Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 6 of 18
Found at i:2310744 original size:5 final size:5
Alignment explanation
Indices: 2310734--2310763 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2310724 TAGCAGGCTC
2310734 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
2310764 CATTTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:2312782 original size:20 final size:20
Alignment explanation
Indices: 2312757--2312794 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2312747 GATAGATAAA
*
2312757 GAATTATTTAAAACATTTAT
1 GAATTATTTAAAAAATTTAT
2312777 GAATTATTTAAAAAATTT
1 GAATTATTTAAAAAATTT
2312795 TAAATAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
GAATTATTTAAAAAATTTAT
Found at i:2317674 original size:30 final size:29
Alignment explanation
Indices: 2317602--2317680 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 29
2317592 TAACCAAAAG
2317602 ATTAAATTAATATTAT-ATATATATTATT
1 ATTAAATTAATATTATAATATATATTATT
*
2317630 TTTAAATT--TA-TATAATATATATTATT
1 ATTAAATTAATATTATAATATATATTATT
* *
2317656 ATTAATTTTAATATTATAATTTATA
1 ATTAA-ATTAATATTATAATATATA
2317681 AAAAAATTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
25 3 0.07
26 18 0.43
27 2 0.05
28 7 0.17
29 2 0.05
30 10 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTAAATTAATATTATAATATATATTATT
Found at i:2317748 original size:25 final size:26
Alignment explanation
Indices: 2317720--2317774 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 26
2317710 ATTGAATTAA
2317720 TTTTATGTTTAATTGA-TTTGATTTT
1 TTTTATGTTTAATTGATTTTGATTTT
*
2317745 TTTTATGTTTGATTGATTTTGATTTT
1 TTTTATGTTTAATTGATTTTGATTTT
2317771 TTTT
1 TTTT
2317775 TAAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (26 bp):
TTTTATGTTTAATTGATTTTGATTTT
Found at i:2322217 original size:2 final size:2
Alignment explanation
Indices: 2322210--2322236 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2322200 GAAATGAAAT
2322210 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2322237 CTTTCTCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2323448 original size:19 final size:18
Alignment explanation
Indices: 2323420--2323484 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
2323410 ACATGTGAAT
*
2323420 AAATTGAATAGAAATAAAA
1 AAATTAAATA-AAATAAAA
*
2323439 AAATTAAATATAAATATAA
1 AAATTAAATA-AAATAAAA
* * *
2323458 AAGTTAATATAAATTAAAC
1 AAATTAA-ATAAAATAAAA
2323477 AAATTAAA
1 AAATTAAA
2323485 GTTAAGTGAG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 1 0.03
19 33 0.89
20 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATTAAATAAAATAAAA
Found at i:2323466 original size:18 final size:19
Alignment explanation
Indices: 2323420--2323475 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
2323410 ACATGTGAAT
* * *
2323420 AAATTGAATAGAAATAAAA
1 AAATTAAATATAAATATAA
2323439 AAATTAAATATAAATATAA
1 AAATTAAATATAAATATAA
*
2323458 AAGTT-AATATAAAT-TAA
1 AAATTAAATATAAATATAA
2323475 A
1 A
2323476 CAAATTAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 4 0.12
18 9 0.27
19 20 0.61
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATTAAATATAAATATAA
Found at i:2325795 original size:55 final size:56
Alignment explanation
Indices: 2325729--2325842 Score: 185
Period size: 55 Copynumber: 2.1 Consensus size: 56
2325719 AGGTGGCTTC
* *
2325729 AATATTTCTAATGCCTAACTCCTATCATTGTAATTTCTTCGTCTCCCTCATTACTT
1 AATATTTCTAATGCCTAAATCCTATCATTGTAATTTCTTCATCTCCCTCATTACTT
* *
2325785 AATA-TTCTAATGCCTAAATCTTATCATTGTAATTTCTTCATCTCCCTCATTGCTT
1 AATATTTCTAATGCCTAAATCCTATCATTGTAATTTCTTCATCTCCCTCATTACTT
2325840 AAT
1 AAT
2325843 TGGTTTTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
55 50 0.93
56 4 0.07
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.45
Consensus pattern (56 bp):
AATATTTCTAATGCCTAAATCCTATCATTGTAATTTCTTCATCTCCCTCATTACTT
Found at i:2331192 original size:9 final size:9
Alignment explanation
Indices: 2331178--2331203 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2331168 AAAGCCTAGG
2331178 ATTGTGGCA
1 ATTGTGGCA
2331187 ATTGTGGCA
1 ATTGTGGCA
2331196 ATTGTGGC
1 ATTGTGGC
2331204 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.35, T:0.35
Consensus pattern (9 bp):
ATTGTGGCA
Found at i:2352343 original size:81 final size:81
Alignment explanation
Indices: 2352255--2352443 Score: 270
Period size: 81 Copynumber: 2.3 Consensus size: 81
2352245 TGAACTAATT
*
2352255 AAAATTTAATTGTTGATCATATAATTTGTCTCTAAATAAATCAAGATAATTTAGAAATAACATTA
1 AAAATTTAATTGTTGATCATATAATTTGTCTATAAATAAATCAAGATAATTTAGAAATAACATTA
2352320 ATATTTTTGACCAATC
66 ATATTTTTGACCAATC
* * * * * *
2352336 AAAATTTAGTTGTTGGTCATATAATTTGTCTATAATTAAATCAAGATAATTTAGAGATAATATTC
1 AAAATTTAATTGTTGATCATATAATTTGTCTATAAATAAATCAAGATAATTTAGAAATAACATTA
* *
2352401 TTATTTTTGATCAATC
66 ATATTTTTGACCAATC
* * *
2352417 AAAATTTAATTATTGCTCATCTAATTT
1 AAAATTTAATTGTTGATCATATAATTT
2352444 ATCTTTAATA
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 95 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (81 bp):
AAAATTTAATTGTTGATCATATAATTTGTCTATAAATAAATCAAGATAATTTAGAAATAACATTA
ATATTTTTGACCAATC
Found at i:2352895 original size:29 final size:29
Alignment explanation
Indices: 2352841--2352896 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2352831 AGCAAGCGAC
* * *
2352841 AACAAAGTTCGTGATTAAGATTAAGTGGA
1 AACAAAGTTCGTAATAAAGATCAAGTGGA
2352870 AACAAAGTTCGTAATCAAAG-TCAAGTG
1 AACAAAGTTCGTAAT-AAAGATCAAGTG
2352897 ATAGTGAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (29 bp):
AACAAAGTTCGTAATAAAGATCAAGTGGA
Found at i:2353092 original size:179 final size:178
Alignment explanation
Indices: 2352839--2353186 Score: 534
Period size: 179 Copynumber: 1.9 Consensus size: 178
2352829 TGAGCAAGCG
* * * * * *
2352839 ACAACAAAGTTCGTGATTAAGATTAAGTGGAAACAAAGTTCGTAATCAAAGTCAAGTGATAGTGA
1 ACAACAAAGTTCATGATTAAGATCAAGCGGAAACAAAGTTCATAATCAAAGTCAAGCGACAGTGA
*
2352904 AGTTCGTGATCTAGATATCAAGCGAAGTTCGTGATCAAGATTAAGTTGTGAAGACTCTTGAAACA
66 AGTTCGTGATCTAGATATCAAGCGAAGTTCATGATCAAGATTAAGTTGTGAAGACTCTTGAAACA
*
2352969 AAGATATCAAGTGTTTATGATCAATATTAAGTCGTTAAGGTCCTTGCA
131 AAGATATCAAGTGTTTATGATCAAGATTAAGTCGTTAAGGTCCTTGCA
** ** *
2353017 ACAACAAAGTTCATGATTAAGATCAAGCGGCAATGAATTTTCATAATCAAGGTCAAGCGACAGTG
1 ACAACAAAGTTCATGATTAAGATCAAGCGG-AAACAAAGTTCATAATCAAAGTCAAGCGACAGTG
* *
2353082 AAGTTCGTGATCTAGATATTAAGCGAAGTTCATGATCAAGATTAAGTTGTGAAGACTCTTGAAAT
65 AAGTTCGTGATCTAGATATCAAGCGAAGTTCATGATCAAGATTAAGTTGTGAAGACTCTTGAAAC
* *
2353147 GAAGATATCAAGTGTTTGTGATCAAGATTAAGTCGTTAAG
130 AAAGATATCAAGTGTTTATGATCAAGATTAAGTCGTTAAG
2353187 AACCTAGAAA
Statistics
Matches: 152, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
178 27 0.18
179 125 0.82
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (178 bp):
ACAACAAAGTTCATGATTAAGATCAAGCGGAAACAAAGTTCATAATCAAAGTCAAGCGACAGTGA
AGTTCGTGATCTAGATATCAAGCGAAGTTCATGATCAAGATTAAGTTGTGAAGACTCTTGAAACA
AAGATATCAAGTGTTTATGATCAAGATTAAGTCGTTAAGGTCCTTGCA
Found at i:2355019 original size:79 final size:80
Alignment explanation
Indices: 2354929--2355181 Score: 313
Period size: 78 Copynumber: 3.2 Consensus size: 80
2354919 AATTTAATTT
* * * * *
2354929 TTATCTCTAAATTAGCAT-AATTA-TTAGAGATAAATTAGATGACCAATAATTAAATTTTGATTG
1 TTATCTCTAAATTATCTTGATTTATTTAGAGAAAAATTA-ATGACCAATAATTAAATTTTGAGTG
*
2354992 GTCAAAAATATGAATA
65 ATCAAAAATATGAATA
* *
2355008 TTATCTCTAAATTATCTTGATTTATTTA-AAAAAAATT-ATGACCAATAACTAAATTTTGAGTGA
1 TTATCTCTAAATTATCTTGATTTATTTAGAGAAAAATTAATGACCAATAATTAAATTTTGAGTGA
2355071 TCAAAAATATGAATA
66 TCAAAAATATGAATA
*
2355086 TTATCTCTAAATTATCTTGATTTATTTAGAGACAAATTATATGACCAATAATTAAATTTT-AGTT
1 TTATCTCTAAATTATCTTGATTTATTTAGAGAAAAATTA-ATGACCAATAATTAAATTTTGAG-T
* * *
2355150 GATC--CAATTTAAATA
64 GATCAAAAATATGAATA
*
2355165 TTATCTTTAAATTATCT
1 TTATCTCTAAATTATCT
2355182 CAAGGGATAA
Statistics
Matches: 153, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
78 66 0.43
79 47 0.31
80 13 0.08
81 27 0.18
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (80 bp):
TTATCTCTAAATTATCTTGATTTATTTAGAGAAAAATTAATGACCAATAATTAAATTTTGAGTGA
TCAAAAATATGAATA
Found at i:2356223 original size:72 final size:72
Alignment explanation
Indices: 2356085--2356241 Score: 170
Period size: 72 Copynumber: 2.2 Consensus size: 72
2356075 TTTTAATAAT
* * * * * * *
2356085 CACATTCACATCTGATGTGAGATGGGGTATCACAATCTCATTTACTCAAATCTTTAATGTCCTCA
1 CACAATCACATCTAATGTGAGATGGGGAATCACAATCCCATCTACTCAAAACCTTAATGTCCTCA
*
2356150 TTAAGGC
66 TTAAAGC
* * * * **
2356157 CACAATCATATCTAATGTGGGATGGGGAATCGCAATCCCATCTACTCAAAACCTTGATGTTGTCA
1 CACAATCACATCTAATGTGAGATGGGGAATCACAATCCCATCTACTCAAAACCTTAATGTCCTCA
2356222 TTAAAGC
66 TTAAAGC
*
2356229 CACACAACACATC
1 CACA-ATCACATC
2356242 ACAATCACCA
Statistics
Matches: 68, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
72 62 0.91
73 6 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (72 bp):
CACAATCACATCTAATGTGAGATGGGGAATCACAATCCCATCTACTCAAAACCTTAATGTCCTCA
TTAAAGC
Found at i:2358444 original size:71 final size:72
Alignment explanation
Indices: 2358355--2358487 Score: 180
Period size: 71 Copynumber: 1.9 Consensus size: 72
2358345 AAGTGATGAA
*
2358355 CTTGAAGAATATCAATACACTTTAAACAAAATGTAAAATTCC-CTAAGTTGAGTTGAAAGTATGG
1 CTTGAAGAATATCAATACACTTTAAACAAAATGTAAAATTCCTC-AAGTTGAGCTGAAAGTATGG
2358419 ACATTGAG
65 ACATTGAG
* * * * **
2358427 CTTGAA-AATATCGATACATTTTAAACAGAATTTAAAATTTTTCAAGTTGAGCTGAAAGTAT
1 CTTGAAGAATATCAATACACTTTAAACAAAATGTAAAATTCCTCAAGTTGAGCTGAAAGTAT
2358488 TGGTGTTTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
71 46 0.87
72 7 0.13
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (72 bp):
CTTGAAGAATATCAATACACTTTAAACAAAATGTAAAATTCCTCAAGTTGAGCTGAAAGTATGGA
CATTGAG
Found at i:2359222 original size:21 final size:21
Alignment explanation
Indices: 2359175--2359240 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2359165 AAATTGCTTC
* *
2359175 AATGATCTTTGAACTTATTTG
1 AATGATCTTTGAACTTGTTTA
* *
2359196 AGTGATCCTTGAACTTGTTTA
1 AATGATCTTTGAACTTGTTTA
* * *
2359217 AATGATTTTTAAAGTTGTTTA
1 AATGATCTTTGAACTTGTTTA
2359238 AAT
1 AAT
2359241 ATAATTTGAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (21 bp):
AATGATCTTTGAACTTGTTTA
Found at i:2359391 original size:22 final size:21
Alignment explanation
Indices: 2359355--2359410 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
2359345 TTGATCTTAT
*
2359355 TTGAATAATTTTTGAAGTTGC
1 TTGAATAGTTTTTGAAGTTGC
* *
2359376 TTGAATGAGTTTTTGAATTTGT
1 TTGAAT-AGTTTTTGAAGTTGC
2359398 TTGAATAGTTTTT
1 TTGAATAGTTTTT
2359411 AAACATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGAATAGTTTTTGAAGTTGC
Found at i:2363201 original size:15 final size:15
Alignment explanation
Indices: 2363183--2363211 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2363173 TCAAAATTAT
2363183 AACTTATAAAAAAAG
1 AACTTATAAAAAAAG
2363198 AACTTATAAAAAAA
1 AACTTATAAAAAAA
2363212 AATTTACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (15 bp):
AACTTATAAAAAAAG
Found at i:2366066 original size:1 final size:1
Alignment explanation
Indices: 2366060--2366093 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
2366050 AGAAAGAAGA
*
2366060 GGGGGGGGGGGGGGGTGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2366094 CCGCGTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:2375823 original size:18 final size:18
Alignment explanation
Indices: 2375780--2375816 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2375770 ATTAATATAA
2375780 TATTTAAAAAATTTCTAAT
1 TATTT-AAAAATTTCTAAT
2375799 TATTTAAAAATTT-TAAT
1 TATTTAAAAATTTCTAAT
2375816 T
1 T
2375817 TTTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTAAAAATTTCTAAT
Found at i:2375930 original size:25 final size:25
Alignment explanation
Indices: 2375896--2375960 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
2375886 ATAAAGTGAT
*
2375896 ATTTTAATTAATAATAA-TTAATTA
1 ATTTAAATTAATAATAATTTAATTA
* *
2375920 ATTATAAATT-ATAAAAATTTATTTA
1 ATT-TAAATTAATAATAATTTAATTA
* *
2375945 ATTTAAAATAAAAATA
1 ATTTAAATTAATAATA
2375961 TAAAACTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 14 0.44
25 18 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAAATTAATAATAATTTAATTA
Found at i:2377620 original size:17 final size:17
Alignment explanation
Indices: 2377590--2377623 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2377580 TATTTAATCG
**
2377590 ATTTGATTTTTTTTAAT
1 ATTTGATTAATTTTAAT
2377607 ATTTGATTAATTTTAAT
1 ATTTGATTAATTTTAAT
2377624 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
ATTTGATTAATTTTAAT
Found at i:2378091 original size:13 final size:12
Alignment explanation
Indices: 2378073--2378101 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2378063 TTGCACACGG
2378073 TTTTTTTTTTAA
1 TTTTTTTTTTAA
2378085 TTTTTTTTTTAA
1 TTTTTTTTTTAA
2378097 TTTTT
1 TTTTT
2378102 CTCATAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:2396394 original size:2 final size:2
Alignment explanation
Indices: 2396387--2396418 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2396377 GTCGACATAC
2396387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2396419 GCCAAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2401631 original size:33 final size:32
Alignment explanation
Indices: 2401591--2401653 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
2401581 CTGAATACTT
* *
2401591 AATTTAAAAATGGTCTAAATCTGAAATAATTGG
1 AATTTAAAAATGATCTAAATC-CAAATAATTGG
*
2401624 AATTTAAAAATTATCTAAATCCAAATAATT
1 AATTTAAAAATGATCTAAATCCAAATAATT
2401654 CATCCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.30
33 19 0.70
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (32 bp):
AATTTAAAAATGATCTAAATCCAAATAATTGG
Found at i:2408656 original size:27 final size:27
Alignment explanation
Indices: 2408599--2408666 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
2408589 AACAACAAAC
* ***
2408599 ATATTTGTTT-GTTTTCAAGAAACTTT
1 ATATTTGTTTCTTTTTCAAGAAAAAAT
*
2408625 TTATTTGTTTCTTTTTCAAGAAAAAAT
1 ATATTTGTTTCTTTTTCAAGAAAAAAT
2408652 ATATTTGTTTCTTTT
1 ATATTTGTTTCTTTT
2408667 CTTCTAATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 9 0.26
27 26 0.74
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.57
Consensus pattern (27 bp):
ATATTTGTTTCTTTTTCAAGAAAAAAT
Found at i:2409184 original size:29 final size:28
Alignment explanation
Indices: 2409145--2409200 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
2409135 NNNNNNNNNN
*
2409145 TCTTGTCTAAATTAAGACTAAACATGTTT
1 TCTTGTCTAAATTAAAAC-AAACATGTTT
2409174 TCTTGTCTAAATTAAAACAAACATGTT
1 TCTTGTCTAAATTAAAACAAACATGTT
2409201 AAAGTTACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAAACAAACATGTTT
Found at i:2415369 original size:34 final size:34
Alignment explanation
Indices: 2415296--2415382 Score: 88
Period size: 34 Copynumber: 2.6 Consensus size: 34
2415286 TTTTAAAGTC
* *
2415296 ATATATTTTATTTTCA-TTTCTTATTATAATCTT
1 ATATATTTTATTTTTATTTTCTTAATATAATCTT
* *
2415329 ACATATTTTATTTTTATTTTTTTAATATAAAT-TT
1 ATATATTTTATTTTTATTTTCTTAATAT-AATCTT
* * *
2415363 TTATATTATATATTTATTTT
1 ATATATTTTATTTTTATTTT
2415383 AATTTTTTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
33 14 0.32
34 27 0.61
35 3 0.07
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (34 bp):
ATATATTTTATTTTTATTTTCTTAATATAATCTT
Found at i:2415411 original size:28 final size:29
Alignment explanation
Indices: 2415364--2415419 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
2415354 TATAAATTTT
*
2415364 TATATTATATATTTATTTTAATTTTTTACC
1 TATATTATATA-TAATTTTAATTTTTTACC
2415394 TATATTATATA-AATTTTAATTTTTTA
1 TATATTATATATAATTTTAATTTTTTA
2415420 TATTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.56
30 11 0.44
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATTATATATAATTTTAATTTTTTACC
Found at i:2415448 original size:47 final size:45
Alignment explanation
Indices: 2415332--2415448 Score: 105
Period size: 47 Copynumber: 2.5 Consensus size: 45
2415322 TAATCTTACA
* *
2415332 TATTTTATTTTTATTT-T-TTTAATATAAATTTTTATATTATATATT
1 TATTTTA-TTTTATTTATAATT-ATATAAATTTTAATATTATATATT
* * *
2415377 TATTTTAATTT-TTTACCTATATTATATAAATTTTAATTTTTTATATTT
1 TATTTTATTTTATTTA--TA-ATTATATAAATTTTAATATTATATA-TT
2415425 TATTTTATTTTAATTTATAATTAT
1 TATTTTATTTT-ATTTATAATTAT
2415449 TAGATTATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
43 3 0.05
44 3 0.05
45 7 0.12
46 1 0.02
47 24 0.41
48 16 0.28
50 4 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (45 bp):
TATTTTATTTTATTTATAATTATATAAATTTTAATATTATATATT
Found at i:2415463 original size:53 final size:52
Alignment explanation
Indices: 2415360--2415468 Score: 125
Period size: 53 Copynumber: 2.1 Consensus size: 52
2415350 TTAATATAAA
*
2415360 TTTTTATATTATATATTTATTTTAATTTTTTACCTATATTATATAAATTTTAAT
1 TTTTTATATTATATATTTATTTTAATTTTTTACCTAGATTATAT-AATTTT-AT
* *
2415414 TTTTTATATTTTAT-TTTATTTTAATTTATAATTA-TTAGATTATAT-ATTTTAT
1 TTTTTATATTATATATTTATTTTAATTT-T--TTACCTAGATTATATAATTTTAT
2415466 TTT
1 TTT
2415469 AATTATAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
52 5 0.10
53 18 0.37
54 14 0.29
55 9 0.18
56 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (52 bp):
TTTTTATATTATATATTTATTTTAATTTTTTACCTAGATTATATAATTTTAT
Found at i:2415473 original size:26 final size:28
Alignment explanation
Indices: 2415430--2415483 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
2415420 TATTTTATTT
*
2415430 TATTTTAATTTATAATTATTAGATTATA
1 TATTTTAATTTATAATTATAAGATTATA
*
2415458 TATTTT-ATTT-TAATTATAATATTATA
1 TATTTTAATTTATAATTATAAGATTATA
2415484 AAATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.58
27 4 0.17
28 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
TATTTTAATTTATAATTATAAGATTATA
Found at i:2424190 original size:2 final size:2
Alignment explanation
Indices: 2424183--2424228 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2424173 AAGCAAAGTT
2424183 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2424225 TA TA
1 TA TA
2424229 AATCCTTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2428795 original size:2 final size:2
Alignment explanation
Indices: 2428788--2428812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2428778 TTATTGGGAA
2428788 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2428813 TTTAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2431106 original size:11 final size:11
Alignment explanation
Indices: 2431092--2431129 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
2431082 TTTCAAAATT
*
2431092 AAATTTCTTAA
1 AAATGTCTTAA
2431103 AAATGTCTTAA
1 AAATGTCTTAA
2431114 AAATGTCTTAA
1 AAATGTCTTAA
2431125 AAATG
1 AAATG
2431130 AGGGGAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (11 bp):
AAATGTCTTAA
Found at i:2433325 original size:11 final size:11
Alignment explanation
Indices: 2433309--2433359 Score: 63
Period size: 10 Copynumber: 4.8 Consensus size: 11
2433299 AGTAATTTTG
2433309 GAAAAAAGAAA
1 GAAAAAAGAAA
2433320 GAAAAAA-AAA
1 GAAAAAAGAAA
2433330 GGAAAAAAGAAA
1 -GAAAAAAGAAA
*
2433342 -AAAAAAGAGA
1 GAAAAAAGAAA
2433352 -AAAAAAGA
1 GAAAAAAGA
2433360 TTTTGTGATC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 20 0.54
11 14 0.38
12 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:2433340 original size:18 final size:19
Alignment explanation
Indices: 2433317--2433356 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
2433307 TGGAAAAAAG
2433317 AAAGAAAAAAAAAG-GAAA
1 AAAGAAAAAAAAAGAGAAA
2433335 AAAGAAAAAAAAAGAGAAA
1 AAAGAAAAAAAAAGAGAAA
2433354 AAA
1 AAA
2433357 AGATTTTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAAAAAGAGAAA
Found at i:2433846 original size:10 final size:10
Alignment explanation
Indices: 2433831--2433865 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
2433821 GGAGGAAATT
2433831 AAAAAAAAGA
1 AAAAAAAAGA
2433841 AAAAAAAAGA
1 AAAAAAAAGA
2433851 AAAGAAACAAGA
1 AAA-AAA-AAGA
2433863 AAA
1 AAA
2433866 TTGAATGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 3 0.13
12 7 0.30
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:2441437 original size:216 final size:217
Alignment explanation
Indices: 2441007--2441437 Score: 693
Period size: 216 Copynumber: 2.0 Consensus size: 217
2440997 TTGATTAGTT
* * *
2441007 ATCCTACATTACACAATCTTATGGAGAGGAAAAGAATTGGATCATCATACATGGATAAGATTACA
1 ATCCTACATTACACAACCTTATGGAGAGGAAAAGAATTGGATCATCATACACGGATAAGACTACA
* *
2441072 TAAAACATAATGAGAGCATAATGGTTATTAATGCACTGAGAAGTAAGATGATATAAAGACAATTT
66 TAAAACATAATGAGAGCAGAATGGTTACTAATGCACT-AGAAGTAAGATGATATAAAGACAATTT
*
2441137 ACTCGTTATCTTGTTACCTGCTCCATCCATAATTGTATACACCAAATGCAACTTTGATGAAGTTT
130 ACTCATTATCTTGTTACCTGCTCCATCCATAATTGTATACACCAAATGCAACTTTGATGAAGTTT
*
2441202 CATGCCTATGTGTTTGAATTAAG
195 CATGCCCATGTGTTTGAATTAAG
* *
2441225 ATCCTACATTACACAACCTTATGGGGAGGAAAAGAATTGGATCATCCTACACGGATAAGACTACA
1 ATCCTACATTACACAACCTTATGGAGAGGAAAAGAATTGGATCATCATACACGGATAAGACTACA
* * *
2441290 TAAAACATAATGAGAGCAGAATGGTTACTGATGCACT-GAAGTAAGATGATATAAAGACAGTTTG
66 TAAAACATAATGAGAGCAGAATGGTTACTAATGCACTAGAAGTAAGATGATATAAAGACAATTTA
* * ** *
2441354 CTCATTATCTTTTTACTTTTTCCATCCTTAATTGTATACACCAAATGCAACTTTGATGAAGTTTC
131 CTCATTATCTTGTTACCTGCTCCATCCATAATTGTATACACCAAATGCAACTTTGATGAAGTTTC
2441419 ATGCCCATGTGTTTGAATT
196 ATGCCCATGTGTTTGAATT
2441438 TCTCAGAGTA
Statistics
Matches: 196, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
216 102 0.52
218 94 0.48
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (217 bp):
ATCCTACATTACACAACCTTATGGAGAGGAAAAGAATTGGATCATCATACACGGATAAGACTACA
TAAAACATAATGAGAGCAGAATGGTTACTAATGCACTAGAAGTAAGATGATATAAAGACAATTTA
CTCATTATCTTGTTACCTGCTCCATCCATAATTGTATACACCAAATGCAACTTTGATGAAGTTTC
ATGCCCATGTGTTTGAATTAAG
Found at i:2445583 original size:28 final size:28
Alignment explanation
Indices: 2445542--2445628 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 28
2445532 TCTCATAATT
2445542 TTATAT-AATATAATTAATTATATTAAATA
1 TTATATAAAT-TAA-TAATTATATTAAATA
*
2445571 -TATATAAATTAATAATTA-ATAAAATA
1 TTATATAAATTAATAATTATATTAAATA
* *
2445597 TTTTTTAAATTAA-ATATT-TATTAAATAA
1 TTATATAAATTAATA-ATTATATTAAAT-A
2445625 TTAT
1 TTAT
2445629 TTTCTCTCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
26 8 0.17
27 25 0.52
28 12 0.25
29 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTATATAAATTAATAATTATATTAAATA
Found at i:2445597 original size:24 final size:28
Alignment explanation
Indices: 2445543--2445597 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2445533 CTCATAATTT
2445543 TATATAATATAATTAATTATATTAAATA
1 TATATAATATAATTAATTATATTAAATA
*
2445571 TATATAA-ATTAA-TAATTA-ATAAAATA
1 TATATAATA-TAATTAATTATATTAAATA
2445597 T
1 T
2445598 TTTTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 7 0.28
28 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TATATAATATAATTAATTATATTAAATA
Found at i:2445611 original size:16 final size:15
Alignment explanation
Indices: 2445592--2445631 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2445582 ATAATTAATA
2445592 AAATATTTTTTAAATT
1 AAATATTTTTTAAA-T
*
2445608 AAATATTTATTAAAT
1 AAATATTTTTTAAAT
*
2445623 AATTATTTT
1 AAATATTTT
2445632 CTCTCACTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATATTTTTTAAAT
Found at i:2447847 original size:354 final size:355
Alignment explanation
Indices: 2447198--2447909 Score: 1074
Period size: 354 Copynumber: 2.0 Consensus size: 355
2447188 CCCTATCTAT
*
2447198 ATAGAATTTATAAAATAAAAGATAATGTTAAGGAATTTGATTTGGATAGATTAAATTCAAATTTT
1 ATAGAATTTATAAAATAAAAGATAATGTTAAGGAATTTGATTTGGATAGATTAAATTCAAAGTTT
*
2447263 AATCAAATCTACTCTACATCTAAATCTAGATACACATAATCAAATATAAGAATTCAAATCAAATT
66 AATCAAATCTACTCTACATCCAAATCTAGATACACATAATCAAATATAAGAATTCAAATCAAATT
* *
2447328 ACACTCATATATCTGGTCTGTTAGGCTATTTGATTTGTCTCGGTTGCTTAGCTTCGTCTAAACTC
131 ACACTCATATATCTGGTCTGTTAGGCTATTTGATTTGCCTCAGTTGCTTAGCTTCGTCTAAACTC
* * *
2447393 TTGAACTGTGACACGATGGACATTTTCATATATATTCATAACATTTCTCCTTAAATGTCTATTAC
196 TTGAACTGTGACACAATGGACATTATCATATATATTCATAACATTCCTCCTTAAATGTCTATTAC
* * *
2447458 ATTAAGAATATATCTTGTTAAAATCTTATTATGAAAAAACCTTA-CAA-AAAAAAATTTGAGTGA
261 ATTAAGAATATATCTTATTAAAATCTTACTATGAAAAAACCTTATCAAGAAAAAAATCTGAGTGA
*
2447521 AGGCAAAAGAGTATATAATATTTTTTAAGA
326 AGGAAAAAGAGTATATAATATTTTTTAAGA
* * *
2447551 ATAGAATTTATAAGATAAAAGATAATGTTAAGGCATTTGATTTGGATAGATTAAATTTCGAAGTT
1 ATAGAATTTATAAAATAAAAGATAATGTTAAGGAATTTGATTTGGATAGATTAAA-TTCAAAGTT
*** * * * *
2447616 TAATTTGATTTACTCTACATCCAAATCTAGATATACATAATCAAATATAAGAGTTTAAATCAAAT
65 TAATCAAATCTACTCTACATCCAAATCTAGATACACATAATCAAATATAAGAATTCAAATCAAAT
* * *
2447681 TACACTCCTATATCTGGTCTGTTAGGCTATTTGGTTTGCCTCAGTTGCTT-GACTTGGTCTAAAC
130 TACACTCATATATCTGGTCTGTTAGGCTATTTGATTTGCCTCAGTTGCTTAG-CTTCGTCTAAAC
* * *
2447745 TCTTAGATC-GTGACATAATGGACATTCAT-ATATATATTCATAACATTCCTCTTTAAATGTCTA
194 TCTT-GAACTGTGACACAATGGACATT-ATCATATATATTCATAACATTCCTCCTTAAATGTCTA
** * *
2447808 TTATGTTAAGAATATATCTTATTAAAATCTTACTATGAAAAAACCTTATGAAGAAATAAATCTGA
257 TTACATTAAGAATATATCTTATTAAAATCTTACTATGAAAAAACCTTATCAAGAAAAAAATCTGA
2447873 GTGAAGGAAAAAGAGTATATAATATTTTTTAAGA
322 GTGAAGGAAAAAGAGTATATAATATTTTTTAAGA
2447907 ATA
1 ATA
2447910 TGTTTTTTAT
Statistics
Matches: 322, Mismatches: 31, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
353 54 0.17
354 216 0.67
355 6 0.02
356 46 0.14
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (355 bp):
ATAGAATTTATAAAATAAAAGATAATGTTAAGGAATTTGATTTGGATAGATTAAATTCAAAGTTT
AATCAAATCTACTCTACATCCAAATCTAGATACACATAATCAAATATAAGAATTCAAATCAAATT
ACACTCATATATCTGGTCTGTTAGGCTATTTGATTTGCCTCAGTTGCTTAGCTTCGTCTAAACTC
TTGAACTGTGACACAATGGACATTATCATATATATTCATAACATTCCTCCTTAAATGTCTATTAC
ATTAAGAATATATCTTATTAAAATCTTACTATGAAAAAACCTTATCAAGAAAAAAATCTGAGTGA
AGGAAAAAGAGTATATAATATTTTTTAAGA
Found at i:2452493 original size:16 final size:16
Alignment explanation
Indices: 2452472--2452504 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2452462 TAACTAATAC
2452472 TCAATTTTCTTTTTAT
1 TCAATTTTCTTTTTAT
2452488 TCAATTTTCTTTTTAT
1 TCAATTTTCTTTTTAT
2452504 T
1 T
2452505 TAAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TCAATTTTCTTTTTAT
Found at i:2452510 original size:17 final size:16
Alignment explanation
Indices: 2452474--2452511 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2452464 ACTAATACTC
*
2452474 AATTTTCTTTTTATTC
1 AATTTTCTTTTTATTA
2452490 AATTTTCTTTTTATTTA
1 AATTTTCTTTTTA-TTA
2452507 AATTT
1 AATTT
2452512 ATTCAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTCTTTTTATTA
Found at i:2463661 original size:13 final size:13
Alignment explanation
Indices: 2463643--2463667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2463633 CATCCAAATA
2463643 TATATATATATAT
1 TATATATATATAT
2463656 TATATATATATA
1 TATATATATATA
2463668 AGAGAAGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATATAT
Found at i:2463678 original size:2 final size:2
Alignment explanation
Indices: 2463668--2463703 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2463658 TATATATATA
2463668 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2463704 TTATAATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2465542 original size:30 final size:31
Alignment explanation
Indices: 2465503--2465561 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
2465493 ACATTAATCA
* *
2465503 TAAGAATTTATTTGACTCAAGACAAAAGTCT
1 TAAGAATTTAATTGACTCAAAACAAAAGTCT
* *
2465534 TAAG-ATTTAATTGGCTCAAAATAAAAGT
1 TAAGAATTTAATTGACTCAAAACAAAAGT
2465562 ATAATGACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (31 bp):
TAAGAATTTAATTGACTCAAAACAAAAGTCT
Found at i:2465610 original size:19 final size:20
Alignment explanation
Indices: 2465584--2465629 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2465574 TTGAATATAA
*
2465584 TAAAAAAA-TAAAAATTTATT
1 TAAAAAAATTAAAAATAT-TT
2465604 TAAAAAAATTAAAAATATTT
1 TAAAAAAATTAAAAATATTT
2465624 TAAAAA
1 TAAAAA
2465630 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAAAAATTAAAAATATTT
Found at i:2465611 original size:21 final size:20
Alignment explanation
Indices: 2465585--2465629 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
2465575 TGAATATAAT
*
2465585 AAAAAAATAAAAATTTATTTA
1 AAAAAAATAAAAATAT-TTTA
*
2465606 AAAAAATTAAAAATATTTTA
1 AAAAAAATAAAAATATTTTA
2465626 AAAA
1 AAAA
2465630 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAAATAAAAATATTTTA
Found at i:2465641 original size:12 final size:11
Alignment explanation
Indices: 2465612--2465640 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2465602 TTTAAAAAAA
2465612 TTAAAAATATT
1 TTAAAAATATT
2465623 TTAAAAATATT
1 TTAAAAATATT
2465634 TTAAAAA
1 TTAAAAA
2465641 AAGCTTCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:2466731 original size:27 final size:27
Alignment explanation
Indices: 2466699--2466752 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2466689 TTTTTTTTTT
*
2466699 GAAAAAAGAAAGTAAAAAAAAAAAAGAG
1 GAAAAGAGAAAG-AAAAAAAAAAAAGAG
* *
2466727 GAAAAGAGAGAGAAAAAAAAAGAAGA
1 GAAAAGAGAAAGAAAAAAAAAAAAGA
2466753 AATAAAACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (27 bp):
GAAAAGAGAAAGAAAAAAAAAAAAGAG
Found at i:2470078 original size:2 final size:2
Alignment explanation
Indices: 2470071--2470109 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2470061 AGGTAACGCT
* *
2470071 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2470110 CTGTAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2470251 original size:52 final size:53
Alignment explanation
Indices: 2470169--2470278 Score: 143
Period size: 52 Copynumber: 2.1 Consensus size: 53
2470159 CGTGTTACGT
* *
2470169 ACTTGGAAACATCTGTGGGCATTACACACTTAGAA-GTCATTATGCATTA-TGC
1 ACTTGAAAACATCTGTGGGCATTACACACTTAGAACGTCACTATGCATTACT-C
* * * *
2470221 ACTTGAAAATATCTGTGGGCGTTACGCACTTGGAACGTCACTATGCATTACTC
1 ACTTGAAAACATCTGTGGGCATTACACACTTAGAACGTCACTATGCATTACTC
2470274 ACTTG
1 ACTTG
2470279 GGATCATCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 30 0.60
53 19 0.38
54 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (53 bp):
ACTTGAAAACATCTGTGGGCATTACACACTTAGAACGTCACTATGCATTACTC
Found at i:2472361 original size:68 final size:68
Alignment explanation
Indices: 2472289--2472424 Score: 202
Period size: 68 Copynumber: 2.0 Consensus size: 68
2472279 CCTCTTTAGT
* * *
2472289 GGAGTCACCAAAATGTAAAGGATTTTTTTAGTAAGGAGAA-AGAACATGTTGTAACAAGTAAAAT
1 GGAGTCACCAAAATGTAAAGGATTATTCTAGTAAGGA-AAGAGAACATGTTGCAACAAGTAAAAT
2472353 AGAA
65 AGAA
* * *
2472357 GGAGTCACCAAAATGTAGAGGGTTATTCTAGTAAGGAAAGAGAACATGTTGCAATAAGTAAAATA
1 GGAGTCACCAAAATGTAAAGGATTATTCTAGTAAGGAAAGAGAACATGTTGCAACAAGTAAAATA
2472422 GAA
66 GAA
2472425 TACACTAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 2 0.03
68 59 0.97
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (68 bp):
GGAGTCACCAAAATGTAAAGGATTATTCTAGTAAGGAAAGAGAACATGTTGCAACAAGTAAAATA
GAA
Found at i:2473133 original size:17 final size:17
Alignment explanation
Indices: 2473111--2473144 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2473101 TAATGAACTG
*
2473111 AAAATCAAGATTATAAT
1 AAAATCAAGATGATAAT
*
2473128 AAAATCATGATGATAAT
1 AAAATCAAGATGATAAT
2473145 CTTAAAAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (17 bp):
AAAATCAAGATGATAAT
Found at i:2474656 original size:2 final size:2
Alignment explanation
Indices: 2474649--2474687 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2474639 CTTCTTTTTA
* * *
2474649 TC TC TC TC TC TC TC TC TC TC TG TT TC TC TC TC CC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2474688 TCCTCTCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2480785 original size:15 final size:15
Alignment explanation
Indices: 2480739--2480779 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
2480729 TTGCAATTAC
2480739 TTTAATATCTAGTAA
1 TTTAATATCTAGTAA
2480754 TTTAATATCTAGTAA
1 TTTAATATCTAGTAA
2480769 TTTAATATCTA
1 TTTAATATCTA
2480780 ACAATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (15 bp):
TTTAATATCTAGTAA
Found at i:2483281 original size:17 final size:17
Alignment explanation
Indices: 2483259--2483292 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2483249 CTTCTTGACC
*
2483259 TTTTTTGTTTTGTTTTG
1 TTTTTTGTTTTCTTTTG
*
2483276 TTTTTTTTTTTCTTTTG
1 TTTTTTGTTTTCTTTTG
2483293 GTCTGTGACG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (17 bp):
TTTTTTGTTTTCTTTTG
Found at i:2484134 original size:16 final size:16
Alignment explanation
Indices: 2484113--2484143 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2484103 AGTGTTTGGT
*
2484113 ATAATAATAAAAAATG
1 ATAATAACAAAAAATG
2484129 ATAATAACAAAAAAT
1 ATAATAACAAAAAAT
2484144 ATGATTGTTG
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:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
ATAATAACAAAAAATG
Found at i:2495903 original size:77 final size:77
Alignment explanation
Indices: 2495768--2495911 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 77
2495758 ACCCTTCTTC
* * * *
2495768 ATAATTTTGCACAAACTAGTAAGGGATGGCAAGAATAGCAAAAAGAAAAAACCCAACTAGGAAAG
1 ATAATTTTGCACAAACTAGTAAAGAATGACAAGAACAGCAAAAAGAAAAAACCCAACTAGGAAAG
2495833 AACCTTTTTTTT
66 AACCTTTTTTTT
* * * *
2495845 ATAATTTTGCACAAATTAGTAAAGAATGAC-AGAAGCAGTAAAAAGAAAGAACCTAACTAGGAAA
1 ATAATTTTGCACAAACTAGTAAAGAATGACAAGAA-CAGCAAAAAGAAAAAACCCAACTAGGAAA
2495909 GAA
65 GAA
2495912 AGGAAGTAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 4 0.07
77 54 0.93
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.21
Consensus pattern (77 bp):
ATAATTTTGCACAAACTAGTAAAGAATGACAAGAACAGCAAAAAGAAAAAACCCAACTAGGAAAG
AACCTTTTTTTT
Found at i:2500269 original size:13 final size:13
Alignment explanation
Indices: 2500251--2500280 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2500241 AAATAATACG
*
2500251 AAATAATTATAAT
1 AAATAAATATAAT
2500264 AAATAAATATAAT
1 AAATAAATATAAT
2500277 AAAT
1 AAAT
2500281 CTTAAACTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATAAATATAAT
Found at i:2500506 original size:16 final size:17
Alignment explanation
Indices: 2500479--2500520 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2500469 TTAATATACA
2500479 AAATTC-AAAT-AATTT
1 AAATTCAAAATAAATTT
* *
2500494 GAATTTAAAATAAATTT
1 AAATTCAAAATAAATTT
2500511 AAATTCAAAA
1 AAATTCAAAA
2500521 CAATCAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 4 0.19
16 4 0.19
17 13 0.62
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATTCAAAATAAATTT
Found at i:2502868 original size:6 final size:6
Alignment explanation
Indices: 2502857--2502882 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2502847 AGCTGTTGTT
2502857 TTTGGC TTTGGC TTTGGC TTTGGC TT
1 TTTGGC TTTGGC TTTGGC TTTGGC TT
2502883 CTTTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.31, T:0.54
Consensus pattern (6 bp):
TTTGGC
Found at i:2505745 original size:17 final size:18
Alignment explanation
Indices: 2505723--2505758 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2505713 ATTTGTGTAA
2505723 AGAGGGAC-AACGGAGAG
1 AGAGGGACTAACGGAGAG
*
2505740 AGAGGGACTAAGGGAGAG
1 AGAGGGACTAACGGAGAG
2505758 A
1 A
2505759 ATTCAGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.08, G:0.47, T:0.03
Consensus pattern (18 bp):
AGAGGGACTAACGGAGAG
Found at i:2511666 original size:2 final size:2
Alignment explanation
Indices: 2511661--2511698 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2511651 TGTGTGAACA
2511661 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2511699 TGAGGGAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2526822 original size:29 final size:31
Alignment explanation
Indices: 2526788--2526852 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 31
2526778 TTTAAAATTA
* *
2526788 AAAAATTAAATTGA-TAAAAT-TTTGAATAT
1 AAAAATTAAATTGACAAAAATATATGAATAT
2526817 AAAAATTAAATTGACAAAAATATATGAATAT
1 AAAAATTAAATTGACAAAAATATATGAATAT
2526848 AAAAA
1 AAAAA
2526853 CTATTTGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 14 0.44
30 5 0.16
31 13 0.41
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (31 bp):
AAAAATTAAATTGACAAAAATATATGAATAT
Found at i:2528641 original size:6 final size:6
Alignment explanation
Indices: 2528630--2528664 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
2528620 TTCTTAACAA
*
2528630 AAAAAG AAAAAG AAAAAG GAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
2528665 TATACTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2546025 original size:13 final size:12
Alignment explanation
Indices: 2546008--2546051 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
2545998 TTTTTATTTA
2546008 TTTTTAAATAAT
1 TTTTTAAATAAT
*
2546020 TATTTTACATAAT
1 T-TTTTAAATAAT
*
2546033 TTTTTGAAT-AT
1 TTTTTAAATAAT
2546044 TTTTTAAA
1 TTTTTAAA
2546052 AATAAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.33
12 7 0.26
13 11 0.41
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
TTTTTAAATAAT
Found at i:2546980 original size:31 final size:33
Alignment explanation
Indices: 2546910--2546972 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
2546900 ATTAAAATAA
*
2546910 AAAATATTTAAATAAAATATATAATATAAGAATC
1 AAAA-ATTAAAATAAAATATATAATATAAGAATC
2546944 AAAAATTAAAATAAAATA-A-AATATAAGAA
1 AAAAATTAAAATAAAATATATAATATAAGAA
2546973 ATTAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 10 0.36
32 1 0.04
33 13 0.46
34 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (33 bp):
AAAAATTAAAATAAAATATATAATATAAGAATC
Found at i:2547084 original size:33 final size:33
Alignment explanation
Indices: 2547006--2547093 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 33
2546996 AAAAGAGATT
* * * *
2547006 AAAATAGAATATATAATATAAAAAATTATATTAA
1 AAAAT-GAAAATAAAATATATAAAATTATAGTAA
*
2547040 AGAAATGAAAATAAAATATATAAGATTATAGTAA
1 A-AAATGAAAATAAAATATATAAAATTATAGTAA
2547074 AAAATGAAAATAAAATATAT
1 AAAATGAAAATAAAATATAT
2547094 TACATTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 19 0.40
34 25 0.52
35 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (33 bp):
AAAATGAAAATAAAATATATAAAATTATAGTAA
Found at i:2547336 original size:15 final size:15
Alignment explanation
Indices: 2547318--2547352 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2547308 CTACAATAAT
2547318 ATTATTTGCAATCAA
1 ATTATTTGCAATCAA
*
2547333 ATTACTTGCAATCAA
1 ATTATTTGCAATCAA
2547348 ATTAT
1 ATTAT
2547353 CTATAATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (15 bp):
ATTATTTGCAATCAA
Found at i:2550284 original size:12 final size:12
Alignment explanation
Indices: 2550267--2550293 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2550257 GCTCAGTTAA
2550267 CAAGTACAAAGC
1 CAAGTACAAAGC
2550279 CAAGTACAAAGC
1 CAAGTACAAAGC
2550291 CAA
1 CAA
2550294 ACCAGTGGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.07
Consensus pattern (12 bp):
CAAGTACAAAGC
Found at i:2557560 original size:2 final size:2
Alignment explanation
Indices: 2557553--2557580 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2557543 AAGTTTGAAT
2557553 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
2557581 GTCTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2559358 original size:2 final size:2
Alignment explanation
Indices: 2559351--2559409 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2559341 TTGTATGTAG
2559351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2559393 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2559410 TTAATGGCTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2559483 original size:17 final size:17
Alignment explanation
Indices: 2559458--2559492 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2559448 GTCTTTTTAG
*
2559458 AATTTTTATAAATTTTT
1 AATTATTATAAATTTTT
2559475 AATTATTATAAATTTTT
1 AATTATTATAAATTTTT
2559492 A
1 A
2559493 TTTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTATTATAAATTTTT
Found at i:2559622 original size:18 final size:17
Alignment explanation
Indices: 2559583--2559621 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2559573 TTTTCACACC
2559583 TTTTTCTCTCTCTCATT
1 TTTTTCTCTCTCTCATT
*
2559600 TTTTTCCTCTTTCTC-TT
1 TTTTT-CTCTCTCTCATT
2559617 TTTTT
1 TTTTT
2559622 TTTATCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTCTCTCTCTCATT
Found at i:2559629 original size:19 final size:19
Alignment explanation
Indices: 2559607--2559645 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2559597 ATTTTTTTCC
* *
2559607 TCTTTCTCTTTTTTTTTTA
1 TCTTTCTATTTTTATTTTA
*
2559626 TCTTTTTATTTTTATTTTA
1 TCTTTCTATTTTTATTTTA
2559645 T
1 T
2559646 TTTTTTACGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (19 bp):
TCTTTCTATTTTTATTTTA
Found at i:2559631 original size:13 final size:13
Alignment explanation
Indices: 2559613--2559652 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
2559603 TTCCTCTTTC
2559613 TCTTTTTTTTTTA
1 TCTTTTTTTTTTA
2559626 TCTTTTTATTTTTA
1 TCTTTTT-TTTTTA
2559640 T-TTTATTTTTTTA
1 TCTTT-TTTTTTTA
2559653 CGTAACTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (13 bp):
TCTTTTTTTTTTA
Found at i:2559650 original size:19 final size:19
Alignment explanation
Indices: 2559615--2559652 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2559605 CCTCTTTCTC
*
2559615 TTTTTTTTTTATCTTTTTA
1 TTTTTATTTTATCTTTTTA
*
2559634 TTTTTATTTTATTTTTTTA
1 TTTTTATTTTATCTTTTTA
2559653 CGTAACTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTATTTTATCTTTTTA
Found at i:2568175 original size:78 final size:77
Alignment explanation
Indices: 2568071--2568236 Score: 235
Period size: 78 Copynumber: 2.2 Consensus size: 77
2568061 AAAGGAGTAT
* * *
2568071 AAAAAATAAAAAGAGGAAAAAATTTATTTTTAATATTTTTTAAACACTAAAATCAATATGATGAT
1 AAAAAATAAAAACAGGAAAAAATTTATTTTTAATATTTTTTAAACAATAAAATAAATATGATGAT
*
2568136 AAAATCTTTTCG
66 AAAATCTTTTCA
* * * * *
2568148 AAAAAATAAATGACAGGAAAAATTTTATTTTTAATATTTTTTCAATAATAAAATAAATTTGATGA
1 AAAAAATAAA-AACAGGAAAAAATTTATTTTTAATATTTTTTAAACAATAAAATAAATATGATGA
2568213 TAAAATCTTTTCA
65 TAAAATCTTTTCA
2568226 AAAAAA-AAAAA
1 AAAAAATAAAAA
2568237 TAAGTGATGA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
76 1 0.01
77 13 0.17
78 64 0.82
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (77 bp):
AAAAAATAAAAACAGGAAAAAATTTATTTTTAATATTTTTTAAACAATAAAATAAATATGATGAT
AAAATCTTTTCA
Found at i:2578649 original size:54 final size:56
Alignment explanation
Indices: 2578588--2578693 Score: 157
Period size: 54 Copynumber: 1.9 Consensus size: 56
2578578 TAAAATAAAA
*
2578588 TATATAATATAAG-AACCAA-AAATTAAAATAAAATA-A-AATATAAGAAATTAAATT
1 TATATAATATAAGTAA--AAGAAATTAAAATAAAATATATAATATAAAAAATTAAATT
2578642 TATATAATATAAGTAAAAGAAATTAAAATAAAATATATAATATAAAAAATTA
1 TATATAATATAAGTAAAAGAAATTAAAATAAAATATATAATATAAAAAATTA
2578694 TGTTAAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
53 2 0.04
54 29 0.62
55 3 0.06
56 13 0.28
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (56 bp):
TATATAATATAAGTAAAAGAAATTAAAATAAAATATATAATATAAAAAATTAAATT
Found at i:2578717 original size:33 final size:33
Alignment explanation
Indices: 2578666--2578748 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
2578656 AAAAGAAATT
* **
2578666 AAAATAAAATATATAATATAAAAAATTATGTTAA
1 AAAATAAAA-ATAAAATATAAAAAATTATAATAA
* *
2578700 AAAATAAAAATAAAATATATAAGATTATAATAA
1 AAAATAAAAATAAAATATAAAAAATTATAATAA
2578733 AAAATAAAAA-AAAATA
1 AAAATAAAAATAAAATA
2578749 AAATATATGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 6 0.14
33 29 0.66
34 9 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (33 bp):
AAAATAAAAATAAAATATAAAAAATTATAATAA
Found at i:2578781 original size:13 final size:16
Alignment explanation
Indices: 2578762--2578802 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 16
2578752 TATATGACAT
2578762 TAAAAAT-ATATT-TA
1 TAAAAATAATATTATA
2578776 -AAAAATAATATTATA
1 TAAAAATAATATTATA
2578791 TAAAAATTAATA
1 TAAAAA-TAATA
2578803 ATAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 5 0.22
15 2 0.09
16 5 0.22
17 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAATAATATTATA
Found at i:2580836 original size:22 final size:21
Alignment explanation
Indices: 2580810--2580854 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2580800 CTGGGGATTG
* *
2580810 GTCCAACTTTATGTTGGATTTT
1 GTCCAACTATATGCT-GATTTT
*
2580832 GTCCAGCTATATGCTGATTTT
1 GTCCAACTATATGCTGATTTT
2580853 GT
1 GT
2580855 TTGTTTGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.47
Consensus pattern (21 bp):
GTCCAACTATATGCTGATTTT
Found at i:2582954 original size:47 final size:47
Alignment explanation
Indices: 2582885--2582980 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
2582875 AGTTTGGGTT
2582885 TATCAGTGCATGAGTGAAGAGTAATTTACCTGGACAAAGATAGCATG
1 TATCAGTGCATGAGTGAAGAGTAATTTACCTGGACAAAGATAGCATG
2582932 TATCAGTGCATGAGTGAAGAGTAATTTACCTGGACAAAGATAGCATG
1 TATCAGTGCATGAGTGAAGAGTAATTTACCTGGACAAAGATAGCATG
2582979 TA
1 TA
2582981 AGTGTTTAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (47 bp):
TATCAGTGCATGAGTGAAGAGTAATTTACCTGGACAAAGATAGCATG
Found at i:2589517 original size:3 final size:3
Alignment explanation
Indices: 2589509--2589535 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2589499 AGCCAAGTAC
2589509 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2589536 AATTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2589834 original size:12 final size:14
Alignment explanation
Indices: 2589805--2589836 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2589795 ATTACTAACC
2589805 AAACAAAAACATAG
1 AAACAAAAACATAG
2589819 AAACAAAAA-A-AG
1 AAACAAAAACATAG
2589831 AAACAA
1 AAACAA
2589837 TGAAATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 1 0.06
14 9 0.50
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.03
Consensus pattern (14 bp):
AAACAAAAACATAG
Found at i:2589865 original size:3 final size:3
Alignment explanation
Indices: 2589840--2589888 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
2589830 GAAACAATGA
*
2589840 AAT AAT GAA- AAT AAT AA- ATAT AAT AAT -AT AAT AAT GAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
2589884 AAT AA
1 AAT AA
2589889 ATACAAGAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 5 0.13
3 31 0.79
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2589872 original size:17 final size:17
Alignment explanation
Indices: 2589850--2589884 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2589840 AATAATGAAA
2589850 ATAATAAAT-ATAATAAT
1 ATAAT-AATGATAATAAT
2589867 ATAATAATGATAATAAT
1 ATAATAATGATAATAAT
2589884 A
1 A
2589885 ATAAATACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAATAATGATAATAAT
Found at i:2592549 original size:29 final size:29
Alignment explanation
Indices: 2592517--2592585 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
2592507 TTTTTTATAT
*
2592517 TTGTTCACGTACAGCCTT-TTCTCTTGTAC
1 TTGTTCACGTACAG-CTTCCTCTCTTGTAC
* *
2592546 TTGTTCATGTACAGCTTCCTCTTTTGTAC
1 TTGTTCACGTACAGCTTCCTCTCTTGTAC
*
2592575 CTGTTCACGTA
1 TTGTTCACGTA
2592586 TAGTTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.45
Consensus pattern (29 bp):
TTGTTCACGTACAGCTTCCTCTCTTGTAC
Found at i:2596697 original size:30 final size:30
Alignment explanation
Indices: 2596661--2596722 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
2596651 AGCTCGCTCC
*
2596661 TCCTACCTAGGAGTGTGATTGAAAACTATG
1 TCCTACCTAGGAGCGTGATTGAAAACTATG
*
2596691 TCCTACCTAGGGGCGTGATTGAAAACTATG
1 TCCTACCTAGGAGCGTGATTGAAAACTATG
2596721 TC
1 TC
2596723 ACAGCGATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (30 bp):
TCCTACCTAGGAGCGTGATTGAAAACTATG
Found at i:2604016 original size:25 final size:25
Alignment explanation
Indices: 2603985--2604057 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
2603975 TTGATGACTT
2603985 GATCTTGATCACGAACTTCGCTTGA
1 GATCTTGATCACGAACTTCGCTTGA
* *
2604010 TATCTTGATCACGAACTTTGCTTGA
1 GATCTTGATCACGAACTTCGCTTGA
*
2604035 GAACTTGATCACGAACTTCGCTT
1 GATCTTGATCACGAACTTCGCTT
2604058 AATGTCTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (25 bp):
GATCTTGATCACGAACTTCGCTTGA
Found at i:2604496 original size:81 final size:80
Alignment explanation
Indices: 2604376--2604548 Score: 208
Period size: 81 Copynumber: 2.2 Consensus size: 80
2604366 AATTTGATTT
* *
2604376 TTATCTCCAAATTATCATAATTTTTTAGAGATAAATTGGATGAC-CAATAAGTAAATTTTTATTG
1 TTATCTCCAAATTACCATAATTTTTTAGAGATAAATTGGATG-CTCAATAAGTAAATTTTAATTG
2604440 GTTAAAAATATGAATA
65 GTTAAAAATATGAATA
* * * * *
2604456 TTATCTCTAAATTACCTTGATTTATTTAGAGATAAGTTGGATGCTCAATAATTAAATTTTAATTG
1 TTATCTCCAAATTACCATAATTT-TTTAGAGATAAATTGGATGCTCAATAAGTAAATTTTAATTG
* * *
2604521 GTT-CACAT-TAAATA
65 GTTAAAAATATGAATA
*
2604535 TTATCTTCAAATTA
1 TTATCTCCAAATTA
2604549 TCTCAAAGGA
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
79 17 0.22
80 23 0.29
81 39 0.49
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.42
Consensus pattern (80 bp):
TTATCTCCAAATTACCATAATTTTTTAGAGATAAATTGGATGCTCAATAAGTAAATTTTAATTGG
TTAAAAATATGAATA
Found at i:2617132 original size:15 final size:15
Alignment explanation
Indices: 2617109--2617164 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
2617099 CTTTACAATA
*
2617109 TAATGTGATTACAAG
1 TAATGTGATTGCAAG
* *
2617124 TAATATGATTGTAAG
1 TAATGTGATTGCAAG
2617139 TAATGTGATTGCAAG
1 TAATGTGATTGCAAG
* *
2617154 CAATGTCATTG
1 TAATGTGATTG
2617165 TAAAGAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (15 bp):
TAATGTGATTGCAAG
Found at i:2617145 original size:30 final size:30
Alignment explanation
Indices: 2617109--2617167 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2617099 CTTTACAATA
* *
2617109 TAATGTGATTACAAGTAATATGATTGTAAG
1 TAATGTGATTACAAGCAATATCATTGTAAG
* *
2617139 TAATGTGATTGCAAGCAATGTCATTGTAA
1 TAATGTGATTACAAGCAATATCATTGTAA
2617168 AGAAAATAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (30 bp):
TAATGTGATTACAAGCAATATCATTGTAAG
Found at i:2617418 original size:33 final size:33
Alignment explanation
Indices: 2617381--2617466 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
2617371 TTTTAATGTC
*
2617381 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATATAATCTT
* * *
2617414 ATATATTTTATTTTCATTTTTTAATATAATTTT
1 ATATATTTTATTTTTATTTATTAATATAATCTT
* *
2617447 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
2617467 TAATTTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 38 0.84
34 7 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTAATATAATCTT
Found at i:2617438 original size:28 final size:30
Alignment explanation
Indices: 2617368--2617435 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
2617358 CTCTTAAATA
* *
2617368 TATTTTTAATGTCATATATTTTATTTTTATT
1 TATTTTTAATCTCATATATTTTATTTTCA-T
*
2617399 TATTATTATAATCTTATATATTTTATTTTCAT
1 TATT-TT-TAATCTCATATATTTTATTTTCAT
2617431 T-TTTT
1 TATTTT
2617436 AATATAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.06
31 6 0.19
32 4 0.12
33 20 0.62
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (30 bp):
TATTTTTAATCTCATATATTTTATTTTCAT
Found at i:2617508 original size:24 final size:25
Alignment explanation
Indices: 2617481--2617554 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
2617471 TTATTTTACC
2617481 TATATTATA-TAAATTTTAATTTTT
1 TATATTATATTAAATTTTAATTTTT
**
2617505 TATATTATATTTTATTTTAA-TTTT
1 TATATTATATTAAATTTTAATTTTT
*
2617529 TATTCTTATATTATATATTTT-ATTTT
1 TA-TATTATATTA-A-ATTTTAATTTT
2617555 AATACTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 15 0.38
25 16 0.40
26 1 0.03
27 8 0.20
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (25 bp):
TATATTATATTAAATTTTAATTTTT
Found at i:2617557 original size:57 final size:57
Alignment explanation
Indices: 2617440--2617545 Score: 166
Period size: 55 Copynumber: 1.9 Consensus size: 57
2617430 TTTTTTAATA
2617440 TAATTTTTTATATTATATATTTTATTTTAATTTATTTTACCTATATTATATAAATTT
1 TAATTTTTTATATTATATATTTTATTTTAATTTATTTTACCTATATTATATAAATTT
*
2617497 TAATTTTTTATA-T-TATATTTTATTTTAATTT-TTATT-CTTATATTATATA
1 TAATTTTTTATATTATATATTTTATTTTAATTTATT-TTACCTATATTATATA
2617546 TTTTATTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
54 14 0.30
55 20 0.43
56 1 0.02
57 12 0.26
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (57 bp):
TAATTTTTTATATTATATATTTTATTTTAATTTATTTTACCTATATTATATAAATTT
Found at i:2625960 original size:2 final size:2
Alignment explanation
Indices: 2625953--2625988 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2625943 CACATGCGTC
2625953 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2625989 GCCATGTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2626969 original size:19 final size:19
Alignment explanation
Indices: 2626945--2626991 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2626935 CCTAACTAGA
2626945 ACCCTAATACATACCCATT
1 ACCCTAATACATACCCATT
*
2626964 ACCCTAATATATACCCATT
1 ACCCTAATACATACCCATT
2626983 ACCCTAATA
1 ACCCTAATA
2626992 ACTACCCGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (19 bp):
ACCCTAATACATACCCATT
Found at i:2626997 original size:19 final size:19
Alignment explanation
Indices: 2626945--2626998 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
2626935 CCTAACTAGA
2626945 ACCCTAAT-ACATACCCATT
1 ACCCTAATAAC-TACCCATT
2626964 ACCCTAATATA-TACCCATT
1 ACCCTAATA-ACTACCCATT
2626983 ACCCTAATAACTACCC
1 ACCCTAATAACTACCC
2626999 GAACTGGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.03
19 30 0.94
21 1 0.03
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (19 bp):
ACCCTAATAACTACCCATT
Found at i:2627209 original size:34 final size:34
Alignment explanation
Indices: 2627171--2627239 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
2627161 AATTTATATT
* *
2627171 TAAAA-AATCACAAACAAATATCTCAAATATCAAC
1 TAAAATAATCAAAAACAAATAT-TCAAATAACAAC
*
2627205 TAAAATAATTAAAAACAAATATTCAAATAACAAC
1 TAAAATAATCAAAAACAAATATTCAAATAACAAC
2627239 T
1 T
2627240 TAAACATTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (34 bp):
TAAAATAATCAAAAACAAATATTCAAATAACAAC
Found at i:2635884 original size:26 final size:26
Alignment explanation
Indices: 2635854--2635936 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 26
2635844 CATTTTCATA
2635854 GTAAAATTATCTATCCACTTCTAGTG
1 GTAAAATTATCTATCCACTTCTAGTG
* ** *
2635880 GTAAAATTA-CTTTTAAATTC-AGATG
1 GTAAAATTATCTATCCACTTCTAG-TG
*
2635905 ATAAAA-TAT-TCATCCACTTCTAGTG
1 GTAAAATTATCT-ATCCACTTCTAGTG
2635930 GTAAAAT
1 GTAAAAT
2635937 AATAATTAGA
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
24 5 0.12
25 26 0.62
26 11 0.26
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (26 bp):
GTAAAATTATCTATCCACTTCTAGTG
Found at i:2636148 original size:53 final size:53
Alignment explanation
Indices: 2636044--2636177 Score: 142
Period size: 53 Copynumber: 2.5 Consensus size: 53
2636034 AGATGGTGCG
* * * * **
2636044 TTCACTTCAAGGAATGAACGAATTTATAATTTTTTATTAGTATCTTGTTTGTCACA
1 TTCACTTCAGGGAATGAAC--ATTCATAA-GTTTTATTAGTAGCTAATTTGTCACA
* * *
2636100 TTCACTTTAGGGAATGAATATTCATAAGTTTTATTAGTAGCTAATTTGTTACA
1 TTCACTTCAGGGAATGAACATTCATAAGTTTTATTAGTAGCTAATTTGTCACA
* *
2636153 TTTACTTCAGGGAATGGACATTCAT
1 TTCACTTCAGGGAATGAACATTCAT
2636178 GGTTTTTCAT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
53 42 0.65
54 7 0.11
56 16 0.25
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (53 bp):
TTCACTTCAGGGAATGAACATTCATAAGTTTTATTAGTAGCTAATTTGTCACA
Found at i:2648555 original size:2 final size:2
Alignment explanation
Indices: 2648550--2648575 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2648540 GCATTCATGA
2648550 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2648576 GTGCTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2650783 original size:2 final size:2
Alignment explanation
Indices: 2650776--2650809 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2650766 AGAACGACAA
2650776 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2650810 GTAGGTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2657365 original size:2 final size:2
Alignment explanation
Indices: 2657358--2657383 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2657348 AGTCAGCTTT
2657358 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2657384 AGGAGGGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2663938 original size:35 final size:35
Alignment explanation
Indices: 2663894--2663986 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
2663884 GAAACATTAT
* * *
2663894 TTCATGCAAAATAATTAGAACAAGTAAAAT-ACTAC
1 TTCACGCAAAACAATTAAAACAAGT-AAATCACTAC
2663929 TTCACGCAAAACAATTAAAACAAGTAAATCACTAC
1 TTCACGCAAAACAATTAAAACAAGTAAATCACTAC
* *
2663964 TTCACGTAAAACAACTAAAACAA
1 TTCACGCAAAACAATTAAAACAA
2663987 TTGAGCACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
34 4 0.08
35 48 0.92
ACGTcount: A:0.53, C:0.19, G:0.06, T:0.22
Consensus pattern (35 bp):
TTCACGCAAAACAATTAAAACAAGTAAATCACTAC
Found at i:2664023 original size:34 final size:34
Alignment explanation
Indices: 2663924--2664011 Score: 86
Period size: 35 Copynumber: 2.6 Consensus size: 34
2663914 CAAGTAAAAT
** * ** *
2663924 ACTACTTCACGCAAAACAATTAAAACAAGTAAATC
1 ACTACTTCACATAAAACAACTAAAACAA-TTGAGC
*
2663959 ACTACTTCACGTAAAACAACTAAAACAATTGAGC
1 ACTACTTCACATAAAACAACTAAAACAATTGAGC
* *
2663993 ACTACTTCATATGAAACAA
1 ACTACTTCACATAAAACAA
2664012 TTAATATAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 19 0.42
35 26 0.58
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.22
Consensus pattern (34 bp):
ACTACTTCACATAAAACAACTAAAACAATTGAGC
Found at i:2665186 original size:22 final size:24
Alignment explanation
Indices: 2665156--2665209 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
2665146 TTTTGTTTTA
* *
2665156 TTATATTTGATGTTATTATT-ATT
1 TTATATTTGATATAATTATTAATT
*
2665179 TTAT-TTTGTTATAATTATTAATT
1 TTATATTTGATATAATTATTAATT
*
2665202 TTAAATTT
1 TTATATTT
2665210 AAATAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 12 0.48
23 10 0.40
24 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TTATATTTGATATAATTATTAATT
Found at i:2670121 original size:9 final size:9
Alignment explanation
Indices: 2670096--2670131 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2670086 AATTGAAAAA
2670096 ATAAATAAAT
1 ATAAAT-AAT
2670106 ATAAATAAT
1 ATAAATAAT
*
2670115 ATTAATAAT
1 ATAAATAAT
2670124 ATAAATAA
1 ATAAATAA
2670132 AAAAAAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAATAAT
Found at i:2674204 original size:6 final size:6
Alignment explanation
Indices: 2674193--2674218 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2674183 GAGCTGATAT
2674193 AGAAGC AGAAGC AGAAGC AGAAGC AG
1 AGAAGC AGAAGC AGAAGC AGAAGC AG
2674219 TATTAGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAAGC
Found at i:2690675 original size:14 final size:14
Alignment explanation
Indices: 2690657--2690694 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
2690647 CCAAATAATG
2690657 AAAAAACAATAAAAC
1 AAAAAA-AATAAAAC
2690672 AAAAAAAATAAAA-
1 AAAAAAAATAAAAC
2690685 AATAAAAAAT
1 AA-AAAAAAT
2690695 CTAATACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 14 0.64
15 6 0.27
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAAATAAAAC
Found at i:2691732 original size:4 final size:4
Alignment explanation
Indices: 2691723--2691764 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
2691713 AGGTTTGGTC
2691723 TAAA TAAA TAAA TAAA TAAAA TAAA TAAA -AATA TAAAA TAAA
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAA-A T-AAA TAAA
2691765 AAGAATAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.06
4 24 0.71
5 6 0.18
6 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:2691746 original size:17 final size:17
Alignment explanation
Indices: 2691724--2691764 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
2691714 GGTTTGGTCT
2691724 AAATAAATAAATAA-ATA
1 AAATAAATAAA-AATATA
2691741 AAATAAATAAAAATATA
1 AAATAAATAAAAATATA
2691758 AAATAAA
1 AAATAAA
2691765 AAGAATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAAATAAAAATATA
Found at i:2691765 original size:13 final size:12
Alignment explanation
Indices: 2691723--2691772 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
2691713 AGGTTTGGTC
*
2691723 TAAATAAATAAA
1 TAAAAAAATAAA
2691735 TAAATAAAATAAA
1 TAAA-AAAATAAA
*
2691748 TAAAAATATAAAA
1 TAAAAAAAT-AAA
2691761 TAAAAAGAATAA
1 TAAAAA-AATAA
2691773 GACCTAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 8 0.25
13 22 0.69
14 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:2702491 original size:2 final size:2
Alignment explanation
Indices: 2702484--2702514 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2702474 GTACAGCACT
2702484 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 T
2702515 GTCATAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2703681 original size:4 final size:4
Alignment explanation
Indices: 2703672--2703708 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
2703662 GATGAGATAC
2703672 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
2703709 TTCAAAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Done.