Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 13 of 332
Found at i:3752802 original size:21 final size:21
Alignment explanation
Indices: 3752776--3752818 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3752766 GTAAACAATA
* *
3752776 TAATGGTTTTGCCTTTTAACT
1 TAATGGTTTTGACATTTAACT
3752797 TAATGGTTTTGACATTTAACT
1 TAATGGTTTTGACATTTAACT
3752818 T
1 T
3752819 TAGAAAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (21 bp):
TAATGGTTTTGACATTTAACT
Found at i:3753718 original size:19 final size:19
Alignment explanation
Indices: 3753694--3753730 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3753684 AGGTTTTTAA
3753694 TCAAATCTAATATATATTC
1 TCAAATCTAATATATATTC
*
3753713 TCAAATTTAATATATATT
1 TCAAATCTAATATATATT
3753731 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (19 bp):
TCAAATCTAATATATATTC
Found at i:3754793 original size:30 final size:29
Alignment explanation
Indices: 3754747--3754803 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
3754737 ATTTTATTAT
*
3754747 TAATTTTTTTTTATTTTAAAGACATTTGC
1 TAATTTTTTATTATTTTAAAGACATTTGC
*
3754776 TAATTTTGTTATTATTTTAAAGGCATTT
1 TAATTTT-TTATTATTTTAAAGACATTT
3754804 ACTTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (29 bp):
TAATTTTTTATTATTTTAAAGACATTTGC
Found at i:3758377 original size:22 final size:22
Alignment explanation
Indices: 3758349--3758400 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
3758339 TAATTCAGTT
3758349 AATCGGTCATTTAACCGATCTA
1 AATCGGTCATTTAACCGATCTA
3758371 AATCGGTCATTTAACCGATCTA
1 AATCGGTCATTTAACCGATCTA
*
3758393 ATTCGGTC
1 AATCGGTC
3758401 GAAGGTCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (22 bp):
AATCGGTCATTTAACCGATCTA
Found at i:3771991 original size:14 final size:14
Alignment explanation
Indices: 3771972--3771998 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3771962 AAATTTTAAA
3771972 AATTATTAAAATTT
1 AATTATTAAAATTT
3771986 AATTATTAAAATT
1 AATTATTAAAATT
3771999 ATTTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTATTAAAATTT
Found at i:3773986 original size:48 final size:48
Alignment explanation
Indices: 3773929--3774063 Score: 136
Period size: 47 Copynumber: 2.9 Consensus size: 48
3773919 ATAAATACTA
*
3773929 AAAT-ATTATATTATAAAAATAATTTAAGTATTTTATAAAGTTAT-AAC
1 AAATAATTATATTATAAAAATAATTTAAATA-TTTATAAAGTTATGAAC
** * * * *
3773976 AAATAATTATATTATTTAAATCA-TAAAATATTTCTAAAGTTATGACC
1 AAATAATTATATTATAAAAATAATTTAAATATTTATAAAGTTATGAAC
* *
3774023 AAAAAATT-TATTATAAAAATAATTTACATA-TTATACAAGTT
1 AAATAATTATATTATAAAAATAATTTAAATATTTATA-AAGTT
3774064 TTCTAATATG
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
46 27 0.39
47 28 0.40
48 15 0.21
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (48 bp):
AAATAATTATATTATAAAAATAATTTAAATATTTATAAAGTTATGAAC
Found at i:3778644 original size:28 final size:28
Alignment explanation
Indices: 3778612--3778669 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
3778602 AGCTTCCTAT
**
3778612 AATGGACTTTGGTGGGAAGAAAAGGAAA
1 AATGGACTTTGGTGAAAAGAAAAGGAAA
3778640 AATGGACTTTGGTGAAAAGAAAAGGAAA
1 AATGGACTTTGGTGAAAAGAAAAGGAAA
3778668 AA
1 AA
3778670 CAGCATCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.48, C:0.03, G:0.31, T:0.17
Consensus pattern (28 bp):
AATGGACTTTGGTGAAAAGAAAAGGAAA
Found at i:3779349 original size:21 final size:22
Alignment explanation
Indices: 3779322--3779367 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3779312 TAAAAAATTG
*
3779322 TTAAAAAATAATAAAAAATGAT
1 TTAAAATATAATAAAAAATGAT
*
3779344 TTAAAATATAA-AAAGAATGCAT
1 TTAAAATATAATAAAAAATG-AT
3779366 TT
1 TT
3779368 CGTATCGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (22 bp):
TTAAAATATAATAAAAAATGAT
Found at i:3782423 original size:3 final size:3
Alignment explanation
Indices: 3782415--3782441 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3782405 GCTGCAAAGT
3782415 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3782442 AGATTAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3798834 original size:10 final size:10
Alignment explanation
Indices: 3798812--3798906 Score: 65
Period size: 10 Copynumber: 9.7 Consensus size: 10
3798802 ATATTTTATC
*
3798812 ATAAAAAT-C
1 ATAAAAATAT
3798821 ATAAAAATAT
1 ATAAAAATAT
3798831 ATAAAAA-ATT
1 ATAAAAATA-T
* *
3798841 ATTAAAATTT
1 ATAAAAATAT
3798851 ATAAAAATAT
1 ATAAAAATAT
3798861 ATTGAAAAAT-T
1 A-T-AAAAATAT
*
3798872 ATAAAAA-AA
1 ATAAAAATAT
**
3798881 ATAAAAAGGT
1 ATAAAAATAT
*
3798891 AT-AAAATTT
1 ATAAAAATAT
3798900 ATAAAAA
1 ATAAAAA
3798907 AAATATATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
9 28 0.41
10 31 0.46
11 3 0.04
12 6 0.09
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:3798839 original size:11 final size:11
Alignment explanation
Indices: 3798823--3798978 Score: 55
Period size: 10 Copynumber: 14.8 Consensus size: 11
3798813 TAAAAATCAT
3798823 AAAAATATATA
1 AAAAATATATA
3798834 AAAAAT-TAT-
1 AAAAATATATA
* *
3798843 TAAAATTTAT-
1 AAAAATATATA
*
3798853 AAAAATATATTG
1 AAAAATATA-TA
3798865 AAAAAT-TATA
1 AAAAATATATA
3798875 AAAAA-A-AT-
1 AAAAATATATA
**
3798883 AAAAAGGTATA
1 AAAAATATATA
** *
3798894 AAATTTATAAA
1 AAAAATATATA
*
3798905 AAAAATATATTTT
1 AAAAATATA--TA
* *
3798918 TAAAATATTTA
1 AAAAATATATA
**
3798929 AAATTTAT-TA
1 AAAAATATATA
3798939 AAAAACTA-ATA
1 AAAAA-TATATA
*
3798950 AAAATTA-ATA
1 AAAAATATATA
*
3798960 AAAACT-TATA
1 AAAAATATATA
*
3798970 AATAATATA
1 AAAAATATA
3798979 AAAGTCATAA
Statistics
Matches: 106, Mismatches: 26, Indels: 26
0.67 0.16 0.16
Matches are distributed among these distances:
8 5 0.05
9 7 0.07
10 43 0.41
11 38 0.36
12 6 0.06
13 7 0.07
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (11 bp):
AAAAATATATA
Found at i:3798839 original size:20 final size:18
Alignment explanation
Indices: 3798812--3799076 Score: 70
Period size: 19 Copynumber: 13.8 Consensus size: 18
3798802 ATATTTTATC
*
3798812 ATAAAAATCATAAAAATAT
1 ATAAAAATTATAAAAA-AT
**
3798831 ATAAAAAATTATTAAAATTT
1 AT-AAAAATTA-TAAAAAAT
*
3798851 ATAAAAATATATTGAAAAATT
1 ATAAAAAT-TA-T-AAAAAAT
** *
3798872 ATAAAAAAAATAAAAAGGT
1 ATAAAAATTATAAAAA-AT
* *
3798891 ATAAAATTTATAAAAAAA
1 ATAAAAATTATAAAAAAT
* * * *
3798909 AT-ATATTTTTAAAATAT
1 ATAAAAATTATAAAAAAT
* *
3798926 TTAAAATTTATTAAAAAACT
1 ATAAAAATTA-TAAAAAA-T
*
3798946 AATAAAAATTAATAAAAACTT
1 -ATAAAAATT-ATAAAAA-AT
*
3798967 ATAAATAA-TAT-AAAAGT
1 ATAAA-AATTATAAAAAAT
*
3798984 CATAAAAACTTATAAACAAGT
1 -ATAAAAA-TTATAAA-AAAT
* * **
3799005 -TATAAATTTTATTAAAT
1 ATAAAAATTATAAAAAAT
** * **
3799022 ATTAAAAAAGATATAACCT
1 A-TAAAAATTATAAAAAAT
3799041 CATAAAAATATATAAAAAAT
1 -ATAAAAAT-TATAAAAAAT
3799061 CATAAAAACTTATAAA
1 -ATAAAAA-TTATAAA
3799077 TATCATAAAA
Statistics
Matches: 183, Mismatches: 41, Indels: 43
0.69 0.15 0.16
Matches are distributed among these distances:
17 18 0.10
18 25 0.14
19 55 0.30
20 45 0.25
21 39 0.21
22 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAAAATTATAAAAAAT
Found at i:3798998 original size:10 final size:10
Alignment explanation
Indices: 3798939--3799010 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
3798929 AAATTTATTA
*
3798939 AAAAACTAAT
1 AAAAACTTAT
3798949 AAAAA-TTAAT
1 AAAAACTT-AT
3798959 AAAAACTTAT
1 AAAAACTTAT
3798969 AAATAA--TAT
1 AAA-AACTTAT
* *
3798978 -AAAAGTCAT
1 AAAAACTTAT
3798987 AAAAACTTAT
1 AAAAACTTAT
*
3798997 AAACAAGTTAT
1 AAA-AACTTAT
3799008 AAA
1 AAA
3799011 TTTTATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
7 2 0.04
8 2 0.04
9 6 0.12
10 27 0.54
11 13 0.26
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (10 bp):
AAAAACTTAT
Found at i:3799095 original size:20 final size:19
Alignment explanation
Indices: 3799040--3799091 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3799030 AGATATAACC
3799040 TCATAAAAATATATAAAAAA
1 TCATAAAAATATAT-AAAAA
*
3799060 TCATAAAAACT-TATAAATA
1 TCATAAAAA-TATATAAAAA
3799079 TCATAAAAATATA
1 TCATAAAAATATA
3799092 ATAAGTTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 12 0.41
21 1 0.03
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
TCATAAAAATATATAAAAA
Found at i:3799600 original size:22 final size:22
Alignment explanation
Indices: 3799575--3799623 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
3799565 TTCATTATGA
3799575 TTTTAAGGGTTTAAATGACTTT
1 TTTTAAGGGTTTAAATGACTTT
*
3799597 TTTTTAGGGTTTAAATGACTTT
1 TTTTAAGGGTTTAAATGACTTT
3799619 TTTTA
1 TTTTA
3799624 TATATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.55
Consensus pattern (22 bp):
TTTTAAGGGTTTAAATGACTTT
Found at i:3799753 original size:10 final size:10
Alignment explanation
Indices: 3799617--3799777 Score: 77
Period size: 10 Copynumber: 16.0 Consensus size: 10
3799607 TTAAATGACT
3799617 TTTTTTATATA
1 TTTTTTATA-A
3799628 TTTTTTAT-A
1 TTTTTTATAA
3799637 -TTTTTAT-A
1 TTTTTTATAA
* *
3799645 TTCTTCATAA
1 TTTTTTATAA
*
3799655 GTTTTTATTAA
1 TTTTTTA-TAA
* *
3799666 -CTTCTATAA
1 TTTTTTATAA
*
3799675 GTTTTTATAA
1 TTTTTTATAA
**
3799685 AATTTTA-AA
1 TTTTTTATAA
3799694 TATATTTTATTAA
1 T-T-TTTTA-TAA
3799707 --TTTTATAA
1 TTTTTTATAA
3799715 CTTTTTTTTATAA
1 ---TTTTTTATAA
* * *
3799728 TTTATTAGAT
1 TTTTTTATAA
3799738 TTTTTTATAA
1 TTTTTTATAA
*
3799748 TTTTTTAT-G
1 TTTTTTATAA
3799757 TTTTTTAATAA
1 TTTTTT-ATAA
3799768 TTTTTTATAA
1 TTTTTTATAA
3799778 CTGTATATCC
Statistics
Matches: 114, Mismatches: 21, Indels: 31
0.69 0.13 0.19
Matches are distributed among these distances:
8 11 0.10
9 22 0.19
10 49 0.43
11 22 0.19
13 10 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:3799772 original size:20 final size:21
Alignment explanation
Indices: 3799717--3799775 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
3799707 TTTTATAACT
*
3799717 TTTTTTTATAATTTATTA-GA
1 TTTTTTTATAATTTTTTATGA
3799737 TTTTTTTATAATTTTTTATG-
1 TTTTTTTATAATTTTTTATGA
*
3799757 TTTTTTAATAATTTTTTAT
1 TTTTTTTATAATTTTTTAT
3799776 AACTGTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 35 0.97
21 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (21 bp):
TTTTTTTATAATTTTTTATGA
Found at i:3803014 original size:5 final size:5
Alignment explanation
Indices: 3803004--3803035 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3802994 GAATTTGTGA
3803004 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
3803036 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:3803029 original size:9 final size:9
Alignment explanation
Indices: 3803005--3803035 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3802995 AATTTGTGAA
3803005 AAATAAAAT
1 AAATAAAAT
3803014 AAAATAAAAT
1 -AAATAAAAT
3803024 AAATAAAAT
1 AAATAAAAT
3803033 AAA
1 AAA
3803036 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:3807458 original size:17 final size:17
Alignment explanation
Indices: 3807436--3807468 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3807426 CTCTGATACC
3807436 AATTTGTGAAAAATAAG
1 AATTTGTGAAAAATAAG
3807453 AATTTGTGAAAAATAA
1 AATTTGTGAAAAATAA
3807469 AATAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (17 bp):
AATTTGTGAAAAATAAG
Found at i:3807472 original size:5 final size:5
Alignment explanation
Indices: 3807462--3807493 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3807452 GAATTTGTGA
3807462 AAAAT AAAAT AAAAT -AAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
3807494 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:3807482 original size:14 final size:14
Alignment explanation
Indices: 3807463--3807493 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3807453 AATTTGTGAA
3807463 AAATAAAATAAAAT
1 AAATAAAATAAAAT
3807477 AAATAAAATAAAAT
1 AAATAAAATAAAAT
3807491 AAA
1 AAA
3807494 GAACACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:3813421 original size:40 final size:40
Alignment explanation
Indices: 3813219--3813396 Score: 295
Period size: 40 Copynumber: 4.5 Consensus size: 40
3813209 GGATGATAAT
3813219 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTC
* *
3813259 CGGGCTAAGTCCCAAAGGCATTTGTGTGAGTTACTAGTTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTC
3813299 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTC
* *
3813339 CGGGCTAAGTCTCGAAGGTATTTGTGCGAGTTACTA-TATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-TC
*
3813379 CGGGCTATGTCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
3813397 TATTCGAGCG
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 1 0.01
40 128 0.99
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTC
Found at i:3817561 original size:59 final size:59
Alignment explanation
Indices: 3817469--3817587 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
3817459 TCAGCCATAC
* *
3817469 TTAACTGGAAGCCTCTGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTGCCGGT
1 TTAACTGGAAGCCTCCGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTACCGGT
3817528 TTAACTGGAAGCCTCCGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTACCGGT
1 TTAACTGGAAGCCTCCGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTACCGGT
3817587 T
1 T
3817588 ACTACCGACG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (59 bp):
TTAACTGGAAGCCTCCGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTACCGGT
Found at i:3826338 original size:15 final size:15
Alignment explanation
Indices: 3826318--3826351 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3826308 TCTGCATGAG
3826318 AAAAATT-AATAATAA
1 AAAAATTAAAT-ATAA
3826333 AAAAATTAAATATAA
1 AAAAATTAAATATAA
3826348 AAAA
1 AAAA
3826352 TCCTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTAAATATAA
Found at i:3832290 original size:18 final size:18
Alignment explanation
Indices: 3832268--3832315 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
3832258 TTGGACTAAA
3832268 TTTTTGGAAAATAG-TTT
1 TTTTTGGAAAATAGATTT
*
3832285 TATTTTGAAAAATAGATTT
1 T-TTTTGGAAAATAGATTT
*
3832304 TTTTTTGAAAAT
1 TTTTTGGAAAAT
3832316 TTTAACATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 21 0.81
19 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (18 bp):
TTTTTGGAAAATAGATTT
Found at i:3832304 original size:19 final size:18
Alignment explanation
Indices: 3832269--3832314 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
3832259 TGGACTAAAT
*
3832269 TTTTGGAAAATAGTTTTA
1 TTTTGAAAAATAGTTTTA
*
3832287 TTTTGAAAAATAGATTTTT
1 TTTTGAAAAATAG-TTTTA
3832306 TTTTGAAAA
1 TTTTGAAAA
3832315 TTTTAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (18 bp):
TTTTGAAAAATAGTTTTA
Found at i:3836774 original size:14 final size:15
Alignment explanation
Indices: 3836750--3836787 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
3836740 TAGAAGGAGC
*
3836750 TCAATTTTTTTTTCT
1 TCAACTTTTTTTTCT
3836765 TCAA-TTTTTTTTCT
1 TCAACTTTTTTTTCT
3836779 TCAACTTTT
1 TCAACTTTT
3836788 AACGTGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (15 bp):
TCAACTTTTTTTTCT
Found at i:3838220 original size:26 final size:25
Alignment explanation
Indices: 3838171--3838222 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
3838161 CCTTTTTGGC
*
3838171 TAAATAGTTAAATATATCGATTTTT
1 TAAATAGTTAAATAGATCGATTTTT
3838196 TAAATTAGTTAAATAGATC-ACTTTTT
1 TAAA-TAGTTAAATAGATCGA-TTTTT
3838222 T
1 T
3838223 TCAAGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (25 bp):
TAAATAGTTAAATAGATCGATTTTT
Found at i:3847456 original size:61 final size:60
Alignment explanation
Indices: 3847345--3847461 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 60
3847335 CTAGAGGAGC
* **
3847345 CTAATTAAATTTGCTAAAAACTTCAAAGAAGAAATGAAATTTTTCAAAAATTTTGGAGGT
1 CTAATTAAATTTGCTAAAAACTTCAAAGAAGAAATCAAAAGTTTCAAAAATTTTGGAGGT
* * * *
3847405 CTAATTAAAATTTTCTTAAAATTTC-AAGAGAGAAATCAAAAGTTTCCAAAATTTTGG
1 CTAATT-AAATTTGCTAAAAACTTCAAAGA-AGAAATCAAAAGTTTCAAAAATTTTGG
3847462 GGGGCATTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 10 0.21
61 38 0.79
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (60 bp):
CTAATTAAATTTGCTAAAAACTTCAAAGAAGAAATCAAAAGTTTCAAAAATTTTGGAGGT
Found at i:3851546 original size:35 final size:35
Alignment explanation
Indices: 3851523--3851715 Score: 266
Period size: 35 Copynumber: 5.5 Consensus size: 35
3851513 GGCAAAGTGC
*
3851523 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
*
3851558 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
* * *
3851593 GAAATATAGGTATGGTATTATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
* *
3851628 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTAT-CCATACCGAGTTGA
* *
3851663 GAAACGTAGGTATGGTATTTTCCATACCGAGTAT-A
1 GAAATGTAGGTATGGTATTATCCATACCGAGT-TGA
3851698 -AAATGTAGGTATGGTATT
1 GAAATGTAGGTATGGTATT
3851716 TCAATGAGGA
Statistics
Matches: 140, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
34 18 0.13
35 120 0.86
36 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
Found at i:3851689 original size:105 final size:104
Alignment explanation
Indices: 3851523--3851715 Score: 300
Period size: 105 Copynumber: 1.8 Consensus size: 104
3851513 GGCAAAGTGC
* *
3851523 GAAATGTAGGTATGGTATTATCCATACCGAGTTGTGAAATGTAGGTATGGTATCATCCATACCGA
1 GAAATGTAGGTATGGCATTATCCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGA
3851588 GT-TGAGAAATATAGGTATGGTATTATCCATACTGAGTTAA
66 GTAT-A-AAATATAGGTATGGTATTATCCATACTGAGTTAA
**
3851628 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTGTGAAACGTAGGTATGGTATTTTCCATACCG
1 GAAATGTAGGTATGGCATTAT-CCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCG
*
3851692 AGTATAAAATGTAGGTATGGTATT
65 AGTATAAAATATAGGTATGGTATT
3851716 TCAATGAGGA
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
104 18 0.22
105 62 0.77
106 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (104 bp):
GAAATGTAGGTATGGCATTATCCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGA
GTATAAAATATAGGTATGGTATTATCCATACTGAGTTAA
Found at i:3856433 original size:18 final size:18
Alignment explanation
Indices: 3856400--3856434 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3856390 TCTTTAATAG
* *
3856400 AAAAGAAACAATTGTAAT
1 AAAAGAAAAAAATGTAAT
3856418 AAAAGAAAAAAATGTAA
1 AAAAGAAAAAAATGTAA
3856435 AATAAAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (18 bp):
AAAAGAAAAAAATGTAAT
Found at i:3856456 original size:15 final size:16
Alignment explanation
Indices: 3856416--3856460 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
3856406 AACAATTGTA
3856416 ATAAAAGAAAAAAATG
1 ATAAAAGAAAAAAATG
*
3856432 -TAAAA-TAAAAAA-G
1 ATAAAAGAAAAAAATG
3856445 ATAAAAGGAAAAAAAT
1 ATAAAA-GAAAAAAAT
3856461 TGTAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
13 1 0.04
14 11 0.48
15 5 0.22
16 6 0.26
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (16 bp):
ATAAAAGAAAAAAATG
Found at i:3856473 original size:29 final size:31
Alignment explanation
Indices: 3856415--3856484 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
3856405 AAACAATTGT
3856415 AATAAAA-GAAAAAAATGTAAAATAAAAAAG
1 AATAAAAGGAAAAAAATGTAAAATAAAAAAG
*
3856445 -ATAAAAGGAAAAAAATTGT-AAA-AAGAAAG
1 AATAAAAGGAAAAAAA-TGTAAAATAAAAAAG
*
3856474 AAAAAAAGGAA
1 AATAAAAGGAA
3856485 TAAATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 12 0.34
30 20 0.57
31 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (31 bp):
AATAAAAGGAAAAAAATGTAAAATAAAAAAG
Found at i:3857852 original size:24 final size:26
Alignment explanation
Indices: 3857810--3857859 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
3857800 ACATAAATTA
*
3857810 TCAAAACAATTTATTTAAA-TACCAT
1 TCAAAACAATTTATGTAAATTACCAT
*
3857835 TCAAATCAA-TTATGTAAATTACCAT
1 TCAAAACAATTTATGTAAATTACCAT
3857860 ATTATAAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (26 bp):
TCAAAACAATTTATGTAAATTACCAT
Found at i:3858680 original size:15 final size:15
Alignment explanation
Indices: 3858655--3858701 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
3858645 ATAACTCACA
3858655 AATTCCAATTCAATAC
1 AATT-CAATTCAATAC
*
3858671 AATTCAATTCAACT-T
1 AATTCAATTCAA-TAC
3858686 AATTCAATTTCAATAC
1 AATTCAA-TTCAATAC
3858702 TACAATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTCAATTCAATAC
Found at i:3859575 original size:23 final size:23
Alignment explanation
Indices: 3859549--3859592 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3859539 AAGTAAATTC
3859549 ATATTTATAATACAAATGTATGT
1 ATATTTATAATACAAATGTATGT
* * *
3859572 ATATTTTTACTACACATGTAT
1 ATATTTATAATACAAATGTAT
3859593 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (23 bp):
ATATTTATAATACAAATGTATGT
Found at i:3859610 original size:22 final size:23
Alignment explanation
Indices: 3859564--3859610 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3859554 TATAATACAA
*
3859564 ATGTATGTATATTTTTACTACAC
1 ATGTATGTATATTTTTACCACAC
* *
3859587 ATGTAT-TTTATTTTTACCATAC
1 ATGTATGTATATTTTTACCACAC
3859609 AT
1 AT
3859611 TTAACATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (23 bp):
ATGTATGTATATTTTTACCACAC
Found at i:3863803 original size:18 final size:18
Alignment explanation
Indices: 3863780--3863816 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3863770 TGTCAGGTTG
3863780 AGGCTTGATTCAAGTAAA
1 AGGCTTGATTCAAGTAAA
3863798 AGGCTTGATTCAAGTAAA
1 AGGCTTGATTCAAGTAAA
3863816 A
1 A
3863817 ACTTTAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (18 bp):
AGGCTTGATTCAAGTAAA
Found at i:3866659 original size:18 final size:18
Alignment explanation
Indices: 3866633--3866679 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3866623 GGTTAATGGC
* *
3866633 GAAGTAGAAGAAGAAGCT
1 GAAGAAGAAGAAGAAGAT
* *
3866651 GAAGGAGAAGAAGATGAT
1 GAAGAAGAAGAAGAAGAT
3866669 GAAGAAGAAGA
1 GAAGAAGAAGA
3866680 GATTGGTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.36, T:0.09
Consensus pattern (18 bp):
GAAGAAGAAGAAGAAGAT
Found at i:3866661 original size:15 final size:15
Alignment explanation
Indices: 3866638--3866679 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3866628 ATGGCGAAGT
*
3866638 AGAAGAAGAAGCTGA
1 AGAAGAAGAAGATGA
*
3866653 AGGAGAAGAAGATGA
1 AGAAGAAGAAGATGA
*
3866668 TGAAGAAGAAGA
1 AGAAGAAGAAGA
3866680 GATTGGTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.36, T:0.07
Consensus pattern (15 bp):
AGAAGAAGAAGATGA
Found at i:3866768 original size:3 final size:3
Alignment explanation
Indices: 3866686--3866721 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3866676 AAGAGATTGG
3866686 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3866722 ATTAGAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:3871261 original size:16 final size:15
Alignment explanation
Indices: 3871235--3871269 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
3871225 TGATGTGAAT
3871235 AATATAAAATATTAA
1 AATATAAAATATTAA
*
3871250 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
3871266 AATA
1 AATA
3871270 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:3871440 original size:20 final size:20
Alignment explanation
Indices: 3871383--3871442 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
3871373 AATACTACAT
3871383 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
3871402 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
3871425 AAATATGTACATAATATA
1 AAATATGTACATAATATA
3871443 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:3871532 original size:25 final size:24
Alignment explanation
Indices: 3871504--3871633 Score: 108
Period size: 23 Copynumber: 5.6 Consensus size: 24
3871494 GTAAAAATAT
*
3871504 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATT-AAG
* *
3871529 ATATATACATAAAATAGTA-TAAT
1 ATATATACATAATATAGTATTAAG
* * *
3871552 ATATATACGTAATATAGAATTTAG
1 ATATATACATAATATAGTATTAAG
* * *
3871576 A-ATATACCTAATATATTA-AAAG
1 ATATATACATAATATAGTATTAAG
* *
3871598 A-ATATATATAATATAATATTAAG
1 ATATATACATAATATAGTATTAAG
*
3871621 AAATATA-ATAATA
1 ATATATACATAATA
3871634 ACAAAAAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
22 17 0.20
23 42 0.49
24 9 0.11
25 17 0.20
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATATACATAATATAGTATTAAG
Found at i:3872141 original size:18 final size:18
Alignment explanation
Indices: 3872118--3872171 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
3872108 ACAAGTGGTG
3872118 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
3872136 GT-G-G--AGT-TGG-TG
1 GTGGAGCAAGTGTGGCTA
3872148 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
3872166 GTGGAG
1 GTGGAG
3872172 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 3 0.11
13 4 0.14
14 4 0.14
16 4 0.14
17 4 0.14
18 9 0.32
ACGTcount: A:0.19, C:0.07, G:0.50, T:0.24
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:3872149 original size:30 final size:30
Alignment explanation
Indices: 3872113--3872181 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
3872103 TAGGTACAAG
3872113 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
3872143 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
3872173 TGGTGGTGG
1 TGGTGGTGG
3872182 CAAAGGCTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.14, C:0.06, G:0.52, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:3889385 original size:22 final size:22
Alignment explanation
Indices: 3889360--3889404 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3889350 TGATTTCCAA
*
3889360 ATGAAATCTCATTCCTATTTAT
1 ATGAAATCTCATGCCTATTTAT
* * *
3889382 ATGAATTTTCATGCCTCTTTAT
1 ATGAAATCTCATGCCTATTTAT
3889404 A
1 A
3889405 GAGACATCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (22 bp):
ATGAAATCTCATGCCTATTTAT
Found at i:3892468 original size:14 final size:15
Alignment explanation
Indices: 3892446--3892522 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3892436 CAATCAAACA
3892446 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
3892460 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
3892475 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
3892495 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
3892509 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
3892523 ACCGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:3892487 original size:20 final size:20
Alignment explanation
Indices: 3892462--3892501 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3892452 AATATTTTCC
*
3892462 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3892482 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3892502 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3892507 original size:34 final size:35
Alignment explanation
Indices: 3892450--3892516 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3892440 CAAACACCAG
*
3892450 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3892485 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3892517 TATTTTACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3895487 original size:114 final size:114
Alignment explanation
Indices: 3895287--3895515 Score: 440
Period size: 114 Copynumber: 2.0 Consensus size: 114
3895277 AGAATAGTCC
3895287 ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAGTAATACTT
1 ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAGTAATACTT
*
3895352 TATAGGATAATCTAATAATATTAGAAAATAAATGAAGGAAAGAAAGAAT
66 TATAGAATAATCTAATAATATTAGAAAATAAATGAAGGAAAGAAAGAAT
3895401 ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAGTAATACTT
1 ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAGTAATACTT
*
3895466 TATAGAATAATCTAATAATATTAGAAAATGAATGAAGGAAAGAAAGAAT
66 TATAGAATAATCTAATAATATTAGAAAATAAATGAAGGAAAGAAAGAAT
3895515 A
1 A
3895516 TTATAATTTG
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.28
Consensus pattern (114 bp):
ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAGTAATACTT
TATAGAATAATCTAATAATATTAGAAAATAAATGAAGGAAAGAAAGAAT
Found at i:3904583 original size:26 final size:26
Alignment explanation
Indices: 3904547--3904602 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
3904537 TGAAATTCCA
3904547 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
3904573 ATCATGGAACATTTAGCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
3904599 ATCA
1 ATCA
3904603 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:3919111 original size:114 final size:114
Alignment explanation
Indices: 3918911--3919139 Score: 431
Period size: 114 Copynumber: 2.0 Consensus size: 114
3918901 AGAATAGTCC
*
3918911 ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAGTAATACTT
1 ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAATAATACTT
3918976 TATAGAATAATCTAATAATATTAGAAAATAAATGAAGGAAAGAAAGAAT
66 TATAGAATAATCTAATAATATTAGAAAATAAATGAAGGAAAGAAAGAAT
*
3919025 ACTACGCACTGAGCAATGTATAACAAGAAACTCAATTTCTATAAAGGATTTCTGTAATAATACTT
1 ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAATAATACTT
*
3919090 TATAGAATAATCTAATAATATTAGAAAATGAATGAAGGAAAGAAAGAAT
66 TATAGAATAATCTAATAATATTAGAAAATAAATGAAGGAAAGAAAGAAT
3919139 A
1 A
3919140 TTATAATTTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (114 bp):
ACTACGCACTGAGCAATGTATAACAAGAAACTAAATTTCTATAAAGGATTTCTGTAATAATACTT
TATAGAATAATCTAATAATATTAGAAAATAAATGAAGGAAAGAAAGAAT
Found at i:3927506 original size:26 final size:26
Alignment explanation
Indices: 3927470--3927530 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
3927460 ATATATTTTC
* *
3927470 TCAAAATTTTACTAGGGGCAAAAAGG
1 TCAAAATTTTACCAGGGGCAAAAACG
* * *
3927496 TCAAAATTTTACCAGTGGTAAAATCG
1 TCAAAATTTTACCAGGGGCAAAAACG
3927522 TCAAAATTT
1 TCAAAATTT
3927531 GTTGGAGGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (26 bp):
TCAAAATTTTACCAGGGGCAAAAACG
Found at i:3931639 original size:42 final size:43
Alignment explanation
Indices: 3931565--3931674 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
3931555 GACTTATAAT
3931565 TTACGTGTAAGACCATGTCAGGGACATCGGCATCG-TAATTGA
1 TTACGTGTAAGACCATGTCAGGGACATCGGCATCGATAATTGA
* * *
3931607 TTCCGTGTAAGACCCTGTCTAGGG-CAGT-GGCATCGATATTTGA
1 TTACGTGTAAGACCATGTC-AGGGACA-TCGGCATCGATAATTGA
* * *
3931650 TTACATGTAAGACCACGTCTGGGAC
1 TTACGTGTAAGACCATGTCAGGGAC
3931675 GTTGGCATTG
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
42 29 0.52
43 27 0.48
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCAGGGACATCGGCATCGATAATTGA
Found at i:3931681 original size:43 final size:43
Alignment explanation
Indices: 3931524--3931682 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
3931514 TATGTGTTTT
* * * *
3931524 CGTGTAAGACCACGTCTAGGAAGTTGGCATCGACT-TATAATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTA
* * * * * *
3931568 CGTGTAAGACCATGTCAGGGACATCGGCATCG-TAATTGATTC
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
3931610 CGTGTAAGACC-CTGTCTAGGG-CAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCT-GGGAC-GTTGGCATCGATATTTGATTA
*
3931653 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
3931683 TGTATGAGCT
Statistics
Matches: 90, Mismatches: 17, Indels: 17
0.73 0.14 0.14
Matches are distributed among these distances:
42 29 0.32
43 34 0.38
44 27 0.30
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:3934168 original size:40 final size:40
Alignment explanation
Indices: 3934113--3934188 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
3934103 TAATCAAAAG
** *
3934113 GGATAAAATTGACCCACCCAGCCCTACACACCAAGTATGA
1 GGATAAAATCAACCCACCCAACCCTACACACCAAGTATGA
*
3934153 GGATAAAATCAACCCATCCAACCCTACACACCAAGT
1 GGATAAAATCAACCCACCCAACCCTACACACCAAGT
3934189 GGTACGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.39, C:0.34, G:0.12, T:0.14
Consensus pattern (40 bp):
GGATAAAATCAACCCACCCAACCCTACACACCAAGTATGA
Found at i:3934655 original size:22 final size:24
Alignment explanation
Indices: 3934607--3934652 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
3934597 GTAAGGCCCC
* *
3934607 TTCTCTTGCTGCTGTTCAATTTCCG
1 TTCTCTTGCTACTGGT-AATTTCCG
3934632 TTCTCTTGCTACTGGT-ATTTC
1 TTCTCTTGCTACTGGTAATTTC
3934653 GTTTCCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
25 14 0.74
ACGTcount: A:0.09, C:0.26, G:0.15, T:0.50
Consensus pattern (24 bp):
TTCTCTTGCTACTGGTAATTTCCG
Found at i:3934679 original size:8 final size:8
Alignment explanation
Indices: 3934666--3934692 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3934656 TCCTTTCTCC
3934666 CTCTCTTT
1 CTCTCTTT
3934674 CTCTCTTT
1 CTCTCTTT
3934682 CTCTCTTT
1 CTCTCTTT
3934690 CTC
1 CTC
3934693 ATGCAATCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (8 bp):
CTCTCTTT
Found at i:3936128 original size:16 final size:16
Alignment explanation
Indices: 3936107--3936200 Score: 80
Period size: 16 Copynumber: 5.8 Consensus size: 16
3936097 AGTCATAGTG
3936107 ATGTGTGAGCTGTGTA
1 ATGTGTGAGCTGTGTA
*** *
3936123 ATGTGTGAGCTACAATG
1 ATGTGTGAGCT-GTGTA
* *
3936140 ATGTGCGAGTTGTGTA
1 ATGTGTGAGCTGTGTA
** *
3936156 ATGTGCAAGCTATGTA
1 ATGTGTGAGCTGTGTA
*
3936172 ATGTGTGAGTTGTAGTA
1 ATGTGTGAGCTGT-GTA
3936189 ATGTGTGAGCTG
1 ATGTGTGAGCTG
3936201 GGAAAATATG
Statistics
Matches: 58, Mismatches: 18, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
16 34 0.59
17 24 0.41
ACGTcount: A:0.23, C:0.07, G:0.34, T:0.35
Consensus pattern (16 bp):
ATGTGTGAGCTGTGTA
Found at i:3936142 original size:33 final size:33
Alignment explanation
Indices: 3936070--3936199 Score: 115
Period size: 33 Copynumber: 3.9 Consensus size: 33
3936060 TGCGAGTTGT
*
3936070 AATGATGTGTGAGCTGTGTAAT-TTTCGAG-T-C
1 AATGATGTGTGAGCTGTGTAATGTGT-GAGCTAC
3936101 ATAGTGATGTGTGAGCTGTGTAATGTGTGAGCTAC
1 A-A-TGATGTGTGAGCTGTGTAATGTGTGAGCTAC
* * **
3936136 AATGATGTGCGAGTTGTGTAATGTGCAAGCTA-
1 AATGATGTGTGAGCTGTGTAATGTGTGAGCTAC
** * *
3936168 TGTAATGTGTGAGTTGTAGTAATGTGTGAGCT
1 AATGATGTGTGAGCTGT-GTAATGTGTGAGCT
3936200 GGGAAAATAT
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
31 1 0.01
32 14 0.17
33 61 0.74
34 4 0.05
35 2 0.02
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (33 bp):
AATGATGTGTGAGCTGTGTAATGTGTGAGCTAC
Found at i:3940230 original size:20 final size:21
Alignment explanation
Indices: 3940205--3940245 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3940195 AAATATTTTC
3940205 AGTAAATCA-TTTTCCAGAAA
1 AGTAAATCATTTTTCCAGAAA
3940225 AGTAAATCATTTTTCCAGAAA
1 AGTAAATCATTTTTCCAGAAA
3940246 TCATTTTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (21 bp):
AGTAAATCATTTTTCCAGAAA
Found at i:3940248 original size:15 final size:15
Alignment explanation
Indices: 3940228--3940266 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
3940218 CCAGAAAAGT
3940228 AAATCATTTTTCCAG
1 AAATCATTTTTCCAG
*
3940243 AAATCA-TTTTCCGG
1 AAATCATTTTTCCAG
*
3940257 AAAACATTTT
1 AAATCATTTT
3940267 ACTGGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (15 bp):
AAATCATTTTTCCAG
Found at i:3942499 original size:42 final size:42
Alignment explanation
Indices: 3942440--3942523 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
3942430 GATTGAAGAA
3942440 ACAAGAAATGCCTTGTGGCGAAAAACTATGTAAATTTTTTTG
1 ACAAGAAATGCCTTGTGGCGAAAAACTATGTAAATTTTTTTG
3942482 ACAAGAAATGCCTTGTGGCGAAAAACTATGTAAATTTTTTTG
1 ACAAGAAATGCCTTGTGGCGAAAAACTATGTAAATTTTTTTG
3942524 GTTATTTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (42 bp):
ACAAGAAATGCCTTGTGGCGAAAAACTATGTAAATTTTTTTG
Found at i:3949109 original size:21 final size:21
Alignment explanation
Indices: 3949084--3949124 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3949074 CACCATCTTT
3949084 TTTTTATATTTTTTGTTTTTG
1 TTTTTATATTTTTTGTTTTTG
*
3949105 TTTTTTTATTTTTTGTTTTT
1 TTTTTATATTTTTTGTTTTT
3949125 TGCTGCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (21 bp):
TTTTTATATTTTTTGTTTTTG
Found at i:3950514 original size:30 final size:30
Alignment explanation
Indices: 3950480--3950538 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3950470 TTATTTTATT
*
3950480 GTTAATTTTCTTATTATTTTAAAGGCATTC
1 GTTAATTTTCTTATTATTTTAAAAGCATTC
*
3950510 GTTAATTTTTTTATTATTTTAAAAGCATT
1 GTTAATTTTCTTATTATTTTAAAAGCATT
3950539 TGCTTGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (30 bp):
GTTAATTTTCTTATTATTTTAAAAGCATTC
Found at i:3964713 original size:26 final size:25
Alignment explanation
Indices: 3964669--3964719 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
3964659 TTTTGAGCAA
* *
3964669 TTTAATTTTTTTTCTTTTATGTTCT
1 TTTAATTTTTTTCCCTTTATGTTCT
*
3964694 TTTAACTTTTTTTCCCTTTATTTTCT
1 TTTAA-TTTTTTTCCCTTTATGTTCT
3964720 ATTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTAATTTTTTTCCCTTTATGTTCT
Found at i:3964998 original size:34 final size:34
Alignment explanation
Indices: 3964956--3965036 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
3964946 AGAATGGAAA
*
3964956 AAAAGAACAAAAAAAGGGAAAGTTAAAAGAACAT
1 AAAAGAACAAAAAAAAGGAAAGTTAAAAGAACAT
3964990 AAAAGAACAAAAAAAAGGAAAGTTAAAAGAACAT
1 AAAAGAACAAAAAAAAGGAAAGTTAAAAGAACAT
3965024 AAAAGAA-AAAAAA
1 AAAAGAACAAAAAA
3965037 GTGCTTAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 6 0.13
34 40 0.87
ACGTcount: A:0.73, C:0.05, G:0.15, T:0.07
Consensus pattern (34 bp):
AAAAGAACAAAAAAAAGGAAAGTTAAAAGAACAT
Found at i:3972690 original size:38 final size:38
Alignment explanation
Indices: 3972634--3972708 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
3972624 GATGTGTATT
* * *
3972634 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
3972672 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATAT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATAT
3972709 TCAGGCCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:3972759 original size:43 final size:43
Alignment explanation
Indices: 3972706--3972873 Score: 248
Period size: 43 Copynumber: 3.9 Consensus size: 43
3972696 GCTGGTATTA
*
3972706 TATTCAGGCCTTCGTGCCTAGCAGACTTAGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGACTTAGTGCCGGTGATGTG
*
3972749 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGACTTAGTGCCGGTGATGTG
* *
3972792 TATTCGGGCCTTCGTGCCTAACAGGA-TTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCA-GACTTAGTGCCGGTGATGTG
* * * *
3972835 TATTCGGGCCTTTGTGCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGACTTAGTGCCGGTGA
3972874 AATGATATGT
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 110 0.98
44 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.33, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGACTTAGTGCCGGTGATGTG
Found at i:3972807 original size:86 final size:85
Alignment explanation
Indices: 3972685--3972873 Score: 265
Period size: 86 Copynumber: 2.2 Consensus size: 85
3972675 GATAAATCCC
* *
3972685 GCAGGCCTAGTGCTGGT-ATTATATTCAGGCCTTCGTGCCTAGCA-GACTTAGTGCCGGTGATGT
1 GCAGGCCTAGTGCCGGTGATTATATTCAGGCCTTCGTGCCTAACAGGA-TTAGTGCCGGTGATGT
3972748 GTATTCGGGCCTTCGTGCCTA
65 GTATTCGGGCCTTCGTGCCTA
* * * *
3972769 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAACAGGATTCGTGCCGGTGATGT
1 GCAGGCCTAGTGCCGGTGAT-TATATTCAGGCCTTCGTGCCTAACAGGATTAGTGCCGGTGATGT
*
3972834 GTATTCGGGCCTTTGTGCCTA
65 GTATTCGGGCCTTCGTGCCTA
* *
3972855 GCAGGCGTAATGCCGGTGA
1 GCAGGCCTAGTGCCGGTGA
3972874 AATGATATGT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 15 0.16
85 2 0.02
86 74 0.80
87 2 0.02
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.30
Consensus pattern (85 bp):
GCAGGCCTAGTGCCGGTGATTATATTCAGGCCTTCGTGCCTAACAGGATTAGTGCCGGTGATGTG
TATTCGGGCCTTCGTGCCTA
Found at i:3975245 original size:19 final size:19
Alignment explanation
Indices: 3975163--3975256 Score: 79
Period size: 19 Copynumber: 5.0 Consensus size: 19
3975153 TATAAAATTT
* *
3975163 TATATTTTTTATATTTCTA
1 TATATTTTTTACATTTTTA
*
3975182 TA-ATCTTTTACTATTTTTA
1 TATATTTTTTAC-ATTTTTA
**
3975201 TA-AAATTTTACAATTTTT-
1 TATATTTTTTAC-ATTTTTA
3975219 TATATTTTTTACATTTTTA
1 TATATTTTTTACATTTTTA
*
3975238 TATTTTTTTCTA-ATTTTTA
1 TATATTTTT-TACATTTTTA
3975257 ATAAAATAGG
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
18 15 0.24
19 45 0.73
20 2 0.03
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (19 bp):
TATATTTTTTACATTTTTA
Found at i:3975255 original size:9 final size:9
Alignment explanation
Indices: 3975160--3975245 Score: 61
Period size: 9 Copynumber: 9.4 Consensus size: 9
3975150 CTTTATAAAA
3975160 TTTTATATT
1 TTTTATATT
3975169 TTTTATA-T
1 TTTTATATT
* *
3975177 TTCTATAATC
1 TTTTAT-ATT
3975187 TTTTACTA-T
1 TTTTA-TATT
**
3975196 TTTTATAAAA
1 TTTTAT-ATT
*
3975206 TTTTACAATT
1 TTTTA-TATT
3975216 TTTTATATT
1 TTTTATATT
*
3975225 TTTTACA-T
1 TTTTATATT
3975233 TTTTATATT
1 TTTTATATT
3975242 TTTT
1 TTTT
3975246 TCTAATTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
8 14 0.24
9 28 0.47
10 16 0.27
11 1 0.02
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTATATT
Found at i:3975431 original size:91 final size:89
Alignment explanation
Indices: 3975259--3975488 Score: 318
Period size: 91 Copynumber: 2.5 Consensus size: 89
3975249 AATTTTTAAT
* * * *
3975259 AAAATAGGGGCTTAATTGCTTTTTCTGAAAAAGTTTAAGGGTCTTTTTGATACATTTTGAAAGTT
1 AAAATAGGAGCTTAATTGCTTTTTTTCAAAAAGTTTGAGGG-CTTTTTGATACATTTTGAAAGTT
*
3975324 CAAATACCCAATTGAGTGCAAAAAA
65 CAAATACCCAAATGAGTGCAAAAAA
* *
3975349 AAATTAGGAGCTTAATTGCTTTTTTTTAAAAAGGTTTGAGGGCATTTTTGATACATTTTGAAAGT
1 AAAATAGGAGCTTAATTGCTTTTTTTCAAAAA-GTTTGAGGGC-TTTTTGATACATTTTGAAAGT
* *
3975414 TCAAGTATCCAAATGAGTGCAAAAAA
64 TCAAATACCCAAATGAGTGCAAAAAA
*
3975440 AAAAGTAGGAGCTTAATTGCATTTTTTCAAAAA-TTGTGAGGGCTTTTTG
1 AAAA-TAGGAGCTTAATTGCTTTTTTTCAAAAAGTT-TGAGGGCTTTTTG
3975489 CACCCTTAAT
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
90 37 0.30
91 62 0.50
92 26 0.21
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (89 bp):
AAAATAGGAGCTTAATTGCTTTTTTTCAAAAAGTTTGAGGGCTTTTTGATACATTTTGAAAGTTC
AAATACCCAAATGAGTGCAAAAAA
Found at i:3976100 original size:17 final size:18
Alignment explanation
Indices: 3976069--3976106 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
3976059 GAGTAATATT
*
3976069 TTTTTTATACCTATATTTG
1 TTTTTTATA-CTATATGTG
3976088 TTTTTTATA-TATATGTG
1 TTTTTTATACTATATGTG
3976105 TT
1 TT
3976107 AATTTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (18 bp):
TTTTTTATACTATATGTG
Found at i:3980758 original size:17 final size:17
Alignment explanation
Indices: 3980736--3980769 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3980726 CAACCGTGGT
3980736 GTTAATATTATTAAAAA
1 GTTAATATTATTAAAAA
* *
3980753 GTTAATGTTTTTAAAAA
1 GTTAATATTATTAAAAA
3980770 AATTATTTTT
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:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
GTTAATATTATTAAAAA
Found at i:3996377 original size:25 final size:26
Alignment explanation
Indices: 3996343--3996391 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3996333 ATAATTTTAA
3996343 TGATTTTT-AAAATAAAAAAATTATT
1 TGATTTTTAAAAATAAAAAAATTATT
*
3996368 TGATTTTTAAAAATTAAAAAATTA
1 TGATTTTTAAAAATAAAAAAATTA
3996392 ATTAAATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
TGATTTTTAAAAATAAAAAAATTATT
Found at i:3996403 original size:27 final size:26
Alignment explanation
Indices: 3996351--3996403 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3996341 AATGATTTTT
** *
3996351 AAAATAAAAAAATTATTTGATTTTTA
1 AAAATAAAAAAATTATTAAATGTTTA
*
3996377 AAAATTAAAAAATTAATTAAATGTTTA
1 AAAATAAAAAAATT-ATTAAATGTTTA
3996404 TGTGGAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
AAAATAAAAAAATTATTAAATGTTTA
Found at i:4003067 original size:30 final size:30
Alignment explanation
Indices: 4003033--4003096 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
4003023 AAATCTTACC
*
4003033 TAAAGCTTGACCCATATAAATAATGGATCT
1 TAAAGCTTCACCCATATAAATAATGGATCT
4003063 TAAAGCTTCACCCATATAAATAATGGATCT
1 TAAAGCTTCACCCATATAAATAATGGATCT
4003093 TAAA
1 TAAA
4003097 TTTTACCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (30 bp):
TAAAGCTTCACCCATATAAATAATGGATCT
Found at i:4004233 original size:42 final size:42
Alignment explanation
Indices: 4004177--4004264 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
4004167 ACCCGCAATC
4004177 TTGTTAGAATAAACTACCCCTTTAGTACTCTGTCATTTATTG
1 TTGTTAGAATAAACTACCCCTTTAGTACTCTGTCATTTATTG
*
4004219 TTGTTAGAATAAACTACCCCTTTAGTACTTTGTCATTTATTG
1 TTGTTAGAATAAACTACCCCTTTAGTACTCTGTCATTTATTG
4004261 TTGT
1 TTGT
4004265 AATCCTAGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (42 bp):
TTGTTAGAATAAACTACCCCTTTAGTACTCTGTCATTTATTG
Found at i:4005002 original size:26 final size:26
Alignment explanation
Indices: 4004966--4005018 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
4004956 TTTTACATTT
4004966 ACCAATTCATTGAATGCTGTATGATA
1 ACCAATTCATTGAATGCTGTATGATA
4004992 ACCAATTCATTGAATGCTGTATGATA
1 ACCAATTCATTGAATGCTGTATGATA
4005018 A
1 A
4005019 ACGCCTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (26 bp):
ACCAATTCATTGAATGCTGTATGATA
Found at i:4007740 original size:34 final size:35
Alignment explanation
Indices: 4007672--4007742 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
4007662 ATAATATGCT
* *
4007672 AATAAAATAAGAGCAGCATAATGAAATAAAAAAGAA
1 AATAAAATAAGAACAG-ATAATAAAATAAAAAAGAA
* *
4007708 AATAAAATAATAACAG-TAATAAAATAATAAAGAA
1 AATAAAATAAGAACAGATAATAAAATAAAAAAGAA
4007742 A
1 A
4007743 TAATAGTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 17 0.55
36 14 0.45
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (35 bp):
AATAAAATAAGAACAGATAATAAAATAAAAAAGAA
Found at i:4007753 original size:17 final size:16
Alignment explanation
Indices: 4007695--4007745 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
4007685 CAGCATAATG
*
4007695 AAATAAAAAAGAAAATA
1 AAATAATAAAG-AAATA
*
4007712 AAATAATAACAGTAATA
1 AAATAATAA-AGAAATA
4007729 AAATAATAAAGAAATA
1 AAATAATAAAGAAATA
4007745 A
1 A
4007746 TAGTAATACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.23
17 21 0.70
18 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATAATAAAGAAATA
Found at i:4008343 original size:7 final size:7
Alignment explanation
Indices: 4008268--4008398 Score: 58
Period size: 8 Copynumber: 17.9 Consensus size: 7
4008258 AAGGGTTTAA
4008268 AATAAAT
1 AATAAAT
*
4008275 AATACAT
1 AATAAAT
4008282 -ATAAGAT
1 AATAA-AT
*
4008289 AAATATAT
1 -AATAAAT
*
4008297 ATTAAA-
1 AATAAAT
4008303 AATATATAT
1 AATA-A-AT
4008312 AATAAGAT
1 AATAA-AT
*
4008320 AACTTAAT
1 AA-TAAAT
4008328 -ATAAAT
1 AATAAAT
*
4008334 AATGAAT
1 AATAAAT
4008341 AATAAAT
1 AATAAAT
4008348 AATTTAAAT
1 AA--TAAAT
4008357 -ATAGAAT
1 AATA-AAT
4008364 AAT-AA-
1 AATAAAT
*
4008369 AATAAACG
1 AATAAA-T
4008377 AATAAAT
1 AATAAAT
4008384 AAATAAAT
1 -AATAAAT
4008392 AAATAAA
1 -AATAAA
4008399 AAGGGGTTAA
Statistics
Matches: 96, Mismatches: 12, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
5 3 0.03
6 16 0.17
7 30 0.31
8 33 0.34
9 14 0.15
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (7 bp):
AATAAAT
Found at i:4008355 original size:23 final size:23
Alignment explanation
Indices: 4008324--4008369 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4008314 TAAGATAACT
4008324 TAATATAAATA-ATGAATAATAAA
1 TAATATAAATATA-GAATAATAAA
*
4008347 TAATTTAAATATAGAATAATAAA
1 TAATATAAATATAGAATAATAAA
4008370 ATAAACGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
TAATATAAATATAGAATAATAAA
Found at i:4010997 original size:93 final size:93
Alignment explanation
Indices: 4010869--4011040 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
4010859 GCCCATAAGT
* * *
4010869 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
4010934 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * * *
4010962 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGTCTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
4011027 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
4011041 CAAATATCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:4011024 original size:46 final size:45
Alignment explanation
Indices: 4010861--4011035 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
4010851 TGTAACCCGC
* *
4010861 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* *
4010907 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** * *
4010953 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
* *
4011000 CCATAAGTGAACTCGGTCTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
4011036 ATGCCCAAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 63 0.61
47 30 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:4013804 original size:13 final size:13
Alignment explanation
Indices: 4013786--4013814 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4013776 TCATTTCATC
4013786 ATAGCTTATGAGA
1 ATAGCTTATGAGA
4013799 ATAGCTTATGAGA
1 ATAGCTTATGAGA
4013812 ATA
1 ATA
4013815 CGTAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (13 bp):
ATAGCTTATGAGA
Found at i:4015212 original size:144 final size:144
Alignment explanation
Indices: 4014952--4015240 Score: 470
Period size: 144 Copynumber: 2.0 Consensus size: 144
4014942 TTGTTCTTCA
* * * *
4014952 TACACACACTCGAGTAACCATCTATTTTATTCTTTTTAAGTGTTGTATTGTCATTGAGTGAGCTT
1 TACACACACTCGAGTAACCACCTATTTTATTCTTTTCAACTGTTGTATTGTCATTGAGTGAACTT
* * *
4015017 TATCATTGTAATATCTTCTTTCAGAGGTGTCTTTAATCATTGTTATTATTTATCATATTTGTAAG
66 TATCATTGTAATATCTTCCTTCAGAGATGTCTTCAATCATTGTTATTATTTATCATATTTGTAAG
4015082 GGTTTGCTTAAGGT
131 GGTTTGCTTAAGGT
* * *
4015096 TACACACACTTGGGTAACCACCTCTTTTATTCTTTTCAACTGTTGTATTGTCATTGAGTGAACTT
1 TACACACACTCGAGTAACCACCTATTTTATTCTTTTCAACTGTTGTATTGTCATTGAGTGAACTT
* *
4015161 TATTATTGTAATATCTTCCTTGAGAGATGTCTTCAATCATTGTTATTATTTATCATATTTGTAAG
66 TATCATTGTAATATCTTCCTTCAGAGATGTCTTCAATCATTGTTATTATTTATCATATTTGTAAG
4015226 GGTTTGCTTAAGGT
131 GGTTTGCTTAAGGT
4015240 T
1 T
4015241 TTTGGGTAGA
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 133 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (144 bp):
TACACACACTCGAGTAACCACCTATTTTATTCTTTTCAACTGTTGTATTGTCATTGAGTGAACTT
TATCATTGTAATATCTTCCTTCAGAGATGTCTTCAATCATTGTTATTATTTATCATATTTGTAAG
GGTTTGCTTAAGGT
Found at i:4016412 original size:29 final size:29
Alignment explanation
Indices: 4016379--4016474 Score: 183
Period size: 29 Copynumber: 3.3 Consensus size: 29
4016369 AATATTGCAA
4016379 TTTTAAATATTAATAATATATTTTAGCAT
1 TTTTAAATATTAATAATATATTTTAGCAT
4016408 TTTTAAATATTAATAATATATTTTAGCAT
1 TTTTAAATATTAATAATATATTTTAGCAT
4016437 TTTTAAATATTAATAATATATTTTAGCAT
1 TTTTAAATATTAATAATATATTTTAGCAT
*
4016466 CTTTAAATA
1 TTTTAAATA
4016475 ATCTTCTTAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTTAAATATTAATAATATATTTTAGCAT
Found at i:4019854 original size:27 final size:27
Alignment explanation
Indices: 4019823--4019875 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4019813 GACATTAATG
4019823 TTGATTTT-GTATAATTATATATAAATA
1 TTGATTTTAGTATAATTAT-TATAAATA
* *
4019850 TTGATTTTATTTTAATTATTATAAAT
1 TTGATTTTAGTATAATTATTATAAAT
4019876 TATTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (27 bp):
TTGATTTTAGTATAATTATTATAAATA
Found at i:4019879 original size:28 final size:28
Alignment explanation
Indices: 4019834--4019888 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
4019824 TGATTTTGTA
* *
4019834 TAATTATATATAAATATTGATTTTATTT
1 TAATTATATATAAATATTAATATTATTT
4019862 TAATTAT-TATAAATTATTAATATTATT
1 TAATTATATATAAA-TATTAATATTATT
4019889 ACTCATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TAATTATATATAAATATTAATATTATTT
Found at i:4021979 original size:17 final size:17
Alignment explanation
Indices: 4021957--4021992 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4021947 GTGAGCCTAT
*
4021957 TTTAGGTTGACTCATAA
1 TTTAGGTTCACTCATAA
4021974 TTTAGGTTCACTCATAA
1 TTTAGGTTCACTCATAA
4021991 TT
1 TT
4021993 ATATTTACTT
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:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (17 bp):
TTTAGGTTCACTCATAA
Found at i:4022092 original size:20 final size:21
Alignment explanation
Indices: 4022049--4022092 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
4022039 GTGTAATTAA
* * *
4022049 ATAAAAATCTAAATTTTATTT
1 ATAAAAATCAAAATTTCATAT
4022070 ATAAAAAT-AAAATTTCATAT
1 ATAAAAATCAAAATTTCATAT
4022090 ATA
1 ATA
4022093 TTTAAATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAAAATCAAAATTTCATAT
Found at i:4022292 original size:22 final size:23
Alignment explanation
Indices: 4022250--4022295 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4022240 ATAAATATAT
*
4022250 TAAATATTTTAAATTTTAATTAA
1 TAAATATATTAAATTTTAATTAA
*
4022273 TAAATATATTATA-TTTAATTAA
1 TAAATATATTAAATTTTAATTAA
4022295 T
1 T
4022296 CTATAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATATATTAAATTTTAATTAA
Found at i:4030668 original size:16 final size:18
Alignment explanation
Indices: 4030641--4030677 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
4030631 TAAACAAATT
4030641 TTTTTAATAATTTTTA-A
1 TTTTTAATAATTTTTACA
4030658 TTTTTAA-AATTTTTACA
1 TTTTTAATAATTTTTACA
4030675 TTT
1 TTT
4030678 AGTTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAATAATTTTTACA
Found at i:4046194 original size:21 final size:21
Alignment explanation
Indices: 4046168--4046208 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4046158 GCGGTGGCGG
*
4046168 TGATGGTGATGGTGGCGATGT
1 TGATGGTGAGGGTGGCGATGT
*
4046189 TGATGGTGGGGGTGGCGATG
1 TGATGGTGAGGGTGGCGATG
4046209 GAGTTGACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.54, T:0.29
Consensus pattern (21 bp):
TGATGGTGAGGGTGGCGATGT
Found at i:4046230 original size:3 final size:3
Alignment explanation
Indices: 4046222--4046262 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
4046212 TTGACTCTGC
* *
4046222 TGG TGG TGG TGG TGG TGA TGG TGA TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
4046263 AAGAAGAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.05, C:0.00, G:0.61, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:4048294 original size:20 final size:18
Alignment explanation
Indices: 4048262--4048308 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
4048252 ATAATTTAAT
4048262 AAATAAAAATAAAAATCTA
1 AAATAAAAATAAAAAT-TA
*
4048281 AAACTAAAACTAAAAATTA
1 AAA-TAAAAATAAAAATTA
4048300 AAATAAAAA
1 AAATAAAAA
4048309 CATATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 12 0.48
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATAAAAATAAAAATTA
Found at i:4048308 original size:19 final size:20
Alignment explanation
Indices: 4048262--4048309 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
4048252 ATAATTTAAT
4048262 AAATAAAAA-TAAAAATCTA
1 AAATAAAAACTAAAAATCTA
4048281 AAACT-AAAACTAAAAAT-TA
1 AAA-TAAAAACTAAAAATCTA
4048300 AAATAAAAAC
1 AAATAAAAAC
4048310 ATATAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.04
19 17 0.65
20 8 0.31
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAAAAACTAAAAATCTA
Found at i:4049636 original size:31 final size:31
Alignment explanation
Indices: 4049598--4049658 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
4049588 TACCCATACA
4049598 ATGTAGGTACTTTAAGGACTTAACTAAAACC
1 ATGTAGGTACTTTAAGGACTTAACTAAAACC
4049629 ATGTAGGTACTTTAAGGACTTAACTAAAAC
1 ATGTAGGTACTTTAAGGACTTAACTAAAAC
4049659 ATTATGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (31 bp):
ATGTAGGTACTTTAAGGACTTAACTAAAACC
Found at i:4060156 original size:7 final size:6
Alignment explanation
Indices: 4060130--4060154 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4060120 AAAATGGGTT
4060130 CTCCCC CTCCCC CTCCCC CTCCCC C
1 CTCCCC CTCCCC CTCCCC CTCCCC C
4060155 CTTTCTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.84, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCCCC
Found at i:4060803 original size:13 final size:13
Alignment explanation
Indices: 4060785--4060809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4060775 TATCGATGCT
4060785 GCCTAACATATTG
1 GCCTAACATATTG
4060798 GCCTAACATATT
1 GCCTAACATATT
4060810 AGCCGTATCA
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:0.24, G:0.12, T:0.32
Consensus pattern (13 bp):
GCCTAACATATTG
Found at i:4068755 original size:19 final size:19
Alignment explanation
Indices: 4068731--4068768 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
4068721 TAGGATTCAA
4068731 TGATTTTGAGGTTT-AGGAT
1 TGATTTTGA-GTTTAAGGAT
4068750 TGATTTTGAGTTTAAGGAT
1 TGATTTTGAGTTTAAGGAT
4068769 GATAATAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (19 bp):
TGATTTTGAGTTTAAGGAT
Found at i:4070390 original size:30 final size:29
Alignment explanation
Indices: 4070348--4070449 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 29
4070338 TTGTAGGTAC
*
4070348 AAGTGGTGGTGGAGCAAGTGTGGCTAGTG
1 AAGTGGTGGTGGAGCAAATGTGGCTAGTG
*
4070377 AAGTAGGTAGTGGAGCAAATGTGGCTAGTG
1 AAGT-GGTGGTGGAGCAAATGTGGCTAGTG
* * *
4070407 GAGTTGGTGGTGGAACAATTGTGGCTAGTGG
1 AAG-TGGTGGTGGAGCAAATGTGGCTAGT-G
*
4070438 AGGTGGTGGTGG
1 AAGTGGTGGTGG
4070450 CAAAGGCTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
29 4 0.06
30 55 0.89
31 3 0.05
ACGTcount: A:0.22, C:0.06, G:0.47, T:0.25
Consensus pattern (29 bp):
AAGTGGTGGTGGAGCAAATGTGGCTAGTG
Found at i:4072207 original size:22 final size:22
Alignment explanation
Indices: 4072169--4072211 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4072159 ATTTATTTTT
*
4072169 ATTTAAATCTCATAATATTCTG
1 ATTTAAATCTCAAAATATTCTG
4072191 ATTTAAAT-TCAAAAATATTCT
1 ATTTAAATCTC-AAAATATTCT
4072212 AATTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTAAATCTCAAAATATTCTG
Found at i:4074442 original size:16 final size:16
Alignment explanation
Indices: 4074423--4074473 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
4074413 TATAAATAAA
*
4074423 TATATTATAAAATTTT
1 TATATAATAAAATTTT
4074439 TATA-ACATAAATTATTTT
1 TATATA-ATAAA--ATTTT
4074457 T-TATAATAAAATTTT
1 TATATAATAAAATTTT
4074472 TA
1 TA
4074474 CCATAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
15 6 0.21
16 9 0.31
17 7 0.24
18 7 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATAATAAAATTTT
Found at i:4075986 original size:27 final size:28
Alignment explanation
Indices: 4075939--4075992 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
4075929 TGAAATTTTA
*
4075939 AAAAAAATAAAATATTATAAAAGTCATG
1 AAAAAAATAAAAAATTATAAAAGTCATG
* *
4075967 AAAAATATAAAAAATT-TAAAATTCAT
1 AAAAAAATAAAAAATTATAAAAGTCAT
4075993 TATCAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAAAATAAAAAATTATAAAAGTCATG
Found at i:4076097 original size:19 final size:21
Alignment explanation
Indices: 4076056--4076103 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
4076046 TTAAATTTTT
4076056 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
4076077 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
4076096 AACTAAAA
1 AACTAAAA
4076104 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:4076130 original size:17 final size:18
Alignment explanation
Indices: 4076094--4076131 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4076084 ATTTAGAATC
4076094 AAAACTAAAATAAATAAT
1 AAAACTAAAATAAATAAT
* *
4076112 AAAATTAAATTAAAT-AT
1 AAAACTAAAATAAATAAT
4076129 AAA
1 AAA
4076132 GATATCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAACTAAAATAAATAAT
Found at i:4077584 original size:17 final size:17
Alignment explanation
Indices: 4077559--4077591 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4077549 TTATTTTTTC
*
4077559 TTTCTGAAAACCCATTG
1 TTTCAGAAAACCCATTG
4077576 TTTCAGAAAACCCATT
1 TTTCAGAAAACCCATT
4077592 TCTTCTTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (17 bp):
TTTCAGAAAACCCATTG
Found at i:4078864 original size:22 final size:23
Alignment explanation
Indices: 4078829--4078879 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
4078819 TAAAATATTA
* *
4078829 ATTTTTAAGTTTTTTAATTTTTT
1 ATTTTTAAGATTTTTAAATTTTT
4078852 ATTTTTAA-ATTTTTAAATTTTT
1 ATTTTTAAGATTTTTAAATTTTT
4078874 ATTTTT
1 ATTTTT
4078880 TGAGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTTTAAGATTTTTAAATTTTT
Found at i:4078874 original size:8 final size:8
Alignment explanation
Indices: 4078828--4078874 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
4078818 CTAAAATATT
4078828 AATTTTTA
1 AATTTTTA
* *
4078836 AGTTTTTT
1 AATTTTTA
4078844 AATTTTT-
1 AATTTTTA
*
4078851 TATTTTTA
1 AATTTTTA
4078859 AATTTTTA
1 AATTTTTA
4078867 AATTTTTA
1 AATTTTTA
4078875 TTTTTTGAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (8 bp):
AATTTTTA
Found at i:4078880 original size:23 final size:23
Alignment explanation
Indices: 4078829--4078879 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
4078819 TAAAATATTA
* *
4078829 ATTTTTAAGTTTTTTAATTTTTT
1 ATTTTTAAATTTTTAAATTTTTT
4078852 ATTTTTAAATTTTTAAA-TTTTT
1 ATTTTTAAATTTTTAAATTTTTT
4078874 ATTTTT
1 ATTTTT
4078880 TGAGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTTTAAATTTTTAAATTTTTT
Found at i:4079491 original size:7 final size:7
Alignment explanation
Indices: 4079479--4079542 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
4079469 CCCATAGCCA
4079479 TTAAACC
1 TTAAACC
4079486 TTAAACC
1 TTAAACC
*
4079493 ATAAAACC
1 -TTAAACC
*
4079501 CTAAACC
1 TTAAACC
* *
4079508 ATAGACC
1 TTAAACC
4079515 TTAAACC
1 TTAAACC
**
4079522 TTAAATA
1 TTAAACC
4079529 TTAAACC
1 TTAAACC
*
4079536 GTAAACC
1 TTAAACC
4079543 AAAAAATAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
7 38 0.86
8 6 0.14
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (7 bp):
TTAAACC
Found at i:4079499 original size:15 final size:15
Alignment explanation
Indices: 4079476--4079526 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
4079466 ATACCCATAG
*
4079476 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
*
4079491 CCATAAAACCCTAAA
1 CCATAAAACCTTAAA
*
4079506 CCAT-AGACCTTAAA
1 CCATAAAACCTTAAA
*
4079520 CCTTAAA
1 CCATAAA
4079527 TATTAAACCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:4079519 original size:36 final size:35
Alignment explanation
Indices: 4079470--4079543 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
4079460 TACTATATAC
4079470 CCATAGCCATTAAACCTTAAACCATAAAACCCTAAA
1 CCATAGCCATTAAACCTTAAA-CATAAAACCCTAAA
* * *
4079506 CCATAGACC-TTAAACCTTAAATATTAAACCGTAAA
1 CCATAG-CCATTAAACCTTAAACATAAAACCCTAAA
4079541 CCA
1 CCA
4079544 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 14 0.41
36 18 0.53
37 2 0.06
ACGTcount: A:0.46, C:0.28, G:0.04, T:0.22
Consensus pattern (35 bp):
CCATAGCCATTAAACCTTAAACATAAAACCCTAAA
Found at i:4079846 original size:40 final size:41
Alignment explanation
Indices: 4079767--4079852 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 41
4079757 GTTATATGAC
* * **
4079767 TTTTAGCGGCGTTTTATCAAAAGCGCCGCTATTGCTCTGT-
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTAATCTGTG
*
4079807 TTTTAGTGGCGTTTTACCAAAAACGCCGCTATTAATCTGTG
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTAATCTGTG
4079848 TTTTA
1 TTTTA
4079853 CAATTTTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 35 0.88
41 5 0.12
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTAATCTGTG
Done.