Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 21
Found at i:942829 original size:40 final size:40
Alignment explanation
Indices: 942774--942923 Score: 115
Period size: 40 Copynumber: 3.5 Consensus size: 40
942764 CGCTAAAAGT
* *
942774 TCGTACTTTAGTGGCATTTTTCTGAAAACACTGCGAAATC
1 TCGTACTCTACTGGCATTTTTCTGAAAACACTGCGAAATC
** *
942814 TCGTACTCTACTGGCATTTTATGCGTTATTGGGGAAATGAC-GCTAAAAGT-
1 TCGTACTCTACTGGCATTTT-T-C-----T---GAAAACACTGC-GAAA-TC
* *
942864 TCGTACTTTAGTGGCATTTTTCTGAAAACACTGCGAAATC
1 TCGTACTCTACTGGCATTTTTCTGAAAACACTGCGAAATC
942904 TCGTACTCTACTGGCATTTT
1 TCGTACTCTACTGGCATTTT
942924 ATTAAAAATG
Statistics
Matches: 84, Mismatches: 12, Indels: 28
0.68 0.10 0.23
Matches are distributed among these distances:
39 1 0.01
40 45 0.54
41 3 0.04
42 1 0.01
43 1 0.01
47 1 0.01
48 1 0.01
49 3 0.04
50 27 0.32
51 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (40 bp):
TCGTACTCTACTGGCATTTTTCTGAAAACACTGCGAAATC
Found at i:942899 original size:90 final size:90
Alignment explanation
Indices: 942746--942925 Score: 360
Period size: 90 Copynumber: 2.0 Consensus size: 90
942736 ACATATAGCG
942746 GCGTTATTGGGGAAATGACGCTAAAAGTTCGTACTTTAGTGGCATTTTTCTGAAAACACTGCGAA
1 GCGTTATTGGGGAAATGACGCTAAAAGTTCGTACTTTAGTGGCATTTTTCTGAAAACACTGCGAA
942811 ATCTCGTACTCTACTGGCATTTTAT
66 ATCTCGTACTCTACTGGCATTTTAT
942836 GCGTTATTGGGGAAATGACGCTAAAAGTTCGTACTTTAGTGGCATTTTTCTGAAAACACTGCGAA
1 GCGTTATTGGGGAAATGACGCTAAAAGTTCGTACTTTAGTGGCATTTTTCTGAAAACACTGCGAA
942901 ATCTCGTACTCTACTGGCATTTTAT
66 ATCTCGTACTCTACTGGCATTTTAT
942926 TAAAAATGCC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (90 bp):
GCGTTATTGGGGAAATGACGCTAAAAGTTCGTACTTTAGTGGCATTTTTCTGAAAACACTGCGAA
ATCTCGTACTCTACTGGCATTTTAT
Found at i:952120 original size:3 final size:3
Alignment explanation
Indices: 952112--952137 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
952102 TCTTTTCTAA
952112 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
952138 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:952144 original size:3 final size:3
Alignment explanation
Indices: 952138--952163 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
952128 CTTCTTCTTC
952138 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
952164 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:957750 original size:15 final size:15
Alignment explanation
Indices: 957730--957774 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
957720 AAAGATTTTT
*
957730 TATATAATAAATTTC
1 TATATAATAAATCTC
*
957745 TATATAATGAATCTC
1 TATATAATAAATCTC
*
957760 TAAAATAATAAATCT
1 T-ATATAATAAATCT
957775 AAATTAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (15 bp):
TATATAATAAATCTC
Found at i:958595 original size:73 final size:73
Alignment explanation
Indices: 958512--958675 Score: 283
Period size: 73 Copynumber: 2.2 Consensus size: 73
958502 TTTATTACAA
* *
958512 GTAAGATAAATAAACTTTATTTGTTACTGTTTTCAATCTTACAATAAGATTCTTTCTTTTATATT
1 GTAACATAAATAAACTTTATTTGTTACTGTTTCCAATCTTACAATAAGATTCTTTCTTTTATATT
958577 CCTCTTAT
66 CCTCTTAT
* *
958585 GTAATATAAATAAACTTTATTTGTTATTGTTTCCAATCTTACAATAAGATTCTTTCTTTTATATT
1 GTAACATAAATAAACTTTATTTGTTACTGTTTCCAATCTTACAATAAGATTCTTTCTTTTATATT
958650 CCTCTTAT
66 CCTCTTAT
*
958658 GTAACATAAGTAAACTTT
1 GTAACATAAATAAACTTT
958676 CTATTATTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 86 1.00
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (73 bp):
GTAACATAAATAAACTTTATTTGTTACTGTTTCCAATCTTACAATAAGATTCTTTCTTTTATATT
CCTCTTAT
Found at i:958676 original size:36 final size:36
Alignment explanation
Indices: 958563--958682 Score: 91
Period size: 36 Copynumber: 3.3 Consensus size: 36
958553 CAATAAGATT
* *
958563 CTTTCTTTTATATTCCTCTTATGTAATATAAATAAA
1 CTTTCTTTTATATTCCTCTTATGTAACATAAGTAAA
* ** ** * * **
958599 CTTTATTTGT-TATTGTTTCCAATCTTACAATAAG-ATT
1 CTTTCTTT-TATATT-CCTCTTATGTAAC-ATAAGTAAA
958636 CTTTCTTTTATATTCCTCTTATGTAACATAAGTAAA
1 CTTTCTTTTATATTCCTCTTATGTAACATAAGTAAA
*
958672 CTTTCTATTAT
1 CTTTCTTTTAT
958683 TTTTATCATA
Statistics
Matches: 58, Mismatches: 21, Indels: 10
0.65 0.24 0.11
Matches are distributed among these distances:
35 5 0.09
36 30 0.52
37 19 0.33
38 4 0.07
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (36 bp):
CTTTCTTTTATATTCCTCTTATGTAACATAAGTAAA
Found at i:958775 original size:45 final size:45
Alignment explanation
Indices: 958726--958815 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
958716 AAGATAAGTA
958726 AACTTTATTTGTTATTGTTTTCAATCCTACAATAAGATTCTTACT
1 AACTTTATTTGTTATTGTTTTCAATCCTACAATAAGATTCTTACT
958771 AACTTTATTTGTTATTGTTTTCAATCCTACAATAAGATTCTTACT
1 AACTTTATTTGTTATTGTTTTCAATCCTACAATAAGATTCTTACT
958816 TTCGGTTCGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (45 bp):
AACTTTATTTGTTATTGTTTTCAATCCTACAATAAGATTCTTACT
Found at i:958879 original size:32 final size:32
Alignment explanation
Indices: 958843--958947 Score: 88
Period size: 32 Copynumber: 3.2 Consensus size: 32
958833 TATGTACAGA
958843 TTGCTTTCAGGTCGGGTTAAATTCAGTTTGGG
1 TTGCTTTCAGGTCGGGTTAAATTCAGTTTGGG
* *
958875 TTGCTTT-TGGATCGGGTTAAAATTC-GTTTTGAG
1 TTGCTTTCAGG-TCGGGTT-AAATTCAG-TTTGGG
* * * * * * *
958908 TTTCATTCAGTTTGGGTTAATTTCAGTTCGGA
1 TTGCTTTCAGGTCGGGTTAAATTCAGTTTGGG
958940 TTGCTTTC
1 TTGCTTTC
958948 GTTTCACTAA
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
31 2 0.04
32 29 0.53
33 23 0.42
34 1 0.02
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (32 bp):
TTGCTTTCAGGTCGGGTTAAATTCAGTTTGGG
Found at i:959620 original size:36 final size:35
Alignment explanation
Indices: 959571--959638 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
959561 AATTTTCCCC
* * *
959571 CAAACATAGCTATTAATAGGGATATTATATTTTTTT
1 CAAACATAACTATTAAGAGGAATATTAT-TTTTTTT
*
959607 CAAATATAACTATTAAGAGGAATATTATTTTT
1 CAAACATAACTATTAAGAGGAATATTATTTTT
959639 CTAGCACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 4 0.14
36 24 0.86
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (35 bp):
CAAACATAACTATTAAGAGGAATATTATTTTTTTT
Found at i:960674 original size:31 final size:31
Alignment explanation
Indices: 960636--960705 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
960626 TTAATGTCTG
960636 GGCACCTAAAATGGTAAC-GAAAAAAACGTTA
1 GGCACCTAAAATGGTAACAG-AAAAAACGTTA
*
960667 GGCACCTAAAATGGTAACAGAGAAAACGTTA
1 GGCACCTAAAATGGTAACAGAAAAAACGTTA
*
960698 GACACCTA
1 GGCACCTA
960706 TTTTTAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.16
Consensus pattern (31 bp):
GGCACCTAAAATGGTAACAGAAAAAACGTTA
Found at i:964637 original size:24 final size:24
Alignment explanation
Indices: 964610--964655 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
964600 TATAAAAAAA
*
964610 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
***
964634 ATCAGGTCAAAATCCAGGTCAA
1 ATCAAAACAAAATCCAGGTCAA
964656 AATTCAGGTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:964641 original size:12 final size:12
Alignment explanation
Indices: 964624--964738 Score: 53
Period size: 12 Copynumber: 9.6 Consensus size: 12
964614 AAACATAATC
*
964624 CAGGTCAAGTAT
1 CAGGTCAAGAAT
964636 CAGGTCAA-AAT
1 CAGGTCAAGAAT
964647 CCAGGTCAA-AATT
1 -CAGGTCAAGAA-T
*
964660 CAGGTCAAGTATT
1 CAGGTCAAG-AAT
*
964673 C-GATC-AGAAT
1 CAGGTCAAGAAT
*
964683 CCAGGTCAAGTAT
1 -CAGGTCAAGAAT
* *
964696 CCGATC-AGAAT
1 CAGGTCAAGAAT
*
964707 CCAGGTCAAGTAT
1 -CAGGTCAAGAAT
* *
964720 CCGATC-AGAAT
1 CAGGTCAAGAAT
964731 CCAGGTCA
1 -CAGGTCA
964739 GGTATTATAA
Statistics
Matches: 75, Mismatches: 17, Indels: 21
0.66 0.15 0.19
Matches are distributed among these distances:
10 2 0.03
11 13 0.17
12 48 0.64
13 11 0.15
14 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (12 bp):
CAGGTCAAGAAT
Found at i:964662 original size:24 final size:24
Alignment explanation
Indices: 964620--964667 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
964610 ATCAAAACAT
*
964620 AATCCAGGTCAAGTATCAGGTCAA
1 AATCCAGGTCAAATATCAGGTCAA
964644 AATCCAGGTCAAA-ATTCAGGTCAA
1 AATCCAGGTCAAATA-TCAGGTCAA
964668 GTATTCGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
AATCCAGGTCAAATATCAGGTCAA
Found at i:964687 original size:24 final size:24
Alignment explanation
Indices: 964660--964743 Score: 150
Period size: 24 Copynumber: 3.5 Consensus size: 24
964650 GGTCAAAATT
*
964660 CAGGTCAAGTATTCGATCAGAATC
1 CAGGTCAAGTATCCGATCAGAATC
964684 CAGGTCAAGTATCCGATCAGAATC
1 CAGGTCAAGTATCCGATCAGAATC
964708 CAGGTCAAGTATCCGATCAGAATC
1 CAGGTCAAGTATCCGATCAGAATC
*
964732 CAGGTCAGGTAT
1 CAGGTCAAGTAT
964744 TATAATAGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCCGATCAGAATC
Found at i:968789 original size:12 final size:12
Alignment explanation
Indices: 968772--968857 Score: 54
Period size: 12 Copynumber: 7.2 Consensus size: 12
968762 AAAACATAAT
968772 TCAGGTCAAGTA
1 TCAGGTCAAGTA
*
968784 TCAGGTCAA-AA
1 TCAGGTCAAGTA
968795 TCCAGGTCAAGTA
1 T-CAGGTCAAGTA
* *
968808 TTC-GATC-AGAA
1 -TCAGGTCAAGTA
968819 TCCAGGTCAAGTA
1 T-CAGGTCAAGTA
* * *
968832 TCCGATC-AGAA
1 TCAGGTCAAGTA
968843 TTCAGGTCAAGTA
1 -TCAGGTCAAGTA
968856 TC
1 TC
968858 CGATCAGCAT
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
10 1 0.02
11 9 0.17
12 34 0.63
13 9 0.17
14 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (12 bp):
TCAGGTCAAGTA
Found at i:968800 original size:24 final size:24
Alignment explanation
Indices: 968773--968880 Score: 153
Period size: 24 Copynumber: 4.5 Consensus size: 24
968763 AAACATAATT
* * *
968773 CAGGTCAAGTATCAGGTCAAAATC
1 CAGGTCAAGTATCCGATCAGAATC
*
968797 CAGGTCAAGTATTCGATCAGAATC
1 CAGGTCAAGTATCCGATCAGAATC
*
968821 CAGGTCAAGTATCCGATCAGAATT
1 CAGGTCAAGTATCCGATCAGAATC
*
968845 CAGGTCAAGTATCCGATCAGCATC
1 CAGGTCAAGTATCCGATCAGAATC
*
968869 CAGGTCATGTAT
1 CAGGTCAAGTAT
968881 TATAATAGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCCGATCAGAATC
Found at i:970041 original size:18 final size:18
Alignment explanation
Indices: 970018--970053 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
970008 TCTTTATCTG
*
970018 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
970036 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
970054 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:972374 original size:14 final size:14
Alignment explanation
Indices: 972355--972382 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
972345 TATGGTATAA
972355 ACCCGAAAATTATG
1 ACCCGAAAATTATG
972369 ACCCGAAAATTATG
1 ACCCGAAAATTATG
972383 TCACAGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
ACCCGAAAATTATG
Found at i:973189 original size:37 final size:37
Alignment explanation
Indices: 973087--973191 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
973077 CCTTTTCGTC
*
973087 CTACTAAGATTCAAACTCCTAAAAATAAGATAAAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
973124 TTGCTAAGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
973161 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
973192 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:973922 original size:13 final size:13
Alignment explanation
Indices: 973904--973930 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
973894 TGTATACTTT
973904 TATATTTGATTTA
1 TATATTTGATTTA
973917 TATATTTGATTTA
1 TATATTTGATTTA
973930 T
1 T
973931 TTTTGTTTTA
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:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TATATTTGATTTA
Found at i:974039 original size:39 final size:38
Alignment explanation
Indices: 973946--974078 Score: 102
Period size: 39 Copynumber: 3.6 Consensus size: 38
973936 TTTTAGTTTT
*
973946 TTTATAT-TATAT-TATATTTTCATATTACTA-TCA-TTA
1 TTTATATATATATATAT-TTTTCATATT-TTACTCATTTA
973982 TTGT-TATGAT-TAT-TATTTTTC-TATTTTACTCATTTA
1 TT-TATAT-ATATATATATTTTTCATATTTTACTCATTTA
* * *
974018 TATATATATATATATATATTTTCATATTTTATTTATTTA
1 TTTATATATATATATAT-TTTTCATATTTTACTCATTTA
* * *
974057 TTTATTTATTTATTTATTTTTC
1 TTTATATATATATATATTTTTC
974079 CTTTTATTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
34 2 0.03
35 10 0.13
36 20 0.25
37 10 0.13
38 11 0.14
39 26 0.33
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.64
Consensus pattern (38 bp):
TTTATATATATATATATTTTTCATATTTTACTCATTTA
Found at i:974052 original size:4 final size:4
Alignment explanation
Indices: 974045--974075 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
974035 ATTTTCATAT
974045 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
974076 TTCCTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:974084 original size:16 final size:16
Alignment explanation
Indices: 974065--974105 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
974055 TATTTATTTA
*
974065 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
974081 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
974096 TATT-TTTATT
1 T-TTATTTATT
974106 CTTGATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:978589 original size:30 final size:28
Alignment explanation
Indices: 978538--978603 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 28
978528 AATCAAGAAC
* *
978538 AAAAAAGAAAATAAGCAAAAAAGCAAAG
1 AAAAAAGAAAATAAGAAAAAAAGCAAAA
* *
978566 AAAAAAGAGAAATAATAACAAAAATCAAAA
1 AAAAAAGA-AAATAAGAA-AAAAAGCAAAA
978596 AGAAAAAG
1 A-AAAAAG
978604 GGACAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 8 0.26
29 7 0.23
30 10 0.32
31 6 0.19
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (28 bp):
AAAAAAGAAAATAAGAAAAAAAGCAAAA
Found at i:979265 original size:22 final size:22
Alignment explanation
Indices: 979237--979292 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
979227 AGCTACCCCA
979237 TCAAACCTTTGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
979259 TCAAACCTTTGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
*
979281 CCAAACCTTTGA
1 TCAAACCTTTGA
979293 CCAAACACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
TCAAACCTTTGAGCATCAAATG
Found at i:979511 original size:24 final size:24
Alignment explanation
Indices: 979483--979545 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
979473 GGGACAATAT
979483 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
* *
979507 TTTCAAAACTCTTGATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
*
979531 TTTCGAAACTCTTTA
1 TTTCAAAACT-TTTA
979546 TTGATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (24 bp):
TTTCAAAACTTTTAATTAAACATC
Found at i:980075 original size:106 final size:106
Alignment explanation
Indices: 979885--980452 Score: 839
Period size: 106 Copynumber: 5.4 Consensus size: 106
979875 TACAGCTTTT
* * ** *
979885 AGAGTCAATTTCAACTTTATGACGAAGGATATTGGACTCCAGACAACGCAATTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
979950 CGAAGGGACCGCTGGTTGTCAAAAAATAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * *
979991 AGAGCCAATTTCAACTTCACAACGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
980056 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
980097 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
980162 CGAAGGGACCGCTGGTTGTCAATAAAAAAATTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* *
980203 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
980268 CGAAGGGACAGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * * * * * *
980309 AGAGCCAATTTAAACTTCACAGCGAAGAATATTGGACTCGAGACAACACAAGTTCAACTTCGCAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * ** *
980374 CGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCGGTTCC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* *
980415 AGAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
980453 TAGAACAATG
Statistics
Matches: 421, Mismatches: 41, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 421 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
Found at i:981181 original size:37 final size:37
Alignment explanation
Indices: 981124--981220 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
981114 CCTTTTCGTC
*
981124 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
1 CTACTAAGATTCAAACTCCTAAAAATAAGATAGAATT
* * * * *
981161 TTGCTAAGATTCAAACTCCTAAGAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAAGATAGAATT
* *
981198 CTACTATGATTTAAACTCCTAAA
1 CTACTAAGATTCAAACTCCTAAA
981221 GATATGATCC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAAGATAGAATT
Found at i:981831 original size:2 final size:2
Alignment explanation
Indices: 981824--981855 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
981814 TATTATTACC
981824 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
981856 TGTAATTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:982111 original size:4 final size:4
Alignment explanation
Indices: 982104--982138 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
982094 TTTTTCATAT
982104 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
982139 TTCCTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:982147 original size:16 final size:16
Alignment explanation
Indices: 982128--982168 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
982118 TATTTATTTA
*
982128 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
982144 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
982159 TATT-TTTATT
1 T-TTATTTATT
982169 CTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:982164 original size:12 final size:12
Alignment explanation
Indices: 982103--982179 Score: 66
Period size: 12 Copynumber: 6.2 Consensus size: 12
982093 TTTTTTCATA
982103 TTTTATTTATTT
1 TTTTATTTATTT
*
982115 ATTTATTTATTT
1 TTTTATTTATTT
*
982127 ATTTATTTATTT
1 TTTTATTTATTT
*
982139 TTCCT-TTTATTTT
1 TT-TTATTTA-TTT
*
982152 TTTTACTTATTT
1 TTTTATTTATTT
* *
982164 TTATTCTTCATTT
1 TT-TTATTTATTT
982177 TTT
1 TTT
982180 CTCTCTAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
12 35 0.66
13 18 0.34
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:983893 original size:30 final size:30
Alignment explanation
Indices: 983850--983922 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
983840 GCGTCCGTTA
*
983850 ATAA-ATTGACATAATTATATATTTGGTCC
1 ATAATATTGACATAATTATACATTTGGTCC
*
983879 ATAATATTGTCATAATTATACATTTGGTCC
1 ATAATATTGACATAATTATACATTTGGTCC
* *
983909 TTAATATTTACATA
1 ATAATATTGACATA
983923 TTCTATCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (30 bp):
ATAATATTGACATAATTATACATTTGGTCC
Found at i:984405 original size:94 final size:91
Alignment explanation
Indices: 984292--984600 Score: 354
Period size: 94 Copynumber: 3.4 Consensus size: 91
984282 TTTTTCTTTA
* *
984292 ACCGTTAATCGAACTGAAATTTATTTGGAAATTATTAACCGAACCAAATTAATTGATTTTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATTGA--TTTTTTC
984357 TTTAACATTAATCGAACGGAAATTATTTG
64 TTTAACATTAATCGAAC-GAAATTATTTG
* **
984386 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAATCGAACCAAATTAACCGAAATTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATTG--ATTTTTTC
*
984451 TTTAACATTAATCCAACCGAAATTATTTG
64 TTTAACATTAATCGAA-CGAAATTATTTG
* * *
984480 ATCGTTTATCGAACCGAAATTTATTTGAAAATT-TT----TAACC--A--AATT-A--TTTTCTT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATTGATTTTTTCTT
* *
984533 TAACCATTAATTGAACCAACATTATTTG
66 TAA-CATTAATCGAACGAA-ATTATTTG
*
984561 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACC
984601 TAATTAACCG
Statistics
Matches: 188, Mismatches: 17, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
80 13 0.07
81 47 0.25
82 3 0.02
85 2 0.01
87 1 0.01
89 4 0.02
93 2 0.01
94 114 0.61
95 1 0.01
96 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (91 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATTGATTTTTTCTT
TAACATTAATCGAACGAAATTATTTG
Found at i:984572 original size:81 final size:80
Alignment explanation
Indices: 984433--984606 Score: 244
Period size: 81 Copynumber: 2.2 Consensus size: 80
984423 ATCGAACCAA
* * *
984433 ATTAACCGAAATT-TTTTCTTTAACATTAATCCAACCGAAATTATTTGATCGTTTATCGAACCGA
1 ATTAACC-AAATTATTTTCTTTAACATTAATCCAACCGAAATTATTTGACCGTTAATCGAACCCA
984497 AATTTATTTGAAAATT
65 AATTTATTTGAAAATT
* **
984513 TTTAACCAAATTATTTTCTTTAACCATTAATTGAACC-AACATTATTTGACCGTTAATCGAACCC
1 ATTAACCAAATTATTTTCTTTAA-CATTAATCCAACCGAA-ATTATTTGACCGTTAATCGAACCC
984577 AAATTTATTTGAAAATT
64 AAATTTATTTGAAAATT
*
984594 ATTAACCTAATTA
1 ATTAACCAAATTA
984607 ACCGAATAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
79 5 0.06
80 18 0.22
81 60 0.72
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (80 bp):
ATTAACCAAATTATTTTCTTTAACATTAATCCAACCGAAATTATTTGACCGTTAATCGAACCCAA
ATTTATTTGAAAATT
Found at i:984890 original size:159 final size:155
Alignment explanation
Indices: 984587--984910 Score: 477
Period size: 159 Copynumber: 2.1 Consensus size: 155
984577 AAATTTATTT
* * * *
984587 GAAAATTATTAACCTAATTAACCGAATAAAATAATTTTTTTTCTTTAACCGTTAATCGAATAGAA
1 GAAATTTATTAACCGAATTAACCGAATAAAATAATTTTTTTTCCTTAACCGTTAATCGAACAGAA
* * *
984652 ATTTATTTAAAAATTATTAACCGAACCAAATCAACCATTTTTTTCTTTAACCATTAATCGAACCG
66 ATTTATTTAAAAATTATTAACCAAACCAAATCAACAATTTTTTTCTTTAACCATTAATCGAACAG
984717 AAATTATTTGACCGTTAATCGAACC
131 AAATTATTTGACCGTTAATCGAACC
* *
984742 GAAATTTATTAATCGAATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACCG
1 GAAATTTATTAACCGAATTAACCGAATAAAAT-AATT-TTTTTTCCTTAACCGTTAATCGAACAG
* * * * *
984807 AAATTTATTTGAAAATTATTAATCAAATCGAATTAACAGAATTTTTTTCTTTAACCATTAATCGA
64 AAATTTATTTAAAAATTATTAACCAAACCAAATCAAC--AATTTTTTTCTTTAACCATTAATCGA
984872 ACAGAAATTATTTGACCGTTAATCGAACC
127 ACAGAAATTATTTGACCGTTAATCGAACC
*
984901 AAAATTTATT
1 GAAATTTATT
984911 TGAAGATTAT
Statistics
Matches: 150, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
155 29 0.19
156 4 0.03
157 55 0.37
159 62 0.41
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (155 bp):
GAAATTTATTAACCGAATTAACCGAATAAAATAATTTTTTTTCCTTAACCGTTAATCGAACAGAA
ATTTATTTAAAAATTATTAACCAAACCAAATCAACAATTTTTTTCTTTAACCATTAATCGAACAG
AAATTATTTGACCGTTAATCGAACC
Found at i:984960 original size:81 final size:81
Alignment explanation
Indices: 984838--985010 Score: 283
Period size: 81 Copynumber: 2.1 Consensus size: 81
984828 ATCAAATCGA
*
984838 ATTAACAGAATTTTTTTCTTTAACCATTAATCGAACAGAAATTATTTGACCGTTAATCGAACCAA
1 ATTAACAGATTTTTTTTCTTTAACCATTAATCGAACAGAAATTATTTGACCGTTAATCGAACCAA
*
984903 AATTTATTTGAAGATT
66 AATTTATTTGAAAATT
* * * *
984919 ATTAACTGATTTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACTGTTAATCGAACCGA
1 ATTAACAGATTTTTTTTCTTTAACCATTAATCGAACAGAAATTATTTGACCGTTAATCGAACCAA
984984 AATTTATTTGAAAATT
66 AATTTATTTGAAAATT
*
985000 ATTAACCGATT
1 ATTAACAGATT
985011 AACGGTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (81 bp):
ATTAACAGATTTTTTTTCTTTAACCATTAATCGAACAGAAATTATTTGACCGTTAATCGAACCAA
AATTTATTTGAAAATT
Found at i:987196 original size:16 final size:15
Alignment explanation
Indices: 987170--987218 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 15
987160 ATCCCAACAA
*
987170 CAAACCCTAGGGTAT
1 CAAAACCTAGGGTAT
987185 CAAAACCATAGGGTAT
1 CAAAACC-TAGGGTAT
987201 CAAAATCCTAGGGTAT
1 CAAAA-CCTAGGGTAT
987217 CA
1 CA
987219 TCTCCCTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
15 6 0.19
16 23 0.74
17 2 0.06
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (15 bp):
CAAAACCTAGGGTAT
Found at i:988219 original size:16 final size:16
Alignment explanation
Indices: 988198--988235 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
988188 TATGAATTAA
988198 ATTACACTATGCTTAT
1 ATTACACTATGCTTAT
988214 ATTACACTATGCTTAT
1 ATTACACTATGCTTAT
988230 ATTACA
1 ATTACA
988236 TGATATTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.42
Consensus pattern (16 bp):
ATTACACTATGCTTAT
Found at i:988264 original size:7 final size:7
Alignment explanation
Indices: 988252--988299 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
988242 TTAGAATTAG
988252 TATTTTT
1 TATTTTT
988259 TATTTTT
1 TATTTTT
988266 TA-TTTT
1 TATTTTT
988272 TATTTTT
1 TATTTTT
* *
988279 AATTTTGA
1 TATTTT-T
*
988287 TATTTTA
1 TATTTTT
988294 TATTTT
1 TATTTT
988300 AATAATGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 6 0.17
7 25 0.69
8 5 0.14
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (7 bp):
TATTTTT
Found at i:988271 original size:13 final size:13
Alignment explanation
Indices: 988255--988300 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
988245 GAATTAGTAT
988255 TTTTTATTTTTTA
1 TTTTTATTTTTTA
*
988268 TTTTTATTTTTAA
1 TTTTTATTTTTTA
* *
988281 TTTTGATATTTTA
1 TTTTTATTTTTTA
988294 TATTTTA
1 T-TTTTA
988301 ATAATGTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:988300 original size:7 final size:7
Alignment explanation
Indices: 988256--988300 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
988246 AATTAGTATT
*
988256 TTTTATT
1 TTTTATA
988263 TTTTAT-
1 TTTTATA
988269 TTTTAT-
1 TTTTATA
988275 TTTTA-A
1 TTTTATA
988281 TTTTGATA
1 TTTT-ATA
988289 TTTTATA
1 TTTTATA
988296 TTTTA
1 TTTTA
988301 ATAATGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 15 0.43
7 15 0.43
8 5 0.14
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:988587 original size:4 final size:4
Alignment explanation
Indices: 988578--988602 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
988568 TTATATCATA
988578 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
988603 AAATATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:990214 original size:36 final size:36
Alignment explanation
Indices: 990151--990219 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
990141 AAGCAATGCA
* * *
990151 CACAGAGATCCTGTTATATTAATACCAAAAGTACTC
1 CACAAAGATCCTGTCAGATTAATACCAAAAGTACTC
990187 CACAAAGATCCTGTCAGATTGAA-ACCAAAAGTA
1 CACAAAGATCCTGTCAGATT-AATACCAAAAGTA
990220 GTCTACAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 27 0.93
37 2 0.07
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (36 bp):
CACAAAGATCCTGTCAGATTAATACCAAAAGTACTC
Found at i:990919 original size:27 final size:26
Alignment explanation
Indices: 990888--990947 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
990878 CATTCACATA
990888 TTTACATTTGCATTTAAATTTGCATTT
1 TTTACATTTGCATTTAAATTTGCA-TT
* * * *
990915 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGCATTTAAATTTGCATT
990941 TTTACAT
1 TTTACAT
990948 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (26 bp):
TTTACATTTGCATTTAAATTTGCATT
Found at i:992906 original size:19 final size:19
Alignment explanation
Indices: 992873--992913 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
992863 CTCATTAGGT
*
992873 AAAAAAAAGGAAAAAAGGGA
1 AAAAAAAAAGAAAAAA-GGA
992893 AAAAAAAAAG-AAAAAGGA
1 AAAAAAAAAGAAAAAAGGA
992911 AAA
1 AAA
992914 TTGAATCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 5 0.25
20 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAGGA
Found at i:994512 original size:20 final size:20
Alignment explanation
Indices: 994482--994558 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
994472 CAGATTGCCT
994482 AGGGGGAACAGATTCCCCCCC
1 AGGGGGAACAGATT-CCCCCC
*
994503 A-GGGGTACAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
994522 AGGGGGAACAGATT--CCCC
1 AGGGGGAACAGATTCCCCCC
*
994540 AGGGGGTACAGATTCCCCC
1 AGGGGGAACAGATTCCCCC
994559 TGAATGGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
18 17 0.34
19 7 0.14
20 25 0.50
21 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.30, T:0.13
Consensus pattern (20 bp):
AGGGGGAACAGATTCCCCCC
Found at i:994539 original size:18 final size:18
Alignment explanation
Indices: 994472--994557 Score: 84
Period size: 18 Copynumber: 4.6 Consensus size: 18
994462 CAAGAAAAAT
* *
994472 CAGATTGCCTAGGGGGAA
1 CAGATTCCCCAGGGGGAA
*
994490 CAGATTCCCCCCCA-GGGGTA
1 CAGATT---CCCCAGGGGGAA
994510 CAGATTCCCCCCAGGGGGAA
1 CAGATT--CCCCAGGGGGAA
*
994530 CAGATTCCCCAGGGGGTA
1 CAGATTCCCCAGGGGGAA
994548 CAGATTCCCC
1 CAGATTCCCC
994558 CTGAATGGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
18 27 0.46
19 7 0.12
20 22 0.37
21 3 0.05
ACGTcount: A:0.23, C:0.33, G:0.29, T:0.15
Consensus pattern (18 bp):
CAGATTCCCCAGGGGGAA
Found at i:995947 original size:19 final size:20
Alignment explanation
Indices: 995923--995970 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
995913 AACGATTTTC
995923 TTTTGAAAACAAAAAT-AAA
1 TTTTGAAAACAAAAATGAAA
* *
995942 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
995962 TTTTGAAAA
1 TTTTGAAAA
995971 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:997466 original size:20 final size:20
Alignment explanation
Indices: 997421--997488 Score: 100
Period size: 20 Copynumber: 3.3 Consensus size: 20
997411 CAGATTGCCT
997421 AGGGGGAACAGATTCCCCCCCC
1 AGGGGGAACAGATT--CCCCCC
* *
997443 AGGGGGTACAGATTCCCCCT
1 AGGGGGAACAGATTCCCCCC
997463 AGGGGGAACAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
997483 AGGGGG
1 AGGGGG
997489 TATCGATTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 29 0.69
22 13 0.31
ACGTcount: A:0.22, C:0.32, G:0.34, T:0.12
Consensus pattern (20 bp):
AGGGGGAACAGATTCCCCCC
Found at i:997468 original size:42 final size:40
Alignment explanation
Indices: 997418--997535 Score: 135
Period size: 40 Copynumber: 3.1 Consensus size: 40
997408 AATCAGATTG
997418 CCTAGGGGGAACAGATTCCCCCCCCAGGGGGTA-CAGATTCCC
1 CCTAGGGGGAACAGATT--CCCCCCAGGGGGTATC-GATTCCC
997460 CCTAGGGGGAACAGATTCCCCCCAGGGGGTATCGATT-CC
1 CCTAGGGGGAACAGATTCCCCCCAGGGGGTATCGATTCCC
* *
997499 CC----GGGAATAGATT--CCCCAGGGGGTATAGATTCCC
1 CCTAGGGGGAACAGATTCCCCCCAGGGGGTATCGATTCCC
997533 CCT
1 CCT
997536 GAATGGTTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
33 17 0.24
34 4 0.06
35 10 0.14
39 4 0.06
40 18 0.25
41 1 0.01
42 17 0.24
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (40 bp):
CCTAGGGGGAACAGATTCCCCCCAGGGGGTATCGATTCCC
Found at i:997496 original size:20 final size:20
Alignment explanation
Indices: 997421--997500 Score: 99
Period size: 20 Copynumber: 3.9 Consensus size: 20
997411 CAGATTGCCT
*
997421 AGGGGGAACAGATTCCCCCCCC
1 AGGGGGTACAGATT--CCCCCC
*
997443 AGGGGGTACAGATTCCCCCT
1 AGGGGGTACAGATTCCCCCC
*
997463 AGGGGGAACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
997483 AGGGGGTATC-GATTCCCC
1 AGGGGGTA-CAGATTCCCC
997501 GGGAATAGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 38 0.73
21 1 0.02
22 13 0.25
ACGTcount: A:0.21, C:0.34, G:0.30, T:0.15
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:997528 original size:18 final size:18
Alignment explanation
Indices: 997439--997533 Score: 88
Period size: 20 Copynumber: 5.2 Consensus size: 18
997429 CAGATTCCCC
*
997439 CCCCAGGGGGTACAGATT
1 CCCCAGGGGGTATAGATT
* *
997457 CCCCCTAGGGGGAACAGATT
1 -CCCC-AGGGGGTATAGATT
*
997477 CCCCCCAGGGGGTATCGATT
1 --CCCCAGGGGGTATAGATT
*
997497 CCCC---GGGAATAGATT
1 CCCCAGGGGGTATAGATT
997512 CCCCAGGGGGTATAGATT
1 CCCCAGGGGGTATAGATT
997530 CCCC
1 CCCC
997534 CTGAATGGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
15 13 0.20
18 18 0.28
19 4 0.06
20 24 0.38
21 5 0.08
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (18 bp):
CCCCAGGGGGTATAGATT
Found at i:997750 original size:21 final size:21
Alignment explanation
Indices: 997717--997756 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
997707 TTTTTGCAGA
*
997717 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
997739 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
997757 ATATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1001762 original size:22 final size:22
Alignment explanation
Indices: 1001734--1001793 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
1001724 TACATCTACA
1001734 CTCTTTTCAAAGATGATAGATT
1 CTCTTTTCAAAGATGATAGATT
*
1001756 CTCTTTTTAAAGATGATAGATT
1 CTCTTTTCAAAGATGATAGATT
1001778 CTCTTTTCAAAGATGA
1 CTCTTTTCAAAGATGA
1001794 AAGCTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
CTCTTTTCAAAGATGATAGATT
Found at i:1002603 original size:166 final size:166
Alignment explanation
Indices: 1002307--1002631 Score: 537
Period size: 166 Copynumber: 2.0 Consensus size: 166
1002297 AAAATGAGCA
1002307 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAAAATTGAGAAAACGA
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAAAATTGAGAAAACGA
**
1002372 TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTCC
66 TTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTCC
*
1002437 TTAGTTTTTTTACTTAGTAAACTATTTCCAACAGCT
131 TTAGTTTTTTTACTTAGTAAACTACTTCCAACAGCT
** *
1002473 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTTGAAAAATAA-TGAGAAAACG
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTA-TTTCAAAAAAAAATTGAGAAAACG
** *
1002537 ATTTTTATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAA-GATTT
65 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACAATTT
1002601 CCTTAGTTTTTTTACTTAGTAAACTACTTCC
129 CCTTAGTTTTTTTACTTAGTAAACTACTTCC
1002632 CACATCTGTA
Statistics
Matches: 148, Mismatches: 9, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
166 110 0.74
167 38 0.26
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (166 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAAAATTGAGAAAACGA
TTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTCC
TTAGTTTTTTTACTTAGTAAACTACTTCCAACAGCT
Found at i:1002966 original size:152 final size:152
Alignment explanation
Indices: 1002640--1002967 Score: 485
Period size: 152 Copynumber: 2.2 Consensus size: 152
1002630 CCCACATCTG
* *
1002640 TAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGTGAGCTTTTTGATGTTTTCAAAGCCTC
1 TAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTC
* * * *
1002705 AGTGTCATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATATT
66 AGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGATTTTTGATATT
* **
1002770 TCCAAAGCCTTAGGGTCATCTG
131 TCCAAAGCCTTAGAGTCATCCA
* *
1002792 TAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTT
1 TAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTC
* *
1002857 AGGGTCATCTGTCAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGATTTTTGATGTT
66 AGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGATTTTTGATATT
* * *
1002922 TTCAAAGTCTTCGAGTCATCCA
131 TCCAAAGCCTTAGAGTCATCCA
* * *
1002944 TAAGACCTGCAGTACATAATGTTT
1 TAAGTCCTGCAGTGCATGATGTTT
1002968 TTTGCTTAAA
Statistics
Matches: 156, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
152 156 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (152 bp):
TAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTC
AGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGATTTTTGATATT
TCCAAAGCCTTAGAGTCATCCA
Found at i:1002967 original size:76 final size:76
Alignment explanation
Indices: 1002634--1002928 Score: 491
Period size: 76 Copynumber: 3.9 Consensus size: 76
1002624 CTACTTCCCA
** *
1002634 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGTGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1002699 AGCCTCAGTGT
66 AGCCTTAGGGT
* * *
1002710 CATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATATTTCCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1002775 AGCCTTAGGGT
66 AGCCTTAGGGT
1002786 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1002851 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
1002862 CATCTGTCAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1002927 AG
66 AG
1002929 TCTTCGAGTC
Statistics
Matches: 205, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 205 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1003523 original size:121 final size:123
Alignment explanation
Indices: 1003398--1003666 Score: 350
Period size: 123 Copynumber: 2.2 Consensus size: 123
1003388 TCATCTGAAA
** * * *
1003398 GAGAAGAATTTGTTCAACCTTTTGTTTGACTCTATCGCAAAAGGAGATAGATCAGCATC-A-ATT
1 GAGAAGAATTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAACATCAACATT
*
1003461 TACAAAAGA-AGTTCATAATGAGAAGAA-TACATCTAAAG-AGAAAGAAGAAGTTCATAAT
66 T-CAAAAGAGAGTTCATAATGACAAGAACT-CATCTAAAGAAG-AAGAAGAAGTTCATAAT
*
1003519 GAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAACATCAACATT
1 GAGAAGAATTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAACATCAACATT
* * * * *
1003584 TCCAGAGAGAGTTCATAATGACAAGAACTCATCTGAAGAAGGAGAATAAGTTCATAAT
66 TCAAAAGAGAGTTCATAATGACAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAAT
* *
1003642 GAGAAGAATTTCTTCAACTTTTTGC
1 GAGAAGAATTTGTTCAACCTTTTGC
1003667 TAAATCACAT
Statistics
Matches: 128, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
121 53 0.41
122 6 0.05
123 66 0.52
124 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (123 bp):
GAGAAGAATTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAACATCAACATT
TCAAAAGAGAGTTCATAATGACAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAAT
Found at i:1015783 original size:2 final size:2
Alignment explanation
Indices: 1015776--1015806 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1015766 GTGTTGTACG
1015776 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
1015807 GAAATTTGAA
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:1020085 original size:21 final size:21
Alignment explanation
Indices: 1020061--1020117 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1020051 AAATCGATGA
*
1020061 GCTCGAAATATAACCCT-AAAG
1 GCTCGAAATATAA-ACTGAAAG
*
1020082 GCTCGACATATAAACTGAAAG
1 GCTCGAAATATAAACTGAAAG
* *
1020103 GCTCGACATGTAAAC
1 GCTCGAAATATAAAC
1020118 CAACGAGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (21 bp):
GCTCGAAATATAAACTGAAAG
Found at i:1022035 original size:8 final size:8
Alignment explanation
Indices: 1022022--1022052 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1022012 CAAATATCAA
1022022 ATTCAAAC
1 ATTCAAAC
1022030 ATTCAAAC
1 ATTCAAAC
1022038 ATTCAAAC
1 ATTCAAAC
*
1022046 ATCCAAA
1 ATTCAAA
1022053 TATATCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (8 bp):
ATTCAAAC
Found at i:1024520 original size:18 final size:18
Alignment explanation
Indices: 1024474--1024509 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1024464 TATATTCTAG
*
1024474 AACTATATCTCCTTTAGT
1 AACTGTATCTCCTTTAGT
1024492 AACTGTATCTCCTTTAGT
1 AACTGTATCTCCTTTAGT
1024510 GACATGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.44
Consensus pattern (18 bp):
AACTGTATCTCCTTTAGT
Found at i:1028178 original size:117 final size:117
Alignment explanation
Indices: 1027956--1028179 Score: 290
Period size: 117 Copynumber: 1.9 Consensus size: 117
1027946 AACTTTCAAA
* *
1027956 TCGAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAATAT
1 TCGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACAT
*
1028021 TTCATTTTGATTTTCAAAATCCATTTTAATTTCTAGAAGAAGTTTGTTTAAT
66 TTCATTTTGATTTTCAAAATCCATTTTAATTTCTAAAAGAAGTTTGTTTAAT
* * * * *
1028073 TCGAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTTTTTCAACA
1 TCGAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACA
* * * * * *
1028137 TTTCTTTTTGTTTTTCCAAGTCTATTTTAGCTTTC-AAAAGAAG
65 TTTCATTTTGATTTTCAAAATCCATTTTA-ATTTCTAAAAGAAG
1028180 ATCATTTTAG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
116 1 0.01
117 86 0.95
118 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (117 bp):
TCGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACAT
TTCATTTTGATTTTCAAAATCCATTTTAATTTCTAAAAGAAGTTTGTTTAAT
Found at i:1036018 original size:2 final size:2
Alignment explanation
Indices: 1036011--1036067 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
1036001 TCGCCCCGAT
* *
1036011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1036051 TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1036068 AAATATTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
1 5 0.10
2 43 0.90
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1041460 original size:22 final size:22
Alignment explanation
Indices: 1041434--1041480 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1041424 TATATTTATT
*
1041434 TAATTTT-TAAAAGAGGTATTAA
1 TAATTTTGT-AAAGAGATATTAA
1041456 TAATTTTGTAAAGAGATATTAA
1 TAATTTTGTAAAGAGATATTAA
1041478 TAA
1 TAA
1041481 AAACTAAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (22 bp):
TAATTTTGTAAAGAGATATTAA
Found at i:1043163 original size:33 final size:34
Alignment explanation
Indices: 1043100--1043183 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 34
1043090 CCCGATTATA
1043100 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
1043134 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
1043167 TATATATAAAATATTTT
1 TATATATATAATATTTT
1043184 CAGGTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 29 0.59
34 20 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:1053777 original size:23 final size:24
Alignment explanation
Indices: 1053750--1053794 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1053740 GTATGTGGAT
*
1053750 TATAGATT-ATGTATTTTATTTAA
1 TATAGATTAATATATTTTATTTAA
1053773 TATAGATTAATATATTTTATTT
1 TATAGATTAATATATTTTATTT
1053795 TTTGGTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (24 bp):
TATAGATTAATATATTTTATTTAA
Found at i:1055231 original size:27 final size:27
Alignment explanation
Indices: 1055201--1055282 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
1055191 TTAGTCACAA
1055201 TATTTTCTCATAATAACACGGCAAATT
1 TATTTTCTCATAATAACACGGCAAATT
** * ** *
1055228 TATTTAGTCACAA-AA-ATCTTC---TA
1 TATTTTCTCATAATAACA-CGGCAAATT
1055251 TATTTTCTCATAATAACACGGCAAATT
1 TATTTTCTCATAATAACACGGCAAATT
1055278 TATTT
1 TATTT
1055283 AGTCACAAAA
Statistics
Matches: 37, Mismatches: 12, Indels: 12
0.61 0.20 0.20
Matches are distributed among these distances:
23 11 0.30
24 4 0.11
25 2 0.05
26 4 0.11
27 16 0.43
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (27 bp):
TATTTTCTCATAATAACACGGCAAATT
Found at i:1055237 original size:40 final size:40
Alignment explanation
Indices: 1055182--1055290 Score: 128
Period size: 50 Copynumber: 2.5 Consensus size: 40
1055172 AAAATTATTT
1055182 CAAATTTATTTAGTCACAATATTTTCTCATAATAACACGG
1 CAAATTTATTTAGTCACAATATTTTCTCATAATAACACGG
1055222 CAAATTTATTTAGTCACAAAAATCTTCTATATTTTCTCATAATAACACGG
1 CAAATTTATTTAGTCAC----A------ATATTTTCTCATAATAACACGG
1055272 CAAATTTATTTAGTCACAA
1 CAAATTTATTTAGTCACAA
1055291 AAAATTATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
40 18 0.31
44 1 0.02
46 1 0.02
50 39 0.66
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (40 bp):
CAAATTTATTTAGTCACAATATTTTCTCATAATAACACGG
Found at i:1063163 original size:19 final size:19
Alignment explanation
Indices: 1063127--1063162 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1063117 GAATAATTTA
1063127 AAACAAAGATTAAGAAAAT
1 AAACAAAGATTAAGAAAAT
1063146 AAACAAAGATT-AGAAAA
1 AAACAAAGATTAAGAAAA
1063163 ACAATTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.69, C:0.06, G:0.11, T:0.14
Consensus pattern (19 bp):
AAACAAAGATTAAGAAAAT
Found at i:1063800 original size:24 final size:24
Alignment explanation
Indices: 1063756--1063801 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1063746 GTTTAAAAAT
*
1063756 AAAACTTAAAATAAAATAAAAACG
1 AAAACTTAAAATAAAAGAAAAACG
1063780 AAAACTTGAAAAT-AAAGAAAAA
1 AAAACTT-AAAATAAAAGAAAAA
1063802 AAGAACTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.15
Consensus pattern (24 bp):
AAAACTTAAAATAAAAGAAAAACG
Found at i:1065319 original size:20 final size:20
Alignment explanation
Indices: 1065290--1065329 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1065280 TTCATCACAC
*
1065290 CAAATTCTCTCAATTTCTCT
1 CAAATACTCTCAATTTCTCT
* *
1065310 CAAATACTCTTATTTTCTCT
1 CAAATACTCTCAATTTCTCT
1065330 ATTTAAGGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (20 bp):
CAAATACTCTCAATTTCTCT
Found at i:1065393 original size:23 final size:22
Alignment explanation
Indices: 1065354--1065398 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1065344 TTATTATATT
*
1065354 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
1065377 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
1065399 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:1065405 original size:17 final size:18
Alignment explanation
Indices: 1065368--1065406 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1065358 ATATTTTGTA
1065368 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
1065386 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
1065403 TTTA
1 TTTA
1065407 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:1065870 original size:36 final size:36
Alignment explanation
Indices: 1065818--1065899 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
1065808 CGATTACACT
* *
1065818 TGAGGATATTGTTATGCACCTGGGGCTTCCGGTGGA
1 TGAGGATGTTGCTATGCACCTGGGGCTTCCGGTGGA
1065854 TGAGGATGTTGCTATGCACCTGGGGCTTCCGGTGGA
1 TGAGGATGTTGCTATGCACCTGGGGCTTCCGGTGGA
1065890 TGAGGATGTT
1 TGAGGATGTT
1065900 ATATTAGGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.16, C:0.16, G:0.38, T:0.30
Consensus pattern (36 bp):
TGAGGATGTTGCTATGCACCTGGGGCTTCCGGTGGA
Found at i:1067512 original size:15 final size:15
Alignment explanation
Indices: 1067492--1067522 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1067482 TCAGGACGAC
*
1067492 GACGACGATGATGAT
1 GACGACGACGATGAT
1067507 GACGACGACGATGAT
1 GACGACGACGATGAT
1067522 G
1 G
1067523 GTGATGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (15 bp):
GACGACGACGATGAT
Found at i:1067795 original size:35 final size:33
Alignment explanation
Indices: 1067756--1067840 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
1067746 GTATTTCAGT
1067756 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
1067791 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
1067826 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1067841 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:1072576 original size:17 final size:17
Alignment explanation
Indices: 1072525--1072576 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1072515 TATAATATTA
1072525 ATAAATTTAATTTAAAT
1 ATAAATTTAATTTAAAT
** * *
1072542 A-AAAAAT-ATATAATT
1 ATAAATTTAATTTAAAT
1072557 ATAAATTTAATTTAAAT
1 ATAAATTTAATTTAAAT
1072574 ATA
1 ATA
1072577 TATATATATA
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
15 7 0.28
16 8 0.32
17 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATTTAATTTAAAT
Found at i:1072621 original size:12 final size:12
Alignment explanation
Indices: 1072606--1072640 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1072596 CGATTCTCGG
1072606 CCCAATACCCGA
1 CCCAATACCCGA
*
1072618 CCCAATACCCGG
1 CCCAATACCCGA
1072630 CCCAATACCCG
1 CCCAATACCCG
1072641 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:1079647 original size:54 final size:54
Alignment explanation
Indices: 1079559--1079732 Score: 267
Period size: 54 Copynumber: 3.2 Consensus size: 54
1079549 AATGTATATA
* * * *
1079559 TTGTGAATTACGGTATTGACACTATGCGTACAACCTAAGTAATTCATAATTAGT
1 TTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATTAGT
1079613 TTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATTAGT
1 TTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATTAGT
* * * * *
1079667 TTGTAAATTACCGTATTGGCACTATATGTGCAACCCACGTAATTCATAATGAGT
1 TTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATTAGT
1079721 TTGTGAATTACC
1 TTGTGAATTACC
1079733 ATAGCAGCAC
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (54 bp):
TTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATTAGT
Found at i:1081569 original size:20 final size:20
Alignment explanation
Indices: 1081534--1081604 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
1081524 AAATGATTTC
*
1081534 ATTTTG-AAAGCAAAATGAA
1 ATTTTGAAAAACAAAATGAA
*
1081553 ATTTTAAAAAACAAAATGAA
1 ATTTTGAAAAACAAAATGAA
1081573 ATTTTGAAAAACAAAATGAA
1 ATTTTGAAAAACAAAATGAA
1081593 ATTTTGAAAAAC
1 ATTTTGAAAAAC
1081605 GATTTTGAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 5 0.10
20 43 0.90
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.27
Consensus pattern (20 bp):
ATTTTGAAAAACAAAATGAA
Found at i:1085266 original size:29 final size:29
Alignment explanation
Indices: 1085234--1085399 Score: 129
Period size: 29 Copynumber: 5.7 Consensus size: 29
1085224 TATGGGGACT
*
1085234 TAATCCCATGCAGAATCAGGACGGGAAAC
1 TAATCCCATGCAGAATCAGGACGGGGAAC
*
1085263 TAATACCATGCAGAATCAGGACGGGGAAC
1 TAATCCCATGCAGAATCAGGACGGGGAAC
** * * * *
1085292 TAATCTTATGTAGAATTAGGATGGGGAAT
1 TAATCCCATGCAGAATCAGGACGGGGAAC
* * * **
1085321 TAATCCCATGCA-AAACTTGGACGAGGATT
1 TAATCCCATGCAGAATC-AGGACGGGGAAC
* * * * *
1085350 TAATCCCATGCAAAAACAAGATGGAG-AC
1 TAATCCCATGCAGAATCAGGACGGGGAAC
*
1085378 TTAATCCCATGCAGAATTAGGA
1 -TAATCCCATGCAGAATCAGGA
1085400 ATGCATCAGA
Statistics
Matches: 105, Mismatches: 29, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
28 2 0.02
29 99 0.94
30 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (29 bp):
TAATCCCATGCAGAATCAGGACGGGGAAC
Found at i:1088162 original size:19 final size:19
Alignment explanation
Indices: 1088140--1088223 Score: 53
Period size: 19 Copynumber: 3.9 Consensus size: 19
1088130 TTGATTTTAT
1088140 TTAGGAATTTAGAGGGAAA
1 TTAGGAATTTAGAGGGAAA
1088159 TTAGGAAATTTTGAGAATATAGGGAAA
1 TTAGG-AA-TTT-AG-----AGGGAAA
1088186 TT-GAGAATTTAGAGGGAAA
1 TTAG-GAATTTAGAGGGAAA
* *
1088205 TTGAGAAATTTAGTGGGAA
1 TT-AGGAATTTAGAGGGAA
1088224 TAGAAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 21
0.69 0.03 0.28
Matches are distributed among these distances:
19 14 0.27
20 14 0.27
21 4 0.08
22 2 0.04
24 2 0.04
25 3 0.06
26 3 0.06
27 10 0.19
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.29
Consensus pattern (19 bp):
TTAGGAATTTAGAGGGAAA
Found at i:1088191 original size:17 final size:18
Alignment explanation
Indices: 1088169--1088211 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1088159 TTAGGAAATT
*
1088169 TTGAGAA-TATAGGGAAA
1 TTGAGAATTAGAGGGAAA
1088186 TTGAGAATTTAGAGGGAAA
1 TTGAGAA-TTAGAGGGAAA
1088205 TTGAGAA
1 TTGAGAA
1088212 ATTTAGTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
19 16 0.70
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (18 bp):
TTGAGAATTAGAGGGAAA
Found at i:1088216 original size:20 final size:19
Alignment explanation
Indices: 1088179--1088223 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
1088169 TTGAGAATAT
1088179 AGGGAAATTGAGAATTTAG
1 AGGGAAATTGAGAATTTAG
1088198 AGGGAAATTGAGAAATTTAG
1 AGGGAAATTGAG-AATTTAG
*
1088218 TGGGAA
1 AGGGAA
1088224 TAGAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.24
Consensus pattern (19 bp):
AGGGAAATTGAGAATTTAG
Found at i:1088234 original size:19 final size:20
Alignment explanation
Indices: 1088191--1088234 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1088181 GGAAATTGAG
* *
1088191 AATTTAGAGGGAAATTGAGA
1 AATTTAGAGGGAAATAGAAA
*
1088211 AATTTAGTGGG-AATAGAAA
1 AATTTAGAGGGAAATAGAAA
1088230 AATTT
1 AATTT
1088235 GGGAAGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (20 bp):
AATTTAGAGGGAAATAGAAA
Found at i:1088471 original size:7 final size:7
Alignment explanation
Indices: 1088454--1088515 Score: 61
Period size: 7 Copynumber: 8.9 Consensus size: 7
1088444 ATAGTTCATA
*
1088454 TAAACCT
1 TAAACCC
*
1088461 TAAATCC
1 TAAACCC
1088468 TAAACCC
1 TAAACCC
*
1088475 TAAACTC
1 TAAACCC
1088482 TAAACCC
1 TAAACCC
**
1088489 TAAACTT
1 TAAACCC
*
1088496 TTAACCC
1 TAAACCC
*
1088503 TAAATCC
1 TAAACCC
1088510 TAAACC
1 TAAACC
1088516 TTAATATATG
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAACCC
Found at i:1088485 original size:21 final size:21
Alignment explanation
Indices: 1088454--1088515 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1088444 ATAGTTCATA
*
1088454 TAAACCTTAAATCCTAAACCC
1 TAAACCCTAAATCCTAAACCC
* * **
1088475 TAAACTCTAAACCCTAAACTT
1 TAAACCCTAAATCCTAAACCC
*
1088496 TTAACCCTAAATCCTAAACC
1 TAAACCCTAAATCCTAAACC
1088516 TTAATATATG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCCTAAATCCTAAACCC
Found at i:1088551 original size:20 final size:19
Alignment explanation
Indices: 1088510--1088566 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
1088500 CCCTAAATCC
* *
1088510 TAAACCTTA-ATATATGTA
1 TAAACCATATATATATATA
*
1088528 TAAACCATGTATAGTATATA
1 TAAACCATATATA-TATATA
*
1088548 TAAACTATATATATATATA
1 TAAACCATATATATATATA
1088567 CCTATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.22
19 9 0.28
20 16 0.50
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAACCATATATATATATA
Found at i:1088556 original size:16 final size:16
Alignment explanation
Indices: 1088537--1088578 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1088527 ATAAACCATG
1088537 TATAGTATATATA-AAC
1 TATA-TATATATATAAC
*
1088553 TATATATATATATACC
1 TATATATATATATAAC
1088569 TATATATATA
1 TATATATATA
1088579 AACCTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (16 bp):
TATATATATATATAAC
Found at i:1088574 original size:14 final size:14
Alignment explanation
Indices: 1088542--1088583 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 14
1088532 CCATGTATAG
1088542 TATATATAAA-CTA
1 TATATATAAACCTA
1088555 TATATATATATACCTA
1 TATATATA-A-ACCTA
1088571 TATATATAAACCT
1 TATATATAAACCT
1088584 TTTTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 2 0.08
16 11 0.42
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATATAAACCTA
Found at i:1088888 original size:33 final size:33
Alignment explanation
Indices: 1088845--1088920 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
1088835 TAAAAACGAC
* *
1088845 CCGACATGAACTCAGTCCGTATCCGATAAACAT
1 CCGACCTGAACTCAATCCGTATCCGATAAACAT
*
1088878 TCGACCTGAACTCAATCCGTATCCGATAAACAT
1 CCGACCTGAACTCAATCCGTATCCGATAAACAT
1088911 CCGACCTGAA
1 CCGACCTGAA
1088921 TTTTATCTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.33, C:0.32, G:0.14, T:0.21
Consensus pattern (33 bp):
CCGACCTGAACTCAATCCGTATCCGATAAACAT
Found at i:1092240 original size:42 final size:40
Alignment explanation
Indices: 1092191--1092329 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 40
1092181 AAAATGAAAC
*
1092191 TTTAGCGGCATTTCTTTAACAAACGCCGCGATAGAGTAGTAA
1 TTTAGCGGCGTTT-TTTAACAAACGCCGCGATAGAGTAGT-A
** * * *
1092233 TTTAGCGGCGTTTTTCGCACAAACGCCGCAATAGTGTTGT-
1 TTTAGCGGCGTTTTT-TAACAAACGCCGCGATAGAGTAGTA
* * *
1092273 TTATAGCGGTGTTTTTTCAACAAACGCCTCGATAAAG-AGTA
1 TT-TAGCGGCGTTTTTT-AACAAACGCCGCGATAGAGTAGTA
1092314 GTTTAGCGGCGTTTTT
1 -TTTAGCGGCGTTTTT
1092330 AGATAAACAC
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
40 4 0.05
41 40 0.52
42 33 0.43
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTTAACAAACGCCGCGATAGAGTAGTA
Found at i:1098742 original size:15 final size:15
Alignment explanation
Indices: 1098722--1098751 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1098712 GACTCACATG
1098722 TGGGAAACAACCTTA
1 TGGGAAACAACCTTA
*
1098737 TGGGAAACAGCCTTA
1 TGGGAAACAACCTTA
1098752 ACCTGCAGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (15 bp):
TGGGAAACAACCTTA
Found at i:1100913 original size:21 final size:21
Alignment explanation
Indices: 1100889--1100934 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1100879 TAAAGCAATG
1100889 ATGGAATTAGCAAGATTGTGA
1 ATGGAATTAGCAAGATTGTGA
1100910 ATGGAATTAGCAAGATTGTGA
1 ATGGAATTAGCAAGATTGTGA
1100931 ATGG
1 ATGG
1100935 CATTGACCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.28
Consensus pattern (21 bp):
ATGGAATTAGCAAGATTGTGA
Found at i:1107946 original size:21 final size:20
Alignment explanation
Indices: 1107903--1108114 Score: 110
Period size: 20 Copynumber: 10.5 Consensus size: 20
1107893 AATAACCAAT
* *
1107903 GAATTCACAACTCG-ATTTC
1 GAATTCGCAACACGAATTTC
*
1107922 GAATTCGCAACACAGAATTTG
1 GAATTCGCAACAC-GAATTTC
*
1107943 GAATTCGCAACACAGAA-GTC
1 GAATTCGCAACAC-GAATTTC
* *
1107963 AAATTCGCAACTCGAATTT-
1 GAATTCGCAACACGAATTTC
1107982 GACAATTTCGCAACACGAATTTC
1 G--AA-TTCGCAACACGAATTTC
*** * * *
1108005 TTTTTCGCAACTCGATTTTT
1 GAATTCGCAACACGAATTTC
* * *
1108025 AAATTCGCAACAAGATTTTC
1 GAATTCGCAACACGAATTTC
* **
1108045 TAATTCGCAA-AGCGCGTTTC
1 GAATTCGCAACA-CGAATTTC
* *
1108065 AAATTCGCAACGCGAATTT-
1 GAATTCGCAACACGAATTTC
* * *
1108084 TATTTTCGCAACACGATTTTC
1 GA-ATTCGCAACACGAATTTC
*
1108105 AAATTCGCAA
1 GAATTCGCAA
1108115 GGCAAATTTA
Statistics
Matches: 146, Mismatches: 36, Indels: 21
0.72 0.18 0.10
Matches are distributed among these distances:
19 16 0.11
20 91 0.62
21 24 0.16
22 15 0.10
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (20 bp):
GAATTCGCAACACGAATTTC
Found at i:1108012 original size:42 final size:40
Alignment explanation
Indices: 1107917--1108114 Score: 139
Period size: 40 Copynumber: 4.9 Consensus size: 40
1107907 TCACAACTCG
* * *
1107917 ATTTCGAATTCGCAACACAGAATTTGGAATTCGCAACACAGA
1 ATTTCTAATTCGCAACTC-GAATTTGAAATTCGCAACA-AGA
* * *
1107959 A-GTCAAATTCGCAACTCGAATTTGACAATTTCGCAACACGA
1 ATTTCTAATTCGCAACTCGAATTTGA-AA-TTCGCAACAAGA
** * *
1108000 ATTTCTTTTTCGCAACTCGATTTTTAAATTCGCAACAAGA
1 ATTTCTAATTCGCAACTCGAATTTGAAATTCGCAACAAGA
* ** ** * **
1108040 TTTTCTAATTCGCAAAGCGCGTTTCAAATTCGCAACGCGA
1 ATTTCTAATTCGCAACTCGAATTTGAAATTCGCAACAAGA
* * * *
1108080 ATTT-TATTTTCGCAACACGATTTTCAAATTCGCAA
1 ATTTCTA-ATTCGCAACTCGAATTTGAAATTCGCAA
1108115 GGCAAATTTA
Statistics
Matches: 124, Mismatches: 28, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
39 2 0.02
40 74 0.60
41 20 0.16
42 28 0.23
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (40 bp):
ATTTCTAATTCGCAACTCGAATTTGAAATTCGCAACAAGA
Found at i:1108285 original size:22 final size:22
Alignment explanation
Indices: 1108250--1108291 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1108240 TCTCTCCAGC
*
1108250 GACATCCATTCCCATCTCCGGT
1 GACATCCATCCCCATCTCCGGT
* *
1108272 GACATCCGTCCCCATGTCCG
1 GACATCCATCCCCATCTCCG
1108292 AGACCCCCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.43, G:0.17, T:0.24
Consensus pattern (22 bp):
GACATCCATCCCCATCTCCGGT
Found at i:1108671 original size:34 final size:34
Alignment explanation
Indices: 1108633--1108705 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
1108623 CAGAAAACTT
*
1108633 AAATTTGCAACACGAAAATCGCAACTCGAAAATG
1 AAATTCGCAACACGAAAATCGCAACTCGAAAATG
*
1108667 AAATTCGCAACACGAGAATCGCAACTCGAAAATG
1 AAATTCGCAACACGAAAATCGCAACTCGAAAATG
1108701 AAATT
1 AAATT
1108706 GGAGTTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.18
Consensus pattern (34 bp):
AAATTCGCAACACGAAAATCGCAACTCGAAAATG
Found at i:1108674 original size:20 final size:20
Alignment explanation
Indices: 1108646--1108705 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
1108636 TTTGCAACAC
*
1108646 GAAAATCGCAACTCGAAAAT
1 GAAATTCGCAACTCGAAAAT
*
1108666 GAAATTCGCAACACG---A-
1 GAAATTCGCAACTCGAAAAT
1108682 G-AA-TCGCAACTCGAAAAT
1 GAAATTCGCAACTCGAAAAT
1108700 GAAATT
1 GAAATT
1108706 GGAGTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
14 9 0.29
15 2 0.06
16 1 0.03
17 2 0.06
18 1 0.03
19 2 0.06
20 14 0.45
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAATTCGCAACTCGAAAAT
Found at i:1108806 original size:34 final size:34
Alignment explanation
Indices: 1108733--1108807 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
1108723 ATTCAACTTG
* *
1108733 CGAATTTCATTTTCGAGTAGCGATTTTCGAGTTG
1 CGAATTTCATTTTCGAGTAGCGATATTCGAGTTA
* * *
1108767 TGAATTTCATTTTCGAGTTGCGATATTCGTGTTA
1 CGAATTTCATTTTCGAGTAGCGATATTCGAGTTA
1108801 CGAATTT
1 CGAATTT
1108808 AAGTTTCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.44
Consensus pattern (34 bp):
CGAATTTCATTTTCGAGTAGCGATATTCGAGTTA
Found at i:1110278 original size:42 final size:42
Alignment explanation
Indices: 1110214--1110313 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
1110204 CCCCACTTTT
* *
1110214 TCATCGAGTCGATTATCCACTTCTACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCAACACCGAGATCCATCACC
*
1110256 TCATCGAGTCGATTCTCTACTTCAACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCAACACCGAGATCCATCACC
*
1110298 TCATCGAGCCGATTCT
1 TCATCGAGTCGATTCT
1110314 ACACCTCAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.25, C:0.35, G:0.13, T:0.27
Consensus pattern (42 bp):
TCATCGAGTCGATTCTCCACTTCAACACCGAGATCCATCACC
Found at i:1110330 original size:42 final size:42
Alignment explanation
Indices: 1110214--1110330 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 42
1110204 CCCCACTTTT
* * * * *
1110214 TCATCGAGTCGATTATCCACTTCTACACCGAGATCCATCACC
1 TCATCGAGCCGATTCTCTACCTCAACACCGAGATCCATCACC
* *
1110256 TCATCGAGTCGATTCTCTACTTCAACACCGAGATCCATCACC
1 TCATCGAGCCGATTCTCTACCTCAACACCGAGATCCATCACC
* *
1110298 TCATCGAGCCGATTCTAC-ACCTCAGCATCGAGA
1 TCATCGAGCCGATTCT-CTACCTCAACACCGAGA
1110331 GCTATCAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 66 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.25
Consensus pattern (42 bp):
TCATCGAGCCGATTCTCTACCTCAACACCGAGATCCATCACC
Found at i:1110514 original size:21 final size:21
Alignment explanation
Indices: 1110484--1110544 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
1110474 CACGGGCTGA
1110484 GTTAGGTGCTTTACGTGATAAG
1 GTTA-GTGCTTTACGTGATAAG
**
1110506 GTTAGTGCTTTACGTGACGAG
1 GTTAGTGCTTTACGTGATAAG
*
1110527 GTTGGTGCTTTACGTGAT
1 GTTAGTGCTTTACGTGAT
1110545 GATAATGGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 31 0.89
22 4 0.11
ACGTcount: A:0.18, C:0.11, G:0.33, T:0.38
Consensus pattern (21 bp):
GTTAGTGCTTTACGTGATAAG
Found at i:1110553 original size:21 final size:21
Alignment explanation
Indices: 1110510--1110553 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1110500 GATAAGGTTA
**
1110510 GTGCTTTACGTGACGAGGTTG
1 GTGCTTTACGTGACGAGAATG
* *
1110531 GTGCTTTACGTGATGATAATG
1 GTGCTTTACGTGACGAGAATG
1110552 GT
1 GT
1110554 ACATGGCGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.18, C:0.11, G:0.34, T:0.36
Consensus pattern (21 bp):
GTGCTTTACGTGACGAGAATG
Found at i:1110608 original size:42 final size:43
Alignment explanation
Indices: 1110562--1110657 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 43
1110552 GTACATGGCG
* *
1110562 TGATGAAGTAGGGT-CTTTACGTGGTAAGGTAACTGCTTTACA
1 TGATGAAGTAGGGTGCTTTACGTGGTAAGGTAACTACTTAACA
* *
1110604 TGATGACA--ATGGTGCTTTACGTGGTGAGGTAACTACTTAACA
1 TGATGA-AGTAGGGTGCTTTACGTGGTAAGGTAACTACTTAACA
*
1110646 TGATGATGTAGG
1 TGATGAAGTAGG
1110658 TGTTCTACGT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.09
42 37 0.84
43 3 0.07
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.32
Consensus pattern (43 bp):
TGATGAAGTAGGGTGCTTTACGTGGTAAGGTAACTACTTAACA
Found at i:1110667 original size:42 final size:40
Alignment explanation
Indices: 1110562--1110668 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 40
1110552 GTACATGGCG
* * *
1110562 TGATGAAGTAGGGTCTTTACGTGGTAAGGTAACTGCTTTACA
1 TGATG-AGTA-GGTGTTTACGTGGTAAGGTAACTACTTAACA
** *
1110604 TGATGACAATGGTGCTTTACGTGGTGAGGTAACTACTTAACA
1 TGATGAGTA-GGTG-TTTACGTGGTAAGGTAACTACTTAACA
1110646 TGATGATGTAGGTGTTCTACGTG
1 TGATGA-GTAGGTGTT-TACGTG
1110669 AGATTGTTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
41 7 0.13
42 45 0.85
43 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (40 bp):
TGATGAGTAGGTGTTTACGTGGTAAGGTAACTACTTAACA
Found at i:1110787 original size:4 final size:4
Alignment explanation
Indices: 1110778--1110819 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1110768 TTTTTCGACA
* * *
1110778 TTAT TTAT TTAT TTAT TTAC TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1110820 TTAGAGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:1110979 original size:21 final size:21
Alignment explanation
Indices: 1110953--1111008 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1110943 GAAGAAGCCT
1110953 GATCCACCTAC-CATTATTCAG
1 GATCCACCT-CTCATTATTCAG
*
1110974 GATCCACCTCTCATTGTTCAG
1 GATCCACCTCTCATTATTCAG
*
1110995 GATTCACCTCTCAT
1 GATCCACCTCTCAT
1111009 CGTTCAAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.23, C:0.34, G:0.11, T:0.32
Consensus pattern (21 bp):
GATCCACCTCTCATTATTCAG
Found at i:1111013 original size:21 final size:21
Alignment explanation
Indices: 1110969--1111059 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 21
1110959 CCTACCATTA
* *
1110969 TTCAGGATCCACCTCTCATTG
1 TTCAGGATGCACCTCTCATCG
*
1110990 TTCAGGATTCACCTCTCATCG
1 TTCAGGATGCACCTCTCATCG
* * *
1111011 TTCAAGAGGCCCCTC-CATCG
1 TTCAGGATGCACCTCTCATCG
* * * *
1111031 TTCAAGAGGCCCCTCCCATCG
1 TTCAGGATGCACCTCTCATCG
1111052 TTCAGGAT
1 TTCAGGAT
1111060 CCACATTCCA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 20 0.33
21 41 0.67
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (21 bp):
TTCAGGATGCACCTCTCATCG
Found at i:1111031 original size:20 final size:20
Alignment explanation
Indices: 1111001--1111055 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 20
1110991 TCAGGATTCA
1111001 CCTCTCATCGTTCAAGAGGCC
1 CCTC-CATCGTTCAAGAGGCC
1111022 CCTCCATCGTTCAAGAGGCC
1 CCTCCATCGTTCAAGAGGCC
1111042 CCTCCCATCGTTCA
1 CCT-CCATCGTTCA
1111056 GGATCCACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.18, C:0.42, G:0.16, T:0.24
Consensus pattern (20 bp):
CCTCCATCGTTCAAGAGGCC
Found at i:1113096 original size:12 final size:12
Alignment explanation
Indices: 1113079--1113103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1113069 AATTTGATTT
1113079 TCGAGTTGTGAA
1 TCGAGTTGTGAA
1113091 TCGAGTTGTGAA
1 TCGAGTTGTGAA
1113103 T
1 T
1113104 TTTAAAATCG
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:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (12 bp):
TCGAGTTGTGAA
Found at i:1113158 original size:20 final size:20
Alignment explanation
Indices: 1113130--1113199 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1113120 GATTTTCATG
1113130 TTGCGAATTTGCATTTT-GAA
1 TTGCGAATTTG-ATTTTCGAA
* * *
1113150 TTGCAAATTCGATTTTCGAG
1 TTGCGAATTTGATTTTCGAA
**
1113170 TTGCGAATTTGATTTTCGTG
1 TTGCGAATTTGATTTTCGAA
1113190 TTGCGAATTT
1 TTGCGAATTT
1113200 TAACTAGGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.12
20 38 0.88
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGATTTTCGAA
Found at i:1113478 original size:11 final size:11
Alignment explanation
Indices: 1113462--1113503 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
1113452 GTATGCATCC
1113462 ACACATAAAAT
1 ACACATAAAAT
*
1113473 ACACATAAAAC
1 ACACATAAAAT
1113484 ACACATAAAAT
1 ACACATAAAAT
1113495 ACACATAAA
1 ACACATAAA
1113504 TTTACCATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (11 bp):
ACACATAAAAT
Found at i:1113486 original size:22 final size:22
Alignment explanation
Indices: 1113461--1113503 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1113451 TGTATGCATC
1113461 CACACATAAAATACACATAAAA
1 CACACATAAAATACACATAAAA
1113483 CACACATAAAATACACATAAA
1 CACACATAAAATACACATAAA
1113504 TTTACCATTG
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:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (22 bp):
CACACATAAAATACACATAAAA
Found at i:1115986 original size:24 final size:24
Alignment explanation
Indices: 1115959--1116012 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1115949 TTGAAACATA
*
1115959 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
*
1115983 ATCAAAGTCCAAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
1116007 ATCAAA
1 ATCAAA
1116013 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCAAGTATTGACCAAG
Found at i:1116771 original size:16 final size:16
Alignment explanation
Indices: 1116752--1116782 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1116742 AAATAATTGA
1116752 AAAATTATATAAAAAT
1 AAAATTATATAAAAAT
*
1116768 AAAATTATGTAAAAA
1 AAAATTATATAAAAA
1116783 AAATTAGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:1116788 original size:14 final size:15
Alignment explanation
Indices: 1116751--1116785 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1116741 GAAATAATTG
1116751 AAAAATTATATAAAA
1 AAAAATTATATAAAA
*
1116766 ATAAAATTATGTAAAA
1 A-AAAATTATATAAAA
1116782 AAAA
1 AAAA
1116786 TTAGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAAATTATATAAAA
Done.