Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 128 of 135
Found at i:38982592 original size:21 final size:20
Alignment explanation
Indices: 38982527--38982583 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
38982517 ATAAATTATA
38982527 AATTTTTATAAAA--ATTTTG
1 AATTTTTA-AAAATTATTTTG
38982546 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
*
38982565 AATTTTTGAAAATTATTTT
1 AATTTTTAAAAATTATTTT
38982584 TTATTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 10 0.29
20 15 0.44
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:38983327 original size:7 final size:7
Alignment explanation
Indices: 38983315--38983342 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
38983305 AAAAATGATG
38983315 AATTATA
1 AATTATA
38983322 AATTATA
1 AATTATA
38983329 AATTATA
1 AATTATA
38983336 AATTATA
1 AATTATA
38983343 TTAATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTATA
Found at i:38990892 original size:6 final size:6
Alignment explanation
Indices: 38990875--38990915 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
38990865 TTTTCTTGGT
*
38990875 TAGGAA TGGGAA TAGGAA TAGGAA TAGGAA TAGGAA TAGGA
1 TAGGAA TAGGAA TAGGAA TAGGAA TAGGAA TAGGAA TAGGA
38990916 TTTGGAATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (6 bp):
TAGGAA
Found at i:38993944 original size:22 final size:22
Alignment explanation
Indices: 38993916--38993969 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
38993906 CTCGATCCAA
38993916 TTATTTTGTTGCTATTTTGCTG
1 TTATTTTGTTGCTATTTTGCTG
* *
38993938 TTATTTTGTTGTTGTTTTGCTG
1 TTATTTTGTTGCTATTTTGCTG
*
38993960 TCATTTTGTT
1 TTATTTTGTT
38993970 ATTATATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (22 bp):
TTATTTTGTTGCTATTTTGCTG
Found at i:38993950 original size:11 final size:11
Alignment explanation
Indices: 38993916--38993974 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
38993906 CTCGATCCAA
38993916 TTATTTTGTTG
1 TTATTTTGTTG
* *
38993927 CTATTTTGCTG
1 TTATTTTGTTG
38993938 TTATTTTGTTG
1 TTATTTTGTTG
* *
38993949 TTGTTTTGCTG
1 TTATTTTGTTG
* *
38993960 TCATTTTGTTA
1 TTATTTTGTTG
38993971 TTAT
1 TTAT
38993975 ATCGCTACTA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.66
Consensus pattern (11 bp):
TTATTTTGTTG
Found at i:39001568 original size:29 final size:28
Alignment explanation
Indices: 39001527--39001581 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
39001517 CAAGTGTAAC
*
39001527 TAAAAAAACAATATAAAA-ATTAAATTTT
1 TAAAAAAAAAATA-AAAAGATTAAATTTT
39001555 TAAAAATAAAAATAAAAAGATTAAATT
1 TAAAAA-AAAAATAAAAAGATTAAATT
39001582 CAAATTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
TAAAAAAAAAATAAAAAGATTAAATTTT
Found at i:39009398 original size:30 final size:30
Alignment explanation
Indices: 39009362--39009419 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39009352 AAAAATAAAA
*
39009362 TATAGAAAAATATTAAAATTTATGAAAACG
1 TATAGAAAAATATTAAAAATTATGAAAACG
* * *
39009392 TATAGAATAATTTTAAAAATTATTAAAA
1 TATAGAAAAATATTAAAAATTATGAAAA
39009420 TATAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (30 bp):
TATAGAAAAATATTAAAAATTATGAAAACG
Found at i:39009436 original size:18 final size:17
Alignment explanation
Indices: 39009405--39009438 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39009395 AGAATAATTT
*
39009405 TAAAAATTATTAAAATA
1 TAAAAATTACTAAAATA
39009422 TAAAAATTTACTAAAAT
1 TAAAAA-TTACTAAAAT
39009439 TTATTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATTACTAAAATA
Found at i:39009522 original size:19 final size:18
Alignment explanation
Indices: 39009464--39009522 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
39009454 GACATTAAAT
*
39009464 AAAA-TTTTAAAATATTA
1 AAAATTTTTAAAATATAA
* *
39009481 AAAATTTATAAAAAAATAGA
1 AAAATTT-TTAAAATATA-A
*
39009501 AAACTTTTTAAAATATAA
1 AAAATTTTTAAAATATAA
39009519 AAAA
1 AAAA
39009523 ATATTAAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 4 0.12
18 6 0.19
19 15 0.47
20 7 0.22
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATTTTTAAAATATAA
Found at i:39009573 original size:104 final size:104
Alignment explanation
Indices: 39009368--39009574 Score: 224
Period size: 104 Copynumber: 2.0 Consensus size: 104
39009358 AAAATATAGA
** **
39009368 AAAATATTAAAATTTATGAAAACGTATAGAATAATTTTAAAAATTATTAAAATATAAAAATTTAC
1 AAAATATTAAAATTTATGAAAACAAATAGAATAATTTTAAAAATTAAAAAAATATAAAAATTTAC
* * *
39009433 TAAAATTTATTATGAAATATAGACATTAAATAAAATTTT
66 TAAAATTTATTATGAAAGATAGAAAATAAATAAAATTTT
* * *
39009472 AAAATATTAAAAATTTAT-AAAA-AAATAGAA-AACTTTTTAAAATATAAAAAAATATTAAATTT
1 AAAATATT-AAAATTTATGAAAACAAATAGAATAA-TTTTAAAAAT-TAAAAAAATATAAAAATT
* * * *
39009534 TATTATAATTTATTATTAAAGATA-AAAATATATAGAAATTT
63 TACTAAAATTTATTATGAAAGATAGAAAATAAATA-AAATTT
39009575 ATTAAAAAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
102 2 0.02
103 22 0.26
104 52 0.61
105 9 0.11
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (104 bp):
AAAATATTAAAATTTATGAAAACAAATAGAATAATTTTAAAAATTAAAAAAATATAAAAATTTAC
TAAAATTTATTATGAAAGATAGAAAATAAATAAAATTTT
Found at i:39012785 original size:27 final size:27
Alignment explanation
Indices: 39012746--39012801 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
39012736 CAAAAAAAAG
* *
39012746 TTAATTAGTAAAATATGTTATTTTTTT
1 TTAATTAGAAAAATAAGTTATTTTTTT
*
39012773 TTAATTTAGAAAAATAAGTTGTTTTTTT
1 TTAA-TTAGAAAAATAAGTTATTTTTTT
39012801 T
1 T
39012802 AGAGAGAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (27 bp):
TTAATTAGAAAAATAAGTTATTTTTTT
Found at i:39014116 original size:12 final size:12
Alignment explanation
Indices: 39014094--39014123 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
39014084 CCCCAAACCT
39014094 TTTTCTTTCTTTC
1 TTTT-TTTCTTTC
39014107 TTTTTTTCTTTC
1 TTTTTTTCTTTC
39014119 TTTTT
1 TTTTT
39014124 CCCTTGCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:39015116 original size:3 final size:3
Alignment explanation
Indices: 39015104--39015150 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
39015094 TATTCTATTC
39015104 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39015151 GGGATGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39017613 original size:23 final size:23
Alignment explanation
Indices: 39017587--39017630 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
39017577 TATCTTGGAT
* *
39017587 TTGGTCTTTCACTTTTATTTTGA
1 TTGGTCGTTCACTTCTATTTTGA
*
39017610 TTGGTCGTTGACTTCTATTTT
1 TTGGTCGTTCACTTCTATTTT
39017631 AAACGACTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.14, G:0.16, T:0.59
Consensus pattern (23 bp):
TTGGTCGTTCACTTCTATTTTGA
Found at i:39023725 original size:17 final size:17
Alignment explanation
Indices: 39023705--39023737 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39023695 AATATTTGAT
39023705 TTTTTA-ATTCTTTTAAC
1 TTTTTATATT-TTTTAAC
39023722 TTTTTATATTTTTTAA
1 TTTTTATATTTTTTAA
39023738 TAATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTATATTTTTTAAC
Found at i:39024187 original size:31 final size:31
Alignment explanation
Indices: 39024152--39024214 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
39024142 AAATTTCAAC
*
39024152 ATTCGAAAAGTACAAGGATTAAAATTGATCA
1 ATTCGAAAAGTACAAGGACTAAAATTGATCA
*
39024183 ATTCGAAAAGTACAAGGACTCAAATTGATCA
1 ATTCGAAAAGTACAAGGACTAAAATTGATCA
39024214 A
1 A
39024215 ATAAAAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.24
Consensus pattern (31 bp):
ATTCGAAAAGTACAAGGACTAAAATTGATCA
Found at i:39024383 original size:3 final size:3
Alignment explanation
Indices: 39024377--39024409 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39024367 AACTTAAAAT
39024377 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39024410 TTTTGGTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39026892 original size:26 final size:29
Alignment explanation
Indices: 39026854--39026909 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
39026844 TATGATATAT
*
39026854 CAAATACACTT-AAAA-ATATTAAAACAA
1 CAAATACAATTAAAAACATATTAAAACAA
39026881 CAAATA-AATTAAAAACGATATTAAAACAA
1 CAAATACAATTAAAAAC-ATATTAAAACAA
39026910 TTCGTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 3 0.12
27 10 0.40
29 12 0.48
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21
Consensus pattern (29 bp):
CAAATACAATTAAAAACATATTAAAACAA
Found at i:39028821 original size:21 final size:21
Alignment explanation
Indices: 39028797--39028837 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39028787 GTTGCTACCT
*
39028797 TTTCCACCACTTCCGCCACCG
1 TTTCCACCACTTCCACCACCG
*
39028818 TTTCCACCCCTTCCACCACC
1 TTTCCACCACTTCCACCACC
39028838 ATCTCTGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.56, G:0.05, T:0.24
Consensus pattern (21 bp):
TTTCCACCACTTCCACCACCG
Found at i:39032702 original size:15 final size:16
Alignment explanation
Indices: 39032677--39032709 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
39032667 TTTCAGATTA
39032677 ATTTTTATTTAAAAAT
1 ATTTTTATTTAAAAAT
39032693 ATTTTT-TTTAAAAAT
1 ATTTTTATTTAAAAAT
39032708 AT
1 AT
39032710 GATACACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTATTTAAAAAT
Found at i:39033207 original size:41 final size:41
Alignment explanation
Indices: 39033162--39033242 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
39033152 TCTTGAGTAT
39033162 CAAATGACTAATTGAGCATTAAATTCATAGTTCAATTTGAA
1 CAAATGACTAATTGAGCATTAAATTCATAGTTCAATTTGAA
39033203 CAAATGACTAATTGAGCATTAAATTCATAGTTCAATTTGA
1 CAAATGACTAATTGAGCATTAAATTCATAGTTCAATTTGA
39033243 GCTGGTCAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (41 bp):
CAAATGACTAATTGAGCATTAAATTCATAGTTCAATTTGAA
Found at i:39038763 original size:21 final size:19
Alignment explanation
Indices: 39038722--39038766 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
39038712 TCATGAAGTT
* *
39038722 AAAAATAAATTTTAATTTA
1 AAAAATAAATTATAATCTA
39038741 AAAAATAAATATAATAATCTA
1 AAAAATAAAT-T-ATAATCTA
39038762 AAAAA
1 AAAAA
39038767 AAGTTTCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 11 0.50
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATAAATTATAATCTA
Found at i:39038949 original size:17 final size:16
Alignment explanation
Indices: 39038923--39038972 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
39038913 TTACTATTTA
39038923 TAATAATATTAATAAT
1 TAATAATATTAATAAT
39038939 TAATAAATATTTAAT-AT
1 TAAT-AATA-TTAATAAT
39038956 TAATGAAT-TTAATAAT
1 TAAT-AATATTAATAAT
39038972 T
1 T
39038973 CTCAATGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.17
16 7 0.23
17 13 0.43
18 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TAATAATATTAATAAT
Found at i:39039220 original size:3 final size:3
Alignment explanation
Indices: 39039214--39039245 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39039204 CAATTTCAGC
39039214 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39039246 AACAGAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39042919 original size:29 final size:29
Alignment explanation
Indices: 39042864--39042924 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
39042854 TATAAATAGT
* * *
39042864 CATTCAACTATAAAAACTTTCATTTTAGG
1 CATTCAACGATAAAAACTTTCAATTTAAG
*
39042893 CATTCAA-GATAAAAAGTTTGCAATTTAAG
1 CATTCAACGATAAAAACTTT-CAATTTAAG
39042922 CAT
1 CAT
39042925 CCACGTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (29 bp):
CATTCAACGATAAAAACTTTCAATTTAAG
Found at i:39043467 original size:2 final size:2
Alignment explanation
Indices: 39043460--39043501 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
39043450 TGAAGAGATG
39043460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39043501 A
1 A
39043502 ATTAGTATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39048468 original size:24 final size:26
Alignment explanation
Indices: 39048436--39048483 Score: 82
Period size: 24 Copynumber: 1.9 Consensus size: 26
39048426 AATCCCCTAA
39048436 TTTTTTTAAAAAAA-T-ATTAAACTC
1 TTTTTTTAAAAAAATTAATTAAACTC
39048460 TTTTTTTAAAAAAATTAATTAAAC
1 TTTTTTTAAAAAAATTAATTAAAC
39048484 CCCAAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 14 0.64
25 1 0.05
26 7 0.32
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTTTTAAAAAAATTAATTAAACTC
Found at i:39050509 original size:6 final size:6
Alignment explanation
Indices: 39050498--39050535 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
39050488 CAATGAGAGA
39050498 GAGGGG GAGGGG GAGGGG GAGGGG GAGGGG GAGGGG GA
1 GAGGGG GAGGGG GAGGGG GAGGGG GAGGGG GAGGGG GA
39050536 TGCATGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.00, G:0.82, T:0.00
Consensus pattern (6 bp):
GAGGGG
Found at i:39056534 original size:20 final size:20
Alignment explanation
Indices: 39056509--39056547 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39056499 ATGTGCCATA
*
39056509 CACTCATTAATAATCTAATC
1 CACTCATTAACAATCTAATC
*
39056529 CACTCATTAGCAATCTAAT
1 CACTCATTAACAATCTAAT
39056548 GAAAGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (20 bp):
CACTCATTAACAATCTAATC
Found at i:39068690 original size:3 final size:3
Alignment explanation
Indices: 39068682--39068726 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
39068672 AGCCCTTTTG
39068682 TTC TTC TTCC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
39068727 ACTTCATCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:39068695 original size:15 final size:15
Alignment explanation
Indices: 39068675--39068720 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
39068665 CCCAATAAGC
*
39068675 CCTTTTGTTCTTCTT
1 CCTTTTCTTCTTCTT
39068690 CCTTTTCTTCTTCTT
1 CCTTTTCTTCTTCTT
39068705 -CTTCTTCTTCTTCTT
1 CCTT-TTCTTCTTCTT
39068720 C
1 C
39068721 TTCTTCACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 3 0.11
15 25 0.89
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (15 bp):
CCTTTTCTTCTTCTT
Found at i:39069485 original size:3 final size:3
Alignment explanation
Indices: 39069477--39069504 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39069467 CATGGAACCT
39069477 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
39069505 AAGCATAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:39072077 original size:13 final size:13
Alignment explanation
Indices: 39072059--39072086 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39072049 TTTCTTACGC
39072059 AATAACATATATA
1 AATAACATATATA
39072072 AATAACATATATA
1 AATAACATATATA
39072085 AA
1 AA
39072087 CATATGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAACATATATA
Found at i:39074316 original size:6 final size:6
Alignment explanation
Indices: 39074307--39074371 Score: 62
Period size: 6 Copynumber: 10.8 Consensus size: 6
39074297 TTAAGTTTAT
* ** *
39074307 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTTCTTA TTTAAA TTT-AC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTT-AAA TTTAAA TTTAAA
39074355 TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
39074372 TCAAATTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
5 8 0.17
6 32 0.68
7 6 0.13
8 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:39074316 original size:17 final size:17
Alignment explanation
Indices: 39074296--39074370 Score: 102
Period size: 17 Copynumber: 4.6 Consensus size: 17
39074286 TTAAATGGAT
*
39074296 TTTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
39074313 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
39074330 TTTAAATTT-TCTT--A
1 TTTAAATTTATTTTAAA
*
39074344 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
39074361 TTTAAATTTA
1 TTTAAATTTA
39074371 ATCAAATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 3 0.06
17 36 0.71
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:39075729 original size:23 final size:23
Alignment explanation
Indices: 39075654--39075790 Score: 152
Period size: 23 Copynumber: 6.0 Consensus size: 23
39075644 AAGTGCTGGG
* * *
39075654 GAAACTGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACAAAGTGC
* ** * *
39075677 -AATCAGTAGGCGTACATAGCGC
1 GAAACAGTAGGCACACAAAGTGC
*
39075699 -AAATCAGTAGGCACACGAAGTGC
1 GAAA-CAGTAGGCACACAAAGTGC
39075722 GAAACAGTAGGCACACAAAGTGC
1 GAAACAGTAGGCACACAAAGTGC
39075745 GAAACAGTAGGCACACAAAGTGC
1 GAAACAGTAGGCACACAAAGTGC
* *
39075768 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACAAAGTGC
39075791 TGAACGGTAA
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.18
23 76 0.79
24 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (23 bp):
GAAACAGTAGGCACACAAAGTGC
Found at i:39075782 original size:69 final size:67
Alignment explanation
Indices: 39075630--39075790 Score: 162
Period size: 69 Copynumber: 2.3 Consensus size: 67
39075620 CGAAGTACTT
* * * ** *
39075630 AACAGTAAGCACACAAGTGCTGGGGAAACTGTAAGCACACACAGTGCAATCAGTAGGCGTACATA
1 AACAGTAAGCACACAAGTGC---GGAAACAGTAAGCACACAAAGTGCAAACAGTAGGCACACAAA
39075695 GCGCA
63 GCGCA
* *
39075700 AATCAGTAGGCACACGAAGTGC-GAAACAGTAGGCACACAAAGTGCGAAACAGTAGGCACACAAA
1 AA-CAGTAAGCACAC-AAGTGCGGAAACAGTAAGCACACAAAGTGC-AAACAGTAGGCACACAAA
*
39075764 GTGCGA
63 GCGC-A
39075770 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACA-AGTGC
39075791 TGAACGGTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
68 21 0.28
69 33 0.43
70 5 0.07
71 11 0.14
72 6 0.08
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (67 bp):
AACAGTAAGCACACAAGTGCGGAAACAGTAAGCACACAAAGTGCAAACAGTAGGCACACAAAGCG
CA
Found at i:39075802 original size:23 final size:23
Alignment explanation
Indices: 39075630--39075790 Score: 139
Period size: 23 Copynumber: 6.9 Consensus size: 23
39075620 CGAAGTACTT
39075630 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
* *
39075656 AACTGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * ** * *
39075678 ATCAGTAGGCGTACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
39075700 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
39075724 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
39075747 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
39075770 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
39075791 TGAACGGTAA
Statistics
Matches: 114, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
22 17 0.15
23 76 0.67
24 3 0.03
26 13 0.11
27 5 0.04
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:39077649 original size:18 final size:18
Alignment explanation
Indices: 39077615--39077659 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
39077605 AATAATGGGT
39077615 TTAATAATAAATATAATA
1 TTAATAATAAATATAATA
*
39077633 TTAATGAT-AATATTAATA
1 TTAATAATAAATA-TAATA
39077651 --AATAATAAA
1 TTAATAATAAA
39077660 AAGAAAGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 5 0.22
17 6 0.26
18 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTAATAATAAATATAATA
Found at i:39078653 original size:59 final size:58
Alignment explanation
Indices: 39078590--39078904 Score: 433
Period size: 59 Copynumber: 5.4 Consensus size: 58
39078580 CTTGGACTGT
*
39078590 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACC-CGATTTCA
* * *
39078649 CCAAAAACTACCATTTTACCCCCAAACTTTTCAAAGTCCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAA-CCCGATTTCA
* *
39078708 CC-AAAACTACCATTTTACTCCCGAAA-TTTCCAAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTAC-CCCCAAACTTTCCAAAATCCCATTTTTAA-CCCGATTTCA
*
39078766 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCC-GATTTCA
* *
39078825 CC-AAAATTACCATTTTACCCCTCAAA-TTTCCTAAAATCTCATTTTTAACCCTGATTTTA
1 CCAAAAATTACCATTTTACCCC-CAAACTTTCC-AAAATCCCATTTTTAACCC-GATTTCA
39078884 CCAAAAATTA-CATTTTTACCC
1 CCAAAAATTACCA-TTTTACCC
39078905 TCGAAAGTTA
Statistics
Matches: 234, Mismatches: 13, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
58 80 0.34
59 137 0.59
60 17 0.07
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCGATTTCA
Found at i:39078806 original size:117 final size:116
Alignment explanation
Indices: 39078593--39078909 Score: 465
Period size: 117 Copynumber: 2.7 Consensus size: 116
39078583 GGACTGTCCA
* * *
39078593 AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAACT
1 AAAATTACCATTTTACCCCCAAA-TTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATT
* * *
39078658 ACCATTTTACCCCCAAACTTTTCAAAGTCCCATTTTTAACCCCGATTTCACC
65 ACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* *
39078710 AAAACTACCATTTTACTCCCGAAATTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTAC-CCCCAAATTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATT
*
39078775 ACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACC
65 ACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * *
39078827 AAAATTACCATTTTACCCCTCAAATTTCCTAAAATCTCATTTTTAACCCTGATTTTACCAAAAAT
1 AAAATTACCATTTTACCCC-CAAATTTCC-AAAATCCCATTTTTAACCCCGATTTCACCAAAAAT
*
39078892 TA-CATTTTTACCCTCGAA
64 TACCA-TTTTACCCCCGAA
39078910 AGTTAAAAAT
Statistics
Matches: 182, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
116 3 0.02
117 127 0.70
118 52 0.29
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (116 bp):
AAAATTACCATTTTACCCCCAAATTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTA
CCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
Found at i:39078889 original size:29 final size:30
Alignment explanation
Indices: 39078746--39078905 Score: 111
Period size: 30 Copynumber: 5.4 Consensus size: 30
39078736 TCCAAAATCC
* *
39078746 CATTTTTAACCCCGATTTCACCAAAAATTA
1 CATTTTTAACCCTGATTTTACCAAAAATTA
* * * **
39078776 CCA-TTTTACCCCCGAACTTT-CC-AAAATCC
1 -CATTTTTAACCCTG-ATTTTACCAAAAATTA
*
39078805 CATTTTTAACCCTGATTTCACC-AAAATTA
1 CATTTTTAACCCTGATTTTACCAAAAATTA
* * * *
39078834 CCA-TTTTACCCCTCAAATTT-CCTAAAATCT-
1 -CATTTTTAACCCT-GATTTTACCAAAAAT-TA
39078864 CATTTTTAACCCTGATTTTACCAAAAATTA
1 CATTTTTAACCCTGATTTTACCAAAAATTA
39078894 CATTTTT-ACCCT
1 CATTTTTAACCCT
39078906 CGAAAGTTAA
Statistics
Matches: 100, Mismatches: 19, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
28 5 0.05
29 44 0.44
30 45 0.45
31 6 0.06
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (30 bp):
CATTTTTAACCCTGATTTTACCAAAAATTA
Found at i:39080429 original size:28 final size:30
Alignment explanation
Indices: 39080398--39080576 Score: 100
Period size: 30 Copynumber: 6.0 Consensus size: 30
39080388 AAATAGGATC
39080398 TTGGAAAGTTCAGAGGT-AAAATCTAA-TT
1 TTGGAAAGTTCAGAGGTCAAAATCTAATTT
* * * *
39080426 TTGGAAAATTTAGGGGTCAAAATGTAATTT
1 TTGGAAAGTTCAGAGGTCAAAATCTAATTT
* * *
39080456 TTAGAAAGTTTTA-AGG-CTAAAATGTAATTT
1 TTGGAAAG-TTCAGAGGTC-AAAATCTAATTT
** * *
39080486 TTAAAAAGTTTA-AGGGTCAAAATGTAATTT
1 TTGGAAAGTTCAGA-GGTCAAAATCTAATTT
* ** * * *
39080516 TTAGAAAGTTTTGGGGTTAAAATATAATTT
1 TTGGAAAGTTCAGAGGTCAAAATCTAATTT
* * *
39080546 TTAGAAAGTTTTAG-GGTCAAAATATAATTT
1 TTGGAAAG-TTCAGAGGTCAAAATCTAATTT
39080576 T
1 T
39080577 CAAAAGGTTT
Statistics
Matches: 128, Mismatches: 15, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
28 14 0.11
29 14 0.11
30 91 0.71
31 9 0.07
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (30 bp):
TTGGAAAGTTCAGAGGTCAAAATCTAATTT
Found at i:39080480 original size:30 final size:30
Alignment explanation
Indices: 39080434--39080635 Score: 273
Period size: 30 Copynumber: 6.7 Consensus size: 30
39080424 TTTTGGAAAA
*
39080434 TTTAGGGGTCAAAATGTAATTTTTAGAAAGT
1 TTTA-GGGTCAAAATATAATTTTTAGAAAGT
* * *
39080465 TTTAAGG-CTAAAATGTAATTTTTAAAAAGT
1 TTTAGGGTC-AAAATATAATTTTTAGAAAGT
* *
39080495 TTAAGGGTCAAAATGTAATTTTTAGAAAGT
1 TTTAGGGTCAAAATATAATTTTTAGAAAGT
* *
39080525 TTTGGGGTTAAAATATAATTTTTAGAAAGT
1 TTTAGGGTCAAAATATAATTTTTAGAAAGT
*
39080555 TTTAGGGTCAAAATATAATTTTCA-AAAGGT
1 TTTAGGGTCAAAATATAATTTTTAGAAA-GT
*
39080585 TTTAGTGTCAAAATATAATTTTTAGAAAGT
1 TTTAGGGTCAAAATATAATTTTTAGAAAGT
39080615 TTTAGGGTCAAAATATAATTT
1 TTTAGGGTCAAAATATAATTT
39080636 CTGAACAATC
Statistics
Matches: 152, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
29 4 0.03
30 140 0.92
31 8 0.05
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.40
Consensus pattern (30 bp):
TTTAGGGTCAAAATATAATTTTTAGAAAGT
Found at i:39080511 original size:60 final size:58
Alignment explanation
Indices: 39080411--39080635 Score: 256
Period size: 60 Copynumber: 3.8 Consensus size: 58
39080401 GAAAGTTCAG
* ** * *
39080411 AGGTAAAATCTAATTTTGGAAAA-TTTAGGGGTCAAAATGTAATTTTTAGAAAGTTTT
1 AGGTAAAATATAATTTTTAAAAAGTTTAAGGGTCAAAATATAATTTTTAGAAAGTTTT
* *
39080468 AAGGCTAAAATGTAATTTTTAAAAAGTTTAAGGGTCAAAATGTAATTTTTAGAAAGTTTT
1 -AGG-TAAAATATAATTTTTAAAAAGTTTAAGGGTCAAAATATAATTTTTAGAAAGTTTT
* * * *
39080528 GGGGTTAAAATATAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTCA-AAAGGTTTT
1 -AGG-TAAAATATAATTTTTAAAAAGTTTAAGGGTCAAAATATAATTTTTAGAAA-GTTTT
* *
39080588 AGTGTCAAAATATAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTT
1 AG-GT-AAAATATAATTTTTAAAAAGTTTAAGGGTCAAAATATAATTT
39080636 CTGAACAATC
Statistics
Matches: 149, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
58 3 0.02
59 22 0.15
60 124 0.83
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (58 bp):
AGGTAAAATATAATTTTTAAAAAGTTTAAGGGTCAAAATATAATTTTTAGAAAGTTTT
Found at i:39082533 original size:18 final size:18
Alignment explanation
Indices: 39082512--39082555 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
39082502 ACATTTATAA
*
39082512 TAATTTTAAAATTTACAT
1 TAATTTTAAAATTTAAAT
*
39082530 TAATTCT-AAATTTAAAT
1 TAATTTTAAAATTTAAAT
*
39082547 TAAATTTAA
1 TAATTTTAA
39082556 CTTTAACATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTTTAAAATTTAAAT
Found at i:39082560 original size:17 final size:16
Alignment explanation
Indices: 39082540--39082579 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
39082530 TAATTCTAAA
39082540 TTTAAATTAAATTTAAC
1 TTTAAA-TAAATTTAAC
*
39082557 TTTAACATAAATTTAAT
1 TTTAA-ATAAATTTAAC
39082574 TTTAAA
1 TTTAAA
39082580 ATGATTTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAATAAATTTAAC
Found at i:39083432 original size:54 final size:54
Alignment explanation
Indices: 39083350--39083635 Score: 527
Period size: 54 Copynumber: 5.3 Consensus size: 54
39083340 TTGGGATTGA
39083350 GATTGAAGGCAATGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
1 GATTGAAGGCAATGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
*
39083404 GATTGAAGGCAATGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTATGTTTGG
1 GATTGAAGGCAATGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
* *
39083458 GATTGAAGGCAATGGAGGAATGCTGGGCAATCCCGGAATTGTTGGTAGGTTTGG
1 GATTGAAGGCAATGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
*
39083512 GATTGAAGGCAACGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
1 GATTGAAGGCAATGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
*
39083566 GATTGAAGGCAATGGAGGTATTCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
1 GATTGAAGGCAATGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
39083620 GATTGAAGGCAATGGA
1 GATTGAAGGCAATGGA
39083636 AGTGGTGGAA
Statistics
Matches: 223, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 223 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (54 bp):
GATTGAAGGCAATGGAGGTATGCTGGGCAATCCGGGAATTGTTGGTAGGTTTGG
Found at i:39083450 original size:27 final size:27
Alignment explanation
Indices: 39083366--39083452 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
39083356 AGGCAATGGA
39083366 GGTATGCTGGGCAATCCGGGAATTGTT
1 GGTATGCTGGGCAATCCGGGAATTGTT
* * * ** * **
39083393 GGTAGGTTTGGG-ATTGAAGGCAA-TGGA
1 GGTATG-CTGGGCAAT-CCGGGAATTGTT
39083420 GGTATGCTGGGCAATCCGGGAATTGTT
1 GGTATGCTGGGCAATCCGGGAATTGTT
39083447 GGTATG
1 GGTATG
39083453 TTTGGGATTG
Statistics
Matches: 40, Mismatches: 16, Indels: 8
0.62 0.25 0.12
Matches are distributed among these distances:
26 8 0.20
27 24 0.60
28 8 0.20
ACGTcount: A:0.21, C:0.10, G:0.40, T:0.29
Consensus pattern (27 bp):
GGTATGCTGGGCAATCCGGGAATTGTT
Found at i:39084101 original size:30 final size:31
Alignment explanation
Indices: 39084027--39084101 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
39084017 CCCCAAAAAA
*
39084027 TTTAAGTACCAACTTAAAAAAAAGTGTCAAG
1 TTTAAGTACCAAATTAAAAAAAAGTGTCAAG
*
39084058 TTT-AGATATCAAATTAAAAAAAA-TGTCAAG
1 TTTAAG-TACCAAATTAAAAAAAAGTGTCAAG
39084088 TTTAAGTACCAAAT
1 TTTAAGTACCAAAT
39084102 ATTATATCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 19 0.49
31 20 0.51
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (31 bp):
TTTAAGTACCAAATTAAAAAAAAGTGTCAAG
Found at i:39085041 original size:20 final size:20
Alignment explanation
Indices: 39084998--39085041 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39084988 CAAAAAATTG
**
39084998 AATTTTTTTATAAAAATATC
1 AATTTTTTTATAAAAATAAA
39085018 AATTTTTTTATAAATAA-AAA
1 AATTTTTTTATAAA-AATAAA
39085038 AATT
1 AATT
39085042 ATATAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTTTTTATAAAAATAAA
Found at i:39085774 original size:25 final size:24
Alignment explanation
Indices: 39085717--39085772 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
39085707 TAAATAAATT
*
39085717 ATATTTTATTTATATTTTTAAATGA
1 ATATTTTACTTATATTTTTAAA-GA
39085742 ATATTTTACTTATACTTTTTAAA-A
1 ATATTTTACTTATA-TTTTTAAAGA
*
39085766 ATTTTTT
1 ATATTTT
39085773 TATACAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 7 0.25
25 13 0.46
26 8 0.29
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATTTTACTTATATTTTTAAAGA
Found at i:39090811 original size:13 final size:13
Alignment explanation
Indices: 39090793--39090817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39090783 ATTTAATCAT
39090793 GTATATATTTTTG
1 GTATATATTTTTG
39090806 GTATATATTTTT
1 GTATATATTTTT
39090818 AATAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
GTATATATTTTTG
Found at i:39091321 original size:93 final size:93
Alignment explanation
Indices: 39091214--39092168 Score: 1670
Period size: 93 Copynumber: 10.5 Consensus size: 93
39091204 TGGGATTCAA
* *
39091214 GGAAGTGCTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATTGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091279 AGGCAATGGAGGTGTGTTGGGCGAGCTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
39091307 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGA-T-----TGGGA-T----T-GA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091360 AGGCAATGGAGGTGTGTTGGGCGAGCTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
39091388 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091453 AGGCAATGGAGGTGTGTTGGGCGAGCTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
39091481 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091546 AGGCAATGGAGGTGTGTTGGGCGAGCTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
*
39091574 GGAAGTGGTGGTAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091639 AGGCAATGGAGGTGTGTTGGGCGAGCTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
39091667 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091732 AGGCAATGGAGGTGTGTTGGGCGAGC--
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
* *
39091758 --------TGG--GAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATCGGGATTGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091813 AGGCAATGGAGGTGTGTTGGGCGAGCTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
39091841 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091906 AGGCAATGGAGGTGTGTTGGGCGAGCTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
39091934 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
*
39091999 AGGCAATGGAGGTGTGTTGGGCGAGTTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
*
39092027 GGAAGTGGTGGTAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
*
39092092 AGGCAATGGAGGTGTGTTGGGTGAGCTG
66 AGGCAATGGAGGTGTGTTGGGCGAGCTG
39092120 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGA
39092169 TTGAAGGCAA
Statistics
Matches: 826, Mismatches: 12, Indels: 48
0.93 0.01 0.05
Matches are distributed among these distances:
81 149 0.18
82 2 0.00
83 3 0.00
86 1 0.00
87 10 0.01
88 1 0.00
91 3 0.00
92 2 0.00
93 655 0.79
ACGTcount: A:0.19, C:0.06, G:0.49, T:0.26
Consensus pattern (93 bp):
GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
AGGCAATGGAGGTGTGTTGGGCGAGCTG
Found at i:39091795 original size:360 final size:360
Alignment explanation
Indices: 39091214--39092212 Score: 1611
Period size: 360 Copynumber: 2.8 Consensus size: 360
39091204 TGGGATTCAA
* *
39091214 GGAAGTGCTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATTGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091279 AGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCT
66 AGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCT
39091344 TTGGGA-T-----TGGGA-T----T-GAAGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGT
131 TTGGGATTGGGACTGGGATTGGGATCGAAGGCAATGGAGGTGTGTTGGGCGAGC----------T
*
39091397 GGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGAAGGCAATGG
186 GG--GAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATTGAAGGCAATGG
39091462 AGGTGTGTTGGGCGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTG
249 AGGTGTGTTGGGCGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTG
39091527 GGACTGGGATTGGGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTG
314 GGACTGGGATTGGGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTG
*
39091574 GGAAGTGGTGGTAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
39091639 AGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCT
66 AGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCT
39091704 TTGGGATTGGGACTGGGATTGGGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGT
131 TTGGGATTGGGACTGGGATTGGGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGT
*
39091769 GGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATCGGGATTGAAGGCAATGGAGGTGTGTTGGG
196 GGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATTGAAGGCAATGGAGGTGTGTTGGG
39091834 CGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTG
261 CGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTG
39091899 GGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTG
326 GGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTG
39091934 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
1 GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
* *
39091999 AGGCAATGGAGGTGTGTTGGGCGAGTTGGGAAGTGGTGGTAGAAGTGGTGGAGTTGGTGGTAGCT
66 AGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCT
*
39092064 TTGGGATTGGGACTGGGATTGGGATCGAAGGCAATGGAGGTGTGTTGGGTGAGCTGGGAAGTGGT
131 TTGGGATTGGGACTGGGATTGGGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGT
* *
39092129 GGAAGAAGTGGTGG-AG--TT-GG--TGGTAGCTTTGGGATTGGGATTGAAGGCAATGGAGGTGT
196 GG-AG--TTGGTGGTAGCTTTGGGATTGGGA-C--TGGGATTGGGATTGAAGGCAATGGAGGTGT
*
39092188 GTTGGGCGAGCTGGGAGGTGGTGGA
255 GTTGGGCGAGCTGGGAAGTGGTGGA
39092213 GTTGGTGGTA
Statistics
Matches: 608, Mismatches: 13, Indels: 36
0.93 0.02 0.05
Matches are distributed among these distances:
357 4 0.01
358 1 0.00
359 2 0.00
360 552 0.91
361 3 0.00
362 5 0.01
363 6 0.01
366 5 0.01
367 1 0.00
371 1 0.00
372 28 0.05
ACGTcount: A:0.19, C:0.06, G:0.50, T:0.25
Consensus pattern (360 bp):
GGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATCGA
AGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCT
TTGGGATTGGGACTGGGATTGGGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTGGGAAGTGGT
GGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTGGGATTGAAGGCAATGGAGGTGTGTTGGG
CGAGCTGGGAAGTGGTGGAAGAAGTGGTGGAGTTGGTGGTAGCTTTGGGATTGGGACTGGGATTG
GGATCGAAGGCAATGGAGGTGTGTTGGGCGAGCTG
Found at i:39092320 original size:18 final size:19
Alignment explanation
Indices: 39092297--39092342 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
39092287 TGGGATTGAA
39092297 GGCAAT-GGAGGTATGCTG
1 GGCAATCGGAGGTATGCTG
39092315 GGCAATCCGGGAGGTATGCTG
1 GGCAAT-C-GGAGGTATGCTG
39092336 GGCAATC
1 GGCAATC
39092343 CCGGAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.24
20 1 0.04
21 18 0.72
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (19 bp):
GGCAATCGGAGGTATGCTG
Found at i:39092329 original size:21 final size:21
Alignment explanation
Indices: 39092303--39092343 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
39092293 TGAAGGCAAT
39092303 GGAGGTATGCTGGGCAATCCG
1 GGAGGTATGCTGGGCAATCCG
39092324 GGAGGTATGCTGGGCAATCC
1 GGAGGTATGCTGGGCAATCC
39092344 CGGAATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGGTATGCTGGGCAATCCG
Found at i:39092372 original size:75 final size:75
Alignment explanation
Indices: 39092249--39092401 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
39092239 TGAAGGCAAT
39092249 GGAGGTATGCTGGGCAATCCCGGAATTGTTGGTAGGTTTGGGATTGAAGGCAATGGAGGTATGCT
1 GGAGGTATGCTGGGCAATCCCGGAATTGTTGGTAGGTTTGGGATTGAAGGCAATGGAGGTATGCT
39092314 GGGCAATCCG
66 GGGCAATCCG
39092324 GGAGGTATGCTGGGCAATCCCGGAATTGTTGGTAGGTTTGGGATTGAAGGCAATGGAGGTATGCT
1 GGAGGTATGCTGGGCAATCCCGGAATTGTTGGTAGGTTTGGGATTGAAGGCAATGGAGGTATGCT
39092389 GGGCAATCCG
66 GGGCAATCCG
39092399 GGA
1 GGA
39092402 ATTGTTGGGA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.25
Consensus pattern (75 bp):
GGAGGTATGCTGGGCAATCCCGGAATTGTTGGTAGGTTTGGGATTGAAGGCAATGGAGGTATGCT
GGGCAATCCG
Found at i:39092403 original size:54 final size:54
Alignment explanation
Indices: 39092324--39092434 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
39092314 GGGCAATCCG
*
39092324 GGAGGTATGCTGGGCAATCCCGGAATTGTTGGTAGGTTTGGGATTGAAGGCAAT
1 GGAGGTATGCTGGGCAATCCCGGAATTGTTGGGAGGTTTGGGATTGAAGGCAAT
*
39092378 GGAGGTATGCTGGGCAATCCGGGAATTGTTGGGAGGTTTGGGATTGAAGGCAAT
1 GGAGGTATGCTGGGCAATCCCGGAATTGTTGGGAGGTTTGGGATTGAAGGCAAT
39092432 GGA
1 GGA
39092435 AGTGGTGGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.23, C:0.10, G:0.41, T:0.26
Consensus pattern (54 bp):
GGAGGTATGCTGGGCAATCCCGGAATTGTTGGGAGGTTTGGGATTGAAGGCAAT
Found at i:39093696 original size:18 final size:20
Alignment explanation
Indices: 39093659--39093701 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
39093649 AAATTATTAA
39093659 ATATTAAAACAATAATATAT
1 ATATTAAAACAATAATATAT
*
39093679 ATATTAAAACTATAATATA-
1 ATATTAAAACAATAATATAT
39093698 ATAT
1 ATAT
39093702 AAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATTAAAACAATAATATAT
Found at i:39096253 original size:20 final size:19
Alignment explanation
Indices: 39096207--39096244 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
39096197 GAACAAAACT
39096207 ATAAAAAATAGTATAAATG
1 ATAAAAAATAGTATAAATG
39096226 ATACAAAAACTA-TATAAAT
1 ATA-AAAAA-TAGTATAAAT
39096245 TATTAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 12 0.71
21 2 0.12
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
ATAAAAAATAGTATAAATG
Found at i:39105381 original size:17 final size:17
Alignment explanation
Indices: 39105359--39105419 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
39105349 ATGAGAATAG
39105359 ATTTTTAATTAATTAAA
1 ATTTTTAATTAATTAAA
* * **
39105376 ATTTTTAAACCTAAATCTA
1 ATTTTT-AA-TTAATTAAA
39105395 ATTTTTAATTAATTAAA
1 ATTTTTAATTAATTAAA
39105412 ATTTTTAA
1 ATTTTTAA
39105420 ACTTAAATCT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 19 0.56
18 4 0.12
19 11 0.32
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTTAATTAATTAAA
Found at i:39105399 original size:36 final size:36
Alignment explanation
Indices: 39105359--39105429 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
39105349 ATGAGAATAG
39105359 ATTTTTAATTAATTAAAATTTTTAAACCTAAATCTA
1 ATTTTTAATTAATTAAAATTTTTAAACCTAAATCTA
*
39105395 ATTTTTAATTAATTAAAATTTTTAAACTTAAATCT
1 ATTTTTAATTAATTAAAATTTTTAAACCTAAATCT
39105430 TAGCTAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (36 bp):
ATTTTTAATTAATTAAAATTTTTAAACCTAAATCTA
Found at i:39105756 original size:26 final size:26
Alignment explanation
Indices: 39105723--39105772 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
39105713 CGCCGCTGAA
39105723 GGCCATGTTCTTTAGCGGCGCTTTTG
1 GGCCATGTTCTTTAGCGGCGCTTTTG
39105749 GGCCATGTTCTTTAGCGGCGCTTT
1 GGCCATGTTCTTTAGCGGCGCTTT
39105773 ATCCAAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.08, C:0.24, G:0.30, T:0.38
Consensus pattern (26 bp):
GGCCATGTTCTTTAGCGGCGCTTTTG
Found at i:39106123 original size:21 final size:21
Alignment explanation
Indices: 39106089--39106141 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
39106079 CTTGTAGTCT
* *
39106089 CTGCTTCCTTCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
*
39106110 CTGTTGCCTCCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
39106131 CTGCTGCCTCC
1 CTGCTGCCTCC
39106142 ACTTTAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.00, C:0.45, G:0.21, T:0.34
Consensus pattern (21 bp):
CTGCTGCCTCCGCTTGCCTCG
Found at i:39106273 original size:65 final size:66
Alignment explanation
Indices: 39106127--39106283 Score: 219
Period size: 65 Copynumber: 2.4 Consensus size: 66
39106117 CTCCGCTTGC
* * *
39106127 CTCGCTGCTGCCTCCACTTTAAGTTGTATGTGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTC
1 CTCGCTGCAGCCTCCTCTTTAAGTTGTATGTGGAGTTCATCATATTTTTTTTGAGACTCTGCTTC
39106192 T
66 T
* * * *
39106193 CTCACTGCAACCTCCTCTTTAAGTTTTA-GATGGAGTTCATCATA-TTTTTTTGAGCCTCTGCTT
1 CTCGCTGCAGCCTCCTCTTTAAGTTGTATG-TGGAGTTCATCATATTTTTTTTGAGACTCTGCTT
39106256 CT
65 CT
*
39106258 CTCGTTGCAGCCTCCTCTTTAAGTTG
1 CTCGCTGCAGCCTCCTCTTTAAGTTG
39106284 AGCAATTTGC
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 43 0.54
66 36 0.46
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43
Consensus pattern (66 bp):
CTCGCTGCAGCCTCCTCTTTAAGTTGTATGTGGAGTTCATCATATTTTTTTTGAGACTCTGCTTC
T
Found at i:39107989 original size:29 final size:31
Alignment explanation
Indices: 39107942--39108003 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
39107932 ATTATGCATC
*
39107942 AACTTTGATTTTATATGTAATTATATATATG
1 AACTTTGATTTTATATGTAATTATATACATG
*
39107973 AACTTT-ATTTTA-GTGTAATTATATACATG
1 AACTTTGATTTTATATGTAATTATATACATG
39108002 AA
1 AA
39108004 ACTCTAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.59
30 6 0.21
31 6 0.21
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (31 bp):
AACTTTGATTTTATATGTAATTATATACATG
Found at i:39110092 original size:21 final size:22
Alignment explanation
Indices: 39110061--39110101 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
39110051 TTTATCTTTT
39110061 TTAAAGTTAAAA-GTCAAAACCA
1 TTAAAGTTAAAATG-CAAAACCA
39110083 TTAAA-TTAAAATGCAAAAC
1 TTAAAGTTAAAATGCAAAAC
39110102 TACGTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.24
Consensus pattern (22 bp):
TTAAAGTTAAAATGCAAAACCA
Found at i:39117920 original size:14 final size:14
Alignment explanation
Indices: 39117903--39117929 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39117893 TTGTTATCTC
39117903 ACTATTTTGTTGTT
1 ACTATTTTGTTGTT
39117917 ACTATTTTGTTGT
1 ACTATTTTGTTGT
39117930 ACTCGTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (14 bp):
ACTATTTTGTTGTT
Found at i:39117974 original size:17 final size:19
Alignment explanation
Indices: 39117941--39117975 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
39117931 CTCGTTTGAA
39117941 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
39117960 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
39117976 ACTATTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:39121080 original size:25 final size:25
Alignment explanation
Indices: 39121046--39121097 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
39121036 TAAAAGTATA
39121046 AATTCATAATGATTCAACGTACTTG
1 AATTCATAATGATTCAACGTACTTG
*
39121071 AATTGATAATGATTCAACGTACTTG
1 AATTCATAATGATTCAACGTACTTG
39121096 AA
1 AA
39121098 ATCTTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (25 bp):
AATTCATAATGATTCAACGTACTTG
Found at i:39124321 original size:22 final size:23
Alignment explanation
Indices: 39124281--39124323 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39124271 GTGATAGATT
39124281 AATTGAAGATAATTCATTATTAG
1 AATTGAAGATAATTCATTATTAG
* *
39124304 AATTTAAGA-AATTGATTATT
1 AATTGAAGATAATTCATTATT
39124324 GGTTTTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (23 bp):
AATTGAAGATAATTCATTATTAG
Found at i:39125517 original size:18 final size:18
Alignment explanation
Indices: 39125483--39125535 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
39125473 ATACAATAAT
39125483 AATA-ATATTTTAATTTTAG
1 AATATATATTTT--TTTTAG
**
39125502 AATATATATTTTTTTTTT
1 AATATATATTTTTTTTAG
*
39125520 AAAATATATTTTTTTT
1 AATATATATTTTTTTT
39125536 TACTTATCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 19 0.63
19 4 0.13
20 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
AATATATATTTTTTTTAG
Found at i:39125533 original size:20 final size:20
Alignment explanation
Indices: 39125483--39125536 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
39125473 ATACAATAAT
** *
39125483 AATA-ATATTTTAATTTTAG
1 AATATATATTTTTTTTTTAA
39125502 AATATATATTTTTTTTTTAA
1 AATATATATTTTTTTTTTAA
39125522 AATATAT-TTTTTTTT
1 AATATATATTTTTTTT
39125537 ACTTATCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
AATATATATTTTTTTTTTAA
Found at i:39126743 original size:2 final size:2
Alignment explanation
Indices: 39126736--39126764 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39126726 ATGTATCATT
39126736 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 T
39126765 TTTAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39135259 original size:22 final size:21
Alignment explanation
Indices: 39135234--39135275 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
39135224 CAATAAACTA
39135234 ATTCATTTGATAATATTTAGCC
1 ATTCATTTGAT-ATATTTAGCC
* *
39135256 ATTCTTTTGATTTATTTAGC
1 ATTCATTTGATATATTTAGC
39135276 ATAACGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (21 bp):
ATTCATTTGATATATTTAGCC
Found at i:39139129 original size:6 final size:6
Alignment explanation
Indices: 39139118--39139151 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
39139108 TTTGAAAGCC
* *
39139118 CCATTT CCATTT CCATTT CCATCT CCATCT CCAT
1 CCATTT CCATTT CCATTT CCATTT CCATTT CCAT
39139152 CTCAACTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.41, G:0.00, T:0.41
Consensus pattern (6 bp):
CCATTT
Found at i:39139133 original size:12 final size:12
Alignment explanation
Indices: 39139118--39139154 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
39139108 TTTGAAAGCC
*
39139118 CCATTTCCATTT
1 CCATTTCCATCT
39139130 CCATTTCCATCT
1 CCATTTCCATCT
*
39139142 CCATCTCCATCT
1 CCATTTCCATCT
39139154 C
1 C
39139155 AACTCACCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.16, C:0.43, G:0.00, T:0.41
Consensus pattern (12 bp):
CCATTTCCATCT
Found at i:39140324 original size:22 final size:23
Alignment explanation
Indices: 39140284--39140326 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39140274 GTGATAGATT
39140284 AATTGAAGATAATTCATTATTAG
1 AATTGAAGATAATTCATTATTAG
* *
39140307 AATTTAAGA-AATTGATTATT
1 AATTGAAGATAATTCATTATT
39140327 GGTTTTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (23 bp):
AATTGAAGATAATTCATTATTAG
Found at i:39141359 original size:32 final size:32
Alignment explanation
Indices: 39141307--39141390 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 32
39141297 CATCAAATGA
*
39141307 TTTTAAAATATTAAAATTATTTTCTAAATTA-TT
1 TTTTAAAATA-TAAAATTATTTT-AAAATTATTT
39141340 TTTTAAAATATAAAATTA--TTAAAATTATTT
1 TTTTAAAATATAAAATTATTTTAAAATTATTT
*
39141370 TTTTGAAATAATAAAATTATT
1 TTTTAAAAT-ATAAAATTATT
39141391 AAATAATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 6 0.13
30 12 0.27
31 9 0.20
32 8 0.18
33 10 0.22
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
TTTTAAAATATAAAATTATTTTAAAATTATTT
Found at i:39141379 original size:30 final size:30
Alignment explanation
Indices: 39141307--39141393 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
39141297 CATCAAATGA
* *
39141307 TTTTAAAATATTAAAATTATTTTCTAAATTATT
1 TTTTAAAATAATAAAATTA--TT-AAAATTATT
39141340 TTTTAAAAT-ATAAAATTATTAAAATTATTT
1 TTTTAAAATAATAAAATTATTAAAATTA-TT
*
39141370 TTTTGAAATAATAAAATTATTAAA
1 TTTTAAAATAATAAAATTATTAAA
39141394 TAATTTTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
29 6 0.12
30 12 0.24
31 14 0.29
32 8 0.16
33 9 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TTTTAAAATAATAAAATTATTAAAATTATT
Found at i:39141400 original size:30 final size:30
Alignment explanation
Indices: 39141307--39141400 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 30
39141297 CATCAAATGA
* *
39141307 TTTTAAAATATTAAAATTATTTTCTAAATTA-TT
1 TTTTAAAATA-TAAAATTA--TT-AAAATAATTT
*
39141340 TTTTAAAATATAAAATTATTAAAATTATTT
1 TTTTAAAATATAAAATTATTAAAATAATTT
*
39141370 TTTTGAAATAATAAAATTATT-AAATAATTT
1 TTTTAAAAT-ATAAAATTATTAAAATAATTT
39141400 T
1 T
39141401 AATTTTCAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
29 6 0.11
30 21 0.38
31 11 0.20
32 8 0.14
33 10 0.18
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
TTTTAAAATATAAAATTATTAAAATAATTT
Found at i:39142337 original size:23 final size:25
Alignment explanation
Indices: 39142289--39142339 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
39142279 AACCTAAAAC
*
39142289 AAATCCTCATTGCAAAAGAGAGAAA
1 AAATCCTCATTACAAAAGAGAGAAA
39142314 AAATCCTCATTACAAAAGAGA-AAA
1 AAATCCTCATTACAAAAGAGAGAAA
39142338 AA
1 AA
39142340 CACGTTAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.16
Consensus pattern (25 bp):
AAATCCTCATTACAAAAGAGAGAAA
Found at i:39145318 original size:24 final size:23
Alignment explanation
Indices: 39145255--39145318 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 23
39145245 AAATAGATTT
39145255 ATGTTAAAAATGTATTTTAAATAAA
1 ATGTTAAAAA--TATTTTAAATAAA
* *
39145280 AT-TTAAGTTATTATTTTAAATAAA
1 ATGTTAA--AAATATTTTAAATAAA
39145304 ATAGTTAAAAATATT
1 AT-GTTAAAAATATT
39145319 AACGATTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
24 24 0.77
25 2 0.06
26 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (23 bp):
ATGTTAAAAATATTTTAAATAAA
Found at i:39155758 original size:2 final size:2
Alignment explanation
Indices: 39155751--39155780 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39155741 AAAACAAATA
39155751 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39155781 GAGGGAGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39161587 original size:30 final size:29
Alignment explanation
Indices: 39161551--39161612 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
39161541 AAGTATTGAG
*
39161551 GGGTTTAATTAAAATTTTTAC-AAATTTTAA
1 GGGTTTAA-GAAAA-TTTTACAAAATTTTAA
39161581 GGGTTTAAGAAAATTTTACAAAAATTTTAA
1 GGGTTTAAGAAAATTTTAC-AAAATTTTAA
39161611 GG
1 GG
39161613 TGGCCTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.21
29 4 0.14
30 19 0.66
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (29 bp):
GGGTTTAAGAAAATTTTACAAAATTTTAA
Found at i:39164551 original size:25 final size:24
Alignment explanation
Indices: 39164523--39164574 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
39164513 CTACAATATG
* * *
39164523 AATATTAATATATTTTTATATCATA
1 AATATCAATATA-TGTTATATAATA
*
39164548 AATATCCATATATGTTATATAATA
1 AATATCAATATATGTTATATAATA
39164572 AAT
1 AAT
39164575 TTATTTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (24 bp):
AATATCAATATATGTTATATAATA
Found at i:39165217 original size:27 final size:25
Alignment explanation
Indices: 39165187--39165244 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
39165177 TACAATATAA
39165187 AAAACAAATAAAATAATTAATATTTTT
1 AAAACAAATAAAATAATT-A-ATTTTT
** *
39165214 AAAAGGAATAAAATAATTACTTTTT
1 AAAACAAATAAAATAATTAATTTTT
39165239 AAAACA
1 AAAACA
39165245 TATTCCTCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 9 0.35
26 1 0.04
27 16 0.62
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (25 bp):
AAAACAAATAAAATAATTAATTTTT
Found at i:39172463 original size:45 final size:46
Alignment explanation
Indices: 39172398--39172494 Score: 169
Period size: 46 Copynumber: 2.1 Consensus size: 46
39172388 ACCAATCAAA
*
39172398 CAACAAATGAAACATTAAAG-TTTAGAGATTCAATTTAATTTTTGCT
1 CAAC-AATGAAACATTAAAGTTTTAGAGATTCAATTTAATTTTTGCC
39172444 CAACAATGAAACATTAAAGTTTTAGAGATTCAATTTAATTTTTGCC
1 CAACAATGAAACATTAAAGTTTTAGAGATTCAATTTAATTTTTGCC
39172490 CAACA
1 CAACA
39172495 TTTGATAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 15 0.31
46 34 0.69
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.35
Consensus pattern (46 bp):
CAACAATGAAACATTAAAGTTTTAGAGATTCAATTTAATTTTTGCC
Found at i:39177916 original size:23 final size:22
Alignment explanation
Indices: 39177890--39177935 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
39177880 TATTGAATAA
*
39177890 ATATAATTATT-TATATATACAAT
1 ATATAAATATTAT-TATAT-CAAT
39177913 ATATAAATATTATTATATCAAT
1 ATATAAATATTATTATATCAAT
39177935 A
1 A
39177936 GTTATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 15 0.71
24 1 0.05
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATAAATATTATTATATCAAT
Found at i:39195547 original size:4 final size:4
Alignment explanation
Indices: 39195538--39195564 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
39195528 GCTTTAAATG
39195538 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
39195565 GTACCTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:39198309 original size:23 final size:23
Alignment explanation
Indices: 39198283--39198427 Score: 202
Period size: 23 Copynumber: 6.3 Consensus size: 23
39198273 ACACTAGTGC
*
39198283 GCTCTCTGATTAGCACCGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
39198306 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
39198329 GCTCTCTGA-TAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
39198351 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
39198374 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
39198397 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
39198420 GCTCTCTG
1 GCTCTCTG
39198428 TTACCCAGCA
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
22 21 0.19
23 89 0.81
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:39198396 original size:68 final size:69
Alignment explanation
Indices: 39198283--39198427 Score: 202
Period size: 68 Copynumber: 2.1 Consensus size: 69
39198273 ACACTAGTGC
* *
39198283 GCTCTCTGATTAGCACCGTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTG-ATAGCACTGT
1 GCTCTCTGATTAGCACCGTGTGTGCTCTCTGATCAGCACTGTGTGTGCTCTCTGTATAGCACTGT
39198347 GTGT
66 GTGT
* ** * * * *
39198351 GCTCTTTGATTAGCACTTTGTGTGCTCTCTGATCAGTACTTTGTGTGCTCTCTGTTTAGCACTTT
1 GCTCTCTGATTAGCACCGTGTGTGCTCTCTGATCAGCACTGTGTGTGCTCTCTGTATAGCACTGT
39198416 GTGT
66 GTGT
39198420 GCTCTCTG
1 GCTCTCTG
39198428 TTACCCAGCA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
68 47 0.71
69 19 0.29
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (69 bp):
GCTCTCTGATTAGCACCGTGTGTGCTCTCTGATCAGCACTGTGTGTGCTCTCTGTATAGCACTGT
GTGT
Found at i:39198428 original size:23 final size:23
Alignment explanation
Indices: 39198283--39198477 Score: 191
Period size: 23 Copynumber: 8.5 Consensus size: 23
39198273 ACACTAGTGC
* **
39198283 GCTCTCTGATTAGCACCGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
39198306 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
39198329 GCTCTCTG-ATAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
39198351 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * *
39198374 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
39198397 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
39198420 GCTCTCTGTTACCCAGCACTTATGTGT
1 GCTCTCTGTT---TAGCACTT-TGTGT
* *
39198447 --TCTCTGTTTAGTACTTCG-GT
1 GCTCTCTGTTTAGCACTTTGTGT
*
39198467 ACTCTCTGTTT
1 GCTCTCTGTTT
39198478 GTTCCGTTTA
Statistics
Matches: 149, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
20 2 0.01
21 1 0.01
22 35 0.23
23 91 0.61
25 8 0.05
26 7 0.05
27 5 0.03
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:39200385 original size:18 final size:19
Alignment explanation
Indices: 39200362--39200400 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
39200352 TGATTAACCG
39200362 AATTAAATTAA-TTTAATC
1 AATTAAATTAACTTTAATC
*
39200380 AATTAATTTAACTTTAATC
1 AATTAAATTAACTTTAATC
39200399 AA
1 AA
39200401 AATTTGAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTAAATTAACTTTAATC
Found at i:39206222 original size:312 final size:312
Alignment explanation
Indices: 39205657--39206288 Score: 1113
Period size: 312 Copynumber: 2.0 Consensus size: 312
39205647 AGGTTCAAAG
*
39205657 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATACAGCAATGCAGTGAATCC
1 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATACAGCAAAGCAGTGAATCC
* *
39205722 TAAAACCGAGACGAGCAAATCTAATCTGCCGAAAGAAGAATGGGAGAAGGCGATACCAACGACTA
66 TAAAACCGAGACGAGCAAATCTAATCTGCCGAAAGAAGAACGGAAGAAGGCGATACCAACGACTA
*
39205787 ATATGGTGGGAAATCATGTAAAATCAAGTGAAAAGGTACAAGGGCAGCAGCAACAGGTAGGAAAG
131 ATATGGTGGGAAATCATGTAAAATCAAGTGAAAACGTACAAGGGCAGCAGCAACAGGTAGGAAAG
* *
39205852 GAACATGGTAAGACTAAAATTCCTCAATTTAGGTGTACTATATGTAACATAACCTGCGGTCGATC
196 GAACATGGTAAGACTAAAATCCCTCAATTTAGGTGTACTATATGCAACATAACCTGCGGTCGATC
*
39205917 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCTAATATTAAA
261 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCCAATATTAAA
*
39205969 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATGCAGCAAAGCAGTGAATCC
1 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATACAGCAAAGCAGTGAATCC
**
39206034 TAAAACCGAGACGAGTGAATCTAATCTGCCGAAAGAAGAACGGAAGAAGGCGATACCAACGACTA
66 TAAAACCGAGACGAGCAAATCTAATCTGCCGAAAGAAGAACGGAAGAAGGCGATACCAACGACTA
* * *
39206099 ATATGGTGGGAAATCATGTAAAATCAAGTGAAAACGTGCAAGGGCAGCAGCAACAGGTTGGGAAG
131 ATATGGTGGGAAATCATGTAAAATCAAGTGAAAACGTACAAGGGCAGCAGCAACAGGTAGGAAAG
*
39206164 GAACATGGTAAGACTAAAATCCCTCAATTTAGGTGTACTATATGCGACATAACCTGCGGTCGATC
196 GAACATGGTAAGACTAAAATCCCTCAATTTAGGTGTACTATATGCAACATAACCTGCGGTCGATC
* *
39206229 TGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCCAATATTGAA
261 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCCAATATTAAA
39206281 AAAC-TGAA
1 AAACATGAA
39206289 TAATCATGGA
Statistics
Matches: 304, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
311 4 0.01
312 300 0.99
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (312 bp):
AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATACAGCAAAGCAGTGAATCC
TAAAACCGAGACGAGCAAATCTAATCTGCCGAAAGAAGAACGGAAGAAGGCGATACCAACGACTA
ATATGGTGGGAAATCATGTAAAATCAAGTGAAAACGTACAAGGGCAGCAGCAACAGGTAGGAAAG
GAACATGGTAAGACTAAAATCCCTCAATTTAGGTGTACTATATGCAACATAACCTGCGGTCGATC
AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCCAATATTAAA
Found at i:39213370 original size:22 final size:22
Alignment explanation
Indices: 39213345--39213387 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39213335 TTCACTGCAA
*
39213345 CAAAAA-TAAACAGCAAAATAAT
1 CAAAAATTAAACA-AAAAATAAT
39213367 CAAAAATTAAACAAAAAATAA
1 CAAAAATTAAACAAAAAATAA
39213388 ATAAATTCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14
Consensus pattern (22 bp):
CAAAAATTAAACAAAAAATAAT
Found at i:39221349 original size:26 final size:26
Alignment explanation
Indices: 39221320--39221385 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
39221310 TTATAGGTTT
* *
39221320 ATAACTACTAAGTAATCCTATTGCTC
1 ATAACAACTAAGTAATCCTATTACTC
39221346 ATAACAACTAAGTAATCCTATTACTC
1 ATAACAACTAAGTAATCCTATTACTC
39221372 AT--CAAGCTAAGTAA
1 ATAACAA-CTAAGTAA
39221386 ACAGATTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 3 0.08
25 8 0.22
26 26 0.70
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (26 bp):
ATAACAACTAAGTAATCCTATTACTC
Found at i:39225187 original size:33 final size:36
Alignment explanation
Indices: 39225108--39225188 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 36
39225098 TGAAATATAA
* *
39225108 ATTTTAAATATTT-TTAAGCAATTAATATTAATTAT
1 ATTTTAAATATTTAATAAGCAATTAATATAAATTAT
*
39225143 -TTATAAA-ATTTAATAAG-AA-T-ATATAAATTAT
1 ATTTTAAATATTTAATAAGCAATTAATATAAATTAT
39225174 ATTTTAAATATTTAA
1 ATTTTAAATATTTAA
39225189 ATATAATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
31 10 0.26
32 7 0.18
33 12 0.31
34 10 0.26
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (36 bp):
ATTTTAAATATTTAATAAGCAATTAATATAAATTAT
Found at i:39227041 original size:17 final size:18
Alignment explanation
Indices: 39227013--39227047 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39227003 AATCCTAATT
*
39227013 TTCCCTTTTTCTTTTTCC
1 TTCCCTTTTTCTTCTTCC
39227031 TTCCC-TTTTCTTCTTCC
1 TTCCCTTTTTCTTCTTCC
39227048 CCTGTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (18 bp):
TTCCCTTTTTCTTCTTCC
Found at i:39227168 original size:14 final size:14
Alignment explanation
Indices: 39227145--39227179 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39227135 AGATATTAGT
39227145 TAATAATAATAAAA
1 TAATAATAATAAAA
* *
39227159 TAATACTAATTAAA
1 TAATAATAATAAAA
39227173 TAATAAT
1 TAATAAT
39227180 TTATATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:39229885 original size:11 final size:11
Alignment explanation
Indices: 39229857--39229890 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
39229847 TTTAGCCTCT
39229857 AATGATTTTTC
1 AATGATTTTTC
*
39229868 TAT-ATTTTTC
1 AATGATTTTTC
39229878 AATGATTTTTC
1 AATGATTTTTC
39229889 AA
1 AA
39229891 AGTCAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (11 bp):
AATGATTTTTC
Found at i:39232257 original size:20 final size:22
Alignment explanation
Indices: 39232215--39232259 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
39232205 AATAAATTAA
*
39232215 TAAAATAAAAAAACATATATTC
1 TAAAATAAAAAAACAGATATTC
*
39232237 TAAAATAAAAACAC-GAT-TTC
1 TAAAATAAAAAAACAGATATTC
39232257 TAA
1 TAA
39232260 GATTAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAAATAAAAAAACAGATATTC
Found at i:39236283 original size:22 final size:22
Alignment explanation
Indices: 39236255--39236298 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39236245 TACTAATTTA
39236255 AGCCTTTTATTGCAAGGTTTTG
1 AGCCTTTTATTGCAAGGTTTTG
*
39236277 AGCCTTTTCTTGCAAGGTTTTG
1 AGCCTTTTATTGCAAGGTTTTG
39236299 GCTTACACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (22 bp):
AGCCTTTTATTGCAAGGTTTTG
Found at i:39247177 original size:11 final size:11
Alignment explanation
Indices: 39247161--39247207 Score: 62
Period size: 10 Copynumber: 4.5 Consensus size: 11
39247151 TTGTATGAAC
39247161 TTTTTTT-TAA
1 TTTTTTTATAA
39247171 TTTTTTT-TAA
1 TTTTTTTATAA
*
39247181 TTTTTTTAAAA
1 TTTTTTTATAA
*
39247192 TATTTTTATAA
1 TTTTTTTATAA
39247203 TTTTT
1 TTTTT
39247208 AAATTATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 17 0.53
11 15 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTTATAA
Found at i:39247627 original size:2 final size:2
Alignment explanation
Indices: 39247620--39247649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39247610 GAATTAACCC
39247620 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
39247650 TGAAATGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39249107 original size:272 final size:265
Alignment explanation
Indices: 39248570--39249270 Score: 815
Period size: 272 Copynumber: 2.6 Consensus size: 265
39248560 AAGCCTTATC
* * *
39248570 ACATGTAGCAGAAGAAGTGGAGATAATACCTCTCTTAAGGTGTGTTTAATTGGGTGAAAAAATAA
1 ACATGTAGCAGAAGAAGTGGAGATAATACCT-TTTTTAGGTGTGCTTAATTGGGTGAAAAAATAA
* * *
39248635 AGGAAT-GAGAGGAGAGAACGGAAAAA-TGGAAATAAAATAAAATTTTG-A-GTGTTTGACAGGG
65 A-GAATGGA-AGGAGAGAAC-GAAAAAGT-GAAAAAAAATAAAA-TTTGAATGTGTTTGGCAGGA
* * * * *
39248696 AAGAAATGAGAGAGGAAAGAAAATAGGATAGAGATTTTTAGGTAATACCAAATTTCAAAGTGAAC
125 AAGAAA-GTGAGAGGAAAGAAAATAGGATAAAAATCTTTAGGAAATACCAAATTTCAAAGTGAAC
*
39248761 AAAAAAATTGCTAGTCTTCAAGCCTTATCACATGTGAAGAATAAGTGTTGAACTAAATCTAAATC
189 AAAAAAATTGCTAGTCTCCAAGCCTTATCACATGTGAAGAATAAGTGTTGAACTAAATCTAAATC
39248826 ATAGTAACAAAA
254 ATAGTAACAAAA
* * * *
39248838 ACATGTAGTATAAGAAGTGGTGATAAAACCTTTTTTAGGTTGTGCTTAATTGGGTGAAAAAATAA
1 ACATGTAGCAGAAGAAGTGGAGATAATACCTTTTTTAGG-TGTGCTTAATTGGGTGAAAAAATAA
* *
39248903 ATGAATGGAAGGAGAGAACGAAAAAGTAAAAAGAAAATAAAATTGGAATGTGTTTGGCAGGAAAG
65 A-GAATGGAAGGAGAGAACGAAAAAGTGAAAA-AAAATAAAATTTGAATGTGTTTGGCAGGAAAG
* * *
39248968 AAACGTGAGAGGAAAGAAAATAAGATATAAATCTTTAGGCAAATGCCAAA-TTCTAAAGTGAACA
128 AAA-GTGAGAGGAAAGAAAATAGGATAAAAATCTTTAGG-AAATACCAAATTTC-AAAGTGAAC-
* * *
39249032 AAAAAAAGTTGCTAGTCTCCAAGCCTTATCACATGTGAGGAATAAGTGTTGAACTGATTCTAAAT
189 AAAAAAA-TTGCTAGTCTCCAAGCCTTATCACATGTGAAGAATAAGTGTTGAACTAAATCTAAAT
*
39249097 CATTGTAACAAAA
253 CATAGTAACAAAA
* * * * * *
39249110 ATATGTAGCAGAAGAAGAGGAGATAATATCTCTCTTAGGATGTGCTTGATTGGGT-AAAAAAGT-
1 ACATGTAGCAGAAGAAGTGGAGATAATACCTTTTTTAGG-TGTGCTTAATTGGGTGAAAAAA-TA
* * * * * *
39249173 AAGGATGGGAGGACAGAGCGGAAAAGTGGAAAAAAAATAAAATTTGAATGTGTTTGGCGGGAAA-
64 AAGAATGGAAGGAGAGAACGAAAAAGT-GAAAAAAAATAAAATTTGAATGTGTTTGGCAGGAAAG
*
39249237 AAGAATGAGAGAGAAAGGAAAATAGGATAAAAAT
128 AA-AGTGAGAG-GAAA-GAAAATAGGATAAAAAT
39249271 GATCATTTCC
Statistics
Matches: 370, Mismatches: 48, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
267 18 0.05
268 77 0.21
269 60 0.16
270 71 0.19
271 34 0.09
272 110 0.30
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (265 bp):
ACATGTAGCAGAAGAAGTGGAGATAATACCTTTTTTAGGTGTGCTTAATTGGGTGAAAAAATAAA
GAATGGAAGGAGAGAACGAAAAAGTGAAAAAAAATAAAATTTGAATGTGTTTGGCAGGAAAGAAA
GTGAGAGGAAAGAAAATAGGATAAAAATCTTTAGGAAATACCAAATTTCAAAGTGAACAAAAAAA
TTGCTAGTCTCCAAGCCTTATCACATGTGAAGAATAAGTGTTGAACTAAATCTAAATCATAGTAA
CAAAA
Found at i:39252189 original size:30 final size:31
Alignment explanation
Indices: 39252122--39252189 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
39252112 TCAAAATTTT
* *
39252122 ATATATAAAATTATACAATGAATTAAAATTC
1 ATATATAAAATTATACAATAAACTAAAATTC
* *
39252153 AGATATAAAA-T-TACAATTAAACTAATATTC
1 ATATATAAAATTATACAA-TAAACTAAAATTC
39252183 ATATATA
1 ATATATA
39252190 TTTTTATATC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 5 0.16
30 17 0.55
31 9 0.29
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.35
Consensus pattern (31 bp):
ATATATAAAATTATACAATAAACTAAAATTC
Found at i:39262075 original size:6 final size:6
Alignment explanation
Indices: 39262064--39262097 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
39262054 TATTTTCAGC
*
39262064 ATAAAA ATAAAA ATTAAA ATAAAA ATTAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA A-TAAAA ATA
39262098 TATATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAAAA
Found at i:39262084 original size:12 final size:12
Alignment explanation
Indices: 39262067--39262094 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39262057 TTTCAGCATA
39262067 AAAATAAAAATT
1 AAAATAAAAATT
39262079 AAAATAAAAATT
1 AAAATAAAAATT
39262091 AAAA
1 AAAA
39262095 ATATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:39273723 original size:21 final size:22
Alignment explanation
Indices: 39273694--39273735 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
39273684 CGTAACCTAC
39273694 AACCTCAAACACTTAAACCTTA
1 AACCTCAAACACTTAAACCTTA
* *
39273716 AACC-CAAACTCTTGAACCTT
1 AACCTCAAACACTTAAACCTT
39273736 GAGCCCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.24
Consensus pattern (22 bp):
AACCTCAAACACTTAAACCTTA
Found at i:39274184 original size:16 final size:16
Alignment explanation
Indices: 39274142--39274193 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
39274132 TATTTAAAGT
*
39274142 AATTTAATTAAAATTA
1 AATTTAATTAAAATAA
39274158 AA-TTAAGTTAAAA-AA
1 AATTTAA-TTAAAATAA
*
39274173 ATATTTAATTAAAATCA
1 A-ATTTAATTAAAATAA
39274190 AATT
1 AATT
39274194 GAATAATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTTAATTAAAATAA
Found at i:39275671 original size:29 final size:29
Alignment explanation
Indices: 39275627--39275684 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
39275617 TGGTGTCGTA
*
39275627 CACTTGGTTGGCACTTGAAAAATGAGGGT
1 CACTTGGTTGGCACTTGAAAAATAAGGGT
* * *
39275656 CACTTTGTTGGTACTTGAAAGATAAGGGT
1 CACTTGGTTGGCACTTGAAAAATAAGGGT
39275685 TAAAACCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (29 bp):
CACTTGGTTGGCACTTGAAAAATAAGGGT
Found at i:39275945 original size:21 final size:19
Alignment explanation
Indices: 39275921--39275966 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
39275911 CTAAACAAAT
*
39275921 TTATTTATAAATATTTTACTA
1 TTATTTAT--ATATTTTAATA
39275942 TTATTTATATATTTTAATA
1 TTATTTATATATTTTAATA
*
39275961 TAATTT
1 TTATTT
39275967 TTTCTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
21 8 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTATATATTTTAATA
Found at i:39280890 original size:431 final size:431
Alignment explanation
Indices: 39280085--39280937 Score: 1458
Period size: 431 Copynumber: 2.0 Consensus size: 431
39280075 AATCCATTTA
* * *
39280085 TTAAAAGTACAATGTATTTTACCATTACATCCAATCATTTATTGATAGTTTTATTTAATTAAATT
1 TTAAAAGTACAATATATTTTACCATTACATCCAATAATTTATTGATAGTATTATTTAATTAAATT
* * * * *
39280150 AAAATTTTCGAATAACCACCCAGGAATGAGGTGATTGATTTTAATTAGTGGACCAAAATGATATG
66 AAAACTTTCGAATAACCACCAAGGAACGAGGTGACTGACTTTAATTAGTGGACCAAAATGATATG
* ** *
39280215 GTGAGGAAGTTGTTAAAACATATGTTATTGAAATTGAATTAGTATATAGATATTTATTCTTCGTT
131 GTGAGGAAGTTCTTAAAACATAAATTATTGAAATTGAATTAGTATATAGATATTTATTCCTCGTT
* *
39280280 TCGACAATTGAAATGTGGAATATAAGCGGAGCAAGTGGACTCAAAATCACTAATTCATTCATACG
196 ACGACAATGGAAATGTGGAATATAAGCGGAGCAAGTGGACTCAAAATCACTAATTCATTCATACG
* *
39280345 GATTCTATCTAATTCATTAATACATTCATACTTGTAATCTAAGTTCTTTTTTTTTTACTATTGAC
261 GATTCTATCTAATTCATTAATACATTCATACTTGTAATCTAAGCTCTTTTTTTTTTACGATTGAC
* *
39280410 TTCATAAAAATATATAATTTTTAAATATAATCACATATACTTTTTATCTGTTTTATAATTTAAAA
326 TTCATAAAAATATAGAATTTTTAAATATAATCACATATACTTATTATCTGTTTTATAATTTAAAA
39280475 TTAATTTTATTAAAATCAGATAATATTCAAATCTAATTTTT
391 TTAATTTTATTAAAATCAGATAATATTCAAATCTAATTTTT
*
39280516 TTAAAAGTACAATATATTTTACCATTACATCCAATAATTTGTTGATAGTATTATTTAATTAAATT
1 TTAAAAGTACAATATATTTTACCATTACATCCAATAATTTATTGATAGTATTATTTAATTAAATT
39280581 AAAACTTTCGAATAACCATCCAAGG-ACGAGGTGACTGACTTTAATTAGTGGACCAAAATGATAT
66 AAAACTTTCGAATAACCA-CCAAGGAACGAGGTGACTGACTTTAATTAGTGGACCAAAATGATAT
*
39280645 GGTGTGGAAGTTCTTAAAACATAAATTATTGAAATTGAATTAGTATATAGATATTTATTCCTCGT
130 GGTGAGGAAGTTCTTAAAACATAAATTATTGAAATTGAATTAGTATATAGATATTTATTCCTCGT
* *
39280710 TACGACAGTGGAAATGTGGAATATAAGCGGAGCAAGTGGACTCAAAATCACTAATTCATTCATAT
195 TACGACAATGGAAATGTGGAATATAAGCGGAGCAAGTGGACTCAAAATCACTAATTCATTCATAC
39280775 GGATTCTATCTAATTCATTAATACATTCATACTTGTAATCTAAGCTCTTTTTTTTTTACGATTGA
260 GGATTCTATCTAATTCATTAATACATTCATACTTGTAATCTAAGCTCTTTTTTTTTTACGATTGA
*
39280840 CTTCATAAAAATATAGAATTTTTAAATATAATCATATATA-TATATTATCTGTTTTATAATTTAA
325 CTTCATAAAAATATAGAATTTTTAAATATAATCACATATACT-TATTATCTGTTTTATAATTTAA
*
39280904 AATTAGTTTTATTAAAATCAGATAATATTCAAAT
389 AATTAATTTTATTAAAATCAGATAATATTCAAAT
39280938 AAAATTCTTC
Statistics
Matches: 396, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
430 1 0.00
431 390 0.98
432 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (431 bp):
TTAAAAGTACAATATATTTTACCATTACATCCAATAATTTATTGATAGTATTATTTAATTAAATT
AAAACTTTCGAATAACCACCAAGGAACGAGGTGACTGACTTTAATTAGTGGACCAAAATGATATG
GTGAGGAAGTTCTTAAAACATAAATTATTGAAATTGAATTAGTATATAGATATTTATTCCTCGTT
ACGACAATGGAAATGTGGAATATAAGCGGAGCAAGTGGACTCAAAATCACTAATTCATTCATACG
GATTCTATCTAATTCATTAATACATTCATACTTGTAATCTAAGCTCTTTTTTTTTTACGATTGAC
TTCATAAAAATATAGAATTTTTAAATATAATCACATATACTTATTATCTGTTTTATAATTTAAAA
TTAATTTTATTAAAATCAGATAATATTCAAATCTAATTTTT
Found at i:39284825 original size:28 final size:26
Alignment explanation
Indices: 39284773--39284825 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
39284763 CTATAATAAC
** *
39284773 AACATTTTAAAAATTTACTTTCCAAA
1 AACATTTTAAAAATTTAAATACCAAA
39284799 AACATTTTATAAAATATTAAATACCAA
1 AACATTTTA-AAAAT-TTAAATACCAA
39284826 TTTAGGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 9 0.41
27 5 0.23
28 8 0.36
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (26 bp):
AACATTTTAAAAATTTAAATACCAAA
Found at i:39292533 original size:33 final size:30
Alignment explanation
Indices: 39292495--39292555 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 30
39292485 TATATTTTAT
39292495 TTAAAATGAGTAAATTAATCTTTTTATGTTAGA
1 TTAAAAT--GTAAATTAAT-TTTTTATGTTAGA
* *
39292528 TTAAAATGTAAATTGATTTTTTTTGTTA
1 TTAAAATGTAAATTAATTTTTTATGTTA
39292556 AAACTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 9 0.35
33 7 0.27
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (30 bp):
TTAAAATGTAAATTAATTTTTTATGTTAGA
Found at i:39292550 original size:31 final size:31
Alignment explanation
Indices: 39292495--39292555 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
39292485 TATATTTTAT
39292495 TTAAAATGAGTAAATTAATCTTTTTATGTTAGA
1 TTAAAAT-AGTAAATTAATCTTTTT-TGTTAGA
* *
39292528 TTAAAAT-GTAAATTGATTTTTTTTGTTA
1 TTAAAATAGTAAATTAATCTTTTTTGTTA
39292556 AAACTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 14 0.54
33 7 0.27
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (31 bp):
TTAAAATAGTAAATTAATCTTTTTTGTTAGA
Found at i:39296295 original size:27 final size:27
Alignment explanation
Indices: 39296264--39296324 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
39296254 TTATCTAAAC
39296264 AGTCCATATTTGTAAAAGGATAACACA
1 AGTCCATATTTGTAAAAGGATAACACA
39296291 AGTCCATATTTGTAAAAGGATAACACA
1 AGTCCATATTTGTAAAAGGATAACACA
*
39296318 AATCCAT
1 AGTCCAT
39296325 TTTAGGCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.26
Consensus pattern (27 bp):
AGTCCATATTTGTAAAAGGATAACACA
Found at i:39296388 original size:8 final size:8
Alignment explanation
Indices: 39296377--39296414 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
39296367 AAAAATATTT
39296377 ATATTATA
1 ATATTATA
39296385 ATATTATA
1 ATATTATA
39296393 ATATTTAATA
1 ATA-TT-ATA
39296403 ATATTAT-
1 ATATTATA
39296410 ATATT
1 ATATT
39296415 TTTTATGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.18
8 13 0.46
9 4 0.14
10 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATATTATA
Done.