Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020987.1 Corchorus olitorius cultivar O-4 contig21020, 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: 193010
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1327 original size:11 final size:11
Alignment explanation
Indices: 1311--1336 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1301 ATAGAGTAAT
1311 AAAAGAAAAAG
1 AAAAGAAAAAG
1322 AAAAGAAAAAG
1 AAAAGAAAAAG
1333 AAAA
1 AAAA
1337 AGGTAGAATT
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:5062 original size:22 final size:21
Alignment explanation
Indices: 5010--5063 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
5000 TGCTTCTTGA
5010 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
5031 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
5050 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
5064 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:7054 original size:12 final size:12
Alignment explanation
Indices: 7037--7062 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7027 CACTATTATA
7037 TTAGTAATGATT
1 TTAGTAATGATT
7049 TTAGTAATGATT
1 TTAGTAATGATT
7061 TT
1 TT
7063 TTCCGATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (12 bp):
TTAGTAATGATT
Found at i:9586 original size:14 final size:14
Alignment explanation
Indices: 9567--9594 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9557 AAATTAAGGC
9567 TTATTTTATTGGGT
1 TTATTTTATTGGGT
9581 TTATTTTATTGGGT
1 TTATTTTATTGGGT
9595 GGAATTCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.64
Consensus pattern (14 bp):
TTATTTTATTGGGT
Found at i:10153 original size:32 final size:32
Alignment explanation
Indices: 10110--10185 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
10100 AAATAAGCCA
*
10110 AAATAGCGGCGTTTCAGTATA-GAAACGCCACT
1 AAATAGTGGCGTTT-AGTATACGAAACGCCACT
** *
10142 AAATAGTGGCGTTTTTTCTACGGAAACGCCACT
1 AAATAGTGGCGTTTAGTATAC-GAAACGCCACT
10175 AAATAGTGGCG
1 AAATAGTGGCG
10186 CTTTTGTACG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 3 0.08
32 13 0.34
33 22 0.58
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (32 bp):
AAATAGTGGCGTTTAGTATACGAAACGCCACT
Found at i:10205 original size:32 final size:32
Alignment explanation
Indices: 10131--10228 Score: 142
Period size: 32 Copynumber: 3.0 Consensus size: 32
10121 TTTCAGTATA
* *
10131 GAAACGCCACTAAATAGTGGCGTTTTTTCTACG
1 GAAACGCCACTAAATAGTGGCG-CTTTTGTACG
10164 GAAACGCCACTAAATAGTGGCGCTTTTGTACG
1 GAAACGCCACTAAATAGTGGCGCTTTTGTACG
* **
10196 GAAAAGCCACTACTTAGTGGCGCTTTTGTACG
1 GAAACGCCACTAAATAGTGGCGCTTTTGTACG
10228 G
1 G
10229 CACCATTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 38 0.63
33 22 0.37
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (32 bp):
GAAACGCCACTAAATAGTGGCGCTTTTGTACG
Found at i:16259 original size:65 final size:65
Alignment explanation
Indices: 16155--16279 Score: 223
Period size: 65 Copynumber: 1.9 Consensus size: 65
16145 GCTTGCTATT
* *
16155 GATTCCAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGTATGGGTTGAAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTTGAAC
*
16220 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTCCCCCATGCATGGGT
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGT
16280 AGGACCAGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.21, C:0.27, G:0.30, T:0.22
Consensus pattern (65 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTTGAAC
Found at i:19691 original size:65 final size:65
Alignment explanation
Indices: 19587--19716 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 65
19577 GCTTGCTATT
* *
19587 GATTCCAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCACGCATGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCACGCATGGGTAGGAC
* * * *
19652 GATTCAAACTTTCTGCACTAGGCTAGGCGTGGGTAGGCCAAGGGTTCCCCATGCATGGGTAGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCACGCATGGGTAGGAC
19717 TAGTTTTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.22
Consensus pattern (65 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCACGCATGGGTAGGAC
Found at i:20911 original size:19 final size:19
Alignment explanation
Indices: 20870--20911 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
20860 ATTTTTTTAT
*
20870 TTATTTACTATTTATATTT
1 TTATTTACTATTTATATTA
*
20889 TTATTTATTAATTTA-ATTA
1 TTATTTACT-ATTTATATTA
20908 TTAT
1 TTAT
20912 CCATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTACTATTTATATTA
Found at i:20921 original size:19 final size:20
Alignment explanation
Indices: 20899--20941 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
20889 TTATTTATTA
*
20899 ATTTAATTA-TTATCCATTT
1 ATTTAACTATTTATCCATTT
*
20918 ATTT-ACTATTTATCCTTTT
1 ATTTAACTATTTATCCATTT
20937 ATTTA
1 ATTTA
20942 TTAATTTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTAACTATTTATCCATTT
Found at i:20937 original size:46 final size:46
Alignment explanation
Indices: 20868--20969 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 46
20858 AGATTTTTTT
* *
20868 ATTTATTTACTATTTATATTTTTATTTATTAATTTAATTATTATCC
1 ATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATCC
* * **
20914 ATTTATTTACTATTTATCCTTTTATTTATTAATTTAGCTATTATTT
1 ATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATCC
20960 ATTTATTTAC
1 ATTTATTTAC
20970 AATTATCTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (46 bp):
ATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATCC
Found at i:21044 original size:8 final size:8
Alignment explanation
Indices: 20996--21073 Score: 50
Period size: 8 Copynumber: 9.6 Consensus size: 8
20986 TTTTACCTAC
20996 CTATTTAT
1 CTATTTAT
*
21004 CTAATTAT
1 CTATTTAT
* *
21012 CTATATAC
1 CTATTTAT
21020 CTATTTAT
1 CTATTTAT
*
21028 CTTTTTAT
1 CTATTTAT
* *
21036 TTATCTAT
1 CTATTTAT
*
21044 -TATTTTT
1 CTATTTAT
*
21051 ACTTATTTTT
1 -C-TATTTAT
21061 CTATTTAT
1 CTATTTAT
*
21069 TTATT
1 CTATT
21074 CATTTATCTA
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
7 5 0.09
8 40 0.75
9 1 0.02
10 7 0.13
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
CTATTTAT
Found at i:22114 original size:21 final size:21
Alignment explanation
Indices: 22090--22136 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
22080 ACCACAACCG
**
22090 GCCATCCGCGCTTTCCTCCGC
1 GCCATCCGCGCTACCCTCCGC
22111 GCCATCCGCGCTACCCTCCGC
1 GCCATCCGCGCTACCCTCCGC
22132 GCCAT
1 GCCAT
22137 ATGCCCGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.09, C:0.53, G:0.19, T:0.19
Consensus pattern (21 bp):
GCCATCCGCGCTACCCTCCGC
Found at i:22268 original size:21 final size:21
Alignment explanation
Indices: 22244--22298 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
22234 CGGCCATTCA
* **
22244 CCGTGCCACCATCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
22265 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
22286 CCGTGCCATCACC
1 CCGTGCCACCACC
22299 ATTCCAAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:24216 original size:29 final size:31
Alignment explanation
Indices: 24164--24223 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
24154 GAAGTTCGTG
*
24164 TTTGAAGACCATTTGAAGACTTATTTGAAGA
1 TTTGAAGACCATTTGAAGACTTATTTCAAGA
*
24195 TTTGAAGA-C-TTTGAAGATTTATTTCAAGA
1 TTTGAAGACCATTTGAAGACTTATTTCAAGA
24224 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
TTTGAAGACCATTTGAAGACTTATTTCAAGA
Found at i:25624 original size:15 final size:16
Alignment explanation
Indices: 25594--25633 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
25584 TTACTTTGCT
25594 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
25610 TTGTTTT-TTGTTTAA
1 TTGTTTTCTAGTTTAA
*
25625 TTGCTTTCT
1 TTGTTTTCT
25634 GTCAACCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:31320 original size:3 final size:3
Alignment explanation
Indices: 31312--31352 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31302 TCTTTCTTAA
31312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31353 ATAAGGTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:36379 original size:27 final size:27
Alignment explanation
Indices: 36349--36419 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
36339 AGTGTACTTG
* *
36349 AAATGACTAAAATGCCCCTGGACGTGT
1 AAATGACCAAAATGCCCATGGACGTGT
36376 AAATGACCAAAATGCCCATGGACGTGT
1 AAATGACCAAAATGCCCATGGACGTGT
*
36403 AAATGGCCAAAATGCCC
1 AAATGACCAAAATGCCC
36420 TTAGTGTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCATGGACGTGT
Found at i:36988 original size:51 final size:50
Alignment explanation
Indices: 36804--36985 Score: 285
Period size: 50 Copynumber: 3.6 Consensus size: 50
36794 GAATCAATTT
* *
36804 CTTTGAATTGTCTTCCAA-TCTAATATTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTC-AATCTTAAAAGGACCGTCTTCCGCTTATC
* *
36854 CTTTGAAATGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
36904 CATTGAACTGTCTTCCAATTCGATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
36955 CTTTGAACTGTCTTCCAATTCAATCTTAAAA
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAA
36986 AGGTAATGTA
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
50 72 0.60
51 49 0.40
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:37072 original size:50 final size:50
Alignment explanation
Indices: 36997--37181 Score: 327
Period size: 50 Copynumber: 3.7 Consensus size: 50
36987 GGTAATGTAC
36997 CGTATGGAAACG-GATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
1 CGTATGGAAACGAG-TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
* * *
37047 CGTATGGAGACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAACTAACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
37097 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
37147 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
37182 AGCATTCGGA
Statistics
Matches: 128, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
50 127 0.99
51 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (50 bp):
CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
Found at i:37964 original size:50 final size:50
Alignment explanation
Indices: 37814--37964 Score: 194
Period size: 50 Copynumber: 3.0 Consensus size: 50
37804 TTAAATGCCC
* * * * * *
37814 TTTGAAAAGTGAATTTTGATCTTGGACTCACAAATGGGATGACATCTTAC
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGAAATCTTAT
* * * *
37864 TTTGAAAAGCGAATTTTAATTTTGAACTCACAAATGGAAAGCAATTTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGAAATCTTAT
* *
37914 TTTGGAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGAAATCTTAT
37964 T
1 T
37965 ATAAAACTTC
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGAAATCTTAT
Found at i:38578 original size:28 final size:29
Alignment explanation
Indices: 38547--38622 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 29
38537 TCTCTCTTGA
38547 TTTTGATTTGATTTGATTTTTTTTTG-TT
1 TTTTGATTTGATTTGATTTTTTTTTGATT
* **
38575 TTTTGCTTT--TTTTTTTGTTTTTTTGATT
1 TTTTGATTTGATTTGATT-TTTTTTTGATT
38603 TTTTGA-TTGA-TTGATTTTTT
1 TTTTGATTTGATTTGATTTTTT
38623 GATTTTTGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
26 5 0.13
27 14 0.37
28 19 0.50
ACGTcount: A:0.09, C:0.01, G:0.13, T:0.76
Consensus pattern (29 bp):
TTTTGATTTGATTTGATTTTTTTTTGATT
Found at i:38579 original size:18 final size:19
Alignment explanation
Indices: 38558--38606 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
38548 TTTGATTTGA
38558 TTTGATTTTTTTTTG-TTT
1 TTTGATTTTTTTTTGTTTT
*
38576 TTTGCTTTTTTTTTTGTTTT
1 TTTG-ATTTTTTTTTGTTTT
38596 TTTGATTTTTT
1 TTTGATTTTTT
38607 GATTGATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 16 0.59
20 7 0.26
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.84
Consensus pattern (19 bp):
TTTGATTTTTTTTTGTTTT
Found at i:38598 original size:20 final size:19
Alignment explanation
Indices: 38558--38635 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 19
38548 TTTGATTTGA
38558 TTTGA-TTTTTTTTTGTTT
1 TTTGATTTTTTTTTTGTTT
*
38576 TTTGCTTTTTTTTTTGTTTT
1 TTTGATTTTTTTTTTG-TTT
38596 TTTGATTTTTTGATTGATTGATTT
1 TTTGATTTTTT--TT--TTG-TTT
*
38620 TTTGATTTTTGTTTTG
1 TTTGATTTTTTTTTTG
38636 AATTTCTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
18 4 0.08
19 10 0.20
20 16 0.32
22 4 0.08
24 16 0.32
ACGTcount: A:0.08, C:0.01, G:0.14, T:0.77
Consensus pattern (19 bp):
TTTGATTTTTTTTTTGTTT
Found at i:38604 original size:16 final size:16
Alignment explanation
Indices: 38585--38629 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
38575 TTTTGCTTTT
38585 TTTTTTGTTTTTTTGA
1 TTTTTTGTTTTTTTGA
* **
38601 TTTTTTGATTGATTGA
1 TTTTTTGTTTTTTTGA
38617 TTTTTTGATTTTT
1 TTTTTTG-TTTTT
38630 GTTTTGAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (16 bp):
TTTTTTGTTTTTTTGA
Found at i:42519 original size:18 final size:18
Alignment explanation
Indices: 42496--42534 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42486 CTCTTGAGAT
42496 AATTCTTCAA-TAGTCTTC
1 AATTCTTCAATTA-TCTTC
42514 AATTCTTCAATTATCTTC
1 AATTCTTCAATTATCTTC
42532 AAT
1 AAT
42535 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (18 bp):
AATTCTTCAATTATCTTC
Found at i:42542 original size:11 final size:10
Alignment explanation
Indices: 42494--42545 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
42484 GCCTCTTGAG
42494 ATAATTCTTCA
1 ATAA-TCTTCA
*
42505 ATAGTCTTCA
1 ATAATCTTCA
42515 AT--TCTTCA
1 ATAATCTTCA
*
42523 ATTATCTTCA
1 ATAATCTTCA
42533 ATAAATCTTCA
1 AT-AATCTTCA
42544 AT
1 AT
42546 CACGAGATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 8 0.22
10 16 0.44
11 12 0.33
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (10 bp):
ATAATCTTCA
Found at i:42543 original size:21 final size:21
Alignment explanation
Indices: 42494--42545 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 21
42484 GCCTCTTGAG
42494 ATAATTCTTCAA-TAGTCTTCA
1 ATAA-TCTTCAATTAGTCTTCA
42515 AT--TCTTCAATTA-TCTTCA
1 ATAATCTTCAATTAGTCTTCA
42533 ATAAATCTTCAAT
1 AT-AATCTTCAAT
42546 CACGAGATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 15 0.56
19 2 0.07
21 10 0.37
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAATCTTCAATTAGTCTTCA
Found at i:49320 original size:40 final size:38
Alignment explanation
Indices: 49220--49813 Score: 417
Period size: 40 Copynumber: 14.7 Consensus size: 38
49210 GGGAATAGGA
* *
49220 ACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAATGATAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTG-G-AA--CTAG
* * *
49262 ACAACACCTTCCGGTGAGGAAGGGCACACTAGTGAACTCG
1 ACAACACCTTCCGATGAGGAAGGGCAAACT-G-GAACTAG
*
49302 ACAACACCTTCCGATGAGGAAGGGCAAACTAGGAAACTTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACT-GG-AACTAG
** * *
49342 ACAACACAATCCGATGAGGAAGGGC-AACTTGGGAAATGTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAAC-T-GG-AA-CTAG
*
49383 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAAACTCG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG--AACTAG
* * * *
49423 CCAACACCTTCTGATGAGGAAGGTCAAACTGGGAAATGTAG
1 ACAACACCTTCCGATGAGGAAGGGCAAACT-GG-AA-CTAG
* * *
49464 ACAACACCTTCCAATGAGGAAGGGCAGACTGGAAATTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-AA-CTAG
* * *
49504 ACAACACCTTCTGATGAGGAAGGGCAGACTGG-ATTA-
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAACTAG
** *
49540 ACAACACCTTCCGATGAGGAAGGGCAAACTAGGGATTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACT--GGAACTAG
* * * ** * *
49580 ACAACACCTTCCGGTGGGGATGGGCAAAACAAGAATTAAA
1 ACAACACCTTCCGATGAGGAAGGGC-AAACTGGAACT-AG
* * * ** *
49620 ACAACACCTTCCAATGGGGAAGCGCAATTTGGGTAAAGCAGACTTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACT--G----G-A-ACTAG
*
49666 AACAACACCTTCCGATGGGGAAGGGCAAACTGGAA-TACTG
1 -ACAACACCTTCCGATGAGGAAGGGCAAACTGGAACTA--G
*
49706 ACAACACCTTCCGATGAGGAAGGGGAAACTGGTAATGCT-G
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-AA--CTAG
* *
49746 ACAACACCTTCCGATG-GCAAAGGGCAAACTGGAACTGCTG
1 ACAACACCTTCCGATGAG-GAAGGGCAAACTGGAACT--AG
49786 ACAACACCTTCCGATGAGGAAGGGCAAA
1 ACAACACCTTCCGATGAGGAAGGGCAAA
49814 ATAGGAAGAG
Statistics
Matches: 455, Mismatches: 63, Indels: 70
0.77 0.11 0.12
Matches are distributed among these distances:
36 28 0.06
37 5 0.01
38 4 0.01
39 47 0.10
40 241 0.53
41 63 0.14
42 33 0.07
43 3 0.01
45 2 0.00
46 1 0.00
47 28 0.06
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (38 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGAACTAG
Found at i:49412 original size:81 final size:80
Alignment explanation
Indices: 49219--49813 Score: 447
Period size: 81 Copynumber: 7.4 Consensus size: 80
49209 AGGGAATAGG
* *
49219 AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAA-TGATAAACAACACCTTCCGGTGAGGAA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTG-GAAACT--TAGACAACACCTTCCGATGAGGAA
* *
49283 GGGCACACTAGTGAACTCG-
63 GGGCACACT-GGGAAAT-GT
**
49302 -ACAACACCTTCCGATGAGGAAGGGCAAACTAGGAAACTT-GACAACACAATCCGATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GGAAACTTAGACAACACCTTCCGATGAGGAAGG
49365 GCA-ACTTGGGAAATGT
65 GCACAC-TGGGAAATGT
* * *
49381 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGAAAAC-TCGCCAACACCTTCTGATGAGGAAG
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAACTTAGACAACACCTTCCGATGAGGAAG
* *
49445 GTCAAACTGGGAAATGT
64 GGCACACTGGGAAATGT
* * * *
49462 AGACAACACCTTCCAATGAGGAAGGGCAGACTGGAAATTTAGACAACACCTTCTGATGAGGAAGG
1 A-ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAACTTAGACAACACCTTCCGATGAGGAAGG
*
49527 GCAGACT-GG--AT-T
65 GCACACTGGGAAATGT
* * * * * *
49539 AACAACACCTTCCGATGAGGAAGGGCAAACTAGG-GATTTAAACAACACCTTCCGGTGGGGATGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GGAAACTTAGACAACACCTTCCGATGAGGAAGG
* ** * **
49603 GCAAAAC-AAGAATTAA
65 GC-ACACTGGGAAATGT
* * * **
49619 AACAACACCTTCCAATGGGGAAGCGCAATTTGGGTAAAGCAGACTT-GAACAACACCTTCCGATG
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GG---A--A-ACTTAG-ACAACACCTTCCGATG
* *
49683 GGGAAGGGCAAACT-GGAATACTG-
58 AGGAAGGGCACACTGGGAA-A-TGT
* * *
49706 -ACAACACCTTCCGATGAGGAAGGGGAAACTGGTAA-TGCT-GACAACACCTTCCGATG-GCAAA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAACT--TAGACAACACCTTCCGATGAG-GAA
* *
49767 GGGCAAACT-GGAACTGCT
63 GGGCACACTGGGAAATG-T
*
49785 GACAACACCTTCCGATGAGGAAGGGCAAA
1 AACAACACCTTCCGATGAGGAAGGGCAAA
49814 ATAGGAAGAG
Statistics
Matches: 424, Mismatches: 54, Indels: 71
0.77 0.10 0.13
Matches are distributed among these distances:
76 54 0.13
77 10 0.02
78 5 0.01
79 40 0.09
80 91 0.21
81 126 0.30
82 36 0.08
83 2 0.00
85 2 0.00
86 31 0.07
87 26 0.06
88 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (80 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAACTTAGACAACACCTTCCGATGAGGAAGGG
CACACTGGGAAATGT
Found at i:49428 original size:121 final size:120
Alignment explanation
Indices: 49220--49820 Score: 541
Period size: 121 Copynumber: 5.0 Consensus size: 120
49210 GGGAATAGGA
*
49220 ACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAATGATAAACAACACCTTCCGGTGAGGAAGG
1 ACAACACCTTCCGATGAGGAAGGGC-AACTG-GAAATG-TAAACAACACCTTCCGATGAGGAAGG
* * **
49285 GCACACTAGTGAACTCGACAACACCTTCCGATGAGGAAGGGCAAACTAGGAAACTT-G
63 GCAAACTGGAAAACTCGACAACACCTTCCGATGAGGAAGGGCAAACTAGGAAACTTAG
**
49342 ACAACACAATCCGATGAGGAAGGGCAACTTGGGAAATGTAAACAACACCTTCCGATGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAC-T-GGAAATGTAAACAACACCTTCCGATGAGGAAGGG
* * * *
49407 CAAACTGGAAAACTCGCCAACACCTTCTGATGAGGAAGGTCAAACTGGGAAA-TGTAG
64 CAAACTGGAAAACTCGACAACACCTTCCGATGAGGAAGGGCAAACTAGGAAACT-TAG
* * * *
49464 ACAACACCTTCCAATGAGGAAGGGCAGACTGGAAATTTAGACAACACCTTCTGATGAGGAAGGGC
1 ACAACACCTTCCGATGAGGAAGGGCA-ACTGGAAATGTAAACAACACCTTCCGATGAGGAAGGGC
* ** * * *
49529 AGACTGG---A-TTAACAACACCTTCCGATGAGGAAGGGCAAACTAGG-GATTTAA
65 AAACTGGAAAACTCGACAACACCTTCCGATGAGGAAGGGCAAACTAGGAAACTTAG
* * * ** * * *
49580 ACAACACCTTCCGGTGGGGATGGGCAAAACAAG-AAT-TAAAACAACACCTTCCAATGGGGAAGC
1 ACAACACCTTCCGATGAGGAAGGGC--AACTGGAAATGT-AAACAACACCTTCCGATGAGGAAGG
** * *
49643 GCAATTTGGGTAAAGCAGACTTGAACAACACCTTCCGATGGGGAAGGGCAAACT-GGAATAC-T-
63 GCAAACT-GG--AA--A-ACTCG-ACAACACCTTCCGATGAGGAAGGGCAAACTAGGAA-ACTTA
49705 G
120 G
* * * *
49706 ACAACACCTTCCGATGAGGAAGGGGAAACTGGTAATGCT-GACAACACCTTCCGATG-GCAAAGG
1 ACAACACCTTCCGATGAGGAA-GGGCAACTGGAAATG-TAAACAACACCTTCCGATGAG-GAAGG
*
49769 GCAAACTGG--AACTGCTGACAACACCTTCCGATGAGGAAGGGCAAAATAGGAA
63 GCAAACTGGAAAACT-C-GACAACACCTTCCGATGAGGAAGGGCAAACTAGGAA
49821 GAGTAGACAA
Statistics
Matches: 389, Mismatches: 60, Indels: 62
0.76 0.12 0.12
Matches are distributed among these distances:
115 1 0.00
116 51 0.13
117 36 0.09
118 5 0.01
119 29 0.07
120 6 0.02
121 112 0.29
122 55 0.14
123 3 0.01
125 8 0.02
126 48 0.12
127 33 0.08
128 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.16
Consensus pattern (120 bp):
ACAACACCTTCCGATGAGGAAGGGCAACTGGAAATGTAAACAACACCTTCCGATGAGGAAGGGCA
AACTGGAAAACTCGACAACACCTTCCGATGAGGAAGGGCAAACTAGGAAACTTAG
Found at i:50995 original size:19 final size:18
Alignment explanation
Indices: 50958--51001 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
50948 CATGCTAACT
50958 TTAATTTAAGAAAAAATC
1 TTAATTTAAGAAAAAATC
* *
50976 TTAACTTTAAGATAAGATC
1 TTAA-TTTAAGAAAAAATC
*
50995 TCAATTT
1 TTAATTT
51002 TCAAATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (18 bp):
TTAATTTAAGAAAAAATC
Found at i:61204 original size:52 final size:52
Alignment explanation
Indices: 61142--61241 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
61132 ATCTGATCAC
* *
61142 TCGAAAAAGATTAATAACGAATCGTTAAAATTGATACAAATACATGTGGCAA
1 TCGAAAAAGATTAATAACGAACCGTTAAAATGGATACAAATACATGTGGCAA
* * *
61194 TCGAACAAGATTAATGACGAACCGTTAAAATGGATACAAATACTTGTG
1 TCGAAAAAGATTAATAACGAACCGTTAAAATGGATACAAATACATGTG
61242 ACTCACTGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (52 bp):
TCGAAAAAGATTAATAACGAACCGTTAAAATGGATACAAATACATGTGGCAA
Found at i:63802 original size:2 final size:2
Alignment explanation
Indices: 63795--63827 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63785 CATACAAATG
63795 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63828 TAAAAATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68852 original size:78 final size:79
Alignment explanation
Indices: 68713--68872 Score: 270
Period size: 78 Copynumber: 2.0 Consensus size: 79
68703 TTTGGTCAGT
* *
68713 ATAACAATGTAGGGAGTTTTCTGATGCAGAGGATCCACTCGAGGGTGGCAACTGTAGAGCATATT
1 ATAACAATGTAGGGAGTTTTCTGATGCAGAGGATCCACTCGAGGGTGGCAACTGCAGAGCATATG
68778 ACTCCTGTTCATTGC
66 ACTCCTG-TCATTGC
*
68793 ATAACAATGTAGGGAG-TTTCTGATGTAGAGGATCCACT-GAGGGTGGCAACTGCAGAGCATATG
1 ATAACAATGTAGGGAGTTTTCTGATGCAGAGGATCCACTCGAGGGTGGCAACTGCAGAGCATATG
68856 ACTCCTGTCATTGC
66 ACTCCTGTCATTGC
68870 ATA
1 ATA
68873 CTAGGCGTAG
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
77 10 0.13
78 30 0.39
79 21 0.27
80 16 0.21
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (79 bp):
ATAACAATGTAGGGAGTTTTCTGATGCAGAGGATCCACTCGAGGGTGGCAACTGCAGAGCATATG
ACTCCTGTCATTGC
Found at i:69128 original size:13 final size:13
Alignment explanation
Indices: 69110--69142 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
69100 AGCCTTGGTC
69110 ATTATTACACACT
1 ATTATTACACACT
*
69123 ATTATTGCACACT
1 ATTATTACACACT
69136 ATTATTA
1 ATTATTA
69143 TATAGTGACT
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:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (13 bp):
ATTATTACACACT
Found at i:76392 original size:23 final size:23
Alignment explanation
Indices: 76362--76407 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
76352 TGGAGGAAGA
*
76362 TGGTTAGTGGTGACTGTTTTGAT
1 TGGTTAGTGGTGACAGTTTTGAT
76385 TGGTTAGTGGTGACAGTTTTGAT
1 TGGTTAGTGGTGACAGTTTTGAT
76408 GCAATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.04, G:0.35, T:0.46
Consensus pattern (23 bp):
TGGTTAGTGGTGACAGTTTTGAT
Found at i:76990 original size:48 final size:48
Alignment explanation
Indices: 76897--76996 Score: 109
Period size: 48 Copynumber: 2.1 Consensus size: 48
76887 TCATGGGCAA
* *
76897 ATATCCCTAATAAATAAATAAATTAATTAAGTTACATTTATTATAGTAG
1 ATATCCCTAATAAATAAATAAATTAATTAAG-TAAATTTATTATAGGAG
76946 ATAT-CCTAATAAATAAATAAA-TAACTTACA-TAAA-TTAGTATATAGGAG
1 ATATCCCTAATAAATAAATAAATTAA-TTA-AGTAAATTTA-T-TATAGGAG
76994 ATA
1 ATA
76997 ATAATTATAG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
46 3 0.07
47 7 0.16
48 30 0.67
49 5 0.11
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.35
Consensus pattern (48 bp):
ATATCCCTAATAAATAAATAAATTAATTAAGTAAATTTATTATAGGAG
Found at i:84032 original size:50 final size:50
Alignment explanation
Indices: 83959--84427 Score: 339
Period size: 50 Copynumber: 9.4 Consensus size: 50
83949 GCTTTAAGTC
** * * *
83959 TTGATTAATTTGTGATAAAAATGAAGCCTTTGAATTAAAGAGATTGAATTT
1 TTGATTAATTTGAAATAAAAATGAAGTCTTTGAACTAAA-AGATTGAACTT
* * * * * * * *
84010 TTGA-TAAATTGAAATAAAAATGAAATCTTTGAAATGAATGGTGGAATTT
1 TTGATTAATTTGAAATAAAAATGAAGTCTTTGAACTAAAAGATTGAACTT
* * * **
84059 TTAATTAATTTGTAAATAAAAGTGAAATCTTTGGGCTAAAAGATTGAACTT
1 TTGATTAATTTG-AAATAAAAATGAAGTCTTTGAACTAAAAGATTGAACTT
**
84110 TTGATTAATTTGTGATAAAAATGGAA-TCTTTGAACTAAAAGATTGAACTT
1 TTGATTAATTTGAAATAAAAAT-GAAGTCTTTGAACTAAAAGATTGAACTT
* *
84160 TTGATTAATTTGTAATAAAAATG-AGATCTTTGGACTAAAAGATTGAAC-T
1 TTGATTAATTTGAAATAAAAATGAAG-TCTTTGAACTAAAAGATTGAACTT
* * * ** * *
84209 TCGATGAATTTGGAAATAAAAATG-AGACCTTTGGGGCTAAAAGATTAAATTT
1 TTGATTAATTT-GAAATAAAAATGAAG-TCTTT-GAACTAAAAGATTGAACTT
* * * * *
84261 TTGGTTAGTTTGTAATAAAAATGAAATCTTTGAACTACAAGATTGAA--T
1 TTGATTAATTTGAAATAAAAATGAAGTCTTTGAACTAAAAGATTGAACTT
** * ** *
84309 TTGATTAACCTGTAAATAAAATTG-AGATCTTTGAGTTGAAAGATT-AACTT
1 TTGATTAATTTG-AAATAAAAATGAAG-TCTTTGAACTAAAAGATTGAACTT
** * * * *
84359 TTGACAAAATTGGAATAAAAATGAAGCCTTT-AAGCTGAAAGATTG-ACTT
1 TTGATTAATTTGAAATAAAAATGAAGTCTTTGAA-CTAAAAGATTGAACTT
* *
84408 TAGATAAATTTGAAATAAAA
1 TTGATTAATTTGAAATAAAA
84428 CCTTTAAGTG
Statistics
Matches: 331, Mismatches: 71, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
48 14 0.04
49 87 0.26
50 145 0.44
51 76 0.23
52 9 0.03
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (50 bp):
TTGATTAATTTGAAATAAAAATGAAGTCTTTGAACTAAAAGATTGAACTT
Found at i:84079 original size:101 final size:100
Alignment explanation
Indices: 83962--84427 Score: 327
Period size: 101 Copynumber: 4.7 Consensus size: 100
83952 TTAAGTCTTG
* * * *
83962 ATTAATTTGTGATAAAAATGAAGCCTTTGAATTAAAGAGATTGAATTTTTGA-TAAATTGAAATA
1 ATTAATTTGTAATAAAAATGAAACCTTTGAACTAAA-AGATTGAACTTTTGATTAAATTGAAATA
* * * *
84026 AAAATGAAATCTTTGAAATGAATGGTGGAATTTTTA
65 AAAATGAAATCTTTGAAATAAAAGATGGAACTTTTA
* * ** * **
84062 ATTAATTTGTAAATAAAAGTGAAATCTTTGGGCTAAAAGATTGAACTTTTGATTAATTTGTGATA
1 ATTAATTTGT-AATAAAAATGAAACCTTTGAACTAAAAGATTGAACTTTTGATTAAATTGAAATA
* * * *
84127 AAAATGGAATCTTTGAACTAAAAGATTGAACTTTTG
65 AAAATGAAATCTTTGAAATAAAAGATGGAACTTTTA
* * * * * *
84163 ATTAATTTGTAATAAAAATGAGATCTTTGGACTAAAAGATTGAAC-TTCGATGAATTTGGAAATA
1 ATTAATTTGTAATAAAAATGAAACCTTTGAACTAAAAGATTGAACTTTTGATTAAATT-GAAATA
* * *** ** * *
84227 AAAATGAGACCTTTGGGGCTAAAAGATTAAATTTTTG
65 AAAATGAAATCTTT-GAAATAAAAGATGGAACTTTTA
* * * * **
84264 GTTAGTTTGTAATAAAAATGAAATCTTTGAACTACAAGATTGAA--TTTGATTAACCTGTAAATA
1 ATTAATTTGTAATAAAAATGAAACCTTTGAACTAAAAGATTGAACTTTTGATTAAATTG-AAATA
* * ** * * *
84327 AAATTGAGATCTTTGAGTTGAAAGAT-TAACTTTTG
65 AAAATGAAATCTTTGAAATAAAAGATGGAACTTTTA
** * * * * *
84362 ACAAAATTGGAATAAAAATGAAGCCTTT-AAGCTGAAAGATTG-ACTTTAGA-TAAATTTGAAAT
1 ATTAATTTGTAATAAAAATGAAACCTTTGAA-CTAAAAGATTGAACTTTTGATTAAA-TTGAAAT
84424 AAAA
64 AAAA
84428 CCTTTAAGTG
Statistics
Matches: 295, Mismatches: 62, Indels: 20
0.78 0.16 0.05
Matches are distributed among these distances:
97 3 0.01
98 47 0.16
99 26 0.09
100 96 0.33
101 123 0.42
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (100 bp):
ATTAATTTGTAATAAAAATGAAACCTTTGAACTAAAAGATTGAACTTTTGATTAAATTGAAATAA
AAATGAAATCTTTGAAATAAAAGATGGAACTTTTA
Found at i:84177 original size:151 final size:150
Alignment explanation
Indices: 83959--84342 Score: 425
Period size: 151 Copynumber: 2.5 Consensus size: 150
83949 GCTTTAAGTC
* * *
83959 TTGATTAATTTGTGATAAAAAT-GAAGCCTTTGAATTAAAGAGATTGAATTTTTGA-TAAATTGA
1 TTGATTAATTTGTGATAAAAATGGAA-TCTTTGAACTAAA-AGATTGAA-TTTTGATTAAATTGT
* * * * * * * * * *
84022 AATAAAAATGAAATCTTTGAAATGAATGGTGGAATTTTTAATTAATTTGTAAATAAAAGTGAAAT
63 AATAAAAATGAGATCTTTGAAATAAAAGATGGAA-CTTCAATGAATTTGGAAATAAAAATGAAAC
*
84087 CTTT-GGGCTAAAAGATTGAACTT
127 CTTTGGGGCTAAAAGATTAAACTT
*
84110 TTGATTAATTTGTGATAAAAATGGAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAA
1 TTGATTAATTTGTGATAAAAATGGAATCTTTGAACTAAAAGATTGAA-TTTTGATTAAATTGTAA
* * * * *
84175 TAAAAATGAGATCTTTGGACTAAAAGATTGAACTTCGATGAATTTGGAAATAAAAATGAGACCTT
65 TAAAAATGAGATCTTTGAAATAAAAGATGGAACTTCAATGAATTTGGAAATAAAAATGAAACCTT
*
84240 TGGGGCTAAAAGATTAAATTT
130 TGGGGCTAAAAGATTAAACTT
* * * * * **
84261 TTGGTTAGTTTGTAATAAAAATGAAATCTTTGAACTACAAGATTGAA-TTTGATTAACCTGTAAA
1 TTGATTAATTTGTGATAAAAATGGAATCTTTGAACTAAAAGATTGAATTTTGATTAAATTGT-AA
*
84325 TAAAATTGAGATCTTTGA
65 TAAAAATGAGATCTTTGA
84343 GTTGAAAGAT
Statistics
Matches: 198, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
149 12 0.06
150 58 0.29
151 125 0.63
152 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (150 bp):
TTGATTAATTTGTGATAAAAATGGAATCTTTGAACTAAAAGATTGAATTTTGATTAAATTGTAAT
AAAAATGAGATCTTTGAAATAAAAGATGGAACTTCAATGAATTTGGAAATAAAAATGAAACCTTT
GGGGCTAAAAGATTAAACTT
Found at i:84980 original size:43 final size:43
Alignment explanation
Indices: 84919--85213 Score: 385
Period size: 43 Copynumber: 6.7 Consensus size: 43
84909 CTTTTATACT
84919 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCATTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCATTTCC
* *
84962 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCATTTCC
*
85005 AAAAATGCCCCTTCCTGGTTGGAAGATCCTTATTCTCATTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCATTTCC
*
85048 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCATTTCC
* * **
85091 AAAAATGCCCCTTCCCGGTCGGAAGGTCCCAATTTTCGATATCTC-TTTTG
1 AAAAATGCCCCTTCCTGGTTGGAAGGT-CC----TT--AT-TCTCATTTCC
* * *
85141 AAAAATGCCCATTCATGGTTGGAAGGTCCTTATTTTCATTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCATTTCC
** *
85184 AAAAATGCCCCTTCCCAGTCGGAAGGTCCT
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCCT
85214 AGTTTTCCTT
Statistics
Matches: 219, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
42 3 0.01
43 177 0.81
44 2 0.01
45 2 0.01
48 2 0.01
49 2 0.01
50 28 0.13
51 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (43 bp):
AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCATTTCC
Found at i:85326 original size:40 final size:40
Alignment explanation
Indices: 85228--85428 Score: 289
Period size: 40 Copynumber: 5.0 Consensus size: 40
85218 TTCCTTCGAT
*
85228 AATTCCCAGTTTGGCCTTCCTTC-TCGGAAGGTGTTGTTTA
1 AATTCCCAGTTTGCCCTTCC-TCATCGGAAGGTGTTGTTTA
85268 AATTTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
1 AA-TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* **
85309 AATTCCCAGTTTGCCCTTTCTCATCAAAAGGTGTTGTTTGA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTT-A
*
85350 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTGTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* *
85390 AATTCTCAGTTTGCCCTTCC-CGGTCGGAAGGTGTTGTTT
1 AATTCCCAGTTTGCCCTTCCTC-ATCGGAAGGTGTTGTTT
85429 TCAATGTTTT
Statistics
Matches: 146, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 73 0.50
41 72 0.49
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (40 bp):
AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
Found at i:85421 original size:81 final size:80
Alignment explanation
Indices: 85228--85428 Score: 280
Period size: 81 Copynumber: 2.5 Consensus size: 80
85218 TTCCTTCGAT
*
85228 AATTCCCAGTTTGGCCTTCCTTC-TCGGAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCTCA
1 AATTCCCAGTTTGCCCTTCC--CATCGGAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCTCA
*
85292 TCGGAAGGTGTTGTTTA
64 TCGGAAGGTGTTGTGTA
* **
85309 AATTCCCAGTTTGCCCTTTCTCATCAAAAGGTGTTGTTTGAAA-TTCCCAGTTTGCCCTTCCTCA
1 AATTCCCAGTTTGCCC-TTCCCATCGGAAGGTGTTGTTT-AAATTTCCCAGTTTGCCCTTCCTCA
85373 TCGGAAGGTGTTGTGTA
64 TCGGAAGGTGTTGTGTA
* *
85390 AATTCTCAGTTTGCCCTTCCCGGTCGGAAGGTGTTGTTT
1 AATTCCCAGTTTGCCCTTCCC-ATCGGAAGGTGTTGTTT
85429 TCAATGTTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
80 5 0.05
81 95 0.90
82 6 0.06
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (80 bp):
AATTCCCAGTTTGCCCTTCCCATCGGAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCTCATC
GGAAGGTGTTGTGTA
Found at i:85517 original size:48 final size:48
Alignment explanation
Indices: 85399--85759 Score: 384
Period size: 49 Copynumber: 7.6 Consensus size: 48
85389 AAATTCTCAG
* *
85399 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTTGTTCTTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATG-TTTTATTCCTGT
* * *
85448 TTTGCCCTTCCCGGTCAGAAGGTGTTGTTTTCAATGTGTTATTCCTAT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGT
**
85496 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGCATTATTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGT
* ** *
85544 TTTGCCCTTCCTGGTCAAAAGGTGTTGTTTTCAATGTTTTTGTTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATG-TTTTATTCCTGT
* ** *
85593 TTTCCCCTTCCC-CACTTGAAGGTGTTGTTTTCAATGTTTTCATTCCTGT
1 TTTGCCCTTCCCGGTC-GGAAGGTGTTGTTTTCAATGTTTT-ATTCCTGT
* * *
85642 TTTGCCTTTCCTGGTCGGAAGGTGTTGTTTTC--------ATTCCGGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGT
* *
85682 TTTTCCCTTCCCGGTCGGAAGGTGTTGTTTTTCAATGTTTTATCCCTAG-
1 TTTGCCCTTCCCGGTCGGAAGGTGTTG-TTTTCAATGTTTTATTCCT-GT
* *
85731 TTTGCCTTTCCTC-ATCGGAAGGTGTTGTT
1 TTTGCCCTTCC-CGGTCGGAAGGTGTTGTT
85760 CCTATTCTCT
Statistics
Matches: 260, Mismatches: 37, Indels: 31
0.79 0.11 0.09
Matches are distributed among these distances:
40 31 0.12
41 5 0.02
48 92 0.35
49 129 0.50
50 3 0.01
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (48 bp):
TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGT
Found at i:85580 original size:145 final size:146
Alignment explanation
Indices: 85399--85674 Score: 421
Period size: 145 Copynumber: 1.9 Consensus size: 146
85389 AAATTCTCAG
** * * **
85399 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTTGTTCTTGTTTTGCCCTT-CCCGGT
1 TTTGCCCTTCCCGGTCAAAAGGTGTTGTTTTCAATGTTTTTGTTCCTGTTTTCCCCTTCCCCACT
85463 CAGAAGGTGTTGTTTTCAATGTGTT-ATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTT
66 -AGAAGGTGTTGTTTTCAATGTGTTCATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTT
85527 CAATGCATTATTCCTGT
130 CAATGCATTATTCCTGT
*
85544 TTTGCCCTTCCTGGTCAAAAGGTGTTGTTTTCAATGTTTTTGTTCCTGTTTTCCCCTTCCCCACT
1 TTTGCCCTTCCCGGTCAAAAGGTGTTGTTTTCAATGTTTTTGTTCCTGTTTTCCCCTTCCCCACT
* * * * *
85609 TGAAGGTGTTGTTTTCAATGTTTTCATTCCTGTTTTGCCTTTCCTGGTCGGAAGGTGTTGTTTTC
66 AGAAGGTGTTGTTTTCAATGTGTTCATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
85674 A
131 A
85675 TTCCGGTTTT
Statistics
Matches: 117, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
145 75 0.64
146 42 0.36
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (146 bp):
TTTGCCCTTCCCGGTCAAAAGGTGTTGTTTTCAATGTTTTTGTTCCTGTTTTCCCCTTCCCCACT
AGAAGGTGTTGTTTTCAATGTGTTCATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
AATGCATTATTCCTGT
Found at i:85684 original size:40 final size:40
Alignment explanation
Indices: 85627--85712 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
85617 TTGTTTTCAA
* * *
85627 TGTTTTCATTCCTGTTTTGCCTTTCCTGGTCGGAAGGTGT
1 TGTTTTCATTCCGGTTTTGCCCTTCCCGGTCGGAAGGTGT
*
85667 TGTTTTCATTCCGGTTTTTCCCTTCCCGGTCGGAAGGTGT
1 TGTTTTCATTCCGGTTTTGCCCTTCCCGGTCGGAAGGTGT
85707 TGTTTT
1 TGTTTT
85713 TCAATGTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.07, C:0.21, G:0.24, T:0.48
Consensus pattern (40 bp):
TGTTTTCATTCCGGTTTTGCCCTTCCCGGTCGGAAGGTGT
Found at i:85690 original size:89 final size:89
Alignment explanation
Indices: 85586--85759 Score: 228
Period size: 89 Copynumber: 2.0 Consensus size: 89
85576 AATGTTTTTG
* * *
85586 TTCCTGTTTTCCCCTTCCCCACT-TGAAGGTGTTG-TTTTCAATGTTTTCATTCCT-GTTTTGCC
1 TTCCGGTTTTCCCCTT-CCCACTCGGAAGGTGTTGTTTTTCAATGTTTT-ATCCCTAG-TTTGCC
**
85648 TTTCCTGGTCGGAAGGTGTTGTTTTCA
63 TTTCCTCATCGGAAGGTGTTGTTTTCA
* **
85675 TTCCGGTTTTTCCCTTCCCGGTCGGAAGGTGTTGTTTTTCAATGTTTTATCCCTAGTTTGCCTTT
1 TTCCGGTTTTCCCCTTCCCACTCGGAAGGTGTTGTTTTTCAATGTTTTATCCCTAGTTTGCCTTT
85740 CCTCATCGGAAGGTGTTGTT
66 CCTCATCGGAAGGTGTTGTT
85760 CCTATTCTCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
88 4 0.05
89 56 0.76
90 14 0.19
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (89 bp):
TTCCGGTTTTCCCCTTCCCACTCGGAAGGTGTTGTTTTTCAATGTTTTATCCCTAGTTTGCCTTT
CCTCATCGGAAGGTGTTGTTTTCA
Found at i:86977 original size:41 final size:41
Alignment explanation
Indices: 86864--87074 Score: 126
Period size: 41 Copynumber: 5.2 Consensus size: 41
86854 TGTTTCCGTT
* * *
86864 TTCACTTTTGTCCCTGATTT-AGTATTTCATTTATTAATTGA
1 TTCAATTTCGTCCCTGATTTAAG-ATTTTATTTATTAATTGA
* * * ** *
86905 TTCAATTTTGTCCCTGATTTAGGGTAATATTTATTTATTGA
1 TTCAATTTCGTCCCTGATTTAAGATTTTATTTATTAATTGA
* *
86946 TTCAATTTCG-CCCTTGATTTAAGATTTTATTT-TTGATTTA
1 TTCAATTTCGTCCC-TGATTTAAGATTTTATTTATTAATTGA
* **** * * * * *
86986 TGCGGCATAGTCCCTGATTTTAGA-TTTATTTCTTGATTAAA
1 TTCAATTTCGTCCCTGATTTAAGATTTTATTTATTAATT-GA
* * * * *
87027 TGCAATTTAGTCCCTGATTTAAGA-TTTAGTTACTACTTGA
1 TTCAATTTCGTCCCTGATTTAAGATTTTATTTATTAATTGA
87067 TTCAATTT
1 TTCAATTT
87075 GATCCTTGAT
Statistics
Matches: 131, Mismatches: 34, Indels: 11
0.74 0.19 0.06
Matches are distributed among these distances:
39 7 0.05
40 36 0.27
41 87 0.66
42 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (41 bp):
TTCAATTTCGTCCCTGATTTAAGATTTTATTTATTAATTGA
Found at i:87055 original size:19 final size:19
Alignment explanation
Indices: 86993--87056 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
86983 TTATGCGGCA
*
86993 TAGTCCCTGATTTTAGATT
1 TAGTCCCTGATTTAAGATT
* * * *
87012 TATTTCTTGATTAAATGCAATT
1 TAGTCCCTGATTTAA-G--ATT
87034 TAGTCCCTGATTTAAGATT
1 TAGTCCCTGATTTAAGATT
87053 TAGT
1 TAGT
87057 TACTACTTGA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 17 0.52
20 1 0.03
21 1 0.03
22 14 0.42
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (19 bp):
TAGTCCCTGATTTAAGATT
Found at i:92668 original size:16 final size:17
Alignment explanation
Indices: 92641--92689 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 17
92631 ACATGTTTTC
92641 AAAAA-GATTTTTCAAA
1 AAAAATGATTTTTCAAA
92657 AAAAATGATTTTTC-AA
1 AAAAATGATTTTTCAAA
*
92673 AAAAATG-GTTTTCAAA
1 AAAAATGATTTTTCAAA
92689 A
1 A
92690 TTTGTTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 5 0.17
16 17 0.57
17 8 0.27
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (17 bp):
AAAAATGATTTTTCAAA
Found at i:94409 original size:36 final size:36
Alignment explanation
Indices: 94210--94772 Score: 523
Period size: 35 Copynumber: 15.6 Consensus size: 36
94200 ATTTCAGATG
* * *
94210 CTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTAT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTT-T
94247 -TT-AGTTTATTTCAGTTGATCCAGGGCGATC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * *
94280 CTTCAGTTAATTTCAGTTGACCCAGGGCGGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * * *
94315 CTTCAATTCATTTTAGTTGA-CCTAGGGTGGTC-CTT
1 CTTCAGTTTATTTCAGTTGATCC-AGGGCGATCTTTT
*
94350 ATTCAGTTTATTTCAGTTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAG-TTGATCCAGGGCGATCTTTT
* * *
94387 CTTCATTTTACTTCAGTTGATCCAAGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * *
94423 CCTCAGTTTACTTCAATTTGATCCAGGGCTATCTTTT
1 CTTCAGTTTATTTC-AGTTGATCCAGGGCGATCTTTT
* * * * * *
94460 CTTTAGTTTATTTCAATTAATCTAGGGTGATCTTTC
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* ** * *
94496 CTCCA-TTTCCTTCAATTGATCTAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
94531 CTTCAGTTTATTTCAGCTGACCCGGGGTGGTCTTTCTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATC-TT-TT
* **
94569 CAATTCATTTTAGCTGACCCAGTTGATCCAGGGCGATCTTTT
1 C--TTCAGTTTA--T--TTCAGTTGATCCAGGGCGATCTTTT
*
94611 CTTCAGTTTATTTCAGTTGATCTAGGGCGAT-TTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * *
94646 CTTCAGTATATTTCAGTTGACCCAGGGCG-GCCTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * *
94681 CTTCAATTTATTTTAGTGGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
94717 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
94753 CTGCAGTTTATTTCAGTTGA
1 CTTCAGTTTATTTCAGTTGA
94773 CCGCAAATTG
Statistics
Matches: 427, Mismatches: 81, Indels: 37
0.78 0.15 0.07
Matches are distributed among these distances:
33 1 0.00
34 6 0.01
35 178 0.42
36 153 0.36
37 49 0.11
38 4 0.01
40 16 0.04
42 4 0.01
43 2 0.00
44 14 0.03
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
Found at i:94667 original size:80 final size:79
Alignment explanation
Indices: 94511--94772 Score: 218
Period size: 80 Copynumber: 3.5 Consensus size: 79
94501 TTTCCTTCAA
* * * * * * * *
94511 TTGATCTAGGGCGATCTTTTCTTCAGTTTATTTCAGCTGACCCGGGGTGGTCTTTCTTCAATTCA
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAGTT-A
* *
94576 TTTTAGCTGACCCAG
65 TTTCAGTTGACCCAG
*
94591 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCTAGGGCGATTTTTCTTCAGTATA
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAGT-TA
94656 TTTCAGTTGACCCAG
65 TTTCAGTTGACCCAG
* * * *
94671 --G--GC--GGC---C-TTTCTTCAATTTATTTTAGTGGATCCAGGGCGATCTTTTCTTCAG---
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT-TTTTCTTCAGTTA
*
94723 TTT-A-TT---TCAG
65 TTTCAGTTGACCCAG
*
94733 TTGATCCAGGGCGATCTTTTCTGCAGTTTATTTCAGTTGA
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGA
94773 CCGCAAATTG
Statistics
Matches: 148, Mismatches: 22, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
62 3 0.02
64 1 0.01
65 2 0.01
66 2 0.01
67 3 0.02
68 3 0.02
70 30 0.20
71 12 0.08
72 19 0.13
74 3 0.02
76 1 0.01
78 1 0.01
80 67 0.45
81 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (79 bp):
TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAGTTAT
TTCAGTTGACCCAG
Found at i:94721 original size:71 final size:71
Alignment explanation
Indices: 94210--94772 Score: 485
Period size: 71 Copynumber: 7.8 Consensus size: 71
94200 ATTTCAGATG
* *
94210 CTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTAT-TT-AGTTTATTTCAGTTGATCCAGGGC
1 CTTCAGTTTATTTCAGTTGATCCAGGGC-GTCTTT-TCTTCAGTTTATTTCAGTTGATCCAGGGC
94273 GATC-TTT
64 GATCTTTT
* * * * * *
94280 CTTCAGTTAATTTCAGTTGACCCAGGGCGGTC-TTTCTTCAATTCATTTTAGTTGA-CCTAGGGT
1 CTTCAGTTTATTTCAGTTGATCCAGGGC-GTCTTTTCTTCAGTTTATTTCAGTTGATCC-AGGGC
* *
94343 GGTC-CTT
64 GATCTTTT
* * * *
94350 ATTCAGTTTATTTCAGTTTGATCCAGGGCGATCTTTTCTTCATTTTACTTCAGTTGATCCAAGGC
1 CTTCAGTTTATTTCAG-TTGATCCAGGGCG-TCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGC
94415 GATCTTTT
64 GATCTTTT
* * * * * * * * *
94423 CCTCAGTTTACTTCAATTTGATCCAGGGCTATCTTTTCTTTAGTTTATTTCAATTAATCTAGGGT
1 CTTCAGTTTATTTC-AGTTGATCCAGGGC-GTCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGC
*
94488 GATCTTTC
64 GATCTTTT
* ** * * * * * *
94496 CTCCA-TTTCCTTCAATTGATCTAGGGCGATCTTTTCTTCAGTTTATTTCAGCTGACCCGGGGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCG-TCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
*
94560 GTCTTTCTT
65 ATC-TT-TT
* ** *
94569 CAATTCATTTTAGCTGACCCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCT
1 C--TTCAGTTTA--T--TTCAGTTGATCCAGGGCG-TCTTTTCTTCAGTTTATTTCAGTTGATCC
94634 AGGGCGAT-TTTT
59 AGGGCGATCTTTT
* * * * * * *
94646 CTTCAGTATATTTCAGTTGACCCAGGGCGGCCTTTCTTCAATTTATTTTAGTGGATCCAGGGCGA
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGTCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA
94711 TCTTTT
66 TCTTTT
*
94717 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTGCAGTTTATTTCAGTTGA
1 CTTCAGTTTATTTCAGTTGATCCAGGGCG-TCTTTTCTTCAGTTTATTTCAGTTGA
94773 CCGCAAATTG
Statistics
Matches: 392, Mismatches: 79, Indels: 42
0.76 0.15 0.08
Matches are distributed among these distances:
68 1 0.00
69 6 0.02
70 99 0.25
71 101 0.26
72 54 0.14
73 66 0.17
74 1 0.00
75 10 0.03
76 3 0.01
77 3 0.01
78 2 0.01
80 46 0.12
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (71 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGTCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA
TCTTTT
Found at i:95067 original size:30 final size:30
Alignment explanation
Indices: 95031--95720 Score: 1058
Period size: 30 Copynumber: 22.9 Consensus size: 30
95021 ACTTTGTCAA
**
95031 TTTATTTCGATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
95061 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
95091 CTTATTTTAATCCTGGCTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
95121 CTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
95151 CTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* **
95181 CTTATTTTAATCCTGGTTTAGGATCGCTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
95211 TTTATTTTAATCCTGGTTTAGGGTCGTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* * *
95241 TTTGTTTTAATCCTGGTTTAGGGTCGTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
95271 TTTGTTTTAATCCTGGTTTAGGATCGTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* * *
95301 TTTGTTTTAATCCTGCTTTAAGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* * **
95331 CTTATTTTAATTCTGGTTTAGGATTTTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
95361 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
95391 TTTATGAGTTAATCCTGGTTTAGGATCGTTGC
1 TTTAT--TTTAATCCTGGTTTAGGATCATTGC
* *
95423 TTTATTTTAATCTTGATTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
95453 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
95483 TTTATTTTAATCCTGATTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
95513 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
95543 TTTATTTTAATCCTGGTTGT-GGATCATTGC
1 TTTATTTTAATCCTGGTT-TAGGATCATTGC
*
95573 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
95603 TTTATTTTAAACCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
95633 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
95663 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
95693 TTTATTTTAATCCTGGTTTAGGATCATT
1 TTTATTTTAATCCTGGTTTAGGATCATT
95721 ACTTCATCAG
Statistics
Matches: 612, Mismatches: 44, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
30 584 0.95
31 1 0.00
32 27 0.04
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTTAGGATCATTGC
Found at i:96476 original size:43 final size:45
Alignment explanation
Indices: 96393--96476 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 45
96383 ATATCCCTGA
* **
96393 TAAATAAATAAATAAATAAAGTTACATTTATTATAGTATATATCC
1 TAAATAAATAAATAAATAAACTTACATAAATTATAGTATATATCC
96438 TAAA-AAATAAATAAAT-AACTTACATAAA-T-TAGTATATAT
1 TAAATAAATAAATAAATAAACTTACATAAATTATAGTATATAT
96477 GAGATAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 10 0.28
42 1 0.03
43 9 0.25
44 12 0.33
45 4 0.11
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (45 bp):
TAAATAAATAAATAAATAAACTTACATAAATTATAGTATATATCC
Found at i:100945 original size:41 final size:41
Alignment explanation
Indices: 100855--100945 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
100845 CTGCTTTTGT
* * * *
100855 ATTTCATTTATTAATTGATTCAATTTTGTCCCTGATTTAGG
1 ATTTTATTTATTAATTGATTCAATTTCGCCCCTGATTTAAG
* ** *
100896 GTAATATTTATTTATTGATTCAATTTCGCCCCTGATTTAAG
1 ATTTTATTTATTAATTGATTCAATTTCGCCCCTGATTTAAG
100937 ATTTTATTT
1 ATTTTATTT
100946 TTGATTTATG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.25, C:0.12, G:0.11, T:0.52
Consensus pattern (41 bp):
ATTTTATTTATTAATTGATTCAATTTCGCCCCTGATTTAAG
Found at i:107148 original size:13 final size:13
Alignment explanation
Indices: 107130--107154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
107120 GAGAAGAAAG
107130 AAGTTGCTCTTAC
1 AAGTTGCTCTTAC
107143 AAGTTGCTCTTA
1 AAGTTGCTCTTA
107155 TTAGGCCTAT
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:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
AAGTTGCTCTTAC
Found at i:110957 original size:17 final size:16
Alignment explanation
Indices: 110911--110959 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
110901 CAATGGAGAT
*
110911 CATGGAGAGGATG-AG
1 CATGGAGAGCATGAAG
*
110926 CATGGAGTGCAATGAAG
1 CATGGAGAGC-ATGAAG
110943 CATGGAGAAGCATGAAG
1 CATGGAG-AGCATGAAG
110960 ATCAAGGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 8 0.29
16 3 0.11
17 15 0.54
18 2 0.07
ACGTcount: A:0.37, C:0.10, G:0.39, T:0.14
Consensus pattern (16 bp):
CATGGAGAGCATGAAG
Found at i:118843 original size:12 final size:12
Alignment explanation
Indices: 118826--118852 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
118816 AATGTAACAT
118826 GAATATGAGTTA
1 GAATATGAGTTA
118838 GAATATGAGTTA
1 GAATATGAGTTA
118850 GAA
1 GAA
118853 AAAAGAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (12 bp):
GAATATGAGTTA
Found at i:120026 original size:35 final size:35
Alignment explanation
Indices: 119575--120018 Score: 555
Period size: 35 Copynumber: 12.7 Consensus size: 35
119565 CGAGTAAAAT
* * *
119575 TGAAGAAAGACCACCTTGGTTCAACTAAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
119610 TGAAGAAAAACCACCCTGGGTCAACTGAAAAAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
119645 TGAAGCAAGACCACCCTGGGTCAACTGAAATAAAT
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
119680 TGAAGAAAGACCGCCCTAGGTCGACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
119715 TGAAGCAAGACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * **
119750 TAAAGAAAGAGCGCATTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
119785 TAAAGAAAGACCGCCCCGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
119820 TGAAGAAAGACCGCCCCGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
*
119855 TGAAGCAAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
119890 TGAAGCAAGACCACCCTGGGTCAACTGAAATAAAT
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
119925 TGAAGAAAGACCACCCTAGGTCGACTGAAATATAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * * * *
119960 TGAGGTAGGATCACCCTGGATCAATTGAAATTAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
119995 TGAAGATAGACCGCCCTGGGTCAA
1 TGAAGAAAGACCACCCTGGGTCAA
120019 TTAAAATTTT
Statistics
Matches: 356, Mismatches: 53, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 356 1.00
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.16
Consensus pattern (35 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
Found at i:121418 original size:15 final size:15
Alignment explanation
Indices: 121398--121436 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
121388 TTATTTCGTT
121398 CTTTTCATTTTTTCC
1 CTTTTCATTTTTTCC
* **
121413 CTTTTCTTTTTTTTT
1 CTTTTCATTTTTTCC
121428 CTTTTCATT
1 CTTTTCATT
121437 CACTTTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTCATTTTTTCC
Found at i:122589 original size:82 final size:82
Alignment explanation
Indices: 122452--122615 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
122442 GAGCCGCCGA
122452 CCCCTTTACTTCCCATCCTTAGATAAGTTTTTCTTCTTTTCTTTAGATGCTCACTCAATTCATGA
1 CCCCTTTACTTCCCATCCTTAGATAAGTTTTTCTTCTTTTCTTTAGATGCTCACTCAATTCATGA
122517 GTGAGTAATCCTTTTCT
66 GTGAGTAATCCTTTTCT
122534 CCCCTTTACTTCCCATCCTTAGATAAGTTTTTCTTCTTTTCTTTAGATGCTCACTCAATTCATGA
1 CCCCTTTACTTCCCATCCTTAGATAAGTTTTTCTTCTTTTCTTTAGATGCTCACTCAATTCATGA
122599 GTGAGTAATCCTTTTCT
66 GTGAGTAATCCTTTTCT
122616 TTTCTCCAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.20, C:0.26, G:0.10, T:0.45
Consensus pattern (82 bp):
CCCCTTTACTTCCCATCCTTAGATAAGTTTTTCTTCTTTTCTTTAGATGCTCACTCAATTCATGA
GTGAGTAATCCTTTTCT
Found at i:123210 original size:22 final size:22
Alignment explanation
Indices: 123168--123210 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
123158 CTTTTAATTA
**
123168 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
123190 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
123211 AATTATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:123594 original size:14 final size:12
Alignment explanation
Indices: 123570--123604 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
123560 GGAAAACCAT
123570 TTTTGAAAAATTA
1 TTTTGAAAAA-TA
123583 TTCTTGAAAAATA
1 TT-TTGAAAAATA
123596 TTTTGAAAA
1 TTTTGAAAA
123605 CATGTGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.33
13 6 0.29
14 8 0.38
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (12 bp):
TTTTGAAAAATA
Found at i:128897 original size:40 final size:41
Alignment explanation
Indices: 128851--128927 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
128841 GTAAATAAAA
* * * *
128851 TCCTAAAGCAGGGGCCATATTGCATCAAAAA-TAAATGGAT
1 TCCTAAAGCAGGGACCAAATCGAATCAAAAAGTAAATGGAT
*
128891 TCCTAAATCAGGGACCAAATCGAATCAAAAAGTAAAT
1 TCCTAAAGCAGGGACCAAATCGAATCAAAAAGTAAAT
128928 AAAAATTCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 26 0.84
41 5 0.16
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (41 bp):
TCCTAAAGCAGGGACCAAATCGAATCAAAAAGTAAATGGAT
Found at i:133875 original size:21 final size:22
Alignment explanation
Indices: 133842--133884 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
133832 GGATTTTAAA
*
133842 TAAAAATATTAATTAAGAAAAC
1 TAAAAATAGTAATTAAGAAAAC
*
133864 TAAAAA-AGTAATTTAGAAAAC
1 TAAAAATAGTAATTAAGAAAAC
133885 AATCAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (22 bp):
TAAAAATAGTAATTAAGAAAAC
Found at i:150312 original size:14 final size:15
Alignment explanation
Indices: 150286--150315 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
150276 CTAAGTCCAA
150286 TCCTTGCTTATTTAT
1 TCCTTGCTTATTTAT
150301 TCCTTG-TTATTTAT
1 TCCTTGCTTATTTAT
150315 T
1 T
150316 TTTCCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (15 bp):
TCCTTGCTTATTTAT
Found at i:150326 original size:17 final size:18
Alignment explanation
Indices: 150293--150326 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
150283 CAATCCTTGC
*
150293 TTATTTATTCCTTGTTAT
1 TTATTTATTCCTAGTTAT
150311 TTATTT-TTCCTAGTTA
1 TTATTTATTCCTAGTTA
150327 GACTTGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (18 bp):
TTATTTATTCCTAGTTAT
Found at i:151018 original size:16 final size:16
Alignment explanation
Indices: 150997--151027 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
150987 GGTTTAATCG
*
150997 AAAAATATAAAAAATA
1 AAAAATAAAAAAAATA
151013 AAAAATAAAAAAAAT
1 AAAAATAAAAAAAAT
151028 TTCGACCAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAAAAATA
Found at i:152605 original size:26 final size:27
Alignment explanation
Indices: 152573--152648 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
152563 ACTAGGGTCA
* *
152573 TCTAGGGGAATTTTGGTCATTTTATAT-
1 TCTAGGGGCATTTTGGTCATTTGA-ATG
152600 TC-AGGGGCATTTTAGG-CATTTGAATG
1 TCTAGGGGCATTTT-GGTCATTTGAATG
*
152626 TCTAGGGGCATTTTGGTCGTTTG
1 TCTAGGGGCATTTTGGTCATTTG
152649 CACACTCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.05
26 20 0.48
27 20 0.48
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (27 bp):
TCTAGGGGCATTTTGGTCATTTGAATG
Found at i:152638 original size:27 final size:27
Alignment explanation
Indices: 152573--152675 Score: 88
Period size: 27 Copynumber: 3.8 Consensus size: 27
152563 ACTAGGGTCA
* *
152573 TCTAGGGGAATTTTGGTCATTTTATAT
1 TCTAGGGGCATTTTGGTCATTTGATAT
152600 TC-AGGGGCATTTTAGG-CATTTGA-AT
1 TCTAGGGGCATTTT-GGTCATTTGATAT
* * *
152625 GTCTAGGGGCATTTTGGTCGTTTGCACAC
1 -TCTAGGGGCATTTTGGTCATTTG-ATAT
*
152654 TCAAGGGGC-TTTGTGGTCATTT
1 TCTAGGGGCATTT-TGGTCATTT
152676 TAAGTTCACA
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
25 2 0.03
26 20 0.32
27 23 0.37
28 17 0.27
29 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (27 bp):
TCTAGGGGCATTTTGGTCATTTGATAT
Found at i:160923 original size:21 final size:22
Alignment explanation
Indices: 160897--160938 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
160887 TTTGCCTCAT
160897 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
*
160918 GCATTCATTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
160939 TAAAGCCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:163451 original size:9 final size:9
Alignment explanation
Indices: 163437--163470 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
163427 AAAGTGAATA
163437 AAAAAAATC
1 AAAAAAATC
163446 AAAAAAATC
1 AAAAAAATC
163455 AAATCAAAATC
1 AAA--AAAATC
163466 AAAAA
1 AAAAA
163471 TCAAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:163460 original size:5 final size:5
Alignment explanation
Indices: 163441--163491 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
163431 TGAATAAAAA
*
163441 AAATC AAA-A AAATC AAATC AAAATC AAAAATC AAATC AAATC AAAATC
1 AAATC AAATC AAATC AAATC -AAATC --AAATC AAATC AAATC -AAATC
163489 AAA
1 AAA
163492 AGAGAATTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 3 0.08
5 21 0.52
6 10 0.25
7 6 0.15
ACGTcount: A:0.69, C:0.16, G:0.00, T:0.16
Consensus pattern (5 bp):
AAATC
Found at i:163463 original size:23 final size:23
Alignment explanation
Indices: 163437--163492 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 23
163427 AAAGTGAATA
163437 AAAAAAATCAAAAAAATCAAATC
1 AAAAAAATCAAAAAAATCAAATC
163460 ---AAAATC--AAAAATCAAATC
1 AAAAAAATCAAAAAAATCAAATC
163478 AAATCAAAATCAAAA
1 AAA--AAAATCAAAA
163493 GAGAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
18 12 0.46
20 6 0.23
23 6 0.23
25 2 0.08
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (23 bp):
AAAAAAATCAAAAAAATCAAATC
Found at i:163464 original size:6 final size:6
Alignment explanation
Indices: 163449--163492 Score: 58
Period size: 5 Copynumber: 7.7 Consensus size: 6
163439 AAAAATCAAA
163449 AAAATC -AAATC AAAATC AAAAATC -AAATC -AAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC -AAAATC AAAATC AAAATC AAAATC AAAA
163493 GAGAATTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 15 0.43
6 14 0.40
7 6 0.17
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:164175 original size:50 final size:50
Alignment explanation
Indices: 164100--164349 Score: 401
Period size: 50 Copynumber: 5.0 Consensus size: 50
164090 AGTTTTACAA
* *
164100 TAAAATTGCTTTCCATTTATGAGTTCAAAATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
164150 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
164200 TAAGATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
164250 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
** * *
164300 TAGGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
164350 GGCATTTAAG
Statistics
Matches: 184, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 184 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:164220 original size:100 final size:100
Alignment explanation
Indices: 164104--164349 Score: 447
Period size: 100 Copynumber: 2.5 Consensus size: 100
164094 TTACAATAAA
* *
164104 ATTGCTTTCCATTTATGAGTTCAAAATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTCCATTTG
1 ATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTCCATTTG
164169 TGAGTTCAAGATCAAAATTTGCTTTTCAAAGTAAG
66 TGAGTTCAAGATCAAAATTTGCTTTTCAAAGTAAG
164204 ATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTCCATTTG
1 ATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTCCATTTG
*
164269 TGAGTTCAAGATCAAAATTTGCTTTTCAAAGTAGG
66 TGAGTTCAAGATCAAAATTTGCTTTTCAAAGTAAG
* *
164304 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 ATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAG
164350 GGCATTTAAG
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 141 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (100 bp):
ATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTCCATTTG
TGAGTTCAAGATCAAAATTTGCTTTTCAAAGTAAG
Found at i:164919 original size:79 final size:80
Alignment explanation
Indices: 164802--164955 Score: 238
Period size: 79 Copynumber: 1.9 Consensus size: 80
164792 GTTATCAAAA
* * * *
164802 TTGACCGCAAATTGGTTCTTTTTCATCATCGATCAAGAAGTTTTCAGTTACAACATCAGACTCAG
1 TTGACCGCAAATTGGTCCTCTTTCATCATCAATCAAGAAGTTGTCAGTTACAACATCAGACTCAG
164867 AGTT-ATTTCTCAAG
66 AGTTAATTTCTCAAG
* * *
164881 TTGACTGCAAATTGGTCCTCTTTCATCATCAATTAAGAAGTTGTCAGTTACAACATCAGATTCAG
1 TTGACCGCAAATTGGTCCTCTTTCATCATCAATCAAGAAGTTGTCAGTTACAACATCAGACTCAG
164946 AGTTAATTTC
66 AGTTAATTTC
164956 CTAAGGTATT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
79 62 0.93
80 5 0.07
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (80 bp):
TTGACCGCAAATTGGTCCTCTTTCATCATCAATCAAGAAGTTGTCAGTTACAACATCAGACTCAG
AGTTAATTTCTCAAG
Found at i:165098 original size:50 final size:50
Alignment explanation
Indices: 165039--165426 Score: 570
Period size: 50 Copynumber: 7.8 Consensus size: 50
165029 CGAATGCTTT
* *
165039 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
165089 GGCTTTTCCAC-ACCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
** *
165138 GGCTTTTTTACAAGCCAAACTCGTTCCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
165188 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
165238 GGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGCCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
165288 GGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * *
165338 GGCTTTT-C-CATG--GAACTCGTTTCCATACGAGTCAACTATCCAAGCCACGTA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAT-CAA--CA--TA
* *
165389 GGCTTTTCCACAAACCGAACTCGTTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
165427 GTTCAAACAT
Statistics
Matches: 309, Mismatches: 19, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
46 24 0.08
47 3 0.01
48 3 0.01
49 48 0.16
50 197 0.64
51 9 0.03
52 1 0.00
53 2 0.01
55 22 0.07
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:165966 original size:27 final size:27
Alignment explanation
Indices: 165902--166005 Score: 88
Period size: 27 Copynumber: 3.8 Consensus size: 27
165892 ACAAGGGTCA
*
165902 TCTAGGGGCATTTTGGTCATTTTTATAT
1 TCTAGGGGCATTTTGGTCA-TTTGATAT
*
165930 TC-AGGGGCATTTTAGTCATTTGA-AT
1 TCTAGGGGCATTTTGGTCATTTGATAT
* * * *
165955 GTCTAGGTGCATTTTGGTCGTTTGCACAC
1 -TCTAGGGGCATTTTGGTCATTTG-ATAT
*
165984 TCAAGGGGC-TTTGTGGTCATTT
1 TCTAGGGGCATTT-TGGTCATTT
166006 TAAGTTCACA
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
25 2 0.03
26 6 0.10
27 35 0.56
28 18 0.29
29 1 0.02
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.42
Consensus pattern (27 bp):
TCTAGGGGCATTTTGGTCATTTGATAT
Found at i:176235 original size:19 final size:18
Alignment explanation
Indices: 176211--176246 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
176201 TGAAGACTTA
176211 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
176230 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
176247 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:176253 original size:30 final size:30
Alignment explanation
Indices: 176199--176258 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
176189 GAAGTTCGTG
* *
176199 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
176229 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
176259 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:182933 original size:169 final size:168
Alignment explanation
Indices: 182633--183046 Score: 702
Period size: 169 Copynumber: 2.5 Consensus size: 168
182623 CCAATAACCA
* * *
182633 AAAGACCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
* * * * * *
182698 AACACAGAGGCACCTATATTCAAGTCCCCAAACACATATATAACATAGGGGCACCTTTATTACAA
65 AACACAGAGGCACCTATATCCAAGTCCCCAAACACATATATAACACAAGGGCAACTCTACTACAA
182763 AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
130 AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
182802 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
182867 ACACAGAGGACATCTATATCCAAGTCCCCAAACACATATATAACACAAGGGCAACTCTACTACAA
66 ACACAGAGG-CACCTATATCCAAGTCCCCAAACACATATATAACACAAGGGCAACTCTACTACAA
*
182932 AGTCCTCAAACACATATATAACACAGAGGCATTTATATC
130 AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
*
182971 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
183036 ACACAGAGGCA
66 ACACAGAGGCA
183047 TTTCTCCTTA
Statistics
Matches: 232, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
168 33 0.14
169 199 0.86
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (168 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCACCTATATCCAAGTCCCCAAACACATATATAACACAAGGGCAACTCTACTACAAA
GTCCTCAAACACATATATAACACAGAGGCATCTATATC
Found at i:183047 original size:43 final size:43
Alignment explanation
Indices: 182641--183047 Score: 512
Period size: 43 Copynumber: 9.6 Consensus size: 43
182631 CAAAAGACCC
* *
182641 CAAACACATATATAACACAGGGGCAAT-TCTATTCCAAAAGTCCT
1 CAAACACATATATAACACAGAGGC-ATCTCTATTAC-AAAGTCCT
* * *
182685 CAAACACATATATAACACAGAGGCACCTATATT-C-AAGTCCC
1 CAAACACATATATAACACAGAGGCATCTCTATTACAAAGTCCT
* * * *
182726 CAAACACATATATAACATAGGGGCACCTTTATTACAAAGTCCT
1 CAAACACATATATAACACAGAGGCATCTCTATTACAAAGTCCT
* *
182769 CAAACACATATATAACACAGAGGCATCTATA-T-CAAAGTCCC
1 CAAACACATATATAACACAGAGGCATCTCTATTACAAAGTCCT
* *
182810 CAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCT
1 CAAACACATATATAACACAGAGGCATCTCTATTACAAAGTCCT
* * *
182853 CAAACACATATATAACACAGAGGACATCTATA-T-CCAAGTCCC
1 CAAACACATATATAACACAGAGG-CATCTCTATTACAAAGTCCT
* *
182895 CAAACACATATATAACACA-AGGGCAACTCTACTACAAAGTCCT
1 CAAACACATATATAACACAGA-GGCATCTCTATTACAAAGTCCT
*
182938 CAAACACATATATAACACAGAGGCAT-T-TA-TATCAAAGTCCC
1 CAAACACATATATAACACAGAGGCATCTCTATTA-CAAAGTCCT
*
182979 CAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCT
1 CAAACACATATATAACACAGAGGCATCTCTATTACAAAGTCCT
183022 CAAACACATATATAACACAGAGGCAT
1 CAAACACATATATAACACAGAGGCAT
183048 TTCTCCTTAT
Statistics
Matches: 318, Mismatches: 31, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.01
41 114 0.36
42 34 0.11
43 131 0.41
44 37 0.12
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.21
Consensus pattern (43 bp):
CAAACACATATATAACACAGAGGCATCTCTATTACAAAGTCCT
Found at i:183049 original size:84 final size:84
Alignment explanation
Indices: 182633--183047 Score: 688
Period size: 84 Copynumber: 4.9 Consensus size: 84
182623 CCAATAACCA
* * *
182633 AAAGACCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
*
182698 AACACAGAGGCACCTATATTC
65 AACACAGAGGCATCTATA-TC
* * *
182719 -AAGTCCCCAAACACATATATAACATAGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
182783 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
182802 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
182867 ACACAGAGGACATCTATATC
66 ACACAGAGG-CATCTATATC
* * *
182887 CAAGTCCCCAAACACATATATAACACAAGGGCAACTCTACTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
182952 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
*
182971 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
183036 ACACAGAGGCAT
66 ACACAGAGGCAT
183048 TTCTCCTTAT
Statistics
Matches: 309, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
83 2 0.01
84 190 0.61
85 117 0.38
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Done.