Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 69 of 204
Found at i:21818641 original size:24 final size:25
Alignment explanation
Indices: 21818609--21818678 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
21818599 AGCTACTCGT
21818609 TATAGGCTCGCATAAGCTTCCTG-AA
1 TATA-GCTCGCATAAGCTTCCTGTAA
** * *
21818634 TATAGCTCTTATGAGCTTCCTGTTA
1 TATAGCTCGCATAAGCTTCCTGTAA
* * *
21818659 TACAGCCCGGATAAGCTTCC
1 TATAGCTCGCATAAGCTTCC
21818679 CGTTACATGG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (25 bp):
TATAGCTCGCATAAGCTTCCTGTAA
Found at i:21820480 original size:21 final size:21
Alignment explanation
Indices: 21820451--21820497 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
21820441 CCCATATATT
*
21820451 TAATGTAAACATACTTTT-TCA
1 TAATATAAACAT-CTTTTCTCA
*
21820472 TAATATAAACATGTTTTCTCA
1 TAATATAAACATCTTTTCTCA
21820493 TAATA
1 TAATA
21820498 CAATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (21 bp):
TAATATAAACATCTTTTCTCA
Found at i:21822269 original size:22 final size:22
Alignment explanation
Indices: 21822244--21822289 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
21822234 AAAGTAGTAG
* * *
21822244 GCACTGAAGTGCGGAACGATAA
1 GCACCGAAGTACGAAACGATAA
*
21822266 GCACCGAAGTACGAAACGGTAA
1 GCACCGAAGTACGAAACGATAA
21822288 GC
1 GC
21822290 GTTAAAACGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.22, G:0.30, T:0.11
Consensus pattern (22 bp):
GCACCGAAGTACGAAACGATAA
Found at i:21824921 original size:45 final size:42
Alignment explanation
Indices: 21824829--21824960 Score: 140
Period size: 45 Copynumber: 3.0 Consensus size: 42
21824819 CAGATACATG
* ***
21824829 GTGGATCAGCACATAGC-ACCACCCTTATAGTCAATGATACTTG
1 GTGGATCAGCACATAGCAACCA-CCTTATAATCAATG-TACCCA
21824872 GTGGATTCAGCACATAGCAACCACCTTCATAATCAATAGTACCCA
1 GTGGA-TCAGCACATAGCAACCACCTT-ATAATCAAT-GTACCCA
*
21824917 GTGGAATCAGCACACAGCAACCACCTTTATAATCAATGGTACCC
1 GTGG-ATCAGCACATAGCAACCACC-TTATAATCAAT-GTACCC
21824961 GGTACACGTA
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
43 5 0.06
44 16 0.21
45 52 0.68
46 4 0.05
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (42 bp):
GTGGATCAGCACATAGCAACCACCTTATAATCAATGTACCCA
Found at i:21825231 original size:17 final size:17
Alignment explanation
Indices: 21825209--21825243 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21825199 CAATTTAGTC
21825209 CAAAAATCACATTTTTG
1 CAAAAATCACATTTTTG
* *
21825226 CAAAAATTATATTTTTG
1 CAAAAATCACATTTTTG
21825243 C
1 C
21825244 CCCTAACGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (17 bp):
CAAAAATCACATTTTTG
Found at i:21828255 original size:21 final size:22
Alignment explanation
Indices: 21828218--21828261 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
21828208 GTGGCATTAC
21828218 ATAATCTGTATAATC-TTTAAA
1 ATAATCTGTATAATCTTTTAAA
*
21828239 ATAATCTG-ATATTTCTTTTAAA
1 ATAATCTGTATA-ATCTTTTAAA
21828261 A
1 A
21828262 CTGAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 10 0.50
22 7 0.35
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
ATAATCTGTATAATCTTTTAAA
Found at i:21837140 original size:18 final size:18
Alignment explanation
Indices: 21837114--21837149 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21837104 AGATTGAATT
*
21837114 ATATTATTAAATTTATTA
1 ATATAATTAAATTTATTA
*
21837132 ATATAATTATATTTATTA
1 ATATAATTAAATTTATTA
21837150 TGCATGTAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATAATTAAATTTATTA
Found at i:21839511 original size:20 final size:21
Alignment explanation
Indices: 21839466--21839511 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
21839456 GCTCATCTGG
* *
21839466 TTTTGCTGCTGCTCCCTCCCT
1 TTTTCCTGCTGCTCCCGCCCT
*
21839487 GTTTCCTGCTGC-CCCGCCCT
1 TTTTCCTGCTGCTCCCGCCCT
21839507 TTTTC
1 TTTTC
21839512 TAATATTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.00, C:0.43, G:0.15, T:0.41
Consensus pattern (21 bp):
TTTTCCTGCTGCTCCCGCCCT
Found at i:21844781 original size:20 final size:22
Alignment explanation
Indices: 21844756--21844799 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
21844746 TAATTTAGAG
21844756 ATCACTTA-AACAAAAA-AAAA
1 ATCACTTATAACAAAAATAAAA
21844776 ATCACTTATAACAAAAATAAAA
1 ATCACTTATAACAAAAATAAAA
21844798 AT
1 AT
21844800 AAGTATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
21 8 0.36
22 6 0.27
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (22 bp):
ATCACTTATAACAAAAATAAAA
Found at i:21845313 original size:10 final size:10
Alignment explanation
Indices: 21845291--21845328 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
21845281 GCGGGTATTT
21845291 TACAAAAATAA
1 TACAAAAA-AA
21845302 TACAAAAAAA
1 TACAAAAAAA
21845312 TA-AAAAAAA
1 TACAAAAAAA
21845321 TACCAAAA
1 TA-CAAAA
21845329 TAGTATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
10 4 0.16
11 12 0.48
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (10 bp):
TACAAAAAAA
Found at i:21845734 original size:154 final size:152
Alignment explanation
Indices: 21845453--21845958 Score: 726
Period size: 154 Copynumber: 3.3 Consensus size: 152
21845443 CAATTGTTCG
* *
21845453 TATTTCAGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTTTTAAAAAATATAATATTTTC
1 TATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTACTTTTAAAAAATATAATATTTTC
*
21845518 TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTTAGTGTGTTTTT
65 TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTGTGTTTTT
21845583 TAAATAAATTTAAAAAAAACCCT
130 TAAATAAATTTAAAAAAAACCCT
** *
21845606 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACCTTCAATAAAAATATATTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTA-CTTTTA-AAAAATATAATATTTT
* * * * * *
21845671 CGT-ATTTTATTATTTTACATTGTTTTAGTACATTATGTTTGAAATGTATTAACTAATTTTGTTT
64 C-TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTGTGTTT
*
21845735 TTTAAATAAATTTAGTAAAAAACCCT
128 TTTAAATAAATTTA-AAAAAAACCCT
* * * *
21845761 TATTTTGACCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACTTTTAAAAAATATACTATTTTC
1 TATTTCGGCCCTTTGTTCGTATTTTTT-CCCGGATTTTATTACTTTTAAAAAATATAATATTTTC
* * *
21845826 TAATTTTATTATTTTACATTATTTTAGTACATTACAATTGAAATGTATTCATTCAGTGTGTTTTT
65 TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTGTGTTTTT
*
21845891 TAAATAAATTTTAAAAAAACCCCT
130 TAAATAAA-TTTAAAAAAAACCCT
* * *
21845915 TATTTCGGTCCTTTGTTCGTATTTTTCCCCTGATTTTATTACTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTT
21845959 GCAAGAAAAA
Statistics
Matches: 311, Mismatches: 35, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
152 19 0.06
153 41 0.13
154 194 0.62
155 44 0.14
156 13 0.04
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (152 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTTTAAAAAATATAATATTTTCT
AATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTGTGTTTTTT
AAATAAATTTAAAAAAAACCCT
Found at i:21850821 original size:45 final size:45
Alignment explanation
Indices: 21850772--21850862 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
21850762 AAAATTGGAG
21850772 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
21850817 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
21850862 A
1 A
21850863 CATTCTCTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.22
Consensus pattern (45 bp):
ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
Found at i:21851634 original size:29 final size:29
Alignment explanation
Indices: 21851592--21851653 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
21851582 TATATTCTAT
21851592 GGTCTAGTTCAACAACTAGCCAAGTAACA
1 GGTCTAGTTCAACAACTAGCCAAGTAACA
21851621 GGTCTAGTTCAACAACTAGCCAAGTAACA
1 GGTCTAGTTCAACAACTAGCCAAGTAACA
21851650 GGTC
1 GGTC
21851654 ATGTACATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (29 bp):
GGTCTAGTTCAACAACTAGCCAAGTAACA
Found at i:21855183 original size:29 final size:29
Alignment explanation
Indices: 21855108--21855196 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
21855098 TTAATTAATT
*
21855108 TTTTAA-AATTTAAAATTATTAAAAATATAA
1 TTTTAATATTTTAAAATT-TTAAAAA-ATAA
21855138 TTTTAATGATTTT--AATTTTAAAAAATAA
1 TTTTAAT-ATTTTAAAATTTTAAAAAATAA
*
21855166 TTTT-ATATTTTTAAAATTTTAAAAATTAA
1 TTTTAATA-TTTTAAAATTTTAAAAAATAA
21855195 TT
1 TT
21855197 AAATGATGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
26 1 0.02
27 6 0.12
28 8 0.15
29 23 0.44
30 10 0.19
32 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TTTTAATATTTTAAAATTTTAAAAAATAA
Found at i:21859654 original size:3 final size:3
Alignment explanation
Indices: 21859646--21859695 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
21859636 CCCTGTTTTC
21859646 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21859694 AT
1 AT
21859696 TGTTGATAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:21870020 original size:15 final size:15
Alignment explanation
Indices: 21869989--21870039 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
21869979 GAGCTATCAT
*
21869989 TAAAATCTAATTAAA
1 TAAAATATAATTAAA
21870004 TAAAATATATATTAATA
1 TAAAATATA-ATTAA-A
* *
21870021 TTAAATAAAATTAAA
1 TAAAATATAATTAAA
21870036 -AAAA
1 TAAAA
21870040 AATCCTCCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.10
15 9 0.30
16 10 0.33
17 8 0.27
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATATAATTAAA
Found at i:21872641 original size:9 final size:8
Alignment explanation
Indices: 21872607--21872642 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
21872597 TAATTTTTTT
21872607 AAAATTTA
1 AAAATTTA
21872615 AAAATTTA
1 AAAATTTA
21872623 AAAATTTA
1 AAAATTTA
21872631 AAAATTATA
1 AAAATT-TA
21872640 AAA
1 AAA
21872643 GTTATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATTTA
Found at i:21872647 original size:9 final size:9
Alignment explanation
Indices: 21872607--21872647 Score: 52
Period size: 8 Copynumber: 4.9 Consensus size: 9
21872597 TAATTTTTTT
21872607 AAAATT-TA
1 AAAATTATA
21872615 AAAATT-TA
1 AAAATTATA
21872623 AAAATT-TA
1 AAAATTATA
21872631 AAAATTATA
1 AAAATTATA
*
21872640 AAAGTTAT
1 AAAATTAT
21872648 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 22 0.71
9 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAATTATA
Found at i:21872661 original size:20 final size:22
Alignment explanation
Indices: 21872627--21872680 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
21872617 AATTTAAAAA
*
21872627 TTTAAAAATTATAAAAGTTATT
1 TTTAAAAATTATAAAAATTATT
21872649 TTTAAAAA-T-TAAAAATTA--
1 TTTAAAAATTATAAAAATTATT
*
21872667 TTAAAAAATTATAA
1 TTTAAAAATTATAA
21872681 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 7 0.25
19 1 0.04
20 11 0.39
21 1 0.04
22 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTAAAAATTATAAAAATTATT
Found at i:21884099 original size:6 final size:6
Alignment explanation
Indices: 21884013--21884096 Score: 141
Period size: 6 Copynumber: 14.0 Consensus size: 6
21884003 TTTATGTGTC
21884013 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * *
21884061 TATGTG TATGTG TATGTG CATGTG GATGTG CATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
21884097 CATTTATAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.17, C:0.02, G:0.35, T:0.46
Consensus pattern (6 bp):
TATGTG
Found at i:21896723 original size:13 final size:14
Alignment explanation
Indices: 21896707--21896736 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
21896697 ATTTATAAAC
21896707 AATATTATG-ATAT
1 AATATTATGTATAT
21896720 AATATTATGTATAT
1 AATATTATGTATAT
21896734 AAT
1 AAT
21896737 CCGTTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
AATATTATGTATAT
Found at i:21899595 original size:4 final size:4
Alignment explanation
Indices: 21899572--21899639 Score: 118
Period size: 4 Copynumber: 16.8 Consensus size: 4
21899562 GTAAGGGCAG
*
21899572 CATA CATTA CATA TATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
21899621 CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CAT
21899640 TCACATATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
4 57 0.93
5 4 0.07
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:21900215 original size:6 final size:6
Alignment explanation
Indices: 21900195--21900231 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
21900185 TTTATCAATC
*
21900195 TCTGAT TCATGAT TCTGAT TCTGGT TCTGAT TCTGAT
1 TCTGAT TC-TGAT TCTGAT TCTGAT TCTGAT TCTGAT
21900232 ATGTTTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (6 bp):
TCTGAT
Found at i:21903007 original size:27 final size:27
Alignment explanation
Indices: 21902963--21903017 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
21902953 TTTTGAAATT
*
21902963 ATTATGTCTTGAATTTGTTAGATATTG
1 ATTATGTCTTGAACTTGTTAGATATTG
21902990 ATTATGTCTT-AAGCTTGTTAGATATTG
1 ATTATGTCTTGAA-CTTGTTAGATATTG
21903017 A
1 A
21903018 ATTTATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.49
Consensus pattern (27 bp):
ATTATGTCTTGAACTTGTTAGATATTG
Found at i:21903034 original size:32 final size:32
Alignment explanation
Indices: 21902945--21903050 Score: 98
Period size: 32 Copynumber: 3.5 Consensus size: 32
21902935 AAATTTTAGT
* * * *
21902945 TTGTTGGATTTTGAAATTATTATGTCTTGAA-T
1 TTGTTAGATATTGAATTTATTATGTCTT-AAGC
21902977 TTGTTAGATATTG-----ATTATGTCTTAAGC
1 TTGTTAGATATTGAATTTATTATGTCTTAAGC
*
21903004 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTGAATTTATTATGTCTTAAGC
* *
21903036 TTGTTGGATGTTGAA
1 TTGTTAGATATTGAA
21903051 ATGATTGACA
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
26 2 0.03
27 23 0.37
32 37 0.60
ACGTcount: A:0.25, C:0.04, G:0.20, T:0.51
Consensus pattern (32 bp):
TTGTTAGATATTGAATTTATTATGTCTTAAGC
Found at i:21904249 original size:20 final size:20
Alignment explanation
Indices: 21904224--21904261 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21904214 ATAATTTAAA
21904224 ATATAAATTTATTAATATGT
1 ATATAAATTTATTAATATGT
21904244 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
21904262 ATGTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:21904271 original size:20 final size:20
Alignment explanation
Indices: 21904228--21904271 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
21904218 TTTAAAATAT
* *
21904228 AAATTTATTAATATGTATAT
1 AAATTTATTAATATATATAA
*
21904248 AAATTTATTAATATATGTAA
1 AAATTTATTAATATATATAA
21904268 AAAT
1 AAAT
21904272 AGTTTTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTTATTAATATATATAA
Found at i:21904373 original size:14 final size:15
Alignment explanation
Indices: 21904354--21904391 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
21904344 CCAGAAACGT
21904354 AAATCATTTTC-CAA
1 AAATCATTTTCTCAA
*
21904368 AAATCATTTTCTGAA
1 AAATCATTTTCTCAA
21904383 AAA-CATTTT
1 AAATCATTTT
21904392 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATCATTTTCTCAA
Found at i:21906009 original size:27 final size:25
Alignment explanation
Indices: 21905945--21906014 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 25
21905935 CTGTACATGT
*
21905945 ATGCTCACACGAGCTGTGAATTAGA
1 ATGCTCACACGAGCTGTGAAATAGA
*
21905970 ATGCTCACACGAGCTGTGAAAATAGGC
1 ATGCTCACACGAGCTGTG-AAATA-GA
*
21905997 CTGCTCACACGAGCTGTG
1 ATGCTCACACGAGCTGTG
21906015 GGTGGAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.45
26 4 0.10
27 18 0.45
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAAATAGA
Found at i:21914468 original size:18 final size:18
Alignment explanation
Indices: 21914445--21914479 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21914435 TATTCATATC
*
21914445 TATTGTTGAAAATAAGAT
1 TATTGTTAAAAATAAGAT
21914463 TATTGTTAAAAATAAGA
1 TATTGTTAAAAATAAGA
21914480 AATTGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (18 bp):
TATTGTTAAAAATAAGAT
Found at i:21914484 original size:17 final size:18
Alignment explanation
Indices: 21914446--21914484 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21914436 ATTCATATCT
* *
21914446 ATTGTTGAAAATAAGATT
1 ATTGTTAAAAATAAGATA
21914464 ATTGTTAAAAATAAGA-A
1 ATTGTTAAAAATAAGATA
21914481 ATTG
1 ATTG
21914485 AATTAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTGTTAAAAATAAGATA
Found at i:21914620 original size:24 final size:25
Alignment explanation
Indices: 21914544--21914627 Score: 134
Period size: 25 Copynumber: 3.4 Consensus size: 25
21914534 GTGGAAAAAT
*
21914544 GATGAATTGATGGTAAAATGCAAAG
1 GATGAATTGACGGTAAAATGCAAAG
21914569 GATGAATTGACGGTAAAATGCAAAG
1 GATGAATTGACGGTAAAATGCAAAG
* *
21914594 GATGAATTGACGGT-ATATGCAAGG
1 GATGAATTGACGGTAAAATGCAAAG
21914618 GATGAATTGA
1 GATGAATTGA
21914628 TGACAAATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 18 0.32
25 38 0.68
ACGTcount: A:0.40, C:0.06, G:0.30, T:0.24
Consensus pattern (25 bp):
GATGAATTGACGGTAAAATGCAAAG
Found at i:21914793 original size:22 final size:21
Alignment explanation
Indices: 21914740--21914794 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
21914730 CTATTTAACC
* *
21914740 CTTATGGGTTTCCGTTCAGCT
1 CTTATGGGTTTCCATTCACCT
* *
21914761 CCTATGAGTTTCCATTCAACCT
1 CTTATGGGTTTCCATTC-ACCT
*
21914783 TTTATGGGTTTC
1 CTTATGGGTTTC
21914795 TGTTAGCACT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (21 bp):
CTTATGGGTTTCCATTCACCT
Found at i:21916523 original size:22 final size:22
Alignment explanation
Indices: 21916498--21916552 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
21916488 TGCACTAATG
21916498 AACAGAGAGCACTA-AAGTGCTA
1 AACAGAGAGCAC-AGAAGTGCTA
* *
21916520 AACAAAGAGCACAGATGTGCTA
1 AACAGAGAGCACAGAAGTGCTA
*
21916542 AACGGAGAGCA
1 AACAGAGAGCA
21916553 TTGTCATGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.11
Consensus pattern (22 bp):
AACAGAGAGCACAGAAGTGCTA
Found at i:21917048 original size:14 final size:14
Alignment explanation
Indices: 21917029--21917058 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21917019 ACACCATTCA
21917029 ATCTCACATTAAAT
1 ATCTCACATTAAAT
21917043 ATCTCACATTAAAT
1 ATCTCACATTAAAT
21917057 AT
1 AT
21917059 TTCCTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (14 bp):
ATCTCACATTAAAT
Found at i:21917499 original size:5 final size:5
Alignment explanation
Indices: 21917489--21917577 Score: 178
Period size: 5 Copynumber: 17.8 Consensus size: 5
21917479 TGTTTGTTTT
21917489 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
21917539 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
21917578 TATTTAACTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 84 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:21921810 original size:10 final size:10
Alignment explanation
Indices: 21921797--21921827 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21921787 TTTTATGTTT
21921797 TTTTTAAATA
1 TTTTTAAATA
21921807 TTTTTAAATA
1 TTTTTAAATA
*
21921817 TTTTTTAATA
1 TTTTTAAATA
21921827 T
1 T
21921828 ATATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:21921843 original size:22 final size:21
Alignment explanation
Indices: 21921818--21921870 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21921808 TTTTAAATAT
* *
21921818 TTTTTAATATATATTTTTTTAA
1 TTTTTAATATA-AGTTTTTGAA
*
21921840 TTTTTATTATAAGTTTTTGAA
1 TTTTTAATATAAGTTTTTGAA
*
21921861 ATTTTAATAT
1 TTTTTAATAT
21921871 TTTTTGTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTAATATAAGTTTTTGAA
Found at i:21921946 original size:23 final size:25
Alignment explanation
Indices: 21921911--21921956 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
21921901 TTTTTATGTA
21921911 TTTTGAGATTTTTT-TTCAAATTATT
1 TTTTGAGATTTTTTATT-AAATTATT
21921936 TTTTGA-A-TTTTTATTAAATTA
1 TTTTGAGATTTTTTATTAAATTA
21921957 AAAGAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.55
24 3 0.15
25 6 0.30
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (25 bp):
TTTTGAGATTTTTTATTAAATTATT
Found at i:21927421 original size:42 final size:41
Alignment explanation
Indices: 21927315--21927468 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 41
21927305 TGAGCTGTGT
* *
21927315 TTTCGTGTAAGACCATGTCTGGGACGTTCGCATCGATTTGAGA
1 TTTCGTGTAAGACCATGTCTGGGAC-ATCGCATCGATAT-AGA
21927358 TTTACGTGTAAGACCATGTCTGGGACATCGACATCG-TATATGA
1 TTT-CGTGTAAGACCATGTCTGGGACATCG-CATCGATATA-GA
* * *
21927401 TTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGA
1 TTTCGTGTAAGACCATGTCTGGGACA-TCGCATCGATA-TAGA
* * * *
21927444 TTACATGGAAGACCACGTCTGGGAC
1 TTTCGTGTAAGACCATGTCTGGGAC
21927469 GTTGGCATTG
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
42 28 0.29
43 39 0.41
44 28 0.29
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TTTCGTGTAAGACCATGTCTGGGACATCGCATCGATATAGA
Found at i:21927491 original size:86 final size:86
Alignment explanation
Indices: 21927312--21927468 Score: 212
Period size: 86 Copynumber: 1.8 Consensus size: 86
21927302 TTCTGAGCTG
* * *
21927312 TGTTTTCGTGTAAGACCATGTCTGGGACGTTCGCATCGATTTGAGATTTACGTGTAAGACCATGT
1 TGTTTTCGTGTAAGACCATGTCTGGGACGTTCGCATCGATTTGAGATTTACATGGAAGACCACGT
21927377 CTGGGACATCGACATCGTATA
66 CTGGGACATCGACATCGTATA
* * * *
21927398 TGATTTCGTGTAAGACCCTGTCTGGGACAG-TGGCATCGATATT-TGA-TTACATGGAAGACCAC
1 TGTTTTCGTGTAAGACCATGTCTGGGAC-GTTCGCATCGAT-TTGAGATTTACATGGAAGACCAC
21927460 GTCTGGGAC
64 GTCTGGGAC
21927469 GTTGGCATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
85 22 0.35
86 37 0.60
87 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (86 bp):
TGTTTTCGTGTAAGACCATGTCTGGGACGTTCGCATCGATTTGAGATTTACATGGAAGACCACGT
CTGGGACATCGACATCGTATA
Found at i:21948321 original size:43 final size:43
Alignment explanation
Indices: 21948260--21948533 Score: 458
Period size: 43 Copynumber: 6.3 Consensus size: 43
21948250 TCTGATGTGT
* *
21948260 GATTTCGTGTAAGACCATAGCTGAGCTATTGGCATCGATCTGA
1 GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
*
21948303 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
1 GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
*
21948346 GATTTCGTGTAAGACCATACCTGGGCTATTGGCATCGATTTGA
1 GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
21948389 GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
1 GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
*
21948432 GATTTCGTGTAAGACCATAGCTGGGCTATTGACATCGATTTGA
1 GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
* **
21948475 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATACGA
1 GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
*
21948518 GATTTCTATGTAAGAC
1 GATTTC-GTGTAAGAC
21948534 TATGTCTGAG
Statistics
Matches: 217, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
43 209 0.96
44 8 0.04
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
Found at i:21951044 original size:34 final size:34
Alignment explanation
Indices: 21951006--21951074 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
21950996 CCTAGCAGCG
21951006 AAAAAATGATATTTATTCAGTTTTAATAACATAT
1 AAAAAATGATATTTATTCAGTTTTAATAACATAT
*
21951040 AAAAAGTGATATTTATTCAGTTTTAATAACATAT
1 AAAAAATGATATTTATTCAGTTTTAATAACATAT
21951074 A
1 A
21951075 TGTTTCGTGC
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:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (34 bp):
AAAAAATGATATTTATTCAGTTTTAATAACATAT
Found at i:21951746 original size:91 final size:90
Alignment explanation
Indices: 21951587--21951790 Score: 257
Period size: 91 Copynumber: 2.3 Consensus size: 90
21951577 CTCTGTTTTG
* * * * * * *
21951587 TGGATAAACCACCAGTG-TTGCAGGTTAATACACTGCCATTAGTAGTGAGTATACAATGGGTTTG
1 TGGATAAACCACCAGTGTTTGCAGGTTAATACACTACCAGTAGTAGTAAATACACAACGGGTTTA
21951651 CAGATAAAAGTTGCCAATAAAAATTA
66 CAGATAAAAGTTGCCAAT-AAAATTA
* * *
21951677 TGGATAAACCACCAGTGTTTGCTGGTTAATACGCTACCAGTAGTTGTAAATACACAACGGGTTTA
1 TGGATAAACCACCAGTGTTTGCAGGTTAATACACTACCAGTAGTAGTAAATACACAACGGGTTTA
* ** *
21951742 CAGATAAAAGTTTCCAATAAGTTTG
66 CAGATAAAAGTTGCCAATAAAATTA
*
21951767 TGGACAAACCACCAGTGTTTGCAG
1 TGGATAAACCACCAGTGTTTGCAG
21951791 ATAAACTACC
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 43 0.44
91 54 0.56
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (90 bp):
TGGATAAACCACCAGTGTTTGCAGGTTAATACACTACCAGTAGTAGTAAATACACAACGGGTTTA
CAGATAAAAGTTGCCAATAAAATTA
Found at i:21961157 original size:9 final size:9
Alignment explanation
Indices: 21961135--21961194 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
21961125 TATTATATAT
21961135 AAAATCAATA
1 AAAAT-AATA
21961145 AAAATAATA
1 AAAATAATA
21961154 AAAAT-ATA
1 AAAATAATA
*
21961162 GAAAATCATAA
1 -AAAATAAT-A
21961173 AAAGATATATA
1 AAA-ATA-ATA
*
21961184 AAAATTATA
1 AAAATAATA
21961193 AA
1 AA
21961195 CAAATATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
8 3 0.07
9 19 0.44
10 12 0.28
11 7 0.16
12 2 0.05
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (9 bp):
AAAATAATA
Found at i:21961160 original size:28 final size:30
Alignment explanation
Indices: 21961129--21961194 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 30
21961119 AATAGGTATT
21961129 ATATATAAAATCA-ATAAAA-ATA-ATAAAA
1 ATATATAAAATCATA-AAAAGATATATAAAA
*
21961157 ATATAGAAAATCATAAAAAGATATATAAAA
1 ATATATAAAATCATAAAAAGATATATAAAA
21961187 AT-TATAAA
1 ATATATAAA
21961195 CAAATATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 16 0.48
29 9 0.27
30 8 0.24
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (30 bp):
ATATATAAAATCATAAAAAGATATATAAAA
Found at i:21961287 original size:9 final size:9
Alignment explanation
Indices: 21961273--21961448 Score: 50
Period size: 9 Copynumber: 19.1 Consensus size: 9
21961263 ACATATTTTT
21961273 TAAAAAATA
1 TAAAAAATA
21961282 T-AAAAATA
1 TAAAAAATA
* *
21961290 TATTAAAATT
1 TA-AAAAATA
** *
21961300 TTTAACATAA
1 TAAAAAAT-A
* *
21961310 TAAAAATTT
1 TAAAAAATA
* *
21961319 TAAAAATTT
1 TAAAAAATA
*
21961328 TAAAAATTA
1 TAAAAAATA
* *
21961337 TATAAATTA
1 TAAAAAATA
* *
21961346 TGAAAAATTG
1 T-AAAAAATA
*
21961356 TAAAAATTA
1 TAAAAAATA
**
21961365 TGTAAAATA
1 TAAAAAATA
**
21961374 TTTAAAATA
1 TAAAAAATA
21961383 TAGAAAAATA
1 TA-AAAAATA
21961393 TTAAAAAATA
1 -TAAAAAATA
* *
21961403 TAGAAAA-G
1 TAAAAAATA
* *
21961411 TGAAAACTA
1 TAAAAAATA
*
21961420 TATAAAATA
1 TAAAAAATA
*
21961429 TAGAAAATTA
1 TA-AAAAATA
*
21961439 TGAAAAATA
1 TAAAAAATA
21961448 T
1 T
21961449 TATTTCAAGT
Statistics
Matches: 125, Mismatches: 34, Indels: 16
0.71 0.19 0.09
Matches are distributed among these distances:
8 12 0.10
9 75 0.60
10 36 0.29
11 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (9 bp):
TAAAAAATA
Found at i:21961297 original size:19 final size:19
Alignment explanation
Indices: 21961275--21961448 Score: 52
Period size: 19 Copynumber: 9.4 Consensus size: 19
21961265 ATATTTTTTA
21961275 AAAAATATAAAAATATATT
1 AAAAATATAAAAATATATT
* * * *
21961294 AAAATTTTTAACATA-A-T
1 AAAAATATAAAAATATATT
*
21961311 AAAAATTTTAAAAAT-T-TT
1 AAAAA-TATAAAAATATATT
* *
21961329 AAAAATTATATAAAT-TATG
1 AAAAA-TATAAAAATATATT
*
21961348 AAAAATTGTAAAAAT-TATGT
1 AAAAA-TATAAAAATATAT-T
* *
21961368 -AAAATATTTAAAATATA-G
1 AAAAATA-TAAAAATATATT
21961386 AAAAATATTAAAAA-ATA-T
1 AAAAATA-TAAAAATATATT
* *
21961404 AGAAAAGT-GAAAACTATA-T
1 A-AAAA-TATAAAAATATATT
*
21961423 -AAAATATAGAAAAT-TATG
1 AAAAATATA-AAAATATATT
21961441 AAAAATAT
1 AAAAATAT
21961449 TATTTCAAGT
Statistics
Matches: 117, Mismatches: 23, Indels: 30
0.69 0.14 0.18
Matches are distributed among these distances:
16 1 0.01
17 12 0.10
18 36 0.31
19 65 0.56
20 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAAATATAAAAATATATT
Found at i:21961301 original size:28 final size:28
Alignment explanation
Indices: 21961270--21961404 Score: 84
Period size: 28 Copynumber: 4.8 Consensus size: 28
21961260 GTTACATATT
21961270 TTTTAAAAAATATAAAAATATATTAAAA
1 TTTTAAAAAATATAAAAATATATTAAAA
* *
21961298 TTTT-TAACATAATAAAAAT-T-TTAAAAA
1 TTTTAAAAAAT-ATAAAAATATATT-AAAA
* * *
21961325 TTTTAAAAATTATATAAAT-TATGAAAAA
1 TTTTAAAAAATATAAAAATATAT-TAAAA
* * *
21961353 TTGTAAAAATTATGTAAAATAT-TTAAAA
1 TTTTAAAAAATAT-AAAAATATATTAAAA
*
21961381 -TATAGAAAAATATTAAAAAATATA
1 TTTTA-AAAAATA-T-AAAAATATA
21961405 GAAAAGTGAA
Statistics
Matches: 82, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
26 2 0.02
27 24 0.29
28 42 0.51
29 13 0.16
30 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (28 bp):
TTTTAAAAAATATAAAAATATATTAAAA
Found at i:21961314 original size:37 final size:34
Alignment explanation
Indices: 21961273--21961399 Score: 94
Period size: 37 Copynumber: 3.4 Consensus size: 34
21961263 ACATATTTTT
21961273 TAAAAAATATAAAAATATATTAAAATTTTTAACATAA
1 TAAAAAATATAAAAAT-TATTAAAATTTTTAA-AT-A
* * *
21961310 TAAAAATTTTAAAAATT-TTAAAAATTATATAAATTA
1 TAAAAAATATAAAAATTATT-AAAATT-TTTAAA-TA
* * *
21961346 TGAAAAATTGTAAAAATTATGTAAAATATTTAAAATA
1 T-AAAAAATATAAAAATTAT-TAAAAT-TTTTAAATA
21961383 TAGAAAAATATTAAAAA
1 TA-AAAAATA-TAAAAA
21961400 ATATAGAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
35 2 0.03
36 11 0.15
37 42 0.58
38 16 0.22
39 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (34 bp):
TAAAAAATATAAAAATTATTAAAATTTTTAAATA
Found at i:21961402 original size:20 final size:20
Alignment explanation
Indices: 21961347--21961409 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
21961337 TATAAATTAT
*
21961347 GAAAAAT-TGTAAAAATTAT-
1 GAAAAATAT-TAAAAAATATA
* *
21961366 GTAAAATATT-TAAAATATA
1 GAAAAATATTAAAAAATATA
21961385 GAAAAATATTAAAAAATATA
1 GAAAAATATTAAAAAATATA
21961405 GAAAA
1 GAAAA
21961410 GTGAAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.17
19 16 0.44
20 14 0.39
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
GAAAAATATTAAAAAATATA
Found at i:21961426 original size:10 final size:9
Alignment explanation
Indices: 21961377--21961436 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
21961367 TAAAATATTT
21961377 AAAATATAG
1 AAAATATAG
*
21961386 AAAAATATTAA
1 -AAAATA-TAG
21961397 AAAATATAG
1 AAAATATAG
*
21961406 AAAA-GT-G
1 AAAATATAG
*
21961413 AAAACTATAT
1 AAAA-TATAG
21961423 AAAATATAG
1 AAAATATAG
21961432 AAAAT
1 AAAAT
21961437 TATGAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
7 5 0.12
8 1 0.03
9 16 0.40
10 16 0.40
11 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (9 bp):
AAAATATAG
Found at i:21961442 original size:28 final size:28
Alignment explanation
Indices: 21961321--21961444 Score: 85
Period size: 28 Copynumber: 4.5 Consensus size: 28
21961311 AAAAATTTTA
* * *
21961321 AAAATTTTAAAAATTATATAAATTAT-G
1 AAAATTATGAAAATTATATAAAATATAG
* * * **
21961348 AAAAATTGTAAAAATTATGTAAAATATTT
1 -AAAATTATGAAAATTATATAAAATATAG
* *
21961377 AAAA-TATAGAAAAATATTAAAAAATATAG
1 AAAATTAT-GAAAATTA-TATAAAATATAG
* *
21961406 AAAA--GTGAAAACTATATAAAATATAG
1 AAAATTATGAAAATTATATAAAATATAG
21961432 AAAATTATGAAAA
1 AAAATTATGAAAA
21961445 ATATTATTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
26 15 0.20
27 9 0.12
28 40 0.53
29 12 0.16
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (28 bp):
AAAATTATGAAAATTATATAAAATATAG
Found at i:21961448 original size:26 final size:25
Alignment explanation
Indices: 21961397--21961448 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
21961387 AAAATATTAA
*
21961397 AAAATATAGAAAAGTGAAAACTATAT
1 AAAATATAGAAAAATGAAAAC-ATAT
21961423 AAAATATAGAAAATTATGAAAA-ATAT
1 AAAATATAGAAAA--ATGAAAACATAT
21961449 TATTTCAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 17 0.74
28 6 0.26
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (25 bp):
AAAATATAGAAAAATGAAAACATAT
Found at i:21961824 original size:9 final size:9
Alignment explanation
Indices: 21961806--21961845 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
21961796 TTTGGTTAAA
*
21961806 AATTACCCG
1 AATTAACCG
21961815 AATTAACCG
1 AATTAACCG
*
21961824 AATTACCCG
1 AATTAACCG
21961833 AATTAACCG
1 AATTAACCG
21961842 AATT
1 AATT
21961846 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:21961829 original size:18 final size:18
Alignment explanation
Indices: 21961806--21961845 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
21961796 TTTGGTTAAA
21961806 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
21961824 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
21961842 AATT
1 AATT
21961846 GAATCACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:21961894 original size:37 final size:37
Alignment explanation
Indices: 21961844--21961918 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
21961834 ATTAACCGAA
21961844 TTGAATCACTACATAAATAAAAACATTACATAAGTCT
1 TTGAATCACTACATAAATAAAAACATTACATAAGTCT
*
21961881 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAAATAAAAACATTACATAAGTCT
21961918 T
1 T
21961919 GAAATTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (37 bp):
TTGAATCACTACATAAATAAAAACATTACATAAGTCT
Found at i:21961912 original size:17 final size:17
Alignment explanation
Indices: 21961853--21961913 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
21961843 ATTGAATCAC
*
21961853 TACATAAATAAAAACAT
1 TACATAATTAAAAACAT
** * *
21961870 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
21961890 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
21961907 TACATAA
1 TACATAA
21961914 GTCTTGAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 20 0.62
20 12 0.38
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:21961932 original size:37 final size:37
Alignment explanation
Indices: 21961844--21961935 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
21961834 ATTAACCGAA
* *
21961844 TTGAATCACTACATAAATAAAAACATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
*
21961881 TTGAATCACTACATAATTAAAAACATTACATAAGTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
21961917 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
21961936 GAAATGTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 45 0.88
38 3 0.06
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:21962059 original size:17 final size:17
Alignment explanation
Indices: 21962039--21962071 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21962029 CTATTTATAT
*
21962039 ATTATTTTTATTTTTAA
1 ATTATTTTCATTTTTAA
21962056 ATTATTTTCATTTTTA
1 ATTATTTTCATTTTTA
21962072 TTTATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTATTTTCATTTTTAA
Found at i:21962070 original size:24 final size:25
Alignment explanation
Indices: 21962042--21962097 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
21962032 TTTATATATT
*
21962042 ATTTTTATTT-TTAAATTATTT-TC
1 ATTTTTATTTATTAAATTATTTGTA
21962065 ATTTTTATTTATTAAATTATTTGTA
1 ATTTTTATTTATTAAATTATTTGTA
21962090 ATTTTTAT
1 ATTTTTAT
21962098 GATTGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 10 0.33
24 11 0.37
25 9 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (25 bp):
ATTTTTATTTATTAAATTATTTGTA
Found at i:21962123 original size:13 final size:13
Alignment explanation
Indices: 21962105--21962137 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
21962095 TATGATTGAG
21962105 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
21962118 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
21962131 TTGGGTT
1 TTGGGTT
21962138 TGGATTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.45, T:0.42
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:21962566 original size:20 final size:20
Alignment explanation
Indices: 21962541--21962583 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
21962531 ATAATATATA
* *
21962541 TTTTAAATTTTTTTATTAAT
1 TTTTAAATATTTTTAATAAT
21962561 TTTTAAATATTTTTAATAAT
1 TTTTAAATATTTTTAATAAT
21962581 TTT
1 TTT
21962584 CCACATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAAATATTTTTAATAAT
Found at i:21962651 original size:15 final size:17
Alignment explanation
Indices: 21962599--21962655 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
21962589 TTTTAAAATC
21962599 ATAATTTTTAATATATTT
1 ATAATTTTTAATAT-TTT
* *
21962617 ATAATTTTTCATAATTT
1 ATAATTTTTAATATTTT
21962634 ATAA-TTTT-ATATTTT
1 ATAATTTTTAATATTTT
21962649 ATAATTT
1 ATAATTT
21962656 AAAATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.29
16 6 0.17
17 7 0.20
18 12 0.34
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTTTAATATTTT
Found at i:21962655 original size:22 final size:24
Alignment explanation
Indices: 21962613--21962682 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 24
21962603 TTTTTAATAT
*
21962613 ATTTATAATT-TTTCATAATTTATA
1 ATTT-TAATTATTTTATAATTTATA
*
21962637 ATTTT-A-TATTTTATAATTTAAA
1 ATTTTAATTATTTTATAATTTATA
*
21962659 ATTTTAATTATTTTAAAATTTATA
1 ATTTTAATTATTTTATAATTTATA
21962683 TTACTTTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 18 0.46
23 2 0.05
24 18 0.46
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTAATTATTTTATAATTTATA
Found at i:21962662 original size:15 final size:15
Alignment explanation
Indices: 21962631--21962679 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
21962621 TTTTTCATAA
* *
21962631 TTTATAATTTTATAT
1 TTTATAATTTAAAAT
21962646 TTTATAATTTAAAAT
1 TTTATAATTTAAAAT
*
21962661 TTTAATTATTTTAAAAT
1 TTT-A-TAATTTAAAAT
21962678 TT
1 TT
21962680 ATATTACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 16 0.55
16 1 0.03
17 12 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTATAATTTAAAAT
Found at i:21962771 original size:18 final size:19
Alignment explanation
Indices: 21962748--21962788 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
21962738 CACTTTACTG
*
21962748 TTTTAT-ATTTTAAAATAT
1 TTTTATAATTGTAAAATAT
*
21962766 TTTTATAATTGTAATATAT
1 TTTTATAATTGTAAAATAT
21962785 TTTT
1 TTTT
21962789 TTTACTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATAATTGTAAAATAT
Found at i:21962819 original size:20 final size:20
Alignment explanation
Indices: 21962807--21962844 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21962797 TTTCTATATT
21962807 TTTA-TGATTTTTTATAATC
1 TTTATTGATTTTTTATAATC
*
21962826 TTTATTGATTTTTAATAAT
1 TTTATTGATTTTTTATAAT
21962845 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTATTGATTTTTTATAATC
Found at i:21962857 original size:12 final size:12
Alignment explanation
Indices: 21962840--21962866 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21962830 TTGATTTTTA
21962840 ATAATTATATAT
1 ATAATTATATAT
21962852 ATAATTATATAT
1 ATAATTATATAT
21962864 ATA
1 ATA
21962867 TATATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAATTATATAT
Found at i:21967490 original size:27 final size:26
Alignment explanation
Indices: 21967436--21967499 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 26
21967426 TTTTGCTTAG
*
21967436 TTTTAATAAAATATACATTTCATGCA
1 TTTTAATAAAATATACATTTCATACA
*
21967462 TTATTAATTAAAATATATATTTCA-ACA
1 TT-TTAA-TAAAATATACATTTCATACA
*
21967489 TTTTAAAAAAA
1 TTTTAATAAAA
21967500 CAAATTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 4 0.12
26 6 0.18
27 8 0.24
28 15 0.45
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTTAATAAAATATACATTTCATACA
Found at i:21968066 original size:21 final size:21
Alignment explanation
Indices: 21968040--21968081 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21968030 CTGCCAGTAA
*
21968040 GTTTGTGGATAAACCACCAGT
1 GTTTGTAGATAAACCACCAGT
*
21968061 GTTTGTAGATAAACTACCAGT
1 GTTTGTAGATAAACCACCAGT
21968082 AGGTTGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (21 bp):
GTTTGTAGATAAACCACCAGT
Found at i:21968075 original size:44 final size:43
Alignment explanation
Indices: 21968027--21968162 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 43
21968017 TTGCAGATAA
* *
21968027 AAACTGCCAGTAAGTTTGTGGATAAACCACCAGTGTTTGTAGAT
1 AAACTACCAGTAAGTTTGTGGATGAACCACCA-TGTTTGTAGAT
* * * * *
21968071 AAACTACCAGT-AGGTTGTGAATGCACAACGCA--TTTGAAGAT
1 AAACTACCAGTAAGTTTGTGGATGAACCAC-CATGTTTGTAGAT
*
21968112 AAAAGCTACAAGTAAGTTTGTGGATGAACCACCAATGTTTGTAGAT
1 -AAA-CTACCAGTAAGTTTGTGGATGAACCACC-ATGTTTGTAGAT
21968158 AAACT
1 AAACT
21968163 GTCAGTAGGT
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
41 8 0.11
42 3 0.04
43 21 0.29
44 29 0.40
45 3 0.04
46 8 0.11
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (43 bp):
AAACTACCAGTAAGTTTGTGGATGAACCACCATGTTTGTAGAT
Found at i:21968097 original size:87 final size:87
Alignment explanation
Indices: 21967951--21968237 Score: 358
Period size: 87 Copynumber: 3.3 Consensus size: 87
21967941 CCGAACACTC
* * * * * * * * *
21967951 AAGTTTATGGATGAACCACCATTGTTTGCAAATAAACTGCCACTTGGTTGTGAATGCACAATGTA
1 AAGTTTGTGGATAAACCACCAATGTTTGTAGATAAACTGCCAGTAGGTTGTGAATGCACAACGAA
* * *
21968016 TTTGCAGATAAAAACTGCCAGT
66 TTTGAAGATAAAAGCTGCAAGT
* * *
21968038 AAGTTTGTGGATAAACCACCAGTGTTTGTAGATAAACTACCAGTAGGTTGTGAATGCACAACGCA
1 AAGTTTGTGGATAAACCACCAATGTTTGTAGATAAACTGCCAGTAGGTTGTGAATGCACAACGAA
*
21968103 TTTGAAGATAAAAGCTACAAGT
66 TTTGAAGATAAAAGCTGCAAGT
* * * *
21968125 AAGTTTGTGGATGAACCACCAATGTTTGTAGATAAACTGTCAGTAGGTTGTGAGTGCACAACAAA
1 AAGTTTGTGGATAAACCACCAATGTTTGTAGATAAACTGCCAGTAGGTTGTGAATGCACAACGAA
*
21968190 TTTGTAGATAAAAGCTGCAAGT
66 TTTGAAGATAAAAGCTGCAAGT
* * *
21968212 AAATTCGCGGATAAACCACCAATGTT
1 AAGTTTGTGGATAAACCACCAATGTT
21968238 GGCAATTATT
Statistics
Matches: 173, Mismatches: 27, Indels: 0
0.87 0.14 0.00
Matches are distributed among these distances:
87 173 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (87 bp):
AAGTTTGTGGATAAACCACCAATGTTTGTAGATAAACTGCCAGTAGGTTGTGAATGCACAACGAA
TTTGAAGATAAAAGCTGCAAGT
Found at i:21968424 original size:38 final size:38
Alignment explanation
Indices: 21968327--21968452 Score: 164
Period size: 38 Copynumber: 3.3 Consensus size: 38
21968317 ACAATATTGA
**
21968327 AACAATAGACATGCTTAATGTGTATTCGGTTCAACAGT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAGT
* * * *
21968365 AA-AATAGACATGCTTATCATGTATTCAGCTCAACGGT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAGT
* *
21968402 AACAATAGCCATGTTTAACATGTATTCGGTTCAACAGT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAGT
*
21968440 AACAATAGGCATG
1 AACAATAGACATG
21968453 AAATCATTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
37 31 0.42
38 43 0.58
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (38 bp):
AACAATAGACATGCTTAACATGTATTCGGTTCAACAGT
Found at i:21970324 original size:29 final size:29
Alignment explanation
Indices: 21970278--21970339 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
21970268 TTTTTCATAA
*
21970278 AATCACATATATAGACATGAATTAAATTC
1 AATCACATATATACACATGAATTAAATTC
21970307 AATCACATATATACACATGAATTAAATTC
1 AATCACATATATACACATGAATTAAATTC
21970336 AATC
1 AATC
21970340 TATAATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (29 bp):
AATCACATATATACACATGAATTAAATTC
Found at i:21978305 original size:18 final size:18
Alignment explanation
Indices: 21978282--21978320 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
21978272 CGTTCTCTCC
21978282 TTTCTCCCCTTCTTTCTT
1 TTTCTCCCCTTCTTTCTT
* *
21978300 TTTCTCTCTTTCTTTCTT
1 TTTCTCCCCTTCTTTCTT
21978318 TTT
1 TTT
21978321 AATACTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTCTCCCCTTCTTTCTT
Found at i:21979442 original size:21 final size:23
Alignment explanation
Indices: 21979402--21979444 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
21979392 ATACGAGAAA
21979402 GAAAATACTTGATAGTAAAAGATG
1 GAAAATAC-TGATAGTAAAAGATG
21979426 GAAAATA-TGAT-GTAAAAGA
1 GAAAATACTGATAGTAAAAGA
21979445 GAGTAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
24 7 0.37
ACGTcount: A:0.53, C:0.02, G:0.21, T:0.23
Consensus pattern (23 bp):
GAAAATACTGATAGTAAAAGATG
Found at i:21980178 original size:24 final size:24
Alignment explanation
Indices: 21980151--21980206 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
21980141 AAGATATGCG
21980151 AAATATTAATAGGCAAAA-ATGTGC
1 AAATATTAATAGGCAAAATA-GTGC
* **
21980175 AAATTTTAATAGGCACCATAGTGC
1 AAATATTAATAGGCAAAATAGTGC
21980199 AAATATTA
1 AAATATTA
21980207 CGAATATCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (24 bp):
AAATATTAATAGGCAAAATAGTGC
Found at i:21981100 original size:27 final size:27
Alignment explanation
Indices: 21981061--21981122 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
21981051 AGAGGGTTTT
*
21981061 TGATTGGCGGCACCAAAGGTGCC-TAAC
1 TGATTGGCAGCACCAAAGGTGCCAT-AC
* * *
21981088 TGATTTGCAGCACCGATGGTGCCATAC
1 TGATTGGCAGCACCAAAGGTGCCATAC
21981115 TGATTGGC
1 TGATTGGC
21981123 GGGACTACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (27 bp):
TGATTGGCAGCACCAAAGGTGCCATAC
Found at i:21981510 original size:45 final size:44
Alignment explanation
Indices: 21981416--21981511 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 44
21981406 GTATTAAGAT
* *
21981416 GTTACTTAGTATTATTGTTAGTAAAAAACTAGTATTATTATTATA
1 GTTAGTTAGTATTATTGTTAGTAAAAAACTAG-ATTATAATTATA
* ** *
21981461 GTTAGTTAGTTATTATTTTTAGTAAAACCCTA-ATTAATAATTTTA
1 GTTAGTTAG-TATTATTGTTAGTAAAAAACTAGATT-ATAATTATA
21981506 GTTAGT
1 GTTAGT
21981512 ATTATTTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
44 3 0.07
45 21 0.49
46 19 0.44
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.48
Consensus pattern (44 bp):
GTTAGTTAGTATTATTGTTAGTAAAAAACTAGATTATAATTATA
Found at i:21984480 original size:11 final size:11
Alignment explanation
Indices: 21984464--21984490 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21984454 GCTTATGCTT
21984464 AAATTGTATCC
1 AAATTGTATCC
21984475 AAATTGTATCC
1 AAATTGTATCC
21984486 AAATT
1 AAATT
21984491 AAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:21987516 original size:44 final size:43
Alignment explanation
Indices: 21987468--21987626 Score: 215
Period size: 44 Copynumber: 3.8 Consensus size: 43
21987458 CTTCCCTCTT
*
21987468 CTTCTTCTTTCTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTCTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
21987512 CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTC-TCTTCTCCTTTCCTTTTCTTTC
21987556 CTTCTTTTTCTTTC---TTTC-C-TCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* *
21987594 CTT-TTCTTTCTTTCTTTCTT-TCTTCTTCTTTCC
1 CTTCTT-TTTCTTTCTTTTTTCTCTTCTCCTTTCC
21987627 CTCTCCTTCT
Statistics
Matches: 105, Mismatches: 3, Indels: 16
0.85 0.02 0.13
Matches are distributed among these distances:
37 2 0.02
38 30 0.29
39 1 0.01
41 7 0.07
42 9 0.09
43 14 0.13
44 42 0.40
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (43 bp):
CTTCTTTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:21987554 original size:10 final size:10
Alignment explanation
Indices: 21987433--21987626 Score: 93
Period size: 10 Copynumber: 19.2 Consensus size: 10
21987423 ATAAAAATTA
*
21987433 CCTTTTTTTT
1 CCTTTTCTTT
* *
21987443 TCTTTTTTTT
1 CCTTTTCTTT
*
21987453 CC-TTTCTTC
1 CCTTTTCTTT
*
21987462 CCTCTTC-TT
1 CCTTTTCTTT
*
21987471 CTTCTTTCTTT
1 CCT-TTTCTTT
21987482 --TTTT-TTT
1 CCTTTTCTTT
*
21987489 CTCTTCTCCTTT
1 C-CTT-TTCTTT
21987501 CCTTTTCTTT
1 CCTTTTCTTT
21987511 CCTTCTT-TTT
1 CCTT-TTCTTT
* *
21987521 CTTTCTTTTTT
1 CCTT-TTCTTT
*
21987532 CTTCTTCTCCTTT
1 C--CTT-TTCTTT
21987545 CCTTTTCTTT
1 CCTTTTCTTT
21987555 CCTTCTT-TTT
1 CCTT-TTCTTT
21987565 -C-TTTCTTT
1 CCTTTTCTTT
* *
21987573 CCTCTCCTTT
1 CCTTTTCTTT
21987583 CCTTTTCTTT
1 CCTTTTCTTT
21987593 CCTTTTCTTT
1 CCTTTTCTTT
*
21987603 CTTTCTTTCTTT
1 C-CT-TTTCTTT
21987615 -CTTCTTCTTT
1 CCTT-TTCTTT
21987625 CC
1 CC
21987627 CTCTCCTTCT
Statistics
Matches: 143, Mismatches: 21, Indels: 39
0.70 0.10 0.19
Matches are distributed among these distances:
7 5 0.03
8 7 0.05
9 14 0.10
10 79 0.55
11 19 0.13
12 11 0.08
13 8 0.06
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
CCTTTTCTTT
Found at i:21987579 original size:38 final size:38
Alignment explanation
Indices: 21987476--21987611 Score: 170
Period size: 38 Copynumber: 3.4 Consensus size: 38
21987466 TTCTTCTTCT
*
21987476 TTCTTTTT-TTT-TTCTCTTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTCTT-TCCTCTCCTTTCCTTTTCTTTCC
21987513 TTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTC---TTTC--C-TCTCCTTTCCTTTTCTTTCC
21987557 TTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCC
21987595 TT-TTCTTTCTTTCTTTC
1 TTCTT-TTTCTTTCTTTC
21987612 TTTCTTCTTC
Statistics
Matches: 89, Mismatches: 1, Indels: 17
0.83 0.01 0.16
Matches are distributed among these distances:
37 10 0.11
38 37 0.42
39 1 0.01
41 6 0.07
42 2 0.02
44 33 0.37
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (38 bp):
TTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCC
Found at i:21987717 original size:27 final size:27
Alignment explanation
Indices: 21987669--21987736 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
21987659 TTATAAGGTT
21987669 GGTGCCGCCAA-CTAGTATGGCACCATC
1 GGTGCCGCCAATC-AGTATGGCACCATC
* *
21987696 GGTGCCGCCAATCAGT-TAGGCACCTTT
1 GGTGCCGCCAATCAGTAT-GGCACCATC
21987723 GGTGCCGCCAATCA
1 GGTGCCGCCAATCA
21987737 AAAACCCTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.03
27 35 0.95
28 1 0.03
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCAATCAGTATGGCACCATC
Found at i:21993927 original size:27 final size:28
Alignment explanation
Indices: 21993897--21993955 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
21993887 TAAATATAGT
*
21993897 AATG-AAGAATTTATAGTATACGATTAA
1 AATGCAAGAATTTATAGTATACAATTAA
*
21993924 AATGCTAATAATTTATAGTATACAATTAA
1 AATGC-AAGAATTTATAGTATACAATTAA
21993953 AAT
1 AAT
21993956 ATTATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
29 24 0.86
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (28 bp):
AATGCAAGAATTTATAGTATACAATTAA
Found at i:21996054 original size:21 final size:20
Alignment explanation
Indices: 21996021--21996059 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21996011 CACTCGCACT
21996021 TTTATTGAAGAGCCACAGCA
1 TTTATTGAAGAGCCACAGCA
*
21996041 TTTATATGTAGAGCCACAG
1 TTTAT-TGAAGAGCCACAG
21996060 TATATGAATA
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:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (20 bp):
TTTATTGAAGAGCCACAGCA
Found at i:21999738 original size:72 final size:72
Alignment explanation
Indices: 21999615--21999853 Score: 374
Period size: 72 Copynumber: 3.3 Consensus size: 72
21999605 AAAATCATAT
**
21999615 ATAAACAACTATTGATAAAACTA-ATTTA-GTATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
*
21999678 GACCAAAC
65 AACCAAAC
*
21999686 ATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
21999751 ACCAAAC
66 ACCAAAC
* * * *
21999758 ATAATCAACCATTGATAAAACTAGATTACACATAAATAAGTATAACATAAATTCAATATCGAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
21999823 ACCAAAC
66 ACCAAAC
*
21999830 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTGATAAAACTAG
21999854 TTTAGCATTG
Statistics
Matches: 154, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
71 25 0.16
72 129 0.84
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:22006905 original size:48 final size:47
Alignment explanation
Indices: 22006850--22007013 Score: 112
Period size: 48 Copynumber: 3.6 Consensus size: 47
22006840 AAGGAGGAAG
22006850 TACTAGCAGTTTAATAATCTGCAAACATTGGTGGTTTATCCATAAACT
1 TACTAGCAGTTT-ATAATCTGCAAACATTGGTGGTTTATCCATAAACT
* * * * * * *
22006898 TACTAGCAATTT-TCATTTGCAAACACATT-GT-G--CATTCA-CAACC
1 TACTAGCAGTTTATAATCTGC-AA-ACATTGGTGGTTTATCCATAAACT
* * *
22006941 TACTGGCAGTTTATTAA-CTTGCAAACACTGGTGGTTTGTCCATAAACT
1 TACTAGCAGTTTA-TAATC-TGCAAACATTGGTGGTTTATCCATAAACT
*
22006989 TACTAGCAGCTTT-T-ATCAGCAAACA
1 TACTAGCAG-TTTATAATCTGCAAACA
22007014 CGTTGTGCAT
Statistics
Matches: 85, Mismatches: 19, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
43 17 0.20
44 8 0.09
45 6 0.07
46 15 0.18
47 9 0.11
48 27 0.32
49 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.34
Consensus pattern (47 bp):
TACTAGCAGTTTATAATCTGCAAACATTGGTGGTTTATCCATAAACT
Found at i:22007011 original size:91 final size:91
Alignment explanation
Indices: 22006850--22007079 Score: 275
Period size: 91 Copynumber: 2.5 Consensus size: 91
22006840 AAGGAGGAAG
* * *
22006850 TACTAGCAGTTTAATAA-TCTGCAAACATTGGTGGTTTATCCATAAACTTACTAGCAATTTTCAT
1 TACTGGCAGTTTATTAACT-TGCAAACACTGGTGGTTTATCCATAAACTTACTAGCAATTTTCAT
**
22006914 TTGCAAACACATTGTGCATTCACAACC
65 CAGCAAACACATTGTGCATTCACAACC
* *
22006941 TACTGGCAGTTTATTAACTTGCAAACACTGGTGGTTTGTCCATAAACTTACTAGCAGCTTTT-AT
1 TACTGGCAGTTTATTAACTTGCAAACACTGGTGGTTTATCCATAAACTTACTAGCA-ATTTTCAT
*
22007005 CAGCAAACACGTTGTGCATTCACAACC
65 CAGCAAACACATTGTGCATTCACAACC
* ** * * ** * *
22007032 TATTGGCAGCATATAAACCTGCAAACACTGAAGGTTCATCCACAAACT
1 TACTGGCAGTTTATTAACTTGCAAACACTGGTGGTTTATCCATAAACT
22007080 GGAGTGTCCG
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
91 114 0.96
92 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (91 bp):
TACTGGCAGTTTATTAACTTGCAAACACTGGTGGTTTATCCATAAACTTACTAGCAATTTTCATC
AGCAAACACATTGTGCATTCACAACC
Found at i:22010019 original size:95 final size:95
Alignment explanation
Indices: 22009856--22010043 Score: 304
Period size: 95 Copynumber: 2.0 Consensus size: 95
22009846 AACCGTTAAA
* * *
22009856 GAGTTTTCATATGTATTTCCCGATGAGTTATTGAGGTTATCTCTAGATCGTGAGAGAGAATTCAG
1 GAGTTTTCATATGTATTTCCCGATGAGTTACTGAGGTTACCTCCAGATCGTGAGAGAGAATTCAG
22009921 AATTGAATTGTTGCCAAGAATCGCTCCAGT
66 AATTGAATTGTTGCCAAGAATCGCTCCAGT
* * * *
22009951 GAGTTTTCATATGTGTTTCCCGATGAGTTACTGAGGTTACCTCCGGGTCGTGAGGGAGAATTCAG
1 GAGTTTTCATATGTATTTCCCGATGAGTTACTGAGGTTACCTCCAGATCGTGAGAGAGAATTCAG
*
22010016 AATTGAATTGTTGCCAGGAATCGCTCCA
66 AATTGAATTGTTGCCAAGAATCGCTCCA
22010044 ATGTCCATTG
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 85 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (95 bp):
GAGTTTTCATATGTATTTCCCGATGAGTTACTGAGGTTACCTCCAGATCGTGAGAGAGAATTCAG
AATTGAATTGTTGCCAAGAATCGCTCCAGT
Found at i:22012925 original size:20 final size:21
Alignment explanation
Indices: 22012884--22012926 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22012874 AATTCTCAAT
**
22012884 TTAAAATTTTTAATTCAATTA
1 TTAAAATTGATAATTCAATTA
22012905 TTAAAATTGATAATT-AATTA
1 TTAAAATTGATAATTCAATTA
22012925 TT
1 TT
22012927 GATGAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAAAATTGATAATTCAATTA
Found at i:22025516 original size:19 final size:19
Alignment explanation
Indices: 22025489--22025527 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
22025479 GCTGCTTTTT
22025489 TATTCTCTTTTTTTATTAC
1 TATTCTCTTTTTTTATTAC
* *
22025508 TATTTTCTTTTTTTTTTAC
1 TATTCTCTTTTTTTATTAC
22025527 T
1 T
22025528 CAAATGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTCTCTTTTTTTATTAC
Found at i:22025556 original size:24 final size:25
Alignment explanation
Indices: 22025509--22025556 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
22025499 TTTTATTACT
* * *
22025509 ATTTTCTTTTTTTTTTACTCAAATG
1 ATTTTCTTTTCTTTTTAATAAAATG
22025534 ATTTT-TTTTCTTTTTAATAAAAT
1 ATTTTCTTTTCTTTTTAATAAAAT
22025557 ATATATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTCTTTTCTTTTTAATAAAATG
Found at i:22026579 original size:31 final size:32
Alignment explanation
Indices: 22026544--22026612 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
22026534 ATTAGTTCCT
* *
22026544 AAATTTGAGATTTTTTT-TTAATTTGGTACTG
1 AAATTTGACATTTTTTTCTTAAGTTGGTACTG
* * *
22026575 AAATTTGACCTTTTTTTCTTAAGTTGGTAGTT
1 AAATTTGACATTTTTTTCTTAAGTTGGTACTG
22026607 AAATTT
1 AAATTT
22026613 ATTGGGATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (32 bp):
AAATTTGACATTTTTTTCTTAAGTTGGTACTG
Found at i:22028098 original size:19 final size:19
Alignment explanation
Indices: 22028068--22028120 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
22028058 GTCAAGTTTT
*
22028068 TCCAAAATAAATTTAAAAA
1 TCCAAAAAAAATTTAAAAA
** *
22028087 TTTAAAAAAAATTGAAAAA
1 TCCAAAAAAAATTTAAAAA
22028106 TCCAAAGAAAAATTT
1 TCCAAA-AAAAATTT
22028121 CAACTGAGCC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (19 bp):
TCCAAAAAAAATTTAAAAA
Found at i:22030498 original size:49 final size:49
Alignment explanation
Indices: 22030377--22030505 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 49
22030367 AGGTCCCCCA
* * *
22030377 TAAGACCATGTCTGAGACATGGCATGGGCACCGATATGAGAACTCCCATG
1 TAAGACCATGTCTGAGACATGGCATTGGCA-CGACAGGAGAACTCCCATG
* *
22030427 TAAGACCATATCTGAGATATGGCATTGGCA-GTACAGGA-AACATCCCATG
1 TAAGACCATGTCTGAGACATGGCATTGGCACG-ACAGGAGAAC-TCCCATG
* *
22030476 TAAGACCATGTCTGGGACATGGCTTTGGCA
1 TAAGACCATGTCTGAGACATGGCATTGGCA
22030506 TGTTATTATT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
48 4 0.06
49 37 0.54
50 27 0.40
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (49 bp):
TAAGACCATGTCTGAGACATGGCATTGGCACGACAGGAGAACTCCCATG
Found at i:22035100 original size:17 final size:17
Alignment explanation
Indices: 22035078--22035112 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22035068 GACTTGACAA
22035078 TGCAGTCAATTCATAAG
1 TGCAGTCAATTCATAAG
22035095 TGCAGTCAATTCATAAG
1 TGCAGTCAATTCATAAG
22035112 T
1 T
22035113 TGTATTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (17 bp):
TGCAGTCAATTCATAAG
Found at i:22037361 original size:24 final size:25
Alignment explanation
Indices: 22037334--22037380 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
22037324 TCTTTTGTGC
* *
22037334 AAGATTGCTTTCTTGT-GATTTTTA
1 AAGATAGCTTTCTTCTCGATTTTTA
*
22037358 AAGATAGTTTTCTTCTCGATTTT
1 AAGATAGCTTTCTTCTCGATTTT
22037381 CTTTAAGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.53
Consensus pattern (25 bp):
AAGATAGCTTTCTTCTCGATTTTTA
Found at i:22037933 original size:89 final size:89
Alignment explanation
Indices: 22037782--22037960 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
22037772 GAAAATTCAA
22037782 ATCCAACATTTCATGAGTATTTTTGTGAAATTCATGCTTATGAGTGTCAAGGTTGAGGGTCTAAT
1 ATCCAACATTTCATGAGTATTTTTGTGAAATTCATGCTTATGAGTGTCAAGGTTGAGGGTCTAAT
22037847 AATAGATTGACAAATGACATATAG
66 AATAGATTGACAAATGACATATAG
22037871 ATCCAACATTTCATGAGTATTTTTGTGAAATTCATGCTTATGAGTGTCAAGGTTGAGGGTCTAAT
1 ATCCAACATTTCATGAGTATTTTTGTGAAATTCATGCTTATGAGTGTCAAGGTTGAGGGTCTAAT
*
22037936 AATAGATTGACAGATGACATATAG
66 AATAGATTGACAAATGACATATAG
22037960 A
1 A
22037961 ATTATTACAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.35
Consensus pattern (89 bp):
ATCCAACATTTCATGAGTATTTTTGTGAAATTCATGCTTATGAGTGTCAAGGTTGAGGGTCTAAT
AATAGATTGACAAATGACATATAG
Found at i:22038303 original size:39 final size:39
Alignment explanation
Indices: 22038247--22038342 Score: 122
Period size: 39 Copynumber: 2.4 Consensus size: 39
22038237 TAGAATCAAA
* *
22038247 ATAGTAAAACTACTCCTATTCACCCTTTACTTCCTATAAT
1 ATAG-AAAAATACTCCTATTCACCCTCTACTTCCTATAAT
* *
22038287 ATA-AAAAATGACTCCTATTCATCCTCTACTTTCTATAAT
1 ATAGAAAAAT-ACTCCTATTCACCCTCTACTTCCTATAAT
*
22038326 ATAGAAAACTACTCCTA
1 ATAGAAAAATACTCCTA
22038343 AAATAAGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 5 0.10
39 36 0.73
40 8 0.16
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (39 bp):
ATAGAAAAATACTCCTATTCACCCTCTACTTCCTATAAT
Found at i:22041805 original size:30 final size:24
Alignment explanation
Indices: 22041743--22041793 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
22041733 CCTGTCAGAC
22041743 CATCAACCCTCATTGCAGTAGTAG
1 CATCAACCCTCATTGCAGTAGTAG
22041767 CATCAACCCTCATTGCAGTAGTAG
1 CATCAACCCTCATTGCAGTAGTAG
22041791 CAT
1 CAT
22041794 TCGCACGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (24 bp):
CATCAACCCTCATTGCAGTAGTAG
Found at i:22043633 original size:34 final size:34
Alignment explanation
Indices: 22043584--22043648 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
22043574 TCCTTCTAAC
*
22043584 ATACATATAATGTATTCAACAATTGATAATAGTT
1 ATACATATAACGTATTCAACAATTGATAATAGTT
* *
22043618 ATACGTATAACGTATTCAACAATTGGTAATA
1 ATACATATAACGTATTCAACAATTGATAATA
22043649 ACTATACAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (34 bp):
ATACATATAACGTATTCAACAATTGATAATAGTT
Found at i:22043655 original size:34 final size:34
Alignment explanation
Indices: 22043580--22043656 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
22043570 AACTTCCTTC
*
22043580 TAAC-ATACATATAATGTATTCAACAATTGATAA
1 TAACTATACATATAACGTATTCAACAATTGATAA
** * *
22043613 TAGTTATACGTATAACGTATTCAACAATTGGTAA
1 TAACTATACATATAACGTATTCAACAATTGATAA
22043647 TAACTATACA
1 TAACTATACA
22043657 GGCATAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (34 bp):
TAACTATACATATAACGTATTCAACAATTGATAA
Found at i:22044198 original size:60 final size:57
Alignment explanation
Indices: 22044117--22044283 Score: 210
Period size: 60 Copynumber: 2.9 Consensus size: 57
22044107 AAGGCTTAAC
* *
22044117 TTTTTTTTAGTCCAAGTTAGTCCTTGAACTTGACAATTATTCTCACATTGAGCTTGGACTT
1 TTTTTTTTA-TCCAAGTTAGTCATTGAACTTGACAATTATTCTCACATTGAGCTT-GA--A
*
22044178 TTTTTTTTATCCAAGTTAGTCTTTGAACTT-AGCAATTATTCTCACATTGAGCTTGAA
1 TTTTTTTTATCCAAGTTAGTCATTGAACTTGA-CAATTATTCTCACATTGAGCTTGAA
* * * * *
22044235 ATTTTTTTATCAAAGTTAGTCATTGAACTGGACAATTGTTTTCACATTG
1 TTTTTTTTATCCAAGTTAGTCATTGAACTTGACAATTATTCTCACATTG
22044284 GAGGCATAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
57 41 0.43
58 1 0.01
59 3 0.03
60 42 0.44
61 9 0.09
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (57 bp):
TTTTTTTTATCCAAGTTAGTCATTGAACTTGACAATTATTCTCACATTGAGCTTGAA
Found at i:22044271 original size:57 final size:58
Alignment explanation
Indices: 22044118--22044283 Score: 201
Period size: 57 Copynumber: 2.8 Consensus size: 58
22044108 AGGCTTAACT
* **
22044118 TTTTTTTAGTCCAAGTTAGTCCTTGAACTTGACAATTATTCTCACATTGAGCTTGGACTTT
1 TTTTTTTA-TCCAAGTTAGTCATTGAAC-TGACAATTATTCTCACATTGAGCTTGGAC-AA
* *
22044179 TTTTTTTATCCAAGTTAGTCTTTGAACTTAGCAATTATTCTCACATTGAGCTT-GA-AA
1 TTTTTTTATCCAAGTTAGTCATTGAACTGA-CAATTATTCTCACATTGAGCTTGGACAA
* * *
22044236 TTTTTTTATCAAAGTTAGTCATTGAACTGGACAATTGTTTTCACATTG
1 TTTTTTTATCCAAGTTAGTCATTGAACT-GACAATTATTCTCACATTG
22044284 GAGGCATAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
57 41 0.44
58 1 0.01
59 4 0.04
60 40 0.43
61 8 0.09
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (58 bp):
TTTTTTTATCCAAGTTAGTCATTGAACTGACAATTATTCTCACATTGAGCTTGGACAA
Found at i:22044517 original size:264 final size:265
Alignment explanation
Indices: 22044032--22044519 Score: 662
Period size: 264 Copynumber: 1.8 Consensus size: 265
22044022 ATATAAGAAA
* *
22044032 TATTTCTTTACAACATTATAATAAAAAGGGTTAATGCAATATTTTGGGCCTAAACTTGACAAGTG
1 TATTTCTTTACAACATTATAATAAAAAGGGTTAATGCAATAGTTGGGGCCTAAACTTGACAAGTG
* *
22044097 TTCCCATATTAAGGCTTAACTTTTTTTTAGTCCAAGTTAGTCCTTGAACTTGACAATTATTCTCA
66 TTCCCATATTAAGGCTTAACTTTTTTTTAGTCCAAGTTAGTACTTAAACTTGACAATTATTCTCA
** * ** * *
22044162 CATTGAGCTTGGACTTTTTTTTTTATCCAAGTTAGTCTTTGAACTTAGCAATTATTCTCACATTG
131 CATTGAGCTTAAAC-TTTTTTTTGATCCAAGTTAACCCTTGAACTTAGAAATTATTCTCACATTG
22044227 AGCTTGAAATTTTTTTATCAAAGTTAGTCATTGAACTGGACAATTGTTTTCACATTGGAGGCATA
195 AGCTTGAAATTTTTTTATCAAAGTTAGTCATTGAACTGGACAATTGTTTTCACATTGGAGGCATA
22044292 AATTAT
260 AATTAT
* * * *
22044298 TATTT-TTTACAACATTATAATAAAAAGGGTTAATGCATTGGTTGGGGTCTAAACTTG-TAAGTG
1 TATTTCTTTACAACATTATAATAAAAAGGGTTAATGCAATAGTTGGGGCCTAAACTTGACAAGTG
* * * * * *
22044361 TTCCTATATTAAGGTTTACCTTTTTTTTAGTCCAAGTTTGTATTTAAACTTTG-TAATTATTCTC
66 TTCCCATATTAAGGCTTAACTTTTTTTTAGTCCAAGTTAGTACTTAAAC-TTGACAATTATTCTC
*
22044425 ACATTGAGGC-TAAAC-TTTTTTTGGTCCAAGTTAACCCTTGAACTTAGAAATTATTCTCACATT
130 ACATTGA-GCTTAAACTTTTTTTTGATCCAAGTTAACCCTTGAACTTAGAAATTATTCTCACATT
* * * *
22044488 GTGACTTGAACCTTTTTTTTTCCAAGTTAGTC
194 GAG-CTTGAA-ATTTTTTTATCAAAGTTAGTC
22044520 CACGATATTT
Statistics
Matches: 192, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
262 44 0.23
263 6 0.03
264 85 0.44
265 52 0.27
266 5 0.03
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (265 bp):
TATTTCTTTACAACATTATAATAAAAAGGGTTAATGCAATAGTTGGGGCCTAAACTTGACAAGTG
TTCCCATATTAAGGCTTAACTTTTTTTTAGTCCAAGTTAGTACTTAAACTTGACAATTATTCTCA
CATTGAGCTTAAACTTTTTTTTGATCCAAGTTAACCCTTGAACTTAGAAATTATTCTCACATTGA
GCTTGAAATTTTTTTATCAAAGTTAGTCATTGAACTGGACAATTGTTTTCACATTGGAGGCATAA
ATTAT
Found at i:22046686 original size:27 final size:27
Alignment explanation
Indices: 22046642--22046883 Score: 287
Period size: 27 Copynumber: 9.0 Consensus size: 27
22046632 CCACGTTAGG
*
22046642 TCGAAATACCCCCATAGGGTAAAATGA
1 TCGAAATACCCCTATAGGGTAAAATGA
* *
22046669 TCAAAATACCCCTGTAGGGTAAAATGA
1 TCGAAATACCCCTATAGGGTAAAATGA
* *
22046696 -CTGAAATATCCCC-GTAGGATAAAATGA
1 TC-GAAATA-CCCCTATAGGGTAAAATGA
22046723 TCGAAATACCCCTATAGGGTAAAATGA
1 TCGAAATACCCCTATAGGGTAAAATGA
* * *
22046750 TCGACATACCCCTGTAGAGTAAAATGA
1 TCGAAATACCCCTATAGGGTAAAATGA
22046777 -CTGAAATA-CCCTATAGGGTAAAATGA
1 TC-GAAATACCCCTATAGGGTAAAATGA
* * *
22046803 CCGAAATACCTCTATAGAGTAAAATGA
1 TCGAAATACCCCTATAGGGTAAAATGA
* *
22046830 TCAAAATACCCCTGTAGGGTAAAATGA
1 TCGAAATACCCCTATAGGGTAAAATGA
*
22046857 TCGAAATA-CCCTCATAAGGTAAAATGA
1 TCGAAATACCCCT-ATAGGGTAAAATGA
22046884 CTGTTATACC
Statistics
Matches: 184, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
26 32 0.17
27 147 0.80
28 5 0.03
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (27 bp):
TCGAAATACCCCTATAGGGTAAAATGA
Found at i:22046879 original size:107 final size:107
Alignment explanation
Indices: 22046642--22046897 Score: 306
Period size: 107 Copynumber: 2.4 Consensus size: 107
22046632 CCACGTTAGG
* * * *
22046642 TCGAAATACCCCCATAGGGTAAAATGA-TCAAAATACCCCTGTAGGGTAAAATGACTGAAATATC
1 TCGAAATA-CCCCATAAGGTAAAATGACT-GAAATACCCCTATAGGGTAAAATGACCGAAATATC
* *
22046706 CCCGTAGGATAAAATGATCGAAATACCCCTATAGGGTAAAATGA
64 CCCATAGGATAAAATGATCAAAATACCCCTATAGGGTAAAATGA
* *
22046750 TCGACATACCCC-TGTAGAGTAAAATGACTGAAATA-CCCTATAGGGTAAAATGACCGAAATA-C
1 TCGAAATACCCCAT-AAG-GTAAAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAATATC
* *
22046812 CTCTATA-GAGTAAAATGATCAAAATACCCCTGTAGGGTAAAATGA
64 C-CCATAGGA-TAAAATGATCAAAATACCCCTATAGGGTAAAATGA
**
22046857 TCGAAATACCCTCATAAGGTAAAATGACTGTTATACCCCTA
1 TCGAAATACCC-CATAAGGTAAAATGACTGAAATACCCCTA
22046898 GGAGACGGAA
Statistics
Matches: 126, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
106 5 0.04
107 90 0.71
108 29 0.23
109 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (107 bp):
TCGAAATACCCCATAAGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAATATCCC
CATAGGATAAAATGATCAAAATACCCCTATAGGGTAAAATGA
Found at i:22060899 original size:15 final size:15
Alignment explanation
Indices: 22060881--22060913 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
22060871 CAAATGCCAA
22060881 AATAATAAATACAAC
1 AATAATAAATACAAC
*
22060896 AATAATAAATACATC
1 AATAATAAATACAAC
22060911 AAT
1 AAT
22060914 GGCATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:22061333 original size:29 final size:31
Alignment explanation
Indices: 22061288--22061346 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
22061278 GTCTAAATAC
*
22061288 AAAAATATTTATTAAAAAAATAAA-ATATAG
1 AAAAATATTCATTAAAAAAATAAATATATAG
22061318 AAAAATATTCA-TAAAAAAATAAATATATA
1 AAAAATATTCATTAAAAAAATAAATATATA
22061347 TACATATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (31 bp):
AAAAATATTCATTAAAAAAATAAATATATAG
Found at i:22061377 original size:27 final size:28
Alignment explanation
Indices: 22061328--22061392 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 28
22061318 AAAAATATTC
*
22061328 ATAAAAAAATAAATATATATACATATGTAG
1 ATAAAATAATAAATATATATACATA--TAG
*
22061358 ATAAAATAAT-AATA-AT-TACATATAT
1 ATAAAATAATAAATATATATACATATAG
22061383 ATAAAATAAT
1 ATAAAATAAT
22061393 TACATTATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 12 0.36
27 6 0.18
28 2 0.06
29 4 0.12
30 9 0.27
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
ATAAAATAATAAATATATATACATATAG
Found at i:22061590 original size:6 final size:6
Alignment explanation
Indices: 22061581--22061606 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22061571 GCGACAGACC
22061581 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
22061607 TGTGCAGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:22063004 original size:44 final size:44
Alignment explanation
Indices: 22062956--22063071 Score: 121
Period size: 44 Copynumber: 2.6 Consensus size: 44
22062946 CTAATCCACT
* * *
22062956 CCACTACAACTTTAGGGAGATAGGA-TTTGTTCATTCAGTCTGCC
1 CCACTACAACTTTAGGGAGATAAGACTTTCTT-ATTCAGTCTACC
** *
22063000 CCACTGTAA-TTTCAGGG-GAATAAGACTTTCTTATTCAGTCTACT
1 CCACTACAACTTT-AGGGAG-ATAAGACTTTCTTATTCAGTCTACC
*
22063044 CCACTACAACTTCAGGGAGATAAGACTT
1 CCACTACAACTTTAGGGAGATAAGACTT
22063072 ACGCGATCTG
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
43 4 0.07
44 46 0.79
45 8 0.14
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
CCACTACAACTTTAGGGAGATAAGACTTTCTTATTCAGTCTACC
Found at i:22063856 original size:44 final size:44
Alignment explanation
Indices: 22063627--22063957 Score: 159
Period size: 44 Copynumber: 7.5 Consensus size: 44
22063617 ACTGTCGGTG
* * *
22063627 CAGGAAGGCAAGATCTGCTATTTTTAACCTGTTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGGTATCTTTAACCTGCTCCGCTGCAACC
* * * * * * * * ****
22063671 TAGGGAGGCAAG-GCTGGTGTCTTTGATCTGCTTCACTGTCGGTA
1 CAGGAAGGCAAGATCTGGTATCTTTAACCTGCTCCGCTG-CAACC
* * *
22063715 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAACC
1 CAGGAAGGCAAGATCTGGTATCTTTAACCTGCTCCGCTGCAACC
* * * ** * * * *****
22063759 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCACTGTTGGTG
1 CAGGAAGGCAAGATCTGGTATCTTTAACCTGCTCCGCTG-CAACC
* *
22063803 CAGAAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGGTATCTTTAACCTGCTCCGCTGCAACC
* * * * * * ******
22063847 CAGGGAGGCAAGGT-TGGTGTCTTTGATCTGCTTCGCTTTTGGTT
1 CAGGAAGGCAAGATCTGGTATCTTTAACCTGCTCCGC-TGCAACC
* *
22063891 TAGGAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGGTATCTTTAACCTGCTCCGCTGCAACC
*
22063935 CAGTG-AGGCAAGA-CTGGTGTCTT
1 CAG-GAAGGCAAGATCTGGTATCTT
22063958 CGATCTACTT
Statistics
Matches: 190, Mismatches: 90, Indels: 15
0.64 0.31 0.05
Matches are distributed among these distances:
43 59 0.31
44 77 0.41
45 54 0.28
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGGTATCTTTAACCTGCTCCGCTGCAACC
Found at i:22064000 original size:88 final size:88
Alignment explanation
Indices: 22063605--22064002 Score: 571
Period size: 88 Copynumber: 4.5 Consensus size: 88
22063595 GTTGGGGTCA
* * * *
22063605 TCGATCTACTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGTTCCGCTGCAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAAC
*
22063670 CTAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * *
22063693 TTGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAAC
22063758 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
22063781 TCGATCTGCTTCACTGTTGGTGCAGAAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAAC
*
22063846 CCAGGGAGGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * **
22063869 TTGATCTGCTTCGCTTTTGGTTTAGGAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAAC
* *
22063934 CCAGTGAGGCAAGACTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
22063957 TCGATCTACTTCGCTGCCGGTGCAGGAAGGCAAGATCTATTATCTT
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGTTATCTT
22064003 CACTGATCTG
Statistics
Matches: 279, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 279 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (88 bp):
TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:22068661 original size:20 final size:20
Alignment explanation
Indices: 22068609--22068662 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
22068599 CTAACTCCTT
*
22068609 TTATTTTATTATAAGATATTA
1 TTATTTTATT-TTAGATATTA
22068630 TT-TTATGT-TTTTAGATATTA
1 TTATT-T-TATTTTAGATATTA
22068650 TTATTTTATTTTA
1 TTATTTTATTTTA
22068663 TTATACATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
19 1 0.04
20 19 0.68
21 7 0.25
22 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (20 bp):
TTATTTTATTTTAGATATTA
Found at i:22078577 original size:59 final size:57
Alignment explanation
Indices: 22078511--22078699 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
22078501 ATTTTATTAA
22078511 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
22078570 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
22078631 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
22078690 ATCATATATT
1 ATCATATATT
22078700 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:22078608 original size:66 final size:64
Alignment explanation
Indices: 22078538--22078736 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
22078528 AAATATATTT
22078538 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
22078603 G
64 G
* * * * * **
22078604 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
22078658 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
22078723 G
64 G
*
22078724 AATATTGATTATT
1 AATATTAATTATT
22078737 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:22078640 original size:61 final size:61
Alignment explanation
Indices: 22078573--22078760 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
22078563 TTATAGTATC
22078573 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
22078634 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
22078692 C
61 T
*
22078693 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
22078754 ATATATT
1 ATATATT
22078761 TTAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Done.