Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 65 of 207
Found at i:18786030 original size:11 final size:11
Alignment explanation
Indices: 18786014--18786039 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18786004 ATTTTTTAAA
18786014 TTTTAAAATAC
1 TTTTAAAATAC
18786025 TTTTAAAATAC
1 TTTTAAAATAC
18786036 TTTT
1 TTTT
18786040 TTTAATTTTT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:18786075 original size:11 final size:11
Alignment explanation
Indices: 18786054--18786093 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
18786044 ATTTTTTTTA
18786054 ATTTT-AAAAT
1 ATTTTAAAAAT
18786064 ATTTTAAAAAT
1 ATTTTAAAAAT
18786075 ATTTTAAAAAT
1 ATTTTAAAAAT
18786086 ACTTTTAA
1 A-TTTTAA
18786094 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:18786093 original size:49 final size:49
Alignment explanation
Indices: 18785997--18786124 Score: 165
Period size: 49 Copynumber: 2.6 Consensus size: 49
18785987 AATTTTTTTA
**
18785997 TTTTTTT-ATTTTTTAA-ATTTTAAAATACTTTTAAAATACTTTTTTTAAT
1 TTTTTTTAATTTTAAAATATTTTAAAATACTTTTAAAATAC--TTTTTAAT
18786046 TTTTTTTAATTTTAAAATATTTTAAAAATA-TTTTAAAAATAC-TTTTAAT
1 TTTTTTTAATTTTAAAATATTTT-AAAATACTTTT-AAAATACTTTTTAAT
18786095 TTTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTTTAATTTTAAAATA-TTTTAAAATA
18786125 AAATTTTTAT
Statistics
Matches: 72, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
49 39 0.54
50 11 0.15
51 9 0.12
52 13 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (49 bp):
TTTTTTTAATTTTAAAATATTTTAAAATACTTTTAAAATACTTTTTAAT
Found at i:18798040 original size:3 final size:3
Alignment explanation
Indices: 18798032--18798064 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
18798022 AATATTTTTG
*
18798032 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18798065 CATTTTCAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18798065 original size:9 final size:9
Alignment explanation
Indices: 18798032--18798068 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
18798022 AATATTTTTG
*
18798032 TATTATTAT
1 TATTATCAT
*
18798041 TATTATTAT
1 TATTATCAT
18798050 TATTATCAT
1 TATTATCAT
18798059 TATTATCAT
1 TATTATCAT
18798068 T
1 T
18798069 TTCAAGTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (9 bp):
TATTATCAT
Found at i:18798522 original size:36 final size:39
Alignment explanation
Indices: 18798459--18798531 Score: 91
Period size: 37 Copynumber: 1.9 Consensus size: 39
18798449 ACAATATCCA
*
18798459 AACAATAACAACAGAAAAGTGGTAAT-AACAA-AATGGC
1 AACAATAACAACAGAAAAGTGGAAATAAACAACAATGGC
*
18798496 AACAA-AACAACATTAAAA-TGGAAATAAACAACAATG
1 AACAATAACAACA-GAAAAGTGGAAATAAACAACAATG
18798532 AAAATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 13 0.42
37 14 0.45
38 4 0.13
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (39 bp):
AACAATAACAACAGAAAAGTGGAAATAAACAACAATGGC
Found at i:18799472 original size:20 final size:20
Alignment explanation
Indices: 18799447--18799491 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
18799437 ATTTATTTAT
* *
18799447 TAAAATAATATTTTTATAAA
1 TAAAATAATAATCTTATAAA
*
18799467 TAAAATAATAATCTTATACA
1 TAAAATAATAATCTTATAAA
18799487 TAAAA
1 TAAAA
18799492 CAATTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATAATAATCTTATAAA
Found at i:18804891 original size:20 final size:21
Alignment explanation
Indices: 18804853--18804891 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18804843 CATTAGTGAC
*
18804853 TAAAATAATAAAATTAAAAAT
1 TAAAATAATAAAATAAAAAAT
*
18804874 TAAAA-AATCAAATAAAAA
1 TAAAATAATAAAATAAAAA
18804892 TACGCTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAATAATAAAATAAAAAAT
Found at i:18808707 original size:15 final size:16
Alignment explanation
Indices: 18808684--18808727 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
18808674 GGTTAGGGTT
*
18808684 TTTAATATTTTT-AGG
1 TTTAGTATTTTTAAGG
18808699 TTTAGTATTTTTTAAGG
1 TTTAGTA-TTTTTAAGG
*
18808716 TTTAGGATTTTT
1 TTTAGTATTTTT
18808728 TGGGTATTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 10 0.40
17 9 0.36
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (16 bp):
TTTAGTATTTTTAAGG
Found at i:18808712 original size:16 final size:17
Alignment explanation
Indices: 18808691--18808728 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18808681 GTTTTTAATA
*
18808691 TTTTT-AGGTTTAGTAT
1 TTTTTAAGGTTTAGGAT
18808707 TTTTTAAGGTTTAGGAT
1 TTTTTAAGGTTTAGGAT
18808724 TTTTT
1 TTTTT
18808729 GGGTATTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63
Consensus pattern (17 bp):
TTTTTAAGGTTTAGGAT
Found at i:18818044 original size:21 final size:21
Alignment explanation
Indices: 18818015--18818058 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
18818005 GGTTAGGGGT
18818015 GTTGCATTTAGTGGTAGCAGA
1 GTTGCATTTAGTGGTAGCAGA
* *
18818036 GTTGTATTTAGTGGTATCAGA
1 GTTGCATTTAGTGGTAGCAGA
18818057 GT
1 GT
18818059 AGGTTTAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.07, G:0.32, T:0.39
Consensus pattern (21 bp):
GTTGCATTTAGTGGTAGCAGA
Found at i:18829693 original size:65 final size:66
Alignment explanation
Indices: 18829586--18829746 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 66
18829576 AGTAGCCTAG
* * * **
18829586 CACGGCCTAGCAGACGGCCGTGTGGCTTGGATGTGTGTCACAAGTCAGTATACTCACCA-TTTTC
1 CACGGCCTAGCAAACGGGCATGTGGCTTGGACATGTGTCACAAGTCAGTATACTCACCATTTTTC
18829650 A
66 A
* * * * * *
18829651 CATGGCCTAGCACACGGGCATGTGGCTTGGCCATGTGTCACAAGTTAGTATGCTCACCATTTTTG
1 CACGGCCTAGCAAACGGGCATGTGGCTTGGACATGTGTCACAAGTCAGTATACTCACCATTTTTC
18829716 A
66 A
18829717 CACGGCCTAGCAAACGGGCATGTGGCTTGG
1 CACGGCCTAGCAAACGGGCATGTGGCTTGG
18829747 TCGTGTGACC
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
65 50 0.60
66 33 0.40
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.25
Consensus pattern (66 bp):
CACGGCCTAGCAAACGGGCATGTGGCTTGGACATGTGTCACAAGTCAGTATACTCACCATTTTTC
A
Found at i:18829785 original size:66 final size:66
Alignment explanation
Indices: 18829586--18829787 Score: 176
Period size: 66 Copynumber: 3.1 Consensus size: 66
18829576 AGTAGCCTAG
* * * *** * * * **
18829586 CACGGCCTAGCAGACGGCCGTGTGGCTTGGATGTGTGTCACAAGTCAGTATACTCACCA-TTTTC
1 CACGGCCTAGCAAACGGGCATGTGGCTTGGCCATGTGACACAAGTTAGTATGCTCACCAGTTTGG
18829650 A
66 A
* * * * *
18829651 CATGGCCTAGCACACGGGCATGTGGCTTGGCCATGTGTCACAAGTTAGTATGCTCACCATTTTTG
1 CACGGCCTAGCAAACGGGCATGTGGCTTGGCCATGTGACACAAGTTAGTATGCTCACCAGTTTGG
18829716 A
66 A
* * * * *
18829717 CACGGCCTAGCAAACGGGCATGTGGCTTGGTCGTGTGACCCAA-TTCAGTGA-GCTTACTAGTTT
1 CACGGCCTAGCAAACGGGCATGTGGCTTGGCCATGTGACACAAGTT-AGT-ATGCTCACCAGTTT
18829780 GGA
64 GGA
18829783 CACGG
1 CACGG
18829788 TCGTGTGTCC
Statistics
Matches: 114, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 52 0.46
66 61 0.54
67 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (66 bp):
CACGGCCTAGCAAACGGGCATGTGGCTTGGCCATGTGACACAAGTTAGTATGCTCACCAGTTTGG
A
Found at i:18830176 original size:51 final size:51
Alignment explanation
Indices: 18830117--18830218 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
18830107 CGGGTTAGGG
18830117 GTGTTACATTTATTAGTATCAGAGCTACAGTTTAGTCAATTCTCAGACTAA
1 GTGTTACATTTATTAGTATCAGAGCTACAGTTTAGTCAATTCTCAGACTAA
* * *
18830168 GTGTTACATTTATTAGTATTAGAGCTACAGTTTAGTCGATTCTCGGACTAA
1 GTGTTACATTTATTAGTATCAGAGCTACAGTTTAGTCAATTCTCAGACTAA
18830219 CGTAGCGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (51 bp):
GTGTTACATTTATTAGTATCAGAGCTACAGTTTAGTCAATTCTCAGACTAA
Found at i:18843015 original size:66 final size:66
Alignment explanation
Indices: 18842893--18843076 Score: 262
Period size: 66 Copynumber: 2.8 Consensus size: 66
18842883 CCTAAAACGG
* * * *
18842893 CCTAGCACACGGGCGTGTGGCTTGGACGTGTGTCACAAGTCTGTATACTCAACATTTTTCACATG
1 CCTAGCACACGGGCGTGTGGCTTGGCCGTGTGTCACAAGTCAGTATGCTCACCATTTTTCACATG
18842958 A
66 A
* *
18842959 CCTAACACACGGACGTGTGGCTTGGCCGTGTGTCACAAGTCAGTATGCTCACCATTTTTCACATG
1 CCTAGCACACGGGCGTGTGGCTTGGCCGTGTGTCACAAGTCAGTATGCTCACCATTTTTCACATG
*
18843024 G
66 A
* * *
18843025 CCTAGCACACGGGCATGTGGCTTGGCCGTGTGACCCAAGTCAGTGA-GCTCAC
1 CCTAGCACACGGGCGTGTGGCTTGGCCGTGTGTCACAAGTCAGT-ATGCTCAC
18843077 TAGTTTGGAC
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 104 0.99
67 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.26
Consensus pattern (66 bp):
CCTAGCACACGGGCGTGTGGCTTGGCCGTGTGTCACAAGTCAGTATGCTCACCATTTTTCACATG
A
Found at i:18853966 original size:14 final size:13
Alignment explanation
Indices: 18853943--18853991 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
18853933 AATTCAAAGT
18853943 AAATAATAATTTA
1 AAATAATAATTTA
18853956 AAATAAATAATTTA
1 AAAT-AATAATTTA
* * *
18853970 CAACAACAATTTA
1 AAATAATAATTTA
18853983 AAA-AATAAT
1 AAATAATAAT
18853992 AATAAAAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 5 0.17
13 14 0.47
14 11 0.37
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAATAATTTA
Found at i:18856071 original size:37 final size:37
Alignment explanation
Indices: 18856021--18856095 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
18856011 ACCTAAACAA
18856021 AAATGACATGTTTCATAAGTAACAAGCAAAAAACCCT
1 AAATGACATGTTTCATAAGTAACAAGCAAAAAACCCT
*
18856058 AAATGACATGTTTCATAAGTAATAAGCAAAAAACCCT
1 AAATGACATGTTTCATAAGTAACAAGCAAAAAACCCT
18856095 A
1 A
18856096 CTTAATTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (37 bp):
AAATGACATGTTTCATAAGTAACAAGCAAAAAACCCT
Found at i:18857597 original size:4 final size:4
Alignment explanation
Indices: 18857588--18857633 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
18857578 ATCAAATTGC
18857588 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
18857634 CTGACACTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:18868538 original size:95 final size:95
Alignment explanation
Indices: 18868407--18868582 Score: 266
Period size: 95 Copynumber: 1.9 Consensus size: 95
18868397 GGCGTCATTA
* * *
18868407 ATAGTAGTGGAATTCATAGTCCAATAAAAGGTAAATGATA-TCATCTCATAGGCATTACATGGTT
1 ATAGTAGTGAAATTCATACTCCAATAAAAGGTAAATGATATTC-TCTCATAAGCATTACATGGTT
*
18868471 GGTAGAAAAGTAACATGACATGACTTCCTTT
65 GATAGAAAAGTAACATGACATGACTTCCTTT
*
18868502 ATAGTAGTGAAATTCATAACT-CGATAAAAGGTAAATGATATTCTCTCATAAGCATTACATGGTT
1 ATAGTAGTGAAATTCAT-ACTCCAATAAAAGGTAAATGATATTCTCTCATAAGCATTACATGGTT
*
18868566 GATGGAAAAGTAACATG
65 GATAGAAAAGTAACATG
18868583 GTCATGGGTC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
95 69 0.95
96 4 0.05
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (95 bp):
ATAGTAGTGAAATTCATACTCCAATAAAAGGTAAATGATATTCTCTCATAAGCATTACATGGTTG
ATAGAAAAGTAACATGACATGACTTCCTTT
Found at i:18872104 original size:13 final size:13
Alignment explanation
Indices: 18872088--18872112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18872078 ATGTTTAGAT
18872088 GAAATGGTTATAC
1 GAAATGGTTATAC
18872101 GAAATGGTTATA
1 GAAATGGTTATA
18872113 TGAGATGATT
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:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (13 bp):
GAAATGGTTATAC
Found at i:18872104 original size:26 final size:26
Alignment explanation
Indices: 18872050--18872115 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
18872040 ATTATGTATT
* *
18872050 AAATGTGTAAATGAAATGGTAAAATG
1 AAATGTTTAAATGAAATGGTAAAACG
* * *
18872076 AAATGTTTAGATGAAATGGTTATACG
1 AAATGTTTAAATGAAATGGTAAAACG
* *
18872102 AAATGGTTATATGA
1 AAATGTTTAAATGA
18872116 GATGATTGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.32
Consensus pattern (26 bp):
AAATGTTTAAATGAAATGGTAAAACG
Found at i:18881709 original size:14 final size:14
Alignment explanation
Indices: 18881690--18881729 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
18881680 TATAATCTTC
18881690 TTTTATATTTTAAT
1 TTTTATATTTTAAT
*
18881704 TTTTATATATTAAAT
1 TTTTATAT-TTTAAT
18881719 TTTTATATTTT
1 TTTTATATTTT
18881730 TATATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTATATTTTAAT
Found at i:18881721 original size:21 final size:22
Alignment explanation
Indices: 18881697--18881739 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18881687 TTCTTTTATA
18881697 TTTTA-ATTTTTATATATTAAAT
1 TTTTATATTTTTATAT-TTAAAT
18881719 TTTTATATTTTTATATTTAAA
1 TTTTATATTTTTATATTTAAA
18881740 AATCTTGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATATTTTTATATTTAAAT
Found at i:18881730 original size:8 final size:8
Alignment explanation
Indices: 18881690--18881736 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
18881680 TATAATCTTC
18881690 TTTTATA-
1 TTTTATAT
18881697 TTTTA-AT
1 TTTTATAT
18881704 TTTTATA-
1 TTTTATAT
* *
18881711 TATTAAAT
1 TTTTATAT
18881719 TTTTATAT
1 TTTTATAT
18881727 TTTTATAT
1 TTTTATAT
18881735 TT
1 TT
18881737 AAAAATCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
6 1 0.03
7 15 0.45
8 17 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTATAT
Found at i:18884527 original size:15 final size:15
Alignment explanation
Indices: 18884507--18884546 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
18884497 GTTATCATTA
18884507 TTTTTACTATTATTG
1 TTTTTACTATTATTG
18884522 TTTTTA--A-TATTG
1 TTTTTACTATTATTG
*
18884534 TTATTACTATTAT
1 TTTTTACTATTAT
18884547 CATGCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
12 10 0.48
13 1 0.05
14 1 0.05
15 9 0.43
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTACTATTATTG
Found at i:18884949 original size:2 final size:2
Alignment explanation
Indices: 18884942--18884984 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
18884932 CATATACATC
* *
18884942 TA TA TA TA TA TA TA TA TA TA TA TA TC TA CA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18884983 TA
1 TA
18884985 CTTTATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18884956 original size:36 final size:36
Alignment explanation
Indices: 18884880--18884956 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
18884870 ACATATCTTT
* * *
18884880 TATATTTTATAATTCACATATACATATATATTTTCC
1 TATATTTTACAATTCACATATACATATATATTATCA
*
18884916 TATATTTTACAACTT-ACATATACATCTATATATAT-A
1 TATATTTTACAA-TTCACATATACATATATAT-TATCA
18884952 TATAT
1 TATAT
18884957 ATATATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (36 bp):
TATATTTTACAATTCACATATACATATATATTATCA
Found at i:18885422 original size:19 final size:19
Alignment explanation
Indices: 18885398--18885437 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
18885388 AATGCTCTTT
*
18885398 AATCAAAAATATAAATAAA
1 AATCAAAAACATAAATAAA
18885417 AATCAAAAACATAAATAAA
1 AATCAAAAACATAAATAAA
18885436 AA
1 AA
18885438 ACTCATTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (19 bp):
AATCAAAAACATAAATAAA
Found at i:18887377 original size:17 final size:17
Alignment explanation
Indices: 18887357--18887391 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18887347 ATTTATTTAA
*
18887357 TCAATTAATTTAATTTC
1 TCAATTAAATTAATTTC
*
18887374 TCAATTAAATTATTTTC
1 TCAATTAAATTAATTTC
18887391 T
1 T
18887392 TAACTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (17 bp):
TCAATTAAATTAATTTC
Found at i:18888776 original size:37 final size:37
Alignment explanation
Indices: 18888706--18888776 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
18888696 CTATCCTAAG
* *
18888706 AAGAAAAGAAAAAACCTAATCTAAAAAATGAAAAGAA
1 AAGAAAAGAAAAAACCTAACCTAAAAAACGAAAAGAA
*
18888743 AAGAAAAG-AAAAACCTAACCTAAAACTACGAAAA
1 AAGAAAAGAAAAAACCTAACCTAAAA-AACGAAAA
18888777 CTAAAGAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.68, C:0.13, G:0.10, T:0.10
Consensus pattern (37 bp):
AAGAAAAGAAAAAACCTAACCTAAAAAACGAAAAGAA
Found at i:18888783 original size:37 final size:36
Alignment explanation
Indices: 18888706--18888791 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
18888696 CTATCCTAAG
* * *
18888706 AAGAAAAGAAAAAACCTAATCTAAAAAATGAAAAGAA
1 AAGAAAAG-AAAAACCTAACCTAAAAAACGAAAACAA
* *
18888743 AAGAAAAGAAAAACCTAACCTAAAACTACGAAAACTA
1 AAGAAAAGAAAAACCTAACCTAAAA-AACGAAAACAA
*
18888780 AAG-AGAGAAAAA
1 AAGAAAAGAAAAA
18888792 TTGTTAGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 24 0.57
37 18 0.43
ACGTcount: A:0.67, C:0.12, G:0.12, T:0.09
Consensus pattern (36 bp):
AAGAAAAGAAAAACCTAACCTAAAAAACGAAAACAA
Found at i:18892430 original size:33 final size:32
Alignment explanation
Indices: 18892359--18892423 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
18892349 TAAGTAATAA
* *
18892359 ATATTAATTA-TTTATAAAATTTAATTAGAAT
1 ATATAAATTATTTTATAAAATTTAAATAGAAT
* *
18892390 ATATAAATTATTTTTTAAATATTTAAATATAAT
1 ATATAAATTATTTTATAAA-ATTTAAATAGAAT
18892423 A
1 A
18892424 ATTAAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 9 0.32
32 7 0.25
33 12 0.43
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (32 bp):
ATATAAATTATTTTATAAAATTTAAATAGAAT
Found at i:18893994 original size:13 final size:13
Alignment explanation
Indices: 18893976--18894004 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18893966 ATGCCGGGTA
18893976 GATTACATATTAG
1 GATTACATATTAG
18893989 GATTACATATTAG
1 GATTACATATTAG
18894002 GAT
1 GAT
18894005 CAAAAGTCCT
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:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (13 bp):
GATTACATATTAG
Found at i:18898702 original size:18 final size:17
Alignment explanation
Indices: 18898679--18898712 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18898669 AGATATTTAT
*
18898679 AACATTTTTTTCAAAGAA
1 AACATTTGTTT-AAAGAA
18898697 AACATTTGTTTAAAGA
1 AACATTTGTTTAAAGA
18898713 TTTATCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
AACATTTGTTTAAAGAA
Found at i:18899531 original size:40 final size:40
Alignment explanation
Indices: 18899477--18899582 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
18899467 GTTTGGATAA
* *
18899477 AAAAAGCCGCTAAAGATCGAGCATTAGTAGCGCTTCT-TGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTT-TATGG
* * *
18899517 AAAACGCCGCTAAAGATTGAGTATTAGCGGCGCTTTATGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTTTATGG
*
18899557 AAAACGCCGCTAAA-AT-AAGCATTAGC
1 AAAACGCCGCTAAAGATCGAGCATTAGC
18899583 CGCGTTTCCC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 8 0.14
39 3 0.05
40 47 0.81
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTTTATGG
Found at i:18899688 original size:41 final size:41
Alignment explanation
Indices: 18899629--18899995 Score: 410
Period size: 41 Copynumber: 9.0 Consensus size: 41
18899619 CGAGGATATT
*
18899629 GCGGCGTTTTT-GAGAAAGCGCCGCTAATGCTTAGGGCTTTA
1 GCGGCGTTTTTGGA-AAAGCGCCGCTAATGCTCAGGGCTTTA
* ** * *
18899670 GTGGCGTTTTTGGAAAAGCGTTGCTAATACTAAGGGCTTTA
1 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGCTTTA
* * *
18899711 GCAGCATTTTTGGGAAAGCGCCGCTAATGCTCAGGGCTTTA
1 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGCTTTA
* * *
18899752 GCAGCGTTTTTAGGAATA-TGCCGCTAATGCTCAGGGCTTTA
1 GCGGCGTTTTT-GGAAAAGCGCCGCTAATGCTCAGGGCTTTA
* *
18899793 GCGGCGTTTTTGG-GAAGCGCCGCTAATGCTCAGGGATTTA
1 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGCTTTA
* *
18899833 ACGGCGTTTTTGG-AAAGCGTCGCTAATGCTCAGGGCTTTA
1 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGCTTTA
18899873 GGCGGCG-TTTTGGAAAAGCGCCGCTAATGCTCAGGGCTTTTA
1 -GCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGC-TTTA
* ***
18899915 GCGGCGTTTTT-GATAAAACGCCG-TGAATGCTC-GATTTTTA
1 GCGGCGTTTTTGGA-AAAGCGCCGCT-AATGCTCAGGGCTTTA
* *
18899955 GCGGCGTTTTCT-AAAAAGCGCCGCTAATGCTCAGGGATTTA
1 GCGGCGTTTT-TGGAAAAGCGCCGCTAATGCTCAGGGCTTTA
18899996 AAATAATTTA
Statistics
Matches: 277, Mismatches: 37, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.00
40 94 0.34
41 153 0.55
42 29 0.10
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (41 bp):
GCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGCTTTA
Found at i:18900266 original size:21 final size:20
Alignment explanation
Indices: 18900240--18900279 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
18900230 TGTGTTAAGG
18900240 GTTTATAGTTGTAGGGTTTAA
1 GTTTATAGTT-TAGGGTTTAA
*
18900261 GTTTATGGTTTAGGGTTTA
1 GTTTATAGTTTAGGGTTTA
18900280 GATTAACTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (20 bp):
GTTTATAGTTTAGGGTTTAA
Found at i:18900278 original size:14 final size:14
Alignment explanation
Indices: 18900182--18900280 Score: 51
Period size: 14 Copynumber: 7.0 Consensus size: 14
18900172 TAGGGGTTAT
*
18900182 GGTTTATGGTTTAT
1 GGTTTATGGTTTAG
* * *
18900196 GGTTTAAAGG-CTGG
1 GGTTT-ATGGTTTAG
*
18900210 GGTTTAAGGTTTAG
1 GGTTTATGGTTTAG
*
18900224 AGG-TTATGTGTTAAG
1 -GGTTTATG-GTTTAG
*
18900239 GGTTTATAGTTGTAG
1 GGTTTATGGTT-TAG
* *
18900254 GGTTTA-AGTTTAT
1 GGTTTATGGTTTAG
*
18900267 GGTTTAGGGTTTAG
1 GGTTTATGGTTTAG
18900281 ATTAACTAGT
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
13 12 0.18
14 31 0.48
15 22 0.34
ACGTcount: A:0.20, C:0.01, G:0.34, T:0.44
Consensus pattern (14 bp):
GGTTTATGGTTTAG
Found at i:18900556 original size:14 final size:15
Alignment explanation
Indices: 18900526--18900579 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 15
18900516 AATAATTATA
18900526 TATGGATTTAAGGAT
1 TATGGATTTAAGGAT
*
18900541 TATGGA-TTAGGGAT
1 TATGGATTTAAGGAT
*
18900555 TATGG-TTTAAGGGT
1 TATGGATTTAAGGAT
18900569 TA-GGATTTAAG
1 TATGGATTTAAG
18900580 ATTTAAGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 2 0.06
14 26 0.76
15 6 0.18
ACGTcount: A:0.30, C:0.00, G:0.31, T:0.39
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:18900572 original size:21 final size:22
Alignment explanation
Indices: 18900529--18900593 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
18900519 AATTATATAT
* *
18900529 GGATTTAAGGA-TTATGGATTAG
1 GGATTTAA-GATTTAAGGGTTAG
* *
18900551 GGA-TTATGGTTTAAGGGTTA-
1 GGATTTAAGATTTAAGGGTTAG
18900571 GGATTTAAGATTTAAGGGTTAG
1 GGATTTAAGATTTAAGGGTTAG
18900593 G
1 G
18900594 AGTTAGGGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.12
21 26 0.76
22 4 0.12
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (22 bp):
GGATTTAAGATTTAAGGGTTAG
Found at i:18910952 original size:22 final size:22
Alignment explanation
Indices: 18910927--18910973 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
18910917 TTATGCTTCT
*
18910927 ATTTTTATAATATAAT-TAGTTA
1 ATTTATATAAT-TAATATAGTTA
*
18910949 ATTTATATAATTAATATGGTTA
1 ATTTATATAATTAATATAGTTA
18910971 ATT
1 ATT
18910974 ATTTCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
ATTTATATAATTAATATAGTTA
Found at i:18912221 original size:6 final size:6
Alignment explanation
Indices: 18912210--18912234 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18912200 CATGAACACC
18912210 ATTTTA ATTTTA ATTTTA ATTTTA A
1 ATTTTA ATTTTA ATTTTA ATTTTA A
18912235 ATATTTTAAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:18913692 original size:57 final size:57
Alignment explanation
Indices: 18913601--18913720 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 57
18913591 TAGATAATAA
* * * * *
18913601 AAAAAATTTAGACCTCAATATAGAAACAATTGTCAAATTCAAGTACCAATTTAGACC
1 AAAAAATTTAAACCTCAATATAGAAACAATTGTCAAATTAAAATACCAACTTAAACC
*
18913658 AAAAAATTTAAACCAT-AATAT-GAGAAC-ATCTGTCAAATTAAAATACTAACTTAAACC
1 AAAAAATTTAAACC-TCAATATAGA-AACAAT-TGTCAAATTAAAATACCAACTTAAACC
18913715 AAAAAA
1 AAAAAA
18913721 AAAAAATCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
56 4 0.07
57 49 0.91
58 1 0.02
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.25
Consensus pattern (57 bp):
AAAAAATTTAAACCTCAATATAGAAACAATTGTCAAATTAAAATACCAACTTAAACC
Found at i:18918901 original size:13 final size:13
Alignment explanation
Indices: 18918883--18918907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18918873 AATTTGATAT
18918883 GTTTATGGTTGAA
1 GTTTATGGTTGAA
18918896 GTTTATGGTTGA
1 GTTTATGGTTGA
18918908 TTTGGTACAC
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:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (13 bp):
GTTTATGGTTGAA
Found at i:18937670 original size:46 final size:45
Alignment explanation
Indices: 18937603--18937892 Score: 359
Period size: 46 Copynumber: 6.6 Consensus size: 45
18937593 TTTGAGTACT
* *
18937603 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
18937649 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ATTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
18937685 TCTGATCAAGTGAAAAAGTAATAAGTGTTAGCCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
18937731 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
18937777 TCTGATCAAGTGACAAATTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
* *
18937823 TCTGATCAAGTGAAAAAGTGATAAGTGATAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
18937868 TCTGATCAAG-G-ACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
18937893 ATCATACGTA
Statistics
Matches: 216, Mismatches: 17, Indels: 25
0.84 0.07 0.10
Matches are distributed among these distances:
36 27 0.12
38 1 0.00
39 1 0.00
40 3 0.01
41 1 0.00
42 4 0.02
43 15 0.07
44 2 0.01
45 23 0.11
46 139 0.64
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:18944774 original size:29 final size:29
Alignment explanation
Indices: 18944700--18944775 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
18944690 ATAATATATC
* *
18944700 AATT-AAAATGTTAACATAAATTTAAATA
1 AATTAAAAATGTTAAAATAAATTGAAATA
* * * *
18944728 AATTAACAATATTGAAATAAGTTGAAATA
1 AATTAAAAATGTTAAAATAAATTGAAATA
18944757 AATTAAAAATGTTAAAATA
1 AATTAAAAATGTTAAAATA
18944776 TTTGAAAGAG
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 4 0.11
29 34 0.89
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.33
Consensus pattern (29 bp):
AATTAAAAATGTTAAAATAAATTGAAATA
Found at i:18948279 original size:23 final size:22
Alignment explanation
Indices: 18948236--18948279 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
18948226 TTTCAAGTCA
18948236 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
18948259 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
18948280 TTAATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:18948476 original size:23 final size:23
Alignment explanation
Indices: 18948378--18948476 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
18948368 ATAAGTGTCA
*
18948378 CACTAATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
18948401 CACTGAAATGTAGCCAAATCTAC
1 CACTGATATGTAGCCGAAGCTAC
18948424 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
18948447 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
18948470 CATTGAT
1 CACTGAT
18948477 CAATAACACT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:18948970 original size:30 final size:30
Alignment explanation
Indices: 18948922--18948980 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
18948912 TCCTTGACTC
*
18948922 AAACTTTTGCAAAATTACAATTTTTCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * * *
18948952 AAACTTTTTCATATTTACACTTTTGCCCC
1 AAACTTTTGCAAAATTACAATTTTGCCCC
18948981 AAAGCTCGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.03, T:0.42
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:18952545 original size:41 final size:41
Alignment explanation
Indices: 18952500--18952603 Score: 174
Period size: 41 Copynumber: 2.5 Consensus size: 41
18952490 GATTTTATAT
18952500 CTAGCAGGCTAAGTGCCGGTGATCAGAATCAGGT-TATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCAGAATCA-GTCTATAAAC
* *
18952541 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGTCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCAGAATCAGTCTATAAAC
18952582 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
18952604 ATATGTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 2 0.03
41 58 0.97
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCAGAATCAGTCTATAAAC
Found at i:18954728 original size:3 final size:3
Alignment explanation
Indices: 18954720--18954760 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
18954710 TCCAGGCTTC
18954720 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
18954761 GGTGAGTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:18960099 original size:15 final size:15
Alignment explanation
Indices: 18960081--18960111 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18960071 AAGGTTTTTT
18960081 TAAACCTTATTAAAC
1 TAAACCTTATTAAAC
18960096 TAAACCTTATTAAAC
1 TAAACCTTATTAAAC
18960111 T
1 T
18960112 TCATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAACCTTATTAAAC
Found at i:18966378 original size:16 final size:15
Alignment explanation
Indices: 18966356--18966410 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
18966346 TAATTGTTAT
18966356 TATCAATAATTTCAA
1 TATCAATAATTTCAA
*
18966371 TATCCAATAAGTTTAAAA
1 TAT-CAATAA-TTT-CAA
*
18966389 AAT-AATAATTTCAA
1 TATCAATAATTTCAA
18966403 TATCAATA
1 TATCAATA
18966411 TCCAACCAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 4 0.12
15 10 0.31
16 11 0.34
17 3 0.09
18 4 0.12
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (15 bp):
TATCAATAATTTCAA
Found at i:18970343 original size:38 final size:39
Alignment explanation
Indices: 18970301--18970378 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
18970291 TTTCAAGCGT
*
18970301 AGTTTAATTTATAATTTTATGAT-TTTTTATTATTTGTA
1 AGTTTAATTTATAATTTTATGATACTTTTATTATTTGTA
18970339 AGTTTAATTTATAATTTTATGATACTTTTATTATTTGTA
1 AGTTTAATTTATAATTTTATGATACTTTTATTATTTGTA
18970378 A
1 A
18970379 ATTCTTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 23 0.61
39 15 0.39
ACGTcount: A:0.31, C:0.01, G:0.08, T:0.60
Consensus pattern (39 bp):
AGTTTAATTTATAATTTTATGATACTTTTATTATTTGTA
Found at i:18971533 original size:12 final size:13
Alignment explanation
Indices: 18971500--18971537 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
18971490 TATTTAAGGT
18971500 TAATTAAGTTAATA
1 TAATTAA-TTAATA
18971514 TTAATTAATTAATA
1 -TAATTAATTAATA
18971528 -AATTAATTAA
1 TAATTAATTAA
18971538 CTAGTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
TAATTAATTAATA
Found at i:18975142 original size:36 final size:36
Alignment explanation
Indices: 18975095--18975184 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
18975085 TATTTCTAAT
* * *
18975095 TTTATCCGACTAGTGCT-AGGCGCAAAATATTATCGG
1 TTTATCCGACTAGTGCTGA-GCACAAAACATTATCGA
*
18975131 TTTATCCGACTAGCGCTGAGCACAAAACATTATCGA
1 TTTATCCGACTAGTGCTGAGCACAAAACATTATCGA
* *
18975167 TTTATTCAACTAGTGCTG
1 TTTATCCGACTAGTGCTG
18975185 GGTACACATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
36 45 0.98
37 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (36 bp):
TTTATCCGACTAGTGCTGAGCACAAAACATTATCGA
Found at i:18975309 original size:76 final size:75
Alignment explanation
Indices: 18975127--18975328 Score: 233
Period size: 76 Copynumber: 2.6 Consensus size: 75
18975117 CAAAATATTA
* * * * *
18975127 TCGGTTTATCCGACTAGCGCTGAGCACAAAACATTATCGATTTATTCAACTAGTGCTGGGTACAC
1 TCGGTTTATCCGACTAGCGCT-AGCACAAAATATTGTTGGTTTATTCAACTAGTGCTGGGCACAC
*
18975192 ATTTGACATGG
65 ATTTGACATCG
* * * * * *
18975203 TCAGTTTATCTGACTAGCACTGGGCACAAAATATTGTTGGTTTATTCGACTAGTGTTGGGCACAC
1 TCGGTTTATCCGACTAGCGCT-AGCACAAAATATTGTTGGTTTATTCAACTAGTGCTGGGCACAC
18975268 ATTTGACATCG
65 ATTTGACATCG
* *
18975279 TCGGTTTATCCGACTAGCGCTAGTCGCAAAATTTTGTTACGGTTTATTCA
1 TCGGTTTATCCGACTAGCGCTAG-CACAAAATATTGTT--GGTTTATTCA
18975329 TCAAGCACTG
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
75 1 0.01
76 94 0.90
78 9 0.09
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (75 bp):
TCGGTTTATCCGACTAGCGCTAGCACAAAATATTGTTGGTTTATTCAACTAGTGCTGGGCACACA
TTTGACATCG
Found at i:18983755 original size:28 final size:28
Alignment explanation
Indices: 18983723--18983777 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
18983713 AAATATTATC
18983723 AAAATTTACAAAAAGGAAATTGAATATG
1 AAAATTTACAAAAAGGAAATTGAATATG
* *
18983751 AAAATTTATAAAAAGTAAATTGAATAT
1 AAAATTTACAAAAAGGAAATTGAATAT
18983778 CCGAATAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (28 bp):
AAAATTTACAAAAAGGAAATTGAATATG
Found at i:18995157 original size:27 final size:27
Alignment explanation
Indices: 18995116--18995167 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
18995106 GAAGAATAGC
18995116 TGGTAATGAATTTGTGTTATCTGGTCT
1 TGGTAATGAATTTGTGTTATCTGGTCT
*
18995143 TGGTAATGACA-TTGTGTTGTCTGGT
1 TGGTAATGA-ATTTGTGTTATCTGGT
18995168 TTTGATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.08, G:0.29, T:0.46
Consensus pattern (27 bp):
TGGTAATGAATTTGTGTTATCTGGTCT
Found at i:18996179 original size:16 final size:16
Alignment explanation
Indices: 18996158--18996226 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
18996148 TTTGGTTCGC
18996158 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
18996174 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
18996190 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
18996207 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
18996223 TGTA
1 TGTA
18996227 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:18996204 original size:33 final size:32
Alignment explanation
Indices: 18996158--18996226 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
18996148 TTTGGTTCGC
18996158 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
18996190 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
18996223 TGTA
1 TGTA
18996227 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:18996291 original size:44 final size:45
Alignment explanation
Indices: 18996207--18996297 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
18996197 GGATTAGAGG
* * *
18996207 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
18996252 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
18996296 TG
1 TG
18996298 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:18996549 original size:157 final size:157
Alignment explanation
Indices: 18996349--18996665 Score: 555
Period size: 157 Copynumber: 2.0 Consensus size: 157
18996339 TAGAATACCC
*
18996349 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
18996414 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAATA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA-A
18996479 ATATATAATTTAATAAAATTCTT-ATAA
130 ATATATAATTTAATAAAATTCTTAATAA
* *
18996506 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
18996571 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
18996636 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
18996663 TTA
1 TTA
18996666 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
156 24 0.16
157 128 0.84
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:18996636 original size:16 final size:16
Alignment explanation
Indices: 18996599--18996640 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
18996589 TTAATCATAT
*
18996599 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
18996615 TT-AAATATATTATAA
1 TTAAAATATATTATAA
18996630 TTAAAATATAT
1 TTAAAATATAT
18996641 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:18996647 original size:14 final size:15
Alignment explanation
Indices: 18996608--18996649 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
18996598 TTTAAACATA
*
18996608 ATTATTATTAAATAT
1 ATTATAATTAAATAT
18996623 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
18996637 A-TATAATTTAATA
1 ATTATAATTAAATA
18996650 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:18996736 original size:120 final size:121
Alignment explanation
Indices: 18996602--18996894 Score: 502
Period size: 120 Copynumber: 2.4 Consensus size: 121
18996592 ATCATATTTA
18996602 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
18996667 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA-GT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAATGTG
18996722 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
18996787 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
* * *
18996843 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
18996895 TAAAATAATT
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 3 0.02
120 160 0.97
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
Found at i:18996767 original size:14 final size:15
Alignment explanation
Indices: 18996728--18996769 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
18996718 AAGTAACATA
*
18996728 ATTATTATTAAATAT
1 ATTATAATTAAATAT
18996743 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
18996757 A-TATAATTTAATA
1 ATTATAATTAAATA
18996770 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:19000438 original size:6 final size:6
Alignment explanation
Indices: 19000429--19000457 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
19000419 TTGATGTTGG
19000429 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
19000458 TGGGGAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:19001116 original size:22 final size:23
Alignment explanation
Indices: 19001075--19001117 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19001065 ATCACCATTA
19001075 TTAAATATATTTATTTATTTAGT
1 TTAAATATATTTATTTATTTAGT
*
19001098 TTAAATATCTTT-TTTATTTA
1 TTAAATATATTTATTTATTTA
19001118 TCATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TTAAATATATTTATTTATTTAGT
Found at i:19001124 original size:22 final size:23
Alignment explanation
Indices: 19001076--19001125 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
19001066 TCACCATTAT
*
19001076 TAAATATATTTATTTATTTAGTT
1 TAAATATATTTATTTATTTAGTA
*
19001099 TAAATATCTTT-TTTATTTA-TCA
1 TAAATATATTTATTTATTTAGT-A
19001121 TAAAT
1 TAAAT
19001126 TACTATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 13 0.54
23 10 0.42
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (23 bp):
TAAATATATTTATTTATTTAGTA
Found at i:19001861 original size:21 final size:21
Alignment explanation
Indices: 19001835--19001892 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
19001825 CTCCAAAACA
*
19001835 AGGGAAAATGGGTTACAATTT
1 AGGGAAAATGGCTTACAATTT
**
19001856 AGGGAAAATATCTTACAATTT
1 AGGGAAAATGGCTTACAATTT
*
19001877 AGGGAAAATGTCTTAC
1 AGGGAAAATGGCTTAC
19001893 CCTTTCAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (21 bp):
AGGGAAAATGGCTTACAATTT
Found at i:19002311 original size:20 final size:20
Alignment explanation
Indices: 19002286--19002325 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19002276 AATATTTTCT
*
19002286 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
19002306 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
19002326 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:19002328 original size:34 final size:34
Alignment explanation
Indices: 19002274--19002339 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
19002264 CAAACACCAG
* *
19002274 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
19002309 AAAACATTTTCCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
19002340 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:19005641 original size:28 final size:26
Alignment explanation
Indices: 19005610--19005673 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
19005600 TTAAAGCACG
*
19005610 AAAGTATATATTAACATAAATATT-TTAA
1 AAAGTATATA--AAAATAAA-ATTGTTAA
19005638 AAAGTATCATAAAAATAAAATTGTTAA
1 AAAGTAT-ATAAAAATAAAATTGTTAA
19005665 AAA-TATATA
1 AAAGTATATA
19005674 GATAATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 3 0.09
26 6 0.18
27 14 0.42
28 7 0.21
29 3 0.09
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (26 bp):
AAAGTATATAAAAATAAAATTGTTAA
Found at i:19007165 original size:44 final size:44
Alignment explanation
Indices: 19007110--19007552 Score: 607
Period size: 44 Copynumber: 10.1 Consensus size: 44
19007100 AGAAACTAAA
* * * * **
19007110 CTTCCACCTATTCCGCTGTTGGTTAGGGAGATAGGACTTGTAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
19007154 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
* * * * *
19007198 CTTCCATCTATTCTACTGCTGGTTAGGGAGATAGGACGTACAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
*
19007242 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACATACAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
* * *
19007286 CTTCAACCTATTCCACTGTTGGTCAGGGAGATAGGGCATACAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
* *
19007330 CATCAACCTATTCCGCTGCTGGTCAGGGAGATAGGACTTACAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
* *
19007374 TTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACATACAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
*
19007418 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACATACAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
* * * * * **
19007462 ATTCCACATATTCCACTGCTGGTCAGAGAGATAGAACTTGTAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
* * * *
19007506 CTTCGACCTATTCCAATGCTGGTCAGGGATATAGGACTGACAAT
1 CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
19007550 CTT
1 CTT
19007553 TGATCTGCTT
Statistics
Matches: 353, Mismatches: 46, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 353 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (44 bp):
CTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAAT
Found at i:19007655 original size:43 final size:41
Alignment explanation
Indices: 19007602--19007815 Score: 121
Period size: 44 Copynumber: 4.9 Consensus size: 41
19007592 TATATTCAAC
19007602 CTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTATCTTCGAT
1 CTGCTCCGCTGCAACC-AGGGAGGCAAGGCT-GTATCTTCGAT
* * *
19007645 CTGCTTCGCTGTCAGTA-CAGGAAGGCAAGGTCTGCTATCTT-AAGT
1 CTGCTCCGCTG-CA--ACCAGGGAGGCAAGG-CTG-TATCTTCGA-T
* * *
19007690 TTGCTCCGCTACAACCGAGGGAGACAAGGCTGGTATCTTCGAT
1 CTGCTCCGCTGCAACC-AGGGAGGCAAGGCT-GTATCTTCGAT
** * * * *
19007733 CTGCTTCACG-T-CGATGCAGGAAGGCAAGATCTGCTATCTTCAAC
1 CTGC-TC-CGCTGC-AACCAGGGAGGCAAG-GCTG-TATCTTCGAT
* *
19007777 CTGCTCCACTACAACCGAGGGAGGCAAGGCTGGTATCTT
1 CTGCTCCGCTGCAACC-AGGGAGGCAAGGCT-GTATCTT
19007816 TAACCTGCTC
Statistics
Matches: 130, Mismatches: 22, Indels: 38
0.68 0.12 0.20
Matches are distributed among these distances:
42 2 0.02
43 47 0.36
44 60 0.46
45 20 0.15
46 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.27, T:0.24
Consensus pattern (41 bp):
CTGCTCCGCTGCAACCAGGGAGGCAAGGCTGTATCTTCGAT
Found at i:19007697 original size:88 final size:87
Alignment explanation
Indices: 19007578--19007815 Score: 311
Period size: 87 Copynumber: 2.7 Consensus size: 87
19007568 TCAGTACAAA
* * * * *
19007578 AAGGCAAGAT-TCGTTATATTCAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTATCTTC
1 AAGGCAAGATCT-GCTATCTTCAACCTGCTCCGCTACAACCGAGGGAGGCAAGGCTGGTATCTTC
*
19007642 GATCTGCTTCGCTGTC-AGTACAGG
65 GATCTGCTTCAC-GTCGA-TACAGG
* ** *
19007666 AAGGCAAGGTCTGCTATCTT-AAGTTTGCTCCGCTACAACCGAGGGAGACAAGGCTGGTATCTTC
1 AAGGCAAGATCTGCTATCTTCAA-CCTGCTCCGCTACAACCGAGGGAGGCAAGGCTGGTATCTTC
*
19007730 GATCTGCTTCACGTCGATGCAGG
65 GATCTGCTTCACGTCGATACAGG
*
19007753 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTGGTATCTT
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTACAACCGAGGGAGGCAAGGCTGGTATCTT
19007816 TAACCTGCTC
Statistics
Matches: 130, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
87 65 0.50
88 64 0.49
89 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (87 bp):
AAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTACAACCGAGGGAGGCAAGGCTGGTATCTTCG
ATCTGCTTCACGTCGATACAGG
Found at i:19007822 original size:43 final size:43
Alignment explanation
Indices: 19007596--19007831 Score: 149
Period size: 43 Copynumber: 5.4 Consensus size: 43
19007586 ATTCGTTATA
* * * *
19007596 TTCAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTATC
1 TTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTGGTATC
* * * * * * *
19007639 TTCGATCTGCTTCGCTGTCAGTA-C-AGGAAGGCAAGGTCTGCTATC
1 TTCAACCTGCTCCACT-ACA--ACCGAGGGAGGCAAGG-CTGGTATC
** * *
19007684 TT-AAGTTTGCTCCGCTACAACCGAGGGAGACAAGGCTGGTATC
1 TTCAA-CCTGCTCCACTACAACCGAGGGAGGCAAGGCTGGTATC
* * * * * * * *
19007727 TTCGATCTGCTTCACGT-CGA-TGCAGGAAGGCAAGATCTGCTATC
1 TTCAACCTGCTCCAC-TACAACCG-AGGGAGGCAAG-GCTGGTATC
19007771 TTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTGGTATC
1 TTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTGGTATC
*
19007814 TTTAACCTGCTCCACTAC
1 TTCAACCTGCTCCACTAC
19007832 TGCTTAGGGA
Statistics
Matches: 147, Mismatches: 33, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
42 2 0.01
43 66 0.45
44 59 0.40
45 19 0.13
46 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (43 bp):
TTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTGGTATC
Found at i:19007824 original size:87 final size:88
Alignment explanation
Indices: 19007548--19007815 Score: 328
Period size: 88 Copynumber: 3.1 Consensus size: 88
19007538 AGGACTGACA
* ** ** * *
19007548 ATCTTTGATCTGCTTCGTTGTCAGTACAAAAAGGCAAGAT-TCGTTATATTCAACCTGCTCCGCT
1 ATCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCT-GCTATCTTCAACCTGCTCCGCT
* * *
19007612 GCAACCTAGGGAGGCAAGGCTAGT
65 ACAACCGAGGGAGGCAAGGCTGGT
* * **
19007636 ATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGGTCTGCTATCTT-AAGTTTGCTCCGCT
1 ATCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAA-CCTGCTCCGCT
*
19007700 ACAACCGAGGGAGACAAGGCTGGT
65 ACAACCGAGGGAGGCAAGGCTGGT
* *
19007724 ATCTTCGATCTGCTTCAC-GTC-GATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 ATCTTCGATCTGCTTCACTGTCAG-TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCT
19007787 ACAACCGAGGGAGGCAAGGCTGGT
65 ACAACCGAGGGAGGCAAGGCTGGT
19007811 ATCTT
1 ATCTT
19007816 TAACCTGCTC
Statistics
Matches: 156, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 65 0.42
88 89 0.57
89 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (88 bp):
ATCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTA
CAACCGAGGGAGGCAAGGCTGGT
Found at i:19007850 original size:87 final size:86
Alignment explanation
Indices: 19007596--19007861 Score: 241
Period size: 87 Copynumber: 3.0 Consensus size: 86
19007586 ATTCGTTATA
* * * * * * * * *
19007596 TTCAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTATCTTCGATCTGCTTCGCTGTCAGT
1 TTCAACCTGCTCCACTACAACCGAGGGAGACAAGGCTGGTATCTTCAACCTGCTCCAC-GTCA-T
* * *
19007661 ACAGGAAGGCAAGGTCTGCTATC
64 GCAGGAAGGCAAGATCTGCCATC
** * * * *
19007684 TT-AAGTTTGCTCCGCTACAACCGAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCACGTCGAT
1 TTCAA-CCTGCTCCACTACAACCGAGGGAGACAAGGCTGGTATCTTCAACCTGCTCCACGTC-AT
*
19007748 GCAGGAAGGCAAGATCTGCTATC
64 GCAGGAAGGCAAGATCTGCCATC
* *
19007771 TTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTGGTATCTTTAACCTGCTCCAC-T-ACTG
1 TTCAACCTGCTCCACTACAACCGAGGGAGACAAGGCTGGTATCTTCAACCTGCTCCACGTCA-TG
* *
19007834 CTTAGGGAGGCCAGATCTGCCATC
65 C--AGGAAGGCAAGATCTGCCATC
19007858 TTCA
1 TTCA
19007862 CTGATCTGTT
Statistics
Matches: 152, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 3 0.02
86 1 0.01
87 96 0.63
88 51 0.34
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (86 bp):
TTCAACCTGCTCCACTACAACCGAGGGAGACAAGGCTGGTATCTTCAACCTGCTCCACGTCATGC
AGGAAGGCAAGATCTGCCATC
Found at i:19009147 original size:20 final size:20
Alignment explanation
Indices: 19009110--19009146 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
19009100 ATTTTTACTT
*
19009110 TTTTCATTCTTTATTTTTCA
1 TTTTCATTCTTCATTTTTCA
19009130 TTTTCATT-TTCATTTTT
1 TTTTCATTCTTCATTTTT
19009147 TTTGACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTCATTCTTCATTTTTCA
Found at i:19015223 original size:28 final size:29
Alignment explanation
Indices: 19015192--19015251 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
19015182 TTTAAAGCAC
*
19015192 AAAAGTATATATAAACATAAATATT-TTAA
1 AAAAGTATATATAAAAATAAA-ATTATTAA
19015221 AAAAGTATA-ATAAAAATAAAATTATTAA
1 AAAAGTATATATAAAAATAAAATTATTAA
19015249 AAA
1 AAA
19015252 TATATAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 3 0.10
28 17 0.59
29 9 0.31
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAGTATATATAAAAATAAAATTATTAA
Found at i:19015257 original size:28 final size:28
Alignment explanation
Indices: 19015192--19015262 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
19015182 TTTAAAGCAC
* *
19015192 AAAAGTATAT-ATAAACATAAATATTTT
1 AAAAATATATAATAAAAATAAATATTTT
19015219 AAAAA-AGTATAATAAAAATAAA-ATTATT
1 AAAAATA-TATAATAAAAATAAATATT-TT
19015247 AAAAATATATAGATAA
1 AAAAATATATA-ATAA
19015263 TATTAGATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 1 0.03
27 10 0.27
28 21 0.57
29 5 0.14
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAAATATATAATAAAAATAAATATTTT
Found at i:19017578 original size:12 final size:13
Alignment explanation
Indices: 19017561--19017590 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
19017551 TATTACATTC
19017561 AATTTGATA-TTT
1 AATTTGATATTTT
19017573 AATTTGATATTTT
1 AATTTGATATTTT
19017586 AATTT
1 AATTT
19017591 ATCATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
AATTTGATATTTT
Found at i:19017830 original size:14 final size:15
Alignment explanation
Indices: 19017810--19017844 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
19017800 TTGTATCTGT
19017810 TTTTTTTTTACAGAA
1 TTTTTTTTTACAGAA
19017825 TTTTTTTTTACAGAA
1 TTTTTTTTTACAGAA
19017840 TTTTT
1 TTTTT
19017845 AAAACTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (15 bp):
TTTTTTTTTACAGAA
Found at i:19017903 original size:34 final size:34
Alignment explanation
Indices: 19017865--19017932 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
19017855 ATGGCCCCTT
19017865 TTTAACTCATAAATACCAACTCATAAATAAGAAG
1 TTTAACTCATAAATACCAACTCATAAATAAGAAG
19017899 TTTAACTCATAAATACCAACTCATAAATAAGAAG
1 TTTAACTCATAAATACCAACTCATAAATAAGAAG
19017933 ATAATCACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.18, G:0.06, T:0.26
Consensus pattern (34 bp):
TTTAACTCATAAATACCAACTCATAAATAAGAAG
Found at i:19023046 original size:23 final size:23
Alignment explanation
Indices: 19023016--19023118 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
19023006 AGTGTTATTG
*
19023016 ATCAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* * ** *
19023039 ATCGGTGGTATCTTTGGCTATAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
19023062 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTACGGCTACAT
* **
19023085 ATCAGTGGTAACTTTGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
19023108 ATCAGT-GTAGC
1 ATCAGTGGTAGC
19023119 ACTTATGTGC
Statistics
Matches: 61, Mismatches: 19, Indels: 1
0.75 0.23 0.01
Matches are distributed among these distances:
22 4 0.07
23 57 0.93
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:19023093 original size:46 final size:46
Alignment explanation
Indices: 19023016--19023118 Score: 145
Period size: 46 Copynumber: 2.3 Consensus size: 46
19023006 AGTGTTATTG
* * *
19023016 ATCAGTGGTAGCTACGACTACATATCGGTGGTATCTTTGGCTATAT
1 ATCAGTGGTAGCTACGACTACATATCAGTGGTAACTTTGGCTACAT
* * *
19023062 TTCAGTGGTAGCTACGGCTACGTATCAGTGGTAACTTTGGCTACAT
1 ATCAGTGGTAGCTACGACTACATATCAGTGGTAACTTTGGCTACAT
19023108 ATCAGT-GTAGC
1 ATCAGTGGTAGC
19023119 ACTTATGTGC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 5 0.10
46 45 0.90
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTACGACTACATATCAGTGGTAACTTTGGCTACAT
Found at i:19024359 original size:49 final size:49
Alignment explanation
Indices: 19024295--19024483 Score: 288
Period size: 49 Copynumber: 3.9 Consensus size: 49
19024285 CAATAAGTGA
*
19024295 TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
* * *
19024344 TATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATCGGTATACGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
* * *
19024393 TATGTGATTAGGTGTAAGACCATAGTTGGGCTATGGCATCGGTATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
* * *
19024442 TATGTGATTACATGTAAGACCATAGTTGGACTATGGCATCGA
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGA
19024484 GAAAATAAGT
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 129 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (49 bp):
TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
Found at i:19029502 original size:25 final size:25
Alignment explanation
Indices: 19029458--19029507 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
19029448 AAACTAAAAT
19029458 TTTAAAATAAATTCACAAATTTAAA
1 TTTAAAATAAATTCACAAATTTAAA
19029483 TTTAAAA-AATATT-ACAAAATTTAAA
1 TTTAAAATAA-ATTCAC-AAATTTAAA
19029508 ATATTCTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (25 bp):
TTTAAAATAAATTCACAAATTTAAA
Found at i:19034106 original size:3 final size:3
Alignment explanation
Indices: 19034098--19034126 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19034088 TATGAGTAAT
19034098 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19034127 CCAATTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19036952 original size:24 final size:25
Alignment explanation
Indices: 19036899--19036954 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
19036889 AGAAATGGTG
*
19036899 AGTTTTAGTATTAAGTAATACGATG
1 AGTTTTAGTATTAAGTAATACGATA
* *
19036924 CGTTTTA-TATTAAGCTAA-ACGGTA
1 AGTTTTAGTATTAAG-TAATACGATA
19036948 AGTTTTA
1 AGTTTTA
19036955 ACAGGCTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (25 bp):
AGTTTTAGTATTAAGTAATACGATA
Found at i:19037226 original size:20 final size:21
Alignment explanation
Indices: 19037184--19037226 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19037174 GATTATTTTA
*
19037184 AAAACTCAATTGACTTAATCC
1 AAAACTCAATTGACTTAACCC
19037205 AAAA-TCAACTTGACTT-ACCC
1 AAAACTCAA-TTGACTTAACCC
19037225 AA
1 AA
19037227 TTGATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAACTCAATTGACTTAACCC
Found at i:19041980 original size:25 final size:25
Alignment explanation
Indices: 19041952--19042001 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
19041942 TACAGAATAT
19041952 TTTAAATTT-TGTAATATT-TTTTAAA
1 TTTAAATTTGTG-AAT-TTATTTTAAA
19041977 TTTAAATTTGTGAATTTATTTTAAA
1 TTTAAATTTGTGAATTTATTTTAAA
19042002 ATTTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.09
25 19 0.83
26 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTAAATTTGTGAATTTATTTTAAA
Found at i:19048222 original size:25 final size:24
Alignment explanation
Indices: 19048166--19048222 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
19048156 TGTTTCATAT
*
19048166 AACTCACCGTTTAGCTTAATATAA
1 AACTCACCATTTAGCTTAATATAA
*
19048190 AACGCACCATATTA-CTTAATACTAA
1 AACTCACCAT-TTAGCTTAATA-TAA
19048215 AACTCACC
1 AACTCACC
19048223 GTTTGGAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.28
Consensus pattern (24 bp):
AACTCACCATTTAGCTTAATATAA
Found at i:19053182 original size:23 final size:23
Alignment explanation
Indices: 19053148--19053207 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
19053138 TTCACACCAA
19053148 AATTT-GGACAGCATATATACAAC
1 AATTTAGG-CAGCATATATACAAC
19053171 AATTTAGGCAGCATATATACAAC
1 AATTTAGGCAGCATATATACAAC
*
19053194 ATATTGA-GCAGCAT
1 A-ATTTAGGCAGCAT
19053208 TTTTGCACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 28 0.82
24 6 0.18
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (23 bp):
AATTTAGGCAGCATATATACAAC
Found at i:19053452 original size:210 final size:211
Alignment explanation
Indices: 19053131--19053557 Score: 757
Period size: 210 Copynumber: 2.0 Consensus size: 211
19053121 CCAAACTAAA
* * * * *
19053131 CAGCAATTTCACACCAAAATTTGGACAGCATATATACAACAATTTAGGCAGCATATATACAACAT
1 CAGCATTTTCACACCAAAAATTGGACAGCATATATACAACAAATTAGGCAGCAAATATACAACAA
19053196 ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
66 ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
*
19053261 AACAAATTGAGTAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAA
131 AACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAA
19053326 TATACAACAAATTGAG
196 TATACAACAAATTGAG
* *
19053342 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATT-GGCAGCAAATATACAACAA
1 CAGCATTTTCACACCAAAAATTGGACAGCATATATACAACAAATTAGGCAGCAAATATACAACAA
*
19053406 ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGATAGCAATTACAC
66 ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
*
19053471 AACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAA
131 AACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAA
19053536 TATACAACAAATTGAG
196 TATACAACAAATTGAG
19053552 CAGCAT
1 CAGCAT
19053558 ATATATACAA
Statistics
Matches: 206, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
210 166 0.81
211 40 0.19
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (211 bp):
CAGCATTTTCACACCAAAAATTGGACAGCATATATACAACAAATTAGGCAGCAAATATACAACAA
ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
AACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAA
TATACAACAAATTGAG
Found at i:19053483 original size:20 final size:22
Alignment explanation
Indices: 19053233--19053549 Score: 112
Period size: 23 Copynumber: 13.6 Consensus size: 22
19053223 GGACAGCTTA
19053233 TACACAACAAATTGGACAGCAAT
1 TACACAACAAATTGGA-AGCAAT
* *
19053256 TACACAACAAATTGAGTAGCATTTT
1 TACACAACAAATTG-GAAGCA--AT
*
19053281 TACACCAA-AAATTGGACAGCTTAT
1 TACA-CAACAAATTGGA-AGC-AAT
* *
19053305 ATA-A-AACAAATTGGCAGCAAA
1 -TACACAACAAATTGGAAGCAAT
* * *
19053326 TATACAACAAATTGAGCAGCATTTT
1 TACACAACAAATTG-GAAGCA--AT
*
19053351 TACACCAA-AAATTGGACAGC-TT
1 TACA-CAACAAATTGGA-AGCAAT
* * *
19053373 ATATACAACAAATTGGCAGCAAA
1 -TACACAACAAATTGGAAGCAAT
* * *
19053396 TATACAACAAATTGAGCAGCATTTT
1 TACACAACAAATTG-GAAGCA--AT
* * *
19053421 TGCACCA-AAATTGGACAGC-TT
1 TACACAACAAATTGGA-AGCAAT
19053442 ATACACAACAAATTGGATAGCAAT
1 -TACACAACAAATTGGA-AGCAAT
* *
19053466 TACACAACAAATTGAGCAGCATTTT
1 TACACAACAAATTG-GAAGCA--AT
*
19053491 TACACCAA-AAATTGGACAGC-TT
1 TACA-CAACAAATTGGA-AGCAAT
* * *
19053513 ATATACAACAAATTGGCAGCAAA
1 -TACACAACAAATTGGAAGCAAT
*
19053536 TATACAACAAATTG
1 TACACAACAAATTG
19053550 AGCAGCATAT
Statistics
Matches: 228, Mismatches: 33, Indels: 67
0.70 0.10 0.20
Matches are distributed among these distances:
20 2 0.01
21 4 0.02
22 63 0.28
23 87 0.38
24 17 0.07
25 46 0.20
26 9 0.04
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (22 bp):
TACACAACAAATTGGAAGCAAT
Found at i:19053574 original size:70 final size:70
Alignment explanation
Indices: 19053131--19053557 Score: 651
Period size: 70 Copynumber: 6.1 Consensus size: 70
19053121 CCAAACTAAA
* * * * * * *
19053131 CAGCAATTTCACACCAAAATTTGGACAGCATATATACAACAATTTAGGCAGCATATATACAACAT
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATT-GGCAGCAAATATACAACAA
19053196 ATTGAG
65 ATTGAG
* * * *
19053202 CAGCATTTTTGCACC-AAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACACAACAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGG-CAGCAAATATACAACAA
19053266 ATTGAG
65 ATTGAG
* *
19053272 TAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
19053337 TTGAG
66 TTGAG
19053342 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
19053407 TTGAG
66 TTGAG
* * * * *
19053412 CAGCATTTTTGCACC-AAAATTGGACAGCTTATACACAACAAATTGGATAGCAATTACACAACAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGG-CAGCAAATATACAACAA
19053476 ATTGAG
65 ATTGAG
19053482 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
19053547 TTGAG
66 TTGAG
19053552 CAGCAT
1 CAGCAT
19053558 ATATATACAA
Statistics
Matches: 323, Mismatches: 29, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
69 32 0.10
70 220 0.68
71 71 0.22
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (70 bp):
CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
TTGAG
Found at i:19054343 original size:28 final size:27
Alignment explanation
Indices: 19054311--19054408 Score: 124
Period size: 28 Copynumber: 3.5 Consensus size: 27
19054301 TTTAATAAGT
* *
19054311 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCT-TATAATTAAAC
* *
19054339 TCGCACACTTAGTGCTTTTCCATTAAAC
1 TCGCACACTTAGTGCTTAT-AATTAAAC
*
19054367 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGC-TTATAATTAAAC
19054395 TCGCACACTTAGTG
1 TCGCACACTTAGTG
19054409 TCGAAAGTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
27 1 0.02
28 58 0.95
29 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
TCGCACACTTAGTGCTTATAATTAAAC
Found at i:19057176 original size:29 final size:29
Alignment explanation
Indices: 19057130--19057192 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
19057120 TGGTGCCTTT
*
19057130 GAACCAATAACTCAGATA-TCACTTGGTTC
1 GAACCAACAACTCAGATACT-ACTTGGTTC
* *
19057159 GAACCAACAGCTCGGATACTACTTGGTTC
1 GAACCAACAACTCAGATACTACTTGGTTC
*
19057188 CAACC
1 GAACC
19057193 TTGGCTCGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (29 bp):
GAACCAACAACTCAGATACTACTTGGTTC
Found at i:19065420 original size:23 final size:23
Alignment explanation
Indices: 19065394--19065442 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
19065384 TAATGACATA
19065394 AAAATGAAAATTTAAATTATTCC
1 AAAATGAAAATTTAAATTATTCC
19065417 AAAATGAAAATTTAAATTATTCC
1 AAAATGAAAATTTAAATTATTCC
19065440 AAA
1 AAA
19065443 TTAAAACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATGAAAATTTAAATTATTCC
Found at i:19070982 original size:2 final size:2
Alignment explanation
Indices: 19070940--19070969 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19070930 TTAGAATGGC
*
19070940 CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19070970 TTTTCATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19072016 original size:59 final size:60
Alignment explanation
Indices: 19071945--19072131 Score: 227
Period size: 59 Copynumber: 3.0 Consensus size: 60
19071935 TTATAAAATT
19071945 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTACTTCATTTAA
1 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTACTTCATTTAA
*
19072005 AA-AAATTGTTTATAATTAAAAAATTATGCCACCTATATTT-AAAATTTACTTCATTTTTCAAAA
1 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTACTTCA---TT-----
19072068 AAATAA
58 ---TAA
*
19072074 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAACAATTAAC-TCATTT
1 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATT-ACTTCATTT
19072132 CTATACTCAG
Statistics
Matches: 110, Mismatches: 3, Indels: 28
0.78 0.02 0.20
Matches are distributed among these distances:
58 12 0.11
59 38 0.35
60 3 0.03
61 2 0.02
68 2 0.02
69 5 0.05
70 38 0.35
71 8 0.07
72 2 0.02
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.40
Consensus pattern (60 bp):
AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTACTTCATTTAA
Found at i:19072830 original size:19 final size:20
Alignment explanation
Indices: 19072808--19072847 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
19072798 GAAGATAAAA
*
19072808 TAAAATATAAAAG-AAATGG
1 TAAAAAATAAAAGAAAATGG
19072827 TAAAAAATAAAAGAAAATGG
1 TAAAAAATAAAAGAAAATGG
19072847 T
1 T
19072848 TTTTTTGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
TAAAAAATAAAAGAAAATGG
Found at i:19076864 original size:40 final size:40
Alignment explanation
Indices: 19076812--19076925 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
19076802 TGGCGTTTGG
*
19076812 ACAAAAAACGCCGCTAAAAATCGAGCATTAGTGGCGCTTT
1 ACAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
* * * *
19076852 ACACAAAACGCCGCTAAAGATCGAGCTTTAGCGGCGCTAT
1 ACAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
* *
19076892 -CAGAAACCGCCGCTAAAAAT-GAGCATTAGCGGCG
1 ACAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCG
19076926 TTTTTTGTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
38 13 0.20
39 17 0.26
40 35 0.54
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (40 bp):
ACAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
Found at i:19077402 original size:14 final size:14
Alignment explanation
Indices: 19077385--19077421 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19077375 GGGTTTAATA
19077385 TATATGATTTAGGG
1 TATATGATTTAGGG
*
19077399 TATATGATTTGGGG
1 TATATGATTTAGGG
19077413 TATATGATT
1 TATATGATT
19077422 AATTTAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (14 bp):
TATATGATTTAGGG
Found at i:19083457 original size:43 final size:43
Alignment explanation
Indices: 19083235--19083530 Score: 218
Period size: 43 Copynumber: 6.7 Consensus size: 43
19083225 GTTAATGTTA
* * * ** *
19083235 TAGCGGCGTTTTTAGTAGAAGCATCGCTAAAGGTCATGAGT-TT
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTG-GTCTT
* *
19083278 TAGCGGCG-TTTTGGGTAAAAGCGTCGCTAAAGGTATTGGTCTT
1 TAGCGGCGTTTTTGGG-AAAAGCGCCGCTAAAGGTCTTGGTCTT
* * * * * * * *
19083321 CAGTGGTGATTTTAGAAAAAGCGTCGCTAAAGGTATTGGTCTT
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
* * ** * ***
19083364 TAGCGGCGATTCTGCAAAAAGCATCGCTAAAGCTAAAGGTCCAAGTCTT
1 TAGCGGCGTTTTTGGGAAAAG---CGC---CGCTAAAGGTCTTGGTCTT
*
19083413 TAGCGGCGTTTTTGGGAAAAGCGCCACTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
* * *
19083456 TAGCGGCGTTTGTGGGACAAGCGCCGCTAAAGGTCTTGGTATT
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
*** *
19083499 TAGCGGCGTTTTTTTAAAAAGCGCTGCTAAAG
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAG
19083531 TTAGCGACGC
Statistics
Matches: 202, Mismatches: 42, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
42 7 0.03
43 154 0.76
44 5 0.02
46 5 0.02
49 31 0.15
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
Found at i:19083530 original size:135 final size:134
Alignment explanation
Indices: 19083260--19083506 Score: 320
Period size: 135 Copynumber: 1.8 Consensus size: 134
19083250 TAGAAGCATC
* * *
19083260 GCTAAAGGTCATGAGTTTTAGCGGCGTTTTGGGTAAAAGCGTCGCTAAAGGTATTGGTCTTCAGT
1 GCTAAAGGTCA-GAGTTTTAGCGGCGTTTTGGGTAAAAGCGCCACTAAAGGTATTGGTCTTCAGC
* * *
19083325 GGTGATTTTAGAAAAAGCGTCGCTAAAGGTATTGGTCTTTAGCGGCGATTCTGCAAAAAGCATCG
65 GGCGATTTTAGAAAAAGCGCCGCTAAAGGTATTGGTATTTAGCGGCGATTCTGCAAAAAGCATCG
19083390 CTAAA
130 CTAAA
* *
19083395 GCTAAAGGTCCA-AGTCTTTAGCGGCGTTTTTGGG-AAAAGCGCCACTAAAGGTCTTGGTCTTTA
1 GCTAAAGGT-CAGAGT-TTTAGCGGCG-TTTTGGGTAAAAGCGCCACTAAAGGTATTGGTCTTCA
* * * *
19083458 GCGGCG-TTTGTGGGACAAGCGCCGCTAAAGGTCTTGGTATTTAGCGGCG
63 GCGGCGATTT-TAGAAAAAGCGCCGCTAAAGGTATTGGTATTTAGCGGCG
19083507 TTTTTTTAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
134 6 0.06
135 81 0.84
136 9 0.09
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (134 bp):
GCTAAAGGTCAGAGTTTTAGCGGCGTTTTGGGTAAAAGCGCCACTAAAGGTATTGGTCTTCAGCG
GCGATTTTAGAAAAAGCGCCGCTAAAGGTATTGGTATTTAGCGGCGATTCTGCAAAAAGCATCGC
TAAA
Found at i:19086132 original size:16 final size:16
Alignment explanation
Indices: 19086107--19086247 Score: 92
Period size: 18 Copynumber: 8.3 Consensus size: 16
19086097 CGAGAAATTT
*
19086107 TTTTTAAAACACGATAA
1 TTTTTGAAACACGA-AA
19086124 -TTTTGAAACAC-AATA
1 TTTTTGAAACACGAA-A
19086139 TTTTTTGAAGACACGGAAA
1 -TTTTTGAA-ACAC-GAAA
*
19086158 TTTTTTAAACA-GAGGAA
1 TTTTTGAAACACGA--AA
19086175 TTTTTTGAAACACGAAA
1 -TTTTTGAAACACGAAA
* *
19086192 CTTTTGAAACATGAAAAA
1 TTTTTGAAACACG--AAA
*
19086210 TTTTTGAAAACATGGAAA
1 TTTTTG-AAACA-CGAAA
*
19086228 -TTTTGAAACACGAGA
1 TTTTTGAAACACGAAA
19086243 TTTTT
1 TTTTT
19086248 TAAAAGGACG
Statistics
Matches: 100, Mismatches: 9, Indels: 31
0.71 0.06 0.22
Matches are distributed among these distances:
14 1 0.01
15 7 0.07
16 30 0.30
17 19 0.19
18 32 0.32
19 8 0.08
20 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (16 bp):
TTTTTGAAACACGAAA
Found at i:19086144 original size:17 final size:16
Alignment explanation
Indices: 19086124--19086202 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 16
19086114 AACACGATAA
19086124 TTTTGAAACACAATATT
1 TTTTGAAACACAA-ATT
19086141 TTTTGAAGACACGGAAATT
1 TTTTGAA-ACAC--AAATT
*
19086160 TTTT-AAACAGAGGAATT
1 TTTTGAAACACA--AATT
*
19086177 TTTTGAAACACGAAA-C
1 TTTTGAAACAC-AAATT
19086193 TTTTGAAACA
1 TTTTGAAACA
19086203 TGAAAAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
15 1 0.02
16 10 0.19
17 20 0.38
18 11 0.21
19 8 0.15
20 2 0.04
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (16 bp):
TTTTGAAACACAAATT
Found at i:19086144 original size:34 final size:34
Alignment explanation
Indices: 19086106--19086252 Score: 113
Period size: 35 Copynumber: 4.3 Consensus size: 34
19086096 ACGAGAAATT
*
19086106 TTTTTTAAAACACGATAA-TTTTGAAACACAA-TA
1 TTTTTTAAAACACGA-AACTTTTGAAACACAAGAA
* * * * *
19086139 TTTTTTGAAGACACGGAAATTTTTTAAACAGAGGAA
1 TTTTTT-AAAACAC-GAAACTTTTGAAACACAAGAA
* * *
19086175 TTTTTTGAAACACGAAACTTTTGAAACATGAAAAA
1 TTTTTTAAAACACGAAACTTTTGAAACA-CAAGAA
* * *
19086210 TTTTTGAAAACATGGAAA-TTTTGAAACACGAG-A
1 TTTTTTAAAACA-CGAAACTTTTGAAACACAAGAA
19086243 TTTTTTAAAA
1 TTTTTTAAAA
19086253 GGACGTATCG
Statistics
Matches: 90, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
33 16 0.18
34 22 0.24
35 41 0.46
36 11 0.12
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (34 bp):
TTTTTTAAAACACGAAACTTTTGAAACACAAGAA
Found at i:19086168 original size:35 final size:32
Alignment explanation
Indices: 19086106--19086248 Score: 110
Period size: 34 Copynumber: 4.2 Consensus size: 32
19086096 ACGAGAAATT
*
19086106 TTTTTTAAAACAC-GATAATTTTGAAACACAATA
1 TTTTTTGAAACACGGA-AATTTTGAAACACAA-A
* *
19086139 TTTTTTGAAGACACGGAAATTTTTTAAACAGAGGAA
1 TTTTTTGAA-ACACGGAAA-TTTTGAAACACA--AA
*
19086175 TTTTTTGAAACAC-GAAACTTTTGAAACATGAAAA
1 TTTTTTGAAACACGGAAA-TTTTGAAACA--CAAA
* * *
19086209 ATTTTTGAAAACATGGAAATTTTGAAACACGAGA
1 TTTTTTG-AAACACGGAAATTTTGAAACAC-AAA
19086243 TTTTTT
1 TTTTTT
19086249 AAAAGGACGT
Statistics
Matches: 89, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
33 8 0.09
34 34 0.38
35 31 0.35
36 15 0.17
37 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (32 bp):
TTTTTTGAAACACGGAAATTTTGAAACACAAA
Found at i:19086248 original size:17 final size:17
Alignment explanation
Indices: 19086106--19086248 Score: 71
Period size: 16 Copynumber: 8.4 Consensus size: 17
19086096 ACGAGAAATT
* *
19086106 TTTTTTAAAACACGATA
1 TTTTTTGAAACACGAGA
* * *
19086123 -ATTTTGAAACACAATA
1 TTTTTTGAAACACGAGA
*
19086139 TTTTTTGAAGACACGGAAA
1 TTTTTTGAA-ACAC-GAGA
19086158 TTTTTT-AAACA-GAGGAA
1 TTTTTTGAAACACGA-G-A
19086175 TTTTTTGAAACACGA-A
1 TTTTTTGAAACACGAGA
** * *
19086191 ACTTTTGAAACATGAAAA
1 TTTTTTGAAACACG-AGA
* *
19086209 ATTTTTGAAAACATG-GA
1 TTTTTTG-AAACACGAGA
**
19086226 AATTTTGAAACACGAGA
1 TTTTTTGAAACACGAGA
19086243 TTTTTT
1 TTTTTT
19086249 AAAAGGACGT
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
15 2 0.02
16 31 0.31
17 31 0.31
18 18 0.18
19 17 0.17
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (17 bp):
TTTTTTGAAACACGAGA
Found at i:19086595 original size:12 final size:13
Alignment explanation
Indices: 19086571--19086603 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
19086561 AAATTGAATT
19086571 AAAT-TAAATTAA
1 AAATATAAATTAA
19086583 AAATATAAA-TAA
1 AAATATAAATTAA
19086595 AAATATAAA
1 AAATATAAA
19086604 AATGCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATATAAATTAA
Found at i:19086741 original size:10 final size:11
Alignment explanation
Indices: 19086721--19086761 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
19086711 GGTTTTTTCC
19086721 TTTTTCTTTTT
1 TTTTTCTTTTT
19086732 TTTTTCTTTTT
1 TTTTTCTTTTT
* *
19086743 TTTCTTCCTCTT
1 TTT-TTCTTTTT
19086755 TTTTTCT
1 TTTTTCT
19086762 GGACTGCTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:19087036 original size:4 final size:4
Alignment explanation
Indices: 19087029--19087086 Score: 57
Period size: 4 Copynumber: 14.0 Consensus size: 4
19087019 TTTTTATTTT
*
19087029 TTTC TTTCC CTTTC -TTC TTCC TTGTC CTTTC -TTC TTTC TTTC TTTC
1 TTTC TTT-C -TTTC TTTC TTTC TT-TC -TTTC TTTC TTTC TTTC TTTC
19087075 TTTC TTTC TTTC
1 TTTC TTTC TTTC
19087087 ACGATCAGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 6 0.13
4 30 0.65
5 5 0.11
6 5 0.11
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:19087059 original size:17 final size:16
Alignment explanation
Indices: 19087032--19087086 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
19087022 TTATTTTTTT
19087032 CTTTCCCTTTCTTCTTC
1 CTTT-CCTTTCTTCTTC
*
19087049 CTTGTCCTTTCTTCTTT
1 CTT-TCCTTTCTTCTTC
*
19087066 CTTT-CTTTCTTTCTTT
1 CTTTCCTTTC-TTCTTC
19087082 CTTTC
1 CTTTC
19087087 ACGATCAGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 5 0.15
16 11 0.32
17 17 0.50
18 1 0.03
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (16 bp):
CTTTCCTTTCTTCTTC
Found at i:19087617 original size:29 final size:29
Alignment explanation
Indices: 19087568--19087711 Score: 128
Period size: 30 Copynumber: 4.9 Consensus size: 29
19087558 AATATCGTAA
* **
19087568 AAATTTTAGGG-CTAAAGTGTAATTTTGGG
1 AAATTTTAGGGTC-AAAATGTAATTTTAAG
*
19087597 AAATTTTAGGGTCAAAATGTAATTCTAAG
1 AAATTTTAGGGTCAAAATGTAATTTTAAG
* * *
19087626 AAAGTTTAAGGGTTAAAATGCAATTTTAAG
1 AAA-TTTTAGGGTCAAAATGTAATTTTAAG
* ** * *
19087656 AAAGTTTAGAGGTTGAAATGTAATTTCAAA
1 AAATTTTAG-GGTCAAAATGTAATTTTAAG
* *
19087686 AAAGTTAAGGGTCAAAATGTAATTTT
1 AAATTTTAGGGTCAAAATGTAATTTT
19087712 TTTTTAAAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
29 44 0.47
30 50 0.53
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (29 bp):
AAATTTTAGGGTCAAAATGTAATTTTAAG
Found at i:19089169 original size:19 final size:19
Alignment explanation
Indices: 19089147--19089189 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
19089137 AAGAAATTTT
* *
19089147 ATTAGGTTATTTTAGGTTA
1 ATTAAGTTAATTTAGGTTA
* *
19089166 ATTAATTTAATTTAGTTTA
1 ATTAAGTTAATTTAGGTTA
19089185 ATTAA
1 ATTAA
19089190 TATTTTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (19 bp):
ATTAAGTTAATTTAGGTTA
Done.