Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 135 of 163
Found at i:43895527 original size:15 final size:16
Alignment explanation
Indices: 43895509--43895547 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
43895499 CTTCTTATCT
*
43895509 TAATTTTA-TATTTCG
1 TAATTTTATTATTTCA
*
43895524 TAATTTTATTATTTTA
1 TAATTTTATTATTTCA
43895540 TAATTTTA
1 TAATTTTA
43895548 AAAATGTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (16 bp):
TAATTTTATTATTTCA
Found at i:43900332 original size:27 final size:25
Alignment explanation
Indices: 43900302--43900352 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
43900292 CTTTTAATGT
43900302 TTATTATAACATATTAATATAATATAC
1 TTATTATAACAT-TT-ATATAATATAC
*
43900329 TTATTATAACATTTATATATTATA
1 TTATTATAACATTTATATAATATA
43900353 ATAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 2 0.09
27 12 0.52
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (25 bp):
TTATTATAACATTTATATAATATAC
Found at i:43901601 original size:154 final size:152
Alignment explanation
Indices: 43901347--43901653 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 152
43901337 ATTTACAATT
43901347 TACCAAAAAATGAATAAATTGTTTTTTTTTGTATGCTTATAAAAAATGAATAAAAGTTTTAATTA
1 TACCAAAAAATGAATAAATTGTTTTTTTTTGTATGCTTATAAAAAATGAATAAAAGTTTTAATTA
*
43901412 AGTCTTCTCCTCAATGTTGCCTCCAAGTGTGGACATGTTGGCTTATTATGTTTTGGGTTCCTACA
66 AGTCTTCTCCTCAATGTTGCCTCCAAGTGTGGACATGTTGGCTTATTATGTCTTGGGTTCCTACA
43901477 ATAACTGCATAACCTCGATTGG
131 ATAACTGCATAACCTCGATTGG
*
43901499 TACCAAAAAATGAATAAATTGTTTTATTTTTGTATGCTTATAAAAAATTGAATAAAATTTTTAAT
1 TACCAAAAAATGAATAAATTGTTTT-TTTTTGTATGCTTATAAAAAA-TGAATAAAAGTTTTAAT
43901564 TAAGTCTTCTCCTCAATGTTGCCTCCAAGTGTGGACATGTTGGCTTATTATGTCTTGGGTTCCTA
64 TAAGTCTTCTCCTCAATGTTGCCTCCAAGTGTGGACATGTTGGCTTATTATGTCTTGGGTTCCTA
*
43901629 CAATAATTGCATAACCTCGATTGG
129 CAATAACTGCATAACCTCGATTGG
43901653 T
1 T
43901654 CTATCTTCTT
Statistics
Matches: 150, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
152 25 0.17
153 21 0.14
154 104 0.69
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (152 bp):
TACCAAAAAATGAATAAATTGTTTTTTTTTGTATGCTTATAAAAAATGAATAAAAGTTTTAATTA
AGTCTTCTCCTCAATGTTGCCTCCAAGTGTGGACATGTTGGCTTATTATGTCTTGGGTTCCTACA
ATAACTGCATAACCTCGATTGG
Found at i:43905240 original size:34 final size:38
Alignment explanation
Indices: 43905172--43905240 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
43905162 TATAGGTAAG
* *
43905172 TTTTATTATTATTATTATTATTATTTGTTATTTTGCAC
1 TTTTATTATTAATATTATTATTATTGGTTATTTTGCAC
43905210 TTTT-TTATTAATATT-TTATT-TTGGTT-TTTTG
1 TTTTATTATTAATATTATTATTATTGGTTATTTTG
43905241 TGATATGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 5 0.17
35 5 0.17
36 5 0.17
37 10 0.34
38 4 0.14
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (38 bp):
TTTTATTATTAATATTATTATTATTGGTTATTTTGCAC
Found at i:43949944 original size:32 final size:33
Alignment explanation
Indices: 43949877--43949952 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 33
43949867 ATAAAAAATT
** *
43949877 AATATTTTATAGTGTTTAGATGAATTTATGTAA
1 AATATTTTATAGTGTTTAGACAAATTTATCTAA
*
43949910 AATATTTTATATTGTTT-GACAAATTT-TCTAAA
1 AATATTTTATAGTGTTTAGACAAATTTATCT-AA
43949942 AATATTTTATA
1 AATATTTTATA
43949953 AAAGTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 2 0.05
32 20 0.53
33 16 0.42
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (33 bp):
AATATTTTATAGTGTTTAGACAAATTTATCTAA
Found at i:43957343 original size:42 final size:44
Alignment explanation
Indices: 43957270--43957362 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 44
43957260 CCTTCTTCTT
*
43957270 CAGCCAAGCCAGTGGCAACTACTGCCGCCTCTGTTCCATCTTCCC
1 CAGCCAAGCCAGTGGCAACTACTG-CGCCTCTGTTCCAACTTCCC
*
43957315 CAGCCAAGTCC-GTGGCAACTAC-G-GCCTCTGTTCCAACTTCTC
1 CAGCCAAG-CCAGTGGCAACTACTGCGCCTCTGTTCCAACTTCCC
43957357 CAGCCA
1 CAGCCA
43957363 GGACAGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
42 23 0.51
44 1 0.02
45 19 0.42
46 2 0.04
ACGTcount: A:0.19, C:0.41, G:0.18, T:0.22
Consensus pattern (44 bp):
CAGCCAAGCCAGTGGCAACTACTGCGCCTCTGTTCCAACTTCCC
Found at i:43962720 original size:20 final size:19
Alignment explanation
Indices: 43962699--43962735 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43962689 TAAAAATATA
*
43962699 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
43962717 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
43962736 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:43962742 original size:19 final size:21
Alignment explanation
Indices: 43962704--43962748 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
43962694 ATATATATAA
* *
43962704 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAATTTTAAAAAATT
43962724 ATTTT-GAATTTTAAAAAATT
1 ATTTTAGAATTTTAAAAAATT
43962744 ATTTT
1 ATTTT
43962749 TGAAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTTTAGAATTTTAAAAAATT
Found at i:43962877 original size:9 final size:9
Alignment explanation
Indices: 43962861--43962891 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43962851 ATTCGATTTG
43962861 ACTCGAATA
1 ACTCGAATA
*
43962870 ATTCGAATA
1 ACTCGAATA
43962879 ACTCGAATA
1 ACTCGAATA
43962888 ACTC
1 ACTC
43962892 TATTTGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
ACTCGAATA
Found at i:43966010 original size:7 final size:7
Alignment explanation
Indices: 43965998--43966023 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43965988 GTTTTTATGG
43965998 GTTGCTT
1 GTTGCTT
43966005 GTTGCTT
1 GTTGCTT
43966012 GTTGCTT
1 GTTGCTT
43966019 GTTGC
1 GTTGC
43966024 AGTAAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.31, T:0.54
Consensus pattern (7 bp):
GTTGCTT
Found at i:43973914 original size:42 final size:41
Alignment explanation
Indices: 43973868--43973995 Score: 104
Period size: 42 Copynumber: 3.1 Consensus size: 41
43973858 TTTGCTATTC
43973868 TTTTACTTTTTAAAAATTTAAATTCGATATTATTTATATTTG
1 TTTTACTTTTTAAAAATTTAAATT-GATATTATTTATATTTG
* *** * * *
43973910 TTTTATCTATTTATTTATTT--ATTTAT-TTATTTGT-TATTC
1 TTTTA-CTTTTTAAAAATTTAAATTGATATTATTTATAT-TTG
*
43973949 TTTTAC-TTTTAAAATATTTAAATTTGATATTATTTAAATTTG
1 TTTTACTTTTTAAAA-ATTTAAA-TTGATATTATTTATATTTG
43973991 TTTTA
1 TTTTA
43973996 TCTATTTATT
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
37 4 0.06
38 6 0.10
39 14 0.22
40 3 0.05
41 7 0.11
42 18 0.29
43 11 0.17
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (41 bp):
TTTTACTTTTTAAAAATTTAAATTGATATTATTTATATTTG
Found at i:43973926 original size:4 final size:4
Alignment explanation
Indices: 43973911--43973941 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
43973901 TTATATTTGT
*
43973911 TTTA TCTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
43973942 GTTATTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:43973933 original size:81 final size:81
Alignment explanation
Indices: 43973842--43974010 Score: 286
Period size: 81 Copynumber: 2.1 Consensus size: 81
43973832 TATGAGTTGT
* *
43973842 TTTATCTATTTATTTATTTGCTATTCTTTTACTTTTTAAAA-ATTTAAATTCGATATTATTTATA
1 TTTATTTATTTATTTATTTGCTATTCTTTTAC-TTTTAAAATATTTAAATTCGATATTATTTAAA
43973906 TTTGTTTTATCTATTTA
65 TTTGTTTTATCTATTTA
* *
43973923 TTTATTTATTTATTTATTTGTTATTCTTTTACTTTTAAAATATTTAAATTTGATATTATTTAAAT
1 TTTATTTATTTATTTATTTGCTATTCTTTTACTTTTAAAATATTTAAATTCGATATTATTTAAAT
43973988 TTGTTTTATCTATTTA
66 TTGTTTTATCTATTTA
43974004 TTTATTT
1 TTTATTT
43974011 GTTATTCTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
80 8 0.10
81 75 0.90
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (81 bp):
TTTATTTATTTATTTATTTGCTATTCTTTTACTTTTAAAATATTTAAATTCGATATTATTTAAAT
TTGTTTTATCTATTTA
Found at i:43973996 original size:69 final size:69
Alignment explanation
Indices: 43973923--43974053 Score: 226
Period size: 69 Copynumber: 1.9 Consensus size: 69
43973913 TATCTATTTA
* *
43973923 TTTATTTATTTATTTATTTGTTATTCTTTTACTTTTAAAATATTTAAATTTGATATTATTTAAAT
1 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAAACATTTAAATTTGATATTATTTAAAT
43973988 TTGT
66 TTGT
* *
43973992 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTTAAACATTTAAGTTTGATATTATTTA
1 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAAACATTTAAATTTGATATTATTTA
43974054 TACTTCCTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (69 bp):
TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAAACATTTAAATTTGATATTATTTAAAT
TTGT
Found at i:43974090 original size:69 final size:69
Alignment explanation
Indices: 43973934--43974080 Score: 197
Period size: 69 Copynumber: 2.1 Consensus size: 69
43973924 TTATTTATTT
* **
43973934 ATTTATTTGTTATTCTTTTACTTTTAAAATATTTAAATTTGATATTATTTAAATTTGTTTTATCT
1 ATTTATTTGTTATTCTTTTACTTTTAAAACATTTAAATTTGATATTATTTAAATTCCTTTTATCT
**
43973999 ATTT
66 ATGC
* * *
43974003 ATTTATTTGTTATTCTTTTACTTTTTAAACATTTAAGTTTGATATTATTTATACTTCCTTTTCAT
1 ATTTATTTGTTATTCTTTTACTTTTAAAACATTTAAATTTGATATTATTTA-AATTCCTTTT-AT
43974068 -TATGC
64 CTATGC
43974073 ATTTATTT
1 ATTTATTT
43974081 TCTTTCTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
69 48 0.71
70 18 0.26
71 2 0.03
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (69 bp):
ATTTATTTGTTATTCTTTTACTTTTAAAACATTTAAATTTGATATTATTTAAATTCCTTTTATCT
ATGC
Found at i:43975286 original size:47 final size:47
Alignment explanation
Indices: 43975224--43975956 Score: 1430
Period size: 47 Copynumber: 15.6 Consensus size: 47
43975214 TGACAGCATA
* * *
43975224 TACATAAATAATTTGATAGCATATACATAAATAATTGGACTGCATTTG
1 TACATCAA-AATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975272 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975319 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975366 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975413 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975460 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975507 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975554 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975601 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975648 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975695 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975742 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975789 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975836 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975883 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
1 TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
43975930 TACATCAAAATTTGACAGCATATACAT
1 TACATCAAAATTTGACAGCATATACAT
43975957 TCATTTACTC
Statistics
Matches: 682, Mismatches: 3, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
47 675 0.99
48 7 0.01
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (47 bp):
TACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTG
Found at i:43976230 original size:14 final size:15
Alignment explanation
Indices: 43976192--43976240 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
43976182 TCACCATGCA
* *
43976192 CATATATATACATTAC
1 CATATAAATAC-TAAC
43976208 CATATAAATACTAAC
1 CATATAAATACTAAC
43976223 CATA-AAATACTAATC
1 CATATAAATACTAA-C
43976238 CAT
1 CAT
43976241 GATTAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 11 0.37
16 10 0.33
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
CATATAAATACTAAC
Found at i:43976974 original size:43 final size:43
Alignment explanation
Indices: 43976927--43977009 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
43976917 AATCACATAC
*
43976927 CGATGCC-ACTATCCCAGACAAGGTCTTACACGAAAACACAAGT
1 CGATGCCGAC-ATCCCAAACAAGGTCTTACACGAAAACACAAGT
* **
43976970 CGATGCCGACGTCCCAAACGTGGTCTTACACGAAAACACA
1 CGATGCCGACATCCCAAACAAGGTCTTACACGAAAACACA
43977010 TACCGGAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 33 0.94
44 2 0.06
ACGTcount: A:0.35, C:0.31, G:0.18, T:0.16
Consensus pattern (43 bp):
CGATGCCGACATCCCAAACAAGGTCTTACACGAAAACACAAGT
Found at i:43979220 original size:22 final size:22
Alignment explanation
Indices: 43979168--43979209 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43979158 ACAAAAAAAA
*
43979168 TGCTATTTTCTTGTTGTTTTGC
1 TGCTATTTTCTTATTGTTTTGC
*
43979190 AGCTATTTTCTTATTGTTTT
1 TGCTATTTTCTTATTGTTTT
43979210 CTTGCTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (22 bp):
TGCTATTTTCTTATTGTTTTGC
Found at i:43984748 original size:24 final size:24
Alignment explanation
Indices: 43984711--43984758 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
43984701 GACTGTGGAC
*
43984711 ATTTTAAAATTTGGTTTTATTTTT
1 ATTTTAAAATTTGGGTTTATTTTT
43984735 ATTTATAAAA-TTGGGTTTATTTTT
1 ATTT-TAAAATTTGGGTTTATTTTT
43984759 GGTTTGCGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.62
Consensus pattern (24 bp):
ATTTTAAAATTTGGGTTTATTTTT
Found at i:43985192 original size:3 final size:3
Alignment explanation
Indices: 43985184--43985208 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43985174 ATTTTTAATT
43985184 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
43985209 AAAACAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43995192 original size:17 final size:17
Alignment explanation
Indices: 43995156--43995198 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
43995146 AACAAGATCT
*
43995156 AAATATAAAAATCTCAA
1 AAATATAAAAATCACAA
*
43995173 AAATGTAAAAATCACTAA
1 AAATATAAAAATCAC-AA
*
43995191 AAACATAA
1 AAATATAA
43995199 GTAGAAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.21
Consensus pattern (17 bp):
AAATATAAAAATCACAA
Found at i:44004712 original size:23 final size:24
Alignment explanation
Indices: 44004668--44004712 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
44004658 AAAATTTTAT
* *
44004668 ATTGATTTTACAAAATATTTGAAA
1 ATTGATTTTACAAAAAAGTTGAAA
*
44004692 ATTG-TTTTATAAAAAAGTTGA
1 ATTGATTTTACAAAAAAGTTGA
44004713 TTTCGCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.42
Consensus pattern (24 bp):
ATTGATTTTACAAAAAAGTTGAAA
Found at i:44007572 original size:24 final size:23
Alignment explanation
Indices: 44007528--44007573 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44007518 AACAAGATAA
* * *
44007528 TATAATATAAAAATTCGCTCCAT
1 TATAATAAAAAAACTCACTCCAT
44007551 TATAATAAAAAAACTCAACTCCA
1 TATAATAAAAAAACTC-ACTCCA
44007574 CCAAATTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (23 bp):
TATAATAAAAAAACTCACTCCAT
Found at i:44011601 original size:19 final size:17
Alignment explanation
Indices: 44011554--44011601 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
44011544 AATTTTTTTT
44011554 ATATTTTTTAA-TTTAA
1 ATATTTTTTAACTTTAA
*
44011570 ATAGTTTTATAACTTTTAA
1 ATA-TTTTTTAAC-TTTAA
44011589 ATTATTTTTTAAC
1 A-TATTTTTTAAC
44011602 ATGACATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.12
17 7 0.27
19 14 0.54
20 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATTTTTTAACTTTAA
Found at i:44020527 original size:20 final size:20
Alignment explanation
Indices: 44020502--44020540 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44020492 TTTGAAGATT
44020502 ATTGATAAATACTTTATATA
1 ATTGATAAATACTTTATATA
*
44020522 ATTGATAAATATTTTATAT
1 ATTGATAAATACTTTATAT
44020541 TTAAGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTGATAAATACTTTATATA
Found at i:44021495 original size:119 final size:120
Alignment explanation
Indices: 44021354--44021591 Score: 469
Period size: 119 Copynumber: 2.0 Consensus size: 120
44021344 TAATTAATTC
44021354 ACTTTAAATAGCAAACATATAGATATATACTCTCTCTTTTTGGTTATTCTTATATTAGACATACA
1 ACTTTAAATAGCAAACATATAGATATATACTCTCTCTTTTTGGTTATTCTTATATTAGACATACA
44021419 ATTATTTTCCTTTTTGATTTTTATTTTAAATTTCTATATATTTAAATTTATAAAA
66 ATTATTTTCCTTTTTGATTTTTATTTTAAATTTCTATATATTTAAATTTATAAAA
44021474 ACTTTAAATA-CAAACATATAGATATATACTCTCTCTTTTTGGTTATTCTTATATTAGACATACA
1 ACTTTAAATAGCAAACATATAGATATATACTCTCTCTTTTTGGTTATTCTTATATTAGACATACA
44021538 ATTATTTTCCTTTTTGATTTTTATTTTAAATTTCTATATATTTAAATTTATAAA
66 ATTATTTTCCTTTTTGATTTTTATTTTAAATTTCTATATATTTAAATTTATAAA
44021592 TATCATGTTT
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 108 0.92
120 10 0.08
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (120 bp):
ACTTTAAATAGCAAACATATAGATATATACTCTCTCTTTTTGGTTATTCTTATATTAGACATACA
ATTATTTTCCTTTTTGATTTTTATTTTAAATTTCTATATATTTAAATTTATAAAA
Found at i:44037870 original size:132 final size:132
Alignment explanation
Indices: 44037633--44038529 Score: 1515
Period size: 132 Copynumber: 6.8 Consensus size: 132
44037623 GTGAAACACC
*
44037633 AGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
44037698 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAGTTGAAGATT
44037763 AT
131 AT
* * * **
44037765 AGATCTTATCTCCCTAAGCAGTAGTGGAGCGGATTGAAAACGATGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * ** *
44037830 GTGGGAAGCAGATTTGAGCCACCAAACCTTGTCTCCCTGAGCAGCAGTAGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAGTTGAAGATT
*
44037895 GT
131 AT
* * *
44037897 AGATTTTATCTCCATAAACAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * *
44037962 GTGGGAAGCAAATTTAAGCCACCAAGCATTGTCTCCCTGAGCAACAGCGGAGAAAGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAGTTGAAGATT
44038027 AT
131 AT
** *
44038029 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATGAATCTTATCTTTCCAAGAGA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
*
44038094 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCACTGAGCAGCAGCGGAGAAAGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAGTTGAAGATT
44038159 AT
131 AT
* *
44038161 ATATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
*
44038226 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAGTTGAAGATT
44038291 AT
131 AT
44038293 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
*
44038358 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAGTTGAAGATT
44038423 AT
131 AT
44038425 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * * * *
44038490 GTGGGAAGCAGATTTGAGCCCCCAAGTCTTATCTTCCTGA
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGA
44038530 AGTTGCAGAG
Statistics
Matches: 712, Mismatches: 53, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 712 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (132 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAGTTGAAGATT
AT
Found at i:44038068 original size:44 final size:44
Alignment explanation
Indices: 44037633--44038465 Score: 181
Period size: 44 Copynumber: 18.9 Consensus size: 44
44037623 GTGAAACACC
* * *
44037633 AGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGC-G
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC--CAT
* *
44037678 A-ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA-
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACCAT
* * * * * * **
44037722 AG-CCTTGTCTCCCTGAGCAGCAGCGGAG-AAAGTTGAAGATTAT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-TTGAAGACCAT
* * *
44037765 AGATCTTATCTCCCTAAGCAGTAGTGGAGCGGATTGAAAACGAT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAT
*
44037809 -GAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTG-AGCCACCA-
1 AG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGA-TTGAAG--ACCAT
* * * * * * * ***
44037854 A-ACCTTGTCTCCCTGAGCAGCAGTAGAGAAGGTTGAAGATTGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAT
* * * * *
44037897 AGATTTTATCTCCATAAACAGTAGTGGAGCAGATCGAAGACGGC-G
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC--CAT
* * *
44037942 A-ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAGCCACCA-
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACCAT
* * ** * * **
44037986 AG--CATTGTCTCCCTGAGCAACAGCGGAG-AAAGTTGAAGATTAT
1 AGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGA-TTGAAGACCAT
* *
44038029 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGAT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAT
* *
44038073 -GAATCTTATCTTTCC-AAG-AG-AGTGGGAAGCAGATTTAAGCCACCA-
1 AG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACCAT
* * * * * * * **
44038118 AG-CCTTGTCTCACTGAGCAGCAGCGGAG-AAAGTTGAAGATTAT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-TTGAAGACCAT
* * * *
44038161 ATATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGC-G
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC--CAT
* *
44038206 A-ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA-
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACCAT
* * * * * * * **
44038250 AG-CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTAT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAT
* *
44038293 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGC-G
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC--CAT
* *
44038338 A-ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA-
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACCAT
* * * * * * * **
44038382 AG-CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTAT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAT
*
44038425 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
44038466 GGCGAATCTT
Statistics
Matches: 549, Mismatches: 151, Indels: 177
0.63 0.17 0.20
Matches are distributed among these distances:
42 34 0.06
43 59 0.11
44 380 0.69
45 48 0.09
46 28 0.05
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (44 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAT
Found at i:44038653 original size:46 final size:46
Alignment explanation
Indices: 44038586--44038679 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
44038576 ATGCAGTAGG
44038586 AAGGAATACTAAAACCCAGCACGACCGAGCAAAACTTGGCATTTTT
1 AAGGAATACTAAAACCCAGCACGACCGAGCAAAACTTGGCATTTTT
44038632 AAGGAATACTAAAACCCAGCACGACCGAGCAAAACTTGGCATTTTT
1 AAGGAATACTAAAACCCAGCACGACCGAGCAAAACTTGGCATTTTT
44038678 AA
1 AA
44038680 AGTCTTTGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (46 bp):
AAGGAATACTAAAACCCAGCACGACCGAGCAAAACTTGGCATTTTT
Found at i:44040579 original size:98 final size:98
Alignment explanation
Indices: 44040452--44040644 Score: 316
Period size: 98 Copynumber: 2.0 Consensus size: 98
44040442 AAAAATCATG
* *
44040452 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTCGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
44040517 AAATCTTGGATAAGTGGATGTTCTTTTAAATTA
66 AAATCTTGGATAAGTGGATGCTCTTTTAAATTA
* *
44040550 AAGGAAATAATTCCGAGTTCG-GATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGGTTTCT
1 AAGGAAAT-ATTCCGAGTTCGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
*
44040614 TAAATCTTGGATGAGTGGATGCTCTTTTAAA
65 TAAATCTTGGATAAGTGGATGCTCTTTTAAA
44040645 ATTTTTATAT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 77 0.88
99 11 0.12
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTCGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGCTCTTTTAAATTA
Found at i:44044209 original size:44 final size:44
Alignment explanation
Indices: 44044146--44044239 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
44044136 GTCTCGACTT
44044146 TCATTTTCATACGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATACGCTTATCAAATATAAGTATTGTATTAACCAAA
*
44044190 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATACGCTTATCAAATATAAGTATTGTATTAACCAAA
44044234 TCATTT
1 TCATTT
44044240 ATTGAATATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.41
Consensus pattern (44 bp):
TCATTTTCATACGCTTATCAAATATAAGTATTGTATTAACCAAA
Found at i:44044233 original size:22 final size:22
Alignment explanation
Indices: 44044164--44044234 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
44044154 ATACGCTTAT
44044164 CAAATATAAGTATTGTATTAAC
1 CAAATATAAGTATTGTATTAAC
** * *
44044186 CAAATCAT-TTTCATATG-CTT-AT
1 CAAAT-ATAAGT-AT-TGTATTAAC
44044208 CAAATATAAGTATTGTATTAAC
1 CAAATATAAGTATTGTATTAAC
44044230 CAAAT
1 CAAAT
44044235 CATTTATTGA
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 19 0.54
23 6 0.17
24 2 0.06
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (22 bp):
CAAATATAAGTATTGTATTAAC
Found at i:44044251 original size:22 final size:21
Alignment explanation
Indices: 44044218--44044261 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
44044208 CAAATATAAG
*
44044218 TATTGTATTAACCAAA-TCATT
1 TATTGAATTAA-CAAATTCATT
44044239 TATTGAATATAACAAATTCATT
1 TATTGAAT-TAACAAATTCATT
44044261 T
1 T
44044262 TCATATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (21 bp):
TATTGAATTAACAAATTCATT
Found at i:44046782 original size:16 final size:16
Alignment explanation
Indices: 44046763--44046795 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44046753 AATTATTATT
*
44046763 AAATAAAAATTAATAA
1 AAATAAAAATAAATAA
44046779 AAATAAAAATAAATAA
1 AAATAAAAATAAATAA
44046795 A
1 A
44046796 TTGATCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAAAATAAATAA
Found at i:44050404 original size:66 final size:66
Alignment explanation
Indices: 44050264--44050424 Score: 171
Period size: 66 Copynumber: 2.4 Consensus size: 66
44050254 GGAAATTTTT
* * * *
44050264 AAATGTAAGACCATAGCTGGGCTGTGGCATTTTAATGAAAAGACCATAACTGAGTTATGACACTT
1 AAATGTAAGACCATGGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGAGTTATGACACTA
*
44050329 T
66 C
* * * * * * * *
44050330 GAACGTAAGACCATGGCTGGGCTATGGCATTCTGATGATAATACCATAATTGGGTTATGGCACTA
1 AAATGTAAGACCATGGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGAGTTATGACACTA
44050395 C
66 C
* *
44050396 AAATGTAAGATCATGG-TAGGGCCATGGCA
1 AAATGTAAGACCATGGCT-GGGCTATGGCA
44050425 ATACATGTGT
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
65 1 0.01
66 76 0.99
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (66 bp):
AAATGTAAGACCATGGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGAGTTATGACACTA
C
Found at i:44059633 original size:21 final size:21
Alignment explanation
Indices: 44059607--44059650 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
44059597 GTTGCAGGTC
44059607 AACAAGTCCCAAATAAGGAGG
1 AACAAGTCCCAAATAAGGAGG
44059628 AACAAGTCCCAAATAAGGAGG
1 AACAAGTCCCAAATAAGGAGG
44059649 AA
1 AA
44059651 TGTGTAGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.09
Consensus pattern (21 bp):
AACAAGTCCCAAATAAGGAGG
Found at i:44061717 original size:43 final size:43
Alignment explanation
Indices: 44061661--44061926 Score: 254
Period size: 43 Copynumber: 6.2 Consensus size: 43
44061651 TCACAAAAAC
* *
44061661 GCCGCTATAGAACATGACCTTTAACGACGCTTTTCCCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGACGCTTTTCCCACAAAT
* * *
44061704 GCTGCTAAAGAACATGACCTATATCGACGCTTTTCCCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGACGCTTTTCCCACAAAT
* * *
44061747 GCCGCTAAAGAACATGACCTTTAGCTG-TGCTTTTCTCC-TAAAC
1 GCCGCTAAAGAACATGACCTTTAGC-GACGCTTTTC-CCACAAAT
* * *
44061790 GCCGCTAAAGAACATGACCTTTAGTTG-CGCTTTT-CCTCAAAC
1 GCCGCTAAAGAACATGACCTTTAG-CGACGCTTTTCCCACAAAT
* * * * *
44061832 ACCGTTAAAGAATATTGACCTTTAGCTACGCTTTT-CCAAAAAT
1 GCCGCTAAAGAACA-TGACCTTTAGCGACGCTTTTCCCACAAAT
* * ** * * *
44061875 GCCTCTAAAGAACATGACATTTAGCGGTGTTTTTCCCAAAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGACGCTTTTCCCACAAAT
44061918 GCCGCTAAA
1 GCCGCTAAA
44061927 AGTCATGTTC
Statistics
Matches: 184, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
41 2 0.01
42 30 0.16
43 149 0.81
44 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGACGCTTTTCCCACAAAT
Found at i:44061925 original size:128 final size:130
Alignment explanation
Indices: 44061647--44061926 Score: 336
Period size: 128 Copynumber: 2.2 Consensus size: 130
44061637 CTTAATGGCG
* ** *
44061647 TTTCTCACAAAAACGCCGCTATAGAACATGACCTTTAACGACGCTTTTCCCACAAATGCTGCTAA
1 TTTCTC-CAAAAACGCCGCTAAAGAACATGACCTTTAACGACGCTTTTCCCACAAACACCGCTAA
* * * *
44061712 AGAACATGACCTATATCGACGCTTTTCCCACAAATGCCGCTAAAGAACATGACCTTTAGCTGTGC
65 AGAACATGACCTATAGCGACGCTTTTCCCAAAAATGCCGCTAAAGAACATGACATTTAGCGGTGC
44061777 T
130 T
* ** * *
44061778 TTTCTCC-TAAACGCCGCTAAAGAACATGACCTTTAGTTG-CGCTTTT-CCTCAAACACCGTTAA
1 TTTCTCCAAAAACGCCGCTAAAGAACATGACCTTTA-ACGACGCTTTTCCCACAAACACCGCTAA
* * * *
44061840 AGAATATTGACCTTTAGCTACGCTTTT-CCAAAAATGCCTCTAAAGAACATGACATTTAGCGGTG
65 AGAACA-TGACCTATAGCGACGCTTTTCCCAAAAATGCCGCTAAAGAACATGACATTTAGCGGTG
*
44061904 TT
129 CT
44061906 TTTC-CCAAAAACGCCGCTAAA
1 TTTCTCCAAAAACGCCGCTAAA
44061927 AGTCATGTTC
Statistics
Matches: 127, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
127 2 0.02
128 67 0.53
129 50 0.39
130 2 0.02
131 6 0.05
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (130 bp):
TTTCTCCAAAAACGCCGCTAAAGAACATGACCTTTAACGACGCTTTTCCCACAAACACCGCTAAA
GAACATGACCTATAGCGACGCTTTTCCCAAAAATGCCGCTAAAGAACATGACATTTAGCGGTGCT
Found at i:44062601 original size:33 final size:33
Alignment explanation
Indices: 44062563--44062651 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
44062553 AGGAAGAAAT
*
44062563 AAAGGGATTTGGGAAATTGGGAATTTTGATCAG
1 AAAGGGATTTGGGAAGTTGGGAATTTTGATCAG
44062596 AAAGGGATTTGGGAAGTTGAGG-ATTTTGATCAG
1 AAAGGGATTTGGGAAGTTG-GGAATTTTGATCAG
44062629 AAAGGGATTTGGGAAGTTGGGAA
1 AAAGGGATTTGGGAAGTTGGGAA
44062652 ATTGGGGAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
32 2 0.04
33 49 0.92
34 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.37, T:0.28
Consensus pattern (33 bp):
AAAGGGATTTGGGAAGTTGGGAATTTTGATCAG
Found at i:44064321 original size:18 final size:19
Alignment explanation
Indices: 44064298--44064337 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
44064288 CATAATGATA
44064298 TATATAATGTA-AT-TTTAT
1 TATATAAT-TACATATTTAT
44064316 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
44064335 TAT
1 TAT
44064338 TTTATTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.10
18 10 0.50
19 8 0.40
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:44064342 original size:95 final size:100
Alignment explanation
Indices: 44064174--44064373 Score: 304
Period size: 95 Copynumber: 2.0 Consensus size: 100
44064164 TTTAAAATAT
44064174 AAAATATATTTAACATAATGATAAATATCACATATATAATTTTTCATTATATAATTACATATTTA
1 AAAATATATTTAACATAATGAT-AATATCACATATATAATTTTTCATTATATAATTACATATTTA
*
44064239 TTGATTTATTTATATAAATAAAAGAGTTATTAATTA
65 TTGATTTATTTATATAAATAAAAAAGTTATTAATTA
* *
44064275 AAAATATATTTAACATAATGAT-ATAT-ATA-ATGTAA-TTTT-ATTATATAATTACATATTTAT
1 AAAATATATTTAACATAATGATAATATCACATATATAATTTTTCATTATATAATTACATATTTAT
*
44064335 T-ATTTTATTTCTATAAATAAAAAAGTTATTAATTA
66 TGA-TTTATTTATATAAATAAAAAAGTTATTAATTA
44064370 AAAA
1 AAAA
44064374 GATGAATTAA
Statistics
Matches: 94, Mismatches: 4, Indels: 8
0.89 0.04 0.08
Matches are distributed among these distances:
94 1 0.01
95 56 0.60
96 4 0.04
97 5 0.05
98 2 0.02
99 4 0.04
101 22 0.23
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (100 bp):
AAAATATATTTAACATAATGATAATATCACATATATAATTTTTCATTATATAATTACATATTTAT
TGATTTATTTATATAAATAAAAAAGTTATTAATTA
Found at i:44064877 original size:24 final size:24
Alignment explanation
Indices: 44064850--44064901 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
44064840 CAAAGTATAC
*
44064850 AGAGAGAAAAAAAAGTAGAATG-TT
1 AGAGAGAAAAAAAAG-AGAAAGATT
* *
44064874 AGAGAGTAATAAAAGAGAAAGATT
1 AGAGAGAAAAAAAAGAGAAAGATT
44064898 AGAG
1 AGAG
44064902 TGCAATTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (24 bp):
AGAGAGAAAAAAAAGAGAAAGATT
Found at i:44090348 original size:24 final size:23
Alignment explanation
Indices: 44090288--44090360 Score: 74
Period size: 24 Copynumber: 3.1 Consensus size: 23
44090278 TACGGGTTGT
44090288 ATAACGGGAAGCTCATAAGAGCC
1 ATAACGGGAAGCTCATAAGAGCC
* **
44090311 ATAATTGGGAAGCTCATGTGAGCC
1 ATAA-CGGGAAGCTCATAAGAGCC
* **
44090335 AATAACGGGCAGCTCCGAAGAGCC
1 -ATAACGGGAAGCTCATAAGAGCC
44090359 AT
1 AT
44090361 TAATCAAGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 6 0.15
24 29 0.74
25 4 0.10
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.16
Consensus pattern (23 bp):
ATAACGGGAAGCTCATAAGAGCC
Found at i:44090420 original size:25 final size:25
Alignment explanation
Indices: 44090345--44090421 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
44090335 AATAACGGGC
* *
44090345 AGCTCCGAAGAGCCATTAATCAAGA
1 AGCTCCGGAGAGCCATTAATCAGGA
* * * *
44090370 AACTCCAGATAGCCA-TATATCGGGA
1 AGCTCCGGAGAGCCATTA-ATCAGGA
*
44090395 AGCTCCGGAGAGCGATTAATCAGGA
1 AGCTCCGGAGAGCCATTAATCAGGA
44090420 AG
1 AG
44090422 ATCACAAAGA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
24 2 0.05
25 35 0.90
26 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (25 bp):
AGCTCCGGAGAGCCATTAATCAGGA
Found at i:44093584 original size:22 final size:20
Alignment explanation
Indices: 44093558--44093602 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
44093548 TAAAATTAAT
*
44093558 ATAAAATTATATTTGATTAAAA
1 ATAAAATCAT-TTTGA-TAAAA
*
44093580 ATAAAATCATTTTTATAAAA
1 ATAAAATCATTTTGATAAAA
44093600 ATA
1 ATA
44093603 CATTCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 9 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAAAATCATTTTGATAAAA
Found at i:44094902 original size:26 final size:24
Alignment explanation
Indices: 44094851--44094909 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
44094841 TTTTTAAAAA
**
44094851 TATTAAAAAAATTGAAACAAAATT
1 TATTAAAAAAATCAAAACAAAATT
*
44094875 TATTAAAAAAATCAAAACACAATT
1 TATTAAAAAAATCAAAACAAAATT
*
44094899 T-TTATAAAAAT
1 TATTAAAAAAAT
44094910 GGATTGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 9 0.29
24 22 0.71
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (24 bp):
TATTAAAAAAATCAAAACAAAATT
Found at i:44106197 original size:30 final size:29
Alignment explanation
Indices: 44106137--44106199 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
44106127 AAAAAAACAA
* *
44106137 TCACTAAACTTTGAAAAGTTACAACTTAG
1 TCACTAAACTTTGAAAAATAACAACTTAG
*
44106166 TCACTGAACTTTAGAAAAATAACAA-TCTAG
1 TCACTAAACTTT-GAAAAATAACAACT-TAG
44106196 TCAC
1 TCAC
44106200 CAATAACCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (29 bp):
TCACTAAACTTTGAAAAATAACAACTTAG
Found at i:44116812 original size:21 final size:22
Alignment explanation
Indices: 44116783--44116829 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
44116773 CTTCTTTAAA
*
44116783 TATCATAAAGTTAATA-TTATT
1 TATCATAAAGTTAAAATTTATT
* *
44116804 TATCTTAAATTTAAAATTTATT
1 TATCATAAAGTTAAAATTTATT
44116826 TATC
1 TATC
44116830 CCTTCATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (22 bp):
TATCATAAAGTTAAAATTTATT
Found at i:44117537 original size:19 final size:20
Alignment explanation
Indices: 44117497--44117539 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
44117487 GTTTTTTTTT
*
44117497 TTTTTAATTTATAACTAATC
1 TTTTTAATATATAACTAATC
44117517 TTTTTAATAT-TAA-TAACTC
1 TTTTTAATATATAACTAA-TC
44117536 TTTT
1 TTTT
44117540 ATTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 9 0.43
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTAATATATAACTAATC
Found at i:44126594 original size:44 final size:44
Alignment explanation
Indices: 44126481--44126595 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 44
44126471 ATTAGGATAT
*
44126481 CATAGCATCTTTCAGCTATTGTCTTAATCATGTTTACCATGATGC
1 CATAGCATCTTTCAGCTATTGTCTT-ATCATGTTCACCATGATGC
* * * * * *
44126526 CATAACGTCTTTCAACCATGGTCTTATCAT-TTCCATCATGATGC
1 CATAGCATCTTTCAGCTATTGTCTTATCATGTT-CACCATGATGC
44126570 CATAGCATCTTTCAGCTATTGTCTTA
1 CATAGCATCTTTCAGCTATTGTCTTA
44126596 CCCATTTTAG
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
43 2 0.04
44 35 0.61
45 20 0.35
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (44 bp):
CATAGCATCTTTCAGCTATTGTCTTATCATGTTCACCATGATGC
Found at i:44129234 original size:111 final size:110
Alignment explanation
Indices: 44129095--44129317 Score: 376
Period size: 111 Copynumber: 2.0 Consensus size: 110
44129085 TCTAAATATA
*
44129095 TTGTTTCAACCAAGGTTAAGTTTTTGTTTGATTTTTAAGAATATTATTTATTTTTATTTCTAGAA
1 TTGTTTCAACCAAGGTTAAGTTTTTGTTTGATTTTTAAGAATATTATTTATTTTTATTTCTAAAA
*
44129160 AAACATTTTTATTTTTT-TAACATATGTTTGGTAAATAGAAATAATT
66 AAACATTTTTATTTTTTCT-A-ATATGTTTGATAAATAGAAATAATT
*
44129206 TTGTTTCAACCAAGGTTAAGTTTTTGTTTGGTTTTTAAGAATATTATTTATTTTTATTTCTAAAA
1 TTGTTTCAACCAAGGTTAAGTTTTTGTTTGATTTTTAAGAATATTATTTATTTTTATTTCTAAAA
* *
44129271 AAACATTTTTCTTTTTTCTAATATGTTTGATAAATATAAATAATT
66 AAACATTTTTATTTTTTCTAATATGTTTGATAAATAGAAATAATT
44129316 TT
1 TT
44129318 TTTAAAAAAT
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
110 25 0.24
111 80 0.75
112 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (110 bp):
TTGTTTCAACCAAGGTTAAGTTTTTGTTTGATTTTTAAGAATATTATTTATTTTTATTTCTAAAA
AAACATTTTTATTTTTTCTAATATGTTTGATAAATAGAAATAATT
Found at i:44130212 original size:43 final size:43
Alignment explanation
Indices: 44130151--44130336 Score: 266
Period size: 43 Copynumber: 4.3 Consensus size: 43
44130141 GCGTCGCTAA
44130151 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
* * *
44130194 CTTTAGCGGCGCTTATCCCACAAACACCGCTAAAGGCCAAGAA
1 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
* * *
44130237 CATTAACGGCGCATT-TCTCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGC-TTATCCCACAAACGCCGCTAAAGACCAAGAC
*
44130280 CTTTAGCAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTT---AGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
44130326 CTTTAGCGGCG
1 CTTTAGCGGCG
44130337 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
43 84 0.67
44 2 0.02
45 2 0.02
46 38 0.30
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.17
Consensus pattern (43 bp):
CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:44133626 original size:61 final size:61
Alignment explanation
Indices: 44133531--44133669 Score: 251
Period size: 61 Copynumber: 2.3 Consensus size: 61
44133521 ATAATGAAAC
* *
44133531 CGAAATACAAATAATATGTTGCTTAAAATCCATTAAACAAAAGTATTAGGAACTCATTAAA
1 CGAAATACAAACAATATGCTGCTTAAAATCCATTAAACAAAAGTATTAGGAACTCATTAAA
44133592 CGAAATACAAACAATATGCTGCTTAAAATCCATTAAACAAAAGTATTAGGAACTCATTAAA
1 CGAAATACAAACAATATGCTGCTTAAAATCCATTAAACAAAAGTATTAGGAACTCATTAAA
*
44133653 TGAAATACAAACAATAT
1 CGAAATACAAACAATAT
44133670 AGCACAAAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 75 1.00
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.26
Consensus pattern (61 bp):
CGAAATACAAACAATATGCTGCTTAAAATCCATTAAACAAAAGTATTAGGAACTCATTAAA
Found at i:44135285 original size:14 final size:14
Alignment explanation
Indices: 44135235--44135302 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
44135225 AAAATTAAAT
* *
44135235 CACTAACTCTTAAC
1 CACTAACCCCTAAC
*
44135249 CACTAACCTCTAAC
1 CACTAACCCCTAAC
*
44135263 CCCTAACCCCTAAC
1 CACTAACCCCTAAC
*
44135277 TACTAACCCCTAAC
1 CACTAACCCCTAAC
*
44135291 C-CCAACCCCTAA
1 CACTAACCCCTAA
44135303 ACATTATTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
13 10 0.22
14 35 0.78
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (14 bp):
CACTAACCCCTAAC
Found at i:44135299 original size:6 final size:7
Alignment explanation
Indices: 44135245--44135302 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
44135235 CACTAACTCT
*
44135245 TAACCAC
1 TAACCCC
*
44135252 TAACCTC
1 TAACCCC
44135259 TAACCCC
1 TAACCCC
44135266 TAACCCC
1 TAACCCC
**
44135273 TAACTAC
1 TAACCCC
44135280 TAACCCC
1 TAACCCC
44135287 TAACCCC
1 TAACCCC
44135294 -AACCCC
1 TAACCCC
44135300 TAA
1 TAA
44135303 ACATTATTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
6 6 0.14
7 38 0.86
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.17
Consensus pattern (7 bp):
TAACCCC
Found at i:44135807 original size:41 final size:41
Alignment explanation
Indices: 44135749--44136228 Score: 708
Period size: 41 Copynumber: 11.7 Consensus size: 41
44135739 AAATGTTTTT
* * *
44135749 GCGGCGCTTTTCTAAAAACACCGTTAAAGGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
*
44135790 GCGGCGCTTTTCCAAAAACGCCGCTAAAAGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
** * * *
44135831 GCGGCGCTTTTTTAAAAACACCGCTATAGGTCTAAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* *
44135872 GCGGCGCTTTTTCAAAAACACCGCTAAAGGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* *
44135913 GCGGCGCTTTTCCATAAACGCCGCTAAAGGTCTAAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* * *
44135954 GCGGCGCCTTTCCAAAAACGCCGCTAAAGCTCTGAGCACTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
*
44135995 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTAAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* * *
44136036 GCGGCGCTTTTCCCAAAATGCCGCTAAAAGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* *
44136077 ACGGCGCTTTTCCAGAAACGCCGCTAAAGGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* * *
44136118 GCGGCGCTTTTCCATAAATGTCGCTAAAGGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
*
44136159 GCGGCGCTTTTCCATAAACGCCGCTAAAGGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* *
44136200 GCGGCGCTTTTTCAAAAATGCCGCTAAAG
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAG
44136229 CCTCGAAAGG
Statistics
Matches: 395, Mismatches: 44, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 395 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
Found at i:44140946 original size:73 final size:74
Alignment explanation
Indices: 44140849--44140997 Score: 291
Period size: 73 Copynumber: 2.0 Consensus size: 74
44140839 TTCAAGACTT
44140849 ATGTAATGTTAGTGATTCAAAGACTTATGTAATATTTTTAATTATGTAGTGATTCAATTCGGTTA
1 ATGTAATGTTAGTGATTCAAAGACTTATGTAATATTTTTAATTATGTAGTGATTCAATTCGGTTA
44140914 ATTCGGGTA
66 ATTCGGGTA
44140923 ATGTAATGTTAG-GATTCAAAGACTTATGTAATATTTTTAATTATGTAGTGATTCAATTCGGTTA
1 ATGTAATGTTAGTGATTCAAAGACTTATGTAATATTTTTAATTATGTAGTGATTCAATTCGGTTA
44140987 ATTCGGGTA
66 ATTCGGGTA
44140996 AT
1 AT
44140998 TCGGTTAATT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 63 0.84
74 12 0.16
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.43
Consensus pattern (74 bp):
ATGTAATGTTAGTGATTCAAAGACTTATGTAATATTTTTAATTATGTAGTGATTCAATTCGGTTA
ATTCGGGTA
Found at i:44140991 original size:9 final size:9
Alignment explanation
Indices: 44140977--44141014 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
44140967 GTAGTGATTC
44140977 AATTCGGTT
1 AATTCGGTT
*
44140986 AATTCGGGT
1 AATTCGGTT
44140995 AATTCGGTT
1 AATTCGGTT
44141004 AATTCGGTT
1 AATTCGGTT
44141013 AA
1 AA
44141015 CCGAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:44142207 original size:46 final size:46
Alignment explanation
Indices: 44142155--44142387 Score: 277
Period size: 46 Copynumber: 5.5 Consensus size: 46
44142145 TTTTTAAAAA
*
44142155 TTTAAAATTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTT
1 TTTAAAATTTTAATATATTTTTAAAATTTTCAAATATTTTTTATTT
*
44142201 TTTAAAATTTTAATATA-TTTT--AA---TC--ATATTCTTTATTT
1 TTTAAAATTTTAATATATTTTTAAAATTTTCAAATATTTTTTATTT
* *
44142239 TTT-AATTTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTT
1 TTTAAAATTTTAATATATTTTTAAAATTTTCAAATATTTTTTATTT
*
44142284 TTTAAAATTTTAATATA-TTTT--AA---TC--ATATTCTTTATTT
1 TTTAAAATTTTAATATATTTTTAAAATTTTCAAATATTTTTTATTT
* *
44142322 TTT-AATTTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTT
1 TTTAAAATTTTAATATATTTTTAAAATTTTCAAATATTTTTTATTT
44142367 TTTAAAATTTTAATATATTTT
1 TTTAAAATTTTAATATATTTT
44142388 AATCATATTC
Statistics
Matches: 156, Mismatches: 13, Indels: 36
0.76 0.06 0.18
Matches are distributed among these distances:
37 22 0.14
38 38 0.24
40 8 0.05
43 8 0.05
45 38 0.24
46 42 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (46 bp):
TTTAAAATTTTAATATATTTTTAAAATTTTCAAATATTTTTTATTT
Found at i:44142237 original size:38 final size:37
Alignment explanation
Indices: 44142188--44142424 Score: 222
Period size: 38 Copynumber: 5.9 Consensus size: 37
44142178 AAATTTTCAA
*
44142188 ATATTTTTTATTTTTTAAAATTTTAATATATTTTAATC
1 ATATTCTTTATTTTTT-AAATTTTAATATATTTTAATC
* *
44142226 ATATTCTTTATTTTTTAATTTTTTATATATTTTTAAAATTTTC
1 ATATTCTTTATTTTTTAAATTTTAATATA-TTTT--AA---TC
*
44142269 AAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATC
1 --ATATTCTTTATTTTTT-AAATTTTAATATATTTTAATC
* *
44142309 ATATTCTTTATTTTTTAATTTTTTATATATTTTTAAAATTTTC
1 ATATTCTTTATTTTTTAAATTTTAATATA-TTTT--AA---TC
*
44142352 AAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATC
1 --ATATTCTTTATTTTTT-AAATTTTAATATATTTTAATC
* *
44142392 ATATTCTTTATTTTTTAATTTTTTATATATTTT
1 ATATTCTTTATTTTTTAAATTTTAATATATTTT
44142425 TTATCATTTT
Statistics
Matches: 166, Mismatches: 15, Indels: 37
0.76 0.07 0.17
Matches are distributed among these distances:
37 37 0.22
38 53 0.32
40 8 0.05
43 8 0.05
45 38 0.23
46 22 0.13
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (37 bp):
ATATTCTTTATTTTTTAAATTTTAATATATTTTAATC
Found at i:44142238 original size:45 final size:46
Alignment explanation
Indices: 44142189--44142416 Score: 223
Period size: 45 Copynumber: 5.4 Consensus size: 46
44142179 AATTTTCAAA
44142189 TATTTTTT-ATTTTTTAAAATTTTAATATATTTTAATCATATTCTT
1 TATTTTTTAATTTTTTAAAATTTTAATATATTTTAATCATATTCTT
* *
44142234 TATTTTTTAATTTTTTATATATTTTTAA-A-A-TTT--TCA-A----A
1 TATTTTTTAATTTTTTA-A-AATTTTAATATATTTTAATCATATTCTT
44142272 TATTTTTT-ATTTTTTAAAATTTTAATATATTTTAATCATATTCTT
1 TATTTTTTAATTTTTTAAAATTTTAATATATTTTAATCATATTCTT
* *
44142317 TATTTTTTAATTTTTTATATATTTTTAA-A-A-TTT--TCA-A----A
1 TATTTTTTAATTTTTTA-A-AATTTTAATATATTTTAATCATATTCTT
44142355 TATTTTTT-ATTTTTTAAAATTTTAATATATTTTAATCATATTCTT
1 TATTTTTTAATTTTTTAAAATTTTAATATATTTTAATCATATTCTT
44142400 TATTTTTTAATTTTTTA
1 TATTTTTTAATTTTTTA
44142417 TATATTTTTT
Statistics
Matches: 148, Mismatches: 8, Indels: 53
0.71 0.04 0.25
Matches are distributed among these distances:
35 14 0.09
36 4 0.03
37 18 0.12
38 22 0.15
40 6 0.04
41 2 0.01
42 2 0.01
43 6 0.04
45 30 0.20
46 26 0.18
47 4 0.03
48 14 0.09
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (46 bp):
TATTTTTTAATTTTTTAAAATTTTAATATATTTTAATCATATTCTT
Found at i:44142256 original size:83 final size:83
Alignment explanation
Indices: 44142162--44142425 Score: 528
Period size: 83 Copynumber: 3.2 Consensus size: 83
44142152 AAATTTAAAA
44142162 TTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATCA
1 TTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATCA
44142227 TATTCTTTATTTTTTAAT
66 TATTCTTTATTTTTTAAT
44142245 TTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATCA
1 TTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATCA
44142310 TATTCTTTATTTTTTAAT
66 TATTCTTTATTTTTTAAT
44142328 TTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATCA
1 TTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATCA
44142393 TATTCTTTATTTTTTAAT
66 TATTCTTTATTTTTTAAT
44142411 TTTTTATATATTTTT
1 TTTTTATATATTTTT
44142426 TATCATTTTT
Statistics
Matches: 181, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 181 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (83 bp):
TTTTTATATATTTTTAAAATTTTCAAATATTTTTTATTTTTTAAAATTTTAATATATTTTAATCA
TATTCTTTATTTTTTAAT
Found at i:44142369 original size:19 final size:18
Alignment explanation
Indices: 44142234--44142350 Score: 80
Period size: 19 Copynumber: 6.3 Consensus size: 18
44142224 TCATATTCTT
*
44142234 TATTTTTTAATTTTTTATA
1 TATTTTTT-ATTTTTTAAA
* * *
44142253 TATTTTTAAAATTTTCAAA
1 TATTTTT-TATTTTTTAAA
44142272 TATTTTTTATTTTTTAAA
1 TATTTTTTATTTTTTAAA
* *
44142290 -ATTTTAATATATTTTAATCA
1 TATTTT-TTATTTTTTAA--A
*
44142310 TATTCTTTATTTTTT-AA
1 TATTTTTTATTTTTTAAA
44142327 T-TTTTTATATATTTTTAAA
1 TATTTTT-TAT-TTTTTAAA
44142346 -ATTTT
1 TATTTT
44142351 CAAATATTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
16 4 0.05
17 10 0.13
18 22 0.29
19 28 0.37
20 8 0.11
21 4 0.05
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTTTATTTTTTAAA
Found at i:44142374 original size:19 final size:19
Alignment explanation
Indices: 44142317--44142409 Score: 64
Period size: 19 Copynumber: 4.9 Consensus size: 19
44142307 TCATATTCTT
*
44142317 TATTTTTTAATTTTTT-ATA
1 TATTTTTT-ATTTTTTAAAA
* ** *
44142336 TATTTTTAAAATTTTCAAA
1 TATTTTTTATTTTTTAAAA
44142355 TATTTTTTATTTTTTAAAA
1 TATTTTTTATTTTTTAAAA
** * *
44142374 T-TTTAATATATTTTAATCA
1 TATTTTTTATTTTTTAA-AA
*
44142393 TATTCTTTATTTTTTAA
1 TATTTTTTATTTTTTAA
44142410 TTTTTTATAT
Statistics
Matches: 55, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
18 17 0.31
19 27 0.49
20 11 0.20
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTTATTTTTTAAAA
Found at i:44151420 original size:52 final size:52
Alignment explanation
Indices: 44151342--44151451 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
44151332 AATATCCTTC
44151342 CATTTGTTTCTTAGACCATTAATCAAGTTATTAGTGTCCTATGTATGTAGGT
1 CATTTGTTTCTTAGACCATTAATCAAGTTATTAGTGTCCTATGTATGTAGGT
44151394 CATTTGTTTCTTAGACCATTAATCAAGTTATTAGTGTCCTATGTATGTAGGT
1 CATTTGTTTCTTAGACCATTAATCAAGTTATTAGTGTCCTATGTATGTAGGT
*
44151446 CCTTTG
1 CATTTG
44151452 ATTGCTACAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.45
Consensus pattern (52 bp):
CATTTGTTTCTTAGACCATTAATCAAGTTATTAGTGTCCTATGTATGTAGGT
Found at i:44154162 original size:16 final size:15
Alignment explanation
Indices: 44154136--44154165 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
44154126 GTTGATAATT
44154136 AAATATATATTAAAA
1 AAATATATATTAAAA
44154151 AAATAGTATATTAAA
1 AAATA-TATATTAAA
44154166 TTGATATAAT
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:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAATATATATTAAAA
Found at i:44154238 original size:9 final size:10
Alignment explanation
Indices: 44154209--44154253 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
44154199 TTTACATACA
44154209 TAATAAATA-
1 TAATAAATAT
*
44154218 TAA-ATATAT
1 TAATAAATAT
44154227 TAATAAAT-T
1 TAATAAATAT
44154236 TAATAAATAT
1 TAATAAATAT
44154246 ATAATAAA
1 -TAATAAA
44154254 GCTTGCATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 4 0.13
9 15 0.50
10 4 0.13
11 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATAAATAT
Found at i:44155107 original size:49 final size:49
Alignment explanation
Indices: 44155052--44155155 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
44155042 TCATGTGTTA
* * ** *
44155052 TAATTTTATACAGTGTTGAGTTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
*
44155101 TAATTTTATAAAGTGTTCCCCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
44155150 T-ATTTT
1 TAATTTT
44155156 GTTTTTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
48 5 0.10
49 44 0.90
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:44157338 original size:39 final size:41
Alignment explanation
Indices: 44157290--44157387 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 41
44157280 CTATTACACA
*
44157290 CCTCTATTCCATTCAACCAAAC-ACAAGAATACC-ATTACG
1 CCTCTATTCCATTCAACCAAACAAAAAGAATACCTATTACG
*
44157329 CCTCTATTCCATTCCATTCAACCAAACAAAAAGATTACCTATTACG
1 CCTC---T--ATTCCATTCAACCAAACAAAAAGAATACCTATTACG
44157375 CCTCTATTCCATT
1 CCTCTATTCCATT
44157388 ACAGCGAACC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
39 4 0.08
41 8 0.16
42 1 0.02
43 1 0.02
44 17 0.34
45 9 0.18
46 10 0.20
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.29
Consensus pattern (41 bp):
CCTCTATTCCATTCAACCAAACAAAAAGAATACCTATTACG
Found at i:44157345 original size:44 final size:46
Alignment explanation
Indices: 44157295--44157387 Score: 154
Period size: 46 Copynumber: 2.1 Consensus size: 46
44157285 ACACACCTCT
*
44157295 ATTCCATTCAACCAAAC-ACAAGAATACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAAGAATACCTATTACGCCTCTATTCC
*
44157339 ATTCCATTCAACCAAACAAAAAGATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAAGAATACCTATTACGCCTCTATTCC
44157385 ATT
1 ATT
44157388 ACAGCGAACC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 17 0.38
45 9 0.20
46 19 0.42
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.28
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAAGAATACCTATTACGCCTCTATTCC
Found at i:44157398 original size:46 final size:44
Alignment explanation
Indices: 44157303--44157401 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 44
44157293 CTATTCCATT
* * *
44157303 CAACCAAACACAAGAATACCATTACGCCTCTATTCCATTCCATT
1 CAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTACATG
*
44157347 CAACCAAACAAAAAGATTACCTATTACGCCTCTATTCCATTACA-G
1 CAACCAAAC-AAAAGAATACC-ATTACGCCTCTATTCCATTACATG
44157392 CGAACCAAAC
1 C-AACCAAAC
44157402 GCACCCTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 9 0.19
45 10 0.21
46 29 0.60
ACGTcount: A:0.39, C:0.32, G:0.06, T:0.22
Consensus pattern (44 bp):
CAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTACATG
Found at i:44161849 original size:9 final size:9
Alignment explanation
Indices: 44161831--44161870 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
44161821 ACATATATTA
*
44161831 AATTCAGTT
1 AATTCGGTT
*
44161840 AATTGGGTT
1 AATTCGGTT
*
44161849 AATTTGGTT
1 AATTCGGTT
44161858 AATTCGGTT
1 AATTCGGTT
44161867 AATT
1 AATT
44161871 TTTGATATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (9 bp):
AATTCGGTT
Found at i:44161858 original size:18 final size:18
Alignment explanation
Indices: 44161837--44161871 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44161827 ATTAAATTCA
*
44161837 GTTAATTGGGTTAATTTG
1 GTTAATTCGGTTAATTTG
44161855 GTTAATTCGGTTAATTT
1 GTTAATTCGGTTAATTT
44161872 TTGATATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (18 bp):
GTTAATTCGGTTAATTTG
Found at i:44171130 original size:20 final size:22
Alignment explanation
Indices: 44171097--44171140 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
44171087 TGTAAAAAAT
44171097 TATTTTCTAAGAA-TA-AATTC
1 TATTTTCTAAGAATTACAATTC
* *
44171117 TATTTTTTAGGAATTACAATTC
1 TATTTTCTAAGAATTACAATTC
44171139 TA
1 TA
44171141 CCAGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 2 0.10
22 7 0.35
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (22 bp):
TATTTTCTAAGAATTACAATTC
Found at i:44172770 original size:3 final size:3
Alignment explanation
Indices: 44172764--44172795 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
44172754 GTAGAAGAAC
*
44172764 AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44172796 AGGAAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:44187289 original size:2 final size:2
Alignment explanation
Indices: 44187282--44187307 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44187272 AAACAAAACA
44187282 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
44187308 CCTCACGCTC
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:44192736 original size:66 final size:66
Alignment explanation
Indices: 44192658--44192781 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
44192648 TTTCTGCACT
* ** * *
44192658 AATGTCGTTGCATGAGTTAATTCCAGATTG-AGTCTGAAATTTTCGCTGCAGTTGACAGATTTTC
1 AATGTCGCTGCATGAGTTAATTCCAGATTGCA-TCCAAAATTGTCGCCGCAGTTGACAGATTTTC
44192722 GC
65 GC
44192724 AATGTCGCTGCATGAGTTAATTCCAGATTGCATCCAAAATTGTCGCCGCAGTTGACAG
1 AATGTCGCTGCATGAGTTAATTCCAGATTGCATCCAAAATTGTCGCCGCAGTTGACAG
44192782 TCGTCTGATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
66 51 0.98
67 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (66 bp):
AATGTCGCTGCATGAGTTAATTCCAGATTGCATCCAAAATTGTCGCCGCAGTTGACAGATTTTCG
C
Found at i:44200754 original size:23 final size:23
Alignment explanation
Indices: 44200723--44200773 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
44200713 ACTTACTTTC
* *
44200723 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
44200746 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
44200769 TTACA
1 TTACA
44200774 TGCTCAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:44203098 original size:19 final size:20
Alignment explanation
Indices: 44203064--44203102 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
44203054 ATGGAGGATA
44203064 AATAATTTAAATTTTATCAAC
1 AATAATTT-AATTTTATCAAC
44203085 AATAATTT-ATTTTATCAA
1 AATAATTTAATTTTATCAA
44203103 TGAACATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATTTAATTTTATCAAC
Found at i:44206406 original size:93 final size:90
Alignment explanation
Indices: 44206309--44206475 Score: 244
Period size: 93 Copynumber: 1.8 Consensus size: 90
44206299 TTCTCTTTTT
* * * *
44206309 TTTTTTTGCACTCAATTGAGCACTTGAACTTTTAAAATGCATAAAAAAAGACCCTCAAACTTCTT
1 TTTTTTTCCACTCAATTGAGCACTTAAACTTTCAAAATGCAT-AAAAAA-ACCCTCAAAATTCTT
44206374 CAGAAAAAGCAATGAAGGCCCTGCTCTC
64 CA-AAAAAGCAATGAAGGCCCTGCTCTC
* * *
44206402 TTTTTTTCCACTCAATTGGGTACTTAAACTTTCAAAATGCATAAAAAAACCCTCAAAATTTTTCA
1 TTTTTTTCCACTCAATTGAGCACTTAAACTTTCAAAATGCATAAAAAAACCCTCAAAATTCTTCA
44206467 AAAAAGCAA
66 AAAAAGCAA
44206476 CTAGGCCCTA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
90 9 0.13
91 15 0.22
92 6 0.09
93 37 0.55
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (90 bp):
TTTTTTTCCACTCAATTGAGCACTTAAACTTTCAAAATGCATAAAAAAACCCTCAAAATTCTTCA
AAAAAGCAATGAAGGCCCTGCTCTC
Found at i:44206536 original size:18 final size:19
Alignment explanation
Indices: 44206515--44206561 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
44206505 AATAAATAAT
44206515 AAATAATAAATTTTAG-AA
1 AAATAATAAATTTTAGTAA
*
44206533 AAATTATTAAATTTTAGTAA
1 AAA-TAATAAATTTTAGTAA
44206553 AAAT-ATAAA
1 AAATAATAAA
44206562 AAAATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.28
19 13 0.52
20 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
AAATAATAAATTTTAGTAA
Found at i:44206705 original size:18 final size:19
Alignment explanation
Indices: 44206669--44206709 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
44206659 NNNNNNNNNN
**
44206669 TTTATATTTTTTTACAATT
1 TTTATATTTTTCCACAATT
44206688 TTTATATTTTTCCA-AATT
1 TTTATATTTTTCCACAATT
44206706 TTTA
1 TTTA
44206710 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATTTTTCCACAATT
Found at i:44207021 original size:90 final size:91
Alignment explanation
Indices: 44206823--44207043 Score: 347
Period size: 90 Copynumber: 2.4 Consensus size: 91
44206813 GAAAAAGTTT
*
44206823 GTCTTTTTGATGCATTTTAAAAGTTTAAATACCCAATTGAGTGCAAAAAAAATAGTAGGGGATTA
1 GTCTTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGTGCAAAAAAAATAGTAGGGGATTA
*
44206888 ATTGCTTTTTTTGAAAAGGTTTGAGT
66 ATTGCTTTTTTTGAAAAGGTTTGAGG
*
44206914 GTCTTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGTGC-AAAAAAATAGTAGGGGCTTA
1 GTCTTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGTGCAAAAAAAATAGTAGGGGATTA
*
44206978 ATTGCTTTTTTTTAAAAGGTTTGAGG
66 ATTGCTTTTTTTGAAAAGGTTTGAGG
* * * *
44207004 G-CTTTTTTTATGTATTTTAAAAGTTCAAGTACACAATTGA
1 GTC-TTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGA
44207044 ATAAAAAAAA
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
89 1 0.01
90 77 0.64
91 43 0.36
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (91 bp):
GTCTTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGTGCAAAAAAAATAGTAGGGGATTA
ATTGCTTTTTTTGAAAAGGTTTGAGG
Found at i:44207053 original size:91 final size:89
Alignment explanation
Indices: 44206826--44207097 Score: 332
Period size: 90 Copynumber: 3.0 Consensus size: 89
44206816 AAAGTTTGTC
* * *
44206826 TTTTTGATGCATTTTAAAAGTTTAAATACCCAATTGAGTGCAAAAAAAATAGTAGGGGATTAATT
1 TTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGT-AAAAAAAAATAGTAGGGGCTTAATT
* *
44206891 GCTTTTTTTGAAAAGGTTTGAGTGT
65 GCTTTTTTTTAAAAGGTTTGAGGGT
**
44206916 CTTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGTGCAAAAAAATAGTAGGGGCTTAATT
1 -TTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGTAAAAAAAAATAGTAGGGGCTTAATT
44206981 GCTTTTTTTTAAAAGGTTTGAGGGCT
65 GCTTTTTTTTAAAAGGTTTGAGGG-T
* * * * * * ** **
44207007 TTTTTTATGTATTTTAAAAGTTCAAGTACACAATTGAATAAAAAAAAAAAACAAAGGCTTAATTG
1 TTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGTAAAAAAAAATAGTAGGGGCTTAATTG
*
44207072 --TTTTTTTAAATAAGTTTGAGGGT
66 CTTTTTTTTAAA-AGGTTTGAGGGT
44207095 TTT
1 TTT
44207098 CACCCTTAAG
Statistics
Matches: 160, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
88 14 0.09
89 10 0.06
90 97 0.61
91 39 0.24
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.39
Consensus pattern (89 bp):
TTTTTGATGCATTTTAAAAGTTCAAATACCCAATTGAGTAAAAAAAAATAGTAGGGGCTTAATTG
CTTTTTTTTAAAAGGTTTGAGGGT
Found at i:44207240 original size:31 final size:29
Alignment explanation
Indices: 44207204--44207292 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
44207194 ATTTTAAAAA
*
44207204 TATACATGAATTTT-AGTTTAATGTGCAATTG
1 TATACATGAATTTTGA-TTT--TATGCAATTG
* *
44207235 TATACATGAACTTTGATTTTATGCAATTT
1 TATACATGAATTTTGATTTTATGCAATTG
* *
44207264 TATACATGAAATTTTGATTTGATTCAATT
1 TATACATG-AATTTTGATTTTATGCAATT
44207293 TTCACAAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.32
30 17 0.34
31 16 0.32
32 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (29 bp):
TATACATGAATTTTGATTTTATGCAATTG
Found at i:44207267 original size:29 final size:30
Alignment explanation
Indices: 44207227--44207294 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
44207217 TAGTTTAATG
* *
44207227 TGCAATTGTATACATG-AACTTTGATTTTA
1 TGCAATTTTATACATGAAACTTTGATTTGA
*
44207256 TGCAATTTTATACATGAAATTTTGATTTGA
1 TGCAATTTTATACATGAAACTTTGATTTGA
*
44207286 TTCAATTTT
1 TGCAATTTT
44207295 CACAAATCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.49
Consensus pattern (30 bp):
TGCAATTTTATACATGAAACTTTGATTTGA
Found at i:44209087 original size:24 final size:24
Alignment explanation
Indices: 44209055--44209126 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
44209045 TATTAAGTTA
*
44209055 TTCGGAGCTTCCTG-TGAATGGCTC
1 TTCGGAGCTACCTGAT-AATGGCTC
*
44209079 TTCGGAGCTACCTGATATTGGCTC
1 TTCGGAGCTACCTGATAATGGCTC
*
44209103 TTCGGAGCTACCTGATATTGGCTC
1 TTCGGAGCTACCTGATAATGGCTC
44209127 GCATGAGCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 44 0.98
25 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.33
Consensus pattern (24 bp):
TTCGGAGCTACCTGATAATGGCTC
Found at i:44209160 original size:24 final size:24
Alignment explanation
Indices: 44209058--44209162 Score: 97
Period size: 24 Copynumber: 4.4 Consensus size: 24
44209048 TAAGTTATTC
* *
44209058 GGAGCTTCCTG-TGAATGGCTCTTC
1 GGAGCTTCCTGAT-ATTGGCTCTTA
* *
44209082 GGAGCTACCTGATATTGGCTCTTC
1 GGAGCTTCCTGATATTGGCTCTTA
* **
44209106 GGAGCTACCTGATATTGGCTCGCA
1 GGAGCTTCCTGATATTGGCTCTTA
*
44209130 TGAGCTTCCTAGATA-TGGCTCTTA
1 GGAGCTTCCT-GATATTGGCTCTTA
*
44209154 TGAGCTTCC
1 GGAGCTTCC
44209163 CGTTAAAAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
24 65 0.93
25 5 0.07
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (24 bp):
GGAGCTTCCTGATATTGGCTCTTA
Found at i:44209218 original size:25 final size:25
Alignment explanation
Indices: 44209184--44209249 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
44209174 CCGGATAAGC
*
44209184 TCCCGTTACATGGCTCACATGAGTT
1 TCCCGTTACATGGCTCACATGAGCT
*
44209209 TCCCTTTACATGGCTCACATGAGCT
1 TCCCGTTACATGGCTCACATGAGCT
44209234 TCCCGATTA-ATGGCTC
1 TCCCG-TTACATGGCTC
44209250 GAGAGAGTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 34 0.92
26 3 0.08
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (25 bp):
TCCCGTTACATGGCTCACATGAGCT
Found at i:44210729 original size:13 final size:13
Alignment explanation
Indices: 44210711--44210737 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44210701 GAGGCGTCCT
44210711 TGGTAGCTATAAC
1 TGGTAGCTATAAC
44210724 TGGTAGCTATAAC
1 TGGTAGCTATAAC
44210737 T
1 T
44210738 AGCTTATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TGGTAGCTATAAC
Found at i:44220116 original size:3 final size:3
Alignment explanation
Indices: 44220110--44220166 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
44220100 CATGTTATAC
*
44220110 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
44220158 CAT TAT TAT
1 TAT TAT TAT
44220167 AGTTATTGCT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:44228414 original size:8 final size:8
Alignment explanation
Indices: 44228401--44228434 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
44228391 GTGTAGCTGA
44228401 TTTATTTG
1 TTTATTTG
44228409 TTTATTTG
1 TTTATTTG
*
44228417 TTTGTTTG
1 TTTATTTG
44228425 TTTATTTG
1 TTTATTTG
44228433 TT
1 TT
44228435 CGATTATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (8 bp):
TTTATTTG
Found at i:44231146 original size:26 final size:26
Alignment explanation
Indices: 44231066--44231148 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
44231056 TTTAGATGAT
* *
44231066 AAATTAATTATTCACTATCAATATTC
1 AAATTAATTATTTACTATCACTATTC
** * *
44231092 AAATTAA--AAGT-CTATAAACT-TTGT
1 AAATTAATTATTTACTAT-CACTATT-C
44231116 AAATTAATTATTTACTATCACTATTC
1 AAATTAATTATTTACTATCACTATTC
44231142 AAATTAA
1 AAATTAA
44231149 AAGTAATGAT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 6 0.15
24 10 0.24
26 19 0.46
27 6 0.15
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (26 bp):
AAATTAATTATTTACTATCACTATTC
Found at i:44234583 original size:20 final size:20
Alignment explanation
Indices: 44234560--44234678 Score: 61
Period size: 19 Copynumber: 5.7 Consensus size: 20
44234550 AACAAATTTT
44234560 AAAAATTTAAAATATTTAT-
1 AAAAATTTAAAATATTTATA
*
44234579 AAAAATTTCAAAATTTATATTTAAAA
1 AAAAATTT--AAA---ATATTT-ATA
44234605 AAAAATTATAATAAT-TTTA-A
1 AAAAATT-TAA-AATATTTATA
* *
44234625 AAAAATCTAAAGA-ATATATA
1 AAAAATTTAAA-ATATTTATA
44234645 AAGAAATTTAAAAT-TTT-TA
1 AA-AAATTTAAAATATTTATA
*
44234664 AAAATTTCTAAAATA
1 AAAAATT-TAAAATA
44234679 ATAATTTTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 31
0.68 0.05 0.27
Matches are distributed among these distances:
18 5 0.06
19 25 0.32
20 13 0.17
21 12 0.15
22 3 0.04
23 2 0.03
24 6 0.08
25 3 0.04
26 8 0.10
27 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATTTAAAATATTTATA
Found at i:44234594 original size:18 final size:18
Alignment explanation
Indices: 44234553--44234597 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
44234543 AAAAAAAAAC
44234553 AAATTT-TAAAAATTTAA
1 AAATTTATAAAAATTTAA
*
44234570 AATATTTATAAAAATTTCA
1 AA-ATTTATAAAAATTTAA
44234589 AAATTTATA
1 AAATTTATA
44234598 TTTAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 11 0.44
19 12 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTATAAAAATTTAA
Found at i:44237712 original size:21 final size:21
Alignment explanation
Indices: 44237679--44237718 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44237669 GCGACGGCGG
* *
44237679 CAACGACATCAACACCACCAT
1 CAACAACAACAACACCACCAT
*
44237700 CAACAACAACAACGCCACC
1 CAACAACAACAACACCACC
44237719 TACAGCAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.45, G:0.05, T:0.05
Consensus pattern (21 bp):
CAACAACAACAACACCACCAT
Found at i:44240572 original size:9 final size:9
Alignment explanation
Indices: 44240558--44240594 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44240548 TATAGTTTGA
44240558 TATTCGAAT
1 TATTCGAAT
44240567 TATTCGAAT
1 TATTCGAAT
*
44240576 TATTCGAGT
1 TATTCGAAT
44240585 TATTCGAAT
1 TATTCGAAT
44240594 T
1 T
44240595 TGAAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44242581 original size:88 final size:89
Alignment explanation
Indices: 44242447--44242623 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 89
44242437 AAATTTAAAA
44242447 AAAAACATGAAGTACACATGAAATATAAGAGGGCTCCTATGTTTAAAATTTTAACATTTTGCTTA
1 AAAAACATGAAGTACACATGAAATATAAGAGGGCTCCTATGTTTAAAATTTTAACATTTTGCTTA
44242512 GTATTTCCATAAAAAAATCAATTT
66 GTATTTCCATAAAAAAATCAATTT
44242536 AAAAACATG-AGTACACATGAAATATAAGAGGGCTCCTATGTTTAAAATTTTAACATTTTGCTTA
1 AAAAACATGAAGTACACATGAAATATAAGAGGGCTCCTATGTTTAAAATTTTAACATTTTGCTTA
44242600 GTATTTCCATAAAAAAATCAATTT
66 GTATTTCCATAAAAAAATCAATTT
44242624 GACTCTTTTT
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 79 0.90
89 9 0.10
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (89 bp):
AAAAACATGAAGTACACATGAAATATAAGAGGGCTCCTATGTTTAAAATTTTAACATTTTGCTTA
GTATTTCCATAAAAAAATCAATTT
Found at i:44242682 original size:30 final size:31
Alignment explanation
Indices: 44242619--44242683 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
44242609 TAAAAAAATC
* * ** *
44242619 AATTTGACTCTTTTTGAAATATTAATGGTCA
1 AATTCGACTCTTTTTAAAATATTAAAAGCCA
44242650 AATTCGACTC-TTTTAAAATATTAAAAGCCA
1 AATTCGACTCTTTTTAAAATATTAAAAGCCA
44242680 AATT
1 AATT
44242684 TAATTAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (31 bp):
AATTCGACTCTTTTTAAAATATTAAAAGCCA
Found at i:44244557 original size:4 final size:4
Alignment explanation
Indices: 44244548--44244579 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
44244538 CCTTACAGAT
44244548 GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG
44244580 AGATTAACGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
GATG
Found at i:44245872 original size:100 final size:103
Alignment explanation
Indices: 44245702--44245897 Score: 290
Period size: 100 Copynumber: 1.9 Consensus size: 103
44245692 GACAGACCGA
*
44245702 CACCAGTATACGAAAAAATAAAAAAAAAAATTTTGATGGTGACCTGCCAATGGCCGGCACCACAT
1 CACCAGTATACGAAAAAAT-AAAAAAAAAA--TTGATAGTGACCTGCCAATGGCCGGCACCACAT
*
44245767 TTATGT-AAAAAAATTTACATTTTGGGGTGTCATTGGCCGG
63 TTATGTAAAAAAAATTTACATTTTCGGGTGTCATTGGCCGG
* * *
44245807 CACCAGTATACGAAAAAAT-AAAAAAAAA-TGGTAGTGGCCTGCCAATGGCCGGCACCACCTTTA
1 CACCAGTATACGAAAAAATAAAAAAAAAATTGATAGTGACCTGCCAATGGCCGGCACCACATTTA
44245870 TGTAAAAAAAAATTTACATTTTCGGGTG
66 TGT-AAAAAAAATTTACATTTTCGGGTG
44245898 CCGATGTAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
100 34 0.40
102 22 0.26
103 9 0.11
105 19 0.23
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.24
Consensus pattern (103 bp):
CACCAGTATACGAAAAAATAAAAAAAAAATTGATAGTGACCTGCCAATGGCCGGCACCACATTTA
TGTAAAAAAAATTTACATTTTCGGGTGTCATTGGCCGG
Found at i:44246168 original size:103 final size:103
Alignment explanation
Indices: 44245914--44246169 Score: 286
Period size: 103 Copynumber: 2.5 Consensus size: 103
44245904 TAAATTTTTT
* * ** *
44245914 TTTACATAAAGGTGGTGCCAACCATTGGCAGGCTACCAC-CAAATTTTTTTTTATTTTTTTGTAT
1 TTTACATAAAGGTGGTGCCAGCCATTGACAGGCTACCACTC-AATTTTTTTAAATTTTTTCGTAT
* *
44245978 ACTGGTGCCGGCCAATAACACCCCAAAATGTAAAAAAAA
65 ACTAGTGCCAGCCAATAACACCCCAAAATGTAAAAAAAA
* * * * *
44246017 TTTACATAAAAGTAGTGCCGGCCATT-AGCAGGTTACCA-TAAATTTTTTTTAAATTTTTTCGTA
1 TTTACATAAAGGTGGTGCCAGCCATTGA-CAGGCTACCACTCAA-TTTTTTTAAATTTTTTCGTA
* *
44246080 TACTAGTGCTAGCCAATGACACCCCAAAATGTAAAAAAAA
64 TACTAGTGCCAGCCAATAACACCCCAAAATGTAAAAAAAA
* * * *
44246120 -TTCCGTAAAGGTGGTGCCAGCCATTGACAGGCCAGCACTCAATGTTTTTT
1 TTTACATAAAGGTGGTGCCAGCCATTGACAGGCTACCACTCAAT-TTTTTT
44246170 TTTTTTTCCT
Statistics
Matches: 124, Mismatches: 23, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
102 30 0.24
103 94 0.76
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (103 bp):
TTTACATAAAGGTGGTGCCAGCCATTGACAGGCTACCACTCAATTTTTTTAAATTTTTTCGTATA
CTAGTGCCAGCCAATAACACCCCAAAATGTAAAAAAAA
Found at i:44246324 original size:128 final size:126
Alignment explanation
Indices: 44246142--44246396 Score: 395
Period size: 128 Copynumber: 2.0 Consensus size: 126
44246132 GGTGCCAGCC
* *
44246142 ATTGACAGGCCAGCACTCAATGTTTTTTTTTTTTTCCTTGTATACCAGTATGATATGATTTTAAA
1 ATTGACAGGCCAGCACTCAATGTTTTTTTTTTTTTCCCTGTATACCAGTATGATACGATTTTAAA
* * *
44246207 AAAATACACTGGTTCCGACCATTGAAAGACCAGAACCAAGAAAATCATTTTTTTAAGTCTG
66 AAAATACACTGATTCCGACCATTGAAAGACCAGAACCAAAAAAATCATTTTTTTAAATCTG
*
44246268 ATTGACGGGCCAGCACTCAAAAT-TTTTTTATTTTTTTCCCTGTATACCAGTATGATACGATTTT
1 ATTGACAGGCCAGCACTC--AATGTTTTTT-TTTTTTTCCCTGTATACCAGTATGATACGATTTT
* * *
44246332 AAAAAAATACACTGATTCCGACCATTGATAGACCAGAACTAAAAAAATTATTTTTTTAAATCTG
63 AAAAAAATACACTGATTCCGACCATTGAAAGACCAGAACCAAAAAAATCATTTTTTTAAATCTG
44246396 A
1 A
44246397 CACAATTATC
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
126 17 0.15
127 6 0.05
128 94 0.80
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (126 bp):
ATTGACAGGCCAGCACTCAATGTTTTTTTTTTTTTCCCTGTATACCAGTATGATACGATTTTAAA
AAAATACACTGATTCCGACCATTGAAAGACCAGAACCAAAAAAATCATTTTTTTAAATCTG
Found at i:44264333 original size:20 final size:20
Alignment explanation
Indices: 44264308--44264345 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44264298 GCAGACCAGG
*
44264308 AAAAAAAGGTAAAAAGAGAA
1 AAAAAAAGGAAAAAAGAGAA
*
44264328 AAAAAAATGAAAAAAGAG
1 AAAAAAAGGAAAAAAGAG
44264346 GGGTCCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.05
Consensus pattern (20 bp):
AAAAAAAGGAAAAAAGAGAA
Found at i:44268838 original size:12 final size:12
Alignment explanation
Indices: 44268823--44268865 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
44268813 ATATCGAAAA
44268823 AAATAAAGTAAT
1 AAATAAAGTAAT
*
44268835 AAATAATA-AAAT
1 AAATAA-AGTAAT
44268847 AAAATAAAGTAAT
1 -AAATAAAGTAAT
44268860 AAATAA
1 AAATAA
44268866 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (12 bp):
AAATAAAGTAAT
Found at i:44268844 original size:15 final size:15
Alignment explanation
Indices: 44268824--44268869 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
44268814 TATCGAAAAA
44268824 AATAAAGTAATAAAT
1 AATAAAGTAATAAAT
44268839 AAT-AA--AAT-AA-
1 AATAAAGTAATAAAT
44268849 AATAAAGTAATAAAT
1 AATAAAGTAATAAAT
44268864 AATAAA
1 AATAAA
44268870 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
10 3 0.12
11 4 0.15
12 3 0.12
13 3 0.12
14 4 0.15
15 9 0.35
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (15 bp):
AATAAAGTAATAAAT
Found at i:44268849 original size:5 final size:5
Alignment explanation
Indices: 44268839--44268880 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
44268829 AGTAATAAAT
* *
44268839 AATAA AATAA AATAA AGTAA TAA-AT AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA -AATAA AATAA AATAA AATAA AA
44268881 ATTGGGTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 2 0.06
5 28 0.90
6 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:44268855 original size:25 final size:25
Alignment explanation
Indices: 44268822--44268879 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
44268812 AATATCGAAA
44268822 AAAATAAAGTAATAAATAATAAAAT
1 AAAATAAAGTAATAAATAATAAAAT
44268847 AAAATAAAGTAATAAATAATAAAAT
1 AAAATAAAGTAATAAATAATAAAAT
44268872 AAAATAAA
1 AAAATAAA
44268880 AATTGGGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.22
Consensus pattern (25 bp):
AAAATAAAGTAATAAATAATAAAAT
Found at i:44268871 original size:8 final size:8
Alignment explanation
Indices: 44268819--44268873 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
44268809 ATTAATATCG
*
44268819 AAAAAAAT
1 AAAATAAT
*
44268827 AAAGTAAT
1 AAAATAAT
44268835 -AAATAAT
1 AAAATAAT
44268842 AAAATAAAAT
1 AAAAT--AAT
*
44268852 AAAGTAAT
1 AAAATAAT
44268860 -AAATAAT
1 AAAATAAT
44268867 AAAATAA
1 AAAATAA
44268874 AATAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
7 12 0.32
8 19 0.50
10 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (8 bp):
AAAATAAT
Found at i:44268872 original size:12 final size:12
Alignment explanation
Indices: 44268832--44268874 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
44268822 AAAATAAAGT
44268832 AATAAATAATAA
1 AATAAATAATAA
*
44268844 AATAAAATAA-AGT
1 AAT-AAATAATA-A
44268857 AATAAATAATAA
1 AATAAATAATAA
44268869 AATAAA
1 AATAAA
44268875 ATAAAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:44269728 original size:11 final size:11
Alignment explanation
Indices: 44269709--44269750 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
44269699 AACACCGAAT
*
44269709 TTTTTGGGTAA
1 TTTTCGGGTAA
44269720 TTTTCGGGTAA
1 TTTTCGGGTAA
44269731 -TTT-GGGTAA
1 TTTTCGGGTAA
44269740 TTTTCGGGTAA
1 TTTTCGGGTAA
44269751 ATCGGTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 6 0.21
10 6 0.21
11 16 0.57
ACGTcount: A:0.19, C:0.05, G:0.29, T:0.48
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:44269736 original size:20 final size:20
Alignment explanation
Indices: 44269711--44269750 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
44269701 CACCGAATTT
44269711 TTTGGGTAATTTTCGGGTAA
1 TTTGGGTAATTTTCGGGTAA
44269731 TTTGGGTAATTTTCGGGTAA
1 TTTGGGTAATTTTCGGGTAA
44269751 ATCGGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (20 bp):
TTTGGGTAATTTTCGGGTAA
Found at i:44269755 original size:9 final size:9
Alignment explanation
Indices: 44269722--44269796 Score: 71
Period size: 9 Copynumber: 8.2 Consensus size: 9
44269712 TTGGGTAATT
44269722 TTCGGGTAA
1 TTCGGGTAA
*
44269731 TTTGGGTAA
1 TTCGGGTAA
44269740 TTTTCGGGTAA
1 --TTCGGGTAA
* *
44269751 ATCGGTTAA
1 TTCGGGTAA
*
44269760 TTCGGTTAA
1 TTCGGGTAA
**
44269769 TTCGATTAA
1 TTCGGGTAA
44269778 -TCGGGTAA
1 TTCGGGTAA
44269786 TTCGGGTAA
1 TTCGGGTAA
44269795 TT
1 TT
44269797 TTTAACCAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
8 6 0.11
9 41 0.75
11 8 0.15
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:44269760 original size:20 final size:20
Alignment explanation
Indices: 44269714--44269761 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
44269704 CGAATTTTTT
* *
44269714 GGGTAATTTTCGGGTAATTT
1 GGGTAATTTTCGGGTAAATC
44269734 GGGTAATTTTCGGGTAAATC
1 GGGTAATTTTCGGGTAAATC
*
44269754 GGTTAATT
1 GGGTAATT
44269762 CGGTTAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.06, G:0.29, T:0.42
Consensus pattern (20 bp):
GGGTAATTTTCGGGTAAATC
Found at i:44269935 original size:12 final size:12
Alignment explanation
Indices: 44269918--44269942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44269908 AGTAATTTCG
44269918 GGTCGGTTAACC
1 GGTCGGTTAACC
44269930 GGTCGGTTAACC
1 GGTCGGTTAACC
44269942 G
1 G
44269943 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:44275215 original size:31 final size:31
Alignment explanation
Indices: 44275180--44275265 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
44275170 TAGCCAAATG
*
44275180 AATTTGAAAAGTACAAGGATTAAAATTGATT
1 AATTTGAAAAGTACAAGGACTAAAATTGATT
* *
44275211 AATTTGAAGAGTACATGGACTAAAATTGATT
1 AATTTGAAAAGTACAAGGACTAAAATTGATT
44275242 AATTT-AAATAGTACATA-GACTAAA
1 AATTTGAAA-AGTACA-AGGACTAAA
44275266 TTTACAACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 2 0.04
31 46 0.96
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (31 bp):
AATTTGAAAAGTACAAGGACTAAAATTGATT
Found at i:44277639 original size:17 final size:17
Alignment explanation
Indices: 44277619--44277660 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
44277609 AAAAGTGATT
44277619 GAAATAAAAAAAAAAAA
1 GAAATAAAAAAAAAAAA
***
44277636 GAAATTTCAAAAAAAAA
1 GAAATAAAAAAAAAAAA
44277653 GAAA-AAAA
1 GAAATAAAA
44277661 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 6, Indels: 1
0.73 0.23 0.04
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.10
Consensus pattern (17 bp):
GAAATAAAAAAAAAAAA
Found at i:44277647 original size:20 final size:21
Alignment explanation
Indices: 44277624--44277662 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
44277614 TGATTGAAAT
*
44277624 AAAAAAAAA-AAAGAAATTTC
1 AAAAAAAAAGAAAAAAATTTC
44277644 AAAAAAAAAGAAAAAAATT
1 AAAAAAAAAGAAAAAAATT
44277663 AAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (21 bp):
AAAAAAAAAGAAAAAAATTTC
Found at i:44277667 original size:20 final size:19
Alignment explanation
Indices: 44277623--44277668 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
44277613 GTGATTGAAA
* *
44277623 TAAAAAAAAAAAAGAAATT
1 TAAAAAAAAAAAAAAAAAT
*
44277642 TCAAAAAAAAAGAAAAAAAT
1 T-AAAAAAAAAAAAAAAAAT
44277662 TAAAAAA
1 TAAAAAA
44277669 TATTTTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (19 bp):
TAAAAAAAAAAAAAAAAAT
Done.