Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:841909 original size:22 final size:22
Alignment explanation
Indices: 841884--841938 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
841874 GATAAAGCTT
*
841884 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* * *
841906 TCATCATTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
841928 TCATCTTTGAA
1 TCATCTTTGAA
841939 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:842387 original size:54 final size:54
Alignment explanation
Indices: 842305--842416 Score: 188
Period size: 54 Copynumber: 2.1 Consensus size: 54
842295 AGAATAGCAG
* * *
842305 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
842359 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
842413 GTTC
1 GTTC
842417 TCAATCATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:844678 original size:114 final size:114
Alignment explanation
Indices: 844478--844695 Score: 357
Period size: 114 Copynumber: 1.9 Consensus size: 114
844468 GATCATGCAG
* * *
844478 TTCATCTTTCAATTCCAATGATTGGTTTTGGGGTTCCTACCAAATCAGATTAGATAACTCAAAGA
1 TTCATCTTTCAATTCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
844543 ATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
*
844592 TTCATCTTTCAAATT-TAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTC-AATTCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
844656 AACACTTCCAGAAGATGCTATTGGATCTTCTTATTTCTAC
65 AACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTAC
844696 CACGATAACG
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
114 92 0.96
115 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAATTCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
Found at i:846833 original size:10 final size:10
Alignment explanation
Indices: 846818--846874 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
846808 CCCCTTCTTC
846818 TTTTTTCCTT
1 TTTTTTCCTT
846828 TTTTTT-CTT
1 TTTTTTCCTT
*
846837 TTTTTTCCCTC
1 TTTTTT-CCTT
*
846848 ATTTTTCCTT
1 TTTTTTCCTT
** *
846858 TTTCATCTTT
1 TTTTTTCCTT
846868 TTTTTTC
1 TTTTTTC
846875 TTTCTTTGCT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
9 9 0.25
10 20 0.56
11 7 0.19
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:846841 original size:20 final size:20
Alignment explanation
Indices: 846812--846877 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
846802 ATTTCTCCCC
*
846812 TTCTTCTTTTTTCCTTTTTT
1 TTCTTTTTTTTTCCTTTTTT
* **
846832 TTCTTTTTTTTCCCTCATTT
1 TTCTTTTTTTTTCCTTTTTT
* ** *
846852 TTCCTTTTTCATCTTTTTTT
1 TTCTTTTTTTTTCCTTTTTT
846872 TTCTTT
1 TTCTTT
846878 CTTTGCTGGA
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (20 bp):
TTCTTTTTTTTTCCTTTTTT
Found at i:846876 original size:10 final size:10
Alignment explanation
Indices: 846812--846877 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 10
846802 ATTTCTCCCC
*
846812 TTCTTCTTTT
1 TTCTTTTTTT
*
846822 TTCCTTTTTT
1 TTCTTTTTTT
846832 TTCTTTTTTT
1 TTCTTTTTTT
* * **
846842 TCCCTCATTT
1 TTCTTTTTTT
* *
846852 TTCCTTTTTC
1 TTCTTTTTTT
*
846862 ATCTTTTTTT
1 TTCTTTTTTT
846872 TTCTTT
1 TTCTTT
846878 CTTTGCTGGA
Statistics
Matches: 41, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:854423 original size:3 final size:3
Alignment explanation
Indices: 854415--854466 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
854405 CTTGGGTTGT
* * * *
854415 ATA ATA ATA ATA ATA TTA ATA ATA AAA ATA ATA ATA ATA GTA ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
854463 ATA A
1 ATA A
854467 AAAACCAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:858491 original size:17 final size:18
Alignment explanation
Indices: 858469--858504 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
858459 ATTAATACCA
858469 TTTA-TTTAATATTATTT
1 TTTATTTTAATATTATTT
*
858486 TTTATTTTTATATTATTT
1 TTTATTTTAATATTATTT
858504 T
1 T
858505 ATTGTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTTAATATTATTT
Found at i:858514 original size:17 final size:16
Alignment explanation
Indices: 858469--858520 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
858459 ATTAATACCA
858469 TTTATTTA-ATATTATTT
1 TTTATTTATATATTA--T
*
858486 TTTATTTTTATATTAT
1 TTTATTTATATATTAT
*
858502 TTTATTGTATATATGAT
1 TTTATT-TATATATTAT
858519 TT
1 TT
858521 ATAATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 7 0.23
17 17 0.57
18 6 0.20
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTATTTATATATTAT
Found at i:864651 original size:165 final size:164
Alignment explanation
Indices: 864378--864706 Score: 606
Period size: 165 Copynumber: 2.0 Consensus size: 164
864368 CAACGAGTAA
864378 TATTAGTAGTTAAAAAAATATTATTTTTATAAATTTTATATTCGAATGTTATGTTTATAGATCAG
1 TATTAGTAGTTAAAAAAATATTATTTTTATAAATTTTATATTCGAATGTTATGTTTATAGATCAG
* *
864443 AGACAAACCTAGGCGGGGTGGGTGGGGAGGTCGCCCCTAAAAGTCTAAAATTATAATGTA-TTTA
66 AGACAAACCTAGACGGGGTGGGTGGGGAGGTCACCCCTAAAAGTCTAAAATTATAATGTATTTTA
864507 GATTTTTTTTCTTTATATTTTGTATTGAAAATTT
131 GATTTTTTTTCTTTATATTTTGTATTGAAAATTT
864541 TATTAGTAGTTAAAAAAATATTATTTTTATAAATTTTATATTCGAATTGTTATGTTTATAGAATC
1 TATTAGTAGTTAAAAAAATATTATTTTTATAAATTTTATATTCGAA-TGTTATGTTTATAG-ATC
864606 AGAGACAAACCTAGACGGGGTGGGTGGGGAGGTCACCCCTAAAAGTCTAAAATTATAATGTATTT
64 AGAGACAAACCTAGACGGGGTGGGTGGGGAGGTCACCCCTAAAAGTCTAAAATTATAATGTATTT
*
864671 TAGATTTTTTTTCTTTATATTTTTTATTGAAAATTT
129 TAGATTTTTTTTCTTTATATTTTGTATTGAAAATTT
864707 GTTTTCGACT
Statistics
Matches: 160, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
163 46 0.29
164 14 0.09
165 63 0.39
166 37 0.23
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (164 bp):
TATTAGTAGTTAAAAAAATATTATTTTTATAAATTTTATATTCGAATGTTATGTTTATAGATCAG
AGACAAACCTAGACGGGGTGGGTGGGGAGGTCACCCCTAAAAGTCTAAAATTATAATGTATTTTA
GATTTTTTTTCTTTATATTTTGTATTGAAAATTT
Found at i:865114 original size:14 final size:16
Alignment explanation
Indices: 865080--865127 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
865070 TTAAAAGAAT
865080 TATTTTATATTTATAA
1 TATTTTATATTTATAA
*
865096 TATTTTAT-TTTATTA
1 TATTTTATATTTATAA
* *
865111 -ATTTTAAATTCATAA
1 TATTTTATATTTATAA
865126 TA
1 TA
865128 ATTGTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.23
15 11 0.42
16 9 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTATATTTATAA
Found at i:871921 original size:28 final size:29
Alignment explanation
Indices: 871890--871956 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
871880 ATCTCTGAGC
*
871890 TTGCTGGCTTAACTTGT-AAAGGCATCCA
1 TTGCTGCCTTAACTTGTAAAAGGCATCCA
**
871918 TTGCTGCCTTTTCTTGTAAAAGGCATCCA
1 TTGCTGCCTTAACTTGTAAAAGGCATCCA
871947 TTGCTGCCTT
1 TTGCTGCCTT
871957 TTCTTGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 14 0.40
29 21 0.60
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (29 bp):
TTGCTGCCTTAACTTGTAAAAGGCATCCA
Found at i:871949 original size:29 final size:28
Alignment explanation
Indices: 871902--871963 Score: 115
Period size: 29 Copynumber: 2.2 Consensus size: 28
871892 GCTGGCTTAA
871902 CTTGTAAAGGCATCCATTGCTGCCTTTT
1 CTTGTAAAGGCATCCATTGCTGCCTTTT
871930 CTTGTAAAAGGCATCCATTGCTGCCTTTT
1 CTTGT-AAAGGCATCCATTGCTGCCTTTT
871959 CTTGT
1 CTTGT
871964 TTCTTTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.15
29 28 0.85
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (28 bp):
CTTGTAAAGGCATCCATTGCTGCCTTTT
Found at i:872853 original size:96 final size:96
Alignment explanation
Indices: 872689--872881 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
872679 GTTGTACGTT
872689 TAATAATATTGTTGATGGAACACATTGATTGTATCCCTCATTTTCTGTTTATTCTCTAGTTTGAA
1 TAATAATATTGTTGATGGAACACATTGATTGTATCCCTCATTTTCTGTTTATTCTCTAGTTTGAA
872754 TGCTGAGTTGTGATTAGTAATAATGCAATAG
66 TGCTGAGTTGTGATTAGTAATAATGCAATAG
872785 TAATAATATTGTTGATGGAACACATTGATTGTATCCCTCATTTTCTGTTTATTCTCTAGTTTGAA
1 TAATAATATTGTTGATGGAACACATTGATTGTATCCCTCATTTTCTGTTTATTCTCTAGTTTGAA
872850 TGCTGAGTTGTGATTAGTAATAATGCAATAG
66 TGCTGAGTTGTGATTAGTAATAATGCAATAG
872881 T
1 T
872882 TCATTTGTGA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (96 bp):
TAATAATATTGTTGATGGAACACATTGATTGTATCCCTCATTTTCTGTTTATTCTCTAGTTTGAA
TGCTGAGTTGTGATTAGTAATAATGCAATAG
Found at i:873092 original size:54 final size:53
Alignment explanation
Indices: 873023--873124 Score: 177
Period size: 54 Copynumber: 1.9 Consensus size: 53
873013 GGCTAACAAT
873023 ATATTTTAACTCTAATAGAAGACATAAATATACCAATGATCATGTCAAGTAACA
1 ATATTTTAACTCTAATAGAAGACATAAA-ATACCAATGATCATGTCAAGTAACA
**
873077 ATATTTTAACTCTAATAGTTGACATAAAATACCAATGATCATGTCAAG
1 ATATTTTAACTCTAATAGAAGACATAAAATACCAATGATCATGTCAAG
873125 AAGTCGTGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 20 0.43
54 26 0.57
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (53 bp):
ATATTTTAACTCTAATAGAAGACATAAAATACCAATGATCATGTCAAGTAACA
Found at i:875943 original size:9 final size:8
Alignment explanation
Indices: 875931--876028 Score: 54
Period size: 7 Copynumber: 12.9 Consensus size: 8
875921 AATATTTTAT
875931 ATATAATTA
1 ATATAA-TA
*
875940 ATATAAAAA
1 ATAT-AATA
875949 ATATAA-A
1 ATATAATA
*
875956 ATATTAT-
1 ATATAATA
875963 ATAT-ATA
1 ATATAATA
875970 AT-TAAT-
1 ATATAATA
875976 ATATAA-A
1 ATATAATA
875983 ATATAA-A
1 ATATAATA
875990 ATATAA-A
1 ATATAATA
*
875997 ATATTAT-
1 ATATAATA
876004 ATAT-ATA
1 ATATAATA
876011 TATATATATA
1 -ATATA-ATA
876021 TATATAAT
1 -ATATAAT
876029 CGGGTAGGGG
Statistics
Matches: 75, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
6 7 0.09
7 40 0.53
8 6 0.08
9 11 0.15
10 11 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:875958 original size:7 final size:7
Alignment explanation
Indices: 875946--876000 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
875936 ATTAATATAA
875946 AAAATAT
1 AAAATAT
875953 AAAATAT
1 AAAATAT
* *
875960 TATATAT
1 AAAATAT
*
875967 ATAAT-T
1 AAAATAT
*
875973 AATATAT
1 AAAATAT
875980 AAAATAT
1 AAAATAT
875987 AAAATAT
1 AAAATAT
875994 AAAATAT
1 AAAATAT
876001 TATATATATA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 4 0.10
7 35 0.90
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATAT
Found at i:875965 original size:2 final size:2
Alignment explanation
Indices: 875956--876026 Score: 59
Period size: 2 Copynumber: 39.5 Consensus size: 2
875946 AAAATATAAA
* *
875956 AT AT -T AT AT AT AT A- AT -T A- AT AT AT A- AA AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
875992 AT A- AA AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
876027 ATCGGGTAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
1 8 0.14
2 50 0.86
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:875966 original size:34 final size:34
Alignment explanation
Indices: 875919--875993 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
875909 CCCGAACCCG
*
875919 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
*
875953 AAAATATTATATATATAATTAATATATAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
875987 AAAATAT
1 AAAATAT
875994 AAAATATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:876007 original size:14 final size:14
Alignment explanation
Indices: 875949--876024 Score: 82
Period size: 14 Copynumber: 5.4 Consensus size: 14
875939 AATATAAAAA
875949 ATATAAAATATTAT
1 ATATAAAATATTAT
* *
875963 ATATATAAT-TAAT
1 ATATAAAATATTAT
* *
875976 ATATAAAATATAAA
1 ATATAAAATATTAT
875990 ATATAAAATATTAT
1 ATATAAAATATTAT
*
876004 ATATATATATATATAT
1 ATATA-AAATAT-TAT
876020 ATATA
1 ATATA
876025 TAATCGGGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
13 11 0.21
14 28 0.54
15 5 0.10
16 8 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATAAAATATTAT
Found at i:878013 original size:25 final size:25
Alignment explanation
Indices: 877979--878035 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
877969 AGAACTTAAG
877979 GGGTTTTGGGGTTTTTTTGGATTTA
1 GGGTTTTGGGGTTTTTTTGGATTTA
878004 GGGTTTTGGGGTTTTTTTGGATTTA
1 GGGTTTTGGGGTTTTTTTGGATTTA
878029 GGGTTTT
1 GGGTTTT
878036 TTTGAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.07, C:0.00, G:0.37, T:0.56
Consensus pattern (25 bp):
GGGTTTTGGGGTTTTTTTGGATTTA
Found at i:880242 original size:14 final size:14
Alignment explanation
Indices: 880213--880242 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
880203 AACATAAATA
880213 AATGAACATAACCG
1 AATGAACATAACCG
*
880227 AATGAACATAATCG
1 AATGAACATAACCG
880241 AA
1 AA
880243 CGTTCACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (14 bp):
AATGAACATAACCG
Found at i:885053 original size:17 final size:17
Alignment explanation
Indices: 884967--885074 Score: 65
Period size: 17 Copynumber: 5.9 Consensus size: 17
884957 AATATTAAAG
*
884967 AAATATATATATAATAAT
1 AAATAAATA-ATAATAAT
* *
884985 AAATAAATAGTAAAAAT
1 AAATAAATAATAATAAT
885002 CAAATGAAAATAATTTAATATAT
1 -AAAT--AAATAA--TAATA-AT
*
885025 ATATACATATAATAATAAT
1 AAATA-A-ATAATAATAAT
* * *
885044 ACATGAATAATAAAAAT
1 AAATAAATAATAATAAT
885061 AAATAAATAA-AATA
1 AAATAAATAATAATA
885075 TCCATATAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
16 3 0.04
17 24 0.34
18 13 0.19
19 5 0.07
20 11 0.16
21 1 0.01
22 11 0.16
23 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
AAATAAATAATAATAAT
Found at i:886403 original size:105 final size:105
Alignment explanation
Indices: 886220--886979 Score: 1128
Period size: 105 Copynumber: 7.3 Consensus size: 105
886210 GCATTGTTCA
* * ***
886220 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAAACTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
886280 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
886320 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
* *
886385 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
886425 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAA---GTTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
886487 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
886527 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
886592 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
886632 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA---GTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
886694 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
886734 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
886799 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
886839 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* ** * * * *
886904 CCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
886945 GAGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
886980 CGCGGATGGC
Statistics
Matches: 609, Mismatches: 36, Indels: 21
0.91 0.05 0.03
Matches are distributed among these distances:
100 35 0.06
101 1 0.00
102 196 0.32
103 2 0.00
104 2 0.00
105 300 0.49
106 47 0.08
107 3 0.00
109 23 0.04
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:886563 original size:207 final size:207
Alignment explanation
Indices: 886220--886979 Score: 1141
Period size: 207 Copynumber: 3.6 Consensus size: 207
886210 GCATTGTTCA
* * *** *
886220 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAAACTG-AA-TGA-AATTTTGTTGACAAGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-GTTGTTGACAAGCA
*
886282 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
65 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
* * *
886347 GAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGTGGTCCCTTCGTCGTGAAGTTGAA
130 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
886412 CTTGCATTGTCTG
195 CTTGCGTTGTCTG
** * *
886425 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTATTGACAAGCAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGACAAGCAG
886490 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTG
*
886555 AAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCATCGTGAAGTTGAAC
131 AAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
886620 TTGCGTTGTCTG
196 TTGCGTTGTCTG
* * * *
886632 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTGACAGGCAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGACAAGCAG
*
886697 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTG
*
886762 AAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
886827 TTGCGTTGTCTG
196 TTGCGTTGTCTG
886839 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---G-TTGTTGACAA
* ** * * * *
886904 CCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG-AGTGCCACGATATCCTCCGTTG
62 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAAGT-CCA--ATATCCTTCGTTG
*
886968 TGGAGTTGAAAT
123 TGAAGTTGAAAT
886980 CGCGGATGGC
Statistics
Matches: 505, Mismatches: 39, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
205 35 0.07
206 1 0.00
207 394 0.78
208 2 0.00
210 1 0.00
211 46 0.09
212 4 0.01
214 22 0.04
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (207 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGACAAGCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTG
Found at i:887718 original size:67 final size:66
Alignment explanation
Indices: 887583--887740 Score: 203
Period size: 68 Copynumber: 2.4 Consensus size: 66
887573 AAGATATATG
* * **
887583 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
887648 TT
65 TT
* *
887650 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGAA-AAAATT-TGTTTTAGGGGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGA-AACAAAATTATGTTTTAAGGGAAATAAATTCAAAG
*
887713 GTT
64 ATT
*
887716 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
887741 ATAGACGAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 30 0.38
69 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:887767 original size:36 final size:36
Alignment explanation
Indices: 887716--887838 Score: 149
Period size: 36 Copynumber: 3.4 Consensus size: 36
887706 TTCAAAGGTT
*
887716 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* * *
887752 TTGTTTCAAGAGAAACTGGCTTAAGAGAGAC-AAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* * *
887787 CTTAGTTCCAAGGGAAACTATCTCAAGAGAGACGAAAT
1 -TT-GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
*
887825 TTATTTCAAGGGAA
1 TTGTTTCAAGGGAA
887839 TGTTTTCAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
35 4 0.06
36 39 0.54
37 26 0.36
38 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
Found at i:889459 original size:18 final size:19
Alignment explanation
Indices: 889420--889462 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
889410 TTTTTTGTCC
889420 CTTTTT-CTTTTTGTTCTT
1 CTTTTTGCTTTTTGTTCTT
*
889438 -TTTTTGCTTTTT-TTTTT
1 CTTTTTGCTTTTTGTTCTT
889455 CTTTTTGC
1 CTTTTTGC
889463 CCTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
CTTTTTGCTTTTTGTTCTT
Found at i:908156 original size:37 final size:37
Alignment explanation
Indices: 908106--908190 Score: 154
Period size: 37 Copynumber: 2.3 Consensus size: 37
908096 CTGTTGTAGG
908106 CCTCCAAGAACGGCCGACAGAGAACGA-AAAAATTGGC
1 CCTCCAAGAACGGCCGACAGAGAACGATAAAAA-TGGC
908143 CCTCCAAGAACGGCCGACAGAGAACGATAAAAATGGC
1 CCTCCAAGAACGGCCGACAGAGAACGATAAAAATGGC
908180 CCTCCAAGAAC
1 CCTCCAAGAAC
908191 AGACAACAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 42 0.89
38 5 0.11
ACGTcount: A:0.40, C:0.29, G:0.22, T:0.08
Consensus pattern (37 bp):
CCTCCAAGAACGGCCGACAGAGAACGATAAAAATGGC
Found at i:912596 original size:30 final size:30
Alignment explanation
Indices: 912560--912625 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
912550 AGTGAACCGG
* * *
912560 CGGTTCAAACCGGTTTTGCCGGTTTTCAGT
1 CGGTTCAAACCGGTTTTCCCGATTTTCAGC
**
912590 CGGTTCACCCCGGTTTTCCCGATTTTCAGC
1 CGGTTCAAACCGGTTTTCCCGATTTTCAGC
912620 CGGTTC
1 CGGTTC
912626 TTCCGGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.11, C:0.30, G:0.24, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTCCCGATTTTCAGC
Found at i:912832 original size:15 final size:16
Alignment explanation
Indices: 912812--912842 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
912802 TTAAGAGATA
912812 AAAAT-ATTTGGAAAT
1 AAAATAATTTGGAAAT
912827 AAAATAATTTGGAAAT
1 AAAATAATTTGGAAAT
912843 TTCAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (16 bp):
AAAATAATTTGGAAAT
Found at i:915125 original size:31 final size:33
Alignment explanation
Indices: 915089--915157 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
915079 CAAATTTCAT
915089 GAATTTCAAACC-AT-CATTTCAATTGGAGAAA
1 GAATTTCAAACCGATCCATTTCAATTGGAGAAA
* * *
915120 GAATTTCATACCGTATCCATTTTAATTGGAGCAA
1 GAATTTCAAACCG-ATCCATTTCAATTGGAGAAA
915154 GAAT
1 GAAT
915158 GAGTATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.34
33 2 0.06
34 19 0.59
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (33 bp):
GAATTTCAAACCGATCCATTTCAATTGGAGAAA
Found at i:918898 original size:14 final size:13
Alignment explanation
Indices: 918867--918896 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
918857 TAGTGTATTA
918867 TTTTAAAATAATT
1 TTTTAAAATAATT
918880 TTTTAAAATAATT
1 TTTTAAAATAATT
918893 TTTT
1 TTTT
918897 TATTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAAATAATT
Found at i:919712 original size:19 final size:20
Alignment explanation
Indices: 919681--919725 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
919671 TAAAATTCGG
919681 ATATTAGAATAATAAATTAAA
1 ATATTAGAATAAT-AATTAAA
*
919702 A-ATTA-AATAATGATTAAA
1 ATATTAGAATAATAATTAAA
919720 ATATTA
1 ATATTA
919726 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 4 0.18
21 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
ATATTAGAATAATAATTAAA
Found at i:920920 original size:3 final size:3
Alignment explanation
Indices: 920902--920955 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
920892 TAGATTTATT
*
920902 TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA T-A
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
920946 TAA TAG TAA T
1 TAA TAA TAA T
920956 GTGGGTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:921854 original size:31 final size:31
Alignment explanation
Indices: 921816--921879 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
921806 ATTCTTATCT
921816 TTTGTAGTTCTATACATGCTCAGAAATTATG
1 TTTGTAGTTCTATACATGCTCAGAAATTATG
921847 TTTGTAGTTCTATACATGCTCAGAAATTATG
1 TTTGTAGTTCTATACATGCTCAGAAATTATG
921878 TT
1 TT
921880 GCTTGAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (31 bp):
TTTGTAGTTCTATACATGCTCAGAAATTATG
Found at i:926534 original size:13 final size:13
Alignment explanation
Indices: 926516--926542 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
926506 AAAATGACCT
926516 AATCTAGAGTGCC
1 AATCTAGAGTGCC
926529 AATCTAGAGTGCC
1 AATCTAGAGTGCC
926542 A
1 A
926543 TAACATAATT
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:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AATCTAGAGTGCC
Found at i:929118 original size:24 final size:24
Alignment explanation
Indices: 929090--929150 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
929080 TTAAAACTTC
* *
929090 TTTTGATAAAGTTGGAACAAAACA
1 TTTTGAAAAAGGTGGAACAAAACA
*
929114 TTTTGAAAAAGGTGGAACAAAACT
1 TTTTGAAAAAGGTGGAACAAAACA
929138 TTGTTAGAAAAAG
1 TT-TT-GAAAAAG
929151 TTTTAGAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 23 0.72
25 2 0.06
26 7 0.22
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.28
Consensus pattern (24 bp):
TTTTGAAAAAGGTGGAACAAAACA
Found at i:935396 original size:22 final size:22
Alignment explanation
Indices: 935370--935425 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
935360 CTCAGAGGGA
935370 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
*
935392 ACCGATT-CCCCCCAATGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
935413 ACCGATTCCCCCC
1 ACCGATTCCCCCC
935426 TGAATGGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGGGGT
Found at i:940163 original size:32 final size:32
Alignment explanation
Indices: 940122--940201 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
940112 GTATAAGAAG
940122 ACGAAGACCATATTGCCTTCAGCAAAACCTGA
1 ACGAAGACCATATTGCCTTCAGCAAAACCTGA
940154 ACGAAGACCATATTGCCTTCAGCAAAACCTGA
1 ACGAAGACCATATTGCCTTCAGCAAAACCTGA
*
940186 ACGAAGATCATATTGC
1 ACGAAGACCATATTGC
940202 TTTGTGATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (32 bp):
ACGAAGACCATATTGCCTTCAGCAAAACCTGA
Found at i:946270 original size:96 final size:98
Alignment explanation
Indices: 946102--946375 Score: 401
Period size: 102 Copynumber: 2.8 Consensus size: 98
946092 TTTGGTCTTG
* * *
946102 TTACTCTAGCATGTCAACTGAAGTTGAACACAACTTCAGTTTGTCCGTAGTCACCGTCTTTGTCA
1 TTACTCTAGCATGTCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTAGTTACCGTCTTTGTTA
*
946167 ACATGTCTGCC-A-GAAGATGAAAATGGGGAAA
66 ACATGTCTGCCAATGAAAATGAAAATGGGGAAA
* *
946198 TTGA-TCTAGCATGTCAACTGAAGCCGAACACAACTTCAGTTTGTTCGTAGTTACCGTCTTTGTT
1 TT-ACTCTAGCATGTCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTAGTTACCGTCTTTGTT
946262 AACATGTCTGCTACAAGATGAAAATGAAAATGGGGAAA
65 AACATGTCTGC--C-A-ATGAAAATGAAAATGGGGAAA
* *
946300 TTACTCTAGCATGCCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTAGTTACCGTCTTTTTTA
1 TTACTCTAGCATGTCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTAGTTACCGTCTTTGTTA
*
946365 ACATATCTGCC
66 ACATGTCTGCC
946376 GGATTTTGAG
Statistics
Matches: 159, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
96 68 0.43
97 1 0.01
98 1 0.01
100 1 0.01
101 2 0.01
102 86 0.54
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (98 bp):
TTACTCTAGCATGTCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTAGTTACCGTCTTTGTTA
ACATGTCTGCCAATGAAAATGAAAATGGGGAAA
Found at i:957793 original size:23 final size:22
Alignment explanation
Indices: 957737--957797 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
957727 TAACTTTACA
*
957737 CATATATATATATATATTTATTT
1 CATATATATA-ATATAGTTATTT
* *
957760 CAAATGTTATAATATAGTTATTTT
1 CATAT-ATATAATATAGTTA-TTT
957784 CATATATATAATAT
1 CATATATATAATAT
957798 CTATGGTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (22 bp):
CATATATATAATATAGTTATTT
Found at i:964421 original size:14 final size:15
Alignment explanation
Indices: 964388--964433 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
964378 TTTTCTTCGA
*
964388 TATTGAAAAATAAA-
1 TATTTAAAAATAAAT
*
964402 TA-TT-AAAATAATT
1 TATTTAAAAATAAAT
964415 TATTTAAAAATAAAT
1 TATTTAAAAATAAAT
964430 TATT
1 TATT
964434 ATTATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
12 7 0.27
13 3 0.12
14 4 0.15
15 12 0.46
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
TATTTAAAAATAAAT
Found at i:965401 original size:17 final size:17
Alignment explanation
Indices: 965379--965411 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
965369 TTTGTTTCTC
965379 TGTATTTCTCT-TCTCTG
1 TGTATTT-TCTGTCTCTG
965396 TGTATTTTCTGTCTCT
1 TGTATTTTCTGTCTCT
965412 CCCTGTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.06, C:0.21, G:0.12, T:0.61
Consensus pattern (17 bp):
TGTATTTTCTGTCTCTG
Found at i:965649 original size:16 final size:16
Alignment explanation
Indices: 965628--965669 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
965618 ACCGTTGGCT
965628 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
965644 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
965660 GAGGCGGCTG
1 GAGGCGGCTG
965670 CGCATGGGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.57, T:0.07
Consensus pattern (16 bp):
GAGGCGGCTGGAGGCA
Found at i:965773 original size:2 final size:2
Alignment explanation
Indices: 965768--965798 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
965758 TTTTTATTAT
965768 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
965799 TTAATAATAA
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:965808 original size:3 final size:3
Alignment explanation
Indices: 965800--965865 Score: 87
Period size: 3 Copynumber: 22.0 Consensus size: 3
965790 TATATATATT
* * *
965800 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
965848 TAA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
965866 ATAAATTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:967206 original size:127 final size:129
Alignment explanation
Indices: 966962--967210 Score: 328
Period size: 127 Copynumber: 1.9 Consensus size: 129
966952 TGCGTCCTGG
* * *
966962 TGTTAAACCTAGTCTACCATCACCATCAAAGTATATTCACGGGACGGGACCGTTGCTTCTTGTGA
1 TGTTAAACCTAGCCTACCATCACCATCAAAGCATATTCAC--GAC-GGACAGTTGCTTCTTGTGA
967027 CTTTCCTTCACCTTTCTTTTCACTTGGTTATTTGTTATATGATAAAAGAAAATGTGTGATATGTT
63 CTTTCCTTCACCTTTCTTTTCACTTGGTTATTTGTTATATGATAAAAGAAAATGTGTGATATGTT
967092 GA
128 GA
* * *
967094 TGTTTAACCTAGCCTACCATCTCCATCGAAGCATATTCAC-A-GGACAGTTGCTTCTTGTGAC-T
1 TGTTAAACCTAGCCTACCATCACCATCAAAGCATATTCACGACGGACAGTTGCTTCTTGTGACTT
* * *
967156 TCTCTTCACCTTTCTTTTCCCTTGGTTCTTTTGTTATTTGACT-AAA-AAAATGTGT
66 TC-CTTCACCTTTCTTTTCACTTGGTT-ATTTGTTATATGA-TAAAAGAAAATGTGT
967211 TAAAATGTGT
Statistics
Matches: 105, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
126 3 0.03
127 51 0.49
128 14 0.13
129 2 0.02
132 35 0.33
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (129 bp):
TGTTAAACCTAGCCTACCATCACCATCAAAGCATATTCACGACGGACAGTTGCTTCTTGTGACTT
TCCTTCACCTTTCTTTTCACTTGGTTATTTGTTATATGATAAAAGAAAATGTGTGATATGTTGA
Found at i:971355 original size:29 final size:29
Alignment explanation
Indices: 971306--971415 Score: 82
Period size: 29 Copynumber: 3.8 Consensus size: 29
971296 TATGACACTC
*
971306 ATTTTAAATTAAACC-CTAAACTTTAAAAT
1 ATTTTAAATTAATCCTC-AAACTTTAAAAT
* *
971335 ATTTTATATTAATCCTCAAACTATAATTCAA-
1 ATTTTAAATTAATCCTCAAACTTTAA---AAT
* *
971366 A-TTTAAATTAATCCTTAAACTTTAAGAT
1 ATTTTAAATTAATCCTCAAACTTTAAAAT
* * * *
971394 AATTTATATTATTCCTTAAACT
1 ATTTTAAATTAATCCTCAAACT
971416 ATCAACATCA
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.02
28 1 0.02
29 39 0.59
30 22 0.33
31 1 0.02
32 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.43
Consensus pattern (29 bp):
ATTTTAAATTAATCCTCAAACTTTAAAAT
Found at i:976417 original size:47 final size:47
Alignment explanation
Indices: 976347--976460 Score: 165
Period size: 47 Copynumber: 2.4 Consensus size: 47
976337 CTCGGTGAAT
** * *
976347 CATCCAATAAGGATGAATTAGCCTGTAACTCGGTGATTGAAATTTAC
1 CATCCAATAAGGATGAACCAGCCTGTAACTCGATAATTGAAATTTAC
*
976394 CATCCAATAAGGATGAACCAGCCTGTAACTCGATAATTGGAATTTAC
1 CATCCAATAAGGATGAACCAGCCTGTAACTCGATAATTGAAATTTAC
* *
976441 CATCCAATAAAGATAAACCA
1 CATCCAATAAGGATGAACCA
976461 ACTTGTAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (47 bp):
CATCCAATAAGGATGAACCAGCCTGTAACTCGATAATTGAAATTTAC
Found at i:977087 original size:19 final size:20
Alignment explanation
Indices: 977054--977091 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
977044 GTCTTTAGAA
977054 AAAGTCAACAGGTTAAAGTC
1 AAAGTCAACAGGTTAAAGTC
977074 AAAGTCAA-AGGTTAAAGT
1 AAAGTCAACAGGTTAAAGT
977092 TAACTCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAGTCAACAGGTTAAAGTC
Found at i:978194 original size:56 final size:56
Alignment explanation
Indices: 978108--978218 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
978098 TTCGTTTATT
* *
978108 AAATGAATCTAAGAATTTTGTTCATACTCGTTTATTTAACTTAGTAAGCGAACATG
1 AAATGAATCTAAGAATTTTGTTCATACTCGTTTATTTAACTTAATAAACGAACATG
*
978164 AAATGAATCTAAGAATTTTGTTCATGCTCGTTTATTTAACTTAATAAACGAACAT
1 AAATGAATCTAAGAATTTTGTTCATACTCGTTTATTTAACTTAATAAACGAACAT
978219 AAACATAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (56 bp):
AAATGAATCTAAGAATTTTGTTCATACTCGTTTATTTAACTTAATAAACGAACATG
Found at i:981760 original size:18 final size:18
Alignment explanation
Indices: 981721--981760 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
981711 TTAATGTTCG
*
981721 TTTATATTTATTTATTTA
1 TTTATATTTATTTAATTA
981739 TTTATATTTAATTTAATT-
1 TTTATATTT-ATTTAATTA
981757 TTTA
1 TTTA
981761 AATCCATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATATTTATTTAATTA
Found at i:981976 original size:29 final size:29
Alignment explanation
Indices: 981923--981994 Score: 135
Period size: 29 Copynumber: 2.4 Consensus size: 29
981913 ATGTTCATAT
981923 GTTTATGTTCGTTTACATTTGTTTAAGCTC
1 GTTTATGTTCG-TTACATTTGTTTAAGCTC
981953 GTTTATGTTCGTTACATTTGTTTAAGCTC
1 GTTTATGTTCGTTACATTTGTTTAAGCTC
981982 GTTTATGTTCGTT
1 GTTTATGTTCGTT
981995 CGTTTGTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 31 0.74
30 11 0.26
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.54
Consensus pattern (29 bp):
GTTTATGTTCGTTACATTTGTTTAAGCTC
Found at i:993766 original size:11 final size:11
Alignment explanation
Indices: 993750--993774 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
993740 TTTTCTTTCT
993750 TTTTATTTTTA
1 TTTTATTTTTA
993761 TTTTATTTTTA
1 TTTTATTTTTA
993772 TTT
1 TTT
993775 GTTTCCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:995012 original size:28 final size:27
Alignment explanation
Indices: 994972--995038 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
994962 GAAGAAGAAG
*
994972 AAGAAGAAAAAGAAGGAAAAATTGTGCA
1 AAGAA-AAAAAGAAAGAAAAATTGTGCA
*
995000 AAGAAAAGAAAGAAAGAGAAATTGTGCA
1 AAGAAAA-AAAGAAAGAAAAATTGTGCA
*
995028 ATGAAAAAAAG
1 AAGAAAAAAAG
995039 GTTATGTGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.17
28 29 0.83
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.10
Consensus pattern (27 bp):
AAGAAAAAAAGAAAGAAAAATTGTGCA
Found at i:997713 original size:39 final size:39
Alignment explanation
Indices: 997670--997759 Score: 126
Period size: 42 Copynumber: 2.2 Consensus size: 39
997660 ATTCTTTTCG
**
997670 TATGTTGATTTAACATTGGAGGTGAGCTAGTTGTTAAAT
1 TATGTTGAAGTAACATTGGAGGTGAGCTAGTTGTTAAAT
*
997709 TATGTTGAAAAAGTAACATTTGAGGTGAGCTAGTTGTTAAAT
1 TATGTTG---AAGTAACATTGGAGGTGAGCTAGTTGTTAAAT
997751 TATGTTGAA
1 TATGTTGAA
997760 AAAGTAGCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
39 9 0.20
42 36 0.80
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.39
Consensus pattern (39 bp):
TATGTTGAAGTAACATTGGAGGTGAGCTAGTTGTTAAAT
Found at i:997734 original size:42 final size:42
Alignment explanation
Indices: 997680--997765 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
997670 TATGTTGATT
997680 TAACATTGGAGGTGAGCTAGTTGTTAAATTATGTTGAAAAAG
1 TAACATTGGAGGTGAGCTAGTTGTTAAATTATGTTGAAAAAG
*
997722 TAACATTTGAGGTGAGCTAGTTGTTAAATTATGTTGAAAAAG
1 TAACATTGGAGGTGAGCTAGTTGTTAAATTATGTTGAAAAAG
997764 TA
1 TA
997766 GCTTGGTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (42 bp):
TAACATTGGAGGTGAGCTAGTTGTTAAATTATGTTGAAAAAG
Found at i:1007265 original size:3 final size:3
Alignment explanation
Indices: 1007257--1007314 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
1007247 TTTGTTTTAT
* *
1007257 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA -TA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1007300 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1007315 AATAAATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 10 0.21
3 38 0.79
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1007298 original size:10 final size:11
Alignment explanation
Indices: 1007253--1007314 Score: 62
Period size: 10 Copynumber: 6.0 Consensus size: 11
1007243 TTCATTTGTT
1007253 TTATT-TATTA
1 TTATTATATTA
* *
1007263 TTATTATTTTG
1 TTATTATATTA
1007274 TT-TTA-A-TA
1 TTATTATATTA
1007282 TTATTATATTA
1 TTATTATATTA
1007293 -TATTATATTA
1 TTATTATATTA
1007303 TTATTATTATTA
1 TTATTA-TATTA
1007315 AATAAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 19 0.45
11 12 0.29
12 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (11 bp):
TTATTATATTA
Found at i:1009986 original size:19 final size:19
Alignment explanation
Indices: 1009964--1010008 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1009954 CTATTATATT
1009964 TAAATTAATCTAATTATAA
1 TAAATTAATCTAATTATAA
1009983 TAAATTAATCTAATTATAA
1 TAAATTAATCTAATTATAA
*
1010002 AAAATTA
1 TAAATTA
1010009 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTAATCTAATTATAA
Found at i:1019657 original size:15 final size:16
Alignment explanation
Indices: 1019637--1019666 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1019627 ATCTTTCACT
1019637 ATAAATAT-ATAAAAG
1 ATAAATATAATAAAAG
1019652 ATAAATATAATAAAA
1 ATAAATATAATAAAA
1019667 CGTTAGGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
ATAAATATAATAAAAG
Found at i:1019919 original size:21 final size:20
Alignment explanation
Indices: 1019893--1019959 Score: 55
Period size: 23 Copynumber: 3.1 Consensus size: 20
1019883 TTAGTTTGAT
1019893 AAAAATAATTTAGGTACTTTA
1 AAAAATAATTTAGGTAC-TTA
* *
1019914 AAAAATGACATTTAGTTTGA-TAA
1 AAAAAT-A-ATTTAG-GT-ACTTA
*
1019937 AAAAATAATTTAAGTACTTA
1 AAAAATAATTTAGGTACTTA
1019957 AAA
1 AAA
1019960 CAAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 11 0.31
22 2 0.06
23 14 0.39
24 1 0.03
25 1 0.03
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.34
Consensus pattern (20 bp):
AAAAATAATTTAGGTACTTA
Found at i:1020199 original size:22 final size:20
Alignment explanation
Indices: 1020165--1020234 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 20
1020155 TTTAAGTACT
1020165 TAAATTATTTTTTATCAAAC
1 TAAATTATTTTTTATCAAAC
*
1020185 TAAATGTCATTTTTT-TGAAGTAC
1 TAAAT-T-ATTTTTTATCAA--AC
1020208 TTAAATTATTTTTTTATCAAAC
1 -TAAATTA-TTTTTTATCAAAC
1020230 TAAAT
1 TAAAT
1020235 CCTTAAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
20 5 0.12
21 9 0.22
22 10 0.24
23 9 0.22
24 8 0.20
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (20 bp):
TAAATTATTTTTTATCAAAC
Found at i:1022993 original size:60 final size:60
Alignment explanation
Indices: 1022882--1023056 Score: 190
Period size: 60 Copynumber: 2.9 Consensus size: 60
1022872 TTTGGGAATG
* ** * *
1022882 AAATTGGAATATTTAAAAGTTTGGGGAATTAATTTAGAATAAGGGTCATAGTTTAAAGATA
1 AAATTGGAATATTCAAAAGTTTAAGG-ACTAATTTAGAATGAGGGTCATAGTTTAAAGATA
* ** * * *
1022943 AAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGTATCATAGTTTGAGGATG
1 AAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGGGTCATAGTTTAAAGATA
* ** *
1023003 CAATTAAAATATTCAAAAGTTTAATGAAC-AATTTAGAATGAGGGTCATAGTTTA
1 AAATTGGAATATTCAAAAGTTTAA-GGACTAATTTAGAATGAGGGTCATAGTTTA
1023057 GAGGCATGTG
Statistics
Matches: 94, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
60 69 0.73
61 25 0.27
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.34
Consensus pattern (60 bp):
AAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGGGTCATAGTTTAAAGATA
Found at i:1027219 original size:21 final size:20
Alignment explanation
Indices: 1027194--1027232 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1027184 TTGCTTCAGG
1027194 GGTATCGATACCCTTGCTATA
1 GGTATCGATACCC-TGCTATA
*
1027215 GGTATTGATACCCTGCTA
1 GGTATCGATACCCTGCTA
1027233 CAGTAACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (20 bp):
GGTATCGATACCCTGCTATA
Found at i:1035599 original size:25 final size:25
Alignment explanation
Indices: 1035570--1035619 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1035560 ATTACTTTTA
* *
1035570 TCTATGTTTCTCTCGCTTCTCTCTC
1 TCTATGCTTCTCTCGCTTCTATCTC
*
1035595 TCTATGCTTCTTTCGCTTCTATCTC
1 TCTATGCTTCTCTCGCTTCTATCTC
1035620 AACTTCTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.06, C:0.34, G:0.08, T:0.52
Consensus pattern (25 bp):
TCTATGCTTCTCTCGCTTCTATCTC
Found at i:1049913 original size:5 final size:5
Alignment explanation
Indices: 1049905--1049930 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1049895 TATTATTATT
1049905 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
1049931 TTATAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1055090 original size:23 final size:23
Alignment explanation
Indices: 1055059--1055116 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1055049 TTGCATTGAT
*
1055059 AGTTCGCAGCAATTACACCAATA
1 AGTTGGCAGCAATTACACCAATA
1055082 AGTTGGCAGCAATTACACCAATA
1 AGTTGGCAGCAATTACACCAATA
1055105 AGTTGGCAGCAA
1 AGTTGGCAGCAA
1055117 CAATTGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (23 bp):
AGTTGGCAGCAATTACACCAATA
Found at i:1059560 original size:15 final size:15
Alignment explanation
Indices: 1059532--1059625 Score: 111
Period size: 15 Copynumber: 6.3 Consensus size: 15
1059522 AAATAATTTT
1059532 AAATAATTTA--ATA
1 AAATAATTTATTATA
* *
1059545 AAGTTATTTATTATA
1 AAATAATTTATTATA
*
1059560 AAATAATTTATTTTAA
1 AAATAATTTATTAT-A
1059576 AAATAATTTATTATA
1 AAATAATTTATTATA
*
1059591 AAATAATTTATTTTA
1 AAATAATTTATTATA
* *
1059606 AAACAAATTATTATA
1 AAATAATTTATTATA
1059621 AAATA
1 AAATA
1059626 TAGATTGATT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
13 8 0.12
15 45 0.67
16 14 0.21
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
AAATAATTTATTATA
Found at i:1059588 original size:31 final size:31
Alignment explanation
Indices: 1059550--1059625 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
1059540 TAATAAAGTT
1059550 ATTTATTATAAAATAATTTATTTTAAAA-ATA
1 ATTTATTATAAAATAATTTATTTTAAAACA-A
1059581 ATTTATTATAAAATAATTTATTTTAAAACAA
1 ATTTATTATAAAATAATTTATTTTAAAACAA
1059612 A-TTATTATAAAATA
1 ATTTATTATAAAATA
1059626 TAGATTGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
30 13 0.30
31 30 0.68
32 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
ATTTATTATAAAATAATTTATTTTAAAACAA
Found at i:1059638 original size:22 final size:22
Alignment explanation
Indices: 1059613--1059713 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
1059603 TTAAAACAAA
*
1059613 TTATTATAAAATATAGATTGAT
1 TTATTTTAAAATATAGATTGAT
** * *
1059635 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATAGA-TTGAT
* * *
1059659 TTAATTTATTAGTATAGATTGAT
1 TTATTTTA-AAATATAGATTGAT
*
1059682 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATAGATTGAT
1059704 TTATTTTAAA
1 TTATTTTAAA
1059714 TAACTTATTA
Statistics
Matches: 60, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 32 0.53
23 13 0.22
24 13 0.22
25 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (22 bp):
TTATTTTAAAATATAGATTGAT
Found at i:1059653 original size:15 final size:14
Alignment explanation
Indices: 1059633--1059668 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1059623 ATATAGATTG
1059633 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
*
1059648 ATTTATTTTAATTA
1 ATTTATTTTAAATA
1059662 ATTTATT
1 ATTTATT
1059669 AGTATAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1059665 original size:14 final size:15
Alignment explanation
Indices: 1059550--1059668 Score: 105
Period size: 15 Copynumber: 7.5 Consensus size: 15
1059540 TAATAAAGTT
*
1059550 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1059565 ATTTATTTTAAAAATA
1 ATTTATTTT-AAAATA
*
1059581 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1059596 ATTTATTTTAAAACA
1 ATTTATTTTAAAATA
* *
1059611 AATTATTATAAAATATAGA
1 ATTTATT-TTAAA-AT--A
1059630 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
*
1059648 ATTTATTTT-AATTA
1 ATTTATTTTAAAATA
1059662 ATTTATT
1 ATTTATT
1059669 AGTATAGATT
Statistics
Matches: 86, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
14 11 0.13
15 42 0.49
16 18 0.21
17 1 0.01
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.05
22 6 0.07
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1059686 original size:32 final size:31
Alignment explanation
Indices: 1059648--1060029 Score: 247
Period size: 32 Copynumber: 12.4 Consensus size: 31
1059638 TTTTAAAATA
*
1059648 ATTTATTTTAATTAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
1059680 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
*
1059702 ATTTATTTTAAATAACTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
*
1059734 ATTTATTTT-AA-AA--TA--A--A-AATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
1059756 ATTTATTTTAAATAATTTATTAGTATCGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
** *
1059788 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTA-TGATTG
* * * * *
1059817 ATTGTAGTTGTATAGATTGATTTATT--T-TAAATA
1 ATT-TA-TT-T-TA-AATAATTTATTAGTATGATTG
* * *
1059850 ATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTG
1 ATTTATT--T-TA-AATAATTTA--TT--AGTAT-GATTG
*
1059890 ATTTATTTTAAATAATTTATTAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
1059922 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
1059954 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
1059986 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
1060018 ATTTATTTTAAA
1 ATTTATTTTAAA
1060030 ATATTGATTG
Statistics
Matches: 289, Mismatches: 18, Indels: 86
0.74 0.05 0.22
Matches are distributed among these distances:
22 27 0.09
23 4 0.01
24 5 0.02
26 6 0.02
27 2 0.01
28 6 0.02
29 3 0.01
30 11 0.04
31 13 0.04
32 174 0.60
33 7 0.02
34 10 0.03
36 7 0.02
37 2 0.01
38 2 0.01
39 1 0.00
40 9 0.03
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.52
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTAGTATGATTG
Found at i:1059711 original size:54 final size:54
Alignment explanation
Indices: 1059648--1060221 Score: 381
Period size: 54 Copynumber: 10.4 Consensus size: 54
1059638 TTTTAAAATA
*
1059648 ATTTATTTTAATTAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* ***
1059702 ATTTATTTTAAATAACTTATTAGTAT-GAATTGATTTATTTTAAAATAAAAATTG
1 ATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATATGGATTG
*
1059756 ATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
*
1059810 ATTTA--TT--AT--TGTAGTT-GTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATAGATTGATTTATTTT-AA-AA--TA-T-G----GATTG
* * * *
1059868 ATTTATTTT-AA-AA--TA-TAG-ATTGATTTATTTTAAATAATTTATTAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGA-TTT--AT--TTTA-AAATATGGATTG
*
1059922 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTG
* *
1059986 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* * *
1060040 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATAGATTGATTTATTTTAAAATATGGATTG
* * * * * * *** *
1060084 A-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATAGATTGATTTA-T-TT-TA-AAATATGGATTG
1060146 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1060200 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
1060222 TTGTAGTTGT
Statistics
Matches: 417, Mismatches: 41, Indels: 124
0.72 0.07 0.21
Matches are distributed among these distances:
43 3 0.01
44 4 0.01
46 1 0.00
47 5 0.01
48 44 0.11
49 6 0.01
50 9 0.02
51 2 0.00
52 6 0.01
53 2 0.00
54 167 0.40
55 10 0.02
56 9 0.02
57 4 0.01
58 37 0.09
59 15 0.04
60 18 0.04
61 3 0.01
62 19 0.05
63 8 0.02
64 45 0.11
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
Found at i:1059843 original size:188 final size:194
Alignment explanation
Indices: 1059648--1059997 Score: 561
Period size: 188 Copynumber: 1.8 Consensus size: 194
1059638 TTTTAAAATA
* *
1059648 ATTTATTTTAATTAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAA
*
1059713 ATAACTTATTAGTATGAATTGATTTATTTT-AA-AA-TA-A-A-AATTGATTTATTTTAAATAAT
66 ATAACTTATTAATATGAATTGATTTATTTTAAATAATTATAGAGAATTGATTTATTTTAAATAAT
1059772 TTATTAGTATCG-ATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTG
131 TTATTAGTAT-GAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTG
1059836 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAA
* *
1059901 ATAATTTATTAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
66 ATAACTTATTAATATGAATTGATTTATTTTAAATAA-TTA-TAG-A-GAATTGATTTATTTTAAA
1059966 TAATTTATTAGTATGAATTGATTTATTTTAAA
127 TAATTTATTAGTATGAATTGATTTATTTTAAA
1059998 TAATTTATTA
Statistics
Matches: 146, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
188 91 0.62
189 2 0.01
190 2 0.01
192 2 0.01
194 1 0.01
196 1 0.01
197 1 0.01
198 46 0.32
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.52
Consensus pattern (194 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAA
ATAACTTATTAATATGAATTGATTTATTTTAAATAATTATAGAGAATTGATTTATTTTAAATAAT
TTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTG
Found at i:1059848 original size:80 final size:85
Alignment explanation
Indices: 1059751--1059965 Score: 316
Period size: 80 Copynumber: 2.6 Consensus size: 85
1059741 TTAAAATAAA
* *
1059751 AATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAATATGGATTGATTTAT
1 AATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTAT
*
1059816 TATT-GT-AGTT-GT-ATA-G
66 T-TTAATAAGTTAGTAATATG
1059832 -ATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTAT
1 AATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTAT
* *
1059896 TTTAAATAATTTATTAATATG
66 TTT-AATAAGTTAGTAATATG
*
1059917 AATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 AATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
1059966 TAATTTATTA
Statistics
Matches: 121, Mismatches: 6, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
79 2 0.02
80 63 0.52
81 1 0.01
82 3 0.02
83 1 0.01
84 3 0.02
85 1 0.01
86 47 0.39
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (85 bp):
AATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTAT
TTTAATAAGTTAGTAATATG
Found at i:1059884 original size:22 final size:22
Alignment explanation
Indices: 1059859--1059901 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1059849 AATTTATTAG
1059859 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
1059881 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
1059902 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:1059909 original size:14 final size:14
Alignment explanation
Indices: 1059890--1060006 Score: 63
Period size: 14 Copynumber: 7.5 Consensus size: 14
1059880 ATATAGATTG
1059890 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1059904 ATTTATTAATATGAATTG
1 ATTTATT--T-T-AAATA
1059922 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
1059936 ATTTATTAGTATGGATTG
1 ATTTATT--T-T-AAATA
1059954 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1059968 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
1059986 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1060000 ATTTATT
1 ATTTATT
1060007 AGTATGGATT
Statistics
Matches: 77, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
14 36 0.47
15 3 0.04
16 6 0.08
17 3 0.04
18 29 0.38
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1059962 original size:64 final size:64
Alignment explanation
Indices: 1059885--1060029 Score: 281
Period size: 64 Copynumber: 2.3 Consensus size: 64
1059875 TTAAAATATA
1059885 GATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAATAATTTATTAGTATG
*
1059949 GATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAATAATTTATTAGTATG
1060013 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
1060030 ATATTGATTG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (64 bp):
GATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAATAATTTATTAGTATG
Found at i:1060074 original size:80 final size:80
Alignment explanation
Indices: 1059976--1060206 Score: 417
Period size: 80 Copynumber: 2.9 Consensus size: 80
1059966 TAATTTATTA
* *
1059976 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1060041 TTTATTATTGTAGTT
66 TTTATTATTGTAGTT
*
1060056 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1060121 TTTATTATTGTAGTT
66 TTTATTATTGTAGTT
* *
1060136 GTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1060201 TTTATT
66 TTTATT
1060207 TTAAATAATT
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 145 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
TTTATTATTGTAGTT
Found at i:1060183 original size:18 final size:17
Alignment explanation
Indices: 1060134--1060184 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
1060124 ATTATTGTAG
1060134 TTGTATAGATTGATTTA
1 TTGTATAGATTGATTTA
* *
1060151 TT-T-TA-AATAATTTA
1 TTGTATAGATTGATTTA
1060165 TTAGTATAGATTGATTTA
1 TT-GTATAGATTGATTTA
1060183 TT
1 TT
1060185 TTAAAATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 2 0.08
17 4 0.15
18 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (17 bp):
TTGTATAGATTGATTTA
Found at i:1060271 original size:31 final size:31
Alignment explanation
Indices: 1060236--1060294 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1060226 AGTTGTATAG
*
1060236 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGTAAAACTAAA
1060267 ATTATTTAAATCTCAGTATTGTAAAACT
1 ATTATTTAAATCTCAGTATTGTAAAACT
1060295 TTTTAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGTAAAACTAAA
Found at i:1065282 original size:22 final size:22
Alignment explanation
Indices: 1065257--1065301 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1065247 CATGTATTTC
1065257 TAATTTCTTGTAATTCTTTAAA
1 TAATTTCTTGTAATTCTTTAAA
* * *
1065279 TAATTTTTTTTAATTTTTTAAA
1 TAATTTCTTGTAATTCTTTAAA
1065301 T
1 T
1065302 CTCATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TAATTTCTTGTAATTCTTTAAA
Found at i:1074352 original size:18 final size:17
Alignment explanation
Indices: 1074327--1074375 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
1074317 ATTTTTTATT
1074327 TTTTAAATCTCATA-AAA
1 TTTTAAATCTC-TAGAAA
*
1074344 TTCTTAAATTATCTAGAAA
1 TT-TTAAA-TCTCTAGAAA
1074363 TTTTAAATCTCTA
1 TTTTAAATCTCTA
1074376 AGGGTTCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 7 0.26
18 12 0.44
19 8 0.30
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTTAAATCTCTAGAAA
Found at i:1074636 original size:13 final size:13
Alignment explanation
Indices: 1074603--1074635 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1074593 TTATGTATTT
1074603 ATATTTTATTTTA
1 ATATTTTATTTTA
1074616 ATATTTTATTTTA
1 ATATTTTATTTTA
1074629 ATTATTT
1 A-TATTT
1074636 AAAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATATTTTATTTTA
Found at i:1075253 original size:13 final size:13
Alignment explanation
Indices: 1075235--1075266 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
1075225 AGCCCAAAGT
1075235 AGGGTAAATCAAA
1 AGGGTAAATCAAA
1075248 AGGGTAAATCAAA
1 AGGGTAAATCAAA
1075261 ATGGGT
1 A-GGGT
1075267 CAATGATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.47, C:0.06, G:0.28, T:0.19
Consensus pattern (13 bp):
AGGGTAAATCAAA
Found at i:1077814 original size:110 final size:110
Alignment explanation
Indices: 1077650--1077866 Score: 317
Period size: 110 Copynumber: 2.0 Consensus size: 110
1077640 ATTAAAGTGT
* * * * * * ** *
1077650 ACTTGAAGCCATGTAAGATGTCTTGATCCTCTAACTTGAGGCATTGAGACTTTGAATTGCTCCTT
1 ACTTGAAGCAATGAAAGATATATTGATCCTCCAACTTAAGGCATTGAGACTTTGAATTAATCCTC
*
1077715 CAACTAGAGGTAGTGGAACTTTTGAAAAATTAAATTGTTCCTACA
66 CAACTAGAGGCAGTGGAACTTTTGAAAAATTAAATTGTTCCTACA
*
1077760 ACTTGAAGCAATGAAAGATATATTGGTCCTCCAACTTAAGGCATTGAGACTTTGAATTAATCCTC
1 ACTTGAAGCAATGAAAGATATATTGATCCTCCAACTTAAGGCATTGAGACTTTGAATTAATCCTC
* *
1077825 CAACTTGAGGCATTGGAACTTTTGAAAAATTAAATTGTTCCT
66 CAACTAGAGGCAGTGGAACTTTTGAAAAATTAAATTGTTCCT
1077867 CAAAATAGAG
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 94 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (110 bp):
ACTTGAAGCAATGAAAGATATATTGATCCTCCAACTTAAGGCATTGAGACTTTGAATTAATCCTC
CAACTAGAGGCAGTGGAACTTTTGAAAAATTAAATTGTTCCTACA
Found at i:1083168 original size:28 final size:29
Alignment explanation
Indices: 1083137--1083191 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
1083127 TTTATAAATA
1083137 ATTTATATTAGT-TAT-TTAAAATATTAAC
1 ATTTATATT-GTATATATTAAAATATTAAC
*
1083165 ATTTATATTTTATATATTAAAATATTA
1 ATTTATATTGTATATATTAAAATATTA
1083192 CTAATGAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 12 0.50
29 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
ATTTATATTGTATATATTAAAATATTAAC
Found at i:1089843 original size:64 final size:64
Alignment explanation
Indices: 1089775--1089995 Score: 239
Period size: 64 Copynumber: 3.5 Consensus size: 64
1089765 TTGAAGGTGT
* * * ** * *
1089775 ATCGATGCACAGGAAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCTTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCAAATGCAATTCGTG
1089838 C
64 C
* *
1089839 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCAAATGTAATTCGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
* * * * * * **
1089903 ATCGATGCATAAGTAGTACATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
* *
1089967 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
1089996 ACCTTCATTA
Statistics
Matches: 133, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
64 127 0.95
65 6 0.05
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
Found at i:1090690 original size:31 final size:31
Alignment explanation
Indices: 1090652--1090714 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
1090642 AGGGTCGAGG
*
1090652 GTTTACCTATGTTCTTC-GGAACATATGGACT
1 GTTTACCTAGGTTCTTCGGGAAC-TATGGACT
*
1090683 GTTTACCTAGGTTCTTCGGGATCTATGGACT
1 GTTTACCTAGGTTCTTCGGGAACTATGGACT
1090714 G
1 G
1090715 GTCCTTCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGAACTATGGACT
Found at i:1093944 original size:64 final size:64
Alignment explanation
Indices: 1093876--1094096 Score: 284
Period size: 64 Copynumber: 3.5 Consensus size: 64
1093866 TTGAAGGTGT
* * * **
1093876 ATCGATGCACAGGAAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTCGTG
1093939 C
64 C
*
1093940 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGC
* * * * **
1094004 ATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGC
* *
1094068 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
1094097 ACCTTCATTA
Statistics
Matches: 140, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
64 134 0.96
65 6 0.04
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGC
Found at i:1094798 original size:31 final size:31
Alignment explanation
Indices: 1094753--1094815 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1094743 AGGGTTGAGG
* *
1094753 GTTTACCTATGTTCTTCG-GAACATATGGACT
1 GTTTACCCAGGTTCTTCGGGAAC-TATGGACT
*
1094784 GTTTACCCAGGTTCTTCGGGATCTATGGACT
1 GTTTACCCAGGTTCTTCGGGAACTATGGACT
1094815 G
1 G
1094816 GTCCTTCGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (31 bp):
GTTTACCCAGGTTCTTCGGGAACTATGGACT
Found at i:1099728 original size:3 final size:3
Alignment explanation
Indices: 1099708--1099755 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
1099698 CCTGCCAAAA
* * *
1099708 AAT AA- AAT -AT ATT AAT AAT AAT ATT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1099754 AA
1 AA
1099756 AGATAATAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1100738 original size:60 final size:60
Alignment explanation
Indices: 1100616--1100740 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
1100606 TAATAATTTA
* * * * * * ** *
1100616 AATTTGAAGATTGATATAAAATATTTTAAACTTTTAGGATTAATTTAAAGTGAGGATCAT
1 AATTTGAAGATAGATATAAAATATTTTAAAATTTAACGATCAATTTAAAATGAAAATAAT
*
1100676 AATTTGAAGATAGATATAGAATATTTTAAAATTTAACGATCAATTTAAAATGAAAATAAT
1 AATTTGAAGATAGATATAAAATATTTTAAAATTTAACGATCAATTTAAAATGAAAATAAT
1100736 AATTT
1 AATTT
1100741 CGAGACATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.38
Consensus pattern (60 bp):
AATTTGAAGATAGATATAAAATATTTTAAAATTTAACGATCAATTTAAAATGAAAATAAT
Found at i:1102603 original size:21 final size:21
Alignment explanation
Indices: 1102577--1102622 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1102567 ATTCTGACTA
1102577 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
*
1102598 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTTCCAAAT
1102619 TCGC
1 TCGC
1102623 AATGCGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:1102628 original size:21 final size:21
Alignment explanation
Indices: 1102583--1102629 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1102573 ACTATCGCGT
**
1102583 TGCGATTTTCCAAATTCGCGT
1 TGCGATTTTCCAAATTCGCAA
*
1102604 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTTCCAAATTCGCAA
1102625 TGCGA
1 TGCGA
1102630 ATACGTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCGCAA
Found at i:1103242 original size:21 final size:21
Alignment explanation
Indices: 1103181--1103259 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
1103171 TTCTAAACTT
1103181 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1103201 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
1103221 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1103242 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
1103260 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1103297 original size:19 final size:19
Alignment explanation
Indices: 1103258--1103302 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1103248 GCAACGAGAG
**
1103258 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
1103277 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
*
1103296 AAACGCA
1 AATCGCA
1103303 TTGCGACAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.27, G:0.18, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1103301 original size:33 final size:33
Alignment explanation
Indices: 1103236--1103297 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1103226 CGCAACGAGA
* **
1103236 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAACCAAAACGC
*
1103269 GAAATGAAAATCGCAACGCGA-AACCAAAA
1 GAAATGAAAATCGCAACGAGAGAACCAAAA
1103298 ACGCATTGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 5 0.20
33 20 0.80
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.08
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAACCAAAACGC
Found at i:1103351 original size:21 final size:21
Alignment explanation
Indices: 1103303--1103351 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1103293 CAAAAACGCA
*
1103303 TTGCGACAGTCATTTTTCACG
1 TTGCGATAGTCATTTTTCACG
1103324 TTGCGATAGTCATTTTTCACG
1 TTGCGATAGTCATTTTTCACG
1103345 TTGCGAT
1 TTGCGAT
1103352 TTTAAGTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (21 bp):
TTGCGATAGTCATTTTTCACG
Found at i:1103831 original size:21 final size:21
Alignment explanation
Indices: 1103807--1103873 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1103797 TCATTCCTCG
1103807 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1103828 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1103849 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1103870 AGAG
1 AGAG
1103874 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1103831 original size:42 final size:42
Alignment explanation
Indices: 1103755--1103873 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1103745 GACTCGCCTG
* * * * * * *
1103755 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1103797 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1103839 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1103874 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1105243 original size:14 final size:14
Alignment explanation
Indices: 1105224--1105259 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1105214 ATTGTTTAAT
1105224 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1105238 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1105252 TGATTTGT
1 TGATTTGT
1105260 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1105383 original size:19 final size:19
Alignment explanation
Indices: 1105367--1105452 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
1105357 AAAAATGACT
*
1105367 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1105386 ATCTCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
1105405 ATCGCAA----AGA-CAAA
1 ATCGCAACGCGAAATGAAA
* *
1105419 ATCGTAACGCGAAACTAAAA
1 ATCGCAACGCGAAA-TGAAA
1105439 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1105453 CTAAATTCGC
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
14 9 0.17
15 2 0.04
18 2 0.04
19 23 0.44
20 16 0.31
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1105439 original size:20 final size:20
Alignment explanation
Indices: 1105416--1105457 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1105406 TCGCAAAGAC
*
1105416 AAAATCGTAACGCGAAACTA
1 AAAATCGCAACGCGAAACTA
1105436 AAAATCGCAACGCGAAACTA
1 AAAATCGCAACGCGAAACTA
1105456 AA
1 AA
1105458 TTCGCGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACTA
Found at i:1105504 original size:33 final size:33
Alignment explanation
Indices: 1105462--1105590 Score: 195
Period size: 33 Copynumber: 3.9 Consensus size: 33
1105452 ACTAAATTCG
* *
1105462 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1105495 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1105528 CATTACGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1105561 CGTTGCGATTTTCATTCTCTCGTTGCGATT
1 CGTTGCGATTTTCATT-TCGCATTGCGATT
1105591 TTCATTTCGC
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 76 0.87
34 11 0.13
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1105579 original size:20 final size:20
Alignment explanation
Indices: 1105554--1105596 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1105544 TCGCATTGCG
1105554 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1105574 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1105594 ATT
1 ATT
1105597 TCGCTTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.12, C:0.23, G:0.14, T:0.51
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1105581 original size:53 final size:53
Alignment explanation
Indices: 1105521--1105629 Score: 173
Period size: 53 Copynumber: 2.1 Consensus size: 53
1105511 TCGCATTGCG
*
1105521 ATTCTCTCATTACGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTCTCTCATTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTC
* * * *
1105574 ATTCTCTCGTTGCGATTTTCATTTCGCTTTGTGATTCCCTCGTTGCGATTTTC
1 ATTCTCTCATTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTC
1105627 ATT
1 ATT
1105630 TCGCATTGCG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.13, C:0.24, G:0.15, T:0.49
Consensus pattern (53 bp):
ATTCTCTCATTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTC
Found at i:1109066 original size:20 final size:19
Alignment explanation
Indices: 1109037--1109075 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1109027 TCGTTGCAAT
1109037 TTACTAAATCGCAATGCGA
1 TTACTAAATCGCAATGCGA
1109056 TTACGTAAATCGCAATGCGA
1 TTAC-TAAATCGCAATGCGA
1109076 ATTAGGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (19 bp):
TTACTAAATCGCAATGCGA
Found at i:1109085 original size:20 final size:20
Alignment explanation
Indices: 1109042--1109085 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1109032 GCAATTTACT
*
1109042 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGG
1109062 AAATCGCAATGCGAATTA-GG
1 AAATCGCAATGCG-ATTACGG
1109082 AAAT
1 AAAT
1109086 AAGGCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (20 bp):
AAATCGCAATGCGATTACGG
Found at i:1112653 original size:52 final size:52
Alignment explanation
Indices: 1112592--1112693 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
1112582 ATATATTTTT
* **
1112592 ATAATATTAATA-TTAAATTATTTTAAAAAT-AAATTTATAATATTTATTTATG
1 ATAATATTAAAATTTAAATTA-TTTAAAAATAAAAAATAT-ATATTTATTTATG
*
1112644 ATAATATTAAAATTTAAATTATTTAAAATTAAAAAATATATATTTATTTA
1 ATAATATTAAAATTTAAATTATTTAAAAATAAAAAATATATATTTATTTA
1112694 ATTATTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 30 0.68
53 14 0.32
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (52 bp):
ATAATATTAAAATTTAAATTATTTAAAAATAAAAAATATATATTTATTTATG
Found at i:1117756 original size:34 final size:34
Alignment explanation
Indices: 1117713--1117781 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1117703 TAAAACTCTC
*
1117713 TCTCTGTATATATATTAGTGTTGCATAGACATGT
1 TCTCTGTATATATATTAGTATTGCATAGACATGT
1117747 TCTCTGTATATATATTAGTATTGCATAGACATGT
1 TCTCTGTATATATATTAGTATTGCATAGACATGT
1117781 T
1 T
1117782 ATGGGGCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (34 bp):
TCTCTGTATATATATTAGTATTGCATAGACATGT
Found at i:1122505 original size:2 final size:2
Alignment explanation
Indices: 1122498--1122551 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1122488 ACATTATAAC
1122498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1122540 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1122552 TAATATGCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1124422 original size:3 final size:3
Alignment explanation
Indices: 1124409--1124443 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1124399 GCAAATGTAA
1124409 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1124444 TTAAAAGACG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1124428 original size:9 final size:8
Alignment explanation
Indices: 1124409--1124449 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
1124399 GCAAATGTAA
1124409 AATAAAAT
1 AATAAAAT
1124417 AATAATAAT
1 AATAA-AAT
1124426 AATAATAAT
1 AATAA-AAT
1124435 AATAAAAT
1 AATAAAAT
*
1124443 ATTAAAA
1 AATAAAA
1124450 GACGAGACGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 14 0.45
9 17 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AATAAAAT
Found at i:1132020 original size:23 final size:23
Alignment explanation
Indices: 1131972--1132031 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1131962 TTGTTTAACG
* * **
1131972 TTCATGAACATATTCATTTAGCA
1 TTCAGGAACATGTTCATTTAAAA
1131995 TTC-GCGAACATGTTCATTTAAAA
1 TTCAG-GAACATGTTCATTTAAAA
1132018 TTCAGGAACATGTT
1 TTCAGGAACATGTT
1132032 TTTTAACGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (23 bp):
TTCAGGAACATGTTCATTTAAAA
Found at i:1133382 original size:26 final size:26
Alignment explanation
Indices: 1133352--1133405 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1133342 GGTGCACAAC
1133352 ATGACGCCATATAGCAAGGGAACACA
1 ATGACGCCATATAGCAAGGGAACACA
1133378 ATGACGCCATATAGCAAGGGAACACA
1 ATGACGCCATATAGCAAGGGAACACA
1133404 AT
1 AT
1133406 TTTTCTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (26 bp):
ATGACGCCATATAGCAAGGGAACACA
Found at i:1138144 original size:115 final size:115
Alignment explanation
Indices: 1137940--1138168 Score: 307
Period size: 115 Copynumber: 2.0 Consensus size: 115
1137930 ACCAAATTTG
* * * * * * *
1137940 TTTTAAGAAAAATAATTTCAAGGTTTGGGTTTCATGAGAAACTGCCTCAAGTGAGACAAATTTTT
1 TTTTAAGAAAAACAATATCAAAGTTTGAGTTTCATGAGAAACTGCCTAAAGCGAGACAAATTTGT
* * *
1138005 TTTAAGAAAAAAATATCAAGAGAGATAAAATCTTAAGTGAGATAATTTTT
66 TCTAAGAAAAAAATATCAAAAGAGATAAAATCTTAAGTGAAATAATTTTT
* *
1138055 TTTTAGGAAAAACAATATCAAAGTTTGAGTTTCATGAGAAACTGTCTAAAGCGAGACGAAATTTG
1 TTTTAAGAAAAACAATATCAAAGTTTGAGTTTCATGAGAAACTGCCTAAAGCGAGAC-AAATTTG
* * *
1138120 TTCTAA-AAAACAATCTCAAAAGAGATAAAATCTTAAGTGAAATGATTTT
65 TTCTAAGAAAAAAATATCAAAAGAGATAAAATCTTAAGTGAAATAATTTT
1138169 GAAGTTTGAT
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
115 87 0.89
116 11 0.11
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (115 bp):
TTTTAAGAAAAACAATATCAAAGTTTGAGTTTCATGAGAAACTGCCTAAAGCGAGACAAATTTGT
TCTAAGAAAAAAATATCAAAAGAGATAAAATCTTAAGTGAAATAATTTTT
Done.