Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 52 of 113
Found at i:13416825 original size:15 final size:17
Alignment explanation
Indices: 13416805--13416836 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
13416795 TACCTCCCAT
13416805 TTTCATC-C-ATTTTAC
1 TTTCATCACAATTTTAC
13416820 TTTCATCACAATTTTAC
1 TTTCATCACAATTTTAC
13416837 CAAGCTAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTCATCACAATTTTAC
Found at i:13426002 original size:18 final size:18
Alignment explanation
Indices: 13425980--13426015 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13425970 TTGAAAAAAA
13425980 AAAAAGGAGAAAATTTTTC
1 AAAAAGGA-AAAATTTTTC
*
13425999 AAAAATGAAAAATTTTT
1 AAAAAGGAAAAATTTTT
13426016 ATTCATGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (18 bp):
AAAAAGGAAAAATTTTTC
Found at i:13426020 original size:21 final size:21
Alignment explanation
Indices: 13425996--13426040 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
13425986 GAGAAAATTT
13425996 TTCAAAAATGAAAAATTTTTA
1 TTCAAAAATGAAAAATTTTTA
***
13426017 TTC-ATGTTGAAAAATTTTTA
1 TTCAAAAATGAAAAATTTTTA
13426037 TTCA
1 TTCA
13426041 TGTGTTATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (21 bp):
TTCAAAAATGAAAAATTTTTA
Found at i:13426029 original size:20 final size:20
Alignment explanation
Indices: 13426004--13426043 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13425994 TTTTCAAAAA
13426004 TGAAAAATTTTTATTCATGT
1 TGAAAAATTTTTATTCATGT
13426024 TGAAAAATTTTTATTCATGT
1 TGAAAAATTTTTATTCATGT
13426044 GTTATTGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (20 bp):
TGAAAAATTTTTATTCATGT
Found at i:13426331 original size:126 final size:124
Alignment explanation
Indices: 13426186--13426782 Score: 553
Period size: 127 Copynumber: 4.9 Consensus size: 124
13426176 AAAAGGAAGG
* * *
13426186 AAAAATTTTTATTTTGAATGTTATTGTACCTTTTGCATTTCATTAGTTTTTGCATTTGGAAATAA
1 AAAAAATTTGATTTTGAATGTTATTGTACCTTTTGCATTTCATTA-TTTTT-CATTTGAAAATAA
* * *
13426251 TAATGTTGTATATACACTTTCATTTCATTTACAAATATTTGAATGGTAGTGTCAATTTTGT
64 TAAAGTTATATATACACTTTCATTTCATGTACAAATATTTGAATGGTAGTGTCAATTTTGT
** * *
13426312 AAAAAATTTGATTTTGAATGTTATTGTACCTTTCACATTTCATTATTTTTTATATTTAAAAATAA
1 AAAAAATTTGATTTTGAATGTTATTGTACCTTTTGCATTTCATTA-TTTTT-CATTTGAAAATAA
* * * * *
13426377 AAAAGTTATATACATACAC-TTCATTTCATGTACAAATATTTGAATAGTAGTTTCAGTTTCGT
64 TAAAGTTATAT--ATACACTTTCATTTCATGTACAAATATTTGAATGGTAGTGTCAATTTTGT
* *
13426439 -AAAAATTGTGATTTTGAATGTTATTGTACCTTTTGTATTTTATTATTTTTCATATTTGAAAATA
1 AAAAAATT-TGATTTTGAATGTTATTGTACCTTTTGCATTTCATTATTTTTC--ATTTGAAAATA
* * * * *
13426503 ATAAAGTTATAAATACA-TTTGATTTCACGTA-TAATATTTGAATGGTAATGTCAATTTTGT
63 ATAAAGTTATATATACACTTTCATTTCATGTACAAATATTTGAATGGTAGTGTCAATTTTGT
* * * * *
13426563 AAAAAATTTTATTCTG-A--TT-TTATA-ATTTT---TTGC---A--TTT-A----AAAATAATA
1 AAAAAATTTGATTTTGAATGTTATTGTACCTTTTGCATTTCATTATTTTTCATTTGAAAATAATA
* *
13426610 AAGTTGTATATACAC-TTCATTTCATGTACAAATATTTGAATGGTAGTGTC-AGTTTG-
66 AAGTTATATATACACTTTCATTTCATGTACAAATATTTGAATGGTAGTGTCAATTTTGT
* * *
13426666 ATAAAAATTTGATTTTGAATGTTATTGTACCTTTCGTATTTCATTATTTTTCACGTTTGGAAATA
1 A-AAAAATTTGATTTTGAATGTTATTGTACCTTTTGCATTTCATTATTTTTCA--TTTGAAAATA
* * * * * *
13426731 ATAAGGTTGTACATATA-TTTCATTTCATGCACAAATGTCTTGAATGGTAGTG
63 ATAAAGTTATATATACACTTTCATTTCATGTACAAATAT-TTGAATGGTAGTG
13426783 AAATTTTCAT
Statistics
Matches: 381, Mismatches: 58, Indels: 65
0.76 0.12 0.13
Matches are distributed among these distances:
103 1 0.00
104 50 0.13
105 20 0.05
107 2 0.01
108 5 0.01
109 3 0.01
111 3 0.01
112 3 0.01
113 1 0.00
115 1 0.00
116 2 0.01
117 3 0.01
118 1 0.00
119 4 0.01
120 4 0.01
121 2 0.01
123 1 0.00
124 66 0.17
125 36 0.09
126 76 0.20
127 91 0.24
128 6 0.02
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (124 bp):
AAAAAATTTGATTTTGAATGTTATTGTACCTTTTGCATTTCATTATTTTTCATTTGAAAATAATA
AAGTTATATATACACTTTCATTTCATGTACAAATATTTGAATGGTAGTGTCAATTTTGT
Found at i:13427043 original size:42 final size:42
Alignment explanation
Indices: 13426997--13427082 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
13426987 GCATTTGATA
13426997 TAAGTACACCATCTTTCATGAAATAGGACATTGCATTCCATG
1 TAAGTACACCATCTTTCATGAAATAGGACATTGCATTCCATG
*
13427039 TAAGTACACCATCTTTCATGAAATAGGACATTGTATTCCATG
1 TAAGTACACCATCTTTCATGAAATAGGACATTGCATTCCATG
13427081 TA
1 TA
13427083 TATATATTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (42 bp):
TAAGTACACCATCTTTCATGAAATAGGACATTGCATTCCATG
Found at i:13431295 original size:31 final size:31
Alignment explanation
Indices: 13431253--13431317 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
13431243 TATCAAGGAA
*
13431253 AAAAGTTTGTCAA-AGAAAAAA-AAAGAGAAAG
1 AAAAGTCTGTCAAGAGAAAAAACAAA-A-AAAG
13431284 AAAAGTCTGTCAAGAGAAAAAACAAAAAAAG
1 AAAAGTCTGTCAAGAGAAAAAACAAAAAAAG
13431315 AAA
1 AAA
13431318 GGAAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 19 0.61
32 9 0.29
33 3 0.10
ACGTcount: A:0.66, C:0.06, G:0.17, T:0.11
Consensus pattern (31 bp):
AAAAGTCTGTCAAGAGAAAAAACAAAAAAAG
Found at i:13431538 original size:23 final size:23
Alignment explanation
Indices: 13431492--13431538 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13431482 AATGGAAAAG
* * *
13431492 TTTTAAGCTCAGTTTAGTTAGCA
1 TTTTAAGCCCAGATTAGCTAGCA
*
13431515 TTTTAAGCCCAGATTAGCTGGCA
1 TTTTAAGCCCAGATTAGCTAGCA
13431538 T
1 T
13431539 CGATAAGATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (23 bp):
TTTTAAGCCCAGATTAGCTAGCA
Found at i:13431636 original size:32 final size:32
Alignment explanation
Indices: 13431556--13431628 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
13431546 ATATAAGCTC
* * * *
13431556 AGTTTAGTAGGCACTAATTAGATTTCAAGTCT
1 AGTTTAGTTGACACAAATTAGATTTCAAGCCT
13431588 AGTTTAGTTGACACAAATTAGATTTCAAGCCT
1 AGTTTAGTTGACACAAATTAGATTTCAAGCCT
13431620 AG-TTAGTTG
1 AGTTTAGTTG
13431629 GTAACAAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 7 0.19
32 30 0.81
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (32 bp):
AGTTTAGTTGACACAAATTAGATTTCAAGCCT
Found at i:13432494 original size:101 final size:102
Alignment explanation
Indices: 13432312--13432495 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 102
13432302 AGGAAAAAAA
**
13432312 TTTTAAATTTTTAAAATTTCAAAGCCTCTAATGAGAAGAACATTCATAGATGTTGAGATTTGTAA
1 TTTTAAATTTTTAAAATTTCAAAGCCTCTAATGAGAAGAACATT-ATAGATGTCAAGATTTGTAA
* *
13432377 AACCTTTAAGCGTTATCTTTAAGTCCTTTAGTAGAAAG
65 AACCTCTAAGCATTATCTTTAAGTCCTTTAGTAGAAAG
* *
13432415 TTTTAAA-TTTTAAAATTTTAAGGCCTCTAATGAGAA-AAGCATT-TAGGATGTCAAGATTTGTA
1 TTTTAAATTTTTAAAATTTCAAAGCCTCTAATGAGAAGAA-CATTATA-GATGTCAAGATTTGTA
*
13432477 AAACCTCTAGGCATTATCT
64 AAACCTCTAAGCATTATCT
13432496 CAAAATCATT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 2 0.03
101 32 0.44
102 31 0.43
103 7 0.10
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (102 bp):
TTTTAAATTTTTAAAATTTCAAAGCCTCTAATGAGAAGAACATTATAGATGTCAAGATTTGTAAA
ACCTCTAAGCATTATCTTTAAGTCCTTTAGTAGAAAG
Found at i:13438014 original size:2 final size:2
Alignment explanation
Indices: 13438007--13438033 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13437997 TCATTTGTTG
13438007 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13438034 GGTTTGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13440588 original size:6 final size:6
Alignment explanation
Indices: 13440577--13440617 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
13440567 ATCCTATTTC
*
13440577 ATTAAT ATTAAT ATTAAT ATT-AT ATT-AT ATTTAT ATTAAT A
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT A
13440618 ACAAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTAAT
Found at i:13442774 original size:12 final size:12
Alignment explanation
Indices: 13442757--13442781 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13442747 AATATTAAAT
13442757 TTAAATAATTTA
1 TTAAATAATTTA
13442769 TTAAATAATTTA
1 TTAAATAATTTA
13442781 T
1 T
13442782 AATTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATAATTTA
Found at i:13443151 original size:2 final size:2
Alignment explanation
Indices: 13443144--13443172 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13443134 ATAAAATTTG
13443144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13443173 AGATTTGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13448290 original size:24 final size:24
Alignment explanation
Indices: 13448258--13448309 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
13448248 ATGTGTTTGT
13448258 TCATCTGTCAAGTCAGACACAAAG
1 TCATCTGTCAAGTCAGACACAAAG
13448282 TCATCTGTCAAGTCAGACACAAAG
1 TCATCTGTCAAGTCAGACACAAAG
13448306 TCAT
1 TCAT
13448310 TCTCCTCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (24 bp):
TCATCTGTCAAGTCAGACACAAAG
Found at i:13449207 original size:23 final size:22
Alignment explanation
Indices: 13449162--13449207 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
13449152 AATTACTTAT
* **
13449162 TATTTATATTTATAATTTTAAA
1 TATTTATATATATAATTAGAAA
13449184 TATTTATAATATATAATTAGAAA
1 TATTTAT-ATATATAATTAGAAA
13449207 T
1 T
13449208 GAGTAAAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTATATATATAATTAGAAA
Found at i:13452588 original size:13 final size:13
Alignment explanation
Indices: 13452552--13452596 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
13452542 ACTGGTCACC
13452552 ATTTTAATTTTTAT
1 ATTTTAA-TTTTAT
*
13452566 ATTTT-TTTTTAT
1 ATTTTAATTTTAT
13452578 ATTTTAATTTTAT
1 ATTTTAATTTTAT
*
13452591 CTTTTA
1 ATTTTA
13452597 TATAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.41
13 11 0.41
14 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTTAATTTTAT
Found at i:13452595 original size:20 final size:19
Alignment explanation
Indices: 13452560--13452599 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
13452550 CCATTTTAAT
13452560 TTTTATATTTTTTTTTATA
1 TTTTATATTTTTTTTTATA
13452579 TTTTA-ATTTTATCTTTTATA
1 TTTTATATTTT-T-TTTTATA
13452599 T
1 T
13452600 AATATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 6 0.32
20 8 0.42
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTATATTTTTTTTTATA
Found at i:13452604 original size:25 final size:25
Alignment explanation
Indices: 13452552--13452611 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
13452542 ACTGGTCACC
* * *
13452552 ATTTTAATTTTTATATTTTTTTTTAT
1 ATTTTAA-TTTTATATTTTATATAAT
*
13452578 ATTTTAATTTTATCTTTTATATAAT
1 ATTTTAATTTTATATTTTATATAAT
*
13452603 ATTATAATT
1 ATTTTAATT
13452612 ATTAAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (25 bp):
ATTTTAATTTTATATTTTATATAAT
Found at i:13452703 original size:22 final size:23
Alignment explanation
Indices: 13452667--13452711 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
13452657 TATTTAATTT
*
13452667 TTTATTTAAATTAATAAAATAAA
1 TTTATTTAAAGTAATAAAATAAA
*
13452690 TTTA-TTAAAGTAATATAATAAA
1 TTTATTTAAAGTAATAAAATAAA
13452712 AATATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TTTATTTAAAGTAATAAAATAAA
Found at i:13452717 original size:22 final size:22
Alignment explanation
Indices: 13452672--13452718 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13452662 AATTTTTTAT
* **
13452672 TTAAATTAATAAAATAAATTTA
1 TTAAAGTAATAAAATAAAAATA
*
13452694 TTAAAGTAATATAATAAAAATA
1 TTAAAGTAATAAAATAAAAATA
13452716 TTA
1 TTA
13452719 TTTGATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAAAGTAATAAAATAAAAATA
Found at i:13453225 original size:61 final size:61
Alignment explanation
Indices: 13453126--13453253 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 61
13453116 ATAAGGTGTT
*
13453126 GATGTGACTGGTTGGTTTACCAGATCTTACGCCGACAGAGGAACGAGTCAATACTACTGCA
1 GATGTGACTGGTTGATTTACCAGATCTTACGCCGACAGAGGAACGAGTCAATACTACTGCA
*
13453187 GATGTGACTGGTTGATTTACCAGATCTTACGCCTACAGAGGAACGAGTCAATACTACTGCA
1 GATGTGACTGGTTGATTTACCAGATCTTACGCCGACAGAGGAACGAGTCAATACTACTGCA
13453248 GATGTG
1 GATGTG
13453254 GCGGTCTATG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (61 bp):
GATGTGACTGGTTGATTTACCAGATCTTACGCCGACAGAGGAACGAGTCAATACTACTGCA
Found at i:13454686 original size:3 final size:3
Alignment explanation
Indices: 13454678--13454703 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13454668 AGTTATATAT
13454678 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
13454704 TTTTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13454782 original size:18 final size:20
Alignment explanation
Indices: 13454761--13454802 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
13454751 TCTGTTAATT
*
13454761 TTATCTGATTCTT-TT-TTA
1 TTATCTGATTATTATTATTA
13454779 TTATCTGATTATTATTATTA
1 TTATCTGATTATTATTATTA
13454799 TTAT
1 TTAT
13454803 TTTTTCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 2 0.10
20 7 0.33
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (20 bp):
TTATCTGATTATTATTATTA
Found at i:13455788 original size:18 final size:19
Alignment explanation
Indices: 13455757--13455804 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
13455747 TTATCTTATT
* *
13455757 TTTATTT-TTGTTTTACT-
1 TTTATTTATTTTTTTAATC
*
13455774 TTTCTTTATTTTTTTAATC
1 TTTATTTATTTTTTTAATC
13455793 TTTATTTATTTT
1 TTTATTTATTTT
13455805 CACTTTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 6 0.24
18 8 0.32
19 11 0.44
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTATTTATTTTTTTAATC
Found at i:13455960 original size:60 final size:60
Alignment explanation
Indices: 13455831--13456186 Score: 487
Period size: 60 Copynumber: 6.0 Consensus size: 60
13455821 TATTTTCTTT
* *
13455831 AAAT-AAATTTTC-AAAAAAATATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTCATTAA
1 AAATCAAATTTTCAAAAAAAATATTTTTAGGG-AAAAGTTGAAAGTATCAATTTTCCTTAG
*
13455889 AAAT-AAA-TTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAG
1 AAATCAAATTTTC-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* * *
13455948 AAGT-AAATTTTCAAAAAAGGA-ATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
1 AAATCAAATTTTCAAAAAA-AATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG
* *
13456007 AAATCAAATTTTCAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
1 AAATCAAATTTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* *
13456067 AAATCAAATTTTCAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
1 AAATCAAATTTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* *
13456127 AAATCAAAGTTTCAAAAAAAAATATTTTTTA-GGAAAAGTTGAAAATATCAATTTTCCTTA
1 AAATCAAATTTTC-AAAAAAAATA-TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
13456187 AAAAATTCCA
Statistics
Matches: 274, Mismatches: 13, Indels: 19
0.90 0.04 0.06
Matches are distributed among these distances:
57 4 0.01
58 8 0.03
59 89 0.32
60 130 0.47
61 37 0.14
62 6 0.02
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (60 bp):
AAATCAAATTTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
Found at i:13456213 original size:47 final size:52
Alignment explanation
Indices: 13456144--13456278 Score: 137
Period size: 43 Copynumber: 2.8 Consensus size: 52
13456134 AGTTTCAAAA
**
13456144 AAAAATATTTTTTAGGAAAAGTTGAAAATATCAATTTTCCTT-AAAAAATTCC
1 AAAAATA-TTTTGGGGAAAAGTTGAAAATATCAATTTTCCTTGAAAAAATTCC
* *
13456196 -AAAATA-TTT-GGG-AAAGTTG--AA-GT-AA-TTTCCTTGAAATAATTCC
1 AAAAATATTTTGGGGAAAAGTTGAAAATATCAATTTTCCTTGAAAAAATTCC
*
13456239 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAATA-TTTTGGGGAAAAGTTGAAAATATCAATTTTCC
13456279 CTACACAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
42 7 0.10
43 11 0.16
44 7 0.10
45 2 0.03
46 3 0.04
47 10 0.15
48 9 0.13
49 3 0.04
50 1 0.01
51 7 0.10
52 2 0.03
53 5 0.07
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (52 bp):
AAAAATATTTTGGGGAAAAGTTGAAAATATCAATTTTCCTTGAAAAAATTCC
Found at i:13460151 original size:9 final size:9
Alignment explanation
Indices: 13460137--13460202 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
13460127 ACAATGGATG
13460137 AAAAATGAA
1 AAAAATGAA
*
13460146 AAAAATGATG
1 AAAAATGA-A
*
13460156 ATAAA--AA
1 AAAAATGAA
13460163 AAAAA-GAA
1 AAAAATGAA
*
13460171 AAAAGA-AAA
1 AAAA-ATGAA
*
13460180 AAAAATAAA
1 AAAAATGAA
13460189 AAAAATGAA
1 AAAAATGAA
13460198 AAAAA
1 AAAAA
13460203 GAGATTCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
7 4 0.09
8 8 0.17
9 31 0.66
10 4 0.09
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAAATGAA
Found at i:13460174 original size:10 final size:10
Alignment explanation
Indices: 13460158--13460202 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
13460148 AAATGATGAT
13460158 AAAAAAAA-A
1 AAAAAAAAGA
*
13460167 AGAAAAAAGA
1 AAAAAAAAGA
*
13460177 AAAAAAAATA
1 AAAAAAAAGA
*
13460187 AAAAAAATGA
1 AAAAAAAAGA
13460197 AAAAAA
1 AAAAAA
13460203 GAGATTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.89, C:0.00, G:0.07, T:0.04
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:13460181 original size:20 final size:20
Alignment explanation
Indices: 13460158--13460202 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
13460148 AAATGATGAT
*
13460158 AAAAAAAA-AAGAAAAAAGA
1 AAAAAAAATAAAAAAAAAGA
*
13460177 AAAAAAAATAAAAAAAATGA
1 AAAAAAAATAAAAAAAAAGA
13460197 AAAAAA
1 AAAAAA
13460203 GAGATTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.89, C:0.00, G:0.07, T:0.04
Consensus pattern (20 bp):
AAAAAAAATAAAAAAAAAGA
Found at i:13461495 original size:41 final size:41
Alignment explanation
Indices: 13461450--13461830 Score: 615
Period size: 41 Copynumber: 9.3 Consensus size: 41
13461440 GGACATGATT
* *
13461450 TTTAG-GGAGTAATTTACTTTTCCAAAGTCGCGGTGCCTCTG
1 TTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTG
*
13461491 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGTCTCTG
1 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
*
13461532 TTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTG
1 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
* *
13461573 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTTTG
1 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
*
13461614 TTTAGAGGAGCAATTTACTTTCCAAAGTTTCGT--TGCCTCTG
1 TTTAGAGGAGCAATTTACTTTTCAAAG--TCGTGGTGCCTCTG
13461655 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
1 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
13461696 TTTAGAGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTG
1 TTTAGAGGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTG
*
13461738 TTTAGATGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
1 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
* *
13461779 TTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTG
1 TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
13461820 TTTAGAGGAGC
1 TTTAGAGGAGC
13461831 TTTGGTAAAA
Statistics
Matches: 318, Mismatches: 16, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.01
41 255 0.80
42 55 0.17
43 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (41 bp):
TTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
Found at i:13461751 original size:165 final size:164
Alignment explanation
Indices: 13461450--13461830 Score: 640
Period size: 165 Copynumber: 2.3 Consensus size: 164
13461440 GGACATGATT
* **
13461450 TTTAG-GGAGTAATTTACTTTTCCAAAGTCGCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC
1 TTTAGAGGAGCAATTTAC-TTTCCAAAGTATCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC
*
13461514 AAAGTCGTGGTGTCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
65 AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
*
13461579 GGAGCAATTTACTTTTCAAAGTCGTGGTACCTTTG
130 GGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTG
* *
13461614 TTTAGAGGAGCAATTTACTTTCCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCA
1 TTTAGAGGAGCAATTTACTTTCCAAAGTATCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCA
13461679 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
66 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-TTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
* *
13461744 TGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG
130 GGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTG
13461779 TTTAGAGGAGCAATTTACTTTCCAAAGTCAT-GGTGCCTCTGTTTAGAGGAGC
1 TTTAGAGGAGCAATTTACTTTCCAAAGT-ATCGGTGCCTCTGTTTAGAGGAGC
13461831 TTTGGTAAAA
Statistics
Matches: 204, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
164 82 0.40
165 121 0.59
166 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (164 bp):
TTTAGAGGAGCAATTTACTTTCCAAAGTATCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCA
AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
GAGCAATTTACTTTTCAAAGTCGTGGTACCTCTG
Found at i:13461879 original size:16 final size:16
Alignment explanation
Indices: 13461837--13461873 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
13461827 GAGCTTTGGT
13461837 AAAAAAA-ACAAAAAC
1 AAAAAAATACAAAAAC
13461852 AAAAAAATACAAAAAC
1 AAAAAAATACAAAAAC
13461868 AAAAAA
1 AAAAAA
13461874 TGACAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAAAAATACAAAAAC
Found at i:13462005 original size:20 final size:21
Alignment explanation
Indices: 13461968--13462008 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
13461958 TGTAGACACC
13461968 CAATTGGGTCCAGGCCCAAAT
1 CAATTGGGTCCAGGCCCAAAT
*
13461989 CAATTGGG-CCTGGCCCAAAT
1 CAATTGGGTCCAGGCCCAAAT
13462009 GGGTAAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (21 bp):
CAATTGGGTCCAGGCCCAAAT
Found at i:13462757 original size:22 final size:22
Alignment explanation
Indices: 13462713--13462757 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
13462703 TCCTAGAAAC
* * **
13462713 CGGTGATCTTTCGATCAGCTTT
1 CGGTGAACTTTCGATAAAATTT
13462735 CGGTGAACTTTCGATAAAATTT
1 CGGTGAACTTTCGATAAAATTT
13462757 C
1 C
13462758 TAGATTTCGA
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:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (22 bp):
CGGTGAACTTTCGATAAAATTT
Found at i:13462775 original size:19 final size:20
Alignment explanation
Indices: 13462743--13462792 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
13462733 TTCGGTGAAC
*
13462743 TTTCGAT-AAAATTTCTAGA
1 TTTCGATGAAATTTTCTAGA
* *
13462762 TTTCGATGACATTTTTTAGA
1 TTTCGATGAAATTTTCTAGA
*
13462782 ATTCGATGAAA
1 TTTCGATGAAA
13462793 ATTCCACCGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (20 bp):
TTTCGATGAAATTTTCTAGA
Found at i:13463037 original size:5 final size:5
Alignment explanation
Indices: 13463021--13463051 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
13463011 CGCCCCCCCT
*
13463021 CCGAG CCAAG CCGAG CCGAG CCGAG CCGAG C
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG C
13463052 TTCCGAGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.42, G:0.35, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:13463186 original size:18 final size:19
Alignment explanation
Indices: 13463155--13463202 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
13463145 TAGTCTTATT
* *
13463155 TTTATTT-TTGTTTTACT-
1 TTTATTTATTTTTTTAATC
*
13463172 TTTCTTTATTTTTTTAATC
1 TTTATTTATTTTTTTAATC
13463191 TTTATTTATTTT
1 TTTATTTATTTT
13463203 CACTTTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 6 0.24
18 8 0.32
19 11 0.44
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTATTTATTTTTTTAATC
Found at i:13463295 original size:60 final size:56
Alignment explanation
Indices: 13463229--13463549 Score: 299
Period size: 60 Copynumber: 5.4 Consensus size: 56
13463219 ATTTGTCTTT
* *
13463229 AAATAAATTTTTCAAAAAATATTTTTGGGAAAAGTTGAAAGTTGATCAATGTTTTCTTAA
1 AAATAAA-TTTTCAAAAAATATTTTTGGGAAAAGTTGAAAG-T-ATCAAT-TTTCCTTAG
13463289 AAATAAA-TTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGT-TC-ATTTTCCTTAG
1 AAATAAATTTTC--AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* * * * *
13463345 AAGTAAATTTTCAAAAAAGAGGATTTTTGAGG-AAAGTTGAAGTGTATCAATTTTTCTTGG
1 AAATAAATTTTC-AAAAA-A-TATTTTTG-GGAAAAGTTGAA-AGTATCAATTTTCCTTAG
* *
13463405 AAATCAAATTTTCAAAAAAAATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTAG
1 AAAT-AAATTTTC--AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAG
** * * *
13463465 AAATAAATTTTCAAAAAGGGATTTTTGAGAAAAAGTTGAAAGTATCAAATTTCCTTGG
1 AAATAAATTTTCAAAAA-ATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG
*
13463523 AAATCAAAGTTTCAAAAAAATATTTTT
1 AAAT-AAATTTTC-AAAAAATATTTTT
13463550 CCAAAAAATA
Statistics
Matches: 219, Mismatches: 24, Indels: 37
0.78 0.09 0.13
Matches are distributed among these distances:
56 19 0.09
57 22 0.10
58 52 0.24
59 23 0.11
60 64 0.29
61 33 0.15
62 6 0.03
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (56 bp):
AAATAAATTTTCAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
Found at i:13463418 original size:118 final size:117
Alignment explanation
Indices: 13463229--13463549 Score: 397
Period size: 118 Copynumber: 2.7 Consensus size: 117
13463219 ATTTGTCTTT
** **
13463229 AAATAAATTTTTCAAAAA-ATATTTTTG-GGAAAAGTTGAAAGT-TGATCAATGTTTTCTTAAAA
1 AAATAAA-TTTTCAAAAAGGGATTTTTGAGG-AAAGTTG-AAGTGT-ATCAAT-TTTTCTTGGAA
* *
13463291 AT-AAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGT-TC-ATTTTCCTTAG
61 ATCAAATTTCAAAAAAAATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTAG
*
13463345 AAGTAAATTTTCAAAAAAGAGGATTTTTGAGGAAAGTTGAAGTGTATCAATTTTTCTTGGAAATC
1 AAATAAATTTTC-AAAAAG-GGATTTTTGAGGAAAGTTGAAGTGTATCAATTTTTCTTGGAAATC
13463410 AAATTTTCAAAAAAAATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTAG
64 AAA-TTTCAAAAAAAATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTAG
* * * *
13463465 AAATAAATTTTCAAAAAGGGATTTTTGAGAAAAAGTTGAA-AGTATCAAATTTCCTTGGAAATCA
1 AAATAAATTTTCAAAAAGGGATTTTTGAG-GAAAGTTGAAGTGTATCAATTTTTCTTGGAAATCA
13463529 AAGTTTC-AAAAAAATATTTTT
65 AA-TTTCAAAAAAAATATTTTT
13463550 CCAAAAAATA
Statistics
Matches: 182, Mismatches: 13, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
115 5 0.03
116 22 0.12
117 27 0.15
118 87 0.48
119 19 0.10
120 22 0.12
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (117 bp):
AAATAAATTTTCAAAAAGGGATTTTTGAGGAAAGTTGAAGTGTATCAATTTTTCTTGGAAATCAA
ATTTCAAAAAAAATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTAG
Found at i:13463572 original size:15 final size:15
Alignment explanation
Indices: 13463532--13463564 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
13463522 GAAATCAAAG
*
13463532 TTTCAAAAAAATATT
1 TTTCCAAAAAATATT
13463547 TTTCCAAAAAATATT
1 TTTCCAAAAAATATT
13463562 TTT
1 TTT
13463565 GTAAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTCCAAAAAATATT
Found at i:13463573 original size:74 final size:72
Alignment explanation
Indices: 13463485--13463621 Score: 206
Period size: 74 Copynumber: 1.9 Consensus size: 72
13463475 TCAAAAAGGG
*
13463485 ATTTTTGAGAAAAAGTTGAAAGTATCAAATTTCCTTGGAAATCAAAGTTT-CAAAAAAATATTTT
1 ATTTTTGAGAAAAAGTTGAAAGTATC-AATTTCCTTGAAAAT-AAA-TTTCCAAAAAAATATTTT
13463549 TCCAAAAAAT
63 TCCAAAAAAT
*
13463559 ATTTTTGTA-AAAAAGTTGAAAGTATCAATTTCCTTGAAAATGAATTTCCAAAAAAATATTTTT
1 ATTTTTG-AGAAAAAGTTGAAAGTATCAATTTCCTTGAAAATAAATTTCCAAAAAAATATTTTT
13463622 AAGGAAAAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
71 3 0.05
72 17 0.29
73 14 0.24
74 24 0.41
75 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (72 bp):
ATTTTTGAGAAAAAGTTGAAAGTATCAATTTCCTTGAAAATAAATTTCCAAAAAAATATTTTTCC
AAAAAAT
Found at i:13464229 original size:3 final size:3
Alignment explanation
Indices: 13464223--13464257 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
13464213 AAAAAATAAT
*
13464223 AAC AAC AAC AAC AAT AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
13464258 TAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:13464262 original size:3 final size:3
Alignment explanation
Indices: 13464256--13464284 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13464246 CAACAACAAC
13464256 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
13464285 GAAAAACTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:13465911 original size:3 final size:3
Alignment explanation
Indices: 13465905--13465939 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
13465895 CTTTAAAATC
13465905 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
13465940 GCATAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13466419 original size:11 final size:11
Alignment explanation
Indices: 13466403--13466444 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
13466393 AATCCTATAA
13466403 GAGATTTGTTT
1 GAGATTTGTTT
*
13466414 GAGATTTGTTA
1 GAGATTTGTTT
13466425 GAGATTTGTTT
1 GAGATTTGTTT
*
13466436 GGGATTTGT
1 GAGATTTGT
13466445 CAGATATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:13466430 original size:22 final size:22
Alignment explanation
Indices: 13466402--13466444 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
13466392 AAATCCTATA
13466402 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
*
13466424 AGAGATTTGTTTGGGATTTGT
1 AGAGATTTGTTTGAGATTTGT
13466445 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:13466586 original size:52 final size:52
Alignment explanation
Indices: 13466501--13466625 Score: 151
Period size: 52 Copynumber: 2.4 Consensus size: 52
13466491 AGAGAAAGAT
* * * *
13466501 GATTCTTAATAGGTAAGTTTGACTTGCAAGAGAAGAGTTCCAAAAAGAAATG
1 GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCCAAAAAGAAAGG
* * * * * *
13466553 GATTCTTAATAGGCAAGTTTGACTTATAGGAGAAGAATTCTAAGAGGAGAGG
1 GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCCAAAAAGAAAGG
*
13466605 GATTCTTAATGGGCAAGTTTG
1 GATTCTTAATAGGCAAGTTTG
13466626 TAAGGTTATA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (52 bp):
GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCCAAAAAGAAAGG
Found at i:13467523 original size:11 final size:11
Alignment explanation
Indices: 13467507--13467548 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
13467497 AATCTCATAA
13467507 GAGATTTGTTT
1 GAGATTTGTTT
*
13467518 GAGATTTATTT
1 GAGATTTGTTT
*
13467529 AAGATTTGTTT
1 GAGATTTGTTT
*
13467540 GAAATTTGT
1 GAGATTTGT
13467549 CAGATATTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:13467661 original size:52 final size:52
Alignment explanation
Indices: 13467605--13467729 Score: 178
Period size: 52 Copynumber: 2.4 Consensus size: 52
13467595 AGAGAAATAT
* * * *
13467605 GATTCTTAATAGGTAAGTTTGACTTGCAAGAGAAGAGTTTTAAAAGGAAAGG
1 GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAGGAAAGG
* * *
13467657 GATTCTTAATAGGCAAGTTTGACTTATAGGAGAAGAATTCTAAAAGGAGAGG
1 GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAGGAAAGG
*
13467709 GATTCTTAATGGGCAAGTTTG
1 GATTCTTAATAGGCAAGTTTG
13467730 TATGGTTATA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (52 bp):
GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAGGAAAGG
Found at i:13476525 original size:28 final size:28
Alignment explanation
Indices: 13476489--13476545 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
13476479 ACATTAAGCT
* * * *
13476489 TTTGCTTTAACATTATGTTATAATGTAA
1 TTTGATTTAACATCATGTAACAATGTAA
*
13476517 TTTGATTTAATATCATGTAACAATGTAA
1 TTTGATTTAACATCATGTAACAATGTAA
13476545 T
1 T
13476546 GGCTTGATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (28 bp):
TTTGATTTAACATCATGTAACAATGTAA
Found at i:13477512 original size:15 final size:16
Alignment explanation
Indices: 13477475--13477515 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
13477465 AAGAAAAATT
*
13477475 ATAAATACTTTAATAG
1 ATAAATATTTTAATAG
13477491 TATAAATATTTTAATA-
1 -ATAAATATTTTAATAG
13477507 ATAAATATT
1 ATAAATATT
13477516 ACTATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
ATAAATATTTTAATAG
Found at i:13477550 original size:17 final size:17
Alignment explanation
Indices: 13477528--13477563 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13477518 TATTTTAATA
13477528 TTAATAAAAATAATATT
1 TTAATAAAAATAATATT
* *
13477545 TTAATAATAGTAATATT
1 TTAATAAAAATAATATT
13477562 TT
1 TT
13477564 TGAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAATAAAAATAATATT
Found at i:13478774 original size:4 final size:4
Alignment explanation
Indices: 13478767--13478798 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
13478757 GTGAGTGGTG
13478767 AGAA AGAA A-AA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
13478799 ATGGAGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:13478963 original size:6 final size:6
Alignment explanation
Indices: 13478952--13478980 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
13478942 TGTAGAGGAT
13478952 TTGGAG TTGGAG TTGGAG TTGGAG TTGGA
1 TTGGAG TTGGAG TTGGAG TTGGAG TTGGA
13478981 CTTACCGATG
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:0.17, C:0.00, G:0.48, T:0.34
Consensus pattern (6 bp):
TTGGAG
Found at i:13479942 original size:18 final size:19
Alignment explanation
Indices: 13479919--13479954 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13479909 ACTTTATTAT
*
13479919 TTTAAAAATTA-ATTTTTA
1 TTTAAAAAATATATTTTTA
13479937 TTTAAAAAATATATTTTT
1 TTTAAAAAATATATTTTT
13479955 GTGATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAAAAATATATTTTTA
Found at i:13481309 original size:18 final size:18
Alignment explanation
Indices: 13481283--13481325 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
13481273 AAATATTGAT
* * *
13481283 AATTGTATTAGAATTAAA
1 AATTATATTACAAATAAA
13481301 AATTATATTACAAATAAA
1 AATTATATTACAAATAAA
13481319 AATTATA
1 AATTATA
13481326 AACATAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (18 bp):
AATTATATTACAAATAAA
Found at i:13481983 original size:4 final size:4
Alignment explanation
Indices: 13481961--13482173 Score: 53
Period size: 4 Copynumber: 54.2 Consensus size: 4
13481951 TCTTTCGTAT
* * * *
13481961 TTTA TGTA TTT- TATTA TTTA TTTA -TTA -TTA -TTA TGTA TTAA TATA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
13482006 TGTA TATC TTTA TTTA TTT- TTT- TTCTG TTAATA TTTA TATGTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TT--TA TTTA T-T-TA -TTTA
* * *
13482054 TTTA TATA GTTA TATA TTTA -TTA TTATA TTATAA TTTA TTTA -TTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TT-T-A TTTA TTTA TTTA TTTA
* * * *
13482102 -TTA -TTA -TTA -TTA TTT- TATA TTTTA TTTA TTTA TCTA ATTA TATA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
* *
13482146 TCTA -TTA -TTA TTTTT TTTA TTTA TTTA T
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA T
13482174 CCTATAATAT
Statistics
Matches: 161, Mismatches: 31, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
3 43 0.27
4 90 0.56
5 18 0.11
6 9 0.06
7 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:13482079 original size:3 final size:3
Alignment explanation
Indices: 13482071--13482157 Score: 65
Period size: 3 Copynumber: 27.7 Consensus size: 3
13482061 AGTTATATAT
*
13482071 TTA TTA TTA -TA TTA TAA TTTA TTTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA
13482116 TTA -TA TT- TTA TTTA TTTA TCTAA TTA TATA TCTA TTA TTA TT
1 TTA TTA TTA TTA -TTA -TTA T-T-A TTA T-TA T-TA TTA TTA TT
13482158 TTTTTTATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 18
0.77 0.03 0.19
Matches are distributed among these distances:
2 8 0.11
3 41 0.57
4 21 0.29
5 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:13482081 original size:12 final size:12
Alignment explanation
Indices: 13482066--13482173 Score: 74
Period size: 11 Copynumber: 9.8 Consensus size: 12
13482056 TATATAGTTA
13482066 TATATTTATTAT
1 TATATTTATTAT
*
13482078 TATA-TTATAAT
1 TATATTTATTAT
13482089 T-TATTTATTAT
1 TATATTTATTAT
13482100 TAT-TATTATTAT
1 TATAT-TTATTAT
13482112 TAT-TTTA-TAT
1 TATATTTATTAT
*
13482122 TTTATTTA-T-T
1 TATATTTATTAT
* *
13482132 TAT-CTAATTA-
1 TATATTTATTAT
*
13482142 TATATCTATTAT
1 TATATTTATTAT
* *
13482154 TATTTTTTTTAT
1 TATATTTATTAT
13482166 T-TATTTAT
1 TATATTTAT
13482174 CCTATAATAT
Statistics
Matches: 74, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
9 2 0.03
10 14 0.19
11 32 0.43
12 26 0.35
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTATTAT
Found at i:13482093 original size:22 final size:22
Alignment explanation
Indices: 13482077--13482144 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 22
13482067 ATATTTATTA
*
13482077 TTATATTATAATTTATTTATTA
1 TTATATTATTATTTATTTATTA
13482099 -T-TATTATTA-TTA-TTATT-
1 TTATATTATTATTTATTTATTA
13482116 TTATATT-TTATTTATTTATCTAA
1 TTATATTATTATTTATTTAT-T-A
13482139 TTATAT
1 TTATAT
13482145 ATCTATTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
18 9 0.24
19 10 0.26
20 11 0.29
21 2 0.05
23 6 0.16
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATATTATTATTTATTTATTA
Found at i:13482130 original size:76 final size:73
Alignment explanation
Indices: 13481967--13482173 Score: 185
Period size: 76 Copynumber: 2.8 Consensus size: 73
13481957 GTATTTTATG
* * * *
13481967 TATTT-TA-TTATTTATTTATTATTAT-TATGTATTAATATATGTATATCTTTATTTATTTTTTT
1 TATTTATATTTATTTATTTATTATTATATATCTATTATTATATGTATATATTTATTTATTTTTTA
*
13482029 TCTGTTAA
66 TCTATTAA
* *
13482037 TATTTATATGTATTTTATTTATATAGTTATATATTTATTATTATAT-TATA-ATTTATTTATTAT
1 TATTTATATTTA-TTTATTTAT-TA-TTATATATCTATTATTATATGTATATATTTATTTATT-T
*
13482100 TATTAT-TATTAT
62 T-TTATCTATTAA
* * *
13482112 TATTTTATATTTTATTTATTTATCTAATTATATATCTATTATTAT-TTTTTTTATTTATTTAT
1 TA-TTTATA-TTTATTTATTTAT-T-ATTATATATCTATTATTATATGTATATATTTATTTAT
13482174 CCTATAATAT
Statistics
Matches: 112, Mismatches: 12, Indels: 19
0.78 0.08 0.13
Matches are distributed among these distances:
70 5 0.04
71 2 0.02
72 2 0.02
73 9 0.08
74 12 0.11
75 17 0.15
76 51 0.46
77 14 0.12
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (73 bp):
TATTTATATTTATTTATTTATTATTATATATCTATTATTATATGTATATATTTATTTATTTTTTA
TCTATTAA
Found at i:13482142 original size:34 final size:34
Alignment explanation
Indices: 13482047--13482170 Score: 112
Period size: 34 Copynumber: 3.5 Consensus size: 34
13482037 TATTTATATG
* *
13482047 TATTTTATTTATATAGTTATATATTTATTATTATATTA
1 TATTTTATTTATTTA-TTA--TA-TTATTATTATTTTA
*
13482085 TAATTTATTTA-TTATTATTATTATTATTATTTTA
1 TATTTTATTTATTTATTA-TATTATTATTATTTTA
13482119 TATTTTATTTATTTATCTA-ATTATATATCTATTATTA
1 TATTTTATTTATTTAT-TATATTAT-TAT-TATT-TTA
13482156 T-TTTT-TTTATTTATT
1 TATTTTATTTATTTATT
13482171 TATCCTATAA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
34 29 0.38
35 18 0.24
36 13 0.17
37 6 0.08
38 10 0.13
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.67
Consensus pattern (34 bp):
TATTTTATTTATTTATTATATTATTATTATTTTA
Found at i:13482152 original size:39 final size:38
Alignment explanation
Indices: 13482047--13482248 Score: 133
Period size: 39 Copynumber: 5.4 Consensus size: 38
13482037 TATTTATATG
* * *
13482047 TATTTTATTTATATAGT-T-ATATATTTATTATTATATTA
1 TATTTTATTTATTTA-TCTAAT-TATATATTATTATTTTA
*
13482085 TAATTTATTTA-TTAT-T-ATTAT-TATTATTATTTTA
1 TATTTTATTTATTTATCTAATTATATATTATTATTTTA
13482119 TATTTTATTTATTTATCTAATTATATATCTATTATTATT-
1 TATTTTATTTATTTATCTAATTATATAT-TATTATT-TTA
* * **
13482158 TTTTTTATTTATTTATCCTATAATATATATATAAGATTTT-
1 TATTTTATTTATTTAT-CTA-ATTATATAT-TATTATTTTA
*
13482198 T-TTTTGATTTATCTGT-TCTAATTATCTATT-TT-TTTTA
1 TATTTT-ATTTAT-T-TATCTAATTATATATTATTATTTTA
13482235 TA-TTTATTTGATTT
1 TATTTTATTT-ATTT
13482249 TTATTTTGGA
Statistics
Matches: 137, Mismatches: 13, Indels: 31
0.76 0.07 0.17
Matches are distributed among these distances:
34 22 0.16
35 8 0.06
36 14 0.10
37 13 0.09
38 14 0.10
39 33 0.24
40 17 0.12
41 15 0.11
42 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.65
Consensus pattern (38 bp):
TATTTTATTTATTTATCTAATTATATATTATTATTTTA
Found at i:13482756 original size:19 final size:20
Alignment explanation
Indices: 13482718--13482761 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
13482708 TCCGGTGAAC
*
13482718 TTCCGACGAAAAAACTCAGA
1 TTCCGACGAAAAAACCCAGA
*
13482738 TTCCGACG-ACAAACCCAGA
1 TTCCGACGAAAAAACCCAGA
*
13482757 ATCCG
1 TTCCG
13482762 GTGAATCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.39, C:0.32, G:0.16, T:0.14
Consensus pattern (20 bp):
TTCCGACGAAAAAACCCAGA
Found at i:13483110 original size:13 final size:12
Alignment explanation
Indices: 13483090--13483125 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
13483080 TTTTTTTAGA
13483090 ATTTTTTTATTT
1 ATTTTTTTATTT
13483102 ATTTGTTTTATTT
1 ATTT-TTTTATTT
*
13483115 ATTTATTTATT
1 ATTTTTTTATT
13483126 AGATTAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:13483117 original size:17 final size:16
Alignment explanation
Indices: 13483091--13483122 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
13483081 TTTTTTAGAA
13483091 TTTTTTTATTTATTTG
1 TTTTTTTATTTATTTG
13483107 TTTTATTTATTTATTT
1 TTTT-TTTATTTATTT
13483123 ATTAGATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTATTTATTTG
Found at i:13483196 original size:23 final size:23
Alignment explanation
Indices: 13483161--13483217 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
13483151 TATCTTTATC
* *
13483161 TTATTTTTATTTTTGTTTT-ACTT
1 TTATTATT-TTTTTATTTTCACTT
*
13483184 TTCTTTATTTTTTTATTTTCACTT
1 TT-ATTATTTTTTTATTTTCACTT
13483208 TTATTATTTT
1 TTATTATTTT
13483218 ATTTTCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (23 bp):
TTATTATTTTTTTATTTTCACTT
Found at i:13483207 original size:24 final size:22
Alignment explanation
Indices: 13483148--13483217 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
13483138 TTTAATCTTC
* *
13483148 TTTTATCTTTA-TCTTATTTTTAT
1 TTTTAT-TTTACTTTTATTATT-T
* *
13483171 TTTTGTTTTACTTTTCTTTATTT
1 TTTTATTTTACTTTT-ATTATTT
13483194 TTTTATTTTCACTTTTATTATTT
1 TTTTATTTT-ACTTTTATTATTT
13483217 T
1 T
13483218 ATTTTCTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.11
23 24 0.63
24 10 0.26
ACGTcount: A:0.14, C:0.09, G:0.01, T:0.76
Consensus pattern (22 bp):
TTTTATTTTACTTTTATTATTT
Found at i:13483359 original size:117 final size:114
Alignment explanation
Indices: 13483232--13483641 Score: 447
Period size: 117 Copynumber: 3.5 Consensus size: 114
13483222 TCTTTAAATA
* *
13483232 AAAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAGAGTATCAATTTTTCTT-AAGA
1 AAAAT-AAAATTTTC-AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAA-A
* ** * *
13483296 AT-AATTTTCAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
63 ATAAAGTTTCAAAAA-AATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTT
13483348 GAAAATCAAAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAA
1 -AAAAT-AAAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAA
* * * *
13483413 TCAAAGTCTCAAAAAAATATTTTTAGGAAAAAATTGAAAATATCAATTGTCCTT
64 T-AAAGTTTCAAAAAAAT-TTTTAAGG-AAAAGTTGAAAATATCAATTTTCCTT
* * *
13483467 ATAAAT-AAATTTTCAAAAAGGA-ATTTTT-GAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAA
1 A-AAATAAAATTTTCAAAAA-AATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTTCTTGAAA
*
13483529 ATCAAAGTTTCAAAAAAAATATATTTTTAAGGAAAAGTTGAAAATATCAATTTTTCTT
63 AT-AAAGTTTC---AAAAA-A-ATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTT
* *
13483587 AAAA-ATAAACTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTC
1 AAAATA-AAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTC
13483642 CTACACAAGA
Statistics
Matches: 254, Mismatches: 22, Indels: 32
0.82 0.07 0.10
Matches are distributed among these distances:
116 47 0.19
117 76 0.30
118 20 0.08
119 64 0.25
120 37 0.15
121 8 0.03
122 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (114 bp):
AAAATAAAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATA
AAGTTTCAAAAAAATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTT
Found at i:13483457 original size:59 final size:58
Alignment explanation
Indices: 13483239--13483641 Score: 435
Period size: 59 Copynumber: 6.9 Consensus size: 58
13483229 ATAAAAATCA
* *
13483239 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAGAGTATCAATTTTTCTT-AAGAAT
1 AAATTTTC-AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAA-AAT
*** *
13483298 -AATTTTC-AAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 AAATTTTCAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT
13483354 CAAAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT
1 --AAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT
* * * * * * *
13483414 CAAAGTCTCAAAAAAATATTTTTAGGAAAAAATTGAAAATATCAATTGTCCTT-ATAAAT
1 -AAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGA-AAAT
* * *
13483473 AAATTTTCAAAAAGGA-ATTTTT-GAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 AAATTTTCAAAAA-AATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT
* * * *
13483531 CAAAGTTTCAAAAAAAATATATTTTTAAGGAAAAGTTGAAAATATCAATTTTTCTTAAAAAT
1 -AAATTTTC--AAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT
* *
13483593 AAACTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTC
1 AAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTC
13483642 CTACACAAGA
Statistics
Matches: 292, Mismatches: 35, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
55 1 0.00
56 39 0.13
57 36 0.12
58 58 0.20
59 65 0.22
60 43 0.15
61 14 0.05
62 36 0.12
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
AAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT
Found at i:13483506 original size:177 final size:175
Alignment explanation
Indices: 13483248--13483637 Score: 563
Period size: 177 Copynumber: 2.2 Consensus size: 175
13483238 AAAATTTCCA
* * * *
13483248 AAAAAAATATTTTTAGGGAAAAGTTGAGAGTATCAATTTTTCTTAAGAATAATTTTCAAAAAGGG
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTGTCCTTAAGAATAATTTTCAAAAAGGA
* *
13483313 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTC-AAAAAA-ATATTT
66 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAAGTTTCAAAAAAATATATTT
* * * *
13483376 TTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTCTC
130 TTAAGGAAAAGTTGAAAATATCAATTTTTCTTAAAAAT-AAACTCTC
* * *
13483423 AAAAAAATATTTTTAGGAAAAAATTGAAAATATCAATTGTCCTTATA-AATAAATTTTCAAAAAG
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTGTCCTTA-AGAAT-AATTTTCAAAAAG
13483487 GAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAATATA
64 G-ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC-AAAAAAATATA
*
13483552 TTTTTAAGGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAACTTTC
127 TTTTTAAGGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAACTCTC
*
13483601 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATT
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATT
13483638 TTTCCTACAC
Statistics
Matches: 191, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
175 42 0.22
176 22 0.12
177 74 0.39
178 12 0.06
179 41 0.21
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (175 bp):
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTGTCCTTAAGAATAATTTTCAAAAAGGA
TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAATATATTTT
TAAGGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAACTCTC
Found at i:13490980 original size:21 final size:21
Alignment explanation
Indices: 13490956--13491018 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
13490946 ATTGTTCAAT
*
13490956 TTAAAATAAGTAAAATAATAA
1 TTAAAATAAATAAAATAATAA
*
13490977 TTAAAGATAGATTAATAATAATAA
1 TTAAA-ATA-AATAA-AATAATAA
*
13491001 -TAATAATAAAAAAAATAA
1 TTAA-AATAAATAAAATAA
13491019 AAAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 10 0.29
22 6 0.17
23 10 0.29
24 9 0.26
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
TTAAAATAAATAAAATAATAA
Found at i:13491027 original size:17 final size:19
Alignment explanation
Indices: 13490957--13491065 Score: 68
Period size: 20 Copynumber: 5.7 Consensus size: 19
13490947 TTGTTCAATT
* *
13490957 TAAAATAAGTAAAATAATAAT
1 TAAAATAAAT-AAATAA-AAA
* * *
13490978 TAAAGATAGATTAATAATAA
1 TAAA-ATAAATAAATAAAAA
13490998 TAATAAT-AATAAA-AAAAA
1 TAA-AATAAATAAATAAAAA
13491016 TAAAA-AAATAAATCTAAAAA
1 TAAAATAAATAAA--TAAAAA
*
13491036 TAAAATAAATAAGT--AAA
1 TAAAATAAATAAATAAAAA
13491053 T-AAATAAATAAAT
1 TAAAATAAATAAAT
13491066 GGAAAACTTG
Statistics
Matches: 71, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
16 11 0.15
17 12 0.17
18 7 0.10
19 5 0.07
20 16 0.23
21 16 0.23
22 4 0.06
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.26
Consensus pattern (19 bp):
TAAAATAAATAAATAAAAA
Found at i:13491028 original size:4 final size:4
Alignment explanation
Indices: 13491013--13491065 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
13491003 ATAATAAAAA
* * *
13491013 AAAT AAAA AAAT AAAT CTAA- AAAT AAAAT AAAT AAGT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
13491062 AAAT
1 AAAT
13491066 GGAAAACTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
3 2 0.05
4 32 0.80
5 6 0.15
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:13492543 original size:66 final size:67
Alignment explanation
Indices: 13492450--13492597 Score: 165
Period size: 67 Copynumber: 2.2 Consensus size: 67
13492440 CCACAAGTAA
* * * * ** ** *
13492450 AAAAAAATTACATGACCTAGACTAAACTGAGAT-CGAAAATGAGCGATCGGGAT-TGAACCACGG
1 AAAAAAATAAAATGAACTAGACCAAACTGAGATAAAAAAATGAGCGATAAGGATCT-AACCACGA
*
13492513 GTT
65 GTC
* *
13492516 AAAAAAATAAAATGAACTAGACCAAACTGAGATAAAAAAATGAGTGATAAGGATCTAATCACGAG
1 AAAAAAATAAAATGAACTAGACCAAACTGAGATAAAAAAATGAGCGATAAGGATCTAACCACGAG
13492581 TC
66 TC
13492583 AAAAAAATAAAATGA
1 AAAAAAATAAAATGA
13492598 TCTGGACTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
66 29 0.43
67 38 0.56
68 1 0.01
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (67 bp):
AAAAAAATAAAATGAACTAGACCAAACTGAGATAAAAAAATGAGCGATAAGGATCTAACCACGAG
TC
Found at i:13494578 original size:19 final size:20
Alignment explanation
Indices: 13494551--13494593 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
13494541 TTCTTATCAA
13494551 TTTTGTCTTTATTTTT-TTC
1 TTTTGTCTTTATTTTTCTTC
*
13494570 TTTTTTCTTTATTTTTCTTC
1 TTTTGTCTTTATTTTTCTTC
13494590 TTTT
1 TTTT
13494594 CCTTTCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTGTCTTTATTTTTCTTC
Found at i:13494585 original size:20 final size:19
Alignment explanation
Indices: 13494551--13494593 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
13494541 TTCTTATCAA
*
13494551 TTTTGTCTTTATTTTTTTC
1 TTTTGTCTTTATTTTCTTC
*
13494570 TTTTTTCTTTATTTTTCTTC
1 TTTTGTCTTTA-TTTTCTTC
13494590 TTTT
1 TTTT
13494594 CCTTTCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTGTCTTTATTTTCTTC
Found at i:13494598 original size:19 final size:19
Alignment explanation
Indices: 13494557--13494598 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
13494547 TCAATTTTGT
*
13494557 CTTTATTTTTTTCTTTTTT
1 CTTTATTTTTTTCTTTTTC
13494576 CTTTATTTTTCTTC-TTTTC
1 CTTTATTTTT-TTCTTTTTC
13494595 CTTT
1 CTTT
13494599 CATAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (19 bp):
CTTTATTTTTTTCTTTTTC
Found at i:13498487 original size:3 final size:3
Alignment explanation
Indices: 13498481--13498535 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
13498471 AATTAAAGAT
13498481 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13498529 ATA ATA A
1 ATA ATA A
13498536 AAAGAAAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13498567 original size:6 final size:6
Alignment explanation
Indices: 13498483--13498606 Score: 78
Period size: 6 Copynumber: 21.0 Consensus size: 6
13498473 TTAAAGATAT
* * * * * * * *
13498483 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
* * * *
13498531 AATAAA AAGAAA AAGAAA AAGAAA ATCTAAA AAT-AA AAT--A AATAAA
1 AATAAA AATAAA AATAAA AATAAA A-ATAAA AATAAA AATAAA AATAAA
13498577 AATGAAA ACA-AAA AAT-AA AATAAA AATAAA
1 AAT-AAA A-ATAAA AATAAA AATAAA AATAAA
13498607 TAAATAAATG
Statistics
Matches: 106, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.04
5 11 0.10
6 82 0.77
7 8 0.08
8 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (6 bp):
AATAAA
Found at i:13498590 original size:28 final size:28
Alignment explanation
Indices: 13498546--13498600 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
13498536 AAAGAAAAAG
*
13498546 AAAAAGAAAATCTAAAAATAAAATAAAT
1 AAAAAGAAAATCAAAAAATAAAATAAAT
13498574 AAAAATGAAAA-CAAAAAATAAAATAAA
1 AAAAA-GAAAATCAAAAAATAAAATAAA
13498601 AATAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (28 bp):
AAAAAGAAAATCAAAAAATAAAATAAAT
Found at i:13498594 original size:19 final size:20
Alignment explanation
Indices: 13498566--13498614 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
13498556 TCTAAAAATA
*
13498566 AAATAAATAAAAATGAAAAC
1 AAATAAATAAAAATAAAAAC
*
13498586 AAA-AAAT-AAAATAAAAAT
1 AAATAAATAAAAATAAAAAC
13498604 AAATAAATAAA
1 AAATAAATAAA
13498615 TGAAAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 12 0.48
19 8 0.32
20 5 0.20
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (20 bp):
AAATAAATAAAAATAAAAAC
Found at i:13498620 original size:19 final size:19
Alignment explanation
Indices: 13498565--13498621 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
13498555 ATCTAAAAAT
13498565 AAAATAAAT-AA-AAATG-
1 AAAATAAATAAATAAATGA
*
13498581 AAAACAAA-AAATAAAAT-A
1 AAAATAAATAAAT-AAATGA
13498599 AAAATAAATAAATAAATGA
1 AAAATAAATAAATAAATGA
13498618 AAAA
1 AAAA
13498622 CTTGCGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
16 9 0.27
18 15 0.45
19 9 0.27
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.16
Consensus pattern (19 bp):
AAAATAAATAAATAAATGA
Found at i:13500973 original size:3 final size:3
Alignment explanation
Indices: 13500965--13500996 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
13500955 ATTTTTAAAG
13500965 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
13500997 AATATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13504001 original size:22 final size:21
Alignment explanation
Indices: 13503956--13504030 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
13503946 TGCCGGATGT
*
13503956 TTAAAAGATTATGCTTGAATGTC
1 TTAAAA-ATTATGCTCGAA-GTC
13503979 TTAAAAATTATGCTCGTAAGTC
1 TTAAAAATTATGCTCG-AAGTC
* *
13504001 TTAGAGATTATG-TCTGAAAGTC
1 TTAAAAATTATGCTC-G-AAGTC
*
13504023 TTACAAAT
1 TTAAAAAT
13504031 CTCAATATCT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.05
22 34 0.77
23 8 0.18
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (21 bp):
TTAAAAATTATGCTCGAAGTC
Found at i:13504253 original size:104 final size:104
Alignment explanation
Indices: 13503998--13504408 Score: 457
Period size: 104 Copynumber: 4.0 Consensus size: 104
13503988 ATGCTCGTAA
* * *
13503998 GTCTTAGAGATTATGTCTGAAA-GTCTTACAAATCTCAATATCTTTGAATGCTCCTTGTATCAAA
1 GTCTTAAAGATTATG-CTCAAAGGTCTTACAAATCTCAATATCTTTGAATGCTCCTCGTATCAAA
* ** * *
13504062 GGCATTGAAACTTTAAAAATTTAAAATGCTTTGCTTGG-G
65 GGCATTGAAACTTTGAAAATTTAAAATATTTTACCTGGAG
* * * * * * *
13504101 GTCATAGAGATTATACTCAAAGGTCTTACAAATCTCAAAATCTTTGAATGTTCCTCATATCAAAA
1 GTCTTAAAGATTATGCTCAAAGGTCTTACAAATCTCAATATCTTTGAATGCTCCTCGTATCAAAG
* * *
13504166 GCATTGAGACTCTGAAGATTTAAAATATTTTACCTGGAG
66 GCATTGAAACTTTGAAAATTTAAAATATTTTACCTGGAG
* * * * * * * * *
13504205 GACTTAAAGATTATGCCCAAAGATTTTACAAATCTCAACAGCTTTGAATGCTCTTTGTACCAAAG
1 GTCTTAAAGATTATGCTCAAAGGTCTTACAAATCTCAATATCTTTGAATGCTCCTCGTATCAAAG
* * *
13504270 GCATTGAAACTTTGAAAATTTAAAATATTTTGCCCGAAG
66 GCATTGAAACTTTGAAAATTTAAAATATTTTACCTGGAG
* * * * * * *
13504309 GTCTTAAACATTATGCTTAGAGGTCTTATAAATCTTAATTTCTTTGAATGCTCCTCGTATCAGAG
1 GTCTTAAAGATTATGCTCAAAGGTCTTACAAATCTCAATATCTTTGAATGCTCCTCGTATCAAAG
*
13504374 GCATTGAAACTTTGAAATTTTAAAATATTTTACCT
66 GCATTGAAACTTTGAAAATTTAAAATATTTTACCT
13504409 AAAGATTTCA
Statistics
Matches: 250, Mismatches: 56, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
102 5 0.02
103 80 0.32
104 165 0.66
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (104 bp):
GTCTTAAAGATTATGCTCAAAGGTCTTACAAATCTCAATATCTTTGAATGCTCCTCGTATCAAAG
GCATTGAAACTTTGAAAATTTAAAATATTTTACCTGGAG
Found at i:13504457 original size:32 final size:32
Alignment explanation
Indices: 13504421--13504484 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
13504411 AGATTTCATA
* * *
13504421 GATTTTGGTGCCAG-CTTGACTAGGTTTAGTTT
1 GATTTGGGTGCCAGTC-TAACTAGGCTTAGTTT
13504453 GATTTGGGTGCCAGTCTAACTAGGCTTAGTTT
1 GATTTGGGTGCCAGTCTAACTAGGCTTAGTTT
13504485 ACCAGGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (32 bp):
GATTTGGGTGCCAGTCTAACTAGGCTTAGTTT
Found at i:13504586 original size:23 final size:23
Alignment explanation
Indices: 13504560--13504610 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
13504550 TAATTTGAGC
*
13504560 TAAATTACTAGTTAATA-TAGGCT
1 TAAATTACTAGCT-ATACTAGGCT
* *
13504583 TAAAGTACTAGCTATACTAGTCT
1 TAAATTACTAGCTATACTAGGCT
13504606 TAAAT
1 TAAAT
13504611 ATCATCTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (23 bp):
TAAATTACTAGCTATACTAGGCT
Found at i:13504669 original size:23 final size:23
Alignment explanation
Indices: 13504643--13504689 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
13504633 GGAGTTTGGG
13504643 TGCTAACTAAT-CTGGGCTTAAAA
1 TGCT-ACTAATACTGGGCTTAAAA
* *
13504666 TGCTAGTTATACTGGGCTTAAAA
1 TGCTACTAATACTGGGCTTAAAA
13504689 T
1 T
13504690 CATCTGAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (23 bp):
TGCTACTAATACTGGGCTTAAAA
Found at i:13504720 original size:77 final size:78
Alignment explanation
Indices: 13504579--13504764 Score: 211
Period size: 77 Copynumber: 2.4 Consensus size: 78
13504569 AGTTAATATA
* * * **
13504579 GGCTTAAAGTACTAGCTATACTAGTCTTAAATATCATCTAGGTGCTAGCTAAATGGAGTTTGGGT
1 GGCTTAAAATGCTAGCTATACTAGGCTTAAATATCATCTAGGTGCTAGCTAAATGGAACTTGGGT
13504644 GCTAACTAATCTG
66 GCTAACTAATCTG
* * *
13504657 GGCTTAAAATGCTAGTTATACTGGGCTTAAA-ATCATCT-GAGTGCTAGTTAAACT-GAACTTGG
1 GGCTTAAAATGCTAGCTATACTAGGCTTAAATATCATCTAG-GTGCTAGCTAAA-TGGAACTTGG
**
13504719 GTGCTAGTTAATCTG
64 GTGCTAACTAATCTG
13504734 GGCTTAAAATG-TCAGCTA-ATCTAGGCTTAAA
1 GGCTTAAAATGCT-AGCTATA-CTAGGCTTAAA
13504765 ATGCCAACTA
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
76 3 0.03
77 62 0.67
78 27 0.29
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (78 bp):
GGCTTAAAATGCTAGCTATACTAGGCTTAAATATCATCTAGGTGCTAGCTAAATGGAACTTGGGT
GCTAACTAATCTG
Found at i:13504781 original size:77 final size:77
Alignment explanation
Indices: 13504638--13504782 Score: 172
Period size: 77 Copynumber: 1.9 Consensus size: 77
13504628 TAAATGGAGT
* * * *
13504638 TTGGGTGCTAACTAATCTGGGCTTAAAATGCTAGTTATACTGGGCTTAAAATCATCTGAGTGCTA
1 TTGGGTGCTAACTAATCTGGGCTTAAAATGCTAGTAATACTAGGCTTAAAATCAACTGAATGCTA
13504703 GTTAAACTGAAC
66 GTTAAACTGAAC
**
13504715 TTGGGTGCTAGTTAATCTGGGCTTAAAATG-TCAGCTAAT-CTAGGCTTAAAATGCCAACT-AAT
1 TTGGGTGCTAACTAATCTGGGCTTAAAATGCT-AG-TAATACTAGGCTTAAAAT--CAACTGAAT
13504777 -CTAGTT
62 GCTAGTT
13504783 TTAAATCTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
76 1 0.02
77 48 0.83
78 5 0.09
79 4 0.07
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (77 bp):
TTGGGTGCTAACTAATCTGGGCTTAAAATGCTAGTAATACTAGGCTTAAAATCAACTGAATGCTA
GTTAAACTGAAC
Found at i:13504787 original size:23 final size:23
Alignment explanation
Indices: 13504727--13504780 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
13504717 GGGTGCTAGT
* * *
13504727 TAATCTGGGCTTAAAATGTCAGC
1 TAATCTAGGCTTAAAATGCCAAC
13504750 TAATCTAGGCTTAAAATGCCAAC
1 TAATCTAGGCTTAAAATGCCAAC
13504773 TAATCTAG
1 TAATCTAG
13504781 TTTTAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (23 bp):
TAATCTAGGCTTAAAATGCCAAC
Found at i:13505325 original size:95 final size:92
Alignment explanation
Indices: 13505206--13505400 Score: 259
Period size: 95 Copynumber: 2.1 Consensus size: 92
13505196 TGCGAATGTT
* *
13505206 TTTCTCATAATGCATATTTAAGTGCAAATACAAGTGATGCAAATGCAAAT-T-TTTCCTCTTTTT
1 TTTCTCATAATACATATGTAAGTGCAAATACAAGTGATGCAAATGCAAATGTCTTT--T-TTTTT
* *
13505269 TTTGGTTTTTTGCAATATTTAGATCAAATATC
63 TTT-G-TTTTTGCAACATGTAGATCAAATATC
* * *
13505301 TTTCTCATAATACATATGTCAGTGCGAATGCAAGTGATGCAAATGCAAATGTCTTTTTTTTTTTT
1 TTTCTCATAATACATATGTAAGTGCAAATACAAGTGATGCAAATGCAAATGTCTTTTTTTTTTTT
*
13505366 GTTTTTGCAACATGTAGATCAAATGTC
66 GTTTTTGCAACATGTAGATCAAATATC
13505393 TTTCTCAT
1 TTTCTCAT
13505401 GATGCACATG
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
92 31 0.34
93 1 0.01
94 8 0.09
95 46 0.51
96 1 0.01
97 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (92 bp):
TTTCTCATAATACATATGTAAGTGCAAATACAAGTGATGCAAATGCAAATGTCTTTTTTTTTTTT
GTTTTTGCAACATGTAGATCAAATATC
Found at i:13505491 original size:90 final size:91
Alignment explanation
Indices: 13505355--13505527 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 91
13505345 GCAAATGTCT
* * * *
13505355 TTTTTTTTTTTGTTTTTGCAACATGTAGATCAAATGTCTTTCTCATGATGCACATGTAATTGATA
1 TTTTTTTTATTGTTTTTGCAACATGTAGATCAAATATCCTTATCATGATGCACATGTAATTGATA
* *
13505420 CAAATGCGATTTTCTTTTGTTTTTTA
66 CAAATGCGAATGTCTTTTGTTTTTTA
* * * * * *
13505446 TTTTTTTTATT-TTTTTGCAATATGTAGGTTAAATATCCTTATCATGATGCATATGTCATTGATG
1 TTTTTTTTATTGTTTTTGCAACATGTAGATCAAATATCCTTATCATGATGCACATGTAATTGATA
13505510 CAAATGCGAATGTCTTTT
66 CAAATGCGAATGTCTTTT
13505528 ATATATATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
90 60 0.86
91 10 0.14
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (91 bp):
TTTTTTTTATTGTTTTTGCAACATGTAGATCAAATATCCTTATCATGATGCACATGTAATTGATA
CAAATGCGAATGTCTTTTGTTTTTTA
Found at i:13508394 original size:103 final size:103
Alignment explanation
Indices: 13508210--13508420 Score: 395
Period size: 103 Copynumber: 2.0 Consensus size: 103
13508200 TAATATTTTA
*
13508210 ATAAATAAAAATAAGTGGTATTATATCATTTATAGTTTACTTTCTTATTTGTACCACAATGGAGT
1 ATAACTAAAAATAAGTGGTATTATATCATTTATAGTTTACTTTCTTATTTGTACCACAATGGAGT
*
13508275 ACCCTAACTCAATCTTTCCACTCCTGCATTTCATACAT
66 ACCCTAACTCAATCTTTCCACTCCTGCATTTAATACAT
13508313 ATAACTAAAAATAAGTGGTATTATATCATTTATAGTTTACTTTCTTATTTGTACCACAATGGAGT
1 ATAACTAAAAATAAGTGGTATTATATCATTTATAGTTTACTTTCTTATTTGTACCACAATGGAGT
*
13508378 ACTCTAACTCAATCTTTCCACTCCTGCATTTAATACAT
66 ACCCTAACTCAATCTTTCCACTCCTGCATTTAATACAT
13508416 ATAAC
1 ATAAC
13508421 AATTAGTAAT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.39
Consensus pattern (103 bp):
ATAACTAAAAATAAGTGGTATTATATCATTTATAGTTTACTTTCTTATTTGTACCACAATGGAGT
ACCCTAACTCAATCTTTCCACTCCTGCATTTAATACAT
Found at i:13511874 original size:17 final size:19
Alignment explanation
Indices: 13511840--13511874 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
13511830 TTGTTTGTCT
13511840 ATTTTCACTCATTTCATAC
1 ATTTTCACTCATTTCATAC
13511859 ATTTT-ACTCA-TTCATA
1 ATTTTCACTCATTTCATA
13511875 GATCATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTCACTCATTTCATAC
Found at i:13517141 original size:41 final size:41
Alignment explanation
Indices: 13517095--13517173 Score: 142
Period size: 41 Copynumber: 1.9 Consensus size: 41
13517085 AAGACCTCTA
13517095 GACATAATCTCTAAGTT-TCCTGGGTAAGATTCATAAGTCTT
1 GACATAATCTCTAAGTTCTCC-GGGTAAGATTCATAAGTCTT
13517136 GACATAATCTCTAAGTTCTCCGGGTAAGATTCATAAGT
1 GACATAATCTCTAAGTTCTCCGGGTAAGATTCATAAGT
13517174 ATTATGAGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 34 0.92
42 3 0.08
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (41 bp):
GACATAATCTCTAAGTTCTCCGGGTAAGATTCATAAGTCTT
Found at i:13517290 original size:84 final size:84
Alignment explanation
Indices: 13517136--13517368 Score: 247
Period size: 84 Copynumber: 2.8 Consensus size: 84
13517126 CATAAGTCTT
** * * * *
13517136 GACATAATCTCTAAGTTCTCCGGGTAAGATTCATAAGTATTATGAGCTAAATATATTTTAGAA-T
1 GACATAATCTCTAAGTTCTTTGGGTAAGATTCATAAGTCTTCTAAGCTAAATCTATTTTA-AAGT
* *
13517200 CGAGATTTACAAAACCTCCA
65 CAAGATTTACAAAACCACCA
* * * *
13517220 GATATAATCTCTAAGTTCTTTGGGCAAGATTCGTAAGTCTTCTAAGCTGAATCTATTTTAAAGTC
1 GACATAATCTCTAAGTTCTTTGGGTAAGATTCATAAGTCTTCTAAGCTAAATCTATTTTAAAGTC
**
13517285 AAGATTTGTAAAACCACCA
66 AAGATTTACAAAACCACCA
* * * * *
13517304 GGCATAATCTCTAA-ATCTTTCAGATAAGATTCATAAGTCTTAC-AAGCTAAATCTATTTTAGAG
1 GACATAATCTCTAAGTTCTTT-GGGTAAGATTCATAAGTCTT-CTAAGCTAAATCTATTTTAAAG
13517367 TC
64 TC
13517369 GATATTTATG
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
83 7 0.06
84 115 0.93
85 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (84 bp):
GACATAATCTCTAAGTTCTTTGGGTAAGATTCATAAGTCTTCTAAGCTAAATCTATTTTAAAGTC
AAGATTTACAAAACCACCA
Found at i:13520859 original size:52 final size:52
Alignment explanation
Indices: 13520777--13520884 Score: 146
Period size: 52 Copynumber: 2.1 Consensus size: 52
13520767 CCTTTGGGAA
* * *
13520777 ATAA-ATTGTTTGTTATGTTTTCATAGATTCAATCAAGTCAAACTAAATAAG
1 ATAATATTGTTTGTTATCTTTCCATAGATTCAATCAAGTCAAAATAAATAAG
* * * *
13520828 ATAATATTGTTTGTTATCTTTCCTTAGATTCAATTAATTGAAAATAAATAAG
1 ATAATATTGTTTGTTATCTTTCCATAGATTCAATCAAGTCAAAATAAATAAG
13520880 ATAAT
1 ATAAT
13520885 TGTGCCATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 4 0.08
52 45 0.92
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (52 bp):
ATAATATTGTTTGTTATCTTTCCATAGATTCAATCAAGTCAAAATAAATAAG
Found at i:13528479 original size:332 final size:332
Alignment explanation
Indices: 13527749--13528680 Score: 1165
Period size: 332 Copynumber: 2.8 Consensus size: 332
13527739 TGAAAGCGGC
* * * * * *
13527749 TTATAATAAAATATGCCTTTAATAATCCAAAAAAAAATTT-TT-GAAAAAATATTTAAGGCATTG
1 TTATAATAAAAAATGCCTTTAATAATCC-AGAAAAATTTTATTAGAAAAATTATTAAAGGCATTA
* * * * *
13527812 TTATCTAAAATCACCTTCAGTAATTATATACAAACTATGATAGGAATTATTAAAGGCGTCTATAT
65 TTTTCT-GAATCACCTTCAGTAATTATATACAAACTATGAAAGGAATTATTAAAGGCATCTATCT
* * *
13527877 TAAATATACGCCTTCAATAAC-GATGTTACAATTTATGTGGTGGTATATAGAAGGTATTTTACAG
129 TAAATATACGCCTTTAATAACAG-TGTTACAATTTGTGTGGTGGTATATAGAAGGCATTTTACAG
* * *
13527941 TAGAAGAAGCCTTTACTAATT-CCAAAATATTTAGTGAAAAAATTTTTAAGGCATCTATTATTAA
193 TAGAAGATGCCTTTACTAATTCCCAAAATATTTAGTGAAAAAATTTTGAAGACATCTATTATTAA
* * **
13528005 CAAACTCCTTCAATAATTGAAGATGCCTTTTCTAATAAATGCCTTCCTTTACCAACGTGATATAT
258 CAAACGCCTTCAATAATTGAAGATGCCTTTTCTAATAAATACCTTCAATTACCAACGTGATATAT
**
13528070 TGAAGGCATT
323 CAAAGGCATT
* * * * **
13528080 TTATAATAAAAAATACCTTTAATAATCCTGAAAACTTTTATTAGAAAAATTATTGAAGGTGTTAT
1 TTATAATAAAAAATGCCTTTAATAATCCAGAAAAATTTTATTAGAAAAATTATTAAAGGCATTAT
* * *
13528145 TTTCTGAATCACCTTCAATAATTATATACAAATTATGAAAGAAATTATTAAAGGCATCTATCTTA
66 TTTCTGAATCACCTTCAGTAATTATATACAAACTATGAAAGGAATTATTAAAGGCATCTATCTTA
*
13528210 AATATACGCCTTTAATAACAGTGTTACAATTTGTGTGGTGGTATATAGAAGGCATTTTACAGTAA
131 AATATACGCCTTTAATAACAGTGTTACAATTTGTGTGGTGGTATATAGAAGGCATTTTACAGTAG
* * *
13528275 AAGATGCCTTTACTAATTCCCAAAATATTTAGTGAAAAAATTTTGATGACGTCTGTTATTAACAA
196 AAGATGCCTTTACTAATTCCCAAAATATTTAGTGAAAAAATTTTGAAGACATCTATTATTAACAA
* * * * ** *
13528340 TCGCCTTCAGTAATTGAAGGTGTCTTTTCTAATATTTACCTTCAATTACCATCGTGATATATCAA
261 ACGCCTTCAATAATTGAAGATGCCTTTTCTAATAAATACCTTCAATTACCAACGTGATATATCAA
*
13528405 AGGTATT
326 AGGCATT
* * * *
13528412 TTATAATGAAAGACGCCTTTAATAATCC-GAGAAAATTTTATTAGGAAAATTATTAAAGGCATTA
1 TTATAATAAAAAATGCCTTTAATAATCCAGA-AAAATTTTATTAGAAAAATTATTAAAGGCATTA
* * * * *
13528476 TTTTTTGAAACAGCCTTCAGTAATTATATACAAACTGTGAGAGGAATTATTAAAGGCATTTATCT
65 TTTTCTGAATCA-CCTTCAGTAATTATATACAAACTATGAAAGGAATTATTAAAGGCATCTATCT
** * * * * ** * *
13528541 TAAATATACATCTTTAATAATAGTGTTACAATATGTATAGCAGTATATAAAAGGCATTTTACAAT
129 TAAATATACGCCTTTAATAACAGTGTTACAATTTGTGTGGTGGTATATAGAAGGCATTTTACAGT
* * * *
13528606 AGAAGATGCCTTTAATAATTCCCAAAATATTTAGTGAAAAAATTTTGAAGGCGTCTATT-TCTAG
194 AGAAGATGCCTTTACTAATTCCCAAAATATTTAGTGAAAAAATTTTGAAGACATCTATTAT-TAA
13528670 CAAACGCCTTC
258 CAAACGCCTTC
13528681 TGTAATGAAT
Statistics
Matches: 517, Mismatches: 77, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
330 7 0.01
331 159 0.31
332 184 0.36
333 167 0.32
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (332 bp):
TTATAATAAAAAATGCCTTTAATAATCCAGAAAAATTTTATTAGAAAAATTATTAAAGGCATTAT
TTTCTGAATCACCTTCAGTAATTATATACAAACTATGAAAGGAATTATTAAAGGCATCTATCTTA
AATATACGCCTTTAATAACAGTGTTACAATTTGTGTGGTGGTATATAGAAGGCATTTTACAGTAG
AAGATGCCTTTACTAATTCCCAAAATATTTAGTGAAAAAATTTTGAAGACATCTATTATTAACAA
ACGCCTTCAATAATTGAAGATGCCTTTTCTAATAAATACCTTCAATTACCAACGTGATATATCAA
AGGCATT
Found at i:13533620 original size:22 final size:20
Alignment explanation
Indices: 13533595--13533646 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
13533585 AAGCCAAATC
13533595 AAAATATTGATAAAACTTAATA
1 AAAATATTGATAAAA-TTAA-A
* * * *
13533617 AAAAAATTAATAATATTTAA
1 AAAATATTGATAAAATTAAA
13533637 AAAATATTGA
1 AAAATATTGA
13533647 AAATACTGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 12 0.50
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATATTGATAAAATTAAA
Found at i:13533758 original size:30 final size:31
Alignment explanation
Indices: 13533719--13533777 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
13533709 TTAAAAATAA
*
13533719 TTATCTT-AAAATATATCAAAATTTATTTAAT
1 TTATCTTAAAAATATA-CAAAATTAATTTAAT
*
13533750 TTAT-TTAAAAATTTACAAAATTAATTTA
1 TTATCTTAAAAATATACAAAATTAATTTA
13533778 TGTAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (31 bp):
TTATCTTAAAAATATACAAAATTAATTTAAT
Found at i:13533849 original size:20 final size:20
Alignment explanation
Indices: 13533813--13533850 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13533803 ATTTAACTTT
*
13533813 TAATTTTAATTTTAATTTAA
1 TAATTTTAATTTAAATTTAA
13533833 TAATTTATAA-TTAAATTT
1 TAATTT-TAATTTAAATTT
13533851 TCATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TAATTTTAATTTAAATTTAA
Found at i:13535147 original size:11 final size:12
Alignment explanation
Indices: 13535105--13535154 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
13535095 ATAGCTTCAT
13535105 ATTTAATATTAATA
1 ATTTAATATT--TA
*
13535119 AATTATATATTT-
1 ATTTA-ATATTTA
13535131 ATTTAA-ATTTA
1 ATTTAATATTTA
13535142 ATTTAATATTTA
1 ATTTAATATTTA
13535154 A
1 A
13535155 GATTTTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 7 0.23
12 10 0.32
13 1 0.03
14 4 0.13
15 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTAATATTTA
Found at i:13535257 original size:16 final size:17
Alignment explanation
Indices: 13535223--13535263 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
13535213 TTTAATTTAT
13535223 ATAATAAAAATTTAAAAA
1 ATAA-AAAAATTTAAAAA
*
13535241 ATAAAAAAATTT-GAAA
1 ATAAAAAAATTTAAAAA
13535257 ATAAAAA
1 ATAAAAA
13535264 TTAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.45
17 8 0.36
18 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
ATAAAAAAATTTAAAAA
Found at i:13542854 original size:22 final size:22
Alignment explanation
Indices: 13542835--13542879 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
13542825 AAATAATATT
13542835 TTTATTATATTACTTTAATAAA
1 TTTATTATATTACTTTAATAAA
* *
13542857 TTTATTTTATTATTTTAAATAAA
1 TTTATTATATTACTTT-AATAAA
13542880 AATAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATATTACTTTAATAAA
Found at i:13542889 original size:11 final size:11
Alignment explanation
Indices: 13542873--13542903 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13542863 TTATTATTTT
*
13542873 AAATAAAAATA
1 AAATAAAAAGA
13542884 AAATAAAAAGA
1 AAATAAAAAGA
13542895 AAATAAAAA
1 AAATAAAAA
13542904 AAGAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (11 bp):
AAATAAAAAGA
Found at i:13543166 original size:294 final size:293
Alignment explanation
Indices: 13542658--13543186 Score: 925
Period size: 294 Copynumber: 1.8 Consensus size: 293
13542648 TGAATTATAA
* *
13542658 TGAGAATATAAAATAATTATTAAGGGTATTAAAATAAAAATGATATGTAATAATAATTTTAAATT
1 TGAGAATATAAAATAATTATTAAAGGTATTAAAATAAAAATGATATGTAATAATAATTTTAAATG
*
13542723 ATTTAATATTTGTAAAATTAGTAAATAATTATTGAATTATTTTTATATAAATAATAATTTTATTA
66 ATTTAATATTTATAAAATTAGTAAATAATTATTGAATTATTTTTATATAAATAATAATTTTATTA
*
13542788 ATAAATAATTAAAAATTAATAAAAATAATAATATAGCAAATAATATTTTTATTATATTACTTTAA
131 ATAAATAATTAAAAAATAATAAAAATAATAATATAGCAAATAATATTTTTATTATATTACTTTAA
*
13542853 TAAATTTATTTTATTATTTTAAATAAAAATAAAATAAAAAGAAAATAAAAAAAGAAATATTATTA
196 TAAATTTATTTTATTATTTTAAATAAAAAGAAAATAAAAAGAAAATAAAAAAAGAAATATTATTA
13542918 AGAAAAGATATTTTAATAATTACAATATTGTAT
261 AGAAAAGATATTTTAATAATTACAATATTGTAT
* * *
13542951 TGAGAATATAAAATAATTATTAAAGGTATTAAAATGAAAATGATATGTATTGATAATTTTAAATG
1 TGAGAATATAAAATAATTATTAAAGGTATTAAAATAAAAATGATATGTAATAATAATTTTAAATG
13543016 ATTTAATATTTATAAAATTAGTAAATAATTATTGAATTATTTTTATATAAAATAATAATTTTATT
66 ATTTAATATTTATAAAATTAGTAAATAATTATTGAATTATTTTTATAT-AAATAATAATTTTATT
* * * *
13543081 AATAAATAATTAAAAAATAATAAAAATGATAGTATATCAAATAATATTTTTATTGTATTACTTTA
130 AATAAATAATTAAAAAATAATAAAAATAATAATATAGCAAATAATATTTTTATTATATTACTTTA
13543146 ATAATATTT-TTTTATTATTTTAAATAAAAAGAAAATAAAAA
195 ATAA-ATTTATTTTATTATTTTAAATAAAAAGAAAATAAAAA
13543187 AAGAATATTT
Statistics
Matches: 222, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
293 107 0.48
294 111 0.50
295 4 0.02
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (293 bp):
TGAGAATATAAAATAATTATTAAAGGTATTAAAATAAAAATGATATGTAATAATAATTTTAAATG
ATTTAATATTTATAAAATTAGTAAATAATTATTGAATTATTTTTATATAAATAATAATTTTATTA
ATAAATAATTAAAAAATAATAAAAATAATAATATAGCAAATAATATTTTTATTATATTACTTTAA
TAAATTTATTTTATTATTTTAAATAAAAAGAAAATAAAAAGAAAATAAAAAAAGAAATATTATTA
AGAAAAGATATTTTAATAATTACAATATTGTAT
Found at i:13545969 original size:18 final size:18
Alignment explanation
Indices: 13545946--13545982 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13545936 TGGACGATAA
13545946 GCCTTTTTTAAAACTTAG
1 GCCTTTTTTAAAACTTAG
13545964 GCCTTTTTTAAAACTTAG
1 GCCTTTTTTAAAACTTAG
13545982 G
1 G
13545983 TTATGAGGTC
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:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (18 bp):
GCCTTTTTTAAAACTTAG
Found at i:13547409 original size:23 final size:23
Alignment explanation
Indices: 13547383--13547426 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
13547373 TATAGTTTTC
*
13547383 TTTCCTTCAAT-TGTTTTCTCTAT
1 TTTCC-TCAATATGTATTCTCTAT
13547406 TTTCCTCAATATGTATTCTCT
1 TTTCCTCAATATGTATTCTCT
13547427 TTATCACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTCCTCAATATGTATTCTCTAT
Found at i:13554037 original size:17 final size:17
Alignment explanation
Indices: 13554004--13554043 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
13553994 TGATAAATAG
* *
13554004 AATG-ATAAGTAATCAA
1 AATGTATAACTAAACAA
13554020 AATGTATAACTAAACAA
1 AATGTATAACTAAACAA
13554037 AATGTAT
1 AATGTAT
13554044 GTGTTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (17 bp):
AATGTATAACTAAACAA
Found at i:13564371 original size:30 final size:30
Alignment explanation
Indices: 13564337--13564401 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
13564327 TCTTTGAGAT
**
13564337 TTTCACAATGAATTTTTTAATTTCTCTTGA
1 TTTCACAATGAATTTTGCAATTTCTCTTGA
*
13564367 TTTCACAATGAATTTTGCAATTTCTTTTGA
1 TTTCACAATGAATTTTGCAATTTCTCTTGA
13564397 TTTCA
1 TTTCA
13564402 TTTTCAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (30 bp):
TTTCACAATGAATTTTGCAATTTCTCTTGA
Found at i:13567048 original size:18 final size:18
Alignment explanation
Indices: 13567021--13567055 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13567011 AGCACTTTAC
*
13567021 TTTATCTTTGGAATTATA
1 TTTATATTTGGAATTATA
*
13567039 TTTATATTTGGACTTAT
1 TTTATATTTGGAATTAT
13567056 TACAGCCTTT
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:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTATATTTGGAATTATA
Found at i:13568986 original size:22 final size:22
Alignment explanation
Indices: 13568955--13569000 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
13568945 ATATTGTTAC
*
13568955 AAAACACTTATTATTGGAAAAA
1 AAAACACTTATTAATGGAAAAA
*
13568977 AAAACCCTTATTAATGGAAAAA
1 AAAACACTTATTAATGGAAAAA
13568999 AA
1 AA
13569001 TAATAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.24
Consensus pattern (22 bp):
AAAACACTTATTAATGGAAAAA
Found at i:13569372 original size:31 final size:31
Alignment explanation
Indices: 13569303--13569381 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
13569293 ATGTATTTAT
*
13569303 ACGAAATTTGAAATTTAGTTTCTATACTCGC
1 ACGAAATTTGAAATTTAGTTTCTATACTCAC
* * *
13569334 ACAAAATTTGAAATTTAGTTTCTGTACTCAT
1 ACGAAATTTGAAATTTAGTTTCTATACTCAC
* *
13569365 ATGAAATTTAAAATTTA
1 ACGAAATTTGAAATTTA
13569382 CTACCTCTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (31 bp):
ACGAAATTTGAAATTTAGTTTCTATACTCAC
Found at i:13569424 original size:19 final size:18
Alignment explanation
Indices: 13569396--13569440 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
13569386 CTCTAATATG
13569396 AAAATATTTTGAATTTTTT
1 AAAATATTTT-AATTTTTT
* *
13569415 AAAATTTTTTAGTTTTTT
1 AAAATATTTTAATTTTTT
13569433 AAAATATT
1 AAAATATT
13569441 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
AAAATATTTTAATTTTTT
Found at i:13569535 original size:32 final size:32
Alignment explanation
Indices: 13569469--13569555 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
13569459 CAATATTCTC
* * *
13569469 TCATAATATTATATCACAATATTGAAAATCTA
1 TCATAATATTCTATCACAATTTTTAAAATCTA
*
13569501 TCATAATATTCTATCACAATTTTTATATAT-TA
1 TCATAATATTCTATCACAATTTTTA-AAATCTA
13569533 TCACTAA-A-TCTATCACAATTTTT
1 TCA-TAATATTCTATCACAATTTTT
13569556 TGTCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 15 0.31
32 28 0.57
33 6 0.12
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (32 bp):
TCATAATATTCTATCACAATTTTTAAAATCTA
Found at i:13570354 original size:16 final size:14
Alignment explanation
Indices: 13570319--13570408 Score: 69
Period size: 14 Copynumber: 6.2 Consensus size: 14
13570309 AATTTTGATA
13570319 TATTAAT-TTAAAT
1 TATTAATATTAAAT
13570332 TATTAATATTATAAT
1 TATTAATATTA-AAT
13570347 TGATTAATA-TAAAT
1 T-ATTAATATTAAAT
* *
13570361 GATAATAATAATAAAAT
1 --TATTAAT-ATTAAAT
* *
13570378 TATTAATATGATAT
1 TATTAATATTAAAT
13570392 TATTAATAATT-AAT
1 TATTAAT-ATTAAAT
13570406 TAT
1 TAT
13570409 ATATAATAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
13 7 0.11
14 23 0.37
15 19 0.31
16 9 0.15
17 4 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:13570378 original size:46 final size:46
Alignment explanation
Indices: 13570328--13570417 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
13570318 ATATTAATTT
*
13570328 AAATTATTAATATTATAATTGATTAAT-ATAAATGATA-ATAATAATA
1 AAATTATTAATATGAT-ATT-ATTAATAATAAATGATATATAATAATA
* *
13570374 AAATTATTAATATGATATTATTAATAATTAATTATATATAATAA
1 AAATTATTAATATGATATTATTAATAATAAATGATATATAATAA
13570418 AAACTAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 6 0.15
45 11 0.28
46 22 0.56
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (46 bp):
AAATTATTAATATGATATTATTAATAATAAATGATATATAATAATA
Done.