC
1 TGAATGCACATTCG-TGCCC
97083 TGTTTTGGCA
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
19 5 0.06
20 71 0.91
21 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (20 bp):
TGAATGCACATTCGTGCCCC
Found at i:98604 original size:34 final size:34
Alignment explanation
Indices: 98561--98625 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
98551 TTCTTACCAT
*
98561 GATTCCTTCATTCGACGACGAACTCAATATCGAC
1 GATTCCTTCATTCGACGACAAACTCAATATCGAC
98595 GATTCCTTCATTCGACGACAAACTCAATATC
1 GATTCCTTCATTCGACGACAAACTCAATATC
98626 AACTTACTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (34 bp):
GATTCCTTCATTCGACGACAAACTCAATATCGAC
Found at i:99568 original size:35 final size:36
Alignment explanation
Indices: 99487--99569 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 36
99477 TCAAAGAGTT
* * * * *
99487 AGTAGATCATTTTCATGGTGTTGCTCCGTAGAGCCA
1 AGTAGATCATTTACATGATGCTACTCCGTAGAGCAA
99523 A-TAGATCATTTACATGATGCTACTCCGTAGAG-AA
1 AGTAGATCATTTACATGATGCTACTCCGTAGAGCAA
*
99557 AGTAGACCATTTA
1 AGTAGATCATTTA
99570 TCCAACCAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.05
35 37 0.93
36 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (36 bp):
AGTAGATCATTTACATGATGCTACTCCGTAGAGCAA
Found at i:101868 original size:14 final size:14
Alignment explanation
Indices: 101845--101890 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
101835 TAAACAATCG
101845 TATTTATTTAGTAT
1 TATTTATTTAGTAT
*
101859 TATTTTTTTAAAG-A-
1 TATTTATTT--AGTAT
101873 TATTTATTTAGTAT
1 TATTTATTTAGTAT
101887 TATT
1 TATT
101891 AACTTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 2 0.08
13 1 0.04
14 20 0.77
15 1 0.04
16 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TATTTATTTAGTAT
Found at i:103672 original size:3 final size:3
Alignment explanation
Indices: 103664--103691 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
103654 AAGTGCCCAA
103664 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
103692 GGGTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:104094 original size:21 final size:21
Alignment explanation
Indices: 104070--104109 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
104060 TTCACTTGCT
*
104070 AAATAAAGATTTTTTTAAAGA
1 AAATAAAGATTTCTTTAAAGA
*
104091 AAATAGAGATTTCTTTAAA
1 AAATAAAGATTTCTTTAAA
104110 AAAGAGAAAG
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:0.50, C:0.03, G:0.10, T:0.38
Consensus pattern (21 bp):
AAATAAAGATTTCTTTAAAGA
Found at i:104318 original size:152 final size:149
Alignment explanation
Indices: 104107--104401 Score: 405
Period size: 152 Copynumber: 2.0 Consensus size: 149
104097 AGATTTCTTT
* * * *
104107 AAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTAGGTTATTTAAAAG-AAAAGT
1 AAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAATCTATTTTTAGATGATTTAAAAGAAAAAGT
* * * * *
104171 TTAAATTTTTTAACGAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAG
66 TTAAATTTTTAAACAAAGTTTT-AATTTTTTTAACTATTTCGAAATAAAAATTTGGA-TTTGAAG
*
104236 TAAAGTAGTGATTTTAATTAA
129 TAAAGTAGTAATTTTAATTAA
* *
104257 AAAAAAAAGAAAATTTAGATTTTTTAAAAAATAAAAATCTGTTTTTTA-ATGATTTTAAAGAAAA
1 AAAAAAAAGAAAATTTAGA-TTTTT-AAAAATAAAAATCT-ATTTTTAGATGATTTAAAAGAAAA
*
104321 AGTTTAAATTTTTAAACAAAGTTTTAATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTGAA
63 AGTTTAAATTTTTAAACAAAGTTTTAATTTTTTTAACTATTTCGAAATAAAAATTTGGATTTGAA
*
104386 GTAAATTAGTAATTTT
128 GTAAAGTAGTAATTTT
104402 GTTTTAATAA
Statistics
Matches: 127, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
150 17 0.13
151 24 0.19
152 54 0.43
153 32 0.25
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.43
Consensus pattern (149 bp):
AAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAATCTATTTTTAGATGATTTAAAAGAAAAAGT
TTAAATTTTTAAACAAAGTTTTAATTTTTTTAACTATTTCGAAATAAAAATTTGGATTTGAAGTA
AAGTAGTAATTTTAATTAA
Found at i:108983 original size:4 final size:4
Alignment explanation
Indices: 108969--109007 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
108959 GTGCTCCAAT
* * *
108969 TTCA ATCA TTCA TTCA TTCA TCCA TTCA TTCA CTCA TTC
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTC
109008 GTTTATTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (4 bp):
TTCA
Found at i:114236 original size:42 final size:42
Alignment explanation
Indices: 114176--114680 Score: 636
Period size: 42 Copynumber: 12.0 Consensus size: 42
114166 GCATTTAGAT
* * **
114176 AGGTGTAGAGGTCCGTTTACTTTTCATCGCATTTAGAGGAGC
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
* * *
114218 AGGTGTGGAGG-CCTGTTTACTTTTCATTGCATTTAGAGGCTC
1 AGGTGTGGAGGTCC-ATTTACTTTTCATCGCATTTAGAGGCCC
* *
114260 AGGTGTGGATG-CCTATTTACTTTTCATTGCATTTAGAGGCCC
1 AGGTGTGGAGGTCC-ATTTACTTTTCATCGCATTTAGAGGCCC
* *
114302 AGGTGTGGAGGTCCATTTATTTTTCATCGCATTTAGAGGCCT
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
** * * * *
114344 AACTGTGGAGGCCCATTTACTTCTCATCGCATTTAGATGTCC
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
* * *
114386 AGGTGTGGAGGTACATTTACTTTTCATTGCATTTAGAGGCTC
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
* * *
114428 AGGTGTGGAGGTCCATTTATTTTTCATCACATTTTGAGGCCC
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
* * * * *
114470 AGGTGTGAAGGCCCATTTACTTTTCCTCACATTTAGAGGCTC
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
* * *
114512 AGGTGTGGAGGTCCATTTACTTTTCATCGTATTTAGAGGTCT
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
* *
114554 AGTTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCTC
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
* *
114596 AGGTGTGGAGGTCCATTTAGTTTTCATTGCATTTAGAGGCCC
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
* * *
114638 AGGTGTGGAGGTTCATTTACTTTTCATTGCATTTTGAGGCCC
1 AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
114680 A
1 A
114681 AGAGTGAGGT
Statistics
Matches: 401, Mismatches: 60, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
41 2 0.00
42 397 0.99
43 2 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (42 bp):
AGGTGTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCC
Found at i:115849 original size:148 final size:149
Alignment explanation
Indices: 115548--115853 Score: 334
Period size: 148 Copynumber: 2.1 Consensus size: 149
115538 AAAAATTTTG
* * *
115548 GTTTTTTAAACAATTTCAAAATAAAATTTTTGATTTTTAAGGAAAATAGTGATTTCTTTAAAAAA
1 GTTTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAGGAAAATAGTGATTTCTTTAAAAAA
* * * * *
115613 GAGAAAGGTTTAGATTTTTAAAAATAAAAAATCTAGTTTTTGGTTATTTTAAAGAGAAGTTTAAA
66 GAGAAAGGTTTAGATTTTTAAAAATAAAAAATATAGTTTTTAGTCATTCTAAAGAAAAGTTTAAA
**** ****
115678 TTTTTAAACAAAATTTTGA
131 TGAAGAAACAAAAGGAAGA
* * * * *
115697 -TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTACGGAAAATAGT-ATTTTTTTTTAAAA
1 GTTTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAGGAAAATAGTGA-TTTCTTTAAAAA
* *
115760 AGAGAAA-GTTTAGATTTTTAAAAAT-AAATATAT-GTTTTTAGTCCTTCTAAAGAAAAGTTTAA
65 AGAGAAAGGTTTAGATTTTTAAAAATAAAAAATATAGTTTTTAGTCATTCTAAAGAAAAGTTTAA
*
115822 ATGAAGAAGATAAAGAGGAAGA
130 ATGAAGAA-ACAAA-AGGAAGA
115844 GTTTTTTTAA
1 GTTTTTTTAA
115854 AATGAGGTTG
Statistics
Matches: 129, Mismatches: 24, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
145 28 0.22
146 10 0.08
147 22 0.17
148 69 0.53
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.41
Consensus pattern (149 bp):
GTTTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAGGAAAATAGTGATTTCTTTAAAAAA
GAGAAAGGTTTAGATTTTTAAAAATAAAAAATATAGTTTTTAGTCATTCTAAAGAAAAGTTTAAA
TGAAGAAACAAAAGGAAGA
Found at i:117501 original size:5 final size:5
Alignment explanation
Indices: 117493--117517 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
117483 TATAATAAAT
117493 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
117518 AATGTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:118719 original size:31 final size:31
Alignment explanation
Indices: 118670--118746 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
118660 TTGTTTTTGA
* *
118670 CCCTCAAATTTTCCAAAAATTCAAATTTAAC
1 CCCTCAAACTTTCCAAAAATCCAAATTTAAC
* * *
118701 CCCTTAAACTTTCTAAAAATCCAAATTTGA-
1 CCCTCAAACTTTCCAAAAATCCAAATTTAAC
*
118731 CCC-CAAATTTTCCAAA
1 CCCTCAAACTTTCCAAA
118747 TAAATTGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 10 0.26
30 3 0.08
31 25 0.66
ACGTcount: A:0.40, C:0.27, G:0.01, T:0.31
Consensus pattern (31 bp):
CCCTCAAACTTTCCAAAAATCCAAATTTAAC
Found at i:118759 original size:30 final size:30
Alignment explanation
Indices: 118724--118786 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
118714 TAAAAATCCA
118724 AATTTGA-CCCCAAATTTTCCAAATAAATTG
1 AATTTGATCCCCAAATTTTCCAAA-AAATTG
* * * *
118754 AATTTGATCCTCGAATTTTCTAAAAATTTG
1 AATTTGATCCCCAAATTTTCCAAAAAATTG
118784 AAT
1 AAT
118787 AACCCTAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (30 bp):
AATTTGATCCCCAAATTTTCCAAAAAATTG
Found at i:130517 original size:43 final size:43
Alignment explanation
Indices: 130454--130536 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
130444 TCTTTTACCT
* * * *
130454 CTAAAGCTGTGGAGGTGCAGATTGAAACCGCAATGACAAACAC
1 CTAAAGCTGTAGAGGGGCAGAATGAAACCACAATGACAAACAC
* *
130497 CTAAAGCTGTAGAGGGGCAGAATGAAGCCACAATGGCAAA
1 CTAAAGCTGTAGAGGGGCAGAATGAAACCACAATGACAAA
130537 TCTCATTCAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (43 bp):
CTAAAGCTGTAGAGGGGCAGAATGAAACCACAATGACAAACAC
Found at i:130674 original size:40 final size:40
Alignment explanation
Indices: 130625--130873 Score: 263
Period size: 40 Copynumber: 6.2 Consensus size: 40
130615 ACAACCTCCA
* * *
130625 ATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCTG
1 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCG
* *
130665 ATCTCTTACCCTAAATAGAGGGCAGATTGAAGACTATCCG
1 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCG
* * * *
130705 ATCTCTTACCCTGACCATG-GGGCAGTTTGAAAACCATCCG
1 ATCTCTTACCCTAACTA-GAGGGCAGATTGAAGACCATCCG
*
130745 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTCG
1 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCG
* ** * * *
130785 ATCTTTTACCCCGA-TCATG-GGGTAGATTGAAGA-AATCCA
1 ATCTCTTACCCTAACT-A-GAGGGCAGATTGAAGACCATCCG
* * * *
130824 ATCTTTTACCCTAACCAGAGGGCAGATCGAAGACCATCAG
1 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCG
130864 ATCTCTTACC
1 ATCTCTTACC
130874 TCGACCATGA
Statistics
Matches: 170, Mismatches: 32, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
38 1 0.01
39 30 0.18
40 137 0.81
41 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (40 bp):
ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCG
Found at i:130735 original size:80 final size:80
Alignment explanation
Indices: 130644--130882 Score: 302
Period size: 80 Copynumber: 3.0 Consensus size: 80
130634 CCTAACTAGA
* * * *
130644 GGGCAAATTGAAGACCATCTGATCTCTTACCCTAAATAGAGGGCAGATTGAAGACTATCCGATCT
1 GGGCAGATTGAAGACCATCCGATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCT
130709 CTTACCCTGACCATG
66 CTTACCCTGACCATG
* * *
130724 GGGCAGTTTGAAAACCATCCGATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTCGATCT
1 GGGCAGATTGAAGACCATCCGATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCT
* * *
130789 TTTACCCCGATCATG
66 CTTACCCTGACCATG
* * * * * * *
130804 GGGTAGATTGAAGA-AATCCAATCTTTTACCCTAACCAGAGGGCAGATCGAAGACCATCAGATCT
1 GGGCAGATTGAAGACCATCCGATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCT
130868 CTTA-CCTCGACCATG
66 CTTACCCT-GACCATG
130883 AGCTGATTGA
Statistics
Matches: 135, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
78 2 0.01
79 52 0.39
80 81 0.60
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (80 bp):
GGGCAGATTGAAGACCATCCGATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCT
CTTACCCTGACCATG
Found at i:130774 original size:120 final size:119
Alignment explanation
Indices: 130617--130873 Score: 299
Period size: 120 Copynumber: 2.2 Consensus size: 119
130607 GTGAAGTTAC
* *
130617 AACC-TCCAATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCA-TCTGATCTCTTACCCTAAA
1 AACCATCCGATCTCTTACCCTAACTAGAGGGCAAATTGAAGACCATTC-GATCTCTTACCC-AAA
* * * * *
130680 T-A-GAGGGCAGATTGAAGACTATCCGATCTCTTACCCTGACCATG-GGGCAGTTTGAA
64 TCATG-GGGCAGATTGAAGA-AATCCAATCTCTTACCCTAACCA-GAGGGCAGATCGAA
* * **
130736 AACCATCCGATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTCGATCTTTTACCCCGATC
1 AACCATCCGATCTCTTACCCTAACTAGAGGGCAAATTGAAGACCATTCGATCTCTTACCCAAATC
* *
130801 ATGGGGTAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAGATCGAA
66 ATGGGGCAGATTGAAGAAATCCAATCTCTTACCCTAACCAGAGGGCAGATCGAA
* *
130855 GACCATCAGATCTCTTACC
1 AACCATCCGATCTCTTACC
130874 TCGACCATGA
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 1 0.01
119 52 0.44
120 62 0.53
121 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (119 bp):
AACCATCCGATCTCTTACCCTAACTAGAGGGCAAATTGAAGACCATTCGATCTCTTACCCAAATC
ATGGGGCAGATTGAAGAAATCCAATCTCTTACCCTAACCAGAGGGCAGATCGAA
Found at i:130858 original size:79 final size:78
Alignment explanation
Indices: 130665--130912 Score: 284
Period size: 80 Copynumber: 3.1 Consensus size: 78
130655 AGACCATCTG
* * * * *
130665 ATCTCTTACCCTAAATAGAGGGCAGATTGAAGACTATCCGATCTCTTACCCTGACCATGGGGCAG
1 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTCGATCTCTTACCCCGACCATGGGGTAG
* *
130730 TTTGAAAACCATCCG
66 ATTGAAAA--ATCCA
* *
130745 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTCGATCTTTTACCCCGATCATGGGGTAG
1 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTCGATCTCTTACCCCGACCATGGGGTAG
130810 ATTGAAGAAATCCA
66 ATTGAA-AAATCCA
* * * * * *
130824 ATCTTTTACCCTAACCAGAGGGCAGATCGAAGACCA-TCAGATCTCTTACCTCGACCATGAGCT-
1 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTC-GATCTCTTACCCCGACCATGGGGTA
*
130887 GATTGAAACAATTCA
65 GATTGAAA-AATCCA
*
130902 ATCTTTTACCC
1 ATCTCTTACCC
130913 CTAAAGTTAT
Statistics
Matches: 147, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
77 1 0.01
78 25 0.17
79 56 0.38
80 63 0.43
81 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTCGATCTCTTACCCCGACCATGGGGTAG
ATTGAAAAATCCA
Found at i:130916 original size:79 final size:76
Alignment explanation
Indices: 130665--130912 Score: 255
Period size: 79 Copynumber: 3.1 Consensus size: 76
130655 AGACCATCTG
* ** * *
130665 ATCTCTTACCCTAAATAGAGGGCAGATTGAAGACTATCCGATCTCTTACCCTGACCATGGGGCAG
1 ATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCAT-CGATCTCTTACCC-GACCAT-GGGCTG
* * *
130730 TTTGAAAACCATCCG
63 ATTG-AAACAATCCA
* * * * *
130745 ATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATTCGATCTTTTACCCCGATCATGGGGTAG
1 ATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCA-TCGATCTCTTA-CCCGACCATGGGCT-G
130810 ATTGAAGA-AATCCA
63 ATTGAA-ACAATCCA
* *
130824 ATCTTTTACCCTAACCAGAGGGCAGATCGAAGACCATCAGATCTCTTACCTCGACCATGAGCTGA
1 ATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATC-GATCTCTTACC-CGACCATGGGCTGA
*
130889 TTGAAACAATTCA
64 TTGAAACAATCCA
130902 ATCTTTTACCC
1 ATCTTTTACCC
130913 CTAAAGTTAT
Statistics
Matches: 144, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
77 1 0.01
78 27 0.19
79 59 0.41
80 53 0.37
81 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (76 bp):
ATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCGATCTCTTACCCGACCATGGGCTGATT
GAAACAATCCA
Found at i:131350 original size:5 final size:5
Alignment explanation
Indices: 131342--131366 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
131332 TATAATAAAT
131342 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
131367 AATGTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:132552 original size:30 final size:29
Alignment explanation
Indices: 132500--132678 Score: 191
Period size: 30 Copynumber: 6.0 Consensus size: 29
132490 TTTTTACCTT
*
132500 CAAATTTTTTAAAAATTCAAATTTGACCC
1 CAAATTTTCTAAAAATTCAAATTTGACCC
* *
132529 CTTAAACTTTCTAAAAA-TCAAATTTGATCC
1 C--AAATTTTCTAAAAATTCAAATTTGACCC
* *
132559 CAAATTTTCTAAAAAAATCAAATTTGATCC
1 CAAATTTTCT-AAAAATTCAAATTTGACCC
* *
132589 CAAATTTTCCAAAAAAATCAAATTTGATCCC
1 CAAATTTT-CTAAAAATTCAAATTTGA-CCC
*
132620 CAAATTTTCCAAAAATTCAAATTTGACCTC
1 CAAATTTTCTAAAAATTCAAATTTGACC-C
* *
132650 TAAAGTTTTC-AAAAATTCCAATTTGACCC
1 CAAA-TTTTCTAAAAATTCAAATTTGACCC
132679 GATTTAATGT
Statistics
Matches: 132, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.06
29 9 0.07
30 87 0.66
31 28 0.21
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (29 bp):
CAAATTTTCTAAAAATTCAAATTTGACCC
Found at i:132709 original size:14 final size:14
Alignment explanation
Indices: 132690--132720 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
132680 ATTTAATGTA
*
132690 ATTTTCTTTTATTT
1 ATTTTCTTTTATAT
132704 ATTTTCTTTTATAT
1 ATTTTCTTTTATAT
132718 ATT
1 ATT
132721 CATAGATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTCTTTTATAT
Found at i:141720 original size:25 final size:25
Alignment explanation
Indices: 141686--141736 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
141676 ATGCTCAGTA
141686 AGTTCAAATGGAAAATACCATACTT
1 AGTTCAAATGGAAAATACCATACTT
* * *
141711 AGTTCAAATGGCAAGTACCATGCTT
1 AGTTCAAATGGAAAATACCATACTT
141736 A
1 A
141737 CCTTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (25 bp):
AGTTCAAATGGAAAATACCATACTT
Found at i:146972 original size:23 final size:23
Alignment explanation
Indices: 146942--147135 Score: 253
Period size: 23 Copynumber: 8.4 Consensus size: 23
146932 TTCTTATATC
146942 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
146965 TATGCTTAAATATTATTGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
146988 TATGCTTAAATGTTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
147011 TATGCTGAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* * * **
147034 TGTACTTAAATACTAATAAGATT
1 TATGCTTAAATATTAATGTGATT
* *
147057 TCTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
147080 TGTGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
147103 TGTGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
**
147126 TGCGCTTAAA
1 TATGCTTAAA
147136 GAATTAAGAT
Statistics
Matches: 149, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 149 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:152006 original size:21 final size:21
Alignment explanation
Indices: 151955--152006 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
151945 GGAGTTTTTA
151955 GTATCGGTAGAAGCAAGACAT
1 GTATCGGTAGAAGCAAGACAT
* * * *
151976 GTTTCAGTAGAAGTC-ATACTT
1 GTATCGGTAGAAG-CAAGACAT
151997 GTATCGGTAG
1 GTATCGGTAG
152007 TATTGTCTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (21 bp):
GTATCGGTAGAAGCAAGACAT
Found at i:157069 original size:21 final size:22
Alignment explanation
Indices: 157015--157070 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
157005 AGAGTTTTTA
*
157015 GTATCGGTAAAAG-CATGACAT
1 GTATCGGTAGAAGTCATGACAT
* * *
157036 GTTTCGCTAGAAGTCAT-ACTT
1 GTATCGGTAGAAGTCATGACAT
157057 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
157071 TGTAGGGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (22 bp):
GTATCGGTAGAAGTCATGACAT
Found at i:157126 original size:92 final size:92
Alignment explanation
Indices: 156959--157152 Score: 318
Period size: 92 Copynumber: 2.1 Consensus size: 92
156949 GGTAGTATGA
*
156959 ATACTTGTATCGGTAGAAGTTGTAGGGTAAAACTTCTTAGCTCTCTAGAGTTTTTAGTATCGGTA
1 ATACTTGTATCGGTAGAAGTTGTAGGGTAAAACTTCTTAGCTCTCTAGAGTTTTTAGTATCAGTA
157024 AAAGCATGACATGTTTCGCTAGAAGTC
66 AAAGCATGACATGTTTCGCTAGAAGTC
*
157051 ATACTTGTATCGGTAGAAGTTGTAGGGTAAAACTTCTTAGCTCT-TCGGAGTTTTTAGTATCAGT
1 ATACTTGTATCGGTAGAAGTTGTAGGGTAAAACTTCTTAGCTCTCT-AGAGTTTTTAGTATCAGT
* * *
157115 AGAAGCTTGACATGTTTCGGTAGAAGTC
65 AAAAGCATGACATGTTTCGCTAGAAGTC
*
157143 AAACTTGTAT
1 ATACTTGTAT
157153 TTGTAGTATT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
91 1 0.01
92 94 0.99
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (92 bp):
ATACTTGTATCGGTAGAAGTTGTAGGGTAAAACTTCTTAGCTCTCTAGAGTTTTTAGTATCAGTA
AAAGCATGACATGTTTCGCTAGAAGTC
Found at i:174101 original size:19 final size:19
Alignment explanation
Indices: 174068--174120 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
174058 CTGTAGATTG
174068 TTTTCA-TGCATTTTTATT
1 TTTTCATTGCATTTTTATT
*
174086 TTTTCATTGTATTTTTATT
1 TTTTCATTGCATTTTTATT
*
174105 TTGTCATTGCATTTTT
1 TTTTCATTGCATTTTT
174121 GTTAAGTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.15, C:0.09, G:0.08, T:0.68
Consensus pattern (19 bp):
TTTTCATTGCATTTTTATT
Found at i:181629 original size:190 final size:193
Alignment explanation
Indices: 181338--181690 Score: 486
Period size: 190 Copynumber: 1.8 Consensus size: 193
181328 GGACATGAGA
* * *
181338 AAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGATTGAGATTTATTCATAAGAACAT
1 AAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGACTGAGATCTATGCATAAG-ACAT
* * *
181403 ATCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAG-TTATATGCACAGATA-C-C-GTATC
65 ATCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTATA-GCACAGACAGCACTGTACC
*
181464 GATGGCT-GAGGTACCGCATATGTTGTGAGTCCTAACAACTCGTGCGAGTAGCATCGTGACTCGG
129 GATAGCTAG-GGTACCGCATATGTTGTGAGTCCTAACAACTCGTGCGAGTAGCATCGTGACTCGG
181528 G
193 G
* * * * *
181529 AAAGAGATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGGGA-CTATGCTTATTG-CAT
1 AAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGACTGAGATCTATGCATA-AGACAT
*
181592 ACTCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTATAGGACAGACAGGCACTGTAC
65 A-TCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTATAGCACAGACA-GCACTGTAC
181657 CGATAGCTAGGGTACCGCATATGTTGTGAGTCCT
128 CGATAGCTAGGGTACCGCATATGTTGTGAGTCCT
181691 CGCCAGCTCG
Statistics
Matches: 141, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
189 4 0.03
190 50 0.35
191 50 0.35
192 1 0.01
193 1 0.01
194 34 0.24
195 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (193 bp):
AAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGACTGAGATCTATGCATAAGACATA
TCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTATAGCACAGACAGCACTGTACCGA
TAGCTAGGGTACCGCATATGTTGTGAGTCCTAACAACTCGTGCGAGTAGCATCGTGACTCGGG
Found at i:187974 original size:17 final size:17
Alignment explanation
Indices: 187952--187989 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
187942 TGGGAGAAAT
187952 AAAGGGTGTTCCCAACA
1 AAAGGGTGTTCCCAACA
187969 AAAGGGTGTTCCCAACA
1 AAAGGGTGTTCCCAACA
187986 AAAG
1 AAAG
187990 CATCCTAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (17 bp):
AAAGGGTGTTCCCAACA
Found at i:197734 original size:3 final size:3
Alignment explanation
Indices: 197726--197750 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
197716 AAAGACCCAA
197726 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
197751 GAGTTTCATG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:198388 original size:168 final size:166
Alignment explanation
Indices: 198183--198492 Score: 473
Period size: 168 Copynumber: 1.9 Consensus size: 166
198173 AATTATGGTT
* * *
198183 TTTTTTAACTAATTTCGAAATAAAAGTTTTAATTTTTAAGTAAAATAGTGATTTTCTT-TAACAA
1 TTTTTTAACTAATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAGTGATTTT-TTAAAAAAA
* * * * *
198247 GATAAAGTTTATATTTTTAAAATTAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAAT
65 GAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAATTATTTT-AA-AAAAA-TTTAAAA
198312 TTTTAAACGAA-GTTTTTAAATTTTTAAACAGGGTTTTGGC
127 TTTTAAAC-AATGTTTTTAAATTTTTAAACAGGGTTTTGGC
*
198352 TTTTTTAACT-ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTTTAAAAAAAG
1 TTTTTTAACTAATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAGTGATTTTTTAAAAAAAG
198416 AGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAATTATTTTAAAAAAATTTAAAATTTT
66 AGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAATTATTTTAAAAAAATTTAAAATTTT
198481 AAACAATGTTTT
131 AAACAATGTTTT
198493 GATTTTTTTA
Statistics
Matches: 130, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
164 2 0.02
165 19 0.15
166 5 0.04
167 4 0.03
168 90 0.69
169 10 0.08
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (166 bp):
TTTTTTAACTAATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAGTGATTTTTTAAAAAAAG
AGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAATTATTTTAAAAAAATTTAAAATTTT
AAACAATGTTTTTAAATTTTTAAACAGGGTTTTGGC
Found at i:198525 original size:145 final size:147
Alignment explanation
Indices: 198326--198839 Score: 607
Period size: 150 Copynumber: 3.5 Consensus size: 147
198316 AAACGAAGTT
* ** **
198326 TTTAAATTTTTAAACAGGGTTTTGGCTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAG
1 TTTAAAATTTTAAACAATGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAG
* *
198391 TAAAATAGTGATTTT-TTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTA
66 TAAAGTAGTGATTTTATTAAAAAAA-AGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTA
198455 ATTATTTT-AA-AAAAA-
130 ATTATTTTAAAGAAAAAG
* * *
198470 TTTAAAATTTTAAACAATGTTTTGATTTTTTTAAAATATTTTGGAATAAAAGTTTGGATTTTTAA
1 TTTAAAATTTTAAACAATGTTTTGATTTTTTT-AACTATTTCGAAATAAAAGTTTGGATTTTTAA
* *
198535 GT-AAGTAGTGATTTTTATTAAAAAAGAAAGAAAG-TTAGATTTCTAAAAAATAAAAATATATTT
65 GTAAAGTAGTGA-TTTTATT-AAAAA-AAAGAAAGTTTAGATTT-TTAAAAATAAAAATCTATTT
* *
198598 TTTAGTGATTTTAAAGAAAAAG
126 TTTAATTATTTTAAAGAAAAAG
* ** *
198620 TTTAAATTTTTTGACAAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAAGTTTGGATTTTT
1 TTTAAAATTTTAAACAATGTTTTGA--TTTTTTTAACTATTTCGAAAT-AAAAGTTTGGATTTTT
*
198685 AAGTAAAGTAGTGATTTTCATTAAAAAGGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTGT
63 AAGTAAAGTAGTGATTTT-ATTAAAAA--AAAGAAAGTTTAGATTTTT-AAAAATAAAAATCTAT
*
198750 TTTTT-TTGTGATTTTAAAGAAAAAG
124 TTTTTAAT-T-ATTTTAAAGAAAAAG
* * *
198775 TTTAAAATTTTAAACAAAT-ATTTGA--TTTTTAACTATTTCGAAATAAAAGTTTTGATTTTAAA
1 TTTAAAATTTTAAAC-AATGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAA
198837 GTA
65 GTA
198840 GTAATTTTAT
Statistics
Matches: 317, Mismatches: 33, Indels: 34
0.83 0.09 0.09
Matches are distributed among these distances:
144 35 0.11
145 35 0.11
146 9 0.03
147 39 0.12
148 4 0.01
149 5 0.02
150 40 0.13
151 30 0.09
152 36 0.11
153 23 0.07
154 27 0.09
155 32 0.10
156 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.44
Consensus pattern (147 bp):
TTTAAAATTTTAAACAATGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAG
TAAAGTAGTGATTTTATTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAA
TTATTTTAAAGAAAAAG
Found at i:198882 original size:145 final size:141
Alignment explanation
Indices: 198352--198888 Score: 460
Period size: 145 Copynumber: 3.6 Consensus size: 141
198342 GGGTTTTGGC
*
198352 TTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTT-AAGTA-AAATAGTGATTTTTTAAAAAAA
1 TTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAAGTAGTAAT--T--TTTTTT-AAAAAA
* * * ** *
198415 GAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAATTATTTT-AA-AAAAA-TTTAAAA
61 GA-AAAGTTTAGATTTTAAAAAATAAAAATCTTTTTTTTTGTGATTTTAAAGAAAAAGTTTAAAA
*
198477 TTTTAAACAATGTTTTGA
125 TTTTAAACAA-ATTTTGA
* * * * *
198495 TTTTTTTAAAATATTTTGGAATAAAAGTTTGGATTTTTAAGTAAGTAGTGATTTTTATTAAAAAA
1 -TTTTTT-AACTATTTCGAAATAAAAGTTTGGATTTTT-A--AAGTAGTAATTTTTTTTAAAAAA
* * *
198560 GAAAGAAAG-TTAGATTTCTAAAAAATAAAAATATATTTTTTAGTGATTTTAAAGAAAAAGTTTA
61 G--A-AAAGTTTAGATTT-TAAAAAATAAAAATCTTTTTTTTTGTGATTTTAAAGAAAAAGTTTA
* **
198624 AATTTTTTGACAAAGTTTTGA
122 AAATTTTAAACAAA-TTTTGA
* **
198645 TTTTTTTTTAACTATTTCGAAATAAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTCATTAAA
1 ---TTTTTTAACTATTTCGAAAT-AAAAGTTTGGA-TTTT---TAAAGTAGTAATTTTTTTTAAA
*
198710 AAGGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTTTTTGTGATTTTAAAGAAAAAG
58 AA--AGA-AAAGTTTAGA-TTTTAAAAAATAAAAATCT-TTTTTTTTGTGATTTTAAAGAAAAAG
198775 TTTAAAATTTTAAACAAATATTTGA
118 TTTAAAATTTTAAACAAAT-TTTGA
*
198800 -TTTTTAACTATTTCGAAATAAAAGTTTTGA-TTTTAAAGTAGTAATTTTATTTTAATCAAAAGA
1 TTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAAGTAGTAATTTT-TTTTAA--AAAAGA
* * * *
198863 AAACTTTTGATTTAAAAAAAAAAAAA
63 AAAGTTTAGATTTTAAAAAATAAAAA
198889 GAAGAAGAAA
Statistics
Matches: 329, Mismatches: 35, Indels: 58
0.78 0.08 0.14
Matches are distributed among these distances:
144 20 0.06
145 56 0.17
146 18 0.05
147 34 0.10
148 9 0.03
149 10 0.03
150 32 0.10
151 30 0.09
152 18 0.05
153 31 0.09
154 21 0.06
155 49 0.15
156 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.43
Consensus pattern (141 bp):
TTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAAGTAGTAATTTTTTTTAAAAAAGAAAA
GTTTAGATTTTAAAAAATAAAAATCTTTTTTTTTGTGATTTTAAAGAAAAAGTTTAAAATTTTAA
ACAAATTTTGA
Found at i:203448 original size:4 final size:4
Alignment explanation
Indices: 203434--203503 Score: 70
Period size: 4 Copynumber: 17.5 Consensus size: 4
203424 GTGCCCCAAT
* * * * *
203434 TTCA ATCA TTCA TTCA TTCA TCCA TCCA -TCTA TTCA TTCC TTCA TCCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTC-A TTCA TTCA TTCA TTCA
*
203482 TTCA TTCA TTCA TTCA CTCA TT
1 TTCA TTCA TTCA TTCA TTCA TT
203504 TGTTTATTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 1 0.02
4 51 0.94
5 2 0.04
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.44
Consensus pattern (4 bp):
TTCA
Found at i:203477 original size:24 final size:24
Alignment explanation
Indices: 203439--203502 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
203429 CCAATTTCAA
203439 TCATTCATTCATTCATCCATCCA-
1 TCATTCATTCATTCATCCATCCAT
* *
203462 TCTATTCATTCCTTCATCCATTCAT
1 TC-ATTCATTCATTCATCCATCCAT
*
203487 TCATTCATTCACTCAT
1 TCATTCATTCATTCAT
203503 TTGTTTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.06
24 31 0.89
25 2 0.06
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.44
Consensus pattern (24 bp):
TCATTCATTCATTCATCCATCCAT
Found at i:203497 original size:20 final size:20
Alignment explanation
Indices: 203440--203497 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
203430 CAATTTCAAT
*
203440 CATTCATTCATTCATCCATC
1 CATTCATTCATTCATTCATC
*
203460 CA-TCTATTCATTCCTTCATC
1 CATTC-ATTCATTCATTCATC
203480 CATTCATTCATTCATTCA
1 CATTCATTCATTCATTCA
203498 CTCATTTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.43
Consensus pattern (20 bp):
CATTCATTCATTCATTCATC
Found at i:204736 original size:30 final size:30
Alignment explanation
Indices: 204702--204771 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
204692 AGGAATCATA
204702 GTTTGAGCAATTTCCTAAAATTCAGACAAG
1 GTTTGAGCAATTTCCTAAAATTCAGACAAG
204732 GTTTGAGCAATTTCCTAAAATTCAGACAAG
1 GTTTGAGCAATTTCCTAAAATTCAGACAAG
204762 GTTTGAGCAA
1 GTTTGAGCAA
204772 AAGACTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (30 bp):
GTTTGAGCAATTTCCTAAAATTCAGACAAG
Found at i:208414 original size:22 final size:22
Alignment explanation
Indices: 208375--208421 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
208365 TTAAATCAAG
*
208375 AAAAAATAAAAAAGAAGAAGAA
1 AAAAAACAAAAAAGAAGAAGAA
208397 AAAAAACAACAAAA-AAGAAGAA
1 AAAAAACAA-AAAAGAAGAAGAA
208419 AAA
1 AAA
208422 TTAGAAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (22 bp):
AAAAAACAAAAAAGAAGAAGAA
Found at i:208890 original size:42 final size:42
Alignment explanation
Indices: 208831--209214 Score: 551
Period size: 42 Copynumber: 9.1 Consensus size: 42
208821 AAAGAAAACA
* *
208831 TTCATTGCATTTAGAGGCCTAGGTATGGAGATCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
208873 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTACATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
208915 TTCATTGTATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
208957 TTCATTGCATTTAGAGGCCTAGATGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTC-CATTTACTT
208999 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
209041 TTCAATGCATTTAGAGGCCCAGGTGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTC-CATTTACTT
*
209083 TTCATTGCATTTAGAGG-CTCGAGTGTGGAGG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAG-GTGTGGAGGTCC-ATTTACTT
* * * *
209125 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
209167 TTCATTGCATTTGGAAGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
209209 TTCATT
1 TTCATT
209215 TCAATTAGCG
Statistics
Matches: 311, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
41 5 0.02
42 303 0.97
43 3 0.01
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
Found at i:210031 original size:21 final size:21
Alignment explanation
Indices: 210007--210058 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
209997 TGGGATAGTA
*
210007 CTACCGATACAAGTGA-GACTT
1 CTACCGATACAAGTCATG-CTT
* *
210028 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
210049 CTACCGATAC
1 CTACCGATAC
210059 TAAAAATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:210787 original size:24 final size:24
Alignment explanation
Indices: 210769--210855 Score: 138
Period size: 24 Copynumber: 3.6 Consensus size: 24
210759 AGCTCCCACA
* *
210769 AGCCTAGAATGGTTAGCTCTTACG
1 AGCCCAGAATGGTTAGCCCTTACG
210793 AGCCCAGAATGGTTAGCCCTTACG
1 AGCCCAGAATGGTTAGCCCTTACG
210817 AGCCCAGAATGGTTAGCCCTTACG
1 AGCCCAGAATGGTTAGCCCTTACG
* *
210841 AGCCTAGAATAGTTA
1 AGCCCAGAATGGTTA
210856 ACCAGTACAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (24 bp):
AGCCCAGAATGGTTAGCCCTTACG
Found at i:210795 original size:49 final size:48
Alignment explanation
Indices: 210732--210843 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
210722 CTTCTAGATT
* *
210732 TTAGCTCATACGAGCACAGATAACATTAGCTCC-CACAAGCCTAGAATGG
1 TTAGCTCTTACGAGCACAGA-AACATTAGC-CCTCACAAGCCCAGAATGG
* *** * *
210781 TTAGCTCTTACGAGCCCAGAATGGTTAGCCCTTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCACAGAAACATTAGCCCTCACAAGCCCAGAATGG
*
210829 TTAGCCCTTACGAGC
1 TTAGCTCTTACGAGC
210844 CTAGAATAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
47 2 0.04
48 33 0.62
49 18 0.34
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (48 bp):
TTAGCTCTTACGAGCACAGAAACATTAGCCCTCACAAGCCCAGAATGG
Found at i:211978 original size:3 final size:3
Alignment explanation
Indices: 211970--211994 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
211960 GGCTGTTACA
211970 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
211995 GGGTTTCATA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:212508 original size:20 final size:19
Alignment explanation
Indices: 212483--212527 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
212473 ATTTTTTAGT
212483 AATTTTAAAGAAAAAGTTTA
1 AATTTTAAA-AAAAAGTTTA
* *
212503 AATTTTTAAACAAAGTTTA
1 AATTTTAAAAAAAAGTTTA
212522 AATTTT
1 AATTTT
212528 TTTTTAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (19 bp):
AATTTTAAAAAAAAGTTTA
Found at i:212605 original size:20 final size:20
Alignment explanation
Indices: 212536--212609 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
212526 TTTTTTTAAC
* *
212536 TATTTTGAAATAAAAGTTTA
1 TATTTTTAAAAAAAAGTTTA
* * *
212556 GATTTTTAAGTAAAATAG-TGA
1 TATTTTTAA--AAAAAAGTTTA
*
212577 TTTTCTTTAAAAAAAAGTTTA
1 TATT-TTTAAAAAAAAGTTTA
212598 TATTTTTAAAAA
1 TATTTTTAAAAA
212610 TAAAAAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
20 21 0.52
21 9 0.22
22 10 0.25
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (20 bp):
TATTTTTAAAAAAAAGTTTA
Found at i:212664 original size:19 final size:20
Alignment explanation
Indices: 212640--212680 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
212630 TATTTTAAAG
212640 AAAAAGTT-TAAATTTTTAA
1 AAAAAGTTCTAAATTTTTAA
* *
212659 AAAAAGTTCTGATTTTTTAA
1 AAAAAGTTCTAAATTTTTAA
212679 AA
1 AA
212681 CTAGTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAAAGTTCTAAATTTTTAA
Found at i:212674 original size:147 final size:145
Alignment explanation
Indices: 212369--213023 Score: 698
Period size: 147 Copynumber: 4.4 Consensus size: 145
212359 TTGGTAAAAT
* * * *
212369 AAAAGTTTTGATTTTTTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGA-TT
1 AAAAGTTTTGATTTTTTAACT-ATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
* * * * *
212433 T--TTAAAAAAGAGAAAGTTTATATTTTAAAAATAAAAATATATTTTTTAGTAATTTTAAAGAAA
65 TCATTAAAAAA-ATAAAGTTTAGATTTTAAAAAAAAAAAAATATTTTTTAGTGATTTTAAAGAAA
212496 AAGTTTAAATTTTTAAA
129 AAGTTTAAATTTTTAAA
* ** * *
212513 CAAAGTTTAAATTTTTTTTTAACTATTTTGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGAT
1 AAAAGTTT---TGATTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGAT
* * * * *
212578 TTTC-TT-TAAAAA-AAAGTTTATATTTTTAAAAATAAAAAAAATATTTTCTAATTATTTTAAAG
63 TTTCATTAAAAAAATAAAGTTTAGA-TTTTAAAAA-AAAAAAAATATTTTTTAGTGATTTTAAAG
212640 AAAAAGTTTAAATTTTTAAA
126 AAAAAGTTTAAATTTTTAAA
* * * * * *
212660 AAAAGTTCTGATTTTTTAAAACTAGTTCAAAATAAAGGTTTGGATTTTTAAGTAAAGTAGTAATT
1 AAAAGTTTTGATTTTTT--AACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATT
* ** **
212725 TTCATTAAAAAAAATAAAGTTTAGATTTTTAAAAAATAAAATCTAACTTTTAGTGATTTTAAAGA
64 TTCATT-AAAAAAATAAAGTTTAGA-TTTTAAAAAAAAAAAAATATTTTTTAGTGATTTTAAAGA
* *
212790 AAAATTTTAAATTTTTAGAC
127 AAAAGTTTAAATTTTTA-AA
* * * *
212810 AAAA-TTTTGATTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAATAAAGTAGTGATTTT
1 AAAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTT
*
212874 CATTAAAAAATAAATAAAGTTTAGATTTTAAAAAAATAAAAATATGTTTTTTAGTGATTTTAAAG
66 CATT--AAAA-AAATAAAGTTTAGATTTTAAAAAAA-AAAAA-ATATTTTTTAGTGATTTTAAAG
*
212939 AAAAAGTTTAAAATTTTAAA
126 AAAAAGTTTAAATTTTTAAA
* ** *
212959 TAATTTTTTGATTTTTTAACTATTT-GAAAATAAAAGTTTTA-ATTTTAAAGTAAAGTAGTGATT
1 AAAAGTTTTGATTTTTTAACTATTTCG-AAATAAAAG-TTTAGATTTTTAAGTAAAGTAGTGATT
213022 TT
64 TT
213024 GTTTTAATTA
Statistics
Matches: 432, Mismatches: 58, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
144 14 0.03
145 10 0.02
146 89 0.21
147 116 0.27
148 17 0.04
149 75 0.17
150 108 0.25
151 3 0.01
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (145 bp):
AAAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTT
CATTAAAAAAATAAAGTTTAGATTTTAAAAAAAAAAAAATATTTTTTAGTGATTTTAAAGAAAAA
GTTTAAATTTTTAAA
Found at i:212830 original size:19 final size:20
Alignment explanation
Indices: 212790--212830 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
212780 ATTTTAAAGA
212790 AAAATTTTAAATTTTTAGAC
1 AAAATTTTAAATTTTTAGAC
* *
212810 AAAATTTTGATTTTTTA-AC
1 AAAATTTTAAATTTTTAGAC
212829 AA
1 AA
212831 TTTCAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
AAAATTTTAAATTTTTAGAC
Found at i:212900 original size:29 final size:26
Alignment explanation
Indices: 212855--212913 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 26
212845 TTTGGATTTT
212855 TAAATAAAGTAGTGATTTTCATTAAAAAA
1 TAAATAAAGTAGTGATTTT-A--AAAAAA
*
212884 TAAATAAAGT-TTAGATTTTAAAAAAA
1 TAAATAAAGTAGT-GATTTTAAAAAAA
212910 TAAA
1 TAAA
212914 AATATGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 10 0.36
28 2 0.07
29 16 0.57
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (26 bp):
TAAATAAAGTAGTGATTTTAAAAAAA
Found at i:212969 original size:150 final size:147
Alignment explanation
Indices: 212369--213023 Score: 706
Period size: 150 Copynumber: 4.4 Consensus size: 147
212359 TTGGTAAAAT
* * * * * *
212369 AAAAGTTTTGATTTTTTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGA-TT
1 AAAATTTTTGATTTTTT-AACAATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTT
* * * *
212433 T-TTAAAAAAGAGAAAGTTTATATTTT--AAAAATAAAAATATATTTTTTAGTAATTTTAAAGAA
65 TCTTAAAAAAAATAAAGTTTAGATTTTAAAAAAATAAAAATATATTTTTTAGTGATTTTAAAGAA
212495 AAAGTTTAAATTTTTAAA
130 AAAGTTTAAATTTTTAAA
* * * ** * *
212513 CAAAGTTTAAATT-TTTTTTTAACTATTTTGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGA
1 -AAAATTT---TTGATTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGA
* * * * *
212577 TTTTCTT--TAAAAA-AAAGTTTATATTTTTAAAAATAA-AAAAA-ATATTTTCTAATTATTTTA
62 TTTTCTTAAAAAAAATAAAGTTTAGA-TTTTAAAAA-AATAAAAATATATTTTTTAGTGATTTTA
212637 AAGAAAAAGTTTAAATTTTTAAA
125 AAGAAAAAGTTTAAATTTTTAAA
* * * *
212660 AAAAGTTCTGATTTTTTAA-AACTAGTTCAAAATAAAGGTTTGGATTTTTAAGTAAAGTAGTAAT
1 AAAATTTTTGATTTTTTAACAA-T--TTCAAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGAT
* * **
212724 TTTCATTAAAAAAAATAAAGTTTAGATTTTTAAAAAAT-AAAATCTAACTTTTAGTGATTTTAAA
63 TTTC-TTAAAAAAAATAAAGTTTAGATTTTAAAAAAATAAAAATATATTTTTTAGTGATTTTAAA
* *
212788 GAAAAATTTTAAATTTTTAGAC
127 GAAAAAGTTTAAATTTTTA-AA
*
212810 AAAA-TTTTGATTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAATAAAGTAGTGATTTT
1 AAAATTTTTGATTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTT
*
212874 CATTAAAAAATAAATAAAGTTTAGATTTTAAAAAAATAAAAATATGTTTTTTAGTGATTTTAAAG
66 C-TT-AAAAA-AAATAAAGTTTAGATTTTAAAAAAATAAAAATATATTTTTTAGTGATTTTAAAG
*
212939 AAAAAGTTTAAAATTTTAAA
128 AAAAAGTTTAAATTTTTAAA
* * * * ** *
212959 TAATTTTTTGATTTTTTAACTATTTGAAAATAAAAGTTTTAATTTTAAAGTAAAGTAGTGATTTT
1 AAAATTTTTGATTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTT
213024 GTTTTAATTA
Statistics
Matches: 430, Mismatches: 55, Indels: 45
0.81 0.10 0.08
Matches are distributed among these distances:
143 2 0.00
144 9 0.02
145 15 0.03
146 89 0.21
147 93 0.22
148 23 0.05
149 90 0.21
150 109 0.25
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (147 bp):
AAAATTTTTGATTTTTTAACAATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTT
CTTAAAAAAAATAAAGTTTAGATTTTAAAAAAATAAAAATATATTTTTTAGTGATTTTAAAGAAA
AAGTTTAAATTTTTAAA
Found at i:226391 original size:49 final size:49
Alignment explanation
Indices: 226337--226436 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
226327 CAATAGGAGC
226337 AAAAGGGTTTAAACACTTAATAAAATGGGTAAATTACACAAAAGGCACA
1 AAAAGGGTTTAAACACTTAATAAAATGGGTAAATTACACAAAAGGCACA
226386 AAAAGGGTTTAAACACTTAATAAAATGGGTAAATTACACAAAAGGCACA
1 AAAAGGGTTTAAACACTTAATAAAATGGGTAAATTACACAAAAGGCACA
226435 AA
1 AA
226437 TAATTAGGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (49 bp):
AAAAGGGTTTAAACACTTAATAAAATGGGTAAATTACACAAAAGGCACA
Found at i:229984 original size:11 final size:11
Alignment explanation
Indices: 229968--229993 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
229958 TTTGTTATGA
229968 TTGTGGTAGAG
1 TTGTGGTAGAG
229979 TTGTGGTAGAG
1 TTGTGGTAGAG
229990 TTGT
1 TTGT
229994 TCATAGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (11 bp):
TTGTGGTAGAG
Found at i:241237 original size:3 final size:3
Alignment explanation
Indices: 241229--241254 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
241219 AAGAAAAGAA
241229 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
241255 AACAGGCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:242963 original size:28 final size:27
Alignment explanation
Indices: 242894--242945 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
242884 AATAGGAATT
*
242894 AATAAAGATATTTTAAGTATAAAAATC
1 AATAGAGATATTTTAAGTATAAAAATC
*
242921 AATAGAAATATTTTAAGTATAAAAA
1 AATAGAGATATTTTAAGTATAAAAA
242946 ATTACTAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (27 bp):
AATAGAGATATTTTAAGTATAAAAATC
Found at i:243049 original size:13 final size:14
Alignment explanation
Indices: 243027--243059 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
243017 ATTTATAAAT
243027 TTTAATTA-TTATA
1 TTTAATTATTTATA
*
243040 TTTAATTATTTTTA
1 TTTAATTATTTATA
243054 TTTAAT
1 TTTAAT
243060 GTGTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTATTTATA
Found at i:246084 original size:25 final size:23
Alignment explanation
Indices: 246056--246101 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
246046 GTTGAATCCA
246056 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
246081 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
246102 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:247150 original size:7 final size:6
Alignment explanation
Indices: 247138--247226 Score: 54
Period size: 6 Copynumber: 13.0 Consensus size: 6
247128 CTCAAAAATA
247138 CTTTTGT CTTTTGT CTTTTT CTTTTT CTTTTT -TTTTCT CAATTTTCT
1 CTTTT-T CTTTT-T CTTTTT CTTTTT CTTTTT CTTTT-T C--TTTT-T
*
247185 CTTCTTT TTTTTT CAATTTTT CTTTTT GACTTTTTT CTTTTT
1 CTT-TTT CTTTTT C--TTTTT CTTTTT --C-TTTTT CTTTTT
247227 AAAATTTAGT
Statistics
Matches: 70, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
5 4 0.06
6 27 0.39
7 18 0.26
8 9 0.13
9 12 0.17
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (6 bp):
CTTTTT
Found at i:247187 original size:21 final size:20
Alignment explanation
Indices: 247159--247211 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 20
247149 TGTCTTTTTC
247159 TTTTTCTTTTTTTTTCTCAA
1 TTTTTCTTTTTTTTTCTCAA
*
247179 TTTTCTCTTCTTTTTTTTTCAA
1 TTTT-TCTT-TTTTTTTCTCAA
247201 TTTTTCTTTTT
1 TTTTTCTTTTT
247212 GACTTTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 7 0.23
21 8 0.27
22 15 0.50
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTCTCAA
Found at i:248091 original size:6 final size:6
Alignment explanation
Indices: 248011--248275 Score: 176
Period size: 6 Copynumber: 44.3 Consensus size: 6
248001 AGTGCATAAT
* * * * * * *
248011 AAAATA AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
248059 AAAATA AAACTA AAAATA AAAAT- AAAATA AAAATG AAAATA AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * * * * * *
248106 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * * * *
248154 AAAATG AAAATG AAAATGA AAATTA AAATTA AAATTA AAAAGA AAAAT-
1 AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA
* * * * * * * *
248202 AAAA-A ATAATGA AAAATG AAAATG AAACTA AAACTG AAAATG AAAATG
1 AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
248250 AAAATG AAAGTA AAAATG AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
248276 TGTACTATTT
Statistics
Matches: 230, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
5 12 0.05
6 209 0.91
7 9 0.04
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:248103 original size:18 final size:18
Alignment explanation
Indices: 248011--248272 Score: 210
Period size: 18 Copynumber: 14.6 Consensus size: 18
248001 AGTGCATAAT
*
248011 AAAATAAAACT-AAAACTA
1 AAAATAAAAATGAAAA-TA
* *
248029 AAACTAAAACT-AAAACTA
1 AAAATAAAAATGAAAA-TA
* * *
248047 AAACTAAAACTAAAAATA
1 AAAATAAAAATGAAAATA
* *
248065 AAACTAAAAATAAAAAT-
1 AAAATAAAAATGAAAATA
248082 AAAATAAAAATGAAAATA
1 AAAATAAAAATGAAAATA
* *
248100 AAAATGAAAATGAAAATG
1 AAAATAAAAATGAAAATA
* *
248118 AAAATGAAAATGAAAATG
1 AAAATAAAAATGAAAATA
* *
248136 AAAATGAAAATGAAAATG
1 AAAATAAAAATGAAAATA
* *
248154 AAAATGAAAATGAAAATG
1 AAAATAAAAATGAAAATA
* *
248172 AAAATTAAAATTAAAATTA
1 AAAATAAAAATGAAAA-TA
*
248191 AAAAGAAAAAT-AAAA-A
1 AAAATAAAAATGAAAATA
* *
248207 ATAATGAAAAATGAAAATG
1 AAAAT-AAAAATGAAAATA
* * *
248226 AAACTAAAACTGAAAATG
1 AAAATAAAAATGAAAATA
* *
248244 AAAATGAAAATGAAAGTA
1 AAAATAAAAATGAAAATA
*
248262 AAAATGAAAAT
1 AAAATAAAAAT
248273 AAATGTACTA
Statistics
Matches: 216, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.02
17 21 0.10
18 174 0.81
19 17 0.08
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.18
Consensus pattern (18 bp):
AAAATAAAAATGAAAATA
Found at i:250460 original size:27 final size:26
Alignment explanation
Indices: 250430--250501 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
250420 GAACTTATAA
250430 AAATAAAAAAAATAAAATGTAAAAATT
1 AAATAAAAAAAATAAAATGTAAAAA-T
* * *
250457 AAATTAAGAACAA-AAAATGTGAAAAT
1 AAA-TAAAAAAAATAAAATGTAAAAAT
*
250483 AAA-AATAAAAATAAGAATG
1 AAATAAAAAAAATAA-AATG
250502 GCTAAATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 6 0.16
25 2 0.05
26 8 0.22
27 14 0.38
28 7 0.19
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.19
Consensus pattern (26 bp):
AAATAAAAAAAATAAAATGTAAAAAT
Found at i:265773 original size:18 final size:20
Alignment explanation
Indices: 265750--265788 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
265740 TTAAAAATCT
265750 GAAAAAAGAA-AACA-ATTA
1 GAAAAAAGAATAACATATTA
*
265768 GAAAAAATAATAACATATTA
1 GAAAAAAGAATAACATATTA
265788 G
1 G
265789 TAAAGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (20 bp):
GAAAAAAGAATAACATATTA
Found at i:267595 original size:36 final size:36
Alignment explanation
Indices: 267555--267637 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 36
267545 TGATGACTGT
267555 TGTGAAAGTGAATATGAT-GGTATGTTATTCATGCCA
1 TGTGAAAGTGAATATG-TGGGTATGTTATTCATGCCA
* *
267591 TGTGACAA-TAAATATGTGGGTATGTTATTCATTCCA
1 TGTGA-AAGTGAATATGTGGGTATGTTATTCATGCCA
267627 TGTGAAAGTGA
1 TGTGAAAGTGA
267638 TTATATTGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 3 0.07
36 36 0.88
37 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.36
Consensus pattern (36 bp):
TGTGAAAGTGAATATGTGGGTATGTTATTCATGCCA
Found at i:268839 original size:21 final size:21
Alignment explanation
Indices: 268815--268866 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
268805 TTCTAAACAG
*
268815 TATCGATACC-CCTTATGAAAC
1 TATCGATACCTCCTT-TAAAAC
* *
268836 TATCCATACCTCCTTTAAAAT
1 TATCGATACCTCCTTTAAAAC
268857 TATCGATACC
1 TATCGATACC
268867 AACGTAACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (21 bp):
TATCGATACCTCCTTTAAAAC
Found at i:276423 original size:26 final size:26
Alignment explanation
Indices: 276356--276463 Score: 119
Period size: 26 Copynumber: 4.2 Consensus size: 26
276346 AACTTTCACA
* **
276356 TTTACGCTTGTCAGCATGAATATAAA
1 TTTACGCTCGTCAGCATGAATATACG
* * *
276382 TTTACGCTCATTAGCATGAAGATACG
1 TTTACGCTCGTCAGCATGAATATACG
* *
276408 TTTACGCTCGTCAGCAAGAACT-CACG
1 TTTACGCTCGTCAGCATGAA-TATACG
*
276434 TTTACGGTCGTCAGCATGAATATACG
1 TTTACGCTCGTCAGCATGAATATACG
276460 TTTA
1 TTTA
276464 TATCACTAGA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
25 1 0.02
26 65 0.98
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (26 bp):
TTTACGCTCGTCAGCATGAATATACG
Found at i:278196 original size:50 final size:51
Alignment explanation
Indices: 278085--278198 Score: 160
Period size: 50 Copynumber: 2.3 Consensus size: 51
278075 ATACTTAGTG
*
278085 GATTTTATTTAGGATGCAAACTTTAACTATCATGAGAGTTACATAATGCAT
1 GATTTTATTTATGATGCAAACTTTAACTATCATGAGAGTTACATAATGCAT
* * * *
278136 G-TCATAATTTATGATGCAAAC-TTAACTATCGTGAGAGTTACATAATGCTT
1 GAT-TTTATTTATGATGCAAACTTTAACTATCATGAGAGTTACATAATGCAT
278186 GATTTTATTTATG
1 GATTTTATTTATG
278199 CAGAACACAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
50 37 0.69
51 17 0.31
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (51 bp):
GATTTTATTTATGATGCAAACTTTAACTATCATGAGAGTTACATAATGCAT
Found at i:283041 original size:24 final size:24
Alignment explanation
Indices: 283011--283060 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
283001 AATCTAAACA
283011 TTTACCGACCTTCTTTTAGTCAAT
1 TTTACCGACCTTCTTTTAGTCAAT
283035 TTTACCGACCTTCTTTTAGTCAAT
1 TTTACCGACCTTCTTTTAGTCAAT
283059 TT
1 TT
283061 ATGTAAGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTACCGACCTTCTTTTAGTCAAT
Found at i:283672 original size:15 final size:15
Alignment explanation
Indices: 283652--283680 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
283642 ATGCCTCACA
283652 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
283667 CACCGTGTTATCAA
1 CACCGTGTTATCAA
283681 GCAACAATAC
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:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:283769 original size:7 final size:7
Alignment explanation
Indices: 283759--283788 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
283749 CAAAATTAAA
283759 AATGTCC
1 AATGTCC
283766 AATGTCC
1 AATGTCC
283773 AATGTCC
1 AATGTCC
283780 AA-GTCC
1 AATGTCC
283786 AAT
1 AAT
283789 TACAACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (7 bp):
AATGTCC
Found at i:289327 original size:2 final size:2
Alignment explanation
Indices: 289314--289349 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
289304 TTGTACAGTA
*
289314 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
289350 TATGTGACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.