Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 135 of 168
Found at i:39502393 original size:61 final size:61
Alignment explanation
Indices: 39502326--39502516 Score: 157
Period size: 61 Copynumber: 3.2 Consensus size: 61
39502316 ATTTCATAGT
*
39502326 ATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGAAAATTAATATAAGAATATTTAATATTAAGAATTTTATTAA
* * * * * *
39502387 ATTATATATT-TTA-ATTAAAATATATTTAATAGT-A-ATTATGTTAAT-TT-A-TATTTTA-CA
1 ATTATATATTATGATTTTAGAA-A-A-TTAATA-TAAGAATAT-TTAATATTAAGAATTTTATTA
*
39502444 GT
61 -A
* * *
39502446 ATCATATATTATGATTTCAGTAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGAAAATTAATATAAGAATATTTAA-TATTAAGAATTTTATTAA
39502507 ATTATATATT
1 ATTATATATT
39502517 TTAATTAACA
Statistics
Matches: 96, Mismatches: 19, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
57 5 0.05
58 9 0.09
59 26 0.27
60 8 0.08
61 35 0.36
62 12 0.12
63 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGAAAATTAATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:39502403 original size:18 final size:17
Alignment explanation
Indices: 39502377--39502411 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39502367 AATATTAAGA
*
39502377 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39502394 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39502412 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39502424 original size:120 final size:120
Alignment explanation
Indices: 39502265--39502553 Score: 429
Period size: 120 Copynumber: 2.4 Consensus size: 120
39502255 AAGTAATTGA
* * * *
39502265 AAATATATATATATT-ATTAAATTATATTTAATAATAATTATGTTAAATTATATTTCATAGTATT
1 AAAT-TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATC
* *
39502329 ATATATTATGATTTTAGAAAATTCATATAAGAATATTTAA-TATTAAGAATTTTATT
65 ATATATTATGATTTCAGAAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATT
* * *
39502385 AAATTATATATTTTAATTAAAATATATTTAATAGTAATTATGTTAATTTATATTTTACAGTATCA
1 AAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCA
*
39502450 TATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATT
66 TATATTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATT
* *
39502505 AAATTATATATTTTAATTAACATATATTTAATAAAAATTATGTTTAAAT
1 AAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
39502554 ATGATTAAAT
Statistics
Matches: 152, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
119 13 0.09
120 134 0.88
121 5 0.03
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (120 bp):
AAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCA
TATATTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATT
Found at i:39502788 original size:16 final size:16
Alignment explanation
Indices: 39502767--39502802 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39502757 GATTTGCTAT
39502767 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
39502783 TACACCTCTAATTCAA
1 TACACCTCTAATCCAA
39502799 TACA
1 TACA
39502803 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:39506166 original size:32 final size:33
Alignment explanation
Indices: 39506104--39506182 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 33
39506094 TAAGCATAAT
*
39506104 AAATTTATGTATATTTTTATGTAGGATTTTAT-G
1 AAATTT-TGTATATTTTCATGTAGGATTTTATGG
* *
39506137 AAATTTTGTGTATTTTCATGTA-TATTTTTATGGG
1 AAATTTTGTATATTTTCATGTAGGA-TTTTAT-GG
*
39506171 AAATTTTTTATA
1 AAATTTTGTATA
39506183 GATAAATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
31 1 0.03
32 20 0.53
33 6 0.16
34 11 0.29
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (33 bp):
AAATTTTGTATATTTTCATGTAGGATTTTATGG
Found at i:39512233 original size:14 final size:14
Alignment explanation
Indices: 39512204--39512249 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
39512194 AATTTACAAC
* *
39512204 ATATACGAATAAAT
1 ATATACAAATACAT
*
39512218 ATTTACAAATACAT
1 ATATACAAATACAT
39512232 ATATACAAATACA-
1 ATATACAAATACAT
39512245 ATATA
1 ATATA
39512250 ACAGTAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (14 bp):
ATATACAAATACAT
Found at i:39525429 original size:26 final size:26
Alignment explanation
Indices: 39525399--39525453 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
39525389 GTATTCAAGA
**
39525399 GATGAAAAAGGCTTGATTGAAA-ACTT
1 GATGAAAAACACTTGA-TGAAAGACTT
39525425 GATGAAAAACACTTGATGAAAGACTT
1 GATGAAAAACACTTGATGAAAGACTT
39525451 GAT
1 GAT
39525454 TAATGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (26 bp):
GATGAAAAACACTTGATGAAAGACTT
Found at i:39536312 original size:43 final size:43
Alignment explanation
Indices: 39536251--39536333 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
39536241 TAAGTAAACA
39536251 AAAAAATTGACATTTGTATGGTTATATAACTTGAGACTTATGT
1 AAAAAATTGACATTTGTATGGTTATATAACTTGAGACTTATGT
39536294 AAAAAATTGACATTTGTATGGTTATATAACTTGAGACTTA
1 AAAAAATTGACATTTGTATGGTTATATAACTTGAGACTTA
39536334 GAGCATTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (43 bp):
AAAAAATTGACATTTGTATGGTTATATAACTTGAGACTTATGT
Found at i:39536327 original size:24 final size:24
Alignment explanation
Indices: 39536257--39536327 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
39536247 AACAAAAAAA
39536257 TTGACATTTGTATGGTTATATAAC
1 TTGACATTTGTATGGTTATATAAC
* * * *
39536281 TTGAGA-CT-TAT-G-TA-AAAAA
1 TTGACATTTGTATGGTTATATAAC
39536300 TTGACATTTGTATGGTTATATAAC
1 TTGACATTTGTATGGTTATATAAC
39536324 TTGA
1 TTGA
39536328 GACTTAGAGC
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 8 0.24
20 3 0.09
21 4 0.12
22 4 0.12
23 3 0.09
24 12 0.35
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (24 bp):
TTGACATTTGTATGGTTATATAAC
Found at i:39543921 original size:24 final size:24
Alignment explanation
Indices: 39543887--39543938 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39543877 TTTTTAGAAG
* **
39543887 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
39543911 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
39543935 ATTT
1 ATTT
39543939 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:39544519 original size:7 final size:7
Alignment explanation
Indices: 39544504--39544600 Score: 122
Period size: 7 Copynumber: 13.6 Consensus size: 7
39544494 ATTTTGTTAT
39544504 ACCCTAA
1 ACCCTAA
*
39544511 ACTCTAA
1 ACCCTAA
39544518 ACCCTAA
1 ACCCTAA
39544525 ACCCTAAA
1 ACCCT-AA
*
39544533 ACTCTAA
1 ACCCTAA
*
39544540 ACACTAA
1 ACCCTAA
*
39544547 ACCTTAAA
1 ACCCT-AA
*
39544555 ACCTTAA
1 ACCCTAA
39544562 ACCCTAA
1 ACCCTAA
*
39544569 ACCTTAA
1 ACCCTAA
39544576 ACCCTAA
1 ACCCTAA
39544583 ACCCTAA
1 ACCCTAA
39544590 ACCCTAA
1 ACCCTAA
39544597 ACCC
1 ACCC
39544601 CAAATTCCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
7 66 0.84
8 13 0.16
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:39544537 original size:22 final size:22
Alignment explanation
Indices: 39544504--39544597 Score: 122
Period size: 22 Copynumber: 4.4 Consensus size: 22
39544494 ATTTTGTTAT
39544504 ACCCT-AAACTCTAAACCCTAA
1 ACCCTAAAACTCTAAACCCTAA
*
39544525 ACCCTAAAACTCTAAACACTAA
1 ACCCTAAAACTCTAAACCCTAA
*
39544547 ACCTTAAAAC-CTTAAACCCTAA
1 ACCCTAAAACTC-TAAACCCTAA
* *
39544569 A-CCTTAAACCCTAAACCCTAA
1 ACCCTAAAACTCTAAACCCTAA
39544590 ACCCTAAA
1 ACCCTAAA
39544598 CCCCAAATTC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
21 23 0.37
22 40 0.63
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (22 bp):
ACCCTAAAACTCTAAACCCTAA
Found at i:39548415 original size:24 final size:24
Alignment explanation
Indices: 39548381--39548432 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39548371 TTTTTAGAAG
* **
39548381 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
39548405 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
39548429 ATTT
1 ATTT
39548433 GACTCTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:39552387 original size:20 final size:20
Alignment explanation
Indices: 39552349--39552387 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39552339 GTCCAATTAG
*
39552349 ATATAAAAATGAATTTAAAA
1 ATATAAAAATGAATGTAAAA
* *
39552369 ATATAAAACTTAATGTAAA
1 ATATAAAAATGAATGTAAA
39552388 TATTTTCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATAAAAATGAATGTAAAA
Found at i:39553810 original size:2 final size:2
Alignment explanation
Indices: 39553803--39553836 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39553793 TTATTGACAA
39553803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39553837 TGTAAGAGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39563170 original size:25 final size:25
Alignment explanation
Indices: 39563136--39563187 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
39563126 GTGACTTCTA
39563136 AATCTATAAAATAAAGGTAAACAAG
1 AATCTATAAAATAAAGGTAAACAAG
39563161 AATCTATAAAATAAAGGTAAACAAG
1 AATCTATAAAATAAAGGTAAACAAG
39563186 AA
1 AA
39563188 CACATGCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.19
Consensus pattern (25 bp):
AATCTATAAAATAAAGGTAAACAAG
Found at i:39563707 original size:43 final size:43
Alignment explanation
Indices: 39563619--39563742 Score: 124
Period size: 43 Copynumber: 2.9 Consensus size: 43
39563609 AGCTCGTACA
* * * * ***
39563619 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCACATACCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAGGTCG
** * *
39563662 ATGCCATTGTCCCAGACAG-GGTCTTTCACGTAAACACAGGTCG
1 ATGCCAACGTCCCAGAC-GTGGTCTTACACGAAAACACAGGTCG
*
39563705 ATGTCAACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACA
39563743 TATCGGAATC
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 1 0.02
43 63 0.97
44 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAGGTCG
Found at i:39564692 original size:5 final size:5
Alignment explanation
Indices: 39564650--39564674 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39564640 GTAATAACTT
39564650 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
39564675 GCTTTATAAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:39568080 original size:40 final size:40
Alignment explanation
Indices: 39568031--39568122 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 40
39568021 AATCGAGAAA
* *
39568031 TAGCAGCGTTTTAGGAAAAGCACCGCTAAAGAGTGAGCAT
1 TAGCGGCGTTTAAGGAAAAGCACCGCTAAAGAGTGAGCAT
*
39568071 TAGCGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCAT
1 TAGCGGCGTTTAAGGAAAAGCACCGCTAAAGAGTGAGCAT
*
39568111 TAACGGCGTTTA
1 TAGCGGCGTTTA
39568123 TAAAAAATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (40 bp):
TAGCGGCGTTTAAGGAAAAGCACCGCTAAAGAGTGAGCAT
Found at i:39569135 original size:2 final size:2
Alignment explanation
Indices: 39569130--39569165 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39569120 AAAAAATCCC
39569130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39569166 TTAGTACTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39569709 original size:2 final size:2
Alignment explanation
Indices: 39569702--39569728 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39569692 TTTATTTTGG
39569702 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
39569729 GAAATGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39572774 original size:17 final size:17
Alignment explanation
Indices: 39572748--39572791 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
39572738 GTTAAATTTA
*
39572748 TTACTTAAATACATTAC
1 TTACTAAAATACATTAC
39572765 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
39572782 TTACTAAAAT
1 TTACTAAAAT
39572792 TTTGTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:39572815 original size:13 final size:13
Alignment explanation
Indices: 39572797--39572838 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
39572787 AAAATTTTGT
*
39572797 TTAAATTTATTAC
1 TTAAATATATTAC
*
39572810 TTAAATATGTTAC
1 TTAAATATATTAC
*
39572823 TTAAATACATTAC
1 TTAAATATATTAC
39572836 TTA
1 TTA
39572839 CTAAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (13 bp):
TTAAATATATTAC
Found at i:39576851 original size:42 final size:41
Alignment explanation
Indices: 39576802--39576964 Score: 238
Period size: 42 Copynumber: 3.9 Consensus size: 41
39576792 GCGTTTTTGT
39576802 ATAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT-
1 ATAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTG
*
39576842 AGTAAAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTTG
1 A-T-AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGC-TTG
* * *
39576886 ATACAAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTGG
1 ATAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT-G
*
39576928 ATTAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
1 ATAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
39576965 TTTTTTTTTT
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 102 0.93
43 3 0.03
44 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
ATAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTG
Found at i:39577252 original size:15 final size:15
Alignment explanation
Indices: 39577232--39577261 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39577222 TAATCTCTTG
39577232 TTCTCCGTAAATACT
1 TTCTCCGTAAATACT
39577247 TTCTCCGTAAATACT
1 TTCTCCGTAAATACT
39577262 CAAGTATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCTCCGTAAATACT
Found at i:39584055 original size:19 final size:20
Alignment explanation
Indices: 39584014--39584058 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
39584004 AAAAAACCTT
*
39584014 TTTTAAAATTTAATTTATTA
1 TTTTAAAATTTAATTTATCA
39584034 TTTTAAAA-TTAATTT-TACA
1 TTTTAAAATTTAATTTAT-CA
39584053 TTTTAA
1 TTTTAA
39584059 TGGAAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAAAATTTAATTTATCA
Found at i:39602927 original size:9 final size:9
Alignment explanation
Indices: 39602913--39602941 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
39602903 TTCTTGTGTC
39602913 TTGGTCTGT
1 TTGGTCTGT
39602922 TTGGTCTGT
1 TTGGTCTGT
39602931 TTGGTCTGT
1 TTGGTCTGT
39602940 TT
1 TT
39602942 ATATTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.31, T:0.59
Consensus pattern (9 bp):
TTGGTCTGT
Found at i:39606399 original size:10 final size:10
Alignment explanation
Indices: 39606384--39606413 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
39606374 AACGAGCTAG
39606384 AGAAAAGGCT
1 AGAAAAGGCT
39606394 AGAAAAGGCT
1 AGAAAAGGCT
39606404 AGAAAAGGCT
1 AGAAAAGGCT
39606414 TTACCAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.30, T:0.10
Consensus pattern (10 bp):
AGAAAAGGCT
Found at i:39608073 original size:18 final size:17
Alignment explanation
Indices: 39608045--39608079 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39608035 AATTATAAGA
*
39608045 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39608062 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39608080 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39608336 original size:16 final size:16
Alignment explanation
Indices: 39608315--39608352 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
39608305 GATTTGCTAT
39608315 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39608331 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39608347 TACACC
1 TACACC
39608353 GAACTTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:39614117 original size:17 final size:17
Alignment explanation
Indices: 39614091--39614124 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39614081 ATAATAAGAC
39614091 TAAAAGATTTTTAAATA
1 TAAAAGATTTTTAAATA
* *
39614108 TAAAATATTTTTTAATA
1 TAAAAGATTTTTAAATA
39614125 AATTTCACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAAAGATTTTTAAATA
Found at i:39614754 original size:19 final size:19
Alignment explanation
Indices: 39614730--39614774 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
39614720 TTATTCTTAT
*
39614730 AATTTTATTTGTAA-TTTAA
1 AATTTTATTT-AAATTTTAA
39614749 AATTTTATTTAAATTTTAA
1 AATTTTATTTAAATTTTAA
39614768 AATTTTA
1 AATTTTA
39614775 AAATGTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
AATTTTATTTAAATTTTAA
Found at i:39614784 original size:25 final size:24
Alignment explanation
Indices: 39614756--39614824 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
39614746 TAAAATTTTA
39614756 TTTAAATTTTA-AAATTTTAAAATGT
1 TTTAAATTTTATAAATTTT-AAAT-T
* * *
39614781 TTTAATTGTTTATATATTTTCAATT
1 TTTAAAT-TTTATAAATTTTAAATT
39614806 TTTATAATTTTATAAATTT
1 TTTA-AATTTTATAAATTT
39614825 ATGTATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 21 0.58
26 9 0.25
27 6 0.17
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTAAATTTTATAAATTTTAAATT
Found at i:39614809 original size:17 final size:16
Alignment explanation
Indices: 39614780--39614817 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
39614770 TTTTAAAATG
39614780 TTTTAATTGTTTATATA
1 TTTTAATTGTTTATA-A
39614797 TTTTCAATT-TTTATAA
1 TTTT-AATTGTTTATAA
39614813 TTTTA
1 TTTTA
39614818 TAAATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.05
16 5 0.25
17 10 0.50
18 4 0.20
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTTAATTGTTTATAA
Found at i:39614844 original size:20 final size:21
Alignment explanation
Indices: 39614821--39614859 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39614811 AATTTTATAA
39614821 ATTTA-TGTATATTTTTAATT
1 ATTTACTGTATATTTTTAATT
* *
39614841 ATTTACTTTTTATTTTTAA
1 ATTTACTGTATATTTTTAA
39614860 GTTTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
ATTTACTGTATATTTTTAATT
Found at i:39622013 original size:4 final size:4
Alignment explanation
Indices: 39622004--39622057 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
39621994 TCAGGCACCT
39622004 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
39622052 TACA TA
1 TACA TA
39622058 ATAATGTTCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:39637837 original size:50 final size:50
Alignment explanation
Indices: 39637775--39638320 Score: 423
Period size: 50 Copynumber: 10.9 Consensus size: 50
39637765 TGCAATGTCG
* * * * **
39637775 GGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACCGCACCGTCA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATCA
** * * ** * *
39637825 GGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATCA
* * * *
39637875 GGGAAACCAGATCCGTCGTTGTAGCTTCAATCTGTTCCACTGTACT-GCTA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATC-A
* ** * * ** * * *
39637925 AGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTACAATATCA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATCA
* * *
39637975 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACT-GCTA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATC-A
* * * * * ** * *
39638025 AGGAAATAAGATCCGCCGTTGTGGCTTCAATTTTTTTAATTGCAATATCA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATCA
* * * **
39638075 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACCGTCA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATCA
** * * * ** * *
39638125 GGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATCA
* * * * *
39638175 TGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACT-GCTA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATC-A
* * * * ** * *
39638225 AGGAAATAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATCA
* *
39638275 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACT
1 GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACT
39638321 GCTAAGGAAG
Statistics
Matches: 361, Mismatches: 129, Indels: 12
0.72 0.26 0.02
Matches are distributed among these distances:
49 3 0.01
50 355 0.98
51 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (50 bp):
GGGAAACAAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTATCA
Found at i:39637930 original size:100 final size:100
Alignment explanation
Indices: 39637749--39638333 Score: 949
Period size: 100 Copynumber: 5.8 Consensus size: 100
39637739 GGTCTGAAAT
* * * * *
39637749 CTTCAATCTATTCAATTGCAATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
39637814 CCGCACCG-TCAGGGAAGTAAGATCCGCCGTTGTGG
66 CTGCACTGCT-AAGGAAGTAAGATCCGCCGTTGTGG
* *
39637849 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGTCGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
*
39637914 CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
*
39637949 CTTCAATCTTTTTAATTACAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
*
39638014 CTGCACTGCTAAGGAAATAAGATCCGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
*
39638049 CTTCAATTTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * * *
39638114 CTGTACCG-TCAGGGAAGTAAGATCTGCCGTTGTGG
66 CTGCACTGCT-AAGGAAGTAAGATCCGCCGTTGTGG
* *
39638149 CTTCAATCTTTTTAATTGCAATATCATGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
*
39638214 CTGCACTGCTAAGGAAATAAGATCCGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
39638249 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
39638314 CTGCACTGCTAAGGAAGTAA
66 CTGCACTGCTAAGGAAGTAA
39638334 AATCTATGGT
Statistics
Matches: 448, Mismatches: 34, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
99 1 0.00
100 445 0.99
101 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (100 bp):
CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
Found at i:39639566 original size:7 final size:7
Alignment explanation
Indices: 39639554--39639582 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
39639544 TTTCATCACC
39639554 TCTTTTT
1 TCTTTTT
39639561 TCTTTTT
1 TCTTTTT
39639568 TCTTTTT
1 TCTTTTT
39639575 TCTTTTT
1 TCTTTTT
39639582 T
1 T
39639583 TTAAGACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TCTTTTT
Found at i:39643927 original size:22 final size:24
Alignment explanation
Indices: 39643893--39643951 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
39643883 TATAGTTTTG
*
39643893 AAAAAAAA-ACATACAT-TAC-AT
1 AAAAAAAATGCATACATATACTAT
*
39643914 AAAAAAAATGCATATATATACTAT
1 AAAAAAAATGCATACATATACTAT
*
39643938 ATAAAGAAATGCAT
1 A-AAAAAAATGCAT
39643952 GCGTATAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 8 0.26
22 6 0.19
23 3 0.10
24 3 0.10
25 11 0.35
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (24 bp):
AAAAAAAATGCATACATATACTAT
Found at i:39643997 original size:18 final size:19
Alignment explanation
Indices: 39643969--39644006 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39643959 GTATAGAAAT
*
39643969 AATAATGATAATGATAATA
1 AATAATGATAATAATAATA
39643988 AATAAT-ATAATAATAATA
1 AATAATGATAATAATAATA
39644006 A
1 A
39644007 TAAAATGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAATGATAATAATAATA
Found at i:39644023 original size:3 final size:3
Alignment explanation
Indices: 39643966--39644009 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
39643956 ATAGTATAGA
* *
39643966 AAT AAT AAT GAT AAT GAT AAT AAAT AAT -AT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
39644010 AATGACAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39650236 original size:16 final size:17
Alignment explanation
Indices: 39650202--39650239 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
39650192 CAGAGATCCA
*
39650202 TATTTATATTATAAATT
1 TATTTATATAATAAATT
*
39650219 TATTTA-ATAATAATTT
1 TATTTATATAATAAATT
39650235 TATTT
1 TATTT
39650240 TTAATTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTATATAATAAATT
Found at i:39652190 original size:16 final size:14
Alignment explanation
Indices: 39652169--39652208 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
39652159 TTTTTTTATC
39652169 TTATTTTTATAATTA
1 TTATTTTTATAA-TA
*
39652184 TTAATTTT-TAATA
1 TTATTTTTATAATA
39652197 TTATTTTTATAA
1 TTATTTTTATAA
39652209 AAAACCACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 6 0.27
15 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTTTATAATA
Found at i:39653191 original size:7 final size:7
Alignment explanation
Indices: 39653179--39653205 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39653169 CAAGTTTCTA
39653179 TTAAAAT
1 TTAAAAT
39653186 TTAAAAT
1 TTAAAAT
39653193 TTAAAAT
1 TTAAAAT
39653200 TTAAAA
1 TTAAAA
39653206 ACATTGGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TTAAAAT
Found at i:39657876 original size:24 final size:25
Alignment explanation
Indices: 39657845--39657898 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
39657835 GGAATCTCCT
*
39657845 TTTA-CAAAGTAAAGTAGTAC-AAC
1 TTTATCAAAGTAAAATAGTACAAAC
39657868 TTTATCAAAGTAAAATAGTACAAAC
1 TTTATCAAAGTAAAATAGTACAAAC
39657893 TTTATC
1 TTTATC
39657899 TACTTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 4 0.14
24 15 0.54
25 9 0.32
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (25 bp):
TTTATCAAAGTAAAATAGTACAAAC
Found at i:39661876 original size:14 final size:14
Alignment explanation
Indices: 39661859--39661904 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
39661849 TAAAAAAATG
39661859 TTATTAAATTATTA
1 TTATTAAATTATTA
*
39661873 TTATTAAATTAGTA
1 TTATTAAATTATTA
39661887 TTATTAAATTATTA
1 TTATTAAATTATTA
39661901 TTAT
1 TTAT
39661905 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:39663049 original size:21 final size:21
Alignment explanation
Indices: 39663016--39663110 Score: 138
Period size: 21 Copynumber: 4.5 Consensus size: 21
39663006 AGGCACTTTA
39663016 TGTGTCGTATATCAGGCACCTCG
1 TGTGTCG--TATCAGGCACCTCG
39663039 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
39663060 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* **
39663081 TGTGTCGTTTCAGGCA-CTTA
1 TGTGTCGTATCAGGCACCTCG
39663101 TGTGTCGTAT
1 TGTGTCGTAT
39663111 ACTGATCAGG
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
20 11 0.16
21 50 0.74
23 7 0.10
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:39663084 original size:42 final size:41
Alignment explanation
Indices: 39663003--39663110 Score: 144
Period size: 42 Copynumber: 2.5 Consensus size: 41
39662993 GGCTTTGCCG
*
39663003 ATCAGGCACTTTATGTGTCGTATATCAGGCACCTCGTGTGTCGT
1 ATCAGGCAC-TCATGTGTCG--TATCAGGCACCTCGTGTGTCGT
*
39663047 ATCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGT
1 ATCAGGCA-CTCATGTGTCGTATCAGGCACCTCGTGTGTCGT
* *
39663089 TTCAGGCACTTATGTGTCGTAT
1 ATCAGGCACTCATGTGTCGTAT
39663111 ACTGATCAGG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
41 12 0.21
42 29 0.50
44 16 0.28
45 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (41 bp):
ATCAGGCACTCATGTGTCGTATCAGGCACCTCGTGTGTCGT
Found at i:39667221 original size:7 final size:7
Alignment explanation
Indices: 39667209--39667249 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
39667199 CAGCTTTCTA
39667209 TTAAAAT
1 TTAAAAT
39667216 TTAAAAT
1 TTAAAAT
39667223 TTAAAAT
1 TTAAAAT
39667230 TTAAAAT
1 TTAAAAT
39667237 TTAAAAT
1 TTAAAAT
39667244 TTAAAA
1 TTAAAA
39667250 GCATTGGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TTAAAAT
Found at i:39671233 original size:12 final size:12
Alignment explanation
Indices: 39671216--39671242 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39671206 TTCGTGTAAA
39671216 AATGATGAATTC
1 AATGATGAATTC
39671228 AATGATGAATTC
1 AATGATGAATTC
39671240 AAT
1 AAT
39671243 TTGAGCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (12 bp):
AATGATGAATTC
Found at i:39675595 original size:13 final size:14
Alignment explanation
Indices: 39675575--39675608 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
39675565 CATTATAAAG
39675575 CCAG-TTTATATTA
1 CCAGATTTATATTA
39675588 CCA-ATTTATATTA
1 CCAGATTTATATTA
39675601 CCAGATTT
1 CCAGATTT
39675609 CACCAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (14 bp):
CCAGATTTATATTA
Found at i:39681432 original size:14 final size:14
Alignment explanation
Indices: 39681413--39681441 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39681403 ATATATTTTT
39681413 TATATTTCTTAAAA
1 TATATTTCTTAAAA
39681427 TATATTTCTTAAAA
1 TATATTTCTTAAAA
39681441 T
1 T
39681442 GTATCAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTTCTTAAAA
Found at i:39687419 original size:20 final size:21
Alignment explanation
Indices: 39687381--39687421 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39687371 TTACAATTAA
*
39687381 CTTTATGAGTTTTAACATTGG
1 CTTTATGAGTTATAACATTGG
*
39687402 CTTTAT-AGTTATAGCATTGG
1 CTTTATGAGTTATAACATTGG
39687422 ATAAGAGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (21 bp):
CTTTATGAGTTATAACATTGG
Found at i:39703127 original size:2 final size:2
Alignment explanation
Indices: 39703122--39703167 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
39703112 ATTTAAAAAA
39703122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39703164 AT AT
1 AT AT
39703168 TCACTTCGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39706971 original size:27 final size:27
Alignment explanation
Indices: 39706935--39707006 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
39706925 CACTTGACTG
* * *
39706935 TGTCATTTCATAGTTCATTTCGCAGTT
1 TGTCACTTCACAGTTCATTTCGCAGCT
*
39706962 TGTCACTTCACGGTTCATTTCGCAGCT
1 TGTCACTTCACAGTTCATTTCGCAGCT
* *
39706989 TGTCACTTTACGGTTCAT
1 TGTCACTTCACAGTTCAT
39707007 CATGTGTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (27 bp):
TGTCACTTCACAGTTCATTTCGCAGCT
Found at i:39720086 original size:17 final size:16
Alignment explanation
Indices: 39720036--39720083 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
39720026 GTTAATGTAA
39720036 TTAATATAAATTATTAT
1 TTAATATAAATT-TTAT
*
39720053 TTAA-ATAAA-ATTA-
1 TTAATATAAATTTTAT
39720066 TTAATATAAATTTTAT
1 TTAATATAAATTTTAT
39720082 TT
1 TT
39720084 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
13 4 0.15
14 8 0.31
15 3 0.12
16 7 0.27
17 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATATAAATTTTAT
Found at i:39720086 original size:30 final size:31
Alignment explanation
Indices: 39720035--39720096 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 31
39720025 TGTTAATGTA
39720035 ATTAATATAAATTATTATTT-AAATAAAATT
1 ATTAATATAAATTATTATTTAAAATAAAATT
39720065 ATTAATATAAATT-TTATTTTAAAAATAAAATT
1 ATTAATATAAATTATTA-TTT-AAAATAAAATT
39720097 TAAAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 3 0.10
30 16 0.55
32 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTAATATAAATTATTATTTAAAATAAAATT
Found at i:39720144 original size:21 final size:19
Alignment explanation
Indices: 39720102--39720171 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 19
39720092 AAATTTAAAA
39720102 TTAATAATACTTTTAA-ATT
1 TTAATAATA-TTTTAATATT
39720121 TTAAGTAATATTCTTAATATT
1 TTAA-TAATATT-TTAATATT
* *
39720142 TTATTGAACATTGTTAATATT
1 TTAAT-AATATT-TTAATATT
39720163 TTAATAATA
1 TTAATAATA
39720172 AATATATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 6 0.14
20 13 0.31
21 23 0.55
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (19 bp):
TTAATAATATTTTAATATT
Found at i:39726396 original size:23 final size:23
Alignment explanation
Indices: 39726359--39726402 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
39726349 AATTGAATTG
39726359 AATTATATTTTTGTTTAATATAT
1 AATTATATTTTTGTTTAATATAT
39726382 AATTA-ATTTTATGTTTAATAT
1 AATTATATTTT-TGTTTAATAT
39726403 GATATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
AATTATATTTTTGTTTAATATAT
Found at i:39726446 original size:29 final size:31
Alignment explanation
Indices: 39726387--39726446 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
39726377 TATATAATTA
* *
39726387 ATTTTATGTTTAATATGATATAAAAATAAAT
1 ATTTTATATTTAAAATGATATAAAAATAAAT
39726418 ATTTTATATTTAAAAT-A-ATAAAAATAAAT
1 ATTTTATATTTAAAATGATATAAAAATAAAT
39726447 TAAAAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.44
30 1 0.04
31 14 0.52
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (31 bp):
ATTTTATATTTAAAATGATATAAAAATAAAT
Found at i:39726997 original size:22 final size:22
Alignment explanation
Indices: 39726950--39727000 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
39726940 AATATTACAT
**
39726950 TTAATTTAATTTAAAATTTAGGA
1 TTAATTTAATAAAAAATTTA-GA
39726973 TTAATTTAATAAAAAATTATA-A
1 TTAATTTAATAAAAAATT-TAGA
39726995 TTAATT
1 TTAATT
39727001 AATTAATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.28
23 16 0.64
24 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTAATTTAATAAAAAATTTAGA
Found at i:39737811 original size:19 final size:19
Alignment explanation
Indices: 39737790--39737825 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39737780 GAATTGGAAT
*
39737790 TTTTTAA-AATTTTTTAAA
1 TTTTTAATAATGTTTTAAA
39737808 TTTTTAATAATGTTTTAA
1 TTTTTAATAATGTTTTAA
39737826 TTGGACCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTTAATAATGTTTTAAA
Found at i:39742904 original size:20 final size:20
Alignment explanation
Indices: 39742879--39742932 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 20
39742869 GGGTTAATAA
39742879 TTTTATGTATCATTTTTAGT
1 TTTTATGTATCATTTTTAGT
*
39742899 TTTTATG--TCATTTTTTGT
1 TTTTATGTATCATTTTTAGT
*
39742917 ATTT-T-TATCATTTTTA
1 TTTTATGTATCATTTTTA
39742933 AAATTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.03
18 21 0.72
20 7 0.24
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTTATGTATCATTTTTAGT
Found at i:39743610 original size:25 final size:25
Alignment explanation
Indices: 39743570--39743617 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
39743560 CTTAGTTTCG
*
39743570 TTTTGTTATTTTTTTTTCTTTTAGC
1 TTTTGTTATTTTTTTTTCATTTAGC
39743595 TTTT-TTATTTTATTTTTCATTTA
1 TTTTGTTATTTT-TTTTTCATTTA
39743618 AAATATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTGTTATTTTTTTTTCATTTAGC
Found at i:39744272 original size:25 final size:27
Alignment explanation
Indices: 39744229--39744296 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
39744219 TTGTATTTTC
* * * *
39744229 TATACATATAAATACGCAT-TTTTTTA
1 TATATATATATATAAGCATATTTTTAA
39744255 TATATA-ATATATAAGCATATTTTTAA
1 TATATATATATATAAGCATATTTTTAA
*
39744281 TATATATATTTATAAG
1 TATATATATATATAAG
39744297 TACGCATCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 10 0.29
26 17 0.49
27 8 0.23
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (27 bp):
TATATATATATATAAGCATATTTTTAA
Found at i:39744563 original size:2 final size:2
Alignment explanation
Indices: 39744556--39744580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39744546 ATTCATCTTC
39744556 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39744581 CTTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39748263 original size:46 final size:46
Alignment explanation
Indices: 39748162--39748533 Score: 493
Period size: 46 Copynumber: 8.6 Consensus size: 46
39748152 TACGTATGAT
*
39748162 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
39748205 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
39748251 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
39748297 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
39748343 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
39748379 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
39748425 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
39748461 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
39748507 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
39748534 AGTACTCAAA
Statistics
Matches: 297, Mismatches: 9, Indels: 43
0.85 0.03 0.12
Matches are distributed among these distances:
36 58 0.20
38 6 0.02
40 4 0.01
41 4 0.01
42 4 0.01
43 10 0.03
44 11 0.04
45 20 0.07
46 180 0.61
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:39748384 original size:36 final size:36
Alignment explanation
Indices: 39748343--39748497 Score: 193
Period size: 36 Copynumber: 4.0 Consensus size: 36
39748333 CTAAGGCTAA
39748343 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
39748379 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A-G
39748421 CTAACACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
39748461 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
39748497 C
1 C
39748498 TAAAGCTACC
Statistics
Matches: 105, Mismatches: 4, Indels: 20
0.81 0.03 0.16
Matches are distributed among these distances:
36 64 0.61
38 3 0.03
40 2 0.02
41 2 0.02
42 2 0.02
44 3 0.03
46 29 0.28
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:39748391 original size:82 final size:82
Alignment explanation
Indices: 39748297--39748533 Score: 429
Period size: 82 Copynumber: 2.9 Consensus size: 82
39748287 CTAAGGCTAC
*
39748297 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
39748362 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
39748379 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
39748444 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
* * * *
39748461 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
39748526 TGATCAGA
66 TGATCAGA
39748534 AGTACTCAAA
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 150 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
TGATCAGATAAGTATAG
Found at i:39748511 original size:128 final size:133
Alignment explanation
Indices: 39748162--39748533 Score: 449
Period size: 128 Copynumber: 2.9 Consensus size: 133
39748152 TACGTATGAT
39748162 CACTTATCACTTGTC-C-C-TGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCAC
1 CACTTATCACTT-TCTCACTTGATCAGATAAG-GTA-CTAAGG--A-CACTTATCACTTTGTCAC
* *
39748223 TTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGC
60 TTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGATAAGTGTAGC
*
39748288 TAAGGCTAC
125 TAAGGCTAA
39748297 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAG-GTA-CTAAGG---ACACTTATCACTTTGTCACT
*
39748362 TGATCAGATAA--GTA--T--AG----CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT
61 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGATAAGTGTAGCT
39748417 AAGGCTAA
126 AAGGCTAA
* *
39748425 CACTTATCACTTTGTCACTTGATCAGATAA-GTA-T-A-G-CACTTATCACTTTTTCACTTGATC
1 CACTTATCACTTTCTCACTTGATCAGATAAGGTACTAAGGACACTTATCACTTTGTCACTTGATC
*
39748485 AGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCTTGATCAGA
66 AGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGA
39748534 AGTACTCAAA
Statistics
Matches: 213, Mismatches: 9, Indels: 37
0.82 0.03 0.14
Matches are distributed among these distances:
118 29 0.14
120 3 0.01
122 2 0.01
123 1 0.00
124 3 0.01
126 3 0.01
128 98 0.46
132 1 0.00
134 3 0.01
135 13 0.06
136 4 0.02
137 19 0.09
138 33 0.15
139 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (133 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGGTACTAAGGACACTTATCACTTTGTCACTTGATC
AGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGGC
TAA
Found at i:39752823 original size:13 final size:13
Alignment explanation
Indices: 39752776--39752821 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
39752766 ATGAAATGAA
39752776 AAAATGAAAAGTG
1 AAAATGAAAAGTG
*
39752789 AAAATGAAAAATG
1 AAAATGAAAAGTG
39752802 AATAATGGAAAAGT-
1 AA-AAT-GAAAAGTG
39752816 AAAATG
1 AAAATG
39752822 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 1 0.03
13 17 0.59
14 5 0.17
15 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (13 bp):
AAAATGAAAAGTG
Found at i:39754161 original size:44 final size:44
Alignment explanation
Indices: 39754098--39755039 Score: 855
Period size: 44 Copynumber: 21.3 Consensus size: 44
39754088 GAAAAGCAGC
39754098 AGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAGT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGT
* *
39754142 AGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
* * *
39754186 GGATCTTGTTTTCATGTATTGACATGAAGTAGATC-AGAGATAGC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGT
* *
39754230 AGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
* * *
39754274 GGATCTTGTCTTCATGTATTGACATGAAGTATATC-AGAGATAGC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGT
* * * *
39754318 AGATCTTATCTTCATGTATTGGCATGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
* * * * *** * *
39754362 AGATATTGTCTTCCTATACTGGTGGTGAAGTAGATCAAAGATAAT
1 AGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCGAAGATAGT
*
39754407 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
* *
39754451 GGATCTTGTCTTCATGTATTGACACGAAGTAGATC-AGAGATAGT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGT
* * * *
39754495 GGGTCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATGGC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
*** * *** * *
39754539 AGATCTTGTCTTCCCATACTGGTGGTCAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCGAAGATAGT
* * * *
39754584 GGATCTTATCTTCATGTATTGACACGAAGTAGATC-AGAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGT
* * * *
39754628 GGGTCTTGTCTTCATGTATTGACATGAAATAGATCGAAGAT-GAC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG-T
*** * ** * *
39754672 AGATCTTGTCTTCCCATACTGGTGATCAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCGAAGATAGT
* * *
39754717 GGATCTTGTCTTCTTGTATTGGCATGAAGTAGATC-AGAGATAGT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGT
* * * *
39754761 -GTCTCTTGTCTTCATGTATTGACATAAAGTAGATCGAAGATGGC
1 AG-ATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
*** * *** *
39754805 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCGAAGATAGT
* *
39754850 GGATCTTGTCTTCATGTATTGACATGAAGTAGAT-TAGAGATAGT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGT
* * * * * *
39754894 GGCTCTTGTCTTCTTGTATTGACATGAAATAGATCGAAGATGGC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
*** * *
39754938 AGATCTTGTCTTCCCATATTG--GTGGAAAAGTAGATCGAATATA-T
1 AGATCTTGTCTTCATGTATTGACAT-G--AAGTAGATCGAAGATAGT
* * * * *
39754982 CAAATCTTGTCTTCATGTAGTGGCGTGAAGTAGATCAAAGATAGT
1 -AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
39755027 AGATCTTGTCTTC
1 AGATCTTGTCTTC
39755040 CAATACTGGT
Statistics
Matches: 721, Mismatches: 149, Indels: 56
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.00
43 8 0.01
44 541 0.75
45 168 0.23
46 1 0.00
47 2 0.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (44 bp):
AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGT
Found at i:39754448 original size:133 final size:132
Alignment explanation
Indices: 39754098--39755039 Score: 1034
Period size: 133 Copynumber: 7.1 Consensus size: 132
39754088 GAAAAGCAGC
* * ***
39754098 AGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAGTAGATCTTATCTTCATGTATT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCCCATATT
*
39754162 GACATGAAGTAGATCGAAGATAATGGATCTTGTTTTCATGTATTGACATGAAGTAGATCAGAGAT
65 GACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
*
39754227 AGC
130 AGT
* *** ***
39754230 AGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTG
* *** * * *
39754295 ACATGAAGTATATC-AGAGATAGCAGATCTTATCTTCATGTATTGGCATGAAGTAGATCAAAGAT
66 ACATGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
*
39754359 AGC
130 AGT
* * * * *** * ** ***
39754362 AGATATTGTCTTCCTATACTGGTGGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATT
*
39754427 GACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACACGAAGTAGATCAGAGAT
65 GACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
39754492 AGT
130 AGT
* * * *
39754495 GGGTCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATGGCAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATA-TT
*** * * *
39754560 GTGGTCAAGTAGATCGAAGATAATGGATCTTATCTTCATGTATTGACACGAAGTAGATCAGAGAT
65 GACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
*
39754625 AAT
130 AGT
* * *
39754628 GGGTCTTGTCTTCATGTATTGACATGAAATAGATCGAAGAT-GACAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG-CAGATCTTGTCTTCCCATA-T
* ** * * *
39754692 GGTGATCAAGTAGATCGAAGATAATGGATCTTGTCTTCTTGTATTGGCATGAAGTAGATCAGAGA
64 TGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGA
39754757 TAGT
129 TAGT
* * *
39754761 -GTCTCTTGTCTTCATGTATTGACATAAAGTAGATCGAAGATGGCAGATCTTGTCTTCCCATACT
1 AG-ATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATA-T
* *** *
39754825 GGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATTAGAGA
64 TGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGA
39754890 TAGT
129 TAGT
* * * * *
39754894 GGCTCTTGTCTTCTTGTATTGACATGAAATAGATCGAAGATGGCAGATCTTGTCTTCCCATATTG
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTG
* * ** * * * *
39754959 --GTGGAAAAGTAGATCGAATAT-ATCAAATCTTGTCTTCATGTAGTGGCGTGAAGTAGATCAAA
66 ACAT-G--AAGTAGATCGAAGATAAT-GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGA
39755021 GATAGT
127 GATAGT
39755027 AGATCTTGTCTTC
1 AGATCTTGTCTTC
39755040 CAATACTGGT
Statistics
Matches: 714, Mismatches: 83, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
130 2 0.00
131 2 0.00
132 169 0.24
133 538 0.75
134 3 0.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (132 bp):
AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTG
ACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA
GT
Found at i:39754903 original size:177 final size:175
Alignment explanation
Indices: 39754099--39755039 Score: 889
Period size: 177 Copynumber: 5.3 Consensus size: 175
39754089 AAAAGCAGCA
*
39754099 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTATCTTCATGTATTGA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTCATGTATTGA
* * * *
39754164 CATGAAGTAGATCGAAGATAATGGATCTTGTTTTCATGTATTGACATGAAGTAGATCAGAGATAG
66 CATGAAGTAGATCGAAGATAGTGGATCTTGTCTTCCTGTATTGGCATGAAGTAGATCAGAGATA-
39754229 CA-GATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
130 -ATGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
* * * *
39754275 GATCTTGTCTTCATGTATTGACATGAAGTATATCAGAGATAGCAGATCTTATCTTCATGTATTGG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTCATGTATTGA
* ** * * * ** *
39754340 CATGAAGTAGATCAAAGATAGCAGATATTGTCTTCCTATACTGGTGGTGAAGTAGATCAAAGATA
66 CATGAAGTAGATCGAAGATAGTGGATCTTGTCTTCCTGTATTGG-CATGAAGTAGATCAGAGATA
*
39754405 ATAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
130 AT-GATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
* * *
39754452 GATCTTGTCTTCATGTATTGACACGAAGTAGATCAGAGATAGTGGGTCTTGTCTTCATGTATTGA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTCATGTATTGA
* ** ** * ** *
39754517 CATGAAGTAGATCGAAGATGGCAGATCTTGTCTTCCCATACTGGTGGTCAAGTAGATC-GAAGAT
66 CATGAAGTAGATCGAAGATAGTGGATCTTGTCTTCCTGTATTGG-CATGAAGTAGATCAG-AGAT
*
39754581 AATGGATCTTATCTTCATGTATTGACACGAAGTAGATC-AGAGATAATG
129 AAT-GATCTTATCTTCATGTATTGACATGAAGTAGATCGA-AGATAATG
* * * ***
39754629 GGTCTTGTCTTCATGTATTGACATGAAATAGATC-GAAGAT-GACAGATCTTGTCTTCCCATACT
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAG-TAGATCTTGTCTTCATGTA-T
* ** * * *
39754692 GGTGATCAAGTAGATCGAAGATAATGGATCTTGTCTTCTTGTATTGGCATGAAGTAGATCAGAGA
63 TGACATGAAGTAGATCGAAGATAGTGGATCTTGTCTTCCTGTATTGGCATGAAGTAGATCAGAGA
* * * * ****
39754757 TAGTGTCTCTTGTCTTCATGTATTGACATAAAGTAGATCGAAGATGGCA
128 TAATG-ATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
*** * *** * *
39754806 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGATAATGGATCTTGTCTTCATGTATT
1 GATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAGTAGATCTTGTCTTCATGTATT
* * * * *
39754870 GACATGAAGTAGAT-TAGAGATAGTGGCTCTTGTCTTCTTGTATTGACATGAAATAGATC-GAAG
64 GACATGAAGTAGATCGA-AGATAGTGGATCTTGTCTTCCTGTATTGGCATGAAGTAGATCAG-AG
* * *** * * *
39754933 ATGGCA-GATCTTGTCTTCCCATATTG--GTGGAAAAGTAGATCGAATAT-ATCA
127 AT--AATGATCTTATCTTCATGTATTGACAT-G--AAGTAGATCGAAGATAAT-G
* * * * *
39754984 AATCTTGTCTTCATGTAGTGGCGTGAAGTAGATCAAAGATAGTAGATCTTGTCTTC
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTC
39755040 CAATACTGGT
Statistics
Matches: 631, Mismatches: 112, Indels: 43
0.80 0.14 0.05
Matches are distributed among these distances:
175 2 0.00
176 102 0.16
177 428 0.68
178 99 0.16
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (175 bp):
GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTCATGTATTGA
CATGAAGTAGATCGAAGATAGTGGATCTTGTCTTCCTGTATTGGCATGAAGTAGATCAGAGATAA
TGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
Found at i:39755023 original size:89 final size:89
Alignment explanation
Indices: 39754897--39755065 Score: 230
Period size: 89 Copynumber: 1.9 Consensus size: 89
39754887 AGATAGTGGC
* * * * * *
39754897 TCTTGTCTTCTTGTATTGACATGAAATAGATCGAAGATGGCAGATCTTGTCTTCCCATATTGGTG
1 TCTTGTCTTCATGTAGTGACATGAAATAGATCAAAGATAGCAGATCTTGTCTTCCAATACTGGTG
39754962 GAAAAGTAGATCGAATATATCAAA
66 GAAAAGTAGATCGAATATATCAAA
* * * *
39754986 TCTTGTCTTCATGTAGTGGCGTGAAGTAGATCAAAGATAGTAGATCTTGTCTTCCAATACTGGTG
1 TCTTGTCTTCATGTAGTGACATGAAATAGATCAAAGATAGCAGATCTTGTCTTCCAATACTGGTG
**
39755051 GCGAAGTAGATCGAA
66 GAAAAGTAGATCGAA
39755066 GATACCAGTC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 68 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (89 bp):
TCTTGTCTTCATGTAGTGACATGAAATAGATCAAAGATAGCAGATCTTGTCTTCCAATACTGGTG
GAAAAGTAGATCGAATATATCAAA
Found at i:39755966 original size:18 final size:18
Alignment explanation
Indices: 39755925--39755969 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
39755915 TTTCTTTTAG
*
39755925 CTTTTTTATTTTATTTTT
1 CTTTTTTATTGTATTTTT
*
39755943 CATTTTTATTGTA-TTTT
1 CTTTTTTATTGTATTTTT
*
39755960 ATTTTTTATT
1 CTTTTTTATT
39755970 TCTCCCATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (18 bp):
CTTTTTTATTGTATTTTT
Found at i:39756183 original size:25 final size:27
Alignment explanation
Indices: 39756140--39756207 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
39756130 TTGTATTTTC
* * * *
39756140 TATACATATAAATACGCAT-TTTTTTA
1 TATATATATATATAAGCATATTTTTAA
39756166 TATATA-ATATATAAGCATATTTTTAA
1 TATATATATATATAAGCATATTTTTAA
*
39756192 TATATATATTTATAAG
1 TATATATATATATAAG
39756208 TACGCATCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 10 0.29
26 17 0.49
27 8 0.23
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (27 bp):
TATATATATATATAAGCATATTTTTAA
Found at i:39756474 original size:2 final size:2
Alignment explanation
Indices: 39756467--39756503 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39756457 ATTCATCTTC
39756467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39756504 CTTTTTACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39758581 original size:335 final size:321
Alignment explanation
Indices: 39757984--39758642 Score: 1003
Period size: 335 Copynumber: 2.0 Consensus size: 321
39757974 GAATTTGGAA
*
39757984 TTATTTTGTTATATCAAAACCTTTGAAAATCAAAATTAACAATCTTACATTATTTTAATATGGCA
1 TTATTTTGTTATATCAAAACCTTTGAAAATCAAAATTAACAATCTTACATTATTTTAATATGACA
* * * *
39758049 TTAGAGCCTTTTGTTCTCAGTCCTAGCCTATACACGTTTTTTCACCCCTTCGTTCAAATGAACAT
66 TTAGAGCCTTTTGTTCTCAATCCTAGCCTATACACATTTTCTCACCCCTTCGTTCAAATGAAAAT
*
39758114 ATTCTTGAACCTTCATATGGGTACAACAATTTATCTTTTTCAACTGAAACAATGTTAATTCTTGT
131 ATTCTTGAACCTTCATATGGCTACAACAATTTATCTTTTTCAACTGAAACAATGTTAATTCTTGT
* * * *
39758179 TCATCAAAGTCAATTAATCAACTTTCTTTTATCACCAACCAATTATTGGCTCCTATATCTATTCA
196 TCATCAAAGTCAATCAAACAACTTTATTTTATCACCAACCAATCATTGGCTCCTATATCTATTCA
* * *
39758244 AAGTGGTGAAGTTCATGTCTAACTATCTTGATAGTCAATAAAGGGGCCTTGCCTAATGGATG
261 AAGTGGAGAAGTTCATGCCTAACTATCTTGATAGTCAAGAAAGGGGCC-TGCCTAATGGATG
*
39758306 TTATTTTGTTATATCAAAACCTTTGAAAATCAAAATTAACAATCTTACATTATTTTAATATTACA
1 TTATTTTGTTATATCAAAACCTTTGAAAATCAAAATTAACAATCTTACATTATTTTAATATGACA
*
39758371 TTAGAGCCTTTTGTTTAACAACATGGTTTTCAATCCTAGCCTATACACATTTTCTCACCCTTTCG
66 TTAGAGCCTTTTG-TT-----C-------TCAATCCTAGCCTATACACATTTTCTCACCCCTTCG
* *
39758436 TTCAAATGAAAATATTCTTGAACCTTTATATGGCTACAACAATTTATCTTTTTCAATTGAAACAA
118 TTCAAATGAAAATATTCTTGAACCTTCATATGGCTACAACAATTTATCTTTTTCAACTGAAACAA
39758501 TGTTAATTCTTGTTCATCAAAGTCAATCAAACAACTTTATTTTATCACCAACCAATCATTGGCTC
183 TGTTAATTCTTGTTCATCAAAGTCAATCAAACAACTTTATTTTATCACCAACCAATCATTGGCTC
* * * *
39758566 CTATATCTATTCAAAGTGGAGAAGTTCATGCCTAACTATCTTGATAGTTAGGAGAGGGGTCTGCC
248 CTATATCTATTCAAAGTGGAGAAGTTCATGCCTAACTATCTTGATAGTCAAGAAAGGGGCCTGCC
39758631 TAATGGATG
313 TAATGGATG
39758640 TTA
1 TTA
39758643 AACCACACCT
Statistics
Matches: 303, Mismatches: 21, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
322 76 0.25
323 2 0.01
328 1 0.00
334 16 0.05
335 208 0.69
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (321 bp):
TTATTTTGTTATATCAAAACCTTTGAAAATCAAAATTAACAATCTTACATTATTTTAATATGACA
TTAGAGCCTTTTGTTCTCAATCCTAGCCTATACACATTTTCTCACCCCTTCGTTCAAATGAAAAT
ATTCTTGAACCTTCATATGGCTACAACAATTTATCTTTTTCAACTGAAACAATGTTAATTCTTGT
TCATCAAAGTCAATCAAACAACTTTATTTTATCACCAACCAATCATTGGCTCCTATATCTATTCA
AAGTGGAGAAGTTCATGCCTAACTATCTTGATAGTCAAGAAAGGGGCCTGCCTAATGGATG
Found at i:39759223 original size:20 final size:20
Alignment explanation
Indices: 39759178--39759228 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
39759168 ACGTAATTCA
*
39759178 AACAGAACAGAACCAAATCG
1 AACAGAACAGAAACAAATCG
* *
39759198 AGCAGAACA-AAACATAATGG
1 AACAGAACAGAAACA-AATCG
*
39759218 AACAGAGCAGA
1 AACAGAACAGA
39759229 GCAATGCTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 4 0.17
20 19 0.79
21 1 0.04
ACGTcount: A:0.55, C:0.20, G:0.20, T:0.06
Consensus pattern (20 bp):
AACAGAACAGAAACAAATCG
Found at i:39759682 original size:13 final size:13
Alignment explanation
Indices: 39759664--39759690 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39759654 TTTTTTAAAG
39759664 CAGACTTATCAAA
1 CAGACTTATCAAA
39759677 CAGACTTATCAAA
1 CAGACTTATCAAA
39759690 C
1 C
39759691 CTCAACAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (13 bp):
CAGACTTATCAAA
Found at i:39760557 original size:37 final size:37
Alignment explanation
Indices: 39760496--39760642 Score: 244
Period size: 37 Copynumber: 4.0 Consensus size: 37
39760486 TACGTATGAT
* *
39760496 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
39760531 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
39760568 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
39760605 CACTTATCACTTTGTTTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
39760642 C
1 C
39760643 GAAGCTATCA
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 93 0.89
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:39760660 original size:7 final size:7
Alignment explanation
Indices: 39760648--39760693 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
39760638 TAGCCGAAGC
39760648 TATCACT
1 TATCACT
39760655 TATCACT
1 TATCACT
39760662 T-TC-CT
1 TATCACT
39760667 TATCACT
1 TATCACT
*
39760674 TTTCACT
1 TATCACT
*
39760681 TGTCACT
1 TATCACT
39760688 TGATCA
1 T-ATCA
39760694 GATAAGTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
5 3 0.09
6 4 0.12
7 23 0.70
8 3 0.09
ACGTcount: A:0.22, C:0.28, G:0.04, T:0.46
Consensus pattern (7 bp):
TATCACT
Found at i:39760707 original size:64 final size:59
Alignment explanation
Indices: 39760655--39760786 Score: 216
Period size: 59 Copynumber: 2.3 Consensus size: 59
39760645 AGCTATCACT
*
39760655 TATCACTT-TC-CTTAT-CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTATCACTT-TCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
39760712 TATCACTTATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGC
1 TATCACTTATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
39760771 TATCACTTATCACTTT
1 TATCACTTATCACTTT
39760787 GTCACTTGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
57 8 0.11
58 3 0.04
59 59 0.84
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (59 bp):
TATCACTTATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:39760740 original size:52 final size:52
Alignment explanation
Indices: 39760665--39760992 Score: 302
Period size: 46 Copynumber: 6.2 Consensus size: 52
39760655 TATCACTTTC
*
39760665 CTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCA
1 CTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCA
*
39760717 CTTATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCA
1 C-T-T-A---T-CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCA
* *
39760776 CTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTA
1 CTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCA
* ** *
39760822 CTGAAGCTATTACTTATCACTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
1 CT-----TATCACTT-T--C--CACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCA
* *
39760884 CTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTA
1 CTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCA
** *
39760930 CTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
1 CTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCA
39760982 CTTATCACTTT
1 CTTATCACTTT
39760993 GTCACTTGAT
Statistics
Matches: 225, Mismatches: 22, Indels: 58
0.74 0.07 0.19
Matches are distributed among these distances:
46 76 0.34
48 1 0.00
50 1 0.00
51 5 0.02
52 47 0.21
53 2 0.01
54 3 0.01
55 1 0.00
56 1 0.00
57 6 0.03
58 2 0.01
59 46 0.20
62 34 0.15
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCA
Found at i:39760879 original size:108 final size:102
Alignment explanation
Indices: 39760670--39761006 Score: 504
Period size: 108 Copynumber: 3.3 Consensus size: 102
39760660 CTTTCCTTAT
* * *
39760670 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTT-CAC-T
* *
39760734 TCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
64 T-CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
39760774 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTGAAGCTATTACTTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT-----TATCACTT-T
39760839 CACTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
60 CACTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
39760882 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTT--C--C
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCACTTC
39760943 ACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 ACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
39760980 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
39761007 AGTACTCAAA
Statistics
Matches: 219, Mismatches: 7, Indels: 20
0.89 0.03 0.08
Matches are distributed among these distances:
98 65 0.30
100 1 0.00
102 1 0.00
103 7 0.03
104 9 0.04
105 37 0.17
108 86 0.39
109 2 0.01
110 10 0.05
111 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (102 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCACTTC
ACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:39760991 original size:98 final size:96
Alignment explanation
Indices: 39760824--39761006 Score: 348
Period size: 98 Copynumber: 1.9 Consensus size: 96
39760814 AGCTATTACT
39760824 GAAGCTATTACTTATCACTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 GAAGCTATTACTTATCACTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
39760889 CACTTTGTCACTTGATCAGATAAGTATAGCC
66 CACTTTGTCACTTGATCAGATAAGTATAGCC
39760920 GAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 GAAGCTATTACTTATCAC-TT-CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTT
39760985 ATCACTTTGTCACTTGATCAGA
64 ATCACTTTGTCACTTGATCAGA
39761007 AGTACTCAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
96 18 0.21
97 2 0.02
98 65 0.76
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (96 bp):
GAAGCTATTACTTATCACTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
CACTTTGTCACTTGATCAGATAAGTATAGCC
Found at i:39763619 original size:18 final size:18
Alignment explanation
Indices: 39763586--39763638 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
39763576 ATTCACCTAA
*
39763586 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
39763605 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
39763623 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
39763639 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:39763677 original size:21 final size:20
Alignment explanation
Indices: 39763653--39763728 Score: 57
Period size: 21 Copynumber: 3.8 Consensus size: 20
39763643 AAAAATTAAA
*
39763653 AAAATTTTAATAAATAAAAAT
1 AAAATTCTAA-AAATAAAAAT
* *
39763674 AAAATTCTAAAACTAAAACT
1 AAAATTCTAAAAATAAAAAT
* **
39763694 -AAA-TCTAAAACTAAAGTCT
1 AAAATTCTAAAAATAAA-AAT
*
39763713 AAAAGTCTAAAAATAA
1 AAAATTCTAAAAATAA
39763729 TTTAATTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
18 12 0.26
19 5 0.11
20 11 0.23
21 19 0.40
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATTCTAAAAATAAAAAT
Found at i:39763715 original size:13 final size:12
Alignment explanation
Indices: 39763680--39763716 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
39763670 AAATAAAATT
*
39763680 CTAAAACTAAAA
1 CTAAATCTAAAA
39763692 CTAAATCTAAAA
1 CTAAATCTAAAA
39763704 CTAAAGTCTAAAA
1 CTAAA-TCTAAAA
39763717 GTCTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.22
Consensus pattern (12 bp):
CTAAATCTAAAA
Found at i:39763762 original size:9 final size:9
Alignment explanation
Indices: 39763748--39763823 Score: 73
Period size: 9 Copynumber: 8.4 Consensus size: 9
39763738 GTAGTGATTC
39763748 AATTCGGTT
1 AATTCGGTT
*
39763757 AATTCGGGT
1 AATTCGGTT
* *
39763766 AATTGGGGT
1 AATTCGGTT
**
39763775 AATTTAGTT
1 AATTCGGTT
39763784 AATTCAGG-T
1 AATTC-GGTT
*
39763793 AATTCAGTT
1 AATTCGGTT
*
39763802 AATTCAGTT
1 AATTCGGTT
39763811 AATTCGGTT
1 AATTCGGTT
39763820 AATT
1 AATT
39763824 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
8 1 0.02
9 54 0.96
10 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39763784 original size:27 final size:27
Alignment explanation
Indices: 39763748--39763823 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
39763738 GTAGTGATTC
* **
39763748 AATTCGGTTAATTCGGGTAATTGGGGT
1 AATTCAGTTAATTCGGGTAATTCAGGT
* * *
39763775 AATTTAGTTAATTCAGGTAATTCAGTT
1 AATTCAGTTAATTCGGGTAATTCAGGT
*
39763802 AATTCAGTTAATTCGGTTAATT
1 AATTCAGTTAATTCGGGTAATT
39763824 TTTAACCAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (27 bp):
AATTCAGTTAATTCGGGTAATTCAGGT
Found at i:39766346 original size:13 final size:13
Alignment explanation
Indices: 39766328--39766358 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39766318 TGGAATCCAA
39766328 TTTATGCATTGAC
1 TTTATGCATTGAC
39766341 TTTATGCATTGAC
1 TTTATGCATTGAC
*
39766354 ATTAT
1 TTTAT
39766359 TGCACCATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (13 bp):
TTTATGCATTGAC
Found at i:39767908 original size:9 final size:9
Alignment explanation
Indices: 39767891--39767927 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
39767881 TGAGTTTTCG
39767891 AATTCGAAT
1 AATTCGAAT
*
39767900 AACTCGAAT
1 AATTCGAAT
39767909 AATTCGAAT
1 AATTCGAAT
39767918 AATTCGAAT
1 AATTCGAAT
39767927 A
1 A
39767928 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:39770903 original size:19 final size:21
Alignment explanation
Indices: 39770879--39770917 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
39770869 GGCTTACTGT
*
39770879 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
39770898 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
39770918 TTAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:39771139 original size:3 final size:3
Alignment explanation
Indices: 39771131--39771202 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
39771121 ACTAATTAAT
* * * *
39771131 TTA TTA TTA TTA TTA TTA TTTA TTA ATC CTA TTA TTA TT- TGTA CTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
39771177 TTA TTG TTA TTA TTA TT- TTCA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TT
39771203 TCTTCTTATC
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 3 0.05
3 47 0.85
4 5 0.09
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:39774410 original size:14 final size:14
Alignment explanation
Indices: 39774391--39774419 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39774381 GTGGTGTCCC
39774391 CTTTCTACCAGAAA
1 CTTTCTACCAGAAA
39774405 CTTTCTACCAGAAA
1 CTTTCTACCAGAAA
39774419 C
1 C
39774420 CAATGTTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (14 bp):
CTTTCTACCAGAAA
Found at i:39776897 original size:44 final size:45
Alignment explanation
Indices: 39776822--39777578 Score: 592
Period size: 44 Copynumber: 17.2 Consensus size: 45
39776812 TAGCTGGTCC
* *
39776822 TGTCTTCCTATATTGGT--AGGAAGTGGATCGAAGAAGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAGAAGCAGATCT
39776865 TGTCTTCCTATATTGGTGGCGGAA-TAGATCGAAGAAAGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAG-AAGCAGATCT
* * **
39776910 TGTCTTCCTATATTGGTAGC-GAAGTGGATCGAAGATTCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAGAAGCAGATCT
* * *
39776954 TGTCTTCCCATACTGGTGGC-GAAGTAGATCAAAGAAAGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAG-AAGCAGATCT
* * * * *
39776999 TGTCTTCATGTA-T--TGGCGTGAAGTAGATCAAAGATAGCAGGTCA
1 TGTCTTCCTATATTGGTGGCG-GAAGTAGATCGAAGA-AGCAGATCT
* * * *
39777043 TGTCTTCCTATATTGGT--AGGAAGTGGATCGAAGATGCAGATTT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAGAAGCAGATCT
* *
39777086 TATCTTTCC-ATACTGGTGGC-GAAGTAGATCGAAGAAAGCAGATCT
1 TGTC-TTCCTATATTGGTGGCGGAAGTAGATCGAAG-AAGCAGATCT
* * * * *
39777131 TATCTT-C-AT-GTGTTGGCGTGAAGTAGATCGAAAATAGCAGGTCT
1 TGTCTTCCTATATTGGTGGCG-GAAGTAGATCGAAGA-AGCAGATCT
* * * *
39777175 TGTCTTCCTATATTGGT--AGGAAGTGGATCAAAGATGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAGAAGCAGATCT
* *
39777218 TGTCTTCCCATACTGGTGGC-GAAGTAGATCGAAGAAAGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAG-AAGCAGATCT
* * * * * *
39777263 TGTCTTCATGTA-T--TGGCGTGAAGTAGATCAAAGATAACAGGTCC
1 TGTCTTCCTATATTGGTGGCG-GAAGTAGATCGAAGA-AGCAGATCT
* * * *
39777307 TATCTTCCTATATTGGT--AGGAAGTGGATCGAAGATGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAGAAGCAGATCT
* * *
39777350 TATCTTCCCATACTGGTGGC-GAAGTAGATCGAAGAAAGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAG-AAGCAGATCT
* * * * *
39777395 TGTCTT--TATGTAT--TGGCATGAAGTAGATCGAAAATAGCAGGTCC
1 TGTCTTCCTATAT-TGGTGGC-GGAAGTAGATCGAAGA-AGCAGATCT
* * * *
39777439 TGTCTTCCTATATTGGT--AGGAAGTGGATCGAAGATGCAAATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAGAAGCAGATCT
* *
39777482 TGTCTTCCCATACTGGTGGC-GAAGTAGATCGAAGAAAGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAG-AAGCAGATCT
* * *
39777527 TGTCTT-ATGTATTGGT-G-TGAAGTAGATCGAAGATAGCAGATCT
1 TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAGA-AGCAGATCT
*
39777570 TGCCTTCCT
1 TGTCTTCCT
39777579 GCACCGACAG
Statistics
Matches: 565, Mismatches: 102, Indels: 93
0.74 0.13 0.12
Matches are distributed among these distances:
42 19 0.03
43 132 0.23
44 278 0.49
45 124 0.22
46 6 0.01
47 6 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
TGTCTTCCTATATTGGTGGCGGAAGTAGATCGAAGAAGCAGATCT
Found at i:39777602 original size:132 final size:132
Alignment explanation
Indices: 39776822--39777578 Score: 1155
Period size: 132 Copynumber: 5.7 Consensus size: 132
39776812 TAGCTGGTCC
* * * * * *
39776822 TGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG-AAGCAGATCTTGTCTTCCTATATTGGTGGC
1 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA-T--TGGC
* * *
39776885 G-GAA-TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATTC
63 GTGAAGTAGATCGAAGATAGCAGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGC
39776948 AGATCT
127 AGATCT
*
39776954 TGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* *
39777019 AAGTAGATCAAAGATAGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
66 AAGTAGATCGAAGATAGCAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
*
39777084 TT
131 CT
* * * *
39777086 TATCTTTCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTGTTGGCGTG
1 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* *
39777151 AAGTAGATCGAAAATAGCAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
66 AAGTAGATCGAAGATAGCAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
39777216 CT
131 CT
39777218 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* * * *
39777283 AAGTAGATCAAAGATAACAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
66 AAGTAGATCGAAGATAGCAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
39777348 CT
131 CT
* * *
39777350 TATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTTATGTATTGGCATG
1 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* * *
39777415 AAGTAGATCGAAAATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAAAT
66 AAGTAGATCGAAGATAGCAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
39777480 CT
131 CT
*
39777482 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT-ATGTATTGGTGTG
1 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* *
39777546 AAGTAGATCGAAGATAGCAGATCTTGCCTTCCT
66 AAGTAGATCGAAGATAGCAGGTCTTGTCTTCCT
39777579 GCACCGACAG
Statistics
Matches: 573, Mismatches: 48, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
131 45 0.08
132 459 0.80
133 49 0.09
134 20 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
AAGTAGATCGAAGATAGCAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
CT
Found at i:39777764 original size:44 final size:44
Alignment explanation
Indices: 39777699--39777904 Score: 238
Period size: 44 Copynumber: 4.7 Consensus size: 44
39777689 TGACCTCAAC
* *
39777699 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTTTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
39777743 CCTATCTCCCTGGTCAACAGTGGAATAGGGTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
39777787 TCTATCTCCCTGGGCAGTAGTGGAAT-GGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGG-TTGAAGATTGTGA-AT
* * *
39777831 CCTATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
39777875 CCTATCTCCCTGAGT-AGCACTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
39777905 GAAAAATANN
Statistics
Matches: 135, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
43 3 0.02
44 128 0.95
45 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:39778398 original size:88 final size:88
Alignment explanation
Indices: 39778081--39778384 Score: 518
Period size: 88 Copynumber: 3.5 Consensus size: 88
39778071 TAGATCGAAG
* * * *
39778081 ATAGTAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACATCAGCCTTGCCTCCTTT
1 ATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
39778146 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
*
39778169 ATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTG
1 ATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
39778234 GGTTGCAGCGGAGCATGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
*
39778257 ATAGTGGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
* *
39778322 GGTTACAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
*
39778345 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGAT
1 ATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGAT
39778385 TGATGACCTC
Statistics
Matches: 203, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 203 1.00
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (88 bp):
ATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGCTAAAA
Found at i:39778464 original size:44 final size:44
Alignment explanation
Indices: 39778398--39778603 Score: 222
Period size: 44 Copynumber: 4.7 Consensus size: 44
39778388 TGACCTCAGC
* *
39778398 CCTATCTCCCTGGTCAGTAGTGGAATAGGTTAAAGATTATGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTATGAAT
*
39778442 CCTATCTCCCTGGTCAGCAGTGGAATAGGGTGAAGATTGA-GAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT-ATGAAT
* * * * *
39778486 GCTATCTCCCTGGGCAGTAGTGGAAT-GGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGG-TTGAAGATTATGA-AT
* * * *
39778530 CATATTTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCATGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTATGAAT
* *
39778574 CCTATCTCCCTGAGT-AGCACTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
39778604 GGAAAATAGC
Statistics
Matches: 133, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
43 3 0.02
44 124 0.93
45 6 0.05
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTATGAAT
Found at i:39779042 original size:23 final size:23
Alignment explanation
Indices: 39779012--39779069 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
39779002 AGATATGATA
39779012 TGTAATCTTAGAAGATGTGATTT
1 TGTAATCTTAGAAGATGTGATTT
39779035 TGTAATCTTAGAAGATGTGATTT
1 TGTAATCTTAGAAGATGTGATTT
39779058 TGTAATCTTAGA
1 TGTAATCTTAGA
39779070 GATTTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (23 bp):
TGTAATCTTAGAAGATGTGATTT
Found at i:39779265 original size:18 final size:21
Alignment explanation
Indices: 39779241--39779279 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
39779231 TGGCTTACTG
*
39779241 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
39779260 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
39779280 TTAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:39779500 original size:3 final size:3
Alignment explanation
Indices: 39779492--39779563 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
39779482 ACTAATTAAT
* * * *
39779492 TTA TTA TTA TTA TTA TTA TTTA TTA ATC CTA TTA TTA TT- TGTA CTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
39779538 TTA TTG TTA TTA TTA TT- TTCA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TT
39779564 TCTTCTTATC
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 3 0.05
3 47 0.85
4 5 0.09
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:39783181 original size:3 final size:3
Alignment explanation
Indices: 39783175--39783224 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
39783165 TTATTATTAT
39783175 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
39783223 TA
1 TA
39783225 TTAAGATGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:39786324 original size:27 final size:27
Alignment explanation
Indices: 39786286--39786362 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
39786276 TAGTATTGGC
39786286 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
39786313 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
39786340 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
39786363 GCCAGGCCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:39786595 original size:19 final size:19
Alignment explanation
Indices: 39786573--39786610 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39786563 AATTTAATTT
*
39786573 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
39786592 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
39786611 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:39786903 original size:27 final size:27
Alignment explanation
Indices: 39786871--39786945 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
39786861 AAAATATTGC
* * *
39786871 AATTTTATATGAATATTGTAATTTTGT
1 AATTTTGTATGAATATTGTAATATTAT
39786898 AATTTTGTATGAATATTGTAATATTAT
1 AATTTTGTATGAATATTGTAATATTAT
39786925 AATTTTGTATGAATATT-TAAT
1 AATTTTGTATGAATATTGTAAT
39786946 GTCGGTATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 4 0.09
27 41 0.91
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (27 bp):
AATTTTGTATGAATATTGTAATATTAT
Found at i:39787063 original size:19 final size:19
Alignment explanation
Indices: 39787041--39787078 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39787031 TATAAATTTA
*
39787041 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
39787060 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
39787079 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:39787644 original size:10 final size:11
Alignment explanation
Indices: 39787616--39787650 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
39787606 CCGTATTTTT
39787616 TTAAAAAAATTA
1 TTAAAAAAA-TA
39787628 TTAAAAAAATA
1 TTAAAAAAATA
39787639 TT-AAAAAATA
1 TTAAAAAAATA
39787649 TT
1 TT
39787651 TTATTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 4 0.17
12 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:39793827 original size:11 final size:11
Alignment explanation
Indices: 39793811--39793837 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
39793801 GCTTAAGCTT
39793811 AAATTGTATCC
1 AAATTGTATCC
39793822 AAATTGTATCC
1 AAATTGTATCC
39793833 AAATT
1 AAATT
39793838 AAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:39796302 original size:13 final size:13
Alignment explanation
Indices: 39796281--39796318 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
39796271 TTCAGTAAAA
39796281 ATATATTATTTTT
1 ATATATTATTTTT
*
39796294 ATATTTTATTATTT
1 ATATATTATT-TTT
39796308 -TATATTATTTT
1 ATATATTATTTT
39796319 AGTGTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 17 0.77
14 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATATATTATTTTT
Found at i:39796310 original size:15 final size:16
Alignment explanation
Indices: 39796284--39796319 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
39796274 AGTAAAAATA
39796284 TATTATTTTTATATTT
1 TATTATTTTTATATTT
39796300 TATTATTTTATATTATTT
1 TATTATTTT-TA-TATTT
39796318 TA
1 TA
39796320 GTGTATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTATTTTTATATTT
Found at i:39796473 original size:158 final size:150
Alignment explanation
Indices: 39796047--39796820 Score: 598
Period size: 158 Copynumber: 4.9 Consensus size: 150
39796037 GCAAGTTGAA
* *
39796047 AAAAAAGTTAGTAAAAACCTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAAAACTCTTACTTC-GCCATTTGTTCGTATTTTTTT-TCCG-ATTTTATTA
* *
39796112 CTTTAAAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATGTTTGAAA
63 TTTTAAAAAATATCGTAATTTCTAATTTTATTATTTTACATTATTTCAGTGCATAATGTTTGAAA
* *
39796177 TTTATTAATTTAGTGTGTTTTTT
128 TTTATTAATTTAGTCTGATTTTT
* * * * * *
39796200 AAATTAATTTGGTGTAAGAAAAAAAC-CTTA-TCCCTGCC-TTTGCTCGTATTATTTTCCCGATT
1 AAA--AA-AT--T-T-AGTAAAAAACTCTTACT-TC-GCCATTTGTTCGTATTTTTTTTCCGA-T
* * * * * * *
39796262 TTTATTACTTTCAGTAAAAATAT-ATTATTTTTATATTTTATTATTTTATATTATTTTAGTGTAT
56 TTTATTA-TTTTA--AAAAATATCGTAATTTCTA-ATTTTATTATTTTACATTATTTCAGTGCAT
** *
39796326 TTTGTTTGAAATTTTTGTATTAA-TTATTTCTGAATTTTT
117 AATGTTTGAAA---TT-TATTAATTTA-GTCTG-ATTTTT
* * *
39796365 AAAAAATTTAGTAATACACTCTTACTTCGACCATTTGTTCGTATTTTTTTATCCGCATTATATTA
1 AAAAAATTTAGTAAAAAACTCTTACTTCG-CCATTTGTTCGTATTTTTTT-TCCG-ATTTTATTA
*
39796430 TTTTAAAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATGTTTGAAA
63 TTTTAAAAAATATCGTAATTTCTAATTTTATTATTTTACATTATTTCAGTGCATAATGTTTGAAA
* *
39796495 TTTATTAATTTAGTGTGTTTTTT
128 TTTATTAATTTAGTCTGATTTTT
* * * *
39796518 AAATTAATTTGGTGTAAGAAAAAAAC-CTTA-TTCCTGCC-TTTGCTCGTATTATTTTTCCGATT
1 AAA--AA-AT--T-T-AGTAAAAAACTCTTACTT-C-GCCATTTGTTCGTATTTTTTTTCCGA-T
* ** * *
39796580 TTTATTACTTTCAATAAAAATATATTATTTTCGT-ATTTTATTATTTTATATTATTTCAGTGCAT
56 TTTATTA-TTT-TA-AAAAATATCGTAATTTC-TAATTTTATTATTTTACATTATTTCAGTGCAT
** * *
39796644 TTTGTTGGAAACTTTTGTATTAA-TTATTTCTGAATTTTT
117 AATGTTTGAAA---TT-TATTAATTTA-GTCTG-ATTTTT
* * *
39796683 AAAAAATTTAGTAATACACTCTTACTTCGGCCATTTGTTCGTAATTTTTTATT-CGCATTATATT
1 AAAAAATTTAGTAAAAAACTCTTACTTC-GCCATTTGTTCGT-ATTTTTT-TTCCG-ATTTTATT
* *
39796747 ATTTTAAAAAATTTCGTAATTTCTAATTTTATTATTTTACATTATTTCAGTGCATAATATTTGAA
62 ATTTTAAAAAATATCGTAATTTCTAATTTTATTATTTTACATTATTTCAGTGCATAATGTTTGAA
*
39796812 ATTTGTTAA
127 ATTTATTAA
39796821 ATATACAATC
Statistics
Matches: 484, Mismatches: 83, Indels: 107
0.72 0.12 0.16
Matches are distributed among these distances:
153 11 0.02
154 14 0.03
155 11 0.02
156 3 0.01
157 23 0.05
158 148 0.31
159 50 0.10
160 144 0.30
161 26 0.05
162 6 0.01
163 14 0.03
164 18 0.04
165 16 0.03
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (150 bp):
AAAAAATTTAGTAAAAAACTCTTACTTCGCCATTTGTTCGTATTTTTTTTCCGATTTTATTATTT
TAAAAAATATCGTAATTTCTAATTTTATTATTTTACATTATTTCAGTGCATAATGTTTGAAATTT
ATTAATTTAGTCTGATTTTT
Found at i:39796631 original size:318 final size:318
Alignment explanation
Indices: 39796047--39796820 Score: 1334
Period size: 318 Copynumber: 2.4 Consensus size: 318
39796037 GCAAGTTGAA
* * * * *
39796047 AAAAAAGTTAGTAA-AAACCTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATT
1 AAAAAATTTAGTAATACA-CTCTTACTTCGGCCATTTGTTCGTATTTTTTTATCCGCATTATATT
*
39796111 ACTTTAAAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATGTTTGAA
65 ATTTTAAAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATGTTTGAA
39796176 ATTTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCTTATCCCTGCCTTT
130 ATTTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCTTATCCCTGCCTTT
* *
39796241 GCTCGTATTATTTTCCCGATTTTTATTACTTTCAGTAAAAATATATTATTTTTATATTTTATTAT
195 GCTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATATTATTTTCATATTTTATTAT
* * * *
39796306 TTTATATTATTTTAGTGTATTTTGTTTGAAATTTTTGTATTAATTATTTCTGAATTTTT
260 TTTATATTATTTCAGTGCATTTTGTTGGAAACTTTTGTATTAATTATTTCTGAATTTTT
*
39796365 AAAAAATTTAGTAATACACTCTTACTTCGACCATTTGTTCGTATTTTTTTATCCGCATTATATTA
1 AAAAAATTTAGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTATCCGCATTATATTA
39796430 TTTTAAAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATGTTTGAAA
66 TTTTAAAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATGTTTGAAA
*
39796495 TTTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCTTATTCCTGCCTTTG
131 TTTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCTTATCCCTGCCTTTG
* *
39796560 CTCGTATTATTTTTCCGATTTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATT
196 CTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATATTATTTTCATATTTTATTATT
39796625 TTATATTATTTCAGTGCATTTTGTTGGAAACTTTTGTATTAATTATTTCTGAATTTTT
261 TTATATTATTTCAGTGCATTTTGTTGGAAACTTTTGTATTAATTATTTCTGAATTTTT
* *
39796683 AAAAAATTTAGTAATACACTCTTACTTCGGCCATTTGTTCGTAATTTTTTATTCGCATTATATTA
1 AAAAAATTTAGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTATCCGCATTATATTA
* * *
39796748 TTTTAAAAAATTTCGTAATTTCTAATTTTATTATTTTACATTATTTCAGTGCATAATATTTGAAA
66 TTTTAAAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATGTTTGAAA
*
39796813 TTTGTTAA
131 TTTATTAA
39796821 ATATACAATC
Statistics
Matches: 432, Mismatches: 23, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
318 430 1.00
319 2 0.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (318 bp):
AAAAAATTTAGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTATCCGCATTATATTA
TTTTAAAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATGTTTGAAA
TTTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCTTATCCCTGCCTTTG
CTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATATTATTTTCATATTTTATTATT
TTATATTATTTCAGTGCATTTTGTTGGAAACTTTTGTATTAATTATTTCTGAATTTTT
Found at i:39797162 original size:5 final size:5
Alignment explanation
Indices: 39797148--39797334 Score: 56
Period size: 5 Copynumber: 38.8 Consensus size: 5
39797138 TAAAAATTAC
* * * ** *
39797148 CTTTT TTTTT CTTTT -TTTT CATTC CTTCC CTCTT CTTCTT C-TTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTTTT CTTTT
* * * * *
39797197 -TTTCT CTTCT CTTCTC CTTTC CTTTT CTTTC CTTCT -TTTT C-TTT CTTTT
1 CTTT-T CTTTT CTT-TT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
* * * * * * * * *
39797246 -TCTT CTTCT CCTTT C-CTT CTTTT -TCTTT CTTTC CTCTC CTTTC CTTTC
1 CTTTT CTTTT CTTTT CTTTT CTTTT CT-TTT CTTTT CTTTT CTTTT CTTTT
*
39797294 CTTTT CTTTC CTTTT C-TTT C-TTT C-TTT C-TTT CTTCTT CTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTTT
39797335 CCCTCTCATT
Statistics
Matches: 137, Mismatches: 31, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
4 40 0.29
5 83 0.61
6 14 0.10
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (5 bp):
CTTTT
Found at i:39797193 original size:10 final size:10
Alignment explanation
Indices: 39797180--39797335 Score: 75
Period size: 10 Copynumber: 15.3 Consensus size: 10
39797170 TCCTTCCCTC
39797180 TTCTTCTTCT
1 TTCTTCTTCT
39797190 TTCTT-TT-T
1 TTCTTCTTCT
39797198 TTC-TCTTC-
1 TTCTTCTTCT
*
39797206 -TCTTCTCCT
1 TTCTTCTTCT
39797215 TTCCTT-TTCT
1 TT-CTTCTTCT
39797225 TTCCTTCTT-T
1 TT-CTTCTTCT
39797235 TTCTTTCTT-T
1 TTC-TTCTTCT
39797245 TTCTTCTTCT
1 TTCTTCTTCT
*
39797255 CCTT-TCCTTCT
1 --TTCTTCTTCT
39797266 TT-TTCTTTCT
1 TTCTTC-TTCT
39797276 TTCCTCTCCTTTCCT
1 TT-CT-T-C-TT-CT
39797291 TTCCTT-TTCT
1 TT-CTTCTTCT
39797301 TTCCTT-TTCT
1 TT-CTTCTTCT
39797311 TTCTTTCTTTCT
1 TTC-TTC-TTCT
39797323 TTCTTCTTCT
1 TTCTTCTTCT
39797333 TTC
1 TTC
39797336 CCTCTCATTC
Statistics
Matches: 122, Mismatches: 4, Indels: 40
0.73 0.02 0.24
Matches are distributed among these distances:
7 3 0.02
8 10 0.08
9 13 0.11
10 57 0.47
11 16 0.13
12 10 0.08
13 1 0.01
14 5 0.04
15 7 0.06
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:39797232 original size:43 final size:43
Alignment explanation
Indices: 39797151--39797335 Score: 129
Period size: 43 Copynumber: 4.3 Consensus size: 43
39797141 AAATTACCTT
* * *
39797151 TTTTTTTCTTT-TTTTTCATTCCTTCCCTCTTC-TT-CTTCTTTC
1 TTTTTTTCTTTCTTCTTC--TCCTTTCCTTTTCTTTCCTTCTTTC
39797193 TTTTTTTCTCTTC-TCTTCTCCTTTCCTTTTCTTTCCTTCTTT-
1 TTTTTTTCT-TTCTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTC
*
39797235 TTCTTTCTT-TTTCTTCTTCTCCTTTCCTTCTT-TTTCTTTCTTTCC
1 TT-TTT-TTCTTTCTTCTTCTCCTTTCCTT-TTCTTTCCTTCTTT-C
* * * *
39797280 TCTCCTTTCCTTTC--CTT-TTCTTTCCTTTTCTTTCTTTCTTTC
1 T-T-TTTTTCTTTCTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTC
39797322 TTTCTTCTTCTTTC
1 TTT-TT-TTCTTTC
39797336 CCTCTCATTC
Statistics
Matches: 119, Mismatches: 9, Indels: 30
0.75 0.06 0.19
Matches are distributed among these distances:
41 14 0.12
42 26 0.22
43 62 0.52
44 7 0.06
45 2 0.02
46 8 0.07
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.69
Consensus pattern (43 bp):
TTTTTTTCTTTCTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTC
Done.