Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015259.1 Kokia drynarioides strain JFW-HI SEQ_130304, 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: 297397
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 540 characters in sequence are not A, C, G, or T
Found at i:840 original size:6 final size:6
Alignment explanation
Indices: 798--922 Score: 96
Period size: 6 Copynumber: 21.2 Consensus size: 6
788 AATGGCTTTG
* * * * *
798 AATTTA ATTTTA AAGTTTA AGTTTTA AAATT- ATTTTA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA A-ATTTA AATTTA AATTTA AATTTA AATTTA
* ** ** *
846 AATTGA AATTTA AA-AGA AATTTA AATTTA AAAATG AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
893 AATTTA AA-GTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA AATTTA A
923 TAAATCTAAA
Statistics
Matches: 89, Mismatches: 24, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
5 14 0.16
6 65 0.73
7 10 0.11
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:842 original size:17 final size:17
Alignment explanation
Indices: 820--922 Score: 91
Period size: 17 Copynumber: 5.9 Consensus size: 17
810 AAGTTTAAGT
* *
820 TTTAAAATTATTTTAAA
1 TTTAAAATAAATTTAAA
* *
837 TTTAAACTAAATTGAAA
1 TTTAAAATAAATTTAAA
*
854 TTTAAAAGAAATTTAAA
1 TTTAAAATAAATTTAAA
*
871 TTTAAAAATGAATTTAAA
1 TTT-AAAATAAATTTAAA
* *
889 TTTAAATTTAAA-GTAAA
1 TTTAAA-ATAAATTTAAA
*
906 TTTAAATTTAAATTTAA
1 TTTAAA-ATAAATTTAA
923 TAAATCTAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
17 49 0.70
18 21 0.30
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:870 original size:23 final size:23
Alignment explanation
Indices: 844--922 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
834 AAATTTAAAC
*
844 TAAATTGAAATTTAAAAGAAATT
1 TAAATTTAAATTTAAAAGAAATT
*
867 TAAATTT-AA---AAATG-AATT
1 TAAATTTAAATTTAAAAGAAATT
885 TAAATTTAAATTT-AAAGTAAATT
1 TAAATTTAAATTTAAAAG-AAATT
908 TAAATTTAAATTTAA
1 TAAATTTAAATTTAA
923 TAAATCTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
18 11 0.24
19 6 0.13
21 3 0.07
22 2 0.04
23 23 0.50
24 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAAAAGAAATT
Found at i:920 original size:35 final size:35
Alignment explanation
Indices: 798--922 Score: 92
Period size: 41 Copynumber: 3.4 Consensus size: 35
788 AATGGCTTTG
* * * * *
798 AATTTAATTTTAAAGTTTAAGTTTTAAAATTATTTTA
1 AATTTAAATTTAAA-TTTAA-ATTTAAAGTAAATTTA
* *
835 AATTTAAA-CTAAATTGAAATTTAAAAG-AAATTTA
1 AATTTAAATTTAAATTTAAATTT-AAAGTAAATTTA
869 AATTTAAAAATGAATTTAAATTTAAATTTAAAGTAAATTTA
1 AATTT----A--AATTTAAATTTAAATTTAAAGTAAATTTA
910 AATTTAAATTTAA
1 AATTTAAATTTAA
923 TAAATCTAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
34 13 0.19
35 14 0.20
36 4 0.06
37 8 0.11
38 1 0.01
40 6 0.09
41 24 0.34
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (35 bp):
AATTTAAATTTAAATTTAAATTTAAAGTAAATTTA
Found at i:1080 original size:21 final size:22
Alignment explanation
Indices: 1040--1080 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1030 AAATACCTTC
* *
1040 AAAATAAATATTATTAATTTAT
1 AAAAAAAATATTAGTAATTTAT
1062 AAAAAAAAT-TTAGTAATTT
1 AAAAAAAATATTAGTAATTT
1081 TCTAGTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAAAAAATATTAGTAATTTAT
Found at i:1539 original size:6 final size:6
Alignment explanation
Indices: 1520--1600 Score: 60
Period size: 6 Copynumber: 13.5 Consensus size: 6
1510 TAAATTGGTA
** **
1520 TAAATT TATTTT TAAATT TAAATT T--ATCT TAAATT TAAATT TATCTTTT
1 TAAATT TAAATT TAAATT TAAATT TAAAT-T TAAATT TAAATT TA--AATT
**
1569 TAAATT TAAATT T-GCTT TAAATT TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA
1601 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
4 2 0.04
5 5 0.09
6 44 0.77
7 2 0.04
8 4 0.07
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.56
Consensus pattern (6 bp):
TAAATT
Found at i:1553 original size:17 final size:18
Alignment explanation
Indices: 1520--1599 Score: 110
Period size: 17 Copynumber: 4.4 Consensus size: 18
1510 TAAATTGGTA
*
1520 TAAATTTATTTTTAAATT
1 TAAATTTATCTTTAAATT
1538 TAAATTTATC-TTAAATT
1 TAAATTTATCTTTAAATT
1555 TAAATTTATCTTTTTAAATT
1 TAAATTTATC--TTTAAATT
*
1575 TAAATTT-GCTTTAAATT
1 TAAATTTATCTTTAAATT
1592 TAAATTTA
1 TAAATTTA
1600 ATCAAATTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
17 32 0.57
18 9 0.16
19 1 0.02
20 14 0.25
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (18 bp):
TAAATTTATCTTTAAATT
Found at i:1576 original size:37 final size:35
Alignment explanation
Indices: 1520--1599 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 35
1510 TAAATTGGTA
*
1520 TAAATTTATTTTTAAATTTAAATTT-ATCTTAAATT
1 TAAATTTATTTTTAAATTTAAATTTGCT-TTAAATT
1555 TAAATTTATCTTTTTAAATTTAAATTTGCTTTAAATT
1 TAAATTTA--TTTTTAAATTTAAATTTGCTTTAAATT
1592 TAAATTTA
1 TAAATTTA
1600 ATCAAATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 8 0.20
37 32 0.78
38 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (35 bp):
TAAATTTATTTTTAAATTTAAATTTGCTTTAAATT
Found at i:1896 original size:25 final size:25
Alignment explanation
Indices: 1862--1930 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
1852 TCCTCCTTCA
1862 GCTCCAACTTGCACTGCCACTAGTT
1 GCTCCAACTTGCACTGCCACTAGTT
1887 GCTCCAACTTGCACTGCCACTAGTT
1 GCTCCAACTTGCACTGCCACTAGTT
1912 GCTCCAAC-TGCTACTGCCA
1 GCTCCAACTTGC-ACTGCCA
1931 TAGCCGAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
24 3 0.07
25 40 0.93
ACGTcount: A:0.20, C:0.38, G:0.16, T:0.26
Consensus pattern (25 bp):
GCTCCAACTTGCACTGCCACTAGTT
Found at i:11988 original size:19 final size:19
Alignment explanation
Indices: 11964--12004 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
11954 AGAAAATTAC
* * *
11964 TAAAATATATTTTCTTATT
1 TAAAATAAATTATATTATT
11983 TAAAATAAATTATATTATT
1 TAAAATAAATTATATTATT
12002 TAA
1 TAA
12005 GGATACTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAATAAATTATATTATT
Found at i:15166 original size:22 final size:20
Alignment explanation
Indices: 15117--15190 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 20
15107 ATTTTATAAT
* *
15117 ATATTTTAAATAATAAAT-A
1 ATATTTTATATAATAATTAA
** *
15136 ATAGCTTATATCATAATTTAA
1 ATATTTTATATAATAA-TTAA
*
15157 ATTATTTTATGTAATAATTAA
1 A-TATTTTATATAATAATTAA
15178 ATATTTTATATAA
1 ATATTTTATATAA
15191 AATATTTTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
19 12 0.29
20 12 0.29
21 7 0.17
22 11 0.26
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
ATATTTTATATAATAATTAA
Found at i:15194 original size:22 final size:22
Alignment explanation
Indices: 15141--15190 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
15131 AAATAATAGC
*
15141 TTATATCATAATTTAAATTATT
1 TTATATAATAATTTAAATTATT
*
15163 TTATGTAATAA-TTAAA-TATT
1 TTATATAATAATTTAAATTATT
15183 TTATATAA
1 TTATATAA
15191 AATATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.44
21 5 0.20
22 9 0.36
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TTATATAATAATTTAAATTATT
Found at i:22718 original size:16 final size:16
Alignment explanation
Indices: 22697--22744 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
22687 TAGATTTTTA
*
22697 TTTAATTTTTATATTT
1 TTTAATTTTTAAATTT
22713 TTTAATTTTTAAATTT
1 TTTAATTTTTAAATTT
*
22729 GTATTATTTTTTAAAT
1 -T-TTAATTTTTAAAT
22745 CATTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 15 0.54
17 1 0.04
18 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTAATTTTTAAATTT
Found at i:28545 original size:19 final size:18
Alignment explanation
Indices: 28519--28554 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28509 TTATTTTTGG
28519 TTTTATTTTTTTAAAATC
1 TTTTATTTTTTTAAAATC
*
28537 TTTTCATTTTTTTTAAAT
1 TTTT-ATTTTTTTAAAAT
28555 TTGCTTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATTTTTTTAAAATC
Found at i:29758 original size:78 final size:74
Alignment explanation
Indices: 29670--29816 Score: 170
Period size: 75 Copynumber: 1.9 Consensus size: 74
29660 ATGAAGATGA
** *
29670 CCACTTCATTG-TTTGACCGACCTACTTCTCTATATCTCATTAGGAAGATAAGGTTTCGAAGTTT
1 CCACTTCATTGATTT-A--GACC-ACTTCTCTATATCTCACCAGGAAAATAAGGTTT-GAAGTTT
*
29734 TACTCACATGAGCT
61 CACTCACATGAGCT
* * **
29748 CCACTTCATTGATTTAGTCCACTTCTCTGTATCTCACCAGGAAAATGGGGTTTGAAGTTTCACTC
1 CCACTTCATTGATTTAGACCACTTCTCTATATCTCACCAGGAAAATAAGGTTTGAAGTTTCACTC
29813 ACAT
66 ACAT
29817 TTGAGCTTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
74 15 0.25
75 27 0.45
76 3 0.05
78 12 0.20
79 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (74 bp):
CCACTTCATTGATTTAGACCACTTCTCTATATCTCACCAGGAAAATAAGGTTTGAAGTTTCACTC
ACATGAGCT
Found at i:29781 original size:75 final size:75
Alignment explanation
Indices: 29693--29869 Score: 196
Period size: 76 Copynumber: 2.3 Consensus size: 75
29683 TGACCGACCT
* ** * *
29693 ACTTCTCTATATCTCATTAGGAAGATAAGGTTTCGAAGTTTTACTCACA-TGAGCTCCACTTCAT
1 ACTTCTCTGTATCTCACCAGGAAGATAAGGTTT-GAAGTTTCACTCACATTGAGCTCCACCTCAT
*
29757 TGA-TTTAGTCC
65 T-ATTTTAGTAC
* ** *
29768 ACTTCTCTGTATCTCACCAGGAAAATGGGGTTTGAAGTTTCACTCACATTTGAGCTTCACCTCAT
1 ACTTCTCTGTATCTCACCAGGAAGATAAGGTTTGAAGTTTCACTCACA-TTGAGCTCCACCTCAT
*
29833 TATTTTGGTAC
65 TATTTTAGTAC
* *
29844 AGTTCTCGGTATCTCACCAGGAAGAT
1 ACTTCTCTGTATCTCACCAGGAAGAT
29870 GACTACTTCA
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
74 14 0.16
75 28 0.33
76 43 0.51
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (75 bp):
ACTTCTCTGTATCTCACCAGGAAGATAAGGTTTGAAGTTTCACTCACATTGAGCTCCACCTCATT
ATTTTAGTAC
Found at i:29783 original size:126 final size:122
Alignment explanation
Indices: 29519--29786 Score: 290
Period size: 126 Copynumber: 2.2 Consensus size: 122
29509 ATTTCGATAT
*** ** *
29519 ACTTCTCTGTATCTCACCAAGAAGATGATTGCTTTGTTGTTTCACCCACTTCTCTATATCTTACC
1 ACTTCTCTGTATCTCACCAAGAAGATGACCACTTCATTGTTTCACCCACTTCTCTATATCTCACC
* * * *
29584 AGGAAGATGGAGTTTGAAGTTTCACTCACATTTGAGTTTCACCTCATTATTTTGGTAC
66 AGGAAGATAGAGTTTGAAGTTTCACTCACA-TTGAGCTCCACCTCATTATTTTAGTAC
* *
29642 ACTTCTCTGTATCTCACCATGAAGATGACCACTTCATTGTTTGACCGACCTACTTCTCTATATCT
1 ACTTCTCTGTATCTCACCAAGAAGATGACCACTTCATTGTTT---C-ACCCACTTCTCTATATCT
** * * *
29707 CATTAGGAAGATA-AGGTTTCGAAGTTTTACTCACA-TGAGCTCCACTTCATTGA-TTTAGTCC
62 CACCAGGAAGATAGA-GTTT-GAAGTTTCACTCACATTGAGCTCCACCTCATT-ATTTTAGTAC
29768 ACTTCTCTGTATCTCACCA
1 ACTTCTCTGTATCTCACCA
29787 GGAAAATGGG
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
123 36 0.30
126 40 0.33
127 31 0.26
128 14 0.12
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (122 bp):
ACTTCTCTGTATCTCACCAAGAAGATGACCACTTCATTGTTTCACCCACTTCTCTATATCTCACC
AGGAAGATAGAGTTTGAAGTTTCACTCACATTGAGCTCCACCTCATTATTTTAGTAC
Found at i:29907 original size:123 final size:123
Alignment explanation
Indices: 29769--30427 Score: 946
Period size: 123 Copynumber: 5.4 Consensus size: 123
29759 ATTTAGTCCA
* *
29769 CTTCTCTGTATCTCACCAGGAAAATGGGGTTTGAAGTTTCACTCACATTTGAGCTTCACCTCATT
1 CTTCTCTGTACCTCACCAGGAAAATGGGGTCTGAAGTTTCACTCACATTTGAGCTTCACCTCATT
* * * *
29834 ATTTTGGTACAGTTCTCGGTATCTCACCAGGAAGATGACTACTTCATTATTTGACCTT
66 ATTTTGGTACACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCTT
* * *
29892 CTTCTCTGTACCTCACCA-AAAAGATGGGGTTTGAAGTTTTACTCACATTTGAGCTTCACCTCAT
1 CTTCTCTGTACCTCACCAGGAAA-ATGGGGTCTGAAGTTTCACTCACATTTGAGCTTCACCTCAT
29956 TATTTTGGTACACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCTT
65 TATTTTGGTACACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCTT
* * * * *
30015 TTTCTCTGCACCTCACCAGGAAGATGGGGTCTGAAGTTTCACTCACATTTAAGCTTCTCCTCATT
1 CTTCTCTGTACCTCACCAGGAAAATGGGGTCTGAAGTTTCACTCACATTTGAGCTTCACCTCATT
* *
30080 ATTTTGGTACACTTCTTTGTATCTCACTAGGAAGATGACCACTTCATTGTTTGACCTT
66 ATTTTGGTACACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCTT
* * * *
30138 TTTCTCTATACCTCACCAGGAAGATGGGGTTTGAAGTTTCACTCACATTTGAGCTTCACCTCATT
1 CTTCTCTGTACCTCACCAGGAAAATGGGGTCTGAAGTTTCACTCACATTTGAGCTTCACCTCATT
* *
30203 ATTTTGATACACTTCTCTGTATCTCACCAGGAAGATGACCACTTTATTGTTTGACCTT
66 ATTTTGGTACACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCTT
* * * *
30261 CTTCTCTGTACTTCACTA-GAAAGATGAGGTCTGAAGTTTCACTCACATTTGAGCTTCTCCTCAT
1 CTTCTCTGTACCTCACCAGGAAA-ATGGGGTCTGAAGTTTCACTCACATTTGAGCTTCACCTCAT
* * * *
30325 TATTTTGGCACACTTCTTTATATCTCACCAGGAAGATGACCTA-TTCATTGTTTGACCTA
65 TATTTTGGTACACTTCTCTGTATCTCACCAGGAAGATGACC-ACTTCATTGTTTGACCTT
* * ** * *
30384 CTTTTTTGTACCTCACCAATAAGATGGGGTCTGGAGTTTCACTC
1 CTTCTCTGTACCTCACCAGGAAAATGGGGTCTGAAGTTTCACTC
30428 CACTCCACTA
Statistics
Matches: 483, Mismatches: 48, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
122 6 0.01
123 472 0.98
124 5 0.01
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (123 bp):
CTTCTCTGTACCTCACCAGGAAAATGGGGTCTGAAGTTTCACTCACATTTGAGCTTCACCTCATT
ATTTTGGTACACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCTT
Found at i:33099 original size:16 final size:17
Alignment explanation
Indices: 33058--33100 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
33048 TTATCATTTG
33058 TTAAAT-AAATATAATC
1 TTAAATAAAATATAATC
*
33074 TTAATTAAAATATAAT-
1 TTAAATAAAATATAATC
33090 TTAAATAAAAT
1 TTAAATAAAAT
33101 GATTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATAAAATATAATC
Found at i:33229 original size:32 final size:32
Alignment explanation
Indices: 33192--33255 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
33182 CATCATAACA
* * *
33192 TATAAATTGATTACTTAAATTTAATAATTCAT
1 TATAAATTAATTAATTAAATTTAATAACTCAT
* *
33224 TATAAATTAATTAATTTAATTTGATAACTCAT
1 TATAAATTAATTAATTAAATTTAATAACTCAT
33256 ATTGGTTGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (32 bp):
TATAAATTAATTAATTAAATTTAATAACTCAT
Found at i:35561 original size:83 final size:83
Alignment explanation
Indices: 35422--35590 Score: 329
Period size: 83 Copynumber: 2.0 Consensus size: 83
35412 ACACAGCCAC
35422 GGTGGAGTGTTGTAATTGTCACAAGCTTAGGAATTTCCAATGGAGTAAATCAAAAAGAGATAGAA
1 GGTGGAGTGTTGTAATTGTCACAAGCTTAGGAATTTCCAATGGAGTAAATCAAAAAGAGATAGAA
35487 GGGAAGAAAGAGAAAAGA
66 GGGAAGAAAGAGAAAAGA
35505 GGTGGAGTGTTGTAATTGTCACAAGCTTAGGAATTTCCAATGGAGTAAATCAAAAAGAGATAGAA
1 GGTGGAGTGTTGTAATTGTCACAAGCTTAGGAATTTCCAATGGAGTAAATCAAAAAGAGATAGAA
*
35570 GGGAAGAAAGAGGAAAGA
66 GGGAAGAAAGAGAAAAGA
35588 GGT
1 GGT
35591 TGTTACTGAA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.21
Consensus pattern (83 bp):
GGTGGAGTGTTGTAATTGTCACAAGCTTAGGAATTTCCAATGGAGTAAATCAAAAAGAGATAGAA
GGGAAGAAAGAGAAAAGA
Found at i:37665 original size:15 final size:14
Alignment explanation
Indices: 37628--37666 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
37618 GGAGTTAAAA
*
37628 TTAAATTTTAATTT
1 TTAAAATTTAATTT
37642 TTAATAATTTATATTT
1 TTAA-AATTTA-ATTT
37658 TTAAAATTT
1 TTAAAATTT
37667 GTAAACGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAAAATTTAATTT
Found at i:41185 original size:56 final size:56
Alignment explanation
Indices: 41119--41261 Score: 171
Period size: 56 Copynumber: 2.6 Consensus size: 56
41109 ATGCTGTTAG
* ** * * *
41119 GATATTATTATGCGATATTATCTTTTAGTAATTTAATTTTTAATGAGG-TATTTTAA
1 GATATTATTATGAGATATTATCTTTTAACAATTCAATTGTTAATG-GGATATTATAA
* * *
41175 GATATTATTATGTGATATTATCTTTTAACAATTCGATTGTTAATGGGATATTATAG
1 GATATTATTATGAGATATTATCTTTTAACAATTCAATTGTTAATGGGATATTATAA
* *
41231 GAAATTATTATGAGATATTATCTCTTAACAA
1 GATATTATTATGAGATATTATCTTTTAACAA
41262 ATTGATTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
55 2 0.03
56 73 0.97
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (56 bp):
GATATTATTATGAGATATTATCTTTTAACAATTCAATTGTTAATGGGATATTATAA
Found at i:47473 original size:21 final size:21
Alignment explanation
Indices: 47447--47501 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
47437 CAATACAGAT
* ** *
47447 TTCTACCGGTACCTGTATTAG
1 TTCTACCGATACAAGTATAAG
47468 TTCTACCGATACAAGTATAAG
1 TTCTACCGATACAAGTATAAG
*
47489 TTCTACCAATACA
1 TTCTACCGATACA
47502 TGTCATGCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAGTATAAG
Found at i:48246 original size:59 final size:60
Alignment explanation
Indices: 48152--48330 Score: 227
Period size: 61 Copynumber: 3.0 Consensus size: 60
48142 GTTTAACTCG
* * *
48152 CATTTATAACTCACGATGACACAAAGTCATCGGACCCTTGTTTGCAT-TA-GAACTCATTT
1 CATTTATTACTCACGATGACATATAGTCATCGGACCCTTGTTT-CATATAGGAACTCATTT
* * *
48211 CATTTATTACTCACGATGACATATAGTCATTGGACCCCTTATTTCGTATAGGAACTCATTT
1 CATTTATTACTCACGATGACATATAGTCATCGGA-CCCTTGTTTCATATAGGAACTCATTT
* * * *
48272 CATTTAATACTCACGATGACATATAATCATCGGACCTCTTGTTCCATATAGGAATTCAT
1 CATTTATTACTCACGATGACATATAGTCATCGGACC-CTTGTTTCATATAGGAACTCAT
48331 ATACTCACGA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
59 32 0.31
60 12 0.12
61 59 0.57
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (60 bp):
CATTTATTACTCACGATGACATATAGTCATCGGACCCTTGTTTCATATAGGAACTCATTT
Found at i:48398 original size:51 final size:53
Alignment explanation
Indices: 48278--48398 Score: 142
Period size: 53 Copynumber: 2.3 Consensus size: 53
48268 ATTTCATTTA
* * **
48278 ATACTCACGATGACA-TATAATCATCGGACCTCTTGTTCCATATAGGAATTCAT
1 ATACTCACGATGACACT-GAGTCATCGGACCTCTTAATCCATATAGGAATTCAT
48331 ATACTCACGATGACACTGAGTCATCGGACCT-TTAATCCATCAT-GG-ATTCAT
1 ATACTCACGATGACACTGAGTCATCGGACCTCTTAATCCAT-ATAGGAATTCAT
* *
48382 TTACTCATGATGACACT
1 ATACTCACGATGACACT
48399 TAGTTATCAG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
51 21 0.35
52 9 0.15
53 29 0.48
54 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (53 bp):
ATACTCACGATGACACTGAGTCATCGGACCTCTTAATCCATATAGGAATTCAT
Found at i:50309 original size:20 final size:21
Alignment explanation
Indices: 50296--50357 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
50286 GATACCTGAT
*
50296 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACCTTTTG
50317 AAAAGGTATCGATA-CTTTTG
1 AAAAGGTATCGATACCTTTTG
50337 AAAAGGTATCGATACCTTTTG
1 AAAAGGTATCGATACCTTTTG
50358 TCATTTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 19 0.49
21 20 0.51
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (21 bp):
AAAAGGTATCGATACCTTTTG
Found at i:56001 original size:24 final size:25
Alignment explanation
Indices: 55923--56019 Score: 115
Period size: 25 Copynumber: 3.8 Consensus size: 25
55913 CAAAGTACTT
* **
55923 AACAGAAGCGCATAAGTATTGGGGA
1 AACAGAAGCACATAAGTGCTGGGGA
*
55948 AACAGAAGCGCATAAGTGCTGGGGA
1 AACAGAAGCACATAAGTGCTGGGGA
55973 AACAGAAGCACATAAGTGCT-GGGA
1 AACAGAAGCACATAAGTGCTGGGGA
* *
55997 AACAGTAGGCACACACAGTGCTG
1 AACAG-AAGCACATA-AGTGCTG
56020 AACAGAAGCA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
24 9 0.14
25 49 0.77
26 6 0.09
ACGTcount: A:0.38, C:0.18, G:0.31, T:0.13
Consensus pattern (25 bp):
AACAGAAGCACATAAGTGCTGGGGA
Found at i:56008 original size:25 final size:24
Alignment explanation
Indices: 55923--56031 Score: 107
Period size: 25 Copynumber: 4.5 Consensus size: 24
55913 CAAAGTACTT
* **
55923 AACAGAAGCGCATAAGTATTGGGGA
1 AACAGAAGCACATAAGTGCT-GGGA
*
55948 AACAGAAGCGCATAAGTGCTGGGGA
1 AACAGAAGCACATAAGTGCT-GGGA
55973 AACAGAAGCACATAAGTGCTGGGA
1 AACAGAAGCACATAAGTGCTGGGA
* *
55997 AACAGTAGGCACACACAGTGCT--G-
1 AACAG-AAGCACATA-AGTGCTGGGA
56020 AACAGAAGCACA
1 AACAGAAGCACA
56032 CACAGCGCTG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
22 6 0.08
23 5 0.07
24 10 0.13
25 49 0.64
26 6 0.08
ACGTcount: A:0.40, C:0.18, G:0.29, T:0.12
Consensus pattern (24 bp):
AACAGAAGCACATAAGTGCTGGGA
Found at i:56031 original size:22 final size:22
Alignment explanation
Indices: 56005--56073 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
55995 GAAACAGTAG
*
56005 GCACACACAGTGCTGAACAGAA
1 GCACACACAGCGCTGAACAGAA
56027 GCACACACAGCGCTGAACAGAA
1 GCACACACAGCGCTGAACAGAA
56049 GCACACACAGCGCTGAACAGTAA
1 GCACACACAGCGCTGAACAG-AA
56072 GC
1 GC
56074 GCTAGCGTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 41 0.91
23 4 0.09
ACGTcount: A:0.39, C:0.30, G:0.23, T:0.07
Consensus pattern (22 bp):
GCACACACAGCGCTGAACAGAA
Found at i:61127 original size:15 final size:15
Alignment explanation
Indices: 61107--61140 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
61097 ACTCTTCAAG
61107 CTTATTGAGAGAAGC
1 CTTATTGAGAGAAGC
61122 CTTATTGAGAGAAGC
1 CTTATTGAGAGAAGC
61137 CTTA
1 CTTA
61141 CTGTGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (15 bp):
CTTATTGAGAGAAGC
Found at i:71678 original size:16 final size:16
Alignment explanation
Indices: 71635--71672 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
71625 GGGCTCGGGC
* *
71635 TTTCTTGAGCTTAGAT
1 TTTCTCGAGCTCAGAT
71651 TTTCTCGAGCTCAGAT
1 TTTCTCGAGCTCAGAT
71667 TTTCTC
1 TTTCTC
71673 AGGCTCGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (16 bp):
TTTCTCGAGCTCAGAT
Found at i:78393 original size:68 final size:69
Alignment explanation
Indices: 78260--78400 Score: 266
Period size: 68 Copynumber: 2.1 Consensus size: 69
78250 CTAATTCAAG
78260 AACCAAGACACAGAAGAGCAGAACTAAAAAAAAAAAATCTTTACGCATCCAAACTTGAAAAACAA
1 AACCAAGACACAGAAGAGCAGAACTAAAAAAAAAAAATCTTTACGCATCCAAACTTGAAAAACAA
78325 CCAA
66 CCAA
*
78329 AACCAAGACACAGAAGAGCAGAACT-AAAAAAAAAAATCTTTACGCATCCAAACTTGAAATACAA
1 AACCAAGACACAGAAGAGCAGAACTAAAAAAAAAAAATCTTTACGCATCCAAACTTGAAAAACAA
78393 CCAA
66 CCAA
78397 AACC
1 AACC
78401 CAATTAAAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 46 0.65
69 25 0.35
ACGTcount: A:0.55, C:0.23, G:0.10, T:0.12
Consensus pattern (69 bp):
AACCAAGACACAGAAGAGCAGAACTAAAAAAAAAAAATCTTTACGCATCCAAACTTGAAAAACAA
CCAA
Found at i:79974 original size:9 final size:11
Alignment explanation
Indices: 79939--79977 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
79929 ATCATGCTAT
79939 TTTTAAGTTATA
1 TTTTAA-TTATA
79951 TTTTAATTATA
1 TTTTAATTATA
*
79962 TTTTAATTATT
1 TTTTAATTATA
79973 TTTTA
1 TTTTA
79978 TGTTGTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTTAATTATA
Found at i:80508 original size:19 final size:19
Alignment explanation
Indices: 80486--80535 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
80476 GAAGATGAAG
80486 AAAATAAAGGAAGAAAA-AA
1 AAAATAAAGGAA-AAAAGAA
80505 AAAATAAA-GAAAAAAGAA
1 AAAATAAAGGAAAAAAGAA
*
80523 ATAAAAAAAGGAA
1 A-AAATAAAGGAA
80536 TAGAGCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.15
18 6 0.22
19 14 0.52
20 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAATAAAGGAAAAAAGAA
Found at i:80514 original size:15 final size:15
Alignment explanation
Indices: 80496--80531 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
80486 AAAATAAAGG
80496 AAGAAAAAAAAAATA
1 AAGAAAAAAAAAATA
*
80511 AAGAAAAAAGAAATA
1 AAGAAAAAAAAAATA
80526 AA-AAAA
1 AAGAAAA
80532 GGAATAGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.06
Consensus pattern (15 bp):
AAGAAAAAAAAAATA
Found at i:84488 original size:32 final size:32
Alignment explanation
Indices: 84452--84513 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
84442 AGCTTTTGGT
84452 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
84484 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
84514 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:85363 original size:23 final size:22
Alignment explanation
Indices: 85334--85463 Score: 111
Period size: 23 Copynumber: 5.7 Consensus size: 22
85324 GGGGAAACAA
*
85334 TAAGCACGCACAGTGCAATCCAG
1 TAAGCACACACAGTGCAAT-CAG
85357 TAAGCACACACAGTGCAATCAG
1 TAAGCACACACAGTGCAATCAG
* * * *
85379 TAGGCGCACATAGCGCAAATCAG
1 TAAGCACACACAGTGC-AATCAG
* *
85402 TAGGCACACGA-AGTGCGAAACAG
1 TAAGCACAC-ACAGTGC-AATCAG
* *
85425 TAAGCACATGA-AGTGCGAAACAG
1 TAAGCACA-CACAGTGC-AATCAG
85448 TAAGCACACACAGTGC
1 TAAGCACACACAGTGC
85464 TGAACAGTAA
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
22 16 0.18
23 74 0.81
24 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.24, T:0.12
Consensus pattern (22 bp):
TAAGCACACACAGTGCAATCAG
Found at i:85469 original size:23 final size:21
Alignment explanation
Indices: 85303--85475 Score: 98
Period size: 23 Copynumber: 7.5 Consensus size: 21
85293 CGAAGAACTT
85303 AACAGTAAGCACACAAGTGCTGGGG
1 AACAGTAAGCACACAAGTGC----G
* *
85328 AAACAATAAGCACGCACAGTGC-
1 -AACAGTAAGCACACA-AGTGCG
85350 AATCCAGTAAGCACACACAGTGC-
1 AA--CAGTAAGCACACA-AGTGCG
* * * *
85373 AATCAGTAGGCGCACATAGCGCA
1 AA-CAGTAAGCACACA-AGTGCG
*
85396 AATCAGTAGGCACACGAAGTGCG
1 AA-CAGTAAGCACAC-AAGTGCG
*
85419 AAACAGTAAGCACATGAAGTGCG
1 -AACAGTAAGCACA-CAAGTGCG
85442 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACA-AGTGC-G
85466 AACAGTAAGC
1 AACAGTAAGC
85476 GCGCTAGCGT
Statistics
Matches: 123, Mismatches: 15, Indels: 21
0.77 0.09 0.13
Matches are distributed among these distances:
21 2 0.02
22 16 0.13
23 83 0.67
24 4 0.03
26 13 0.11
27 5 0.04
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (21 bp):
AACAGTAAGCACACAAGTGCG
Found at i:85576 original size:24 final size:26
Alignment explanation
Indices: 85538--85585 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
85528 TCGACATGAG
85538 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
85564 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
85586 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:86418 original size:23 final size:22
Alignment explanation
Indices: 86389--86518 Score: 111
Period size: 23 Copynumber: 5.7 Consensus size: 22
86379 GGGGAAACAA
*
86389 TAAGCACGCACAGTGCAATCCAG
1 TAAGCACACACAGTGCAAT-CAG
86412 TAAGCACACACAGTGCAATCAG
1 TAAGCACACACAGTGCAATCAG
* * * *
86434 TAGGCGCACATAGCGCAAATCAG
1 TAAGCACACACAGTGC-AATCAG
* *
86457 TAGGCACACGA-AGTGCGAAACAG
1 TAAGCACAC-ACAGTGC-AATCAG
* *
86480 TAAGCACATGA-AGTGCGAAACAG
1 TAAGCACA-CACAGTGC-AATCAG
86503 TAAGCACACACAGTGC
1 TAAGCACACACAGTGC
86519 TGAACAGTAA
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
22 16 0.18
23 74 0.81
24 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.24, T:0.12
Consensus pattern (22 bp):
TAAGCACACACAGTGCAATCAG
Found at i:86524 original size:23 final size:21
Alignment explanation
Indices: 86358--86530 Score: 98
Period size: 23 Copynumber: 7.5 Consensus size: 21
86348 CGAAGAACTT
86358 AACAGTAAGCACACAAGTGCTGGGG
1 AACAGTAAGCACACAAGTGC----G
* *
86383 AAACAATAAGCACGCACAGTGC-
1 -AACAGTAAGCACACA-AGTGCG
86405 AATCCAGTAAGCACACACAGTGC-
1 AA--CAGTAAGCACACA-AGTGCG
* * * *
86428 AATCAGTAGGCGCACATAGCGCA
1 AA-CAGTAAGCACACA-AGTGCG
*
86451 AATCAGTAGGCACACGAAGTGCG
1 AA-CAGTAAGCACAC-AAGTGCG
*
86474 AAACAGTAAGCACATGAAGTGCG
1 -AACAGTAAGCACA-CAAGTGCG
86497 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACA-AGTGC-G
86521 AACAGTAAGC
1 AACAGTAAGC
86531 GCGCTAGCGT
Statistics
Matches: 123, Mismatches: 15, Indels: 21
0.77 0.09 0.13
Matches are distributed among these distances:
21 2 0.02
22 16 0.13
23 83 0.67
24 4 0.03
26 13 0.11
27 5 0.04
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (21 bp):
AACAGTAAGCACACAAGTGCG
Found at i:86631 original size:24 final size:26
Alignment explanation
Indices: 86593--86640 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
86583 TCGACATGAG
86593 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
86619 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
86641 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:91947 original size:23 final size:23
Alignment explanation
Indices: 91872--91952 Score: 94
Period size: 23 Copynumber: 3.4 Consensus size: 23
91862 ACACTAGCGC
*
91872 GCTCTCTG-T-TTAGCACGTCTCGT
1 GCTCTCTGTTATTAGCAC-TGT-GT
91895 GCTCTCTGTTATTAGCACTGTGT
1 GCTCTCTGTTATTAGCACTGTGT
91918 GCTCTCTGTTATTAGCACTTTGTGT
1 GCTCTCTGTTATTAGCAC--TGTGT
*
91943 GCTCTTTGTT
1 GCTCTCTGTT
91953 TGTACTTTGG
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
23 28 0.54
24 3 0.06
25 21 0.40
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (23 bp):
GCTCTCTGTTATTAGCACTGTGT
Found at i:91970 original size:21 final size:22
Alignment explanation
Indices: 91934--91976 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
91924 TGTTATTAGC
*
91934 ACTTTGTGTGCTCTTTGTTTGT
1 ACTTTGTGTACTCTTTGTTTGT
91956 ACTTTG-GTACTCTTTGTTTGT
1 ACTTTGTGTACTCTTTGTTTGT
91977 TCTGTATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.58
Consensus pattern (22 bp):
ACTTTGTGTACTCTTTGTTTGT
Found at i:96581 original size:19 final size:19
Alignment explanation
Indices: 96557--96600 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
96547 TTATGATATT
*
96557 AAATAACAATAAATAATA-A
1 AAATAACAA-AAATAAAATA
*
96576 AAATAACCAAAATAAAATA
1 AAATAACAAAAATAAAATA
96595 AAATAA
1 AAATAA
96601 AATTCAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (19 bp):
AAATAACAAAAATAAAATA
Found at i:96910 original size:3 final size:3
Alignment explanation
Indices: 96904--96937 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
96894 TACAAGAAGA
96904 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
96938 TTAAAGTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:106998 original size:21 final size:22
Alignment explanation
Indices: 106950--106999 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
106940 CCTAGTTGTG
*
106950 TTATAACTACCTTACTAAAAAA
1 TTATAATTACCTTACTAAAAAA
* *
106972 TAATAATTACTTTACT-AAAAA
1 TTATAATTACCTTACTAAAAAA
106993 TTATAAT
1 TTATAAT
107000 ATTTATGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TTATAATTACCTTACTAAAAAA
Found at i:117282 original size:163 final size:163
Alignment explanation
Indices: 117012--117339 Score: 638
Period size: 163 Copynumber: 2.0 Consensus size: 163
117002 GAATGTAGAC
117012 TAAAATATTGGAGAGTTGATCATTTTTTCATCGTCCTAGGGTTTATTTGTAGGTATGGTCTCATG
1 TAAAATATTGGAGAGTTGATCATTTTTTCATCGTCCTAGGGTTTATTTGTAGGTATGGTCTCATG
117077 TCAAGTGACGTTCATCATTGTGGGATGCGTGGAAAAGATGTCTGTGATGGGACGTGTCATCATTC
66 TCAAGTGACGTTCATCATTGTGGGATGCGTGGAAAAGATGTCTGTGATGGGACGTGTCATCATTC
*
117142 CCTCTAAATCATTGTACGAAATAGTTGAGTTCA
131 CCTCTAAATCATTGTACGAAATAGTTGAATTCA
117175 TAAAATATTGGAGAGTTGATCATTTTTTCATCGTCCTAGGGTTTATTTGTAGGTATGGTCTCATG
1 TAAAATATTGGAGAGTTGATCATTTTTTCATCGTCCTAGGGTTTATTTGTAGGTATGGTCTCATG
*
117240 TCAAGTGACGTTCATCATTGTGGGATGCGTGGAAAAGATGTCTGTGATGGGACGTGTTATCATTC
66 TCAAGTGACGTTCATCATTGTGGGATGCGTGGAAAAGATGTCTGTGATGGGACGTGTCATCATTC
117305 CCTCTAAATCATTGTACGAAATAGTTGAATTCA
131 CCTCTAAATCATTGTACGAAATAGTTGAATTCA
117338 TA
1 TA
117340 TGGGGTTCGA
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 163 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (163 bp):
TAAAATATTGGAGAGTTGATCATTTTTTCATCGTCCTAGGGTTTATTTGTAGGTATGGTCTCATG
TCAAGTGACGTTCATCATTGTGGGATGCGTGGAAAAGATGTCTGTGATGGGACGTGTCATCATTC
CCTCTAAATCATTGTACGAAATAGTTGAATTCA
Found at i:128592 original size:2 final size:2
Alignment explanation
Indices: 128585--128609 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
128575 CCATCGCCTA
128585 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
128610 AATTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:134144 original size:21 final size:20
Alignment explanation
Indices: 134098--134147 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
134088 ATGTAAAAAA
*
134098 TAAATTAAAAGCAAAAATAT
1 TAAATTAAAAGAAAAAATAT
* *
134118 TAAAATTAAAATAAAAAATGT
1 T-AAATTAAAAGAAAAAATAT
134139 CTAAATTAA
1 -TAAATTAA
134148 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (20 bp):
TAAATTAAAAGAAAAAATAT
Found at i:136032 original size:74 final size:74
Alignment explanation
Indices: 135953--136101 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
135943 AAACATATAA
135953 TAAAAGGATTTTGTTTATAGAATTTGACCAATCAAATCCATTATTAGTAAAGCTATAAATCTAAC
1 TAAAAGGATTTTGTTTATAGAATTTGACCAATCAAATCCATTATTAGTAAAGCTATAAATCTAAC
136018 CTTTAATAT
66 CTTTAATAT
136027 TAAAAGGATTTTGTTTATAGAATTTGACCAATCAAATCCATTATTAGTAAAGCTATAAATCTAAC
1 TAAAAGGATTTTGTTTATAGAATTTGACCAATCAAATCCATTATTAGTAAAGCTATAAATCTAAC
136092 CTTTAATAT
66 CTTTAATAT
136101 T
1 T
136102 TACATTTCTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (74 bp):
TAAAAGGATTTTGTTTATAGAATTTGACCAATCAAATCCATTATTAGTAAAGCTATAAATCTAAC
CTTTAATAT
Found at i:149586 original size:47 final size:47
Alignment explanation
Indices: 149517--149701 Score: 300
Period size: 47 Copynumber: 3.9 Consensus size: 47
149507 TTTTAACTTG
*
149517 ATGCCTTTTAGGGACTCTTTGGCTT-TCGGTTTCACTACGAGTAGTTT
1 ATGCCTTTCAGGGACTCTTTGGCTTGT-GGTTTCACTACGAGTAGTTT
149564 ATGCCTTTCAGGGACTCTTTGGCTTGTGGTTTCACTACGAGTAGTTT
1 ATGCCTTTCAGGGACTCTTTGGCTTGTGGTTTCACTACGAGTAGTTT
* *
149611 ATGCCTTTCAGGGACTCTTTGGCTTGTGGTTTCACTATGAGTATTTT
1 ATGCCTTTCAGGGACTCTTTGGCTTGTGGTTTCACTACGAGTAGTTT
* * *
149658 ATGCCTTTCAGGGACTCTTTGGCTTTTGGTTTCATTATGAGTAG
1 ATGCCTTTCAGGGACTCTTTGGCTTGTGGTTTCACTACGAGTAG
149702 CAAAGATATT
Statistics
Matches: 131, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
47 130 0.99
48 1 0.01
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (47 bp):
ATGCCTTTCAGGGACTCTTTGGCTTGTGGTTTCACTACGAGTAGTTT
Found at i:158182 original size:6 final size:6
Alignment explanation
Indices: 158158--158216 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
158148 CGAGCGAGAC
* * * * *
158158 GAAGAA GAAGAA GAAGAT GATGAT GACGTT GAAGAT GAAGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
158206 GAAAAT GAAGA
1 GAAGAT GAAGA
158217 AGAGGAAGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.32, T:0.15
Consensus pattern (6 bp):
GAAGAT
Found at i:164666 original size:37 final size:37
Alignment explanation
Indices: 164616--164690 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
164606 GTAAACATAG
164616 TACCCAATGGCCTAGAGATTCCTCGGTTAGTATTCTT
1 TACCCAATGGCCTAGAGATTCCTCGGTTAGTATTCTT
164653 TACCCAATGGCCTAGAGATTCCTCGGTTAGTATTCTT
1 TACCCAATGGCCTAGAGATTCCTCGGTTAGTATTCTT
164690 T
1 T
164691 CTCGAGTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (37 bp):
TACCCAATGGCCTAGAGATTCCTCGGTTAGTATTCTT
Found at i:173033 original size:3 final size:3
Alignment explanation
Indices: 173025--173059 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
173015 CAGGTTGAGT
173025 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
173060 TTGCAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:180676 original size:10 final size:11
Alignment explanation
Indices: 180647--180684 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
180637 TTGAACTAAT
180647 TCATTAAATAAA
1 TCATTAAA-AAA
180659 TCATTAAAAAA
1 TCATTAAAAAA
*
180670 T-ATTAAAAAT
1 TCATTAAAAAA
180680 TCATT
1 TCATT
180685 CAATCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 7 0.29
12 8 0.33
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (11 bp):
TCATTAAAAAA
Found at i:182999 original size:19 final size:17
Alignment explanation
Indices: 182961--182993 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
182951 TTGATCGTAA
182961 AAAAAAATTATTATTTT
1 AAAAAAATTATTATTTT
182978 AAAAAAA-TA-TATTTT
1 AAAAAAATTATTATTTT
182993 A
1 A
182994 TTTAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAAAATTATTATTTT
Found at i:185405 original size:21 final size:22
Alignment explanation
Indices: 185372--185421 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
185362 AACTTTTTGC
185372 AATAAATTCTTAATAAATATAT
1 AATAAATTCTTAATAAATATAT
* **
185394 AATACATT-TTAATTGATATAT
1 AATAAATTCTTAATAAATATAT
185415 ATATAAA
1 A-ATAAA
185422 ATCAAATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
AATAAATTCTTAATAAATATAT
Found at i:194727 original size:21 final size:19
Alignment explanation
Indices: 194701--194740 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
194691 ATGAGAAAAA
194701 AAAATTAGAAATATCAACTTT
1 AAAATTAGAAAT-TC-ACTTT
*
194722 AAAATTATAAATTCACTTT
1 AAAATTAGAAATTCACTTT
194741 CCTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAATTAGAAATTCACTTT
Found at i:196166 original size:25 final size:23
Alignment explanation
Indices: 196138--196184 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
196128 TAATATTCTA
196138 TTGTAAACATTATAAAATTATTAAG
1 TTGTAAACA-TATAAAATT-TTAAG
* *
196163 TTGTCAATATATAAAATTTTAA
1 TTGTAAACATATAAAATTTTAA
196185 CAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 7 0.35
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (23 bp):
TTGTAAACATATAAAATTTTAAG
Found at i:198688 original size:29 final size:30
Alignment explanation
Indices: 198642--198698 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
198632 TTTGAATCAC
* *
198642 AATTAGAATTTCACATATATAATTACACCA
1 AATTAGAAATTCACATATACAATTACACCA
*
198672 AATTA-AAATTCATATATACAATTACAC
1 AATTAGAAATTCACATATACAATTACAC
198699 ATTAACTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (30 bp):
AATTAGAAATTCACATATACAATTACACCA
Found at i:202598 original size:22 final size:22
Alignment explanation
Indices: 202573--202614 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
202563 AATTTGGCAC
* *
202573 AATAATAAATTTAATTTTTAAA
1 AATAAAAAAATTAATTTTTAAA
202595 AATAAAAAAATTAATTTTTA
1 AATAAAAAAATTAATTTTTA
202615 TATATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAAAAAAATTAATTTTTAAA
Found at i:204437 original size:2 final size:2
Alignment explanation
Indices: 204430--204457 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
204420 AAGTTTTGTT
204430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
204458 AATTTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:207782 original size:59 final size:59
Alignment explanation
Indices: 207700--208124 Score: 551
Period size: 59 Copynumber: 7.2 Consensus size: 59
207690 AAAATGGTGG
* * *
207700 TTTTGGAAGGTTCGAAGTTAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* * * *
207759 TTTCGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* *
207818 TTTTAGAAGGTTTCG-GGTCAAAAATGGGATTTTTGGAAGTT-TAGGGGTAAAATGGTAAT
1 TTTTGGAAGG-TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAAT
* * *
207877 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTT-GATGTTC-AGAGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAG-GGTAAAATGGTAAT
* * * * *
207935 TTTCGGAAGTTTCCAGGTAAAAAATGGGATTTTTGAAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
*
207994 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* **
208053 TTTTGAAAGGTTCG-GGGAAAAAATGGGATTTTTGGAAGGTTCG-GGGTCAAAAATGG-AAT
1 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAA-GTTCGAGGGT--AAAATGGTAAT
208112 TTTTGGAA-GTTCG
1 TTTTGGAAGGTTCG
208125 GGGACCTTTG
Statistics
Matches: 325, Mismatches: 31, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
57 1 0.00
58 82 0.25
59 229 0.70
60 13 0.04
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (59 bp):
TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
Found at i:207985 original size:176 final size:175
Alignment explanation
Indices: 207685--208120 Score: 569
Period size: 176 Copynumber: 2.5 Consensus size: 175
207675 CGAATGCACG
* ** * ** * *
207685 GGGGAAAAATGGTGGTTTTGGAAGGTTCGAAGTTAAAAATGAGATTTTTGGAAGTTCGAGGGTAA
1 GGGGTAAAATGGTAATTTTTGAAGGTTCGGGGTAAAAAATGGGATTTTT-GAAGTTCGAGGGTAA
* * * *
207750 AATGGTAATTTTCGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAATGGT
65 AATGGTAATTTTCGGAAGGTTCCAGGTAAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAATGGT
*
207815 AATTTTTAGAAGGTTTCG-GGTCAAAAATGGGATTTTTGGAAGTTTA
130 AATTTTTAGAAGG-TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCA
* *
207861 GGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGATGTTC-AGAGGTA
1 GGGGTAAAATGGTAATTTTT-GAAGGTTCGGGGTAAAAAATGGGATTTTTGAAGTTCGAG-GGTA
*
207925 AAATGGTAATTTTCGGAAGTTTCCAGGTAAAAAATGGGATTTTT-GAAAGTTCGAGGGTAAAATG
64 AAATGGTAATTTTCGGAAGGTTCCAGGTAAAAAATGGGATTTTTAG-AAGTTCGAGGGTAAAATG
* *
207989 GTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCG
128 GTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCA
208037 GGGGTAAAATGGTAATTTTTGAAAGGTTCGGGG-AAAAAATGGGATTTTTGGAAGGTTCG-GGGT
1 GGGGTAAAATGGTAATTTTTG-AAGGTTCGGGGTAAAAAATGGGATTTTT-GAA-GTTCGAGGGT
*
208100 CAAAAATGG-AATTTTTGGAAG
63 --AAAATGGTAATTTTCGGAAG
208121 TTCGGGGACC
Statistics
Matches: 230, Mismatches: 20, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
175 23 0.10
176 159 0.69
177 41 0.18
178 7 0.03
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.32
Consensus pattern (175 bp):
GGGGTAAAATGGTAATTTTTGAAGGTTCGGGGTAAAAAATGGGATTTTTGAAGTTCGAGGGTAAA
ATGGTAATTTTCGGAAGGTTCCAGGTAAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAATGGTA
ATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCA
Found at i:208125 original size:29 final size:28
Alignment explanation
Indices: 207700--208127 Score: 316
Period size: 29 Copynumber: 14.6 Consensus size: 28
207690 AAAATGGTGG
* *
207700 TTTTGGAAGGTTCGAAGTTAAAAAT-GAGAT
1 TTTTGGAA-GTTCG-GGGTAAAAATGGA-AT
207730 TTTTGGAAGTTCGAGGGT-AAAATGGTAAT
1 TTTTGGAAGTTCG-GGGTAAAAATGG-AAT
* * *
207759 TTTCGGAAGGTTCGAGGTCAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGT-AAAAATGGAAT
* *
207789 TTTTAGAAGTTTGGGGGT-AAAATGGTAAT
1 TTTTGGAAG-TTCGGGGTAAAAATGG-AAT
* *
207818 TTTTAGAAGGTTTC-GGGTCAAAAATGGGAT
1 TTTTGGAA-G-TTCGGGGT-AAAAATGGAAT
*
207848 TTTTGGAAGTTTAGGGGT-AAAATGGTAAT
1 TTTTGGAAG-TTCGGGGTAAAAATGG-AAT
* *
207877 TTTTAGAAGGTTCGGGGTCAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGT-AAAAATGGAAT
* *
207907 TTTT-GATGTTCAGAGGT-AAAATGGTAAT
1 TTTTGGAAGTTC-GGGGTAAAAATGG-AAT
* ** *
207935 TTTCGGAAGTTTCCAGGTAAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGT-AAAAATGGAAT
*
207965 TTTTGAAAGTTCGAGGGT-AAAATGGTAAT
1 TTTTGGAAGTTCG-GGGTAAAAATGG-AAT
* *
207994 TTTTGGAAGGTTCGAGGTCAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGT-AAAAATGGAAT
208024 TTTTGGAAGTTCGGGGGT-AAAATGGTAAT
1 TTTTGGAAGTTC-GGGGTAAAAATGG-AAT
* * *
208053 TTTTGAAAGGTTCGGGGAAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTAAAAATGGAAT
208082 TTTTGGAAGGTTCGGGGTCAAAAATGGAAT
1 TTTTGGAA-GTTCGGGGT-AAAAATGGAAT
208112 TTTTGGAAGTTCGGGG
1 TTTTGGAAGTTCGGGG
208128 ACCTTTGGGG
Statistics
Matches: 326, Mismatches: 41, Indels: 63
0.76 0.10 0.15
Matches are distributed among these distances:
27 7 0.02
28 42 0.13
29 127 0.39
30 115 0.35
31 35 0.11
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (28 bp):
TTTTGGAAGTTCGGGGTAAAAATGGAAT
Found at i:209976 original size:17 final size:17
Alignment explanation
Indices: 209956--210035 Score: 106
Period size: 18 Copynumber: 4.6 Consensus size: 17
209946 TAGTTTTATT
*
209956 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
209973 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
209990 TAAATTTAAATTTTTAAA
1 TAAATTTAAA-TTTAAAA
* *
210008 CAAATTTAATTTTTAAAA
1 TAAATTTAA-ATTTAAAA
210026 TAAATTTAAA
1 TAAATTTAAA
210036 GGGAGTTTGG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
17 26 0.48
18 28 0.52
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:209990 original size:7 final size:6
Alignment explanation
Indices: 209953--210002 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
209943 TTTTAGTTTT
* * *
209953 ATTTAA ATTTAA ATTCAA A-ATAA ATTTAA ATTTAA A-ATAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
209999 ATTT
1 ATTT
210003 TTAAACAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 7 0.19
6 29 0.81
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:210014 original size:18 final size:18
Alignment explanation
Indices: 209956--210035 Score: 94
Period size: 17 Copynumber: 4.6 Consensus size: 18
209946 TAGTTTTATT
**
209956 TAAATTTAAA-TTCAAAA
1 TAAATTTAAATTTTTAAA
*
209973 TAAATTTAAA-TTTAAAA
1 TAAATTTAAATTTTTAAA
209990 TAAATTTAAATTTTTAAA
1 TAAATTTAAATTTTTAAA
*
210008 CAAATTT-AATTTTTAAAA
1 TAAATTTAAATTTTT-AAA
210026 TAAATTTAAA
1 TAAATTTAAA
210036 GGGAGTTTGG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
17 33 0.59
18 21 0.38
19 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTTTAAA
Found at i:211976 original size:16 final size:16
Alignment explanation
Indices: 211937--211978 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
211927 TAATTTTAAC
*
211937 ATAACTTTTAATAAAT
1 ATAATTTTTAATAAAT
211953 ATATATTTTTACATAAA-
1 ATA-ATTTTTA-ATAAAT
211970 ATAATTTTT
1 ATAATTTTT
211979 TTATCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATTTTTAATAAAT
Found at i:212402 original size:20 final size:20
Alignment explanation
Indices: 212365--212402 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
212355 GAATAATAAG
*
212365 AAGTTTATTGTTTTATTTAA
1 AAGTTTATTGTTTAATTTAA
212385 AAGTTTA-TGTTTGAATTT
1 AAGTTTATTGTTT-AATTT
212403 TCTAAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (20 bp):
AAGTTTATTGTTTAATTTAA
Found at i:222171 original size:74 final size:74
Alignment explanation
Indices: 222050--222196 Score: 294
Period size: 74 Copynumber: 2.0 Consensus size: 74
222040 CAAAAACATA
222050 GTAAGTACGTGGATTAAGTTTTAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATATAATT
1 GTAAGTACGTGGATTAAGTTTTAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATATAATT
222115 TTGAGTGTT
66 TTGAGTGTT
222124 GTAAGTACGTGGATTAAGTTTTAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATATAATT
1 GTAAGTACGTGGATTAAGTTTTAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATATAATT
222189 TTGAGTGT
66 TTGAGTGT
222197 GTTGAAGTGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (74 bp):
GTAAGTACGTGGATTAAGTTTTAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATATAATT
TTGAGTGTT
Found at i:222188 original size:39 final size:39
Alignment explanation
Indices: 222071--222188 Score: 115
Period size: 39 Copynumber: 3.1 Consensus size: 39
222061 GATTAAGTTT
222071 TAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATA
1 TAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATA
* * * * *
222110 TAATTTTGAGT-GT-TGTAAGTAC-G-TG--GAT-TAAGTTT
1 TAA-TTCGATTAGTATG--AGTACTGTTGTTAATGTAAGATA
222145 TAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATA
1 TAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATA
222184 TAATT
1 TAATT
222189 TTGAGTGTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
34 10 0.17
35 11 0.19
36 6 0.10
38 6 0.10
39 16 0.27
40 10 0.17
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.43
Consensus pattern (39 bp):
TAATTCGATTAGTATGAGTACTGTTGTTAATGTAAGATA
Found at i:229400 original size:2 final size:2
Alignment explanation
Indices: 229393--229434 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
229383 GATCATATTG
229393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
229435 TCATGTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:232343 original size:18 final size:18
Alignment explanation
Indices: 232320--232362 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
232310 GAATATGTTG
232320 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
232338 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
232356 TTAATTA
1 TTAATTA
232363 CACTTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:241525 original size:37 final size:36
Alignment explanation
Indices: 241472--241553 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 36
241462 CTATTAATAA
*
241472 TTTTTTT-ATCACCCAATTATTCG-AATTTTTCTTTT
1 TTTTTTTCATCACCCAATTATT-GAAAATTTTCTTTT
*
241507 TTTTTTTCCATCATCCAATTATTGAAAATTTTCTTTT
1 TTTTTTT-CATCACCCAATTATTGAAAATTTTCTTTT
*
241544 TTCTTTTCAT
1 TTTTTTTCAT
241554 TAGCCATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 7 0.17
36 4 0.10
37 30 0.73
ACGTcount: A:0.21, C:0.17, G:0.02, T:0.60
Consensus pattern (36 bp):
TTTTTTTCATCACCCAATTATTGAAAATTTTCTTTT
Found at i:244195 original size:11 final size:11
Alignment explanation
Indices: 244179--244203 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
244169 AAAACTTTCG
244179 AATAATTTAAT
1 AATAATTTAAT
244190 AATAATTTAAT
1 AATAATTTAAT
244201 AAT
1 AAT
244204 TTTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTTAAT
Found at i:247525 original size:2 final size:2
Alignment explanation
Indices: 247489--247513 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
247479 GGTAAAAGAG
247489 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
247514 AACGTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:248897 original size:14 final size:14
Alignment explanation
Indices: 248879--248907 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
248869 ATTTATTTTT
248879 ATTTTT-TAAATAC
1 ATTTTTATAAATAC
248892 ATTTTTATAAATAC
1 ATTTTTATAAATAC
248906 AT
1 AT
248908 GTTGTTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTTTATAAATAC
Found at i:251375 original size:30 final size:31
Alignment explanation
Indices: 251341--251398 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
251331 GGACAGAAAA
* *
251341 AAGTTCAGGCTC-AATGTGAGAACAATTGCT
1 AAGTTCAGGCCCTAATATGAGAACAATTGCT
*
251371 AAGTTTAGGCCCTAATATGAGAACAATT
1 AAGTTCAGGCCCTAATATGAGAACAATT
251399 ATCAAGTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (31 bp):
AAGTTCAGGCCCTAATATGAGAACAATTGCT
Found at i:253701 original size:19 final size:19
Alignment explanation
Indices: 253648--253704 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
253638 TATGCGCTTA
*
253648 TGCGTCAGGATGCACTTCG
1 TGCGCCAGGATGCACTTCG
** * *
253667 TGTTCCAGATATGCACTTTG
1 TGCGCCAG-GATGCACTTCG
253687 TGCGCCAGGATGCACTTC
1 TGCGCCAGGATGCACTTC
253705 ATGTGTTAGT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (19 bp):
TGCGCCAGGATGCACTTCG
Found at i:266801 original size:3 final size:3
Alignment explanation
Indices: 266793--266819 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
266783 AATTGATTTA
266793 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
266820 TGAGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:267478 original size:38 final size:38
Alignment explanation
Indices: 267436--267534 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 38
267426 AAAGTGTTAA
**
267436 AATAAAAG-TCT-TTATATTAAAAACACTACCATAAATAT
1 AATAAAAGTTCTATTATATTAAAAACA--AAAATAAATAT
* *
267474 AATAAATGTTTTATTATATTAAAAACAAAAATAAATAT
1 AATAAAAGTTCTATTATATTAAAAACAAAAATAAATAT
* *
267512 AATAAATA-TTTTATTGTATTAAA
1 AATAAA-AGTTCTATTATATTAAA
267535 TATTATTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
38 36 0.69
39 2 0.04
40 14 0.27
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (38 bp):
AATAAAAGTTCTATTATATTAAAAACAAAAATAAATAT
Found at i:267492 original size:40 final size:38
Alignment explanation
Indices: 267447--267534 Score: 122
Period size: 38 Copynumber: 2.3 Consensus size: 38
267437 ATAAAAGTCT
** *
267447 TTATATTAAAAACACTACCATAAATATAATAAATGTTTTA
1 TTATATTAAAAACA--AAAATAAATATAATAAATATTTTA
267487 TTATATTAAAAACAAAAATAAATATAATAAATATTTTA
1 TTATATTAAAAACAAAAATAAATATAATAAATATTTTA
*
267525 TTGTATTAAA
1 TTATATTAAA
267535 TATTATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 30 0.68
40 14 0.32
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATATTAAAAACAAAAATAAATATAATAAATATTTTA
Found at i:271146 original size:156 final size:156
Alignment explanation
Indices: 270840--271308 Score: 643
Period size: 156 Copynumber: 3.0 Consensus size: 156
270830 CAGAATAATC
** * * * *
270840 AAACAGTGACACGTGATAACACATATACCTTATCCTGAGGTATAGTGACCAATTTTTAACAATAT
1 AAACAGTGACACGTGATGCCACATATACCTCATCCTGACGTATAGTGACCAGTTTTTAACAATAA
* * *
270905 AAATGGAT-GAATTTTTAATAGAATGACTAGTTTGCTGTTTGATCTAACCTACTGGAACTAATTT
66 AAATGGATGGAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
* *
270969 GCCCATATTTTGAGTAAAGGGGGTAA
131 GCCCATTTTTTGAGTAGAGGGGGTAA
* * * *
270995 AAGCAGTGACACGTGATGCCACCTATACCTCATCCTGATGTACAGTGACCAGTTTTTAACAATAA
1 AAACAGTGACACGTGATGCCACATATACCTCATCCTGACGTATAGTGACCAGTTTTTAACAATAA
*
271060 AAATGGATGGAATTTTTAATAGAATGACTAGTTTGTTCTTTGATCTAACCTAATAGAACTAATTT
66 AAATGGATGGAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
* **
271125 GCCCATTTTTTTAGTAGAGGGGACAA
131 GCCCATTTTTTGAGTAGAGGGGGTAA
* * *
271151 AAATAGTGACACATGATGCCACATATACCTCATCCTGACGTATAGTGACCAGTTTTTAACAATAG
1 AAACAGTGACACGTGATGCCACATATACCTCATCCTGACGTATAGTGACCAGTTTTTAACAATAA
* * * * * *
271216 AAATAGATGAAATTTTTAATAGAATGACTGGTTTGCTCTTTGATCTAATCTAGTAGAACCAATTT
66 AAATGGATGGAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
* * * *
271281 ACCCATTTTTGGAATAGAGAGGGTAA
131 GCCCATTTTTTGAGTAGAGGGGGTAA
271307 AA
1 AA
271309 TGCAATTTAG
Statistics
Matches: 274, Mismatches: 39, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
155 64 0.23
156 210 0.77
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (156 bp):
AAACAGTGACACGTGATGCCACATATACCTCATCCTGACGTATAGTGACCAGTTTTTAACAATAA
AAATGGATGGAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
GCCCATTTTTTGAGTAGAGGGGGTAA
Found at i:274892 original size:12 final size:12
Alignment explanation
Indices: 274875--274899 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
274865 CTAAAACTTG
274875 AATATTAAGGAA
1 AATATTAAGGAA
274887 AATATTAAGGAA
1 AATATTAAGGAA
274899 A
1 A
274900 TTTGACTAAA
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:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
AATATTAAGGAA
Found at i:283855 original size:21 final size:20
Alignment explanation
Indices: 283823--283861 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
283813 AAACTATCTT
*
283823 TTAAATAGTAAAATTATAAG
1 TTAAATAATAAAATTATAAG
283843 TTAATATAATAAAATTATA
1 TTAA-ATAATAAAATTATA
283862 TTTTGATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTAAATAATAAAATTATAAG
Found at i:284239 original size:15 final size:15
Alignment explanation
Indices: 284206--284239 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
284196 AGTATGCCTG
* *
284206 AAAACTTTAAAATTT
1 AAAACTTTAAAAATA
284221 AAAACTTTAAAAATA
1 AAAACTTTAAAAATA
284236 AAAA
1 AAAA
284240 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAACTTTAAAAATA
Found at i:287841 original size:208 final size:207
Alignment explanation
Indices: 287329--288015 Score: 906
Period size: 208 Copynumber: 3.4 Consensus size: 207
287319 TATAATCACT
* * * *
287329 CCATTTCATTAACCCACTAGCAAATACTAAAATCCAGCTAAAACAACCAATTTTAAGCTGT-AAC
1 CCATTTCATTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAAC
* * * *
287393 CCATAAATTTTCTCCA-TAGTTT---AATCAACAATTACCCCATTTCGTT-ATCCACTAGCAATA
66 CCATAAATTTCCTCCACT-GTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATT
* * * *
287453 ACT-AAA---AG-----CCACCAATTTTAAGCTGTAAACCCATAAATCTCTTCCATTGTTTAACA
130 ACTAAAACCCAGCTAAACCACCAATTTTAAGCTGTAAACCCATAAAACTCCTACATAGTTTAACA
*
287509 ATCAACAATCACC
195 ATCAACAATAACC
* * *
287522 CCATTTCATTAATCCGCTAGCAAATACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAAC
1 CCATTTCATTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAAC
* *
287587 CCATAAATTTCCTCCACTGTTTAACAATCAACAATAACCTCATTTCATTAATCCACTAGTAATTA
66 CCATAAATTTCCTCCACTGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATTA
*
287652 CTAAAACCCAGCTGAAACCACCAATTTTTAAGCTGTAAACCCATAAAACTCCTACAAAGTTTAAC
131 CTAAAACCCAGCT-AAACCACCAA-TTTTAAGCTGTAAACCCATAAAACTCCTACATAGTTTAAC
*
287717 TATCAACAATAACC
194 AATCAACAATAACC
*
287731 CCATTTCATTAATCCATTATCAATTACTAAAATCCAGCTAAAACCACC-ATTTTAAGCTGTAAAC
1 CCATTTCATTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAAC
* *
287795 CCATAAATTTCCTCCA-TGGTTTAACAATCAACAATCACCCCATTTCATTGATCCACTAGCAATT
66 CCATAAATTTCCTCCACT-GTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATT
* *
287859 ACTAAAATCCAGCTAAACTCACCAATTTTAAGCTGTAAACCCATAAAATTCCTACATAGTTTAAC
130 ACTAAAACCCAGCTAAAC-CACCAATTTTAAGCTGTAAACCCATAAAACTCCTACATAGTTTAAC
287924 AATCAACAATAACC
194 AATCAACAATAACC
* ** ** * *
287938 CCATTTCATTAATCCACTGTCAATTACTAAAATCCAGCTAAAGTCGTCAATTTTAAGCTGTGAAG
1 CCATTTCATTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAAC
288003 CCA-AAATTATCCT
66 CCATAAATT-TCCT
288016 AAAAAAGACA
Statistics
Matches: 437, Mismatches: 36, Indels: 27
0.87 0.07 0.05
Matches are distributed among these distances:
193 58 0.13
194 22 0.05
195 1 0.00
197 21 0.05
198 15 0.03
199 3 0.01
202 2 0.00
207 103 0.24
208 121 0.28
209 91 0.21
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (207 bp):
CCATTTCATTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAAC
CCATAAATTTCCTCCACTGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATTA
CTAAAACCCAGCTAAACCACCAATTTTAAGCTGTAAACCCATAAAACTCCTACATAGTTTAACAA
TCAACAATAACC
Found at i:288016 original size:104 final size:104
Alignment explanation
Indices: 287461--288016 Score: 759
Period size: 104 Copynumber: 5.3 Consensus size: 104
287451 TAACTAAAAG
* * * * *
287461 CCACCAATTTTAAGCTGTAAACCCATAAATCTCTTCCATTGTTTAACAATCAACAATCACCCCAT
1 CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCAT
* *
287526 TTCATTAATCCGCTAG-CAAATACTAAAATCCAGCTAAAA
66 TTCATTAATCCACTAGTCAATTACTAAAATCCAGCT-AAA
* *
287565 CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACT-GTTTAACAATCAACAATAACCTCA
1 CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTACA-TAGTTTAACAATCAACAATAACCCCA
*
287629 TTTCATTAATCCACTAGT-AATTACTAAAACCCAGCTGAAA
65 TTTCATTAATCCACTAGTCAATTACTAAAATCCAGCT-AAA
** * *
287669 CCACCAATTTTTAAGCTGTAAACCCATAAAACTCCTACAAAGTTTAACTATCAACAATAACCCCA
1 CCACCAA-TTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCA
*
287734 TTTCATTAATCCATTA-TCAATTACTAAAATCCAGCTAAAA
65 TTTCATTAATCCACTAGTCAATTACTAAAATCCAGCT-AAA
* * *
287774 CCACC-ATTTTAAGCTGTAAACCCATAAATTTCCTCCATGGTTTAACAATCAACAATCACCCCAT
1 CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCAT
*
287838 TTCATTGATCCACTAG-CAATTACTAAAATCCAGCTAAA
66 TTCATTAATCCACTAGTCAATTACTAAAATCCAGCTAAA
*
287876 CTCACCAATTTTAAGCTGTAAACCCATAAAATTCCTACATAGTTTAACAATCAACAATAACCCCA
1 C-CACCAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCA
287941 TTTCATTAATCCACT-GTCAATTACTAAAATCCAGCTAAA
65 TTTCATTAATCCACTAGTCAATTACTAAAATCCAGCTAAA
* ** * *
287980 GTCGTCAATTTTAAGCTGTGAAGCCA-AAATTATCCTA
1 -CCACCAATTTTAAGCTGTAAACCCATAAATT-TCCTA
288017 AAAAAGACAA
Statistics
Matches: 404, Mismatches: 37, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
102 4 0.01
103 92 0.23
104 217 0.54
105 91 0.23
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (104 bp):
CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCAT
TTCATTAATCCACTAGTCAATTACTAAAATCCAGCTAAA
Found at i:292904 original size:6 final size:6
Alignment explanation
Indices: 292893--292917 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
292883 ACACGTGTTT
292893 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
292918 ATATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:293260 original size:4 final size:4
Alignment explanation
Indices: 293251--293314 Score: 69
Period size: 4 Copynumber: 16.0 Consensus size: 4
293241 AAATAAACGG
* *
293251 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA G-AA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
293300 G-AA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA
293315 TGTAATGTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
3 6 0.12
4 38 0.73
5 8 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:293297 original size:20 final size:19
Alignment explanation
Indices: 293250--293314 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
293240 CAAATAAACG
*
293250 GGAAAGAAAGAAAGGAAAGAA
1 GGAAAGAAAG-AA-GAAGGAA
*
293271 AGAAAGAAAGAAGAAGGAGA
1 GGAAAGAAAGAAGAAGGA-A
293291 GGAAAGAAAGAAGAAGGAA
1 GGAAAGAAAGAAGAAGGAA
*
293310 AGAAA
1 GGAAA
293315 TGTAATGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.26
20 20 0.51
21 9 0.23
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (19 bp):
GGAAAGAAAGAAGAAGGAA
Found at i:293312 original size:28 final size:29
Alignment explanation
Indices: 293250--293314 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
293240 CAAATAAACG
293250 GGAAAGAAAGAAAGGAAAGAAAGAAAGAA
1 GGAAAGAAAGAAAGGAAAGAAAGAAAGAA
* * *
293279 AG-AAGAAGGAGAGGAAAGAAAG-AAGAA
1 GGAAAGAAAGAAAGGAAAGAAAGAAAGAA
293306 GGAAAGAAA
1 GGAAAGAAA
293315 TGTAATGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 6 0.20
28 23 0.77
29 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (29 bp):
GGAAAGAAAGAAAGGAAAGAAAGAAAGAA
Found at i:296424 original size:21 final size:21
Alignment explanation
Indices: 296398--296441 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
296388 TTAGGGTCCA
*
296398 ATTGCCCCGGAGGAGTAGAGT
1 ATTGCCCCGGAGGAATAGAGT
*
296419 ATTGCCCGGGAGGAATAGAGT
1 ATTGCCCCGGAGGAATAGAGT
296440 AT
1 AT
296442 CGCGATGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.36, T:0.20
Consensus pattern (21 bp):
ATTGCCCCGGAGGAATAGAGT
Found at i:296563 original size:45 final size:45
Alignment explanation
Indices: 296448--296572 Score: 151
Period size: 45 Copynumber: 2.8 Consensus size: 45
296438 GTATCGCGAT
* * * ** * * *
296448 GGCTCGTCAAACTCAGCCTGATATCATTCCCTTGTGTATTGCGGT
1 GGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGCATTGCGGC
* *
296493 GGCTCGTCAAATTGAGGCTGATATCCTTGGTTTGAGCATTGCGGC
1 GGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGCATTGCGGC
*
296538 GGCTCGTCAAACTGAGGTTGATATCCTTGGCTTGA
1 GGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGA
296573 TGAGCTATGC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.32
Consensus pattern (45 bp):
GGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGCATTGCGGC
Done.