Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015193.1 Kokia drynarioides strain JFW-HI SEQ_130237, 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: 594178
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 490 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1198 original size:21 final size:21
Alignment explanation
Indices: 1172--1212 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1162 AATATGGGTG
*
1172 AAATATT-ATGTGTTTAATTAT
1 AAATATTGAT-TGTGTAATTAT
1193 AAATATTGATTGTGTAATTA
1 AAATATTGATTGTGTAATTA
1213 ATTGGTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
AAATATTGATTGTGTAATTAT
Found at i:1334 original size:27 final size:24
Alignment explanation
Indices: 1288--1336 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
1278 AGAGAAATGT
1288 AAATGAGATATATGAAATTATGAG
1 AAATGAGATATATGAAATTATGAG
*
1312 AAATGATGTTATATGAGATATTATG
1 AAATGA-GATATATGA-A-ATTATG
1337 CCCATATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 8 0.38
26 1 0.05
27 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (24 bp):
AAATGAGATATATGAAATTATGAG
Found at i:1429 original size:22 final size:22
Alignment explanation
Indices: 1399--1500 Score: 132
Period size: 22 Copynumber: 4.4 Consensus size: 22
1389 ATGCTAGTGC
*
1399 GCTTACTGTTCATCACTGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
1422 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
1444 GCTTCTGTTTCCCCAGCACTATGTGT
1 GCTTCTG-TT---CAGCACTGTGTGT
*
1470 GCTTCTGCTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
1492 GCTTCTGTT
1 GCTTCTGTT
1501 TCCCCAGCAA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
22 44 0.63
23 6 0.09
25 1 0.01
26 19 0.27
ACGTcount: A:0.10, C:0.25, G:0.24, T:0.41
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:1473 original size:48 final size:48
Alignment explanation
Indices: 1412--1509 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
1402 TACTGTTCAT
* *
1412 CACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTTCCCCAG
1 CACTATGTGTGCTTCTGCTCAGCACTGTGTGTGCTTCTGTTTCCCCAG
1460 CACTATGTGTGCTTCTGCTCAGCACTGTGTGTGCTTCTGTTTCCCCAG
1 CACTATGTGTGCTTCTGCTCAGCACTGTGTGTGCTTCTGTTTCCCCAG
1508 CA
1 CA
1510 ATTATGTACT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.10, C:0.29, G:0.23, T:0.38
Consensus pattern (48 bp):
CACTATGTGTGCTTCTGCTCAGCACTGTGTGTGCTTCTGTTTCCCCAG
Found at i:3704 original size:22 final size:21
Alignment explanation
Indices: 3673--3727 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
3663 ACTAAAATTT
*
3673 CAAAATTTAAAAAATACAAAAA
1 CAAAAATTAAAAAATA-AAAAA
* *
3695 CTAAAATTAATCAAATAAAAAA
1 CAAAAATTAA-AAAATAAAAAA
*
3717 CAAAAACTAAA
1 CAAAAATTAAA
3728 CCCATAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (21 bp):
CAAAAATTAAAAAATAAAAAA
Found at i:4326 original size:20 final size:20
Alignment explanation
Indices: 4301--4343 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
4291 AAAATTTATC
4301 TAGTATATCATATC-GATAAA
1 TAGTAT-TCATATCAGATAAA
*
4321 TAGTATTCATATCATATAAA
1 TAGTATTCATATCAGATAAA
4341 TAG
1 TAG
4344 ATAAATCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (20 bp):
TAGTATTCATATCAGATAAA
Found at i:11608 original size:26 final size:28
Alignment explanation
Indices: 11571--11623 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
11561 ACCAATCATT
11571 GCATAGTCATGAATGAAGCAAA-GAAAA
1 GCATAGTCATGAATGAAGCAAATGAAAA
*
11598 GCAT-GTCATGAATTAAGCAAATGAAA
1 GCATAGTCATGAATGAAGCAAATGAAA
11624 GAAAATTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (28 bp):
GCATAGTCATGAATGAAGCAAATGAAAA
Found at i:16079 original size:77 final size:78
Alignment explanation
Indices: 15887--16105 Score: 289
Period size: 79 Copynumber: 2.8 Consensus size: 78
15877 ACGCAAAATC
* * * * *
15887 GTTGGTTAATCCAACTAGAGTTGGGTTCACTTTTGCAGTTTATCCTCTAGTTACTGGGTGACAAG
1 GTTGGTTAATCCAACTAGAGTTGGGCTCACTTTTGCGGTTTATCCGCTAGGTACTGGGTGCCAAG
15952 ATTTGACGAACATT
66 ATTTGACGAACA-T
** * *
15966 GTTGGTTAATTTAACTAGAGTTGGGCTCACTTTTGCGGTTTATCAGCTAGGTACTAGGTGCCAAG
1 GTTGGTTAATCCAACTAGAGTTGGGCTCACTTTTGCGGTTTATCCGCTAGGTACTGGGTGCCAAG
16031 ATTTGAC-AGAC-T
66 ATTTGACGA-ACAT
* * * *
16043 GTTGGTTAATCCAATTAGAGCTGGACTCACTTTTGCGGTTTATCCGCTAGGCACTGGGTGCCA
1 GTTGGTTAATCCAACTAGAGTTGGGCTCACTTTTGCGGTTTATCCGCTAGGTACTGGGTGCCA
16106 GGATCGTCGA
Statistics
Matches: 122, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
77 56 0.46
78 1 0.01
79 65 0.53
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (78 bp):
GTTGGTTAATCCAACTAGAGTTGGGCTCACTTTTGCGGTTTATCCGCTAGGTACTGGGTGCCAAG
ATTTGACGAACAT
Found at i:16361 original size:79 final size:80
Alignment explanation
Indices: 16144--16361 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 80
16134 AGCGCAAAAC
* * * * **
16144 CGTTGGTTAATCCAACTAGAGCTGAGCTCACTTATTGCAGTTTATCCGTTAGGCACTGGGTGCCA
1 CGTTGGTTAATCCAACTAGAGTTG-GCTCACTT-TTGCGGTTTATCAGTAAGGCACTAAGTGCCA
*
16209 GGAATGGACGGAATTAT
64 AGAATGGACGGAATTAT
* * * * *
16226 CGTTGGTTAATCCAGCTAGAGCTAGGCTTACTTTTGCGGTTTATCCACTAA-ACACTAAGTGCCA
1 CGTTGGTTAATCCAACTAGAG-TTGGCTCACTTTTGCGGTTTAT-CAGTAAGGCACTAAGTGCCA
* * *
16290 AGATTTGATGGACA-T-T
64 AGAATGGACGGA-ATTAT
* *
16306 -GTTGGTTAATCCAACTAGAGTTGGCCTCACTTTTGTGGTTTATCTGTAAGGCACTA
1 CGTTGGTTAATCCAACTAGAGTTGG-CTCACTTTTGCGGTTTATCAGTAAGGCACTA
16362 GGTGTTAGGA
Statistics
Matches: 109, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
78 7 0.06
79 40 0.37
80 1 0.01
81 29 0.27
82 31 0.28
83 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (80 bp):
CGTTGGTTAATCCAACTAGAGTTGGCTCACTTTTGCGGTTTATCAGTAAGGCACTAAGTGCCAAG
AATGGACGGAATTAT
Found at i:16374 original size:263 final size:260
Alignment explanation
Indices: 15847--16488 Score: 812
Period size: 263 Copynumber: 2.5 Consensus size: 260
15837 GAATTATTAA
*
15847 AGGATCGTCGGTTTATCCGACTAGCGCT-AGACGCAAAATCGTTGGTTAATCCAACTAGAGTTGG
1 AGGATCGTCGGTTTATCCGACTAGCGCTGAG-CGCAAAACCGTTGGTTAATCCAACTAGAGTT-G
* ** * * *
15911 GTTCACTT-TTGCAGTTTATCC-TCTAGTTACTGGGTGACAAGATTTGAC-GAA-CATTGTTGGT
64 GCTCACTTATTGCAGTTTATCCGT-TAGGCACTGGGTGACAAGAATTGACGGAATTATCGTTGGT
** * * *** *
15972 TAATTTAACTAGAGTTGGGCTCACTTTTGCGGTTTATCAGCTAGGTACTAGGTGCCAAGATTTGA
128 TAATCCAACTAGAGCTAGGCTCACTTTTGCGGTTTATCAGCTAAACACTAAGTGCCAAGATTTGA
* *
16037 CAGACTGTTGGTTAATCCAATTAGAGCTGGACTCACTTTTGCGGTTTATCCGCTAGGCACTGGGT
193 CAGACTGTTGGTTAATCCAACTAGAGCTGGACTCACTTTTGCGGTTTATCCGCTAGGCACTAGGT
16102 GCC
258 GCC
* *
16105 AGGATCGTCGATTTATCCGACTAGCGCTGAGCGCAAAACCGTTGGTTAATCCAACTAGAGCTGAG
1 AGGATCGTCGGTTTATCCGACTAGCGCTGAGCGCAAAACCGTTGGTTAATCCAACTAGAGTTG-G
* * *
16170 CTCACTTATTGCAGTTTATCCGTTAGGCACTGGGTGCCAGGAATGGACGGAATTATCGTTGGTTA
65 CTCACTTATTGCAGTTTATCCGTTAGGCACTGGGTGACAAGAATTGACGGAATTATCGTTGGTTA
* * *
16235 ATCCAGCTAGAGCTAGGCTTACTTTTGCGGTTTATCCA-CTAAACACTAAGTGCCAAGATTTGAT
130 ATCCAACTAGAGCTAGGCTCACTTTTGCGGTTTAT-CAGCTAAACACTAAGTGCCAAGATTTGAC
* * * * *
16299 GGACATTGTTGGTTAATCCAACTAGAGTTGGCCTCACTTTTGTGGTTTATCTG-TAAGGCACTAG
194 AGAC--TGTTGGTTAATCCAACTAGAGCTGGACTCACTTTTGCGGTTTATCCGCT-AGGCACTAG
**
16363 GTGTT
256 GTGCC
*
16368 AGGATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAAACCGTTGGTTAATCCAACTAGAGTTGGA
1 AGGATCGTCGGTTTATCCGACTAGCGCTGAGCGCAAAACCGTTGGTTAATCCAACTAGAGTTGG-
* * * * *
16433 CTCACTTATTGCAGTTTATCCGCTAGGCACCGGGTGTCATGAATTGACGGATTTAT
65 CTCACTTATTGCAGTTTATCCGTTAGGCACTGGGTGACAAGAATTGACGGAATTAT
16489 ACGGTGATAA
Statistics
Matches: 332, Mismatches: 41, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
257 1 0.00
258 63 0.19
259 34 0.10
260 4 0.01
261 63 0.19
262 4 0.01
263 163 0.49
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (260 bp):
AGGATCGTCGGTTTATCCGACTAGCGCTGAGCGCAAAACCGTTGGTTAATCCAACTAGAGTTGGC
TCACTTATTGCAGTTTATCCGTTAGGCACTGGGTGACAAGAATTGACGGAATTATCGTTGGTTAA
TCCAACTAGAGCTAGGCTCACTTTTGCGGTTTATCAGCTAAACACTAAGTGCCAAGATTTGACAG
ACTGTTGGTTAATCCAACTAGAGCTGGACTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCC
Found at i:25913 original size:9 final size:9
Alignment explanation
Indices: 25896--25928 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
25886 ATGTAATGTG
*
25896 AATGAATGC
1 AATGCATGC
25905 AATGCATGC
1 AATGCATGC
25914 AATGCATGC
1 AATGCATGC
25923 AATGCA
1 AATGCA
25929 AGAGAAGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (9 bp):
AATGCATGC
Found at i:29988 original size:30 final size:29
Alignment explanation
Indices: 29897--29993 Score: 108
Period size: 30 Copynumber: 3.3 Consensus size: 29
29887 AAAAAATCAA
* *
29897 GGTCAAAAATGGAATTTTTAGAAGTTTGG
1 GGTCAAAAATGTAATTTTTGGAAGTTTGG
* *
29926 GG--ATAAATTGGTAATTTTTGGAAAATTTGG
1 GGTCA-AAAAT-GTAATTTTTGG-AAGTTTGG
29956 GGTCAAAAATGTAATTTTTGGAAGTTTAGG
1 GGTCAAAAATGTAATTTTTGGAAGTTT-GG
29986 GGTCAAAA
1 GGTCAAAA
29994 TATGATTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.02
28 4 0.07
29 16 0.29
30 30 0.54
31 4 0.07
32 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
GGTCAAAAATGTAATTTTTGGAAGTTTGG
Found at i:30001 original size:29 final size:29
Alignment explanation
Indices: 29897--30016 Score: 88
Period size: 30 Copynumber: 4.0 Consensus size: 29
29887 AAAAAATCAA
*
29897 GGTCAAAAATGGAATTTTTAGAAGTTT-GG
1 GGTCAAAAAT-GAATTTTTGGAAGTTTAGG
* *
29926 GG--ATAAATTGGTAATTTTTGGAAAATTT-GG
1 GGTCA-AAAAT-G-AATTTTTGG-AAGTTTAGG
29956 GGTCAAAAATGTAATTTTTGGAAGTTTAGG
1 GGTCAAAAATG-AATTTTTGGAAGTTTAGG
* *
29986 GGTCAAAATATG-ATTTCTAGATAGTTTAGG
1 GGTCAAAA-ATGAATTTTTGGA-AGTTTAGG
30016 G
1 G
30017 ACCTCTAGAG
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
27 1 0.01
28 6 0.08
29 22 0.29
30 39 0.51
31 7 0.09
32 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
GGTCAAAAATGAATTTTTGGAAGTTTAGG
Found at i:31696 original size:34 final size:34
Alignment explanation
Indices: 31652--31721 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
31642 TTTGTTAAGG
* * * *
31652 TTTTAGGGTTTGGGTCACTTGGGCTCGTCTATGC
1 TTTTAAGGTTTAGGTCACTTCGGCCCGTCTATGC
*
31686 TTTTAAGGTTTAGGTCACTTCGGCCCGTCTGTGC
1 TTTTAAGGTTTAGGTCACTTCGGCCCGTCTATGC
31720 TT
1 TT
31722 GGGTCATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.10, C:0.20, G:0.29, T:0.41
Consensus pattern (34 bp):
TTTTAAGGTTTAGGTCACTTCGGCCCGTCTATGC
Found at i:31882 original size:17 final size:17
Alignment explanation
Indices: 31860--31916 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
31850 TATTTCAAAT
31860 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
31877 TTTAAATTTAAAAT-AA
1 TTTAAATTTAAAATAAA
* *
31893 TTCTAAACTTAGAATAAA
1 TT-TAAATTTAAAATAAA
31911 TTTAAA
1 TTTAAA
31917 ATAAAGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.11
17 28 0.78
18 4 0.11
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:33725 original size:38 final size:38
Alignment explanation
Indices: 33674--33749 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
33664 GAATTCGAAC
33674 TACTTATATATTATTAAAAGTTTTAAATATAAAAATTA
1 TACTTATATATTATTAAAAGTTTTAAATATAAAAATTA
33712 TACTTATATATTATTAAAAGTTTTAAATATAAAAATTA
1 TACTTATATATTATTAAAAGTTTTAAATATAAAAATTA
33750 AGTTATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (38 bp):
TACTTATATATTATTAAAAGTTTTAAATATAAAAATTA
Found at i:33741 original size:19 final size:19
Alignment explanation
Indices: 33681--33741 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
33671 AACTACTTAT
33681 ATATTATTAAAAGTTTTAA
1 ATATTATTAAAAGTTTTAA
* *
33700 ATA-TA--AAAATTATACTTAT
1 ATATTATTAAAAGT-T--TTAA
33719 ATATTATTAAAAGTTTTAA
1 ATATTATTAAAAGTTTTAA
33738 ATAT
1 ATAT
33742 AAAAATTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 5 0.16
17 1 0.03
18 2 0.06
19 16 0.50
20 2 0.06
21 1 0.03
22 5 0.16
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTATTAAAAGTTTTAA
Found at i:34061 original size:12 final size:11
Alignment explanation
Indices: 34044--34090 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
34034 CAACATTATG
34044 TCATTTTCATTT
1 TCATTTT-ATTT
34056 TCATTTTATTT
1 TCATTTTATTT
*
34067 GT-TTTATTATTT
1 -TCATT-TTATTT
34079 TCATTTTATTT
1 TCATTTTATTT
34090 T
1 T
34091 TACATGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 14 0.47
12 16 0.53
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (11 bp):
TCATTTTATTT
Found at i:34200 original size:24 final size:25
Alignment explanation
Indices: 34149--34201 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
34139 CGTTAGTAAT
* * *
34149 TTTAGTTATATAAATTTTTAATATA
1 TTTAATTATATAAATTTTGAATAAA
34174 TTTAATTATATAAA-TTTGAATAAA
1 TTTAATTATATAAATTTTGAATAAA
34198 TTTA
1 TTTA
34202 GATAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTAATTATATAAATTTTGAATAAA
Found at i:41184 original size:45 final size:45
Alignment explanation
Indices: 41134--41222 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 45
41124 CTTTCTTTAC
41134 AAAGTATATTTATATT-ATTTTGAGAAG-TTTTTGTCATTTTATAAT
1 AAAGTATATTTATATTAATTTT-AG-AGCTTTTTGTCATTTTATAAT
* *
41179 AAAGTATGTTTATATTAATTTTAGGGTCTTTTTGTCATTTTATA
1 AAAGTATATTTATATTAATTTTAGAG-CTTTTTGTCATTTTATA
41223 TAATTTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 1 0.03
45 17 0.44
46 21 0.54
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.54
Consensus pattern (45 bp):
AAAGTATATTTATATTAATTTTAGAGCTTTTTGTCATTTTATAAT
Found at i:41593 original size:6 final size:7
Alignment explanation
Indices: 41578--41603 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41568 ATATTTTCTG
41578 TTTTATT
1 TTTTATT
41585 TTTTATT
1 TTTTATT
41592 TTTTATT
1 TTTTATT
41599 TTTTA
1 TTTTA
41604 AAAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:45938 original size:117 final size:117
Alignment explanation
Indices: 45732--45970 Score: 478
Period size: 117 Copynumber: 2.0 Consensus size: 117
45722 GAGTGCTTTT
45732 TTGATTGAATCTATTTGCAGCGTTCATGCATGCATATTACAATGGGTTAACTGAGTTTTCTTCAT
1 TTGATTGAATCTATTTGCAGCGTTCATGCATGCATATTACAATGGGTTAACTGAGTTTTCTTCAT
45797 GTCCTTAAGACTTAAAATATTGTTGCGGATGGCATGGCGAAGATAAGGTCTC
66 GTCCTTAAGACTTAAAATATTGTTGCGGATGGCATGGCGAAGATAAGGTCTC
45849 TTGATTGAATCTATTTGCAGCGTTCATGCATGCATATTACAATGGGTTAACTGAGTTTTCTTCAT
1 TTGATTGAATCTATTTGCAGCGTTCATGCATGCATATTACAATGGGTTAACTGAGTTTTCTTCAT
45914 GTCCTTAAGACTTAAAATATTGTTGCGGATGGCATGGCGAAGATAAGGTCTC
66 GTCCTTAAGACTTAAAATATTGTTGCGGATGGCATGGCGAAGATAAGGTCTC
45966 TTGAT
1 TTGAT
45971 ATTGGGTTGT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 122 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (117 bp):
TTGATTGAATCTATTTGCAGCGTTCATGCATGCATATTACAATGGGTTAACTGAGTTTTCTTCAT
GTCCTTAAGACTTAAAATATTGTTGCGGATGGCATGGCGAAGATAAGGTCTC
Found at i:47010 original size:11 final size:9
Alignment explanation
Indices: 46980--47040 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
46970 GCATTTTAAA
46980 TTTTATAA-
1 TTTTATAAT
46988 TTTTATAAT
1 TTTTATAAT
46997 TTTTATATAT
1 TTTTATA-AT
47007 TTTTATAAAATT
1 TTTTAT--AA-T
47019 TTTTATAAT
1 TTTTATAAT
* *
47028 TTTCATGAT
1 TTTTATAAT
47037 TTTT
1 TTTT
47041 TAAACATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.18
9 18 0.40
10 10 0.22
11 1 0.02
12 8 0.18
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:47010 original size:19 final size:17
Alignment explanation
Indices: 46972--47040 Score: 61
Period size: 22 Copynumber: 3.8 Consensus size: 17
46962 TCCCTTTTGC
46972 ATTTTA-AA-TTTTATA
1 ATTTTATAATTTTTATA
46987 ATTTTATAATTTTTATA
1 ATTTTATAATTTTTATA
47004 TATTTTTATAAAATTTTTTATA
1 -A-TTTTAT--AA-TTTTTATA
*
47026 ATTTTCATGATTTTT
1 ATTTT-ATAATTTTT
47041 TAAACATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
15 6 0.13
16 2 0.04
17 7 0.16
18 6 0.13
19 7 0.16
20 4 0.09
21 5 0.11
22 8 0.18
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (17 bp):
ATTTTATAATTTTTATA
Found at i:47030 original size:8 final size:8
Alignment explanation
Indices: 46972--47014 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
46962 TCCCTTTTGC
46972 ATTTTA-A
1 ATTTTATA
46979 ATTTTATA
1 ATTTTATA
46987 ATTTTATA
1 ATTTTATA
46995 ATTTTTATA
1 A-TTTTATA
47004 TATTTTTATA
1 -A-TTTTATA
47014 A
1 A
47015 AATTTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.18
8 10 0.30
9 8 0.24
10 9 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
ATTTTATA
Found at i:47041 original size:19 final size:17
Alignment explanation
Indices: 46980--47042 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 17
46970 GCATTTTAAA
46980 TTTTATAATTTTATAATT
1 TTTTATAATTTTAT-ATT
*
46998 TTTATATATTTTTATAAAATT
1 TTT-TATAATTTTAT---ATT
47019 TTTTATAATTTTCATGATT
1 TTTTATAATTTT-AT-ATT
47038 TTTTA
1 TTTTA
47043 AACATTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.08
19 18 0.47
20 8 0.21
21 9 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTATAATTTTATATT
Found at i:47050 original size:30 final size:31
Alignment explanation
Indices: 46988--47060 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
46978 AATTTTATAA
*
46988 TTTTATAATTTTTATATATTTTTATAAAATT
1 TTTTATAATTTTCATATATTTTTATAAAATT
*
47019 TTTTATAATTTTCATGAT-TTTTTA-AACATT
1 TTTTATAATTTTCAT-ATATTTTTATAAAATT
*
47049 TTTTTTAATTTT
1 TTTTATAATTTT
47061 AAAAGTGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.42
31 20 0.53
32 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (31 bp):
TTTTATAATTTTCATATATTTTTATAAAATT
Found at i:47602 original size:23 final size:23
Alignment explanation
Indices: 47576--47621 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
47566 AATATCTATA
* *
47576 TAAAATTATTAATCAAAATTATT
1 TAAAACTAATAATCAAAATTATT
* *
47599 TAAAACTAATATTCATAATTATT
1 TAAAACTAATAATCAAAATTATT
47622 AATACCCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAACTAATAATCAAAATTATT
Found at i:49793 original size:6 final size:7
Alignment explanation
Indices: 49772--49801 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
49762 GACCATTAAC
49772 TTTGTTT
1 TTTGTTT
49779 TTTGTTT
1 TTTGTTT
49786 TTTGTTT
1 TTTGTTT
*
49793 TTTCTTT
1 TTTGTTT
49800 TT
1 TT
49802 GAGACAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (7 bp):
TTTGTTT
Found at i:52369 original size:15 final size:15
Alignment explanation
Indices: 52337--52377 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
52327 GCTAAAACTA
52337 TATTCTGAA-ATAGC
1 TATTCTGAACATAGC
*
52351 TATTCTGAACATAGT
1 TATTCTGAACATAGC
52366 TATTCTTGAACA
1 TATTC-TGAACA
52378 ACAGTTGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.38
15 9 0.38
16 6 0.25
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (15 bp):
TATTCTGAACATAGC
Found at i:53327 original size:17 final size:20
Alignment explanation
Indices: 53287--53327 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
53277 ATTATTGTTA
*
53287 ATTTAATAAATATATTTTTC
1 ATTTAATAAATATATTTATC
53307 ATTTAATAAA-AT-TTTAT-
1 ATTTAATAAATATATTTATC
53324 ATTT
1 ATTT
53328 GTTTACATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 4 0.20
19 2 0.10
20 10 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTAATAAATATATTTATC
Found at i:56636 original size:21 final size:22
Alignment explanation
Indices: 56591--56635 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
56581 GATTTTAATA
*
56591 TTCAATTTGGTACCTAAGTTTT
1 TTCAAATTGGTACCTAAGTTTT
* *
56613 TTCAAATTGGTACTTGAGTTTT
1 TTCAAATTGGTACCTAAGTTTT
56635 T
1 T
56636 CTTTGTCCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.51
Consensus pattern (22 bp):
TTCAAATTGGTACCTAAGTTTT
Found at i:60305 original size:38 final size:40
Alignment explanation
Indices: 60254--60340 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 40
60244 TTACTTTCAC
*
60254 AAAAAATTATAAAATTTTATAAAA-TCGTAAG-AAAATTAT
1 AAAAAATTATAAAA-TATATAAAATTCGTAAGAAAAATTAT
* *
60293 AAAAAA-TCTAAAATATATAAAATTTGTAAGAAAAATTAT
1 AAAAAATTATAAAATATATAAAATTCGTAAGAAAAATTAT
60332 -AAAAATTAT
1 AAAAAATTAT
60341 CGTACCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 8 0.20
38 17 0.41
39 16 0.39
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (40 bp):
AAAAAATTATAAAATATATAAAATTCGTAAGAAAAATTAT
Found at i:72631 original size:23 final size:23
Alignment explanation
Indices: 72588--72632 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
72578 AAGTAAAATA
*
72588 GTGTCACAAGACAGAGAAAAAAC
1 GTGTCACAAAACAGAGAAAAAAC
*
72611 GTGTCACAAAAACAGATAAAAA
1 GTGTCAC-AAAACAGAGAAAAA
72633 TTAGAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.11
Consensus pattern (23 bp):
GTGTCACAAAACAGAGAAAAAAC
Found at i:74070 original size:24 final size:26
Alignment explanation
Indices: 74017--74071 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
74007 CTTAGTTATT
* **
74017 AATTAATTTTTTAAATTATATATTTT
1 AATTAATTTTTTAAATAATATATTCG
74043 AATTAA-TTTTTAAATAAT-TATTCG
1 AATTAATTTTTTAAATAATATATTCG
74067 AATTA
1 AATTA
74072 TTAAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 9 0.35
25 11 0.42
26 6 0.23
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
AATTAATTTTTTAAATAATATATTCG
Found at i:75004 original size:17 final size:19
Alignment explanation
Indices: 74984--75019 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
74974 AAAAAAAAGA
74984 AAAT-AAAAGG-CTAAATT
1 AAATAAAAAGGACTAAATT
75001 AAATAAAAAGGACTAAATT
1 AAATAAAAAGGACTAAATT
75020 GAAACCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 6 0.35
19 7 0.41
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.22
Consensus pattern (19 bp):
AAATAAAAAGGACTAAATT
Found at i:75008 original size:28 final size:28
Alignment explanation
Indices: 74952--75029 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 28
74942 GAAGAAATAC
74952 AGAAAATTAAAACCTAAATTGCAAAAAAA
1 AGAAAATTAAAACCTAAATT-CAAAAAAA
*
74981 AGAAAA-TAAAAGGCTAAATT-AAATAAAA
1 AGAAAATTAAAA-CCTAAATTCAAA-AAAA
*
75009 AGGACTAAATTGAAACCTAAA
1 A-GA--AAATTAAAACCTAAA
75030 CAAAATTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
27 3 0.08
28 10 0.25
29 15 0.38
31 8 0.20
32 4 0.10
ACGTcount: A:0.63, C:0.09, G:0.10, T:0.18
Consensus pattern (28 bp):
AGAAAATTAAAACCTAAATTCAAAAAAA
Found at i:81781 original size:7 final size:7
Alignment explanation
Indices: 81753--81804 Score: 52
Period size: 8 Copynumber: 6.9 Consensus size: 7
81743 TTTTTTTTTT
81753 TTTTTAA
1 TTTTTAA
81760 GTTTTTATA
1 -TTTTTA-A
81769 TATTTTAA
1 T-TTTTAA
81777 TTTTTAA
1 TTTTTAA
81784 -TTTTAA
1 TTTTTAA
81790 TTTTTGAA
1 TTTTT-AA
81798 TTATTTA
1 TT-TTTA
81805 TTGATGTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.15
7 10 0.26
8 14 0.36
9 9 0.23
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (7 bp):
TTTTTAA
Found at i:81788 original size:13 final size:14
Alignment explanation
Indices: 81770--81799 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
81760 GTTTTTATAT
81770 ATTTTAATTTTT-A
1 ATTTTAATTTTTGA
81783 ATTTTAATTTTTGA
1 ATTTTAATTTTTGA
81797 ATT
1 ATT
81800 ATTTATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
ATTTTAATTTTTGA
Found at i:84108 original size:126 final size:126
Alignment explanation
Indices: 83953--84384 Score: 399
Period size: 126 Copynumber: 3.4 Consensus size: 126
83943 CTCCTGAAGT
* * * *
83953 ATCATCTCCAGGACCAGCATACTCACCCAAGCATCATGGCCCTGTTTTTGAACCCCCTGAAACAT
1 ATCATCTCCAGGACCAGCACACTCACCCAAGCATCATGGCCCTGTTGTAGAACCCCCAGAAACAT
* * *
84018 CAATTCTAGAGCCAGAACACTCTCTCAAGCA-TCACGGCCCCGTTCTAGAATCTGTCAAAGC
66 CAATTCTAGAGCCAGAACACTCTCTCAAGCACT-ATGGCCCTGTTCTAGAACCTGTCAAAGC
* * * * * * * * *
84079 ATCATCTCCGGGGCCAGCATACTCACCCAAACATCATAGCCCTGTTGTGGAACCTCCAGAAGCCT
1 ATCATCTCCAGGACCAGCACACTCACCCAAGCATCATGGCCCTGTTGTAGAACCCCCAGAAACAT
* * * * *
84144 C-ATCTCTAGAGCAAGTACAGTCT-TCAGAGCACTATGGCCCTGTTGC-AGAACCAGCCAAAGC
66 CAAT-TCTAGAGCCAGAACACTCTCTCA-AGCACTATGGCCCTGTT-CTAGAACCTGTCAAAGC
* ** * * *
84205 CTCATCTCCATCACCAGCACACTCACCCAAGTATCATGGCTCC-ATTGTAGAGCCCCCAGAAACA
1 ATCATCTCCAGGACCAGCACACTCACCCAAGCATCATGGC-CCTGTTGTAGAACCCCCAGAAACA
* * * * * * * *
84269 TCAATTCTAGAGACAAAAAATTCTCCCAAG-ACCTATGGACCTGTTCTAGAACCTCTGAAAGC
65 TCAATTCTAGAGCCAGAACACTCTCTCAAGCA-CTATGGCCCTGTTCTAGAACCTGTCAAAGC
** * * **
84331 ATCATCTCTTGGGCCAGCACACTCTCCGGAGCATCATGGCCCTGTTGTAGAACC
1 ATCATCTCCAGGACCAGCACACTCACCCAAGCATCATGGCCCTGTTGTAGAACC
84385 AGCCAAAGCC
Statistics
Matches: 239, Mismatches: 57, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
125 9 0.04
126 222 0.93
127 8 0.03
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (126 bp):
ATCATCTCCAGGACCAGCACACTCACCCAAGCATCATGGCCCTGTTGTAGAACCCCCAGAAACAT
CAATTCTAGAGCCAGAACACTCTCTCAAGCACTATGGCCCTGTTCTAGAACCTGTCAAAGC
Found at i:84382 original size:63 final size:63
Alignment explanation
Indices: 84303--84574 Score: 196
Period size: 63 Copynumber: 4.3 Consensus size: 63
84293 CCCAAGACCT
* **
84303 ATGGACCTGTTCTAGAACCTCTGAAAGCATCATCTCTTGGGCCAGCACACTCTCCGGAGCATC
1 ATGGCCCTGTTCTAGAACCTCTGAAAGCATCATCTCTTGGGCCAGCACACTCTCCTAAGCATC
* * * * ** * *
84366 ATGGCCCTGTTGTAGAACCAGC-CAAAGCCTCATCTCCGGGGCCAGCACACTCACCCAAGCATC
1 ATGGCCCTGTTCTAGAACC-TCTGAAAGCATCATCTCTTGGGCCAGCACACTCTCCTAAGCATC
* * * * * ** * * *
84429 ATGGCTCTGTTCTAGAACCACCAGAAA-TATCAAT-TC-TGGAGACAAAAAATTCTCTTAAGCA-
1 ATGGCCCTGTTCTAGAACC-TCTGAAAGCATC-ATCTCTTGG-GCCAGCACACTCTCCTAAGCAT
84490 C
63 C
** * * * *
84491 AATGAACCTCTTCTAGAACCTCTGAAAGCATCATCTCTAGGGCCAGCACACTCTCCTGACCATC
1 -ATGGCCCTGTTCTAGAACCTCTGAAAGCATCATCTCTTGGGCCAGCACACTCTCCTAAGCATC
*
84555 ATGACCCTGTTGC-AGAACCT
1 ATGGCCCTGTT-CTAGAACCT
84575 GCCGAAGCCC
Statistics
Matches: 156, Mismatches: 43, Indels: 20
0.71 0.20 0.09
Matches are distributed among these distances:
62 10 0.06
63 136 0.87
64 10 0.06
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (63 bp):
ATGGCCCTGTTCTAGAACCTCTGAAAGCATCATCTCTTGGGCCAGCACACTCTCCTAAGCATC
Found at i:84455 original size:189 final size:189
Alignment explanation
Indices: 84177--84606 Score: 585
Period size: 189 Copynumber: 2.3 Consensus size: 189
84167 TCAGAGCACT
* * *
84177 ATGGCCCTGTTGCAGAACCAGCCAAAGCCTCATCTCCATCACCAGCACACTCACCCAAGTATCAT
1 ATGGCCCTGTTGCAGAACCAGCCAAAGCCTCATCTCCAGCGCCAGCACACTCACCCAAGCATCAT
* * * *
84242 GGCTCCATTGTAGAGCCCCCAGAAACATCAATTCTAGAGACAAAAAATTCTCCCAAG-ACCTATG
66 GGCTCCATTCTAGAACCACCAGAAACATCAATTCTAGAGACAAAAAATTCTCCCAAGCA-CAATG
* * * *
84306 GACCTGTTCTAGAACCTCTGAAAGCATCATCTCTTGGGCCAGCACACTCTCCGGAGCATC
130 AACCTCTTCTAGAACCTCTGAAAGCATCATCTCTAGGGCCAGCACACTCTCCGGACCATC
* * *
84366 ATGGCCCTGTTGTAGAACCAGCCAAAGCCTCATCTCCGGGGCCAGCACACTCACCCAAGCATCAT
1 ATGGCCCTGTTGCAGAACCAGCCAAAGCCTCATCTCCAGCGCCAGCACACTCACCCAAGCATCAT
** * * **
84431 GGCTCTGTTCTAGAACCACCAGAAATATCAATTCTGGAGACAAAAAATTCTCTTAAGCACAATGA
66 GGCTCCATTCTAGAACCACCAGAAACATCAATTCTAGAGACAAAAAATTCTCCCAAGCACAATGA
*
84496 ACCTCTTCTAGAACCTCTGAAAGCATCATCTCTAGGGCCAGCACACTCTCCTGACCATC
131 ACCTCTTCTAGAACCTCTGAAAGCATCATCTCTAGGGCCAGCACACTCTCCGGACCATC
* * * * * *
84555 ATGACCCTGTTGCAGAACCTGCCGAAGCCCCAT-TCCCTGTGCCAGCACACTC
1 ATGGCCCTGTTGCAGAACCAGCCAAAGCCTCATCT-CCAGCGCCAGCACACTC
84607 TTCCAAGCTC
Statistics
Matches: 211, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
188 1 0.00
189 209 0.99
190 1 0.00
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (189 bp):
ATGGCCCTGTTGCAGAACCAGCCAAAGCCTCATCTCCAGCGCCAGCACACTCACCCAAGCATCAT
GGCTCCATTCTAGAACCACCAGAAACATCAATTCTAGAGACAAAAAATTCTCCCAAGCACAATGA
ACCTCTTCTAGAACCTCTGAAAGCATCATCTCTAGGGCCAGCACACTCTCCGGACCATC
Found at i:92091 original size:28 final size:29
Alignment explanation
Indices: 92060--92118 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
92050 ATTTGCGCGA
*
92060 TTAAAATTTAATTCTTTTA-CTTTTAATT
1 TTAAAAATTAATTCTTTTATCTTTTAATT
*
92088 TTAAAAATTAATTTTTTTATTCTTTTAATT
1 TTAAAAATTAATTCTTTTA-TCTTTTAATT
92118 T
1 T
92119 AATAGTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 17 0.63
30 10 0.37
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (29 bp):
TTAAAAATTAATTCTTTTATCTTTTAATT
Found at i:94493 original size:28 final size:28
Alignment explanation
Indices: 94461--94707 Score: 250
Period size: 28 Copynumber: 9.0 Consensus size: 28
94451 ATAAACATTA
* *
94461 GTTTACGCTTGTCAGCTTACACATATGC
1 GTTTACGCTCGTCAGCTTATACATATGC
* *
94489 GTTTACGCTTGTCAGC-T-TACACA--C
1 GTTTACGCTCGTCAGCTTATACATATGC
* * **
94513 GTTTACTCTCGTCAGCTTATACATCTAA
1 GTTTACGCTCGTCAGCTTATACATATGC
* *
94541 GTTTACGCTCGTCAGCTTATATATATAC
1 GTTTACGCTCGTCAGCTTATACATATGC
* *
94569 GTTTACGCTCATTAGCTTATACATATGC
1 GTTTACGCTCGTCAGCTTATACATATGC
* *
94597 GTTTACGCTCGCCAGTTTATACATATGC
1 GTTTACGCTCGTCAGCTTATACATATGC
* * **
94625 GTTTATGCTCGTCAACTTATACATATAT
1 GTTTACGCTCGTCAGCTTATACATATGC
* * * **
94653 GTTTATGCTCGCCAGTTTGCACATATGC
1 GTTTACGCTCGTCAGCTTATACATATGC
*
94681 GTTTATGCTCGTCAGCTTATACATATG
1 GTTTACGCTCGTCAGCTTATACATATG
94708 AACTATATAT
Statistics
Matches: 179, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
24 15 0.08
25 1 0.01
26 8 0.04
27 1 0.01
28 154 0.86
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (28 bp):
GTTTACGCTCGTCAGCTTATACATATGC
Found at i:95836 original size:17 final size:18
Alignment explanation
Indices: 95814--95852 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
95804 TAAAAATAAT
95814 TTTTATAAT-TT-TACCAA
1 TTTTATAATATTATA-CAA
95831 TTTTATAATATTATACAA
1 TTTTATAATATTATACAA
95849 TTTT
1 TTTT
95853 TATTTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 9 0.45
19 2 0.10
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATAATATTATACAA
Found at i:95979 original size:8 final size:8
Alignment explanation
Indices: 95961--95993 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
95951 AAATATGTAA
95961 TTTTTAGAT
1 TTTTTA-AT
95970 TTTTTAAT
1 TTTTTAAT
95978 TTTTTAAT
1 TTTTTAAT
95986 TTTTTAAT
1 TTTTTAAT
95994 ATATATTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (8 bp):
TTTTTAAT
Found at i:101506 original size:24 final size:27
Alignment explanation
Indices: 101473--101531 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 27
101463 GCATTAATTG
*
101473 AATTAATAATAA-TAATAA-TATTAAT
1 AATTAATAATAACCAATAATTATTAAT
*
101498 -ATTAATAATAACCATTAATTATTAAT
1 AATTAATAATAACCAATAATTATTAAT
101524 AATTAATA
1 AATTAATA
101532 TTATTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 11 0.38
25 4 0.14
26 7 0.24
27 7 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
AATTAATAATAACCAATAATTATTAAT
Found at i:101534 original size:20 final size:18
Alignment explanation
Indices: 101474--101534 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 18
101464 CATTAATTGA
*
101474 ATTAATAATAATAATAAT
1 ATTAATATTAATAATAAT
*
101492 ATTAATATTAATAATAACC
1 ATTAATATTAATAATAA-T
101511 ATTAATTATTAATAATTAAT
1 ATTAA-TATTAATAA-TAAT
101531 ATTA
1 ATTA
101535 TTTTAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 16 0.43
19 5 0.14
20 13 0.35
21 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATATTAATAATAAT
Found at i:102712 original size:30 final size:29
Alignment explanation
Indices: 102589--102819 Score: 111
Period size: 29 Copynumber: 7.9 Consensus size: 29
102579 GAAGGTCCCA
*
102589 AACTGTCCAAAAATTA-CATTTTTACCCCTG
1 AACT-TCCAAAAATTACCA-TTTTACCCCCG
* * ****
102619 AACTCCCAAAAATT-CTGATTTTGACCTTAA
1 AACTTCCAAAAATTAC-CATTTT-ACCCCCG
* *
102649 AACTTTCAAAAATCA-CATTTTGA-CCCCG
1 AACTTCCAAAAATTACCATTTT-ACCCCCG
102677 AAACTTCCAAAAATTACCATTTTACCCCCCG
1 -AACTTCCAAAAATTACCATTTTA-CCCCCG
*** *
102708 AACTTTTTGAAAATTA-CATTTTTACCCTCG
1 AAC-TTCCAAAAATTACCA-TTTTACCCCCG
* * *
102738 AACTTCTC-AAAGTT-CCATTTTAACCTCG
1 AACTTC-CAAAAATTACCATTTTACCCCCG
** **
102766 ATTTTTCCAAAAATTACTTTTTTACCCCCG
1 A-ACTTCCAAAAATTACCATTTTACCCCCG
102796 AACTT-CAAAAATTATCC-TTTTACC
1 AACTTCCAAAAATTA-CCATTTTACC
102820 TTCGGATGTC
Statistics
Matches: 151, Mismatches: 34, Indels: 34
0.69 0.16 0.16
Matches are distributed among these distances:
28 29 0.19
29 54 0.36
30 49 0.32
31 19 0.13
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTACCATTTTACCCCCG
Found at i:114995 original size:109 final size:109
Alignment explanation
Indices: 114802--115000 Score: 301
Period size: 109 Copynumber: 1.8 Consensus size: 109
114792 TCGATGTGAG
* * * *
114802 CAAATCTTCGAACCCTAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATAAAATGGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGATAAGATACTAAGAAGCAAGTCGAAGCAATAAAAAGGATA
*
114867 GCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAATACGAA
66 GCTTCCTGATGAGACACAGAGAAGTATACCAACTCAAATACGAA
* * *
114911 CAAATTTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGAG-CGCAGCAATAAAAAGGAT
1 CAAATCTTCGAACCCCAGCTTCCTGATAAGATACTAAGAAGCA-AGTCGAAGCAATAAAAAGGAT
*
114975 AGCTTCTTGATGAGACACAGAGAAGT
65 AGCTTCCTGATGAGACACAGAGAAGT
115001 GGATCAAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 78 0.98
110 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (109 bp):
CAAATCTTCGAACCCCAGCTTCCTGATAAGATACTAAGAAGCAAGTCGAAGCAATAAAAAGGATA
GCTTCCTGATGAGACACAGAGAAGTATACCAACTCAAATACGAA
Found at i:115412 original size:6 final size:6
Alignment explanation
Indices: 115394--115442 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
115384 AAACTTTTCT
* *
115394 TTTAAA GTTTAAA TTTAAA -TTAAG TTTAAA TTTAAA -TTGAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
115441 TT
1 TT
115443 GAATTAAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 8 0.22
6 22 0.61
7 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:115420 original size:17 final size:18
Alignment explanation
Indices: 115398--115442 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
115388 TTTTCTTTTA
115398 AAGTTTAAATTTAAATT-
1 AAGTTTAAATTTAAATTG
115415 AAGTTTAAATTTAAATTG
1 AAGTTTAAATTTAAATTG
115433 AA-TTTAAATT
1 AAGTTTAAATT
115443 GAATTAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 25 0.93
18 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (18 bp):
AAGTTTAAATTTAAATTG
Found at i:115443 original size:11 final size:11
Alignment explanation
Indices: 115422--115447 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
115412 ATTAAGTTTA
115422 AATTTAAATTG
1 AATTTAAATTG
115433 AATTTAAATTG
1 AATTTAAATTG
115444 AATT
1 AATT
115448 AAGGAAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTAAATTG
Found at i:116127 original size:20 final size:18
Alignment explanation
Indices: 116073--116127 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
116063 CATTAATTGA
* *
116073 ATTAATAACAATAATAAT
1 ATTAATAATAATATTAAT
*
116091 ATTAATAATAACCATTAATT
1 ATTAATAATAA-TATTAA-T
116111 ATTAATAATTAATATTA
1 ATTAATAA-TAATATTA
116128 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 10 0.33
19 4 0.13
20 13 0.43
21 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAATAATAATATTAAT
Found at i:117287 original size:29 final size:28
Alignment explanation
Indices: 117255--117529 Score: 109
Period size: 29 Copynumber: 9.4 Consensus size: 28
117245 AACTGTCTAG
*
117255 AAATTACATTTTTACCCTCGAACTTCAAA
1 AAATTACATTTTTACCCTCAAACTTC-AA
* *
117284 AAATT-CTAATTTTAACCC-CAAAACTTTCTA
1 AAATTAC--ATTTTTACCCTC-AAAC-TTCAA
*
117314 AAATTACCA--TTT-CCC-CGAACTTCCAA
1 AAATTA-CATTTTTACCCTCAAACTT-CAA
* * **
117340 AAATTCCATTTTTGACCCTAAAACTTTTGA
1 AAATTACATTTTT-ACCCTCAAAC-TTCAA
* * * *
117370 AAATCACATTTTGACCATAAAACTTTCAA
1 AAATTACATTTTTACCCTCAAAC-TTCAA
* *
117399 ATATTACCA-TTTTACCC-CTAAACTTTCCA
1 AAATTA-CATTTTTACCCTC-AAAC-TTCAA
* **
117428 AAATTCCATTTTTAACCCT-AATTTTCCCAA
1 AAATTACATTTTT-ACCCTCAAACTT--CAA
* *
117458 AAATTACATTTTTACCCTCGAACTTCCA
1 AAATTACATTTTTACCCTCAAACTTCAA
* * *
117486 AAATTTCTAATTTTAACCTCGAAACTTCCAA
1 AAATTAC-ATTTTTACCCTC-AAACTT-CAA
117517 AAATTACCATTTT
1 AAATTA-CATTTT
117530 ACCTTCGGAT
Statistics
Matches: 181, Mismatches: 40, Indels: 48
0.67 0.15 0.18
Matches are distributed among these distances:
25 4 0.02
26 10 0.06
27 7 0.04
28 15 0.08
29 66 0.36
30 61 0.34
31 16 0.09
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (28 bp):
AAATTACATTTTTACCCTCAAACTTCAA
Found at i:117530 original size:59 final size:58
Alignment explanation
Indices: 117240--117532 Score: 153
Period size: 59 Copynumber: 5.0 Consensus size: 58
117230 CCCTGGAGGT
* * * * * * *
117240 CCCTAAACTGTCTAGAAATTACATTTTTACCCTCG-AACTTCAAAAAATT-CTAATTTTAAC
1 CCCTAAACTTTCCA-AAATTCCAATTTTAACC-CGAAACTTCCAAAAATTAC-CATTTT-AC
* * *
117300 CCCAAAACTTTCTAAAATTACC-A-TTT-CCCCG-AACTTCCAAAAATT-CCATTTTTGA-
1 CCCTAAACTTTCCAAAATT-CCAATTTTAACCCGAAACTTCCAAAAATTACCA-TTTT-AC
** * ** * *
117355 CCCTAAAACTTTTGAAAA-T-CACATTTTGACCATAAAACTTTCAAATATTACCATTTTAC
1 CCCT-AAACTTTCCAAAATTCCA-ATTTTAACC-CGAAACTTCCAAAAATTACCATTTTAC
* * **
117414 CCCTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTCCCAAAAATTA-CATTTTTA-
1 CCCTAAACTTTCCAAAATTCCAATTTTAACCCGAAACTT-CCAAAAATTACCA-TTTTAC
* *
117472 CCCTCGAAC-TTCCAAAATTTCTAATTTTAACCTCGAAACTTCCAAAAATTACCATTTTAC
1 CCCT-AAACTTTCCAAAA-TTCCAATTTTAACC-CGAAACTTCCAAAAATTACCATTTTAC
117532 C
1 C
117533 TTCGGATGTC
Statistics
Matches: 182, Mismatches: 31, Indels: 40
0.72 0.12 0.16
Matches are distributed among these distances:
53 1 0.01
55 6 0.03
56 35 0.19
57 5 0.03
58 33 0.18
59 76 0.42
60 26 0.14
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAATTCCAATTTTAACCCGAAACTTCCAAAAATTACCATTTTAC
Found at i:117604 original size:29 final size:29
Alignment explanation
Indices: 117572--117651 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
117562 CTCGATTTTT
117572 TCTAAAAGTTACCGTTTTACCCTCGAA-TG
1 TCTAAAAGTTACCGTTTTACCCT-GAACTG
* * *
117601 TCT-AAAGTTCCCTTTTTAACCCTGAACTT
1 TCTAAAAGTTACCGTTTT-ACCCTGAACTG
*
117630 TCCCAAAA-TTACCGTTTTACCC
1 T-CTAAAAGTTACCGTTTTACCC
117652 CTTGAGAGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
28 15 0.37
29 14 0.34
30 9 0.22
31 3 0.07
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.36
Consensus pattern (29 bp):
TCTAAAAGTTACCGTTTTACCCTGAACTG
Found at i:118616 original size:22 final size:21
Alignment explanation
Indices: 118591--118633 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
118581 GCAATTAGCA
118591 TTAA-TAAAAAATAATATTTAAT
1 TTAATTAAAAAAT-AT-TTTAAT
*
118613 TTAATTATAAAATATTTTAAT
1 TTAATTAAAAAATATTTTAAT
118634 ATTATACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTAAAAAATATTTTAAT
Found at i:119175 original size:21 final size:21
Alignment explanation
Indices: 119133--119176 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
119123 TTTCTTCAAT
* *
119133 TTGTTTTTGATTTATTATATA
1 TTGTTTTTGAATTATTAGATA
119154 TTGTTTTTAGAATTA-TAGATA
1 TTGTTTTT-GAATTATTAGATA
119175 TT
1 TT
119177 CTCAACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.61
Consensus pattern (21 bp):
TTGTTTTTGAATTATTAGATA
Found at i:124550 original size:172 final size:172
Alignment explanation
Indices: 124264--124607 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
124254 TATTAATCGT
124264 GACTATTATAAATAAATATTAATAACTCTTAAGACTTAGTCTCTCGAATTTATGGTTTAAGGTCT
1 GACTATTATAAATAAATATTAATAACTCTTAAGACTTAGTCTCTCGAATTTATGGTTTAAGGTCT
124329 CGGATTTAAGGGGTTGAATTGGTATTTTAAGATTCTTTTCAAACTTCTTTAAATGATAAGGAAAT
66 CGGATTTAAGGGGTTGAATTGGTATTTTAAGATTCTTTTCAAACTTCTTTAAATGATAAGGAAAT
124394 AGAAGAAAAACTTAGACAATTTAATTTATAATGGTTTGGCTC
131 AGAAGAAAAACTTAGACAATTTAATTTATAATGGTTTGGCTC
124436 GACTATTATAAATAAATATTAATAACTCTTAAGACTTAGTCTCTCGAATTTATGGTTTAAGGTCT
1 GACTATTATAAATAAATATTAATAACTCTTAAGACTTAGTCTCTCGAATTTATGGTTTAAGGTCT
124501 CGGATTTAAGGGGTTGAATTGGTATTTTAAGATTCTTTTCAAACTTCTTTAAATGATAAGGAAAT
66 CGGATTTAAGGGGTTGAATTGGTATTTTAAGATTCTTTTCAAACTTCTTTAAATGATAAGGAAAT
124566 AGAAGAAAAACTTAGACAATTTAATTTATAATGGTTTGGCTC
131 AGAAGAAAAACTTAGACAATTTAATTTATAATGGTTTGGCTC
124608 AAATTGCTTA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (172 bp):
GACTATTATAAATAAATATTAATAACTCTTAAGACTTAGTCTCTCGAATTTATGGTTTAAGGTCT
CGGATTTAAGGGGTTGAATTGGTATTTTAAGATTCTTTTCAAACTTCTTTAAATGATAAGGAAAT
AGAAGAAAAACTTAGACAATTTAATTTATAATGGTTTGGCTC
Found at i:131581 original size:21 final size:21
Alignment explanation
Indices: 131539--131581 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
131529 AGTAAGTACT
**
131539 TTAGATTTCTTTTTTACCTAA
1 TTAGATTTCTTTTTTAAATAA
*
131560 TTAGATTTTTTTTTTAAATAA
1 TTAGATTTCTTTTTTAAATAA
131581 T
1 T
131582 AAGTTAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
TTAGATTTCTTTTTTAAATAA
Found at i:134652 original size:18 final size:18
Alignment explanation
Indices: 134610--134645 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
134600 TATTAGCCTT
134610 ATTCTTTCAAGTTTTCTG
1 ATTCTTTCAAGTTTTCTG
134628 ATTCTTTCAAGTTTTCTG
1 ATTCTTTCAAGTTTTCTG
134646 TCTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.56
Consensus pattern (18 bp):
ATTCTTTCAAGTTTTCTG
Found at i:135097 original size:26 final size:25
Alignment explanation
Indices: 135056--135104 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
135046 TAAATTGATT
135056 TTATTTTATTAAAAAATTGAAATAAA
1 TTATTTTATTAAAAAA-TGAAATAAA
* *
135082 TTATTTTTTTATAAAATGAAATA
1 TTATTTTATTAAAAAATGAAATA
135105 TTCAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
TTATTTTATTAAAAAATGAAATAAA
Found at i:145993 original size:417 final size:412
Alignment explanation
Indices: 145196--146000 Score: 1170
Period size: 413 Copynumber: 1.9 Consensus size: 412
145186 TCCACATTCT
* * *
145196 CCTGTTGGCTAACACTCCGGCGGTATGCAAGATATGACATCGATGTCCACGTACGACATCCACTC
1 CCTGTTGGCTAACACTCCGACGATATGCAAGATATGACATCGATGTCCACGTACAACATCCACTC
* *
145261 AAACTGAAAAACATATTTAAAAAATAACGTTATATATGAATTTTTGTAACCAATCATAAAGTAAT
66 AAACTGAAAAAAATATTTAAAAAATAACGTTATATATGAATTTTAGTAACCAATCATAAAGTAAT
*
145326 CAATATAAGATCGAAAGAATAACTAACCTCGCGTTTCGAACATAGATCTATCAACAACCTAAGAT
131 CAATATAAGATCGAAAGAATAACTAACCTCGCGTTTCAAACATAGATC-ATCAACAACCTAAGAT
* * * *
145391 CTTTTAACTCATCGGGCACATCCATGTAGCTTGACCTATGGTTCCACTTGTATAAACGATGTGCT
195 CTTCTAACTCATCGGGCACATCCATGTAGCTCGACCCATGGTTCCACTTGTACAAACGATGTGCT
* *
145456 AGTCGAAACGTATAATAAAAAAATACTTTGCAGACTAAGTATTTGTTAAGAAATGATGTTTACTT
260 AGTCAAAACGTATAATAAAAAAATACTTTACAGACTAAGTATTTGTTAAGAAATGATGTTTACTT
* * *
145521 CGTCACATACAAAAAAATATATGGGTTGATCATACTGGGACGTAGAAACGGTAGTCGCCACCAAC
325 CGTCACAAACAAAAAAATATATGGGTTGATCACACTGGGACATAGAAACGGTAGTCGCCACCAAC
145586 GGCACCTTCGCATCTCACATCCG
390 GGCACCTTCGCATCTCACATCCG
* * * * * **
145609 CCTGTTGGCTAACACTTCGACTATATGTAAGATATGACATCGATGTCGATGTACAACATTTACTC
1 CCTGTTGGCTAACACTCCGACGATATGCAAGATATGACATCGATGTCCACGTACAACATCCACTC
* * *
145674 AAACTGAAAACAAAT-TTTAAAAAATATCGTTATGTATGAATTTTAGTAACCAATCATAAGGTAA
66 AAACTGAAAA-AAATATTTAAAAAATAACGTTATATATGAATTTTAGTAACCAATCATAAAGTAA
* *
145738 TTAATATAAGATCGAAAGTATAAGTAACTAACCTCGCG-TTCTAAACATTGATC-T-AACAACCT
130 TCAATATAAGATCGAAAG---AA-TAACTAACCTCGCGTTTC-AAACATAGATCATCAACAACCT
* * *
145800 AAGATCTTCTAACTCATCGGGCACATCCATGTAGCTCGGCCCATGGTTCCACTTTTACAAATGAT
190 AAGATCTTCTAACTCATCGGGCACATCCATGTAGCTCGACCCATGGTTCCACTTGTACAAACGAT
* *
145865 GTGTTAGT-AAAAGCGTAATAATAATAAAAAATACTTTACAGACTATGTATTTGTTAAGAAATGA
255 GTGCTAGTCAAAA-CGT-ATAAT-A-AAAAAATACTTTACAGACTAAGTATTTGTTAAGAAATGA
* *
145929 TGTTTACTTCGTCACAAACGAAAAAATATATGGGTTGATCACACTGGGACATAGACACGGTAGTC
316 TGTTTACTTCGTCACAAACAAAAAAATATATGGGTTGATCACACTGGGACATAGAAACGGTAGTC
145994 GCCACCA
381 GCCACCA
146001 GACTTACGAT
Statistics
Matches: 348, Mismatches: 34, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
413 130 0.37
414 79 0.23
415 6 0.02
416 6 0.02
417 127 0.36
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (412 bp):
CCTGTTGGCTAACACTCCGACGATATGCAAGATATGACATCGATGTCCACGTACAACATCCACTC
AAACTGAAAAAAATATTTAAAAAATAACGTTATATATGAATTTTAGTAACCAATCATAAAGTAAT
CAATATAAGATCGAAAGAATAACTAACCTCGCGTTTCAAACATAGATCATCAACAACCTAAGATC
TTCTAACTCATCGGGCACATCCATGTAGCTCGACCCATGGTTCCACTTGTACAAACGATGTGCTA
GTCAAAACGTATAATAAAAAAATACTTTACAGACTAAGTATTTGTTAAGAAATGATGTTTACTTC
GTCACAAACAAAAAAATATATGGGTTGATCACACTGGGACATAGAAACGGTAGTCGCCACCAACG
GCACCTTCGCATCTCACATCCG
Found at i:147444 original size:25 final size:25
Alignment explanation
Indices: 147416--147463 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
147406 AAACAAATAA
*
147416 CAAAACCCAAAACCAAAATCAAATC
1 CAAAAACCAAAACCAAAATCAAATC
** *
147441 CAAAAACTTAATCCAAAATCAAA
1 CAAAAACCAAAACCAAAATCAAA
147464 AGTCCGGAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.12
Consensus pattern (25 bp):
CAAAAACCAAAACCAAAATCAAATC
Found at i:148248 original size:11 final size:11
Alignment explanation
Indices: 148232--148345 Score: 79
Period size: 11 Copynumber: 10.0 Consensus size: 11
148222 ATCGGGCCCC
148232 TTTTAAATTTA
1 TTTTAAATTTA
*
148243 TTTTAAGATTAA
1 TTTTAA-ATTTA
* *
148255 ATTT-ATTTTAA
1 TTTTAAATTT-A
* *
148266 ATTTAGATTTA
1 TTTTAAATTTA
148277 TTTTAAATTTAAA
1 TTTTAAATTT--A
* *
148290 TTTAAAATTAA
1 TTTTAAATTTA
148301 TTTTAAATTTGA
1 TTTTAAATTT-A
*
148313 ATTT-AATTTAA
1 TTTTAAATTT-A
*
148324 GTTTAAATTTA
1 TTTTAAATTTA
148335 TTTTAAATTTA
1 TTTTAAATTTA
148346 AAATTATTAT
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
10 2 0.03
11 50 0.62
12 19 0.24
13 9 0.11
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:148256 original size:17 final size:17
Alignment explanation
Indices: 148233--148364 Score: 131
Period size: 17 Copynumber: 7.4 Consensus size: 17
148223 TCGGGCCCCT
148233 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
148251 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
148267 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
148284 TTTAAATTTAAAATTAATTTTAAA
1 TTTAAA--T----TT-ATTTTAAA
* * *
148308 TTTGAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
148325 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
148342 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
148359 TTTAAA
1 TTTAAA
148365 ATAAATAAGG
Statistics
Matches: 96, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.01
17 76 0.79
18 2 0.02
19 1 0.01
22 1 0.01
23 2 0.02
24 13 0.14
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:148270 original size:6 final size:6
Alignment explanation
Indices: 148233--148364 Score: 100
Period size: 6 Copynumber: 23.0 Consensus size: 6
148223 TCGGGCCCCT
* * * *
148233 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTAGA TTT-AT
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
148278 TTTAAA TTTAAA TTTAAA ATTAAT TTTAAA TTTGAA TTT-AA TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
148325 TTTAAA TTT-AT TTTAAA TTTAAA ATT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
148365 ATAAATAAGG
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
4 2 0.02
5 22 0.23
6 70 0.72
7 3 0.03
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:148323 original size:58 final size:58
Alignment explanation
Indices: 148236--148347 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 58
148226 GGCCCCTTTT
* * *
148236 AAATTTATTTTAAGATTAAATTTATTTTAAATTTAGATTTATTTTAAATTTAAATTTA
1 AAATTAATTTTAAGATTAAATTTAATTTAAATTTAAATTTATTTTAAATTTAAATTTA
* *
148294 AAATTAATTTTAA-ATTTGAATTTAATTTAAGTTTAAATTTATTTTAAATTTAAA
1 AAATTAATTTTAAGA-TTAAATTTAATTTAAATTTAAATTTATTTTAAATTTAAA
148348 ATTATTATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 1 0.02
58 47 0.98
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (58 bp):
AAATTAATTTTAAGATTAAATTTAATTTAAATTTAAATTTATTTTAAATTTAAATTTA
Found at i:148361 original size:58 final size:58
Alignment explanation
Indices: 148254--148366 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
148244 TTTAAGATTA
* * * * *
148254 AATTTATTTTAAATTTAGATTTATTTTAAATTTAAATTTAAAATTAATTTTAAATTTG
1 AATTTAATTTAAATTTAAATTTATTTTAAATTTAAAATTAAAATAAATTTAAAATTTG
* **
148312 AATTTAATTTAAGTTTAAATTTATTTTAAATTTAAAATTATTATAAATTTAAAAT
1 AATTTAATTTAAATTTAAATTTATTTTAAATTTAAAATTAAAATAAATTTAAAAT
148367 AAATAAGGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (58 bp):
AATTTAATTTAAATTTAAATTTATTTTAAATTTAAAATTAAAATAAATTTAAAATTTG
Found at i:150336 original size:29 final size:29
Alignment explanation
Indices: 150283--150587 Score: 217
Period size: 29 Copynumber: 10.4 Consensus size: 29
150273 CCTTGGAGGT
150283 CCCT-AAACTGTCCAAAAATTACATTTTTA
1 CCCTCAAACT-TCCAAAAATTACATTTTTA
* * *
150312 CCTTCGAACTTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTT-A
* * ***
150342 CCTTAAAACTTTTGAAAATTACATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
** * *
150371 CCCT-AAACTTTAAAAAATTCCATTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* *
150399 CCC-CAAAACTTTCAAAATTTACATTTTTA
1 CCCTC-AAACTTCCAAAAATTACATTTTTA
* * * * *
150428 CCCCCAAATTTCAAAAAAAATTCCATTTTAA
1 CCCTCAAACTTC--CAAAAATTACATTTTTA
* *
150459 CTCAT-AAACTTCCAAAAATTACAATTTTA
1 C-CCTCAAACTTCCAAAAATTACATTTTTA
* * *
150488 CCCCCCAAACTTCTAAAAATTTCATTTTTGA
1 -CCCTCAAACTTCCAAAAATTACATTTTT-A
* * *
150519 CCCTAAAACTT-CTAAAATTACTTTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
*
150547 CCCTCAAACTTCCAAAAATCT-CAATTTTGA
1 CCCTCAAACTTCCAAAAAT-TAC-ATTTTTA
*
150577 CCCTGAAACTT
1 CCCTCAAACTT
150588 TTGAAAATTA
Statistics
Matches: 215, Mismatches: 47, Indels: 27
0.74 0.16 0.09
Matches are distributed among these distances:
28 34 0.16
29 85 0.40
30 74 0.34
31 21 0.10
32 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTTA
Found at i:150604 original size:30 final size:29
Alignment explanation
Indices: 150325--150609 Score: 150
Period size: 30 Copynumber: 9.7 Consensus size: 29
150315 TCGAACTTCC
*
150325 AAAAATTCCATTTTTGACCTTAAAACTTTT
1 AAAAATTCCA-TTTTGACCCTAAAACTTTT
* * * *
150355 GAAAATTACATTTTTACCCT-AAACTTTA
1 AAAAATTCCATTTTGACCCTAAAACTTTT
* *
150383 AAAAATTCCATTTTGACCCCAAAACTTTC
1 AAAAATTCCATTTTGACCCTAAAACTTTT
* * * ** *
150412 AAAATTTACATTTTTACCCCCAAA-TTTCAAA
1 AAAAATTCCATTTTGACCCTAAAACTTT---T
* * **
150443 AAAAATTCCATTTTAACTC-ATAAACTTCC
1 AAAAATTCCATTTTGACCCTA-AAACTTTT
* ** *
150472 AAAAATTACAATTTT-ACCCCCCAAACTTCT
1 AAAAATT-CCATTTTGA-CCCTAAAACTTTT
* *
150502 AAAAATTTCATTTTTGACCCTAAAACTTCT
1 AAAAATTCCA-TTTTGACCCTAAAACTTTT
* * * * **
150532 -AAAATTACTTTTTTACCCTCAAACTTCC
1 AAAAATTCCATTTTGACCCTAAAACTTTT
* *
150560 AAAAATCTCAATTTTGACCCTGAAACTTTT
1 AAAAAT-TCCATTTTGACCCTAAAACTTTT
*
150590 GAAAATTACCATTTTG-CCCT
1 AAAAATT-CCATTTTGACCCT
150610 CGAATGTCCA
Statistics
Matches: 197, Mismatches: 44, Indels: 29
0.73 0.16 0.11
Matches are distributed among these distances:
28 42 0.21
29 61 0.31
30 73 0.37
31 19 0.10
32 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAATTCCATTTTGACCCTAAAACTTTT
Found at i:150610 original size:59 final size:58
Alignment explanation
Indices: 150297--150626 Score: 244
Period size: 59 Copynumber: 5.6 Consensus size: 58
150287 AAACTGTCCA
* * * *
150297 AAAATTA-CATTTTTACCTTCGAACTTCCAAAAATTCCATTTTTGACCTTAAAACTTTTG
1 AAAATTACCA-TTTTACCCTCAAACTTCCAAAAATT-CAATTTTGACCCTAAAACTTTTG
** * * *
150356 AAAATTA-CATTTTTACCCT-AAACTTTAAAAAATTCCATTTTGACCCCAAAAC-TTTC
1 AAAATTACCA-TTTTACCCTCAAACTTCCAAAAATTCAATTTTGACCCTAAAACTTTTG
* * * * * * ***
150412 AAAATTTA-CATTTTTACCCCCAAATTTCAAAAAAAATTCCATTTTAACTC-ATAAACTTCCA
1 AAAA-TTACCA-TTTTACCCTCAAACTTC--CAAAAATTCAATTTTGACCCTA-AAACTTTTG
* * * * *
150473 AAAATTACAATTTTACCCCCCAAACTTCTAAAAATTTCATTTTTGACCCTAAAACTTCT-
1 AAAATTACCATTTTA-CCCTCAAACTTCCAAAAA-TTCAATTTTGACCCTAAAACTTTTG
** *
150532 AAAATTACTTTTTTACCCTCAAACTTCCAAAAATCTCAATTTTGACCCTGAAACTTTTG
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAAT-TCAATTTTGACCCTAAAACTTTTG
* *
150591 AAAATTACCATTTTGCCCTCGAA-TGTCCAAAAATTC
1 AAAATTACCATTTTACCCTCAAACT-TCCAAAAATTC
150627 CGCTTTTGAT
Statistics
Matches: 222, Mismatches: 36, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
56 7 0.03
57 29 0.13
58 56 0.25
59 65 0.29
60 47 0.21
61 18 0.08
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCAATTTTGACCCTAAAACTTTTG
Found at i:157419 original size:30 final size:30
Alignment explanation
Indices: 157383--157491 Score: 132
Period size: 30 Copynumber: 3.7 Consensus size: 30
157373 CCTAGAAGGT
*
157383 CCCTAAAATTTTCAAAAATCATATTTTGAC
1 CCCTAAAATTTTCAAAAATTATATTTTGAC
*
157413 CCCTAAACTTTT-ATAAAATTATATTTTGAC
1 CCCTAAAATTTTCA-AAAATTATATTTTGAC
* * *
157443 CACTAAAATTTTCTAAAATTACATTTTGA-
1 CCCTAAAATTTTCAAAAATTATATTTTGAC
* *
157472 CCCTAAACTTTTCCAAAATT
1 CCCTAAAATTTTCAAAAATT
157492 GCATTTTTGC
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
29 18 0.26
30 50 0.74
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (30 bp):
CCCTAAAATTTTCAAAAATTATATTTTGAC
Found at i:157489 original size:29 final size:29
Alignment explanation
Indices: 157383--157675 Score: 165
Period size: 29 Copynumber: 10.1 Consensus size: 29
157373 CCTAGAAGGT
* * * *
157383 CCCTAAAATTTTCAAAAATCATATTTTGA
1 CCCTAAACTTTTCCAAAATTACATTTTGA
** *
157412 CCCCTAAACTTTTATAAAATTATATTTTGA
1 -CCCTAAACTTTTCCAAAATTACATTTTGA
* *
157442 CCACTAAAATTTTCTAAAATTACATTTTGA
1 CC-CTAAACTTTTCCAAAATTACATTTTGA
*
157472 CCCTAAACTTTTCCAAAATTGCATTTTTG-
1 CCCTAAACTTTTCCAAAATTACA-TTTTGA
* * *
157501 CCCTGAAC--TTCCAAAAATCACATTTTTA
1 CCCTAAACTTTTCC-AAAATTACATTTTGA
** *
157529 CCCCCGAAC--TTCCAAAAATCACATTTT-A
1 -CCCTAAACTTTTCC-AAAATTACATTTTGA
* * * * *
157557 CCTTGAA-TTTCTCAAAAATGACATTTTCA
1 CCCTAAACTTT-TCCAAAATTACATTTTGA
* * * *
157586 CCCCAAACATTCCCAAAATTACATTTTTA
1 CCCTAAACTTTTCCAAAATTACATTTTGA
* *
157615 CCCCTAAAC-TTTCCAAAAGTACATTTTAA
1 -CCCTAAACTTTTCCAAAATTACATTTTGA
* *
157644 CCCCAAAC-TCTCCAAAACTT-CATTTTCGA
1 CCCTAAACTTTTCCAAAA-TTACATTTT-GA
157673 CCC
1 CCC
157676 CTTTTTTNNN
Statistics
Matches: 215, Mismatches: 35, Indels: 27
0.78 0.13 0.10
Matches are distributed among these distances:
27 13 0.06
28 42 0.20
29 95 0.44
30 65 0.30
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATTACATTTTGA
Found at i:157500 original size:30 final size:30
Alignment explanation
Indices: 157383--157531 Score: 123
Period size: 30 Copynumber: 5.1 Consensus size: 30
157373 CCTAGAAGGT
* *
157383 CCCTAAAATTTT-CAAAAATCATATTTTGA
1 CCCTAAACTTTTCCAAAATTCATATTTTGA
**
157412 CCCCTAAACTTTTATAAAATT-ATATTTTGA
1 -CCCTAAACTTTTCCAAAATTCATATTTTGA
* * *
157442 CCACTAAAATTTTCTAAAATT-ACATTTTGA
1 CC-CTAAACTTTTCCAAAATTCATATTTTGA
157472 CCCTAAACTTTTCCAAAATTGCAT-TTTTG-
1 CCCTAAACTTTTCCAAAATT-CATATTTTGA
* * * *
157501 CCCTGAAC--TTCCAAAAATCACATTTTTA
1 CCCTAAACTTTTCCAAAATTCATATTTTGA
157529 CCC
1 CCC
157532 CCGAACTTCC
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
26 2 0.02
27 13 0.13
28 3 0.03
29 25 0.25
30 51 0.51
31 6 0.06
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTCATATTTTGA
Found at i:157500 original size:60 final size:60
Alignment explanation
Indices: 157385--157652 Score: 164
Period size: 57 Copynumber: 4.6 Consensus size: 60
157375 TAGAAGGTCC
* *
157385 CTAAAATTTTCAAAAATCATATTTTGACCCCTAAACTTTTATAAAATTATATTTTGACCA
1 CTAAAATTTTCAAAAATCACATTTTGACCCCTAAACTTTTACAAAATTATATTTTGACCA
* * *
157445 CTAAAATTTTCTAAAATTACATTTTGA-CCCTAAACTTTTCCAAAATTGCAT-TTTTG-CC-
1 CTAAAATTTTCAAAAATCACATTTTGACCCCTAAACTTTTACAAAATT--ATATTTTGACCA
* * * * ** ** * *
157503 CT-GAACTTCCAAAAATCACATTTTTACCCCCGAACTTCCA-AAAATCACATTTT-A-C-
1 CTAAAATTTTCAAAAATCACATTTTGACCCCTAAACTTTTACAAAATTATATTTTGACCA
** * * * ** * * *
157558 CTTGAATTTCTCAAAAATGACATTTTCACCCC-AAACATTCCCAAAATTACATTTTTACCC
1 CTAAAATTT-TCAAAAATCACATTTTGACCCCTAAACTTTTACAAAATTATATTTTGACCA
* * * *
157618 CTAAACTTTCCAAAAGT-ACATTTTAACCCC-AAACT
1 CTAAAATTTTCAAAAATCACATTTTGACCCCTAAACT
157653 CTCCAAAACT
Statistics
Matches: 163, Mismatches: 34, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
55 4 0.02
56 14 0.09
57 54 0.33
58 27 0.17
59 27 0.17
60 35 0.21
61 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.35
Consensus pattern (60 bp):
CTAAAATTTTCAAAAATCACATTTTGACCCCTAAACTTTTACAAAATTATATTTTGACCA
Found at i:157547 original size:57 final size:55
Alignment explanation
Indices: 157457--157669 Score: 180
Period size: 57 Copynumber: 3.7 Consensus size: 55
157447 AAAATTTTCT
* * * * *
157457 AAAATTACATTTTGACCCTAAACTTTTCC-AAAATTGCATTTTTGCCCTGAACTTCC
1 AAAAATACATTTTTACCCCAAAC--TTCCAAAAATTACATTTTTACCCTGAACTTCC
* * * *
157513 AAAAATCACATTTTTACCCCCGAACTTCCAAAAATCACA-TTTTACCTTGAATTTCTC
1 AAAAAT-ACATTTTTA-CCCCAAACTTCCAAAAATTACATTTTTACCCTGAACTTC-C
* * *
157570 AAAAATGACATTTTCACCCCAAACATTCCCAAAATTACATTTTTACCCCTAAACTTTCC
1 AAAAAT-ACATTTTTACCCCAAAC-TTCCAAAAATTACATTTTTA-CCCTGAAC-TTCC
* * *
157629 AAAAGTACATTTTAACCCCAAACTCTCCAAAACTT-CATTTT
1 AAAAATACATTTTTACCCCAAACT-TCCAAAAATTACATTTT
157670 CGACCCCTTT
Statistics
Matches: 127, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
56 29 0.23
57 49 0.39
58 35 0.28
59 11 0.09
60 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (55 bp):
AAAAATACATTTTTACCCCAAACTTCCAAAAATTACATTTTTACCCTGAACTTCC
Found at i:157904 original size:19 final size:20
Alignment explanation
Indices: 157873--157910 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
157863 TTATCGTTAA
157873 TTGCATAGCTCATATTTATT
1 TTGCATAGCTCATATTTATT
*
157893 TTGCAT-GCTCATTTTTAT
1 TTGCATAGCTCATATTTAT
157911 CTCTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.53
Consensus pattern (20 bp):
TTGCATAGCTCATATTTATT
Found at i:162606 original size:17 final size:16
Alignment explanation
Indices: 162584--162632 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
162574 TTGAAAACTA
162584 CAAAAATATTATAAATGG
1 CAAAAA-ATTATAAAT-G
*
162602 CAAAAAAATATAAAATG
1 CAAAAAATTAT-AAATG
162619 CAAAAAATTA-AAAT
1 CAAAAAATTATAAAT
162633 TTATTAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
17 14 0.50
18 10 0.36
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.22
Consensus pattern (16 bp):
CAAAAAATTATAAATG
Found at i:162650 original size:27 final size:24
Alignment explanation
Indices: 162620--162687 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 24
162610 TATAAAATGC
* *
162620 AAAAAATTAAAATTTATTAACATAGTA
1 AAAAAATTAAAAATTA-TAA-A-AATA
162647 AAAAAATTAAAAATTATAAAAATA
1 AAAAAATTAAAAATTATAAAAATA
162671 AAAAAATTTATAAAATT
1 AAAAAA-TTA-AAAATT
162688 TGTGGAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.24
25 4 0.11
26 9 0.24
27 15 0.41
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (24 bp):
AAAAAATTAAAAATTATAAAAATA
Found at i:163077 original size:25 final size:26
Alignment explanation
Indices: 163030--163079 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
163020 GCTAGAAGGC
* *
163030 TTGGTGAACTAGGGTTCACCAATAGA
1 TTGGCGAACTAGGATTCACCAATAGA
163056 TTGGCGAACT-GGATTCACCAATAG
1 TTGGCGAACTAGGATTCACCAATAG
163080 GATAGCGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (26 bp):
TTGGCGAACTAGGATTCACCAATAGA
Found at i:163087 original size:25 final size:26
Alignment explanation
Indices: 163035--163089 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
163025 AAGGCTTGGT
* *
163035 GAACTAGGGTTCACCAATAGATTGGC
1 GAACTAGGATTCACCAATAGATTAGC
163061 GAACT-GGATTCACCAATAGGA-TAGC
1 GAACTAGGATTCACCAATA-GATTAGC
163086 GAAC
1 GAAC
163090 CGGGGTTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (26 bp):
GAACTAGGATTCACCAATAGATTAGC
Found at i:165682 original size:24 final size:24
Alignment explanation
Indices: 165632--165682 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
165622 GTATACTGGT
*
165632 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAAC
**
165656 TAACCATTCTGGGCTCGTGTGAAC
1 TAACCATTCTGGGCTCGTAAGAAC
165680 TAA
1 TAA
165683 AGTTACCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAAC
Found at i:166405 original size:21 final size:20
Alignment explanation
Indices: 166381--166456 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 20
166371 AGAGTTTTTA
166381 GTATCGGTAGAAGCAAG-ACTT
1 GTATCGGTAGAA--AAGCACTT
166402 GTATCGGTAGAAAAGTCACTT
1 GTATCGGTAGAAAAG-CACTT
** *
166423 GTATCGGTAGAACTGTCACTG
1 GTATCGGTAGAAAAG-CACTT
166444 GTATCGGTAGAAA
1 GTATCGGTAGAAA
166457 TCTGCACTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.06
21 46 0.94
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGGTAGAAAAGCACTT
Found at i:168053 original size:18 final size:18
Alignment explanation
Indices: 168032--168148 Score: 59
Period size: 18 Copynumber: 6.7 Consensus size: 18
168022 TTTATCAAAA
168032 TTTATTATTTTTAATAAT
1 TTTATTATTTTTAATAAT
*
168050 TTTA-T-TTTTT-ACAAT
1 TTTATTATTTTTAATAAT
* * * *
168065 TTCATAATTTATCA-AAT
1 TTTATTATTTTTAATAAT
* *
168082 TTT-TAATTTTTAAATATT
1 TTTATTATTTTT-AATAAT
**
168100 TTTATT-TTTTTTGTAAT
1 TTTATTATTTTTAATAAT
*
168117 TTTAATTATTTTTTATAA-
1 TTT-ATTATTTTTAATAAT
*
168135 TATATATATTTTTA
1 TTTAT-TATTTTTA
168149 TCATTTATAA
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
15 7 0.09
16 12 0.16
17 19 0.25
18 27 0.36
19 10 0.13
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (18 bp):
TTTATTATTTTTAATAAT
Found at i:168068 original size:50 final size:50
Alignment explanation
Indices: 168013--168109 Score: 144
Period size: 50 Copynumber: 1.9 Consensus size: 50
168003 TACCTACAAT
168013 ATTTCAAAATTTATCAAAATTTATT-ATTTTT-AATAATTTTATTTTTTACA
1 ATTTCAAAATTTATC-AAATTT-TTAATTTTTAAATAATTTTATTTTTTACA
* *
168063 ATTTCATAATTTATCAAATTTTTAATTTTTAAATATTTTTATTTTTT
1 ATTTCAAAATTTATCAAATTTTTAATTTTTAAATAATTTTATTTTTT
168110 TTGTAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 2 0.05
49 12 0.28
50 29 0.67
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (50 bp):
ATTTCAAAATTTATCAAATTTTTAATTTTTAAATAATTTTATTTTTTACA
Found at i:168101 original size:16 final size:15
Alignment explanation
Indices: 168029--168108 Score: 54
Period size: 16 Copynumber: 5.0 Consensus size: 15
168019 AAATTTATCA
168029 AAATTTATT-ATTTTT
1 AAATTT-TTAATTTTT
* *
168044 AATAATTTTATTTTTT
1 AA-ATTTTTAATTTTT
* *
168060 ACAATTTCATAATTTATC
1 A-AATTT-TTAATTT-TT
168078 AAATTTTTAATTTTT
1 AAATTTTTAATTTTT
*
168093 AAATATTTTTATTTTT
1 AAAT-TTTTAATTTTT
168109 TTTGTAATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
15 9 0.18
16 28 0.56
17 11 0.22
18 2 0.04
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATTTTTAATTTTT
Found at i:168128 original size:19 final size:18
Alignment explanation
Indices: 168097--168135 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
168087 ATTTTTAAAT
* *
168097 ATTTTTATTTTTTTTGTA
1 ATTTTAATTTTTTTTATA
168115 ATTTTAATTATTTTTTATA
1 ATTTTAATT-TTTTTTATA
168134 AT
1 AT
168136 ATATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
ATTTTAATTTTTTTTATA
Found at i:179007 original size:12 final size:13
Alignment explanation
Indices: 178990--179031 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
178980 AAAAATAAAC
178990 AAAAG-AGAAGAG
1 AAAAGAAGAAGAG
179002 AAAAGAAGAA-AG
1 AAAAGAAGAAGAG
179014 CAAAAGAAGAAG-G
1 -AAAAGAAGAAGAG
179027 AAAAG
1 AAAAG
179032 TTAAAGAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAGAG
Found at i:180171 original size:35 final size:35
Alignment explanation
Indices: 180125--180202 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
180115 GTGTTGCCCT
* * * * *
180125 AAAGGGCCTATAGATCGTTTACACTGTGTCACTTC
1 AAAGGACCTATAGACCATTTACACAGTGTCACCTC
* *
180160 AAAGGACCTATATACCATTTACACAGTGTCGCCTC
1 AAAGGACCTATAGACCATTTACACAGTGTCACCTC
180195 AAAGGACC
1 AAAGGACC
180203 AGTCGATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (35 bp):
AAAGGACCTATAGACCATTTACACAGTGTCACCTC
Found at i:181663 original size:20 final size:21
Alignment explanation
Indices: 181631--181677 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
181621 TCATTTTAGT
181631 ATTT-TTATATTTTGGAA-AC
1 ATTTCTTATATTTTGGAAGAC
* * *
181650 GTTTCTTATTTTTTTGAAGAC
1 ATTTCTTATATTTTGGAAGAC
181671 ATTTCTT
1 ATTTCTT
181678 GTAGTAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (21 bp):
ATTTCTTATATTTTGGAAGAC
Found at i:182173 original size:28 final size:28
Alignment explanation
Indices: 182133--182202 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
182123 TTTTGATTTA
182133 GTCGAGTTGACGAATCGAGTCAAATCGT
1 GTCGAGTTGACGAATCGAGTCAAATCGT
182161 GTCGAGTTGACGAATCGAGTCAAATCGT
1 GTCGAGTTGACGAATCGAGTCAAATCGT
*
182189 GTCGAGTTAACGAA
1 GTCGAGTTGACGAA
182203 ACCTATTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (28 bp):
GTCGAGTTGACGAATCGAGTCAAATCGT
Found at i:185897 original size:43 final size:43
Alignment explanation
Indices: 185815--185897 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
185805 GAAAGGTTTT
* * *
185815 TTATGAGGGTTTTAACAAGAAATGGATTTGTGTTTGTTTCTAA
1 TTATGAGGGTTTTAAAAAGAAATGGATTTGTATTAGTTTCTAA
* *
185858 TTATTAGGGTTTTAAAAAGATAA-GGATTTTTATTAGTTTC
1 TTATGAGGGTTTTAAAAAGA-AATGGATTTGTATTAGTTTC
185898 AAAATTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 32 0.94
44 2 0.06
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (43 bp):
TTATGAGGGTTTTAAAAAGAAATGGATTTGTATTAGTTTCTAA
Found at i:186560 original size:11 final size:10
Alignment explanation
Indices: 186539--186620 Score: 82
Period size: 11 Copynumber: 8.2 Consensus size: 10
186529 AAAAATTTTG
186539 AAATATGTAA
1 AAATATGTAA
186549 AAATATGCTAA
1 AAATATG-TAA
*
186560 AAATATGGATA
1 AAATATGTA-A
186571 AAATATG--A
1 AAATATGTAA
*
186579 AAATATGAAA
1 AAATATGTAA
186589 AAATATGTAA
1 AAATATGTAA
186599 AAA-ATGTATAA
1 AAATATG--TAA
186610 AAATATG-AA
1 AAATATGTAA
186619 AA
1 AA
186621 TATTAGGCAT
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
8 8 0.13
9 7 0.11
10 21 0.33
11 24 0.38
12 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.11, T:0.26
Consensus pattern (10 bp):
AAATATGTAA
Found at i:186620 original size:39 final size:40
Alignment explanation
Indices: 186539--186623 Score: 129
Period size: 39 Copynumber: 2.1 Consensus size: 40
186529 AAAAATTTTG
*
186539 AAATATGTAAAAATATGCTAAAAATATGGATAAAATATGA
1 AAATATGAAAAAATATGCTAAAAATATGGATAAAATATGA
*
186579 AAATATGAAAAAATATG-TAAAAA-ATGTATAAAAATATGA
1 AAATATGAAAAAATATGCTAAAAATATGGAT-AAAATATGA
186618 AAATAT
1 AAATAT
186624 TAGGCATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
38 5 0.12
39 21 0.50
40 16 0.38
ACGTcount: A:0.61, C:0.01, G:0.11, T:0.27
Consensus pattern (40 bp):
AAATATGAAAAAATATGCTAAAAATATGGATAAAATATGA
Found at i:189502 original size:20 final size:22
Alignment explanation
Indices: 189479--189524 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
189469 TAGTACAAGT
*
189479 ATTTTGACATG-TTT-AAAATC
1 ATTTTAACATGATTTGAAAATC
*
189499 ATTTTAACATGATTTGAAAATT
1 ATTTTAACATGATTTGAAAATC
189521 ATTT
1 ATTT
189525 CAAACTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 3 0.14
22 9 0.41
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (22 bp):
ATTTTAACATGATTTGAAAATC
Found at i:194201 original size:30 final size:30
Alignment explanation
Indices: 194167--194230 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
194157 AAATAATTCT
194167 ATTATTTAAAATATCTACAACTTTACACCC
1 ATTATTTAAAATATCTACAACTTTACACCC
*
194197 ATTATTTACAATATCTACAACTTTACACCC
1 ATTATTTAAAATATCTACAACTTTACACCC
194227 ATTA
1 ATTA
194231 GACTCAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (30 bp):
ATTATTTAAAATATCTACAACTTTACACCC
Found at i:197424 original size:80 final size:80
Alignment explanation
Indices: 197340--197500 Score: 286
Period size: 80 Copynumber: 2.0 Consensus size: 80
197330 AATCATTTTA
*
197340 ACTTGATTTGAAAATTGTTTTAAACTTTTCTAAGAGCTCAAGCTAGGAGTTTAAATTTTACCTCT
1 ACTTGATTTGAAAATTGTTTTAAACTTTTCTAAGAGCTCAAGATAGGAGTTTAAATTTTACCTCT
*
197405 TAGATTTTAAAATTG
66 AAGATTTTAAAATTG
* *
197420 ACTTGATTTGAAAATTGTTTTAAACTTTTCTAAGAGTTCAAGATATGAGTTTAAATTTTACCTCT
1 ACTTGATTTGAAAATTGTTTTAAACTTTTCTAAGAGCTCAAGATAGGAGTTTAAATTTTACCTCT
197485 AAGATTTTAAAATTG
66 AAGATTTTAAAATTG
197500 A
1 A
197501 TAAATAATTT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (80 bp):
ACTTGATTTGAAAATTGTTTTAAACTTTTCTAAGAGCTCAAGATAGGAGTTTAAATTTTACCTCT
AAGATTTTAAAATTG
Found at i:201300 original size:19 final size:20
Alignment explanation
Indices: 201278--201315 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
201268 AATCCAAAGT
*
201278 TATTTTCAAAAA-TTCAATA
1 TATTTACAAAAATTTCAATA
201297 TATTTACAAAAATTTCAAT
1 TATTTACAAAAATTTCAAT
201316 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTTACAAAAATTTCAATA
Found at i:201343 original size:17 final size:18
Alignment explanation
Indices: 201323--201373 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
201313 AATTTTTTTT
201323 AAATATTTTAAAAAT-TA
1 AAATATTTTAAAAATGTA
201340 AAATA-TTTAAAAATGTA
1 AAATATTTTAAAAATGTA
201357 AAA-ATTTATAAAAATGT
1 AAATATTT-TAAAAATGT
201374 TTAAAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.32
17 12 0.39
18 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (18 bp):
AAATATTTTAAAAATGTA
Found at i:201348 original size:16 final size:17
Alignment explanation
Indices: 201323--201369 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
201313 AATTTTTTTT
201323 AAATATTTTAAAAAT-TA
1 AAATA-TTTAAAAATGTA
201340 AAATATTTAAAAATGTA
1 AAATATTTAAAAATGTA
201357 AAA-ATTTATAAAA
1 AAATATTTA-AAAA
201370 ATGTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATATTTAAAAATGTA
Found at i:201368 original size:18 final size:17
Alignment explanation
Indices: 201322--201373 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
201312 CAATTTTTTT
*
201322 TAAATATTTTAAAAAT-
1 TAAAAATTTTAAAAATG
201338 T-AAAATATTTAAAAATG
1 TAAAAAT-TTTAAAAATG
201355 TAAAAATTTATAAAAATG
1 TAAAAATTT-TAAAAATG
201373 T
1 T
201374 TTAAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 3 0.10
18 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
TAAAAATTTTAAAAATG
Found at i:206526 original size:27 final size:27
Alignment explanation
Indices: 206496--206564 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
206486 TATGAGATGT
206496 ATTTTTATATTTTTATTATCGAAA-ATA
1 ATTTTTATATTTTTATTATC-AAATATA
206523 ATTTTT-TATTTTTATTTATCAAATATA
1 ATTTTTATATTTTTA-TTATCAAATATA
*
206550 TTTTTTA-ATTTTTAT
1 ATTTTTATATTTTTAT
206565 AAAATAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 12 0.32
27 26 0.68
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (27 bp):
ATTTTTATATTTTTATTATCAAATATA
Found at i:206527 original size:26 final size:25
Alignment explanation
Indices: 206495--206564 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 25
206485 TTATGAGATG
206495 TATTTTTATATTTTTATTATCGAAA-A
1 TATTTTT-TATTTTTATTATC-AAATA
206521 TAATTTTTTATTTTTATTTATCAAATA
1 T-ATTTTTTATTTTTA-TTATCAAATA
206548 TATTTTTTAATTTTTAT
1 TATTTTTT-ATTTTTAT
206565 AAAATAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
26 20 0.50
27 20 0.50
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (25 bp):
TATTTTTTATTTTTATTATCAAATA
Found at i:210390 original size:13 final size:13
Alignment explanation
Indices: 210372--210396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210362 TTATGTCTTT
210372 TTTTTTAAATATA
1 TTTTTTAAATATA
210385 TTTTTTAAATAT
1 TTTTTTAAATAT
210397 TTTATTATAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAAATATA
Found at i:211369 original size:31 final size:31
Alignment explanation
Indices: 211333--211397 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
211323 CTGTAAGTAT
* * * *
211333 TAATTTGGACTAAAAAACTAAGTTCATGTAC
1 TAATTTGAACCAAAAAACCAAGTTCAGGTAC
*
211364 TAATTTGAACCAAGAAACCAAGTTCAGGTAC
1 TAATTTGAACCAAAAAACCAAGTTCAGGTAC
211395 TAA
1 TAA
211398 AATGTGTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (31 bp):
TAATTTGAACCAAAAAACCAAGTTCAGGTAC
Found at i:215407 original size:20 final size:21
Alignment explanation
Indices: 215365--215407 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
215355 TGATCCGAGG
*
215365 AACTTTTAATATTTTAAAGTT
1 AACTTTTAATATTTTAAACTT
* *
215386 AACTTTTTA-ATTTTAATCTT
1 AACTTTTAATATTTTAAACTT
215406 AA
1 AA
215408 GTATTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (21 bp):
AACTTTTAATATTTTAAACTT
Found at i:215472 original size:13 final size:12
Alignment explanation
Indices: 215440--215478 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
215430 ACTTGATATA
*
215440 TAATTATTAAAT
1 TAATTAATAAAT
215452 TAAGTTAATAAAT
1 TAA-TTAATAAAT
215465 CTAATTAATAAAT
1 -TAATTAATAAAT
215478 T
1 T
215479 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 17 0.71
14 3 0.12
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (12 bp):
TAATTAATAAAT
Found at i:221229 original size:40 final size:40
Alignment explanation
Indices: 221141--221354 Score: 241
Period size: 40 Copynumber: 5.4 Consensus size: 40
221131 TGTGTGAAGG
* * *
221141 CACTGTAAACATTGCAACATTATTATTG-ACTAGCAGTGA
1 CACTGTAAACACTGCAATATTATTACTGAACTAGCAGTGA
* * * *
221180 CACTGTAAACACTGCGATATTATTACTGAATTGGCAATGA
1 CACTGTAAACACTGCAATATTATTACTGAACTAGCAGTGA
* *
221220 CATTGTAAACACTGCAATACTATTACTGAACTAGCAGTGA
1 CACTGTAAACACTGCAATATTATTACTGAACTAGCAGTGA
* * ** *
221260 CACTGGAAACATTGTGATATTACTACTGAACTAGCAGTGA
1 CACTGTAAACACTGCAATATTATTACTGAACTAGCAGTGA
* * ***
221300 CACTGTAAACACTACAATATTATTATTGAACTAATTGTGA
1 CACTGTAAACACTGCAATATTATTACTGAACTAGCAGTGA
*
221340 CACTTTAAACACTGC
1 CACTGTAAACACTGC
221355 TAGACTACCA
Statistics
Matches: 142, Mismatches: 32, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
39 24 0.17
40 118 0.83
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (40 bp):
CACTGTAAACACTGCAATATTATTACTGAACTAGCAGTGA
Found at i:221261 original size:80 final size:80
Alignment explanation
Indices: 221141--221354 Score: 268
Period size: 80 Copynumber: 2.7 Consensus size: 80
221131 TGTGTGAAGG
* * *
221141 CACTGTAAACATTGCAACATTATTATTG-ACTAGCAGTGACACTGTAAACACTGCGATATTATTA
1 CACTGTAAACACTGCAATATTATTATTGAACTAGCAGTGACACTGTAAACACTGCGATATTACTA
* *
221205 CTGAATTGGCAATGA
66 CTGAACTAGCAATGA
* * * * * *
221220 CATTGTAAACACTGCAATACTATTACTGAACTAGCAGTGACACTGGAAACATTGTGATATTACTA
1 CACTGTAAACACTGCAATATTATTATTGAACTAGCAGTGACACTGTAAACACTGCGATATTACTA
*
221285 CTGAACTAGCAGTGA
66 CTGAACTAGCAATGA
* *** *
221300 CACTGTAAACACTACAATATTATTATTGAACTAATTGTGACACTTTAAACACTGC
1 CACTGTAAACACTGCAATATTATTATTGAACTAGCAGTGACACTGTAAACACTGC
221355 TAGACTACCA
Statistics
Matches: 111, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
79 23 0.21
80 88 0.79
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (80 bp):
CACTGTAAACACTGCAATATTATTATTGAACTAGCAGTGACACTGTAAACACTGCGATATTACTA
CTGAACTAGCAATGA
Found at i:223245 original size:35 final size:35
Alignment explanation
Indices: 223206--223276 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
223196 CCATAGAATA
*
223206 TTTTTAGATTTTTTGCACCTTTGG-AATATTTTTTTT
1 TTTTTAGATTTTTTGCA--TGTGGAAATATTTTTTTT
* *
223242 TTTTTCGATTTTTTTCATGTGGAAATATTTTTTTT
1 TTTTTAGATTTTTTGCATGTGGAAATATTTTTTTT
223277 CACTGTATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 4 0.13
35 12 0.39
36 15 0.48
ACGTcount: A:0.17, C:0.07, G:0.11, T:0.65
Consensus pattern (35 bp):
TTTTTAGATTTTTTGCATGTGGAAATATTTTTTTT
Found at i:234086 original size:30 final size:30
Alignment explanation
Indices: 234050--234113 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
234040 ATTTAATTAA
*
234050 AAAAATTATAATTT-AATCATTAAACTATTT
1 AAAAATTATAATTTAAATCACTAAACTA-TT
* * *
234080 AAAAATTTTCATTTAAATCGCTAAACTATT
1 AAAAATTATAATTTAAATCACTAAACTATT
234110 AAAA
1 AAAA
234114 TCAATGTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAAATTATAATTTAAATCACTAAACTATT
Found at i:236146 original size:24 final size:22
Alignment explanation
Indices: 236103--236156 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
236093 AAATACATTA
236103 AATTATTTTTATATCGAATAATAT
1 AATTATTTTTATATC-AAT-ATAT
236127 AATTATTTATGTATAT-AATATAT
1 AATTATTT-T-TATATCAATATAT
*
236150 AAATATT
1 AATTATT
236157 AATAACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 10 0.37
24 11 0.41
25 1 0.04
26 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
AATTATTTTTATATCAATATAT
Found at i:241822 original size:466 final size:466
Alignment explanation
Indices: 240935--241870 Score: 1489
Period size: 466 Copynumber: 2.0 Consensus size: 466
240925 GACAATCAAT
* * *
240935 GTGTTATTCATATCACAATCAATTGGGTTCCCAACAAAAACCTACTTAACCCAGTCGCAAACTGC
1 GTGTTATTCAGATCACAATCAATTAGGTTCCCAACAAAAACCTACTTAACCCAGTCACAAACTGC
*
241000 ATCCCCGATTGCGTCCCACTACCTCCGAAAAATAAACACATGGAAACTATCACTTCCTAAGGCTT
66 ATCCCCGATTGCGTCCCACTACCTCCGAAAAATAAACACATGGAAACCATCACTTCCTAAGGCTT
* * *
241065 TTAGAACTGCCATATCAAAAAGGGCTGCCTTAATTTCAATATTGGACACTAGTTTACCCAAAAAT
131 TCAAAACTGCCATATCAAAAAGGGCTGCCTTAATTTCAATACTGGACACTAGTTTACCCAAAAAT
* *
241130 TGAGGTCTTCAGACTCAAGCTGAGGGAATCGACTTCAAGGAAACGTACCACAAGGTCCCAAATGT
196 TGAGGTCTTCAGACTCAAGCTAAGGGAATCGACTTCAAGGAAAAGTACCACAAGGTCCCAAATGT
241195 TCCCCATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAATCAA
261 TCCCCATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAATCAA
* *
241260 ATTATCGTCAGAATTACGAATAGCTAATATGCAATTACTCTTCCGTCGTTGCAAGGTACGAGTAT
326 ATTATCGTCAAAATTACGAATAGCTAATATGCAATTACTCTTCCGTCGTTGCAAGGTACAAGTAT
* * *
241325 AAAAAAACTTAGCATTATTATCCCCCAGTTTCAACCAGTCATAATGTGCTTTCTGTTTCCAAATG
391 AAAAAAACTTAGCATTACTATCCCCCAGTTTCAACCAATCATAACGTGCTTTCTGTTTCCAAATG
*
241390 AGCTCTTTATG
456 AGCTCTTAATG
* * * *
241401 GTGTTATTCAGATCACGATCAATTAGGTTCCCAATAAAGACCTGCTTAACCCAGTCACAAACTGC
1 GTGTTATTCAGATCACAATCAATTAGGTTCCCAACAAAAACCTACTTAACCCAGTCACAAACTGC
* *
241466 ATCCCCGATTGCGTCCCACTGCCTCC-AGAAAATAAGCACATGGAAACCATCACTTCCTAAGGCT
66 ATCCCCGATTGCGTCCCACTACCTCCGA-AAAATAAACACATGGAAACCATCACTTCCTAAGGCT
241530 TTCAAAACTGCCATATCAAAAAGGGCTGCCTTAATTTCAATACTGGACACTAGTTTACCCAAAAA
130 TTCAAAACTGCCATATCAAAAAGGGCTGCCTTAATTTCAATACTGGACACTAGTTTACCC-AAAA
** * * *
241595 ATTGAGGTCTTCAGACTCAAGCTAAGGGAATCGACTTTGAGGAAAAGTACCACAGGGTCTCAGAT
194 ATTGAGGTCTTCAGACTCAAGCTAAGGGAATCGACTTCAAGGAAAAGTACCACAAGGTCCCAAAT
*
241660 GTTTCCCATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAATC
259 GTTCCCCATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAATC
* * * * *
241725 CAATTGTCGTCAAAATTACGAATAGCTGATATGCGATTACTCTTCCGTCGTTGCAGGGTACAAGT
324 AAATTATCGTCAAAATTACGAATAGCTAATATGCAATTACTCTTCCGTCGTTGCAAGGTACAAGT
** * * * * *
241790 ATGGAAAAACTTAGTATTCCTAT-TCTCAGTTTCAACCAATCATAACGTTCTTTCTGTTTCCAAA
389 ATAAAAAAACTTAGCATTACTATCCCCCAGTTTCAACCAATCATAACGTGCTTTCTGTTTCCAAA
241854 TGAGCTCTTAATG
454 TGAGCTCTTAATG
241867 GTGT
1 GTGT
241871 AGAACAATGT
Statistics
Matches: 429, Mismatches: 39, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
465 1 0.00
466 226 0.53
467 202 0.47
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (466 bp):
GTGTTATTCAGATCACAATCAATTAGGTTCCCAACAAAAACCTACTTAACCCAGTCACAAACTGC
ATCCCCGATTGCGTCCCACTACCTCCGAAAAATAAACACATGGAAACCATCACTTCCTAAGGCTT
TCAAAACTGCCATATCAAAAAGGGCTGCCTTAATTTCAATACTGGACACTAGTTTACCCAAAAAT
TGAGGTCTTCAGACTCAAGCTAAGGGAATCGACTTCAAGGAAAAGTACCACAAGGTCCCAAATGT
TCCCCATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAATCAA
ATTATCGTCAAAATTACGAATAGCTAATATGCAATTACTCTTCCGTCGTTGCAAGGTACAAGTAT
AAAAAAACTTAGCATTACTATCCCCCAGTTTCAACCAATCATAACGTGCTTTCTGTTTCCAAATG
AGCTCTTAATG
Found at i:248956 original size:31 final size:31
Alignment explanation
Indices: 248911--248976 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
248901 AAAAAAAAAG
*
248911 TTCAATCCCCAATATCG-AAACAATTACCTAA
1 TTCAAGCCCCAATAT-GAAAACAATTACCTAA
* * *
248942 TTCAAGCCCTAATATGAAAACAATTATCTAG
1 TTCAAGCCCCAATATGAAAACAATTACCTAA
248973 TTCA
1 TTCA
248977 GACCTCAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (31 bp):
TTCAAGCCCCAATATGAAAACAATTACCTAA
Found at i:249700 original size:10 final size:10
Alignment explanation
Indices: 249687--249729 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
249677 AAAAATCGTA
249687 AAAAAAATAT
1 AAAAAAATAT
*
249697 AAAAATATAT
1 AAAAAAATAT
* *
249707 AGAAATATA-
1 AAAAAAATAT
249716 AAAAAAATAT
1 AAAAAAATAT
249726 AAAA
1 AAAA
249730 TTTTATAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:249731 original size:59 final size:60
Alignment explanation
Indices: 249652--249778 Score: 168
Period size: 59 Copynumber: 2.1 Consensus size: 60
249642 AGAAAAAATG
* * *
249652 TATATAAAAAATTGTAAAATTTTATAAAAATCGTAAAAAAAATATA-AAAATATATAGAAA
1 TATATAAAAAAATATAAAATTTTAT-AAAATCGTAAAAAAAATATACAAAATATAAAGAAA
* * * *
249712 TATA-AAAAAAATATAAAATTTTATAAAGTCGTAAGAAAATTATACAAAATGTAAAGAAA
1 TATATAAAAAAATATAAAATTTTATAAAATCGTAAAAAAAATATACAAAATATAAAGAAA
249771 TATATAAA
1 TATATAAA
249779 TTTCCTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 17 0.29
59 34 0.59
60 7 0.12
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (60 bp):
TATATAAAAAAATATAAAATTTTATAAAATCGTAAAAAAAATATACAAAATATAAAGAAA
Found at i:249736 original size:29 final size:29
Alignment explanation
Indices: 249652--249738 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
249642 AGAAAAAATG
* *
249652 TATATAAAAAATTGTAAAATTTTATAAAAA
1 TATA-AAAAAAATATAAAATTTTATAAAAA
* * * *
249682 TCGTAAAAAAAATATAAAAATATATAGAAA
1 T-ATAAAAAAAATATAAAATTTTATAAAAA
249712 TATAAAAAAAATATAAAATTTTATAAA
1 TATAAAAAAAATATAAAATTTTATAAA
249739 GTCGTAAGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 22 0.48
30 22 0.48
31 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (29 bp):
TATAAAAAAAATATAAAATTTTATAAAAA
Found at i:249750 original size:29 final size:29
Alignment explanation
Indices: 249657--249755 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 29
249647 AAATGTATAT
* *
249657 AAAAAATTGTAAAATTTTATAAAAATCGTA
1 AAAAAAATATAAAATTTTAT-AAAATCGTA
* * *
249687 AAAAAAATATAAAAATATATAGAAAT-ATA
1 AAAAAAATATAAAATTTTATA-AAATCGTA
*
249716 AAAAAAATATAAAATTTTATAAAGTCGTA
1 AAAAAAATATAAAATTTTATAAAATCGTA
* *
249745 AGAAAATTATA
1 AAAAAAATATA
249756 CAAAATGTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.05
29 33 0.59
30 20 0.36
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (29 bp):
AAAAAAATATAAAATTTTATAAAATCGTA
Done.