Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001993.1 Hibiscus syriacus cultivar Beakdansim tig00004075_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 637348
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:12430 original size:1 final size:1
Alignment explanation
Indices: 12419--12498 Score: 61
Period size: 1 Copynumber: 80.0 Consensus size: 1
12409 ATGCTTGAAG
* * * * * * * * * *
12419 AAAAGAAAAAAAGAAGAAGAAAGAAAAAAAAAAAAGAAAAAAAAAGAAAGAAAAGAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
12484 AAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAA
12499 GGGGGGGTCA
Statistics
Matches: 57, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:12439 original size:19 final size:18
Alignment explanation
Indices: 12416--12498 Score: 95
Period size: 18 Copynumber: 4.8 Consensus size: 18
12406 ATTATGCTTG
12416 AAGAAAAGAAAAAAAGAA
1 AAGAAAAGAAAAAAAGAA
12434 GAAG-AAAGAAAAAAA-AA
1 -AAGAAAAGAAAAAAAGAA
*
12451 AA-AGAA-AAAAAAAG-A
1 AAGAAAAGAAAAAAAGAA
12466 AAGAAAAGAAAAAAAAGAA
1 AAGAAAAG-AAAAAAAGAA
*
12485 AAAAAAAGAAAAAA
1 AAGAAAAGAAAAAA
12499 GGGGGGGTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
15 10 0.18
16 7 0.13
17 2 0.04
18 25 0.45
19 11 0.20
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAGAAAAGAAAAAAAGAA
Found at i:12440 original size:14 final size:13
Alignment explanation
Indices: 12419--12498 Score: 83
Period size: 13 Copynumber: 5.9 Consensus size: 13
12409 ATGCTTGAAG
12419 AAAAGAA-AAAAA
1 AAAAGAAGAAAAA
12431 GAAGAAGAAAGAAAAA
1 -AA-AAG-AAGAAAAA
*
12447 AAAAAAAGAAAAA
1 AAAAGAAGAAAAA
12460 AAAAGAAAGAAAAGA
1 AAAAG-AAGAAAA-A
*
12475 AAAAAAAGAAAAA
1 AAAAGAAGAAAAA
12488 AAAAGAA-AAAA
1 AAAAGAAGAAAA
12499 GGGGGGGTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
12 4 0.07
13 21 0.36
14 19 0.33
15 9 0.16
16 5 0.09
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAA
Found at i:12444 original size:23 final size:23
Alignment explanation
Indices: 12416--12498 Score: 98
Period size: 23 Copynumber: 3.6 Consensus size: 23
12406 ATTATGCTTG
*
12416 AAGAAAAGAAAAAAAGAAGAAGA
1 AAGAAAAGAAAAAAAGAAAAAGA
* *
12439 AAGAAAAAAAAAAAAGAAAAAAA
1 AAGAAAAGAAAAAAAGAAAAAGA
12462 AAG-AAAGAAAAGAAA-AAAAAGAA
1 AAGAAAAGAAAA-AAAGAAAAAG-A
*
12485 AAAAAAAGAAAAAA
1 AAGAAAAGAAAAAA
12499 GGGGGGGTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
22 12 0.24
23 31 0.61
24 8 0.16
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (23 bp):
AAGAAAAGAAAAAAAGAAAAAGA
Found at i:12454 original size:31 final size:31
Alignment explanation
Indices: 12419--12499 Score: 116
Period size: 27 Copynumber: 2.7 Consensus size: 31
12409 ATGCTTGAAG
12419 AAAAGAAAAAAAGAAGAAGAAAGAAAA-AAAA
1 AAAAGAAAAAAA-AAGAAGAAAGAAAAGAAAA
12450 AAAAG--AAAAAAA-AAGAAAGAAAAGAAAA
1 AAAAGAAAAAAAAAGAAGAAAGAAAAGAAAA
*
12478 AAAAGAAAAAAAAAGAAAAAAG
1 AAAAGAAAAAAAAAGAAGAAAG
12500 GGGGGGTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
27 11 0.24
28 11 0.24
29 5 0.11
30 7 0.16
31 11 0.24
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (31 bp):
AAAAGAAAAAAAAAGAAGAAAGAAAAGAAAA
Found at i:12477 original size:28 final size:28
Alignment explanation
Indices: 12416--12495 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 28
12406 ATTATGCTTG
* *
12416 AAGAAAAGAAAA-AAAGAAGAAGAAAGAA
1 AAGAAAA-AAAAGAAAAAAAAAGAAAGAA
12444 AA-AAAAAAAAGAAAAAAAAAGAAAGAA
1 AAGAAAAAAAAGAAAAAAAAAGAAAGAA
12471 AAGAAAAAAAAGAAAAAAAAAGAAA
1 AAGAAAAAAAAGAAAAAAAAAGAAA
12496 AAAGGGGGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.08
27 20 0.42
28 24 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (28 bp):
AAGAAAAAAAAGAAAAAAAAAGAAAGAA
Found at i:12496 original size:10 final size:10
Alignment explanation
Indices: 12419--12498 Score: 103
Period size: 10 Copynumber: 8.1 Consensus size: 10
12409 ATGCTTGAAG
12419 AAAAGAAAAA
1 AAAAGAAAAA
12429 AAGAAGAAGAAA
1 AA-AAGAA-AAA
*
12441 GAAA-AAAAA
1 AAAAGAAAAA
12450 AAAAGAAAAA
1 AAAAGAAAAA
*
12460 AAAAG-AAAG
1 AAAAGAAAAA
12469 AAAAG-AAAA
1 AAAAGAAAAA
12478 AAAAGAAAAA
1 AAAAGAAAAA
12488 AAAAGAAAAA
1 AAAAGAAAAA
12498 A
1 A
12499 GGGGGGGTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
9 22 0.35
10 29 0.47
11 7 0.11
12 4 0.06
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:13808 original size:76 final size:78
Alignment explanation
Indices: 13622--14238 Score: 774
Period size: 76 Copynumber: 7.9 Consensus size: 78
13612 TAATAGACTC
*
13622 ATAGCATCTTCTGGAAGTGTTCTTTGAG-TATCTGATCTGGGTTTAAGAAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GGTTTGAG-AACCAATCATTGAATT
* *
13686 TAGAGATGAATGTTC
64 TGGAGATGAATGTTT
13701 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAGAACCAATCATTGAA-TTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAGAACCAATCATTGAATTTG
13765 GA-ATGAATGTATT
66 GAGATGAATGT-TT
* *
13778 ATAACATCTT-TGGAAGTGTTCTTTGAGTTATCTGA--TGG-TTGAGAA-CAATCATTGAATTTA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAGAACCAATCATTGAATTTG
13838 GAGATGAATGTTT
66 GAGATGAATGTTT
13851 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGAGAA-CAATCATTGAA-
1 --ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-GAGAACCAATCATTGAAT
* * *
13914 TTGAAGATGAA-ATTA
63 TTGGAGATGAATGTTT
*
13929 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGTAGAACCAATCATTGAATTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-AGAACCAATCATTGAATTT
13994 GGAAGATGAATGTGTT
65 GG-AGATGAATGT-TT
14010 CATAGCATC-TCTGGAA--G-TC-TTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAA-
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG--AGAACCAATCATTGAAT
**
14069 TTGGAAGATGAATGTGCCA
63 TTGG-AGATGAATGT--TT
*
14088 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAGAACCAATCATTGAATTTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAGAACCAATCATTGAATTT-
*
14153 GGAAGATGAAT-TTG
65 GG-AGATGAATGTTT
* *
14167 CTAGCATC-TCTGGAAGTGTTCTTTGAGTTATCTGAT-TGGTTTGGTAGAACCAATCA-T-AAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-G-AGAACCAATCATTGAATT
14228 TGGAGATGAAT
64 TGGAGATGAAT
14239 TTCAATGAAC
Statistics
Matches: 484, Mismatches: 25, Indels: 62
0.85 0.04 0.11
Matches are distributed among these distances:
72 11 0.02
73 13 0.03
74 11 0.02
75 18 0.04
76 107 0.22
77 78 0.16
78 77 0.16
79 72 0.15
80 44 0.09
81 13 0.03
82 40 0.08
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (78 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAGAACCAATCATTGAATTTG
GAGATGAATGTTT
Found at i:14105 original size:235 final size:230
Alignment explanation
Indices: 13622--14238 Score: 837
Period size: 235 Copynumber: 2.7 Consensus size: 230
13612 TAATAGACTC
13622 ATAGCATCTTCTGGAAGTGTTCTTTGAG-TATCTGATCTGGGTTTA-AGAAACCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GGTTTAGAG-AACCAATCATTGAAT
* * * *
13685 TTAGAGATGAATGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-AGA
64 TGA-AGATGAA-ATTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGTAGA
*
13749 ACCAATCATTGAATTGGA-ATGAATGTATTATAACATCTTTGGAAGTGTTCTTTGAGTTATCTGA
127 ACCAATCATTGAATTGGAGATGAATGTATTATAACATCTCTGGAAG-GTTCTTTGAGTTATCTGA
* **
13813 TGGTTGAGAACAATCATTGAATTTAGAGATGAATGTTTCA
191 TGGTTGAGAACAATCATTGAATTGAGAGATGAATGTGCCA
13853 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGAGAA-CAATCATTGAATTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGAGAACCAATCATTGAATTG
13917 AAGATGAAATTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGTAGAACCA
66 AAGATGAAATTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGTAGAACCA
* *
13982 ATCATTGAATTTGGAAGATGAATGTGTTCATAGCATCTCTGGAA-G-TC-TTGAGTTATCTGATC
131 ATCATTGAA-TTGG-AGATGAATGTATT-ATAACATCTCTGGAAGGTTCTTTGAGTTATCTGA--
14044 TGGTTTGACAGAACCAATCATTGAATTG-GAAGATGAATGTGCCA
191 TGG-TTG--AGAA-CAATCATTGAATTGAG-AGATGAATGTGCCA
*
14088 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGAGAACCAATCATTGAATTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGAGAACCAATCATTGAA-TT
* **
14152 GGGAAGATGAATTTGCTAGCATC-TCTGGAAGTGTTCTTTGAGTTATCTGAT-TGGTTTGGTAGA
65 --GAAGATGAAATTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTAGA
*
14215 ACCAATCA-TAAATTGGAGATGAAT
127 ACCAATCATTGAATTGGAGATGAAT
14239 TTCAATGAAC
Statistics
Matches: 352, Mismatches: 15, Indels: 35
0.88 0.04 0.09
Matches are distributed among these distances:
228 46 0.13
229 36 0.10
230 20 0.06
231 41 0.12
232 25 0.07
233 13 0.04
234 20 0.06
235 81 0.23
236 8 0.02
237 44 0.12
238 18 0.05
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (230 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGAGAACCAATCATTGAATTG
AAGATGAAATTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGTAGAACCA
ATCATTGAATTGGAGATGAATGTATTATAACATCTCTGGAAGGTTCTTTGAGTTATCTGATGGTT
GAGAACAATCATTGAATTGAGAGATGAATGTGCCA
Found at i:15271 original size:108 final size:110
Alignment explanation
Indices: 14966--15711 Score: 930
Period size: 107 Copynumber: 7.0 Consensus size: 110
14956 TTTCAAAGAT
*
14966 TGAATCCATCATTGAT-GA--AGCTTTT-CAGAGAAAG-TCATAAT--GAAGAACTCATCTGAAG
1 TGAATTCATCATTGATGGATCAGCTTTTCCAGAG--AGTTCATAATGAGAAGAACTCATCTGAAG
**
15024 -AAGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAATTTTTTG-C
64 AAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
* *
15068 TAAATTC--CCTTGATGGATCAGCTTTTCCAGA-AGTTCATAATGAGAAGAAACTCATCTGAAG-
1 TGAATTCATCATTGATGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAG-AACTCATCTGAAGA
* * *
15129 AAG-A-AAGAAATTCATAATGAGAAGAATTTGTTCAA-TTTTTGCT
65 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
* *
15172 TAAATTCATCCCTTGATGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 TGAATTCAT-CATTGATGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
15237 AAG-AGAA-AAATTCATAATGAGAAGAATTTGTTCAA--TTTTG-C
65 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
*
15278 T-AATTCATCCCTTG-TGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 TGAATTCAT-CATTGATGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
15341 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
15387 TGAATTCATCATTGATGGAT---CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 TGAATTCATCATTGATGGATCAGCTTTTCCAGAG--AGTTCATAATGAGAAGAACTCATCTGAAG
*
15449 -AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTACC
64 AAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
* * *
15494 TGAATCCATCATTGATGGAGCATCTTTT-CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAA
1 TGAATTCATCATTGATGGATCAGCTTTTCCAGAG--AGTTCATAATGAGAAGAACTCATCTG-AA
* *
15558 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
63 GAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
* * *
15606 TGAA-TCATCATTGATGGATTATCTTTTCCAGAAAGTTCATAATGAGAAGAACTCA--TGAAG-A
1 TGAATTCATCATTGATGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
* *
15667 AGAAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTTGC
66 AG-AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
15712 ATAATTCTAT
Statistics
Matches: 589, Mismatches: 22, Indels: 61
0.88 0.03 0.09
Matches are distributed among these distances:
100 6 0.01
101 4 0.01
102 12 0.02
103 15 0.03
104 94 0.16
105 33 0.06
106 30 0.05
107 119 0.20
108 92 0.16
109 70 0.12
110 42 0.07
111 58 0.10
112 14 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (110 bp):
TGAATTCATCATTGATGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
AGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
Found at i:16037 original size:3 final size:3
Alignment explanation
Indices: 16029--16065 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
16019 ACCCATATAA
16029 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16066 AAAATATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16049 original size:17 final size:17
Alignment explanation
Indices: 16024--16065 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
16014 TTTTTACCCA
*
16024 TATAATATTATTATTAT
1 TATATTATTATTATTAT
16041 TATATTATTATTATTAT
1 TATATTATTATTATTAT
16058 TATTATTA
1 TA-TATTA
16066 AAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTATTATTATTAT
Found at i:19548 original size:22 final size:22
Alignment explanation
Indices: 19523--19564 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
19513 CAATTCATTT
19523 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
19545 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
19565 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:19932 original size:13 final size:13
Alignment explanation
Indices: 19914--19938 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19904 AAAAGGCAAA
19914 AAAAGGCAAAAAC
1 AAAAGGCAAAAAC
19927 AAAAGGCAAAAA
1 AAAAGGCAAAAA
19939 AATAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGGCAAAAAC
Found at i:19947 original size:23 final size:24
Alignment explanation
Indices: 19894--19948 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
19884 TTGTTTTTCA
19894 AAAAAAACAAAAAAGGCAAAAAAAG
1 AAAAAAAC-AAAAAGGCAAAAAAAG
** *
19919 GCAAAAAC-AAAAGGCAAAAAAAT
1 AAAAAAACAAAAAGGCAAAAAAAG
19942 AAAAAAA
1 AAAAAAA
19949 AAGTCAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 19 0.76
25 6 0.24
ACGTcount: A:0.78, C:0.09, G:0.11, T:0.02
Consensus pattern (24 bp):
AAAAAAACAAAAAGGCAAAAAAAG
Found at i:19957 original size:10 final size:10
Alignment explanation
Indices: 19902--19940 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
19892 CAAAAAAAAC
19902 AAAAAAGGCA
1 AAAAAAGGCA
19912 AAAAAAGGCAAA
1 AAAAAAGGC--A
19924 AACAAAAGGCA
1 AA-AAAAGGCA
19935 AAAAAA
1 AAAAAA
19941 TAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 13 0.50
11 3 0.12
12 3 0.12
13 7 0.27
ACGTcount: A:0.74, C:0.10, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGGCA
Found at i:24148 original size:22 final size:22
Alignment explanation
Indices: 24123--24164 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
24113 CAATTCATTT
24123 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
24145 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
24165 CCAGTACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:29061 original size:9 final size:9
Alignment explanation
Indices: 29047--29086 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
29037 TTAATGAAAT
29047 AAGAAATGA
1 AAGAAATGA
29056 AAGAAA-GA
1 AAGAAATGA
29064 AATGAAATGA
1 AA-GAAATGA
29074 TAAGAAATGA
1 -AAGAAATGA
29084 AAG
1 AAG
29087 GGATAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.14
9 13 0.46
10 9 0.32
11 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (9 bp):
AAGAAATGA
Found at i:29080 original size:15 final size:14
Alignment explanation
Indices: 29045--29086 Score: 68
Period size: 13 Copynumber: 3.0 Consensus size: 14
29035 GATTAATGAA
29045 ATAAGAAATGAAAG
1 ATAAGAAATGAAAG
29059 A-AAGAAATGAAATG
1 ATAAGAAATGAAA-G
29073 ATAAGAAATGAAAG
1 ATAAGAAATGAAAG
29087 GGATAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (14 bp):
ATAAGAAATGAAAG
Found at i:29094 original size:15 final size:13
Alignment explanation
Indices: 29039--29086 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
29029 GAACTGGATT
*
29039 AATGAAATA-AGA
1 AATGAAAGATAGA
*
29051 AATGAAAGAAAGA
1 AATGAAAGATAGA
29064 AATGAAATGATAAGA
1 AATGAAA-GAT-AGA
29079 AATGAAAG
1 AATGAAAG
29087 GGATAGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 8 0.26
13 10 0.32
14 3 0.10
15 10 0.32
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (13 bp):
AATGAAAGATAGA
Found at i:29667 original size:19 final size:20
Alignment explanation
Indices: 29621--29658 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29611 CCCCTTTGAA
29621 AATACATGATTTTTAATGAG
1 AATACATGATTTTTAATGAG
*
29641 AATGCATGA-TTTTAATGA
1 AATACATGATTTTTAATGA
29659 AGGTACATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (20 bp):
AATACATGATTTTTAATGAG
Found at i:33697 original size:47 final size:45
Alignment explanation
Indices: 33599--33724 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
33589 GTAACCATGC
** * *
33599 AAATAAGCTTTTGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
33643 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
* *
33690 AACTAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
33725 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.15
46 1 0.01
47 38 0.54
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:37823 original size:47 final size:45
Alignment explanation
Indices: 37726--37851 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
37716 GTAACCATGC
* * * *
37726 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAGGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
37770 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
*
37817 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
37852 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:39343 original size:5 final size:5
Alignment explanation
Indices: 39333--39389 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
39323 TGGAGTACAA
*
39333 AAAAG AAAAG AAAAG AAAAA AAGAAG AAAA- ATTCAAA- AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG A---AAAG AAAAG AAAAG
39380 AAAAG AAAAG
1 AAAAG AAAAG
39390 CCAAAAAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 33 0.73
6 4 0.09
7 4 0.09
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:39359 original size:16 final size:15
Alignment explanation
Indices: 39332--39389 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
39322 TTGGAGTACA
39332 AAAAAGAAAAGAAAAG
1 AAAAA-AAAAGAAAAG
39348 AAAAAAAGAAGAAAA-
1 AAAAAAA-AAGAAAAG
*
39363 ATTCAAAAAAAGAAAAG
1 A--AAAAAAAAGAAAAG
*
39380 AAAAGAAAAG
1 AAAAAAAAAG
39390 CCAAAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 10 0.29
16 19 0.54
17 6 0.17
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:39401 original size:27 final size:25
Alignment explanation
Indices: 39343--39401 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
39333 AAAAGAAAAG
* **
39343 AAAAGAAA-AAAAGAAGAAAAATTC
1 AAAAGAAAGAAAAGAAAAAAAAGCC
39367 AAAA-AAAGAAAAGAAAAGAAAAGCC
1 AAAAGAAAGAAAAGAAAA-AAAAGCC
39392 AAAAAGAAAG
1 -AAAAGAAAG
39402 CAAGCCAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 3 0.11
24 12 0.43
25 5 0.18
26 4 0.14
27 4 0.14
ACGTcount: A:0.76, C:0.05, G:0.15, T:0.03
Consensus pattern (25 bp):
AAAAGAAAGAAAAGAAAAAAAAGCC
Found at i:47063 original size:31 final size:30
Alignment explanation
Indices: 47019--47079 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
47009 AAAGGATGAA
*
47019 GAAAAGAAGGAATTAGGTTGTTAGAAATTT
1 GAAAAGAAGGAATTAGGTTGCTAGAAATTT
* * *
47049 GAAAGAGAATGAATTAGTTTGCTGGAAATTT
1 GAAA-AGAAGGAATTAGGTTGCTAGAAATTT
47080 AGAATGGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.41, C:0.02, G:0.26, T:0.31
Consensus pattern (30 bp):
GAAAAGAAGGAATTAGGTTGCTAGAAATTT
Found at i:54216 original size:19 final size:19
Alignment explanation
Indices: 54192--54241 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
54182 CCAAATATCA
54192 TCAAAGAAATTG-AAGCAC
1 TCAAAGAAATTGTAAGCAC
54210 TCAAAAGAATAAATTGTAAGCAC
1 TC-AAAG---AAATTGTAAGCAC
54233 TCAAAGAAA
1 TCAAAGAAA
54242 GAAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
18 2 0.07
19 7 0.26
22 10 0.37
23 8 0.30
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (19 bp):
TCAAAGAAATTGTAAGCAC
Found at i:55309 original size:14 final size:14
Alignment explanation
Indices: 55290--55320 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55280 ATATGAAAAA
*
55290 AGTTGGAATTTATG
1 AGTTGGAATTGATG
55304 AGTTGGAATTGATG
1 AGTTGGAATTGATG
55318 AGT
1 AGT
55321 GTAGAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (14 bp):
AGTTGGAATTGATG
Found at i:58159 original size:18 final size:19
Alignment explanation
Indices: 58125--58162 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
58115 CCTTAACATG
58125 ATATGTATTATAATAGTAT
1 ATATGTATTATAATAGTAT
58144 ATATG-ATTA-AACTAGTAT
1 ATATGTATTATAA-TAGTAT
58162 A
1 A
58163 AAGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 11 0.61
19 5 0.28
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (19 bp):
ATATGTATTATAATAGTAT
Found at i:60717 original size:16 final size:16
Alignment explanation
Indices: 60681--60714 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
60671 CACGTGAGGA
60681 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
60697 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
60714 T
1 T
60715 ATTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:67082 original size:19 final size:21
Alignment explanation
Indices: 67045--67087 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
67035 TAACATTTTC
67045 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
67065 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
67085 TTT
1 TTT
67088 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:67093 original size:19 final size:20
Alignment explanation
Indices: 67044--67093 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
67034 TTAACATTTT
*
67044 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
67064 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
67083 CTTTTACCTTT
1 CTTTTACCTTT
67094 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:70951 original size:16 final size:16
Alignment explanation
Indices: 70915--70948 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
70905 CACGTGAGGA
70915 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
70931 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
70948 T
1 T
70949 ATTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:72355 original size:22 final size:21
Alignment explanation
Indices: 72323--72363 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
72313 CTATCTCTAT
72323 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
72344 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
72364 TTTTGGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:75815 original size:22 final size:23
Alignment explanation
Indices: 75770--75820 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
75760 TTTCTTTTCT
75770 TTTCTTCCTTTGAGTGATTACAA
1 TTTCTTCCTTTGAGTGATTACAA
* *
75793 TTTCTTCTTTTGAGTGCTT-CAA
1 TTTCTTCCTTTGAGTGATTACAA
75815 TTTCTT
1 TTTCTT
75821 TGCTGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.55
Consensus pattern (23 bp):
TTTCTTCCTTTGAGTGATTACAA
Found at i:77581 original size:142 final size:142
Alignment explanation
Indices: 77403--77684 Score: 447
Period size: 142 Copynumber: 2.0 Consensus size: 142
77393 GTGTTCATGC
* *
77403 TAAGTTATTTATTAGTTACATAACTAGTAACCTTAACATGATATGTATTATAATAACATATATGA
1 TAAGTTATCTATTAGCTACATAACTAGTAACCTTAACATGATATGTATTATAATAACATATATGA
* * * * * *
77468 TTAAACTAGTATAATGTAAATATAACATTGAAATGTTCAAGAGTACTCCCTTTGTATGTGAAAAT
66 TCAAACTAATATAAAGTAAATATAACATAGAAATGTTCAAGAATACTCCCTTTGTATGTGAAAAC
*
77533 GTCCTTGCATCA
131 GTACTTGCATCA
* *
77545 TAAGTTATCTGTTAGCTACATAACTAGTAACCTTAACATGATATGTATTATAATAGCATATATGA
1 TAAGTTATCTATTAGCTACATAACTAGTAACCTTAACATGATATGTATTATAATAACATATATGA
* *
77610 TCAATCTAATATAAAGTAAATATAACATAGAAATTTTCAAGAATACTCCCTTTGTATGTGAAAAC
66 TCAAACTAATATAAAGTAAATATAACATAGAAATGTTCAAGAATACTCCCTTTGTATGTGAAAAC
77675 GTACTTGCAT
131 GTACTTGCAT
77685 TATCCCTCAT
Statistics
Matches: 127, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
142 127 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (142 bp):
TAAGTTATCTATTAGCTACATAACTAGTAACCTTAACATGATATGTATTATAATAACATATATGA
TCAAACTAATATAAAGTAAATATAACATAGAAATGTTCAAGAATACTCCCTTTGTATGTGAAAAC
GTACTTGCATCA
Found at i:80251 original size:22 final size:23
Alignment explanation
Indices: 80206--80257 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
80196 TTATTTTCTT
80206 TTTCTTTCTTTGAGTGCTTACAA
1 TTTCTTTCTTTGAGTGCTTACAA
80229 TTTC-TTCTTTTGAGTGCTT-CAA
1 TTTCTTTC-TTTGAGTGCTTACAA
80251 TTTCTTT
1 TTTCTTT
80258 GCTGATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.13, C:0.17, G:0.12, T:0.58
Consensus pattern (23 bp):
TTTCTTTCTTTGAGTGCTTACAA
Found at i:81927 original size:142 final size:142
Alignment explanation
Indices: 81746--82027 Score: 465
Period size: 142 Copynumber: 2.0 Consensus size: 142
81736 GTGTTCATGC
* *
81746 TAAGTTATTTATTAGTTACATAACTAGTAACCTTAACATGATATGTATTATAATAGCATATATGA
1 TAAGTTATCTATTAGCTACATAACTAGTAACCTTAACATGATATGTATTATAATAGCATATATGA
* * * *
81811 TTAAACTAATATAAAGTAAATATAACATTGAAATGTTCAAGAGTACTCCCTTTGTATGTGAAAAC
66 TCAAACTAATATAAAGTAAATATAACATAGAAATATTCAAGAATACTCCCTTTGTATGTGAAAAC
81876 GTCCTTGCATCA
131 GTCCTTGCATCA
*
81888 TAAGTTATCTATTAGCTACATAACTAGTAACCTTAACATGATATGTATTATTATAGCATATATGA
1 TAAGTTATCTATTAGCTACATAACTAGTAACCTTAACATGATATGTATTATAATAGCATATATGA
* * *
81953 TCAATCTAATATAAAGTAAATATAACATAGGAATATTCAATAATACTCCCTTTGTATGTGAAAAC
66 TCAAACTAATATAAAGTAAATATAACATAGAAATATTCAAGAATACTCCCTTTGTATGTGAAAAC
*
82018 GTGCTTGCAT
131 GTCCTTGCAT
82028 TATCCCTCAT
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 129 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (142 bp):
TAAGTTATCTATTAGCTACATAACTAGTAACCTTAACATGATATGTATTATAATAGCATATATGA
TCAAACTAATATAAAGTAAATATAACATAGAAATATTCAAGAATACTCCCTTTGTATGTGAAAAC
GTCCTTGCATCA
Found at i:89211 original size:327 final size:326
Alignment explanation
Indices: 88614--89273 Score: 926
Period size: 327 Copynumber: 2.0 Consensus size: 326
88604 ATCTCCATCT
* * ***
88614 CCTTGAAATAATCTTCAACGCTCCGGCTTCCTTGTTTAAGATTTTGTCGCTTATGATAAAGATAT
1 CCTTGAAATAATCTTCAACGCACCAGCTTCCTTGTTTAAGATTTTAAAGCTTATGATAAAGATAT
*
88679 CAGTGATAGTGAGTAGGCACAAACCTTTTTCTCATAATGGCCTTCATTTCTTCCTAAGTATTGAT
66 CAGTGATAGTGAGTAGGCACAAA-CTTTTTCTCATAATGGCCTTCATTTATTCCTAAGTATTGAT
* * *
88744 TAGGCGTTCACCATTTCGTCTTCTGGAACTTACCAATTTATCCCACCAAACTAGGGCATAGTCCA
130 GAGGCATTCACCATTTCGTCTTCTGGAACTTACCAATTGATCCCACCAAACTAGGGCATAGTCCA
* *
88809 CAAATTCCATAGCAGCAAACCATACTTTATTTTGCTTCGTATAGTTTTAACATTAAAAAATATGC
195 CAAATTCCATAGCAGCAAACCATACTTTATTTTGCTCCATATAGTTTTAACATTAAAAAATATGC
* *
88874 TCGATCTTGATTACCTAATCAATATAGGCTTCAGGATCAGTTCGTCCTCGAAATGGAGGAATGGT
260 TCGATCTTGATTACCCAATCAAGATAGGCTTCAGGATCAGTTCGTCCTCGAAATGGAGGAATGGT
88939 TA
325 TA
* * * * *
88941 CCTTGAAATAATCTTCAATGCACCAGTTTCCTTGTTTAAGATTTTAAAGCTTATTATCAAGATCT
1 CCTTGAAATAATCTTCAACGCACCAGCTTCCTTGTTTAAGATTTTAAAGCTTATGATAAAGATAT
* *
89006 CAGTGATAGTGAGTAGGCACGAA-TATTTTCATCATAATGGCCTTTATTTATTCCTAAGTATTGA
66 CAGTGATAGTGAGTAGGCACAAACT-TTTTC-TCATAATGGCCTTCATTTATTCCTAAGTATTGA
* * * * *
89070 TGAGGCATTCTCCATTTCTTCTTCTTGAACTTACTAATTGATCCCACCAAACTAGGGCGTAGTCC
129 TGAGGCATTCACCATTTCGTCTTCTGGAACTTACCAATTGATCCCACCAAACTAGGGCATAGTCC
* * ** * * * *
89135 ACAAATTCCATTGCAGTAAGGCTTACTTTCTTTTGCTCCATGTAGTTTTAACATTCAAAAATATG
194 ACAAATTCCATAGCAGCAAACCATACTTTATTTTGCTCCATATAGTTTTAACATTAAAAAATATG
* * * ** * *
89200 TTCGTTCTTGATTACCCAGTCAAGATAGGCTTTGGGATCAGTTCGTCCTTGAAATGGAGGAATTG
259 CTCGATCTTGATTACCCAATCAAGATAGGCTTCAGGATCAGTTCGTCCTCGAAATGGAGGAATGG
89265 TTA
324 TTA
89268 CCTTGA
1 CCTTGA
89274 TGTTGTTGAA
Statistics
Matches: 291, Mismatches: 40, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
325 1 0.00
326 5 0.02
327 285 0.98
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (326 bp):
CCTTGAAATAATCTTCAACGCACCAGCTTCCTTGTTTAAGATTTTAAAGCTTATGATAAAGATAT
CAGTGATAGTGAGTAGGCACAAACTTTTTCTCATAATGGCCTTCATTTATTCCTAAGTATTGATG
AGGCATTCACCATTTCGTCTTCTGGAACTTACCAATTGATCCCACCAAACTAGGGCATAGTCCAC
AAATTCCATAGCAGCAAACCATACTTTATTTTGCTCCATATAGTTTTAACATTAAAAAATATGCT
CGATCTTGATTACCCAATCAAGATAGGCTTCAGGATCAGTTCGTCCTCGAAATGGAGGAATGGTT
A
Found at i:95242 original size:16 final size:16
Alignment explanation
Indices: 95218--95250 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
95208 TAGTTAGCTC
95218 ATTTACATTCTAACAT
1 ATTTACATTCTAACAT
*
95234 ATTTGCATTCTAACAT
1 ATTTACATTCTAACAT
95250 A
1 A
95251 GGTGGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTTACATTCTAACAT
Found at i:104950 original size:16 final size:16
Alignment explanation
Indices: 104929--104961 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
104919 TTGTTCCACC
104929 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
104945 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
104961 T
1 T
104962 GAGCTAACTA
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:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:105838 original size:13 final size:14
Alignment explanation
Indices: 105803--105844 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
105793 TCCTTCTTAG
*
105803 TCTTTCTATCACCA
1 TCTTTCCATCACCA
105817 TCTTTCCATCACCA
1 TCTTTCCATCACCA
*
105831 TC-TTCCATAACCA
1 TCTTTCCATCACCA
105844 T
1 T
105845 TCACACCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (14 bp):
TCTTTCCATCACCA
Found at i:110738 original size:24 final size:23
Alignment explanation
Indices: 110699--110756 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
110689 GGTGATCCAC
*
110699 AAGACATGT-CCTTTGACATTTC-A
1 AAGA-ATGTACCTTTGA-AATTCAA
*
110722 AAGGATGTACCTCTTGAAATTCAA
1 AAGAATGTACCT-TTGAAATTCAA
110746 AAGAATGTACC
1 AAGAATGTACC
110757 GATAGAAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 4 0.14
23 10 0.34
24 15 0.52
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (23 bp):
AAGAATGTACCTTTGAAATTCAA
Found at i:112736 original size:22 final size:21
Alignment explanation
Indices: 112699--112739 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
112689 CCATCTCCAT
112699 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
112720 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
112740 TTTTCGCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:113098 original size:33 final size:33
Alignment explanation
Indices: 113061--113123 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
113051 GCAAAAAGAA
*
113061 AGAAAAAAACAAAAGAAAAAAAAATAAAAATTC
1 AGAAAAAAACAAAAGAAAAAAAAAGAAAAATTC
* * *
113094 AGAAAAGAAGAAAAGAAAAGAAAAGAAAAA
1 AGAAAAAAACAAAAGAAAAAAAAAGAAAAA
113124 GAAAATCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (33 bp):
AGAAAAAAACAAAAGAAAAAAAAAGAAAAATTC
Found at i:113113 original size:38 final size:36
Alignment explanation
Indices: 113059--113145 Score: 106
Period size: 38 Copynumber: 2.4 Consensus size: 36
113049 GTGCAAAAAG
*
113059 AAAGAAAAAAACAAAAGAAAA-AAAAATAAAAATTCAGA
1 AAAGAAGAAAACAAAAGAAAAGAAAAA-AAAAA-TCA-A
* *
113097 AAAGAAGAAAAGAAAAGAAAAGAAAAAGAAAATCAA
1 AAAGAAGAAAACAAAAGAAAAGAAAAAAAAAATCAA
113133 AAAG-AGAAAACAA
1 AAAGAAGAAAACAA
113146 GCCAAGGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
35 8 0.18
36 5 0.11
37 3 0.07
38 23 0.52
39 5 0.11
ACGTcount: A:0.78, C:0.05, G:0.13, T:0.05
Consensus pattern (36 bp):
AAAGAAGAAAACAAAAGAAAAGAAAAAAAAAATCAA
Found at i:113115 original size:18 final size:16
Alignment explanation
Indices: 113094--113128 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
113084 ATAAAAATTC
113094 AGAAAAGAAGAAAAGAAA
1 AGAAAAG-A-AAAAGAAA
113112 AGAAAAGAAAAAGAAA
1 AGAAAAGAAAAAGAAA
113128 A
1 A
113129 TCAAAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAAAGAAA
Found at i:117345 original size:22 final size:21
Alignment explanation
Indices: 117308--117348 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
117298 CCATCTCCAT
117308 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
117329 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
117349 TTTTCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:120973 original size:3 final size:3
Alignment explanation
Indices: 120965--120989 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
120955 CCAATTTAAA
120965 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
120990 CATTTTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:126429 original size:81 final size:77
Alignment explanation
Indices: 126334--126503 Score: 196
Period size: 77 Copynumber: 2.2 Consensus size: 77
126324 CTGTCAAATG
* *
126334 CACAGCTAGTCCATTATTCTTTTACTCAACAATGTTTAACCATTCATCTAACTAGAATCATTGAC
1 CACAGTTAGGCCATTATTCTTTTACTCAA-AA-G--TAACCATTCATCTAACTAGAATCATTGAC
* *
126399 ACCTTTTTGCCAATTA
62 ACCTTTCTCCCAATTA
* * * * * * *
126415 CATAGTTAGGCCATTATTCTTTTACTTAATAGTGACCGTTCATCTAACTGGCATCATTGACACCT
1 CACAGTTAGGCCATTATTCTTTTACTCAAAAGTAACCATTCATCTAACTAGAATCATTGACACCT
*
126480 TTCTCCCAATTG
66 TTCTCCCAATTA
126492 CACAGTTAGGCC
1 CACAGTTAGGCC
126504 TCAAAGGCAC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
77 49 0.64
79 1 0.01
80 1 0.01
81 25 0.33
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (77 bp):
CACAGTTAGGCCATTATTCTTTTACTCAAAAGTAACCATTCATCTAACTAGAATCATTGACACCT
TTCTCCCAATTA
Found at i:126859 original size:58 final size:59
Alignment explanation
Indices: 126788--127019 Score: 362
Period size: 59 Copynumber: 4.0 Consensus size: 59
126778 TATATTTCCC
* * **
126788 ATACGGAAATTCATACACTTAGTATGAGTTTCTTATC-TTTTTGCACATAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCA
126846 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACCG-AGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACA-CGAAGTGCCCA
* **
126905 ATACGGAAATTCATACAGTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCATA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCA
*
126964 ATACGGAAATTCATACACTTAGTATCAATTTCTTAAC-TTTTTGCACACGAAGTGCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCC
127020 ATTTTGGTAT
Statistics
Matches: 161, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
58 55 0.34
59 106 0.66
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (59 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCA
Found at i:127516 original size:75 final size:75
Alignment explanation
Indices: 127376--127521 Score: 213
Period size: 75 Copynumber: 1.9 Consensus size: 75
127366 CAATACTTCT
* ** * * *
127376 ATACTATGGTACCGATATCCCCTTCCGGTATCGATACCAATTTTAGGTTTGATGCTGCCTGGTAT
1 ATACTATGGTACCGATATCCCCTTCCGATATCGATACCAATTTTACCTTCGATGATGCCTAGTAT
127441 CGATACTACC
66 CGATACTACC
*
127451 ATACTATGGTACCGATA-CCACCTTCCGATATCGATACCAATTTTACCTTCGATGATGCTTAGTA
1 ATACTATGGTACCGATATCC-CCTTCCGATATCGATACCAATTTTACCTTCGATGATGCCTAGTA
127515 TCGATAC
65 TCGATAC
127522 CCTTACCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
74 2 0.03
75 61 0.97
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (75 bp):
ATACTATGGTACCGATATCCCCTTCCGATATCGATACCAATTTTACCTTCGATGATGCCTAGTAT
CGATACTACC
Found at i:130527 original size:15 final size:14
Alignment explanation
Indices: 130507--130552 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
130497 AAATAATTAA
130507 ATTTTATAAAATAT
1 ATTTTATAAAATAT
* *
130521 ATATT-TAAAATCT
1 ATTTTATAAAATAT
*
130534 ATTTTATTAAATAT
1 ATTTTATAAAATAT
130548 -TTTTA
1 ATTTTA
130553 AATATATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTTATAAAATAT
Found at i:130529 original size:13 final size:12
Alignment explanation
Indices: 130513--130562 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
130503 TTAAATTTTA
130513 TAAAATATATATT
1 TAAAATATAT-TT
*
130526 TAAAATCTATTT
1 TAAAATATATTT
130538 TATTAAATAT-TTT
1 TA--AAATATATTT
130551 T-AAATATATTT
1 TAAAATATATTT
130562 T
1 T
130563 TCCCATTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 6 0.19
11 4 0.12
12 4 0.12
13 13 0.41
14 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
TAAAATATATTT
Found at i:131504 original size:29 final size:29
Alignment explanation
Indices: 131462--131528 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
131452 AATCCATGTT
131462 GTTGGGTCGTATCCTAGTATACATTTTAA
1 GTTGGGTCGTATCCTAGTATACATTTTAA
131491 GTTGGGTCGTATCCTAGTATACATTTTAA
1 GTTGGGTCGTATCCTAGTATACATTTTAA
131520 GTTGGGTCG
1 GTTGGGTCG
131529 ACCTCCTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.40
Consensus pattern (29 bp):
GTTGGGTCGTATCCTAGTATACATTTTAA
Found at i:138524 original size:60 final size:59
Alignment explanation
Indices: 138450--138620 Score: 188
Period size: 60 Copynumber: 2.8 Consensus size: 59
138440 ATATGTTAAT
* *
138450 ATTATTATTAAAAT-ATTATTTATATAATT-TTATAAATAA-AAATATTATAAATTATATTA
1 ATTATTATTAAAATAAGTATTT-TAT-ATTATTA-AAATAATAAATATTATAAATTATATCA
*
138509 ATTATTTATTAAAATAAGTATTTTATATTATTAAAATAATAAATATTATTAATTATATCA
1 ATTA-TTATTAAAATAAGTATTTTATATTATTAAAATAATAAATATTATAAATTATATCA
* **
138569 ATTGCTTATGCAAATAAGGATATTGTTATATTATTAAAATAA-AAATATTATA
1 ATT-ATTATTAAAATAA-G-TATT-TTATATTATTAAAATAATAAATATTATA
138621 TTATAATTTA
Statistics
Matches: 97, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
59 13 0.13
60 47 0.48
61 7 0.07
62 13 0.13
63 17 0.18
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (59 bp):
ATTATTATTAAAATAAGTATTTTATATTATTAAAATAATAAATATTATAAATTATATCA
Found at i:140241 original size:18 final size:16
Alignment explanation
Indices: 140195--140254 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
140185 ATCATGCTAC
140195 TTCATTTAAGCATG-A
1 TTCATTTAAGCATGCA
140210 GTTCATTTAAGCATGCA
1 -TTCATTTAAGCATGCA
140227 TTGCATTTAAAGCAT-CTA
1 TT-CATTT-AAGCATGC-A
140245 TTTCATTTAA
1 -TTCATTTAA
140255 TAAAGTTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 16 0.41
17 9 0.23
18 12 0.31
19 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (16 bp):
TTCATTTAAGCATGCA
Found at i:140281 original size:17 final size:17
Alignment explanation
Indices: 140261--140319 Score: 100
Period size: 17 Copynumber: 3.5 Consensus size: 17
140251 TTAATAAAGT
* *
140261 TAGTTCATTAATTAAAC
1 TAGTTCATAAATCAAAC
140278 TAGTTCATAAATCAAAC
1 TAGTTCATAAATCAAAC
140295 TAGTTCATAAATCAAAC
1 TAGTTCATAAATCAAAC
140312 TAGTTCAT
1 TAGTTCAT
140320 TTATTAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (17 bp):
TAGTTCATAAATCAAAC
Found at i:140328 original size:17 final size:17
Alignment explanation
Indices: 140261--140330 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
140251 TTAATAAAGT
140261 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
140278 TAGTTCATAAATCAAAC
1 TAGTTCATTAATTAAAC
* *
140295 TAGTTCATAAATCAAAC
1 TAGTTCATTAATTAAAC
*
140312 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
140329 TA
1 TA
140331 ACTCTTAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:140329 original size:34 final size:34
Alignment explanation
Indices: 140246--140330 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
140236 AAGCATCTAT
* * * *
140246 TTCATTTAATAAAGTTAGTTCATTAATTAAACTAG
1 TTCATTTATTAAA-CTAGTTCATAAATCAAACTAG
** *
140281 TTCATAAATCAAACTAGTTCATAAATCAAACTAG
1 TTCATTTATTAAACTAGTTCATAAATCAAACTAG
140315 TTCATTTATTAAACTA
1 TTCATTTATTAAACTA
140331 ACTCTTAATT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
34 31 0.77
35 9 0.22
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (34 bp):
TTCATTTATTAAACTAGTTCATAAATCAAACTAG
Found at i:143379 original size:17 final size:17
Alignment explanation
Indices: 143359--143411 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
143349 TTAATAAAGT
143359 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* * *
143376 TAGTTTATAAATCAAAC
1 TAGTTCATTAATTAAAC
* *
143393 TTGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
143410 TA
1 TA
143412 AATCTTAATT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:145040 original size:11 final size:12
Alignment explanation
Indices: 145024--145052 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
145014 ATTAAGAAGA
145024 TTTCAT-ATTTG
1 TTTCATCATTTG
145035 TTTCATCATTTG
1 TTTCATCATTTG
145047 TTTCAT
1 TTTCAT
145053 TATCTTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.17, C:0.14, G:0.07, T:0.62
Consensus pattern (12 bp):
TTTCATCATTTG
Found at i:146708 original size:17 final size:17
Alignment explanation
Indices: 146673--146740 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
146663 AAGCACCTAT
* *
146673 TTCATTTAATAAAGTTAG
1 TTCATTAAATAAA-CTAG
*
146691 TTCATTAACTAAACTAG
1 TTCATTAAATAAACTAG
146708 TTCA-TAAATCAAACTAG
1 TTCATTAAAT-AAACTAG
* *
146725 TTCATTTATTAAACTA
1 TTCATTAAATAAACTA
146741 ACTCTTAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
16 4 0.10
17 24 0.57
18 14 0.33
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (17 bp):
TTCATTAAATAAACTAG
Found at i:154997 original size:21 final size:20
Alignment explanation
Indices: 154956--154993 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
154946 TCTACCATGT
154956 TTAAGAAGTATGAATTTTGG
1 TTAAGAAGTATGAATTTTGG
154976 TTAATGAAGT-TGAATTTT
1 TTAA-GAAGTATGAATTTT
154994 TGGTCATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (20 bp):
TTAAGAAGTATGAATTTTGG
Found at i:158038 original size:21 final size:20
Alignment explanation
Indices: 157966--158038 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
157956 AAGGTTGGTC
* *
157966 TCCATACCAGAGGACTGATA
1 TCCATACCAAAGGATTGATA
157986 TCCATACCAAA-GATTGAGTA
1 TCCATACCAAAGGATTGA-TA
*
158006 TCCATACCAAAGGTTTGATA
1 TCCATACCAAAGGATTGATA
*
158026 TCAATACCTAAAG
1 TCCATACC-AAAG
158039 TGGTTGAGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 5 0.11
20 32 0.70
21 9 0.20
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (20 bp):
TCCATACCAAAGGATTGATA
Found at i:158862 original size:19 final size:20
Alignment explanation
Indices: 158840--158883 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
158830 ATTGGTATCA
*
158840 ATACTCAAGG-TGAGTATTG
1 ATACTCAAGGATCAGTATTG
*
158859 ATACCCAAGGATCAGTATTG
1 ATACTCAAGGATCAGTATTG
158879 ATACT
1 ATACT
158884 TCTGGTATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (20 bp):
ATACTCAAGGATCAGTATTG
Found at i:162514 original size:59 final size:59
Alignment explanation
Indices: 162443--162562 Score: 197
Period size: 59 Copynumber: 2.0 Consensus size: 59
162433 AGTGTAATTG
* * *
162443 TACCATTAAAG-AAAATATGGCTGATTTGGGGAAGATTTTTTTTGTTGTTTTACGTTGCA
1 TACCATTAAAGAAAAATATGGCTAATTTGGGAAAGA-TTTTGTTGTTGTTTTACGTTGCA
162502 TACCATTAAAGAAAAATATGGCTAATTTGGGAAAGATTTTGTTGTTGTTTTACGTTGCA
1 TACCATTAAAGAAAAATATGGCTAATTTGGGAAAGATTTTGTTGTTGTTTTACGTTGCA
162561 TA
1 TA
162563 TTTTGGGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 35 0.61
60 22 0.39
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (59 bp):
TACCATTAAAGAAAAATATGGCTAATTTGGGAAAGATTTTGTTGTTGTTTTACGTTGCA
Found at i:163378 original size:20 final size:19
Alignment explanation
Indices: 163353--163393 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
163343 TAAGGTTGTA
*
163353 GTATCGATGTCAGATGCTCG
1 GTATCGATAT-AGATGCTCG
*
163373 GTATCGATATGGATGCTCG
1 GTATCGATATAGATGCTCG
163392 GT
1 GT
163394 CTCAAGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.32
Consensus pattern (19 bp):
GTATCGATATAGATGCTCG
Found at i:163477 original size:20 final size:21
Alignment explanation
Indices: 163449--163492 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
163439 CTCTATATTG
*
163449 AAGGATTGATATCCATACC-A
1 AAGGATTGATATCAATACCTA
*
163469 AAGGCTTGATATCAATACCTA
1 AAGGATTGATATCAATACCTA
163490 AAG
1 AAG
163493 TGGTTGACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (21 bp):
AAGGATTGATATCAATACCTA
Found at i:172744 original size:23 final size:25
Alignment explanation
Indices: 172712--172759 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
172702 TAGGCATGAT
172712 CATTGAGTCC-TC-ATAGGTCACGTC
1 CATTGAGTCCTTCTA-AGGTCACGTC
172736 CATTG-GTCCTTCTAAGGTCACGTC
1 CATTGAGTCCTTCTAAGGTCACGTC
172760 TTTTGGGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 17 0.77
25 1 0.05
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (25 bp):
CATTGAGTCCTTCTAAGGTCACGTC
Found at i:175963 original size:36 final size:35
Alignment explanation
Indices: 175860--175975 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 35
175850 TAGTTAAGGA
* * *
175860 ATGGTGATGATATAGGTGTGAAATGGTGATAGAGG
1 ATGGTGATGATATAGGTGTGAAATGGTAATGGAAG
* * *
175895 ATGGTGATGATATAGGCGTGCAATGGTTATGGAAG
1 ATGGTGATGATATAGGTGTGAAATGGTAATGGAAG
* *
175930 ATGATGATGTTATAGGTGTGAAAATGGTAATGGAAG
1 ATGGTGATGATATAGGTGTG-AAATGGTAATGGAAG
175966 ATGGTGATGA
1 ATGGTGATGA
175976 ATAAATAGTA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 47 0.69
36 21 0.31
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.29
Consensus pattern (35 bp):
ATGGTGATGATATAGGTGTGAAATGGTAATGGAAG
Found at i:176529 original size:27 final size:27
Alignment explanation
Indices: 176488--176551 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
176478 CACGCATGGC
* *
176488 ACATGGGTGGTTGGTTATGAGGCACTA
1 ACATGGGTGGCTGGTCATGAGGCACTA
176515 ACATGGGTGGCTGGTCATGAGGCACTA
1 ACATGGGTGGCTGGTCATGAGGCACTA
*
176542 AGATGGGTGG
1 ACATGGGTGG
176552 TATAGGGTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.41, T:0.25
Consensus pattern (27 bp):
ACATGGGTGGCTGGTCATGAGGCACTA
Found at i:190016 original size:21 final size:21
Alignment explanation
Indices: 189992--190040 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
189982 GTTTTGCTAC
*
189992 AAGAATTT-ATGGCCTCGACA
1 AAGAATTTCATGGCCTCAACA
*
190012 AA-AGATTTCATGGCTTCAACA
1 AAGA-ATTTCATGGCCTCAACA
190033 AAGAATTT
1 AAGAATTT
190041 GATGCATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 6 0.25
21 16 0.67
22 1 0.04
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (21 bp):
AAGAATTTCATGGCCTCAACA
Found at i:194589 original size:14 final size:14
Alignment explanation
Indices: 194570--194605 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
194560 TTCCTTCAAA
194570 CTTTTCTCTTAAAT
1 CTTTTCTCTTAAAT
194584 CTTTTCTCTTAAAT
1 CTTTTCTCTTAAAT
194598 CTTTTCTC
1 CTTTTCTC
194606 CACATCCCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (14 bp):
CTTTTCTCTTAAAT
Found at i:229467 original size:23 final size:23
Alignment explanation
Indices: 229419--229464 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
229409 GGTGTTTGAT
* *
229419 ATACAACATCATCAACATATTCC
1 ATACAACATCAACAACATAATCC
*
229442 ATACAACATCAACACCATCAATC
1 ATACAACATCAACAACAT-AATC
229465 ATATTCCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.22
Consensus pattern (23 bp):
ATACAACATCAACAACATAATCC
Found at i:229483 original size:29 final size:29
Alignment explanation
Indices: 229422--229484 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
229412 GTTTGATATA
* *
229422 CAACATCATCAACATATTCCATACAACAT
1 CAACACCATCAACATATTCCATACAACAC
*
229451 CAACACCATCAATCATATTCCAT-CAATAC
1 CAACACCATCAA-CATATTCCATACAACAC
229480 CAACA
1 CAACA
229485 ACAACTTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (29 bp):
CAACACCATCAACATATTCCATACAACAC
Found at i:246965 original size:17 final size:17
Alignment explanation
Indices: 246921--246969 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
246911 GAAGAGGGAG
*
246921 AAGAAGAAGAATAAGGAAA
1 AAGAAGAA-AAT-GGGAAA
*
246940 ATGAGAGAAAATGGGAAA
1 AAGA-AGAAAATGGGAAA
246958 AAGAAGAAAATG
1 AAGAAGAAAATG
246970 AAAGAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.31
18 8 0.31
19 6 0.23
20 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.08
Consensus pattern (17 bp):
AAGAAGAAAATGGGAAA
Found at i:256195 original size:21 final size:21
Alignment explanation
Indices: 256157--256200 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
256147 GTTTTTCGGC
*
256157 AAGTACATAATTTTTAA-TGA
1 AAGTACATAATCTTTAATTGA
256177 AAGTACATAATGCTTTAATTGA
1 AAGTACATAAT-CTTTAATTGA
256199 AA
1 AA
256201 AAAGGAGTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 5 0.24
22 5 0.24
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (21 bp):
AAGTACATAATCTTTAATTGA
Found at i:258143 original size:29 final size:29
Alignment explanation
Indices: 258111--258170 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
258101 TCGTTGAGCC
*
258111 ATTGTAGTTTATATGGACTTGGATGTTTT
1 ATTGTAGTTTATATGGACTTGGATGCTTT
258140 ATTGTAGTTTATATGGACTTGGATGCTTT
1 ATTGTAGTTTATATGGACTTGGATGCTTT
258169 AT
1 AT
258171 GGGTTTTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.22, C:0.05, G:0.23, T:0.50
Consensus pattern (29 bp):
ATTGTAGTTTATATGGACTTGGATGCTTT
Found at i:266968 original size:17 final size:18
Alignment explanation
Indices: 266933--266970 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
266923 ATAGGTTAGG
266933 ATGGAAAGAAAAGAAGAA
1 ATGGAAAGAAAAGAAGAA
*
266951 ATGGAAAGATAA-AAGAA
1 ATGGAAAGAAAAGAAGAA
266968 ATG
1 ATG
266971 ATTTAAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (18 bp):
ATGGAAAGAAAAGAAGAA
Found at i:267837 original size:20 final size:21
Alignment explanation
Indices: 267812--267856 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
267802 GTGATTCGAC
*
267812 AAGTACATAAT-TTTTAATGA
1 AAGTACATAATATTTAAATGA
267832 AAGTACATAATGATTTAAATGA
1 AAGTACATAAT-ATTTAAATGA
267854 AAG
1 AAG
267857 AATGAGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
22 11 0.50
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (21 bp):
AAGTACATAATATTTAAATGA
Found at i:272013 original size:363 final size:367
Alignment explanation
Indices: 271344--272077 Score: 1406
Period size: 363 Copynumber: 2.0 Consensus size: 367
271334 TGTTCTTCTT
271344 TTAGGTCACATCTCCTGATTATTTGATTGCCACATTGCTTAAATAGGAATGGTTCATCCCAGTGA
1 TTAGGTCACATCTCCTGATTATTTGATTGCCACATTGCTTAAATAGGAATGGTTCATCCCAGTGA
271409 TAGTATCGCACATCATGTCAGAATTGTTTTCTCCTTTGCTAGAAAAATCTGGAGGTATAATACCA
66 -AGTATCGCACATCATGTCAGAATTGTTTTCTCCTTTGCTAGAAAAATCTGGAGGTATAATACCA
271474 CTAACAAGAAAATTGACTATGTCAGCGTACCACGACACAACCATGATAAATAAAATTTTATCATC
130 CTAACAAGAAAATTGACTATGTCAGCGTACCACGACACAACCATGATAAATAAAATTTTATCATC
271539 AGGGAAATCCTCATAGATGTCCTTCATATCATGAAAAATGATTTCGTTTTCAAGGCTTGACAAGT
195 AGGGAAATCCTCATAGATGTCCTTCATATCATGAAAAATGATTTCGTTTTCAAGGCTTGACAAGT
271604 GATTTGATACTTGGTCTTTAGTATCCTTTCTATCCTTCACCTCTAAATCAAACTCTTATAGTTGC
260 GATTTGATACTTGGTCTTTAGTATCCTTTCTATCCTTCACCTCTAAATCAAACTCTTATAGTTGC
271669 AATATCCATCTAATGAGCCCAGGCTTTGCATC-TTTTTATTGA
325 AATATCCATCTAATGAGCCCAGGCTTTGCATCTTTTTTATTGA
271711 TTAGGTCACATCTCCTGATTATTTGATTGCCACATTGCTTAAATAGGAATGGTTCATCCCAGTG-
1 TTAGGTCACATCTCCTGATTATTTGATTGCCACATTGCTTAAATAGGAATGGTTCATCCCAGTGA
271775 AGTATCGCACATCATGTCAGAATTGTTTTCTCCTTTGCTAGAAAAATCTGGAGGTATAATACCAC
66 AGTATCGCACATCATGTCAGAATTGTTTTCTCCTTTGCTAGAAAAATCTGGAGGTATAATACCAC
271840 T-ACAAGAAAAATTGACTATGTCAGCGTACCACGACACAACCATGAT-AAT-AAATTTTATCATC
131 TAACAAG-AAAATTGACTATGTCAGCGTACCACGACACAACCATGATAAATAAAATTTTATCATC
271902 AGGGAAATCCTCATAGATGTCCTTCATATCATGAAAAATGATTTCGTTTTCAAGGCTTGACAAGT
195 AGGGAAATCCTCATAGATGTCCTTCATATCATGAAAAATGATTTCGTTTTCAAGGCTTGACAAGT
271967 GATTTGATACTTGGTCTTTAGTATCCTTTCTATCCTTCACCTCTAAATCAAACTCTTATAGTTGC
260 GATTTGATACTTGGTCTTTAGTATCCTTTCTATCCTTCACCTCTAAATCAAACTCTTATAGTTGC
*
272032 GATATCCATCTAATGAGCCCAGGCTTTGCATCTTTTTTATTGA
325 AATATCCATCTAATGAGCCCAGGCTTTGCATCTTTTTTATTGA
272075 TTA
1 TTA
272078 AATACTTAAC
Statistics
Matches: 364, Mismatches: 1, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
363 174 0.48
364 21 0.06
365 105 0.29
367 64 0.18
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (367 bp):
TTAGGTCACATCTCCTGATTATTTGATTGCCACATTGCTTAAATAGGAATGGTTCATCCCAGTGA
AGTATCGCACATCATGTCAGAATTGTTTTCTCCTTTGCTAGAAAAATCTGGAGGTATAATACCAC
TAACAAGAAAATTGACTATGTCAGCGTACCACGACACAACCATGATAAATAAAATTTTATCATCA
GGGAAATCCTCATAGATGTCCTTCATATCATGAAAAATGATTTCGTTTTCAAGGCTTGACAAGTG
ATTTGATACTTGGTCTTTAGTATCCTTTCTATCCTTCACCTCTAAATCAAACTCTTATAGTTGCA
ATATCCATCTAATGAGCCCAGGCTTTGCATCTTTTTTATTGA
Found at i:273869 original size:110 final size:110
Alignment explanation
Indices: 273676--273896 Score: 442
Period size: 110 Copynumber: 2.0 Consensus size: 110
273666 AGGAATGAGT
273676 AGTTCGATAGGAAGGGCAGATAGATGAACCATCATCGATATCAGCCGAAAATGAAAAAATGCACG
1 AGTTCGATAGGAAGGGCAGATAGATGAACCATCATCGATATCAGCCGAAAATGAAAAAATGCACG
273741 ACGACCGACTTGGGTTTCGATGAAGCTTCCCTCATTCATTTCCCG
66 ACGACCGACTTGGGTTTCGATGAAGCTTCCCTCATTCATTTCCCG
273786 AGTTCGATAGGAAGGGCAGATAGATGAACCATCATCGATATCAGCCGAAAATGAAAAAATGCACG
1 AGTTCGATAGGAAGGGCAGATAGATGAACCATCATCGATATCAGCCGAAAATGAAAAAATGCACG
273851 ACGACCGACTTGGGTTTCGATGAAGCTTCCCTCATTCATTTCCCG
66 ACGACCGACTTGGGTTTCGATGAAGCTTCCCTCATTCATTTCCCG
273896 A
1 A
273897 TGAACGGCGG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (110 bp):
AGTTCGATAGGAAGGGCAGATAGATGAACCATCATCGATATCAGCCGAAAATGAAAAAATGCACG
ACGACCGACTTGGGTTTCGATGAAGCTTCCCTCATTCATTTCCCG
Found at i:276144 original size:18 final size:18
Alignment explanation
Indices: 276118--276159 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
276108 CCAAGCATTT
*
276118 GGGTCGGACAGGCGGGTC
1 GGGTTGGACAGGCGGGTC
*
276136 GGGTTGGACAGGCGGGTT
1 GGGTTGGACAGGCGGGTC
276154 GGGTTG
1 GGGTTG
276160 ATCCAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.57, T:0.19
Consensus pattern (18 bp):
GGGTTGGACAGGCGGGTC
Found at i:285104 original size:43 final size:43
Alignment explanation
Indices: 285047--285177 Score: 153
Period size: 43 Copynumber: 3.1 Consensus size: 43
285037 GTTTGTTCCA
*
285047 AAAAC-GCCGCTACAGATATGACCTTTTACGGTGTTTTTATCC
1 AAAACTGCTGCTACAGATATGACCTTTTACGGTGTTTTTATCC
* *
285089 AAAACTGCTGCTACAGATATGACCTTTTGCGGCG--TTTATCC
1 AAAACTGCTGCTACAGATATGACCTTTTACGGTGTTTTTATCC
* * * *
285130 AAAAAAATGCTGCTACA-ATATGACCTTTTACAGTGTTTGTATAC
1 --AAAACTGCTGCTACAGATATGACCTTTTACGGTGTTTTTATCC
285174 AAAA
1 AAAA
285178 ACGCCGCTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
41 7 0.09
42 24 0.32
43 39 0.52
44 5 0.07
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (43 bp):
AAAACTGCTGCTACAGATATGACCTTTTACGGTGTTTTTATCC
Found at i:285199 original size:85 final size:86
Alignment explanation
Indices: 285046--285204 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 86
285036 CGTTTGTTCC
* * * * * *
285046 AAAAACGCCGCTACAGATATGACCTTTTACGGTGTTTTTATCCAAAACTGCTGCTACAGATATGA
1 AAAAACGCCGCTACAGATATGACCTTTTACAGTGTTTGTATCAAAAACTGCCGCTACAAATATAA
285111 CCTTTTGCGGCGTTTATCCAA
66 CCTTTTGCGGCGTTTATCCAA
* * * *
285132 AAAAATGCTGCTACA-ATATGACCTTTTACAGTGTTTGTATACAAAAAC-GCCGCTATAAATCTA
1 AAAAACGCCGCTACAGATATGACCTTTTACAGTGTTTGTAT-CAAAAACTGCCGCTACAAATATA
285195 ACCTTTTGCG
65 ACCTTTTGCG
285205 TTTTGTTCCA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
85 43 0.69
86 19 0.31
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (86 bp):
AAAAACGCCGCTACAGATATGACCTTTTACAGTGTTTGTATCAAAAACTGCCGCTACAAATATAA
CCTTTTGCGGCGTTTATCCAA
Found at i:285314 original size:42 final size:42
Alignment explanation
Indices: 285165--285316 Score: 157
Period size: 44 Copynumber: 3.6 Consensus size: 42
285155 TTTTACAGTG
* *
285165 TTTGTATACAAAAACGCCGCTATAAATCTAACCTTTTGC-G-T
1 TTTGT-TACAAAAACGCCGCTATAGATCTAACCTTTTGCGGCA
* * * *
285206 TTTGTTCCAAAAACGCCGATATAGATCTCAACCTTTTGTGGCG
1 TTTGTTACAAAAACGCCGCTATAGATCT-AACCTTTTGCGGCA
*
285249 TTTGTATACAAAAACGCCTCTATAGATCTGAA-CTTTTGCGGCA
1 TTTGT-TACAAAAACGCCGCTATAGATCT-AACCTTTTGCGGCA
* **
285292 TTTGTTTCAAAAATTCCGCTATAGA
1 TTTGTTACAAAAACGCCGCTATAGA
285317 ACTTGACTTT
Statistics
Matches: 92, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
40 20 0.22
41 14 0.15
42 17 0.18
43 19 0.21
44 22 0.24
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (42 bp):
TTTGTTACAAAAACGCCGCTATAGATCTAACCTTTTGCGGCA
Found at i:288248 original size:11 final size:11
Alignment explanation
Indices: 288232--288256 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
288222 AATAATCCCG
288232 AATATAGATTT
1 AATATAGATTT
288243 AATATAGATTT
1 AATATAGATTT
288254 AAT
1 AAT
288257 TAATTTGAAA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
AATATAGATTT
Found at i:292656 original size:16 final size:16
Alignment explanation
Indices: 292635--292672 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
292625 GCACTCAAAG
292635 AAGAAAACA-AAAAAAA
1 AAGAAAA-AGAAAAAAA
*
292651 AAGAAAAAGAAAAGAA
1 AAGAAAAAGAAAAAAA
292667 AAGAAA
1 AAGAAA
292673 GAAAAGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAAAAA
Found at i:307025 original size:36 final size:34
Alignment explanation
Indices: 306936--307027 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 34
306926 ATCTTATGAC
* * *
306936 TATAATTTGAATATTGACTATAATATATAAGATG
1 TATAATTTTAATATTAATTATAATATATAAGATG
* *
306970 TAT-ATTTTTATCATTAATTATAATATAATATATAT-
1 TATAATTTTAAT-ATTAATTATAATAT-ATA-AGATG
307005 TATAATTTTAATATTAAATTATA
1 TATAATTTTAATATT-AATTATA
307028 TTTTTTAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
33 6 0.13
34 15 0.32
35 9 0.19
36 17 0.36
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (34 bp):
TATAATTTTAATATTAATTATAATATATAAGATG
Found at i:307036 original size:26 final size:23
Alignment explanation
Indices: 306983--307031 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
306973 ATTTTTATCA
306983 TTAATTATAATATAATATATATT
1 TTAATTATAATATAATATATATT
* *
307006 ATAATTTTAATATTAA-ATTATATT
1 TTAATTATAATA-TAATA-TATATT
307030 TT
1 TT
307032 TTAATGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATTATAATATAATATATATT
Found at i:322494 original size:13 final size:13
Alignment explanation
Indices: 322472--322504 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
322462 TAATATAAAT
322472 ATTAAATCCATCA
1 ATTAAATCCATCA
*
322485 ATTAATTCCATCA
1 ATTAAATCCATCA
322498 ATTAAAT
1 ATTAAAT
322505 TCACTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTAAATCCATCA
Found at i:335170 original size:40 final size:40
Alignment explanation
Indices: 335048--335177 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
335038 GCCAAGTTGA
* *
335048 CATCTTTGGTTGGTGGCCAACTTGTACACATTGGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTGCACATTGGAAAATT
* * *
335088 CATCTTTGGTAGGCGGTCAACTTGTGCACATTTGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTGCACATTGGAAAATT
* * *
335128 CATCTTTGGTAGGTGGCCAAACTTTTGCACA-TGGGAATTT
1 CATCTTTGGTAGGTGGCC-AACTTGTGCACATTGGAAAATT
*
335168 CATATTTGGT
1 CATCTTTGGT
335178 TCCTAAAATA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 66 0.86
41 11 0.14
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (40 bp):
CATCTTTGGTAGGTGGCCAACTTGTGCACATTGGAAAATT
Found at i:340317 original size:2 final size:2
Alignment explanation
Indices: 340310--340360 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
340300 GAACCTCCCA
340310 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
340352 TC TC TC TC T
1 TC TC TC TC T
340361 ATGATGATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:341887 original size:90 final size:90
Alignment explanation
Indices: 341715--341887 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 90
341705 TACCGTGTAT
* *
341715 CCAATACCAAAGTGTTGGCCCTACAAGGGGAATCGAATGCCCAAACTAGATTAAATTAAATAAAT
1 CCAATACCAAAGTGTTGGCCCTACAAGGGGAA-CAAATGCCCAAACTAAATTAAATTAAATAAAT
* * **
341780 TTTCTCTCGTTAAAAACCTTGAATAC
65 TGTATCTCGGGAAAAACCTTGAATAC
* * *
341806 CCAATACCGAAGTGTTGGTCCTACAAGGGGAA-AAAGTGCTCAAACTAAATTAAATTAAATAAAT
1 CCAATACCAAAGTGTTGGCCCTACAAGGGGAACAAA-TGCCCAAACTAAATTAAATTAAATAAAT
*
341870 TGTATCTCGGGACAAACC
65 TGTATCTCGGGAAAAACC
341888 GAGTAAAATT
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
89 2 0.03
90 39 0.55
91 30 0.42
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (90 bp):
CCAATACCAAAGTGTTGGCCCTACAAGGGGAACAAATGCCCAAACTAAATTAAATTAAATAAATT
GTATCTCGGGAAAAACCTTGAATAC
Found at i:346319 original size:94 final size:95
Alignment explanation
Indices: 346150--346348 Score: 274
Period size: 94 Copynumber: 2.1 Consensus size: 95
346140 ACTGAGATGG
* * **
346150 GTATCGATACTATGAGGAAGGTATCGATACCATTTATTCCAGAATGTAGAAATGGTATCGATACT
1 GTATCGATACTAAGAGAAAGGTATCGATACCATGGATTCCAGAATGTAGAAATGGTATCGATACT
* * * *
346215 GTAATAGAGTATCAGTACCATAGTATAGAA
66 GAAAGAGAGTATCAGTACCACAATATAGAA
* * *
346245 GTATCGGTACTAAGAGAAAGGTATCGATATCATGGA-TCCAGAATGTAGAAGTGGTATCGATACT
1 GTATCGATACTAAGAGAAAGGTATCGATACCATGGATTCCAGAATGTAGAAATGGTATCGATACT
* *
346309 GAAAGGGAGTATCGGTACCACAATATAGAA
66 GAAAGAGAGTATCAGTACCACAATATAGAA
346339 GTATCGATAC
1 GTATCGATAC
346349 CATAGTAAGG
Statistics
Matches: 90, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
94 60 0.67
95 30 0.33
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (95 bp):
GTATCGATACTAAGAGAAAGGTATCGATACCATGGATTCCAGAATGTAGAAATGGTATCGATACT
GAAAGAGAGTATCAGTACCACAATATAGAA
Found at i:346784 original size:54 final size:54
Alignment explanation
Indices: 346668--346914 Score: 379
Period size: 54 Copynumber: 4.6 Consensus size: 54
346658 ACCAAAGAGA
* * **
346668 CACTATGTGTGCAACATAAGAAATTCAT-ATAAGTTTATTAATTTCCGTATTAA
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
*
346721 CACTTTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
* * *
346775 CACTATGTGTGCAACCCAAGAAATTCATAATAAGTTTATGAATTTTCGTATAGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
** *
346829 CACTATGTGTATAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
*
346883 CACTATGTGTGCAACCTAATAAATTCATAATA
1 CACTATGTGTGCAACCTAAGAAATTCATAATA
346915 GGTGACATAA
Statistics
Matches: 175, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 26 0.15
54 149 0.85
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (54 bp):
CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
Found at i:350433 original size:6 final size:6
Alignment explanation
Indices: 350422--350508 Score: 83
Period size: 6 Copynumber: 14.8 Consensus size: 6
350412 ATCTAAAGAA
* *
350422 AAAAAG AAAAAG AAAAAG AAAGA- AAAAAG AAAAA- AGAGAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG
* * *
350469 AAAAAG AGAAAG AGAAA- AAAGAG AGAAAA- AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAA
350509 AAGGACAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
5 12 0.18
6 51 0.76
7 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:350451 original size:23 final size:22
Alignment explanation
Indices: 350416--350510 Score: 102
Period size: 25 Copynumber: 4.1 Consensus size: 22
350406 AGATTCATCT
350416 AAAGAAAAAAAGAAAAAGAAAAA
1 AAAG-AAAAAAGAAAAAGAAAAA
350439 GAAAGAAAAAAGAAAAAAGAGAAGAA
1 -AAAGAAAAAAG-AAAAAGA-AA-AA
*
350465 AAAGAAAAAGAGAAAGAGAAAAA
1 AAAGAAAAA-AGAAAAAGAAAAA
* *
350488 AGAGAGAAAA-AAAAAGAAAAA
1 AAAGAAAAAAGAAAAAGAAAAA
350509 AA
1 AA
350511 GGACAAGAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
21 11 0.18
22 1 0.02
23 16 0.26
24 13 0.21
25 17 0.27
26 4 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAGAAAAAGAAAAA
Found at i:350470 original size:41 final size:42
Alignment explanation
Indices: 350416--350508 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 42
350406 AGATTCATCT
350416 AAAGAA-AAAAAGAAAAAGA-AAA-AGAAAGAAA-AAAGAAAA
1 AAAGAAGAAAAAGAAAAAGAGAAAGAGAAA-AAAGAAAGAAAA
*
350455 AAGAGAAGAAAAAGAAAAAGAGAAAGAGAAAAAAGAGAGAAAA
1 AA-AGAAGAAAAAGAAAAAGAGAAAGAGAAAAAAGAAAGAAAA
350498 AAA-AAGAAAAA
1 AAAGAAGAAAAA
350509 AAGGACAAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
39 2 0.04
40 4 0.08
41 21 0.44
42 7 0.15
43 14 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (42 bp):
AAAGAAGAAAAAGAAAAAGAGAAAGAGAAAAAAGAAAGAAAA
Found at i:352284 original size:75 final size:74
Alignment explanation
Indices: 352080--352317 Score: 286
Period size: 75 Copynumber: 3.2 Consensus size: 74
352070 AGCAAATATC
* * *
352080 AGAAATTTATCTCACTTGAGA-GTGTTTTTCTCAAAACGAGTTTTGTCTCACTAGAGATAGTTTT
1 AGAAATTTATCTCACTTGAGATG-GTTTTTCTCAAAACAAGTTTCGTCTCACTAGAGACAG-TTT
*
352144 CCCTTGAAA-C
64 CCCTTGAAATA
** * * *
352154 A-AAATTTATCTCACTTGAGATTTTTTTTC-CATAACAAGTTTCATCTCACTGGAGACAGTTTCC
1 AGAAATTTATCTCACTTGAGATGGTTTTTCTCAAAACAAGTTTCGTCTCACTAGAGACAGTTTCC
*
352217 CCTGAAATA
66 CTTGAAATA
* *
352226 AGAAATTTTATCTCACTTGAGATGGTTTTTCTTAAAACCAGTTTCGTCTCACTAGAGACAGTTTC
1 AGAAA-TTTATCTCACTTGAGATGGTTTTTCTCAAAACAAGTTTCGTCTCACTAGAGACAGTTTC
*
352291 ACTTGAAATA
65 CCTTGAAATA
*
352301 AGAAATTTTATCCCACT
1 AGAAA-TTTATCTCACT
352318 CATGTTTGAG
Statistics
Matches: 139, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
71 11 0.08
72 24 0.17
73 28 0.20
74 24 0.17
75 52 0.37
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (74 bp):
AGAAATTTATCTCACTTGAGATGGTTTTTCTCAAAACAAGTTTCGTCTCACTAGAGACAGTTTCC
CTTGAAATA
Found at i:357860 original size:69 final size:69
Alignment explanation
Indices: 357773--357905 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 69
357763 CCAACAACTC
* * *
357773 GAGATGGTTTTTCTTAAAACCAACTTCGTATTGCTTGAGA-AAGTTTTCGCTTGAAACAAAATTT
1 GAGATGGTTTTTCTTAAAACCAACTTCATATCGCTTGAGATAA-TTTTCCCTTGAAACAAAATTT
357837 CACTT
65 CACTT
*
357842 GAGATGGTTTTTCTTAAAACCAACTTCATCTCGCTTGAGATAATTTTCCCTTGAAACAAAATTT
1 GAGATGGTTTTTCTTAAAACCAACTTCATATCGCTTGAGATAATTTTCCCTTGAAACAAAATTT
357906 TCTAATCTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 57 0.97
70 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (69 bp):
GAGATGGTTTTTCTTAAAACCAACTTCATATCGCTTGAGATAATTTTCCCTTGAAACAAAATTTC
ACTT
Found at i:357879 original size:36 final size:36
Alignment explanation
Indices: 357773--357882 Score: 93
Period size: 36 Copynumber: 3.1 Consensus size: 36
357763 CCAACAACTC
* *
357773 GAGATGGTTTTTCTTAAAACCAACTTCGTATTGCTT
1 GAGATGGTTTTTCTTAAAACCAACTTCATATCGCTT
** * * * * *
357809 GAGAAAGTTTTCGCTTGAAA-CAA---AATTTCACTT
1 GAGATGGTTTT-TCTTAAAACCAACTTCATATCGCTT
*
357842 GAGATGGTTTTTCTTAAAACCAACTTCATCTCGCTT
1 GAGATGGTTTTTCTTAAAACCAACTTCATATCGCTT
357878 GAGAT
1 GAGAT
357883 AATTTTCCCT
Statistics
Matches: 53, Mismatches: 16, Indels: 10
0.67 0.20 0.13
Matches are distributed among these distances:
32 6 0.11
33 17 0.32
36 24 0.45
37 6 0.11
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (36 bp):
GAGATGGTTTTTCTTAAAACCAACTTCATATCGCTT
Found at i:358577 original size:136 final size:134
Alignment explanation
Indices: 358277--358779 Score: 595
Period size: 134 Copynumber: 3.7 Consensus size: 134
358267 TAAACCGATC
* * *
358277 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCTGACTGAGGGAGAAGAAGTTCATAA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAA
* * * ** * * *
358342 TGAGAAAAGTTTGTTC-ACCTATCACTCGATTCATGACATTTCAAATCAGGGACACCTCGCTTGA
66 TGAGAAGAG-TTGTTCGACCTATCACTCGATTCACGATATTTTGAATCAGTGACGCCTCGCTTAA
*
358406 GGAAT
130 GGATT
** * * * *
358411 AACATTTCAAATGGAGAGTTTGTAATGAGAATAACTCATCCAAAAGAG-GTAGAATAAGTTCATA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAG-AGAAGAAGTTCATA
*
358475 ATGAGAAGAGCTTGTTCGAGCTATCACTCGATTCAC-AGTATTTTGAATCAGTGACGCCT-GACT
65 ATGAGAAGAG-TTGTTCGACCTATCACTCGATTCACGA-TATTTTGAATCAGTGACGCCTCG-CT
358538 TAAAGGATT
127 T-AAGGATT
* * *
358547 AACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCATCTGACAGAGAGAGAA-AACGTTCGTA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAA-GTTCATA
* * * *
358611 ATGAGAAGA-TTGTTTGACCTATCACTCGATTAACGATATTTTGAATCAGTGATGCCTCGTTTGA
65 ATGAGAAGAGTTGTTCGACCTATCACTCGATTCACGATATTTTGAATCAGTGACGCCTCGCTT-A
*
358675 GGGATT
129 AGGATT
* * * * *
358681 AACATTTCATATGGAGAGTTCATAATGAGAAGAACACATTCGATAGAGAGATAAGAAGTTCATAA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAA
358746 TGAGAAGAGATTGTTCGACCTATCACTCGATTCA
66 TGAGAAGAG-TTGTTCGACCTATCACTCGATTCA
358780 TGGCATTTCG
Statistics
Matches: 313, Mismatches: 44, Indels: 22
0.83 0.12 0.06
Matches are distributed among these distances:
133 1 0.00
134 183 0.58
135 41 0.13
136 87 0.28
137 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (134 bp):
AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAA
TGAGAAGAGTTGTTCGACCTATCACTCGATTCACGATATTTTGAATCAGTGACGCCTCGCTTAAG
GATT
Found at i:358762 original size:270 final size:270
Alignment explanation
Indices: 358277--358779 Score: 690
Period size: 270 Copynumber: 1.9 Consensus size: 270
358267 TAAACCGATC
* * *
358277 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCTGACTGAGGGAGAAGAAGTTCATAA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCATCTGACAGAGAGAGAAGAAGTTCATAA
* *
358342 TGAGAAAAGTTTGTTCACCTATCACTCGATTCATGACATTTCAAATCAGGGACACCTCGCTTGAG
66 TGAGAAAAGTTTGTTCACCTATCACTCGATTAACGACATTTCAAATCAGGGACACCTCGCTTGAG
** * * *
358407 GAATAACATTTCAAATGGAGAGTTTGTAATGAGAATAACTCATCCAAAAGAGGTAGAATAAGTTC
131 GAATAACATTTCAAATGGAGAGTTCATAATGAGAAGAACACATCCAAAAGAGGTAGAAGAAGTTC
* *
358472 ATAATGAGAAGAGCTTGTTCGAGCTATCACTCGATTCACAGTATTTTGAATCAGTGACGCCTGAC
196 ATAATGAGAAGAGATTGTTCGACCTATCACTCGATTCACAGTATTTTGAATCAGTGACGCCTGAC
358537 TTAAAGGATT
261 TTAAAGGATT
*
358547 AACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCATCTGACAGAGAGAGAA-AACGTTCGTA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCATCTGACAGAGAGAGAAGAA-GTTCATA
* * * ** * ** *
358611 ATGAG--AAGATTGTTTGACCTATCACTCGATTAACGATATTTTGAATCAGTGATGCCTCGTTTG
65 ATGAGAAAAGTTTG-TTCACCTATCACTCGATTAACGACATTTCAAATCAGGGACACCTCGCTTG
* * * * * *
358674 AGGGATTAACATTTCATATGGAGAGTTCATAATGAGAAGAACACATTCGATAGAGAG-ATAAGAA
129 A-GGAATAACATTTCAAATGGAGAGTTCATAATGAGAAGAACACATCCAAAAGAG-GTAGAAGAA
358738 GTTCATAATGAGAAGAGATTGTTCGACCTATCACTCGATTCA
192 GTTCATAATGAGAAGAGATTGTTCGACCTATCACTCGATTCA
358780 TGGCATTTCG
Statistics
Matches: 201, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
268 6 0.03
269 43 0.21
270 151 0.75
271 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (270 bp):
AACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCATCTGACAGAGAGAGAAGAAGTTCATAA
TGAGAAAAGTTTGTTCACCTATCACTCGATTAACGACATTTCAAATCAGGGACACCTCGCTTGAG
GAATAACATTTCAAATGGAGAGTTCATAATGAGAAGAACACATCCAAAAGAGGTAGAAGAAGTTC
ATAATGAGAAGAGATTGTTCGACCTATCACTCGATTCACAGTATTTTGAATCAGTGACGCCTGAC
TTAAAGGATT
Found at i:362278 original size:28 final size:28
Alignment explanation
Indices: 362217--362281 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
362207 ATCGATCCAT
* * * *
362217 TGCTTGAAACATTATGTTGTCGAGATAG
1 TGCTTGAAACATTATGCTATCAAGACAG
* *
362245 TACTTGAAATATTATGCTATCAAGACAG
1 TGCTTGAAACATTATGCTATCAAGACAG
362273 TGCTTGAAA
1 TGCTTGAAA
362282 GCAACAACGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (28 bp):
TGCTTGAAACATTATGCTATCAAGACAG
Found at i:367263 original size:43 final size:43
Alignment explanation
Indices: 366953--367315 Score: 347
Period size: 43 Copynumber: 8.5 Consensus size: 43
366943 CCGCTAAAAT
* *
366953 TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTAGAGTTCTA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTCGAGATCTA
** * * * *
366996 TAGCAACGTTTTTTGAACAAACGTCGCAATAGGTAGAGTTTTA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTCGAGATCTA
* * * *
367039 TAACGACGTTTTTGGAACAAACGTCGCAATAGGTAGAGTTCTA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTCGAGATCTA
* * *
367082 TAGCGACGTTTTTGGAACAAACATCGCAATAGGTCGAGATTTA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTCGAGATCTA
* * ** ***
367125 TAGCAGCATTTTTTTAACAAATACCGCAATAGGTCGAGATCTA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTCGAGATCTA
* * *
367168 TAGCGGCATTTTTTGAACAAACGTCGCAAAAGGTC-AGATCTA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTCGAGATCTA
* * * * * *
367210 TAGTGCCGTTTTTGAAATAAACGCCACAATAGGTCGAGATCTA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTCGAGATCTA
* * * * * *
367253 TAGTGGCGTTTCTAGAGA-AAACG-AGCAAAAAGTCGA-ATCTA
1 TAGCGGCGTTTTTGGA-ACAAACGTCGCAATAGGTCGAGATCTA
*
367294 TAGCGGCGTTTTTGGAATAAAC
1 TAGCGGCGTTTTTGGAACAAAC
367316 ACCGCTAATT
Statistics
Matches: 270, Mismatches: 47, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
40 1 0.00
41 22 0.08
42 42 0.16
43 204 0.76
44 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTTTGGAACAAACGTCGCAATAGGTCGAGATCTA
Found at i:367275 original size:85 final size:84
Alignment explanation
Indices: 367151--367315 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 84
367141 ACAAATACCG
* * * * *
367151 CAATAGGTCGAGATCTATAGCGGCATTTTTTGAACAAACGTCGCAAAAGGTC-AGATCTATAGTG
1 CAATAGGTCGAGATCTATAGCGGCATTTCTAGAACAAACG-AGCAAAAAGTCGA-ATCTATAGCG
367215 CCGTTTTTGAAATAAACGCCA
64 CCGTTTTTGAAATAAACGCCA
* * *
367236 CAATAGGTCGAGATCTATAGTGGCGTTTCTAGAGA-AAACGAGCAAAAAGTCGAATCTATAGCGG
1 CAATAGGTCGAGATCTATAGCGGCATTTCTAGA-ACAAACGAGCAAAAAGTCGAATCTATAGCGC
*
367300 CGTTTTTGGAATAAAC
65 CGTTTTTGAAATAAAC
367316 ACCGCTAATT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 33 0.48
85 35 0.51
86 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (84 bp):
CAATAGGTCGAGATCTATAGCGGCATTTCTAGAACAAACGAGCAAAAAGTCGAATCTATAGCGCC
GTTTTTGAAATAAACGCCA
Found at i:375291 original size:64 final size:64
Alignment explanation
Indices: 375205--375360 Score: 217
Period size: 64 Copynumber: 2.4 Consensus size: 64
375195 TGCACTAAGA
* * * *
375205 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AACAAGCCCGAGTGCATCGATGTATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCCGAGTGCATCGATGCATGGAA
375268 T
64 T
* **
375269 GTGCATCGATGCATAAAATGCATTTGATGTTTTCATAAAACTTGAGTGCATCGATGCATGGAAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCGAGTGCATCGATGCATGGAAT
375333 GTGCATCGATGCATAAAATGCATTCGAT
1 GTGCATCGATGCATAAAATGCATTCGAT
375361 TTCAATTTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
64 73 0.89
65 7 0.09
66 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCGAGTGCATCGATGCATGGAAT
Found at i:375352 original size:19 final size:19
Alignment explanation
Indices: 375314--375352 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
375304 TAAAACTTGA
**
375314 GTGCATCGATGCATGGAAT
1 GTGCATCGATGCATAAAAT
375333 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCATAAAAT
375352 G
1 G
375353 CATTCGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (19 bp):
GTGCATCGATGCATAAAAT
Found at i:375401 original size:64 final size:63
Alignment explanation
Indices: 375205--375404 Score: 196
Period size: 64 Copynumber: 3.1 Consensus size: 63
375195 TGCACTAAGA
* * * *
375205 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AACAAGCCCGAGTGCATCGATGTATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA--CTGAGTGCATCGATGCATGGAT
375267 AT
63 -T
* *
375269 GTGCATCGATGCATAAAATGCATTTGATGTTTTCATAAAACTTGAGTGCATCGATGCATGGAAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAC-TGAGTGCATCGATGCATGGATT
* **
375333 GTGCATCGATGCATAAAATGCATTCGAT-TTCAATTTATTCAA-TG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTT---TTCATAAAACTGAGTGCATCGATGCATGGAT
375395 T
63 T
375396 GGTGCATCG
1 -GTGCATCG
375405 CTACACTCTT
Statistics
Matches: 117, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
63 21 0.18
64 81 0.69
65 7 0.06
66 8 0.07
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTGAGTGCATCGATGCATGGATT
Found at i:377694 original size:90 final size:89
Alignment explanation
Indices: 377555--377731 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 89
377545 TAATCCCGAA
* * * * * *
377555 TATTTAATTTCAATTAATTAAATATAGATTTATTAATTTGAAATAATAAAATCCCTGATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTAATTAATTTGAAATAATAAAAACCCTAATATGACT
377620 AGGGTAACTTGGATATAAAAGGAT
66 AGGGTAACTTGGATATAAAAGGAT
*
377644 TATTAAATTCCAATTAATTAAATATAGATATAATTAATTTGAAATAATAAAAACCTTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGAT-TAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
377709 TAGGGTAACTTGGCTATAAAAGG
65 TAGGGTAACTTGGATATAAAAGG
377732 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 27 0.34
90 52 0.66
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTAATTAATTTGAAATAATAAAAACCCTAATATGACT
AGGGTAACTTGGATATAAAAGGAT
Found at i:384485 original size:90 final size:90
Alignment explanation
Indices: 384364--384541 Score: 275
Period size: 90 Copynumber: 2.0 Consensus size: 90
384354 TAATCCCGAA
* * * * * *
384364 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTTGATATGAA
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAA
384429 TAAGGTAACTTGGATATAAAAGGAT
66 TAAGGTAACTTGGATATAAAAGGAT
*
384454 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAA
* *
384519 TAGGGTAACTTGGCTATAAAAGG
66 TAAGGTAACTTGGATATAAAAGG
384542 GTGTTTTAGG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAA
TAAGGTAACTTGGATATAAAAGGAT
Found at i:385452 original size:36 final size:35
Alignment explanation
Indices: 385355--385459 Score: 129
Period size: 35 Copynumber: 3.0 Consensus size: 35
385345 GGTGGTTATT
* * * *
385355 TAGGCTTGAAATGATGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGATGATGGAAGATGGTGATGTTA
* * *
385390 TAGGCGTGCAATGGTAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGATGATGGAAGATGGTGATGTTA
*
385425 TAGGCGTGAAAATGTTGATGGAAGATGGTGATGTT
1 TAGGCGTG-AAATGATGATGGAAGATGGTGATGTT
385460 TATGTAGTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
35 36 0.61
36 23 0.39
ACGTcount: A:0.32, C:0.04, G:0.34, T:0.30
Consensus pattern (35 bp):
TAGGCGTGAAATGATGATGGAAGATGGTGATGTTA
Found at i:388256 original size:45 final size:41
Alignment explanation
Indices: 388140--388263 Score: 124
Period size: 45 Copynumber: 2.8 Consensus size: 41
388130 AAAACCCTAT
* * *
388140 GGATGCATCGATGCATGTCCTTGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCAT-TTCATGTGTATCGATGCACATTCAA
*
388182 GGAGTGCATC-AGTGCATCTTCATGATGTATCGATTCACATTCAAA
1 GGA-TGCATCGA-TGCAT-TTCATG-TGTATCGATGCACATTC-AA
388227 GGGATGCATCGATGCACTTTCATAGTGTATCGATGCA
1 -GGATGCATCGATGCA-TTTCAT-GTGTATCGATGCA
388264 TTAAGCATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
42 4 0.06
43 15 0.22
44 15 0.22
45 28 0.41
46 6 0.09
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (41 bp):
GGATGCATCGATGCATTTCATGTGTATCGATGCACATTCAA
Found at i:394273 original size:64 final size:64
Alignment explanation
Indices: 394088--394246 Score: 214
Period size: 64 Copynumber: 2.5 Consensus size: 64
394078 TGCACTAAGA
* * * * *
394088 GTGCATAGATGCATGAAGTGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATTCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-ACTGAGTGCATCGATGCATGGTA
394151 T
64 T
* *
394152 GTGCATTGATGCATAAAATGCATTCGATGTTTTCATAAAAACTGAGTGCATCGATGCATTGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACTGAGTGCATCGATGCATGGTAT
*
394216 GTGCATCGATGCATAAAATGCATTTGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
394247 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
64 76 0.89
65 7 0.08
66 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACTGAGTGCATCGATGCATGGTAT
Found at i:395350 original size:16 final size:16
Alignment explanation
Indices: 395329--395359 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
395319 GTTTGATATT
395329 TATTTCAATCATAATA
1 TATTTCAATCATAATA
395345 TATTTCAATCATAAT
1 TATTTCAATCATAAT
395360 CTAAATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTCAATCATAATA
Found at i:398676 original size:15 final size:15
Alignment explanation
Indices: 398656--398690 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
398646 AAGGTTCCAC
*
398656 TAATATTTCTTGAGG
1 TAATATTTCTTCAGG
398671 TAATATTTCTTCAGG
1 TAATATTTCTTCAGG
398686 TAATA
1 TAATA
398691 GACAAGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (15 bp):
TAATATTTCTTCAGG
Found at i:400097 original size:27 final size:27
Alignment explanation
Indices: 400049--400137 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 27
400039 TCGGTTTTGG
** *
400049 AGTTCAAGGTATTCCGACCATTTTAG-
1 AGTTCAAGGTATTTTGATCATTTTAGA
*
400075 AGTTCAAGGGTATTTTGATCATTTTAGT
1 AGTTCAA-GGTATTTTGATCATTTTAGA
* * * *
400103 ACTTGAAGTTATTTTGATAATTTT-GA
1 AGTTCAAGGTATTTTGATCATTTTAGA
*
400129 AGCTCAAGG
1 AGTTCAAGG
400138 GTAATTCATT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
26 13 0.27
27 31 0.63
28 5 0.10
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.40
Consensus pattern (27 bp):
AGTTCAAGGTATTTTGATCATTTTAGA
Done.