Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 21
Found at i:4156813 original size:128 final size:129
Alignment explanation
Indices: 4156415--4156977 Score: 604
Period size: 128 Copynumber: 4.3 Consensus size: 129
4156405 TGTTGATCCA
* * * * * * *
4156415 TTCCACTGTCACTCAGGGAATATCAAATCTT-GAAAGAGAGGGATTTGTTTCACTTCTTTTGACG
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAA-AG-TGGA-CT-TTCCACTTCTTCTAAAG
* * *
4156479 GGAATATCAGATCTTGAGGGAGTTGATCCATTCCTCTGTCACTCAGGGAAGATTGAATCGGGGCA
62 GGAATATC--ATATGGA-GGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCA
4156544 GACTTG
124 GACTTG
* *
4156550 TTCCGCTGTCACTTAGGGAATATCAAATCTTGG-AAAGTGAGACTTAATCCACTTCTTCTAAAGA
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGTG-GACTT--TCCACTTCTTCTAAAGG
* * * * *
4156614 GAATATTAGATCTGGATGAGTTGATCAATTCCGCTGTCACTCAGGGAAGATTGAATC-GGGCATA
63 GAATA-T-CATATGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGA
4156678 CTTG
126 CTTG
* * **
4156682 TTCCGTTGTCACTCAGTGAATATCAAATCTTGGAAAAGTTGGACATGTTCTGCTTCTTCT-AAGG
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAG-TGGAC-T-TTCCACTTCTTCTAAAGG
*
4156746 GAATATCATATGG-GGAG-TGATCCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGCA-ACT
63 GAATATCATATGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACT
4156808 TG
128 TG
* *
4156810 TTCCGCTGTCACTAAGGGAATATCAAATCTTGGAAAAGAGGGACTTTCCACTTCTTCTGAAA-GG
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAG-TGGACTTTCCACTTCTTCT-AAAGGG
* * * *
4156874 -ATATCATATCTGGAAGAGTTGATCCATTCCGCTGTCACTCAGTGAAGGTTTAATCGGGGCAGAC
64 AATATCATA--TGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGAC
*
4156938 TTA
127 TTG
* * *
4156941 TTCTGCTGTCACTCAAGGAATATCAAATATTGGAAAA
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAA
4156978 AAAAGGTTTG
Statistics
Matches: 367, Mismatches: 43, Indels: 40
0.82 0.10 0.09
Matches are distributed among these distances:
126 19 0.05
127 3 0.01
128 83 0.23
129 11 0.03
130 43 0.12
131 38 0.10
132 49 0.13
133 57 0.16
134 30 0.08
135 33 0.09
136 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (129 bp):
TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGTGGACTTTCCACTTCTTCTAAAGGGAA
TATCATATGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTG
Found at i:4179253 original size:16 final size:16
Alignment explanation
Indices: 4179229--4179260 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4179219 ATTTTCTTTT
*
4179229 AATCGTAAAATTTATA
1 AATCATAAAATTTATA
4179245 AATCATAAAATTTATA
1 AATCATAAAATTTATA
4179261 TACCTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AATCATAAAATTTATA
Found at i:4182325 original size:18 final size:18
Alignment explanation
Indices: 4182302--4182344 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4182292 CTTTATATTA
* *
4182302 TTTATTTATTTATTTTCT
1 TTTATTTAATTATTATCT
*
4182320 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
4182338 TTTATTT
1 TTTATTT
4182345 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:4182424 original size:35 final size:35
Alignment explanation
Indices: 4182385--4182474 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 35
4182375 TCTTTAGTAC
*
4182385 TATTATTTATTATTTTATT-ATTTTCCCTTTTT-ATT
1 TATTA-TTATTATTTTATTAATTTT-CCTTTTTAAAT
*
4182420 TATTATTATTTATTTTATTAATTTTTCTTTTTAAAT
1 TATTATTA-TTATTTTATTAATTTTCCTTTTTAAAT
*
4182456 TATAATTATCTATTTTATT
1 TATTATTAT-TATTTTATT
4182475 TTATTAAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
34 3 0.06
35 22 0.46
36 23 0.48
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (35 bp):
TATTATTATTATTTTATTAATTTTCCTTTTTAAAT
Found at i:4182478 original size:20 final size:20
Alignment explanation
Indices: 4182428--4182478 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
4182418 TTTATTATTA
*
4182428 TTTATTTTATTAATTTTTCTT
1 TTTATTTTA-TAATTTATCTT
**
4182449 TTTAAATTATAA-TTATCTAT
1 TTTATTTTATAATTTATCT-T
4182469 TTTATTTTAT
1 TTTATTTTAT
4182479 TAAATCTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTTATAATTTATCTT
Found at i:4187490 original size:14 final size:14
Alignment explanation
Indices: 4187471--4187497 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4187461 ATTTCGTTCT
4187471 ATTTTTTTTATTTC
1 ATTTTTTTTATTTC
4187485 ATTTTTTTTATTT
1 ATTTTTTTTATTT
4187498 TATTATTTAG
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:0.04, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTTTTATTTC
Found at i:4187498 original size:5 final size:5
Alignment explanation
Indices: 4187470--4187564 Score: 60
Period size: 5 Copynumber: 19.2 Consensus size: 5
4187460 CATTTCGTTC
* *
4187470 TATTT T-TTT TATTT CATTT T-TTT TATTT TA--T TATTT AGCAATCTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT ---TAT-TT
*
4187515 TATTT TCATTC TA-TT TATTT TATTT T-TATT TA-TT TATTT TATTT TATTT
1 TATTT T-ATTT TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT
4187564 T
1 T
4187565 TCTCTGAACA
Statistics
Matches: 71, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
3 3 0.04
4 16 0.23
5 42 0.59
6 6 0.08
8 2 0.03
9 2 0.03
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:4189504 original size:19 final size:19
Alignment explanation
Indices: 4189482--4189583 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 19
4189472 GTTTAAATAG
4189482 GTTTTAGTATTTTAATTAA
1 GTTTTAGTATTTTAATTAA
*
4189501 GTTTTAG-A--AT-ATT-A
1 GTTTTAGTATTTTAATTAA
* **
4189515 TTTTTA-TATTTT-ATCTTT
1 GTTTTAGTATTTTAAT-TAA
4189533 GTTTTAGGTATTTTAATTTAAATA
1 GTTTTA-GTATTTTAA-TT--A-A
4189557 GGTTTTAGTATTTTAATTAA
1 -GTTTTAGTATTTTAATTAA
4189577 GTTTTAG
1 GTTTTAG
4189584 GATATTATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 26
0.66 0.07 0.27
Matches are distributed among these distances:
14 7 0.11
15 3 0.05
16 4 0.06
17 1 0.02
18 6 0.10
19 14 0.22
20 7 0.11
21 3 0.05
22 1 0.02
23 2 0.03
24 9 0.14
25 6 0.10
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (19 bp):
GTTTTAGTATTTTAATTAA
Found at i:4189524 original size:76 final size:76
Alignment explanation
Indices: 4189426--4189651 Score: 384
Period size: 76 Copynumber: 3.0 Consensus size: 76
4189416 TAAGATAATA
4189426 TTTTA-AATATTATATTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGT
1 TTTTAGAATATTAT-TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGT
4189490 ATTTTAATTAAG
65 ATTTTAATTAAG
*
4189502 TTTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAATTTAAATAGGTTTTAGTA
1 TTTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
4189567 TTTTAATTAAG
66 TTTTAATTAAG
* *
4189578 TTTTAGGATATTATTTTTACATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGT
1 TTTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGT
*
4189642 GTTTTAATTA
65 ATTTTAATTA
4189652 GGATTTAAGA
Statistics
Matches: 143, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
75 5 0.03
76 130 0.91
77 8 0.06
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (76 bp):
TTTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
TTTTAATTAAG
Found at i:4189996 original size:100 final size:100
Alignment explanation
Indices: 4189823--4190029 Score: 396
Period size: 100 Copynumber: 2.1 Consensus size: 100
4189813 TGTTTACAAC
4189823 AATTGCTAAGTATGACTTTGGTCATGCTTAGCTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
1 AATTGCTAAGTATGACTTTGGTCATGCTTAGCTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
4189888 GCTCAATTCCAAACGTGAGAATTGTAAGGTACTTA
66 GCTCAATTCCAAACGTGAGAATTGTAAGGTACTTA
*
4189923 AATTGCTAAGTATGACTTTGGTCATGCTTAGTTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
1 AATTGCTAAGTATGACTTTGGTCATGCTTAGCTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
*
4189988 GCTCAATTCCAAATGTGAGAATTGTAAGGTACTTA
66 GCTCAATTCCAAACGTGAGAATTGTAAGGTACTTA
4190023 AATTGCT
1 AATTGCT
4190030 TCGGATTTTT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 105 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (100 bp):
AATTGCTAAGTATGACTTTGGTCATGCTTAGCTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
GCTCAATTCCAAACGTGAGAATTGTAAGGTACTTA
Found at i:4190386 original size:18 final size:18
Alignment explanation
Indices: 4190363--4190404 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
4190353 TTTATATTAC
4190363 TTATTTAATTATTTTCTT
1 TTATTTAATTATTTTCTT
4190381 TTATTTAATTATTTTCTT
1 TTATTTAATTATTTTCTT
4190399 TTATTT
1 TTATTT
4190405 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTAATTATTTTCTT
Found at i:4200384 original size:4 final size:4
Alignment explanation
Indices: 4200351--4200404 Score: 63
Period size: 4 Copynumber: 12.8 Consensus size: 4
4200341 TATAACAATT
* *
4200351 TTTG TTTTG TTTTG TTATG TGTG CTTG TTTG TTTG TTTG TTTG TTTG TTTG
1 TTTG -TTTG -TTTG TT-TG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG
4200402 TTT
1 TTT
4200405 ATTTCTTTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
4 32 0.73
5 12 0.27
ACGTcount: A:0.02, C:0.02, G:0.24, T:0.72
Consensus pattern (4 bp):
TTTG
Found at i:4200420 original size:13 final size:13
Alignment explanation
Indices: 4200402--4200439 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
4200392 TGTTTGTTTG
4200402 TTTATTTCTTTAC
1 TTTATTTCTTTAC
4200415 TTTATTTCTTTAC
1 TTTATTTCTTTAC
*
4200428 TTTATTTATTTA
1 TTTATTTCTTTA
4200440 TTGTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTCTTTAC
Found at i:4203529 original size:31 final size:33
Alignment explanation
Indices: 4203460--4203529 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
4203450 TCTCCAAAAA
* *
4203460 CTATATATATATATATGTTTTCAAAAATATAGT
1 CTATATATATATACATATTTTCAAAAATATAGT
* * *
4203493 GTATATATATATGCATATTTT-AAAATTATA-T
1 CTATATATATATACATATTTTCAAAAATATAGT
4203524 CTATAT
1 CTATAT
4203530 TTTTAAAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 6 0.19
32 8 0.26
33 17 0.55
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (33 bp):
CTATATATATATACATATTTTCAAAAATATAGT
Found at i:4203535 original size:20 final size:19
Alignment explanation
Indices: 4203510--4203548 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
4203500 TATATGCATA
*
4203510 TTTTAAAATTATATCTATAT
1 TTTTAAAAGTATA-CTATAT
4203530 TTTTAAAAGTATACTATAT
1 TTTTAAAAGTATACTATAT
4203549 ATTATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
TTTTAAAAGTATACTATAT
Found at i:4203566 original size:35 final size:35
Alignment explanation
Indices: 4203525--4203592 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
4203515 AAATTATATC
*
4203525 TATATTTTTA-AAAGTATACTATATAT-TATATATTT
1 TATA-TTTTAGAAACTATA-TATATATATATATATTT
*
4203560 TATATTTTAGAAACTTTATATATATATATATAT
1 TATATTTTAGAAACTATATATATATATATATAT
4203593 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 12 0.41
35 17 0.59
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (35 bp):
TATATTTTAGAAACTATATATATATATATATATTT
Found at i:4203583 original size:2 final size:2
Alignment explanation
Indices: 4203576--4203614 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4203566 TTAGAAACTT
4203576 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4203615 GTTTCAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4217000 original size:54 final size:54
Alignment explanation
Indices: 4216916--4217311 Score: 508
Period size: 54 Copynumber: 7.3 Consensus size: 54
4216906 CTATGTGTAC
* *
4216916 TACAGGCATTAAGTGTGCAATTCAC-AGAATTCATCATGAGTTGATGAACAACCG
1 TACAGGCACTATGTGTGCAATTCACGA-AATTCATCATGAGTTGATGAACAACCG
* * * *
4216970 TACAGGCACTATGTGTTCAATTCACGGAATTCATCATGAGTTGATGAACAGCTG
1 TACAGGCACTATGTGTGCAATTCACGAAATTCATCATGAGTTGATGAACAACCG
* * * **
4217024 TATAGGCACTATGTGTTCAATTCACGAAATTCATCATGAGTTGATGAAAAATTG
1 TACAGGCACTATGTGTGCAATTCACGAAATTCATCATGAGTTGATGAACAACCG
* * * *
4217078 TATAGGCACTATGTGTACAATTCACGGAATTCATCATGATTTGATGAACAACCG
1 TACAGGCACTATGTGTGCAATTCACGAAATTCATCATGAGTTGATGAACAACCG
* *
4217132 TACAGGCACTATGTGTGCAATTCACGAAATTCATCATGAGTTGATGAGCAACTG
1 TACAGGCACTATGTGTGCAATTCACGAAATTCATCATGAGTTGATGAACAACCG
* * *
4217186 TACAGGCACTATGTGGGCAATCCATGAAATTCATCATGAGTTGATGAACAACCG
1 TACAGGCACTATGTGTGCAATTCACGAAATTCATCATGAGTTGATGAACAACCG
* * * * **
4217240 TATAGGCACTATGTGTGCAA-CCAATGAAATTCATCATGAGTTGATAAATTACCG
1 TACAGGCACTATGTGTGCAATTC-ACGAAATTCATCATGAGTTGATGAACAACCG
* *
4217294 TATAGGCACTACGTGTGC
1 TACAGGCACTATGTGTGC
4217312 GTCTTAATAA
Statistics
Matches: 306, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
53 2 0.01
54 304 0.99
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (54 bp):
TACAGGCACTATGTGTGCAATTCACGAAATTCATCATGAGTTGATGAACAACCG
Found at i:4222755 original size:32 final size:31
Alignment explanation
Indices: 4222717--4222790 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 31
4222707 GATGATCTTG
*
4222717 GGTAGGCTCTAAGGCCCGAAGGCATTTCCTT
1 GGTAGGCTCTAAGGCCCGAAGGCACTTCCTT
* *
4222748 GGATAGGCTCTAAGGCCCTAAGGTACTTCCTT
1 GG-TAGGCTCTAAGGCCCGAAGGCACTTCCTT
4222780 GTGTAGGCTCT
1 G-GTAGGCTCT
4222791 TTGGTACTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 2 0.05
32 35 0.92
33 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.28
Consensus pattern (31 bp):
GGTAGGCTCTAAGGCCCGAAGGCACTTCCTT
Found at i:4226939 original size:32 final size:32
Alignment explanation
Indices: 4226902--4226990 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
4226892 AAGAAATTTC
*
4226902 CTTGGGTAGGCTCTAAGGCCCCAAGGTGC-TT
1 CTTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
* * *
4226933 CTTTGGGTAGGCTCTTAGGCCCTAATGTACTTT
1 C-TTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
* *
4226966 CTTGGGTAGTCTCTCAGGCCCCAAG
1 CTTGGGTAGGCTCTAAGGCCCCAAG
4226991 ATATTCCTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 1 0.02
32 44 0.92
33 3 0.06
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (32 bp):
CTTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
Found at i:4230821 original size:2 final size:2
Alignment explanation
Indices: 4230814--4230847 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4230804 GTATAAGTGG
4230814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4230848 TATGGTTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4232219 original size:160 final size:164
Alignment explanation
Indices: 4231934--4232258 Score: 613
Period size: 160 Copynumber: 2.0 Consensus size: 164
4231924 CCTACGGTGC
4231934 TAGGGAGGTTACCAATGGTGTCAGTCATGCATGGTAGGGTGACAGCCTCCTTTTCCCCCCTTTAT
1 TAGGGAGGTTACCAATGGTGTCAGTCATGCATGGTAGGGTGACAGCCTCCTTTTCCCCCC-TTAT
4231999 ATTATACTCTCAACGGCAACAACATAATCGGCAATCCAATCTTGGCTGTGTGGACGGTTGAACCG
65 ATTATACTCTCAACGGCAACAACATAATCGGCAATCCAATCTTGGCTGTGTGGACGGTTGAACCG
4232064 AATCAA-TTTTTTGTCGAACAAAAC-AAAAACAGA
130 AATCAATTTTTTTGTCGAACAAAACAAAAAACAGA
4232097 TAGGGAGGTTACCAATGGTGTCAGTCATGCATGGTAGGGTGACAGCCTCCTTTTCCCCCC-T-TA
1 TAGGGAGGTTACCAATGGTGTCAGTCATGCATGGTAGGGTGACAGCCTCCTTTTCCCCCCTTATA
4232160 TTATACTCTCAACGGCAACAACATAATCGGCAATCCAATCTTGGCTGTGTGGACGGTTGAACCGA
66 TTATACTCTCAACGGCAACAACATAATCGGCAATCCAATCTTGGCTGTGTGGACGGTTGAACCGA
4232225 ATCAATTTTTTTGTCGAACAAAACAAAAAACAGA
131 ATCAATTTTTTTGTCGAACAAAACAAAAAACAGA
4232259 AAAGAAGTGG
Statistics
Matches: 160, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
160 72 0.45
161 19 0.12
162 9 0.06
163 60 0.38
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (164 bp):
TAGGGAGGTTACCAATGGTGTCAGTCATGCATGGTAGGGTGACAGCCTCCTTTTCCCCCCTTATA
TTATACTCTCAACGGCAACAACATAATCGGCAATCCAATCTTGGCTGTGTGGACGGTTGAACCGA
ATCAATTTTTTTGTCGAACAAAACAAAAAACAGA
Found at i:4236084 original size:20 final size:20
Alignment explanation
Indices: 4236039--4236076 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4236029 AACGGTCAGA
*
4236039 TCGATTTGGGTTGACTCATG
1 TCGATTTGGGTTAACTCATG
*
4236059 CCGATTTGGGTTAACTCA
1 TCGATTTGGGTTAACTCA
4236077 ATTCGATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
TCGATTTGGGTTAACTCATG
Found at i:4240082 original size:17 final size:17
Alignment explanation
Indices: 4240060--4240094 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4240050 AGCTTTTGAA
*
4240060 ATACACTTACTGCATGT
1 ATACACTTACTACATGT
4240077 ATACACTTACTACATGT
1 ATACACTTACTACATGT
4240094 A
1 A
4240095 ATTTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (17 bp):
ATACACTTACTACATGT
Found at i:4244338 original size:60 final size:59
Alignment explanation
Indices: 4244242--4244365 Score: 203
Period size: 60 Copynumber: 2.1 Consensus size: 59
4244232 GCTCCTTTTC
*
4244242 AGGTAGTGGTTCGTGGCATCAGGTGCTGAGGTTGAAGATAAGGGTCTTTGTTTCCTAAG
1 AGGTAGTGGTTCGTGGCATCAGGTGCTGAGGTTGAAGATAAGGGTCCTTGTTTCCTAAG
* * *
4244301 AGGTAGTGGTTCGTGGCATTCAGGTGCTGAGGTTGAAGGTAAGGGTCCTTGTTTCGTTAG
1 AGGTAGTGGTTCGTGGCA-TCAGGTGCTGAGGTTGAAGATAAGGGTCCTTGTTTCCTAAG
4244361 AGGTA
1 AGGTA
4244366 TGGGCTTGTG
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 18 0.30
60 42 0.70
ACGTcount: A:0.19, C:0.11, G:0.37, T:0.32
Consensus pattern (59 bp):
AGGTAGTGGTTCGTGGCATCAGGTGCTGAGGTTGAAGATAAGGGTCCTTGTTTCCTAAG
Found at i:4247226 original size:16 final size:16
Alignment explanation
Indices: 4247207--4247251 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
4247197 CATGTATTAG
*
4247207 TACATACATGCAT-TCA
1 TACATATATGCATGT-A
*
4247223 TACATATATGCGTGTA
1 TACATATATGCATGTA
4247239 TACATATATGCAT
1 TACATATATGCAT
4247252 ACATTCTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (16 bp):
TACATATATGCATGTA
Found at i:4247255 original size:12 final size:12
Alignment explanation
Indices: 4247238--4247440 Score: 92
Period size: 12 Copynumber: 16.1 Consensus size: 12
4247228 ATATGCGTGT
*
4247238 ATACATATATGC
1 ATACATATATAC
* *
4247250 ATACAT-TCTCTC
1 ATACATATAT-AC
*
4247262 ATACATACATAC
1 ATACATATATAC
* *
4247274 ATACATATAGAT
1 ATACATATATAC
* *
4247286 AGACATACATACGC
1 ATACATATATA--C
4247300 ATACATTCATCATAC
1 ATACA-T-AT-ATAC
*
4247315 ATACATATATAT
1 ATACATATATAC
*
4247327 ATACATACATAC
1 ATACATATATAC
4247339 ATACATATAGATAGGC
1 ATACATAT--ATA--C
4247355 AT-CATATATAC
1 ATACATATATAC
* *
4247366 ATACATACATTC
1 ATACATATATAC
*
4247378 ACT-CATACATAC
1 A-TACATATATAC
*
4247390 ATACATACATATAG
1 ATACAT--ATATAC
*
4247404 ATAGGCATACATAC
1 ATA--CATATATAC
*
4247418 ATAC--ATACAC
1 ATACATATATAC
4247428 ATACATATATAC
1 ATACATATATAC
4247440 A
1 A
4247441 CCCCATACAT
Statistics
Matches: 143, Mismatches: 28, Indels: 40
0.68 0.13 0.19
Matches are distributed among these distances:
10 8 0.06
11 6 0.04
12 78 0.55
13 7 0.05
14 22 0.15
15 12 0.08
16 7 0.05
17 3 0.02
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (12 bp):
ATACATATATAC
Found at i:4247270 original size:4 final size:4
Alignment explanation
Indices: 4247261--4247570 Score: 149
Period size: 4 Copynumber: 78.5 Consensus size: 4
4247251 TACATTCTCT
* * * * *
4247261 CATA CATA CATA CATA CATA TAGA TAGA CATA CATA CGCATA CATT CAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA --CATA CATA CATA
* * *
4247310 CATA CATA CATA TATA TATA CATA CATA CATA CAT- -ATA GATA GGCAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA --CATA
* *
4247357 CATA TATA CATA CATA CATT CACT- CATA CATA CATA CATA CAT- -ATA
1 CATA CATA CATA CATA CATA CA-TA CATA CATA CATA CATA CATA CATA
* * **
4247403 GATA GGCATA CATA CATA CATA C--A CATA CATA TATA CACCC CATA CATA
1 CATA --CATA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA CATA
* * * * * * * * * * *
4247452 CATG TATG CATC CATG CACA CTTA CATA CATC CGTG CACA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
4247500 CATG CATA CATA C--A CACA CATA CATA CACA CATA TATA TATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
4247546 TATA TATA TATA TATA -ATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
4247571 CATAATAGAC
Statistics
Matches: 245, Mismatches: 41, Indels: 40
0.75 0.13 0.12
Matches are distributed among these distances:
2 8 0.03
3 10 0.04
4 215 0.88
5 3 0.01
6 9 0.04
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:4247536 original size:2 final size:2
Alignment explanation
Indices: 4247531--4247561 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4247521 ACATACACAC
4247531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4247562 ATACATACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4247606 original size:8 final size:8
Alignment explanation
Indices: 4247606--4247880 Score: 68
Period size: 8 Copynumber: 34.4 Consensus size: 8
4247596 ACATATACAC
4247606 ACACATAT
1 ACACATAT
4247614 ACACAT-T
1 ACACATAT
4247621 -CACATAT
1 ACACATAT
*
4247628 ACACACAT
1 ACACATAT
* *
4247636 TCACACAT
1 ACACATAT
4247644 ACACATAT
1 ACACATAT
*
4247652 ATACATAT
1 ACACATAT
*
4247660 ATACATACGT
1 ACACATA--T
*
4247670 ATACATATT
1 ACACATA-T
*
4247679 AGCACATAC
1 A-CACATAT
* * *
4247688 ATATACAT
1 ACACATAT
4247696 ACACATAT
1 ACACATAT
**
4247704 ATGCAT-T
1 ACACATAT
* *
4247711 -CATACAT
1 ACACATAT
*
4247718 ACGCATAT
1 ACACATAT
*
4247726 --ACATAA
1 ACACATAT
*
4247732 ACACACACT
1 ACACATA-T
* *
4247741 ACATAAAT
1 ACACATAT
*
4247749 ACACACAT
1 ACACATAT
*
4247757 ACATA-AT
1 ACACATAT
4247764 ACA-A-AT
1 ACACATAT
* *
4247770 AGACATAC
1 ACACATAT
4247778 ACACATAT
1 ACACATAT
* *
4247786 ACATATAC
1 ACACATAT
**
4247794 ACACATGC
1 ACACATAT
*
4247802 ACACAAAT
1 ACACATAT
*
4247810 ACACATACAC
1 ACACAT--AT
4247820 ACACATGCAT
1 ACACAT--AT
4247830 ACACATTAT
1 ACACA-TAT
*
4247839 ACAC--AC
1 ACACATAT
* *
4247845 ACACAAAA
1 ACACATAT
4247853 ACACATAT
1 ACACATAT
* *
4247861 ACATACAT
1 ACACATAT
4247869 ACACATAAT
1 ACACAT-AT
4247878 ACA
1 ACA
4247881 TACATACATA
Statistics
Matches: 193, Mismatches: 56, Indels: 35
0.68 0.20 0.12
Matches are distributed among these distances:
6 20 0.10
7 10 0.05
8 116 0.60
9 19 0.10
10 27 0.14
11 1 0.01
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.22
Consensus pattern (8 bp):
ACACATAT
Found at i:4247609 original size:12 final size:12
Alignment explanation
Indices: 4247562--4247634 Score: 65
Period size: 12 Copynumber: 5.8 Consensus size: 12
4247552 TATATATATA
*
4247562 ATACATACACAT
1 ATACACACACAT
*
4247574 AATAGACACGACAT
1 -ATACACAC-ACAT
***
4247588 ATATGTACACAT
1 ATACACACACAT
4247600 ATACACACACAT
1 ATACACACACAT
4247612 ATACACATTCACAT
1 ATACACA--CACAT
4247626 ATACACACA
1 ATACACACA
4247635 TTCACACATA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
12 22 0.45
13 11 0.22
14 16 0.33
ACGTcount: A:0.48, C:0.26, G:0.04, T:0.22
Consensus pattern (12 bp):
ATACACACACAT
Found at i:4247631 original size:24 final size:24
Alignment explanation
Indices: 4247593--4247886 Score: 91
Period size: 24 Copynumber: 11.8 Consensus size: 24
4247583 GACATATATG
4247593 TACACATATACACACACATATACACA
1 TACACATAT--ACACACATATACACA
*
4247619 TTCACATATACACACAT-TCACACA
1 TACACATATACACACATAT-ACACA
* * *
4247643 TACACATATATACATATATACATACG
1 TACACATATACACACATATAC--ACA
* * * *
4247669 TATACATATTAGCACATACATATACA
1 TACACATA-TA-CACACATATACACA
* * *
4247695 TACACATATATGCATTCATACATACGCA
1 TACACATATA--CA--CACATATACACA
* * * * *
4247723 TATACATAAACACACACTACATAAA
1 TACACATATACACACA-TATACACA
* * *
4247748 TACACACAT--ACATA-ATACAAA
1 TACACATATACACACATATACACA
* *
4247769 TAGAC--ATACACACATATACATA
1 TACACATATACACACATATACACA
* * *
4247791 TACACACATGCACACAAATACACA
1 TACACATATACACACATATACACA
* *
4247815 TACACACACATGCATACACATTATACACA
1 T--ACACATAT--ACACACA-TATACACA
* *
4247844 CACACA-A-AAACACATATACATACA
1 TACACATATACACACATATAC--ACA
*
4247868 TACACATAATACATACATA
1 TACACAT-ATACACACATA
4247887 CATACAGACC
Statistics
Matches: 201, Mismatches: 42, Indels: 49
0.69 0.14 0.17
Matches are distributed among these distances:
19 2 0.01
21 13 0.06
22 15 0.07
23 11 0.05
24 55 0.27
25 12 0.06
26 41 0.20
27 14 0.07
28 31 0.15
29 7 0.03
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.22
Consensus pattern (24 bp):
TACACATATACACACATATACACA
Found at i:4247745 original size:15 final size:16
Alignment explanation
Indices: 4247724--4247762 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
4247714 ACATACGCAT
4247724 ATACATAAACACACAC
1 ATACATAAACACACAC
*
4247740 -TACATAAATACACAC
1 ATACATAAACACACAC
4247755 ATACATAA
1 ATACATAA
4247763 TACAAATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (16 bp):
ATACATAAACACACAC
Found at i:4247764 original size:15 final size:15
Alignment explanation
Indices: 4247724--4247799 Score: 68
Period size: 14 Copynumber: 5.1 Consensus size: 15
4247714 ACATACGCAT
4247724 ATACATAA-ACACAC
1 ATACATAATACACAC
4247738 ACTACATAAATACACAC
1 A-TACAT-AATACACAC
* *
4247755 ATACATAATACAAAT
1 ATACATAATACACAC
* * *
4247770 AGACAT-ACACACAT
1 ATACATAATACACAC
4247784 ATACAT-ATACACAC
1 ATACATAATACACAC
4247798 AT
1 AT
4247800 GCACACAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
14 20 0.39
15 17 0.33
16 7 0.14
17 7 0.14
ACGTcount: A:0.54, C:0.25, G:0.01, T:0.20
Consensus pattern (15 bp):
ATACATAATACACAC
Found at i:4247815 original size:26 final size:26
Alignment explanation
Indices: 4247776--4247828 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
4247766 AAATAGACAT
* * *
4247776 ACACACATATACATATACACACATGC
1 ACACAAATACACATACACACACATGC
4247802 ACACAAATACACATACACACACATGC
1 ACACAAATACACATACACACACATGC
4247828 A
1 A
4247829 TACACATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.32, G:0.04, T:0.15
Consensus pattern (26 bp):
ACACAAATACACATACACACACATGC
Found at i:4247881 original size:17 final size:16
Alignment explanation
Indices: 4247600--4247888 Score: 106
Period size: 16 Copynumber: 18.6 Consensus size: 16
4247590 ATGTACACAT
*
4247600 ATACACACACATATAC
1 ATACATACACATATAC
*
4247616 --ACATTCACATATAC
1 ATACATACACATATAC
* *
4247630 ACACATTCACACATACAC
1 ATACA-T-ACACATATAC
* *
4247648 ATATATACATATATAC
1 ATACATACACATATAC
* *
4247664 ATACGTATACATATTAGC
1 ATACATACACATA-TA-C
4247682 --ACAT--ACATATAC
1 ATACATACACATATAC
* * * *
4247694 ATACACATATATGCATTC
1 ATACATACACAT--ATAC
*
4247712 ATACATACGCATATAC
1 ATACATACACATATAC
*
4247728 ATA-A-ACACACACTAC
1 ATACATACACATA-TAC
* *
4247743 ATAAATACACACATAC
1 ATACATACACATATAC
* *
4247759 ATA-ATACAAATAGAC
1 ATACATACACATATAC
4247774 ATAC--ACACATATAC
1 ATACATACACATATAC
* * **
4247788 ATATACACACATGCAC
1 ATACATACACATATAC
* * *
4247804 ACAAATACACATACAC
1 ATACATACACATATAC
* * *
4247820 ACACAT--GCATACAC
1 ATACATACACATATAC
* * *
4247834 AT-TATACACACACAC
1 ATACATACACATATAC
*
4247849 A-A-AAACACATATAC
1 ATACATACACATATAC
4247863 ATACATACACATAATAC
1 ATACATACACAT-ATAC
4247880 ATACATACA
1 ATACATACA
4247889 TACAGACCCA
Statistics
Matches: 204, Mismatches: 45, Indels: 47
0.69 0.15 0.16
Matches are distributed among these distances:
12 1 0.00
13 4 0.02
14 54 0.26
15 27 0.13
16 71 0.35
17 24 0.12
18 23 0.11
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.22
Consensus pattern (16 bp):
ATACATACACATATAC
Found at i:4247884 original size:43 final size:44
Alignment explanation
Indices: 4247716--4247911 Score: 135
Period size: 43 Copynumber: 4.4 Consensus size: 44
4247706 GCATTCATAC
* * * * *
4247716 ATACGCATATACATAAACACACACTACATAAATACACACATACATA
1 ATACACATATACATACATACACA-TACATATATACACACACACA-A
* * * * *
4247762 ATACAAATAGACATACACACATATACATATACACACATGCACACAA
1 ATACACATATACATACATACACATACATATATACACA--CACACAA
* * * * *
4247808 ATACACATACACACACATGCATACACAT-TATACACACACACAA
1 ATACACATATACATACATACACATACATATATACACACACACAA
* * * * *
4247851 AAACACATATACATACATACACATA-ATACATACATACATACAG
1 ATACACATATACATACATACACATACATATATACACACACACAA
** *
4247894 ACCCACACATACATACAT
1 ATACACATATACATACAT
4247912 GCATGCATAC
Statistics
Matches: 119, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
42 2 0.02
43 52 0.44
45 19 0.16
46 41 0.34
47 5 0.04
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (44 bp):
ATACACATATACATACATACACATACATATATACACACACACAA
Found at i:4247935 original size:4 final size:4
Alignment explanation
Indices: 4247859--4247922 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
4247849 AAAAACACAT
* *
4247859 ATAC ATAC ATAC --AC ATA- ATAC ATAC ATAC ATAC AGACCC ACAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA--C ATAC ATAC
* *
4247906 ATAC ATGC ATGC ATAC A
1 ATAC ATAC ATAC ATAC A
4247923 CATGTACATA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
2 2 0.04
3 3 0.06
4 42 0.84
6 3 0.06
ACGTcount: A:0.47, C:0.28, G:0.05, T:0.20
Consensus pattern (4 bp):
ATAC
Found at i:4247969 original size:8 final size:8
Alignment explanation
Indices: 4247958--4248096 Score: 53
Period size: 8 Copynumber: 18.1 Consensus size: 8
4247948 ACATGTGTAC
4247958 ATATACAT
1 ATATACAT
*
4247966 ATAT--GT
1 ATATACAT
*
4247972 ATATGCAT
1 ATATACAT
4247980 ATATACAT
1 ATATACAT
*
4247988 ACATACA-
1 ATATACAT
*
4247995 A-ATATAT
1 ATATACAT
*
4248002 ATACACAT
1 ATATACAT
* *
4248010 ACATGCAT
1 ATATACAT
4248018 ATATAC--
1 ATATACAT
*
4248024 -TACACAT
1 ATATACAT
4248031 ATATACAT
1 ATATACAT
* *
4248039 ACACACAT
1 ATATACAT
* *
4248047 ACATAACAC
1 ATAT-ACAT
4248056 ATGCATAC--
1 AT--ATACAT
4248064 ATATACAT
1 ATATACAT
**
4248072 GCATACAT
1 ATATACAT
*
4248080 ATATATAT
1 ATATACAT
4248088 ATATACAT
1 ATATACAT
4248096 A
1 A
4248097 CACACATACA
Statistics
Matches: 94, Mismatches: 25, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
5 4 0.04
6 13 0.14
7 2 0.02
8 67 0.71
9 4 0.04
10 2 0.02
11 2 0.02
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (8 bp):
ATATACAT
Found at i:4247991 original size:4 final size:4
Alignment explanation
Indices: 4247977--4248166 Score: 79
Period size: 4 Copynumber: 49.0 Consensus size: 4
4247967 TATGTATATG
* * * * * *
4247977 CATA TATA CATA CATA CA-A -ATA TATA TACA CATA CATG CATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
4248023 CTACA CATA TATA CATA CACA CATA CATA -ACA CATG CATA CAT- -ATA
1 C-ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * *
4248069 CATG CATA CATA TATA TATA TATA CATA CACA CATA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * *
4248117 TACA CATA CACA CATA C--A CACA CACA CACA CACA CATA CATA AATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4248163 CATA
1 CATA
4248167 TATAAACACA
Statistics
Matches: 144, Mismatches: 34, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
2 5 0.03
3 4 0.03
4 132 0.92
5 3 0.02
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:4248033 original size:13 final size:14
Alignment explanation
Indices: 4248000--4248142 Score: 67
Period size: 14 Copynumber: 10.1 Consensus size: 14
4247990 ATACAAATAT
*
4248000 ATATACACATACATGC
1 ATATATACATACA--C
4248016 ATATATAC-TACAC
1 ATATATACATACAC
4248029 ATATATACATACAC
1 ATATATACATACAC
*
4248043 --ACATACATAACAC
1 ATATATACAT-ACAC
** *
4248056 ATGCATACATATAC
1 ATATATACATACAC
* * * *
4248070 ATGCATACATATATAT
1 AT--ATATACATACAC
4248086 ATATATACATACAC
1 ATATATACATACAC
* * *
4248100 ACATACACACACAC
1 ATATATACATACAC
* *
4248114 ACATACACATACAC
1 ATATATACATACAC
* * *
4248128 ACATACACACACAC
1 ATATATACATACAC
4248142 A
1 A
4248143 CACACACACA
Statistics
Matches: 103, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
12 7 0.07
13 13 0.13
14 56 0.54
15 11 0.11
16 16 0.16
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.22
Consensus pattern (14 bp):
ATATATACATACAC
Found at i:4248107 original size:6 final size:6
Alignment explanation
Indices: 4248096--4248152 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
4248086 ATATATACAT
* * * *
4248096 ACACAC ATACAC ACACAC ACATAC ACATAC ACACAT ACACAC ACACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
4248144 ACACAC ACA
1 ACACAC ACA
4248153 TACATAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.51, C:0.42, G:0.00, T:0.07
Consensus pattern (6 bp):
ACACAC
Found at i:4248111 original size:12 final size:12
Alignment explanation
Indices: 4248090--4248411 Score: 178
Period size: 12 Copynumber: 26.1 Consensus size: 12
4248080 ATATATATAT
*
4248090 ATACATACACAC
1 ATACACACACAC
4248102 ATACACACACACAC
1 AT--ACACACACAC
4248116 ATACACATACACAC
1 ATACAC--ACACAC
4248130 ATACACACACAC
1 ATACACACACAC
*
4248142 ACACACACACATAC
1 ATACACACAC--AC
* * * *
4248156 ATAAATACATAT
1 ATACACACACAC
* * *
4248168 ATAAACACAAAA
1 ATACACACACAC
* *
4248180 ATAAAAACAGACAC
1 AT--ACACACACAC
* *
4248194 AAACACAGACAC
1 ATACACACACAC
* *
4248206 AT-CATACACAT
1 ATACACACACAC
4248217 ATGTACACACACAC
1 A--TACACACACAC
** *
4248231 ATACGTACATAC
1 ATACACACACAC
* * *
4248243 GTACATACATAC
1 ATACACACACAC
* * * *
4248255 ATGCATACATAT
1 ATACACACACAC
** * * *
4248267 AGGCATACATAT
1 ATACACACACAC
*
4248279 GTACACACACAC
1 ATACACACACAC
*
4248291 ACACACACACAC
1 ATACACACACAC
*
4248303 ACACACACACAC
1 ATACACACACAC
*
4248315 ACACACACACAC
1 ATACACACACAC
*
4248327 ACACACACACAC
1 ATACACACACAC
*
4248339 ACACACACACAC
1 ATACACACACAC
*
4248351 ACACACACACAC
1 ATACACACACAC
*
4248363 ACACACACACAC
1 ATACACACACAC
*
4248375 ACACACACACAC
1 ATACACACACAC
*
4248387 ACACACACACAC
1 ATACACACACAC
*
4248399 ACACACACACAC
1 ATACACACACAC
4248411 A
1 A
4248412 CACGTGTGTG
Statistics
Matches: 261, Mismatches: 38, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
11 7 0.03
12 206 0.79
13 1 0.00
14 47 0.18
ACGTcount: A:0.50, C:0.37, G:0.03, T:0.10
Consensus pattern (12 bp):
ATACACACACAC
Found at i:4248288 original size:2 final size:2
Alignment explanation
Indices: 4248281--4248414 Score: 268
Period size: 2 Copynumber: 67.0 Consensus size: 2
4248271 ATACATATGT
4248281 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4248323 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4248365 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4248407 AC AC AC AC
1 AC AC AC AC
4248415 GTGTGTGCAC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 132 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4248428 original size:4 final size:4
Alignment explanation
Indices: 4248421--4248459 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
4248411 ACACGTGTGT
4248421 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCA
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCA
4248460 TACATACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.49, G:0.26, T:0.00
Consensus pattern (4 bp):
GCAC
Found at i:4248712 original size:19 final size:20
Alignment explanation
Indices: 4248677--4248724 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
4248667 TTCAAAATTA
*
4248677 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATTCCATTTTG
4248697 TTTTTCAAAA-TCCATTTTG
1 TTTTTCAAAATTCCATTTTG
4248716 TTTTT-AAAA
1 TTTTTCAAAA
4248725 AGAAAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 4 0.15
19 13 0.48
20 10 0.37
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTCAAAATTCCATTTTG
Found at i:4250293 original size:10 final size:10
Alignment explanation
Indices: 4250240--4250286 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
4250230 GCTGCTGGAA
4250240 ACCGGTTT-G
1 ACCGGTTTCG
*
4250249 ACCGGTTTTCA
1 ACCGG-TTTCG
*
4250260 ACCGGTTTTG
1 ACCGGTTTCG
4250270 ACCGGTTTCG
1 ACCGGTTTCG
4250280 ACCGGTT
1 ACCGGTT
4250287 CGAACCGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 5 0.16
10 22 0.69
11 5 0.16
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.34
Consensus pattern (10 bp):
ACCGGTTTCG
Found at i:4250293 original size:20 final size:20
Alignment explanation
Indices: 4250239--4250286 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
4250229 CGCTGCTGGA
4250239 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTTTC
4250259 AACCGGTTTTGACCGG-TTTC
1 AACCGG-TTTGACCGGTTTTC
*
4250279 GACCGGTT
1 AACCGGTT
4250287 CGAACCGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.58
21 9 0.35
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTTC
Found at i:4250343 original size:17 final size:17
Alignment explanation
Indices: 4250305--4250355 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
4250295 TACCGGTCTT
*
4250305 ACCCGACCCGACC-CT-
1 ACCCGACCCGACCGTTG
4250320 A-CCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
4250336 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
4250353 ACC
1 ACC
4250356 GTTGACAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 11 0.34
15 2 0.06
16 1 0.03
17 18 0.56
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.10
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:4257514 original size:9 final size:9
Alignment explanation
Indices: 4257500--4257553 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
4257490 CGCTGCTGGA
4257500 AACCGGTTT
1 AACCGGTTT
4257509 AACCGGTTCT
1 AACCGGTT-T
*
4257519 AACCGTTTT
1 AACCGGTTT
* *
4257528 GACCGGTCTG
1 AACCGGT-TT
4257538 AACCGGTTT
1 AACCGGTTT
*
4257547 AGCCGGT
1 AACCGGT
4257554 CTGACCCGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:4257541 original size:19 final size:18
Alignment explanation
Indices: 4257500--4257557 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
4257490 CGCTGCTGGA
4257500 AACCGGTTTAACCGGTTCT-
1 AACCGGTTT-ACCGG-TCTG
*
4257519 AACCGTTTTGACCGGTCTG
1 AACCGGTTT-ACCGGTCTG
4257538 AACCGGTTTAGCCGGTCTG
1 AACCGGTTTA-CCGGTCTG
4257557 A
1 A
4257558 CCCGACCCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.12
19 30 0.88
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (18 bp):
AACCGGTTTACCGGTCTG
Found at i:4263737 original size:25 final size:24
Alignment explanation
Indices: 4263696--4263758 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
4263686 AAAATAAACT
*
4263696 TAATTAAAATAATTAAAACAAAAAA
1 TAATTAAAATAAGTAAAA-AAAAAA
*
4263721 TAATTAAAA-ATAGTAAAAAAAGAA
1 TAATTAAAATA-AGTAAAAAAAAAA
*
4263745 TAAAATAAAATAAG
1 T-AATTAAAATAAG
4263759 GACCAAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 7 0.22
25 24 0.75
26 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (24 bp):
TAATTAAAATAAGTAAAAAAAAAA
Found at i:4263867 original size:29 final size:28
Alignment explanation
Indices: 4263830--4263887 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
4263820 GTCAAATAAG
4263830 AAATAAATAGTGACCAAAATGCAAAAATTA
1 AAATAAATAGT-ACCAAAAT-CAAAAATTA
* *
4263860 AAAT-AATAGTAGCTAAATCAAAAATTA
1 AAATAAATAGTACCAAAATCAAAAATTA
4263887 A
1 A
4263888 CAGTGACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 6 0.23
29 6 0.23
30 4 0.15
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (28 bp):
AAATAAATAGTACCAAAATCAAAAATTA
Found at i:4265473 original size:117 final size:117
Alignment explanation
Indices: 4265288--4265637 Score: 460
Period size: 117 Copynumber: 3.0 Consensus size: 117
4265278 GGGGATGTCA
* * *
4265288 ATCCACTTCCTTCTGTGATGGAA-T-CACCAAGGTTGAATAAGTTCTTCTCATTATGAACTTCCT
1 ATCCACATCCTTCTGTGATGGAATTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCT
*
4265351 CTCCCTCGTCGGATGAGTTATTCTCATTATGAACTTTCCACTGGAAATATTG
66 CTCCCTCGTCGGATGAGTTCTTCTCATTATGAACTTTCCACTGGAAATATTG
* *
4265403 ATCCACCTCCTTCTATGATGGAATTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCT
1 ATCCACATCCTTCTGTGATGGAATTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCT
* * *
4265468 CTCCCTCGTCGGATGAGTTCTTCTCATTATAAACTCTCC-CATTGAAA-AGTTG
66 CTCCCTCGTCGGATGAGTTCTTCTCATTATGAACTTTCCAC-TGGAAATA-TTG
* * * * **
4265520 ATCCACATACTTCTGTGATGAAATTGAA-CAACGTTGAACAAGTTCTTCTTATTATGAACTTATT
1 ATCCACATCCTTCTGTGATGGAATTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCT
* * * *
4265584 CTCCCTCGTCGAATGAGTTCTTCTTATTATGAACTCTT-CACTGGATATGTTG
66 CTCCCTCGTCGGATGAGTTCTTCTCATTATGAACT-TTCCACTGGAAATATTG
4265636 AT
1 AT
4265638 TCAAGGTTGA
Statistics
Matches: 205, Mismatches: 23, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
115 21 0.10
116 77 0.38
117 107 0.52
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (117 bp):
ATCCACATCCTTCTGTGATGGAATTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCT
CTCCCTCGTCGGATGAGTTCTTCTCATTATGAACTTTCCACTGGAAATATTG
Found at i:4265707 original size:91 final size:91
Alignment explanation
Indices: 4265552--4266011 Score: 656
Period size: 91 Copynumber: 5.0 Consensus size: 91
4265542 ATTGAACAAC
* * * * *
4265552 GTTGAACAAGTTCTTCTTATTATGAACTTATTCTCCCTCGTCGAATGAGTTCTTCTTATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * *
4265617 CTCTTCACTGGATATGTTGATTCAAG
66 CTCTCCACTGGAAATGTTGATGCAAG
*
4265643 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* **
4265708 CTCTCCACTGGAAATGTTAACCCAAG
66 CTCTCCACTGGAAATGTTGATGCAAG
4265734 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
** * *
4265799 CTC-CCTGTTGAAAATGTTGATGCAAT
66 CTCTCC-ACTGGAAATGTTGATGCAAG
*
4265825 GTTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTC-TATCGGATGAGTTCTTCTCATTATG
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGT-T-GGATGAGTTCTTCTCATTATG
*
4265889 AACTCTCCATTGGAAAATGTTGA-GTCAAG
64 AACTCTCCACTGG-AAATGTTGATG-CAAG
* * * *
4265918 GTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCTTTGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
4265983 CTCTCCACTGGAAATGTTGATGCAAG
66 CTCTCCACTGGAAATGTTGATGCAAG
4266009 GTT
1 GTT
4266012 TATCTTCTCT
Statistics
Matches: 332, Mismatches: 29, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
90 3 0.01
91 215 0.65
92 64 0.19
93 49 0.15
94 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (91 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
CTCTCCACTGGAAATGTTGATGCAAG
Found at i:4268084 original size:5 final size:5
Alignment explanation
Indices: 4268067--4268247 Score: 113
Period size: 5 Copynumber: 34.6 Consensus size: 5
4268057 TTTTAAAAAA
* * *
4268067 TTTCT TTTAT TTTCTT TTTCTT TTTCTT TTTCT TTT-T CTT-T TTTCA
1 TTTCT TTTCT TTTC-T TTTC-T TTTC-T TTTCT TTTCT TTTCT TTTCT
* * *
4268113 TTTCT TTT-T ATTTTT TTTAT TTTAT TTT-T TTTCT TTTCCT TTTCT TTTCT
1 TTTCT TTTCT -TTTCT TTTCT TTTCT TTTCT TTTCT TTT-CT TTTCT TTTCT
*
4268163 TTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCT TTTCCT TTTCT
1 TTTCT TTT-CT TTT-CT TTT-CT TTT-CT TTT-CT TTTCT TTT-CT TTTCT
* *
4268214 TTT-T TTAT-T TTTATT TTTCT ATTTTT TTTCT TTT
1 TTTCT TT-TCT TTT-CT TTTCT -TTTCT TTTCT TTT
4268248 TTCATCTTCA
Statistics
Matches: 152, Mismatches: 12, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
4 15 0.10
5 72 0.47
6 65 0.43
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:4268087 original size:6 final size:6
Alignment explanation
Indices: 4268076--4268248 Score: 122
Period size: 6 Copynumber: 28.7 Consensus size: 6
4268066 ATTTCTTTTA
* *
4268076 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT-T CATTTCT TTTTAT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT TTTTCT
* * * *
4268124 TTTT-T TTATT-T TATTT-T TTTTCT TTTCCT TTTCTTT TCTTTCC TTTTCC
1 TTTTCT TT-TTCT T-TTTCT TTTTCT TTTTCT TTT-TCT T-TTTCT TTTTCT
* * * * * * *
4268173 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCT TTTCCT TTTCTTT TTTTAT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTT-TCT TTTTCT
* *
4268222 TTTTAT TTTTCT ATTT-T TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
4268249 TCATCTTCAA
Statistics
Matches: 142, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
5 11 0.08
6 119 0.84
7 10 0.07
8 2 0.01
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:4268137 original size:14 final size:14
Alignment explanation
Indices: 4268118--4268149 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4268108 TTTCATTTCT
4268118 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
*
4268132 TTTTATTTTTTTTC
1 TTTTATTTTTTTTA
4268146 TTTT
1 TTTT
4268150 CCTTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:4270846 original size:37 final size:38
Alignment explanation
Indices: 4270790--4270878 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
4270780 TCTAATTCAT
* *
4270790 ATATTCGGGTCGGGTCGGGTC-GGGTTTTTTAAGTGTG
1 ATATTCGGGTCGAGACGGGTCAGGGTTTTTTAAGTGTG
*
4270827 ATATTCGGGTCGAGACGGGTCAGGTTTTTTTAAGTGTG
1 ATATTCGGGTCGAGACGGGTCAGGGTTTTTTAAGTGTG
4270865 ATATTCGGGTCGAG
1 ATATTCGGGTCGAG
4270879 TTCGGGTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 19 0.40
38 29 0.60
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.36
Consensus pattern (38 bp):
ATATTCGGGTCGAGACGGGTCAGGGTTTTTTAAGTGTG
Found at i:4271433 original size:17 final size:18
Alignment explanation
Indices: 4271411--4271457 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
4271401 TATGGAATTG
*
4271411 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
4271428 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
4271446 GATTCCAATTCC
1 GATTCCAATTCC
4271458 CTTATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:4273646 original size:29 final size:31
Alignment explanation
Indices: 4273589--4273646 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
4273579 AAATAAGAGC
*
4273589 AGACAAAAGGAAATCAATGTTAGTAGAAACA
1 AGACAAAAAGAAATCAATGTTAGTAGAAACA
*
4273620 AGACAAAAAG-AATCAA-GTTAGTTGAAA
1 AGACAAAAAGAAATCAATGTTAGTAGAAA
4273647 TGATTAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.55, C:0.09, G:0.19, T:0.17
Consensus pattern (31 bp):
AGACAAAAAGAAATCAATGTTAGTAGAAACA
Found at i:4275725 original size:51 final size:50
Alignment explanation
Indices: 4275634--4275779 Score: 136
Period size: 52 Copynumber: 2.9 Consensus size: 50
4275624 CCTAATTGCA
* * * *
4275634 TAAATATAAAACAAA-AATGACTAAAATGCAAGAAAATAAAAGT-TAGTAG-
1 TAAATAAAAAATAAATAGTGACTAAAATG-AAAAAAATAAAA-TATAGTAGC
* *
4275683 TCAAATAAGAAATAAATAGTGACCAAAATGAAAAAAATTAAAATAATAGTAGC
1 T-AAATAAAAAATAAATAGTGACTAAAATGAAAAAAA-TAAAAT-ATAGTAGC
* * *
4275736 TAAATAAAAAATGAATAGTGACTAAAATAAAATAAAACAAAATA
1 TAAATAAAAAATAAATAGTGACTAAAATGAAA-AAAATAAAATA
4275780 GAATGATAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
49 1 0.01
50 18 0.23
51 17 0.22
52 38 0.48
53 5 0.06
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (50 bp):
TAAATAAAAAATAAATAGTGACTAAAATGAAAAAAATAAAATATAGTAGC
Found at i:4275760 original size:22 final size:22
Alignment explanation
Indices: 4275722--4275767 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4275712 GAAAAAAATT
4275722 AAAATAATAGTAGCT-AAATAA
1 AAAATAATAGTAGCTAAAATAA
4275743 AAAATGAATAGT-GACTAAAATAA
1 AAAAT-AATAGTAG-CTAAAATAA
4275766 AA
1 AA
4275768 TAAAACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.63, C:0.04, G:0.11, T:0.22
Consensus pattern (22 bp):
AAAATAATAGTAGCTAAAATAA
Found at i:4275767 original size:21 final size:20
Alignment explanation
Indices: 4275716--4275770 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
4275706 CAAAATGAAA
4275716 AAAATTAAAATAATAGTAGCT
1 AAAA-TAAAATAATAGTAGCT
*
4275737 AAATAAAAAATGAATAGT-GACT
1 AAA-ATAAAAT-AATAGTAG-CT
4275759 AAAATAAAATAA
1 AAAATAAAATAA
4275771 AACAAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 2 0.07
21 15 0.52
22 12 0.41
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.24
Consensus pattern (20 bp):
AAAATAAAATAATAGTAGCT
Found at i:4288538 original size:22 final size:24
Alignment explanation
Indices: 4288512--4288560 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4288502 AACTTTGGCC
4288512 TATA-TTT-TAATTTAAAATAATA
1 TATATTTTCTAATTTAAAATAATA
* *
4288534 TATATTTTCTTATTTAAAATATTA
1 TATATTTTCTAATTTAAAATAATA
4288558 TAT
1 TAT
4288561 TTAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 3 0.13
24 16 0.70
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTTTCTAATTTAAAATAATA
Found at i:4295247 original size:29 final size:29
Alignment explanation
Indices: 4295210--4295298 Score: 142
Period size: 29 Copynumber: 3.1 Consensus size: 29
4295200 GTTGCTGTAA
*
4295210 TTGTGCCACGTTGGTTGTGTGATTGGTTG
1 TTGTGCCACGTTGGTTGTGTGACTGGTTG
*
4295239 TTGTGCCACATTGGTTGTGTGACTGGTTG
1 TTGTGCCACGTTGGTTGTGTGACTGGTTG
* *
4295268 TTGTGCCACGCTGGATGTGTGACTGGTTG
1 TTGTGCCACGTTGGTTGTGTGACTGGTTG
4295297 TT
1 TT
4295299 AGGAGGTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.09, C:0.13, G:0.36, T:0.42
Consensus pattern (29 bp):
TTGTGCCACGTTGGTTGTGTGACTGGTTG
Found at i:4295253 original size:17 final size:17
Alignment explanation
Indices: 4295231--4295276 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
4295221 TGGTTGTGTG
4295231 ATTGGTTGTTGTGCCAC
1 ATTGGTTGTTGTGCCAC
4295248 ATTGGTTG-TGTG--AC
1 ATTGGTTGTTGTGCCAC
4295262 --TGGTTGTTGTGCCAC
1 ATTGGTTGTTGTGCCAC
4295277 GCTGGATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 2 0.08
15 2 0.08
16 4 0.15
17 8 0.31
ACGTcount: A:0.11, C:0.15, G:0.33, T:0.41
Consensus pattern (17 bp):
ATTGGTTGTTGTGCCAC
Found at i:4295319 original size:22 final size:20
Alignment explanation
Indices: 4295291--4295330 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
4295281 GATGTGTGAC
4295291 TGGTTGTTAGGAGGTTGTTACT
1 TGGTTGTTA-GA-GTTGTTACT
4295313 TGGTTGTTAGAGTTGTTA
1 TGGTTGTTAGAGTTGTTA
4295331 AAGATAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.15, C:0.03, G:0.35, T:0.47
Consensus pattern (20 bp):
TGGTTGTTAGAGTTGTTACT
Found at i:4299504 original size:26 final size:26
Alignment explanation
Indices: 4299468--4299528 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
4299458 TCCAGCATTA
4299468 TAAGTCCCATAAGTGAATAATAGGTC
1 TAAGTCCCATAAGTGAATAATAGGTC
4299494 TAAGTCCCATAAGTGAATAATAGGTC
1 TAAGTCCCATAAGTGAATAATAGGTC
*
4299520 CAAGTCCCA
1 TAAGTCCCA
4299529 AACGTCCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (26 bp):
TAAGTCCCATAAGTGAATAATAGGTC
Found at i:4301194 original size:64 final size:63
Alignment explanation
Indices: 4301125--4301334 Score: 228
Period size: 65 Copynumber: 3.3 Consensus size: 63
4301115 TGCACTAAGA
** *
4301125 GTGCATCGATGCATCAAGGGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
**
4301189 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
4301253 T
63 G
* ** *
4301254 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--
4301317 TG
62 TG
*
4301319 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
4301335 CTTTGATAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.38
65 67 0.54
66 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:4302012 original size:14 final size:15
Alignment explanation
Indices: 4301993--4302021 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4301983 TCAAGAATTT
4301993 AACAATCCA-AAACA
1 AACAATCCAGAAACA
4302007 AACAATCCAGAAACA
1 AACAATCCAGAAACA
4302022 TAAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:4302376 original size:21 final size:21
Alignment explanation
Indices: 4302352--4302395 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4302342 CCGAAGGGGG
*
4302352 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
4302373 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
4302394 AG
1 AG
4302396 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:4303885 original size:23 final size:22
Alignment explanation
Indices: 4303856--4303934 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
4303846 CATGGCCTTA
*
4303856 TGCATCGATGCATATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-G
* * *
4303879 TGCATCGCTGCACCTTC-ATGG
1 TGCATCGATGCACATTCAAGGG
* *
4303900 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGG
4303922 TGCATCGATGCAC
1 TGCATCGATGCAC
4303935 TGCTAGGTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 16 0.36
23 14 0.31
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGG
Found at i:4303911 original size:21 final size:22
Alignment explanation
Indices: 4303855--4303934 Score: 90
Period size: 21 Copynumber: 3.6 Consensus size: 22
4303845 GCATGGCCTT
*
4303855 ATGCATCGATGCATATTCAAGG
1 ATGCATCGATGCACATTCAAGG
* * * *
4303877 CGTGCATCGCTGCACCTTCATGG
1 -ATGCATCGATGCACATTCAAGG
*
4303900 -TGTATCGATGCACATTCAAGG
1 ATGCATCGATGCACATTCAAGG
4303921 ATGCATCGATGCAC
1 ATGCATCGATGCAC
4303935 TGCTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 17 0.37
22 12 0.26
23 17 0.37
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (22 bp):
ATGCATCGATGCACATTCAAGG
Found at i:4309702 original size:18 final size:17
Alignment explanation
Indices: 4309648--4309696 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
4309638 TTGGACCCTT
* *
4309648 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
4309666 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
4309684 AGTGCATTCGATG
1 AGTGCA-TCGATG
4309697 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:4309816 original size:65 final size:65
Alignment explanation
Indices: 4309668--4309827 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
4309658 TGCACTAAGA
* *
4309668 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCATAGTGCATAGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCATAGTACATAGATGCATGGCTG
* * *
4309732 GTGCATCGATGCATCAAATGCATTCGATGTTTTGATAAA-ATCC-TCAGTACATCGATGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAT-AGTACATAGATGCATGGC
*
4309794 TAT
64 T-G
* *
4309797 GTGCATCGATGCATGAAATGCATTTGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
4309828 CAATTTAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 30 0.36
65 51 0.61
66 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCATAGTACATAGATGCATGGCTG
Found at i:4311606 original size:65 final size:65
Alignment explanation
Indices: 4311501--4311666 Score: 194
Period size: 65 Copynumber: 2.6 Consensus size: 65
4311491 GACCTAGTGT
* * * *
4311501 ATCGGTACA-ATAATTATATTCGATGTTTCAA-AAGAGCTAGGAGTGTATC-AGTGCATGGTGTG
1 ATCGGTACACA-AAATACATTCGATGTTTCAATAA-AACTAGGAGTGTATCTA-TGCATGGTCTG
4311563 TGC
63 TGC
* *
4311566 ATCGGTACACAAAATACATTCGATGTTTCAATAAAACTAGGAGTGTATCTATGTATTGTCTGTGC
1 ATCGGTACACAAAATACATTCGATGTTTCAATAAAACTAGGAGTGTATCTATGCATGGTCTGTGC
* * * *
4311631 ATCAGTACACAAAATGCATTCTATGTTTTAATAAAA
1 ATCGGTACACAAAATACATTCGATGTTTCAATAAAA
4311667 TAAAGATGTA
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
65 84 0.95
66 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (65 bp):
ATCGGTACACAAAATACATTCGATGTTTCAATAAAACTAGGAGTGTATCTATGCATGGTCTGTGC
Found at i:4312020 original size:13 final size:13
Alignment explanation
Indices: 4312002--4312035 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
4311992 TAATATTTTC
4312002 TTTGAAAATCATT
1 TTTGAAAATCATT
4312015 TTTG-AAATCATT
1 TTTGAAAATCATT
4312027 TTTGAAAAT
1 TTTGAAAAT
4312036 AACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:4314268 original size:21 final size:21
Alignment explanation
Indices: 4314242--4314317 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
4314232 CAAGGACGGC
4314242 ATCGATGCACTTTCATAGTGT
1 ATCGATGCACTTTCATAGTGT
* *
4314263 ATCGATGCACATTC-TAGGGAT
1 ATCGATGCACTTTCATAGTG-T
* * *
4314284 ACATCGGTACACTATCATAGTGT
1 --ATCGATGCACTTTCATAGTGT
4314307 ATCGATGCACT
1 ATCGATGCACT
4314318 GCGTATAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
20 4 0.10
21 23 0.55
23 11 0.26
24 4 0.10
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (21 bp):
ATCGATGCACTTTCATAGTGT
Found at i:4314289 original size:44 final size:44
Alignment explanation
Indices: 4314214--4314316 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 44
4314204 TACACTGCAG
* * * *
4314214 AGTGTATCGATACACATTCAAGGACGGCATCGATGCACTTTCAT
1 AGTGTATCGATGCACATTCAAGGACGACATCGATACACTATCAT
* * *
4314258 AGTGTATCGATGCACATTCTAGGGA-TACATCGGTACACTATCAT
1 AGTGTATCGATGCACATTC-AAGGACGACATCGATACACTATCAT
4314302 AGTGTATCGATGCAC
1 AGTGTATCGATGCAC
4314317 TGCGTATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 47 0.92
45 4 0.08
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGACGACATCGATACACTATCAT
Found at i:4318573 original size:15 final size:12
Alignment explanation
Indices: 4318542--4318566 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4318532 TCCAACATTT
4318542 TTCTTTGTCTCA
1 TTCTTTGTCTCA
4318554 TTCTTTGTCTCA
1 TTCTTTGTCTCA
4318566 T
1 T
4318567 CCTTCTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TTCTTTGTCTCA
Found at i:4321369 original size:65 final size:65
Alignment explanation
Indices: 4321300--4321436 Score: 163
Period size: 65 Copynumber: 2.1 Consensus size: 65
4321290 ACACTAATTA
* * * *
4321300 CATTCAATGTTTC-AAATGA-GCCTGGAGTGCATCGATGCATAGT-TTGTGCATCGGTACACAAA
1 CATTCAATGTTTCAAAAT-ATGCC-AGAGTACATAGATGCAT-GTCGTGTGCATCGGTACACAAA
4321362 ATG
63 ATG
* * *
4321365 CATTCGATGTTTCAAAATATTCCAGAGTACATAGATGCATGTCGTGTGCATCGTTACACAAAATG
1 CATTCAATGTTTCAAAATATGCCAGAGTACATAGATGCATGTCGTGTGCATCGGTACACAAAATG
4321430 CATTCAA
1 CATTCAA
4321437 AATGGGTGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
64 2 0.03
65 53 0.87
66 6 0.10
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (65 bp):
CATTCAATGTTTCAAAATATGCCAGAGTACATAGATGCATGTCGTGTGCATCGGTACACAAAATG
Found at i:4321798 original size:17 final size:17
Alignment explanation
Indices: 4321778--4321811 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4321768 AGATTTTCAT
*
4321778 TGAAAATCATTTTTGAA
1 TGAAAATCATTTATGAA
4321795 TGAAAATCATTTATGAA
1 TGAAAATCATTTATGAA
4321812 ACCAAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
TGAAAATCATTTATGAA
Found at i:4329336 original size:26 final size:27
Alignment explanation
Indices: 4329307--4329358 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
4329297 ATAAGCATTC
* *
4329307 AAATTTAAACA-TCCAACATCCAAAAT
1 AAATTCAAACATTCAAACATCCAAAAT
4329333 AAATTCAAACATTCAAACATCCAAAA
1 AAATTCAAACATTCAAACATCCAAAA
4329359 CATATGAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (27 bp):
AAATTCAAACATTCAAACATCCAAAAT
Found at i:4335280 original size:13 final size:13
Alignment explanation
Indices: 4335243--4335281 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
4335233 GCTCAATGAA
*
4335243 CGTCATAAATGCG
1 CGTCATAAATGTG
4335256 CGTCATAAATGTG
1 CGTCATAAATGTG
*
4335269 TGTCATAAATGTG
1 CGTCATAAATGTG
4335282 ACGCACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:4338865 original size:21 final size:20
Alignment explanation
Indices: 4338839--4338883 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
4338829 GATTATTTTC
*
4338839 ATTTTTCAATTTTGAAATATA
1 ATTTTTCAATTTT-AAAAATA
**
4338860 ATTTTTGTATTTTAAAAATA
1 ATTTTTCAATTTTAAAAATA
4338880 ATTT
1 ATTT
4338884 CTCATAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTTCAATTTTAAAAATA
Found at i:4340891 original size:65 final size:65
Alignment explanation
Indices: 4340807--4340957 Score: 178
Period size: 65 Copynumber: 2.3 Consensus size: 65
4340797 AGGGGAGCAT
* * ** * ** *
4340807 CGGTACACTAATTACATTCGATGTTTC-AAATGAGCCTGGAGTGCATCGATGCATGGTTTGTGGA
1 CGGTACACAAATTGCATTCGATGTTTCAAAAT-AGCCAAGAGAGCATCGATGCATGGCGTGTGCA
4340871 C
65 C
** *
4340872 CGGTACACAAATTGCATTCGATGTTTCAAAATATTCAAGAGAGCATCGATGCATGGCGTGTGCAT
1 CGGTACACAAATTGCATTCGATGTTTCAAAATAGCCAAGAGAGCATCGATGCATGGCGTGTGCAC
*
4340937 CGGTACACAAAATGCATTCGA
1 CGGTACACAAATTGCATTCGA
4340958 AATGGGTGTG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
65 69 0.95
66 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (65 bp):
CGGTACACAAATTGCATTCGATGTTTCAAAATAGCCAAGAGAGCATCGATGCATGGCGTGTGCAC
Found at i:4342953 original size:17 final size:19
Alignment explanation
Indices: 4342917--4342953 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4342907 TTAATTAACT
*
4342917 TTCCATTGTTTCTCTTCAA
1 TTCCATTGTTTCTATTCAA
4342936 TTCCATT-TTTC-ATTCAA
1 TTCCATTGTTTCTATTCAA
4342953 T
1 T
4342954 CAAAATTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.54
Consensus pattern (19 bp):
TTCCATTGTTTCTATTCAA
Found at i:4343235 original size:3 final size:3
Alignment explanation
Indices: 4343209--4343272 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
4343199 TGTCCCGTTT
* * * * *
4343209 TTA TTT TTA TTT TTA TT- TTT TTA TTA TT- CTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
4343255 ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
4343273 CAGGCCCAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
2 3 0.06
3 45 0.94
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4344540 original size:21 final size:20
Alignment explanation
Indices: 4344514--4344558 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
4344504 AATTAAGGCC
4344514 TTTAAT-TTATATATTTTACAT
1 TTTAATCTTAT-TATTTTA-AT
4344535 TTTAATCTTATTATTTTAAT
1 TTTAATCTTATTATTTTAAT
4344555 TTTA
1 TTTA
4344559 TTTGCTTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAATCTTATTATTTTAAT
Found at i:4349345 original size:3 final size:3
Alignment explanation
Indices: 4349332--4349362 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
4349322 GGGCATGCTC
4349332 GAA GTAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA
4349363 AGAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:4351628 original size:54 final size:54
Alignment explanation
Indices: 4351536--4351687 Score: 180
Period size: 54 Copynumber: 2.8 Consensus size: 54
4351526 ATCTGTGTAA
* * * * * *
4351536 AAACCACAGGAAATGATGAATGTATTGTCAAATGTTTTACGAGCATTTGGGTAG
1 AAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAG
* * * * *
4351590 AAGCCACATGAAAGGATTAATGCT-TTGTCAAATATTTTACGAACATCTATGCAG
1 AAACCACAGGAAAGGATGAATG-TGTTGTCAAATGTTTTACGAACATCTAGGCAG
*
4351644 AAACCACAGGAAGGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 AAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
4351688 CAGTGATTAT
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 79 0.98
55 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (54 bp):
AAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAG
Found at i:4353216 original size:3 final size:3
Alignment explanation
Indices: 4353208--4353262 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
4353198 ATGAACAAAA
** * *
4353208 ATT ATT ATT ACA ATT ATT ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4353256 ATT ATT A
1 ATT ATT A
4353263 CAATCCCGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:4354549 original size:20 final size:21
Alignment explanation
Indices: 4354506--4354559 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
4354496 AATTAATTCC
4354506 TTTAATTTATATATTTTACAT
1 TTTAATTTATATATTTTACAT
4354527 TTTAATCTTAT-TATTTT-CAT
1 TTTAAT-TTATATATTTTACAT
* *
4354547 TTTTATTTGTATA
1 TTTAATTTATATA
4354560 AGTTACTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 3 0.10
20 10 0.34
21 12 0.41
22 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTAATTTATATATTTTACAT
Found at i:4355712 original size:192 final size:192
Alignment explanation
Indices: 4355385--4355766 Score: 665
Period size: 192 Copynumber: 2.0 Consensus size: 192
4355375 TCCTATTTAT
* * *
4355385 TTAATGGTTCTTGATGATTTTTAATGAATATTTGTGATTTTTAAAGAGCTAATGTTGTTATAAAA
1 TTAATGGTTCTTGATGATTTGTAATGAATATTTGTGATTTTTAAAGAGCTAATGCTATTATAAAA
* *
4355450 TCATATTTGAAATTTAGATTAAAGAAATTAAAGTTTACTAAGCAAAATGAATCAGTCTAGGTTAT
66 TCATATTTGAAATTTAGATTAAAGAAATTAAAATTTACTAAGCAAAATAAATCAGTCTAGGTTAT
*
4355515 TTTCTAGAAATTCGGATTACCTTTGAGTTGTTGTTGATGATATTTTGGAGATGTTTTAAACA
131 TTTCTAGAAATTCGGATTACCTATGAGTTGTTGTTGATGATATTTTGGAGATGTTTTAAACA
4355577 TTAATGGTTCTTGATGATTTGTAATGAATATTTGTGATTTTTAAAGAGCTAATGCTATTATAAAA
1 TTAATGGTTCTTGATGATTTGTAATGAATATTTGTGATTTTTAAAGAGCTAATGCTATTATAAAA
4355642 TCATATTTGAAATTTAGATTAAAGAAATTAAAATTTACTAAGCAAAATAAATCAGTCTAGGTTAT
66 TCATATTTGAAATTTAGATTAAAGAAATTAAAATTTACTAAGCAAAATAAATCAGTCTAGGTTAT
** * * *
4355707 TTTCTAGAAATTTTGATTACCTATGATTTGTTGTTGATGATGTTTTGGATATGTTTTAAA
131 TTTCTAGAAATTCGGATTACCTATGAGTTGTTGTTGATGATATTTTGGAGATGTTTTAAA
4355767 ATCATTTTTG
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
192 179 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (192 bp):
TTAATGGTTCTTGATGATTTGTAATGAATATTTGTGATTTTTAAAGAGCTAATGCTATTATAAAA
TCATATTTGAAATTTAGATTAAAGAAATTAAAATTTACTAAGCAAAATAAATCAGTCTAGGTTAT
TTTCTAGAAATTCGGATTACCTATGAGTTGTTGTTGATGATATTTTGGAGATGTTTTAAACA
Found at i:4365925 original size:22 final size:22
Alignment explanation
Indices: 4365900--4365947 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
4365890 GTTGAATGCG
4365900 AAAAAAATAACAGTTCGAACGA
1 AAAAAAATAACAGTTCGAACGA
* * *
4365922 AAAAAAATGACTGTTCGAATGA
1 AAAAAAATAACAGTTCGAACGA
4365944 AAAA
1 AAAA
4365948 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (22 bp):
AAAAAAATAACAGTTCGAACGA
Found at i:4379083 original size:28 final size:28
Alignment explanation
Indices: 4379049--4379115 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
4379039 GAAAAATGTT
4379049 TTAAATATATGTATGAATTTGAGTTTAG
1 TTAAATATATGTATGAATTTGAGTTTAG
4379077 TTAAATATATGTATGAATTTGAGTTTAG
1 TTAAATATATGTATGAATTTGAGTTTAG
4379105 TTAAATATATG
1 TTAAATATATG
4379116 GTTATTGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.46
Consensus pattern (28 bp):
TTAAATATATGTATGAATTTGAGTTTAG
Found at i:4381225 original size:21 final size:21
Alignment explanation
Indices: 4381176--4381227 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
4381166 GAGGGTCTAC
* *
4381176 GCGGTCCTTCGGGACATATAT
1 GCGGTCCTTTGGAACATATAT
***
4381197 GTAATCCTTTGGAACATATAT
1 GCGGTCCTTTGGAACATATAT
4381218 GCGGTCCTTT
1 GCGGTCCTTT
4381228 AAGACATATA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
GCGGTCCTTTGGAACATATAT
Found at i:4384451 original size:12 final size:12
Alignment explanation
Indices: 4384422--4384462 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
4384412 TCCATTACAT
4384422 TTTTTACTTTTA
1 TTTTTACTTTTA
*
4384434 TCTTTACTTTT-
1 TTTTTACTTTTA
4384445 TGTTTTA-TTTTA
1 T-TTTTACTTTTA
4384457 TTTTTA
1 TTTTTA
4384463 TTCATTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTACTTTTA
Found at i:4385929 original size:18 final size:18
Alignment explanation
Indices: 4385889--4385931 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4385879 CTTGTTAAAT
*
4385889 ATTGTTTGGAATGCTATG
1 ATTGTTTGGAATACTATG
*
4385907 CTTGTTTGGGAATAC-ATG
1 ATTGTTT-GGAATACTATG
4385925 ATTGTTT
1 ATTGTTT
4385932 AGGTTAGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.47
Consensus pattern (18 bp):
ATTGTTTGGAATACTATG
Found at i:4388385 original size:23 final size:23
Alignment explanation
Indices: 4388359--4388425 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
4388349 ATTTTATATA
*
4388359 GCACTTTGGTACATTTCTACGCG
1 GCACTTCGGTACATTTCTACGCG
* *
4388382 GCACTTCGGTGA-AATTCTACGTG
1 GCACTTCGGT-ACATTTCTACGCG
* *
4388405 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTACATTTCTACG
4388426 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
GCACTTCGGTACATTTCTACGCG
Found at i:4396112 original size:26 final size:25
Alignment explanation
Indices: 4396076--4396130 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
4396066 GATAAGCTTA
*
4396076 TGTATGGAATGCATATATTATGCAGT
1 TGTATGGAATGCATATATAATGCA-T
* * *
4396102 TGTATTGAATGGATGTATAATGCAT
1 TGTATGGAATGCATATATAATGCAT
4396127 TGTA
1 TGTA
4396131 CTCCATTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (25 bp):
TGTATGGAATGCATATATAATGCAT
Found at i:4397736 original size:28 final size:28
Alignment explanation
Indices: 4397700--4397759 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
4397690 GTCAAAACGA
*
4397700 GCCATTAATAATGCACTATGTCAAAAAT
1 GCCATTAATAATGCACCATGTCAAAAAT
4397728 GCCATTAATAATGCACCATGTCAAAAAT
1 GCCATTAATAATGCACCATGTCAAAAAT
4397756 GCCA
1 GCCA
4397760 ACAACTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.25
Consensus pattern (28 bp):
GCCATTAATAATGCACCATGTCAAAAAT
Found at i:4398585 original size:23 final size:23
Alignment explanation
Indices: 4398559--4398605 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
4398549 GTAATGTTTG
4398559 TCCTATTTACCTCCTTAAGGTAA
1 TCCTATTTACCTCCTTAAGGTAA
*
4398582 TCCTATTTACGTCCTTAAGGTAA
1 TCCTATTTACCTCCTTAAGGTAA
4398605 T
1 T
4398606 GAATTAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (23 bp):
TCCTATTTACCTCCTTAAGGTAA
Found at i:4402285 original size:9 final size:9
Alignment explanation
Indices: 4402253--4402277 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4402243 TAAAAGGGAA
4402253 AAATAAAAT
1 AAATAAAAT
4402262 AAATAAAAT
1 AAATAAAAT
4402271 AAATAAA
1 AAATAAA
4402278 TAAGATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:4402344 original size:2 final size:2
Alignment explanation
Indices: 4402337--4402365 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4402327 GAAAAAGGAA
4402337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4402366 CATCAAAGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4403375 original size:35 final size:35
Alignment explanation
Indices: 4403336--4403407 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
4403326 CTAAAAAACC
4403336 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
4403371 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
4403406 CT
1 CT
4403408 TCTTTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:4404077 original size:106 final size:105
Alignment explanation
Indices: 4403891--4404624 Score: 976
Period size: 106 Copynumber: 7.0 Consensus size: 105
4403881 TGTATTGTTC
* * * * * *
4403891 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTATTTATTGAC
1 CGAGTCCAATATCCTTCGAT-GTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGAC
* * * * *
4403955 AGCCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCAGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGC-GTCT
* * * *
4403997 TGAGTCTAATATCCTTCGATGCGAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
*
4404062 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
*
4404103 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT-AGCTCTGAAATTGGGAAATTATTTGTTGAC
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGA-CTCTGAAATTGGGAAATTATTTGTTGAC
4404167 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-GTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCGTCT
*
4404207 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
4404272 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
* * * * *
4404313 CGAGTCCAATATCCTACG--CT--A-TTG-----G-CTCTGAAATTGGTAGATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* * *
4404367 ACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTAT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
*
4404408 TGAGTCCAATATCCTTC-ACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGAC
1 CGAGTCCAATATCCTTCGA-TGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGAC
* *
4404472 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
* * *
4404514 CGAGTCCAACATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* *
4404579 ACCAGCCGTCCCTTCGTTGTGAACTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
4404620 CGAGT
1 CGAGT
4404625 GGCACGATAT
Statistics
Matches: 561, Mismatches: 48, Indels: 38
0.87 0.07 0.06
Matches are distributed among these distances:
95 78 0.14
96 1 0.00
97 1 0.00
99 1 0.00
100 3 0.01
101 3 0.01
102 1 0.00
104 101 0.18
105 3 0.01
106 366 0.65
107 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCGTCT
Found at i:4412837 original size:9 final size:9
Alignment explanation
Indices: 4412805--4412829 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4412795 TAAAAGGGAA
4412805 AAATAAAAT
1 AAATAAAAT
4412814 AAATAAAAT
1 AAATAAAAT
4412823 AAATAAA
1 AAATAAA
4412830 TAAGATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:4412901 original size:2 final size:2
Alignment explanation
Indices: 4412896--4412956 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
4412886 AAAAAAAAAA
4412896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4412938 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
4412957 CATCAAAGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4413278 original size:2 final size:2
Alignment explanation
Indices: 4413234--4413262 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4413224 ATAAAAAATA
4413234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4413263 AAGTTATAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4413450 original size:2 final size:2
Alignment explanation
Indices: 4413443--4413492 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
4413433 TATTAAAGAA
4413443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4413484 AT AA AT AT A
1 AT AT AT AT A
4413493 GTAAAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4413570 original size:17 final size:18
Alignment explanation
Indices: 4413542--4413576 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
4413532 ATATACGTAT
4413542 AAAATAATATGAATAAAA
1 AAAATAATATGAATAAAA
4413560 AAAATAA-ATGAATAAAA
1 AAAATAATATGAATAAAA
4413577 TATCCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAATAATATGAATAAAA
Found at i:4413990 original size:35 final size:35
Alignment explanation
Indices: 4413951--4414027 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
4413941 CAAAAAAACC
*
4413951 CTATTTTAGACTAGTATTTAAGTCCTAATCCAACT
1 CTATTTTAAACTAGTATTTAAGTCCTAATCCAACT
*
4413986 CTATTTTAAACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAAACTAGTATTTAAGTCCTAATCCAACT
*
4414021 CTTTTTT
1 CTATTTT
4414028 TTGTTACATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (35 bp):
CTATTTTAAACTAGTATTTAAGTCCTAATCCAACT
Found at i:4415663 original size:17 final size:18
Alignment explanation
Indices: 4415641--4415680 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
4415631 ATAAAATACA
4415641 AATAAAAATATA-ATTAT
1 AATAAAAATATATATTAT
* *
4415658 AATAAAAATTTATTTTAT
1 AATAAAAATATATATTAT
4415676 AATAA
1 AATAA
4415681 CTCACTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAAAAATATATATTAT
Found at i:4429088 original size:24 final size:24
Alignment explanation
Indices: 4429061--4429118 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
4429051 AAATACCCTG
*
4429061 AAACCACCCATCACTTTCCAAGAA
1 AAACTACCCATCACTTTCCAAGAA
4429085 AAACTACCCATCACTTTCCAAGAA
1 AAACTACCCATCACTTTCCAAGAA
*
4429109 ACACTACCCA
1 AAACTACCCA
4429119 CCCACCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.41, C:0.38, G:0.03, T:0.17
Consensus pattern (24 bp):
AAACTACCCATCACTTTCCAAGAA
Found at i:4433649 original size:19 final size:19
Alignment explanation
Indices: 4433627--4433688 Score: 106
Period size: 19 Copynumber: 3.3 Consensus size: 19
4433617 TAGTGTATCA
4433627 GTGCACTAAGAGTGCATCG
1 GTGCACTAAGAGTGCATCG
4433646 GTGCACTAAGAGTGCATCG
1 GTGCACTAAGAGTGCATCG
*
4433665 GTTCACTAAGAGTGCATCG
1 GTGCACTAAGAGTGCATCG
*
4433684 ATGCA
1 GTGCA
4433689 TAAAATGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (19 bp):
GTGCACTAAGAGTGCATCG
Found at i:4433809 original size:65 final size:65
Alignment explanation
Indices: 4433676--4433836 Score: 197
Period size: 65 Copynumber: 2.5 Consensus size: 65
4433666 TTCACTAAGA
4433676 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGACTG
* * * *
4433740 GTGCATCGTTACATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGTATAGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CTGAGTGCATCGATGCAT-G-
4433803 A-T-
62 ACTG
* *
4433805 GTGCATCGATGCATGAAATGCATTTGATGTTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTT
4433837 ATTTTATTCC
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
64 27 0.32
65 51 0.61
66 5 0.06
67 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGACTG
Found at i:4433874 original size:65 final size:63
Alignment explanation
Indices: 4433676--4433883 Score: 181
Period size: 65 Copynumber: 3.2 Consensus size: 63
4433666 TTCACTAAGA
* * * *
4433676 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTT-ATATTAACCTGAGTGCATCGATGCATGATTG
* * * * *
4433740 GTGCATCGTTACATCAAATGCATTCGATGTTT-TCATAAAACTCTGAGTGCATCGATGTAT-AGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTAT-AT-TAAC-CTGAGTGCATCGATGCATGA-T
4433803 AT-
62 -TG
* * * *
4433805 GTGCATCGATGCATGAAATGCATTTGATGTTTATTTTATTCCATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTATATTA-ACC-TGAGTGCATCGATGCAT-GATT
4433869 G
63 G
*
4433870 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
4433884 CACTTTGAAA
Statistics
Matches: 115, Mismatches: 18, Indels: 21
0.75 0.12 0.14
Matches are distributed among these distances:
63 1 0.01
64 48 0.42
65 63 0.55
66 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTATATTAACCTGAGTGCATCGATGCATGATTG
Found at i:4436561 original size:23 final size:22
Alignment explanation
Indices: 4436531--4436612 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
4436521 GCATGGCCTT
4436531 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
4436553 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
4436575 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
4436598 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
4436613 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Done.