Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 11 of 295
Found at i:3402236 original size:12 final size:12
Alignment explanation
Indices: 3402219--3402244 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3402209 TTAATCCCTT
3402219 TCAATTTTGATA
1 TCAATTTTGATA
3402231 TCAATTTTGATA
1 TCAATTTTGATA
3402243 TC
1 TC
3402245 GAGTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (12 bp):
TCAATTTTGATA
Found at i:3406459 original size:18 final size:20
Alignment explanation
Indices: 3406436--3406472 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
3406426 ATTTAATCCC
3406436 TTTATTTT-TTAAA-ATAAA
1 TTTATTTTATTAAATATAAA
3406454 TTTATTTTATTAAATATAA
1 TTTATTTTATTAAATATAA
3406473 GTTCAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTTTATTAAATATAAA
Found at i:3406960 original size:34 final size:34
Alignment explanation
Indices: 3406902--3406971 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
3406892 TTTTGGCCCC
*
3406902 AATAATGATAAAATTAGGATTTAGTCCTTATAAA
1 AATAATGATAAAATTAGGATTTAGTCCTCATAAA
* * *
3406936 AATACTGATAAAATT-GTATCTTAGTTCTCATAAA
1 AATAATGATAAAATTAGGAT-TTAGTCCTCATAAA
3406970 AA
1 AA
3406972 ATTATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 3 0.10
34 28 0.90
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.36
Consensus pattern (34 bp):
AATAATGATAAAATTAGGATTTAGTCCTCATAAA
Found at i:3408469 original size:32 final size:33
Alignment explanation
Indices: 3408428--3408495 Score: 129
Period size: 32 Copynumber: 2.1 Consensus size: 33
3408418 ACTTGTAGTA
3408428 AAAGTGAAGTTATTGTGATG-TTTTTTTTTGTC
1 AAAGTGAAGTTATTGTGATGTTTTTTTTTTGTC
3408460 AAAGTGAAGTTATTGTGATGTTTTTTTTTTGTC
1 AAAGTGAAGTTATTGTGATGTTTTTTTTTTGTC
3408493 AAA
1 AAA
3408496 TCTAATGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.25, C:0.03, G:0.21, T:0.51
Consensus pattern (33 bp):
AAAGTGAAGTTATTGTGATGTTTTTTTTTTGTC
Found at i:3416148 original size:37 final size:37
Alignment explanation
Indices: 3416086--3416158 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
3416076 ATTTAGTTGA
*
3416086 GAAATAATTTAAAGATAGTTATTTTTATAAAATAAAG
1 GAAATAATTTAAAAATAGTTATTTTTATAAAATAAAG
* *
3416123 GAAATAATTTAAAAATTA-TTGTTTTTATAAAGTAAA
1 GAAATAATTTAAAAA-TAGTTATTTTTATAAAATAAA
3416159 TTATATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.40
Consensus pattern (37 bp):
GAAATAATTTAAAAATAGTTATTTTTATAAAATAAAG
Found at i:3427466 original size:19 final size:20
Alignment explanation
Indices: 3427419--3427468 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
3427409 TACATTACAA
3427419 AAAAAAAATTATAAAATTTC
1 AAAAAAAATTATAAAATTTC
3427439 ATAAAAAAATTA-AAAATTAT-
1 A-AAAAAAATTATAAAATT-TC
3427459 AAAAAAAATT
1 AAAAAAAATT
3427469 CTAAGCAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.32
20 8 0.29
21 11 0.39
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAAATTATAAAATTTC
Found at i:3431560 original size:9 final size:9
Alignment explanation
Indices: 3431533--3431573 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
3431523 TGGCTGAAGC
3431533 TCTTCCTCT
1 TCTTCCTCT
* *
3431542 TCCTCATCT
1 TCTTCCTCT
3431551 TCTTCCTCT
1 TCTTCCTCT
3431560 TCTTCCTCT
1 TCTTCCTCT
3431569 TCTTC
1 TCTTC
3431574 TTCACCTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:3431752 original size:21 final size:21
Alignment explanation
Indices: 3431728--3431767 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3431718 ATCTTCCTCC
3431728 TCACCTGCAT-CTTCATCTTGA
1 TCACCTGC-TGCTTCATCTTGA
3431749 TCACCTGCTGCTTCATCTT
1 TCACCTGCTGCTTCATCTT
3431768 CCTCATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.15, C:0.35, G:0.10, T:0.40
Consensus pattern (21 bp):
TCACCTGCTGCTTCATCTTGA
Found at i:3431775 original size:24 final size:24
Alignment explanation
Indices: 3431717--3431775 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 24
3431707 TCACCTGATC
*
3431717 CATCTTCCTCCTCACCTGCATCTT
1 CATCTTCCTCATCACCTGCATCTT
*
3431741 CATC-T--TGATCACCTGC-TGCTT
1 CATCTTCCTCATCACCTGCAT-CTT
3431762 CATCTTCCTCATCA
1 CATCTTCCTCATCA
3431776 TCATTGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 1 0.04
23 1 0.04
24 9 0.32
ACGTcount: A:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (24 bp):
CATCTTCCTCATCACCTGCATCTT
Found at i:3436378 original size:13 final size:13
Alignment explanation
Indices: 3436360--3436389 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3436350 TTATTAATAA
3436360 TTTAATAAGATAC
1 TTTAATAAGATAC
*
3436373 TTTAATAAGATAT
1 TTTAATAAGATAC
3436386 TTTA
1 TTTA
3436390 TTATTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (13 bp):
TTTAATAAGATAC
Found at i:3451716 original size:34 final size:32
Alignment explanation
Indices: 3451673--3451748 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
3451663 GCCTGTAATA
*
3451673 GATAATATTAATGATAATTAATTTATTATTTTTT
1 GATAATATTAA--ATAACTAATTTATTATTTTTT
*
3451707 GATAATATT-AATAACTGATTTATTATTTTTT
1 GATAATATTAAATAACTAATTTATTATTTTTT
3451738 GA-AA-ATTAAAT
1 GATAATATTAAAT
3451749 GACTCAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 3 0.08
30 5 0.13
31 21 0.54
33 1 0.03
34 9 0.23
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (32 bp):
GATAATATTAAATAACTAATTTATTATTTTTT
Found at i:3452269 original size:16 final size:18
Alignment explanation
Indices: 3452238--3452270 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3452228 TCTTCGTTTA
3452238 GGTTTTATTATTATTGTT
1 GGTTTTATTATTATTGTT
3452256 GGTTTT-TT-TTATTGT
1 GGTTTTATTATTATTGT
3452271 GCATGTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70
Consensus pattern (18 bp):
GGTTTTATTATTATTGTT
Found at i:3458087 original size:21 final size:22
Alignment explanation
Indices: 3458058--3458104 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
3458048 CAGAAGGAGT
* *
3458058 GAGTAGTACTTCGCTGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3458080 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3458101 GAGT
1 GAGT
3458105 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3463443 original size:15 final size:14
Alignment explanation
Indices: 3463423--3463453 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3463413 ATAATATTGG
3463423 ATATGCTGCAAGTGA
1 ATATGCTGCAA-TGA
3463438 ATATGCTGCAATGA
1 ATATGCTGCAATGA
3463452 AT
1 AT
3463454 CTGGTTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (14 bp):
ATATGCTGCAATGA
Found at i:3470067 original size:27 final size:27
Alignment explanation
Indices: 3470016--3470068 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3470006 CCATTTTTAT
** * *
3470016 TTATTAAATATAATTTTTTTCTTGAAA
1 TTATTAAATATAAAATTATTATTGAAA
3470043 TTATTAAATATAAAATTATTATTGAA
1 TTATTAAATATAAAATTATTATTGAA
3470069 TCACATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (27 bp):
TTATTAAATATAAAATTATTATTGAAA
Found at i:3471805 original size:76 final size:73
Alignment explanation
Indices: 3471653--3471912 Score: 233
Period size: 75 Copynumber: 3.5 Consensus size: 73
3471643 GCTACCATAT
* * *
3471653 CTTATAGAAGATTCTAGAAGTGCTAAAGAGATGGGTA-AGACTAAGGA-GA-TGAACATTGAATT
1 CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATA-A-TATGGAGGAGTGAACATCGAATT
3471715 GTCACCAAAG
64 GTCACCAAAG
* *
3471725 CTTATAGAAGATTCTACAAGTACTAAAAGAGATGGGTCATAATATGGAGGAGTGGAGCATCGAAT
1 CTTATAGAAGATTCTACAAGTGCT-AAAGAGATGGGT-ATAATATGGAGGAGT-GAACATCGAAT
*
3471790 TGAT-ATCAAAG
63 TG-TCACCAAAG
* * * * * *
3471801 CTTATAGAAGATTCTCCAAGTGCTAAAGAGATAGATATGAATATGGAGGAGGAGAACGTTGAATT
1 CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAT-AATATGGAGGA-GTGAACATCGAATT
** * **
3471866 GAT-GGCGATT
64 G-TCACCAAAG
* *
3471876 CTTATAGAAGATTCTTCAAATGCTAAAGAGATGGGTA
1 CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTA
3471913 AGGATGTGGC
Statistics
Matches: 156, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
72 22 0.14
73 17 0.11
74 6 0.04
75 70 0.45
76 40 0.26
77 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.26
Consensus pattern (73 bp):
CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATAATATGGAGGAGTGAACATCGAATTGT
CACCAAAG
Found at i:3476283 original size:19 final size:19
Alignment explanation
Indices: 3476259--3476308 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3476249 TTGTTTGATA
3476259 AAATTAATCTTATTTTATT
1 AAATTAATCTTATTTTATT
*
3476278 AAATTAA--TTA-TTTCTT
1 AAATTAATCTTATTTTATT
3476294 AAATCTAATCTTATT
1 AAAT-TAATCTTATT
3476309 AATTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 9 0.35
17 6 0.23
19 10 0.38
20 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATTAATCTTATTTTATT
Found at i:3476973 original size:18 final size:18
Alignment explanation
Indices: 3476948--3476996 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
3476938 ATTAGCAAGT
3476948 AATT-AAATTTTTTAAAA
1 AATTAAAATTTTTTAAAA
* *
3476965 ATTTAAAATTTATTAAAA
1 AATTAAAATTTTTTAAAA
*
3476983 AATTATAATTTTTT
1 AATTAAAATTTTTT
3476997 TTTTGTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTAAAATTTTTTAAAA
Found at i:3481917 original size:16 final size:17
Alignment explanation
Indices: 3481893--3481944 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
3481883 AATTAACAGA
3481893 AATATTTATTGTTTTC-
1 AATATTTATTGTTTTCT
*
3481909 AATACTTATATAGTTTTCT
1 AATA-TT-TATTGTTTTCT
*
3481928 AATATTTGTTGTTTTCT
1 AATATTTATTGTTTTCT
3481945 TATTTGTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 11 0.37
18 11 0.37
19 4 0.13
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.60
Consensus pattern (17 bp):
AATATTTATTGTTTTCT
Found at i:3482436 original size:30 final size:29
Alignment explanation
Indices: 3482382--3482438 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
3482372 ATAAAATTAT
**
3482382 ATATGAATTTTAATTTTATGTAATTTTAA
1 ATATGAATTTTAATTCGATGTAATTTTAA
*
3482411 ATATGAAATTTTAATTCGATTTAATTTT
1 ATATG-AATTTTAATTCGATGTAATTTT
3482439 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (29 bp):
ATATGAATTTTAATTCGATGTAATTTTAA
Found at i:3483658 original size:9 final size:9
Alignment explanation
Indices: 3483646--3483677 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
3483636 TCGAGGTCGA
3483646 CGCCTAGAT
1 CGCCTAGAT
3483655 CGCCTAGAT
1 CGCCTAGAT
3483664 CGCCTAGAT
1 CGCCTAGAT
3483673 CGCCT
1 CGCCT
3483678 TACTTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.19, C:0.38, G:0.22, T:0.22
Consensus pattern (9 bp):
CGCCTAGAT
Found at i:3484764 original size:21 final size:21
Alignment explanation
Indices: 3484738--3484781 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3484728 GTGATGATAC
3484738 TCACTATTACATACTCATAAT
1 TCACTATTACATACTCATAAT
3484759 TCACTATTACATACTCATAAT
1 TCACTATTACATACTCATAAT
3484780 TC
1 TC
3484782 GATTGAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (21 bp):
TCACTATTACATACTCATAAT
Found at i:3485903 original size:30 final size:30
Alignment explanation
Indices: 3485847--3485903 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3485837 TCTATGTATA
* *
3485847 AATATTAAATTTATATATGAATTTTTGTCT
1 AATATTAAATTTATACATGAAATTTTGTCT
*
3485877 AATATTCAATTTGATACAT-AAATTTTG
1 AATATTAAATTT-ATACATGAAATTTTG
3485904 ATTCGATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (30 bp):
AATATTAAATTTATACATGAAATTTTGTCT
Found at i:3486150 original size:29 final size:30
Alignment explanation
Indices: 3486118--3486182 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
3486108 CCAAAATTTT
3486118 ATATATAAAATTACACA-AAATTAAAACTC
1 ATATATAAAATTACACATAAATTAAAACTC
* * *
3486147 ATATATAACATTGCACATTAAATTAAAATTC
1 ATATATAAAATTACACA-TAAATTAAAACTC
3486178 ATATA
1 ATATA
3486183 AAACTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 15 0.48
31 16 0.52
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
ATATATAAAATTACACATAAATTAAAACTC
Found at i:3486624 original size:17 final size:16
Alignment explanation
Indices: 3486602--3486635 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3486592 ATCAACAAAG
*
3486602 TTATTAAATACATCTTT
1 TTATTAAAGACAT-TTT
3486619 TTATTAAAGACATTTT
1 TTATTAAAGACATTTT
3486635 T
1 T
3486636 ACCCTAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (16 bp):
TTATTAAAGACATTTT
Found at i:3490337 original size:12 final size:12
Alignment explanation
Indices: 3490320--3490345 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3490310 CTTGTAACCC
3490320 TGTTTGAGTTCA
1 TGTTTGAGTTCA
3490332 TGTTTGAGTTCA
1 TGTTTGAGTTCA
3490344 TG
1 TG
3490346 CCTCACACGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50
Consensus pattern (12 bp):
TGTTTGAGTTCA
Found at i:3493209 original size:5 final size:5
Alignment explanation
Indices: 3493190--3493224 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
3493180 TAGCAGTTTG
3493190 TAAAA TAATAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAAA
3493225 TCCGACTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:3498654 original size:14 final size:14
Alignment explanation
Indices: 3498617--3498664 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3498607 TATATTTAAA
3498617 AAAATATAAAAACTT
1 AAAATATAAAAA-TT
* * *
3498632 TATACATAAAAATT
1 AAAATATAAAAATT
*
3498646 AAAATATAAAAACT
1 AAAATATAAAAATT
3498660 AAAAT
1 AAAAT
3498665 TTAATTTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:3499887 original size:295 final size:294
Alignment explanation
Indices: 3499347--3499911 Score: 672
Period size: 298 Copynumber: 1.9 Consensus size: 294
3499337 CATATTATTA
* * * * * * *
3499347 ATATATACAATTTATGGAGATAATAAAGTGTGTATAGTAAAACAAAAATGTACAAAATATATTTA
1 ATATATACAATTGATGGAGATAATAAAGTATATATAGTAAAACAAAAATGTAAAAAAGACATTAA
* * * **
3499412 AATAAAGCTTTGGTTGAATGGTGAATTTAAGGTTTTAGTAATTTAATTGGTGCGATTCAAATCTC
66 AATAAAGCTTTGGTTGAACGATGAATTTAAGGTTTTAGTAATCTAATTAATGCGATTCAAATCTC
* *
3499477 ACCATATATAAGCTTTAATTGATTTTTGTTAAAATGAAAAGACTAAAATGCCTTCGAATAATATA
131 ACCATATATAAGATTTAATTGATTTTTGTTAAAATGAAAAGACTAAAATACCTTCGAATAATATA
* * * * *
3499542 ATTTTTTTAAAATTACGGAAGAATATTTTCGTAATTTCTTGGCCAAGTTGGTGACCAGATTGAGG
196 ATTTTTTT---ATTAAGGAAGAACATTTTCGTAATTTCATGACCAAGTTGGTGACCAGATTAAGG
3499607 GTGACACCAATTAAGTCAAAAGCTTAATAAATAGTAT
258 GTGACACCAATTAAGTCAAAAGCTTAATAAATAGTAT
* * * * *
3499644 ATATATACAATTGATGGAGATAATAAATTATATATATTAAAATAGAATTGTATAAAAAGACATTA
1 ATATATACAATTGATGGAGATAATAAAGTATATATAGTAAAACAAAAATGTA-AAAAAGACATTA
* * * *
3499709 AAATGAAGCTTTGGTTGAACGATGAATTTAATGTTTTAGTAATCTAATTAATGCGGGTTTAAAT-
65 AAATAAAGCTTTGGTTGAACGATGAATTTAAGGTTTTAGTAATCTAATTAATGC-GATTCAAATC
** * * * *
3499773 TC-CGTTATATGCATATTTCAATTGGTTTTTGTTAAAATGAGAAGACTAAAATACTCTT-GAATA
129 TCACCATATAT-AAGATTT-AATTGATTTTTGTTAAAATGAAAAGACTAAAATAC-CTTCGAATA
** *
3499836 ATATTAA-TTTTTT-TTAAGGAAGAACATTTTCGTAATTTCATGATTAAGTTGGTGACCCGATTA
191 ATA-TAATTTTTTTATTAAGGAAGAACATTTTCGTAATTTCATGACCAAGTTGGTGACCAGATTA
*
3499899 AGGGTGATACCAA
255 AGGGTGACACCAA
3499912 CTCAGTCATG
Statistics
Matches: 224, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
295 54 0.24
297 50 0.22
298 61 0.27
299 53 0.24
300 6 0.03
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (294 bp):
ATATATACAATTGATGGAGATAATAAAGTATATATAGTAAAACAAAAATGTAAAAAAGACATTAA
AATAAAGCTTTGGTTGAACGATGAATTTAAGGTTTTAGTAATCTAATTAATGCGATTCAAATCTC
ACCATATATAAGATTTAATTGATTTTTGTTAAAATGAAAAGACTAAAATACCTTCGAATAATATA
ATTTTTTTATTAAGGAAGAACATTTTCGTAATTTCATGACCAAGTTGGTGACCAGATTAAGGGTG
ACACCAATTAAGTCAAAAGCTTAATAAATAGTAT
Found at i:3504982 original size:19 final size:20
Alignment explanation
Indices: 3504958--3505005 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
3504948 TTTTTCATAA
* *
3504958 AATGAAAA-AATAAGAAAAT
1 AATGAAAATAAGAAAAAAAT
3504977 AATGAAAATAAGAAAAAAAT
1 AATGAAAATAAGAAAAAAAT
3504997 -ATGAAAATA
1 AATGAAAATA
3505006 CCTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (20 bp):
AATGAAAATAAGAAAAAAAT
Found at i:3517572 original size:17 final size:17
Alignment explanation
Indices: 3517543--3517576 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3517533 TTTTTTATAT
3517543 ATTTAAAATTATTAAAA
1 ATTTAAAATTATTAAAA
3517560 ATTTATAAA-TATTAAAA
1 ATTTA-AAATTATTAAAA
3517577 TAGAGACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAATTATTAAAA
Found at i:3542628 original size:22 final size:20
Alignment explanation
Indices: 3542602--3542660 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
3542592 AGTTTATACA
*
3542602 TAATTTATATATTACAAATTT
1 TAATTTATATATTA-AAATCT
*
3542623 TCAATTTAAAATATTAAAATCT
1 T-AATTT-ATATATTAAAATCT
3542645 TAATTT-TATAGTTAAA
1 TAATTTATATA-TTAAA
3542661 TTACAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 6 0.19
22 11 0.34
23 7 0.22
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATTTATATATTAAAATCT
Found at i:3544705 original size:32 final size:32
Alignment explanation
Indices: 3544639--3544706 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
3544629 TTTTGGTTAA
* *
3544639 TGTTGGATTCTAAAATTTTAGTTTATTATATT
1 TGTTGGATTCTAAAATTTTAGTCTATGATATT
*
3544671 TGTTGGATTCTGAAATTATTATGTCT-TGAT-TT
1 TGTTGGATTCTAAAATT-TTA-GTCTATGATATT
3544703 TGTT
1 TGTT
3544707 AGATATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 22 0.71
33 6 0.19
34 3 0.10
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.56
Consensus pattern (32 bp):
TGTTGGATTCTAAAATTTTAGTCTATGATATT
Found at i:3544732 original size:27 final size:27
Alignment explanation
Indices: 3544702--3544774 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
3544692 TGTCTTGATT
3544702 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
3544729 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
3544761 TTGTTGGATATTGA
1 TTGTTAGATATTGA
3544775 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:3544754 original size:32 final size:32
Alignment explanation
Indices: 3544715--3544775 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3544705 TTAGATATTG
3544715 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
3544747 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
3544776 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:3545794 original size:22 final size:22
Alignment explanation
Indices: 3545726--3545814 Score: 92
Period size: 22 Copynumber: 4.0 Consensus size: 22
3545716 GATACTTTTA
3545726 ATGTGGTGTAATATTAGTTATGC
1 ATGTGGTGTAATATTAGTTAT-C
** *
3545749 ACT-TGG-ACAATATTGTTGTTATC
1 A-TGTGGTGTAATA-T-TAGTTATC
3545772 ATGTGGTGTAATATTAGTTATC
1 ATGTGGTGTAATATTAGTTATC
*
3545794 ATATGGTGTAATATTAGTTAT
1 ATGTGGTGTAATATTAGTTAT
3545815 GCACTTGGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
22 32 0.59
23 11 0.20
24 11 0.20
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (22 bp):
ATGTGGTGTAATATTAGTTATC
Found at i:3545874 original size:68 final size:68
Alignment explanation
Indices: 3545729--3545877 Score: 210
Period size: 68 Copynumber: 2.2 Consensus size: 68
3545719 ACTTTTAATG
* * *
3545729 TGGTGTAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATATTAGTTATC
1 TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
3545794 ATA
66 ATA
* * *
3545797 TGGTGTAATATTAGTTATGCACTTGGATAATGTTGTTGTTATCATGTGGTGTAATACTAATTATG
1 TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTAT-
* *
3545862 TATT
65 CATA
3545866 TGG-ATAATATTA
1 TGGTATAATATTA
3545878 TTAATTTCTA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 68 0.93
69 5 0.07
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (68 bp):
TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
ATA
Found at i:3546058 original size:18 final size:19
Alignment explanation
Indices: 3546032--3546067 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3546022 TTGAGTATTA
3546032 TTATATATTTA-AAATAAT
1 TTATATATTTATAAATAAT
*
3546050 TTATTTATTTATAAATAA
1 TTATATATTTATAAATAA
3546068 ATCATTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATATTTATAAATAAT
Found at i:3546296 original size:14 final size:14
Alignment explanation
Indices: 3546274--3546340 Score: 75
Period size: 14 Copynumber: 4.7 Consensus size: 14
3546264 CCAGAAAAGT
*
3546274 AAATCATTTTCTAA
1 AAATTATTTTCTAA
3546288 AAATTATTTT-TCAA
1 AAATTATTTTCT-AA
3546302 TAAATTATTTTCTAA
1 -AAATTATTTTCTAA
*
3546317 AAATTATTTTCCGAA
1 AAATTATTTT-CTAA
3546332 AAA-TATTTT
1 AAATTATTTT
3546341 ATCTGTAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.02
14 27 0.57
15 18 0.38
16 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (14 bp):
AAATTATTTTCTAA
Found at i:3546306 original size:15 final size:15
Alignment explanation
Indices: 3546280--3546340 Score: 74
Period size: 15 Copynumber: 4.2 Consensus size: 15
3546270 AAGTAAATCA
3546280 TTTTCTAAAAATTAT
1 TTTTCTAAAAATTAT
3546295 TTTTC-AATAAATTA-
1 TTTTCTAA-AAATTAT
3546309 TTTTCTAAAAATTAT
1 TTTTCTAAAAATTAT
* *
3546324 TTTCCGAAAAA-TAT
1 TTTTCTAAAAATTAT
3546338 TTT
1 TTT
3546341 ATCTGTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 19 0.46
15 22 0.54
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTTCTAAAAATTAT
Found at i:3546335 original size:29 final size:29
Alignment explanation
Indices: 3546273--3546340 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
3546263 ACCAGAAAAG
* *
3546273 TAAATCATTTTCTAAAAATTATTTTTCAA
1 TAAATTATTTTCTAAAAATTATTTTCCAA
3546302 TAAATTATTTTCTAAAAATTATTTTCCGAA
1 TAAATTATTTTCTAAAAATTATTTTCC-AA
3546332 -AAA-TATTTT
1 TAAATTATTTT
3546341 ATCTGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 6 0.17
29 28 0.78
30 2 0.06
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAATTATTTTCTAAAAATTATTTTCCAA
Found at i:3548952 original size:14 final size:14
Alignment explanation
Indices: 3548935--3548963 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3548925 TTTGACTGAC
3548935 TTTTGACTAAAGTT
1 TTTTGACTAAAGTT
3548949 TTTTGACTAAAGTT
1 TTTTGACTAAAGTT
3548963 T
1 T
3548964 AAAGAACTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTTGACTAAAGTT
Found at i:3561908 original size:7 final size:7
Alignment explanation
Indices: 3561896--3561936 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
3561886 CAACAAAACA
3561896 CCCTACT
1 CCCTACT
3561903 CCCTACT
1 CCCTACT
3561910 CCCTACT
1 CCCTACT
3561917 CCCTACT
1 CCCTACT
3561924 CCCTACT
1 CCCTACT
3561931 CCCTAC
1 CCCTAC
3561937 ACTTTTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.15, C:0.59, G:0.00, T:0.27
Consensus pattern (7 bp):
CCCTACT
Found at i:3564607 original size:3 final size:3
Alignment explanation
Indices: 3564599--3564626 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3564589 TTCTTAATTT
3564599 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3564627 GCCATGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3565811 original size:22 final size:22
Alignment explanation
Indices: 3565783--3565826 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3565773 ACAAGGCTGA
3565783 GACACACGCCAGTGTCTCTACC
1 GACACACGCCAGTGTCTCTACC
3565805 GACACACGCCAGTGTCTCTACC
1 GACACACGCCAGTGTCTCTACC
3565827 CTTGTGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.41, G:0.18, T:0.18
Consensus pattern (22 bp):
GACACACGCCAGTGTCTCTACC
Found at i:3566694 original size:18 final size:18
Alignment explanation
Indices: 3566623--3566694 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 18
3566613 TATTATCAAT
3566623 ATTATTCAGTAAC-GATCA
1 ATTATTCAGTAACAG-TCA
* * * *
3566641 ATTGTTTAGTGACAATCA
1 ATTATTCAGTAACAGTCA
* * *
3566659 GTTATTCAATATCAGTCA
1 ATTATTCAGTAACAGTCA
*
3566677 ATTATTCAGTAACTGTCA
1 ATTATTCAGTAACAGTCA
3566695 GTATCATTCA
Statistics
Matches: 38, Mismatches: 15, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
ATTATTCAGTAACAGTCA
Found at i:3566873 original size:18 final size:18
Alignment explanation
Indices: 3566832--3566873 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3566822 GTAACGATAA
*
3566832 CAGTAACAGTAACAGTAG
1 CAGTAGCAGTAACAGTAG
*
3566850 CAGTAGCAGTGACAGTAG
1 CAGTAGCAGTAACAGTAG
*
3566868 CTGTAG
1 CAGTAG
3566874 ACAGAGTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.19
Consensus pattern (18 bp):
CAGTAGCAGTAACAGTAG
Found at i:3568180 original size:17 final size:16
Alignment explanation
Indices: 3568154--3568186 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3568144 TTGTCTTTCT
3568154 TTTATTTATTTAATTA
1 TTTATTTATTTAATTA
3568170 TTTACTTTATTTAATTA
1 TTTA-TTTATTTAATTA
3568187 ATAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTATTTAATTA
Found at i:3574878 original size:16 final size:14
Alignment explanation
Indices: 3574849--3574882 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
3574839 TAAGTCAATA
3574849 ATAATATTAAATTT
1 ATAATATTAAATTT
3574863 ATAATATATAACATTT
1 ATAATAT-TAA-ATTT
3574879 ATAA
1 ATAA
3574883 GTAAGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 3 0.17
16 8 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATATTAAATTT
Found at i:3580338 original size:23 final size:22
Alignment explanation
Indices: 3580302--3580356 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
3580292 GTTTTTATAT
3580302 ATATTATAAATAAATATAATAA-A
1 ATATTATAAATAAA-A-AATAACA
* *
3580325 ATATTATTACTAAAAAATAACA
1 ATATTATAAATAAAAAATAACA
3580347 ATAATTATAA
1 AT-ATTATAA
3580357 TTGTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 18 0.67
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATTATAAATAAAAAATAACA
Found at i:3580349 original size:27 final size:27
Alignment explanation
Indices: 3580298--3580350 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3580288 TCGTGTTTTT
*
3580298 ATATATATTATAAATAAATATAATAAA
1 ATATATATTATAAATAAATACAATAAA
3580325 ATAT-TATTACTAAA-AAATAACAATAA
1 ATATATATTA-TAAATAAAT-ACAATAA
3580351 TTATAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATATATTATAAATAAATACAATAAA
Found at i:3583572 original size:117 final size:117
Alignment explanation
Indices: 3583366--3583598 Score: 439
Period size: 117 Copynumber: 2.0 Consensus size: 117
3583356 TAACATCGAG
3583366 GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGCTTACCTTGAGGTTTGCTTATGAAAGATG
1 GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGCTTACCTTGAGGTTTGCTTATGAAAGATG
*
3583431 AAGTGCAAAGGTAGTCGTGGGAGCTGGAAATAGGTGTGGAGACTTTGTGGTT
66 AAGTGCAAAGATAGTCGTGGGAGCTGGAAATAGGTGTGGAGACTTTGTGGTT
*
3583483 GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGTTTACCTTGAGGTTTGCTTATGAAAGATG
1 GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGCTTACCTTGAGGTTTGCTTATGAAAGATG
*
3583548 AAGTGCAAAGATAGTCGTGGGAGCTGGAAATGGGTGTGGAGACTTTGTGGT
66 AAGTGCAAAGATAGTCGTGGGAGCTGGAAATAGGTGTGGAGACTTTGTGGT
3583599 CCTCAACGAA
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 113 1.00
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.29
Consensus pattern (117 bp):
GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGCTTACCTTGAGGTTTGCTTATGAAAGATG
AAGTGCAAAGATAGTCGTGGGAGCTGGAAATAGGTGTGGAGACTTTGTGGTT
Found at i:3586846 original size:40 final size:40
Alignment explanation
Indices: 3586800--3586876 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
3586790 TTAGGCATAA
*
3586800 ATAGAAGATTGAGTAGTTAATCTCTTTAATTGTACTAGTC
1 ATAGAAGATTGAGTAGTCAATCTCTTTAATTGTACTAGTC
3586840 ATAGAAGATTGAGTAGTCAATCTCTTTAATTGTACTA
1 ATAGAAGATTGAGTAGTCAATCTCTTTAATTGTACTA
3586877 TTTAGTGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (40 bp):
ATAGAAGATTGAGTAGTCAATCTCTTTAATTGTACTAGTC
Found at i:3588621 original size:5 final size:5
Alignment explanation
Indices: 3588607--3588636 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3588597 TCTAGAACAT
*
3588607 TAAAA TAAAA GAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
3588637 AAGGGAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:3595588 original size:16 final size:13
Alignment explanation
Indices: 3595556--3595581 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3595546 AATTGTAATA
3595556 AATATTAATTATT
1 AATATTAATTATT
3595569 AATATTAATTATT
1 AATATTAATTATT
3595582 TTTAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTAATTATT
Found at i:3595689 original size:16 final size:16
Alignment explanation
Indices: 3595670--3595700 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3595660 AATTTATTAA
3595670 AATAATATATTATATT
1 AATAATATATTATATT
*
3595686 AATAATTTATTATAT
1 AATAATATATTATAT
3595701 GACTAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATAATATATTATATT
Found at i:3597377 original size:37 final size:37
Alignment explanation
Indices: 3597327--3597402 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
3597317 TAACACAGGC
3597327 CAAATATATGATTTATGTTTGGTTAGGCGAGTCCTTA
1 CAAATATATGATTTATGTTTGGTTAGGCGAGTCCTTA
*
3597364 CAAATATATGATTTATGTTTGGTTGGGCGAGTCCTTA
1 CAAATATATGATTTATGTTTGGTTAGGCGAGTCCTTA
3597401 CA
1 CA
3597403 GATAGTGTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.39
Consensus pattern (37 bp):
CAAATATATGATTTATGTTTGGTTAGGCGAGTCCTTA
Found at i:3601063 original size:18 final size:18
Alignment explanation
Indices: 3601040--3601079 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
3601030 GCTAGTAATG
3601040 AAAGCAAAATATTTTCCA
1 AAAGCAAAATATTTTCCA
3601058 AAAGCAAAATATTTTCCA
1 AAAGCAAAATATTTTCCA
3601076 AAAG
1 AAAG
3601080 GGGATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (18 bp):
AAAGCAAAATATTTTCCA
Found at i:3603114 original size:14 final size:15
Alignment explanation
Indices: 3603097--3603127 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3603087 TATAGTGTAG
3603097 TAAATAT-TAAAAAA
1 TAAATATATAAAAAA
3603111 TAAATATATAAAAAA
1 TAAATATATAAAAAA
3603126 TA
1 TA
3603128 GGACATGTGA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATATATAAAAAA
Found at i:3607474 original size:3 final size:3
Alignment explanation
Indices: 3607436--3607463 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3607426 TCAGACTACT
3607436 ACC ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC A
3607464 TTTGACCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:3613246 original size:17 final size:19
Alignment explanation
Indices: 3613213--3613252 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
3613203 CGTGTGGACT
3613213 ACCCGTGTGGACCCACAC-
1 ACCCGTGTGGACCCACACG
3613231 ACCCGTGTGG-CCCACACG
1 ACCCGTGTGGACCCACACG
3613249 ACCC
1 ACCC
3613253 AAATCAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.20, C:0.47, G:0.23, T:0.10
Consensus pattern (19 bp):
ACCCGTGTGGACCCACACG
Found at i:3631770 original size:4 final size:4
Alignment explanation
Indices: 3631759--3631788 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3631749 AAAAAAAAGT
3631759 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
3631789 CATTGTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:3644620 original size:26 final size:24
Alignment explanation
Indices: 3644583--3644633 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
3644573 TATTAAAAAT
*
3644583 TAAAAAGGTAATTTAGA-TATTTTAA
1 TAAAAAGATAA-TTA-ATTATTTTAA
3644608 TAAAAATGATAATTAATTATTTTAA
1 TAAAAA-GATAATTAATTATTTTAA
3644633 T
1 T
3644634 TATTTATGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 1 0.04
25 18 0.78
26 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (24 bp):
TAAAAAGATAATTAATTATTTTAA
Found at i:3653528 original size:78 final size:78
Alignment explanation
Indices: 3653431--3653669 Score: 433
Period size: 78 Copynumber: 3.1 Consensus size: 78
3653421 GTAGATCAGT
* *
3653431 TGATGGCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGATACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
3653496 CCAAATCCAAGGA
66 CCAAATCCAAGGA
*
3653509 TGATGTCGCTTCAAGAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
3653574 CCAAATCCAAGGA
66 CCAAATCCAAGGA
* *
3653587 GGATGTCACTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
3653652 CCAAATCCAAGGA
66 CCAAATCCAAGGA
3653665 TGATG
1 TGATG
3653670 ACAATGTTAC
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 154 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (78 bp):
TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
CCAAATCCAAGGA
Found at i:3653580 original size:42 final size:42
Alignment explanation
Indices: 3653455--3653661 Score: 123
Period size: 42 Copynumber: 5.2 Consensus size: 42
3653445 AAGTAGGCAA
*
3653455 CAAATCCAAAAATGAGGACACTGGTGATACACCCAAGTCTAC
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
** * * * **** * *
3653497 CAAATCCAAGGATGATGTCGCT--T--CA-AGAGTAGGC-AA
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
3653533 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
** * * * **** * *
3653575 CAAATCCAAGGAGGATGTCACT--T--CA-AAAGTAGGC-AA
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
3653611 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
3653653 CAAATCCAA
1 CAAATCCAA
3653662 GGATGATGAC
Statistics
Matches: 108, Mismatches: 45, Indels: 24
0.61 0.25 0.14
Matches are distributed among these distances:
36 36 0.33
37 8 0.07
38 5 0.05
40 6 0.06
41 8 0.07
42 45 0.42
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (42 bp):
CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
Found at i:3658471 original size:17 final size:17
Alignment explanation
Indices: 3658451--3658484 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3658441 GGTCAAGTTG
3658451 ATAAAAAAATTTAATAA
1 ATAAAAAAATTTAATAA
* *
3658468 ATAAATAAATTTGATAA
1 ATAAAAAAATTTAATAA
3658485 TTTTTTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATAAAAAAATTTAATAA
Found at i:3660596 original size:18 final size:18
Alignment explanation
Indices: 3660573--3660607 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3660563 GAAAATATTT
3660573 TAAATT-TTATTTCAAAAA
1 TAAATTATTATTT-AAAAA
3660591 TAAATTATTATTTAAAA
1 TAAATTATTATTTAAAA
3660608 CCATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATTATTATTTAAAAA
Found at i:3660977 original size:17 final size:17
Alignment explanation
Indices: 3660936--3660980 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3660926 AATTTTTCAG
3660936 TATTTCTTTTTCAACGCT
1 TATTT-TTTTTCAACGCT
* **
3660954 TAATTTTTTTCAACTTT
1 TATTTTTTTTCAACGCT
3660971 TATTTTTTTT
1 TATTTTTTTT
3660981 TCAATTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTTTTTTCAACGCT
Found at i:3660988 original size:16 final size:17
Alignment explanation
Indices: 3660957--3660989 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3660947 CAACGCTTAA
3660957 TTTTTTTCAACTTTTATT
1 TTTTTTTCAAC-TTTATT
3660975 TTTTTTTCAA-TTTAT
1 TTTTTTTCAACTTTAT
3660990 AAACTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTCAACTTTATT
Found at i:3674701 original size:2 final size:2
Alignment explanation
Indices: 3674694--3674718 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3674684 GCAACACGCA
3674694 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 T
3674719 TCCTCCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3690617 original size:16 final size:16
Alignment explanation
Indices: 3690578--3690610 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3690568 TAGCTGCTAC
3690578 TCAAAGCCCAAGCGAT
1 TCAAAGCCCAAGCGAT
3690594 TCAAAGCCCAAGCGAT
1 TCAAAGCCCAAGCGAT
3690610 T
1 T
3690611 ATGAGCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.15
Consensus pattern (16 bp):
TCAAAGCCCAAGCGAT
Found at i:3690685 original size:105 final size:105
Alignment explanation
Indices: 3690503--3690697 Score: 390
Period size: 105 Copynumber: 1.9 Consensus size: 105
3690493 AACTATGAAA
3690503 ATTATGAGCCTCAAAATTAAAGACAAGTAGAAATAAGTGAACATGAATGCACATGTATGTCTGTA
1 ATTATGAGCCTCAAAATTAAAGACAAGTAGAAATAAGTGAACATGAATGCACATGTATGTCTGTA
3690568 TAGCTGCTACTCAAAGCCCAAGCGATTCAAAGCCCAAGCG
66 TAGCTGCTACTCAAAGCCCAAGCGATTCAAAGCCCAAGCG
3690608 ATTATGAGCCTCAAAATTAAAGACAAGTAGAAATAAGTGAACATGAATGCACATGTATGTCTGTA
1 ATTATGAGCCTCAAAATTAAAGACAAGTAGAAATAAGTGAACATGAATGCACATGTATGTCTGTA
3690673 TAGCTGCTACTCAAAGCCCAAGCGA
66 TAGCTGCTACTCAAAGCCCAAGCGA
3690698 GTGTTGGATA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 90 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (105 bp):
ATTATGAGCCTCAAAATTAAAGACAAGTAGAAATAAGTGAACATGAATGCACATGTATGTCTGTA
TAGCTGCTACTCAAAGCCCAAGCGATTCAAAGCCCAAGCG
Found at i:3694356 original size:23 final size:26
Alignment explanation
Indices: 3694324--3694381 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
3694314 AAGGAGCTTA
*
3694324 AAAATAAAT-A-ATATAAAA-ATTTT
1 AAAATAAATAACATATAAAACAGTTT
*
3694347 AAAATGAATAACATATAAAACAGTTT
1 AAAATAAATAACATATAAAACAGTTT
*
3694373 AAATTAAAT
1 AAAATAAAT
3694382 GTCATATACG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.29
24 1 0.04
25 8 0.29
26 11 0.39
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAATAAATAACATATAAAACAGTTT
Found at i:3694583 original size:28 final size:27
Alignment explanation
Indices: 3694541--3694629 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 27
3694531 ACTAAAAAAC
*
3694541 ATATAAAAGATTTTAAAATAGATAATAT
1 ATATAAAATA-TTTAAAATAGATAATAT
*
3694569 ATATAAAATAGTTTAAAAT-GAAAGATAT
1 ATATAAAATA-TTTAAAATAGATA-ATAT
* ** *
3694597 ATATGAAATA-TCGAAATAAATAATAT
1 ATATAAAATATTTAAAATAGATAATAT
3694623 ATATAAA
1 ATATAAA
3694630 GTCTAAAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
26 15 0.30
27 5 0.10
28 30 0.60
ACGTcount: A:0.58, C:0.01, G:0.08, T:0.33
Consensus pattern (27 bp):
ATATAAAATATTTAAAATAGATAATAT
Found at i:3695311 original size:127 final size:127
Alignment explanation
Indices: 3695130--3695451 Score: 396
Period size: 132 Copynumber: 2.5 Consensus size: 127
3695120 AACGAAAAAC
* * * * **
3695130 CGAAACCCAGTACGGTAGGGCACGATTCCTCGAACTTCCAAACATTGAACATTGCCTTGTTTTAG
1 CGAAACCCAGCAC-GTAGGGCATGATTCCCCGAATTTCCAAACATCAAACATTGCCTTGTTTTAG
* * * *
3695195 AATTT-AAAGAATACGAATGAAATTCTAAAGGAATATTTGATTATTTTGAATAAACGAGG-AAT
65 AATTTAAAAAAACACGAATGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACG-GGAAAT
* *
3695257 CGAAACCCAGCACGATAGGGCATGGTTCCCCGAATTTCCAAGCATCAAACATTGCCCTTGTTTTA
1 CGAAACCCAGCACG-TAGGGCATGATTCCCCGAATTTCCAAACATCAAACATTG-CCTTGTTTTA
** *
3695322 GAATTTAGAAAAAAAACACGTGTGAAATTCTAAAGGAATGTTCGATTATTTTGAACAAACGGGAA
64 GAATTT---AAAAAAACACGAATGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAA
3695387 AT
126 AT
* *
3695389 CGAAACCCAGCACCGTAGGGCATGATTTCCCGAATTTTCAAACATCAAACATTGCCTTCGTTT
1 CGAAACCCAGCA-CGTAGGGCATGATTCCCCGAATTTCCAAACATCAAACATTGCCTT-GTTT
3695452 GAAGGAATTT
Statistics
Matches: 167, Mismatches: 19, Indels: 13
0.84 0.10 0.07
Matches are distributed among these distances:
126 1 0.01
127 44 0.26
128 16 0.10
131 6 0.04
132 98 0.59
133 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (127 bp):
CGAAACCCAGCACGTAGGGCATGATTCCCCGAATTTCCAAACATCAAACATTGCCTTGTTTTAGA
ATTTAAAAAAACACGAATGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAAT
Found at i:3696459 original size:32 final size:30
Alignment explanation
Indices: 3696418--3696485 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
3696408 ACTTTAAAAG
* *
3696418 AAAT-TACATATGCAAAATAAAATGAGATTAA
1 AAATATACATA-G-AAAATAAAAGGAGAGTAA
* *
3696449 TAATATACATAGAATATAAAAGGAGAGTAA
1 AAATATACATAGAAAATAAAAGGAGAGTAA
3696479 AAATATA
1 AAATATA
3696486 TAATAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 21 0.68
31 4 0.13
32 6 0.19
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (30 bp):
AAATATACATAGAAAATAAAAGGAGAGTAA
Found at i:3696574 original size:31 final size:31
Alignment explanation
Indices: 3696513--3696575 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
3696503 AGGAAATACT
* * * *
3696513 TATACGTATAATAGATTTAAAAACATATATA
1 TATACATATAATAAATTTAAAAAAAAATATA
3696544 TATACATA-AATAAATTTAGAAAAAAAATATA
1 TATACATATAATAAATTTA-AAAAAAAATATA
3696575 T
1 T
3696576 GCAAGAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (31 bp):
TATACATATAATAAATTTAAAAAAAAATATA
Found at i:3701722 original size:120 final size:120
Alignment explanation
Indices: 3701525--3701787 Score: 517
Period size: 120 Copynumber: 2.2 Consensus size: 120
3701515 TTTTCAAGTT
3701525 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
3701590 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
3701645 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
3701710 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
3701765 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
3701788 TAAATATGAT
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 142 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
Found at i:3701764 original size:18 final size:17
Alignment explanation
Indices: 3701736--3701770 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3701726 ATTATTAAGA
*
3701736 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3701753 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3701771 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3702000 original size:44 final size:45
Alignment explanation
Indices: 3701935--3702020 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
3701925 ACCTCTATTC
* *
3701935 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTA
***
3701979 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCA
3702021 ATATACCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 19 0.53
45 17 0.47
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.28
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTA
Found at i:3702030 original size:16 final size:16
Alignment explanation
Indices: 3702006--3702057 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
3701996 GATTAGCTAT
3702006 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
3702022 TATACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
3702038 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
3702054 TACA
1 TACA
3702058 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.35, G:0.02, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3704916 original size:13 final size:13
Alignment explanation
Indices: 3704898--3704922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3704888 TGTTGAATAA
3704898 ATTAATTATTTTT
1 ATTAATTATTTTT
3704911 ATTAATTATTTT
1 ATTAATTATTTT
3704923 GAATTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTAATTATTTTT
Found at i:3705651 original size:7 final size:7
Alignment explanation
Indices: 3705641--3705672 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3705631 AAAAAATCTA
*
3705641 AAAATAG
1 AAAATAT
3705648 AAAATAT
1 AAAATAT
3705655 AAAATAT
1 AAAATAT
3705662 AAAATAT
1 AAAATAT
3705669 AAAA
1 AAAA
3705673 AAAAAAAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (7 bp):
AAAATAT
Found at i:3705657 original size:15 final size:15
Alignment explanation
Indices: 3705633--3705673 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
3705623 AAAATTTTAA
*
3705633 AAAATCTAAAAATAG
1 AAAATATAAAAATAG
*
3705648 AAAATAT-AAAATAT
1 AAAATATAAAAATAG
3705662 AAAATATAAAAA
1 AAAATATAAAAA
3705674 AAAAAAGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATATAAAAATAG
Found at i:3705679 original size:14 final size:14
Alignment explanation
Indices: 3705631--3705679 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3705621 ATAAAATTTT
*
3705631 AAAAAATCTAAAAA
1 AAAAAATATAAAAA
* *
3705645 TAGAAAATATAAAAT
1 -AAAAAATATAAAAA
*
3705660 ATAAAATATAAAAA
1 AAAAAATATAAAAA
3705674 AAAAAA
1 AAAAAA
3705680 GCTTCAGGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (14 bp):
AAAAAATATAAAAA
Found at i:3709381 original size:12 final size:10
Alignment explanation
Indices: 3709355--3709382 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3709345 GTAGTTTTAA
3709355 TTATATAAAC
1 TTATATAAAC
3709365 TTATATAAAC
1 TTATATAAAC
3709375 TTATATAA
1 TTATATAA
3709383 TATCTGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TTATATAAAC
Found at i:3709843 original size:8 final size:7
Alignment explanation
Indices: 3709822--3709846 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3709812 TAAATTAATA
3709822 TAATTTT
1 TAATTTT
3709829 TAATTTT
1 TAATTTT
3709836 TAATTTT
1 TAATTTT
3709843 TAAT
1 TAAT
3709847 GATAAATTTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TAATTTT
Found at i:3714761 original size:45 final size:44
Alignment explanation
Indices: 3714702--3714792 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
3714692 TTTGGTTCGC
* * *
3714702 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
3714747 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
3714791 TG
1 TG
3714793 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:3714984 original size:18 final size:17
Alignment explanation
Indices: 3714957--3714991 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3714947 TTATTTTTAA
*
3714957 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3714975 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3714992 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3715057 original size:157 final size:157
Alignment explanation
Indices: 3714844--3715160 Score: 553
Period size: 157 Copynumber: 2.0 Consensus size: 157
3714834 TAGAATACCC
* *
3714844 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAATTTATTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
* * *
3714909 TTATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTTTTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
3714974 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
3715001 TTAGCAAAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAATTTATTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
* *
3715066 ATATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
3715131 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
3715158 TTA
1 TTA
3715161 ATATTCTTAT
Statistics
Matches: 151, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 151 1.00
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (157 bp):
TTAGCAAAAATTTATTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:3715131 original size:16 final size:16
Alignment explanation
Indices: 3715094--3715135 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3715084 TTAATCATAT
*
3715094 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
3715110 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3715125 TTAAAATATAT
1 TTAAAATATAT
3715136 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3715142 original size:14 final size:15
Alignment explanation
Indices: 3715103--3715144 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3715093 TTTAAACATA
*
3715103 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3715118 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3715132 A-TATAATTTAATA
1 ATTATAATTAAATA
3715145 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3718163 original size:11 final size:11
Alignment explanation
Indices: 3718147--3718172 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3718137 TCGGGAGGCA
3718147 AAGGTAGAACG
1 AAGGTAGAACG
3718158 AAGGTAGAACG
1 AAGGTAGAACG
3718169 AAGG
1 AAGG
3718173 AAGAGGCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.38, T:0.08
Consensus pattern (11 bp):
AAGGTAGAACG
Found at i:3720271 original size:12 final size:12
Alignment explanation
Indices: 3720254--3720292 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3720244 TTATATTTAT
3720254 TATTTTTAAAAA
1 TATTTTTAAAAA
3720266 TATTTTTAAGAAA
1 TATTTTTAA-AAA
* *
3720279 AATTTTAAAAAA
1 TATTTTTAAAAA
3720291 TA
1 TA
3720293 AAAATGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
TATTTTTAAAAA
Found at i:3720978 original size:15 final size:17
Alignment explanation
Indices: 3720958--3720989 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3720948 TACTAAATTG
3720958 TGCATAT-TA-AAAAAA
1 TGCATATATATAAAAAA
3720973 TGCATATATATAAAAAA
1 TGCATATATATAAAAAA
3720990 ATCAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (17 bp):
TGCATATATATAAAAAA
Found at i:3721489 original size:170 final size:170
Alignment explanation
Indices: 3721207--3721548 Score: 684
Period size: 170 Copynumber: 2.0 Consensus size: 170
3721197 CAATAAGCTA
3721207 AACTCATACTTCAAGTTGTTTCACGCCTTAAATAAAAACACTCAATAAATCCGTTGGACAAGTGG
1 AACTCATACTTCAAGTTGTTTCACGCCTTAAATAAAAACACTCAATAAATCCGTTGGACAAGTGG
3721272 ATTCACATCTCTTACAACCAGCACAATCTTCTGTTCTTGGAGTGGAAGCAATTTGCTTAGCTTTA
66 ATTCACATCTCTTACAACCAGCACAATCTTCTGTTCTTGGAGTGGAAGCAATTTGCTTAGCTTTA
3721337 CATCCATCCCAATGTATCATTTCTAACACATTGGAGGTGC
131 CATCCATCCCAATGTATCATTTCTAACACATTGGAGGTGC
3721377 AACTCATACTTCAAGTTGTTTCACGCCTTAAATAAAAACACTCAATAAATCCGTTGGACAAGTGG
1 AACTCATACTTCAAGTTGTTTCACGCCTTAAATAAAAACACTCAATAAATCCGTTGGACAAGTGG
3721442 ATTCACATCTCTTACAACCAGCACAATCTTCTGTTCTTGGAGTGGAAGCAATTTGCTTAGCTTTA
66 ATTCACATCTCTTACAACCAGCACAATCTTCTGTTCTTGGAGTGGAAGCAATTTGCTTAGCTTTA
3721507 CATCCATCCCAATGTATCATTTCTAACACATTGGAGGTGC
131 CATCCATCCCAATGTATCATTTCTAACACATTGGAGGTGC
3721547 AA
1 AA
3721549 GCTCGGACAA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 172 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (170 bp):
AACTCATACTTCAAGTTGTTTCACGCCTTAAATAAAAACACTCAATAAATCCGTTGGACAAGTGG
ATTCACATCTCTTACAACCAGCACAATCTTCTGTTCTTGGAGTGGAAGCAATTTGCTTAGCTTTA
CATCCATCCCAATGTATCATTTCTAACACATTGGAGGTGC
Found at i:3724259 original size:30 final size:30
Alignment explanation
Indices: 3724224--3724297 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
3724214 TGGCAAAAAA
3724224 CTCTCAAATTTCTCCATAAATTTCTCAAAG
1 CTCTCAAATTTCTCCATAAATTTCTCAAAG
*
3724254 CTCTCAAATTTCTCCTTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCATAAATTTCTCAAAG
3724284 CTCTCAAATTTCTC
1 CTCTCAAATTTCTC
3724298 AAAGATCGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.39
Consensus pattern (30 bp):
CTCTCAAATTTCTCCATAAATTTCTCAAAG
Found at i:3724264 original size:18 final size:18
Alignment explanation
Indices: 3724241--3724301 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
3724231 ATTTCTCCAT
3724241 AAATTTCTCAAAGCTCTC
1 AAATTTCTCAAAGCTCTC
3724259 AAATTTCTC----CT-T-
1 AAATTTCTCAAAGCTCTC
3724271 AAATTTCTCAAAGCTCTC
1 AAATTTCTCAAAGCTCTC
3724289 AAATTTCTCAAAG
1 AAATTTCTCAAAG
3724302 ATCGCTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
12 9 0.24
13 1 0.03
14 2 0.05
16 2 0.05
17 1 0.03
18 22 0.59
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (18 bp):
AAATTTCTCAAAGCTCTC
Found at i:3724267 original size:9 final size:9
Alignment explanation
Indices: 3724225--3724300 Score: 62
Period size: 9 Copynumber: 7.8 Consensus size: 9
3724215 GGCAAAAAAC
3724225 TCTCAAATT
1 TCTCAAATT
3724234 TCTCCATAAATT
1 TCT-C--AAATT
**
3724246 TCTCAAAGC
1 TCTCAAATT
3724255 TCTCAAATT
1 TCTCAAATT
3724264 TCTCCTTAAATT
1 TCT-C--AAATT
**
3724276 TCTCAAAGC
1 TCTCAAATT
3724285 TCTCAAATT
1 TCTCAAATT
3724294 TCTCAAA
1 TCTCAAA
3724301 GATCGCTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 33 0.62
10 2 0.04
11 2 0.04
12 16 0.30
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (9 bp):
TCTCAAATT
Found at i:3724530 original size:25 final size:24
Alignment explanation
Indices: 3724479--3724529 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
3724469 TTGAATATTA
*
3724479 TTTAATATTTTTTATTTGTATAAT
1 TTTAATAATTTTTATTTGTATAAT
3724503 TTTAATTAATTTTTATTT-TATAAT
1 TTTAA-TAATTTTTATTTGTATAAT
3724527 TTT
1 TTT
3724530 TTATAACAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTAATAATTTTTATTTGTATAAT
Found at i:3726074 original size:18 final size:18
Alignment explanation
Indices: 3726051--3726093 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3726041 TGCCAGGTGC
*
3726051 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
*
3726069 GTATCCTAATCCTTATAT
1 GTATCCTAACCCTTATAT
*
3726087 GTTTCCT
1 GTATCCT
3726094 GTTGAAACCA
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:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:3727158 original size:28 final size:27
Alignment explanation
Indices: 3727103--3727175 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
3727093 ATCTAACATG
* *
3727103 AATAAAATGTAAAAC-AATTTGAAATAA
1 AATAATATGTAAAACAAATTTCAAAT-A
*
3727130 AATAATATATAAAACAAATTTCAAATA
1 AATAATATGTAAAACAAATTTCAAATA
* *
3727157 AACAATATGTTAAACAAAT
1 AATAATATGTAAAACAAAT
3727176 CAAGATGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 30 0.77
28 9 0.23
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (27 bp):
AATAATATGTAAAACAAATTTCAAATA
Found at i:3727288 original size:27 final size:27
Alignment explanation
Indices: 3727232--3727306 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 27
3727222 ATAAAAGAGC
3727232 TTAAAATAAATAATATGTAAAAGAGAAA
1 TTAAAATAAAT-ATATGTAAAAGAGAAA
*
3727260 TTTAAAATAAATAT-TGTACAAGA-ATAA
1 -TTAAAATAAATATATGTAAAAGAGA-AA
*
3727287 TTAAAA-AAATATATATAAAA
1 TTAAAATAAATATATGTAAAA
3727307 ATCCAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 6 0.15
26 12 0.29
27 10 0.24
28 2 0.05
29 11 0.27
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (27 bp):
TTAAAATAAATATATGTAAAAGAGAAA
Found at i:3727336 original size:22 final size:22
Alignment explanation
Indices: 3727287--3727338 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3727277 ACAAGAATAA
*
3727287 TTAAAAAAATATATATAAAAAT
1 TTAAAATAATATATATAAAAAT
** *
3727309 CCAAAATAATATATATAAAAGT
1 TTAAAATAATATATATAAAAAT
3727331 TTAAAATA
1 TTAAAATA
3727339 GGTAACATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAAATAATATATATAAAAAT
Found at i:3732729 original size:127 final size:126
Alignment explanation
Indices: 3732444--3732808 Score: 529
Period size: 127 Copynumber: 2.9 Consensus size: 126
3732434 ATTGATGTGT
* *
3732444 GAGCTTTTTTCA-TCAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTGACAATATTTGTT
1 GAGCTTTTTTCAGT-AATTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTT
* *
3732508 CAGAACCGTCTTCTTAATATTATTTTTTCAGGAACTACTAG-AGAAAAAGAGCGTCCACGTAG
65 CAGAACCGTCTTCTTAAAATTATTTTTTCAGGAATTACT-GTAGAAAAAGAGCGTCCACGTAG
* * * * *
3732570 GAGATTTTTTCAGTAATTTTGCTGATAGTGCATTCTGCTTAAAGCGCTTTCGACACTATTTGTTC
1 GAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTC
* * * *
3732635 AGAAACGTCTTCTCAAAATTATTTTTTTCAGGAATTACTGTAGAAAAATAGCGTCCACGTGG
66 AGAACCGTCTTCTTAAAATTA-TTTTTTCAGGAATTACTGTAGAAAAAGAGCGTCCACGTAG
*
3732697 GAGCTTTTTTCAGTAATTTTGCTGACAATGCATCCTGCTTGAAGCGTTTTTC-ACACTATTTGTT
1 GAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCG-TTTTCGACACTATTTGTT
* *
3732761 CAGAACCGTATTCTTAAAATTATTTTTTCAAGAATTACTGTAGAAAAA
65 CAGAACCGTCTTCTTAAAATTATTTTTTCAGGAATTACTGTAGAAAAA
3732809 ATAAAATCCT
Statistics
Matches: 212, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
126 100 0.47
127 108 0.51
128 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (126 bp):
GAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTC
AGAACCGTCTTCTTAAAATTATTTTTTCAGGAATTACTGTAGAAAAAGAGCGTCCACGTAG
Found at i:3732906 original size:35 final size:35
Alignment explanation
Indices: 3732865--3732989 Score: 116
Period size: 34 Copynumber: 3.6 Consensus size: 35
3732855 AACACAATAT
**
3732865 TATTTTTTTTAAAA-ACTAAAACCTAATTTAATTA
1 TATTTTTTAAAAAACACTAAAACCTAATTTAATTA
* **
3732899 TTTTTTTTAAAAAACACTAAGCCCTAATTTAATTA
1 TATTTTTTAAAAAACACTAAAACCTAATTTAATTA
* *
3732934 -ATTTATTT--AAAACCCTTAAACCCTAATTTAATTA
1 TATTT-TTTAAAAAACAC-TAAAACCTAATTTAATTA
3732968 -ATTTTTTAAAAAGAACACTAAA
1 TATTTTTT-AAAA-AACACTAAA
3732990 TACTTATTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
33 9 0.12
34 35 0.47
35 21 0.28
36 6 0.08
37 4 0.05
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.42
Consensus pattern (35 bp):
TATTTTTTAAAAAACACTAAAACCTAATTTAATTA
Found at i:3733109 original size:15 final size:15
Alignment explanation
Indices: 3733085--3733123 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3733075 TTATTTTAAC
* * *
3733085 AAAACACTAACCCTA
1 AAAACCCTAAACCAA
3733100 AAAACCCTAAACCAA
1 AAAACCCTAAACCAA
3733115 AAAACCCTA
1 AAAACCCTA
3733124 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAACCCTAAACCAA
Found at i:3733109 original size:42 final size:42
Alignment explanation
Indices: 3733027--3733105 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
3733017 AATCCAGAAC
*
3733027 CCTAAATTATTTTAACAAAACACTAAAACCTACAAACCTAAG
1 CCTAAATTATTTTAACAAAACACTAAAACCTAAAAACCTAAG
*
3733069 CCTAAATTATTTTAACAAAACACT-AACCCTAAAAACC
1 CCTAAATTATTTTAACAAAACACTAAAACCTAAAAACC
3733106 CTAAACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 11 0.31
42 24 0.69
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.24
Consensus pattern (42 bp):
CCTAAATTATTTTAACAAAACACTAAAACCTAAAAACCTAAG
Found at i:3735813 original size:17 final size:17
Alignment explanation
Indices: 3735791--3735828 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3735781 GAATGAAAAA
3735791 AAAAGAAAATAAAAGTT
1 AAAAGAAAATAAAAGTT
3735808 AAAAGAAAATAAAAGTT
1 AAAAGAAAATAAAAGTT
3735825 AAAA
1 AAAA
3735829 ATTAAATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (17 bp):
AAAAGAAAATAAAAGTT
Found at i:3736061 original size:2 final size:2
Alignment explanation
Indices: 3736054--3736087 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3736044 TAAAAATGAC
3736054 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
3736088 GCAACTTTCA
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:3742496 original size:13 final size:12
Alignment explanation
Indices: 3742473--3742519 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
3742463 TCACGTTTTC
3742473 TTTTTTG-TTAT
1 TTTTTTGTTTAT
3742484 TTTTTTGTCTTAT
1 TTTTTTGT-TTAT
*
3742497 TTGTTTTATTTAT
1 TT-TTTTGTTTAT
*
3742510 TTTATTGTTT
1 TTTTTTGTTT
3742520 CTAATTTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 7 0.23
12 6 0.20
13 12 0.40
14 5 0.17
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTGTTTAT
Found at i:3750503 original size:17 final size:17
Alignment explanation
Indices: 3750472--3750531 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
3750462 TTAAAAAATA
3750472 TTAAAAGAT-TATATATT
1 TTAAAA-ATATATATATT
**
3750489 TTAAAAATATATATAAA
1 TTAAAAATATATATATT
*
3750506 TTATAAATATATA-ATT
1 TTAAAAATATATATATT
3750522 GTCTAAAAAT
1 -T-TAAAAAT
3750532 TAAAAATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
16 3 0.09
17 25 0.74
18 6 0.18
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAAAATATATATATT
Found at i:3751279 original size:22 final size:21
Alignment explanation
Indices: 3751244--3751289 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
3751234 TTCTAATAAA
3751244 TTTTAGTAATTTTTATATTGTTT
1 TTTTAGTAATTTTTATA--GTTT
*
3751267 TTTTTGTAA-TTTTATAGTTT
1 TTTTAGTAATTTTTATAGTTT
3751287 TTT
1 TTT
3751290 AATTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
22 7 0.32
23 8 0.36
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTTAGTAATTTTTATAGTTT
Found at i:3751304 original size:16 final size:16
Alignment explanation
Indices: 3751285--3751341 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
3751275 ATTTTATAGT
3751285 TTTTTAATTTTTTTTA
1 TTTTTAATTTTTTTTA
* * *
3751301 TTTTTAATAAATTTGTCA
1 TTTTTAAT--TTTTTTTA
3751319 TTTTATAA-TTTTTTTA
1 TTTT-TAATTTTTTTTA
3751335 TTTTTAA
1 TTTTTAA
3751342 AAATTCTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
15 3 0.09
16 17 0.53
18 9 0.28
19 3 0.09
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTTTAATTTTTTTTA
Found at i:3751357 original size:35 final size:35
Alignment explanation
Indices: 3751237--3751357 Score: 94
Period size: 34 Copynumber: 3.5 Consensus size: 35
3751227 TTTAAACTTC
* *
3751237 TAATAAATTTTAGTAATTTT-TATATTGTTTTT-TTTG
1 TAATAAA-TTTA-TAATTTTATA-ATTTTTTTTATTTT
* *
3751273 TAAT---TTTATAGTTTTTTAATTTTTTTTATTTT
1 TAATAAATTTATAATTTTATAATTTTTTTTATTTT
* *
3751305 TAATAAATTTGTCATTTTATAA-TTTTTTTATTTT
1 TAATAAATTTATAATTTTATAATTTTTTTTATTTT
3751339 TAA-AAATTCTATAAATTTT
1 TAATAAATT-TAT-AATTTT
3751358 TTTTTGGATG
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
31 14 0.20
32 13 0.19
33 5 0.07
34 17 0.25
35 16 0.23
36 4 0.06
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (35 bp):
TAATAAATTTATAATTTTATAATTTTTTTTATTTT
Found at i:3753794 original size:10 final size:10
Alignment explanation
Indices: 3753762--3753795 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
3753752 TGTAAAATAA
3753762 TTTTTATAGTT
1 TTTTTATA-TT
3753773 TTTTTATAATT
1 TTTTTAT-ATT
3753784 TTTTTATATT
1 TTTTTATATT
3753794 TT
1 TT
3753796 AAAAGATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 16 0.73
12 1 0.05
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTTTATATT
Found at i:3766878 original size:18 final size:18
Alignment explanation
Indices: 3766855--3766893 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3766845 TCTATATTAG
3766855 AATGAGAAATAGTAAATA
1 AATGAGAAATAGTAAATA
3766873 AATGAGAAATAGTAAATA
1 AATGAGAAATAGTAAATA
3766891 AAT
1 AAT
3766894 ACCATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
AATGAGAAATAGTAAATA
Found at i:3770426 original size:23 final size:23
Alignment explanation
Indices: 3770400--3770493 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
3770390 AAGTTAGAAG
3770400 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
3770423 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
3770446 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
3770469 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
3770492 AG
1 AG
3770494 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:3774932 original size:23 final size:23
Alignment explanation
Indices: 3774906--3775000 Score: 127
Period size: 23 Copynumber: 4.1 Consensus size: 23
3774896 AAGTTAGAAG
3774906 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
3774929 AGTGAAAAAAACTTGAATATGAAT
1 AGTG-AAGAGACTTGAATATGAAA
*
3774953 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
3774976 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
3774999 AG
1 AG
3775001 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
23 41 0.67
24 20 0.33
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:3775658 original size:15 final size:15
Alignment explanation
Indices: 3775638--3775689 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
3775628 AGTGAATTGG
3775638 AAATAAAAATATATT
1 AAATAAAAATATATT
3775653 AAATAAAAA-ATAATTT
1 AAATAAAAATAT-A-TT
3775669 ATTAATAAAATATATATT
1 A--AATAAAA-ATATATT
3775687 AAA
1 AAA
3775690 ATGATTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.06
15 10 0.32
16 5 0.16
18 10 0.32
19 2 0.06
20 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATAAAAATATATT
Done.