Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 21 of 125
Found at i:3684070 original size:2 final size:2
Alignment explanation
Indices: 3684058--3684087 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3684048 ACCGTTTCAA
*
3684058 AT AT GT 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
3684088 GAACATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3688882 original size:20 final size:20
Alignment explanation
Indices: 3688831--3688888 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
3688821 ATTTTTATTC
3688831 ATTTTTATTTTA-GATTTTT
1 ATTTTTATTTTATGATTTTT
* *
3688850 -TATTTCATATTTATCATTTTT
1 AT-TTTTAT-TTTATGATTTTT
3688871 ATTTTTATTTTATGATTT
1 ATTTTTATTTTATGATTT
3688889 ATTTTCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 13 0.42
21 11 0.35
22 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (20 bp):
ATTTTTATTTTATGATTTTT
Found at i:3691354 original size:62 final size:57
Alignment explanation
Indices: 3691262--3691421 Score: 196
Period size: 62 Copynumber: 2.7 Consensus size: 57
3691252 ATTTCAAGAA
*
3691262 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGCTTTCCAC
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAG-TTT---C
* *
3691323 AAAAAAATATTTTTGGGAAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTC
1 AAAAAAATATTTTTGGG--AAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGTTTC
* *
3691382 AAAAGAATATTTTTGGGGAAAAGTTGAAAGTATTAATTTT
1 AAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTT
3691422 TCCTGCAAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
58 21 0.23
59 14 0.16
60 5 0.06
61 15 0.17
62 32 0.36
63 3 0.03
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (57 bp):
AAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGTTTC
Found at i:3691891 original size:80 final size:80
Alignment explanation
Indices: 3691758--3691920 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
3691748 AAGGACCCTT
3691758 AAACTTAGGTGTTCCCTGAAAGGATAAATTCCTTAGGTGACCAATCACACCTAGATAAAAAAGAT
1 AAACTTAGGTGTTCCCTGAAAGGATAAATTCCTTAGGTGACCAATCACACCTAGATAAAAAAGAT
3691823 TGGTGACGACTCCTA
66 TGGTGACGACTCCTA
*
3691838 AAACTTAGGTGTTCCCTGAAAGGATATATTCCTTAGGTGACCAATCACACCTAGATAAAAAAGAT
1 AAACTTAGGTGTTCCCTGAAAGGATAAATTCCTTAGGTGACCAATCACACCTAGATAAAAAAGAT
3691903 TGGTGACGACTCCTA
66 TGGTGACGACTCCTA
3691918 AAA
1 AAA
3691921 GTCAATGTCT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (80 bp):
AAACTTAGGTGTTCCCTGAAAGGATAAATTCCTTAGGTGACCAATCACACCTAGATAAAAAAGAT
TGGTGACGACTCCTA
Found at i:3696473 original size:11 final size:11
Alignment explanation
Indices: 3696459--3696486 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3696449 TAAATTAAAA
3696459 AAAATTACTTT
1 AAAATTACTTT
3696470 AAAATTACTTT
1 AAAATTACTTT
3696481 AAAATT
1 AAAATT
3696487 GAAATGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (11 bp):
AAAATTACTTT
Found at i:3697748 original size:20 final size:20
Alignment explanation
Indices: 3697700--3697755 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
3697690 AGTACTGCAG
* *
3697700 CCACCGTTACAGTACCACCA
1 CCACCGCTACAGTACTACCA
** *
3697720 CTGCTGCTACAGTACTACCA
1 CCACCGCTACAGTACTACCA
*
3697740 CCACCGCTATAGTACT
1 CCACCGCTACAGTACT
3697756 GCTACAGTGA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.39, G:0.12, T:0.21
Consensus pattern (20 bp):
CCACCGCTACAGTACTACCA
Found at i:3699387 original size:15 final size:15
Alignment explanation
Indices: 3699367--3699397 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3699357 ACACATTTAG
3699367 TTTTTTT-TTTAAAA
1 TTTTTTTATTTAAAA
3699381 TTTTTTTATTTAAAA
1 TTTTTTTATTTAAAA
3699396 TT
1 TT
3699398 GTCATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTTATTTAAAA
Found at i:3702981 original size:2 final size:2
Alignment explanation
Indices: 3702891--3702962 Score: 85
Period size: 2 Copynumber: 36.5 Consensus size: 2
3702881 ATACTAACTT
* * *
3702891 TA TA TA TA TA TA TA TG TA TG TA T- TA TA TA TA -A CTT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
3702932 TA TA TA TA TA TA GA 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 T
3702963 GTATGCATGC
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3704847 original size:14 final size:14
Alignment explanation
Indices: 3704825--3704863 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3704815 TTGATTTTAT
3704825 ATTTGATTTGAA-TA
1 ATTT-ATTTGAATTA
3704839 ATTTAATTTGAATTA
1 ATTT-ATTTGAATTA
3704854 ATTTATTTGA
1 ATTTATTTGA
3704864 TTTAGGCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (14 bp):
ATTTATTTGAATTA
Found at i:3705424 original size:16 final size:16
Alignment explanation
Indices: 3705403--3705509 Score: 64
Period size: 16 Copynumber: 6.9 Consensus size: 16
3705393 ATAAAAAAAA
*
3705403 AAAACCTTGAAACCCT
1 AAAACCTTAAAACCCT
* * *
3705419 AAAACCCTAAAATCTT
1 AAAACCTTAAAACCCT
* *
3705435 GAAATCC-TAAAACCTT
1 -AAAACCTTAAAACCCT
* *
3705451 ATAACCTTGAAACCCT
1 AAAACCTTAAAACCCT
3705467 -AAA-CTTCAAAACCCT
1 AAAACCTT-AAAACCCT
3705482 AAAA-C-T-AAACCCT
1 AAAACCTTAAAACCCT
* *
3705495 AAACCCTAAAAACCC
1 AAAACCTTAAAACCC
3705510 ACAAAAACCC
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
13 10 0.14
14 4 0.06
15 14 0.20
16 37 0.53
17 5 0.07
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAACCTTAAAACCCT
Found at i:3705430 original size:24 final size:24
Alignment explanation
Indices: 3705403--3705469 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
3705393 ATAAAAAAAA
3705403 AAAACCTTGAAACCCTAAAACCCT
1 AAAACCTTGAAACCCTAAAACCCT
* * *
3705427 AAAATCTTGAAATCCTAAAACCTT
1 AAAACCTTGAAACCCTAAAACCCT
*
3705451 ATAACCTTGAAACCCTAAA
1 AAAACCTTGAAACCCTAAA
3705470 CTTCAAAACC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.46, C:0.27, G:0.04, T:0.22
Consensus pattern (24 bp):
AAAACCTTGAAACCCTAAAACCCT
Found at i:3708473 original size:4 final size:4
Alignment explanation
Indices: 3708466--3708575 Score: 72
Period size: 4 Copynumber: 28.0 Consensus size: 4
3708456 TATTTAAAGA
* *
3708466 AAAT AAAT AAAT AAAT -AA- AAAT AAA- AATAA AAAT AAAAT AAA- ATAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT -AAAT AAAT A-AAT
* * * *
3708513 AAAT -AGT AAAT AATT CTAAT CTAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3708562 -AAT -AAT AAAT AAAT
1 AAAT AAAT AAAT AAAT
3708576 GAAAAAAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
3 15 0.17
4 59 0.67
5 14 0.16
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:3708753 original size:3 final size:3
Alignment explanation
Indices: 3708739--3708787 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
3708729 ATGCAAAAAT
*
3708739 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3708787 A
1 A
3708788 ATTTTATGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3709425 original size:17 final size:18
Alignment explanation
Indices: 3709395--3709453 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
3709385 ATAACTTTTA
* *
3709395 ATAAATTATAATTAAATTT
1 ATAAATT-TTATTAAATAT
*
3709414 A-AAATTTTATTAAAAAT
1 ATAAATTTTATTAAATAT
*
3709431 ATAAATTTTAATAAATA-
1 ATAAATTTTATTAAATAT
3709448 ATAAAT
1 ATAAAT
3709454 CACATATAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 15 0.44
18 18 0.53
19 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATTTTATTAAATAT
Found at i:3710172 original size:4 final size:4
Alignment explanation
Indices: 3710163--3710187 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3710153 TTCATCTCTC
3710163 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
3710188 ATATATGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3717605 original size:25 final size:27
Alignment explanation
Indices: 3717569--3717624 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
3717559 TATTCTCAAA
*
3717569 TAATTAATAGTATA-CT-AATTTTTTTT
1 TAATTAATAGTA-ACCTCAATTCTTTTT
3717595 TAATT-ATAGTAACCTCAATTCTTTTT
1 TAATTAATAGTAACCTCAATTCTTTTT
3717621 TAAT
1 TAAT
3717625 ATTATAAGCG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 1 0.04
25 8 0.30
26 18 0.67
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.54
Consensus pattern (27 bp):
TAATTAATAGTAACCTCAATTCTTTTT
Found at i:3718029 original size:25 final size:26
Alignment explanation
Indices: 3717995--3718045 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
3717985 CAGCATTTTC
*
3717995 AATATATAATATATT-TAAATAAATA
1 AATAAATAATATATTATAAATAAATA
* *
3718020 AATAAATAATTTATTATAATTAAATA
1 AATAAATAATATATTATAAATAAATA
3718046 GGCGAATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATAAATAATATATTATAAATAAATA
Found at i:3718630 original size:24 final size:25
Alignment explanation
Indices: 3718603--3718698 Score: 79
Period size: 26 Copynumber: 3.8 Consensus size: 25
3718593 AATTTAACAT
*
3718603 TATTTTTTAATAGTATTAT-AAATA
1 TATTTTTTAATAATATTATAAAATA
* *
3718627 TATTTTTTATTAATATTTTAAAATA
1 TATTTTTTAATAATATTATAAAATA
** * *
3718652 TATTTTAAAATTAAAATTAAAAAATA
1 TATTTTTTAA-TAATATTATAAAATA
3718678 T-TTTTATTAATTAAGTATTAT
1 TATTTT-TTAA-TAA-TATTAT
3718699 TTTAAACTGA
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
24 16 0.29
25 16 0.29
26 19 0.35
27 4 0.07
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATTTTTTAATAATATTATAAAATA
Found at i:3718650 original size:25 final size:25
Alignment explanation
Indices: 3718595--3718657 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
3718585 TTCAAATAAA
* *
3718595 TTTAACAT-TATTTTTTAATAGTAT
1 TTTAAAATATATTTTTTAATAATAT
* *
3718619 TAT-AAATATATTTTTTATTAATAT
1 TTTAAAATATATTTTTTAATAATAT
3718643 TTTAAAATATATTTT
1 TTTAAAATATATTTT
3718658 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 3 0.09
24 18 0.56
25 11 0.34
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTAAAATATATTTTTTAATAATAT
Found at i:3719719 original size:19 final size:17
Alignment explanation
Indices: 3719695--3719734 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
3719685 TTTTATTGAC
*
3719695 AAAATATTTGTTGATAAAA
1 AAAATATTT-ATGA-AAAA
3719714 AAAATATTTATGAAAAA
1 AAAATATTTATGAAAAA
3719731 AAAA
1 AAAA
3719735 AAGGTACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (17 bp):
AAAATATTTATGAAAAA
Found at i:3719731 original size:18 final size:19
Alignment explanation
Indices: 3719695--3719735 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3719685 TTTTATTGAC
* *
3719695 AAAATATTTGTTGATAAAA
1 AAAATATTTGATGAAAAAA
3719714 AAAATATTT-ATGAAAAAA
1 AAAATATTTGATGAAAAAA
3719732 AAAA
1 AAAA
3719736 AGGTACCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAATATTTGATGAAAAAA
Found at i:3720017 original size:13 final size:13
Alignment explanation
Indices: 3719999--3720025 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3719989 GTATTTTTAG
3719999 ATGAAAAATAGTA
1 ATGAAAAATAGTA
3720012 ATGAAAAATAGTA
1 ATGAAAAATAGTA
3720025 A
1 A
3720026 CGACGATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (13 bp):
ATGAAAAATAGTA
Found at i:3720269 original size:6 final size:7
Alignment explanation
Indices: 3720244--3720268 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3720234 GCAAAACAAT
3720244 AAAAATA
1 AAAAATA
3720251 AAAAATA
1 AAAAATA
3720258 AAAAATA
1 AAAAATA
3720265 AAAA
1 AAAA
3720269 TGGCAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:3720276 original size:7 final size:7
Alignment explanation
Indices: 3720266--3720293 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3720256 TAAAAAATAA
3720266 AAATGGC
1 AAATGGC
3720273 AAATGGC
1 AAATGGC
3720280 AAATGGC
1 AAATGGC
3720287 AAATGGC
1 AAATGGC
3720294 GTTGGGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (7 bp):
AAATGGC
Found at i:3725630 original size:31 final size:31
Alignment explanation
Indices: 3725563--3725631 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
3725553 GTATGTCGTT
* *
3725563 AAAATATTAATTTTTTTTAAATTTTAGTGATT
1 AAAATATTAATTTTTTTTAAATTTTAG-AATA
3725595 AAAAT-TTAATTTTTTTTTATAATTTTA-AATA
1 AAAATATTAA-TTTTTTTTA-AATTTTAGAATA
3725626 AAAATA
1 AAAATA
3725632 ATAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
31 11 0.34
32 14 0.44
33 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
AAAATATTAATTTTTTTTAAATTTTAGAATA
Found at i:3729304 original size:41 final size:40
Alignment explanation
Indices: 3729225--3729333 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 40
3729215 TTTATGTCGA
3729225 ATTTATTTCATATT-AAATATATATAATATAAAAATTATTTT
1 ATTTATTT-ATATTAAAATATATATAATATAAAAATTA-TTT
* * *
3729266 ATTATAATTTATCTTAAAATAT-TA-AATATTAAATTTATTT
1 ATT-T-ATTTATATTAAAATATATATAATATAAAAATTATTT
*
3729306 ATTTATTTATATTAAATTTATATATAAT
1 ATTTATTTATATTAAA-ATATATATAAT
3729334 TTTTTATTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
38 11 0.19
39 4 0.07
40 8 0.14
41 17 0.30
42 7 0.12
43 10 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (40 bp):
ATTTATTTATATTAAAATATATATAATATAAAAATTATTT
Found at i:3729326 original size:15 final size:15
Alignment explanation
Indices: 3729224--3729331 Score: 53
Period size: 15 Copynumber: 6.8 Consensus size: 15
3729214 TTTTATGTCG
3729224 AATTTATTTCATATTA
1 AATTTATTT-ATATTA
* * *
3729240 AATATATATAATATAA
1 AATTTAT-TTATATTA
*
3729256 AAATTATTT-TATTA
1 AATTTATTTATATTA
3729270 TAATTTATCTTAAAATATTA
1 -AATTTAT-TT---ATATTA
3729290 AATATTAAATTTAT-TT-
1 AAT-TT--ATTTATATTA
3729306 -ATTTATTTATATTA
1 AATTTATTTATATTA
*
3729320 AATTTATATATA
1 AATTTATTTATA
3729332 ATTTTTTATT
Statistics
Matches: 70, Mismatches: 9, Indels: 27
0.66 0.08 0.25
Matches are distributed among these distances:
12 6 0.09
13 2 0.03
14 6 0.09
15 19 0.27
16 18 0.26
17 3 0.04
18 2 0.03
19 3 0.04
20 7 0.10
21 2 0.03
22 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTATTTATATTA
Found at i:3729341 original size:23 final size:23
Alignment explanation
Indices: 3729257--3729348 Score: 73
Period size: 23 Copynumber: 3.9 Consensus size: 23
3729247 ATAATATAAA
3729257 AATTATTT-TATTATAATTTATCTT
1 AATTATTTATATTA-AATTTAT-TT
* *
3729281 AAAATATTAAATATTAAATTTATTT
1 -AATTATT-TATATTAAATTTATTT
*
3729306 ATTTATTTATATTAAATTTATATAT
1 AATTATTTATATTAAATTTAT-T-T
*
3729331 AATT-TTT-TATTAATTTTA
1 AATTATTTATATTAAATTTA
3729349 AGTTGTATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
23 23 0.41
24 9 0.16
25 12 0.21
26 7 0.12
27 5 0.09
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTATTTATATTAAATTTATTT
Found at i:3730445 original size:2 final size:2
Alignment explanation
Indices: 3730438--3730466 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3730428 TGTTTGGTCC
3730438 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3730467 GGGCTGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3745558 original size:6 final size:6
Alignment explanation
Indices: 3745549--3745587 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
3745539 CAACACCAAA
*
3745549 AAAAAC AAAAA- ATAAAAA AAAAAC AAAAAC AAAAAC AAA
1 AAAAAC AAAAAC A-AAAAC AAAAAC AAAAAC AAAAAC AAA
3745588 CTTTTTCCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 1 0.03
6 28 0.93
7 1 0.03
ACGTcount: A:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:3745582 original size:17 final size:18
Alignment explanation
Indices: 3745546--3745583 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
3745536 GACCAACACC
*
3745546 AAAAAAAACAAAAAATAA
1 AAAAAAAACAAAAAACAA
3745564 AAAAAAAAC-AAAAACAA
1 AAAAAAAACAAAAAACAA
3745581 AAA
1 AAA
3745584 CAAACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (18 bp):
AAAAAAAACAAAAAACAA
Found at i:3751666 original size:29 final size:29
Alignment explanation
Indices: 3751634--3751702 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
3751624 TGAGTAGAGA
* **
3751634 TTTCTAAGATATCTTTAGGTGAGAAAATT
1 TTTCTAAGAAATCCCTAGGTGAGAAAATT
*
3751663 TTTCTAAGAAATCCCTATGTGAGAAAATT
1 TTTCTAAGAAATCCCTAGGTGAGAAAATT
3751692 TTTCTAA-AAAT
1 TTTCTAAGAAAT
3751703 ACTGCTAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 4 0.11
29 32 0.89
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (29 bp):
TTTCTAAGAAATCCCTAGGTGAGAAAATT
Found at i:3754000 original size:14 final size:13
Alignment explanation
Indices: 3753946--3754003 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
3753936 AAATATATAT
* *
3753946 ATATAATATAAAA
1 ATATTATATTAAA
* *
3753959 ATTATTTTATTATA
1 A-TATTATATTAAA
3753973 AT-TTATATTAAA
1 ATATTATATTAAA
3753985 ATATTATATATAAA
1 ATATTATAT-TAAA
3753999 ATATT
1 ATATT
3754004 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
12 10 0.28
13 8 0.22
14 18 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTATATTAAA
Found at i:3755215 original size:14 final size:14
Alignment explanation
Indices: 3755198--3755241 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3755188 ATATTATATC
3755198 AAATAATTTAAAAT
1 AAATAATTTAAAAT
*
3755212 AAATAATTATAAATT
1 AAATAATT-TAAAAT
*
3755227 ATAT-ATTTAAAAT
1 AAATAATTTAAAAT
3755240 AA
1 AA
3755242 TCTTAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 6 0.24
14 11 0.44
15 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATAATTTAAAAT
Found at i:3755613 original size:22 final size:22
Alignment explanation
Indices: 3755567--3755613 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3755557 GTTAATGATT
*
3755567 TTTTAATAATATTTTGATATTA
1 TTTTAATAATATTTTGATATGA
*
3755589 TTTTAGTAATATTTTTGAT-TGA
1 TTTTAATAATA-TTTTGATATGA
3755611 TTT
1 TTT
3755614 GATATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.62
Consensus pattern (22 bp):
TTTTAATAATATTTTGATATGA
Found at i:3757244 original size:11 final size:11
Alignment explanation
Indices: 3757207--3757238 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
3757197 AATATTTAAT
3757207 AAAACAAACAAA
1 AAAACAAA-AAA
3757219 AAAACAAAAAA
1 AAAACAAAAAA
3757230 AAAACAAAA
1 AAAACAAAA
3757239 CGAAAATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:3757333 original size:21 final size:20
Alignment explanation
Indices: 3757289--3757346 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 20
3757279 ACTGTCCCCG
3757289 ACCAACTCCCTGTCAGCCACCCA
1 ACCAACTCCCTG--A-CCACCCA
3757312 ACCAACTCCCTGACCAACCCA
1 ACCAACTCCCTGACC-ACCCA
*
3757333 ACCAACCCCCTGAC
1 ACCAACTCCCTGAC
3757347 TAGCTCTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 2 0.06
21 19 0.58
23 12 0.36
ACGTcount: A:0.29, C:0.53, G:0.07, T:0.10
Consensus pattern (20 bp):
ACCAACTCCCTGACCACCCA
Found at i:3757566 original size:17 final size:17
Alignment explanation
Indices: 3757540--3757577 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3757530 AAGGGCACAG
*
3757540 AAACGTAAAAAAAAAAA
1 AAACGCAAAAAAAAAAA
*
3757557 AAACGCAAAAAAAAAGA
1 AAACGCAAAAAAAAAAA
3757574 AAAC
1 AAAC
3757578 AAAAACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.11, G:0.08, T:0.03
Consensus pattern (17 bp):
AAACGCAAAAAAAAAAA
Found at i:3757571 original size:22 final size:22
Alignment explanation
Indices: 3757546--3757589 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3757536 ACAGAAACGT
3757546 AAAA-AAAAAAAAAACGCAAAAA
1 AAAAGAAAAAAAAAAC-CAAAAA
*
3757568 AAAAGAAAACAAAAACCAAAAA
1 AAAAGAAAAAAAAAACCAAAAA
3757590 TAACATAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAAAACCAAAAA
Found at i:3759281 original size:194 final size:196
Alignment explanation
Indices: 3758929--3759303 Score: 657
Period size: 194 Copynumber: 1.9 Consensus size: 196
3758919 TACATAATTT
* * * *
3758929 TTACGAAAAGTAAATTCAGATCTTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTT
1 TTACGAAAAATAAATTCAGAGCCTCCAAAGATGAGATTCTAAAAGTATTCCGAATAGAGATGCTT
3758994 TAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTATCAACGTACTGGAACATTTTAAGAAT
66 TAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTATCAACGTACTGGAACATTTTAAGAAT
*
3759059 TATTTCAATAAAAAGGTTTTAATTTATTTTTCTTGAGAATAA-ATTTTTTTTAACATGACATTTT
131 TATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATATTTTTTTTAACATGACATTTT
3759123 C
196 C
*
3759124 TTACGAAAAATAAATTC-GAGCCTCCAAAGATGAGATTCTAAAAGTATTCCGAATAGAGATGTTT
1 TTACGAAAAATAAATTCAGAGCCTCCAAAGATGAGATTCTAAAAGTATTCCGAATAGAGATGCTT
3759188 TAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTA-CTAACGTACTGGAACATTTTAAGAA
66 TAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTATC-AACGTACTGGAACATTTTAAGAA
*
3759252 TTATTTCAATAAAAAGGTTTTGATTTATTTTTCTCGAGAATAATATTTTTTT
130 TTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATATTTTTTT
3759304 AATAAATAAA
Statistics
Matches: 171, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
193 1 0.01
194 146 0.85
195 24 0.14
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (196 bp):
TTACGAAAAATAAATTCAGAGCCTCCAAAGATGAGATTCTAAAAGTATTCCGAATAGAGATGCTT
TAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTATCAACGTACTGGAACATTTTAAGAAT
TATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATATTTTTTTTAACATGACATTTT
C
Found at i:3759814 original size:15 final size:13
Alignment explanation
Indices: 3759767--3759813 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
3759757 CATTTTTAGT
3759767 AAAAAAAAAACAA
1 AAAAAAAAAACAA
3759780 AAAAAAACAAATCAA
1 AAAAAAA-AAA-CAA
*
3759795 AAAATAAAAAGCAA
1 AAAA-AAAAAACAA
3759809 AAAAA
1 AAAAA
3759814 TTCACACACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.27
14 10 0.33
15 9 0.30
16 3 0.10
ACGTcount: A:0.85, C:0.09, G:0.02, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:3768154 original size:47 final size:49
Alignment explanation
Indices: 3768090--3768508 Score: 550
Period size: 49 Copynumber: 8.6 Consensus size: 49
3768080 AGATGAGAAA
* * * *
3768090 TTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGC-TTTTTC-AGAAAGAA
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGAGAGAT
* * * *
3768137 TTTTAAAGTTGTTGAGCCTTTGCTGAAAGGAGC-TTTTTCAAGATAAGAT
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGA-GAGAT
3768186 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGAGAGAT
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGAGAGAT
*
3768235 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGAAGCTTTTTTC-A-AGAGAT
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGAGAGAT
* *
3768282 TTTTAAAGTTGTGAAGCCTCTGTTGAGAGGAGCTTTTTTTC-AGATGAGAT
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGC-TTTTTTCAAGA-GAGAT
3768332 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTTCAAGAGAGAAT
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGC-TTTTTTCAAGAGAG-AT
*
3768383 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGAAGCTTTTTTC-A-AGAGAT
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGAGAGAT
* ** * *
3768430 TTTTAAAGTTGTGAAGCCTCTATTGAGAGGAGC-TTTTTCTAGATGAAAT
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGA-GAGAT
* *
3768479 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGG
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGG
3768509 TGCCCTTTTC
Statistics
Matches: 335, Mismatches: 26, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
46 6 0.02
47 103 0.31
48 17 0.05
49 108 0.32
50 64 0.19
51 37 0.11
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (49 bp):
TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGAGAGAT
Found at i:3768203 original size:96 final size:97
Alignment explanation
Indices: 3768090--3768508 Score: 555
Period size: 96 Copynumber: 4.3 Consensus size: 97
3768080 AGATGAGAAA
* * * * *
3768090 TTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGC-TTTTTCAGAAAGAATTTTAAAGTTGTTGAGC
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAGAGAGATTTTTAAAGTTGTGGAGC
* *
3768154 CTTTGCTGAAAGGAGC-TTTTTCAAGATAAGAT
66 CTCTGCTGAGAGGAGCTTTTTTCAAGA-AAGAT
3768186 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGAGAGATTTTTAAAGTTGTGGAG
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTC-AGAGAGATTTTTAAAGTTGTGGAG
*
3768251 CCTCTGCTGAGAGAAGCTTTTTTCAAG--AGAT
65 CCTCTGCTGAGAGGAGCTTTTTTCAAGAAAGAT
* *
3768282 TTTTAAAGTTGTGAAGCCTCTGTTGAGAGGAGCTTTTTTTCAGATGAGATTTTTAAAGTTGTGGA
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGC-TTTTTTCAGA-GAGATTTTTAAAGTTGTGGA
*
3768347 GCCTCTGCTGAGAGGAGCTTTTTTTCAAGAGAGAAT
64 GCCTCTGCTGAGAGGAGC-TTTTTTCAAGAAAG-AT
* *
3768383 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGAAGCTTTTTTCA-AGAGATTTTTAAAGTTGTGAAGC
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAGAGAGATTTTTAAAGTTGTGGAGC
** *
3768447 CTCTATTGAGAGGAGC-TTTTTCTAGATGAA-AT
66 CTCTGCTGAGAGGAGCTTTTTTCAAGA--AAGAT
* *
3768479 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGG
1 TTTTAAAGTTGTGGAGCCTCTGCTGAGAGG
3768509 TGCCCTTTTC
Statistics
Matches: 290, Mismatches: 22, Indels: 22
0.87 0.07 0.07
Matches are distributed among these distances:
96 107 0.37
97 50 0.17
98 81 0.28
99 10 0.03
100 10 0.03
101 32 0.11
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (97 bp):
TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTTCAGAGAGATTTTTAAAGTTGTGGAGC
CTCTGCTGAGAGGAGCTTTTTTCAAGAAAGAT
Found at i:3768689 original size:9 final size:8
Alignment explanation
Indices: 3768675--3768714 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
3768665 AATAATATTT
3768675 AACAAAACA
1 AACAAAA-A
3768684 AACAAAAA
1 AACAAAAA
*
3768692 AATAAAAA
1 AACAAAAA
*
3768700 AAAAAAAA
1 AACAAAAA
3768708 AACAAAA
1 AACAAAA
3768715 CAAAACGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.03
Consensus pattern (8 bp):
AACAAAAA
Found at i:3768708 original size:16 final size:17
Alignment explanation
Indices: 3768675--3768719 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
3768665 AATAATATTT
*
3768675 AACAAAACAAACAAAAA
1 AACAAAACAAAAAAAAA
*
3768692 AATAAAA-AAAAAAAAA
1 AACAAAACAAAAAAAAA
3768708 AACAAAACAAAA
1 AACAAAACAAAA
3768720 CGAAAATAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (17 bp):
AACAAAACAAAAAAAAA
Found at i:3768814 original size:35 final size:35
Alignment explanation
Indices: 3768768--3768834 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
3768758 AAACTGCCCC
*
3768768 GACCAACTCCCTGTCAGCCACCTAACCAACTCCGT
1 GACCAACTCCCTGTCAGCCACCCAACCAACTCCGT
3768803 GACCAACTCCCTGTCAGCCACCCAACCAACTC
1 GACCAACTCCCTGTCAGCCACCCAACCAACTC
3768835 TCCGACCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.27, C:0.48, G:0.10, T:0.15
Consensus pattern (35 bp):
GACCAACTCCCTGTCAGCCACCCAACCAACTCCGT
Found at i:3768842 original size:35 final size:34
Alignment explanation
Indices: 3768765--3768844 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 34
3768755 GTCAAACTGC
*
3768765 CCCGACCAACTCCCTGTCAGCCACCTAACCAACT
1 CCCGACCAACTCCCTGTCAGCCACCCAACCAACT
*
3768799 CCGTGACCAACTCCCTGTCAGCCACCCAACCAACT
1 CC-CGACCAACTCCCTGTCAGCCACCCAACCAACT
3768834 CTCCGACCAAC
1 C-CCGACCAAC
3768845 CCAACCAACC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 2 0.05
35 38 0.93
36 1 0.02
ACGTcount: A:0.26, C:0.50, G:0.10, T:0.14
Consensus pattern (34 bp):
CCCGACCAACTCCCTGTCAGCCACCCAACCAACT
Found at i:3769066 original size:24 final size:23
Alignment explanation
Indices: 3769039--3769094 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
3769029 TAGATCTAGC
* *
3769039 AAAAAAAAAAGGCACAAAAACGTA
1 AAAAAAAAAAGGCAAAAAAAC-CA
*
3769063 AAAAAAAAAATGCAAAAAAACCA
1 AAAAAAAAAAGGCAAAAAAACCA
3769086 AAAAAAAAA
1 AAAAAAAAA
3769095 CTAAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.79, C:0.11, G:0.07, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAAGGCAAAAAAACCA
Found at i:3770768 original size:194 final size:194
Alignment explanation
Indices: 3770412--3770791 Score: 640
Period size: 194 Copynumber: 2.0 Consensus size: 194
3770402 ACATTACATA
* *
3770412 ATTTTTACGAAAAGTAAATTCAGACCTTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGAT
1 ATTTTTACAAAAAATAAATTCAGACCTTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGAT
3770477 GCTTTAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGAAACATTTTAA
66 GCTTTAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGAAACATTTTAA
*
3770542 GAATTATTTCAATAAAAAAGTTTTAATTTATTTTTCTTGAGAATAAATATT-TTTTTAACATGAC
131 GAATTATTTCAATAAAAAAGTTTTAATTTATTTTTCTCGAGAAT-AATATTCTTTTTAACATGAC
*
3770606 ATTTCTTACAAAAAATAAATTC-GAGCC-TCCAAAGATGAGATTCTAAAAGTATTTCGAGTAGAG
1 ATTT-TTACAAAAAATAAATTCAGA-CCTTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAG
* *
3770669 ATGCTTTAAGAAATCTTTATGTGAGAAAGAGTTCTTTTAGTGTTACCAACGTACTGAAACATTTT
64 ATGCTTTAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGAAACATTTT
* *
3770734 AAGAATTATTTCAATAAAAAGGTTTTGATTTATTTTTCTCGAGAATAATATTCTTTTT
129 AAGAATTATTTCAATAAAAAAGTTTTAATTTATTTTTCTCGAGAATAATATTCTTTTT
3770792 TAATAAATAA
Statistics
Matches: 175, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
193 6 0.03
194 152 0.87
195 17 0.10
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (194 bp):
ATTTTTACAAAAAATAAATTCAGACCTTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGAT
GCTTTAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGAAACATTTTAA
GAATTATTTCAATAAAAAAGTTTTAATTTATTTTTCTCGAGAATAATATTCTTTTTAACATGAC
Found at i:3771302 original size:2 final size:2
Alignment explanation
Indices: 3771295--3771320 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3771285 AACTCCACAA
3771295 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
3771321 TGTAGGATTC
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):
AT
Found at i:3774109 original size:3 final size:3
Alignment explanation
Indices: 3774101--3774133 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3774091 TAATCTGCAA
3774101 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3774134 GCAGAAACCC
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:3775840 original size:21 final size:21
Alignment explanation
Indices: 3775815--3775865 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3775805 GATTAAAGTG
* *
3775815 AAATTAATTATTGTAATAATA
1 AAATTAAATATTATAATAATA
3775836 AAATTAAATATTATAATAATA
1 AAATTAAATATTATAATAATA
3775857 AAATTAAAT
1 AAATTAAAT
3775866 TAGTGATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTAAATATTATAATAATA
Found at i:3776515 original size:14 final size:15
Alignment explanation
Indices: 3776498--3776527 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3776488 ATTCTACGAG
3776498 TTTAAAA-TAATTTT
1 TTTAAAATTAATTTT
3776512 TTTAAAATTAATTTT
1 TTTAAAATTAATTTT
3776527 T
1 T
3776528 AATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAAAATTAATTTT
Found at i:3789834 original size:30 final size:30
Alignment explanation
Indices: 3789800--3789871 Score: 117
Period size: 33 Copynumber: 2.3 Consensus size: 30
3789790 AAGGAAACGC
3789800 AAGTGAAGAGGATTGAACGTTTATTTGAGA
1 AAGTGAAGAGGATTGAACGTTTATTTGAGA
3789830 AAGTGATAAAGAGGATTGAACGTTTATTTGAGA
1 AAGTG---AAGAGGATTGAACGTTTATTTGAGA
3789863 AAGTGAAGA
1 AAGTGAAGA
3789872 TTAACGTCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
30 9 0.23
33 30 0.77
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.28
Consensus pattern (30 bp):
AAGTGAAGAGGATTGAACGTTTATTTGAGA
Found at i:3789843 original size:33 final size:33
Alignment explanation
Indices: 3789805--3789868 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
3789795 AACGCAAGTG
3789805 AAGAGGATTGAACGTTTATTTGAGAAAGTGATA
1 AAGAGGATTGAACGTTTATTTGAGAAAGTGATA
3789838 AAGAGGATTGAACGTTTATTTGAGAAAGTGA
1 AAGAGGATTGAACGTTTATTTGAGAAAGTGA
3789869 AGATTAACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.28, T:0.30
Consensus pattern (33 bp):
AAGAGGATTGAACGTTTATTTGAGAAAGTGATA
Found at i:3790460 original size:26 final size:27
Alignment explanation
Indices: 3790405--3790471 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
3790395 ATTCTCTTGT
* *
3790405 ATTAT-ATAAAGTAGAATTGAAATAAG
1 ATTATAATAAAATAAAATTGAAATAAG
* *
3790431 ATTATAATAAAATAAAATTGAATTCA-
1 ATTATAATAAAATAAAATTGAAATAAG
3790457 ATTATAAATAAAATA
1 ATTAT-AATAAAATA
3790472 GAGAAGGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.29
27 25 0.71
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (27 bp):
ATTATAATAAAATAAAATTGAAATAAG
Found at i:3791834 original size:233 final size:228
Alignment explanation
Indices: 3791559--3792091 Score: 558
Period size: 233 Copynumber: 2.3 Consensus size: 228
3791549 TTTTTGGGGG
* * *
3791559 AAAAATCCTGCATATTTGAGTTTTCTATTTTTCCATATAAAAAATGATAGATAAGACAACAAAAA
1 AAAAAT-CTACATATTTGA-TTTTCT-TTTTCCCATA-AAAAAATGACAGATAAGACAACAAAAA
* ** * **
3791624 TAATAA-TCACACATCTCTCTGTCACCATGTGCCTTGAACTTTACCTACGATA-TGGAGTTTATT
62 CAATAACT-ACACATCTCTCTGTCA-CACCTGCCTTGAACTTTACCTACCATACT-GAGTACATT
*
3791687 TGTTTTAAGG-TATGGAAAAATTTAAAAAAAAAAAAAAACGAAAGAAAAAAGATTTTGGGTAAGA
124 TGTTTT-AGGCTATGGAAAAA-TT-AAAAAAAAAAAAAA-GAAAG---AAAGATTTGGGGTAAGA
3791751 AAATACCATT-TTTTCTTATATTCACTTGATAGGCTTTTTT-AGGAAA
182 AAATACCATTATTTTCTTATATTCACTTGATAGG-TTTTTTGAGGAAA
3791797 AAAAATCT-CATATTTGATTTTACTTTTTCCCATAAAAAAAGTGACAGATAA-ACAACAAAAACA
1 AAAAATCTACATATTTGATTTT-CTTTTTCCCATAAAAAAA-TGACAGATAAGACAACAAAAACA
* ** * * * *
3791860 ATAACTATATGTCTCTGTGTCACACCTGCCTTGAACTTTGCCTGCCATACTTAGTACATTTGTTT
64 ATAACTACACATCTCTCTGTCACACCTGCCTTGAACTTTACCTACCATACTGAGTACATTTGTTT
* * * *
3791925 TAGGCTATGGAAAAATTAAAAAAAAAAAGAAGAAAGAAAGATTTGGGGTAAGAGAATGCTATTAT
129 TAGGCTATGGAAAAATTAAAAAAAAAAAAAAGAAAGAAAGATTTGGGGTAAGAAAATACCATTAT
* * * *
3791990 TTTCTTATATTTAGTTGTTAGGTTTTTTGAGGGAA
194 TTTCTTATATTCACTTGATAGGTTTTTTGAGGAAA
* * * * * * *
3792025 AAAAATCTTATATATTTCAGTTTGCCTCTTCTCATAAAAAAATGACAGATAAGACAACAAAACCA
1 AAAAATC-TACATATTTGA-TTTTCTTTTTCCCATAAAAAAATGACAGATAAGACAACAAAAACA
3792090 AT
64 AT
3792092 GACCACATGT
Statistics
Matches: 253, Mismatches: 31, Indels: 30
0.81 0.10 0.10
Matches are distributed among these distances:
227 29 0.11
228 32 0.13
229 11 0.04
230 40 0.16
231 16 0.06
232 5 0.02
233 44 0.17
234 34 0.13
235 23 0.09
236 11 0.04
237 2 0.01
238 6 0.02
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (228 bp):
AAAAATCTACATATTTGATTTTCTTTTTCCCATAAAAAAATGACAGATAAGACAACAAAAACAAT
AACTACACATCTCTCTGTCACACCTGCCTTGAACTTTACCTACCATACTGAGTACATTTGTTTTA
GGCTATGGAAAAATTAAAAAAAAAAAAAAGAAAGAAAGATTTGGGGTAAGAAAATACCATTATTT
TCTTATATTCACTTGATAGGTTTTTTGAGGAAA
Found at i:3794374 original size:2 final size:2
Alignment explanation
Indices: 3794367--3794408 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3794357 AGGATGATAA
3794367 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3794409 GGATATAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3796026 original size:1 final size:1
Alignment explanation
Indices: 3796020--3796049 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3796010 TAAAATCTAG
3796020 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3796050 CCAACTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3799164 original size:20 final size:20
Alignment explanation
Indices: 3799126--3799165 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3799116 AAATTTTAAA
* *
3799126 TTATTTAATATTTATAAATT
1 TTATTTAATATATAAAAATT
*
3799146 TTATTTATTATATAAAAATT
1 TTATTTAATATATAAAAATT
3799166 GCTAATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTAATATATAAAAATT
Found at i:3799180 original size:20 final size:20
Alignment explanation
Indices: 3799157--3799202 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3799147 TATTTATTAT
*
3799157 ATAAAAATTGCTAATAAATA
1 ATAAAAATTACTAATAAATA
* * *
3799177 ATAAAATTTATTAATAAGTA
1 ATAAAAATTACTAATAAATA
3799197 ATAAAA
1 ATAAAA
3799203 TATTTTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
ATAAAAATTACTAATAAATA
Found at i:3806272 original size:31 final size:29
Alignment explanation
Indices: 3806237--3806296 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
3806227 ATGAATGATC
3806237 TTTAAATTATAATAAAATATTAAATATAATA
1 TTTAAATT-TAA-AAAATATTAAATATAATA
* *
3806268 TTTAAATTTTAAAAATATTTAATATAATA
1 TTTAAATTTAAAAAATATTAAATATAATA
3806297 CATGAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 17 0.63
30 2 0.07
31 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTAAATTTAAAAAATATTAAATATAATA
Found at i:3806304 original size:29 final size:29
Alignment explanation
Indices: 3806239--3806309 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
3806229 GAATGATCTT
**
3806239 TAAATTATAATAAAATATTAAATATAATATT
1 TAAATTAT-A-AAAATATTAAATATAATACA
* *
3806270 TAAATTTTAAAAATATTTAATATAATACA
1 TAAATTATAAAAATATTAAATATAATACA
*
3806299 TGAATTATAAA
1 TAAATTATAAA
3806310 TTTTTAGCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 26 0.76
30 1 0.03
31 7 0.21
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
TAAATTATAAAAATATTAAATATAATACA
Found at i:3808783 original size:9 final size:9
Alignment explanation
Indices: 3808766--3808821 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
3808756 ACAACAAGAT
*
3808766 ACAAATAAA
1 ACAATTAAA
3808775 ACAATTAAA
1 ACAATTAAA
3808784 ACCAA-TAAA
1 A-CAATTAAA
3808793 ACAATTAAA
1 ACAATTAAA
* *
3808802 ATAAATAAA
1 ACAATTAAA
*
3808811 TAAAATTAAA
1 -ACAATTAAA
3808821 A
1 A
3808822 AAACTGTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 3 0.08
9 26 0.67
10 10 0.26
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (9 bp):
ACAATTAAA
Found at i:3808790 original size:18 final size:18
Alignment explanation
Indices: 3808766--3808821 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
3808756 ACAACAAGAT
3808766 ACAAATAAAACAATTAAA
1 ACAAATAAAACAATTAAA
*
3808784 ACCAATAAAACAATTAAA
1 ACAAATAAAACAATTAAA
* *
3808802 ATAAATAAATAAAATTAAA
1 ACAAATAAA-ACAATTAAA
3808821 A
1 A
3808822 AAACTGTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
18 24 0.73
19 9 0.27
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (18 bp):
ACAAATAAAACAATTAAA
Found at i:3809361 original size:51 final size:50
Alignment explanation
Indices: 3809323--3809435 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 50
3809313 ATTTTCTTGT
* *
3809323 AGGGATTGATTAGTTATGTTTTCTAAATGAACTGATCGATCCCCTCTTTAA
1 AGGGATCGATTAGTTAAGTTTTCTAAATGAACTGATCGATCCCCTCTTT-A
* * *
3809374 AGGGATCGATTAGTTAAGTTTTCTAAATGAATTTATCGATCCCCCCTTTAA
1 AGGGATCGATTAGTTAAGTTTTCTAAATGAACTGATCGATCCCCTCTTT-A
*
3809425 AGGGATTGATT
1 AGGGATCGATT
3809436 CATTTTTATC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (50 bp):
AGGGATCGATTAGTTAAGTTTTCTAAATGAACTGATCGATCCCCTCTTTA
Found at i:3815249 original size:22 final size:22
Alignment explanation
Indices: 3815218--3815265 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3815208 GATTACATTG
*
3815218 AAAATGTTATAATGTATA-TTT
1 AAAATGTTATAATGCATACTTT
*
3815239 AAAATAGTTATATTGCATACTTT
1 AAAAT-GTTATAATGCATACTTT
3815262 AAAA
1 AAAA
3815266 AAAATGGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 11 0.48
23 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (22 bp):
AAAATGTTATAATGCATACTTT
Found at i:3823204 original size:2 final size:2
Alignment explanation
Indices: 3823197--3823228 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3823187 TTTCTTTTCC
3823197 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3823229 TCATTCACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3831668 original size:20 final size:20
Alignment explanation
Indices: 3831645--3831687 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3831635 TTTTTAAAAC
*
3831645 TTTATTTGAAAAGATATTTT
1 TTTATCTGAAAAGATATTTT
* *
3831665 TTTATCTGACAAGATGTTTT
1 TTTATCTGAAAAGATATTTT
3831685 TTT
1 TTT
3831688 TCTTTATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.56
Consensus pattern (20 bp):
TTTATCTGAAAAGATATTTT
Found at i:3831777 original size:14 final size:15
Alignment explanation
Indices: 3831760--3831792 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3831750 AAAAAAGCCA
3831760 AAAAAATAAT-ACAT
1 AAAAAATAATAACAT
3831774 AAAAAATAATAACAT
1 AAAAAATAATAACAT
3831789 AAAA
1 AAAA
3831793 TAAGTGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAATAATAACAT
Found at i:3831831 original size:19 final size:19
Alignment explanation
Indices: 3831803--3831850 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
3831793 TAAGTGGGTT
3831803 AAAAAT-AAAATAAAATCA
1 AAAAATAAAAATAAAATCA
*
3831821 AAAAATAAAAATAAAATGA
1 AAAAATAAAAATAAAATCA
*
3831840 AAAAAGAAAAA
1 AAAAATAAAAA
3831851 CCTGTGATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.12
Consensus pattern (19 bp):
AAAAATAAAAATAAAATCA
Found at i:3832547 original size:2 final size:2
Alignment explanation
Indices: 3832542--3832571 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3832532 TCTCTCTCTC
3832542 TA TA 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 TA TA
3832572 ATGCCATCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3833057 original size:20 final size:20
Alignment explanation
Indices: 3833034--3833071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3833024 AATAAAATAT
3833034 TATTTTTTAAAATATAAAAA
1 TATTTTTTAAAATATAAAAA
* *
3833054 TATTTTTTTAGATATAAA
1 TATTTTTTAAAATATAAA
3833072 TATTTAAATA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTTTTAAAATATAAAAA
Found at i:3833081 original size:8 final size:8
Alignment explanation
Indices: 3833065--3833110 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
3833055 ATTTTTTTAG
3833065 ATATAAAT
1 ATATAAAT
*
3833073 ATTTAAAT
1 ATATAAAT
* *
3833081 ATATTATT
1 ATATAAAT
3833089 ATATAAAT
1 ATATAAAT
3833097 ATATAAAT
1 ATATAAAT
*
3833105 AAATAA
1 ATATAA
3833111 TTAAATAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:3833108 original size:12 final size:13
Alignment explanation
Indices: 3833067--3833127 Score: 60
Period size: 12 Copynumber: 5.1 Consensus size: 13
3833057 TTTTTTAGAT
3833067 ATAAATAT-TTAA
1 ATAAATATATTAA
* *
3833079 ATATAT-TATTAT
1 ATAAATATATTAA
3833091 ATAAATATA-TAA
1 ATAAATATATTAA
3833103 ATAAATA-ATTAA
1 ATAAATATATTAA
*
3833115 ATAATTA-ATTAA
1 ATAAATATATTAA
3833127 A
1 A
3833128 AATTTTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAAATATATTAA
Found at i:3833113 original size:24 final size:24
Alignment explanation
Indices: 3833065--3833118 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3833055 ATTTTTTTAG
* * *
3833065 ATATAAATATTTAAATATATTATT
1 ATATAAATATATAAATAAATAATT
3833089 ATATAAATATATAAATAAATAATT
1 ATATAAATATATAAATAAATAATT
*
3833113 AAATAA
1 ATATAA
3833119 TTAATTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATAAATATATAAATAAATAATT
Found at i:3833460 original size:21 final size:21
Alignment explanation
Indices: 3833436--3833482 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3833426 CCCGAAATTA
3833436 ATAAAATAATATTTTTAAAAT
1 ATAAAATAATATTTTTAAAAT
* *
3833457 ATAAAATATTATTTTTTAAAT
1 ATAAAATAATATTTTTAAAAT
3833478 ATAAA
1 ATAAA
3833483 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAAATAATATTTTTAAAAT
Found at i:3833978 original size:2 final size:2
Alignment explanation
Indices: 3833971--3833997 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3833961 GTGTAACACA
3833971 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3833998 AGGTAAAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3838955 original size:22 final size:21
Alignment explanation
Indices: 3838921--3838965 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3838911 AAAATTAAAA
* *
3838921 AATAAAATTTAAAATTTTGAT
1 AATAAAATATAAAATTTTAAT
3838942 AATAATAATATAAAATTTTAAT
1 AATAA-AATATAAAATTTTAAT
3838964 AA
1 AA
3838966 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AATAAAATATAAAATTTTAAT
Found at i:3847248 original size:20 final size:19
Alignment explanation
Indices: 3847212--3847257 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3847202 ATATATAAAA
* *
3847212 ATTTATTTTTTAATTATTT
1 ATTTATTTTATAATTATAT
*
3847231 ATTTACTTTTATATTTATAT
1 ATTTA-TTTTATAATTATAT
3847251 ATTTATT
1 ATTTATT
3847258 AAATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTATTTTATAATTATAT
Found at i:3847253 original size:24 final size:24
Alignment explanation
Indices: 3847226--3847274 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3847216 ATTTTTTAAT
* * *
3847226 TATTTATTTACTTTTATATTTATA
1 TATTTATTAAATTTAATATTTATA
3847250 TATTTATTAAATTTAATATTTATA
1 TATTTATTAAATTTAATATTTATA
3847274 T
1 T
3847275 TTAAAAATAA
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:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTATTAAATTTAATATTTATA
Found at i:3852451 original size:54 final size:54
Alignment explanation
Indices: 3852376--3852480 Score: 131
Period size: 54 Copynumber: 1.9 Consensus size: 54
3852366 AATTTAAGAT
* *
3852376 CTCCAATCCAACAGGCTCAAAAAAGAGCT-GGGTAATTGCTTAATTGGGCCAACG
1 CTCCAATCCAACAGGCCCAAAAAAGAGCTAGGG-AATTGCTTAAGTGGGCCAACG
* * * * *
3852430 CTCCACTCCAACGGGCCCAAAAATGAGCTAGGGAGTTTCTTAAGTGGGCCA
1 CTCCAATCCAACAGGCCCAAAAAAGAGCTAGGGAATTGCTTAAGTGGGCCA
3852481 GCCAGCTCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 40 0.93
55 3 0.07
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (54 bp):
CTCCAATCCAACAGGCCCAAAAAAGAGCTAGGGAATTGCTTAAGTGGGCCAACG
Found at i:3865762 original size:2 final size:2
Alignment explanation
Indices: 3865755--3865803 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
3865745 CCGAATTTAG
* *
3865755 AT AT AT AT AT AT AT AT AT TT AT -T AT TT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3865795 TT AT AT AT A
1 AT AT AT AT A
3865804 AATTAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:3865786 original size:15 final size:15
Alignment explanation
Indices: 3865748--3865803 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
3865738 ATTCAATCCG
*
3865748 AATTTAGATATATAT
1 AATTTATATATATAT
* *
3865763 -ATATATATATTTAT
1 AATTTATATATATAT
*
3865777 TATTTATATATATAT
1 AATTTATATATATAT
3865792 AATTTATATATA
1 AATTTATATATA
3865804 AATTAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 11 0.32
15 23 0.68
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
AATTTATATATATAT
Found at i:3866152 original size:13 final size:14
Alignment explanation
Indices: 3866136--3866164 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3866126 ATTTAAAAAA
3866136 AATTTTAAT-TATT
1 AATTTTAATATATT
3866149 AATTTTAATATATT
1 AATTTTAATATATT
3866163 AA
1 AA
3866165 AAAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTTAATATATT
Found at i:3868911 original size:20 final size:19
Alignment explanation
Indices: 3868885--3868933 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
3868875 AATTTTTATA
3868885 TATTATTTTAATATAAAAT
1 TATTATTTTAATATAAAAT
* *
3868904 TTTATATTTTGATATAAAAT
1 TAT-TATTTTAATATAAAAT
3868924 TATTATTTTA
1 TATTATTTTA
3868934 TTTTATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTATTTTAATATAAAAT
Found at i:3869463 original size:25 final size:24
Alignment explanation
Indices: 3869425--3869483 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
3869415 TTTTCATTGA
* *
3869425 AATATTTTTTTCAATCACAGCTAT
1 AATAATTTTTTCAATCACAACTAT
* *
3869449 AATAACTTTTTTCAATCCCAATTAT
1 AATAA-TTTTTTCAATCACAACTAT
3869474 AATAATTTTT
1 AATAATTTTT
3869484 ATTATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.47
Consensus pattern (24 bp):
AATAATTTTTTCAATCACAACTAT
Found at i:3870613 original size:29 final size:29
Alignment explanation
Indices: 3870565--3870677 Score: 80
Period size: 27 Copynumber: 4.0 Consensus size: 29
3870555 TATATAAAAA
**
3870565 TATATATTAT-TT-ATTTAATTTTATATT
1 TATATATTATATTAATAAAATTTTATATT
*
3870592 TATATATTATATTAATAAAATTAT-TATT
1 TATATATTATATTAATAAAATTTTATATT
* *
3870620 TA-ATATTTTAATTTAATAAAAATATTATATT
1 TATATATTAT-A-TTAAT-AAAATTTTATATT
3870651 TATA-A-TA-ATTAAAATAAAA-TTTATATT
1 TATATATTATATT--AATAAAATTTTATATT
3870678 AAAAATAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
27 25 0.36
28 14 0.20
29 15 0.22
30 7 0.10
31 7 0.10
32 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATATTATATTAATAAAATTTTATATT
Found at i:3870618 original size:24 final size:24
Alignment explanation
Indices: 3870591--3870665 Score: 62
Period size: 29 Copynumber: 2.9 Consensus size: 24
3870581 AATTTTATAT
3870591 TTATATATTATATTAATAAAATTA
1 TTATATATTATATTAATAAAATTA
* *
3870615 TTATTTAATATTTTAATTTAATAAAAATA
1 TTA--T-ATATTAT-A-TTAATAAAATTA
*
3870644 TTATAT-TTATAATAATTAAAAT
1 TTATATATTATATTAA-TAAAAT
3870666 AAAATTTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
23 3 0.08
24 9 0.22
25 3 0.08
26 3 0.08
27 7 0.17
28 1 0.03
29 14 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATATATTATATTAATAAAATTA
Found at i:3870677 original size:27 final size:27
Alignment explanation
Indices: 3870589--3870687 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 27
3870579 TTAATTTTAT
* **
3870589 ATTTATATATTATATTAA-TAAAATTATT
1 ATTTATAT-TTATAATAATTAAAA-TAAA
*
3870617 ATTTAATATTT-TAAT--TTAATA-AAA
1 ATTT-ATATTTATAATAATTAAAATAAA
3870641 ATATTATATTTATAATAATTAAAATAAA
1 AT-TTATATTTATAATAATTAAAATAAA
* *
3870669 ATTTATATTAAAAATAATT
1 ATTTATATTTATAATAATT
3870688 TTTTATTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
24 9 0.16
25 6 0.11
26 4 0.07
27 23 0.40
28 11 0.19
29 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTTATATTTATAATAATTAAAATAAA
Found at i:3870701 original size:39 final size:39
Alignment explanation
Indices: 3870629--3870709 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
3870619 TTAATATTTT
3870629 AATTTAATAAAAATATTATATTTATAATAATTAAAATAA
1 AATTTAATAAAAATATTATATTTATAATAATTAAAATAA
*
3870668 AATTTATATTAAAAATAATT-T-TTTATTAT-ATTAAAATAA
1 AATTTA-A-TAAAAAT-ATTATATTTATAATAATTAAAATAA
3870707 AAT
1 AAT
3870710 AAAATAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
39 19 0.50
40 8 0.21
41 8 0.21
42 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (39 bp):
AATTTAATAAAAATATTATATTTATAATAATTAAAATAA
Found at i:3871050 original size:3 final size:3
Alignment explanation
Indices: 3871042--3871092 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3871032 TAGAGAGGCG
3871042 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3871090 AAT
1 AAT
3871093 TACGTTTGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3871254 original size:22 final size:19
Alignment explanation
Indices: 3871229--3871268 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
3871219 AAATTATAAC
3871229 TTAATTATATATAAATATATTG
1 TTAATTA-AT-TAAA-ATATTG
3871251 TTAATTAATTAAAATATT
1 TTAATTAATTAAAATATT
3871269 AAATAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 2 0.11
22 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTAATTAATTAAAATATTG
Found at i:3871271 original size:28 final size:28
Alignment explanation
Indices: 3871235--3871328 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 28
3871225 TAACTTAATT
3871235 ATATATAAAT-ATATTGTTAATTAATTAAA
1 ATATATAAATAATATT-TTAATTAA-TAAA
*
3871264 ATAT-TAAATAATATTTTTATTAATAAA
1 ATATATAAATAATATTTTAATTAATAAA
* * *
3871291 ATACATATATATAA-ATTAAATAAATAATAAA
1 AT--ATATAAATAATATT--TTAATTAATAAA
3871322 ATATATA
1 ATATATA
3871329 TATTCTTTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
27 6 0.11
28 12 0.22
29 19 0.35
30 6 0.11
31 11 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATATAAATAATATTTTAATTAATAAA
Found at i:3871635 original size:16 final size:17
Alignment explanation
Indices: 3871606--3871645 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3871596 AATAATTTTT
3871606 TATAAAATTTATATAAA
1 TATAAAATTTATATAAA
3871623 TATAAAA-TTATATAAA
1 TATAAAATTTATATAAA
3871639 TAATAAA
1 T-ATAAA
3871646 TATATATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAAATTTATATAAA
Found at i:3871651 original size:17 final size:16
Alignment explanation
Indices: 3871610--3871652 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3871600 ATTTTTTATA
*
3871610 AAATTTATATAAATAT
1 AAATATATATAAATAT
3871626 AAA-ATTATATAAATAAT
1 AAATA-TATATAAAT-AT
3871643 AAATATATAT
1 AAATATATAT
3871653 TGTTATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 12 0.52
17 10 0.43
18 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATATAAATAT
Found at i:3872176 original size:19 final size:19
Alignment explanation
Indices: 3872129--3872187 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
3872119 TGAGTTTTTT
**
3872129 ATAAAAATTATCTAATAAA
1 ATAAAAATTATAAAATAAA
* *
3872148 AAATAAAATTATAAAATTAA
1 ATA-AAAATTATAAAATAAA
*
3872168 ATAAAAATTATAAAACAAA
1 ATAAAAATTATAAAATAAA
3872187 A
1 A
3872188 AATTAAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAAATTATAAAATAAA
Found at i:3872196 original size:27 final size:28
Alignment explanation
Indices: 3872160--3872224 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 28
3872150 ATAAAATTAT
3872160 AAAATT-AAATAAAAATT-ATAAAACAA
1 AAAATTAAAATAAAAATTAATAAAACAA
* * *
3872186 AAAATTAAAAT-AAATTTAATAAAATAT
1 AAAATTAAAATAAAAATTAATAAAACAA
3872213 AAAA-TAAAATAA
1 AAAATTAAAATAA
3872225 TAGAGATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 17 0.52
27 16 0.48
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (28 bp):
AAAATTAAAATAAAAATTAATAAAACAA
Found at i:3872900 original size:25 final size:25
Alignment explanation
Indices: 3872872--3872953 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
3872862 ATTATATATT
3872872 TATATTATATTTTATATAAAAATTA
1 TATATTATATTTTATATAAAAATTA
*
3872897 TATATAATGA-TTTATATAAAAATATAA
1 TATATTAT-ATTTTATATAAAAAT-T-A
* * * * *
3872924 AATATTAAATTTTTTATTAAATTTA
1 TATATTATATTTTATATAAAAATTA
3872949 TATAT
1 TATAT
3872954 AATTATTATA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
25 25 0.56
26 4 0.09
27 16 0.36
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (25 bp):
TATATTATATTTTATATAAAAATTA
Found at i:3873001 original size:24 final size:24
Alignment explanation
Indices: 3872931--3873001 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 24
3872921 TAAAATATTA
** *
3872931 AATTTTT-TATTAAATTTATATAT
1 AATTTTTATATTTTATTTTTATAT
* ** *
3872954 AATTATTATAATTTTA-AATCATAT
1 AATTTTTAT-ATTTTATTTTTATAT
3872978 AATTTTTATATTTTATTTTTATAT
1 AATTTTTATATTTTATTTTTATAT
3873002 CATATTATTT
Statistics
Matches: 34, Mismatches: 11, Indels: 5
0.68 0.22 0.10
Matches are distributed among these distances:
23 12 0.35
24 18 0.53
25 4 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTTTTATATTTTATTTTTATAT
Found at i:3873011 original size:16 final size:16
Alignment explanation
Indices: 3872965--3873012 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
3872955 ATTATTATAA
* *
3872965 TTTTAAATCATATAAT
1 TTTTATATCATATTAT
3872981 TTTTATAT--T-TTAT
1 TTTTATATCATATTAT
3872994 TTTTATATCATATTAT
1 TTTTATATCATATTAT
3873010 TTT
1 TTT
3873013 ATCATATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 11 0.41
14 1 0.04
15 1 0.04
16 14 0.52
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATATCATATTAT
Found at i:3875620 original size:86 final size:87
Alignment explanation
Indices: 3875516--3875689 Score: 332
Period size: 86 Copynumber: 2.0 Consensus size: 87
3875506 CTGACGACGG
*
3875516 TTGATGATGACGATGGAGGGCCGGGCCTTTGAATTTGACTGTAATAAT-GATTTTGGGGTCACAC
1 TTGATGATGACGACGGAGGGCCGGGCCTTTGAATTTGACTGTAATAATGGATTTTGGGGTCACAC
3875580 CACTGCTAGATAAGACGCGCAC
66 CACTGCTAGATAAGACGCGCAC
3875602 TTGATGATGACGACGGAGGGCCGGGCCTTTGAATTTGACTGTAATAATGGATTTTGGGGTCACAC
1 TTGATGATGACGACGGAGGGCCGGGCCTTTGAATTTGACTGTAATAATGGATTTTGGGGTCACAC
3875667 CACTGCTAGATAAGACGCGCAC
66 CACTGCTAGATAAGACGCGCAC
3875689 T
1 T
3875690 CAAATATTTA
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 47 0.55
87 39 0.45
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (87 bp):
TTGATGATGACGACGGAGGGCCGGGCCTTTGAATTTGACTGTAATAATGGATTTTGGGGTCACAC
CACTGCTAGATAAGACGCGCAC
Found at i:3876180 original size:17 final size:17
Alignment explanation
Indices: 3876149--3876184 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3876139 AGGTAATATA
3876149 ATTATCAAAATAATTTT
1 ATTATCAAAATAATTTT
*
3876166 ATTATTAAAATAATTTT
1 ATTATCAAAATAATTTT
3876183 AT
1 AT
3876185 CACTGAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATCAAAATAATTTT
Found at i:3876739 original size:22 final size:21
Alignment explanation
Indices: 3876701--3876741 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3876691 TTACATATCA
*
3876701 TTTTATTTTTGTGATAAAATT
1 TTTTATTTTTGTAATAAAATT
*
3876722 TTTTATTTTTTTAAATAAAA
1 TTTTATTTTTGT-AATAAAA
3876742 ATTATATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTATTTTTGTAATAAAATT
Found at i:3877445 original size:5 final size:5
Alignment explanation
Indices: 3877431--3877466 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
3877421 CTCGGAGAGA
*
3877431 AAAAG GAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
3877467 GGTTGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3883736 original size:20 final size:20
Alignment explanation
Indices: 3883696--3883747 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
3883686 GTTTTAGTTA
3883696 TATTATTTTAA-ATGAATTTT
1 TATTATTTTAATAT-AATTTT
3883716 TACTTATTTTAATAT-ATTTT
1 TA-TTATTTTAATATAATTTT
*
3883736 TATTATATTAAT
1 TATTATTTTAAT
3883748 TCCAGATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 9 0.31
20 9 0.31
21 9 0.31
22 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTATTTTAATATAATTTT
Found at i:3891552 original size:1 final size:1
Alignment explanation
Indices: 3891512--3891542 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
3891502 TTAAAAACTC
3891512 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3891543 GCTAGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3893727 original size:75 final size:76
Alignment explanation
Indices: 3893604--3893750 Score: 244
Period size: 75 Copynumber: 1.9 Consensus size: 76
3893594 TGACTCACGA
* *
3893604 TTTTGTCATACAAAATGTGTCTCACAAGAAAGAGATGGTGTAGACCCTTATATA-CCCCTTTTAT
1 TTTTGTCATACAAAAGGTGCCTCACAAGAAAGAGATGGTGTAGACCCTTATATACCCCCTTTTAT
3893668 ATTCGATACAG
66 ATTCGATACAG
*
3893679 TTTTGTCATACAAAAGGTGCCTCACAAGGAAGAGATGGTGT-GAACCCTTATATACCCCCTTTTA
1 TTTTGTCATACAAAAGGTGCCTCACAAGAAAGAGATGGTGTAG-ACCCTTATATACCCCCTTTTA
3893743 TATTCGAT
65 TATTCGAT
3893751 GTAAGATTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
74 1 0.01
75 49 0.73
76 17 0.25
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (76 bp):
TTTTGTCATACAAAAGGTGCCTCACAAGAAAGAGATGGTGTAGACCCTTATATACCCCCTTTTAT
ATTCGATACAG
Found at i:3894302 original size:19 final size:19
Alignment explanation
Indices: 3894278--3894326 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
3894268 CTAATTAATT
3894278 ATCTTTTCAGTTTTTTTTA
1 ATCTTTTCAGTTTTTTTTA
3894297 ATCTTTTCAGTTTTTTTTA
1 ATCTTTTCAGTTTTTTTTA
3894316 ATCTTTTCAGT
1 ATCTTTTCAGT
3894327 ATTTAGATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.65
Consensus pattern (19 bp):
ATCTTTTCAGTTTTTTTTA
Found at i:3894731 original size:24 final size:25
Alignment explanation
Indices: 3894690--3894737 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3894680 ATTTTTTCTT
3894690 ATAAAAAAAAGTCAAAAT-TTAAAA
1 ATAAAAAAAAGTCAAAATGTTAAAA
* **
3894714 ATAAAAAAAATTGTAAATGTTAAA
1 ATAAAAAAAAGTCAAAATGTTAAA
3894738 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (25 bp):
ATAAAAAAAAGTCAAAATGTTAAAA
Found at i:3896897 original size:14 final size:14
Alignment explanation
Indices: 3896878--3896912 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
3896868 ATGTCCAAAG
3896878 GGCAACATAGTTTT
1 GGCAACATAGTTTT
3896892 GGCAACATAGTTTT
1 GGCAACATAGTTTT
3896906 GGCAACA
1 GGCAACA
3896913 ATTAGAGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (14 bp):
GGCAACATAGTTTT
Found at i:3903841 original size:22 final size:22
Alignment explanation
Indices: 3903806--3903847 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3903796 TAATATAATT
**
3903806 TAAAATTTTTAAATAAATTTAG
1 TAAAATTTAAAAATAAATTTAG
*
3903828 TAAAATTTAAAAATATATTT
1 TAAAATTTAAAAATAAATTT
3903848 TATATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TAAAATTTAAAAATAAATTTAG
Found at i:3903878 original size:37 final size:37
Alignment explanation
Indices: 3903837--3903928 Score: 104
Period size: 37 Copynumber: 2.5 Consensus size: 37
3903827 GTAAAATTTA
3903837 AAAATATATTTTATATTTTAATATCGATATAAAT-TAT
1 AAAATATATTTTATATTTTAATAT-GATATAAATGTAT
*
3903874 AAAATATAATTTT-TATTTAAAATATGATATAAATGTAT
1 AAAATAT-ATTTTATATTT-TAATATGATATAAATGTAT
*
3903912 -ACAT-T-TTTTATATTTTA
1 AAAATATATTTTATATTTTA
3903929 TATTACATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
34 5 0.10
35 5 0.10
36 1 0.02
37 24 0.50
38 13 0.27
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (37 bp):
AAAATATATTTTATATTTTAATATGATATAAATGTAT
Found at i:3904815 original size:20 final size:20
Alignment explanation
Indices: 3904792--3904837 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
3904782 TCATAATTTT
3904792 TAATGTTAAAAA-ATAAAAAA
1 TAAT-TTAAAAATATAAAAAA
3904812 TAATTTAAAAATATAAAAAA
1 TAATTTAAAAATATAAAAAA
*
3904832 TGATTT
1 TAATTT
3904838 TTAGATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
TAATTTAAAAATATAAAAAA
Found at i:3905212 original size:13 final size:13
Alignment explanation
Indices: 3905185--3905253 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
3905175 AGCAATATTG
*
3905185 ATAATTTAA-AAT
1 ATAATATAATAAT
3905197 ATAATATAATAAT
1 ATAATATAATAAT
3905210 ATAATATAAAATAAT
1 ATAATAT--AATAAT
* *
3905225 ACGAATA-AAAAAT
1 A-TAATATAATAAT
3905238 ATAA-AT-ATAAT
1 ATAATATAATAAT
3905249 ATAAT
1 ATAAT
3905254 TTAAAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
11 9 0.20
12 10 0.22
13 16 0.35
15 7 0.15
16 4 0.09
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:3905308 original size:22 final size:22
Alignment explanation
Indices: 3905258--3905308 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3905248 TATAATTTAA
* *
3905258 AATTTTAATAAAATTTATAAAT
1 AATTTTAATAAAATTAAAAAAT
*
3905280 AAATTTAATAAAA-TAAAAAAT
1 AATTTTAATAAAATTAAAAAAT
3905301 ATATTTTA
1 A-ATTTTA
3905309 TATTTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTTTAATAAAATTAAAAAAT
Found at i:3907388 original size:21 final size:21
Alignment explanation
Indices: 3907359--3907400 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3907349 GTAATACATG
*
3907359 GAGAGGAGGAATATTAAGATA
1 GAGAAGAGGAATATTAAGATA
3907380 GAGAAGAGGAATATTAAGATA
1 GAGAAGAGGAATATTAAGATA
3907401 ATCTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (21 bp):
GAGAAGAGGAATATTAAGATA
Found at i:3907729 original size:10 final size:10
Alignment explanation
Indices: 3907714--3907742 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3907704 AAAACCGCTT
3907714 CTCTCACTCA
1 CTCTCACTCA
3907724 CTCTCACTCA
1 CTCTCACTCA
3907734 CTCTCACTC
1 CTCTCACTC
3907743 TTTCCCCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.52, G:0.00, T:0.31
Consensus pattern (10 bp):
CTCTCACTCA
Found at i:3910264 original size:20 final size:20
Alignment explanation
Indices: 3910239--3910279 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3910229 TTAAGATTTC
3910239 ACATAAAAGTGTATGCTTTT
1 ACATAAAAGTGTATGCTTTT
3910259 ACATAAAAGTGTATGCTTTT
1 ACATAAAAGTGTATGCTTTT
3910279 A
1 A
3910280 TGTGTATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (20 bp):
ACATAAAAGTGTATGCTTTT
Found at i:3911021 original size:34 final size:34
Alignment explanation
Indices: 3910957--3911021 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
3910947 TTATTCTTGA
* **
3910957 GGTATATTTCATTTTCTAGTTTGAATAGTCCTTT
1 GGTATATTTCATTTACTAGTTCCAATAGTCCTTT
*
3910991 GGTATGTTTCATTTACTAGTCTCCAA-AGTCC
1 GGTATATTTCATTTACTAGT-TCCAATAGTCC
3911022 AAAGCCACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
34 23 0.88
35 3 0.12
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (34 bp):
GGTATATTTCATTTACTAGTTCCAATAGTCCTTT
Done.