Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 133 of 185
Found at i:40874276 original size:101 final size:101
Alignment explanation
Indices: 40874151--40874356 Score: 376
Period size: 101 Copynumber: 2.0 Consensus size: 101
40874141 ATCTTCTAAC
*
40874151 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGGGGTGGAAAAGCACTTTTTGACAGCACA
1 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
*
40874216 AGCAATGCCAAACAATCAGCTTTAACATCAAATTAA
66 AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
*
40874252 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCATA
1 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
*
40874317 AACAATGCCAAACAATCAGCTTTAACATCAAATTAG
66 AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
40874353 TTTT
1 TTTT
40874357 TCAACCCAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (101 bp):
TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
Found at i:40881227 original size:3 final size:3
Alignment explanation
Indices: 40881219--40881251 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
40881209 CAAATTTGAC
40881219 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40881252 GTTAACAACT
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):
AAT
Found at i:40881423 original size:21 final size:21
Alignment explanation
Indices: 40881384--40881424 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40881374 AATTTATTAT
**
40881384 TATATTTATAATTGTAATATA
1 TATATTTATAATTAAAATATA
*
40881405 TATATTTATTATTAAAATAT
1 TATATTTATAATTAAAATAT
40881425 TAATATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATATTTATAATTAAAATATA
Found at i:40881430 original size:21 final size:21
Alignment explanation
Indices: 40881381--40881430 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
40881371 AAAAATTTAT
**
40881381 TATT-ATATTTATAATTGTAA
1 TATTAATATTTATAATTAAAA
*
40881401 TA-TATATATTTATTATTAAAA
1 TATTA-ATATTTATAATTAAAA
40881422 TATTAATAT
1 TATTAATAT
40881431 AAATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.04
20 2 0.08
21 19 0.79
22 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTAATATTTATAATTAAAA
Found at i:40881492 original size:17 final size:19
Alignment explanation
Indices: 40881456--40881495 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
40881446 ATATATCAAG
40881456 AATATTATTTAAAATTTAAA
1 AATATTATTTAAAA-TTAAA
40881476 AATATTA-TTAAAA-TAAA
1 AATATTATTTAAAATTAAA
40881493 AAT
1 AAT
40881496 GTAATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTATTTAAAATTAAA
Found at i:40881546 original size:26 final size:27
Alignment explanation
Indices: 40881517--40881568 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
40881507 TAATTTATTA
* *
40881517 AAATAATTCATTATAT-TATTAAATAT
1 AAATAATTAAATATATATATTAAATAT
*
40881543 AAATAATTAAATATGTATATTAAATA
1 AAATAATTAAATATATATATTAAATA
40881569 ATATTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATAATTAAATATATATATTAAATAT
Found at i:40881551 original size:22 final size:21
Alignment explanation
Indices: 40881511--40881551 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
40881501 ATTAAATAAT
* *
40881511 TTATTAAAATAATTCATTATA
1 TTATTAAAATAAATAATTATA
40881532 TTATTAAATATAAATAATTA
1 TTATTAAA-ATAAATAATTA
40881552 AATATGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATTAAAATAAATAATTATA
Found at i:40881594 original size:22 final size:22
Alignment explanation
Indices: 40881569--40881611 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40881559 ATATTAAATA
40881569 ATATTAAAA-TTTATAATATTTG
1 ATATTAAAATTTTA-AATATTTG
*
40881591 ATATTAATATTTTAAATATTT
1 ATATTAAAATTTTAAATATTT
40881612 TCAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTAAAATTTTAAATATTTG
Found at i:40888679 original size:14 final size:14
Alignment explanation
Indices: 40888660--40888687 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40888650 AAAAAAAGAA
40888660 AGGAAATAAAGTTT
1 AGGAAATAAAGTTT
40888674 AGGAAATAAAGTTT
1 AGGAAATAAAGTTT
40888688 CAAGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
AGGAAATAAAGTTT
Found at i:40891637 original size:20 final size:21
Alignment explanation
Indices: 40891609--40891656 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
40891599 AATGGTTATA
* *
40891609 GAAAATAATTTTTA-AAAAAT
1 GAAATTAATTTTAATAAAAAT
40891629 GAAATTAATTTTAATAAAAAT
1 GAAATTAATTTTAATAAAAAT
40891650 GATAATT
1 GA-AATT
40891657 CCGGGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (21 bp):
GAAATTAATTTTAATAAAAAT
Found at i:40893676 original size:20 final size:20
Alignment explanation
Indices: 40893651--40893689 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40893641 CGCCTATGTG
* *
40893651 AAGGAGGCATACGCCCGTGA
1 AAGGAGGCACACGACCGTGA
40893671 AAGGAGGCACACGACCGTG
1 AAGGAGGCACACGACCGTG
40893690 TGTCGATAAC
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:0.31, C:0.26, G:0.36, T:0.08
Consensus pattern (20 bp):
AAGGAGGCACACGACCGTGA
Found at i:40901914 original size:14 final size:14
Alignment explanation
Indices: 40901891--40901924 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40901881 TGGTATGGTT
40901891 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
40901904 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
40901918 TTATAGG
1 TTATAGG
40901925 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:40902079 original size:22 final size:23
Alignment explanation
Indices: 40902054--40902100 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
40902044 GAGGAAAGTT
40902054 TAAAGAACATAAAA-GAAAAAAA
1 TAAAGAACATAAAACGAAAAAAA
** *
40902076 TAAATTACTTAAAACGAAAAAAA
1 TAAAGAACATAAAACGAAAAAAA
40902099 TA
1 TA
40902101 TGGGGATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.17
Consensus pattern (23 bp):
TAAAGAACATAAAACGAAAAAAA
Found at i:40904096 original size:27 final size:27
Alignment explanation
Indices: 40904032--40904096 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
40904022 TATTTTATTA
40904032 TTATTATTTATTTCTTTTTGGTCACTTT
1 TTATTATTT-TTTCTTTTTGGTCACTTT
* * *
40904060 CTATCT-TTTTTTCTTCTTT-TTCATTTT
1 TTAT-TATTTTTTCTT-TTTGGTCACTTT
40904087 TTATTATTTT
1 TTATTATTTT
40904097 GTTAATCGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.03
27 19 0.63
28 9 0.30
29 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (27 bp):
TTATTATTTTTTCTTTTTGGTCACTTT
Found at i:40908844 original size:16 final size:16
Alignment explanation
Indices: 40908813--40908842 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40908803 TGATATCTCT
40908813 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
40908829 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
40908843 TACTATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:40922837 original size:26 final size:26
Alignment explanation
Indices: 40922770--40922831 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
40922760 CTTGTAAGTG
* *
40922770 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATATATGCTACGATA
* *
40922796 TTCTGAAAGTGATATATGTTACGATA
1 TTCTGAAACTGATATATGCTACGATA
40922822 TTCTGAAACT
1 TTCTGAAACT
40922832 ACTATAGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (26 bp):
TTCTGAAACTGATATATGCTACGATA
Found at i:40922956 original size:31 final size:33
Alignment explanation
Indices: 40922894--40922957 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
40922884 GTCTGCCCAA
*
40922894 AAAATAGGAGGTTTCGGGTAAAAATATAGGCCC
1 AAAATAGGAGGTTTCGGGCAAAAATATAGGCCC
*
40922927 AAAATATG-GGTTT-GGGCAAAAA-ATGAGGCCC
1 AAAATAGGAGGTTTCGGGCAAAAATAT-AGGCCC
40922958 GTTTTCCTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.07
31 14 0.50
32 5 0.18
33 7 0.25
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.20
Consensus pattern (33 bp):
AAAATAGGAGGTTTCGGGCAAAAATATAGGCCC
Found at i:40923060 original size:17 final size:17
Alignment explanation
Indices: 40923040--40923072 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40923030 TATATTTTTA
*
40923040 TTTTTAATTAAATATAC
1 TTTTTAATCAAATATAC
40923057 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
40923073 TATATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:40931597 original size:13 final size:13
Alignment explanation
Indices: 40931575--40931604 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40931565 TCTTTAGGTA
*
40931575 TTTAATTGACTTG
1 TTTAACTGACTTG
40931588 TTTAACTGACTTG
1 TTTAACTGACTTG
40931601 TTTA
1 TTTA
40931605 GTTTGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTAACTGACTTG
Found at i:40935297 original size:9 final size:9
Alignment explanation
Indices: 40935279--40935320 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
40935269 TTTGGTTAAA
40935279 AATTAACCG
1 AATTAACCG
*
40935288 AATTACCCG
1 AATTAACCG
*
40935297 AATTAACTG
1 AATTAACCG
40935306 AATTAACCG
1 AATTAACCG
40935315 AATTAA
1 AATTAA
40935321 ATCACTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:40935420 original size:18 final size:18
Alignment explanation
Indices: 40935397--40935450 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
40935387 AATTTTTATG
40935397 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
* *
40935415 ATTGGGTTGAGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
40935433 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
40935451 TTAGGTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.13, C:0.02, G:0.44, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:40936172 original size:30 final size:30
Alignment explanation
Indices: 40936136--40936199 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
40936126 ATTACATTCC
40936136 AATAATTCTAATAAGAATACAACATCCTTA
1 AATAATTCTAATAAGAATACAACATCCTTA
40936166 AATAATTCTAATAAGAATACAACATCCTTA
1 AATAATTCTAATAAGAATACAACATCCTTA
40936196 AATA
1 AATA
40936200 TTTGATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.30
Consensus pattern (30 bp):
AATAATTCTAATAAGAATACAACATCCTTA
Found at i:40938039 original size:42 final size:42
Alignment explanation
Indices: 40937949--40938041 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
40937939 TTTAACCCTA
* * *
40937949 ATGGGTTTCAGTTAAGCTCTTTTGAGCTTCAGTTTAACCCCT
1 ATGGGTTTCAGTTAAGCTCTTATGAGCTTCAGTTCAACACCT
* * * * *
40937991 ACGGGTTTCCGTTCAGCTCTTATGAGCTTCCGTTCAACACTT
1 ATGGGTTTCAGTTAAGCTCTTATGAGCTTCAGTTCAACACCT
*
40938033 TTGGGTTTC
1 ATGGGTTTC
40938042 TGTTTAGCAC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (42 bp):
ATGGGTTTCAGTTAAGCTCTTATGAGCTTCAGTTCAACACCT
Found at i:40945846 original size:20 final size:21
Alignment explanation
Indices: 40945814--40945857 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
40945804 CAATCACTTT
40945814 ATAATATAATTAAAAAATAAA
1 ATAATATAATTAAAAAATAAA
**
40945835 ATAATA-AATTAAGTAATAAA
1 ATAATATAATTAAAAAATAAA
40945855 ATA
1 ATA
40945858 TATTCATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
ATAATATAATTAAAAAATAAA
Found at i:40947877 original size:21 final size:21
Alignment explanation
Indices: 40947853--40947892 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40947843 TTTTAAATTT
40947853 TAAAAATTATTAAA-AAAATCA
1 TAAAAATTA-TAAACAAAATCA
40947874 TAAAAATTATAAACAAAAT
1 TAAAAATTATAAACAAAAT
40947893 TTATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATTATAAACAAAATCA
Found at i:40948048 original size:13 final size:12
Alignment explanation
Indices: 40948022--40948054 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40948012 AATATAATTT
40948022 TAAATTTTTTTA
1 TAAATTTTTTTA
40948034 TAAATTTTGTTTA
1 TAAATTTT-TTTA
40948047 T-AATTTTT
1 TAAATTTTT
40948055 ATGGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 14 0.70
13 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
TAAATTTTTTTA
Found at i:40950487 original size:2 final size:2
Alignment explanation
Indices: 40950482--40950506 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40950472 TGTCAAATTC
40950482 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 A
40950507 AAGCACATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40965986 original size:40 final size:41
Alignment explanation
Indices: 40965856--40965987 Score: 137
Period size: 41 Copynumber: 3.2 Consensus size: 41
40965846 TCGCATAGCG
* * * * * *
40965856 GAAGCTATTAT-AATCCCGCACTCTAAGTGCCTTACATAGCC
1 GAAGCTATTCTCAAT-CTGCACACTAAGTGCCATAAATAGTC
40965897 GAAGCTA-TCTCAATCT-CACAGACTAAGTGCCATATATATAGTC
1 GAAGCTATTCTCAATCTGCAC--ACTAAGTGCCATA-A-ATAGTC
40965940 GAAGCTATTCTCAAT-TGCACACTAAGTGCCATAAATAGTC
1 GAAGCTATTCTCAATCTGCACACTAAGTGCCATAAATAGTC
40965980 GAAGCTAT
1 GAAGCTAT
40965988 CTCGAGTCGA
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
39 3 0.04
40 17 0.22
41 22 0.28
42 13 0.17
43 13 0.17
44 10 0.13
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (41 bp):
GAAGCTATTCTCAATCTGCACACTAAGTGCCATAAATAGTC
Found at i:40967942 original size:25 final size:27
Alignment explanation
Indices: 40967914--40967963 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
40967904 ATTTGTAAAT
40967914 TAGAAAAATATC-TCA-AGAATTTTTC
1 TAGAAAAATATCTTCAGAGAATTTTTC
* *
40967939 TAGAATAATCTCTTCAGAGAATTTT
1 TAGAAAAATATCTTCAGAGAATTTT
40967964 CTCTCTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 3 0.14
27 8 0.38
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (27 bp):
TAGAAAAATATCTTCAGAGAATTTTTC
Found at i:40970041 original size:43 final size:43
Alignment explanation
Indices: 40969927--40970042 Score: 155
Period size: 43 Copynumber: 2.7 Consensus size: 43
40969917 TATTTTTTTG
* * * *
40969927 TGTAAGACCACGTCTGGGACGTCGGCATCGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATTGACTTGTGATTACA
*
40969970 TGTAAGACCATGTCTGGGACAG-TGGCATTGA-TATGTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATTGACT-TGTGATTACA
40970013 TGTAAGACCACGTCTGGGACGTTGGCATTG
1 TGTAAGACCACGTCTGGGACGTTGGCATTG
40970043 TACGAGTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
42 2 0.03
43 61 0.95
44 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATTGACTTGTGATTACA
Found at i:40971373 original size:15 final size:14
Alignment explanation
Indices: 40971352--40971387 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
40971342 ATAATCCTTA
*
40971352 ATAATTATCTTAAT
1 ATAATTATCCTAAT
40971366 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
40971381 ATAATTA
1 ATAATTA
40971388 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:40980900 original size:18 final size:18
Alignment explanation
Indices: 40980864--40980900 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40980854 TAAACTTTCG
* *
40980864 AATTCAAATAATCTCAAT
1 AATTCAAATAAACTAAAT
40980882 AATTCAAATAAACTAAAT
1 AATTCAAATAAACTAAAT
40980900 A
1 A
40980901 TCAAATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTCAAATAAACTAAAT
Found at i:40981105 original size:27 final size:28
Alignment explanation
Indices: 40981058--40981126 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
40981048 CTTTTTCTTT
* **
40981058 TCCCCTAAAACTTTTGTTTCCACC-AAA
1 TCCCCTAAAATTTTTACTTCCACCTAAA
*
40981085 TCCCCTAAAATTTTTACTTCCTCCTAAA
1 TCCCCTAAAATTTTTACTTCCACCTAAA
40981113 --CCCTAAAATCTTTT
1 TCCCCTAAAAT-TTTT
40981127 TTTTTTGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.25
27 24 0.67
28 3 0.08
ACGTcount: A:0.29, C:0.32, G:0.01, T:0.38
Consensus pattern (28 bp):
TCCCCTAAAATTTTTACTTCCACCTAAA
Found at i:40981468 original size:19 final size:19
Alignment explanation
Indices: 40981444--40981480 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40981434 AAGTTAAAAT
40981444 CAAATTTGATTACGGTGGA
1 CAAATTTGATTACGGTGGA
*
40981463 CAAATTTGATTATGGTGG
1 CAAATTTGATTACGGTGG
40981481 GTGGCGATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (19 bp):
CAAATTTGATTACGGTGGA
Found at i:40987130 original size:21 final size:23
Alignment explanation
Indices: 40987104--40987148 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40987094 GAAAGGTATC
*
40987104 TACAAATTA-AATC-TCTAATAT
1 TACAAAATAGAATCTTCTAATAT
*
40987125 TACAAAATAGTATCTTCTAATAT
1 TACAAAATAGAATCTTCTAATAT
40987148 T
1 T
40987149 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (23 bp):
TACAAAATAGAATCTTCTAATAT
Found at i:40992093 original size:9 final size:9
Alignment explanation
Indices: 40992079--40992104 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40992069 CAAACCTAAA
40992079 ACCCAACAG
1 ACCCAACAG
40992088 ACCCAACAG
1 ACCCAACAG
40992097 ACCCAACA
1 ACCCAACA
40992105 CCCAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.46, G:0.08, T:0.00
Consensus pattern (9 bp):
ACCCAACAG
Found at i:40993537 original size:2 final size:2
Alignment explanation
Indices: 40993530--40993555 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40993520 CTTCTGAATC
40993530 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40993556 CATTTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40993611 original size:31 final size:30
Alignment explanation
Indices: 40993559--40993623 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
40993549 ATATATACAT
*
40993559 TTTCTTTTAAATCTATTTATGTA-TATATTA
1 TTTCTTTTAAATCTATATATGTAGTAT-TTA
40993589 TTTCTTCTTAAATC-ATCATATGTAGTATTTA
1 TTTCTT-TTAAATCTAT-ATATGTAGTATTTA
40993620 TTTC
1 TTTC
40993624 GAGATCCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 8 0.26
31 20 0.65
32 3 0.10
ACGTcount: A:0.28, C:0.11, G:0.05, T:0.57
Consensus pattern (30 bp):
TTTCTTTTAAATCTATATATGTAGTATTTA
Found at i:41000111 original size:21 final size:23
Alignment explanation
Indices: 41000085--41000129 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41000075 GAAAGGTATC
*
41000085 TACAAATTA-AATC-TCTAATAT
1 TACAAAATAGAATCTTCTAATAT
*
41000106 TACAAAATAGTATCTTCTAATAT
1 TACAAAATAGAATCTTCTAATAT
41000129 T
1 T
41000130 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (23 bp):
TACAAAATAGAATCTTCTAATAT
Found at i:41010715 original size:24 final size:23
Alignment explanation
Indices: 41010688--41010733 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
41010678 TTTTTTTGAA
*
41010688 TTTCGAGTTCAAATCAAGTTAAAC
1 TTTCGAGTTCAAAT-AACTTAAAC
*
41010712 TTTCGATTTCAAATAACTTAAA
1 TTTCGAGTTCAAATAACTTAAA
41010734 TAATTCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
TTTCGAGTTCAAATAACTTAAAC
Found at i:41011303 original size:19 final size:19
Alignment explanation
Indices: 41011279--41011316 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41011269 AAAGTTAAAA
41011279 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
41011298 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
41011317 GTGGCGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:41014816 original size:23 final size:23
Alignment explanation
Indices: 41014764--41014816 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
41014754 TAGGGTAGAT
* *
41014764 AATTAAATTATTAGAAATTAGTA
1 AATTAAAATATTAGAAATAAGTA
* *
41014787 AAATAAAATATTA-AAATAATTA
1 AATTAAAATATTAGAAATAAGTA
41014809 GAATTAAA
1 -AATTAAA
41014817 TTTTTAGGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (23 bp):
AATTAAAATATTAGAAATAAGTA
Found at i:41017286 original size:17 final size:18
Alignment explanation
Indices: 41017264--41017300 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41017254 TTTTGGGTTG
41017264 TGTGGG-CCACACGGGCA
1 TGTGGGCCCACACGGGCA
*
41017281 TGTGGGCCCACATGGGCA
1 TGTGGGCCCACACGGGCA
41017299 TG
1 TG
41017301 CAGCATGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (18 bp):
TGTGGGCCCACACGGGCA
Found at i:41019329 original size:22 final size:21
Alignment explanation
Indices: 41019303--41019348 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
41019293 ATAGAGACCA
41019303 CCATTCAGTGGTATCGCGATAT
1 CCATTCAG-GGTATCGCGATAT
**
41019325 CCATTTTGGGTATCGCGATAT
1 CCATTCAGGGTATCGCGATAT
41019346 CCA
1 CCA
41019349 CCTGCCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (21 bp):
CCATTCAGGGTATCGCGATAT
Found at i:41022881 original size:28 final size:28
Alignment explanation
Indices: 41022844--41022931 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
41022834 CATACAGTAG
* *
41022844 CAGTCTGGGCCTAAGCCCAATAAAGCAA
1 CAGTGTGGGCCTTAGCCCAATAAAGCAA
* * * *
41022872 TAGT-TGGGGCCTTATCCCAATACAGTAA
1 CAGTGT-GGGCCTTAGCCCAATAAAGCAA
* *
41022900 CAGTGTGGGCCTTAGCCCAATACAGTAA
1 CAGTGTGGGCCTTAGCCCAATAAAGCAA
41022928 CAGT
1 CAGT
41022932 ATAATGCAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
27 1 0.02
28 49 0.96
29 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATAAAGCAA
Found at i:41023098 original size:26 final size:26
Alignment explanation
Indices: 41023069--41023118 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
41023059 TAATAATGAT
*
41023069 GCAACAAAGCTGCCAGTAACAGTAAC
1 GCAAAAAAGCTGCCAGTAACAGTAAC
41023095 GCAAAAAAGCTGCCAGTAACAGTA
1 GCAAAAAAGCTGCCAGTAACAGTA
41023119 TATGTGGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (26 bp):
GCAAAAAAGCTGCCAGTAACAGTAAC
Found at i:41023315 original size:27 final size:27
Alignment explanation
Indices: 41023293--41023603 Score: 301
Period size: 27 Copynumber: 11.5 Consensus size: 27
41023283 AGGGGTATAA
* *
41023293 CAGTCATTTTACCTTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* * *
41023320 CGGTAATTTTACCCTTCCAAGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
41023347 CAGTAATCTTT-CCCTTTGAGGGTATTT
1 CAGTAAT-TTTACCCTTCGAGGGTATTT
* **
41023374 TAGTAATTTTA-CCTTTTAGGAGTATTT
1 CAGTAATTTTACCCTTCGAGG-GTATTT
*
41023401 C-GATAATTTTACCTTTCGAGGGTATTT
1 CAG-TAATTTTACCCTTCGAGGGTATTT
*
41023428 CAGTAATTTTACCCATCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* *
41023455 TAGTAATTTTACCCATCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* *
41023482 TAGTAATTTTACCCTTCAAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
** *
41023509 TGGTAATTTTACCCTTCAAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* * *
41023536 C-GATAATTTTA-CTTATCAACGGTATTT
1 CAG-TAATTTTACCCT-TCGAGGGTATTT
* * *
41023563 TAGTAGTTTTACCCCATCGAGGGTATTT
1 CAGTAATTTTA-CCCTTCGAGGGTATTT
*
41023591 -GGTAATTTTACCC
1 CAGTAATTTTACCC
41023604 ACGAATCGTA
Statistics
Matches: 241, Mismatches: 32, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
26 18 0.07
27 201 0.83
28 21 0.09
29 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.43
Consensus pattern (27 bp):
CAGTAATTTTACCCTTCGAGGGTATTT
Found at i:41028476 original size:32 final size:32
Alignment explanation
Indices: 41028421--41028544 Score: 140
Period size: 32 Copynumber: 3.9 Consensus size: 32
41028411 ATAAGTACAT
* * * * *
41028421 TAATATGATTGGCACAAAACCATCAATAGTAG
1 TAATATGATCGGCATAAAGCCATCAGTAATAG
* *
41028453 TAATATGATCGGCATACAGCCATCAGTAATGG
1 TAATATGATCGGCATAAAGCCATCAGTAATAG
* *
41028485 TAACATGATCGGCATAAAGCCATCAGTAACAG
1 TAATATGATCGGCATAAAGCCATCAGTAATAG
* * *
41028517 TAATATGATCGGTAAAAAACCATCAGTA
1 TAATATGATCGGCATAAAGCCATCAGTA
41028545 GCATCGCAGC
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (32 bp):
TAATATGATCGGCATAAAGCCATCAGTAATAG
Found at i:41028719 original size:24 final size:24
Alignment explanation
Indices: 41028690--41028747 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
41028680 CCATTCTCAG
41028690 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* * *
41028714 ATTCAGTTATACCAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
41028738 AATCAATCAT
1 AATCAGTCAT
41028748 TTACACTCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:41029010 original size:27 final size:27
Alignment explanation
Indices: 41028770--41029011 Score: 222
Period size: 27 Copynumber: 9.0 Consensus size: 27
41028760 AGCAAAATAG
* * * *
41028770 TCATTT-ACCCTCTAAGGGTATTATGG
1 TCATTTAACCCTATAGGGGTATTACGA
* *
41028796 TCATTTTAA-CTTATAGGGGTATTACGG
1 TCA-TTTAACCCTATAGGGGTATTACGA
* * * * *
41028823 TTATTT-TCTCTATAGGGTTATTACGG
1 TCATTTAACCCTATAGGGGTATTACGA
* *
41028849 TCATTTAACCCTATAGGGGTACTACGG
1 TCATTTAACCCTATAGGGGTATTACGA
* * * * *
41028876 TTATTTTACCCCATAGAGGCATTACGA
1 TCATTTAACCCTATAGGGGTATTACGA
* *
41028903 TCATTTTACCCTACAGGGGTATTAC-A
1 TCATTTAACCCTATAGGGGTATTACGA
* *
41028929 GTCATTTAACCCTATGGGGGTATTACAA
1 -TCATTTAACCCTATAGGGGTATTACGA
*
41028957 TCATTTTACCCTATAGGGGTATTACGA
1 TCATTTAACCCTATAGGGGTATTACGA
*
41028984 TCATTTAACCCTATGGGGGTATTACGA
1 TCATTTAACCCTATAGGGGTATTACGA
41029011 T
1 T
41029012 TGTTTTACAA
Statistics
Matches: 176, Mismatches: 34, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
26 27 0.15
27 147 0.84
28 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (27 bp):
TCATTTAACCCTATAGGGGTATTACGA
Found at i:41029125 original size:19 final size:19
Alignment explanation
Indices: 41029101--41029138 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41029091 CCCAATGCCA
41029101 ATTTTCGGCCCACGTAGGC
1 ATTTTCGGCCCACGTAGGC
41029120 ATTTTCGGCCCACGTAGGC
1 ATTTTCGGCCCACGTAGGC
41029139 CTACACGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.26
Consensus pattern (19 bp):
ATTTTCGGCCCACGTAGGC
Found at i:41029826 original size:31 final size:32
Alignment explanation
Indices: 41029791--41029932 Score: 90
Period size: 32 Copynumber: 4.5 Consensus size: 32
41029781 GAATGGCTAC
* *
41029791 AAGCCATAAGTA-CATTAATATGATTGGCACA
1 AAGCCATAAGTAGCAGTAATATGATCGGCACA
* * *
41029822 AAGCCATCAGTAGTAGTAATATGATCGGCATA
1 AAGCCATAAGTAGCAGTAATATGATCGGCACA
* * * * *
41029854 CAA-CCATCAGTAACGGTAATATGATCGGGAAA
1 -AAGCCATAAGTAGCAGTAATATGATCGGCACA
* * ** ** * *
41029886 AATCTATTCGTAATAGTAATATAATCAGCACA
1 AAGCCATAAGTAGCAGTAATATGATCGGCACA
*
41029918 AAGCCATCAGTAGCA
1 AAGCCATAAGTAGCA
41029933 TTGCAGCAAA
Statistics
Matches: 83, Mismatches: 25, Indels: 5
0.73 0.22 0.04
Matches are distributed among these distances:
31 13 0.16
32 68 0.82
33 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (32 bp):
AAGCCATAAGTAGCAGTAATATGATCGGCACA
Found at i:41029844 original size:32 final size:32
Alignment explanation
Indices: 41029806--41029929 Score: 117
Period size: 32 Copynumber: 3.9 Consensus size: 32
41029796 ATAAGTACAT
* *
41029806 TAATATGATTGGCACAAAGCCATCAGTAGTAG
1 TAATATGATCGGCACAAAGCCATCAGTAATAG
* **
41029838 TAATATGATCGGCATACAA-CCATCAGTAACGG
1 TAATATGATCGGCACA-AAGCCATCAGTAATAG
* * * *
41029870 TAATATGATCGGGAAAAATCTATTC-GTAATAG
1 TAATATGATCGGCACAAAGCCA-TCAGTAATAG
* *
41029902 TAATATAATCAGCACAAAGCCATCAGTA
1 TAATATGATCGGCACAAAGCCATCAGTA
41029930 GCATTGCAGC
Statistics
Matches: 72, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
31 4 0.06
32 64 0.89
33 4 0.06
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAATAG
Found at i:41030140 original size:24 final size:24
Alignment explanation
Indices: 41030113--41030161 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
41030103 AGTTATACCA
*
41030113 ATCACAGACAAATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
**
41030137 ATCATGGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
41030161 A
1 A
41030162 CTCGAGGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:41030228 original size:27 final size:27
Alignment explanation
Indices: 41030198--41030484 Score: 308
Period size: 27 Copynumber: 10.6 Consensus size: 27
41030188 CTCTAAGGAC
* * *
41030198 ATTATGGTCATTTTACCTTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* *
41030225 ATTACGGTTATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
41030252 ATTACGGTTATTTAACCCTATAAGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
41030279 ATTACGGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
** *
41030306 ATTATAGTCA-TTTATCCCTATGGGGGGT
1 ATTACGGTCATTTTA-CCCTAT-AGGGGT
*
41030334 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
41030361 ATTACGATCATTTAACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * * *
41030388 ATTACAGTTATTTAACCTTATAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
*
41030415 ATTACGGTCATTTTACCCTACT-GGGGC
1 ATTACGGTCATTTTACCCTA-TAGGGGT
* * *
41030442 ATTACGGTTATTTAACCCTATTGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* *
41030469 ATTACAGTTATTTTAC
1 ATTACGGTCATTTTAC
41030485 AACCTTTTCG
Statistics
Matches: 220, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
26 5 0.02
27 192 0.87
28 19 0.09
29 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTATAGGGGT
Found at i:41030374 original size:109 final size:108
Alignment explanation
Indices: 41030204--41030473 Score: 346
Period size: 109 Copynumber: 2.5 Consensus size: 108
41030194 GGACATTATG
* * * *
41030204 GTCATTTTACCTTACAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGGTTATTTAACC
1 GTCATTTTACCCTACTGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATCATTTAACC
* * *
41030269 CTATAAGGGTATTACGGTCATTTTACCCTATAGGGGTATTATA
66 CTATAAGGGTATTACAGTCATTTAACCCTATAGGGGTATTACA
*
41030312 GTCA-TTTATCCCTA-TGGGGGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTA
1 GTCATTTTA-CCCTACT--GGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATCATTTA
** * * *
41030375 ACCCTATGGGGGTATTACAGTTATTTAACCTTATAGGGGTATTACG
63 ACCCTATAAGGGTATTACAGTCATTTAACCCTATAGGGGTATTACA
* * **
41030421 GTCATTTTACCCTACTGGGGCATTACGGTTATTTAACCCTATTGGGGTATTAC
1 GTCATTTTACCCTACTGGGGTATTACGGTTATTTTACCCTACAGGGGTATTAC
41030474 AGTTATTTTA
Statistics
Matches: 139, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
107 4 0.03
108 40 0.29
109 90 0.65
110 5 0.04
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (108 bp):
GTCATTTTACCCTACTGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATCATTTAACC
CTATAAGGGTATTACAGTCATTTAACCCTATAGGGGTATTACA
Found at i:41036954 original size:28 final size:28
Alignment explanation
Indices: 41036923--41036982 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
41036913 CATGCAGTAG
41036923 CAGTCTGGGCCTGAGCCCAATACAACAA
1 CAGTCTGGGCCTGAGCCCAATACAACAA
* * *
41036951 CAGTGTGGGCCTTAGCCCAATACAATAA
1 CAGTCTGGGCCTGAGCCCAATACAACAA
41036979 CAGT
1 CAGT
41036983 ACAATGCAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (28 bp):
CAGTCTGGGCCTGAGCCCAATACAACAA
Found at i:41037334 original size:27 final size:27
Alignment explanation
Indices: 41037304--41037364 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
41037294 TCAACTCCTA
*
41037304 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATAACAGCCATTTTACCCTATG
*** *
41037331 GGGGTATTTTAGCCATTTTACCCTTTG
1 GGGGTATAACAGCCATTTTACCCTATG
41037358 GGGGTAT
1 GGGGTAT
41037365 TTCGATAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (27 bp):
GGGGTATAACAGCCATTTTACCCTATG
Found at i:41037375 original size:27 final size:27
Alignment explanation
Indices: 41037345--41037676 Score: 400
Period size: 27 Copynumber: 12.3 Consensus size: 27
41037335 TATTTTAGCC
*
41037345 ATTTTACCCTTTGGGGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
41037372 ATTTTACCC-TTGAGGGGTATTTCG-TA
1 ATTTTACCCTTTGA-GGGTATTTCGATA
* * *
41037398 ATCTTACCCTTTAAGGGTATTTCAATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* * *
41037425 ATCTTACCCTTTTAGGGTATTTCGGTA
1 ATTTTACCCTTTGAGGGTATTTCGATA
*
41037452 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* * * *
41037479 ATTTTACCCTTCGAGGATATTTTGGTA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* * * *
41037506 AATTTAACCTTCGAGGGTATTT-TAGTA
1 ATTTTACCCTTTGAGGGTATTTCGA-TA
* * *
41037533 ATTTTACTCATTGAGGGTATTTTGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
*
41037560 ATTTTACCCTTTGAGGGCATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* *
41037587 GTTTTACCCTTTGAGGGTATTTCGATT
1 ATTTTACCCTTTGAGGGTATTTCGATA
*
41037614 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* *
41037641 ATTTTACCCTTCGAGGTTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
41037668 ATTTTACCC
1 ATTTTACCC
41037677 ACGAATCGTA
Statistics
Matches: 264, Mismatches: 36, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
26 22 0.08
27 241 0.91
28 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTTGAGGGTATTTCGATA
Found at i:41041347 original size:42 final size:42
Alignment explanation
Indices: 41041280--41041459 Score: 152
Period size: 42 Copynumber: 4.3 Consensus size: 42
41041270 TTTCGGTATA
* ** * *
41041280 GCACACTTGGTGCCCGTTATTCAACATCATCATTTTAATTTC
1 GCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTC
41041322 GCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTC
1 GCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTC
* * * ** * ** *
41041364 ACACACTTAGTTCCGTTCATATAGCC-GTAGC--TA-TTCGATACTC
1 GCACACTTAGTGCC--T-AT-TATCCAACATCATTATTTTAAT-TTC
41041407 GCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTC
1 GCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTC
*
41041449 ACACACTTAGT
1 GCACACTTAGT
41041460 TCCGTTCATA
Statistics
Matches: 105, Mismatches: 24, Indels: 18
0.71 0.16 0.12
Matches are distributed among these distances:
39 4 0.04
40 4 0.04
41 1 0.01
42 67 0.64
43 20 0.19
44 1 0.01
45 4 0.04
46 4 0.04
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (42 bp):
GCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTC
Found at i:41041412 original size:85 final size:85
Alignment explanation
Indices: 41041320--41041504 Score: 370
Period size: 85 Copynumber: 2.2 Consensus size: 85
41041310 CATTTTAATT
41041320 TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTCACACACTTAGTTCCGTTCATA
1 TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTCACACACTTAGTTCCGTTCATA
41041385 TAGCCGTAGCTATTCGATAC
66 TAGCCGTAGCTATTCGATAC
41041405 TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTCACACACTTAGTTCCGTTCATA
1 TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTCACACACTTAGTTCCGTTCATA
41041470 TAGCCGTAGCTATTCGATAC
66 TAGCCGTAGCTATTCGATAC
41041490 TCGCACACTTAGTGC
1 TCGCACACTTAGTGC
41041505 TAAATATTGA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 100 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (85 bp):
TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTCACACACTTAGTTCCGTTCATA
TAGCCGTAGCTATTCGATAC
Found at i:41047050 original size:28 final size:29
Alignment explanation
Indices: 41046994--41047213 Score: 166
Period size: 28 Copynumber: 7.8 Consensus size: 29
41046984 TTTTTTGTAG
* * *
41046994 AATAGTGGTAAAACTGTAAAATCT-AAAA
1 AATAGTGGCAAAACTGTAAAATTTGGAAA
41047022 AATAGTGG-AAAACTGTAAAATTTGGAAA
1 AATAGTGGCAAAACTGTAAAATTTGGAAA
* * * *
41047050 AATAATGGC-AAATTATAAAATCTGGAAA
1 AATAGTGGCAAAACTGTAAAATTTGGAAA
** *
41047078 ACCAG-AGCAAAACTGTAAAATTTAGG-AA
1 AATAGTGGCAAAACTGTAAAATTT-GGAAA
* * * *
41047106 AATTGTGGTAGAACTGTAAAATTGGGAAA
1 AATAGTGGCAAAACTGTAAAATTTGGAAA
* * ** *
41047135 AATAGTGGCAGAACTATAAAAGATGTAAA
1 AATAGTGGCAAAACTGTAAAATTTGGAAA
* *
41047164 ACCTA-TGGCAAAATTGTAAAATTT-GAAA
1 A-ATAGTGGCAAAACTGTAAAATTTGGAAA
* *
41047192 AATAGTGGCAGAACTATAAAAT
1 AATAGTGGCAAAACTGTAAAAT
41047214 CTGTAAAATG
Statistics
Matches: 146, Mismatches: 38, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
27 18 0.12
28 71 0.49
29 55 0.38
30 2 0.01
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.24
Consensus pattern (29 bp):
AATAGTGGCAAAACTGTAAAATTTGGAAA
Found at i:41050274 original size:64 final size:65
Alignment explanation
Indices: 41050167--41050296 Score: 226
Period size: 64 Copynumber: 2.0 Consensus size: 65
41050157 TTTTAAAAAT
* *
41050167 ATTACTTTCCATCTTGCTTGATAGACATGAGATACATTGACAATTACCGTAAAGTATTATTAGTC
1 ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
*
41050232 ATTAATTTCCTTCTTGC-TGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
1 ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
41050296 A
1 A
41050297 GGAACCTACT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 47 0.76
65 15 0.24
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (65 bp):
ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
Found at i:41055250 original size:13 final size:13
Alignment explanation
Indices: 41055219--41055256 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41055209 AATTTCAAGT
41055219 ATTGT-ATAAAAA
1 ATTGTGATAAAAA
41055231 ATATGTGATAAAAA
1 AT-TGTGATAAAAA
*
41055245 CTTGTGATAAAA
1 ATTGTGATAAAA
41055257 TTAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 2 0.09
13 13 0.57
14 8 0.35
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (13 bp):
ATTGTGATAAAAA
Found at i:41056985 original size:19 final size:19
Alignment explanation
Indices: 41056961--41056999 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41056951 AGCAGACCAA
*
41056961 TTAAGTCTGTTGGGGTTGT
1 TTAAGTCTGTTAGGGTTGT
*
41056980 TTAAGTTTGTTAGGGTTGT
1 TTAAGTCTGTTAGGGTTGT
41056999 T
1 T
41057000 AACTTCAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.33, T:0.51
Consensus pattern (19 bp):
TTAAGTCTGTTAGGGTTGT
Found at i:41062635 original size:27 final size:27
Alignment explanation
Indices: 41062595--41062923 Score: 328
Period size: 27 Copynumber: 12.2 Consensus size: 27
41062585 ATAATGGGCC
41062595 TAAAATGACCGAAATACCCTCGAAGGA
1 TAAAATGACCGAAATACCCTCGAAGGA
**
41062622 TAAAATGATTGAAATACTCC-CGAAAGG-
1 TAAAATGACCGAAATAC-CCTCG-AAGGA
* *
41062649 TAAAATGACCGAAATACCCCCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGA
* *
41062676 TCAAATGACCGAAATACCCTCAAAGGA
1 TAAAATGACCGAAATACCCTCGAAGGA
* * * *
41062703 TAAAATGATCAAAATACCTTC-ACAGGT
1 TAAAATGACCGAAATACCCTCGA-AGGA
** * *
41062730 TAAAATGACTAAAATACCCCCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGA
* ** *
41062757 TAAAAAGACTAAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGA
* *
41062784 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGA
** * *
41062811 TAAAATGATTGAAATACCCCCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGA
*
41062838 TAAAATGACCGAAATA-CCTCCGAAAGA
1 TAAAATGACCGAAATACCCT-CGAAGGA
**
41062865 TAAAATGATTGAAATACCC-CTGAAGGA
1 TAAAATGACCGAAATACCCTC-GAAGGA
41062892 TAAAATGACCGAAATACCC-CGAAGGA
1 TAAAATGACCGAAATACCCTCGAAGGA
41062918 TAAAAT
1 TAAAAT
41062924 AATTATTATA
Statistics
Matches: 259, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.08
27 228 0.88
28 9 0.03
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGA
Found at i:41062734 original size:81 final size:80
Alignment explanation
Indices: 41062595--41062923 Score: 375
Period size: 81 Copynumber: 4.1 Consensus size: 80
41062585 ATAATGGGCC
* *
41062595 TAAAATGACCGAAATACCCTCGAAGGATAAAATGATTGAAATACTCC-CGAAAGGTAAAATGACC
1 TAAAATGACCGAAATACCCTCAAAGGATAAAATGATCGAAATAC-CCTCG-AAGGTAAAATGACC
41062659 GAAATACCCCCGAAGGG
64 GAAATACCCCCGAAGGG
* * * *
41062676 TCAAATGACCGAAATACCCTCAAAGGATAAAATGATCAAAATACCTTC-ACAGGTTAAAATGACT
1 TAAAATGACCGAAATACCCTCAAAGGATAAAATGATCGAAATACCCTCGA-AGG-TAAAATGACC
*
41062740 AAAATACCCCCGAAGGG
64 GAAATACCCCCGAAGGG
* ** * * **
41062757 TAAAAAGACTAAAATACCCTCGAAGGGTAAAATGA-CTGAAATACCCTCGAAGGGTAAAATGATT
1 TAAAATGACCGAAATACCCTCAAAGGATAAAATGATC-GAAATACCCTCGAA-GGTAAAATGACC
41062821 GAAATACCCCCGAAGGG
64 GAAATACCCCCGAAGGG
*
41062838 TAAAATGACCGAAATA-CCTCCGAAA-GATAAAATGATTGAAATACCC-CTGAAGGATAAAATGA
1 TAAAATGACCGAAATACCCT-C-AAAGGATAAAATGATCGAAATACCCTC-GAAGG-TAAAATGA
*
41062900 CCGAAATA-CCCCGAAGGA
62 CCGAAATACCCCCGAAGGG
41062918 TAAAAT
1 TAAAAT
41062924 AATTATTATA
Statistics
Matches: 211, Mismatches: 26, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
79 1 0.00
80 26 0.12
81 179 0.85
82 5 0.02
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (80 bp):
TAAAATGACCGAAATACCCTCAAAGGATAAAATGATCGAAATACCCTCGAAGGTAAAATGACCGA
AATACCCCCGAAGGG
Found at i:41063161 original size:26 final size:26
Alignment explanation
Indices: 41063102--41063176 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
41063092 TGCCACATAT
* *
41063102 ACTATTACTGGCAGCTTTACTGCATT
1 ACTATTACTGGCAGCTTTGCTGCATC
* *
41063128 GCTGTTACTGGCAGCTTTGCTGCATC
1 ACTATTACTGGCAGCTTTGCTGCATC
* *
41063154 ATTATTACTGGTAGCTTTGCTGC
1 ACTATTACTGGCAGCTTTGCTGC
41063177 GATTTTGGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (26 bp):
ACTATTACTGGCAGCTTTGCTGCATC
Found at i:41071740 original size:17 final size:18
Alignment explanation
Indices: 41071718--41071751 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41071708 TGTGGTTGGT
41071718 AGGAAA-AAAATGAAAAG
1 AGGAAAGAAAATGAAAAG
41071735 AGGAAAGAAAATGAAAA
1 AGGAAAGAAAATGAAAA
41071752 AAATGAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (18 bp):
AGGAAAGAAAATGAAAAG
Found at i:41087378 original size:18 final size:19
Alignment explanation
Indices: 41087355--41087391 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41087345 TTTTTAAAAA
41087355 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
41087373 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
41087392 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:41087392 original size:18 final size:18
Alignment explanation
Indices: 41087355--41087408 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
41087345 TTTTTAAAAA
41087355 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAA-TTT
41087373 TATAAATATTTAGAATTT
1 TATAAATATTTAGAATTT
* *
41087391 TAAAAATTATTTTGAATT
1 TATAAA-TATTTAGAATT
41087409 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TATAAATATTTAGAATTT
Found at i:41088642 original size:5 final size:5
Alignment explanation
Indices: 41088632--41088657 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41088622 TTCTTCGTGT
41088632 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
41088658 ATATATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:41088666 original size:15 final size:15
Alignment explanation
Indices: 41088632--41088665 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41088622 TTCTTCGTGT
*
41088632 TTTTATTTTATTTTA
1 TTTTATTTTATTATA
41088647 TTTTATTTTATATATA
1 TTTTATTTTAT-TATA
41088663 TTT
1 TTT
41088666 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTATTATA
Found at i:41088919 original size:30 final size:30
Alignment explanation
Indices: 41088848--41088978 Score: 115
Period size: 30 Copynumber: 4.4 Consensus size: 30
41088838 AAAAAAATAT
* * *
41088848 AAATTACA-TTCGGACTCCTAAATTTTCTTT
1 AAATTACATTTTGGAC-CCTAAACTTTCTTA
* **
41088878 GAATTGTATTTTGGACCCTAAACTTTCTTA
1 AAATTACATTTTGGACCCTAAACTTTCTTA
* * *
41088908 AAATTTCATTTT-GACCACTTAACTTTCTAA
1 AAATTACATTTTGGACC-CTAAACTTTCTTA
* * *
41088938 AAATTACATTTTGG-CCCCATATTTTCTTA
1 AAATTACATTTTGGACCCTAAACTTTCTTA
41088967 AAATTACATTTT
1 AAATTACATTTT
41088979 TTCCCAGAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
29 24 0.30
30 50 0.62
31 7 0.09
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (30 bp):
AAATTACATTTTGGACCCTAAACTTTCTTA
Found at i:41089701 original size:19 final size:20
Alignment explanation
Indices: 41089668--41089713 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
41089658 TTGGGTTTTC
*
41089668 GAAAGAAGAAAAAAGTAGAA
1 GAAAGAAGAAAAAAGAAGAA
*
41089688 GGAAGAAG-AAAAAGAAGAA
1 GAAAGAAGAAAAAAGAAGAA
41089707 GAAAGAA
1 GAAAGAA
41089714 AATAAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (20 bp):
GAAAGAAGAAAAAAGAAGAA
Found at i:41089712 original size:16 final size:16
Alignment explanation
Indices: 41089670--41089715 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
41089660 GGGTTTTCGA
*
41089670 AAGAAGAAA-AAAGTAG
1 AAGAAGAAAGAAA-AAG
41089686 AAGGAAG-AAGAAAAAG
1 AA-GAAGAAAGAAAAAG
41089702 AAGAAGAAAGAAAA
1 AAGAAGAAAGAAAA
41089716 TAAAAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:41089724 original size:19 final size:19
Alignment explanation
Indices: 41089684--41089733 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
41089674 AGAAAAAAGT
* *
41089684 AGAAGGAAGAAGAA-AAAGA
1 AGAAGAAAGAA-AATAAAAA
41089703 AGAAGAAAGAAAATAAAAA
1 AGAAGAAAGAAAATAAAAA
41089722 AG-AGAAA-AAAAT
1 AGAAGAAAGAAAAT
41089734 TTAAATCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.18
18 7 0.25
19 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (19 bp):
AGAAGAAAGAAAATAAAAA
Found at i:41089935 original size:17 final size:19
Alignment explanation
Indices: 41089913--41089955 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
41089903 AGGCCAACTA
*
41089913 CCAGGCCAG-CA-CAGCGC
1 CCAGGCCAGCCAGCAGCCC
*
41089930 CCAGGCGAGCCAGCAGCCC
1 CCAGGCCAGCCAGCAGCCC
41089949 CCAGGCC
1 CCAGGCC
41089956 CAGCGTAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 11 0.52
ACGTcount: A:0.21, C:0.49, G:0.30, T:0.00
Consensus pattern (19 bp):
CCAGGCCAGCCAGCAGCCC
Found at i:41090625 original size:17 final size:16
Alignment explanation
Indices: 41090539--41090803 Score: 91
Period size: 17 Copynumber: 14.9 Consensus size: 16
41090529 AAAAAATCAA
41090539 AAAAATTTCGTGTTTC
1 AAAAATTTCGTGTTTC
* *
41090555 AAAAATCTTTGTGCTTC
1 AAAAAT-TTCGTGTTTC
* *
41090572 CAAAATTTCGGTATTTC
1 AAAAATTTC-GTGTTTC
* *
41090589 AAAAATTTTTCATATTTTC
1 AAAAA--TTTCGT-GTTTC
*
41090608 AAAAATTTCCGTGCTTC
1 AAAAATTT-CGTGTTTC
* *
41090625 AAAAAAAAATTCGTCCTTTC
1 ---AAAAATTTCGT-GTTTC
* *
41090645 AACAATTTTCGTG-TTA
1 AA-AAATTTCGTGTTTC
*
41090661 AAAAAATTCGTGTTTC
1 AAAAATTTCGTGTTTC
41090677 AAAAAAATTCTCGTGTTTC
1 --AAAAATT-TCGTGTTTC
* *
41090696 ATAAATTTTTGTGTTTTC
1 A-AAAATTTCGTG-TTTC
*
41090714 AAAAAAAAAATTTCTCGTGCTTC
1 -----AAAAA-TT-TCGTGTTTC
*
41090737 GAAAATTTCGTGTTTTC
1 AAAAATTTCGTG-TTTC
* *
41090754 AAAAGTTTTTGTGTTTC
1 AAAA-ATTTCGTGTTTC
* * *
41090771 GAAATTTTCGTGTCTC
1 AAAAATTTCGTGTTTC
41090787 AATAAATTCTCGTGTTT
1 AA-AAATT-TCGTGTTT
41090804 TTTAAATATT
Statistics
Matches: 182, Mismatches: 39, Indels: 54
0.66 0.14 0.20
Matches are distributed among these distances:
15 8 0.04
16 30 0.16
17 54 0.30
18 42 0.23
19 25 0.14
20 10 0.05
22 3 0.02
23 6 0.03
24 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:41090645 original size:37 final size:32
Alignment explanation
Indices: 41090604--41090681 Score: 84
Period size: 37 Copynumber: 2.3 Consensus size: 32
41090594 TTTTTCATAT
41090604 TTTCAAAAATTTCCGTGCTTCAAAAAAAAATTCGTCC
1 TTTCAAAAATTTCCGTG-TT---AAAAAAATTCGT-C
* * *
41090641 TTTCAACAATTTTCGTGTTAAAAAAATTCGTG
1 TTTCAAAAATTTCCGTGTTAAAAAAATTCGTC
41090673 TTTCAAAAA
1 TTTCAAAAA
41090682 AATTCTCGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 8 0.22
33 12 0.32
36 2 0.05
37 15 0.41
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (32 bp):
TTTCAAAAATTTCCGTGTTAAAAAAATTCGTC
Found at i:41090690 original size:19 final size:18
Alignment explanation
Indices: 41090535--41090720 Score: 86
Period size: 18 Copynumber: 10.5 Consensus size: 18
41090525 AAGAAAAAAA
41090535 TCAAAAAAATTTCGTGTT
1 TCAAAAAAATTTCGTGTT
** *
41090553 TCAAAAATCTTT-GTGCT
1 TCAAAAAAATTTCGTGTT
* *
41090570 TC--CAAAATTTCGGTATT
1 TCAAAAAAATTTC-GTGTT
** * *
41090587 TCAAAAATTTTTCATATTT
1 TCAAAAAAATTTCGT-GTT
*
41090606 TC--AAAAATTTCCGTGCT
1 TCAAAAAAATTT-CGTGTT
* *
41090623 TCAAAAAAAAATTCGTCCTT
1 TC-AAAAAAATTTCGT-GTT
* *
41090643 TC-AACAATTTTCGTG-T
1 TCAAAAAAATTTCGTGTT
41090659 T-AAAAAAA-TTCGTGTT
1 TCAAAAAAATTTCGTGTT
41090675 TCAAAAAAATTCTCGTGTT
1 TCAAAAAAATT-TCGTGTT
* * *
41090694 TC-ATAAATTTTTGTGTTT
1 TCAAAAAAATTTCGTG-TT
41090712 TCAAAAAAA
1 TCAAAAAAA
41090721 AAATTTCTCG
Statistics
Matches: 119, Mismatches: 32, Indels: 33
0.65 0.17 0.18
Matches are distributed among these distances:
15 11 0.09
16 8 0.07
17 31 0.26
18 33 0.28
19 26 0.22
20 10 0.08
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (18 bp):
TCAAAAAAATTTCGTGTT
Found at i:41090750 original size:40 final size:40
Alignment explanation
Indices: 41090677--41090757 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
41090667 TTCGTGTTTC
* *
41090677 AAAAAAATTCTCGTGTTTCATAAATTTTTGTGTTTTCAAA
1 AAAAAAATTCTCGTGCTTCATAAATTTTCGTGTTTTCAAA
41090717 AAAAAAATTTCTCGTGCTTCGA-AAA-TTTCGTGTTTTCAAA
1 AAAAAAA-TTCTCGTGCTTC-ATAAATTTTCGTGTTTTCAAA
41090757 A
1 A
41090758 GTTTTTGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 22 0.59
41 14 0.38
42 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (40 bp):
AAAAAAATTCTCGTGCTTCATAAATTTTCGTGTTTTCAAA
Found at i:41099246 original size:75 final size:76
Alignment explanation
Indices: 41099033--41099700 Score: 745
Period size: 75 Copynumber: 8.7 Consensus size: 76
41099023 AGAATTATAT
41099033 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CT
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC-
*
41099097 ATACACCGAGGTA
65 AT-CACTGAGGTA
* *
41099110 TTTTTAATTTATGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
41099174 TC-CTAAGGTA
66 TCACTGAGGTA
*
41099184 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTAAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
41099249 TC-CTGAGGTA
66 TCACTGAGGTA
* * *
41099259 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
41099324 TC-CTGAGGTA
66 TCACTGAGGTA
* * * *
41099334 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGTCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
41099399 -CGCTGAGGTA
66 TCACTGAGGTA
* * *
41099409 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCTG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-T-
*
41099474 CA-CGCTGAGGTA
64 CATCACTGAGGTA
* * * *
41099486 TTTTTTTAATTTAT-TTTAAAAAAAATCAAATCAAAACCAACTCATAATGCGAGAGGTGAGTTGA
1 --TTTTCAATTTCTGTTT-------TTCAAA--AAAATCAACTCATAATGCGAGAGGTGAGTTGA
* *
41099550 GACTTGGG-CTATACACTGAGGTA
55 GCCTCGGGTC-AT-CACTGAGGTA
* * * * *
41099573 TTTTTAATTTCTGTTTTTC--AAAAATCAACTTATATTGTGAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
41099636 T-ATGCCGAGGTA
66 TCA--CTGAGGTA
* ** *
41099648 TTTTTCAATTTCTATTTTTC--AAAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 -TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGC-GAGAGGTGAGTTGA
41099701 ACTTCGAATC
Statistics
Matches: 522, Mismatches: 44, Indels: 51
0.85 0.07 0.08
Matches are distributed among these distances:
73 1 0.00
74 24 0.05
75 298 0.57
76 89 0.17
77 31 0.06
78 2 0.00
79 12 0.02
84 1 0.00
85 17 0.03
86 3 0.01
87 44 0.08
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (76 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
TCACTGAGGTA
Found at i:41100183 original size:30 final size:29
Alignment explanation
Indices: 41100149--41100220 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
41100139 AAACTTTTTT
* *
41100149 AAAATTTCATTTTGACCCCTTAATTTTCTA
1 AAAATTACATTTTGACCCCAT-ATTTTCTA
* * *
41100179 AAAATTACATTTTGGCCTCATATTTTTTA
1 AAAATTACATTTTGACCCCATATTTTCTA
41100208 AAAATTACATTTT
1 AAAATTACATTTT
41100221 CCCCAGAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.47
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCATATTTTCTA
Found at i:41100752 original size:18 final size:19
Alignment explanation
Indices: 41100726--41100776 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
41100716 GCCAAAATAG
*
41100726 AAGAGAAAGAGAAAGAA-A
1 AAGAAAAAGAGAAAGAACA
*
41100744 AAGAAAAAGGGAAA-AACA
1 AAGAAAAAGAGAAAGAACA
*
41100762 AAAAAAAAGAGAAAG
1 AAGAAAAAGAGAAAG
41100777 CTTTTCGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (19 bp):
AAGAAAAAGAGAAAGAACA
Found at i:41100922 original size:10 final size:10
Alignment explanation
Indices: 41100904--41100968 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
41100894 AGGGTTTTCG
41100904 AAAGAAGAAA
1 AAAGAAGAAA
* *
41100914 AAAGTAGAAG
1 AAAGAAGAAA
*
41100924 GAAGAAGAAAA
1 AAAGAAG-AAA
41100935 AGAAGAAGAAAGA
1 A-AAGAAG-AA-A
41100948 AAAGAA-AAA
1 AAAGAAGAAA
41100957 AAAG-AGAAA
1 AAAGAAGAAA
41100966 AAA
1 AAA
41100969 ATTTAAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.02
9 11 0.24
10 15 0.33
11 2 0.04
12 14 0.31
13 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (10 bp):
AAAGAAGAAA
Found at i:41100936 original size:19 final size:20
Alignment explanation
Indices: 41100903--41100965 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
41100893 TAGGGTTTTC
*
41100903 GAAAGAAGAAAAAAGTAGAA
1 GAAAGAAGAAAAAAGAAGAA
*
41100923 GGAAGAAG-AAAAAGAAGAA
1 GAAAGAAGAAAAAAGAAGAA
41100942 GAAAGAAAAGAAAAAA-AAG-A
1 GAAAG--AAGAAAAAAGAAGAA
41100962 GAAA
1 GAAA
41100966 AAAATTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 14 0.38
20 12 0.32
21 6 0.16
22 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (20 bp):
GAAAGAAGAAAAAAGAAGAA
Found at i:41100941 original size:12 final size:12
Alignment explanation
Indices: 41100924--41100969 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
41100914 AAAGTAGAAG
41100924 GAAGAAGAAAAA
1 GAAGAAGAAAAA
41100936 GAAGAAGAAAGAA
1 GAAGAAGAAA-AA
*
41100949 -AAGAAAAAAAA
1 GAAGAAGAAAAA
41100960 G-AGAA-AAAAA
1 GAAGAAGAAAAA
41100970 TTTAAATCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 5 0.16
11 6 0.19
12 18 0.58
13 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:41100947 original size:16 final size:16
Alignment explanation
Indices: 41100905--41100950 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
41100895 GGGTTTTCGA
*
41100905 AAGAAGAAA-AAAGTAG
1 AAGAAGAAAGAAA-AAG
41100921 AAGGAAG-AAGAAAAAG
1 AA-GAAGAAAGAAAAAG
41100937 AAGAAGAAAGAAAA
1 AAGAAGAAAGAAAA
41100951 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:41101309 original size:16 final size:16
Alignment explanation
Indices: 41101288--41101324 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
41101278 GCAGCAGCAA
41101288 AAAAAAAAGAGA-AAAG
1 AAAAAAAAG-GACAAAG
41101304 AAAAAAAAGGACAAAG
1 AAAAAAAAGGACAAAG
41101320 AAAAA
1 AAAAA
41101325 GAAAAAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGGACAAAG
Found at i:41101309 original size:17 final size:17
Alignment explanation
Indices: 41101287--41101329 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
41101277 GGCAGCAGCA
41101287 AAAAAAAAAGAGA-AAAG
1 AAAAAAAAAG-GACAAAG
41101304 -AAAAAAAAGGACAAAG
1 AAAAAAAAAGGACAAAG
41101320 AAAAAGAAAA
1 AAAAA-AAAA
41101330 AGGAAAGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 13 0.57
17 4 0.17
18 4 0.17
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGGACAAAG
Found at i:41101336 original size:17 final size:16
Alignment explanation
Indices: 41101286--41101336 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
41101276 CGGCAGCAGC
41101286 AAAAAAAAAAGAGAAA-
1 AAAAAAAAAAG-GAAAG
*
41101302 AGAAAAAAAAGGACAAAG
1 AAAAAAAAAAGG--AAAG
41101320 AAAAAGAAAAAGGAAAG
1 AAAAA-AAAAAGGAAAG
41101337 GCCCAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 1 0.03
16 10 0.34
17 7 0.24
18 4 0.14
19 7 0.24
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGGAAAG
Found at i:41101856 original size:18 final size:17
Alignment explanation
Indices: 41101796--41102051 Score: 141
Period size: 17 Copynumber: 14.5 Consensus size: 17
41101786 ATAAAAAAAA
41101796 TTCGTGTTTCAAAAATCT
1 TTCGTGTTTCAAAAAT-T
*
41101814 TT-GTGTTTCCAAAA-T
1 TTCGTGTTTCAAAAATT
*
41101829 TTCGGTATTTCAAAAATTT
1 TTC-GTGTTTCAAAAA-TT
* *
41101848 TTCGTATTTTTAAAAATT
1 TTCGT-GTTTCAAAAATT
* **
41101866 TCCGTGTTTCAAAAAAAA
1 TTCGTGTTTC-AAAAATT
*
41101884 TT-GTGTTTTCAACAATT
1 TTCGTG-TTTCAAAAATT
*
41101901 TTCGTGTTT-AAAAA-A
1 TTCGTGTTTCAAAAATT
41101916 TTCGTGTTTCAAAAAAATT
1 TTCGTGTTTC--AAAAATT
* *
41101935 CTCGTGTTTCATAAATT
1 TTCGTGTTTCAAAAATT
41101952 TTCGTGTTTTCAAAAAAAAATT
1 TTCGTG-TTTC----AAAAATT
* *
41101974 TCCCGTGCTTT-GAAAA-T
1 T-TCGTG-TTTCAAAAATT
*
41101991 TTCGTGTTTTCAAAAGTT
1 TTCGTG-TTTCAAAAATT
* *
41102009 TTTGTGTTTC-GAAATT
1 TTCGTGTTTCAAAAATT
*
41102025 TTCGTGTCTCAATAAATT
1 TTCGTGTTTCAA-AAATT
*
41102043 CTCGTGTTT
1 TTCGTGTTT
41102052 TTTTTAAATA
Statistics
Matches: 180, Mismatches: 36, Indels: 44
0.69 0.14 0.17
Matches are distributed among these distances:
15 12 0.07
16 23 0.13
17 56 0.31
18 54 0.30
19 21 0.12
22 7 0.04
23 7 0.04
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (17 bp):
TTCGTGTTTCAAAAATT
Found at i:41101994 original size:39 final size:37
Alignment explanation
Indices: 41101903--41102005 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 37
41101893 CAACAATTTT
* *
41101903 CGTGTTTAAAAAATTCGTG-TTTC--AAAAAAATTCT
1 CGTGTTTAAAAATTTCGTGTTTTCAAAAAAAAATTCC
*
41101937 CGTGTTTCATAAATTTTCGTGTTTTCAAAAAAAAATTTCC
1 CGTGTTT-A-AAAATTTCGTGTTTTCAAAAAAAAA-TTCC
*
41101977 CGTGCTTTGAAAATTTCGTGTTTTCAAAA
1 CGTG-TTTAAAAATTTCGTGTTTTCAAAA
41102006 GTTTTTGTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
34 7 0.12
35 1 0.02
36 9 0.16
37 4 0.07
39 26 0.46
40 7 0.12
41 3 0.05
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (37 bp):
CGTGTTTAAAAATTTCGTGTTTTCAAAAAAAAATTCC
Found at i:41103908 original size:16 final size:16
Alignment explanation
Indices: 41103875--41103908 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41103865 GCTTATTGTT
* *
41103875 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
41103891 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
41103907 AA
1 AA
41103909 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:41106736 original size:21 final size:21
Alignment explanation
Indices: 41106710--41106750 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41106700 AGACGAGCAA
* *
41106710 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
41106731 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
41106751 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:41108689 original size:16 final size:16
Alignment explanation
Indices: 41108656--41108689 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41108646 GGAGATTGTT
* *
41108656 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
41108672 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
41108688 AA
1 AA
41108690 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:41117295 original size:114 final size:114
Alignment explanation
Indices: 41117175--41117891 Score: 807
Period size: 114 Copynumber: 6.3 Consensus size: 114
41117165 GCGCTTACGA
* * * * * *
41117175 AAAAACGCCGGTAATGTATAGTATTAGCGGCGCTTATGGGAAGCGCCGCAAA-CGATGTTAACCA
1 AAAAACGCCGCTAAAGTATAGTATTAGCGGCGTTTGTCGGAAGCGCCGCAAATC-ATCTTAACCA
* * *
41117239 AAACGCAGAG-TTTGGTCTTGATGTA-TATT-GCAATTAGTGGCGCTT-ATAA
65 AAACGCAGAGTTTTGGTCTTTA-GGAGTATTAG-AATTAGTGGCGCTTGAT-T
* * * ** * *
41117288 ATAAAACGCCGCTAATGTATAGTATTAGCGGCGCATAG-CATTAAACGCCGCAAGAT-ATCCTAA
1 A-AAAACGCCGCTAAAGTATAGTATTAGCGGCG-TTTGTC-GGAAGCGCCGCAA-ATCATCTTAA
* *** * * * * * **
41117351 TCAAAACGCTCCGTTTTGGTCTTGATGTA-TACTATAATTAGTGGCG-TTTAAG
62 CCAAAACGCAGAGTTTTGGTCTTTA-GGAGTATTAGAATTAGTGGCGCTTGATT
* * * * *
41117403 GAAAACGCCAG-TAAAGGATAGT-TATAGCAGCGTTTGGTGGGAAGCGCCTCCAAAT-ATCTTAA
1 AAAAACGCC-GCTAAAGTATAGTAT-TAGCGGCGTTT-GTCGGAAGCGCC-GCAAATCATCTTAA
41117465 CCAAAACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTGGCGCTTGATT
62 CCAAAACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTGGCGCTTGATT
* *
41117518 AAAAACGCCGCTAAAGTATA-TCATCAGCGGCGTTTGTCGGATGCGCCGCAAATCATCTTAACCA
1 AAAAACGCCGCTAAAGTATAGT-ATTAGCGGCGTTTGTCGGAAGCGCCGCAAATCATCTTAACCA
*
41117582 AAACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTCGCGCTTGATT
65 AAACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTGGCGCTTGATT
* *
41117632 AAAAACGCCGCTAAAGTATA-TCATCAGCGGCGTTTGTCGGATGCGCCGCAAATCATCTTAACCA
1 AAAAACGCCGCTAAAGTATAGT-ATTAGCGGCGTTTGTCGGAAGCGCCGCAAATCATCTTAACCA
41117696 AAACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTGGCGCTTGATT
65 AAACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTGGCGCTTGATT
* * *
41117746 AAAAACGCCGCTAAAGTATA-TCATCAGCGGCATTTGTCGGATGCGCCGCAAATCATCTTAACCA
1 AAAAACGCCGCTAAAGTATAGT-ATTAGCGGCGTTTGTCGGAAGCGCCGCAAATCATCTTAACCA
*
41117810 AAACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTGGCGCTTGGTT
65 AAACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTGGCGCTTGATT
*
41117860 AAAAACGCCGCTGAAGTATAGTATTAGCGGCG
1 AAAAACGCCGCTAAAGTATAGTATTAGCGGCG
41117892 CTTTTACGAA
Statistics
Matches: 529, Mismatches: 55, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
113 10 0.02
114 427 0.81
115 60 0.11
116 32 0.06
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (114 bp):
AAAAACGCCGCTAAAGTATAGTATTAGCGGCGTTTGTCGGAAGCGCCGCAAATCATCTTAACCAA
AACGCAGAGTTTTGGTCTTTAGGAGTATTAGAATTAGTGGCGCTTGATT
Found at i:41118018 original size:18 final size:18
Alignment explanation
Indices: 41117997--41118032 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
41117987 TCATTTTATA
41117997 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
41118015 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
41118033 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:41118114 original size:10 final size:11
Alignment explanation
Indices: 41118093--41118122 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
41118083 AATAGTATTA
41118093 TTTAAAATAAT
1 TTTAAAATAAT
41118104 TTTAAAA-AAT
1 TTTAAAATAAT
41118114 TTTAAAATA
1 TTTAAAATA
41118123 CATGACTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTAAAATAAT
Found at i:41118964 original size:7 final size:7
Alignment explanation
Indices: 41118943--41119022 Score: 106
Period size: 7 Copynumber: 11.3 Consensus size: 7
41118933 TTTATTGCTC
41118943 GGGGTTTT
1 GGGG-TTT
41118951 GGGGTTT
1 GGGGTTT
*
41118958 AGGGTTT
1 GGGGTTT
*
41118965 GGGATTT
1 GGGGTTT
41118972 GGGGTTT
1 GGGGTTT
*
41118979 AGGGTTT
1 GGGGTTT
41118986 GGGGTTT
1 GGGGTTT
41118993 GGGGTTT
1 GGGGTTT
41119000 GGGGTTT
1 GGGGTTT
*
41119007 GAGGTTT
1 GGGGTTT
*
41119014 GGGGATT
1 GGGGTTT
41119021 GG
1 GG
41119023 TTTTTGAGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
7 59 0.94
8 4 0.06
ACGTcount: A:0.06, C:0.00, G:0.53, T:0.41
Consensus pattern (7 bp):
GGGGTTT
Found at i:41119022 original size:21 final size:21
Alignment explanation
Indices: 41118948--41119034 Score: 106
Period size: 21 Copynumber: 4.1 Consensus size: 21
41118938 TGCTCGGGGT
41118948 TTTGGGGTTTAGGGTTTG-GG
1 TTTGGGGTTTAGGGTTTGAGG
*
41118968 ATTTGGGGTTTAGGGTTTGGGG
1 -TTTGGGGTTTAGGGTTTGAGG
*
41118990 TTTGGGGTTTGGGGTTTGAGG
1 TTTGGGGTTTAGGGTTTGAGG
* *
41119011 TTTGGGGATT-GGTTTTTGAGG
1 TTTGGGGTTTAGG-GTTTGAGG
41119032 TTT
1 TTT
41119035 AAGGATTAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.46
Consensus pattern (21 bp):
TTTGGGGTTTAGGGTTTGAGG
Found at i:41121647 original size:31 final size:31
Alignment explanation
Indices: 41121609--41121672 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
41121599 GAACGACGAA
*
41121609 CTGTATGAGGGATCAAAATTTTCAAAAATGT
1 CTGTATGAGGGATCAAAATATTCAAAAATGT
41121640 CTGTATGAGGGATCAAAATATTCAAAAATGT
1 CTGTATGAGGGATCAAAATATTCAAAAATGT
41121671 CT
1 CT
41121673 TTCTATGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (31 bp):
CTGTATGAGGGATCAAAATATTCAAAAATGT
Found at i:41126572 original size:21 final size:21
Alignment explanation
Indices: 41126546--41126615 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
41126536 CAACAACTTA
* *
41126546 AAGCAGAGGCGACAGCGCGAG
1 AAGCAGAAGCGACAGCGAGAG
*
41126567 AAGCAGAAGCTACAGCGAGAG
1 AAGCAGAAGCGACAGCGAGAG
*
41126588 AAGCAGAAGCTG-CAGCAAGAG
1 AAGCAGAAGC-GACAGCGAGAG
41126609 AAGCAGA
1 AAGCAGA
41126616 GCAGGCCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.41, C:0.20, G:0.36, T:0.03
Consensus pattern (21 bp):
AAGCAGAAGCGACAGCGAGAG
Found at i:41127203 original size:42 final size:42
Alignment explanation
Indices: 41126977--41127261 Score: 394
Period size: 43 Copynumber: 6.7 Consensus size: 42
41126967 AAGAATAAAT
*
41126977 GCCGCTAAAAGAGCAT-TGTCTTTAGCGGCGTTTCTTTTCTAAGC
1 GCCGCT-AAAGAACATGT-TCTTTAGCGGCGTTTC-TTTCTAAGC
* *
41127021 GTCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTTTTAAAGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTTCT-AAGC
* * *
41127064 GCCGCTAAAGAACATTTTCTTTAGTGGCGTTTCTTTTTAAAGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTTCT-AAGC
* *
41127107 ACCGCTAAAGAACATTTTCTTTAGCGGCGTTTCTTTTCTAAGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTC-TTTCTAAGC
*
41127150 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCGTTCTAAGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTTCTAAGC
*
41127192 GCCGCTGAAGAACATGTTCTTTAGCGGCGTTT-TTTCCTAAGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTT-CTAAGC
*
41127234 GCCGCTAAAGAACATGGTCTTTAGCGGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGC
41127262 ACTTTTATTT
Statistics
Matches: 221, Mismatches: 16, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
41 2 0.01
42 75 0.34
43 134 0.61
44 10 0.05
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTTCTAAGC
Found at i:41131656 original size:89 final size:89
Alignment explanation
Indices: 41131449--41131678 Score: 277
Period size: 92 Copynumber: 2.6 Consensus size: 89
41131439 AAGCCCTTTT
* * *
41131449 TTTTTGTTTGCACTCAATTGGGTATTTGAACTTTCAAAATGCATCAAAAAAGCCCTCAAACTATT
1 TTTTT-TTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCAT-TAAAAAGCCCGCAAAC--TT
*
41131514 TTAAAAAAAAAAGCAATTAAGCCCCTAC
62 TTAAAAAAAAAAGCAATTAAGCCACTAC
* *
41131542 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCTCGCAAGC-TTTAA
1 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCCCGCAAACTTTTAA
* *
41131606 AAAATAAAA-CAATTAAGCCATTGAG
66 AAAA-AAAAGCAATTAAGCCACT-AC
* ** *
41131631 TTTTTTTGGCACTCAATTTAGTACTTGAACTGT-AAAATGCATTAAAAA
1 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAA
41131679 TACTCTCTGA
Statistics
Matches: 123, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
88 35 0.28
89 34 0.28
91 12 0.10
92 37 0.30
93 5 0.04
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (89 bp):
TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCCCGCAAACTTTTAA
AAAAAAAAGCAATTAAGCCACTAC
Found at i:41132293 original size:77 final size:77
Alignment explanation
Indices: 41132166--41132318 Score: 279
Period size: 77 Copynumber: 2.0 Consensus size: 77
41132156 TTTAGAGGAG
*
41132166 TTTGAAAGTGTTTCAAATTAGAGGTGTTGAGAGATTTGGGGAGTAGAATTAGGGGTGTAGTAGTA
1 TTTGAAAGTGTTTCAAATTAGAGGTGTTGAGAGATTTGGGGAGTAGAATTAAGGGTGTAGTAGTA
41132231 GTTGGCTGAAAT
66 GTTGGCTGAAAT
* *
41132243 TTTGAAAGTGTTTCAAATTAGGGGTGTTGAGAGATTTGGGGAGTGGAATTAAGGGTGTAGTAGTA
1 TTTGAAAGTGTTTCAAATTAGAGGTGTTGAGAGATTTGGGGAGTAGAATTAAGGGTGTAGTAGTA
41132308 GTTGGCTGAAA
66 GTTGGCTGAAA
41132319 GTAGGTTTCC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.33
Consensus pattern (77 bp):
TTTGAAAGTGTTTCAAATTAGAGGTGTTGAGAGATTTGGGGAGTAGAATTAAGGGTGTAGTAGTA
GTTGGCTGAAAT
Found at i:41133701 original size:27 final size:27
Alignment explanation
Indices: 41133650--41134228 Score: 685
Period size: 27 Copynumber: 21.5 Consensus size: 27
41133640 AAAGGTTATT
* *
41133650 AAATGACCATAATGTCCCTTGTAGGGTA
1 AAATGACCGTAATG-CCCCTGTAGGGTA
* * * * *
41133678 AAATTATCGTAATACCCCTATAGGGAA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* **
41133705 AAATGACCGTAATACCCCCATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * * * **
41133732 AAATAACCGTAATACTCCTATAGAATA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
41133759 AAATGACCGTAATACCCC-ATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
41133785 AAATAACCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * ** * * *
41133812 AATTAATTGTAATACCTCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * * *
41133839 AAATGATCGTAATACCCTTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
41133866 AAATGACCGTAATGCCCTTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
41133893 AAATGACCGTAATGCCCTTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
41133920 AAATGACCGTAATGCCCCTGTAGGGT-
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
41133946 AAATGTCCGTAATGCCTCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
41133973 AAATGACCGTAATGCCTCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
41134000 AAATAATCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
41134027 AAATGACCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
41134054 AAATGACCGTAATGCCCTTATAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
41134081 AAATGACCATAATGCCCTTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
41134108 AAATGACCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
41134135 AAATGATCATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
41134162 AAATGATCGTAATGCCCTTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
41134189 AAATGACCGTAATGCCCCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
41134216 AAATGATCGTAAT
1 AAATGACCGTAAT
41134229 ACCCTCGAGG
Statistics
Matches: 483, Mismatches: 66, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
26 45 0.09
27 428 0.89
28 10 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
AAATGACCGTAATGCCCCTGTAGGGTA
Found at i:41134293 original size:24 final size:24
Alignment explanation
Indices: 41134265--41134323 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
41134255 TCTACAGTTA
* *
41134265 AATGACTGATTTTTTTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
* *
41134289 TATGATTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
41134313 AATGACTGATT
1 AATGACTGATT
41134324 CTGAGCATGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.20, C:0.05, G:0.24, T:0.51
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:41134477 original size:26 final size:26
Alignment explanation
Indices: 41134448--41134498 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
41134438 TATACTATAT
*
41134448 TGGCAGCTTTGCTGCGATACTACTGC
1 TGGCAACTTTGCTGCGATACTACTGC
* *
41134474 TGGCAACTTTGTTGCGATGCTACTG
1 TGGCAACTTTGCTGCGATACTACTG
41134499 ATGCCTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (26 bp):
TGGCAACTTTGCTGCGATACTACTGC
Found at i:41134539 original size:32 final size:31
Alignment explanation
Indices: 41134494--41134682 Score: 189
Period size: 32 Copynumber: 5.9 Consensus size: 31
41134484 GTTGCGATGC
* *
41134494 TACTGATGCCTTTGTGCCGATCATATTATCAT
1 TACTGATG-CTTTGTGCCGATCATATTACCGT
* *
41134526 CACTGATAGCTTTGTGCCAATCATATTACCGT
1 TACTGAT-GCTTTGTGCCGATCATATTACCGT
* *
41134558 TATTGATGATTTTGTGCCGATCATATTACCGT
1 TACTGATG-CTTTGTGCCGATCATATTACCGT
*
41134590 TACTGATGGCTTTGTACCGATCATATTACCGT
1 TACTGAT-GCTTTGTGCCGATCATATTACCGT
* * * * *
41134622 TATTGATGGCTGTGTGCCGATCATATCACTGC
1 TACTGAT-GCTTTGTGCCGATCATATTACCGT
* * *
41134654 TATTGATGGCTTTGTGCCAAACATATTAC
1 TACTGAT-GCTTTGTGCCGATCATATTAC
41134683 TGTACTTATG
Statistics
Matches: 133, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
31 1 0.01
32 130 0.98
33 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (31 bp):
TACTGATGCTTTGTGCCGATCATATTACCGT
Found at i:41134602 original size:64 final size:64
Alignment explanation
Indices: 41134497--41134682 Score: 237
Period size: 64 Copynumber: 2.9 Consensus size: 64
41134487 GCGATGCTAC
* * * * *
41134497 TGATGCCTTTGTGCCGATCATATTATCATCACTGATAGCTTTGTGCCAATCATATTACCGTTAT
1 TGATGACTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGCCAATCATATTACCGTTAT
* * *
41134561 TGATGATTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTACCGATCATATTACCGTTAT
1 TGATGACTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGCCAATCATATTACCGTTAT
* * * * * * *
41134625 TGATGGCTGTGTGCCGATCATATCACTGCTATTGATGGCTTTGTGCCAAACATATTAC
1 TGATGACTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGCCAATCATATTAC
41134683 TGTACTTATG
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 104 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (64 bp):
TGATGACTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGCCAATCATATTACCGTTAT
Found at i:41134658 original size:96 final size:95
Alignment explanation
Indices: 41134494--41134696 Score: 235
Period size: 96 Copynumber: 2.1 Consensus size: 95
41134484 GTTGCGATGC
* * * * * *
41134494 TACTGATGCCTTTGTGCCGATCATATTATCATCACTGATAGCTTTGTGCCAATCATATTACCGTT
1 TACTGATGGCTTTGTACCGATCATATTACCATCACTGATAGCTGTGTGCCAATCATATCACCGCT
* * *
41134559 ATTGATGATTTTGTGCCGATCATATTACCG
66 ATTGATGACTTTGTGCCAAACATATTACCG
* * * * * *
41134589 TTACTGATGGCTTTGTACCGATCATATTACCGTTATTGATGGCTGTGTGCCGATCATATCACTGC
1 -TACTGATGGCTTTGTACCGATCATATTACCATCACTGATAGCTGTGTGCCAATCATATCACCGC
* *
41134654 TATTGATGGCTTTGTGCCAAACATATTACTG
65 TATTGATGACTTTGTGCCAAACATATTACCG
*
41134685 TACTTATGGCTT
1 TACTGATGGCTT
41134697 GTAGCCATTC
Statistics
Matches: 89, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
95 11 0.12
96 78 0.88
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (95 bp):
TACTGATGGCTTTGTACCGATCATATTACCATCACTGATAGCTGTGTGCCAATCATATCACCGCT
ATTGATGACTTTGTGCCAAACATATTACCG
Found at i:41134713 original size:22 final size:22
Alignment explanation
Indices: 41134688--41134734 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
41134678 ATTACTGTAC
* * *
41134688 TTATGGCTTGTAGCCATTCTGT
1 TTATAGCTTATAGCCATCCTGT
*
41134710 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCCATCCTGT
41134732 TTA
1 TTA
41134735 CGACTCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTGT
Found at i:41135710 original size:9 final size:9
Alignment explanation
Indices: 41135698--41135769 Score: 63
Period size: 9 Copynumber: 7.4 Consensus size: 9
41135688 AAATTAGGAA
41135698 AAAAATTAT
1 AAAAATTAT
*
41135707 AAAAATCGTAA
1 AAAAAT--TAT
41135718 AAGAAATTAT
1 AA-AAATTAT
*
41135728 AAAATATTGT
1 AAAA-ATTAT
41135738 AAAAATTTAT
1 AAAAA-TTAT
* *
41135748 AAAAGTCAT
1 AAAAATTAT
41135757 AAAAATTAT
1 AAAAATTAT
41135766 AAAA
1 AAAA
41135770 GGCATCAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
9 23 0.46
10 19 0.38
11 4 0.08
12 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:41135724 original size:21 final size:21
Alignment explanation
Indices: 41135674--41135751 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
41135664 AATACAAATA
* *
41135674 TAAAAATATTATTAAAAT-TAG
1 TAAAAAAATTA-TAAAATATCG
*
41135695 GAAAAAAATTATAAAA-ATCG
1 TAAAAAAATTATAAAATATCG
*
41135715 TAAAAGAAATTATAAAATATTG
1 TAAAA-AAATTATAAAATATCG
*
41135737 T-AAAAATTTATAAAA
1 TAAAAAAATTATAAAA
41135752 GTCATAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 21 0.44
21 23 0.48
22 4 0.08
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (21 bp):
TAAAAAAATTATAAAATATCG
Found at i:41135747 original size:20 final size:20
Alignment explanation
Indices: 41135696--41135769 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
41135686 TAAAATTAGG
41135696 AAAAAAATTATAAAAATCGT
1 AAAAAAATTATAAAAATCGT
*
41135716 AAAAGAAATTATAAAATATTGT
1 AAAA-AAATTATAAAA-ATCGT
* *
41135738 -AAAAATTTATAAAAGTC--
1 AAAAAAATTATAAAAATCGT
*
41135755 ATAAAAATTATAAAA
1 AAAAAAATTATAAAA
41135770 GGCATCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 12 0.27
19 1 0.02
20 14 0.31
21 14 0.31
22 4 0.09
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAAAATTATAAAAATCGT
Found at i:41135770 original size:18 final size:19
Alignment explanation
Indices: 41135737--41135780 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
41135727 TAAAATATTG
*
41135737 TAAAAATTTATAAAAGTCA
1 TAAAAATTTATAAAAGGCA
41135756 TAAAAA-TTATAAAAGGCA
1 TAAAAATTTATAAAAGGCA
41135774 TCAAAAA
1 T-AAAAA
41135781 GACTAACGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (19 bp):
TAAAAATTTATAAAAGGCA
Found at i:41135952 original size:9 final size:10
Alignment explanation
Indices: 41135921--41136096 Score: 72
Period size: 9 Copynumber: 18.3 Consensus size: 10
41135911 AGTACGATAA
41135921 TTTTATAATT
1 TTTTATAATT
41135931 TTTTATGAA--
1 TTTTAT-AATT
41135940 TTTTAT-ATT
1 TTTTATAATT
41135949 TTTTATAATT
1 TTTTATAATT
*
41135959 TTCTTACAA--
1 TT-TTATAATT
* **
41135968 CTTTATAAAA
1 TTTTATAATT
41135978 TTTTATAATT
1 TTTTATAATT
41135988 TTTT-T-ATAT
1 TTTTATAAT-T
* *
41135997 TTCTAT-ATA
1 TTTTATAATT
*
41136006 TTTTCTAA-T
1 TTTTATAATT
*
41136015 TTTTATGA-T
1 TTTTATAATT
**
41136024 TTTTATAAAA
1 TTTTATAATT
*
41136034 TTTTACAA-T
1 TTTTATAATT
41136043 TTTTATATATT
1 TTTTATA-ATT
41136054 TTTTA-AGA-T
1 TTTTATA-ATT
*
41136063 TTTCATAACTT
1 TTTTATAA-TT
* *
41136074 TTTTGTAATA
1 TTTTATAATT
*
41136084 TTTAATAATT
1 TTTTATAATT
41136094 TTT
1 TTT
41136097 AAATATTATT
Statistics
Matches: 124, Mismatches: 26, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
7 1 0.01
8 7 0.06
9 48 0.39
10 48 0.39
11 20 0.16
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:41135954 original size:28 final size:28
Alignment explanation
Indices: 41135920--41136046 Score: 109
Period size: 28 Copynumber: 4.5 Consensus size: 28
41135910 TAGTACGATA
41135920 ATTTTATAATTTTTTATGAATTTTATAT
1 ATTTTATAATTTTTTATGAATTTTATAT
* * * *
41135948 TTTTTATAATTTTCTTA-CAACTTTATAAA
1 ATTTTATAATTTT-TTATGAATTTTAT-AT
41135977 ATTTTATAATTTTTT-T-ATATTTCTATAT
1 ATTTTATAATTTTTTATGA-ATTT-TATAT
* * *
41136005 ATTTTCTAA-TTTTTATGATTTTTATAAA
1 ATTTTATAATTTTTTATGAATTTTAT-AT
*
41136033 ATTTTACAATTTTT
1 ATTTTATAATTTTT
41136047 ATATATTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
27 9 0.12
28 45 0.58
29 24 0.31
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (28 bp):
ATTTTATAATTTTTTATGAATTTTATAT
Done.