Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_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: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1537156 original size:21 final size:21
Alignment explanation
Indices: 1537116--1537170 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1537106 CGGAAAATGA
* *
1537116 AGCAAGAGAAGCAGAGAGAGC
1 AGCAACAGAAGCAGACAGAGC
* * * *
1537137 AGCAGCGGAAGCAGCCAGAGT
1 AGCAACAGAAGCAGACAGAGC
1537158 AGCAACAGAAGCA
1 AGCAACAGAAGCA
1537171 TAGAAAGAAG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.20, G:0.35, T:0.02
Consensus pattern (21 bp):
AGCAACAGAAGCAGACAGAGC
Found at i:1537182 original size:21 final size:21
Alignment explanation
Indices: 1537158--1537203 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1537148 CAGCCAGAGT
1537158 AGCAACAGA-AGCATAGAAAGA
1 AGCAAC-GACAGCATAGAAAGA
*
1537179 AGCAACGACAGCATAGAGAGA
1 AGCAACGACAGCATAGAAAGA
1537200 AGCA
1 AGCA
1537204 GTGCCAGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.52, C:0.17, G:0.26, T:0.04
Consensus pattern (21 bp):
AGCAACGACAGCATAGAAAGA
Found at i:1537211 original size:21 final size:21
Alignment explanation
Indices: 1537167--1537226 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
1537157 TAGCAACAGA
* *
1537167 AGCATAGAAAGAAGCAACGAC
1 AGCATAGAGAGAAGCAGCGAC
* *
1537188 AGCATAGAGAGAAGCAGTGCC
1 AGCATAGAGAGAAGCAGCGAC
*
1537209 AGCACAGAGAGAAGCAGC
1 AGCATAGAGAGAAGCAGC
1537227 ATATTAGCAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.45, C:0.20, G:0.30, T:0.05
Consensus pattern (21 bp):
AGCATAGAGAGAAGCAGCGAC
Found at i:1537729 original size:43 final size:43
Alignment explanation
Indices: 1537608--1537729 Score: 154
Period size: 43 Copynumber: 2.8 Consensus size: 43
1537598 GTTTGTATGG
*
1537608 AAACGCCGCTAAATCTCAACACCTATTACGACGTTTTCAATAA
1 AAACGCCGCTAAATCTCAACACCTATTGCGACGTTTTCAATAA
* * * * *
1537651 AAACGCCGCTAATTCTCAACACTTATTGCGTCGTTTTCGATAC
1 AAACGCCGCTAAATCTCAACACCTATTGCGACGTTTTCAATAA
* * * *
1537694 AAACGCCGCTAAATATGAAAACCTACTGCGACGTTT
1 AAACGCCGCTAAATCTCAACACCTATTGCGACGTTT
1537730 GTGGGAAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAATCTCAACACCTATTGCGACGTTTTCAATAA
Found at i:1537741 original size:43 final size:44
Alignment explanation
Indices: 1537694--1537900 Score: 190
Period size: 43 Copynumber: 4.8 Consensus size: 44
1537684 TTTTCGATAC
* * *
1537694 AAACGCCGCTAAATATGAAAACCTACTGCGACGTTTGT-GGGAA
1 AAACGCCGCTAAATATCAAAACCTACTACGGCGTTTGTAGGGAA
* ** * *
1537737 AAACGCCGCTAAACATCATCACATTCTACGGCGTTTGT--GGAA
1 AAACGCCGCTAAATATCAAAACCTACTACGGCGTTTGTAGGGAA
* * * * * *
1537779 AAACGCCGCAAAATATCAAAACCTTCTGCGGTGTTTGTAAGTAA
1 AAACGCCGCTAAATATCAAAACCTACTACGGCGTTTGTAGGGAA
* * **
1537823 AAA-GCCGCTAAATCTCAACACCTACTACGGTATTTGTAGGG-A
1 AAACGCCGCTAAATATCAAAACCTACTACGGCGTTTGTAGGGAA
* * *
1537865 AAATGCCGCTAAACATCAAAACCTATTACGGCGTTT
1 AAACGCCGCTAAATATCAAAACCTACTACGGCGTTT
1537901 TTTGTCAGAA
Statistics
Matches: 131, Mismatches: 30, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
42 39 0.30
43 86 0.66
44 6 0.05
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (44 bp):
AAACGCCGCTAAATATCAAAACCTACTACGGCGTTTGTAGGGAA
Found at i:1537808 original size:85 final size:86
Alignment explanation
Indices: 1537608--1537889 Score: 218
Period size: 86 Copynumber: 3.3 Consensus size: 86
1537598 GTTTGTATGG
* * * * * *
1537608 AAACGCCGCTAAATCTCAACACCTATTACGACGTTT-TCAA-TAAAAACGCCGCTAATTCTCAAC
1 AAACGCCGCTAAATATCAAAACCTACTGCGACGTTTGT-AAGGAAAAA-GCCGCTAAATCTCAAC
* * * * * *
1537671 ACTTATTGCGTCGTTT-T-CGATA
64 ACATACTACGGCATTTGTAGGA-A
* * *
1537693 CAAACGCCGCTAAATATGAAAACCTACTGCGACGTTTGT-GGGAAAAACGCCGCTAAA-CATCAT
1 -AAACGCCGCTAAATATCAAAACCTACTGCGACGTTTGTAAGGAAAAA-GCCGCTAAATC-TCAA
* *
1537756 CACATTCTACGGCGTTTGT-GGAA
63 CACATACTACGGCATTTGTAGGAA
* * ** *
1537779 AAACGCCGCAAAATATCAAAACCTTCTGCGGTGTTTGTAAGTAAAAAGCCGCTAAATCTCAACAC
1 AAACGCCGCTAAATATCAAAACCTACTGCGACGTTTGTAAGGAAAAAGCCGCTAAATCTCAACAC
* * *
1537844 CTACTACGGTATTTGTAGGGA
66 ATACTACGGCATTTGTAGGAA
* *
1537865 AAATGCCGCTAAACATCAAAACCTA
1 AAACGCCGCTAAATATCAAAACCTA
1537890 TTACGGCGTT
Statistics
Matches: 157, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
85 61 0.39
86 92 0.59
87 4 0.03
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTAAATATCAAAACCTACTGCGACGTTTGTAAGGAAAAAGCCGCTAAATCTCAACAC
ATACTACGGCATTTGTAGGAA
Found at i:1538291 original size:9 final size:10
Alignment explanation
Indices: 1538268--1538293 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1538258 ATTTATGCAT
1538268 TTTTTTGGCC
1 TTTTTTGGCC
1538278 TTTTTTGGCC
1 TTTTTTGGCC
1538288 TTTTTT
1 TTTTTT
1538294 TTTGGCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (10 bp):
TTTTTTGGCC
Found at i:1538402 original size:17 final size:17
Alignment explanation
Indices: 1538376--1538411 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1538366 TGATAAGAGC
*
1538376 TAAAGGAGTAAAAAAAT
1 TAAAGAAGTAAAAAAAT
*
1538393 TAAAGAAGTATAAAAAT
1 TAAAGAAGTAAAAAAAT
1538410 TA
1 TA
1538412 TTAAAACCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (17 bp):
TAAAGAAGTAAAAAAAT
Found at i:1538863 original size:4 final size:4
Alignment explanation
Indices: 1538849--1538886 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
1538839 GTATAATGAG
*
1538849 ATAA A-AA ATAA ATAA ACAA ATAAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA AT
1538887 TGAGATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:1538875 original size:17 final size:17
Alignment explanation
Indices: 1538853--1538886 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1538843 AATGAGATAA
1538853 AAAATAAATAAACAAAT
1 AAAATAAATAAACAAAT
*
1538870 AAAATAAATAAATAAAT
1 AAAATAAATAAACAAAT
1538887 TGAGATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAAATAAACAAAT
Found at i:1541657 original size:22 final size:22
Alignment explanation
Indices: 1541616--1541657 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1541606 TTTATTAGTA
* * *
1541616 TTAATATTAGTTTTTTTATAAG
1 TTAATATCAGTATTTATATAAG
1541638 TTAATATCAGTATTTATATA
1 TTAATATCAGTATTTATATA
1541658 GTGTACGCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
TTAATATCAGTATTTATATAAG
Found at i:1541706 original size:13 final size:14
Alignment explanation
Indices: 1541678--1541713 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1541668 ATATATTTAA
1541678 TTATTTATTCTTTT
1 TTATTTATTCTTTT
*
1541692 TTATTT-TTGTTTT
1 TTATTTATTCTTTT
1541705 TTATTTATT
1 TTATTTATT
1541714 ACTATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (14 bp):
TTATTTATTCTTTT
Found at i:1541759 original size:3 final size:3
Alignment explanation
Indices: 1541709--1541821 Score: 57
Period size: 3 Copynumber: 40.0 Consensus size: 3
1541699 TGTTTTTTAT
* * * * *
1541709 TTA TTA CTA TTA -TA TTA -TA CTA TT- TTA TTT TTA TT- TTT TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1541753 -TA TTA TT- TTCA TTA TTC TT- TTA TCT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* *
1541796 TTA TCA -TA TGTA TT- TTA TTA TCA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA
1541822 ACATCTTTCT
Statistics
Matches: 85, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
2 18 0.21
3 61 0.72
4 6 0.07
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1541782 original size:26 final size:25
Alignment explanation
Indices: 1541729--1541794 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
1541719 TATATTATAC
* *
1541729 TATT-TTATTTTTATTTTTTTACTA
1 TATTATTATTATTATTCTTTTACTA
*
1541753 TATTATT-TTCATTATTCTTTTATCTT
1 TATTATTATT-ATTATTCTTTTA-CTA
1541779 TATTATTATTATTATT
1 TATTATTATTATTATT
1541795 ATTATCATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 6 0.17
25 12 0.34
26 15 0.43
27 2 0.06
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (25 bp):
TATTATTATTATTATTCTTTTACTA
Found at i:1541784 original size:9 final size:9
Alignment explanation
Indices: 1541709--1541821 Score: 57
Period size: 8 Copynumber: 13.3 Consensus size: 9
1541699 TGTTTTTTAT
*
1541709 TTATTACTA
1 TTATTATTA
1541718 TTA-TATTA
1 TTATTATTA
*
1541726 -TACTATT-
1 TTATTATTA
*
1541733 TTATTTTTA
1 TTATTATTA
*
1541742 TT-TTTTTA
1 TTATTATTA
*
1541750 CTA-TATTA
1 TTATTATTA
1541758 TT-TTCATTA
1 TTATT-ATTA
*
1541767 TTCTT-TTA
1 TTATTATTA
1541775 TCT-TTATTA
1 T-TATTATTA
1541784 TTATTATTA
1 TTATTATTA
*
1541793 TTATTATCA
1 TTATTATTA
1541802 -TATGTATT-
1 TTAT-TATTA
*
1541810 TTATTATCA
1 TTATTATTA
1541819 TTA
1 TTA
1541822 ACATCTTTCT
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
7 2 0.02
8 39 0.48
9 39 0.48
10 2 0.02
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (9 bp):
TTATTATTA
Found at i:1542051 original size:11 final size:11
Alignment explanation
Indices: 1542037--1542086 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1542027 TTTTGGTTTA
1542037 TTTAATATTTT
1 TTTAATATTTT
*
1542048 TTTATTATTTT
1 TTTAATATTTT
* *
1542059 TTTAAAATTGTA
1 TTTAATATT-TT
*
1542071 TTTATTATTTT
1 TTTAATATTTT
1542082 TTTAA
1 TTTAA
1542087 ATTATTCTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTAATATTTT
Found at i:1542157 original size:28 final size:28
Alignment explanation
Indices: 1542104--1542158 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
1542094 TTTTCCTATG
* *
1542104 ATTTATTTTTATTTGTTTATTTATTTTC
1 ATTTATTTTGATTTGTTTATTCATTTTC
*
1542132 ATTTCATTTTGATTTTTTTA-TCATTTT
1 ATTT-ATTTTGATTTGTTTATTCATTTT
1542159 TTCCTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (28 bp):
ATTTATTTTGATTTGTTTATTCATTTTC
Found at i:1544971 original size:95 final size:94
Alignment explanation
Indices: 1544793--1545035 Score: 276
Period size: 95 Copynumber: 2.7 Consensus size: 94
1544783 TATAATATTA
* * * * *
1544793 TATATATCCAATAAAGCTTGAGTTTTCTCTCTAGAGCAATTGGTTAAACGCTCTGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
* * *
1544858 AAATATTCGGCTAGCCTGATAAAGGTGAG
66 AAAGATTCAGCTAACCTGATAAAGGTGAG
1544887 TATACTATACAATAAAGCTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTTATG
*
1544951 GATAAGATTCAGCTAACCTGATAAAGGT--G
64 GAAAAGATTCAGCTAACCTGATAAAGGTGAG
* * *
1544980 T-T-TAT----T-TA--TTGAGTTTTCCCTCTAGAGCAATTGGTTAAACGTCCCGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
1545036 TCCAGCTAGC
Statistics
Matches: 134, Mismatches: 12, Indels: 17
0.82 0.07 0.10
Matches are distributed among these distances:
83 44 0.33
84 1 0.01
85 1 0.01
86 1 0.01
90 3 0.02
92 1 0.01
93 2 0.01
94 5 0.04
95 76 0.57
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
AAAGATTCAGCTAACCTGATAAAGGTGAG
Found at i:1546426 original size:22 final size:22
Alignment explanation
Indices: 1546385--1546426 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1546375 TTTATTAGTA
*
1546385 TTAATATTAGTTTTTTTATAAG
1 TTAATATTAGTTTTTATATAAG
1546407 TTAATATTA-TTATTTATATA
1 TTAATATTAGTT-TTTATATA
1546427 GTATACGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TTAATATTAGTTTTTATATAAG
Found at i:1546564 original size:3 final size:3
Alignment explanation
Indices: 1546486--1546599 Score: 66
Period size: 3 Copynumber: 40.0 Consensus size: 3
1546476 GGTTTTTTAT
* * * * *
1546486 TTA TTA CTA TTA CTA TTA -TA TTA TTT TTA TTT TTA TT- TT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1546531 -TA TTA TT- TTCA TTA TTC TT- TTA TCT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* *
1546574 TTA TCA -TA TGTA TT- TTA TTA TCA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA
1546600 ACATATATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 22
0.70 0.11 0.18
Matches are distributed among these distances:
2 16 0.19
3 64 0.74
4 6 0.07
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1546664 original size:12 final size:14
Alignment explanation
Indices: 1546623--1546657 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1546613 TCTCTAAACG
* *
1546623 TTTTTCAACCTCTT
1 TTTTTCAACTTTTT
1546637 TTTTTCAACTTTTT
1 TTTTTCAACTTTTT
1546651 TTTTTCA
1 TTTTTCA
1546658 TTTTTTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTCAACTTTTT
Found at i:1546678 original size:23 final size:23
Alignment explanation
Indices: 1546635--1546678 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1546625 TTTCAACCTC
*
1546635 TTTTTTTCAACTTTTTTTTTTCA
1 TTTTTTTCAACTTTTTATTTTCA
1546658 TTTTTTTC-ACTTTTTCATTTT
1 TTTTTTTCAACTTTTT-ATTTT
1546679 TTCAACCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTTTCAACTTTTTATTTTCA
Found at i:1546717 original size:19 final size:19
Alignment explanation
Indices: 1546676--1546718 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1546666 ACTTTTTCAT
*
1546676 TTTTTCAACCTCTTCCAAC
1 TTTTTCAACATCTTCCAAC
*
1546695 TTTTTCAACAT-TTTCAAC
1 TTTTTCAACATCTTCCAAC
*
1546713 ATTTTC
1 TTTTTC
1546719 CTCTTTTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTCAACATCTTCCAAC
Found at i:1546827 original size:19 final size:18
Alignment explanation
Indices: 1546803--1546857 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
1546793 AAACGTTTTA
1546803 TATATTTTTTATTTCATTT
1 TATATTTTTTATTT-ATTT
**
1546822 TATATTTTTGGTTTATTT
1 TATATTTTTTATTTATTT
*
1546840 AATATTTTTTA-TTATTT
1 TATATTTTTTATTTATTT
1546857 T
1 T
1546858 TTAAATTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 6 0.20
18 12 0.40
19 12 0.40
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (18 bp):
TATATTTTTTATTTATTT
Found at i:1546901 original size:18 final size:18
Alignment explanation
Indices: 1546880--1546922 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1546870 TTCTTTTAAA
*
1546880 TTATTCTTT-TCCTTTTAT
1 TTATT-TTTATCCGTTTAT
*
1546898 TTATTTTTATTCGTTTAT
1 TTATTTTTATCCGTTTAT
1546916 TTATTTT
1 TTATTTT
1546923 CATTTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.74
Consensus pattern (18 bp):
TTATTTTTATCCGTTTAT
Found at i:1546979 original size:21 final size:21
Alignment explanation
Indices: 1546955--1547017 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 21
1546945 ATTTTTTCCT
1546955 TTTTTAATTTTATTTATTTA-A
1 TTTTT-ATTTTATTTATTTAGA
*
1546976 TTTTTCTTTTGATTTATTTAGTA
1 TTTTTATTTT-ATTTATTTAG-A
1546999 TTTGTT-TATTTATTTATTT
1 TTT-TTAT-TTTATTTATTT
1547018 TCTCTAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 4 0.11
21 14 0.39
23 13 0.36
24 5 0.14
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTTATTTTATTTATTTAGA
Found at i:1549218 original size:28 final size:28
Alignment explanation
Indices: 1549186--1549247 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
1549176 TTGGATTACG
*
1549186 AAATTTCCGATGTGATTTTAAAGAAATA
1 AAATTTCCGATATGATTTTAAAGAAATA
1549214 AAATTTCCGATATGATTTTAAAGAAATA
1 AAATTTCCGATATGATTTTAAAGAAATA
1549242 AAATTT
1 AAATTT
1549248 TACCGGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.37
Consensus pattern (28 bp):
AAATTTCCGATATGATTTTAAAGAAATA
Found at i:1550421 original size:197 final size:197
Alignment explanation
Indices: 1550086--1550686 Score: 1175
Period size: 197 Copynumber: 3.1 Consensus size: 197
1550076 AAAGAGTACA
1550086 TTTATTTTGTGAAGGCGAGAGATTAAAACTATTGAAGAAGTGAAACTTTAAAAGTCATATTGGAA
1 TTTATTTTGTGAAGGCGAGAGATTAAAACTATTGAAGAAGTGAAACTTTAAAAGTCATATTGGAA
1550151 AAACTTCTCTTTTTCCTTAGCTGTCATCGGTCTTTTTTTCTTCATCTTTGTAATCAGCGGCGACA
66 AAACTTCTCTTTTTCCTTAGCTGTCATCGGTCTTTTTTTCTTCATCTTTGTAATCAGCGGCGACA
*
1550216 TCAATTTTGATGCTGATCATCGACTATCGTTATTCATTGTTTTTCCTTCTTTTTATTATAACATA
131 TCAATTTTGATGCTGATCATCGACTATCGTTATTCATTGTTTTTCCTTCTTTTTATTATAACGTA
1550281 TT
196 TT
1550283 TTTATTTTGTGAAGGCGAGAGATTAAAACTATTGAAGAAGTGAAACTTTAAAAGTCATATTGGAA
1 TTTATTTTGTGAAGGCGAGAGATTAAAACTATTGAAGAAGTGAAACTTTAAAAGTCATATTGGAA
1550348 AAACTTCTCTTTTTCCTTAGCTGTCATCGGTCTTTTTTTCTTCATCTTTGTAATCAGCGGCGACA
66 AAACTTCTCTTTTTCCTTAGCTGTCATCGGTCTTTTTTTCTTCATCTTTGTAATCAGCGGCGACA
1550413 TCAATTTTGATGCTGATCATCGACTATCGTTATTCATTGTTTTTCCTTCTTTTTATTATAACGTA
131 TCAATTTTGATGCTGATCATCGACTATCGTTATTCATTGTTTTTCCTTCTTTTTATTATAACGTA
1550478 TT
196 TT
1550480 TTTATTTTGTGAAGGCGAGAGATTAAAACTATTGAAGAAGTGAAACTTTAAAAGTCATATTGGAA
1 TTTATTTTGTGAAGGCGAGAGATTAAAACTATTGAAGAAGTGAAACTTTAAAAGTCATATTGGAA
* *
1550545 AAACTTCTCTTTTTCCTTAGCTGTCATCAGTCTTTTTTTCTTCATCTTTGTAATCAGCGACGACA
66 AAACTTCTCTTTTTCCTTAGCTGTCATCGGTCTTTTTTTCTTCATCTTTGTAATCAGCGGCGACA
1550610 TCAATTTTGATGCTGATCATCGACTATCGTTATTCATTGTTTTTCCTTCTTTTTATTATAACGTA
131 TCAATTTTGATGCTGATCATCGACTATCGTTATTCATTGTTTTTCCTTCTTTTTATTATAACGTA
1550675 TT
196 TT
1550677 TTTATTTTGT
1 TTTATTTTGT
1550687 TCTTTTTTTA
Statistics
Matches: 401, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
197 401 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (197 bp):
TTTATTTTGTGAAGGCGAGAGATTAAAACTATTGAAGAAGTGAAACTTTAAAAGTCATATTGGAA
AAACTTCTCTTTTTCCTTAGCTGTCATCGGTCTTTTTTTCTTCATCTTTGTAATCAGCGGCGACA
TCAATTTTGATGCTGATCATCGACTATCGTTATTCATTGTTTTTCCTTCTTTTTATTATAACGTA
TT
Found at i:1551431 original size:21 final size:21
Alignment explanation
Indices: 1551407--1551464 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1551397 AAAAATAATC
* *
1551407 ATATTTAAATTGCTTGCATCT
1 ATATTTTAATTGCTAGCATCT
1551428 ATATTTTAATTGCTAGCATCT
1 ATATTTTAATTGCTAGCATCT
1551449 ATATTTTAATTGCTAG
1 ATATTTTAATTGCTAG
1551465 ACCACCTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.48
Consensus pattern (21 bp):
ATATTTTAATTGCTAGCATCT
Found at i:1552776 original size:16 final size:16
Alignment explanation
Indices: 1552757--1552834 Score: 75
Period size: 16 Copynumber: 4.9 Consensus size: 16
1552747 GTTAAATTCG
* *
1552757 GTTCAGGTTGCTTTCA
1 GTTCGGGTTACTTTCA
* * *
1552773 GTTCAGGTTAATTTCG
1 GTTCGGGTTACTTTCA
* *
1552789 GTTTGGGTTACTTTCG
1 GTTCGGGTTACTTTCA
*
1552805 GTTCGGGTTAATTTCA
1 GTTCGGGTTACTTTCA
*
1552821 GTTCGGGTTGCTTT
1 GTTCGGGTTACTTT
1552835 TGGTTTCGAT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.12, C:0.14, G:0.28, T:0.46
Consensus pattern (16 bp):
GTTCGGGTTACTTTCA
Found at i:1552783 original size:32 final size:32
Alignment explanation
Indices: 1552725--1552834 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 32
1552715 ATTTTAATAT
* * * * *
1552725 GTTCGGGTTGTTTTCGGGTCATGTTAAATTCG
1 GTTCGGGTTGCTTTCAGTTCAGGTTAATTTCG
*
1552757 GTTCAGGTTGCTTTCAGTTCAGGTTAATTTCG
1 GTTCGGGTTGCTTTCAGTTCAGGTTAATTTCG
* * * * *
1552789 GTTTGGGTTACTTTCGGTTCGGGTTAATTTCA
1 GTTCGGGTTGCTTTCAGTTCAGGTTAATTTCG
1552821 GTTCGGGTTGCTTT
1 GTTCGGGTTGCTTT
1552835 TGGTTTCGAT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.12, C:0.14, G:0.29, T:0.45
Consensus pattern (32 bp):
GTTCGGGTTGCTTTCAGTTCAGGTTAATTTCG
Found at i:1552848 original size:32 final size:32
Alignment explanation
Indices: 1552748--1552850 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 32
1552738 TCGGGTCATG
* * * * *
1552748 TTAAATTCGGTTCAGGTTGCTTTCAGTTCAGG-
1 TTAATTTCAGTTCGGGTTACTTTCGGTTC-GGA
* * *
1552780 TTAATTTCGGTTTGGGTTACTTTCGGTTCGGG
1 TTAATTTCAGTTCGGGTTACTTTCGGTTCGGA
* *
1552812 TTAATTTCAGTTCGGGTTGCTTTTGGTTTC-GA
1 TTAATTTCAGTTCGGGTTACTTTCGG-TTCGGA
1552844 TTAATTT
1 TTAATTT
1552851 TGGTTTCGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 2 0.03
32 54 0.92
33 3 0.05
ACGTcount: A:0.15, C:0.13, G:0.25, T:0.48
Consensus pattern (32 bp):
TTAATTTCAGTTCGGGTTACTTTCGGTTCGGA
Found at i:1552907 original size:54 final size:54
Alignment explanation
Indices: 1552800--1552904 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 54
1552790 TTTGGGTTAC
* * * *
1552800 TTTCGGTTCGGGTTAATTTCAGTTCGGGTTGCTTTTGGTTTCGATTAATTTTGG
1 TTTCGGTTCGGGTTAACTTCAGTTCGGGTTGATTTTGGTTTCCACTAATTTTGG
* * **
1552854 TTTCGGTTTGGGTTAACTTCGGTTTTGGTTGATTTTGG-TTCCACTAATTTT
1 TTTCGGTTCGGGTTAACTTCAGTTCGGGTTGATTTTGGTTTCCACTAATTTT
1552905 TGGATCGGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
53 11 0.26
54 32 0.74
ACGTcount: A:0.11, C:0.11, G:0.26, T:0.51
Consensus pattern (54 bp):
TTTCGGTTCGGGTTAACTTCAGTTCGGGTTGATTTTGGTTTCCACTAATTTTGG
Found at i:1553688 original size:2 final size:2
Alignment explanation
Indices: 1553681--1553715 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1553671 AGGGAAAGGA
1553681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1553716 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1553720 original size:2 final size:2
Alignment explanation
Indices: 1553715--1553745 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1553705 ATATATATAT
1553715 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1553746 ATATAATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1554497 original size:2 final size:2
Alignment explanation
Indices: 1554492--1554563 Score: 92
Period size: 2 Copynumber: 36.0 Consensus size: 2
1554482 ATCTAATTCT
*
1554492 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TGC -C
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC
* * *
1554534 TC TG TC TC TC TC TA TC TC TC TC TA TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1554564 ATGGAGGTCT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
1 1 0.02
2 58 0.97
3 1 0.02
ACGTcount: A:0.03, C:0.47, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1557350 original size:20 final size:20
Alignment explanation
Indices: 1557325--1557377 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1557315 GACCAACAAA
1557325 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
1557345 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
1557365 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1557378 TCTGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:1557409 original size:20 final size:20
Alignment explanation
Indices: 1557398--1557604 Score: 258
Period size: 20 Copynumber: 10.4 Consensus size: 20
1557388 GCAACACAGA
1557398 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
1557418 AGTCAAATTCGTAACGCGAC
1 AGTCAAATTCGCAACGCGAT
1557438 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* * * *
1557458 AGTCAAATTTGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
1557478 AGTCAAATTCGCAACGCGAATT
1 AGTCAAATTCGCAACGCG-A-T
* * *
1557500 TGT-AAA-TCGCAACAC-AA
1 AGTCAAATTCGCAACGCGAT
1557517 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
1557537 AGTCAAATTCGCAACGTGAT
1 AGTCAAATTCGCAACGCGAT
*
1557557 AGTCAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
1557577 AGTCAAATTCGCAATGCGAA
1 AGTCAAATTCGCAACGCGAT
1557597 AGTCAAAT
1 AGTCAAAT
1557605 GTTTTTATGC
Statistics
Matches: 160, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
17 2 0.01
18 4 0.03
19 8 0.05
20 140 0.88
21 4 0.03
22 2 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:1557409 original size:40 final size:41
Alignment explanation
Indices: 1557365--1557590 Score: 258
Period size: 40 Copynumber: 5.7 Consensus size: 41
1557355 AGTTTCCAAT
*
1557365 TTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAAT-AGTCAAATTCGCAACACAGAAGTCAAA
* *
1557405 TTCGCAACGCG-ATAGTCAAATTCGTAACGC-GACAGTCAAA
1 TTCGCAACGCGAATAGTCAAATTCGCAACACAGA-AGTCAAA
* *
1557445 TTCGCAACGCG-ATAGTCAAATTTGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATAGTCAAATTCGCAACACAGAAGTCAAA
*
1557485 TTCGCAACGCGAATTTGT-AAA-TCGCAACACA-AAGTCAAA
1 TTCGCAACGCGAA-TAGTCAAATTCGCAACACAGAAGTCAAA
**
1557524 TTCGCAACGCG-ATAGTCAAATTCGCAAC-GTGATAGTCAAA
1 TTCGCAACGCGAATAGTCAAATTCGCAACACAGA-AGTCAAA
*
1557564 TTCGCAATGCG-ATAGTCAAATTCGCAA
1 TTCGCAACGCGAATAGTCAAATTCGCAA
1557591 TGCGAAAGTC
Statistics
Matches: 163, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
37 3 0.02
38 6 0.04
39 34 0.21
40 112 0.69
41 5 0.03
42 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
TTCGCAACGCGAATAGTCAAATTCGCAACACAGAAGTCAAA
Found at i:1557545 original size:99 final size:99
Alignment explanation
Indices: 1557418--1557596 Score: 277
Period size: 99 Copynumber: 1.8 Consensus size: 99
1557408 GCAACGCGAT
* *
1557418 AGTCAAATTCGTAACGCGACAGTCAAATTCGCAACGCGATAGTCAAATTTGCAACACAAAAGTCA
1 AGTCAAATTCGCAACGCGACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCA
1557483 AATTCGCAACGCGAATTTGTAAATCGCAACACAA
66 AATTCGCAACGCGAATTTGTAAATCGCAACACAA
* * ** * *
1557517 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGTGATAGTCAAATTCGCAATGCGATAGTCA
1 AGTCAAATTCGCAACGCGACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCA
*
1557582 AATTCGCAATGCGAA
66 AATTCGCAACGCGAA
1557597 AGTCAAATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 71 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (99 bp):
AGTCAAATTCGCAACGCGACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCA
AATTCGCAACGCGAATTTGTAAATCGCAACACAA
Found at i:1557576 original size:119 final size:120
Alignment explanation
Indices: 1557365--1557604 Score: 392
Period size: 119 Copynumber: 2.0 Consensus size: 120
1557355 AGTTTCCAAT
*
1557365 TTCGCAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGT
1 TTCGCAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
*
1557430 AACGCGACAGTCAAATTCGCAACGCGATAGTCAAATTTGCAACACAAAAGTCAAA
66 AACGCGACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
*
1557485 TTCGCAACGCGAATTTGTAAATCGCAACACA-AAGTCAAATTCGCAACGCGATAGTCAAATTCGC
1 TTCGCAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
* * * ** *
1557549 AACGTGATAGTCAAATTCGCAATGCGATAGTCAAATTCGCAATGCGAAAGTCAAA
66 AACGCGACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
1557604 T
1 T
1557605 GTTTTTATGC
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
119 81 0.73
120 30 0.27
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (120 bp):
TTCGCAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
AACGCGACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:1560314 original size:42 final size:43
Alignment explanation
Indices: 1560267--1560358 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 43
1560257 GATGCACTTA
* * *
1560267 TCATCATTC-AAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCGAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTC
*
1560309 TCATCA-TCGAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTG
1 TCATCATTCGAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTC
1560351 TCATCATT
1 TCATCATT
1560359 TAAAAGGTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 2 0.05
42 41 0.93
43 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (43 bp):
TCATCATTCGAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTC
Found at i:1560355 original size:21 final size:21
Alignment explanation
Indices: 1560267--1560355 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 21
1560257 GATGCACTTA
* *
1560267 TCATCATTCAAGAGGCGCCTC
1 TCATCGTTCAAGAGGCCCCTC
1560288 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
1560309 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* *
1560330 CCATCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
1560351 TCATC
1 TCATC
1560356 ATTTAAAAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
20 3 0.05
21 49 0.89
22 3 0.05
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1561868 original size:66 final size:60
Alignment explanation
Indices: 1561737--1561876 Score: 183
Period size: 66 Copynumber: 2.2 Consensus size: 60
1561727 TTTTACATTG
1561737 AAAGTTGATTTGTTTAATTGATGAGGAAATAAAATTTATTTTTTTATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAAATTTATTTTTTTATTAATTGATTTGTA
* * *
1561797 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATGATT-TTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAA-AAT--TTATTTTT--TT-ATTAATTGATTTG
1561861 TA
59 TA
1561863 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
1561877 GTTTCTAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
60 17 0.24
61 13 0.19
62 3 0.04
63 5 0.07
64 2 0.03
65 2 0.03
66 28 0.40
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (60 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAAATTTATTTTTTTATTAATTGATTTGTA
Found at i:1561960 original size:20 final size:20
Alignment explanation
Indices: 1561935--1561972 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1561925 GTTGAAGGTA
*
1561935 CAAATTTGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
1561955 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
1561973 TAAGCGTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1562301 original size:39 final size:39
Alignment explanation
Indices: 1562245--1562331 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1562235 TCAAGTTGTA
1562245 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
1562284 GATTTTGATTTCTTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1562323 GATTTTGAT
1 GATTTTGAT
1562332 GAGCATCGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1562658 original size:12 final size:12
Alignment explanation
Indices: 1562643--1562677 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1562633 ATTTATATTG
1562643 AAATTCAAACTT
1 AAATTCAAACTT
* *
1562655 AAATTGAAATTT
1 AAATTCAAACTT
1562667 AAATTCAAACT
1 AAATTCAAACT
1562678 CCAATTACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.34
Consensus pattern (12 bp):
AAATTCAAACTT
Found at i:1563120 original size:20 final size:20
Alignment explanation
Indices: 1563097--1563158 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
1563087 TGTACAACAT
*
1563097 GAAAGTTAAATTCGCAACGC
1 GAAAGTCAAATTCGCAACGC
* *
1563117 GAAAGTCAAATTTGCAACGA
1 GAAAGTCAAATTCGCAACGC
*
1563137 GAAAGCCAAATTCGCAACGC
1 GAAAGTCAAATTCGCAACGC
1563157 GA
1 GA
1563159 TTTTCGGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGC
Found at i:1564066 original size:19 final size:20
Alignment explanation
Indices: 1564037--1564074 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1564027 AGAAATTCGT
1564037 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
1564057 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
1564075 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:1564118 original size:63 final size:62
Alignment explanation
Indices: 1564044--1564200 Score: 190
Period size: 63 Copynumber: 2.5 Consensus size: 62
1564034 CGTTGAAGGT
* * * *
1564044 GCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCAGG
1 GCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCAGG
** ** *
1564107 GCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAGT
1 GCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCAGG
1564170 GCATCGATGCATCAGGAGTGCATCGATGCAT
1 GCATCGATGCAT-AGGAGTGCATCGATGCAT
1564201 GCCTCCATTA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
63 77 0.94
64 5 0.06
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (62 bp):
GCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCAGG
Found at i:1565535 original size:18 final size:18
Alignment explanation
Indices: 1565512--1565547 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1565502 AGGAATGATA
1565512 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1565530 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1565548 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1565549 original size:62 final size:62
Alignment explanation
Indices: 1565483--1565670 Score: 146
Period size: 62 Copynumber: 3.1 Consensus size: 62
1565473 TGATCCCTAG
*
1565483 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCAGGA
* * * * * * *
1565545 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCCCT
1 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTT
1565602 -A-G-
58 CAGGA
*
1565604 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTAGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCAGGA
1565666 CATAT
1 CATAT
1565671 ATGTATTCTT
Statistics
Matches: 92, Mismatches: 15, Indels: 38
0.63 0.10 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 19 0.21
60 12 0.13
61 11 0.12
62 24 0.26
63 7 0.08
64 6 0.07
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (62 bp):
CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCAGGA
Found at i:1565666 original size:18 final size:18
Alignment explanation
Indices: 1565633--1565668 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1565623 AGGAATGATA
*
1565633 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCAGGACAT
*
1565651 TGTGGTCCTTTAGGACAT
1 TGTGGTCCTTCAGGACAT
1565669 ATATGTATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCAGGACAT
Found at i:1565772 original size:121 final size:121
Alignment explanation
Indices: 1565409--1565760 Score: 650
Period size: 121 Copynumber: 2.9 Consensus size: 121
1565399 CGAGGGTCTA
1565409 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1565474 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
1565530 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1565595 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
** **
1565651 TGTGGTCCTTTAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
1565716 GATCCCTAATATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
1565761 ATTATGGACA
Statistics
Matches: 225, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 225 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:1565840 original size:23 final size:23
Alignment explanation
Indices: 1565779--1565847 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1565769 CATTATTATA
* *
1565779 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCATTTCTATG
*
1565802 CGGCACTACGGTGCATTTCTATG
1 TGGCACTACGGTGCATTTCTATG
* *
1565825 TGGCACTTCGGTGCATTTATATG
1 TGGCACTACGGTGCATTTCTATG
1565848 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTATG
Found at i:1569655 original size:19 final size:20
Alignment explanation
Indices: 1569626--1569663 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1569616 AGAAATTTGT
1569626 TGAAGGTGCATCAATGCATA
1 TGAAGGTGCATCAATGCATA
*
1569646 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCAATGCAT
1569664 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCAATGCATA
Found at i:1569764 original size:62 final size:62
Alignment explanation
Indices: 1569631--1569788 Score: 203
Period size: 62 Copynumber: 2.5 Consensus size: 62
1569621 TTTGTTGAAG
* * * * * *
1569631 GTGCATCAATGCATATGAAGTGCATCGATGCATTAATTTAAATACAAACATCGAATGTCATCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCATT-ATCTAAATAAAAACATCGAATGCCATCA
*
1569694 GTGCATCGATGCATAAGGAGTGCATCGATGCATT-TCT-AATAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCATTATCTAAATAAA--AACATCGAATGCCATCA
*
1569756 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGGAGTGCATCGATGCAT
1569789 GCCTCCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
60 5 0.06
61 2 0.02
62 47 0.55
63 31 0.36
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAAGGAGTGCATCGATGCATTATCTAAATAAAAACATCGAATGCCATCA
Found at i:1571267 original size:116 final size:114
Alignment explanation
Indices: 1570979--1571304 Score: 452
Period size: 116 Copynumber: 2.9 Consensus size: 114
1570969 CGAGGGTCTA
*
1570979 TGTGGTCCTTCGGACATATATTATTCTTTGGAACATGTGTGAAGTCT-GTGAGACACATACTTAA
1 TGTGGTCCTT-GGACATATATTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
* *
1571043 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
65 TCCCTATCATATGTATATGATTCTTAAGG-A--ATATGTGGT-CTTCGAGACAT
* *
1571097 TGTGGTCCTT---C--GTACTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 TGTGGTCCTTGGACATATATTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
1571157 CCCTATCATATGTATATAATTCTTAAGGAATATGTGGT-TTCGAGACAT
66 CCCTATCATATGTATATGATTCTTAAGGAATATGTGGTCTTCGAGACAT
*
1571205 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCC-TT-GGACATATAT-TATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1571270 GATCCCTAGT-ATATGTATATGATTCTTAAGGAATA
63 GATCCCTA-TCATATGTATATGATTCTTAAGGAATA
1571305 ATATGTGGTC
Statistics
Matches: 188, Mismatches: 10, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
108 17 0.09
109 2 0.01
110 9 0.05
112 29 0.15
113 44 0.23
114 1 0.01
115 2 0.01
116 73 0.39
117 1 0.01
118 10 0.05
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (114 bp):
TGTGGTCCTTGGACATATATTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTATCATATGTATATGATTCTTAAGGAATATGTGGTCTTCGAGACAT
Found at i:1571383 original size:23 final size:23
Alignment explanation
Indices: 1571333--1571393 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1571323 CATTATTATA
*
1571333 TGGCACTACGGTGCAATTCTACG
1 TGGCACTATGGTGCAATTCTACG
* **
1571356 CGGCACTATGGTGCAATTCTTTG
1 TGGCACTATGGTGCAATTCTACG
1571379 TGGCACT-TCGGTGCA
1 TGGCACTAT-GGTGCA
1571394 TTTATATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTATGGTGCAATTCTACG
Found at i:1574415 original size:24 final size:24
Alignment explanation
Indices: 1574381--1574434 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1574371 CCATCATATC
1574381 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1574405 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1574429 ATCAAA
1 ATCAAA
1574435 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1574448 original size:24 final size:24
Alignment explanation
Indices: 1574381--1574448 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1574371 CCATCATATC
* * *
1574381 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1574405 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1574429 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1574449 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1575183 original size:14 final size:15
Alignment explanation
Indices: 1575147--1575184 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1575137 GAAATCATTG
1575147 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1575162 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1575177 AAAAATTA
1 AAAAATTA
1575185 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1575369 original size:19 final size:19
Alignment explanation
Indices: 1575341--1575431 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
1575331 ACTAAAACCT
*
1575341 GTTGCAAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
1575360 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
1575379 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
** **
1575400 GTTGCGAATTTGACTTTGT
1 GTTGCGAATTTGAAATTCA
1575419 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1575432 CTATCGCGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
19 48 0.75
20 1 0.02
21 15 0.23
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:1575423 original size:40 final size:39
Alignment explanation
Indices: 1575360--1575505 Score: 159
Period size: 40 Copynumber: 3.7 Consensus size: 39
1575350 TTGAAATTCA
** **
1575360 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAA-ATTCCGC
1 GTTGCGAATTTGACTTTGTGTTGCGAATTTGAATA-T-CGC
*
1575400 GTTGCGAATTTGACTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTGTGTTGCGAATTTGAATATCGC
* ** *
1575439 GTTGCGAATTTGACTATCGCATTGCGAATTTGAGTATCGC
1 GTTGCGAATTTGACT-TTGTGTTGCGAATTTGAATATCGC
*
1575479 GTTTCGAATTTGACTTATGTGTTGCGA
1 GTTGCGAATTTGACTT-TGTGTTGCGA
1575506 TTTACAAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
39 19 0.21
40 70 0.78
41 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (39 bp):
GTTGCGAATTTGACTTTGTGTTGCGAATTTGAATATCGC
Found at i:1575444 original size:20 final size:20
Alignment explanation
Indices: 1575379--1575493 Score: 144
Period size: 20 Copynumber: 5.8 Consensus size: 20
1575369 TTGAAATTCA
*
1575379 GTTGCGAATTTGA-AATTCCGC
1 GTTGCGAATTTGACTA-T-CGC
* *
1575400 GTTGCGAATTTGACT-TTGT
1 GTTGCGAATTTGACTATCGC
1575419 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
1575439 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* *
1575459 ATTGCGAATTTGAGTATCGC
1 GTTGCGAATTTGACTATCGC
*
1575479 GTTTCGAATTTGACT
1 GTTGCGAATTTGACT
1575494 TATGTGTTGC
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.20
20 53 0.65
21 13 0.16
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:1575488 original size:60 final size:60
Alignment explanation
Indices: 1575379--1575525 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 60
1575369 TTGAAATTCA
* * *
1575379 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGAAATTCCGCATTGCGAATTTGACTTCGCGTTGCGAATTTGACTATCGC
* * * *
1575439 GTTGCGAATTTG-ACTAT-CGCATTGCGAATTTGAGTATCGCGTTTCGAATTTGACTTAT-GT
1 GTTGCGAATTTGAAAT-TCCGCATTGCGAATTTGACT-TCGCGTTGCGAATTTGAC-TATCGC
*
1575499 GTTGCG-ATTTACAAATT-CGCATTGCGA
1 GTTGCGAATTT-GAAATTCCGCATTGCGA
1575526 TTTACAGATT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
59 22 0.30
60 46 0.63
61 5 0.07
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (60 bp):
GTTGCGAATTTGAAATTCCGCATTGCGAATTTGACTTCGCGTTGCGAATTTGACTATCGC
Found at i:1575544 original size:80 final size:79
Alignment explanation
Indices: 1575379--1575570 Score: 207
Period size: 80 Copynumber: 2.4 Consensus size: 79
1575369 TTGAAATTCA
* * * *
1575379 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGC
1 GTTGCGAATTTGAGATT-CGCGTTTCGAATTTGACTTTGTGTTGCGAATTTGACAATCGCATTGC
*
1575444 GAATTTGACTATCGC
65 GAATTTGACGATCGC
*
1575459 ATTGCGAATTTGAG-TATCGCGTTTCGAATTTGACTTATGTGTTGCG-ATTT-ACAAATTCGCAT
1 GTTGCGAATTTGAGAT-TCGCGTTTCGAATTTGACTT-TGTGTTGCGAATTTGAC-AA-TCGCAT
1575521 TGCG-ATTT-ACAGATTCGC
62 TGCGAATTTGAC-GA-TCGC
*
1575539 GTTGCG-ATTTACAGATTCGCGTTTCGAATTTG
1 GTTGCGAATTT-GAGATTCGCGTTTCGAATTTG
1575571 GAAAATCGCA
Statistics
Matches: 96, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
78 4 0.04
79 33 0.34
80 58 0.60
81 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (79 bp):
GTTGCGAATTTGAGATTCGCGTTTCGAATTTGACTTTGTGTTGCGAATTTGACAATCGCATTGCG
AATTTGACGATCGC
Found at i:1575559 original size:20 final size:20
Alignment explanation
Indices: 1575499--1575561 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
1575489 TGACTTATGT
*
1575499 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAGATTCGC
*
1575519 ATTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
1575539 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
1575559 GTT
1 GTT
1575562 TCGAATTTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:1575992 original size:46 final size:46
Alignment explanation
Indices: 1575941--1576038 Score: 112
Period size: 46 Copynumber: 2.1 Consensus size: 46
1575931 TATAAAATAT
*
1575941 TAAAAATA-TTTAAAAAATATGAAAATAGAC-ATAATAATATTA-AAAA
1 TAAAAATACTATAAAAAATATGAAAA-AGACAATAA-AAT-TTAGAAAA
* * *
1575987 TAAAAATACTATAAAAAATTTTAAAAATACAATAAAATTTAGAAAA
1 TAAAAATACTATAAAAAATATGAAAAAGACAATAAAATTTAGAAAA
1576033 TAAAAA
1 TAAAAA
1576039 ATGATAATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 3 0.07
46 24 0.53
47 18 0.40
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (46 bp):
TAAAAATACTATAAAAAATATGAAAAAGACAATAAAATTTAGAAAA
Found at i:1576010 original size:27 final size:28
Alignment explanation
Indices: 1575920--1576015 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 28
1575910 AAACTTAAGG
1575920 ATTTTAAAAATTATAAAATA-T-TAAAAA
1 ATTTTAAAAA-TATAAAATACTATAAAAA
* *
1575947 TATTTAAAAAATATGAAAATAGAC-AT-AATA
1 -ATTTTAAAAATAT-AAAAT--ACTATAAAAA
*
1575977 ATATTAAAAATA-AAAATACTATAAAAA
1 ATTTTAAAAATATAAAATACTATAAAAA
1576004 ATTTTAAAAATA
1 ATTTTAAAAATA
1576016 CAATAAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 22 0.40
28 14 0.25
29 10 0.18
30 4 0.07
31 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
ATTTTAAAAATATAAAATACTATAAAAA
Found at i:1576558 original size:155 final size:157
Alignment explanation
Indices: 1576361--1576749 Score: 480
Period size: 155 Copynumber: 2.5 Consensus size: 157
1576351 TTATTCTTTC
* * * * *
1576361 ATTTTAAGTCTATTTTTTTTACCAAATTTGAACTACACGCTCCTAAACCATAGTAGAATGCGTGT
1 ATTTTAAGTC-A-CTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGT
* * * *
1576426 GTAATTTTAATTCCTCTTTGTGATAACAAAATTTTAT-TTTTCAATTTAGTCTTTTAATTTTTCA
64 GT-ACTTTAATTCCTCTTTGTGATAACAAAATTTTATATTTTCAATTTAGTCCTTCAATTCTTCA
*
1576490 TAATCTCCTTATTTCTTCAATTCGTCATTT
128 TAATCTCCTTATTCCTTCAATTCGTCATTT
* *
1576520 ATTTTTAGTC-C-TTTTTACCAAATTTGAGCCACATGCTCCTAAACCATAGTAGAATACATGTGT
1 ATTTTAAGTCACTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTGT
* * * *
1576583 ACTTTCATTCCTCTTTTTTATAACAAAATTTTTTATTTTCAATTTAGTCCTTCAATTCTTCATAA
66 ACTTTAATTCCTCTTTGTGATAACAAAATTTTATATTTTCAATTTAGTCCTTCAATTCTTCATAA
* *
1576648 TCTCCTTATTCCTTCAATTTGTGATTT
131 TCTCCTTATTCCTTCAATTCGTCATTT
* * * * * * *
1576675 ATTTTAAGTCACTTTTTTTACC-AATTTAAACCACATGCTCATATACCACAATAGAATACCTATG
1 ATTTTAAGTCAC-TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
1576739 TAACTTTAATT
65 T-ACTTTAATT
1576750 GTTATTTTTT
Statistics
Matches: 197, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
154 29 0.15
155 107 0.54
156 1 0.01
157 35 0.18
158 16 0.08
159 9 0.05
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (157 bp):
ATTTTAAGTCACTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTGT
ACTTTAATTCCTCTTTGTGATAACAAAATTTTATATTTTCAATTTAGTCCTTCAATTCTTCATAA
TCTCCTTATTCCTTCAATTCGTCATTT
Found at i:1580526 original size:2 final size:2
Alignment explanation
Indices: 1580521--1580560 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1580511 AAGAGAAAAA
*
1580521 AT AT AT AA AT A- AT AT AT AT -T AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1580560 A
1 A
1580561 ATAAGGACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1581093 original size:31 final size:31
Alignment explanation
Indices: 1581058--1581124 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1581048 ATAAAGTTTG
* *
1581058 GTCACTTTCATTTCGTTTTAGTTAAGATTTT
1 GTCACTTTCATTTCGTTTTAATTAAGATGTT
* *
1581089 GTCACTTTCGTTTTGTTTTAATTAAGATGTT
1 GTCACTTTCATTTCGTTTTAATTAAGATGTT
1581120 GTCAC
1 GTCAC
1581125 AAAATGTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.52
Consensus pattern (31 bp):
GTCACTTTCATTTCGTTTTAATTAAGATGTT
Found at i:1581325 original size:31 final size:31
Alignment explanation
Indices: 1581257--1581325 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1581247 CAAAAAACAT
* ** *
1581257 AAGTTTTGGTCACTTACGTTATTGTTTTATT
1 AAGTTTTGGTCACTTACATTATCATTTTATC
* * *
1581288 ATGTTTTGTTCACTTATATTATCATTTTATC
1 AAGTTTTGGTCACTTACATTATCATTTTATC
1581319 AAGTTTT
1 AAGTTTT
1581326 AATGACTTGG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (31 bp):
AAGTTTTGGTCACTTACATTATCATTTTATC
Found at i:1583541 original size:23 final size:23
Alignment explanation
Indices: 1583515--1583579 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
1583505 CAGCTGGTAT
1583515 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* * **
1583538 AATTGCACCGGAGCGCCGCGTAG
1 AATTGCACCGAAGTGCCATGTAG
*
1583561 AATTGCACCGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
1583580 ATAATAATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:1588826 original size:23 final size:23
Alignment explanation
Indices: 1588800--1588844 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1588790 CACCACAGCT
*
1588800 CGTATAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
* *
1588823 CGTAGAGTTGCACCGTAGTGCC
1 CGTAGAATTGCACCGGAGTGCC
1588845 ATATAATAAT
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:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCG
Found at i:1590460 original size:21 final size:21
Alignment explanation
Indices: 1590436--1590478 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1590426 TCTGGTTTGT
* * *
1590436 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1590457 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1590478 T
1 T
1590479 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1591596 original size:15 final size:16
Alignment explanation
Indices: 1591576--1591607 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1591566 AAAATTGTAA
1591576 TTTAATTA-ATATTAT
1 TTTAATTATATATTAT
1591591 TTTAATTATATATTAT
1 TTTAATTATATATTAT
1591607 T
1 T
1591608 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATTATATATTAT
Found at i:1595430 original size:26 final size:26
Alignment explanation
Indices: 1595362--1595432 Score: 133
Period size: 26 Copynumber: 2.7 Consensus size: 26
1595352 TTCTGGTTCA
*
1595362 GTAACTAAAACATCAGGAACTCACGT
1 GTAACTAAAACATCAGTAACTCACGT
1595388 GTAACTAAAACATCAGTAACTCACGT
1 GTAACTAAAACATCAGTAACTCACGT
1595414 GTAACTAAAACATCAGTAA
1 GTAACTAAAACATCAGTAA
1595433 TATCAAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (26 bp):
GTAACTAAAACATCAGTAACTCACGT
Found at i:1597443 original size:24 final size:24
Alignment explanation
Indices: 1597408--1597454 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1597398 TTTGATCCTA
* *
1597408 AACTTTATATAAAATATAAATTTT
1 AACTTTAGATAAAACATAAATTTT
*
1597432 AACTTTAGATAAAACATCAATTT
1 AACTTTAGATAAAACATAAATTT
1597455 AACATATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (24 bp):
AACTTTAGATAAAACATAAATTTT
Found at i:1597956 original size:2 final size:2
Alignment explanation
Indices: 1597949--1597973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1597939 ATTGCATGTT
1597949 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 T
1597974 TCGTTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1601472 original size:2 final size:2
Alignment explanation
Indices: 1601465--1601491 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1601455 TTAATTAAAT
1601465 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 T
1601492 TAAATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1601675 original size:2 final size:2
Alignment explanation
Indices: 1601670--1601703 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1601660 TATATATATA
*
1601670 TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1601704 AAATAATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:1602199 original size:2 final size:2
Alignment explanation
Indices: 1602192--1602219 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1602182 AAGCTAAATA
1602192 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
1602220 TTAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1604420 original size:20 final size:20
Alignment explanation
Indices: 1604354--1604470 Score: 76
Period size: 20 Copynumber: 5.8 Consensus size: 20
1604344 TAACATGTTG
* * *
1604354 AAATTTGACAAATCCAATTT
1 AAATTTGACAAAACCGATTA
* * *
1604374 CAATTTGACAAAA-CAAGTAA
1 AAATTTGACAAAACCGA-TTA
1604394 CAAATTTGACAAAACCGATTA
1 -AAATTTGACAAAACCGATTA
* * *
1604415 AAATTTGACAAAATCGGTTG
1 AAATTTGACAAAACCGATTA
* * *
1604435 AAATTTGACGAAACTTG-TTT
1 AAATTTGACAAAAC-CGATTA
*
1604455 TAATTTGACAAAACCG
1 AAATTTGACAAAACCG
1604471 GTAAAAAGCT
Statistics
Matches: 76, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
19 4 0.05
20 55 0.72
21 15 0.20
22 2 0.03
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
AAATTTGACAAAACCGATTA
Found at i:1604791 original size:197 final size:197
Alignment explanation
Indices: 1604451--1604814 Score: 557
Period size: 197 Copynumber: 1.8 Consensus size: 197
1604441 GACGAAACTT
* * *
1604451 GTTTTAATTTGACAAAACCGGTAAAAAGCTACCAGAATTGTTGAAATTTGTATTGATACGTTTAT
1 GTTTCAATTTGACAAAACCGGTAAAAAGCTACCAGAATTGTTGAAATTTGTATCGATACATTTAT
** * * *
1604516 AAGTATATTTACAAAAGTATCGAAACTGTATGAATTTAAAAGAATTGTAATAATAGCGGCTATAA
66 AAGTATAAGTACAAAAGTATCGAAACTGTAGGAATTTAAAAGAATTGCAATAATAGCGACTATAA
1604581 AGTATCGATACCTTACACACATGTATCGATACATGACAATATAACATGATGAAAATTAACAAAAT
131 AGTATCGATACCTTACACACATGTATCGATACATGACAATATAACATGATGAAAATTAACAAAAT
1604646 CA
196 CA
* ** * *
1604648 GTTTCAATTTGACAAAACCGGTAAAGATTTATCGGAATTGTTGAAATTTGTATCGATACATTTAT
1 GTTTCAATTTGACAAAACCGGTAAAAAGCTACCAGAATTGTTGAAATTTGTATCGATACATTTAT
* * ** *
1604713 AAGTATAAGTACCAATGTATCGGTACTTTAGGAATTTAAAAGAATTGCAATAATAGCGACTATAA
66 AAGTATAAGTACAAAAGTATCGAAACTGTAGGAATTTAAAAGAATTGCAATAATAGCGACTATAA
*
1604778 AGTATCGATACCTTAGACACATGTATCGATACATGAC
131 AGTATCGATACCTTACACACATGTATCGATACATGAC
1604815 TGTCGGAACC
Statistics
Matches: 148, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
197 148 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (197 bp):
GTTTCAATTTGACAAAACCGGTAAAAAGCTACCAGAATTGTTGAAATTTGTATCGATACATTTAT
AAGTATAAGTACAAAAGTATCGAAACTGTAGGAATTTAAAAGAATTGCAATAATAGCGACTATAA
AGTATCGATACCTTACACACATGTATCGATACATGACAATATAACATGATGAAAATTAACAAAAT
CA
Found at i:1605164 original size:19 final size:19
Alignment explanation
Indices: 1605140--1605180 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1605130 GTTAAATAAG
*
1605140 AAATAATAAA-TAAATATTA
1 AAATAAAAAATTAAAT-TTA
1605159 AAATAAAAAATTAAATTTA
1 AAATAAAAAATTAAATTTA
1605178 AAA
1 AAA
1605181 ACGAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATAAAAAATTAAATTTA
Found at i:1607486 original size:106 final size:106
Alignment explanation
Indices: 1607301--1608432 Score: 1834
Period size: 106 Copynumber: 10.7 Consensus size: 106
1607291 GGTAAGTTTT
* * * * * * * * * *
1607301 GTTGTCTAGAGGCAAATATCCTCCGCCGTGAAGTTAAAATTGACTCTGAAACTGGAAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1607366 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1607407 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAACTGGCTCTGAAATTGGGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
*
1607472 GTTGACAACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
** * *
1607513 GTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1607578 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1607619 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1607684 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA-TATGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT-TGC
*
1607725 GTTGTCTGTAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
*
1607790 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
1607831 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
* *
1607896 GTTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACATGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * * * * * * *
1607937 GTTGTCTGGAGACCAATATCCTCCGCCGTGAAGTTAAAATTGACTCTGAAACTGGAAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1608002 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
1608043 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAACTGGCTCTGAAATTGAGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
*
1608108 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGT
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
1608149 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
*
1608214 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
1608255 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
*
1608320 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
1608361 GTTGTCTGGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1608426 GTTGACA
66 GTTGACA
1608433 TATAACTTTT
Statistics
Matches: 957, Mismatches: 67, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
105 1 0.00
106 955 1.00
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
Found at i:1611248 original size:20 final size:19
Alignment explanation
Indices: 1611212--1611249 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1611202 TGCATGTGAT
*
1611212 GGAAATAAAATAAAAGAGA
1 GGAAAAAAAATAAAAGAGA
1611231 GGAAAAAAAATAAAA-AGA
1 GGAAAAAAAATAAAAGAGA
1611249 G
1 G
1611250 TTAGTAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (19 bp):
GGAAAAAAAATAAAAGAGA
Found at i:1614043 original size:20 final size:20
Alignment explanation
Indices: 1614014--1614053 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1614004 CAATATAACA
1614014 GGTTTAAATTTGACAAAACC
1 GGTTTAAATTTGACAAAACC
*
1614034 GGTTTCAATTTGACAAAACC
1 GGTTTAAATTTGACAAAACC
1614054 CCTAAAGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
GGTTTAAATTTGACAAAACC
Found at i:1614146 original size:21 final size:21
Alignment explanation
Indices: 1614122--1614185 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1614112 CAAAGTATCA
1614122 ATACTTTATATATGTGTATTG
1 ATACTTTATATATGTGTATTG
*
1614143 ATACATTTATA-A---GTATCG
1 ATAC-TTTATATATGTGTATTG
*
1614161 ATACTTTAAATATGTGTATTG
1 ATACTTTATATATGTGTATTG
1614182 ATAC
1 ATAC
1614186 ATTTTGCGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 5 0.14
18 10 0.29
21 14 0.40
22 6 0.17
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.45
Consensus pattern (21 bp):
ATACTTTATATATGTGTATTG
Found at i:1614168 original size:39 final size:39
Alignment explanation
Indices: 1614114--1614189 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
1614104 ATATGTACCA
*
1614114 AAGTATCAATACTTTATATATGTGTATTGATACATTTAT
1 AAGTATCAATACTTTAAATATGTGTATTGATACATTTAT
*
1614153 AAGTATCGATACTTTAAATATGTGTATTGATACATTT
1 AAGTATCAATACTTTAAATATGTGTATTGATACATTT
1614190 TGCGTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.45
Consensus pattern (39 bp):
AAGTATCAATACTTTAAATATGTGTATTGATACATTTAT
Found at i:1614440 original size:20 final size:20
Alignment explanation
Indices: 1614391--1614440 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1614381 CTTGCGTAAT
1614391 TACCAAGTATCGATACTTTTA
1 TACC-AGTATCGATACTTTTA
* *
1614412 TA-TAGGTATGGATACTTTTA
1 TACCA-GTATCGATACTTTTA
1614432 TACCAGTAT
1 TACCAGTAT
1614441 ACTTCTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
TACCAGTATCGATACTTTTA
Found at i:1620354 original size:3 final size:3
Alignment explanation
Indices: 1620342--1620390 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
1620332 ATATATATAT
* * *
1620342 ATA ATAA ATA ATA ATA ATA ATA ATA TATT ATA TTA ATA ATA ATT ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
1620389 AT
1 AT
1620391 TATTATTATG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:1620368 original size:28 final size:28
Alignment explanation
Indices: 1620320--1620399 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 28
1620310 ATGTAATTTG
1620320 TAATATATATATATATATATATATAATAAATAA
1 TAATA-ATA-ATA-ATATAT-TAT-ATAAATAA
*
1620353 TAATAATAATAATATATTATATTAATAA
1 TAATAATAATAATATATTATATAAATAA
* *
1620381 TAATTATAATTAT-TATTAT
1 TAATAATAATAATATATTAT
1620400 GAAAAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.14
28 18 0.41
29 3 0.07
30 6 0.14
31 3 0.07
32 3 0.07
33 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATAATAATAATATATTATATAAATAA
Found at i:1620381 original size:22 final size:22
Alignment explanation
Indices: 1620353--1620398 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1620343 TAATAAATAA
1620353 TAATAATAATAATATATTA-TAT
1 TAATAATAATAATA-ATTATTAT
*
1620375 TAATAATAATTATAATTATTAT
1 TAATAATAATAATAATTATTAT
1620397 TA
1 TA
1620399 TGAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATAATTATTAT
Found at i:1620392 original size:16 final size:16
Alignment explanation
Indices: 1620343--1620392 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1620333 TATATATATA
*
1620343 TAATAAATAATAATAA-
1 TAAT-AATAATTATAAT
1620359 TAATAATATATTAT-AT
1 TAATAATA-ATTATAAT
1620375 TAATAATAATTATAAT
1 TAATAATAATTATAAT
1620391 TA
1 TA
1620393 TTATTATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATAATTATAAT
Found at i:1620394 original size:19 final size:19
Alignment explanation
Indices: 1620320--1620395 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 19
1620310 ATGTAATTTG
1620320 TAATATATATATATATATATATA
1 TAATA-ATATA-ATATAT-TA-A
1620343 TAATAA-ATAATA-A-TAA
1 TAATAATATAATATATTAA
*
1620359 TAATAATATATTATATTAA
1 TAATAATATAATATATTAA
1620378 TAATAATTATAAT-TATTA
1 TAATAA-TATAATATATTA
1620396 TTATGAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
16 7 0.15
17 7 0.15
18 1 0.02
19 15 0.32
20 8 0.17
21 3 0.06
22 1 0.02
23 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATAATATAATATATTAA
Found at i:1620833 original size:37 final size:36
Alignment explanation
Indices: 1620774--1621047 Score: 242
Period size: 37 Copynumber: 7.5 Consensus size: 36
1620764 GAAATAACTG
1620774 TCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAA
* * * ** **
1620811 TCTCAAGTGAGATAAATTTTTGTTTCAAGTGAAACTG
1 TCTCAAGCGAGACAAA-TTTTGTTTTAAGAAAAACAA
*
1620848 TCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
* * * ** ** **
1620884 TCTCAAGTGAGATAAAGTTCTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAA-TTTTGTTTTAAGAAAAACAA
1620921 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
** * * ** ** **
1620957 TCTCAAATGAGATAAAGTTCTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAA-TTTTGTTTTAAGAAAAACAA
*
1620994 TCTCAAGCGAGACAAATTTTCTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
* *
1621030 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGACAAATT
1621048 GCTATTTGAA
Statistics
Matches: 177, Mismatches: 57, Indels: 7
0.73 0.24 0.03
Matches are distributed among these distances:
36 82 0.46
37 94 0.53
38 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
Found at i:1620889 original size:73 final size:73
Alignment explanation
Indices: 1620769--1621045 Score: 491
Period size: 73 Copynumber: 3.8 Consensus size: 73
1620759 AACTCGAAAT
* *
1620769 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
*
1620834 TTCAAGTGA
65 TTCGAGTGA
*
1620843 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1620908 TCGAGTGA
66 TCGAGTGA
*
1620916 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAATGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1620981 TCGAGTGA
66 TCGAGTGA
*
1620989 AACTGTCTCAAGCGAGACAAATTTTCTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1621046 TTGCTATTTG
Statistics
Matches: 195, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
73 174 0.89
74 21 0.11
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (73 bp):
AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCGAGTGA
Found at i:1621362 original size:166 final size:166
Alignment explanation
Indices: 1621089--1621414 Score: 548
Period size: 166 Copynumber: 2.0 Consensus size: 166
1621079 TATGGATGTG
* * * *
1621089 GGAAATAGTTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTT
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTT
**
1621154 AGAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
1621219 T-GGTAACATGACCCAATCTCAAGATAATGTTGTTT
131 TGGGTAACATGACCCAATCTCAAGATAATGTTGTTT
1621254 GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCA-TT
1 GGAAATAGTTTACTAAGT--AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTT
* *
1621318 TTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATATCATGTTG
64 TTAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTG
1621383 ATTGGGTAACATGACCCAATCTCAAGATAATG
129 ATTGGGTAACATGACCCAATCTCAAGATAATG
1621415 CTCATTCTTG
Statistics
Matches: 150, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
165 18 0.12
166 66 0.44
167 66 0.44
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (166 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTT
AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
TGGGTAACATGACCCAATCTCAAGATAATGTTGTTT
Found at i:1621954 original size:22 final size:22
Alignment explanation
Indices: 1621929--1621983 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1621919 AATAAAGCTT
1621929 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1621951 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1621973 TCATCTTTGAA
1 TCATCTTTGAA
1621984 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1628412 original size:14 final size:14
Alignment explanation
Indices: 1628393--1628421 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1628383 TTGAAAACAG
1628393 TAAATCAACAACTT
1 TAAATCAACAACTT
1628407 TAAATCAACAACTT
1 TAAATCAACAACTT
1628421 T
1 T
1628422 TCATTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATCAACAACTT
Found at i:1634100 original size:2 final size:2
Alignment explanation
Indices: 1634093--1634160 Score: 85
Period size: 2 Copynumber: 37.0 Consensus size: 2
1634083 GTAATTTGTA
1634093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1634134 AT AA AT A- AT A- AT A- AT A- AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1634161 TAATAATAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
1 6 0.10
2 52 0.90
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1634164 original size:16 final size:17
Alignment explanation
Indices: 1634091--1634174 Score: 77
Period size: 16 Copynumber: 4.9 Consensus size: 17
1634081 ATGTAATTTG
1634091 TAAT-ATATATATATATA
1 TAATAATATAT-TATATA
1634108 TATATATATATATATATATA
1 TA-ATA-ATATAT-TATATA
* *
1634128 TATATAATAAATAATA-A
1 TA-ATAATATATTATATA
1634145 TAATAATATATTATAT-
1 TAATAATATATTATATA
1634161 TAATAATA-ATTATA
1 TAATAATATATTATA
1634175 ATTATTATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
15 6 0.10
16 19 0.32
17 5 0.08
18 5 0.08
19 5 0.08
20 19 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATAATATATTATATA
Found at i:1634167 original size:22 final size:22
Alignment explanation
Indices: 1634139--1634184 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1634129 ATATAATAAA
1634139 TAATAATAATAATATATTA-TAT
1 TAATAATAATAATA-ATTATTAT
*
1634161 TAATAATAATTATAATTATTAT
1 TAATAATAATAATAATTATTAT
1634183 TA
1 TA
1634185 TGAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATAATTATTAT
Found at i:1635129 original size:131 final size:131
Alignment explanation
Indices: 1634916--1635375 Score: 737
Period size: 131 Copynumber: 3.5 Consensus size: 131
1634906 TAGTTCAACA
*
1634916 GAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGGTAAACGTTTT-TATCGGTA
1 GAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGGTAAAC-TTTTCTACCGGTA
*
1634980 TAATGAAAATAGGCGTAAATGTCCAACTATTGATACTCATATACAAATTATCGATACTTATAATT
65 TAATAAAAATAGGCGTAAATGTCCAACTATTGATACTCATATACAAATTATCGATACTTATAATT
1635045 TC
130 TC
* *
1635047 GAAACCTATTATTTTAAAGTAATAGGTAAATTAACAATGTACACAGTAAACTTTTCTACCGGTAT
1 GAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGGTAAACTTTTCTACCGGTAT
*
1635112 AATAAAAATAGACGTAAATGTCCAACTATTGATACTCATATACAAATTATCGATACTTATAATTT
66 AATAAAAATAGGCGTAAATGTCCAACTATTGATACTCATATACAAATTATCGATACTTATAATTT
1635177 C
131 C
*
1635178 GAAACCTATTA-TTTAGAAGTAATAGGTAAATTAACAATGTACACGGTAAACTTTTCTATCGGTA
1 GAAACCTATTACTTTA-AAGTAATAGGTAAATTAACAATGTACACGGTAAACTTTTCTACCGGTA
* * * * * *
1635242 TAATAAAAATAGGCGTAAATATCCAAGTATCGATACTCATATACAAAATATCTAAACTTATAATT
65 TAATAAAAATAGGCGTAAATGTCCAACTATTGATACTCATATACAAATTATCGATACTTATAATT
*
1635307 TT
130 TC
* * *
1635309 GAAACCTATTACTTTAAAGTAACAAGTAAATTAACAATGTACACGGTAGAC-TTTCTACCGGTAT
1 GAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGGTAAACTTTTCTACCGGTAT
1635373 AAT
66 AAT
1635376 GGAAATATGC
Statistics
Matches: 307, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
130 23 0.07
131 280 0.91
132 4 0.01
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (131 bp):
GAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGGTAAACTTTTCTACCGGTAT
AATAAAAATAGGCGTAAATGTCCAACTATTGATACTCATATACAAATTATCGATACTTATAATTT
C
Found at i:1636465 original size:37 final size:37
Alignment explanation
Indices: 1636391--1636465 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1636381 TACTATAATT
**
1636391 AATTTATATATTTTCTTTAAAAATTTTAAATTTATAA
1 AATTTATATATTTTCTTTAAAAATTTTAAATAGATAA
*
1636428 AATTTATATAATTTTTTTTACAAAA-TTTAAA-AGATAA
1 AATTTATAT-ATTTTCTTTA-AAAATTTTAAATAGATAA
1636465 A
1 A
1636466 GAGATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 15 0.45
39 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAATTTTAAATAGATAA
Found at i:1637270 original size:37 final size:38
Alignment explanation
Indices: 1637185--1637271 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 38
1637175 CATTAATATT
*
1637185 TTTTATATTTTTAATTTTATAAAATAAATTATATAAATA
1 TTTTATA-ATTTAATTTTATAAAATAAATTATATAAATA
*
1637224 --TTATGAATTTAATTTTTTTAAAA-AAA-TATATAAATA
1 TTTTAT-AATTTAA-TTTTATAAAATAAATTATATAAATA
1637260 TTTTATAATTTA
1 TTTTATAATTTA
1637272 TAATATTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
36 10 0.24
37 18 0.43
38 14 0.33
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (38 bp):
TTTTATAATTTAATTTTATAAAATAAATTATATAAATA
Found at i:1637291 original size:18 final size:17
Alignment explanation
Indices: 1637246--1637294 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1637236 TTTTTTTAAA
*
1637246 AAAATATATAAATATTTT
1 AAAATATAT-AATATTAT
* *
1637264 ATAATTTATAATATTAT
1 AAAATATATAATATTAT
1637281 ACAAATATATAATA
1 A-AAATATATAATA
1637295 AAGATAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATATAATATTAT
Found at i:1640424 original size:21 final size:21
Alignment explanation
Indices: 1640400--1640443 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1640390 AGCTGTCTTT
1640400 TCAGTCTGCCAAGCTTTAAGC
1 TCAGTCTGCCAAGCTTTAAGC
* *
1640421 TCAGTCTGCCGATCTTTAAGC
1 TCAGTCTGCCAAGCTTTAAGC
1640442 TC
1 TC
1640444 TCGGGTCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (21 bp):
TCAGTCTGCCAAGCTTTAAGC
Found at i:1645592 original size:30 final size:31
Alignment explanation
Indices: 1645525--1645596 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 31
1645515 GAGTCGAGGG
1645525 TTACCTATGTCTTTCGGGACATATGGACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACA-GA
1645557 TTACCTATGTCTTTCGGGACATATGGACA-A
1 TTACCTATGTCTTTCGGGACATATGGACAGA
1645587 TTACCTATGT
1 TTACCTATGT
1645597 TCTTCAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 11 0.28
32 29 0.73
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACAGA
Found at i:1645609 original size:30 final size:31
Alignment explanation
Indices: 1645525--1645613 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 31
1645515 GAGTCGAGGG
***
1645525 TTACCTATGTCTTTCGGGACATATGGACAGGA
1 TTACCTATGTCTTTCAAAACATATGGACA-GA
***
1645557 TTACCTATGTCTTTCGGGACATATGGACA-A
1 TTACCTATGTCTTTCAAAACATATGGACAGA
1645587 TTACCTATGT-TCTTCAAAACATATGGA
1 TTACCTATGTCT-TTCAAAACATATGGA
1645614 TAGGTCATTC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 1 0.02
30 23 0.43
32 29 0.55
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCTTTCAAAACATATGGACAGA
Found at i:1646615 original size:19 final size:20
Alignment explanation
Indices: 1646585--1646622 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1646575 CTATTTCCAC
1646585 AGTATCAGTACTATTCATAT
1 AGTATCAGTACTATTCATAT
1646605 AGTAT-AGTACTATTCATA
1 AGTATCAGTACTATTCATA
1646623 AAAACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
AGTATCAGTACTATTCATAT
Found at i:1647196 original size:16 final size:17
Alignment explanation
Indices: 1647168--1647202 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1647158 ATTTTTAGTC
1647168 GCTTTGTAAAAGTAAAT
1 GCTTTGTAAAAGTAAAT
*
1647185 GCTTTG-AAAAGTCAAT
1 GCTTTGTAAAAGTAAAT
1647201 GC
1 GC
1647203 GACACTTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (17 bp):
GCTTTGTAAAAGTAAAT
Found at i:1650788 original size:3 final size:3
Alignment explanation
Indices: 1650773--1650845 Score: 110
Period size: 3 Copynumber: 24.0 Consensus size: 3
1650763 CATTACTGTG
* *
1650773 ATA ATA TTA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
*
1650819 ATA ATA ATA ATA ATA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1650846 TGTGAAACAA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1652594 original size:11 final size:11
Alignment explanation
Indices: 1652578--1652610 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1652568 GAGATGGATC
*
1652578 AAAAGGGGTTG
1 AAAAGGGGTCG
1652589 AAAAGGGGTCG
1 AAAAGGGGTCG
1652600 AAAAGGGGTCG
1 AAAAGGGGTCG
1652611 TTTTTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.45, T:0.12
Consensus pattern (11 bp):
AAAAGGGGTCG
Found at i:1654369 original size:2 final size:2
Alignment explanation
Indices: 1654362--1654391 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1654352 ACAATTCTTT
*
1654362 TA TA TA TA TG 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
1654392 ATAATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1656089 original size:18 final size:18
Alignment explanation
Indices: 1656062--1656167 Score: 131
Period size: 18 Copynumber: 5.9 Consensus size: 18
1656052 GAGGGTCTAT
*
1656062 GTGGTCTTTCGGGACATA
1 GTGGTCCTTCGGGACATA
**
1656080 GTGGTATTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
1656098 ATGGTCCTTCAGGACATA
1 GTGGTCCTTCGGGACATA
* *
1656116 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
1656134 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
1656152 GTGGTCATACGGGACA
1 GTGGTCCTTCGGGACA
1656168 AATTCTACGT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 77 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1659436 original size:18 final size:18
Alignment explanation
Indices: 1659331--1659428 Score: 142
Period size: 18 Copynumber: 5.4 Consensus size: 18
1659321 GAGGGTCTAT
1659331 ATGGTCCTTCGAGACATA
1 ATGGTCCTTCGAGACATA
1659349 ATGGTCCTTCGAGACATA
1 ATGGTCCTTCGAGACATA
*
1659367 ATGGTCCTTCAAGACATA
1 ATGGTCCTTCGAGACATA
* *
1659385 ATGGTCCTTCGGGACACA
1 ATGGTCCTTCGAGACATA
* * *
1659403 GTGGTCCTTTGGGACATA
1 ATGGTCCTTCGAGACATA
1659421 ATGGTCCT
1 ATGGTCCT
1659429 ACGGGACAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (18 bp):
ATGGTCCTTCGAGACATA
Done.