Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_pilon, 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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 19
Found at i:1992573 original size:110 final size:110
Alignment explanation
Indices: 1992422--1992628 Score: 315
Period size: 110 Copynumber: 1.9 Consensus size: 110
1992412 GACTGGGAAA
* *
1992422 TTGTTTGTTGACAGCCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATA
1 TTGTTTGTTGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
* * *
1992487 TCCTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
66 TCCCTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* * * * *
1992532 TTGTTTGTTGACAATCAGTCGCTCCTTCGTTGTGAAGTTGAGCTTTTGTTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
*
1992597 TCCCTCGCTATGAAGTTGAAATTGGCTCTGAA
66 TCCCTCGCTATGAAGTTGAAATTGACTCTGAA
1992629 ACTGGGAAGC
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (110 bp):
TTGTTTGTTGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
TCCCTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
Found at i:1993459 original size:36 final size:36
Alignment explanation
Indices: 1993419--1993626 Score: 184
Period size: 36 Copynumber: 5.9 Consensus size: 36
1993409 TATTTCAAGG
1993419 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAA
* *
1993455 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAAA
* * **
1993492 GAAAATGTCTCAAGGGAGATGAAATTTGTTTCAAATA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAA-A
* * **
1993529 -AAACATAT-TC-----A-A-ATAATTTGTTTCAAGG
1 GAAAC-TGTCTCAAGAGAGACAAAATTTGTTTCAAAA
* **
1993557 GAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAA
*
1993593 GAAACTGTCTCAAGAGAGA-AGAAATTTATTTCAA
1 GAAACTGTCTCAAGAGAGACA-AAATTTGTTTCAA
1993627 GGGAAATGTT
Statistics
Matches: 142, Mismatches: 17, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.01
29 18 0.13
30 1 0.01
31 1 0.01
34 1 0.01
35 2 0.01
36 84 0.59
37 33 0.23
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAA
Found at i:1993501 original size:37 final size:36
Alignment explanation
Indices: 1993419--1993510 Score: 139
Period size: 37 Copynumber: 2.5 Consensus size: 36
1993409 TATTTCAAGG
* *
1993419 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
1993455 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
* *
1993492 GAAAATGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
1993511 TGAAATTTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 24 0.47
37 27 0.53
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.21
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:1993656 original size:101 final size:101
Alignment explanation
Indices: 1993441--1993713 Score: 305
Period size: 101 Copynumber: 2.7 Consensus size: 101
1993431 AGAGAGACAA
* * * ** *
1993441 AATTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAG
* * * *
1993506 GGAGATGAAATTTGTTTCAAATAAAACATATTCAAAT
65 AGAGAAGAAATTTATTTCAAAGAAAACATATTCAAAT
*
1993543 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA
* * ** *
1993608 GAGAAGAAATTTATTTCAAGGGAAATGTTTTC-AAT
66 GAGAAGAAATTTATTTCAAAGAAAACATATTCAAAT
** * * * *
1993643 GTTTATGTTTCAAGAGAAACCGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTATTTCAAGGGAAACTGTCTCAA
*
1993708 GCGAGA
64 GAGAGA
1993714 TAAAATATTC
Statistics
Matches: 145, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
100 5 0.03
101 73 0.50
102 67 0.46
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (101 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA
GAGAAGAAATTTATTTCAAAGAAAACATATTCAAAT
Found at i:1993699 original size:37 final size:37
Alignment explanation
Indices: 1993648--1993719 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1993638 TCAATGTTTA
* *
1993648 TGTTTCAAGAGAAACCGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACCATCTCAAGCGAGACAAAATTT
* * *
1993685 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACCATCTCAAGCGAGACAAAAT
1993720 ATTCTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACCATCTCAAGCGAGACAAAATTT
Found at i:1995232 original size:13 final size:13
Alignment explanation
Indices: 1995196--1995253 Score: 66
Period size: 13 Copynumber: 4.4 Consensus size: 13
1995186 TCTTGTCTTT
1995196 TTTTTAATTTTC-C
1 TTTTT-ATTTTCTC
*
1995209 TTTGTTTTTTTCTC
1 TTT-TTATTTTCTC
1995223 TTTTTATTTTCTC
1 TTTTTATTTTCTC
1995236 TTTGTT-TTTTCTC
1 TTT-TTATTTTCTC
1995249 TTTTT
1 TTTTT
1995254 TCTGATTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 2 0.05
13 30 0.75
14 8 0.20
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTTATTTTCTC
Found at i:1995253 original size:26 final size:27
Alignment explanation
Indices: 1995196--1995253 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
1995186 TCTTGTCTTT
1995196 TTTTTAATTTTCCTTTGTTTTTTTCTC
1 TTTTTAATTTTCCTTTGTTTTTTTCTC
1995223 TTTTT-ATTTTCTCTTTG-TTTTTTCTC
1 TTTTTAATTTTC-CTTTGTTTTTTTCTC
1995249 TTTTT
1 TTTTT
1995254 TCTGATTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (27 bp):
TTTTTAATTTTCCTTTGTTTTTTTCTC
Found at i:1995254 original size:27 final size:26
Alignment explanation
Indices: 1995195--1995254 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 26
1995185 ATCTTGTCTT
1995195 TTTTTTAATTTTCCTTTGTTTTTTTC
1 TTTTTTAATTTTCCTTTGTTTTTTTC
1995221 TCTTTTT-ATTTTCTCTTTGTTTTTTCTC
1 T-TTTTTAATTTTC-CTTTGTTTTTT-TC
1995249 TTTTTT
1 TTTTTT
1995255 CTGATTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.23
27 21 0.68
28 3 0.10
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.78
Consensus pattern (26 bp):
TTTTTTAATTTTCCTTTGTTTTTTTC
Found at i:1999785 original size:16 final size:16
Alignment explanation
Indices: 1999764--1999794 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1999754 AACAGGTAAA
*
1999764 AAATAATAATAATAAT
1 AAATAATAAAAATAAT
1999780 AAATAATAAAAATAA
1 AAATAATAAAAATAA
1999795 ACAAAATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAATAAAAATAAT
Found at i:2000040 original size:25 final size:26
Alignment explanation
Indices: 1999970--2000079 Score: 79
Period size: 25 Copynumber: 4.3 Consensus size: 26
1999960 GGTAAAACAA
* * *
1999970 ATAAA-AAATAAAGATATACAT-GAT
1 ATAAAGAAATAAAAATATAAATAAAT
*
1999994 ATTAAG-AA-AAAAATAATAAATAAAT
1 ATAAAGAAATAAAAAT-ATAAATAAAT
*
2000019 A-AAAGGAAATAAAAATAT-AATATAT
1 ATAAA-GAAATAAAAATATAAATAAAT
* *
2000044 ATAAATAAATAAAAATAAAAATAGAAT
1 ATAAAGAAATAAAAATATAAATA-AAT
*
2000071 ATTAAGAAA
1 ATAAAGAAA
2000080 ATATATATAA
Statistics
Matches: 66, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
23 5 0.08
24 13 0.20
25 22 0.33
26 11 0.17
27 15 0.23
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (26 bp):
ATAAAGAAATAAAAATATAAATAAAT
Found at i:2000051 original size:31 final size:30
Alignment explanation
Indices: 2000000--2000109 Score: 89
Period size: 31 Copynumber: 3.4 Consensus size: 30
1999990 TGATATTAAG
* *
2000000 AAAAAAATAATA-AATAAATAAA-AGGAAAT
1 AAAAATATAATATAATAAATAAATA-AAAAT
2000029 AAAAATATAATATATATAAATAAATAAAAAT
1 AAAAATATAATATA-ATAAATAAATAAAAAT
* *
2000060 AAAAATAGAATATTAAGAAAATATATATAAAAACGT
1 AAAAATATAATA-TAA-TAAATA-A-ATAAAAA--T
2000096 ATAAAATATAATAT
1 A-AAAATATAATAT
2000110 TAAGAAACAA
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
29 11 0.17
30 1 0.02
31 25 0.38
32 8 0.12
33 1 0.02
34 7 0.11
36 3 0.05
37 10 0.15
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAAATATAATATAATAAATAAATAAAAAT
Found at i:2007471 original size:18 final size:18
Alignment explanation
Indices: 2007448--2007483 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2007438 ATAATATTAT
*
2007448 TCTTAATAATATTATATA
1 TCTTAATAATACTATATA
2007466 TCTTAATAATACTATATA
1 TCTTAATAATACTATATA
2007484 GAAATATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
TCTTAATAATACTATATA
Found at i:2008523 original size:15 final size:18
Alignment explanation
Indices: 2008467--2008521 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
2008457 AGATGCTACT
*
2008467 TTATAATCACTAATTATA
1 TTATCATCACTAATTATA
2008485 TTATCATCACTAATTATA
1 TTATCATCACTAATTATA
2008503 TTATCATCACTAATTATA
1 TTATCATCACTAATTATA
2008521 T
1 T
2008522 CACTATTTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATCATCACTAATTATA
Found at i:2010106 original size:15 final size:16
Alignment explanation
Indices: 2010068--2010109 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2010058 ATGTAGGCTT
*
2010068 AATATACTATTAAAAA
1 AATATATTATTAAAAA
2010084 AATATATTATTAAAAA
1 AATATATTATTAAAAA
*
2010100 TAT-TATTATT
1 AATATATTATT
2010110 TTTTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATTATTAAAAA
Found at i:2010292 original size:44 final size:44
Alignment explanation
Indices: 2010189--2010292 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
2010179 AAATCGGTAG
* *
2010189 AAAAAATAATATTTTACATAGCGCCCAATATTAATATTTCTAGT
1 AAAAAATAATATTTTACATAACGCCCAATATTAATATTTCTACT
** *
2010233 AAAAAATAAGGTTTTA-AGTAACGTCCAATATTAATATTTC-ACT
1 AAAAAATAATATTTTACA-TAACGCCCAATATTAATATTTCTACT
2010276 AGAAAAATAATATTTTA
1 A-AAAAATAATATTTTA
2010293 GATAGTGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
43 4 0.08
44 47 0.92
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (44 bp):
AAAAAATAATATTTTACATAACGCCCAATATTAATATTTCTACT
Found at i:2024879 original size:27 final size:27
Alignment explanation
Indices: 2024846--2024910 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
2024836 AATTTTTCCC
* *
2024846 TAATATTTATTATTATAGGCTTATTTT
1 TAATATTTATTATTAGAGACTTATTTT
*
2024873 TAATATTTATTATTGGAGACTTATTTT
1 TAATATTTATTATTAGAGACTTATTTT
2024900 T-ATAATTTATT
1 TAAT-ATTTATT
2024911 TTTTCTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (27 bp):
TAATATTTATTATTAGAGACTTATTTT
Found at i:2025230 original size:72 final size:71
Alignment explanation
Indices: 2025095--2025231 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
2025085 TGGATTTTCA
* * * * * *
2025095 ATTTTTTAATATTTTTTATTATGAACATACTATTAAAATTTATCTTTTTTTAATATTTGTTATTA
1 ATTTTTTAATACTTATTATTATGAACATACTATTAAAATTTATCTTTTTTCAACACTTATTATTA
2025160 GGGACT
66 GGGACT
*
2025166 ATTTTTTCAATACTTATTATTATGAAGATACCT-TTAAAATTTTAT-TTTTTTCAACACTTATTA
1 ATTTTTT-AATACTTATTATTATGAACATA-CTATTAAAA-TTTATCTTTTTTCAACACTTATTA
2025229 TTA
63 TTA
2025232 TGACAGTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
71 7 0.12
72 42 0.75
73 7 0.12
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (71 bp):
ATTTTTTAATACTTATTATTATGAACATACTATTAAAATTTATCTTTTTTCAACACTTATTATTA
GGGACT
Found at i:2033191 original size:9 final size:9
Alignment explanation
Indices: 2033179--2033204 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2033169 ATCAAAAAAA
2033179 TTATTATTT
1 TTATTATTT
2033188 TTATTATTT
1 TTATTATTT
2033197 TTATTATT
1 TTATTATT
2033205 ATTAGGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTATTT
Found at i:2033605 original size:21 final size:21
Alignment explanation
Indices: 2033563--2033605 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2033553 CTGGTAAAAA
**
2033563 TTACCTAAAAAATTATTATTT
1 TTACCTAAAAAACAATTATTT
2033584 TTACCTAAAACAACAATT-TTT
1 TTACCTAAAA-AACAATTATTT
2033605 T
1 T
2033606 AACATTTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (21 bp):
TTACCTAAAAAACAATTATTT
Found at i:2039117 original size:102 final size:102
Alignment explanation
Indices: 2038941--2039135 Score: 243
Period size: 102 Copynumber: 1.9 Consensus size: 102
2038931 ATAAGCTGGT
* * * ** ** *
2038941 AGTTGAATGTCTTCCCCTTGAACCTGAAGGCATCGTGTCATATGAGTTTTGAATTGAGTGTTGTG
1 AGTTGAATGTCCTCCCCTGGAACCTGAAGGCATCGTGTCAAATGAGTACTGAACAGAGTGTTGTA
*
2039006 TCGCAGGCATCTCCATATTGAGGTCAAAGCAGCTCGC
66 TCGCAGGCATCTCCATATTAAGGTCAAAGCAGCTCGC
* *
2039043 AGTTGAATG-CCTCCTCCTGGAACTTGAAGGCATCGTGTCAAATGAGTACTGAACAGATTGCTT-
1 AGTTGAATGTCCTCC-CCTGGAACCTGAAGGCATCGTGTCAAATGAGTACTGAACAGAGTG-TTG
2039106 TATCG-AGGGCATCTCCATATTAAGGTCAAA
64 TATCGCA-GGCATCTCCATATTAAGGTCAAA
2039136 AAATTGGCAG
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
101 5 0.06
102 72 0.91
103 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (102 bp):
AGTTGAATGTCCTCCCCTGGAACCTGAAGGCATCGTGTCAAATGAGTACTGAACAGAGTGTTGTA
TCGCAGGCATCTCCATATTAAGGTCAAAGCAGCTCGC
Found at i:2039964 original size:13 final size:14
Alignment explanation
Indices: 2039941--2039969 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2039931 AACAAAATCT
2039941 ATTTGATAGAAGGA
1 ATTTGATAGAAGGA
2039955 ATTT-ATAGAAGGA
1 ATTTGATAGAAGGA
2039968 AT
1 AT
2039970 AATGTGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.31
Consensus pattern (14 bp):
ATTTGATAGAAGGA
Found at i:2042024 original size:23 final size:21
Alignment explanation
Indices: 2041978--2042024 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2041968 AATGAAGAAT
2041978 AAAAATAAAAAAAAATAAAGG
1 AAAAATAAAAAAAAATAAAGG
* *
2041999 AAAAATAATTAAATAAATAAATG
1 AAAAATAA--AAAAAAATAAAGG
2042022 AAA
1 AAA
2042025 TATTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (21 bp):
AAAAATAAAAAAAAATAAAGG
Found at i:2042109 original size:18 final size:18
Alignment explanation
Indices: 2042066--2042116 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
2042056 AAAATAGAAA
*
2042066 AATAATAATCATAACA-AT
1 AATAATAAT-ATAAAATAT
2042084 AATAATAATATGAAAATAT
1 AATAATAATAT-AAAATAT
2042103 AAT-ATAATATAAAA
1 AATAATAATATAAAA
2042117 AAAATCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.20
18 19 0.63
19 5 0.17
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
AATAATAATATAAAATAT
Found at i:2042359 original size:19 final size:21
Alignment explanation
Indices: 2042326--2042365 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
2042316 TAAAAAAAGT
*
2042326 ATATATATATATAAATAATAA
1 ATATATATATATAAAAAATAA
2042347 ATATA-ATAT-TAAAAAATAA
1 ATATATATATATAAAAAATAA
2042366 CCAAATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATATATATATAAAAAATAA
Found at i:2042363 original size:22 final size:22
Alignment explanation
Indices: 2042318--2042395 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
2042308 ATATTTTTTA
*
2042318 AAAAAAGTATATATATATATAAAT
1 AAAAAA-TATA-ATATAAATAAAT
*
2042342 AATAAATATAATATTAAA-AAAT
1 AAAAAATATAATA-TAAATAAAT
* *
2042364 AACCAAAT-GAATATAAATAAAT
1 AA-AAAATATAATATAAATAAAT
2042386 AAAAAATATA
1 AAAAAATATA
2042396 TGTATAGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 8 0.18
22 20 0.45
23 11 0.25
24 5 0.11
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (22 bp):
AAAAAATATAATATAAATAAAT
Found at i:2042406 original size:23 final size:24
Alignment explanation
Indices: 2042375--2042423 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2042365 ACCAAATGAA
2042375 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
2042398 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
2042422 TA
1 TA
2042424 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:2042939 original size:37 final size:37
Alignment explanation
Indices: 2042889--2042996 Score: 144
Period size: 37 Copynumber: 2.9 Consensus size: 37
2042879 ATACTTGTGG
* *
2042889 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATATTTAGGAGTTTGAATCATAGTAGAACTCT
* * *
2042926 ATCCTATATTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATATTTAGGAGTTTGAATCATAGTAGAACTCT
* * *
2042963 ATCTTATTTTTAGGAGTTTGAATCCTAGTAGAAC
1 ATCCTATATTTAGGAGTTTGAATCATAGTAGAAC
2042997 GAAAAGGTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATATTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:2044009 original size:106 final size:106
Alignment explanation
Indices: 2043697--2045385 Score: 2486
Period size: 106 Copynumber: 16.0 Consensus size: 106
2043687 GCATTGTTCT
* * * *** * * *
2043697 GAGTCAAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCAGGAAATTATTTTTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * * *
2043761 ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2043803 GAGTCCAATAACCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
2043862 TCAGCAGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* *
2043904 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2043968 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
2044009 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGTTATAAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
2044074 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2044115 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2044180 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2044221 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
2044286 CCAGCAGTCCCTTTGTTGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2044327 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
2044392 CCAGTGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2044433 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
2044498 -CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2044538 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
2044603 CCAACGATCCATTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2044644 GAGTCCAATATCCTACGCTGTGAATTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
2044709 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2044750 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2044815 CCATC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
2044855 GAGTCCAATATCCTTCATTGTGAAGTTGAAATT-GCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
2044919 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2044960 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2045025 TCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
2045066 GAGTCCAATATCCTTCGTTGTGGAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
2045131 CCAGCGGTCCCTTCGTTGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2045172 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
2045237 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2045277 -AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
2045341 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2045382 GAGT
1 GAGT
2045386 GGCACGATAT
Statistics
Matches: 1442, Mismatches: 127, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
100 77 0.05
101 5 0.00
102 4 0.00
104 134 0.09
105 234 0.16
106 987 0.68
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2044665 original size:317 final size:318
Alignment explanation
Indices: 2043696--2045385 Score: 2677
Period size: 317 Copynumber: 5.3 Consensus size: 318
2043686 AGCATTGTTC
* * * *** * *
2043696 TGAGTCAAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCAGGAAATTATTTTTTGAC
1 TGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAC
* * * * * * *
2043760 AACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATAACCTTCGCTGTG
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
* * * *
2043825 AAGTTGAAATTGACTCTG-AA-TGA-AA--T-TTTGTTGACAATCAGCAGCCCCTTCGTCGTGAA
130 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
* * * *
2043884 GTTGAGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATT
195 GTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
2043948 GGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
259 GGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
2044008 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGTTATAAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
2044073 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* *
2044138 AGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAG
131 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
2044203 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGG
196 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * *
2044268 GAAGTTGTTTATTGACAACCAGCAGTCCCTTTGTTGTGAAGTTGAACTTGCGTTGTCT
261 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
2044326 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* *
2044391 ACCAGTGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
2044456 AGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA-CAGCGGTCCCTTCGTCGTGAAG
131 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
2044520 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGG
196 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * * * *
2044585 GAAGTTATTTATTGACAACCAACGATCCATTCGTCGTGAAGTTGAACTTGTGTTGTCT
261 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
2044643 TGAGTCCAATATCCTACGCTGTGAATTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
*
2044708 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
2044773 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCATC-GTCCCTTCGTCGTGAAG
131 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
**
2044837 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATT-GCTCTGAAATTGG
196 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
*
2044901 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCT
261 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
2044959 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* *
2045024 ATCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGG
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* *
2045089 AGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAG
131 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
2045154 TTAAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA
196 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
*
2045219 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-
261 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
2045276 T-AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * *
2045340 ACCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTGAGT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
2045386 GGCACGATAT
Statistics
Matches: 1273, Mismatches: 94, Indels: 18
0.92 0.07 0.01
Matches are distributed among these distances:
312 125 0.10
313 3 0.00
314 3 0.00
315 2 0.00
316 333 0.26
317 433 0.34
318 374 0.29
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (318 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:2046214 original size:22 final size:22
Alignment explanation
Indices: 2046189--2046265 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
2046179 TTATGTTTGG
*
2046189 TCAAAGGTTTGGCATTTGATTC
1 TCAAAGGTTTGGCATTTGATGC
2046211 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2046233 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2046255 TCAACGGTTTG
1 TCAAAGGTTTG
2046266 ATGGGGTAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:2046934 original size:172 final size:173
Alignment explanation
Indices: 2046641--2046987 Score: 574
Period size: 172 Copynumber: 2.0 Consensus size: 173
2046631 TAAATAGGCC
*
2046641 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTTATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAA-CA-GTCCTG
*
2046706 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTAAGTGATTCGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTAAGTGATTCGGGAATA
* *
2046771 ATTTTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGTCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
* *
2046816 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTGTGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAACAGTCCTGCT
*
2046878 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATA
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTAAGTGATTCGGGAATA
2046943 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
2046988 TTTAGGGAAT
Statistics
Matches: 163, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
170 14 0.09
172 98 0.60
174 1 0.01
175 50 0.31
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTAAGTGATTCGGGAATAAT
TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:2047059 original size:7 final size:7
Alignment explanation
Indices: 2047020--2047092 Score: 51
Period size: 7 Copynumber: 9.7 Consensus size: 7
2047010 TTTTTGTCCC
2047020 TTTTTCT
1 TTTTTCT
2047027 TTTTGAT-T
1 TTTT--TCT
2047035 TTTGTTCT
1 TTT-TTCT
2047043 TGTTTCTCT
1 T-TTT-TCT
2047052 TTTTTCT
1 TTTTTCT
*
2047059 TTATT-T
1 TTTTTCT
*
2047065 TTTTGCT
1 TTTTTCT
2047072 TTTTTGCT
1 TTTTT-CT
2047080 TCTTTTCT
1 T-TTTTCT
2047088 TTTTT
1 TTTTT
2047093 GTTCTTGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
6 4 0.08
7 21 0.40
8 16 0.30
9 12 0.23
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:2047091 original size:16 final size:16
Alignment explanation
Indices: 2047065--2047098 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2047055 TTCTTTATTT
2047065 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
2047082 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
2047097 TT
1 TT
2047099 GATTGGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:2050547 original size:20 final size:20
Alignment explanation
Indices: 2050513--2050550 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2050503 TGCAGATGAT
2050513 GGAAATAAAATAAAAGAGAG
1 GGAAATAAAATAAAAGAGAG
2050533 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
2050551 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.08
Consensus pattern (20 bp):
GGAAATAAAATAAAAGAGAG
Found at i:2051637 original size:12 final size:12
Alignment explanation
Indices: 2051620--2051690 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
2051610 AGGGAAAAAT
2051620 AAATAAATGAAA
1 AAATAAATGAAA
2051632 AAATAAA-GAATAA
1 AAATAAATG-A-AA
* *
2051645 AAATAAGTAAAA
1 AAATAAATGAAA
* *
2051657 AAATAAAAGGAA
1 AAATAAATGAAA
*
2051669 AAAT-AATTAAA
1 AAATAAATGAAA
2051680 TAAATAAATGA
1 -AAATAAATGA
2051691 TATATATATA
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
11 5 0.11
12 26 0.59
13 13 0.30
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (12 bp):
AAATAAATGAAA
Found at i:2051648 original size:13 final size:13
Alignment explanation
Indices: 2051615--2051663 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
2051605 GTCCGAGGGA
2051615 AAAATAAATAAA-T
1 AAAA-AAATAAAGT
*
2051628 GAAAAAATAAAG-
1 AAAAAAATAAAGT
2051640 AATAAAAAT-AAGT
1 AA-AAAAATAAAGT
2051653 AAAAAAATAAA
1 AAAAAAATAAA
2051664 AGGAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 17 0.57
13 13 0.43
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAAAAATAAAGT
Found at i:2051670 original size:24 final size:25
Alignment explanation
Indices: 2051620--2051687 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 25
2051610 AGGGAAAAAT
* *
2051620 AAATAAATGAAAAAATAAAGAATAA
1 AAATAAATAAAAAAATAAAGAAGAA
* *
2051645 AAATAAGTAAAAAAATAAA-AGGAA
1 AAATAAATAAAAAAATAAAGAAGAA
* *
2051669 AAATAATTAAATAAATAAA
1 AAATAAATAAAAAAATAAA
2051688 TGATATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 20 0.54
25 17 0.46
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (25 bp):
AAATAAATAAAAAAATAAAGAAGAA
Found at i:2051776 original size:18 final size:18
Alignment explanation
Indices: 2051728--2051781 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 18
2051718 AAAATAGAAA
2051728 AATAATAATCATAACAATAAT
1 AATAATAAT-ATAA-AAT-AT
2051749 AATAATAATATGAAAATAT
1 AATAATAATAT-AAAATAT
2051768 AAT-ATAATATAAAA
1 AATAATAATATAAAA
2051782 AAACCAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.12
18 7 0.22
19 5 0.16
20 5 0.16
21 11 0.34
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAATAATATAAAATAT
Found at i:2051782 original size:18 final size:20
Alignment explanation
Indices: 2051728--2051782 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
2051718 AAAATAGAAA
*
2051728 AATAATAATCATAACAATAAT
1 AATAATAAT-ATAAAAATAAT
*
2051749 AATAATAATATGAAAAT-AT
1 AATAATAATATAAAAATAAT
2051768 AAT-ATAATATAAAAA
1 AATAATAATATAAAAA
2051783 AACCAAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.35
19 5 0.16
20 6 0.19
21 9 0.29
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
AATAATAATATAAAAATAAT
Found at i:2051799 original size:20 final size:21
Alignment explanation
Indices: 2051773--2051823 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
2051763 AATATAATAT
2051773 AATATAAAAAA-ACCAAAACCA
1 AATATAAAAAATA-CAAAACCA
*
2051794 AA-ATAAATAAATATAAAACCA
1 AATATAAA-AAATACAAAACCA
2051815 AATATAAAA
1 AATATAAAA
2051824 GTATACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.19
21 15 0.58
22 6 0.23
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.16
Consensus pattern (21 bp):
AATATAAAAAATACAAAACCA
Found at i:2052018 original size:19 final size:19
Alignment explanation
Indices: 2051976--2052024 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2051966 ATATTTTTTT
*
2051976 TAAAAAAGTATATATATATA
1 TAAAAAA-TAAATATATATA
*
2051996 TAAATAATAAATATAGTAT-
1 TAAAAAATAAATATA-TATA
2052015 TAAAAAATAA
1 TAAAAAATAA
2052025 CCAAATGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
TAAAAAATAAATATATATA
Found at i:2052599 original size:37 final size:37
Alignment explanation
Indices: 2052558--2052657 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 37
2052548 GGATCATATC
* * *
2052558 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATA
1 TTTAGGAGTTTGAATCCTAGTAGAACTATATCCTATA
* * * * *
2052595 TTTAGGAGTTTGAATCCTAGCAAAATTATATCTTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTATATCCTATA
*
2052632 TTTAGGAGTTTGAATCCTATTAGAAC
1 TTTAGGAGTTTGAATCCTAGTAGAAC
2052658 GAAAAAGTAT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTATATCCTATA
Found at i:2056533 original size:26 final size:26
Alignment explanation
Indices: 2056504--2056558 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
2056494 TAATGAAAGT
*
2056504 AAATAAATAATATAAATA-AAATAATA
1 AAATAAAAAATATAAATATAAAT-ATA
*
2056530 AAATAAAAAATATATATATAAATATA
1 AAATAAAAAATATAAATATAAATATA
2056556 AAA
1 AAA
2056559 ATGTATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (26 bp):
AAATAAAAAATATAAATATAAATATA
Found at i:2056552 original size:19 final size:20
Alignment explanation
Indices: 2056510--2056583 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
2056500 AAGTAAATAA
2056510 ATAATATAAATAAA-ATA-AT
1 ATAATATAAA-AAATATATAT
2056529 A-AA-ATAAAAAATATATAT
1 ATAATATAAAAAATATATAT
* *
2056547 ATAA-ATATAAAAATGTATGT
1 ATAATATA-AAAAATATATAT
2056567 ATAATATAATAAAATAT
1 ATAATATAA-AAAATAT
2056584 TAAATAGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 3 0.07
17 8 0.17
18 5 0.11
19 6 0.13
20 15 0.33
21 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
ATAATATAAAAAATATATAT
Found at i:2056599 original size:29 final size:27
Alignment explanation
Indices: 2056499--2056601 Score: 70
Period size: 29 Copynumber: 3.6 Consensus size: 27
2056489 AAACATAATG
2056499 AAAGTAAATAAATAATATAAATAAAATAATA
1 AAAGT-AAT-AATAATAT-AATAAAAT-ATA
2056530 AAA-TAA-AA-AATATATATATAAATATAA
1 AAAGTAATAATAATATA-ATA-AAATAT-A
*
2056557 AAATGT-ATGTATAATATAATAAAATATTA
1 AAA-GTAAT-AATAATATAATAAAATA-TA
2056586 AATAGTAATAATAATA
1 AA-AGTAATAATAATA
2056602 ATAAATGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 24
0.69 0.02 0.28
Matches are distributed among these distances:
25 1 0.02
26 10 0.17
27 10 0.17
28 1 0.02
29 19 0.32
30 9 0.15
31 9 0.15
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (27 bp):
AAAGTAATAATAATATAATAAAATATA
Found at i:2056652 original size:28 final size:28
Alignment explanation
Indices: 2056585--2056652 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
2056575 ATAAAATATT
*
2056585 AAATAGTAAT-A-ATAATAATAAATGAA
1 AAATAGTAATCATATAATAATAAATAAA
* * *
2056611 AAATAAT-ATACATATAATATTAACTAAA
1 AAATAGTAAT-CATATAATAATAAATAAA
2056639 AAATAGTAATCATA
1 AAATAGTAATCATA
2056653 GAAATATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
25 2 0.06
26 6 0.18
27 1 0.03
28 22 0.67
29 2 0.06
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (28 bp):
AAATAGTAATCATATAATAATAAATAAA
Found at i:2064572 original size:255 final size:257
Alignment explanation
Indices: 2064121--2064626 Score: 982
Period size: 255 Copynumber: 2.0 Consensus size: 257
2064111 ATCTAGGGAC
2064121 CGGGGCGTTACACCATCAGTTAGATTTTGTTCGGAGTAGGGCGATGAACTTAATGGTGGTGGCAT
1 CGGGGCGTTACACCATCAGTTAGATTTTGTTCGGAGTAGGGCGATGAACTTAATGGTGGTGGCAT
2064186 GTAACATACAATCAACCATAGCCGTTAGAAAACAACGAATGAAAACTTAAAAACTAACGACCCTT
66 GTAACATACAATCAACCATAGCCGTTAGAAAACAACGAATGAAAACTTAAAAACTAACGACCCTT
2064251 TGAGATATTTTTCATGACAATCAACATAGTTTACGATTGGTTTGGGGACTAGATTTTTGTCGTGG
131 TGAGATATTTTTCATGACAATCAACATAGTTTACGATTGGTTTGGGGACTAGATTTTTGTCGTGG
2064316 CAATGAGAC-ATTTTGATGATGTCAACGGTGACAGCCACATACC-GTGATGTGATTAGGAGA
196 CAATGAGACAATTTTGATGATGTCAACGGTGACAGCCACATACCGGTGATGTGATTAGGAGA
2064376 CGGGGCGTTACACCATCAGTTAGATTTTGTTCGGAGTAGGGCGATGAACTTAATGGTGGTGGCAT
1 CGGGGCGTTACACCATCAGTTAGATTTTGTTCGGAGTAGGGCGATGAACTTAATGGTGGTGGCAT
2064441 GTAACATACAATCAACCATAGCCGTTAGAAAACAACGAATGAAAACTTAAAAACTAACGACCCTT
66 GTAACATACAATCAACCATAGCCGTTAGAAAACAACGAATGAAAACTTAAAAACTAACGACCCTT
2064506 TGAGATATTTTTCATGACAATCAACATAGTTTCACGATTGG-TTGGGGACTAGATTTTTGTCGTG
131 TGAGATATTTTTCATGACAATCAACATAGTTT-ACGATTGGTTTGGGGACTAGATTTTTGTCGTG
2064570 GCAATGAGACAATTTTGATGATGTCAACGGTGACAGCCACATACCGGTGATGTGATT
195 GCAATGAGACAATTTTGATGATGTCAACGGTGACAGCCACATACCGGTGATGTGATT
2064627 TTGTTTTTTT
Statistics
Matches: 248, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
255 195 0.79
256 42 0.17
257 11 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (257 bp):
CGGGGCGTTACACCATCAGTTAGATTTTGTTCGGAGTAGGGCGATGAACTTAATGGTGGTGGCAT
GTAACATACAATCAACCATAGCCGTTAGAAAACAACGAATGAAAACTTAAAAACTAACGACCCTT
TGAGATATTTTTCATGACAATCAACATAGTTTACGATTGGTTTGGGGACTAGATTTTTGTCGTGG
CAATGAGACAATTTTGATGATGTCAACGGTGACAGCCACATACCGGTGATGTGATTAGGAGA
Found at i:2065741 original size:14 final size:14
Alignment explanation
Indices: 2065722--2065763 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2065712 TATTTTTAAA
2065722 AATTTAAATAATAT
1 AATTTAAATAATAT
2065736 AATTTAAAT-AT-T
1 AATTTAAATAATAT
* *
2065748 ATTTTAAATAAAAT
1 AATTTAAATAATAT
2065762 AA
1 AA
2065764 CTAAAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTAAATAATAT
Found at i:2066323 original size:19 final size:18
Alignment explanation
Indices: 2066290--2066325 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2066280 ATATTCGTAA
*
2066290 ATATTAAATTTAAAAAAT
1 ATATTAAAATTAAAAAAT
2066308 ATATTCAAAATTAAAAAA
1 ATATT-AAAATTAAAAAA
2066326 AATCACTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATTAAAATTAAAAAAT
Found at i:2068415 original size:28 final size:26
Alignment explanation
Indices: 2068364--2068416 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
2068354 AAATATTAGA
* *
2068364 ATTATTTATTTATTTATTATTAAAAC
1 ATTATTTATTAATTTATTAATAAAAC
2068390 ATTATTTATATAATTTTATTAATAAAA
1 ATTATTTAT-TAA-TTTATTAATAAAA
2068417 AGATTAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 2 0.09
28 12 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTATTTATTAATTTATTAATAAAAC
Found at i:2068511 original size:28 final size:30
Alignment explanation
Indices: 2068456--2068526 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
2068446 AAAAATATTT
* *
2068456 ATAA-ATTATATTATTTATTTATTAAAGTA
1 ATAATATTATATTATATATTTATGAAAGTA
2068485 ATAATATTATATTATAT-TTTA-GAAAGTA
1 ATAATATTATATTATATATTTATGAAAGTA
* *
2068513 TTAATTAATATATT
1 ATAA-TATTATATT
2068527 TTAAATATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.25
29 16 0.44
30 11 0.31
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
ATAATATTATATTATATATTTATGAAAGTA
Found at i:2068695 original size:27 final size:28
Alignment explanation
Indices: 2068659--2068726 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
2068649 TAATTTATTA
*
2068659 TATAGTATTAAAATATAATAT-AATATCT
1 TATAATATTAAAATATAAT-TGAATATCT
* * *
2068687 TA-ATTATTATAATATAATTGAATATTT
1 TATAATATTAAAATATAATTGAATATCT
2068714 TATAATATTAAAA
1 TATAATATTAAAA
2068727 AATCTAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 1 0.03
27 22 0.67
28 10 0.30
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (28 bp):
TATAATATTAAAATATAATTGAATATCT
Found at i:2072092 original size:26 final size:26
Alignment explanation
Indices: 2072049--2072110 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
2072039 AAGTCAATGA
* * *
2072049 TCAACGGATCAGTTAAACGGGTTGGG
1 TCAACGGGTCAATCAAACGGGTTGGG
2072075 TCAACGGGTCAATCAAACGGGTTGGG
1 TCAACGGGTCAATCAAACGGGTTGGG
2072101 TCAACGGGTC
1 TCAACGGGTC
2072111 GGTTATTGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (26 bp):
TCAACGGGTCAATCAAACGGGTTGGG
Found at i:2074558 original size:26 final size:26
Alignment explanation
Indices: 2074508--2074566 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
2074498 GTGGCATGGT
* *
2074508 TTTTCAAAAATCATTTTTCATATTT-
1 TTTTAAAAAATCATTTTTCAAATTTG
2074533 TTTCTAAAAAATC-TTTTTGCAAATTTG
1 TTT-TAAAAAATCATTTTT-CAAATTTG
2074560 TTTTAAA
1 TTTTAAA
2074567 CAAAATTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 8 0.28
26 18 0.62
27 3 0.10
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.53
Consensus pattern (26 bp):
TTTTAAAAAATCATTTTTCAAATTTG
Found at i:2075335 original size:19 final size:19
Alignment explanation
Indices: 2075313--2075353 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2075303 CAAACGGGCA
2075313 GAATCGAACTGAGTTGAGC
1 GAATCGAACTGAGTTGAGC
2075332 GAATCGAACTGAGTTGAGC
1 GAATCGAACTGAGTTGAGC
2075351 GAA
1 GAA
2075354 AACAGTCAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.20
Consensus pattern (19 bp):
GAATCGAACTGAGTTGAGC
Found at i:2084713 original size:36 final size:36
Alignment explanation
Indices: 2084672--2084743 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2084662 TTCTCTAGTA
2084672 TTAAAATTAAAAATTCAAAAATATATTTAATTTATT
1 TTAAAATTAAAAATTCAAAAATATATTTAATTTATT
2084708 TTAAAATTAAAAATTCAAAAATATATTTAATTTATT
1 TTAAAATTAAAAATTCAAAAATATATTTAATTTATT
2084744 ATTTCAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (36 bp):
TTAAAATTAAAAATTCAAAAATATATTTAATTTATT
Found at i:2084750 original size:25 final size:27
Alignment explanation
Indices: 2084721--2084784 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
2084711 AAATTAAAAA
* *
2084721 TTCAAAAATATATTTA-ATTTA-TTAT
1 TTCAAAAATATAATAATATTTATTTAT
2084746 TTCAAAATTATATAATAATATTTATTTAT
1 TTCAAAA--ATATAATAATATTTATTTAT
2084775 TT-AAAAATAT
1 TTCAAAAATAT
2084785 TAGAAAAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 7 0.21
26 4 0.12
27 7 0.21
28 9 0.27
29 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
TTCAAAAATATAATAATATTTATTTAT
Found at i:2085313 original size:2 final size:2
Alignment explanation
Indices: 2085306--2085387 Score: 150
Period size: 2 Copynumber: 42.0 Consensus size: 2
2085296 TAAATTGTAC
2085306 AT AT AT AT AT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2085346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2085388 TCTGTAAGGA
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2085970 original size:11 final size:10
Alignment explanation
Indices: 2085947--2085994 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
2085937 TATCTCTTCC
2085947 TTTCGTTTTTT
1 TTTC-TTTTTT
2085958 TTTCTTTTCTT
1 TTTCTTTT-TT
2085969 TTT-TTTTTGT
1 TTTCTTTTT-T
2085979 TTTCTATTTTT
1 TTTCT-TTTTT
2085990 TTTCT
1 TTTCT
2085995 CTCTCTCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 12 0.36
11 16 0.48
12 4 0.12
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:2085971 original size:16 final size:16
Alignment explanation
Indices: 2085947--2085994 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
2085937 TATCTCTTCC
*
2085947 TTTCGTTTTTTTTTCT
1 TTTCTTTTTTTTTTCT
*
2085963 TTTCTTTTTTTTTTGT
1 TTTCTTTTTTTTTTCT
*
2085979 TTTCTATTTTTTTTCT
1 TTTCTTTTTTTTTTCT
2085995 CTCTCTCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.83
Consensus pattern (16 bp):
TTTCTTTTTTTTTTCT
Found at i:2086776 original size:76 final size:76
Alignment explanation
Indices: 2086599--2087006 Score: 673
Period size: 76 Copynumber: 5.4 Consensus size: 76
2086589 GAAATGTTGA
*
2086599 AAACATCATGCACTGAAGG-CTTACAGATGACCCTAAGGCTTTGAAAAACATCAAAAAGCTCCTG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG-AAAACATCAAAAAGCTCCCG
2086663 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
2086675 AAACATCATGCACTGTAGGAC-TACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2086739 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
2086750 AAACATCATGCACTGTAGGACTTACAGATGACTCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2086815 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2086826 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-AAGAACATCAAAAAGCTCTCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAA-AACATCAAAAAGCTCCCG
2086890 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
2086902 AAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2086966 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2086977 AAA-ATCATGCACTGAAGGACTTATAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
2087007 GGGAAATAGT
Statistics
Matches: 317, Mismatches: 11, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
74 26 0.08
75 97 0.31
76 193 0.61
77 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2086957 original size:151 final size:151
Alignment explanation
Indices: 2086599--2087006 Score: 671
Period size: 151 Copynumber: 2.7 Consensus size: 151
2086589 GAAATGTTGA
*
2086599 AAACATCATGCACTGAAGG-CTTACAGATGACCCTAAGGCTTTGAAAAACATCAAAAAGCTCCTG
1 AAACATCATGCACTGAAGGACTTACAGATGA-CCTAAGGCTTT-AAAAACATCAAAAAGCTCCCG
* *
2086663 AAGGCTTTTTGGAAACATCATGCACTGTAGGAC-TACAGATGACCCTAAGGCTTTGAAAACATCA
64 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
2086727 AAAAGCTCCCGAAGGCTTTTTGG
129 AAAAGCTCCCGAAGGCTTTTTGG
* * *
2086750 AAACATCATGCACTGTAGGACTTACAGATGACTCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGAC-CTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
2086815 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-AAGAACATCA
65 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAA-AACATCA
*
2086879 AAAAGCTCTCGAAGGCTTTTTGG
129 AAAAGCTCCCGAAGGCTTTTTGG
*
2086902 AAACATCATGCACTGAAGGACTTACAGATGACCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAA
1 AAACATCATGCACTGAAGGACTTACAGATGACCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAA
*
2086967 GGCTTTTTGGAAA-ATCATGCACTGAAGGACTTATAGATGA
66 GGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
2087007 GGGAAATAGT
Statistics
Matches: 241, Mismatches: 12, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
150 26 0.11
151 115 0.48
152 100 0.41
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (151 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAA
GGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAA
AAGCTCCCGAAGGCTTTTTGG
Found at i:2087557 original size:107 final size:111
Alignment explanation
Indices: 2087384--2087993 Score: 718
Period size: 113 Copynumber: 5.7 Consensus size: 111
2087374 GATAGAATAT
* *
2087384 GCAAAAAGTTGAAC-AATTCTT-TTATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
2087444 ATTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
66 ATTATGAACTTCTCTGGAAAAG-TGATCCATCAAATGATGGATTTAA
2087491 GCAAAAGGTTGAAC-AATTC-T-T-ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-TC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
2087551 ATTATGAACCTTCTCTGGCAAAA-TAATCCATCAAGTGAT-GAATTCA
66 ATTATGAA-CTTCTCTGG-AAAAGTGATCCATCAAATGATGGATTTAA
*
2087597 G-ACAAAGGTTGAACAAA---TT-TCAATATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCA-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * ** *
2087654 CATTATGAACTTTCTCTGG-AATGATGATCCATCAAATAATATATTCAA
65 CATTATGAAC-TTCTCTGGAAAAG-TGATCCATCAAATGATGGATTTAA
* *
2087702 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
2087767 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
66 ATTATGAAC-TTCTCTGGAAAAG-TGATCCATCAAATGATGGATTTAA
* *
2087815 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
2087880 ATTATGAACTTCTATGG-AAA-TG-TCAATC-CATGATGGATTTGA
66 ATTATGAACTTCTCTGGAAAAGTGATCCATCAAATGATGGATTTAA
*
2087922 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-C--CTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2087984 ATTATGAACT
66 ATTATGAACT
2087994 CGACCTGGAA
Statistics
Matches: 450, Mismatches: 30, Indels: 49
0.85 0.06 0.09
Matches are distributed among these distances:
102 2 0.00
103 27 0.06
104 59 0.13
105 29 0.06
106 28 0.06
107 95 0.21
108 42 0.09
109 15 0.03
111 2 0.00
112 53 0.12
113 98 0.22
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (111 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTCTCTGGAAAAGTGATCCATCAAATGATGGATTTAA
Found at i:2087838 original size:113 final size:111
Alignment explanation
Indices: 2087384--2088027 Score: 739
Period size: 107 Copynumber: 6.0 Consensus size: 111
2087374 GATAGAATAT
* *
2087384 GCAAAAAGTTGAAC-AATTCTTTTATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAATTCTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * **
2087445 TTATGAAC-TTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
66 TTATGAACTTTCTCTGG-AATGATGATCCATCAAATGATGGATTCAA
2087491 GCAAAAGGTTGAAC-AATTC-TT-ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-TCA
1 GCAAAAGGTTGAACAAATTCTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
2087552 TTATGAACCTTCTCTGGCAA-AATAATCCATCAAGTGATGAATTC-A
66 TTATGAACTTTCTCTGG-AATGATGATCCATCAAATGATGGATTCAA
*
2087597 G-ACAAAGGTTGAACAAA---TTTCAATATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCA-AAAGGTTGAACAAATTCTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* **
2087655 ATTATGAACTTTCTCTGGAATGATGATCCATCAAATAATATATTCAA
65 ATTATGAACTTTCTCTGGAATGATGATCCATCAAATGATGGATTCAA
* *
2087702 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTT-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2087767 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
65 ATTATGAACTTTCTCTGG-AATGATGATCCATCAAATGATGGATTCAA
* *
2087815 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTT-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
2087880 ATTATGAAC-TTCTATGGAA--ATG-TCAATC-CATGATGGATTTGA
65 ATTATGAACTTTCTCTGGAATGATGATCCATCAAATGATGGATTCAA
*
2087922 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-C--CTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTT-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * **
2087984 ATTATGAACTCGAC-CTGGAATGTTGATCCATTGAATGATGGATT
65 ATTATGAACT-TTCTCTGGAATGATGATCCATCAAATGATGGATT
2088028 GAACTTTGCT
Statistics
Matches: 473, Mismatches: 38, Indels: 50
0.84 0.07 0.09
Matches are distributed among these distances:
103 28 0.06
104 64 0.14
105 32 0.07
106 25 0.05
107 102 0.22
108 47 0.10
109 22 0.05
111 2 0.00
112 53 0.11
113 98 0.21
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (111 bp):
GCAAAAGGTTGAACAAATTCTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAATGATGATCCATCAAATGATGGATTCAA
Found at i:2087869 original size:24 final size:23
Alignment explanation
Indices: 2087834--2087878 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2087824 TGAACAAATT
2087834 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
2087858 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
2087879 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:2088454 original size:21 final size:21
Alignment explanation
Indices: 2088430--2088471 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2088420 TTTTCATTTG
*
2088430 AAAAGAGAATCTGTCATCTTT
1 AAAAGAGAATCTATCATCTTT
2088451 AAAAGAGAATCTATCATCTTT
1 AAAAGAGAATCTATCATCTTT
2088472 GAAGAGTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (21 bp):
AAAAGAGAATCTATCATCTTT
Found at i:2096919 original size:218 final size:216
Alignment explanation
Indices: 2096544--2096977 Score: 818
Period size: 218 Copynumber: 2.0 Consensus size: 216
2096534 TTTTGGTAAA
2096544 TCTATCAGAACCCTTGGTTACCAAATTAGGTCGATCATTTACCATAACTGTAAGGTTCCATGATC
1 TCTATCAGAACCCTTGGTTACCAAATTAGGTCGATCATTTACCATAACTGTAAGGTTCCATGATC
2096609 CAAAAGACTTTGGATTCGCGTTGAAGGCAAGACAATTCTCGATGGTATGTCCTTGAGCTCCGGCA
66 CAAAAGACTTTGGATTCGCGTTGAAGGCAAGACAATTCTCGATGGTATGTCCTTGAGCTCCGGCA
2096674 TGATATTCACAATGAACGTTGATGTCATACCAATTTGGATACGGAGGTTGGAACGG-TTTAT-AT
131 TGATATTCACAATGAACGTTGATGTCATACCAATTTGGATACGGAGGTTGGAACGGTTTTATAAT
2096737 ATAGGATCCACTTCTCGTGCTT
196 AT-GGATCCACTTCTCGTGCTT
2096759 TCTATCAGAACCCTTGGTTACCAAATTAGGTCGATCATTTACCATAACTTGTAAGGTTCCATGAT
1 TCTATCAGAACCCTTGGTTACCAAATTAGGTCGATCATTTACCATAAC-TGTAAGGTTCCATGAT
2096824 CCAAAAGACTTTGGATTCAGCGTTTGAAGGCAAGACAATTCTCGATGGTATGTCCTTGAGCTCCG
65 CCAAAAGACTTTGGATTC-GCG-TTGAAGGCAAGACAATTCTCGATGGTATGTCCTTGAGCTCCG
2096889 GCATGATATTCACAATGAACGTTGATGTCATACCAATTTGGATACGGAGGTTGGAACGGTTTTAT
128 GCATGATATTCACAATGAACGTTGATGTCATACCAATTTGGATACGGAGGTTGGAACGGTTTTAT
2096954 AATATGGATCCACTTCTCGTGCTT
193 AATATGGATCCACTTCTCGTGCTT
2096978 CAAGTAGCTT
Statistics
Matches: 214, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
215 48 0.22
216 34 0.16
217 3 0.01
218 101 0.47
219 24 0.11
220 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (216 bp):
TCTATCAGAACCCTTGGTTACCAAATTAGGTCGATCATTTACCATAACTGTAAGGTTCCATGATC
CAAAAGACTTTGGATTCGCGTTGAAGGCAAGACAATTCTCGATGGTATGTCCTTGAGCTCCGGCA
TGATATTCACAATGAACGTTGATGTCATACCAATTTGGATACGGAGGTTGGAACGGTTTTATAAT
ATGGATCCACTTCTCGTGCTT
Found at i:2098846 original size:15 final size:16
Alignment explanation
Indices: 2098822--2098854 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2098812 GCTCTTTTCT
2098822 TTGATATT-AATAAAA
1 TTGATATTAAATAAAA
*
2098837 TTGATTTTAAATAAAA
1 TTGATATTAAATAAAA
2098853 TT
1 TT
2098855 AAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGATATTAAATAAAA
Found at i:2098977 original size:23 final size:24
Alignment explanation
Indices: 2098941--2098985 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2098931 TTCGATATTG
2098941 AAAAATATTAAAATAATTTATTTTA
1 AAAAATATTAAAATAA-TTATTTTA
*
2098966 AAAAATA-T-AAATTATTATTT
1 AAAAATATTAAAATAATTATTT
2098986 ATCATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 1 0.05
25 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAAATATTAAAATAATTATTTTA
Found at i:2099941 original size:16 final size:16
Alignment explanation
Indices: 2099917--2099965 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
2099907 TATCTCTTCC
*
2099917 TTTCGTTTTTTTTTCT
1 TTTCTTTTTTTTTTCT
*
2099933 TTTCTTTTTTTTTTGT
1 TTTCTTTTTTTTTTCT
*
2099949 TTTCTATTTTTTGTTCT
1 TTTCT-TTTTTTTTTCT
2099966 CTCTCTCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTTTTTTCT
Found at i:2100424 original size:3 final size:3
Alignment explanation
Indices: 2100416--2100456 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2100406 ATTTTTTATT
*
2100416 TAA TAA TAA TAA T-A TAA TAA -AT TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
2100457 AATGAACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2104150 original size:11 final size:11
Alignment explanation
Indices: 2104130--2104164 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
2104120 ACCACCACGT
2104130 AAACTCGAATC
1 AAACTCGAATC
*
2104141 AAACTTGAATC
1 AAACTCGAATC
2104152 AAACTCGAATC
1 AAACTCGAATC
2104163 AA
1 AA
2104165 GCTCTAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.09, T:0.20
Consensus pattern (11 bp):
AAACTCGAATC
Found at i:2129805 original size:24 final size:24
Alignment explanation
Indices: 2129778--2129847 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
2129768 ATTATATAAG
2129778 TATTTATATATTTTATAATATTAA
1 TATTTATATATTTTATAATATTAA
* * * * *
2129802 TATTAATTTATTTAAAAAAATTAA
1 TATTTATATATTTTATAATATTAA
2129826 -ATTTATGATATTTATTATAATA
1 TATTTAT-ATA-TT-TTATAATA
2129848 GAATACAAGT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 5 0.15
24 21 0.64
25 2 0.06
26 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TATTTATATATTTTATAATATTAA
Found at i:2129976 original size:31 final size:34
Alignment explanation
Indices: 2129941--2130019 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 34
2129931 TTAGTTATTT
* *
2129941 AATATTTAAAT-TAATT-TTTTTAAAATAAAT-A
1 AATATTTAAATAAAATTATTTTAAAAATAAATAA
*
2129972 AATATTAAAATGAAAAATTATTTTAAAAATAAATAA
1 AATATTTAAAT--AAAATTATTTTAAAAATAAATAA
2130008 AATATTATAAAT
1 AATATT-TAAAT
2130020 CATATTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 10 0.26
34 4 0.11
35 13 0.34
36 7 0.18
37 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (34 bp):
AATATTTAAATAAAATTATTTTAAAAATAAATAA
Found at i:2131749 original size:5 final size:5
Alignment explanation
Indices: 2131739--2131768 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2131729 AATTTTAATG
2131739 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
2131769 TTGTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2135547 original size:36 final size:36
Alignment explanation
Indices: 2135507--2135588 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
2135497 ACTAAACCTG
2135507 TCCCCGTCCCCATCCCCGTTTAACATAAACGATTTT
1 TCCCCGTCCCCATCCCCGTTTAACATAAACGATTTT
* * *
2135543 TCCCCGTCCCCGTCCCCGTTTAACATAAATGGTTTT
1 TCCCCGTCCCCATCCCCGTTTAACATAAACGATTTT
*
2135579 TCCCCATCCC
1 TCCCCGTCCC
2135589 GTTTAATTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.18, C:0.41, G:0.10, T:0.30
Consensus pattern (36 bp):
TCCCCGTCCCCATCCCCGTTTAACATAAACGATTTT
Found at i:2136509 original size:16 final size:16
Alignment explanation
Indices: 2136478--2136548 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
2136468 ACGAGACGAG
*
2136478 TAATGAGCATCGAGCT
1 TAATGAGCAACGAGCT
* *
2136494 TAACGAGTAACGAGCT
1 TAATGAGCAACGAGCT
*
2136510 TAATGAGCAACGAACT
1 TAATGAGCAACGAGCT
*
2136526 TAATGAGCAACGAGTT
1 TAATGAGCAACGAGCT
2136542 TAATGAG
1 TAATGAG
2136549 TAACAAGTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (16 bp):
TAATGAGCAACGAGCT
Found at i:2136708 original size:31 final size:31
Alignment explanation
Indices: 2136637--2136719 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 31
2136627 AAAAATTTAT
*
2136637 GTACTAAAACGAAACAAAAAGTTAACAGCGA
1 GTACTAAAATGAAACAAAAAGTTAACAGCGA
**
2136668 GATACTAAAATGAAACAAAAAGTTAACTATTG-
1 G-TACTAAAATGAAACAAAAAGTTAAC-AGCGA
*
2136700 GTACTAAAATGAAATAAAAA
1 GTACTAAAATGAAACAAAAA
2136720 CTAAACTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
31 19 0.41
32 25 0.54
33 2 0.04
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (31 bp):
GTACTAAAATGAAACAAAAAGTTAACAGCGA
Found at i:2136807 original size:2 final size:2
Alignment explanation
Indices: 2136800--2136842 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2136790 ATAATAAAAG
2136800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2136842 T
1 T
2136843 TATGATAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2138286 original size:12 final size:13
Alignment explanation
Indices: 2138259--2138290 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2138249 TAATATTATT
2138259 TTTTTTAAAATAA
1 TTTTTTAAAATAA
2138272 TTTTTTAAAAT-A
1 TTTTTTAAAATAA
2138284 TTTTTTA
1 TTTTTTA
2138291 TATGCATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTAAAATAA
Found at i:2145597 original size:18 final size:18
Alignment explanation
Indices: 2145571--2145605 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2145561 TGTGGTGGAG
* *
2145571 AATCGAGGAAGAAATGAT
1 AATCAAGGAACAAATGAT
2145589 AATCAAGGAACAAATGA
1 AATCAAGGAACAAATGA
2145606 GAACCGATGA
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:0.54, C:0.09, G:0.23, T:0.14
Consensus pattern (18 bp):
AATCAAGGAACAAATGAT
Found at i:2150927 original size:25 final size:25
Alignment explanation
Indices: 2150893--2150969 Score: 136
Period size: 25 Copynumber: 3.1 Consensus size: 25
2150883 TATTGGTCCC
* *
2150893 CCCGTCCCCGTCCCCGTTTAAAAAA
1 CCCGTACCCGTCCCCGCTTAAAAAA
2150918 CCCGTACCCGTCCCCGCTTAAAAAA
1 CCCGTACCCGTCCCCGCTTAAAAAA
2150943 CCCGTACCCGTCCCCGCTTAAAAAA
1 CCCGTACCCGTCCCCGCTTAAAAAA
2150968 CC
1 CC
2150970 GCGGGGATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.26, C:0.45, G:0.12, T:0.17
Consensus pattern (25 bp):
CCCGTACCCGTCCCCGCTTAAAAAA
Found at i:2153278 original size:29 final size:29
Alignment explanation
Indices: 2153214--2153271 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2153204 CAATAGACTG
2153214 AAATAAATACAACATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
*
2153243 AAATAAATACAAGATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
2153272 GATTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.17
Consensus pattern (29 bp):
AAATAAATACAACATACAAATTAGAAACC
Found at i:2154944 original size:2 final size:2
Alignment explanation
Indices: 2154933--2154965 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2154923 AAATTTATTA
2154933 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2154966 TATTTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2155035 original size:13 final size:12
Alignment explanation
Indices: 2154979--2155023 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
2154969 TTTTAATATT
2154979 TATCGGG-CTGGG
1 TATCGGGTC-GGG
2154991 TATCGGGTCGGG
1 TATCGGGTCGGG
*
2155003 TATCGGGGCGGG
1 TATCGGGTCGGG
2155015 TAATCGGGT
1 T-ATCGGGT
2155024 AATCGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 22 0.76
13 7 0.24
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (12 bp):
TATCGGGTCGGG
Found at i:2155090 original size:6 final size:6
Alignment explanation
Indices: 2155079--2155109 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2155069 TAAACGGTTT
*
2155079 TCCCCG TCCCCG TCCCCG TCCTCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG T
2155110 TTAGCGTCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.61, G:0.16, T:0.23
Consensus pattern (6 bp):
TCCCCG
Found at i:2162943 original size:21 final size:21
Alignment explanation
Indices: 2162917--2162957 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2162907 TTTGAATTTA
*
2162917 ATGAAGGAGTACCGATACCCT
1 ATGAAGGAGTACCAATACCCT
*
2162938 ATGAAGGGGTACCAATACCC
1 ATGAAGGAGTACCAATACCC
2162958 CATGTACGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (21 bp):
ATGAAGGAGTACCAATACCCT
Found at i:2165940 original size:18 final size:18
Alignment explanation
Indices: 2165917--2165973 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
2165907 TATATTTTCC
2165917 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
*
2165935 AACAATTGATATCATTTTGTT
1 AACAATTGGTATC--TTT-TT
* *
2165956 AATAATTGGTATATTTTT
1 AACAATTGGTATCTTTTT
2165974 CATTAAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 14 0.44
19 3 0.09
20 3 0.09
21 12 0.38
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.51
Consensus pattern (18 bp):
AACAATTGGTATCTTTTT
Found at i:2165962 original size:21 final size:20
Alignment explanation
Indices: 2165933--2165972 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2165923 TGGTATCTTT
2165933 TTAACAATTGATATCATTTTG
1 TTAACAATTGATAT-ATTTTG
* *
2165954 TTAATAATTGGTATATTTT
1 TTAACAATTGATATATTTT
2165973 TCATTAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (20 bp):
TTAACAATTGATATATTTTG
Found at i:2166308 original size:15 final size:16
Alignment explanation
Indices: 2166259--2166308 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 16
2166249 GAATGTAAAG
2166259 AGGGTACCGATACCCCCC
1 AGGGTACCGATA--CCCC
2166277 AGGGTTATCCG-TACCCC
1 AGGG-TA-CCGATACCCC
2166294 -GGGTACCGATACCCC
1 AGGGTACCGATACCCC
2166309 CTGCAGGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 3 0.10
17 4 0.14
18 4 0.14
19 4 0.14
20 3 0.10
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (16 bp):
AGGGTACCGATACCCC
Found at i:2166722 original size:34 final size:32
Alignment explanation
Indices: 2166683--2166752 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2166673 TTTTGTAAAG
* *
2166683 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2166717 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2166749 GGGA
1 GGGA
2166753 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2179500 original size:23 final size:23
Alignment explanation
Indices: 2179474--2179517 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2179464 CGCCACTGCT
*
2179474 GACTGGATCTTCTAGAAGCTACC
1 GACTGGACCTTCTAGAAGCTACC
*
2179497 GACTGGGCCTTCTAGAAGCTA
1 GACTGGACCTTCTAGAAGCTA
2179518 TTAACTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
GACTGGACCTTCTAGAAGCTACC
Found at i:2179524 original size:23 final size:23
Alignment explanation
Indices: 2179482--2179526 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2179472 CTGACTGGAT
*
2179482 CTTCTAGAAGCTACCGACTGGGC
1 CTTCTAGAAGCTACCAACTGGGC
**
2179505 CTTCTAGAAGCTATTAACTGGG
1 CTTCTAGAAGCTACCAACTGGG
2179527 TGCCACGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (23 bp):
CTTCTAGAAGCTACCAACTGGGC
Found at i:2180056 original size:2 final size:2
Alignment explanation
Indices: 2180049--2180094 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2180039 TATTAACTTT
* *
2180049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA AA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2180090 TA TA T
1 TA TA T
2180095 TTATTTACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2180110 original size:23 final size:23
Alignment explanation
Indices: 2180066--2180111 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2180056 ATATATATAT
* *
2180066 ATATATATATATATTTATAAATA
1 ATATATATATATACTTAGAAATA
* *
2180089 ATATATTTATTTACTTAGAAATA
1 ATATATATATATACTTAGAAATA
2180112 TCAGAAAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATATATATATACTTAGAAATA
Found at i:2180407 original size:21 final size:21
Alignment explanation
Indices: 2180383--2180425 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2180373 CTAAATAGTG
2180383 ACTAAAATAAATAAAAT-TAAA
1 ACTAAAAT-AATAAAATATAAA
* *
2180404 ACTATAATATTAAAATATAAA
1 ACTAAAATAATAAAATATAAA
2180425 A
1 A
2180426 TGAAAGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
ACTAAAATAATAAAATATAAA
Found at i:2180415 original size:14 final size:13
Alignment explanation
Indices: 2180393--2180426 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2180383 ACTAAAATAA
2180393 ATAAAATTAAAACT
1 ATAAAATTAAAA-T
*
2180407 ATAATATTAAAAT
1 ATAAAATTAAAAT
2180420 ATAAAAT
1 ATAAAAT
2180427 GAAAGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAATTAAAAT
Found at i:2181755 original size:3 final size:3
Alignment explanation
Indices: 2181740--2181836 Score: 103
Period size: 3 Copynumber: 33.0 Consensus size: 3
2181730 GACCTGTTTG
* *
2181740 TAA TAA TAC TAA TAA TAA TAA AAA TAAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * *
2181785 TAA TAA T-A TAAA TAA -AA TAA -AA TAA TAT TAA TAT TAA TAT TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2181828 TAA TAA TAA
1 TAA TAA TAA
2181837 AAAATGGATA
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
2 8 0.10
3 65 0.83
4 5 0.06
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2182436 original size:123 final size:122
Alignment explanation
Indices: 2182209--2182529 Score: 484
Period size: 122 Copynumber: 2.6 Consensus size: 122
2182199 AGGCTATGTT
* * *
2182209 GAACAAATTCTTCCTCATTATAAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACA
1 GAACAAATTCTT-CTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA-A
* * * *
2182274 CTT-T-TGGAAATGTTTATGCTGATCTATCTCCTTCTGTGATAGCGTCATGCAAAAGGTA
64 TTTCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAGT-ATGCAAAAGGTA
* * *
2182332 GAATAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTTATTATGAAATT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAATT
*
2182397 TCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAGTATGCAAAAGGTT
66 TCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAGTATGCAAAAGGTA
* *
2182454 GAACAAATTCTTCTCATTATGAACTTCTTATTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAATT
2182519 TCTCTGGAAAA
66 TCTCTGGAAAA
2182530 TGTTGATCTA
Statistics
Matches: 180, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
121 3 0.02
122 128 0.71
123 49 0.27
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (122 bp):
GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAATT
TCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAGTATGCAAAAGGTA
Found at i:2182584 original size:113 final size:119
Alignment explanation
Indices: 2182206--2182591 Score: 414
Period size: 122 Copynumber: 3.2 Consensus size: 119
2182196 TTAAGGCTAT
* * * * *
2182206 GTTGAACAAATTCTTCCTCATTATAAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTT-CTCATTATGAACTTATTATTCCTCTTCAGATAAGTTCTTCTCATTATGA
* * * * *
2182271 ACACTT-T-TGGAAATGTTTATGCTGATCTATCTCCTTCTGTGATAGCGTCATGCAAAAG
65 A-ATTTCTCTGGAAAAG-TGAT-CTGATCTATCT-CATCTGTGATAGAGT-ATGCAAAAG
* * * *
2182329 GTAGAATAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTTATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTATTATTCCTCTTCAGATAAGTTCTTCTCATTATGAA
*
2182394 ATTTCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAGTATGCAAAAG
66 ATTTCTCTGGAAAAGTG-AT-CTGATCTATCT-CATCTGTGATAGAGTATGCAAAAG
*
2182451 GTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTCTTCAGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTATTATTCCTCTTCAGATAAGTTCTTCTCATTATGAA
* **
2182516 CTTTCTCTGGAAAA-TG-T-TGATCTATCT-AT-TGATGA-ATTCG-A-GCAAAAG
66 ATTTCTCTGGAAAAGTGATCTGATCTATCTCATCTG-TGATA-GAGTATGCAAAAG
* *
2182564 GTTGAACAAGTTCTTTTCATTATGAACT
1 GTTGAACAAATTCTTCTCATTATGAACT
2182592 CTTTCGGAAA
Statistics
Matches: 236, Mismatches: 22, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
113 33 0.14
114 4 0.02
115 5 0.02
117 10 0.04
119 1 0.00
121 5 0.02
122 129 0.55
123 49 0.21
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (119 bp):
GTTGAACAAATTCTTCTCATTATGAACTTATTATTCCTCTTCAGATAAGTTCTTCTCATTATGAA
ATTTCTCTGGAAAAGTGATCTGATCTATCTCATCTGTGATAGAGTATGCAAAAG
Found at i:2183051 original size:22 final size:22
Alignment explanation
Indices: 2182980--2183052 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
2182970 AAATCCAATA
* * *
2182980 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
2183002 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
* *
2183024 AATCTATTATCTTTGAAGATAG
1 AATCTATCATCTTTGAAGAGAG
2183046 AATCTAT
1 AATCTAT
2183053 AATATGCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:2183495 original size:53 final size:53
Alignment explanation
Indices: 2183426--2183561 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
2183416 AAATTTTTAG
* *
2183426 AACACATTCATTCTTTCCTGTGGCTTCTGCCTAATGTTCGTAAAGT-ATTTGAC
1 AACACATTCATCCTTTCCTGTGGTTTCTGCCTAATGTTCGTAAA-TCATTTGAC
2183479 AACACATTCATCCTTTCCTGTGGTTTCTGCCTAATGTTCGTAAATCATTTGAC
1 AACACATTCATCCTTTCCTGTGGTTTCTGCCTAATGTTCGTAAATCATTTGAC
2183532 AACACATTCATCCTTTCCTGTGGTTTCTGC
1 AACACATTCATCCTTTCCTGTGGTTTCTGC
2183562 TCAGATGCCT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
52 1 0.01
53 79 0.99
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (53 bp):
AACACATTCATCCTTTCCTGTGGTTTCTGCCTAATGTTCGTAAATCATTTGAC
Found at i:2184057 original size:18 final size:18
Alignment explanation
Indices: 2184031--2184068 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2184021 TATATAAAAG
2184031 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCGAA
*
2184049 AATACATTGAATTTCGAA
1 AATAAATTGAATTTCGAA
2184067 AA
1 AA
2184069 GATAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCGAA
Found at i:2195136 original size:14 final size:14
Alignment explanation
Indices: 2195113--2195144 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2195103 ACCTAAAAAA
2195113 ATAAAAAAGAATAT
1 ATAAAAAAGAATAT
*
2195127 ATAAAGAAGAATAT
1 ATAAAAAAGAATAT
2195141 ATAA
1 ATAA
2195145 TAAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (14 bp):
ATAAAAAAGAATAT
Found at i:2195701 original size:2 final size:2
Alignment explanation
Indices: 2195689--2195721 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2195679 TATTAACTTT
*
2195689 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2195722 TTTATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2195906 original size:11 final size:11
Alignment explanation
Indices: 2195890--2195916 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2195880 AGATTTTTTC
2195890 ATAAAAAACAA
1 ATAAAAAACAA
2195901 ATAAAAAACAA
1 ATAAAAAACAA
2195912 ATAAA
1 ATAAA
2195917 TAAATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.11
Consensus pattern (11 bp):
ATAAAAAACAA
Found at i:2197427 original size:3 final size:3
Alignment explanation
Indices: 2197419--2197519 Score: 84
Period size: 3 Copynumber: 34.0 Consensus size: 3
2197409 GACCTATTTG
* * *
2197419 TAA TAA TAA TAA TAA AAA TAAA TAA TAA TAA TAG TATA GAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA
* * *
2197466 TAA TAA TAG T-A TAAA TAA -AA TAA -AA T-A GAA TAA TAA TAA TAT
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2197508 TAA TCA TAA TAA
1 TAA TAA TAA TAA
2197520 AAACAAATGG
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
2 6 0.08
3 65 0.84
4 6 0.08
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2197444 original size:19 final size:20
Alignment explanation
Indices: 2197420--2197506 Score: 89
Period size: 19 Copynumber: 4.7 Consensus size: 20
2197410 ACCTATTTGT
2197420 AATAATAATAATAAAAATA-
1 AATAATAATAATAAAAATAG
**
2197439 AATAATAATAAT-AGTATAG
1 AATAATAATAATAAAAATAG
2197458 AATAATAATAAT---AATAG
1 AATAATAATAATAAAAATAG
*
2197475 TATAAATAA-AAT-AAAATAG
1 AAT-AATAATAATAAAAATAG
2197494 AATAATAATAATA
1 AATAATAATAATA
2197507 TTAATCATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.16
18 14 0.25
19 34 0.60
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AATAATAATAATAAAAATAG
Found at i:2197447 original size:22 final size:22
Alignment explanation
Indices: 2197419--2197545 Score: 93
Period size: 22 Copynumber: 5.9 Consensus size: 22
2197409 GACCTATTTG
2197419 TAATAATAATAATAAAAATAAA
1 TAATAATAATAATAAAAATAAA
* *
2197441 TAATAATAATAGTATAGAAT-AA
1 TAATAATAATAATA-AAAATAAA
* *
2197463 TAATAATAATAGTATAAATAAAA
1 TAATAATAATAATAAAAAT-AAA
* *
2197486 TAA-AAT-AGAATAATAAT-AA
1 TAATAATAATAATAAAAATAAA
* * *
2197505 TATTAATCATAATAAAAACAAA
1 TAATAATAATAATAAAAATAAA
* *
2197527 TGGATAA-AATAAAAAAAAT
1 T-AATAATAATAATAAAAAT
2197546 TAGTATCTTC
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
19 4 0.05
20 3 0.04
21 18 0.22
22 44 0.54
23 12 0.15
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (22 bp):
TAATAATAATAATAAAAATAAA
Found at i:2210181 original size:23 final size:23
Alignment explanation
Indices: 2210155--2210200 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2210145 CTTCACGCCA
*
2210155 CTGCTGACTGGATCTTCTAGAAG
1 CTGCTGACTGGACCTTCTAGAAG
* *
2210178 CTGCTGATTGGGCCTTCTAGAAG
1 CTGCTGACTGGACCTTCTAGAAG
2210201 ATGTTGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (23 bp):
CTGCTGACTGGACCTTCTAGAAG
Found at i:2210208 original size:23 final size:23
Alignment explanation
Indices: 2210168--2210212 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2210158 CTGACTGGAT
*
2210168 CTTCTAGAAGCTGCTGATTGGGC
1 CTTCTAGAAGATGCTGATTGGGC
*
2210191 CTTCTAGAAGATGTTGATTGGG
1 CTTCTAGAAGATGCTGATTGGG
2210213 TGCCATGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (23 bp):
CTTCTAGAAGATGCTGATTGGGC
Found at i:2213322 original size:27 final size:25
Alignment explanation
Indices: 2213274--2213327 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
2213264 AATTTTATAA
*
2213274 AATTTTGAGTTTTTAAAATAAATTAT
1 AATTTTAAGTTTTTAAAATAAA-TAT
**
2213300 AATTTTAAGGTTTTTAATTTAAATAT
1 AATTTTAA-GTTTTTAAAATAAATAT
2213326 AA
1 AA
2213328 ATAAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (25 bp):
AATTTTAAGTTTTTAAAATAAATAT
Found at i:2216063 original size:117 final size:115
Alignment explanation
Indices: 2215750--2216035 Score: 446
Period size: 117 Copynumber: 2.5 Consensus size: 115
2215740 GCTCCTTTGT
* *
2215750 TGTGTGCTCAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGAATCTACACATTG
1 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCGGGAATCTACACATTG
* **
2215815 TAGTGATTGGAATGACTGGATGGGGAAGTTATTACCGCAGGCTCCTTTGC
66 TAGTGATTGGAGTGACTGGATGGGGAAGTTATTACCGCAGGCTCCTCGGC
*
2215865 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACAT
1 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTC--GGGAATCTACACAT
*
2215930 TGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTGCAGGCTCCTCGGC
64 TGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACCGCAGGCTCCTCGGC
* * * * *
2215982 TTTGTGCTTAGGGTAAGTCCTTATTGGTGTGCATGTGGGTGTATGTTTCGGGAA
1 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCGGGAA
2216036 AATATACAAA
Statistics
Matches: 157, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
115 53 0.34
117 104 0.66
ACGTcount: A:0.18, C:0.14, G:0.35, T:0.33
Consensus pattern (115 bp):
TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCGGGAATCTACACATTG
TAGTGATTGGAGTGACTGGATGGGGAAGTTATTACCGCAGGCTCCTCGGC
Found at i:2217041 original size:20 final size:20
Alignment explanation
Indices: 2216947--2217315 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2216937 GATTTTCCAT
* ** *
2216947 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2216967 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2216987 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2217007 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2217027 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2217047 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2217067 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2217087 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2217107 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2217127 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2217147 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2217167 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2217187 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2217207 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2217227 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2217247 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2217267 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2217287 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2217307 AATCACAAC
1 AATCGCAAC
2217316 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2218028 original size:24 final size:24
Alignment explanation
Indices: 2217989--2218035 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2217979 AAATTTGGTC
2217989 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2218013 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2218036 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2218227 original size:12 final size:12
Alignment explanation
Indices: 2218210--2218234 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2218200 ATATAATCCT
2218210 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2218222 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2218234 G
1 G
2218235 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2220563 original size:19 final size:19
Alignment explanation
Indices: 2220541--2220847 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
2220531 CGGAAAATAC
*
2220541 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2220560 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2220574 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2220594 AATCGCAA--CG--AT-AG
1 AATCGCAATGCGAAATGAA
2220608 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2220627 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2220646 AATCGCAA--CG--AT-AG
1 AATCGCAATGCGAAATGAA
2220660 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2220679 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
2220698 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
2220712 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
2220731 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
2220750 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2220769 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2220788 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
2220802 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2220821 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2220840 AATCGCAA
1 AATCGCAA
2220848 CGAGATAATC
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 43 0.17
15 6 0.02
16 16 0.06
17 15 0.06
18 7 0.03
19 149 0.60
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2220656 original size:52 final size:53
Alignment explanation
Indices: 2220569--2220847 Score: 358
Period size: 52 Copynumber: 5.2 Consensus size: 53
2220559 AAATCCCAAC
*
2220569 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGATAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGATAAAATCGCAATGCGAA
*
2220622 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGATAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGATAAAATCGCAATGCGAA
* * *
2220674 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGATAAAATCGCAATGCGAA
* *
2220726 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--AT-AAAATCGCAATGCGAA
2220783 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--AT-AAAATCGCAATGCGAA
2220835 ATGAAAATCGCAA
1 ATGAAAATCGCAA
2220848 CGAGATAATC
Statistics
Matches: 212, Mismatches: 8, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
51 2 0.01
52 156 0.74
53 18 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGATAAAATCGCAATGCGAA
Found at i:2220692 original size:71 final size:71
Alignment explanation
Indices: 2220608--2220847 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
2220598 GCAACGATAG
2220608 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGA
2220673 AATGAA
66 AATGAA
* * *
2220679 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-TAGAATCGCAA
*
2220739 TACGAAATGAA
61 TGCGAAATGAA
*
2220750 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGA
2220815 AATGAA
66 AATGAA
2220821 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
2220848 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 5 0.03
70 3 0.02
71 114 0.76
72 3 0.02
73 5 0.03
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGA
AATGAA
Found at i:2220793 original size:142 final size:137
Alignment explanation
Indices: 2220541--2220879 Score: 497
Period size: 142 Copynumber: 2.4 Consensus size: 137
2220531 CGGAAAATAC
* * * *
2220541 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
2220604 ATAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAAT
63 ATAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
2220669 GCGAAATGAA
128 GCGAAATGAA
2220679 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
2220744 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 -AT-AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
2220809 ATGCGAAATGAA
126 ATGCGAAATGAA
2220821 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
2220880 TTGCGATTTT
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 33 0.18
139 3 0.02
141 2 0.01
142 122 0.66
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGATA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Done.