Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007741.1 Hibiscus syriacus cultivar Beakdansim tig00110004_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: 1550271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:986765 original size:25 final size:26
Alignment explanation
Indices: 986736--986799 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 26
986726 ATTTTTCTCT
986736 TTTAACATTTTTTTAC-C-TT-TTTTA
1 TTTAA-ATTTTTTTACTCTTTATTTTA
986760 TCTT-AATTTTTTT-CTCTTTATTTTA
1 T-TTAAATTTTTTTACTCTTTATTTTA
986785 TTTAATATTTTTTTA
1 TTTAA-ATTTTTTTA
986800 ATCTAACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
22 1 0.03
23 9 0.27
24 6 0.18
25 9 0.27
26 8 0.24
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTAAATTTTTTTACTCTTTATTTTA
Found at i:986770 original size:24 final size:25
Alignment explanation
Indices: 986736--986799 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
986726 ATTTTTCTCT
*
986736 TTTAACATTTTTTTACCTT-TTTTA
1 TTTAATATTTTTTTACCTTATTTTA
*
986760 TCTTAAT-TTTTTTCT-CTTTATTTTA
1 T-TTAATATTTTTT-TACCTTATTTTA
986785 TTTAATATTTTTTTA
1 TTTAATATTTTTTTA
986800 ATCTAACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTAATATTTTTTTACCTTATTTTA
Found at i:992555 original size:96 final size:97
Alignment explanation
Indices: 992396--992649 Score: 379
Period size: 96 Copynumber: 2.6 Consensus size: 97
992386 CTATTATAGT
* * * * *
992396 ATAGCTCAAGGCGAGAAGGGTTATATGTCAATAAAAACCTT-GAGTTTGATTCCATTCAGCTCAA
1 ATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCTATTCAGCTCAA
* * *
992460 GGGAACATCAATATTCCAGTCAAATTTATATC
66 GGGAACATCAATATTCCAGCCAAATTTACAGC
992492 ATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCTATTCA-CTCAA
1 ATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCTATTCAGCTCAA
*
992556 GGGCACATCAATATTCCAGCCAAATTTACAGC
66 GGGAACATCAATATTCCAGCCAAATTTACAGC
* * *
992588 ATAGCTCAAGGTGATAAGGGTTATCTGTAAACAAAAATCTTCGAGTTCGATT-TATTCAGCTC
1 ATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCTATTCAGCTC
992650 GATGACATAT
Statistics
Matches: 144, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
95 6 0.04
96 123 0.85
97 15 0.10
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (97 bp):
ATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCTATTCAGCTCAA
GGGAACATCAATATTCCAGCCAAATTTACAGC
Found at i:993359 original size:38 final size:37
Alignment explanation
Indices: 993317--993570 Score: 113
Period size: 37 Copynumber: 6.5 Consensus size: 37
993307 TCGATTTTCG
993317 AAAATATATATATTATATAATTTTAAAAACGATATT-A
1 AAAATATATATATTATATAATTTTAAAAAC-ATATTGA
* * *
993354 AAAA-ATATATATTATATAGTTTTGAAAACATTTTGA
1 AAAATATATATATTATATAATTTTAAAAACATATTGA
** *
993390 ATATATATATATATATATATATATATTATATAGTTTTGAAAATATTTTGA
1 A-A-A-ATATATATAT-TATATA-ATT-T-TA----AAAACATA--TTGA
** * * * * *
993440 AGGCATATATAGAATATATAGTTTTTGAAAACAT-TTTA
1 A-AAATATATATATTATATA-ATTTTAAAAACATATTGA
* * * *
993478 AAAATATATATAATATATAGTTTTTAAAAATATTTTG-
1 AAAATATATATATTATATA-ATTTTAAAAACATATTGA
* * * *
993515 AAAATATATATAATATATAGTTTTAAAAATATTTTTG-
1 AAAATATATATATTATATAATTTTAAAAACA-TATTGA
*
993552 AAAATATATATAATATATA
1 AAAATATATATATTATATA
993571 TCTTTGAAAA
Statistics
Matches: 172, Mismatches: 28, Indels: 34
0.74 0.12 0.15
Matches are distributed among these distances:
35 4 0.02
36 36 0.21
37 75 0.44
38 7 0.04
39 1 0.01
40 8 0.05
41 10 0.06
42 2 0.01
43 1 0.01
44 1 0.01
45 1 0.01
46 1 0.01
47 8 0.05
48 12 0.07
50 5 0.03
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAATATATATATTATATAATTTTAAAAACATATTGA
Found at i:993368 original size:36 final size:36
Alignment explanation
Indices: 993316--993408 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 36
993306 ATCGATTTTC
993316 GAAAATATATATATTATATAATTTTAAAAACGATATT
1 GAAAATATATATATTATATAATTTTAAAAAC-ATATT
* * * *
993353 -AAAAAATATATATTATATAGTTTTGAAAACATTTT
1 GAAAATATATATATTATATAATTTTAAAAACATATT
*
993388 GAATATATATATATATATATA
1 GAAAATATATATAT-TATATA
993409 TATATATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
35 4 0.08
36 38 0.79
37 6 0.12
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (36 bp):
GAAAATATATATATTATATAATTTTAAAAACATATT
Found at i:993397 original size:2 final size:2
Alignment explanation
Indices: 993390--993421 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
993380 AACATTTTGA
993390 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
993422 GTTTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:993420 original size:86 final size:87
Alignment explanation
Indices: 993320--993496 Score: 216
Period size: 86 Copynumber: 2.0 Consensus size: 87
993310 ATTTTCGAAA
* *
993320 ATATATATATTATATAATTTTAAAAACGATATT-AA-AAAATATATATTATATAG-TTTTGAAAA
1 ATATATATATTATATAATTTTAAAAA-GATATTGAAGAAAATATAGAATATATAGTTTTTGAAAA
* *
993382 CATTTTGAATATATATATATATAT
65 CATTTTAAAAATATATATA-ATAT
* * * * * *
993406 ATATATATATTATATAGTTTTGAAAATATTTTGAAGGCATATATAGAATATATAGTTTTTGAAAA
1 ATATATATATTATATAATTTTAAAAAGATATTGAA-GAAAATATAGAATATATAGTTTTTGAAAA
993471 CATTTTAAAAATATATATAATAT
65 CATTTTAAAAATATATATAATAT
993494 ATA
1 ATA
993497 GTTTTTAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
85 4 0.05
86 26 0.34
88 21 0.27
89 26 0.34
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (87 bp):
ATATATATATTATATAATTTTAAAAAGATATTGAAGAAAATATAGAATATATAGTTTTTGAAAAC
ATTTTAAAAATATATATAATAT
Found at i:993448 original size:50 final size:49
Alignment explanation
Indices: 993358--993459 Score: 150
Period size: 50 Copynumber: 2.1 Consensus size: 49
993348 ATATTAAAAA
* * *
993358 ATATATATTATATAGTTTTGAAAACATTTTGAATATATATATATATATAT
1 ATATATATTATATAGTTTTGAAAACATTTTGAAGACATATATAGA-ATAT
* *
993408 ATATATATTATATAGTTTTGAAAATATTTTGAAGGCATATATAGAATAT
1 ATATATATTATATAGTTTTGAAAACATTTTGAAGACATATATAGAATAT
993457 ATA
1 ATA
993460 GTTTTTGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 7 0.15
50 40 0.85
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (49 bp):
ATATATATTATATAGTTTTGAAAACATTTTGAAGACATATATAGAATAT
Found at i:993638 original size:42 final size:42
Alignment explanation
Indices: 993591--993681 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
993581 TATTTTTGAA
* *
993591 AATATATTATATAG-TTTAAAAAATAATTTTTTAA-TATATAT
1 AATATATTATAT-GTTTTAAAAAATAATTTTTAAAGCATATAT
*
993632 ATATATATTATATGTTTTGAAAAATAATTTTTAAAGCATATAT
1 A-ATATATTATATGTTTTAAAAAATAATTTTTAAAGCATATAT
993675 AATATAT
1 AATATAT
993682 GGTTTTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
41 2 0.05
42 35 0.80
43 7 0.16
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (42 bp):
AATATATTATATGTTTTAAAAAATAATTTTTAAAGCATATAT
Found at i:993692 original size:37 final size:36
Alignment explanation
Indices: 993406--993698 Score: 288
Period size: 37 Copynumber: 7.9 Consensus size: 36
993396 ATATATATAT
* * * *
993406 ATATATATATTATATAGTTTTGAAAATATTTTGAAGGC
1 ATATATATAATATATAGTTTTAAAAATATTTTTAA--A
* * * *
993444 ATATATAGAATATATAGTTTTTGAAAACATTTTAAAA
1 ATATATATAATATATAG-TTTTAAAAATATTTTTAAA
*
993481 ATATATATAATATATAGTTTTTAAAAATATTTTGAAA
1 ATATATATAATATATAG-TTTTAAAAATATTTTTAAA
993518 ATATATATAATATATAGTTTTAAAAATATTTTTGAAA
1 ATATATATAATATATAGTTTTAAAAATATTTTT-AAA
* *
993555 ATATATATAATATATA-TCTTTGAAAATATTTTTGAA
1 ATATATATAATATATAGT-TTTAAAAATATTTTTAAA
* *
993591 A-ATATAT--TATATAGTTTAAAAAATAATTTTTTAAT
1 ATATATATAATATATAGTTTTAAAAAT-A-TTTTTAAA
993626 ATATATATATATATTATATGTTTTGAAAAATAATTTTTAAA
1 ATATATATA-ATA-TATA-GTTTT-AAAAAT-ATTTTTAAA
** *
993667 GCATATATAATATATGGTTTTAAAAATGATTT
1 ATATATATAATATATAGTTTTAAAAAT-ATTT
993699 ATTTATTACC
Statistics
Matches: 220, Mismatches: 22, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
33 13 0.06
34 2 0.01
35 13 0.06
36 25 0.11
37 93 0.42
38 20 0.09
39 21 0.10
40 7 0.03
41 18 0.08
42 8 0.04
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTAAAAATATTTTTAAA
Found at i:993693 original size:112 final size:112
Alignment explanation
Indices: 993400--993698 Score: 319
Period size: 112 Copynumber: 2.7 Consensus size: 112
993390 ATATATATAT
* * *
993400 ATATATATATATATATTATATAGTTTTG-AAAATATTTTGAAGGCATATATAGAATATATAGTTT
1 ATATATATATATATATTATAT-GTTTTGAAAAATATTTTTAAAGCATATAT--AATATAT-GATT
* *
993464 TTGAAAACATTTTAAAAATATATATAATATATAGTTTTTAAAAATATTTTGA
62 TTGAAAATATTTTAAAAATATATAT-ATATATAGTTTTAAAAAATATTTTGA
* **
993516 AAATATATATA-ATA-TATA-GTTTT-AAAAATATTTTTGAAAATATATATAATATAT-ATCTTT
1 ATATATATATATATATTATATGTTTTGAAAAATATTTTT-AAAGCATATATAATATATGAT-TTT
** *
993576 GAAAATATTTTTGAAA-ATATAT-TATATAG-TTTAAAAAATAATTTTTTA
64 GAAAATATTTTAAAAATATATATATATATAGTTTTAAAAAAT-A-TTTTGA
* *
993624 ATATATATATATATATTATATGTTTTGAAAAATAATTTTTAAAGCATATATAATATATGGTTTTA
1 ATATATATATATATATTATATGTTTTGAAAAAT-ATTTTTAAAGCATATATAATATATGATTTTG
993689 AAAATGATTT
65 AAAAT-ATTT
993699 ATTTATTACC
Statistics
Matches: 155, Mismatches: 16, Indels: 27
0.78 0.08 0.14
Matches are distributed among these distances:
106 9 0.06
107 8 0.05
108 15 0.10
109 10 0.06
110 20 0.13
111 12 0.08
112 45 0.29
113 19 0.12
114 4 0.03
115 3 0.02
116 10 0.06
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (112 bp):
ATATATATATATATATTATATGTTTTGAAAAATATTTTTAAAGCATATATAATATATGATTTTGA
AAATATTTTAAAAATATATATATATATAGTTTTAAAAAATATTTTGA
Found at i:994061 original size:22 final size:23
Alignment explanation
Indices: 994013--994066 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
994003 ACGGGGGTAA
*
994013 AACAACCCCTGAAGTTAAAGGAG
1 AACAACCCCTGAAGCTAAAGGAG
994036 AACAACCCCTGAAGCTAAA-GAG
1 AACAACCCCTGAAGCTAAAGGAG
994058 AACAACCCC
1 AACAACCCC
994067 GATGGGAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.44, C:0.30, G:0.17, T:0.09
Consensus pattern (23 bp):
AACAACCCCTGAAGCTAAAGGAG
Found at i:996439 original size:133 final size:136
Alignment explanation
Indices: 996164--996569 Score: 459
Period size: 133 Copynumber: 3.0 Consensus size: 136
996154 GAACCTAGAG
* * * *
996164 AATTAAACCTAAAAATGTAGGCTCT-AATATTAATCCAAATCATTTTTAATAAATTATTGAGTCG
1 AATTAAACCT-AAAATGAAGGCTCTAAATATTAA-CCTAATCAATTTTAATAAATTATTGATTCG
* *
996228 AACAGTTAAAATGGAACCTCGAGCATGAAAA-TGATGACCAAATAAAAAATT-CTTCTAAATTAA
64 -A-A-TTAAAATGGAACCTCGAG-A--AAAAGTGAGGACCAAATAAAAAATTACTCCTAAATTAA
*
996291 AGAACTAAGTTTGA
123 AGAACTAAGTATGA
* * * *
996305 AATTAAACGTAAAATGAAGGCTCTAAATATTAACCTATTCAATTTCAATAAATTATTTATTCGAA
1 AATTAAACCTAAAATGAAGGCTCTAAATATTAACCTAATCAATTTTAATAAATTATTGATTCGAA
*
996370 -T-AAATGGAACCTCGAGAAAAAGTGAGGACCAAATAAAAAATTAC-CCTAAGTTAAA-AGACTA
66 TTAAAATGGAACCTCGAGAAAAAGTGAGGACCAAATAAAAAATTACTCCTAAATTAAAGA-ACTA
996431 AGTATGA
130 AGTATGA
* * *
996438 AATTAAACCTAAAATGGAGGCTCTAAATATTAACCTACTCAATTTTAATCAATTATTGATTCAAA
1 AATTAAACCTAAAATGAAGGCTCTAAATATTAACCTAATCAATTTTAATAAATTATTGATTC---
* * * * **
996503 TAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATTAAAAATTA-TATTAAATTAAAGAAC
63 GAATTAAAATGGAACCTCGAGAAAAAGTGAGGACCAAATAAAAAATTACTCCTAAATTAAAGAAC
996567 TAA
128 TAA
996570 ATTATAAAGG
Statistics
Matches: 229, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
132 5 0.02
133 94 0.41
134 2 0.01
135 15 0.07
136 3 0.01
137 1 0.00
138 53 0.23
139 2 0.01
140 37 0.16
141 17 0.07
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (136 bp):
AATTAAACCTAAAATGAAGGCTCTAAATATTAACCTAATCAATTTTAATAAATTATTGATTCGAA
TTAAAATGGAACCTCGAGAAAAAGTGAGGACCAAATAAAAAATTACTCCTAAATTAAAGAACTAA
GTATGA
Found at i:996863 original size:14 final size:14
Alignment explanation
Indices: 996846--996897 Score: 104
Period size: 14 Copynumber: 3.7 Consensus size: 14
996836 TAATGGACTG
996846 AATTTAAAGGTTGA
1 AATTTAAAGGTTGA
996860 AATTTAAAGGTTGA
1 AATTTAAAGGTTGA
996874 AATTTAAAGGTTGA
1 AATTTAAAGGTTGA
996888 AATTTAAAGG
1 AATTTAAAGG
996898 ACTAAAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (14 bp):
AATTTAAAGGTTGA
Found at i:996866 original size:28 final size:29
Alignment explanation
Indices: 996831--996910 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 29
996821 TTAAAAAATG
*
996831 GAAA-TTAATGGACTG-AATTTAAAGGTT
1 GAAATTTAAAGGACTGAAATTTAAAGGTT
*
996858 GAAATTTAAAGG-TTGAAATTTAAAGGTT
1 GAAATTTAAAGGACTGAAATTTAAAGGTT
* *
996886 GAAATTTAAAGGACTAAAATGTAAA
1 GAAATTTAAAGGACTGAAATTTAAA
996911 TAATAGAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
27 6 0.13
28 30 0.67
29 9 0.20
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (29 bp):
GAAATTTAAAGGACTGAAATTTAAAGGTT
Found at i:999281 original size:16 final size:15
Alignment explanation
Indices: 999255--999284 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
999245 GATTGCAAGA
999255 ATAAAATAAAAATAT
1 ATAAAATAAAAATAT
999270 ATAAATATAAAAATA
1 ATAAA-ATAAAAATA
999285 AAAGTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAAATAAAAATAT
Found at i:999319 original size:6 final size:6
Alignment explanation
Indices: 999254--999327 Score: 57
Period size: 6 Copynumber: 12.3 Consensus size: 6
999244 GGATTGCAAG
* *
999254 AATAA- AATAAA AATATAT AA-ATAT AAAAAT AA-AAGT AATAAT AGA-AAT
1 AATAAT AATAAT AATA-AT AATA-AT AATAAT AATAA-T AATAAT A-ATAAT
*
999302 AATAAT AATAAT ATTAAT AATAAT AA
1 AATAAT AATAAT AATAAT AATAAT AA
999328 CGTCGGGACG
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
5 8 0.14
6 44 0.75
7 7 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (6 bp):
AATAAT
Found at i:999319 original size:9 final size:9
Alignment explanation
Indices: 999254--999327 Score: 57
Period size: 9 Copynumber: 8.2 Consensus size: 9
999244 GGATTGCAAG
999254 AATAA-AAT
1 AATAATAAT
*
999262 AAAAATATAT
1 AATAATA-AT
*
999272 AA-ATATAAA
1 AATA-ATAAT
999281 AATAA-AAGT
1 AATAATAA-T
999290 AATAATAGA-
1 AATAATA-AT
999299 AATAATAAT
1 AATAATAAT
*
999308 AATAATATT
1 AATAATAAT
999317 AATAATAAT
1 AATAATAAT
999326 AA
1 AA
999328 CGTCGGGACG
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
8 7 0.13
9 36 0.68
10 9 0.17
11 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (9 bp):
AATAATAAT
Found at i:999818 original size:136 final size:136
Alignment explanation
Indices: 999516--999972 Score: 690
Period size: 135 Copynumber: 3.4 Consensus size: 136
999506 CTAATATGAG
* * *
999516 ATCTGGAAATGTTGATTCATTCCAC-TGTTCTTCAGGGAAGATTGAATCGAGGCAAACTTGTTCC
1 ATCTAGAAATGTTGATTCATTCCACTTATTCTTCAGGGAAGATTGAATCGAGGCATACTTGTTCC
* *
999580 ATTGTACCTCATGGAAGATCAAATCTATAAAAAAGAGGGATCTGTTTCGCTGCTTCTTGAGGGAA
66 ACTGTACCTCATGGAAGATCAAATCTATAAAAAAGAGGGATCTATTTCGCTGCTTCTTGAGGGAA
999645 AATCAT
131 AATCAT
* *
999651 ATCTAGAAATGTTGATTCATTCC-GTTATTCTTCAGGAAAGATTGAATCGAGGCATACTTGTTCC
1 ATCTAGAAATGTTGATTCATTCCACTTATTCTTCAGGGAAGATTGAATCGAGGCATACTTGTTCC
999715 ACTGTACCTCATGGAAGATCAAATCTATAAAAAAAGAGGGATCTATTTCGCTGCTTCTTGAGGGA
66 ACTGTACCTCATGGAAGATCAAATCTAT-AAAAAAGAGGGATCTATTTCGCTGCTTCTTGAGGGA
999780 AAATCAT
130 AAATCAT
999787 ATCTAGAAATGTTGATTCATTCCACTT-TTCTTCAGGGAAGATTGAATCGAGGCATACTTGTTCC
1 ATCTAGAAATGTTGATTCATTCCACTTATTCTTCAGGGAAGATTGAATCGAGGCATACTTGTTCC
* * * * * ** * * *
999851 GCTATTCCTCAAGGAAGATCAAATATGGAAAAAATAGGGTTCTATTCCGCTGCTTCTTGAGGGAA
66 ACTGTACCTCATGGAAGATCAAATCTATAAAAAAGAGGGATCTATTTCGCTGCTTCTTGAGGGAA
999916 AATCAT
131 AATCAT
* *
999922 ATCT-GAAAATGTTGATTAATT-CAATTATTCTTCAGGGAAGATTGAATCGAG
1 ATCTAG-AAATGTTGATTCATTCCACTTATTCTTCAGGGAAGATTGAATCGAG
999973 TTCGATTCGT
Statistics
Matches: 296, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
134 5 0.02
135 167 0.56
136 122 0.41
137 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (136 bp):
ATCTAGAAATGTTGATTCATTCCACTTATTCTTCAGGGAAGATTGAATCGAGGCATACTTGTTCC
ACTGTACCTCATGGAAGATCAAATCTATAAAAAAGAGGGATCTATTTCGCTGCTTCTTGAGGGAA
AATCAT
Found at i:1006452 original size:21 final size:22
Alignment explanation
Indices: 1006423--1006472 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
1006413 TAAGATAAAA
*
1006423 TAGACATAGAACACAAACGGGT
1 TAGACATAGAACACAAACGAGT
1006445 TAGA-ATAGAACACAAACGAGT
1 TAGACATAGAACACAAACGAGT
1006466 TAG-CATA
1 TAGACATA
1006473 CATAAGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (22 bp):
TAGACATAGAACACAAACGAGT
Found at i:1007445 original size:12 final size:13
Alignment explanation
Indices: 1007416--1007451 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1007406 CAAGTTTAAG
1007416 TTTTTAAAAGTGA
1 TTTTTAAAAGTGA
1007429 TTTTTAAAAGTGA
1 TTTTTAAAAGTGA
1007442 TTTTTAAAAG
1 TTTTTAAAAG
1007452 ATATCATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (13 bp):
TTTTTAAAAGTGA
Found at i:1008148 original size:131 final size:131
Alignment explanation
Indices: 1007905--1008255 Score: 459
Period size: 131 Copynumber: 2.7 Consensus size: 131
1007895 ATAATTCTAA
** * *
1007905 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGGTCTCTCATAACTTAAATCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAACCA
** * * ** * *
1007970 ATCATTTATTACTTTAATTGAAATGAAGATATATCACTATTTTGTCTTAAAATTCTATATTGATT
66 ATCATTTATTACTCCAATCGAAATAAAGATATATCACTATTACGTCTTAAAAATCAATATTGATT
1008035 C
131 C
* * * * * * *
1008036 GAGTGAAAACAATAATATCTAATGATTTTCAATCGAGAATAAATGACCTCTAATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAACCA
*
1008101 ATAATTTATTACTCCAATCGAAATAAAGATATATCACTATTACGTCTTAAAAATCAATATTGATT
66 ATCATTTATTACTCCAATCGAAATAAAGATATATCACTATTACGTCTTAAAAATCAATATTGATT
*
1008166 T
131 C
* * * * *
1008167 GAGAGAAAAGGGTAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATTCCATGAACCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAACCA
*
1008232 GTCATTTATTACTCCAATCGAAAT
66 ATCATTTATTACTCCAATCGAAAT
1008256 GAAAAGGTAT
Statistics
Matches: 187, Mismatches: 33, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
131 187 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAACCA
ATCATTTATTACTCCAATCGAAATAAAGATATATCACTATTACGTCTTAAAAATCAATATTGATT
C
Found at i:1009063 original size:24 final size:24
Alignment explanation
Indices: 1009036--1009193 Score: 280
Period size: 24 Copynumber: 6.6 Consensus size: 24
1009026 CTATTCTTTC
*
1009036 GCTTCAATTGAGCTCGAATTTCAG
1 GCTTCAATCGAGCTCGAATTTCAG
1009060 GCTTCAATCGAGCTCGAATTTCAG
1 GCTTCAATCGAGCTCGAATTTCAG
1009084 GCTTCAATCGAGCTCGAATTTCAG
1 GCTTCAATCGAGCTCGAATTTCAG
*
1009108 GCTTCAATCGAGTTCGAATTTCAG
1 GCTTCAATCGAGCTCGAATTTCAG
* *
1009132 GCTTTAATCGAGCTAGAATTTCAG
1 GCTTCAATCGAGCTCGAATTTCAG
1009156 GCTTCAATCGAGCTCGAATTTCAG
1 GCTTCAATCGAGCTCGAATTTCAG
1009180 GCTTCAATCGAGCT
1 GCTTCAATCGAGCT
1009194 TCTAATTTTT
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 127 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (24 bp):
GCTTCAATCGAGCTCGAATTTCAG
Found at i:1011577 original size:12 final size:12
Alignment explanation
Indices: 1011532--1011579 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1011522 TATTATAAAT
*
1011532 ATAAAAATA-AA
1 ATAATAATATAA
*
1011543 AGTAATAATAGAA
1 A-TAATAATATAA
*
1011556 ATAATAATATTA
1 ATAATAATATAA
1011568 ATAATAATATAA
1 ATAATAATATAA
1011580 CGTCAAGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 1 0.03
12 27 0.87
13 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
ATAATAATATAA
Found at i:1011785 original size:27 final size:28
Alignment explanation
Indices: 1011737--1011791 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1011727 ATAAAAAATG
*
1011737 AAATTAATTATATTCTTATTAAAATTTA
1 AAATTAATAATATTCTTATTAAAATTTA
*
1011765 AAATTAAATAATATT-TT-TTAATATTTA
1 AAATT-AATAATATTCTTATTAAAATTTA
1011792 TTTAATAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.38
28 7 0.29
29 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATTAATAATATTCTTATTAAAATTTA
Found at i:1012899 original size:3 final size:3
Alignment explanation
Indices: 1012893--1012944 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
1012883 TCTTTTTTTA
* ** *
1012893 TAT TAT TTT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1012940 TAT TA
1 TAT TA
1012945 ATTTACATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1018863 original size:22 final size:22
Alignment explanation
Indices: 1018838--1018905 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 22
1018828 AATATCATAT
*
1018838 CAAAGCGAAGAGAACAAAAAAA
1 CAAAGAGAAGAGAACAAAAAAA
*
1018860 CAAAGAGAAAAGAAACAAAGAAAAAA
1 CAAAGAGAAGAG-AAC--A-AAAAAA
1018886 CAAAGAGCAAGAGAA-AAAAA
1 CAAAGAG-AAGAGAACAAAAA
1018906 GAAAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
22 14 0.37
23 4 0.11
25 1 0.03
26 15 0.39
27 4 0.11
ACGTcount: A:0.72, C:0.10, G:0.18, T:0.00
Consensus pattern (22 bp):
CAAAGAGAAGAGAACAAAAAAA
Found at i:1018867 original size:17 final size:15
Alignment explanation
Indices: 1018853--1018905 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1018843 CGAAGAGAAC
1018853 AAAAAAACAAAGAGA
1 AAAAAAACAAAGAGA
*
1018868 AAAGAAACAAAGA-A
1 AAAAAAACAAAGAGA
*
1018882 AAAACAAAGAGCAAGAGA
1 AAAA-AAACA--AAGAGA
1018900 AAAAAA
1 AAAAAA
1018906 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 4 0.13
15 16 0.52
17 6 0.19
18 5 0.16
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAAGAGA
Found at i:1018898 original size:49 final size:49
Alignment explanation
Indices: 1018845--1018938 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
1018835 TATCAAAGCG
* * *
1018845 AAGAGAACAAAA-AAACAAAGAGAAAAGAAACAAAGAAAA-AACAAAGAGC
1 AAGAGAAAAAAAGAAAAAAAAAG-AAA-AAACAAAGAAAAGAACAAAGAGC
*
1018894 AAGAGAAAAAAAGAAAAAAAAAGCAAAAACAAAGAAAAGAACAAA
1 AAGAGAAAAAAAGAAAAAAAAAGAAAAAACAAAGAAAAGAACAAA
1018939 TAACAAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 12 0.31
49 19 0.49
50 8 0.21
ACGTcount: A:0.77, C:0.09, G:0.15, T:0.00
Consensus pattern (49 bp):
AAGAGAAAAAAAGAAAAAAAAAGAAAAAACAAAGAAAAGAACAAAGAGC
Found at i:1018900 original size:27 final size:26
Alignment explanation
Indices: 1018854--1018938 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
1018844 GAAGAGAACA
*
1018854 AAAAAACAAAGAGAAAAGAAACAAAG
1 AAAAAACAAAGAGCAAAGAAACAAAG
*
1018880 AAAAAACAAAGAGCAAGAGAAAAAAAG
1 AAAAAACAAAGAGCAA-AGAAACAAAG
1018907 -AAAAA-AAA-AGC-AA-AAACAAAG
1 AAAAAACAAAGAGCAAAGAAACAAAG
1018928 AAAAGAACAAA
1 AAAA-AACAAA
1018939 TAACAAAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
21 7 0.13
22 4 0.08
23 3 0.06
24 6 0.12
25 3 0.06
26 20 0.38
27 9 0.17
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (26 bp):
AAAAAACAAAGAGCAAAGAAACAAAG
Found at i:1018931 original size:19 final size:19
Alignment explanation
Indices: 1018868--1018945 Score: 54
Period size: 19 Copynumber: 4.2 Consensus size: 19
1018858 AACAAAGAGA
* *
1018868 AAAGAAACAAAGAAAAAAC
1 AAAGAAAAAAAGCAAAAAC
** *
1018887 AAAGAGCAAGAG-AAAAA-
1 AAAGAAAAAAAGCAAAAAC
*
1018904 AAGAAAAAAAAAGCAAAAAC
1 AA-AGAAAAAAAGCAAAAAC
*
1018924 AAAGAAAAGAA-CAAATAAC
1 AAAGAAAAAAAGCAAA-AAC
1018943 AAA
1 AAA
1018946 AAGATGAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
17 2 0.04
18 15 0.33
19 26 0.58
20 2 0.04
ACGTcount: A:0.77, C:0.09, G:0.13, T:0.01
Consensus pattern (19 bp):
AAAGAAAAAAAGCAAAAAC
Found at i:1020137 original size:4 final size:4
Alignment explanation
Indices: 1020128--1020261 Score: 54
Period size: 4 Copynumber: 33.8 Consensus size: 4
1020118 ATCAATAGAT
* * * * * * * * *
1020128 ACAC ACAC ACAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * *
1020176 ATAC ACAC ACAC ACA- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * *
1020223 ACAT ACAT ACAT ACAT ACAT ACAC ACAC ACAC ACAC ACA
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACA
1020262 TGCATGCATG
Statistics
Matches: 126, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 3 0.02
4 123 0.98
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (4 bp):
ACAC
Found at i:1020149 original size:8 final size:8
Alignment explanation
Indices: 1020139--1020532 Score: 490
Period size: 8 Copynumber: 49.5 Consensus size: 8
1020129 CACACACACA
*
1020139 CATACATA
1 CATACATG
*
1020147 CATACATA
1 CATACATG
*
1020155 CATACATA
1 CATACATG
*
1020163 CATACATA
1 CATACATG
*
1020171 CATACATA
1 CATACATG
*
1020179 CACACA--
1 CATACATG
* *
1020185 CACACA-A
1 CATACATG
*
1020192 CATACATA
1 CATACATG
*
1020200 CATACATA
1 CATACATG
*
1020208 CATACATA
1 CATACATG
*
1020216 CATACATA
1 CATACATG
*
1020224 CATACATA
1 CATACATG
*
1020232 CATACATA
1 CATACATG
**
1020240 CATACACA
1 CATACATG
* **
1020248 CACACACA
1 CATACATG
*
1020256 CACACATG
1 CATACATG
*
1020264 CATGCATG
1 CATACATG
*
1020272 CATGCATG
1 CATACATG
* *
1020280 CATGCATC
1 CATACATG
* *
1020288 CATCCATC
1 CATACATG
*
1020296 CATCCACATA
1 CAT--ACATG
*
1020306 CATACATA
1 CATACATG
1020314 CATACATG
1 CATACATG
1020322 CATACATG
1 CATACATG
1020330 CATACATG
1 CATACATG
1020338 CATACATG
1 CATACATG
1020346 CATACATG
1 CATACATG
1020354 CATACATG
1 CATACATG
1020362 CATACATG
1 CATACATG
1020370 CATACATG
1 CATACATG
1020378 CATACATG
1 CATACATG
1020386 CATACATG
1 CATACATG
1020394 CATACATG
1 CATACATG
1020402 CATACATG
1 CATACATG
1020410 CATACATG
1 CATACATG
1020418 CATACATG
1 CATACATG
1020426 CATACATG
1 CATACATG
1020434 CATACATG
1 CATACATG
1020442 CATACATG
1 CATACATG
1020450 CATACATG
1 CATACATG
1020458 CATACATG
1 CATACATG
1020466 CATACATG
1 CATACATG
1020474 CATACATG
1 CATACATG
1020482 CATACATG
1 CATACATG
1020490 CATACATG
1 CATACATG
1020498 CATACATG
1 CATACATG
1020506 CATAC-TG
1 CATACATG
1020513 CATACATG
1 CATACATG
1020521 CATACATG
1 CATACATG
1020529 CATA
1 CATA
1020533 TTTTGTCTCA
Statistics
Matches: 368, Mismatches: 13, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
6 6 0.02
7 12 0.03
8 344 0.93
10 6 0.02
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (8 bp):
CATACATG
Found at i:1020868 original size:36 final size:36
Alignment explanation
Indices: 1020738--1020875 Score: 122
Period size: 36 Copynumber: 3.8 Consensus size: 36
1020728 GTTTCACATT
* **
1020738 AAACAAA-GTTGATCTCACTTGAGATCGTTTTCTC-AA
1 AAACAAATGTTG-TATCACTTGAGA-CAATTTCTCTAA
*
1020774 AAACAAACT-TTGTCA-CGCTTGAGACAATTTCTCTAA
1 AAACAAA-TGTTGT-ATCACTTGAGACAATTTCTCTAA
* * * **
1020810 AAACAATTATTGTCTCGTTTGAGACAATTTCTCTAA
1 AAACAAATGTTGTATCACTTGAGACAATTTCTCTAA
*
1020846 AAACAAATGTTGTATCACTTGAGGCAATTT
1 AAACAAATGTTGTATCACTTGAGACAATTT
1020876 TCCAAATTAT
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
35 8 0.10
36 72 0.87
37 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (36 bp):
AAACAAATGTTGTATCACTTGAGACAATTTCTCTAA
Found at i:1020928 original size:32 final size:32
Alignment explanation
Indices: 1020891--1020972 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
1020881 ATTATGAATT
* *
1020891 TGTTTCACTGGAAACAAACATCATCTTTGAGTC
1 TGTTTCACTTGAAACAAA-AGCATCTTTGAGTC
** *
1020924 -GTTTCTTTTGAAAC-AAAGGATCTTTGAGTC
1 TGTTTCACTTGAAACAAAAGCATCTTTGAGTC
1020954 TGTTTCACTTGAAACAAAA
1 TGTTTCACTTGAAACAAAA
1020973 TGAAAAAATC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 12 0.30
31 14 0.35
32 14 0.35
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTTTCACTTGAAACAAAAGCATCTTTGAGTC
Found at i:1021525 original size:39 final size:39
Alignment explanation
Indices: 1021439--1021527 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 39
1021429 CTTTGAATTG
1021439 TTTC-TTTG-AAAACAAAATTTTGTCTCACTTAGATACA
1 TTTCTTTTGAAAAACAAAATTTTGTCTCACTTAGATACA
* * * *
1021476 ATT-TTCTGAAAAACAAAGTTTTGTCTCTCTTGAGATA-A
1 TTTCTTTTGAAAAACAAAATTTTGTCTCACTT-AGATACA
1021514 TTTCTTTTGAAAAA
1 TTTCTTTTGAAAAA
1021528 TCATTGAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
37 5 0.12
38 23 0.55
39 14 0.33
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (39 bp):
TTTCTTTTGAAAAACAAAATTTTGTCTCACTTAGATACA
Found at i:1021622 original size:65 final size:62
Alignment explanation
Indices: 1021486--1021624 Score: 161
Period size: 63 Copynumber: 2.2 Consensus size: 62
1021476 ATTTTCTGAA
* * *
1021486 AAACAAAGTTTTGTCTCTCTTGAGATAATTTCTTTTGAAAAATCATTGAATATGTTTTTTTG
1 AAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAAAAATCATTGAATATGTTTTTTGG
* * * * * *
1021548 ATAACAAAATTTTTTCTCTTTTGAGACAATTTCTTTTAAGAAAAATCTTTTAGTCTGTTTCTTTG
1 A-AACAAAATTTTGTCTCTCTTGAGACAATTTCTTTT--GAAAAATCATTGAATATGTTT-TTTG
1021613 G
62 G
1021614 AAACAAAATTT
1 AAACAAAATTT
1021625 ATGATCTTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 1 0.02
63 31 0.48
65 27 0.42
66 5 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (62 bp):
AAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAAAAATCATTGAATATGTTTTTTGG
Found at i:1021633 original size:65 final size:63
Alignment explanation
Indices: 1021505--1021633 Score: 143
Period size: 65 Copynumber: 2.0 Consensus size: 63
1021495 TTTGTCTCTC
* * * **
1021505 TTGAGATAATTTCTTTTGAAAAATCATTGAATATGTTTTTTTGATAACAAAATTTTTTCTCTT
1 TTGAGACAATTTCTTTTGAAAAATCATTGAATATGTTTTTTGGATAACAAAATTTATGATCTT
* * * *
1021568 TTGAGACAATTTCTTTTAAGAAAAATCTTTTAGTCTGTTTCTTTGGA-AACAAAATTTATGATCT
1 TTGAGACAATTTCTTTT--GAAAAATCATTGAATATGTTT-TTTGGATAACAAAATTTATGATCT
1021632 T
63 T
1021633 T
1 T
1021634 GAGTTTGTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
63 16 0.30
65 33 0.61
66 5 0.09
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (63 bp):
TTGAGACAATTTCTTTTGAAAAATCATTGAATATGTTTTTTGGATAACAAAATTTATGATCTT
Found at i:1021930 original size:28 final size:28
Alignment explanation
Indices: 1021830--1021939 Score: 98
Period size: 28 Copynumber: 3.8 Consensus size: 28
1021820 TTTTGTCTCT
* * *
1021830 TTTGAGACAGTTGCTTTTGAAACACATCACC
1 TTTGAGTCAGTTTCTTTTGAAACA-A--ATC
**
1021861 TTTGAGTTTGTTT-TTCTTGAAACAAATC
1 TTTGAGTCAGTTTCTT-TTGAAACAAATC
1021889 TTTGAGTCCA-TTTCTTTTGAAACAAATC
1 TTTGAGT-CAGTTTCTTTTGAAACAAATC
**
1021917 TTTGAGTCAGTTTCCCTTGAAAC
1 TTTGAGTCAGTTTCTTTTGAAAC
1021940 CATAATCACT
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.03
28 42 0.64
29 2 0.03
30 3 0.05
31 17 0.26
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (28 bp):
TTTGAGTCAGTTTCTTTTGAAACAAATC
Found at i:1022188 original size:134 final size:134
Alignment explanation
Indices: 1021968--1022300 Score: 386
Period size: 134 Copynumber: 2.5 Consensus size: 134
1021958 CCAGTCGTCC
* * ** *
1021968 TCATCACGTATGAGTAGTGTCATCCCCTGACCAGATCTCTTCATCGTTTAGGAGTCGTGTCACCC
1 TCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCATCACTTAGGAGCCGTGTCACCC
* * * * * *
1022033 CTAGATAACTAGATGTCCTCA-TCACGTAGGAACCGTGTTATTGC-CT-TTTCTAAAAATGACTA
66 ATAGATAACCAGACGTCCTCATTCA-GTAGGAACCGTGTTA-T-CACTCCTCCTAAAAATGACCA
1022095 GAACTCT
128 GAACTCT
* *
1022102 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCC
1 TCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCATCACTTAGGAGCCGTGTCACCC
* * * *
1022167 ATAGATAACCA-ACCGTCCTCATTGAGTAGGGACCGTGTTATCACTCCTCCTAAAGATGGCCAGA
66 ATAGATAACCAGA-CGTCCTCATTCAGTAGGAACCGTGTTATCACTCCTCCTAAAAATGACCAGA
1022231 ACTCT
130 ACTCT
* ** * * * *
1022236 TCATTACGTATGAGCAGTGTCATCCTTTGACAAAATTTCCTCATCACTTAGGAACCGTGTCACCC
1 TCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCATCACTTAGGAGCCGTGTCACCC
1022301 TTATATGACC
Statistics
Matches: 169, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
132 1 0.01
133 4 0.02
134 162 0.96
135 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (134 bp):
TCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCATCACTTAGGAGCCGTGTCACCC
ATAGATAACCAGACGTCCTCATTCAGTAGGAACCGTGTTATCACTCCTCCTAAAAATGACCAGAA
CTCT
Found at i:1022502 original size:3 final size:3
Alignment explanation
Indices: 1022496--1022559 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
1022486 TCTTTTTTTA
** *
1022496 TAT TAT TAT TAT TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1022543 TAT TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1022560 ATTTACATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1022944 original size:21 final size:21
Alignment explanation
Indices: 1022918--1022962 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1022908 AGGGGATTTA
1022918 ACAGAGGCCATCACCAATCAC
1 ACAGAGGCCATCACCAATCAC
1022939 ACAGAGGCCATCACCAATCAC
1 ACAGAGGCCATCACCAATCAC
1022960 ACA
1 ACA
1022963 TGCAAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.38, G:0.13, T:0.09
Consensus pattern (21 bp):
ACAGAGGCCATCACCAATCAC
Found at i:1023981 original size:2 final size:2
Alignment explanation
Indices: 1023974--1024006 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1023964 CTTTTATAGG
1023974 TA TA TA 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
1024007 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1025920 original size:60 final size:59
Alignment explanation
Indices: 1025783--1025942 Score: 152
Period size: 60 Copynumber: 2.7 Consensus size: 59
1025773 ATTAGTATAT
* * *
1025783 AAGT-ATAGTTTGA-GATGAAATTAAAATGTTCAAAAAGTTTGGGGACCAACCTAGAATG
1 AAGTCATAGTTTGAGGATGAAATTGAAAT-TTTAAAAAGTTTGAGGACCAACCTAGAATG
* * **
1025841 AATGTCATAGTTTGGGGATGAAATTGAAATTTTAAAAAGTTTGAGGACTAATTTAGAATGG
1 AA-GTCATAGTTTGAGGATGAAATTGAAATTTTAAAAAGTTTGAGGACCAACCTAGAAT-G
1025902 TAA-TCATAG-TTGAAGGATGAAATTAGAACA-TTT-AAAAGTTT
1 -AAGTCATAGTTTG-AGGATGAAATT-GAA-ATTTTAAAAAGTTT
1025943 AAGAAACAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
58 2 0.02
59 5 0.06
60 56 0.65
61 20 0.23
62 3 0.03
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (59 bp):
AAGTCATAGTTTGAGGATGAAATTGAAATTTTAAAAAGTTTGAGGACCAACCTAGAATG
Found at i:1029392 original size:74 final size:74
Alignment explanation
Indices: 1029291--1029501 Score: 253
Period size: 74 Copynumber: 2.8 Consensus size: 74
1029281 ATTTCAAGGG
* * * * * *
1029291 AAACTTTCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTTAAGTGAAATGAAATTTCTT
1 AAACTATCTCAAACGAGAT-CAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC-T
*
1029356 ATTTTGAGTAA
64 ATTTTGAATAA
* * * * *
1029367 AAATTGTCTCAAATGAGA-CAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTGT
1 AAACTATCTCAAACGAGATCAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTAT
*
1029431 TTTGAATGA
66 TTTGAATAA
* *
1029440 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT
1 AAACTATCTCAAACGAGATCAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT
1029502 TTGTTTCGAG
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
73 23 0.20
74 40 0.35
75 38 0.33
76 14 0.12
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (74 bp):
AAACTATCTCAAACGAGATCAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTAT
TTTGAATAA
Found at i:1029566 original size:74 final size:76
Alignment explanation
Indices: 1029401--1029833 Score: 329
Period size: 74 Copynumber: 5.8 Consensus size: 76
1029391 GTTTTAAGAA
* * * *
1029401 AAACAATCTCAAGTGAGATAAAATTTCTGTTTTGAATGAAAACTATCTCAAGCGAGATGAATCTT
1 AAACTATCTCAAGTGAGATAAAATTTTTGTTTTGAGTG-AAACTATCTCAAGCGAGATAAATCTT
* * **
1029466 GT-TTT-AAGAA
65 CTATTTCGAGTG
* * * *
1029476 AAACAATCTCAAGTGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAAGCTATA-AAAT-TTC
1 AAACTATCTCAAGTGAGATAAAATTTTTGTTTTGAGTGAAACTATCTCAAGCGAGATAAATCTTC
1029539 TATTTCGAGTG
66 TATTTCGAGTG
* * * ** *
1029550 GAACTATCTCAAGTGAGATGAAA--TTTGTTTTAAGAAAAAC-ATTCTCAAGAGAGATAAAAT-T
1 AAACTATCTCAAGTGAGATAAAATTTTTGTTTTGAGTGAAACTA-TCTCAAGCGAGAT-AAATCT
* *
1029611 TTTGTTTCGAGTG
64 TCTATTTCGAGTG
* * * * * * *
1029624 AAACTATTTCAA-TCGAGAT-GAA-TCTTGTTTTTAG-AAAAATAATCTCAAGTGAGATAAATCT
1 AAACTATCTCAAGT-GAGATAAAATTTTTGTTTTGAGTGAAACT-ATCTCAAGCGAGATAAATCT
*
1029685 TCTACTTCGAGTG
64 TCTATTTCGAGTG
* * * *
1029698 AAACTATCTCAAGCGAGATAAAATTTTT-TCTTCGAGTGAAACAATCTCAAGCGAGATGAATCTT
1 AAACTATCTCAAGTGAGATAAAATTTTTGT-TTTGAGTGAAACTATCTCAAGCGAGATAAATCTT
* * **
1029762 GT-TTT-AAGAA
65 CTATTTCGAGTG
* * * *
1029772 AAACAATCTCAAGTGAGATAAATTTTTTTTGTATTAAGTGAAACTATCTCAAGCGAGATAAA
1 AAACTATCTCAAGTGAGATAAA--ATTTTTGTTTTGAGTGAAACTATCTCAAGCGAGATAAA
1029834 AGTTTTGCTT
Statistics
Matches: 284, Mismatches: 56, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
71 1 0.00
72 25 0.09
73 17 0.06
74 139 0.49
75 41 0.14
76 57 0.20
77 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (76 bp):
AAACTATCTCAAGTGAGATAAAATTTTTGTTTTGAGTGAAACTATCTCAAGCGAGATAAATCTTC
TATTTCGAGTG
Found at i:1029571 original size:110 final size:111
Alignment explanation
Indices: 1029418--1029635 Score: 341
Period size: 110 Copynumber: 2.0 Consensus size: 111
1029408 CTCAAGTGAG
* *
1029418 ATAAAATTTCTGTTTTGAATGAAAACTATCTCAAGCGAGATG-AATCTTGTTTTAAGAAAAACAA
1 ATAAAATTTCTATTTCGAATGAAAACTATCTCAAGCGAGATGAAAT-TTGTTTTAAGAAAAACAA
*
1029482 TCTCAAGTGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAAGCT
65 TCTCAAGAGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAAGCT
* * * *
1029529 ATAAAATTTCTATTTCGAGTG-GAACTATCTCAAGTGAGATGAAATTTGTTTTAAGAAAAACATT
1 ATAAAATTTCTATTTCGAATGAAAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAAT
*
1029593 CTCAAGAGAGATAAAATTTTTGTTTCGAGTGAAACTATTTCAA
66 CTCAAGAGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAA
1029636 TCGAGATGAA
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
110 77 0.79
111 21 0.21
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (111 bp):
ATAAAATTTCTATTTCGAATGAAAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAAT
CTCAAGAGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAAGCT
Found at i:1029596 original size:36 final size:36
Alignment explanation
Indices: 1029291--1029801 Score: 176
Period size: 36 Copynumber: 13.9 Consensus size: 36
1029281 ATTTCAAGGG
* *
1029291 AAACTTTCTCAAGCGAGATGAAATTTGTTTTAAGAA
1 AAACATTCTCAAGTGAGATGAAATTTGTTTTAAGAA
* * * * *
1029327 AAACAATCTTAAGTGAAATGAAATTTCTTATTTTGAGTAA
1 AAACATTCTCAAGTGAGATGAAA--T-TTGTTTTAAG-AA
* * * *
1029367 AAA-TTGTCTCAAATGAGA--CAGTTTGTTTTAAGAA
1 AAACAT-TCTCAAGTGAGATGAAATTTGTTTTAAGAA
* *
1029401 AAACAATCTCAAGTGAGATAAAATTTCTGTTTTGAATG-A
1 AAACATTCTCAAGTGAGATGAAA-TT-TGTTTT-AA-GAA
*
1029440 AAAC-TATCTCAAGCGAGATG-AATCTTGTTTTAAGAA
1 AAACAT-TCTCAAGTGAGATGAAAT-TTGTTTTAAGAA
* * ** **
1029476 AAACAATCTCAAGTGAGATAAAATTTTTGTTTCGAGTG
1 AAACATTCTCAAGTGAGATGAAA--TTTGTTTTAAGAA
* * * **
1029514 AAAC-TATCTCAAGCT---ATAAAATTTCTATTTCGAGTG
1 AAACAT-TCTCAAG-TGAGATGAAATTTGT-TTT-AAGAA
*
1029550 GAAC-TATCTCAAGTGAGATGAAATTTGTTTTAAGAA
1 AAACAT-TCTCAAGTGAGATGAAATTTGTTTTAAGAA
* * ** **
1029586 AAACATTCTCAAGAGAGATAAAATTTTTGTTTCGAGTG
1 AAACATTCTCAAGTGAGATGAAA--TTTGTTTTAAGAA
*
1029624 AAACTATT-TCAA-TCGAGATG-AATCTTGTTTTTAGAA
1 AAAC-ATTCTCAAGT-GAGATGAAAT-TTGTTTTAAGAA
* * * ** **
1029660 AAATAATCTCAAGTGAGAT-AAATCTTCTACTTCGAGTG
1 AAACATTCTCAAGTGAGATGAAAT-TTGT--TTTAAGAA
* * * * **
1029698 AAAC-TATCTCAAGCGAGATAAAATTTTTTCTTCGAGTG
1 AAACAT-TCTCAAGTGAGATGAAATTTGTT-TT-AAGAA
* *
1029736 AAACAATCTCAAGCGAGATG-AATCTTGTTTTAAGAA
1 AAACATTCTCAAGTGAGATGAAAT-TTGTTTTAAGAA
* *
1029772 AAACAATCTCAAGTGAGAT-AAATTTTTTTT
1 AAACATTCTCAAGTGAGATGAAATTTGTTTT
1029802 GTATTAAGTG
Statistics
Matches: 358, Mismatches: 73, Indels: 89
0.69 0.14 0.17
Matches are distributed among these distances:
34 20 0.06
35 21 0.06
36 133 0.37
37 24 0.07
38 109 0.30
39 36 0.10
40 15 0.04
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (36 bp):
AAACATTCTCAAGTGAGATGAAATTTGTTTTAAGAA
Found at i:1029821 original size:40 final size:37
Alignment explanation
Indices: 1029401--1029833 Score: 209
Period size: 36 Copynumber: 11.6 Consensus size: 37
1029391 GTTTTAAGAA
* * *
1029401 AAACAATCTCAAGTGAGATAAAATTTCTGTTTTGAA-TG
1 AAACAATCTCAAGCGAGATAAATTTTTTG-TTT-AAGTG
* * * * **
1029439 AAAACTATCTCAAGCGAGATGAATCTTGT-TTTAAGAA
1 -AAACAATCTCAAGCGAGATAAATTTTTTGTTTAAGTG
* * *
1029476 AAACAATCTCAAGTGAGATAAAATTTTTGTTTCGAGTG
1 AAACAATCTCAAGCGAGATAAATTTTTTGTTT-AAGTG
* * * * **
1029514 AAACTATCTCAAGCTATA-AAATTTCTAT-TTCGAGTG
1 AAACAATCTCAAGCGAGATAAATTT-TTTGTTTAAGTG
* * * * **
1029550 GAACTATCTCAAGTGAGATGAAA-TTTGT-TTTAAGAA
1 AAACAATCTCAAGCGAGAT-AAATTTTTTGTTTAAGTG
* * * *
1029586 AAACATTCTCAAGAGAGATAAAATTTTTGTTTCGAGTG
1 AAACAATCTCAAGCGAGATAAATTTTTTGTTT-AAGTG
* * * * * **
1029624 AAACTATTTCAATCGAGATGAATCTTGTT-TTT-AGAA
1 AAACAATCTCAAGCGAGATAAAT-TTTTTGTTTAAGTG
* * * ** **
1029660 AAATAATCTCAAGTGAGATAAATCTTCTACTTCGAGTG
1 AAACAATCTCAAGCGAGATAAAT-TTTTTGTTTAAGTG
* * **
1029698 AAACTATCTCAAGCGAGATAAAATTTTTTCTTCGAGTG
1 AAACAATCTCAAGCGAGAT-AAATTTTTTGTTTAAGTG
* * * **
1029736 AAACAATCTCAAGCGAGATGAATCTTGT-TTTAAGAA
1 AAACAATCTCAAGCGAGATAAATTTTTTGTTTAAGTG
*
1029772 AAACAATCTCAAGTGAGATAAATTTTTTTTGTATTAAGTG
1 AAACAATCTCAAGCGAGATAAA--TTTTTTGT-TTAAGTG
*
1029812 AAACTATCTCAAGCGAGATAAA
1 AAACAATCTCAAGCGAGATAAA
1029834 AGTTTTGCTT
Statistics
Matches: 294, Mismatches: 83, Indels: 33
0.72 0.20 0.08
Matches are distributed among these distances:
35 3 0.01
36 115 0.39
37 26 0.09
38 94 0.32
39 31 0.11
40 25 0.09
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (37 bp):
AAACAATCTCAAGCGAGATAAATTTTTTGTTTAAGTG
Found at i:1029850 original size:38 final size:37
Alignment explanation
Indices: 1029401--1029861 Score: 285
Period size: 38 Copynumber: 12.3 Consensus size: 37
1029391 GTTTTAAGAA
* * * *
1029401 AAACAATCTCAAGTGAGATAAAATTTCTGTTTTGAATG
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTCGAGTG
* * ** **
1029439 AAAACTATCTCAAGCGAGAT-GAATCTTGTTTTAAGAA
1 -AAACTATCTCAAGCGAGATAAAATTTTGTTTCGAGTG
* *
1029476 AAACAATCTCAAGTGAGATAAAATTTTTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAA-TTTTGTTTCGAGTG
* *
1029514 AAACTATCTCAAGC--TATAAAATTTCTATTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTCGAGTG
* * * ** **
1029550 GAACTATCTCAAGTGAGATGAAA-TTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCGAGTG
*
1029586 AAAC-ATTCTCAAGAGAGATAAAATTTTTGTTTCGAGTG
1 AAACTA-TCTCAAGCGAGATAAAA-TTTTGTTTCGAGTG
* * * * ** *
1029624 AAACTATTTCAATCGAGAT-GAATCTTGTTTTTAG-A
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCGAGTG
* * **
1029659 AAAATAATCTCAAGTGAGAT-AAATCTTCTACTTCGAGTG
1 AAACT-ATCTCAAGCGAGATAAAAT-TT-TGTTTCGAGTG
*
1029698 AAACTATCTCAAGCGAGATAAAATTTTTTCTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATTTTGT-TTCGAGTG
* * * ** **
1029736 AAACAATCTCAAGCGAGAT-GAATCTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCGAGTG
* * * *
1029772 AAACAATCTCAAGTGAGATAAATTTTTTTTGTATT-AAGTG
1 AAACTATCTCAAGCGAGATAAA---ATTTTGT-TTCGAGTG
* *
1029812 AAACTATCTCAAGCGAGATAAAAGTTTTGCTTCTAGTG
1 AAACTATCTCAAGCGAGATAAAA-TTTTGTTTCGAGTG
*
1029850 AAACTATTTCAA
1 AAACTATCTCAA
1029862 ACAAGATGAA
Statistics
Matches: 321, Mismatches: 79, Indels: 45
0.72 0.18 0.10
Matches are distributed among these distances:
35 8 0.02
36 114 0.36
37 24 0.07
38 119 0.37
39 26 0.08
40 28 0.09
41 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (37 bp):
AAACTATCTCAAGCGAGATAAAATTTTGTTTCGAGTG
Found at i:1029873 original size:114 final size:112
Alignment explanation
Indices: 1029592--1029910 Score: 419
Period size: 112 Copynumber: 2.8 Consensus size: 112
1029582 AGAAAAACAT
* * *
1029592 TCTCAAGAGAGATAAAATTTTTGTTTCGAGTGAAACTATTTCAATCGAGATGAATCTTGTTTTTA
1 TCTCAAGCGAGATAAAATTTTTGCTTCGAGTGAAACTATTTCAAACGAGATGAATCTTG-TTTTA
* * * *
1029657 GAAAAATAATCTCAAGTGAGATAAA-TCTTCTACTTCGAGTGAAACTA
65 GAAAAACAATCTCAAGTGAGATAAATTTTTTTACTTCAAGTGAAACTA
* * * *
1029704 TCTCAAGCGAGATAAAATTTTTTCTTCGAGTGAAACAATCTCAAGCGAGATGAATCTTGTTTTAA
1 TCTCAAGCGAGATAAAATTTTTGCTTCGAGTGAAACTATTTCAAACGAGATGAATCTTGTTTT-A
** *
1029769 GAAAAACAATCTCAAGTGAGATAAATTTTTTTTGTATTAAGTGAAACTA
65 GAAAAACAATCTCAAGTGAGATAAATTTTTTTACT-TCAAGTGAAACTA
* * *
1029818 TCTCAAGCGAGATAAAAGTTTTGCTTCTAGTGAAACTATTTCAAACAAGATGAATCTTGTTTTAG
1 TCTCAAGCGAGATAAAATTTTTGCTTCGAGTGAAACTATTTCAAACGAGATGAATCTTGTTTTAG
* *
1029883 AAAAGCAATCTCAAGT-A-ATATATTTTTT
66 AAAAACAATCTCAAGTGAGATAAATTTTTT
1029911 CTATTAAATG
Statistics
Matches: 182, Mismatches: 22, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
111 14 0.08
112 79 0.43
113 22 0.12
114 67 0.37
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (112 bp):
TCTCAAGCGAGATAAAATTTTTGCTTCGAGTGAAACTATTTCAAACGAGATGAATCTTGTTTTAG
AAAAACAATCTCAAGTGAGATAAATTTTTTTACTTCAAGTGAAACTA
Found at i:1032719 original size:29 final size:30
Alignment explanation
Indices: 1032669--1032728 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1032659 AAAACACAAG
1032669 ACAAGACAAAAAGAAGTCAAGTCAGTAGAA
1 ACAAGACAAAAAGAAGTCAAGTCAGTAGAA
* *
1032699 ACAAGACAAAAAGAA-TCAAGTTAGTTGAA
1 ACAAGACAAAAAGAAGTCAAGTCAGTAGAA
1032728 A
1 A
1032729 TGATTAGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.57, C:0.12, G:0.18, T:0.13
Consensus pattern (30 bp):
ACAAGACAAAAAGAAGTCAAGTCAGTAGAA
Found at i:1042921 original size:20 final size:20
Alignment explanation
Indices: 1042896--1042944 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1042886 AAACTCGAAC
1042896 AACTCGACTTGAATTTCTTA
1 AACTCGACTTGAATTTCTTA
1042916 AACTCGACTTGAATTTCTTA
1 AACTCGACTTGAATTTCTTA
1042936 AACTCGACT
1 AACTCGACT
1042945 CGACGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (20 bp):
AACTCGACTTGAATTTCTTA
Found at i:1042953 original size:25 final size:24
Alignment explanation
Indices: 1042897--1042953 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 24
1042887 AACTCGAACA
1042897 ACTCGACTTGAATTTCTTAAACTCG
1 ACTCGAC-TGAATTTCTTAAACTCG
1042922 ACT----TGAATTTCTTAAACTCG
1 ACTCGACTGAATTTCTTAAACTCG
1042942 ACTCGACGTGAA
1 ACTCGAC-TGAA
1042954 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
20 20 0.74
25 7 0.26
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (24 bp):
ACTCGACTGAATTTCTTAAACTCG
Found at i:1044792 original size:26 final size:26
Alignment explanation
Indices: 1044769--1044823 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1044759 GGTTAATGTG
1044769 CATCGATGCACTCTCAAATAAATGAA
1 CATCGATGCACTCTCAAATAAATGAA
1044795 CATCGATGCACTCTCAAATAAATGAA
1 CATCGATGCACTCTCAAATAAATGAA
1044821 CAT
1 CAT
1044824 TAAATGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.24
Consensus pattern (26 bp):
CATCGATGCACTCTCAAATAAATGAA
Found at i:1045702 original size:18 final size:18
Alignment explanation
Indices: 1045679--1045748 Score: 131
Period size: 18 Copynumber: 3.9 Consensus size: 18
1045669 GGGTCTACGC
*
1045679 GGTCCTTCGGGACATAGT
1 GGTCCTTCAGGACATAGT
1045697 GGTCCTTCAGGACATAGT
1 GGTCCTTCAGGACATAGT
1045715 GGTCCTTCAGGACATAGT
1 GGTCCTTCAGGACATAGT
1045733 GGTCCTTCAGGACATA
1 GGTCCTTCAGGACATA
1045749 TGTGTTATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (18 bp):
GGTCCTTCAGGACATAGT
Found at i:1056650 original size:22 final size:22
Alignment explanation
Indices: 1056556--1056657 Score: 93
Period size: 21 Copynumber: 4.7 Consensus size: 22
1056546 ATAACCCGTG
*
1056556 GGGGGTATCGATT-CCC-TCAA
1 GGGGGTATCGATTCCCCTTTAA
* * * *
1056576 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGTATCGATTCCCCTT-TAA
* * *
1056600 GGGGGAATTGGTTCCCCTTTAA
1 GGGGGTATCGATTCCCCTTTAA
1056622 -GGGGTATCGATTCCCCTTTAA
1 GGGGGTATCGATTCCCCTTTAA
1056643 GGGGGTATCGATTCC
1 GGGGGTATCGATTCC
1056658 TCTGCACTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.03
21 27 0.40
22 18 0.27
23 16 0.24
24 4 0.06
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTTTAA
Found at i:1074859 original size:13 final size:15
Alignment explanation
Indices: 1074839--1074870 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1074829 AATTTCGAAA
1074839 TAAAAAA-ATTATTT
1 TAAAAAATATTATTT
1074853 TAAAAAATATTATTT
1 TAAAAAATATTATTT
1074868 TAA
1 TAA
1074871 TTGATGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAAAATATTATTT
Found at i:1081533 original size:19 final size:19
Alignment explanation
Indices: 1081509--1081546 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1081499 GCTTTTGGAC
1081509 ACATGATAAACATAGTCAT
1 ACATGATAAACATAGTCAT
1081528 ACATGATAAACATAGTCAT
1 ACATGATAAACATAGTCAT
1081547 GTATAATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
ACATGATAAACATAGTCAT
Found at i:1094391 original size:19 final size:19
Alignment explanation
Indices: 1094342--1094414 Score: 55
Period size: 19 Copynumber: 4.0 Consensus size: 19
1094332 TTTAATATAT
*
1094342 TTATTAAA-ATATTTTTAA
1 TTATTAAATATATTATTAA
* *
1094360 ATA-TAAATAATATTATTCA
1 TTATTAAAT-ATATTATTAA
* **
1094379 TTATTAAATATATAATTTT
1 TTATTAAATATATTATTAA
1094398 TTATT--ATATATTATTAA
1 TTATTAAATATATTATTAA
1094415 AATAAAAACA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
17 13 0.31
18 2 0.05
19 22 0.52
20 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTAAATATATTATTAA
Found at i:1094487 original size:19 final size:19
Alignment explanation
Indices: 1094460--1094520 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
1094450 TGATTATTTT
* *
1094460 ATATAATATTAAAAAAATA
1 ATATTATATTAAATAAATA
*
1094479 ATATTATATTATATAAATA
1 ATATTATATTAAATAAATA
* * *
1094498 TTAATA-AATAAATAAATA
1 ATATTATATTAAATAAATA
1094516 ATATT
1 ATATT
1094521 TTGATGAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
18 13 0.39
19 20 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATTATATTAAATAAATA
Found at i:1094803 original size:42 final size:42
Alignment explanation
Indices: 1094692--1094810 Score: 179
Period size: 41 Copynumber: 2.9 Consensus size: 42
1094682 ATGAATTACA
*
1094692 TTCCGGAAAACCAATTACGTGAAACAAACACAGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
*
1094734 TT-CGAAAAACGAATTACGT-AGAACAAACACAGGAAAACATT
1 TTCCGGAAAACGAATTACGTGA-AACAAACACAGGAAAACATT
* *
1094775 TTCCGGAAAATGAATTACGTGAAACAAACACTGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAA
1094811 TTCGAGAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
40 1 0.01
41 37 0.54
42 30 0.43
43 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
Found at i:1095047 original size:36 final size:36
Alignment explanation
Indices: 1094965--1095109 Score: 186
Period size: 36 Copynumber: 4.1 Consensus size: 36
1094955 TTTGGTTCAT
* * *
1094965 TTGGAGGTTGATGTTCAGTTTCAACAGTTGGTTCT--
1 TTGGAGGTTGAGGTTCAGTTTCAACAATTTGTT-TAG
*
1095000 TTGGAGGTTGAGGTTCAGTTTCAACAAATTGTTTAG
1 TTGGAGGTTGAGGTTCAGTTTCAACAATTTGTTTAG
* * *
1095036 TTGGATGTTGAGGTTCAGTTTCAACAGTTTGTTCAG
1 TTGGAGGTTGAGGTTCAGTTTCAACAATTTGTTTAG
* *
1095072 TTGGATGTTGAGGTTTAGTTTCAACAATTTGTTTAG
1 TTGGAGGTTGAGGTTCAGTTTCAACAATTTGTTTAG
1095108 TT
1 TT
1095110 TCAACAGTTG
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
34 1 0.01
35 29 0.30
36 67 0.69
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.43
Consensus pattern (36 bp):
TTGGAGGTTGAGGTTCAGTTTCAACAATTTGTTTAG
Found at i:1095052 original size:71 final size:72
Alignment explanation
Indices: 1094965--1095109 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 72
1094955 TTTGGTTCAT
* *
1094965 TTGGAGGTTGATGTTCAGTTTCAACAGTTGGTTC-TTTGGAGGTTGAGGTTCAGTTTCAACAAAT
1 TTGGAGGTTGAGGTTCAGTTTCAACAGTTGGTTCAGTTGGAGGTTGAGGTTCAGTTTCAACAAAT
1095029 TGTTTAG
66 TGTTTAG
* * * * *
1095036 TTGGATGTTGAGGTTCAGTTTCAACAGTTTGTTCAGTTGGATGTTGAGGTTTAGTTTCAACAATT
1 TTGGAGGTTGAGGTTCAGTTTCAACAGTTGGTTCAGTTGGAGGTTGAGGTTCAGTTTCAACAAAT
1095101 TGTTTAG
66 TGTTTAG
1095108 TT
1 TT
1095110 TCAACAGTTG
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
71 31 0.47
72 35 0.53
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.43
Consensus pattern (72 bp):
TTGGAGGTTGAGGTTCAGTTTCAACAGTTGGTTCAGTTGGAGGTTGAGGTTCAGTTTCAACAAAT
TGTTTAG
Found at i:1095110 original size:54 final size:54
Alignment explanation
Indices: 1095047--1095160 Score: 183
Period size: 54 Copynumber: 2.1 Consensus size: 54
1095037 TGGATGTTGA
* * *
1095047 GGTTCAGTTTCAACAGTTTGTTCAGTTGGATGTTGAGGTTTAGTTTCAACAATT
1 GGTTTAGTTTCAACAGTTGGTTCAGTTGGAGGTTGAGGTTTAGTTTCAACAATT
* *
1095101 TGTTTAGTTTCAACAGTTGGTTCATTTGGAGGTTGAGGTTTAGTTTCAACAATT
1 GGTTTAGTTTCAACAGTTGGTTCAGTTGGAGGTTGAGGTTTAGTTTCAACAATT
1095155 GGTTTA
1 GGTTTA
1095161 TTTGGAGGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.44
Consensus pattern (54 bp):
GGTTTAGTTTCAACAGTTGGTTCAGTTGGAGGTTGAGGTTTAGTTTCAACAATT
Found at i:1095123 original size:72 final size:70
Alignment explanation
Indices: 1094977--1095124 Score: 181
Period size: 72 Copynumber: 2.1 Consensus size: 70
1094967 GGAGGTTGAT
* ** *
1094977 GTTCAGTTTCAACAGTTGGTTCTTTGGAGGTTGAGGTTCAGTTTCAACAAATTGTTTAGTTGGAT
1 GTTCAGTTTCAACAGTTGGTTCGTTGGAGGTTGAGGTTCAGTTTCAACAAATTGTTTAGTTCAAA
1095042 GTTGAG
66 GTT-AG
* * * *
1095048 GTTCAGTTTCAACAGTTTGTTCAGTTGGATGTTGAGGTTTAGTTTCAACAATTTGTTTAGTTTCA
1 GTTCAGTTTCAACAGTTGGTTC-GTTGGAGGTTGAGGTTCAGTTTCAACAAATTGTTTAG-TTCA
1095113 ACAGTT-G
64 A-AGTTAG
1095120 GTTCA
1 GTTCA
1095125 TTTGGAGGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
71 21 0.32
72 39 0.59
73 3 0.05
74 3 0.05
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.43
Consensus pattern (70 bp):
GTTCAGTTTCAACAGTTGGTTCGTTGGAGGTTGAGGTTCAGTTTCAACAAATTGTTTAGTTCAAA
GTTAG
Found at i:1095149 original size:36 final size:36
Alignment explanation
Indices: 1095102--1095170 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1095092 TCAACAATTT
*
1095102 GTTTAGTTTCAACAGTTGGTTCATTTGGAGGTTGAG
1 GTTTAGTTTCAACAATTGGTTCATTTGGAGGTTGAG
*
1095138 GTTTAGTTTCAACAATTGGTTTATTTGGAGGTT
1 GTTTAGTTTCAACAATTGGTTCATTTGGAGGTT
1095171 CATGTGCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.45
Consensus pattern (36 bp):
GTTTAGTTTCAACAATTGGTTCATTTGGAGGTTGAG
Found at i:1096080 original size:2 final size:2
Alignment explanation
Indices: 1096062--1096104 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1096052 AGGTGTGCAT
*
1096062 TA TA TT TA TA TA T- 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
1096103 TA
1 TA
1096105 ACATGTTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1096443 original size:5 final size:5
Alignment explanation
Indices: 1096433--1096459 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1096423 TATATATAGC
1096433 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
1096460 AATTCACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:1097673 original size:2 final size:2
Alignment explanation
Indices: 1097666--1097716 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
1097656 AATTTTGATA
* *
1097666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT CT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1097706 AT GT AT AT AT A
1 AT AT AT AT AT A
1097717 CACGAGCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1100553 original size:48 final size:48
Alignment explanation
Indices: 1100497--1100589 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
1100487 TACTTTTCTG
*
1100497 TTGTTCATTTTCTTATGTAACTTTATAGAAATATATAGTTGTTATATT
1 TTGTTCATTTTCTTATATAACTTTATAGAAATATATAGTTGTTATATT
1100545 TTGTTCATTTTCTTATATAACTTTATAGAAATATATAGTTGTTAT
1 TTGTTCATTTTCTTATATAACTTTATAGAAATATATAGTTGTTAT
1100590 GTGTTTAACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (48 bp):
TTGTTCATTTTCTTATATAACTTTATAGAAATATATAGTTGTTATATT
Found at i:1102090 original size:5 final size:5
Alignment explanation
Indices: 1102080--1102116 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
1102070 TAGATTTACC
*
1102080 TTTCT TTTCTT TTTCT TTTCT GTTCT TTTCT TTTCT T
1 TTTCT TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT T
1102117 ATTTAGTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:1103022 original size:36 final size:36
Alignment explanation
Indices: 1102976--1103083 Score: 162
Period size: 36 Copynumber: 3.0 Consensus size: 36
1102966 TTATTATAAA
* * * * *
1102976 AACATCACTAAGGTACATGACTATTGCGGCATTTAT
1 AACACCACTAAAGTACATGATTATTGTGGCGTTTAT
1103012 AACACCACTAAAGTACATGATTATTGTGGCGTTTAT
1 AACACCACTAAAGTACATGATTATTGTGGCGTTTAT
*
1103048 AAAACCACTAAAGTACATGATTATTGTGGCGTTTAT
1 AACACCACTAAAGTACATGATTATTGTGGCGTTTAT
1103084 TATAAAAACG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (36 bp):
AACACCACTAAAGTACATGATTATTGTGGCGTTTAT
Found at i:1103147 original size:41 final size:41
Alignment explanation
Indices: 1102971--1103186 Score: 145
Period size: 36 Copynumber: 5.5 Consensus size: 41
1102961 GGTGTTTATT
* * * *
1102971 ATAAAAACATCACTAAGGTACATGACTATTGCGGCATTT--
1 ATAAAAACGTCACTAAAGTACATGACTAATGCGGCGTTTGA
* * * *
1103010 AT-AACAC--CACTAAAGTACATGATTATTGTGGCGTTT--
1 ATAAAAACGTCACTAAAGTACATGACTAATGCGGCGTTTGA
* * *
1103046 AT-AAAAC--CACTAAAGTACATGATTATTGTGGCGTTT-A
1 ATAAAAACGTCACTAAAGTACATGACTAATGCGGCGTTTGA
*
1103083 TTATAAAAACG-CAACTAACGTACATGACTAATGCGGCGTTTGA
1 --ATAAAAACGTC-ACTAAAGTACATGACTAATGCGGCGTTTGA
* * * *
1103126 ACAAAAATGTCACTAAAGTACA-AATCTATAT-CGGCGTTTGT
1 ATAAAAACGTCACTAAAGTACATGA-CTA-ATGCGGCGTTTGA
1103167 ATAAAAACGTCACTAAAGTA
1 ATAAAAACGTCACTAAAGTA
1103187 TAAGTCTATC
Statistics
Matches: 150, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
36 60 0.40
38 4 0.03
39 4 0.03
40 6 0.04
41 48 0.32
42 27 0.18
43 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (41 bp):
ATAAAAACGTCACTAAAGTACATGACTAATGCGGCGTTTGA
Found at i:1103195 original size:41 final size:41
Alignment explanation
Indices: 1103116--1103195 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
1103106 ATGACTAATG
*
1103116 CGGCGTTTGAACAAAAATGTCACTAAAGTACAAATCTATAT
1 CGGCGTTTGAACAAAAACGTCACTAAAGTACAAATCTATAT
* * * *
1103157 CGGCGTTTGTATAAAAACGTCACTAAAGTATAAGTCTAT
1 CGGCGTTTGAACAAAAACGTCACTAAAGTACAAATCTAT
1103196 CTCGACCGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (41 bp):
CGGCGTTTGAACAAAAACGTCACTAAAGTACAAATCTATAT
Found at i:1103625 original size:42 final size:42
Alignment explanation
Indices: 1103533--1103615 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1103523 AACAAAAGCG
*
1103533 CCACTAAAGTACAAGTCTATAGCGACGTTTGTATAAAAAAAC
1 CCACTAAAATACAAGTCTATAGCGACGTTTGTATAAAAAAAC
* * *
1103575 CCACTAAAATATAAGTCTATAGCGTCGTTTG-ATAGAAAAAC
1 CCACTAAAATACAAGTCTATAGCGACGTTTGTATAAAAAAAC
1103616 AGCGCTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 9 0.24
42 28 0.76
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (42 bp):
CCACTAAAATACAAGTCTATAGCGACGTTTGTATAAAAAAAC
Found at i:1103926 original size:41 final size:40
Alignment explanation
Indices: 1103881--1104023 Score: 110
Period size: 41 Copynumber: 3.5 Consensus size: 40
1103871 TATTACAACA
* *
1103881 TTTGTATAAAAACACCACAAAAGTAGTACTTTGTTGCGACG
1 TTTGT-TAAAAACACCACTAAAGTAGTACTATGTTGCGACG
* * ** * *
1103922 TTTGTTAAAAA-ATGCCACTATAG-ATGAACCCTATTGCAACG
1 TTTGTTAAAAACA--CCACTAAAGTA-GTACTATGTTGCGACG
* * * *
1103963 TTTGTATAAAAACATCGCTAAAGTACTACTATGTTGCGGCG
1 TTTGT-TAAAAACACCACTAAAGTAGTACTATGTTGCGACG
1104004 TTTGTTGAAAAACACCACTA
1 TTTGTT-AAAAACACCACTA
1104024 TAGATAAACA
Statistics
Matches: 76, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
39 1 0.01
40 8 0.11
41 59 0.78
42 7 0.09
43 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (40 bp):
TTTGTTAAAAACACCACTAAAGTAGTACTATGTTGCGACG
Found at i:1103967 original size:82 final size:82
Alignment explanation
Indices: 1103713--1104066 Score: 370
Period size: 82 Copynumber: 4.3 Consensus size: 82
1103703 ATAATTACGG
** * * ** **
1103713 CGTTTGTATAAAAACGTCGCTAAAGTACTACTCTATTAG-GGCGTTTGTTGGAAAACACCACTAT
1 CGTTTGTATAAAAACACCGCTAAAGTACTACTATGTT-GCGGCGTTTGTTAAAAAATGCCACTAT
1103777 AGATGAACCCTATTACAA
65 AGATGAACCCTATTACAA
* * * *
1103795 CATTTTATATAAAAATACCGCTAAAGTACTACTATGTTGCGGC-TTTTTTGAAAAAAATGCCACT
1 C-GTTTGTATAAAAACACCGCTAAAGTACTACTATGTTGCGGCGTTTGTT--AAAAAATGCCACT
* *
1103859 ATAGATTAATCCTATTACAA
63 ATAGATGAACCCTATTACAA
* * * * * *
1103879 CATTTGTATAAAAACACCACAAAAGTAGTACTTTGTTGCGACGTTTGTTAAAAAATGCCACTATA
1 CGTTTGTATAAAAACACCGCTAAAGTACTACTATGTTGCGGCGTTTGTTAAAAAATGCCACTATA
*
1103944 GATGAACCCTATTGCAA
66 GATGAACCCTATTACAA
* * **
1103961 CGTTTGTATAAAAACATCGCTAAAGTACTACTATGTTGCGGCGTTTGTTGAAAAACACCACTATA
1 CGTTTGTATAAAAACACCGCTAAAGTACTACTATGTTGCGGCGTTTGTTAAAAAATGCCACTATA
* * * *
1104026 GATAAACACTATTGCGA
66 GATGAACCCTATTACAA
* * *
1104043 CGTTTGTATATAAACGCTGCTAAA
1 CGTTTGTATAAAAACACCGCTAAA
1104067 TTTACCATTT
Statistics
Matches: 224, Mismatches: 43, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
82 126 0.56
83 65 0.29
84 33 0.15
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (82 bp):
CGTTTGTATAAAAACACCGCTAAAGTACTACTATGTTGCGGCGTTTGTTAAAAAATGCCACTATA
GATGAACCCTATTACAA
Found at i:1104041 original size:41 final size:39
Alignment explanation
Indices: 1103914--1104049 Score: 116
Period size: 41 Copynumber: 3.3 Consensus size: 39
1103904 TAGTACTTTG
*
1103914 TTGCGACGTTTGTTAAAAA-ATGCCACTATAGATGAACCCTA
1 TTGCGACGTTTGTTAAAAACA--CCACTATAGAT-AACACTA
* * * *
1103955 TTGCAACGTTTGTATAAAAACATCGCTAAAG-T-ACTACTA
1 TTGCGACGTTTGT-TAAAAACACCACTATAGATAAC-ACTA
*
1103994 TGTTGCGGCGTTTGTTGAAAAACACCACTATAGATAAACACTA
1 --TTGCGACGTTTGTT-AAAAACACCACTATAGAT-AACACTA
1104037 TTGCGACGTTTGT
1 TTGCGACGTTTGT
1104050 ATATAAACGC
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
38 2 0.03
39 3 0.04
40 2 0.03
41 54 0.72
42 7 0.09
43 5 0.07
44 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (39 bp):
TTGCGACGTTTGTTAAAAACACCACTATAGATAACACTA
Found at i:1105326 original size:265 final size:262
Alignment explanation
Indices: 1104921--1105444 Score: 689
Period size: 265 Copynumber: 2.0 Consensus size: 262
1104911 AATATGAAAA
* *
1104921 ATTAAATTTAACAGAAATCCGAACAACTTGACTAAACTAAAATTTTGTAAACTCGACTTAACTCG
1 ATTAAATTTAACAGAAATCCGAACAACTCGACTAAACTAAAATTTTATAAACTCGACTTAACTCG
** * *
1104986 AAAAATTTTCAAATTTGAGTTGAGTTATAAAATAAAACTTGAATAACTAGAATTTTTTAGTAATT
66 AAAAATTTTCAAATTTGAGTCAAGCTATAAAATAAAACTCGAATAACTAGAATTTTTTAGTAATT
* * *
1105051 AGTGGATTGATTTTCAAGTCTGAGTCGAGTTCCTCAATTTT-TATGATATATGTATATCACATA-
131 AGTAGATTGATTTTCAAGTCTGAGTCGAATCCCTCAATTTTGTATGATATATGTATATCACATAT
* *
1105114 TGAAAAAATATGAAGAAAAAATATATGTATTGTATATGGTCATATAAAACCATTTAAATTGAAAT
196 TG-AAAAATATGAAG-AAAAATATATGTATTATATATGGTCATAGAAAACCATTTAAATT-AAAT
1105179 TTACG
258 TTACG
** * * *
1105184 ATTAAATTTAAACAGAAATTTGAACAACTCGACTCAACTACAATTTTATAAACTCAGA-TTGACT
1 ATTAAATTT-AACAGAAATCCGAACAACTCGACTAAACTAAAATTTTATAAACTC-GACTTAACT
* * * * *
1105248 C-AAAATTTTTTTTAAATTTGAGTCAAGCTATAAAGTAGAACTCGAATAACTCA-ATTTTTTTAG
64 CGAAAA--ATTTTCAAATTTGAGTCAAGCTATAAAATAAAACTCGAATAACT-AGAATTTTTTAG
* * *
1105311 TAATTAGTAGATTGATTTTCAATTTTGAGTTGAATCCCTCAATTTTGTATGATATATGTATATCA
126 TAATTAGTAGATTGATTTTCAAGTCTGAGTCGAATCCCTCAATTTTGTATGATATATGTATATCA
* * * *
1105376 CATATTGAAAAATATGAAGAAATATATATGTATTATATATGGTTATAGGAAATCATTTAAATTAA
191 CATATTGAAAAATATGAAGAAAAATATATGTATTATATATGGTCATAGAAAACCATTTAAATTAA
1105441 ATTT
256 ATTT
1105445 TATTATAATA
Statistics
Matches: 226, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
263 13 0.06
264 51 0.23
265 125 0.55
266 35 0.15
267 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (262 bp):
ATTAAATTTAACAGAAATCCGAACAACTCGACTAAACTAAAATTTTATAAACTCGACTTAACTCG
AAAAATTTTCAAATTTGAGTCAAGCTATAAAATAAAACTCGAATAACTAGAATTTTTTAGTAATT
AGTAGATTGATTTTCAAGTCTGAGTCGAATCCCTCAATTTTGTATGATATATGTATATCACATAT
TGAAAAATATGAAGAAAAATATATGTATTATATATGGTCATAGAAAACCATTTAAATTAAATTTA
CG
Found at i:1105860 original size:339 final size:331
Alignment explanation
Indices: 1105292--1105912 Score: 751
Period size: 337 Copynumber: 1.8 Consensus size: 331
1105282 GTAGAACTCG
* * **
1105292 AATAACTCAATTTTTTTAGTAATTAGTAGATTGATTTTCAATTTTGAGTTGAATCCCTCAATTTT
1 AATAACTCAATATTTTTAGTAATTAGTAGATTGATTTTCAAGTTTGAGTTGAATAACTCAATTTT
1105357 GTATGATATATGTATATCACATATTGAAAAATATGAAGAAATATATATGTATTATATATGGTTAT
66 GTATGATATA-GTATATCACATATTGAAAAATATGAAGAAATATATATGTATTATATATGGTTAT
* ** * *
1105422 AGGAAATCATTTAAATTAAATTTTATTATAATATTATAAATATTTACAAATAAATTTAAATATAA
130 AGAAAATCATTTAAATTAAATTTTACCATAATATTATAAATATTTACAAATAAATTTAAACAGAA
* *
1105487 ACTCGAACAATTAGACTCGAATCTAAAAAATTTCAAATTTGAGTCAAGTTATAAAATAGAACTCG
195 ACTC-AACAATCAGACTCGAA--TAAAAAATTTC-AAGTT--G---AGTTATAAAATAGAACTCG
1105552 AATAACTTGAAAT-TTTTTAACTCGACTCAACTAAAAAAATTAAATTCTAGTCGAGTTGAGTTAT
251 AATAACTTGAAATATTTTTAACTCGACTCAACTAAAAAAATTAAATTCTAGTCGAGTTGAGTTAT
1105616 AAAATAGATCTCGAAC
316 AAAATAGATCTCGAAC
* * *
1105632 AATAACTCAA-ATTTTTAGTAATTAGT-GAATT-AGTTTTTAAGTTTGAGTTGAGTAATTCAATT
1 AATAACTCAATATTTTTAGTAATTAGTAG-ATTGA-TTTTCAAGTTTGAGTTGAATAACTCAATT
** * * *
1105694 TTGTATGATATA-TATATCATGTA-TGAAAAATTATGAGGAAATATATTTGTATTGTATATGGTT
64 TTGTATGATATAGTATATCACATATTGAAAAA-TATGAAGAAATATATATGTATTATATATGGTT
**
1105757 ATAGAAAATCATTTAAATTAGAATTAAAAATTTACCATAATATTATAAATATTTACACTTAAAAT
128 ATAGAAAATCATTTAAATTA-AA-T-----TTTACCATAATATTATAAATATTTACAAAT-AAAT
*
1105822 TTAAACAGAGACTC-A-AA-CA-ACTCGAA-AAAATCAATTTCAAGTTGAGTTATAAAATAGAAC
185 TTAAACAGAAACTCAACAATCAGACTCGAATAAAA--AATTTCAAGTTGAGTTATAAAATAGAAC
*
1105882 TCGAATAACTTGAAATATTTTTTACTCGACT
248 TCGAATAACTTGAAATATTTTTAACTCGACT
1105913 TGACTCGGTC
Statistics
Matches: 244, Mismatches: 23, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
333 32 0.13
334 13 0.05
336 8 0.03
337 61 0.25
338 8 0.03
339 60 0.25
340 17 0.07
341 1 0.00
342 2 0.01
343 1 0.00
344 26 0.11
345 15 0.06
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (331 bp):
AATAACTCAATATTTTTAGTAATTAGTAGATTGATTTTCAAGTTTGAGTTGAATAACTCAATTTT
GTATGATATAGTATATCACATATTGAAAAATATGAAGAAATATATATGTATTATATATGGTTATA
GAAAATCATTTAAATTAAATTTTACCATAATATTATAAATATTTACAAATAAATTTAAACAGAAA
CTCAACAATCAGACTCGAATAAAAAATTTCAAGTTGAGTTATAAAATAGAACTCGAATAACTTGA
AATATTTTTAACTCGACTCAACTAAAAAAATTAAATTCTAGTCGAGTTGAGTTATAAAATAGATC
TCGAAC
Found at i:1108977 original size:56 final size:56
Alignment explanation
Indices: 1108917--1109023 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
1108907 ATTTTGTCTG
* * * * *
1108917 AAAATTAAAGAGGGAACTAAATGTAAGGACCAAACTTGCAATTGTACCATTGTCCA
1 AAAATTAAACAGGAAACAAAATGTAAGGACCAAACTTACAATTATACCATTGTCCA
*
1108973 AAAATTATACAGGAAACAAAATGTAAGGACCAAACTTACAATTATACCATT
1 AAAATTAAACAGGAAACAAAATGTAAGGACCAAACTTACAATTATACCATT
1109024 TGTAATTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (56 bp):
AAAATTAAACAGGAAACAAAATGTAAGGACCAAACTTACAATTATACCATTGTCCA
Found at i:1110179 original size:16 final size:16
Alignment explanation
Indices: 1110137--1110185 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
1110127 CTGCTAACCA
1110137 CTAACCGCTAACTTTT
1 CTAACCGCTAACTTTT
**
1110153 CTAACAACTAACTTTT
1 CTAACCGCTAACTTTT
1110169 CTAACCGCTAATCTTTT
1 CTAACCGCTAA-CTTTT
1110186 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.39
Consensus pattern (16 bp):
CTAACCGCTAACTTTT
Found at i:1110394 original size:33 final size:29
Alignment explanation
Indices: 1110330--1110394 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
1110320 TTTATTTCTG
* *
1110330 TTATTTAATTTTATGAATTTTTATTTTCT
1 TTATTTAATTTTATGAATTTTTACTTGCT
1110359 TTATTTAATTTTAGTGTATACTTTTTACTTGCT
1 TTATTTAATTTTA-TG-A-A-TTTTTACTTGCT
1110392 TTA
1 TTA
1110395 ATGTTCTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 13 0.43
30 2 0.07
31 1 0.03
32 1 0.03
33 13 0.43
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (29 bp):
TTATTTAATTTTATGAATTTTTACTTGCT
Found at i:1114607 original size:12 final size:11
Alignment explanation
Indices: 1114601--1114651 Score: 66
Period size: 13 Copynumber: 4.3 Consensus size: 11
1114591 CAAAGCAAAG
1114601 AAAAAAGAAAA
1 AAAAAAGAAAA
1114612 AAAAAAGAAAA
1 AAAAAAGAAAA
1114623 AAAGAAAGAAAGA
1 AAA-AAAGAAA-A
1114636 AAAAGAAGAAAGA
1 AAAA-AAGAAA-A
1114649 AAA
1 AAA
1114652 TTGATCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 14 0.38
12 8 0.22
13 15 0.41
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:1114639 original size:17 final size:17
Alignment explanation
Indices: 1114592--1114650 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
1114582 TGCAAAGATC
*
1114592 AAAGCAAAGAAAAAAGAAA
1 AAAG-AAAGAAAAAA-AAG
*
1114611 AAAAAAAG-AAAAAAAG
1 AAAGAAAGAAAAAAAAG
*
1114627 AAAGAAAGAAAAAGAAG
1 AAAGAAAGAAAAAAAAG
1114644 AAAGAAA
1 AAAGAAA
1114651 ATTGATCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 9 0.26
17 19 0.54
18 4 0.11
19 3 0.09
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAAAG
Found at i:1114648 original size:4 final size:4
Alignment explanation
Indices: 1114592--1114650 Score: 59
Period size: 4 Copynumber: 14.8 Consensus size: 4
1114582 TGCAAAGATC
* * *
1114592 AAAG CAAAG AAA- AAAG AAA- AAAA AAAG AAAA AAAG AAAG AAAG AAAA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1114639 AGAAG AAAG AAA
1 A-AAG AAAG AAA
1114651 ATTGATCAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
3 6 0.13
4 33 0.72
5 7 0.15
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1117090 original size:36 final size:36
Alignment explanation
Indices: 1117050--1117230 Score: 133
Period size: 36 Copynumber: 5.2 Consensus size: 36
1117040 TTCGTCTCGT
1117050 TTGAGACAATTTTTCTTGAAACAAAATTGGTCTCAC
1 TTGAGACAATTTTTCTTGAAACAAAATTGGTCTCAC
** ** * * * *
1117086 TTGAGATTATTTTCTCTAAAAACAAATTTTGTTTCGC
1 TTGAGACAATTTT-TCTTGAAACAAAATTGGTCTCAC
*
1117123 TTGAGACAATTTCTCTTGAAACACAAA------TC-C
1 TTGAGACAATTTTTCTTGAAACA-AAATTGGTCTCAC
*** * * * *
1117153 TTGAGATTGTTTCTCTTGAAACAAATTTCGTCTCGC
1 TTGAGACAATTTTTCTTGAAACAAAATTGGTCTCAC
* *
1117189 TTGAGACAGTTTTTCTTGAAACAAAATTGATCTCAC
1 TTGAGACAATTTTTCTTGAAACAAAATTGGTCTCAC
1117225 TTGAGA
1 TTGAGA
1117231 TTATTTTCCT
Statistics
Matches: 111, Mismatches: 25, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
29 2 0.02
30 21 0.19
31 2 0.02
35 2 0.02
36 55 0.50
37 29 0.26
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (36 bp):
TTGAGACAATTTTTCTTGAAACAAAATTGGTCTCAC
Found at i:1117338 original size:67 final size:67
Alignment explanation
Indices: 1117015--1117535 Score: 502
Period size: 67 Copynumber: 7.6 Consensus size: 67
1117005 TGTCACCTTG
* ** * * *
1117015 GAGATTTTTTCTCTCTAAACAAA-TTTTCGTCTCGTTTGAGACAATTTTTCTTGAAACA-AAATT
1 GAGATTGTTTCTCTAGAAACAAAGTTTT-GTCTCGCTTGAGACAGTTTCTCTTGAAACATAAA--
1117078 GGTCTCACTT
63 ---C-CA-TT
* * * * *
1117088 GAGATTATTTTCTCTAAAAACAAA-TTTTGTTTCGCTTGAGACAATTTCTCTTGAAACACAAATC
1 GAGATT-GTTTCTCTAGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAA-C
1117152 C-TT
64 CATT
* * * *
1117155 GAGATTGTTTCTCTTGAAACAAA-TTTCGTCTCGCTTGAGACAGTTTTTCTTGAAACAAAATTGA
1 GAGATTGTTTCTCTAGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAA---A
1117219 TCTCACTT
63 -C-CA-TT
* * * * *
1117227 GAGATTATTT-TCCTA-AAA-AAACTTTTGTCTCTCTTGAGATAGTTTCTCTTGACACATAAACC
1 GAGATTGTTTCT-CTAGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACC
*
1117289 TTT
65 ATT
* * *
1117292 GAGATTATTTCTCTAGAAACAAAGTTTTATCTCGCTTGAGACAGTTTCACTTGAAACATAAACCA
1 GAGATTGTTTCTCTAGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCA
1117357 TT
66 TT
* *
1117359 GAGATTGTTTCTCTCA-AAACAAAGTTTTATCTCACTTGAGACAGTTTCTCTTGAAACATAAACC
1 GAGATTGTTTCTCT-AGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACC
*
1117423 TTT
65 ATT
* * *
1117426 GAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCACTTGAGATAGTTTCTCTTGAAACATAAACCA
1 GAGATTGTTTCTCTAGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCA
1117491 TT
66 TT
* ** * *
1117493 GATATTGTTTCTCTCCAAAAAAAGTTTCGTCTCGCTTGAGACA
1 GAGATTGTTTCTCTAGAAACAAAGTTTTGTCTCGCTTGAGACA
1117536 ATTTTCCATT
Statistics
Matches: 389, Mismatches: 44, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
65 15 0.04
66 51 0.13
67 208 0.53
68 2 0.01
69 4 0.01
70 6 0.02
71 35 0.09
72 13 0.03
73 33 0.08
74 22 0.06
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (67 bp):
GAGATTGTTTCTCTAGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCA
TT
Found at i:1117369 original size:30 final size:30
Alignment explanation
Indices: 1117335--1117446 Score: 91
Period size: 30 Copynumber: 3.5 Consensus size: 30
1117325 GCTTGAGACA
*
1117335 GTTTCACTTGAAACATAAACCATTGAGATT
1 GTTTCTCTTGAAACATAAACCATTGAGATT
** **
1117365 GTTTCTCTCAAAACA-AAGTTTTATCTCACTTGAGACA
1 GTTTCTCTTGAAACATAA-----A-C-CA-TTGAGATT
*
1117402 GTTTCTCTTGAAACATAAACCTTTGAGATT
1 GTTTCTCTTGAAACATAAACCATTGAGATT
1117432 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1117447 AAGTTTTGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
29 2 0.03
30 33 0.52
31 1 0.02
32 1 0.02
33 1 0.02
34 1 0.02
35 1 0.02
36 2 0.03
37 19 0.30
38 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (30 bp):
GTTTCTCTTGAAACATAAACCATTGAGATT
Found at i:1117416 original size:37 final size:37
Alignment explanation
Indices: 1117357--1117483 Score: 126
Period size: 37 Copynumber: 3.6 Consensus size: 37
1117347 ACATAAACCA
* **
1117357 TTGAGATTGTTTCTCTCAAAACAAAGTTTTATCTCAC
1 TTGAGATAGTTTCTCTTGAAACAAAGTTTTATCTCAC
* *
1117394 TTGAGACAGTTTCTCTTGAAACATAA-----A-C-C-T
1 TTGAGATAGTTTCTCTTGAAACA-AAGTTTTATCTCAC
* *
1117424 TTGAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCAC
1 TTGAGATAGTTTCTCTTGAAACAAAGTTTTATCTCAC
1117461 TTGAGATAGTTTCTCTTGAAACA
1 TTGAGATAGTTTCTCTTGAAACA
1117484 TAAACCATTG
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
29 2 0.03
30 21 0.30
31 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 1 0.01
37 41 0.58
38 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (37 bp):
TTGAGATAGTTTCTCTTGAAACAAAGTTTTATCTCAC
Found at i:1117421 original size:134 final size:133
Alignment explanation
Indices: 1117009--1117535 Score: 557
Period size: 134 Copynumber: 3.9 Consensus size: 133
1116999 GCTGTCTGTC
* * * * *
1117009 ACCTTGGAGATTTTTTCTCTCT-AAACAAA-TTTTCGTCTCGTTTGAGACAATTTTTCTTGAAAC
1 ACCTTTGAGATTGTTTCTCT-TGAAACAAAGTTTT-GTCTCGCTTGAGACAGTTTCTCTTGAAAC
* * * *
1117072 A-AAATTGGTCTCACTTGAGATTATTT-TCTCTAAAAACAAATTTTGTTTCGCTTGAGACAATTT
64 ATAAA-----C-CA-TTGAGATTGTTTCTCTC-AAAAA-AAGTTTTGTCTCGCTTGAGACAGTTT
*
1117135 CTCTTGAAACACAA
120 CTCTTGAAACATAA
* *
1117149 ATCC-TTGAGATTGTTTCTCTTGAAACAAA-TTTCGTCTCGCTTGAGACAGTTTTTCTTGAAACA
1 A-CCTTTGAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
* * * * *
1117212 AAATTGATCTCACTTGAGATTATTT-TC-CTAAAAAAACTTTTGTCTCTCTTGAGATAGTTTCTC
65 TAA---A-C-CA-TTGAGATTGTTTCTCTC-AAAAAAAGTTTTGTCTCGCTTGAGACAGTTTCTC
*
1117275 TTGACACATAA
123 TTGAAACATAA
* * * *
1117286 ACCTTTGAGATTATTTCTCTAGAAACAAAGTTTTATCTCGCTTGAGACAGTTTCACTTGAAACAT
1 ACCTTTGAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAT
* *
1117351 AAACCATTGAGATTGTTTCTCTCAAAACAAAGTTTTATCTCACTTGAGACAGTTTCTCTTGAAAC
66 AAACCATTGAGATTGTTTCTCTCAAAA-AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAAC
1117416 ATAA
130 ATAA
* *
1117420 ACCTTTGAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCACTTGAGATAGTTTCTCTTGAAACAT
1 ACCTTTGAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAT
* *
1117485 AAACCATTGATATTGTTTCTCTCCAAAAAAAGTTTCGTCTCGCTTGAGACA
66 AAACCATTGAGATTGTTTCTCT-CAAAAAAAGTTTTGTCTCGCTTGAGACA
1117536 ATTTTCCATT
Statistics
Matches: 340, Mismatches: 35, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
132 11 0.03
133 8 0.02
134 138 0.41
135 6 0.02
136 2 0.01
137 57 0.17
138 39 0.11
139 49 0.14
140 27 0.08
141 2 0.01
143 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (133 bp):
ACCTTTGAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAT
AAACCATTGAGATTGTTTCTCTCAAAAAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
TAA
Found at i:1117506 original size:201 final size:202
Alignment explanation
Indices: 1117086--1117618 Score: 566
Period size: 201 Copynumber: 2.6 Consensus size: 202
1117076 TTGGTCTCAC
* *
1117086 TTGAGATTATTTTCTCTAAAAACAAA-TTTTGTTTCGCTTGAGACAATTTCTCTTGAAACACAAA
1 TTGAGATTA-TTTCTCTAAAAACAAAGTTTTGTCTCGCTTGAGACAATTTCACTTGAAACACAAA
** * * *
1117150 TCCTTGAGATTGTTTCTCTTGAAACAAATTTCGTCTCGCTTGAGACAGTTTTTCTTGAAACAAAA
65 TCCTTGAGATTGTTTCTCTCAAAACAAATTTCATCTCACTTGAGACAGTTTCTCTTGAAACAAAA
* *
1117215 TTGATCTCACTTGAGATTATTTTCCTAAAAAAACTTTTGTCTCTCTTGAGATAGTTTCTCTTGAC
130 -T-ATCTCACTTGAGATTATTTTCCTAAAAAAACTTTTGTCTCACTTGAGATAGTTTCTCTTGAA
*
1117280 ACATAAACCT
193 ACATAAACCA
* * * *
1117290 TTGAGATTATTTCTCTAGAAACAAAGTTTTATCTCGCTTGAGACAGTTTCACTTGAAACATAAA-
1 TTGAGATTATTTCTCTAAAAACAAAGTTTTGTCTCGCTTGAGACAATTTCACTTGAAACACAAAT
* *
1117354 CCATTGAGATTGTTTCTCTCAAAACAAAGTTTTATCTCACTTGAGACAGTTTCTCTTGAAACATA
66 CC-TTGAGATTGTTTCTCTCAAAACAAA-TTTCATCTCACTTGAGACAGTTTCTCTTGAAACAAA
* * * * *
1117419 A-A-C-C-TTTGAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCACTTGAGATAGTTTCTCTTGA
129 ATATCTCACTTGAGATTATTT-TCCT-AAAAAAACTTTTGTCTCACTTGAGATAGTTTCTCTTGA
1117480 AACATAAACCA
192 AACATAAACCA
* * * * *
1117491 TTGATATTGTTTCTCTCCAAAA-AAAGTTTCGTCTCGCTTGAGACAATTTTC-CATTGAAACAAA
1 TTGAGATTATTTCTCT-AAAAACAAAGTTTTGTCTCGCTTGAGACAA-TTTCAC-TTGAAACACA
* ** * * ** * *
1117554 AAT-TTTGA-AACGTTTCACTCGAAATA-AAATTTTATCTCACCCGAGATAGCTTCTCTTGAAAC
63 AATCCTTGAGATTGTTTCTCTC-AAA-ACAAATTTCATCTCACTTGAGACAGTTTCTCTTGAAAC
1117616 AAA
126 AAA
1117619 TTTCTTTCCA
Statistics
Matches: 280, Mismatches: 38, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
199 11 0.04
200 44 0.16
201 91 0.32
202 20 0.07
203 17 0.06
204 65 0.23
205 32 0.11
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (202 bp):
TTGAGATTATTTCTCTAAAAACAAAGTTTTGTCTCGCTTGAGACAATTTCACTTGAAACACAAAT
CCTTGAGATTGTTTCTCTCAAAACAAATTTCATCTCACTTGAGACAGTTTCTCTTGAAACAAAAT
ATCTCACTTGAGATTATTTTCCTAAAAAAACTTTTGTCTCACTTGAGATAGTTTCTCTTGAAACA
TAAACCA
Found at i:1117561 original size:134 final size:135
Alignment explanation
Indices: 1117086--1117616 Score: 526
Period size: 134 Copynumber: 3.9 Consensus size: 135
1117076 TTGGTCTCAC
* * * * *
1117086 TTGAGATTATTT-TCTCTAAAAACAAATTTTGTTTCGCTTGAGACAA-TTTCTCTTGAAACACAA
1 TTGAGATTGTTTCTCTCCAAAAA-AAGTTTTGTCTCGCTTGAGACAAGTTTCTCTTGAAACATAA
* * ** * * *
1117149 ATCCTTGAGATTGTTTCTCTTGAAACAAA-TTTCGTCTCGCTTGAGACAGTTTTTCTTGAAACAA
65 AACTTTGAGATTGTTTCTCTTGAAACAAAGTTTTATCTCACTTGAGACAGTTTCTCTTGAAACAT
1117213 AATTGATCTCA
130 AA---A-C-CA
* * * * * *
1117224 CTTGAGATTATTT-TC-CTAAAAAAACTTTTGTCTCTCTTGAGA-TAGTTTCTCTTGACACATAA
1 -TTGAGATTGTTTCTCTCCAAAAAAAGTTTTGTCTCGCTTGAGACAAGTTTCTCTTGAAACATAA
* * * * *
1117286 ACCTTTGAGATTATTTCTCTAGAAACAAAGTTTTATCTCGCTTGAGACAGTTTCACTTGAAACAT
65 AACTTTGAGATTGTTTCTCTTGAAACAAAGTTTTATCTCACTTGAGACAGTTTCTCTTGAAACAT
1117351 AAACCA
130 AAACCA
* *
1117357 TTGAGATTGTTTCTCT-CAAAACAAAGTTTTATCTCACTTGAGAC-AGTTTCTCTTGAAACATAA
1 TTGAGATTGTTTCTCTCCAAAA-AAAGTTTTGTCTCGCTTGAGACAAGTTTCTCTTGAAACATAA
* * *
1117420 ACCTTTGAGATTGTTTCTCTTGAAACAAAGTTTTGTCTCACTTGAGATAGTTTCTCTTGAAACAT
65 AACTTTGAGATTGTTTCTCTTGAAACAAAGTTTTATCTCACTTGAGACAGTTTCTCTTGAAACAT
1117485 AAACCA
130 AAACCA
* * *
1117491 TTGATATTGTTTCTCTCCAAAAAAAGTTTCGTCTCGCTTGAGACAATTTTC-CATTGAAACA-AA
1 TTGAGATTGTTTCTCTCCAAAAAAAGTTTTGTCTCGCTTGAGACAAGTTTCTC-TTGAAACATAA
* ** * * * * ** * *
1117554 AATTTTGA-AACGTTTCACTCGAAATAAAATTTTATCTCACCCGAGATAGCTTCTCTTGAAACA
65 AACTTTGAGATTGTTTCTCTTGAAACAAAGTTTTATCTCACTTGAGACAGTTTCTCTTGAAACA
1117617 AATTTCTTTC
Statistics
Matches: 339, Mismatches: 44, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
132 11 0.03
133 53 0.16
134 145 0.43
135 19 0.06
136 1 0.00
137 57 0.17
138 39 0.12
139 14 0.04
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (135 bp):
TTGAGATTGTTTCTCTCCAAAAAAAGTTTTGTCTCGCTTGAGACAAGTTTCTCTTGAAACATAAA
ACTTTGAGATTGTTTCTCTTGAAACAAAGTTTTATCTCACTTGAGACAGTTTCTCTTGAAACATA
AACCA
Found at i:1118005 original size:139 final size:139
Alignment explanation
Indices: 1117742--1118665 Score: 955
Period size: 139 Copynumber: 6.7 Consensus size: 139
1117732 TGACAACCAT
* * *
1117742 GACCAGAACTCCTCAACGCGAATGAGCAGTGTCATCCTCAGATAATCAGATGTCCTCATCACGTA
1 GACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGATGTCCTCATCACGTA
* * * * *
1117807 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATGACTAGATGTCCTTATCA-AGAAGGAATAAT
66 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACA-TAGGAACAAT
1117871 TTCGTCCACC
130 TTCGTCCACC
* *
1117881 GACCAGATCTCCTCAACGCGAAGGAGCAGCGTCATCCTCGGACAATCAGATGTCCTCATCACGTA
1 GACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGATGTCCTCATCACGTA
* * *
1117946 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATTGCTAGACATCCTCATCACATAGGAACAATG
66 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATT
1118011 TCGTCCACC
131 TCGTCCACC
* * * * * * * * *
1118020 TACCAGATCTCCTCAATGCAAAGGAACAATTTTATTCTCAGACAATCAGACGTCCTCATCACGTA
1 GACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGATGTCCTCATCACGTA
* * * *
1118085 TGAACCATATT-TCTCTAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATG
66 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAAT-
1118149 TT-GTCCACC
130 TTCGTCCACC
* * * *
1118158 GACCAGATCTCCTCAATGCGAAGGAGCAGTGTCATCCTCAGACAATCAGAAGTTCTCATCACATA
1 GACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGATGTCCTCATCACGTA
* ** * * *
1118223 GGGATTGTATTGTCTCCAAATTATCCCTAAATATGGCTAGACGTCCTCATCGCGA-AGGAACAAT
66 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCAC-ATAGGAACAAT
* *
1118287 ATCTTCCACC
130 TTCGTCCACC
* * * * * * *
1118297 GACCATATCTCCTCAACGCGAAGGAGTAGTGTCATCATTAGACAATCAGACT-TTCTAATCATGT
1 GACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGA-TGTCCTCATCACGT
* * * * * *
1118361 AGGAACCATGTTGTCTTCAAATTATCCCTAAAGACGGCTAGAAGTCCTCACCACGA-AGGAAAAA
65 AGGAACCGTGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCAC-ATAGGAACAA
* *
1118425 TGTCGTCTACC
129 TTTCGTCCACC
* * * * * * * * * * ** *
1118436 GACTAGACCTCCTCAACACAAAGTAGTAGTGTCATCCTCAAACAATCAAATTTTCTCATCGTGAA
1 GACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGATGTCCTCATCACGTA
* *** * *
1118501 AGAACTAAGTTATCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACATAGGAACAATG
66 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAAT-
*
1118566 TT-GTGCACC
130 TTCGTCCACC
* * * * * * * * * *
1118575 GAACAGATCTCTTCAACACAAAGGAGTAATGTCATCCCCAGACAACCAGACT-TCCTCAACACGA
1 GACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGA-TGTCCTCATCACGT
* **
1118639 AGGAACCGCGTTGTCTTTAAATTATCC
65 AGGAACCGTGTTGTCTCCAAATTATCC
1118666 AGATTGACCA
Statistics
Matches: 655, Mismatches: 120, Indels: 20
0.82 0.15 0.03
Matches are distributed among these distances:
138 120 0.18
139 531 0.81
140 4 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (139 bp):
GACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGATGTCCTCATCACGTA
GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATT
TCGTCCACC
Found at i:1120076 original size:124 final size:124
Alignment explanation
Indices: 1119916--1120142 Score: 350
Period size: 124 Copynumber: 1.8 Consensus size: 124
1119906 ACTCTTGTTA
* * * * *
1119916 TTTATTTATTGTTTATAATATTCTATTTGACCTTGTGGTGATCCGATCCGGGGTATGATCCACAT
1 TTTATTAATTGTTTATAATATTCGATTAGACCTTGTGGTGACCCGATCCGAGGTATGATCCACAT
*
1119981 TATTATGGTTCGAACTCTGCTAACCACT-AATTTTTTATATATTTTATTTTATTTTATT
66 TATTATGGTCCGAACTCTGCTAACCACTAAATTTTTTATATATTTTATTTTATTTTATT
*
1120039 TTTATTAATTTGTTT-TAATTATTCGATTAGATCTTGTGGTGACCCGATCCGAGGTATGATCCAC
1 TTTATTAA-TTGTTTATAA-TATTCGATTAGACCTTGTGGTGACCCGATCCGAGGTATGATCCAC
*
1120103 ATTATTATGGTCCGGACTCTGCTAACCACTAAATTTTTTA
64 ATTATTATGGTCCGAACTCTGCTAACCACTAAATTTTTTA
1120143 ACATCTAACC
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
123 10 0.11
124 74 0.80
125 9 0.10
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (124 bp):
TTTATTAATTGTTTATAATATTCGATTAGACCTTGTGGTGACCCGATCCGAGGTATGATCCACAT
TATTATGGTCCGAACTCTGCTAACCACTAAATTTTTTATATATTTTATTTTATTTTATT
Found at i:1120323 original size:16 final size:16
Alignment explanation
Indices: 1120302--1120332 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1120292 TCGATACTAA
*
1120302 CATTTTATTTTTATTG
1 CATTTTATTTCTATTG
1120318 CATTTTATTTCTATT
1 CATTTTATTTCTATT
1120333 ATTTAATTTT
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:0.19, C:0.10, G:0.03, T:0.68
Consensus pattern (16 bp):
CATTTTATTTCTATTG
Found at i:1121393 original size:18 final size:19
Alignment explanation
Indices: 1121359--1121396 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1121349 ATTTTTTAAA
1121359 TAAAGTCATAATTATTTTT
1 TAAAGTCATAATTATTTTT
1121378 TAAA-TCAT-ATTAATTTTT
1 TAAAGTCATAATT-ATTTTT
1121396 T
1 T
1121397 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 11 0.61
19 4 0.22
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
TAAAGTCATAATTATTTTT
Found at i:1121394 original size:17 final size:19
Alignment explanation
Indices: 1121359--1121395 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1121349 ATTTTTTAAA
*
1121359 TAAAGTCATAATTATTTTT
1 TAAAGTCATAATTAATTTT
1121378 TAAA-TCAT-ATTAATTTT
1 TAAAGTCATAATTAATTTT
1121395 T
1 T
1121396 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
TAAAGTCATAATTAATTTT
Found at i:1123182 original size:14 final size:15
Alignment explanation
Indices: 1123157--1123186 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1123147 TCTCTCTAAA
1123157 AACCCACAAAAATAG
1 AACCCACAAAAATAG
1123172 AACCC-CAAAAATAG
1 AACCCACAAAAATAG
1123186 A
1 A
1123187 TCCAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.60, C:0.27, G:0.07, T:0.07
Consensus pattern (15 bp):
AACCCACAAAAATAG
Found at i:1123353 original size:16 final size:17
Alignment explanation
Indices: 1123332--1123369 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1123322 TTCATTATGG
1123332 TTTTCCC-CTAT-TTTCT
1 TTTTCCCTCTATGTTT-T
1123348 TTTTCCCTCTATGTTTT
1 TTTTCCCTCTATGTTTT
1123365 TTTTC
1 TTTTC
1123370 TGCTTAGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 10 0.50
18 3 0.15
ACGTcount: A:0.05, C:0.26, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTCCCTCTATGTTTT
Found at i:1124019 original size:3 final size:3
Alignment explanation
Indices: 1124013--1124071 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
1124003 ATAACAGAAA
* * *
1124013 AAT AAT ATT AAT AAT AAT AAT AGT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1124061 AAT AAT AAT AA
1 AAT AAT AAT AA
1124072 ATAAAAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1129090 original size:45 final size:47
Alignment explanation
Indices: 1129025--1129124 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 47
1129015 TAATGAATAA
1129025 AATAATAACAAACTAAAATGTCTTAAC-T-C-TAATTCCTAATAAAAT
1 AATAATAACAAAC-AAAATGTCTTAACTTACTTAATTCCTAATAAAAT
*
1129070 AATAATAACTAAA-AATAATGTTTTAACTTAACCTTAATTCCTAATAAAAT
1 AATAATAAC-AAACAA-AATGTCTTAACTT-A-CTTAATTCCTAATAAAAT
1129120 AATAA
1 AATAA
1129125 ATCTAATCCT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
44 2 0.04
45 19 0.40
46 4 0.09
49 1 0.02
50 21 0.45
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (47 bp):
AATAATAACAAACAAAATGTCTTAACTTACTTAATTCCTAATAAAAT
Found at i:1133249 original size:59 final size:59
Alignment explanation
Indices: 1133129--1133241 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
1133119 AAATAGTGGA
*
1133129 TAAGTATCCTATCGAACCCTCCTAGTCGCAATGAAAAGACAAACTCGATAATATAACTC
1 TAAGTATCCTATCGAACCCTCCTAGTCGCAACGAAAAGACAAACTCGATAATATAACTC
*
1133188 TAAGTATCCTATCGAACCCTCCTAGTCGTAACGAAAATGA-AAACTCGATAATAT
1 TAAGTATCCTATCGAACCCTCCTAGTCGCAACGAAAA-GACAAACTCGATAATAT
1133242 GGCTCTAACC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
59 49 0.96
60 2 0.04
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (59 bp):
TAAGTATCCTATCGAACCCTCCTAGTCGCAACGAAAAGACAAACTCGATAATATAACTC
Found at i:1134906 original size:65 final size:62
Alignment explanation
Indices: 1134771--1134917 Score: 163
Period size: 65 Copynumber: 2.3 Consensus size: 62
1134761 AAATAGCCAA
1134771 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCAATGCATGAT
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCAATGCATGAT
* * **
1134835 ATGTGCATCGATGCATGAAATGCATTTGATG-TTCAATTTAAT-TCATGGTGCATCAATGCATGG
1 A-GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCAATGCAT-G
1134898 ATT
61 A-T
*
1134901 AGTGCATCGGTGCATCA
1 AGTGCATCGATGCATCA
1134918 CTTTGATAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 20 0.28
65 43 0.61
66 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (62 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCAATGCATGAT
Found at i:1135950 original size:21 final size:21
Alignment explanation
Indices: 1135926--1135969 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1135916 CCGGTGCCGG
1135926 AGGAGGAGCACGAGAAGAGCT
1 AGGAGGAGCACGAGAAGAGCT
* * *
1135947 AGGAGTAGCTCGTGAAGAGCT
1 AGGAGGAGCACGAGAAGAGCT
1135968 AG
1 AG
1135970 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.41, T:0.11
Consensus pattern (21 bp):
AGGAGGAGCACGAGAAGAGCT
Found at i:1137528 original size:24 final size:22
Alignment explanation
Indices: 1137501--1137603 Score: 104
Period size: 24 Copynumber: 4.6 Consensus size: 22
1137491 CATGGCCTTG
1137501 TGCATCGATGCACATTCAAGGCCA
1 TGCATCGATGCACATTCAAGG--A
* *
1137525 TGCATCGATGTACATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-A
*
1137548 TGCATC-AGTGCATC-TTCATGG-
1 TGCATCGA-TGCA-CATTCAAGGA
*
1137569 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
1137591 TGCATCGATGCAC
1 TGCATCGATGCAC
1137604 TGTTAGGTGT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.01
21 15 0.22
22 14 0.21
23 16 0.24
24 21 0.31
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:1137619 original size:20 final size:21
Alignment explanation
Indices: 1137504--1137622 Score: 75
Period size: 21 Copynumber: 5.4 Consensus size: 21
1137494 GGCCTTGTGC
*
1137504 ATCGATGCACATTCAAGGCCATGC
1 ATCGATGCACATTCAAGG---TGT
* *
1137528 ATCGATGTACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
*
1137551 ATC-AGTGCATC-TTCATGGTGT
1 ATCGA-TGCA-CATTCAAGGTGT
*
1137572 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
1137594 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
1137614 ATCGATGCA
1 ATCGATGCA
1137623 TGAAGCACAA
Statistics
Matches: 79, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
20 12 0.15
21 20 0.25
22 16 0.20
23 13 0.16
24 16 0.20
25 1 0.01
26 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:1137622 original size:42 final size:44
Alignment explanation
Indices: 1137528--1137622 Score: 117
Period size: 42 Copynumber: 2.2 Consensus size: 44
1137518 AAGGCCATGC
* *
1137528 ATCGATGTACATTCAAGGCGTGCATCAGTGCATCTTCATGGTGT
1 ATCGATGCACATTCAAGGCATGCATCAGTGCATCTTCATGGTGT
*
1137572 ATCGATGCACATTCAAGG-ATGCATC-GATGCA-CTGTTA-GGTGT
1 ATCGATGCACATTCAAGGCATGCATCAG-TGCATCT-TCATGGTGT
1137614 ATCGATGCA
1 ATCGATGCA
1137623 TGAAGCACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 17 0.37
43 12 0.26
44 17 0.37
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCATGCATCAGTGCATCTTCATGGTGT
Found at i:1143452 original size:18 final size:17
Alignment explanation
Indices: 1143398--1143446 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1143388 TTGGACCCTT
* *
1143398 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1143416 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1143434 AGTGCATTCGATG
1 AGTGCA-TCGATG
1143447 TTTCAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1143619 original size:65 final size:64
Alignment explanation
Indices: 1143417--1143627 Score: 214
Period size: 65 Copynumber: 3.3 Consensus size: 64
1143407 GTGCACTAAG
* * * *
1143417 AGTGCATCGATGCATCAAGTGCATTCGATGTTTC--AAAATCGCCAGAGTGCATCGATGTATGGT
1 AGTGCATCGATGCATCAAATGAATTCGATGTTTCATAAAAT--CCATAGTGCATCGATGCATGGT
1143480 T
64 T
* * *
1143481 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGATGCATGG-T
1 AGTGCATCGATGCATCAAATGAATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGGTT
* * ** * *
1143545 ATGTCCATCGATGCATGAAATGAATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGA
1 A-GTGCATCGATGCATCAAATGAATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-
1143609 TT
63 TT
*
1143611 AGTGCATCGGTGCATCA
1 AGTGCATCGATGCATCA
1143628 CTTTGATAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
63 3 0.02
64 52 0.42
65 61 0.50
66 2 0.02
67 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
AGTGCATCGATGCATCAAATGAATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTT
Found at i:1147229 original size:65 final size:63
Alignment explanation
Indices: 1147105--1147236 Score: 178
Period size: 65 Copynumber: 2.0 Consensus size: 63
1147095 TTTTTTAAAC
* * *
1147105 ACTCATATTTAGGTGTTTTTCCTGCTTGAGTACAATTAATACAGTTCTCCTAATGTACTACTTG
1 ACTCATATCTAGGTGTTTTT-CTGCTTGAGTACAATTAATACAGTTCCCCTAATATACTACTTG
1147169 ACTCATATCTAGGTGCTTTTT-TGCTTGAGTAAATCAATTAATACA-TTCCCCTAATATACTACT
1 ACTCATATCTAGGTG-TTTTTCTGCTTGAGT--A-CAATTAATACAGTTCCCCTAATATACTACT
1147232 TG
62 TG
1147234 ACT
1 ACT
1147237 TTCTATAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
63 9 0.15
64 14 0.23
65 27 0.44
66 11 0.18
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (63 bp):
ACTCATATCTAGGTGTTTTTCTGCTTGAGTACAATTAATACAGTTCCCCTAATATACTACTTG
Found at i:1161391 original size:6 final size:6
Alignment explanation
Indices: 1161380--1161413 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1161370 GCTCGGCTCA
1161380 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGT
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGT
1161414 AATACGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
TGGTCG
Found at i:1170432 original size:64 final size:63
Alignment explanation
Indices: 1170342--1170503 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
1170332 AATTGTTCAG
* * * * * * *
1170342 AGTGTATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAGTT
1 AGTGCATCGATACATAGGTAGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGGCAATT
* *
1170406 AGTGCATCGATACATTAGG-AGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTAATT
1 AGTGCATCGATACA-TAGGTAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATT
* * * *
1170470 TGTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 AGTGCATCGATACATAGGTAGTGCATCGATGCAC
1170504 ATGTTAAAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 4 0.05
64 71 0.86
65 8 0.10
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (63 bp):
AGTGCATCGATACATAGGTAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
Found at i:1172022 original size:23 final size:23
Alignment explanation
Indices: 1171954--1172022 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1171944 ACATTTTATA
*
1171954 TGGCACTTCAGTGCAATCCTACG
1 TGGCACTTCAGTGCAATTCTACG
* * *
1171977 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCAGTGCAATTCTACG
*
1172000 TGGCACTTCAGTGCAATTATACG
1 TGGCACTTCAGTGCAATTCTACG
1172023 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (23 bp):
TGGCACTTCAGTGCAATTCTACG
Found at i:1174693 original size:20 final size:20
Alignment explanation
Indices: 1174665--1174749 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
1174655 TTCCTAATTT
*
1174665 GCAATGCGAATACGTAAATC
1 GCAACGCGAATACGTAAATC
** *
1174685 GCAACGCGAATTTGGAAAATC
1 GCAACGCGAA-TACGTAAATC
*
1174706 GCAACGCGATTACGTAAATC
1 GCAACGCGAATACGTAAATC
1174726 GCAACGCGAATACGTAAATC
1 GCAACGCGAATACGTAAATC
1174746 GCAA
1 GCAA
1174750 AGAGATTCTG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 39 0.71
21 16 0.29
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (20 bp):
GCAACGCGAATACGTAAATC
Found at i:1175638 original size:24 final size:24
Alignment explanation
Indices: 1175611--1175664 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1175601 GTATTCAAAA
1175611 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1175635 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1175659 TTTGAT
1 TTTGAT
1175665 GATTTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1178228 original size:33 final size:32
Alignment explanation
Indices: 1178184--1178271 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 32
1178174 ATGTCTATCA
* *
1178184 CAACGCAGAAATAAAAATCGCAACGAGAGAATCG
1 CAACGC-GAAAT-AAAATCGCAACGACAAAATCG
*
1178218 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAACGCGAAAT-AAAATCGCAACGACAAAATCG
1178251 CAACGCGAAACTAAAATCGCA
1 CAACGCGAAA-TAAAATCGCA
1178272 GCGCGGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 42 0.88
34 6 0.12
ACGTcount: A:0.49, C:0.23, G:0.18, T:0.10
Consensus pattern (32 bp):
CAACGCGAAATAAAATCGCAACGACAAAATCG
Found at i:1178281 original size:53 final size:53
Alignment explanation
Indices: 1178224--1178427 Score: 141
Period size: 53 Copynumber: 3.9 Consensus size: 53
1178214 ATCGCAATGC
*
1178224 GAAATGAAAATCGCAACGACAAAATCGCAACGCGAAACT-AAAATCGCAGCGCG
1 GAAATGAAAATCGCAACGACAAAATCGCAACACGAAA-TGAAAATCGCAGCGCG
* * * * *
1178277 GAAATGAAAATCGCGACGAGAGAATCGCAATACGAAATGAAAATCGCAACGAC-
1 GAAATGAAAATCGCAACGACAAAATCGCAACACGAAATGAAAATCGCAGCG-CG
* * * * ** * **
1178330 AAAATCG-CAA-CGCAA-AACTAAAATCGCAACGCGGAAATGACTATCACAATGC-
1 GAAAT-GAAAATCGCAACGAC-AAAATCGCAACAC-GAAATGAAAATCGCAGCGCG
* * * **
1178382 GAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCG
1 GAAATGAAAATCGCAACGACAAAATCGCAACACGAAATGAAAATCG
1178428 TAAAGAGGGA
Statistics
Matches: 115, Mismatches: 28, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
51 2 0.02
52 32 0.28
53 78 0.68
54 3 0.03
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (53 bp):
GAAATGAAAATCGCAACGACAAAATCGCAACACGAAATGAAAATCGCAGCGCG
Found at i:1178286 original size:20 final size:19
Alignment explanation
Indices: 1178213--1178362 Score: 66
Period size: 19 Copynumber: 8.6 Consensus size: 19
1178203 GCAACGAGAG
*
1178213 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
1178232 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
1178246 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
1178265 AATCGCAGCGCGGAAA-TGAA
1 AATCGCAACGC-GAAACT-AA
* * *
1178285 AATCGCGA--CG--A-GAG
1 AATCGCAACGCGAAACTAA
**
1178299 AATCGCAATACGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
1178318 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
1178332 AATCGCAACGCAAAACTAA
1 AATCGCAACGCGAAACTAA
1178351 AATCGCAACGCG
1 AATCGCAACGCG
1178363 GAAATGACTA
Statistics
Matches: 102, Mismatches: 10, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
14 28 0.27
15 3 0.03
16 5 0.05
17 5 0.05
18 6 0.06
19 43 0.42
20 12 0.12
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Done.