Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 1 of 208
Found at i:2128 original size:19 final size:19
Alignment explanation
Indices: 2094--2144 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
2084 ACATTATTTG
2094 ATTAAAAACCCT-AAATTA
1 ATTAAAAACCCTAAAATTA
2112 ATTAAAAACCCTAAAATTA
1 ATTAAAAACCCTAAAATTA
2131 ATTAAAAACCCTAA
1 ATTAAAAACCCTAA
2145 CTAACCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 12 0.38
19 20 0.62
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (19 bp):
ATTAAAAACCCTAAAATTA
Found at i:2220 original size:27 final size:27
Alignment explanation
Indices: 2128--3001 Score: 846
Period size: 27 Copynumber: 33.0 Consensus size: 27
2118 AACCCTAAAA
*
2128 TTAATTAAAAACCCTAA-CTAACCTAA-
1 TTAATT-AAAACCCTAACCTAACTTAAT
2154 TTAATTAAAACCCTAACCTAACTTAAT
1 TTAATTAAAACCCTAACCTAACTTAAT
*
2181 TTAATTAAAA----ACCCTAACTTAA-
1 TTAATTAAAACCCTAACCTAACTTAAT
*
2203 TTAATTAAAACCCTAACCTAACCTAACCTAAC
1 TTAATTAAAACCCTAACCTAA-CT----TAAT
* * ***** *
2235 CTAATTGAATTAAAAACCCTAACCTAACT
1 TTAATTAAAACCCTAA-CCTAACTTAA-T
*
2264 AATTAATT-AAACCCTAAAACCTAACCTAA-
1 --TTAATTAAAACCCT--AACCTAACTTAAT
2293 TTAATTAAAACCCTAACCTAACTTAA-
1 TTAATTAAAACCCTAACCTAACTTAAT
*
2319 TTAATTAAAAACCCTAACCTAACCTAAT
1 TTAATT-AAAACCCTAACCTAACTTAAT
2347 TTAATTAAAACCCTAA-C-AAC-TAA-
1 TTAATTAAAACCCTAACCTAACTTAAT
*
2370 TTAATTAAAACCCTAAACCCTAACCTAACT
1 TTAATTAAAACCCT-AA-CCTAACTTAA-T
*
2400 AATTAATTAAAAACCCTAACCTAACCTAAT
1 --TTAATT-AAAACCCTAACCTAACTTAAT
2430 TTAATTAAAACCCTAACCTAA-TTAAT
1 TTAATTAAAACCCTAACCTAACTTAAT
2456 TTAATT-AAACCCTAACCCTAAC-TAAT
1 TTAATTAAAACCCTAA-CCTAACTTAAT
*
2482 TTAATTAAAAACCCTAACCCTAACCTAAT
1 TTAATT-AAAACCCTAA-CCTAACTTAAT
2511 TTAATTAAAAACCCTAACCTAACTTAAT
1 TTAATT-AAAACCCTAACCTAACTTAAT
2539 TTAATTAAAA-CCTAACC---C-TAA-
1 TTAATTAAAACCCTAACCTAACTTAAT
2560 TTAATTAAAACCCTAACCTAA-TTAAT
1 TTAATTAAAACCCTAACCTAACTTAAT
2586 TTAATTAAAAACCCTAACCCTAAC-TAAT
1 TTAATT-AAAACCCTAA-CCTAACTTAAT
*
2614 TTAATTAAAACCCTAACCTAACCTAA-
1 TTAATTAAAACCCTAACCTAACTTAAT
2640 TTAATTAAAA-CCTAACC--A-TTAAT
1 TTAATTAAAACCCTAACCTAACTTAAT
*
2663 TTAATTAAAAACCTAACCCTAAC-TAAT
1 TTAATTAAAACCCTAA-CCTAACTTAAT
* *
2690 TTAATTAAAACCCTAACCCAACCTAAT
1 TTAATTAAAACCCTAACCTAACTTAAT
2717 TTAATTAAAACCCTAACCTAAC----T
1 TTAATTAAAACCCTAACCTAACTTAAT
2740 TTAATTAAAAACCCTAACCCTAACTTAAT
1 TTAATT-AAAACCCTAA-CCTAACTTAAT
2769 TTAATT-AAA----AACCTAACTTAAT
1 TTAATTAAAACCCTAACCTAACTTAAT
2791 TTAATTAAAAACCCTAACCTAAC-TAAT
1 TTAATT-AAAACCCTAACCTAACTTAAT
2818 TTAATT-AAACCCTAACCTAAC-----
1 TTAATTAAAACCCTAACCTAACTTAAT
*
2839 -CAATTAAAA-CCTAACCTAACTTAAT
1 TTAATTAAAACCCTAACCTAACTTAAT
*
2864 TTAATTAAAAACCCTAACCCTAACCTAAT
1 TTAATT-AAAACCCTAA-CCTAACTTAAT
2893 TTAATTAAAACCCTAACCTAAC-TAAT
1 TTAATTAAAACCCTAACCTAACTTAAT
*
2919 TTAATTAAAAACCCTAACCCTAACCTAAT
1 TTAATT-AAAACCCTAA-CCTAACTTAAT
*
2948 TTAATT-AAACCCTAACCCTAACCTAA-
1 TTAATTAAAACCCTAA-CCTAACTTAAT
2974 TTAATTAAAAACCCTAACCTAAC-TAAT
1 TTAATT-AAAACCCTAACCTAACTTAAT
3001 T
1 T
3002 AAACCCTAAA
Statistics
Matches: 738, Mismatches: 29, Indels: 161
0.80 0.03 0.17
Matches are distributed among these distances:
20 15 0.02
21 13 0.02
22 40 0.05
23 46 0.06
24 23 0.03
25 55 0.07
26 121 0.16
27 197 0.27
28 110 0.15
29 54 0.07
30 3 0.00
31 28 0.04
32 20 0.03
33 13 0.02
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (27 bp):
TTAATTAAAACCCTAACCTAACTTAAT
Found at i:2224 original size:5 final size:5
Alignment explanation
Indices: 2214--2238 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2204 TAATTAAAAC
2214 CCTAA CCTAA CCTAA CCTAA CCTAA
1 CCTAA CCTAA CCTAA CCTAA CCTAA
2239 TTGAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CCTAA
Found at i:2285 original size:64 final size:59
Alignment explanation
Indices: 2165--2450 Score: 218
Period size: 59 Copynumber: 5.0 Consensus size: 59
2155 TAATTAAAAC
* *
2165 CCTAACCTAACTTAATTTAATTAAAAACCCTAACTTAATTAATTAAAACCCTAACCTAA
1 CCTAACCTAACCTAATTGAATTAAAAACCCTAACTTAATTAATTAAAACCCTAACCTAA
* * *
2224 CCTAACCTAACCTAATTGAATTAAAAACCCTAACCTAACTAATTAATTAA----ACCCTAA
1 CCTAACCTAACCTAATTGAATTAAAAACCCTAACTTAATTAATTAA--AACCCTAACCTAA
* * *
2281 ---AACCTAACCTAATT-AATT-AAAACCCTAACCTAACTTAATT--AA--TTAA--AAA
1 CCTAACCTAACCTAATTGAATTAAAAACCCTAACTTAA-TTAATTAAAACCCTAACCTAA
* * *
2330 CCCTAACCTAACCTAATTTAATT-AAAACCCTAACAACTAATTAATTAAAACCCTAA---AC
1 -CCTAACCTAACCTAATTGAATTAAAAACCCTAAC--TTAATTAATTAAAACCCTAACCTAA
2388 CCTAACCTAA-CTAATT-AATTAAAAACCCTAACCTAACCTAATTTAATTAAAACCCTAACCTAA
1 CCTAACCTAACCTAATTGAATTAAAAACCCTAA-CT----TAA-TTAATTAAAACCCTAACCTAA
2451 TTAATTTAAT
Statistics
Matches: 189, Mismatches: 12, Indels: 48
0.76 0.05 0.19
Matches are distributed among these distances:
49 4 0.02
51 1 0.01
52 15 0.08
53 23 0.12
54 29 0.15
55 10 0.05
56 20 0.11
57 19 0.10
58 1 0.01
59 48 0.25
60 16 0.08
61 2 0.01
63 1 0.01
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (59 bp):
CCTAACCTAACCTAATTGAATTAAAAACCCTAACTTAATTAATTAAAACCCTAACCTAA
Found at i:3017 original size:21 final size:21
Alignment explanation
Indices: 2961--3017 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
2951 ATTAAACCCT
*
2961 AACCCTAACCTAATTAATTAAA
1 AACCCTAACCTAACTAATT-AA
2983 AACCCTAACCTAACTAATT-A
1 AACCCTAACCTAACTAATTAA
3003 AACCCTAAACCTAAC
1 AACCCT-AACCTAAC
3018 CCTAACATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 18 0.55
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCTAACCTAACTAATTAA
Found at i:3917 original size:125 final size:124
Alignment explanation
Indices: 3702--3957 Score: 318
Period size: 125 Copynumber: 2.1 Consensus size: 124
3692 CCACGAGGGC
**
3702 GCGATTTGACACTATTTGCTCAGAAATGTAAAAAAAAATTATTTCCAGCATGACCAACTGTAGCG
1 GCGATTTGACACTATTTGCTCAGAAACATAAAAAAAAATTATTTCCAGCATGACCAACTGTAGCG
* * ** * **
3767 AAGTCGCGTCCAAGAGGGCGTGATTTAACAATTTCTGCCCAATATAGCATCCTTGTATCA
66 AAATCGCGTCCAAGAGGCCACGATTTAACAATTTCTGCCCAA-ATAGCATCCTAGTAGAA
* * * *
3827 GCGATTTTATACTATTTGCTCAGAAAACATCAAAAAAAATTATTTCTTA-CATGACC-ACTGTAG
1 GCGATTTGACACTATTTGCTCAG-AAACATAAAAAAAAATTATTTC-CAGCATGACCAACTGTAG
* * * *
3890 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
64 CGAAATCGCGTCCAAGAGGCCACGATTTAACAATTTCTGCCCAAATAGCATCCTAGTAGAA
3951 GCGATTT
1 GCGATTT
3958 CCCATTATTT
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
124 21 0.19
125 64 0.57
126 26 0.23
127 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (124 bp):
GCGATTTGACACTATTTGCTCAGAAACATAAAAAAAAATTATTTCCAGCATGACCAACTGTAGCG
AAATCGCGTCCAAGAGGCCACGATTTAACAATTTCTGCCCAAATAGCATCCTAGTAGAA
Found at i:6420 original size:47 final size:47
Alignment explanation
Indices: 6351--6443 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
6341 TTCAATACAG
*
6351 TTACATACAATATATTTACCTGATTCAAAC-CACCTAATCAAGCTTTA
1 TTACATACAATATATCTACCTGATTC-AACTCACCTAATCAAGCTTTA
* *
6398 TTACATACAATATCTCTACCTGATTCAGCTCACCTAATCAAGCTTT
1 TTACATACAATATATCTACCTGATTCAACTCACCTAATCAAGCTTT
6444 GTACATTAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
46 2 0.05
47 40 0.95
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (47 bp):
TTACATACAATATATCTACCTGATTCAACTCACCTAATCAAGCTTTA
Found at i:15042 original size:104 final size:105
Alignment explanation
Indices: 14862--15129 Score: 450
Period size: 104 Copynumber: 2.6 Consensus size: 105
14852 TAACCGTTAT
* **
14862 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
14927 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
14966 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
15031 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
15071 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
15130 TTATATACAA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 82 0.53
105 71 0.46
106 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:15498 original size:30 final size:30
Alignment explanation
Indices: 15464--15521 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
15454 CCACCCAACT
15464 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
*** * *
15494 TTTTGCGTAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
15522 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:22801 original size:23 final size:23
Alignment explanation
Indices: 22758--22801 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
22748 AATGTCCAAA
*
22758 ATTTTCGTAACTCATTATTTATT
1 ATTTTCGTAACTCATGATTTATT
* *
22781 ATTTTCTTAACTCATGCTTTA
1 ATTTTCGTAACTCATGATTTA
22802 GGGACTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.55
Consensus pattern (23 bp):
ATTTTCGTAACTCATGATTTATT
Found at i:25207 original size:23 final size:23
Alignment explanation
Indices: 25180--25255 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
25170 AGTGTTATTG
*
25180 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
25203 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
25226 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
25249 ATTAGTG
1 ATCAGTG
25256 TTGCACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:32988 original size:15 final size:15
Alignment explanation
Indices: 32968--32998 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
32958 AAATAAGTTA
32968 TAATTTTTTTATTTT
1 TAATTTTTTTATTTT
32983 TAATTTTTTTATTTT
1 TAATTTTTTTATTTT
32998 T
1 T
32999 TATAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TAATTTTTTTATTTT
Found at i:33026 original size:18 final size:17
Alignment explanation
Indices: 33001--33050 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
32991 TTATTTTTTA
33001 TAAA-ATAAATAAAATT
1 TAAACATAAATAAAATT
33017 TAACACAT-AATAAAATT
1 TAA-ACATAAATAAAATT
*
33034 TAAACTTAAAATAAAAT
1 TAAACAT-AAATAAAAT
33051 AATTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 6 0.21
17 13 0.45
18 10 0.34
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAACATAAATAAAATT
Found at i:44236 original size:27 final size:27
Alignment explanation
Indices: 44183--44239 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
44173 GTGCAAACGA
*
44183 CACTTTGGTGCAAATTAACGATTGTGG
1 CACTTTGGTGCAAATTAACGATAGTGG
**
44210 CACTTTGGTGC-AATTCAGTGATAGTGG
1 CACTTTGGTGCAAATT-AACGATAGTGG
44237 CAC
1 CAC
44240 CTCAACGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (27 bp):
CACTTTGGTGCAAATTAACGATAGTGG
Found at i:45323 original size:21 final size:21
Alignment explanation
Indices: 45282--45342 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
45272 AAATAGAAGG
*
45282 GAAAG-AAGGGAAAAA-AAAA
1 GAAAGAAAAGGAAAAAGAAAA
* *
45301 GAAAGAAAATGAGAAAGAAAA
1 GAAAGAAAAGGAAAAAGAAAA
45322 GAAAGAAAAGGAAAAAGAAAA
1 GAAAGAAAAGGAAAAAGAAAA
45343 AGAGAGAGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 5 0.14
20 7 0.20
21 23 0.66
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
GAAAGAAAAGGAAAAAGAAAA
Found at i:47469 original size:17 final size:17
Alignment explanation
Indices: 47440--47474 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
47430 GTGTTAAAAT
47440 AGTGAATTGTG-AATAA
1 AGTGAATTGTGAAATAA
47456 AGTGAATATGTGAAATAA
1 AGTGAAT-TGTGAAATAA
47474 A
1 A
47475 AATATACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (17 bp):
AGTGAATTGTGAAATAA
Found at i:52905 original size:8 final size:8
Alignment explanation
Indices: 52892--52920 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
52882 AGTTAAATAT
52892 ATATTATA
1 ATATTATA
52900 ATATTATA
1 ATATTATA
52908 ATATTAT-
1 ATATTATA
52915 ATATTA
1 ATATTA
52921 ATGTTTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATATTATA
Found at i:52934 original size:41 final size:41
Alignment explanation
Indices: 52884--52963 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
52874 ATATTTAAAG
*
52884 TTAAATATATATTATAATAT-TATAATATTATATATTAATGT
1 TTAAATATATA-TATAATATATATAATATTATATAATAATGT
* ** *
52925 TTAAGTATATATATTTTATATATTATATTATATAATAAT
1 TTAAATATATATATAATATATATAATATTATATAATAAT
52964 AAAACAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 6 0.18
41 27 0.82
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (41 bp):
TTAAATATATATATAATATATATAATATTATATAATAATGT
Found at i:52951 original size:16 final size:16
Alignment explanation
Indices: 52888--52957 Score: 60
Period size: 15 Copynumber: 4.5 Consensus size: 16
52878 TTAAAGTTAA
52888 ATATATATTATAATATT
1 ATATATATTAT-ATATT
52905 ATA-ATATTATATATT
1 ATATATATTATATATT
*
52920 A-ATGT-TTA-AGTA-T
1 ATATATATTATA-TATT
*
52933 ATATATTTTATATATT
1 ATATATATTATATATT
52949 ATATTATAT
1 ATA-TATAT
52958 AATAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
13 3 0.07
14 9 0.21
15 12 0.28
16 12 0.28
17 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATATATATTATATATT
Found at i:53499 original size:41 final size:39
Alignment explanation
Indices: 53454--53579 Score: 139
Period size: 37 Copynumber: 3.2 Consensus size: 39
53444 TCGATGAAAT
* *
53454 ACTGGGTGTCAATTTACTACTTCGGATTAATTCGGTGAGGC
1 ACTGGGTGTCAATTTA-TACTTCGGATT-ATCCGATGAGGC
* * * *
53495 ACTGGGTGTCAATTTAT--TTCGGTTTAGCAGATGAGAC
1 ACTGGGTGTCAATTTATACTTCGGATTATCCGATGAGGC
*
53532 ACTGGGTGTCAATTTATTACTTCGAATTATCCGATGAGGC
1 ACTGGGTGTCAATTTA-TACTTCGGATTATCCGATGAGGC
*
53572 ACTAGGTG
1 ACTGGGTG
53580 CCAAACTGGT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
37 23 0.33
38 8 0.11
40 23 0.33
41 16 0.23
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (39 bp):
ACTGGGTGTCAATTTATACTTCGGATTATCCGATGAGGC
Found at i:57422 original size:20 final size:21
Alignment explanation
Indices: 57394--57433 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
57384 TATAATTATA
*
57394 TAATTAGATA-AATATTATTT
1 TAATGAGATATAATATTATTT
*
57414 TAATGAGATATATTATTATT
1 TAATGAGATATAATATTATT
57434 ATTTTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TAATGAGATATAATATTATTT
Found at i:59272 original size:101 final size:101
Alignment explanation
Indices: 59114--59336 Score: 331
Period size: 101 Copynumber: 2.2 Consensus size: 101
59104 CCATAACTAA
59114 GTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAAC
1 GTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAAC
*
59179 TGAGTTATGGCATTCTGATGATAATACAATCTCTAG
66 TGAGCTATGGCATTCTGATGATAATACAATCTCTAG
* * * *
59215 GTTATGGCACTATGAACGTAAGACCATGGTTGGACTATGGCAGTGTTTATATGTAAGACCATAGC
1 GTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAAC
* * * * *
59280 TGGGCTATGGCATTCTGATGATAAGACCAT-ACTGG
66 TGAGCTATGGCATTCTGATGATAATACAATCTCTAG
* *
59315 GTTATGACACTACGAATGTAAA
1 GTTATGACACTATGAACGTAAA
59337 GGATGAATTG
Statistics
Matches: 108, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 21 0.19
101 87 0.81
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (101 bp):
GTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAAC
TGAGCTATGGCATTCTGATGATAATACAATCTCTAG
Found at i:61865 original size:40 final size:41
Alignment explanation
Indices: 61788--61875 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 41
61778 AGCGGCTCTT
*
61788 TTAGCGGCGCTTGGAAAAAAAACGCCGATAAAAATCGAGCA
1 TTAGCGGCGCTTGCAAAAAAAACGCCGATAAAAATCGAGCA
** *
61829 TTAGCGGCGCTT-CAAGGAAAACGCC-ACTAAAGATCGAGCA
1 TTAGCGGCGCTTGCAAAAAAAACGCCGA-TAAAAATCGAGCA
61869 TTAGCGG
1 TTAGCGG
61876 AGTTTTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 1 0.02
40 29 0.69
41 12 0.29
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (41 bp):
TTAGCGGCGCTTGCAAAAAAAACGCCGATAAAAATCGAGCA
Found at i:64013 original size:43 final size:43
Alignment explanation
Indices: 63884--64125 Score: 231
Period size: 43 Copynumber: 5.6 Consensus size: 43
63874 ATAATTTTTT
* * * * *
63884 TAAAGGTTATGTT-TTTAGCGGCGTTTTTGTGAGAAGCGCCGC
1 TAAAGGTCAGGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * * * ** *
63926 TAAAGGTTC--GATCTATAGCTGCATTTGTGACAAAAAAGCACCGC
1 TAAAGG-TCAGGTTCTTTAGCGGCGTTTGTG--GGAAAAGCGCCGC
*
63970 TAAAGATCAGGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCAGGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
** * *
64013 TAAAGGTCTTGTTCTTTAGCGGTGTTTGTAGGAAAAGCGCCGC
1 TAAAGGTCAGGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
64056 TAAAGGTCATGG-TCTTTAGCGGCGTTTGTGGGAAAAGCGCAGC
1 TAAAGGTCA-GGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
** *
64099 TAAAGGTCTTGTTCTTTAGCAGCGTTT
1 TAAAGGTCAGGTTCTTTAGCGGCGTTT
64126 TTTTTAAAAA
Statistics
Matches: 161, Mismatches: 31, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.01
42 19 0.12
43 109 0.68
44 15 0.09
45 16 0.10
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (43 bp):
TAAAGGTCAGGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:64081 original size:86 final size:88
Alignment explanation
Indices: 63884--64118 Score: 282
Period size: 86 Copynumber: 2.7 Consensus size: 88
63874 ATAATTTTTT
* * * * * * * * *
63884 TAAAGGTTAT-GTTTTTAGCGGCGTTTTTGTGAGAAGCGCCGCTAAAGGT-TCGATCTATAGCTG
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGCGG
63947 CATTTGTGACAAAAAAGCACCGC
66 CATTTGTGACAAAAAAGCACCGC
*
63970 TAAAGATCA-GGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGCG
1 TAAAGGTCATGG-TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGCG
** ** *
64034 GTGTTTGT-A-GGAAAAGCGCCGC
65 GCATTTGTGACAAAAAAGCACCGC
*
64056 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAGGTCTTGTTCTTTAGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGC
64119 AGCGTTTTTT
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
86 76 0.59
87 37 0.29
88 15 0.12
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (88 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGCGG
CATTTGTGACAAAAAAGCACCGC
Found at i:64234 original size:22 final size:22
Alignment explanation
Indices: 64202--64245 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
64192 TATCGGCGCT
* *
64202 AAAAAGTGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
64224 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
64246 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.25, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:66731 original size:27 final size:25
Alignment explanation
Indices: 66701--66760 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
66691 AGCACATAAT
*
66701 CAAGAAGCACTTTCTCGAGCCATGTAA
1 CAAGAAGCAC-ATCT-GAGCCATGTAA
* *
66728 CAAGAAGCTCATGTGAGCCATGTAA
1 CAAGAAGCACATCTGAGCCATGTAA
*
66753 CAGGAAGC
1 CAAGAAGC
66761 TTATCCGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 18 0.62
26 2 0.07
27 9 0.31
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (25 bp):
CAAGAAGCACATCTGAGCCATGTAA
Found at i:68961 original size:16 final size:17
Alignment explanation
Indices: 68937--68969 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
68927 GATATTAAAA
68937 TAAAAAAAAT-AAATTT
1 TAAAAAAAATGAAATTT
*
68953 TAAATAAAATGAAATTT
1 TAAAAAAAATGAAATTT
68970 AAACATAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAAAAAATGAAATTT
Found at i:74353 original size:32 final size:32
Alignment explanation
Indices: 74317--74385 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
74307 ATTCTTGTGA
74317 ATGATGCACTTTGCTATATTTTGTTCCAAGTG
1 ATGATGCACTTTGCTATATTTTGTTCCAAGTG
74349 ATGATGCACTTTGCTATATTTTGTTCCAAGTG
1 ATGATGCACTTTGCTATATTTTGTTCCAAGTG
74381 ATGAT
1 ATGAT
74386 CTTGCATCGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.43
Consensus pattern (32 bp):
ATGATGCACTTTGCTATATTTTGTTCCAAGTG
Found at i:77383 original size:22 final size:22
Alignment explanation
Indices: 77338--77384 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
77328 CAAAATGCTG
* *
77338 TAAGAGAAATTATGAAGAATTC
1 TAAGAGAAATTAAGAAGAACTC
*
77360 TAAGAGAAATTAAGATGAACTC
1 TAAGAGAAATTAAGAAGAACTC
77382 TAA
1 TAA
77385 TGTAGCTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (22 bp):
TAAGAGAAATTAAGAAGAACTC
Found at i:78114 original size:49 final size:49
Alignment explanation
Indices: 78033--78130 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
78023 CCAACTTGCC
78033 AATGATCACTTGAAATGAAGCATCGGCGAACCCCTTA-CATAATATGTCT
1 AATGATCACTTGAAATGAAGCATCGGCGAACCCCTTAGC-TAATATGTCT
* * * *
78082 AATGATCTCTTGATATGAAGCATTGGCTAACCCCTTAGCTAATATGTCT
1 AATGATCACTTGAAATGAAGCATCGGCGAACCCCTTAGCTAATATGTCT
78131 GCCATCTACC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 43 0.98
50 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (49 bp):
AATGATCACTTGAAATGAAGCATCGGCGAACCCCTTAGCTAATATGTCT
Found at i:80168 original size:20 final size:20
Alignment explanation
Indices: 80140--80179 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
80130 AAACTAATTT
80140 TTATATAAAT-TTAATTATAA
1 TTATATAAATATTAA-TATAA
*
80160 TTATCTAAATATTAATATAA
1 TTATATAAATATTAATATAA
80180 AGCTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATATAAATATTAATATAA
Found at i:86937 original size:171 final size:171
Alignment explanation
Indices: 86652--86998 Score: 685
Period size: 171 Copynumber: 2.0 Consensus size: 171
86642 GCTATATAAT
*
86652 ATTCAGGAAAGGTCAATTGCATTGATTCTCTTTTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
1 ATTCAGGAAAGGTCAATTGCATTGATTCTCTTCTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
86717 TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
66 TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
86782 TCCATCCTCAATACTTCTGAATCATGTATACTTGATAATCA
131 TCCATCCTCAATACTTCTGAATCATGTATACTTGATAATCA
86823 ATTCAGGAAAGGTCAATTGCATTGATTCTCTTCTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
1 ATTCAGGAAAGGTCAATTGCATTGATTCTCTTCTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
86888 TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
66 TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
86953 TCCATCCTCAATACTTCTGAATCATGTATACTTGATAATCA
131 TCCATCCTCAATACTTCTGAATCATGTATACTTGATAATCA
86994 ATTCA
1 ATTCA
86999 AGCTTGGACA
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 175 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (171 bp):
ATTCAGGAAAGGTCAATTGCATTGATTCTCTTCTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
TCCATCCTCAATACTTCTGAATCATGTATACTTGATAATCA
Found at i:89759 original size:20 final size:21
Alignment explanation
Indices: 89730--89770 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
89720 TATATTAAAT
89730 TTTATAAAAG-TACAAAATAA
1 TTTATAAAAGTTACAAAATAA
* *
89750 TTTATCAAAGTTTCAAAATAA
1 TTTATAAAAGTTACAAAATAA
89771 AATTCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (21 bp):
TTTATAAAAGTTACAAAATAA
Found at i:97157 original size:14 final size:14
Alignment explanation
Indices: 97138--97164 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
97128 CATTTGCTCA
97138 TCTCTTGTGGTTTG
1 TCTCTTGTGGTTTG
97152 TCTCTTGTGGTTT
1 TCTCTTGTGGTTT
97165 TTTCAAGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.26, T:0.59
Consensus pattern (14 bp):
TCTCTTGTGGTTTG
Found at i:99709 original size:25 final size:24
Alignment explanation
Indices: 99627--100225 Score: 181
Period size: 23 Copynumber: 25.7 Consensus size: 24
99617 ATCTATCCTG
* *
99627 TTTGGACAGC-TCTTTTACATC-AA
1 TTTGGACAGCAT-TTATACACCAAA
*
99650 TTTGGACAGCATTTATATACCAAA
1 TTTGGACAGCATTTATACACCAAA
* *
99674 -CTAGACAGCATTT-TCACACCAAAA
1 TTTGGACAGCATTTAT-ACACC-AAA
* *
99698 TTTGGACAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
99722 -TTGGGCAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* *
99745 -TT-GAGCAGCATTTTTACATCAAAA
1 TTTGGA-CAGCATTTATACA-CCAAA
* *
99769 ATTGGACAGCA--TATATA-C-AA
1 TTTGGACAGCATTTATACACCAAA
* * *
99789 ----CACAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
99809 TTGGGCAGCA-TATATATAC-C-AAA
1 TTTGG-A-CAGCATTTATACACCAAA
* *
99832 -TT-GAGCAGCATTTTTACATCAAA
1 TTTGGA-CAGCATTTATACACCAAA
* * *
99855 ATTGGACAGCATATATACAAC-AA
1 TTTGGACAGCATTTATACACCAAA
* * ** *
99878 TATGGGCAGCATAAATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
*
99902 -TT-GAGCAGCATTTTTACACCAAAA
1 TTTGGA-CAGCATTTATACACC-AAA
* * * *
99926 ATTGGACATCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
** * *
99950 -TTGGGTAGCATATATATACCAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
99973 -TT-GAGCAACATTTTTACATCAAA
1 TTTGGA-CAGCATTTATACACCAAA
* * *
99996 ATTGGAC-GACATATATACAAC-AA
1 TTTGGACAG-CATTTATACACCAAA
* ** *
100019 TTTGGGCAGCATAAATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* *
100043 -TTGTG-CAACATTTTTACACCAAAA
1 TTTG-GACAGCATTTATACACC-AAA
* * *
100067 ATTGGACAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
100091 -TTGGGCAGCATATATATACCAAA
1 TTTGGACAGCATTTATACACCAAA
* *
100114 -TT-GAGCAGCATTTTTACATCAAA
1 TTTGGA-CAGCATTTATACACCAAA
* * *
100137 ATTGGACAGCATATATACAAC-AA
1 TTTGGACAGCATTTATACACCAAA
** *
100160 TTTGGACAGCATAAATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
*
100184 -TT-GAGCAGCATTTTTACACCAAAAA
1 TTTGGA-CAGCATTTATACACC--AAA
*
100209 TTTGGACAGCATATATA
1 TTTGGACAGCATTTATA
100226 TAACAATTTG
Statistics
Matches: 434, Mismatches: 93, Indels: 95
0.70 0.15 0.15
Matches are distributed among these distances:
16 6 0.01
18 5 0.01
19 1 0.00
20 8 0.02
21 7 0.02
22 8 0.02
23 240 0.55
24 73 0.17
25 66 0.15
26 18 0.04
27 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (24 bp):
TTTGGACAGCATTTATACACCAAA
Found at i:99730 original size:23 final size:23
Alignment explanation
Indices: 99699--100243 Score: 406
Period size: 23 Copynumber: 23.5 Consensus size: 23
99689 ACACCAAAAT
*
99699 TTGGACAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
99722 TTGGGCAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * *
99745 TTGAGCAGCATTTTTACATCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
*
99770 TTGGACAGCATATATACAAC--A
1 TTGGGCAGCATATATACAACAAA
99791 -----CAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
99809 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * *
99832 TTGAGCAGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
*
99856 TTGGACAGCATATATACAAC-AA
1 TTGGGCAGCATATATACAACAAA
*
99878 TATGGGCAGCATAAATACAACAAA
1 T-TGGGCAGCATATATACAACAAA
* * * *
99902 TTGAGCAGCATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
* *
99927 TTGGACATCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * *
99950 TTGGGTAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
99973 TTGAGCAACATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
99997 TTGGAC-GACATATATACAACAAT
1 TTGGGCAG-CATATATACAACAAA
*
100020 TTGGGCAGCATAAATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
100043 TTGTGCAACATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
*
100068 TTGGACAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
100091 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * *
100114 TTGAGCAGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
100138 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
* *
100161 TTGGACAGCATAAATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * *
100184 TTGAGCAGCATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
* * *
100209 TTTGGACAGCATATATATAACAAT
1 -TTGGGCAGCATATATACAACAAA
*
100233 TTGGGTAGCAT
1 TTGGGCAGCAT
100244 TTAAGCATCA
Statistics
Matches: 399, Mismatches: 100, Indels: 46
0.73 0.18 0.08
Matches are distributed among these distances:
16 15 0.04
18 1 0.00
21 1 0.00
22 3 0.01
23 251 0.63
24 59 0.15
25 56 0.14
26 13 0.03
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (23 bp):
TTGGGCAGCATATATACAACAAA
Found at i:99795 original size:16 final size:16
Alignment explanation
Indices: 99774--99806 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
99764 CAAAAATTGG
99774 ACAGCATATATACAAC
1 ACAGCATATATACAAC
99790 ACAGCATATATACAAC
1 ACAGCATATATACAAC
99806 A
1 A
99807 AATTGGGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.06, T:0.18
Consensus pattern (16 bp):
ACAGCATATATACAAC
Found at i:99849 original size:87 final size:86
Alignment explanation
Indices: 99703--100158 Score: 328
Period size: 93 Copynumber: 5.0 Consensus size: 86
99693 CAAAATTTGG
99703 ACAGCATATATACAACAAATTGGGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAA
1 ACAGCATATATACAACAAATTGGGCAGCATATATACAACAAATTGAGCAGCATTTTTACATC-AA
99768 AATTGGACAGCATATATACAAC
65 AATTGGACAGCATATATACAAC
* *
99790 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
1 ACAGCATATATACAACAAATTGGGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAA
99855 ATTGGACAGCATATATACAAC
66 ATTGGACAGCATATATACAAC
* * * * * * *
99876 AATATGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATTG-GACATCATAT
1 ---A----CAGCATATATACAACAAATTGGGCAGCATATATACA--ACAAATTGAG-CAGCATTT
* * ** *
99940 ATACAAC-AAATTGGGTAGCATATATATACCAAATTG
56 TTACATCAAAATTGGACAGC--ATATATA-C-AA--C
* * * * * * * *** *
99976 AGCAACATTTTTACATCAAAATTGGAC-GACATATATACAACAATTTGGGCAGCATAAATACAAC
1 A-CAGCATATATACAAC-AAATTGGGCAG-CATATATACAACAAATTGAGCAGCATTTTTACATC
* * * *
100040 -AAATTGTG-CAACATTTTTACACCAAAAATTGG
63 AAAATTG-GACAGCA--TATATA-C---AA---C
* *
100072 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
1 ACAGCATATATACAACAAATTGGGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAA
100137 ATTGGACAGCATATATACAAC
66 ATTGGACAGCATATATACAAC
100158 A
1 A
100159 ATTTGGACAG
Statistics
Matches: 290, Mismatches: 51, Indels: 57
0.73 0.13 0.14
Matches are distributed among these distances:
86 25 0.09
87 60 0.21
89 3 0.01
91 1 0.00
92 1 0.00
93 68 0.23
94 61 0.21
95 57 0.20
96 10 0.03
97 2 0.01
98 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (86 bp):
ACAGCATATATACAACAAATTGGGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAA
ATTGGACAGCATATATACAAC
Found at i:99875 original size:70 final size:71
Alignment explanation
Indices: 99790--100243 Score: 639
Period size: 70 Copynumber: 6.4 Consensus size: 71
99780 TATATACAAC
* * * *
99790 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATC-AA
1 ACAGCATATATACAACAAATTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
99854 AATTGG
66 AATTGG
99860 ACAGCATATATACAAC-AATATGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAA
1 ACAGCATATATACAACAAAT-TGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAA
99924 AAATTGG
65 AAATTGG
* * * * * * *
99931 ACATCATATATACAACAAATTGGGTAGCATATATATACCAAATTGAGCAACATTTTTACATC-AA
1 ACAGCATATATACAACAAATTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
99995 AATTGG
66 AATTGG
* * *
100001 AC-GACATATATACAACAATTTGGGCAGCATAAATACAACAAATTGTGCAACATTTTTACACCAA
1 ACAG-CATATATACAACAAATTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAA
100065 AAATTGG
65 AAATTGG
* * * *
100072 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATC-AA
1 ACAGCATATATACAACAAATTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
100136 AATTGG
66 AATTGG
* *
100142 ACAGCATATATACAACAATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
1 ACAGCATATATACAACAAATTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
100207 AATTTGG
66 AA-TTGG
* * *
100214 ACAGCATATATATAACAATTTGGGTAGCAT
1 ACAGCATATATACAACAAATTGGGCAGCAT
100244 TTAAGCATCA
Statistics
Matches: 341, Mismatches: 35, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
69 3 0.01
70 179 0.52
71 124 0.36
72 35 0.10
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (71 bp):
ACAGCATATATACAACAAATTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
AATTGG
Found at i:99919 original size:157 final size:158
Alignment explanation
Indices: 99642--99947 Score: 483
Period size: 157 Copynumber: 1.9 Consensus size: 158
99632 ACAGCTCTTT
* * *
99642 TACATCAATTTGGACAGCATTTATATACCAAACTAGACAGCATTTTCACACCAAAATTTGGACAG
1 TACAACAAATTGGACAGCATATATATACCAAACTAGACAGCATTTTCACACCAAAATTTGGACAG
* *
99707 CATATATACAACAAATTGGGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAAAATT
66 CATATATACAACAAATTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATT
99772 GGACAGCATATATACAACACAGCATATA
131 GGACAGCATATATACAACACAGCATATA
* * * *
99800 TACAACAAATTGGGCAGCATATATATACCAAA-TTGAGCAGCATTTTTACATCAAAA-TTGGACA
1 TACAACAAATTGGACAGCATATATATACCAAACTAGA-CAGCATTTTCACACCAAAATTTGGACA
99863 GCATATATACAAC-AATATGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAA
65 GCATATATACAACAAAT-TGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAA
*
99927 TTGGACATCATATATACAACA
129 TTGGACAGCATATATACAACA
99948 AATTGGGTAG
Statistics
Matches: 136, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
156 3 0.02
157 88 0.65
158 45 0.33
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.25
Consensus pattern (158 bp):
TACAACAAATTGGACAGCATATATATACCAAACTAGACAGCATTTTCACACCAAAATTTGGACAG
CATATATACAACAAATTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATT
GGACAGCATATATACAACACAGCATATA
Found at i:99967 original size:141 final size:141
Alignment explanation
Indices: 99790--100243 Score: 793
Period size: 141 Copynumber: 3.2 Consensus size: 141
99780 TATATACAAC
99790 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
1 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
*
99855 ATTGGACAGCATATATACAACAATATGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACA
66 ATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACA
99920 CCAAAAATTGG
131 CCAAAAATTGG
* * *
99931 ACATCATATATACAACAAATTGGGTAGCATATATATACCAAATTGAGCAACATTTTTACATCAAA
1 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
* *
99996 ATTGGAC-GACATATATACAACAATTTGGGCAGCATAAATACAACAAATTGTGCAACATTTTTAC
66 ATTGGACAG-CATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTAC
100060 ACCAAAAATTGG
130 ACCAAAAATTGG
100072 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
1 ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
*
100137 ATTGGACAGCATATATACAACAATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTTACA
66 ATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACA
100202 CCAAAAATTTGG
131 CCAAAAA-TTGG
* * *
100214 ACAGCATATATATAACAATTTGGGTAGCAT
1 ACAGCATATATACAACAAATTGGGCAGCAT
100244 TTAAGCATCA
Statistics
Matches: 295, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
140 1 0.00
141 262 0.89
142 32 0.11
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (141 bp):
ACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
ATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACA
CCAAAAATTGG
Found at i:100256 original size:49 final size:49
Alignment explanation
Indices: 99884--100245 Score: 172
Period size: 48 Copynumber: 7.6 Consensus size: 49
99874 ACAATATGGG
*
99884 CAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAA-TTGGA
1 CAGCATAAATACAACAAATTGAGCAGCATTTTAACACCAAAAATTTGGA
* * * * * *
99932 CATCATATATACAACAAATTGGGTAGCA-TATATATACC--AAA-TT-GA
1 CAGCATAAATACAACAAATTGAGCAGCATTTTA-ACACCAAAAATTTGGA
* *** * * * * *
99977 GCAACATTTTTACATCAAAATTG-G-ACGACA-TAT-ATA-CAACAATTTGGG
1 -CAGCATAAATACAAC-AAATTGAGCA-G-CATTTTAACACCAAAAATTTGGA
* * *
100025 CAGCATAAATACAACAAATTGTGCAACATTTTTACACCAAAAA-TTGGA
1 CAGCATAAATACAACAAATTGAGCAGCATTTTAACACCAAAAATTTGGA
* * * *
100073 CAGCATATATACAACAAATTGGGCAGCA-TATATATACC--AAA-TT-GA
1 CAGCATAAATACAACAAATTGAGCAGCATTTTA-ACACCAAAAATTTGGA
*** * * * *
100118 GCAGCATTTTTACATCAAAATTG-GACAGCA-TAT-ATA-CAACAATTTGGA
1 -CAGCATAAATACAAC-AAATTGAG-CAGCATTTTAACACCAAAAATTTGGA
*
100166 CAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATTTGGA
1 CAGCATAAATACAACAAATTGAGCAGCATTTTAACACCAAAAATTTGGA
* * * * *
100215 CAGCATATATATAACAATTTGGGTAGCATTT
1 CAGCATAAATACAACAAATTGAGCAGCATTT
100246 AAGCATCAAA
Statistics
Matches: 243, Mismatches: 45, Indels: 51
0.72 0.13 0.15
Matches are distributed among these distances:
44 2 0.01
45 11 0.05
46 59 0.24
47 60 0.25
48 69 0.28
49 42 0.17
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (49 bp):
CAGCATAAATACAACAAATTGAGCAGCATTTTAACACCAAAAATTTGGA
Found at i:100999 original size:28 final size:28
Alignment explanation
Indices: 100967--101064 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
100957 TTTAATAAGT
*
100967 TCGCACACCTAGTGTTTAATAATCAATC
1 TCGCACACTTAGTGTTTAATAATCAATC
*
100995 TCGCACACTTAGTGCTTAATAATCAATC
1 TCGCACACTTAGTGTTTAATAATCAATC
* * * *
101023 TCGCATACTTAGTGATTT-ACAATTAAAC
1 TCGCACACTTAGTG-TTTAATAATCAATC
101051 TCGCACACTTAGTG
1 TCGCACACTTAGTG
101065 CTAATCTCAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 59 0.97
29 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (28 bp):
TCGCACACTTAGTGTTTAATAATCAATC
Found at i:109180 original size:24 final size:23
Alignment explanation
Indices: 109094--109172 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
109084 TAAATTAAAT
* *
109094 GAACTTGTTCATGACTACTTAAT-
1 GAACATGTTCATGAATA-TTAATC
* * * *
109117 GAATATATTCAAGAATATTAATT
1 GAACATGTTCATGAATATTAATC
109140 GAACATGTTCATGAATATATAATC
1 GAACATGTTCATGAATAT-TAATC
*
109164 GAATATGTT
1 GAACATGTT
109173 TGTGAATAAG
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 5 0.11
23 27 0.61
24 12 0.27
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (23 bp):
GAACATGTTCATGAATATTAATC
Found at i:119270 original size:20 final size:21
Alignment explanation
Indices: 119221--119270 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
119211 AGAAAAAAAT
* *
119221 TTAAAGTAGAAGTGAAGACGG
1 TTAAAGAAAAAGTGAAGACGG
* *
119242 TTGAGGAAAAAGTGAAGA-GG
1 TTAAAGAAAAAGTGAAGACGG
119262 TTAAAGAAA
1 TTAAAGAAA
119271 TAATGTAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.48, C:0.02, G:0.32, T:0.18
Consensus pattern (21 bp):
TTAAAGAAAAAGTGAAGACGG
Found at i:130511 original size:3 final size:3
Alignment explanation
Indices: 130490--130526 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
130480 CAAAGCTAAA
* *
130490 AAT AAT GAT AAT GAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
130527 CTTGGCCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:147001 original size:41 final size:41
Alignment explanation
Indices: 146956--147038 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
146946 TATAAAACCT
* *
146956 TAGTTTTGATTTTAGTATTTTGCTTTACTTTTGAAATTTTC
1 TAGTTTTGATTTTAGTATTCTGCTTTACTTTTGAAAATTTC
146997 TAGTTTTGATTTTAGTATTCTGCTTTACTTTTGAAAATTTC
1 TAGTTTTGATTTTAGTATTCTGCTTTACTTTTGAAAATTTC
147038 T
1 T
147039 TTTTATTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.59
Consensus pattern (41 bp):
TAGTTTTGATTTTAGTATTCTGCTTTACTTTTGAAAATTTC
Found at i:159526 original size:59 final size:58
Alignment explanation
Indices: 159393--159527 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 58
159383 TTTTCAAAGA
*
159393 TTAACTTGGACAAAAAAATTCTAATCCCAATGTGAGAACATTTATCAAGTTCTAGGGC
1 TTAACTTGGACAAAAAAATTCTAATCCCAATGTGAGAACAATTATCAAGTTCTAGGGC
* * * *
159451 TTAACTTGGACCAAAAAAAGTAT-TAGTCCTAATGTGGGAACAATTATCAAGTT-TAAGG-
1 TTAACTTGGA-CAAAAAAA-T-TCTAATCCCAATGTGAGAACAATTATCAAGTTCTAGGGC
159509 TCTAACTTGGACAAAAAAA
1 T-TAACTTGGACAAAAAAA
159528 ATTTTAAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
58 19 0.28
59 21 0.31
60 27 0.40
61 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (58 bp):
TTAACTTGGACAAAAAAATTCTAATCCCAATGTGAGAACAATTATCAAGTTCTAGGGC
Found at i:159557 original size:59 final size:58
Alignment explanation
Indices: 159393--159563 Score: 163
Period size: 59 Copynumber: 2.9 Consensus size: 58
159383 TTTTCAAAGA
* *
159393 TTAACTTGGAC-AAAAAAATTCTAA-TCCCAATGTGAGAACATTTATCAAGTTCTAGGGC
1 TTAACTTGGACAAAAAAAATTTTAAGTCCCAATGTG-GAA-AATTATCAAGTTCTAGGGC
* * * *
159451 TTAACTTGGACCAAAAAAAGTATT-AGTCCTAATGTGGGAACAATTATCAAGTT-TAAGG-
1 TTAACTTGGA-CAAAAAAAATTTTAAGTCCCAATGT-GGAA-AATTATCAAGTTCTAGGGC
* *
159509 TCTAACTTGGACAAAAAAAATTTTAAGCCCCAACGTCGGAAAAGTTATCAAGTTC
1 T-TAACTTGGACAAAAAAAATTTTAAGTCCCAATGT-GGAAAA-TTATCAAGTTC
159564 AAGCTCAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
58 24 0.26
59 37 0.40
60 31 0.33
61 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (58 bp):
TTAACTTGGACAAAAAAAATTTTAAGTCCCAATGTGGAAAATTATCAAGTTCTAGGGC
Found at i:165248 original size:6 final size:6
Alignment explanation
Indices: 165237--165365 Score: 195
Period size: 6 Copynumber: 21.5 Consensus size: 6
165227 CAACGATGGG
* *
165237 TCCGGT TCCGGT TCTGGT TCCGGT TCTGGT TCCGGT TCCGGT TCCGGT
1 TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT
* * *
165285 TCCGGT TCTGGT TCCGAT TCCGGT TCCGGT TCCGGT TCCGGT TCTGGT
1 TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT
* *
165333 TACGAT TCCGGT TCCGGT TCCGGT TCCGGT TCC
1 TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCC
165366 AGCTCCAAGA
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 109 1.00
ACGTcount: A:0.02, C:0.30, G:0.31, T:0.36
Consensus pattern (6 bp):
TCCGGT
Found at i:173692 original size:17 final size:17
Alignment explanation
Indices: 173667--173700 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
173657 ACTATCAATT
*
173667 ATTTAGAAAAATTCGAA
1 ATTTAGAAAAAGTCGAA
*
173684 ATTTTGAAAAAGTCGAA
1 ATTTAGAAAAAGTCGAA
173701 CGAAACCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (17 bp):
ATTTAGAAAAAGTCGAA
Found at i:176700 original size:24 final size:24
Alignment explanation
Indices: 176668--176718 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
176658 ATGCTTCCCA
176668 TTAATTGCTCTTCAAAGCTACCCG
1 TTAATTGCTCTTCAAAGCTACCCG
**
176692 TTAATTGCTCTTTGAAGCTACCCG
1 TTAATTGCTCTTCAAAGCTACCCG
176716 TTA
1 TTA
176719 TAGGCTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (24 bp):
TTAATTGCTCTTCAAAGCTACCCG
Found at i:176729 original size:24 final size:26
Alignment explanation
Indices: 176682--176746 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
176672 TTGCTCTTCA
* *
176682 AAGCTACCCGTTA-ATTGCTCTTTG-
1 AAGCTACCCGTTATATGGCTATTTGT
176706 AAGCTACCCGTTATA-GGCTATTTGT
1 AAGCTACCCGTTATATGGCTATTTGT
* *
176731 GAGCTTCCCGTTATAT
1 AAGCTACCCGTTATAT
176747 TGCTCGGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 20 0.59
25 14 0.41
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (26 bp):
AAGCTACCCGTTATATGGCTATTTGT
Found at i:187374 original size:18 final size:17
Alignment explanation
Indices: 187343--187377 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
187333 GATTTAGGGT
187343 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
187360 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
187378 AAATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:191114 original size:16 final size:17
Alignment explanation
Indices: 191093--191124 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
191083 AAATATGCAA
191093 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
191109 TCACATAACTTCATAT
1 TCACATAACTTCATAT
191125 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:191351 original size:43 final size:43
Alignment explanation
Indices: 191285--191454 Score: 208
Period size: 43 Copynumber: 4.0 Consensus size: 43
191275 GACTCGTACA
*
191285 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
191328 ATGCC-ACTGTCCCAGACAG-GGTCTTACACG-AATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* * * *
191369 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATA-TCG
191412 ATGCCAACGTCCCAGACGTGGTCTTACACGATAA-CACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-TAATCACATATCG
191455 GAAATCCTAT
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
41 28 0.26
42 16 0.15
43 59 0.55
44 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:191426 original size:84 final size:84
Alignment explanation
Indices: 191285--191442 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
191275 GACTCGTACA
* * * *
191285 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAGAC-GTGG
191349 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
*
191369 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCAATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCAATGCC-ACTGTCCCAGACGTG
191432 GTCTTACACGA
64 GTCTTACACGA
191443 TAACACATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 2 0.03
84 62 0.94
85 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:192841 original size:7 final size:7
Alignment explanation
Indices: 192829--192853 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
192819 AGAGAGCACT
192829 GATATGA
1 GATATGA
192836 GATATGA
1 GATATGA
192843 GATATGA
1 GATATGA
192850 GATA
1 GATA
192854 GTAGTGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (7 bp):
GATATGA
Found at i:195187 original size:34 final size:34
Alignment explanation
Indices: 195149--195227 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
195139 CAAATGACCT
* *
195149 ATGTAAATCATGTATTCCGTGTAGTTTATAAACC
1 ATGTAAATCATGTATTCCATGTAATTTATAAACC
* *
195183 ATGTAAATCATGTATTTCATGTAATTTATAATCC
1 ATGTAAATCATGTATTCCATGTAATTTATAAACC
*
195217 TTGTAAATCAT
1 ATGTAAATCAT
195228 ATAACTCTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (34 bp):
ATGTAAATCATGTATTCCATGTAATTTATAAACC
Found at i:195432 original size:22 final size:23
Alignment explanation
Indices: 195404--195494 Score: 107
Period size: 23 Copynumber: 4.0 Consensus size: 23
195394 TTGAGCTGGT
*
195404 AAACGGTAAGCTCTATCGAGCTG
1 AAACGGTAAGCTCTATAGAGCTG
*
195427 -AACGGTAAGCTCCATAGAGCTG
1 AAACGGTAAGCTCTATAGAGCTG
*
195449 AAATGGTAAGCTCGTA-AGAGCTG
1 AAACGGTAAGCTC-TATAGAGCTG
*
195472 AAACGGTAAGTTC-ATACGAGCTG
1 AAACGGTAAGCTCTATA-GAGCTG
195495 TTGTGAGTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.02
22 21 0.36
23 35 0.60
24 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (23 bp):
AAACGGTAAGCTCTATAGAGCTG
Found at i:195458 original size:45 final size:46
Alignment explanation
Indices: 195408--195494 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
195398 GCTGGTAAAC
*
195408 GGTAAGCTC-TATCGAGCTG-AACGGTAAGCTCCATA-GAGCTGAAAT
1 GGTAAGCTCGTA-AGAGCTGAAACGGTAAG-TCCATACGAGCTGAAAT
*
195453 GGTAAGCTCGTAAGAGCTGAAACGGTAAGTTCATACGAGCTG
1 GGTAAGCTCGTAAGAGCTGAAACGGTAAGTCCATACGAGCTG
195495 TTGTGAGTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
45 20 0.54
46 17 0.46
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (46 bp):
GGTAAGCTCGTAAGAGCTGAAACGGTAAGTCCATACGAGCTGAAAT
Found at i:200462 original size:12 final size:13
Alignment explanation
Indices: 200442--200473 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
200432 CCGCCCGTAT
200442 TAATTTTTTT-TA
1 TAATTTTTTTATA
200454 T-ATTTTTTTATA
1 TAATTTTTTTATA
200466 TAATTTTT
1 TAATTTTT
200474 AAATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.44
12 4 0.22
13 6 0.33
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TAATTTTTTTATA
Found at i:204583 original size:3 final size:3
Alignment explanation
Indices: 204575--204610 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
204565 ATCGTATCAG
204575 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
204611 TATTGCTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:219763 original size:6 final size:6
Alignment explanation
Indices: 219752--219782 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
219742 TAGTTGAGTA
219752 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT G
1 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT G
219783 GTTTATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.16
Consensus pattern (6 bp):
GAGCCT
Found at i:224573 original size:4 final size:4
Alignment explanation
Indices: 224566--224595 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
224556 GAGCATATGT
224566 ATGG ATGG ATGG ATGG ATGG ATGG ATGG AT
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG AT
224596 ACCTGAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.47, T:0.27
Consensus pattern (4 bp):
ATGG
Found at i:225655 original size:20 final size:20
Alignment explanation
Indices: 225633--225669 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
225623 ATTTTAGGAT
225633 TTTTATA-ATTTTTTAAAGA
1 TTTTATATATTTTTTAAAGA
225652 TTTTATATATTTTTTAAA
1 TTTTATATATTTTTTAAA
225670 TTTCCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATATATTTTTTAAAGA
Found at i:241119 original size:14 final size:13
Alignment explanation
Indices: 241093--241143 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
241083 GTTTATTTGA
241093 AATATAATAATAT
1 AATATAATAATAT
241106 AATATAATTAATAT
1 AATATAA-TAATAT
* *
241120 AAT-TTACAATAT
1 AATATAATAATAT
*
241132 AATAAAATAATA
1 AATATAATAATA
241144 ATATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:260895 original size:5 final size:5
Alignment explanation
Indices: 260885--260909 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
260875 TCTATGTATG
260885 TTCTC TTCTC TTCTC TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC
260910 CCTACAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCTC
Found at i:261245 original size:6 final size:6
Alignment explanation
Indices: 261234--261265 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
261224 AGTGAGGGGA
261234 GCGGAG GCGGAG GCGGAG GCGGAAG GCGGAG G
1 GCGGAG GCGGAG GCGGAG GCGG-AG GCGGAG G
261266 GAGGAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.19, C:0.16, G:0.66, T:0.00
Consensus pattern (6 bp):
GCGGAG
Found at i:285538 original size:16 final size:17
Alignment explanation
Indices: 285500--285538 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
285490 AACTTCAAAT
285500 TATTTTTTTATATATAA
1 TATTTTTTTATATATAA
285517 -AGTTTTTTTAT-TATAA
1 TA-TTTTTTTATATATAA
285533 TATTTT
1 TATTTT
285539 ACCACAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTTTTTTATATATAA
Found at i:296232 original size:5 final size:5
Alignment explanation
Indices: 296222--296246 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
296212 TCTATGTATG
296222 TTCTC TTCTC TTCTC TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC
296247 CCTACAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCTC
Found at i:296581 original size:6 final size:6
Alignment explanation
Indices: 296566--296605 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
296556 ATTATTGAGT
296566 GAGG-G GAGGCG GAGGCG GAGGCG GAGGCG GAAGGCG GAGG
1 GAGGCG GAGGCG GAGGCG GAGGCG GAGGCG G-AGGCG GAGG
296606 GAGGAAAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 4 0.12
6 23 0.70
7 6 0.18
ACGTcount: A:0.20, C:0.12, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGGCG
Found at i:329298 original size:5 final size:5
Alignment explanation
Indices: 329288--329312 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
329278 TCTATGTATG
329288 TTCTC TTCTC TTCTC TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC
329313 CCTACAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCTC
Found at i:329646 original size:6 final size:6
Alignment explanation
Indices: 329632--329672 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
329622 ATTATTGAGT
*
329632 GAGGGG GAGGCG GAGGCG GAGGCG GAGGCG GAAGGCG GAGG
1 GAGGCG GAGGCG GAGGCG GAGGCG GAGGCG G-AGGCG GAGG
329673 GAGGAAAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.20, C:0.12, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGGCG
Found at i:343409 original size:20 final size:22
Alignment explanation
Indices: 343372--343412 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
343362 CCGGCCTATT
343372 TTTTAATAAATATTAAAAAATTA
1 TTTTAATAAATA-TAAAAAATTA
343395 TTTTAA-AAATA-AAAAAAT
1 TTTTAATAAATATAAAAAAT
343413 AAAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTAATAAATATAAAAAATTA
Found at i:343416 original size:26 final size:25
Alignment explanation
Indices: 343387--343438 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
343377 ATAAATATTA
343387 AAAAATTATTTTAAAAATAAAAAAAT
1 AAAAA-TATTTTAAAAATAAAAAAAT
* *
343413 AAAAATATTTTAAAATTTAAAAAAT
1 AAAAATATTTTAAAAATAAAAAAAT
343438 A
1 A
343439 TATTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAATATTTTAAAAATAAAAAAAT
Found at i:345759 original size:36 final size:36
Alignment explanation
Indices: 345712--345785 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
345702 AACAACTTAA
345712 TCAAATTCTACTATTAATTTTTATGTGTAAATTGCC
1 TCAAATTCTACTATTAATTTTTATGTGTAAATTGCC
345748 TCAAATTCTACTATTAATTTTTATGTGTAAATTGCC
1 TCAAATTCTACTATTAATTTTTATGTGTAAATTGCC
345784 TC
1 TC
345786 TCTTCTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (36 bp):
TCAAATTCTACTATTAATTTTTATGTGTAAATTGCC
Found at i:350890 original size:7 final size:7
Alignment explanation
Indices: 350878--350902 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
350868 GCTGCTTGCT
350878 TTTTGGC
1 TTTTGGC
350885 TTTTGGC
1 TTTTGGC
350892 TTTTGGC
1 TTTTGGC
350899 TTTT
1 TTTT
350903 AGGATCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.24, T:0.64
Consensus pattern (7 bp):
TTTTGGC
Found at i:351294 original size:28 final size:29
Alignment explanation
Indices: 351235--351294 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
351225 AATCTTTCAT
* **
351235 AATTAATTTTGAAAAGAAAATTAAAATTA
1 AATTAATTTTGAAAAGAAAATAAAAAGGA
351264 AATT-ATTTTAGAAAAGAAAA-AAAAAGGA
1 AATTAATTTT-GAAAAGAAAATAAAAAGGA
351292 AAT
1 AAT
351295 CAAACATCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (29 bp):
AATTAATTTTGAAAAGAAAATAAAAAGGA
Found at i:365257 original size:18 final size:19
Alignment explanation
Indices: 365224--365262 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
365214 ATGAGTGCTA
*
365224 ATAATTCTACTTCAAACTT
1 ATAATCCTACTTCAAACTT
*
365243 ATAATCCTA-TTCAAATTT
1 ATAATCCTACTTCAAACTT
365261 AT
1 AT
365263 TATCAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATCCTACTTCAAACTT
Found at i:367590 original size:17 final size:16
Alignment explanation
Indices: 367562--367614 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
367552 TTTGGTTCGC
*
367562 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
367578 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
367595 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
367611 TGTA
1 TGTA
367615 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 20 0.57
17 15 0.43
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:367867 original size:16 final size:16
Alignment explanation
Indices: 367830--367884 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
367820 TTAATCATAT
*
367830 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
367846 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
367861 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
367879 -TAAAAT
1 TTAAAAT
367885 TCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:367877 original size:18 final size:18
Alignment explanation
Indices: 367836--367884 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
367826 ATATTTAAAC
367836 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
367854 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
367870 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
367885 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:368003 original size:67 final size:67
Alignment explanation
Indices: 367932--368144 Score: 168
Period size: 67 Copynumber: 3.1 Consensus size: 67
367922 ATTGTTAATG
*
367932 TTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAAT
367997 TA
66 TA
* * * * * * ***
367999 TTATTAAATATATTTTAATTAAAATATATAATT-T-AATAA-AATTCTTATAAT--TAGCAGAAA
1 TTATT---TAAATTTTAA-TAAGAT-TATTATTATCAATAATAAATATTTTAATCATA-TTTAAA
** * *
368059 TTTGTTATTG
60 --CATAATTA
* *
368069 TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAAT
368134 TA
66 TA
368136 TTA-TTAAAT
1 TTATTTAAAT
368145 ACATTATAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 27
0.65 0.18 0.17
Matches are distributed among these distances:
65 5 0.05
66 12 0.12
67 28 0.27
68 11 0.11
69 12 0.12
70 24 0.23
71 6 0.06
72 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (67 bp):
TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAAT
TA
Found at i:368021 original size:156 final size:156
Alignment explanation
Indices: 367737--368064 Score: 620
Period size: 156 Copynumber: 2.1 Consensus size: 156
367727 TAGAATACCC
* *
367737 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
367802 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
367867 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
367893 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
367958 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
368023 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
*
368049 TTAGCAGAAATTTGTT
1 TTAGCAGAAAATTGTT
368065 ATTGTTATTT
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 168 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTATAA
Found at i:368027 original size:18 final size:17
Alignment explanation
Indices: 368006--368040 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
367996 TTATTATTAA
*
368006 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
368024 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
368041 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:368031 original size:137 final size:137
Alignment explanation
Indices: 367742--368182 Score: 315
Period size: 156 Copynumber: 3.1 Consensus size: 137
367732 TACCCTTAGC
*
367742 ATAAAATTGTT-TTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
1 ATAAAATTCTTATTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
*
367806 CAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAATATA
66 CAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
367871 TAATTTA
131 TAATTTA
* * * * * *
367878 ATAAAATTCTTATAATTAGCAGAAAATTG-TT-TTGGTAAATGATTATTGTTAATGTTATTTAA-
1 ATAAAATTC-T-T-ATT-G--GTAAA-TGATTATT-GTTATTG-TTATT-TAAATTTTA-ATAAG
* * * * ** *
367940 ATT-TTA--ATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTA
55 ATTATTATTATCAG-TAATAAATAT-TTTAAT-CATA---T--T--T----AAACATAATTATTA
368002 TTAAATATATTTTAATTAAAATATATAATTTA
106 TTAAATATATTTTAATTAAAATATATAATTTA
*** * * *
368034 ATAAAATTCTTATAATTAGCA-GA-AATTTGTTATTGTTATTTAAATTTTAATAAGATTATTAAT
1 ATAAAATTCTTATTGGTA-AATGATTA-TTGTTATTGTTATTTAAATTTTAATAAGATTATTATT
* * * * ****
368097 ATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATACATTATAATTTTGGTA
64 ATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATA
368162 TATAATTTA
129 TATAATTTA
368171 ATAAAATTCTTA
1 ATAAAATTCTTA
368183 ATAATTCATA
Statistics
Matches: 230, Mismatches: 41, Indels: 67
0.68 0.12 0.20
Matches are distributed among these distances:
136 8 0.03
137 53 0.23
138 1 0.00
140 2 0.01
141 2 0.01
142 6 0.03
143 19 0.08
144 14 0.06
145 14 0.06
146 3 0.01
147 3 0.01
148 14 0.06
149 13 0.06
150 13 0.06
151 6 0.03
152 1 0.00
153 2 0.01
154 1 0.00
155 1 0.00
156 54 0.23
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (137 bp):
ATAAAATTCTTATTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
CAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
TAATTTA
Found at i:368222 original size:137 final size:135
Alignment explanation
Indices: 367944--368222 Score: 339
Period size: 137 Copynumber: 2.0 Consensus size: 135
367934 ATTTAAATTT
* * *
367944 TAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
* * * *
368009 TATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAGAAATTTGTTATTGTTATT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTA-CA-AAATTTCTTATTGTTACT
* **
368074 TAAATTT
129 CAAATCA
368081 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
**** *
368146 CATTATAATTTTGGTATATAATTTAATAAAATTCTTAATAATT-C-ATA-TTCTTATATGAATTT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTT-ATAATTACAAAATTTCTTAT-TG---TT
368208 ACTCAAATCA
126 ACTCAAATCA
368218 TAATA
1 TAATA
368223 TATGATACTA
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
133 6 0.05
134 4 0.03
136 1 0.01
137 105 0.86
138 6 0.05
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (135 bp):
TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTACAAAATTTCTTATTGTTACTCA
AATCA
Found at i:371677 original size:8 final size:9
Alignment explanation
Indices: 371657--371691 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
371647 ATATTACAAC
371657 AAAAATTTA
1 AAAAATTTA
371666 AAAAATTTA
1 AAAAATTTA
371675 AAAAATTT-
1 AAAAATTTA
371683 AAAAATTTA
1 AAAAATTTA
371692 GAAGAGTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAAATTTA
Found at i:371680 original size:18 final size:17
Alignment explanation
Indices: 371657--371691 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
371647 ATATTACAAC
371657 AAAAATTTAAAAAATTTA
1 AAAAATTT-AAAAATTTA
371675 AAAAATTTAAAAATTTA
1 AAAAATTTAAAAATTTA
371692 GAAGAGTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATTTAAAAATTTA
Found at i:379715 original size:48 final size:49
Alignment explanation
Indices: 379656--379755 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 49
379646 CACCTCGGCT
* *
379656 TCTTTTATCCCTATCATGATCGTCATCACTTTCAGTTCTCCGGTGCC-A
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
379704 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
379753 TCT
1 TCT
379756 GTCCGTTCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 45 0.92
49 4 0.08
ACGTcount: A:0.17, C:0.32, G:0.11, T:0.40
Consensus pattern (49 bp):
TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
Found at i:391109 original size:27 final size:26
Alignment explanation
Indices: 391047--391114 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
391037 TTAAATCTTT
* *
391047 TAAAAATTTTAAATTGATAAAAATAA
1 TAAAAATTTTAATTTCATAAAAATAA
*
391073 -AATTATATTTTAATTTCACTAAAAATAA
1 TAA--AAATTTTAATTTCA-TAAAAATAA
391101 TAAAAA-TTTAATTT
1 TAAAAATTTTAATTT
391115 AATACTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.06
26 8 0.24
27 13 0.38
28 9 0.26
29 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (26 bp):
TAAAAATTTTAATTTCATAAAAATAA
Found at i:401923 original size:160 final size:160
Alignment explanation
Indices: 401655--401974 Score: 631
Period size: 160 Copynumber: 2.0 Consensus size: 160
401645 CAGGGATCAC
401655 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
1 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
401720 TACAAATTCTAAATATCTATAGGATTCAAATTTATAGCAGTCAATTAGAAGTAATATTAAATTCC
66 TACAAATTCTAAATATCTATAGGATTCAAATTTATAGCAGTCAATTAGAAGTAATATTAAATTCC
401785 TTTCAAACATAGGACGACACAATTAATGCT
131 TTTCAAACATAGGACGACACAATTAATGCT
401815 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
1 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
*
401880 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
66 TACAAATTCTAAATATCTATAGGATTCAAATTTATAGCAGTCAATTAGAAGTAATATTAAATTCC
401945 TTTCAAACATAGGACGACACAATTAATGCT
131 TTTCAAACATAGGACGACACAATTAATGCT
401975 ATATTTGAAC
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 159 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (160 bp):
TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
TACAAATTCTAAATATCTATAGGATTCAAATTTATAGCAGTCAATTAGAAGTAATATTAAATTCC
TTTCAAACATAGGACGACACAATTAATGCT
Found at i:409306 original size:24 final size:24
Alignment explanation
Indices: 409279--409330 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
409269 TTAGTAAGTC
*
409279 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
409303 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
409327 AAAT
1 AAAT
409331 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:411276 original size:24 final size:24
Alignment explanation
Indices: 411249--411300 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
411239 TTAGTAAGTC
*
411249 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
411273 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
411297 AAAT
1 AAAT
411301 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:415168 original size:6 final size:6
Alignment explanation
Indices: 415157--415181 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
415147 GGTTATTGGT
415157 TTAGGG TTAGGG TTAGGG TTAGGG T
1 TTAGGG TTAGGG TTAGGG TTAGGG T
415182 GTTTTTAAGT
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:0.48, T:0.36
Consensus pattern (6 bp):
TTAGGG
Found at i:415573 original size:48 final size:48
Alignment explanation
Indices: 415516--415629 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 48
415506 TTAAAAGAAT
*
415516 TTCACTTATATTAAAAATTGTCTTATTTAAAACGTTATTGTAAAAAAA
1 TTCAATTATATTAAAAATTGTCTTATTTAAAACGTTATTGTAAAAAAA
* * *
415564 TTCAATTATA-AAAAAATTTGTCTTATTTAAAACGTTATTGTAAAGAAT
1 TTCAATTATATTAAAAA-TTGTCTTATTTAAAACGTTATTGTAAAAAAA
*
415612 TTCGATTATATTAAAAAT
1 TTCAATTATATTAAAAAT
415630 ATTAAAGTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 5 0.09
48 48 0.83
49 5 0.09
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (48 bp):
TTCAATTATATTAAAAATTGTCTTATTTAAAACGTTATTGTAAAAAAA
Found at i:416222 original size:18 final size:18
Alignment explanation
Indices: 416196--416238 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
416186 GACTCGAAAA
* * *
416196 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
416214 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
416232 AGGATAC
1 AGGATAC
416239 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:418122 original size:12 final size:11
Alignment explanation
Indices: 418083--418125 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
418073 AAATAGGGAT
418083 TTGAGA-GAAA
1 TTGAGAGGAAA
418093 CTTGAGAGGAAA
1 -TTGAGAGGAAA
418105 TTGAGAGGAAA
1 TTGAGAGGAAA
418116 TT-AGA-GAAA
1 TTGAGAGGAAA
418125 T
1 T
418126 GATTTATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.16
10 3 0.10
11 19 0.61
12 4 0.13
ACGTcount: A:0.47, C:0.02, G:0.30, T:0.21
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:418391 original size:14 final size:14
Alignment explanation
Indices: 418359--418392 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
418349 CCCCTGACAT
418359 TGCGCTGACGTAGA
1 TGCGCTGACGTAGA
* *
418373 CGCGCTGACGTGGA
1 TGCGCTGACGTAGA
418387 TGCGCT
1 TGCGCT
418393 TTCAAGGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.38, T:0.21
Consensus pattern (14 bp):
TGCGCTGACGTAGA
Found at i:418464 original size:38 final size:38
Alignment explanation
Indices: 418413--418486 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
418403 TGGGCCAATC
418413 CGGTAATTAATTTATTTTTTTAAACCTTCAAACTAATT
1 CGGTAATTAATTTATTTTTTTAAACCTTCAAACTAATT
*
418451 CGGTAATTAATTTATTTTTTTGAACCTTCAAACTAA
1 CGGTAATTAATTTATTTTTTTAAACCTTCAAACTAA
418487 CGCTTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.46
Consensus pattern (38 bp):
CGGTAATTAATTTATTTTTTTAAACCTTCAAACTAATT
Found at i:418739 original size:20 final size:19
Alignment explanation
Indices: 418711--418834 Score: 58
Period size: 19 Copynumber: 6.3 Consensus size: 19
418701 CTAAACCATA
*
418711 TCAACATTTAATTAAAAATT
1 TCAAAATTT-ATTAAAAATT
*
418731 TCAAAATTTA-TAGAATATT
1 TCAAAATTTATTA-AAAATT
** *
418750 TTTAAATTT-TTGTAAAATT
1 TCAAAATTTATT-AAAAATT
*
418769 TCAAATTTTCATTAAAAATAT
1 TCAAAATTT-ATTAAAAAT-T
* *
418790 TCAAAA-ATATATAAAAATA
1 TCAAAATTTAT-TAAAAATT
* *
418809 T-AAAAGTTATTTAAAGTATT
1 TCAAAATTTA-TTAAA-AATT
418829 TCAAAA
1 TCAAAA
418835 AGTATAAAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
18 6 0.08
19 34 0.44
20 25 0.32
21 12 0.16
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (19 bp):
TCAAAATTTATTAAAAATT
Found at i:420374 original size:14 final size:13
Alignment explanation
Indices: 420354--420394 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
420344 TTTGATTGCC
420354 TGTAAAATATTTT
1 TGTAAAATATTTT
420367 TCGTAAAATGATTTT
1 T-GTAAAAT-ATTTT
*
420382 TGAAAAATATTTT
1 TGTAAAATATTTT
420395 ACTTTTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (13 bp):
TGTAAAATATTTT
Found at i:434362 original size:40 final size:40
Alignment explanation
Indices: 434318--434454 Score: 186
Period size: 41 Copynumber: 3.4 Consensus size: 40
434308 AAATATATTT
* *
434318 ATTTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
*
434358 ATTTTTTTTAAATTTTTAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTT-AATTTTAAAATATTTTTAAAATAC-TTTTTTA
**
434400 A-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTAAA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
*
434439 ATACTTTTTTAATTTT
1 AT-TTTTTTTAATTTT
434455 TTAAAATAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
39 6 0.07
40 32 0.37
41 40 0.47
42 8 0.09
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.63
Consensus pattern (40 bp):
ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:434406 original size:51 final size:50
Alignment explanation
Indices: 434329--434456 Score: 154
Period size: 51 Copynumber: 2.5 Consensus size: 50
434319 TTTTTTTTAA
** *
434329 TTTTAAAATA-TTTTTTACATACTTTTTTAATTTTTTTTAA-ATTTTT-AAATAT
1 TTTTAAAATACTTTTTTA-AT--TTTTTTAA--TTTTAAAATATTTTTAAAATAC
434381 TTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTAAAATAC-TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
434432 TTTTAAAATACTTTTTTAATTTTTT
1 TTTTAAAATACTTTTTTAATTTTTT
434457 AAAATAAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
49 6 0.09
50 20 0.29
51 24 0.35
52 10 0.14
53 2 0.03
54 7 0.10
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (50 bp):
TTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:434424 original size:11 final size:11
Alignment explanation
Indices: 434410--434462 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
434400 ATTTTTTTAA
434410 TTTTAAAATAT
1 TTTTAAAATAT
*
434421 TTTTAAAATAC
1 TTTTAAAATAT
434432 TTTTAAAATACT
1 TTTTAAAATA-T
*
434444 TTTT-TAAT-T
1 TTTTAAAATAT
434453 TTTTAAAATA
1 TTTTAAAATA
434463 AAAATTGGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 5 0.14
10 3 0.09
11 23 0.66
12 4 0.11
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:434949 original size:43 final size:42
Alignment explanation
Indices: 434916--435057 Score: 212
Period size: 43 Copynumber: 3.3 Consensus size: 42
434906 GAATCGTACT
*
434916 TTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCA-GTTC
*
434959 TTTAGCGGCGTTTGTGATAAAAGGGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCA-GTTC
* **
435002 TTTAGTGGCGTTTGTGATAAAAGCGTTGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCA-GTTC
435045 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
435058 ACATGTTCTT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 92 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCAGTTC
Found at i:435064 original size:21 final size:21
Alignment explanation
Indices: 435038--435078 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
435028 TGCTAAAGAT
435038 CATGTTCTTTAGCGGCGTTTA
1 CATGTTCTTTAGCGGCGTTTA
435059 CATGTTCTTTAGCGGCGTTT
1 CATGTTCTTTAGCGGCGTTT
435079 TGTTTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (21 bp):
CATGTTCTTTAGCGGCGTTTA
Found at i:439606 original size:3 final size:3
Alignment explanation
Indices: 439594--439624 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
439584 GAATAATAAT
*
439594 AAG AAT AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
439625 TTATCTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:444009 original size:29 final size:30
Alignment explanation
Indices: 443950--444007 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
443940 TCCGAGCCTT
*
443950 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
443980 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
444008 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:444237 original size:13 final size:13
Alignment explanation
Indices: 444219--444250 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
444209 TTTCCAGCAA
444219 TTATGAATTTATT
1 TTATGAATTTATT
444232 TTATGAATTTATT
1 TTATGAATTTATT
*
444245 TGATGA
1 TTATGA
444251 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:444456 original size:50 final size:51
Alignment explanation
Indices: 444345--444543 Score: 233
Period size: 50 Copynumber: 3.8 Consensus size: 51
444335 ATTTGGGTAA
444345 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GATCATG
* * *
444401 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA-GATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCATG
* * * * *
444451 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCATG
*
444501 AGAACATCCCATGTAAGACCATGTCTGGGACATGG-ATTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCA
444544 TGTTATTATC
Statistics
Matches: 126, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
49 1 0.01
50 48 0.38
51 35 0.28
55 2 0.02
56 40 0.32
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (51 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCATG
Found at i:444542 original size:101 final size:102
Alignment explanation
Indices: 444357--444543 Score: 261
Period size: 101 Copynumber: 1.8 Consensus size: 102
444347 AGATCCCATG
* * **
444357 TAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCATGTAAGACCAT
1 TAAGACCATGTCTGGGACATGGCATGGGCATCC---A-ATCACGAGACATCCCATGTAAGACCAT
*
444422 GTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTA
62 GTCTGGGACATGGAGTTGGCACCGAGATGAGAGGTCCCCTA
444463 TAAGACCATGTCTGGGACATGGCATGGGCA-CC-ATCACGAGAACATCCCATGTAAGACCATGTC
1 TAAGACCATGTCTGGGACATGGCATGGGCATCCAATCACGAG-ACATCCCATGTAAGACCATGTC
*
444526 TGGGACATGGATTTGGCA
65 TGGGACATGGAGTTGGCA
444544 TGTTATTATC
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
100 7 0.09
101 36 0.49
105 2 0.03
106 29 0.39
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (102 bp):
TAAGACCATGTCTGGGACATGGCATGGGCATCCAATCACGAGACATCCCATGTAAGACCATGTCT
GGGACATGGAGTTGGCACCGAGATGAGAGGTCCCCTA
Found at i:445972 original size:103 final size:104
Alignment explanation
Indices: 445793--446057 Score: 415
Period size: 103 Copynumber: 2.6 Consensus size: 104
445783 AACCGTTATT
* * * * *
445793 GGTGGATCTCGCACTGAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
445858 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
445896 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
445961 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
446000 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
446058 TTATGTACAA
Statistics
Matches: 148, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 82 0.55
104 66 0.45
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:446418 original size:30 final size:29
Alignment explanation
Indices: 446384--446448 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
446374 TAATCCACCA
446384 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
446414 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
446444 CCCAA
1 CCCAA
446449 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:446422 original size:31 final size:30
Alignment explanation
Indices: 446391--446448 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
446381 CCACCCAACT
446391 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
446421 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
446449 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:454242 original size:29 final size:30
Alignment explanation
Indices: 454183--454240 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
454173 TCCGAGCCTT
*
454183 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
454213 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
454241 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:454470 original size:13 final size:13
Alignment explanation
Indices: 454452--454483 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
454442 TTTCCAGCAA
454452 TTATGAATTTATT
1 TTATGAATTTATT
454465 TTATGAATTTATT
1 TTATGAATTTATT
*
454478 TGATGA
1 TTATGA
454484 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:454685 original size:50 final size:51
Alignment explanation
Indices: 454578--454776 Score: 249
Period size: 50 Copynumber: 3.8 Consensus size: 51
454568 ATTTGGGTAA
454578 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GATCATG
* *
454634 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCATG
* * * * *
454684 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCATG
* *
454734 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
454777 TGTTATTATC
Statistics
Matches: 128, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
49 1 0.01
50 48 0.38
51 36 0.28
55 2 0.02
56 41 0.32
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.22
Consensus pattern (51 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCATG
Done.