Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012777.1 Corchorus olitorius cultivar O-4 contig12810, 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: 71097
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2993 original size:16 final size:15
Alignment explanation
Indices: 2955--2996 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
2945 AAAGAGGTTG
2955 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
2970 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
2985 ACTAGAAAACAA
1 AC-AGAAAACAA
2997 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:6829 original size:18 final size:18
Alignment explanation
Indices: 6803--6841 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
6793 TCATCACGAA
6803 CAATCATATTTATCAAAG
1 CAATCATATTTATCAAAG
*
6821 CAATGATATTTATCAAAG
1 CAATCATATTTATCAAAG
6839 CAA
1 CAA
6842 GGCAATAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (18 bp):
CAATCATATTTATCAAAG
Found at i:11167 original size:16 final size:16
Alignment explanation
Indices: 11146--11176 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11136 AGGAATAAGC
11146 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
11162 AATCAATTAAAGCAA
1 AATCAATCAAAGCAA
11177 AACAATGCAA
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:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:17276 original size:33 final size:33
Alignment explanation
Indices: 17224--17298 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
17214 ACAAGCTGCA
* *
17224 TCTTGACAAGTTGCATCTAAATAATTTTATGCC
1 TCTTGACAAGTTACATCTAAATAATTTTACGCC
* *
17257 TCTTGACAATTTACCTCTAAATAATTTTACGCC
1 TCTTGACAAGTTACATCTAAATAATTTTACGCC
17290 TCTTGACAA
1 TCTTGACAA
17299 ATACCCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (33 bp):
TCTTGACAAGTTACATCTAAATAATTTTACGCC
Found at i:21989 original size:33 final size:33
Alignment explanation
Indices: 21947--22015 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
21937 CTTCAAGGAG
21947 ATAAACTTGGACTACCTATGAGGAAATGCAATT
1 ATAAACTTGGACTACCTATGAGGAAATGCAATT
21980 ATAAACTTGGACTACCTATGAGGAAATGCAATT
1 ATAAACTTGGACTACCTATGAGGAAATGCAATT
22013 ATA
1 ATA
22016 CCCTATATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (33 bp):
ATAAACTTGGACTACCTATGAGGAAATGCAATT
Found at i:24139 original size:48 final size:48
Alignment explanation
Indices: 24083--24181 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
24073 AATTGAAGCA
* *
24083 CAATGACAACTTCAAGCGTCAAACATATTATGTGACAATTTCTGGTGT
1 CAATGACAACTTCAAGCGTCAAACATACTATGTGACAACTTCTGGTGT
*
24131 CAATGACAACTTCAGGCGTCAAACATACTATGTGACAACTTCTGGTGT
1 CAATGACAACTTCAAGCGTCAAACATACTATGTGACAACTTCTGGTGT
24179 CAA
1 CAA
24182 AATAAAAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (48 bp):
CAATGACAACTTCAAGCGTCAAACATACTATGTGACAACTTCTGGTGT
Found at i:24270 original size:37 final size:37
Alignment explanation
Indices: 24211--24318 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
24201 ATCCCAACCT
* *
24211 CAGCATGACAACTTCTAGTGTCAAAGTTTAATTTCCC
1 CAGCGTGACAACTTCTAGTGTCAAAATTTAATTTCCC
* *
24248 CAGCGTGATAACTTCTAGTGTCAAAATTTAATTTCCT
1 CAGCGTGACAACTTCTAGTGTCAAAATTTAATTTCCC
* *
24285 CTGCGTGACAACTTCTAGTGTCAAAA-ATAATTTC
1 CAGCGTGACAACTTCTAGTGTCAAAATTTAATTTC
24319 TTAATGTGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 7 0.11
37 57 0.89
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (37 bp):
CAGCGTGACAACTTCTAGTGTCAAAATTTAATTTCCC
Found at i:24387 original size:35 final size:35
Alignment explanation
Indices: 24216--24379 Score: 154
Period size: 37 Copynumber: 4.6 Consensus size: 35
24206 AACCTCAGCA
** * *
24216 TGACAACTTCTAGTGTCAAAGTTTAATTTC-CCCAGCG
1 TGACAACTTCTAGTGTCAAA-AATAATTTCTCTC--TG
* *
24253 TGATAACTTCTAGTGTCAAAATTTAATTTC-CTCTGCG
1 TGACAACTTCTAGTGTCAAAA-ATAATTTCTCTCT--G
*
24290 TGACAACTTCTAGTGTCAAAAATAATTTCT-TAATG
1 TGACAACTTCTAGTGTCAAAAATAATTTCTCT-CTG
* *
24325 TGACAACATCTAATGTCAAAAATAATTTCTCTCTG
1 TGACAACTTCTAGTGTCAAAAATAATTTCTCTCTG
*
24360 TGACAGCTTCTAGTGTCAAA
1 TGACAACTTCTAGTGTCAAA
24380 TTAAATTTAC
Statistics
Matches: 108, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
35 48 0.44
36 9 0.08
37 51 0.47
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (35 bp):
TGACAACTTCTAGTGTCAAAAATAATTTCTCTCTG
Found at i:24387 original size:70 final size:72
Alignment explanation
Indices: 24216--24387 Score: 181
Period size: 70 Copynumber: 2.4 Consensus size: 72
24206 AACCTCAGCA
* * * * * *
24216 TGACAACTTCTAGTGTCAAAGTTTAATTTCCCCAGCGTGATAACTTCTAGTGTCAAAATTTAATT
1 TGACAACTTCTAGTGTCAAA-TTAAATTTCCCCAACGTGACAACATCTAATGTCAAAATATAATT
24281 TCCTCTGCG
65 TCCTCT-CG
* ** *
24290 TGACAACTTCTAGTGTCAAA-AATAATTT-CTTAATGTGACAACATCTAATGTCAAAA-ATAATT
1 TGACAACTTCTAGTGTCAAATTA-AATTTCCCCAACGTGACAACATCTAATGTCAAAATATAATT
24352 T-CTCTCTG
65 TCCTCTC-G
*
24360 TGACAGCTTCTAGTGTCAAATTAAATTT
1 TGACAACTTCTAGTGTCAAATTAAATTT
24388 ACTAGAACAA
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
69 1 0.01
70 29 0.35
71 7 0.08
72 21 0.25
73 5 0.06
74 20 0.24
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (72 bp):
TGACAACTTCTAGTGTCAAATTAAATTTCCCCAACGTGACAACATCTAATGTCAAAATATAATTT
CCTCTCG
Found at i:26533 original size:115 final size:114
Alignment explanation
Indices: 26269--26684 Score: 474
Period size: 115 Copynumber: 3.7 Consensus size: 114
26259 AAAATTGAAG
* * *
26269 ATAGCAGCGTTTCTTGGTCT-AAACGCCGCTAAATGGGGGCGTTTGA-GTTTAAAACACCGCCAT
1 ATAGCGGCGTTTC-T-GTCTAAAACGCCGCTAAATGGGGGCGTTTGAGGTGTAAAACGCCGCCAT
* * * *
26332 A-TTCA-TTTTTTTCCGGGAAATGCAAATT-GGTAGAAATGATACTAAAAT
64 ATTTAATTTTTTTTCCGGAAAATGCAAATTGGGTAAAAATAATACTAAAAT
* * * *
26380 ATAGCGGCGCTTTCAGGCTAAAACACCGCTAAATGGGGGCGTTTGAGGTGTAAAATGCCGCCATA
1 ATAGCGGCG-TTTCTGTCTAAAACGCCGCTAAATGGGGGCGTTTGAGGTGTAAAACGCCGCCATA
*
26445 TTTAATTTTTTTTCCAGAAAATGCAAATTGGGTAAAAATAAATACTAAAAT
65 TTTAATTTTTTTTCCGGAAAATGCAAATTGGGTAAAAAT-AATACTAAAAT
* * *
26496 ATAGCGGCGTTTCTTTCTAAAACGCCGCTAAATGGGGGCGTTT-AGG-GTAGACAATGCTGCCAT
1 ATAGCGGCGTTTCTGTCTAAAACGCCGCTAAATGGGGGCGTTTGAGGTGTA-A-AACGCCGCCAT
* *
26559 ATTTAATTTTTTTCCCCGGAAAATGCAAA-TGGGTAAAAATGAATACTAAGAT
64 ATTTAATTTTTTT-TCCGGAAAATGCAAATTGGGTAAAAAT-AATACTAAAAT
* * * * *
26611 -TAGCGGTGTTTCTGTCCAAAACGCCGCTAAATGGGGGAGTTTAAGGT-TGAAAACGCCTCCATA
1 ATAGCGGCGTTTCTGTCTAAAACGCCGCTAAATGGGGGCGTTTGAGGTGT-AAAACGCCGCCATA
*
26674 ATTAATTTTTT
65 TTTAATTTTTT
26685 CCCGCTAAAA
Statistics
Matches: 263, Mismatches: 29, Indels: 23
0.83 0.09 0.07
Matches are distributed among these distances:
110 3 0.01
111 33 0.13
112 19 0.07
113 6 0.02
114 82 0.31
115 87 0.33
116 33 0.13
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (114 bp):
ATAGCGGCGTTTCTGTCTAAAACGCCGCTAAATGGGGGCGTTTGAGGTGTAAAACGCCGCCATAT
TTAATTTTTTTTCCGGAAAATGCAAATTGGGTAAAAATAATACTAAAAT
Found at i:26653 original size:114 final size:112
Alignment explanation
Indices: 26269--26684 Score: 441
Period size: 114 Copynumber: 3.7 Consensus size: 112
26259 AAAATTGAAG
* ** ** *
26269 ATAGCAGCGTTTCTTGGTCT-AAACGCCGCTAAATGGGGGCGTTTGAGTTTA-AAACACCGCCAT
1 ATAGCGGCGTTTC-T-GTCTAAAACGCCGCTAAATGGGGGCGTTT-AGGGTAGAAATGCTGCCAT
* * * *
26332 A-TTCATTTTTTTCCGGGAAATGCAAATTGGTAGAAATG-ATACTAAAAT
63 ATTTAATTTTTTTCCGGAAAATGCAAATGGGTAAAAATGAATACTAAAAT
* * * *
26380 ATAGCGGCGCTTTCAGGCTAAAACACCGCTAAATGGGGGCGTTTGAGGTGTA-AAATGCCGCCAT
1 ATAGCGGCG-TTTCTGTCTAAAACGCCGCTAAATGGGGGCGTTT-AGG-GTAGAAATGCTGCCAT
* *
26444 ATTTAATTTTTTTTCCAGAAAATGCAAATTGGGTAAAAATAAATACTAAAAT
63 ATTTAA-TTTTTTTCCGGAAAATGCAAA-TGGGTAAAAATGAATACTAAAAT
*
26496 ATAGCGGCGTTTCTTTCTAAAACGCCGCTAAATGGGGGCGTTTAGGGTAGACAATGCTGCCATAT
1 ATAGCGGCGTTTCTGTCTAAAACGCCGCTAAATGGGGGCGTTTAGGGTAGA-AATGCTGCCATAT
*
26561 TTAATTTTTTTCCCCGGAAAATGCAAATGGGTAAAAATGAATACTAAGAT
65 TTAATTTTTTT--CCGGAAAATGCAAATGGGTAAAAATGAATACTAAAAT
* * * * * *
26611 -TAGCGGTGTTTCTGTCCAAAACGCCGCTAAATGGGGGAGTTTAAGGTTGAAAACGCCT-CCATA
1 ATAGCGGCGTTTCTGTCTAAAACGCCGCTAAATGGGGGCGTTTAGGGTAG-AAATG-CTGCCATA
*
26674 ATTAATTTTTT
64 TTTAATTTTTT
26685 CCCGCTAAAA
Statistics
Matches: 262, Mismatches: 30, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
110 3 0.01
111 34 0.13
112 17 0.06
113 6 0.02
114 91 0.35
115 79 0.30
116 32 0.12
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (112 bp):
ATAGCGGCGTTTCTGTCTAAAACGCCGCTAAATGGGGGCGTTTAGGGTAGAAATGCTGCCATATT
TAATTTTTTTCCGGAAAATGCAAATGGGTAAAAATGAATACTAAAAT
Found at i:28617 original size:33 final size:33
Alignment explanation
Indices: 28573--28639 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
28563 AAAAAAGCCA
*
28573 AAATAGCGGCGTTTCTTGTACGGAAACGCCGCT
1 AAATAGCGGCGTTTCTTGTACGAAAACGCCGCT
* *
28606 AAATAGTGGCGTTTCTTGTACGAAAACGCTGCT
1 AAATAGCGGCGTTTCTTGTACGAAAACGCCGCT
28639 A
1 A
28640 TTCCGGAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (33 bp):
AAATAGCGGCGTTTCTTGTACGAAAACGCCGCT
Found at i:30230 original size:10 final size:9
Alignment explanation
Indices: 30216--30279 Score: 69
Period size: 10 Copynumber: 6.9 Consensus size: 9
30206 GCTTTTTTAA
30216 ATATTTTTT
1 ATATTTTTT
*
30225 ATTATTTTCT
1 A-TATTTTTT
30235 A-ATTTTTT
1 ATATTTTTT
30243 ATATATTTTT
1 ATAT-TTTTT
30253 -TATATTTTT
1 ATAT-TTTTT
30262 ATATTTTTT
1 ATATTTTTT
30271 AATATTTTT
1 -ATATTTTT
30280 AAACCGGCTC
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
8 7 0.15
9 17 0.35
10 24 0.50
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
ATATTTTTT
Found at i:30240 original size:29 final size:28
Alignment explanation
Indices: 30208--30279 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 28
30198 CCTACGTGGC
30208 TTTTTTAAATATTTTTTATTATTTTCTA-A
1 TTTTTTAAATATTTTTTA-TATTTT-TATA
*
30237 TTTTTTATATATTTTTTATATTTTTATA
1 TTTTTTAAATATTTTTTATATTTTTATA
30265 TTTTTT-AATATTTTT
1 TTTTTTAAATATTTTT
30280 AAACCGGCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 10 0.25
28 13 0.32
29 17 0.43
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTTTTAAATATTTTTTATATTTTTATA
Found at i:30241 original size:18 final size:18
Alignment explanation
Indices: 30209--30280 Score: 76
Period size: 18 Copynumber: 3.8 Consensus size: 18
30199 CTACGTGGCT
30209 TTTTTAAATATTTTTTATTA
1 TTTTT-AATA-TTTTTATTA
30229 TTTTCTAAT-TTTTTATATA
1 TTTT-TAATATTTTTAT-TA
*
30248 TTTTTTATATTTTTA-TA
1 TTTTTAATATTTTTATTA
30265 TTTTTTAATATTTTTA
1 -TTTTTAATATTTTTA
30281 AACCGGCTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.04
18 24 0.52
19 12 0.26
20 7 0.15
21 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTAATATTTTTATTA
Found at i:30281 original size:9 final size:9
Alignment explanation
Indices: 30209--30281 Score: 69
Period size: 9 Copynumber: 7.8 Consensus size: 9
30199 CTACGTGGCT
30209 TTTTTAAATA
1 TTTTT-AATA
*
30219 TTTTTTATTA
1 -TTTTTAATA
30229 TTTTCTAAT-
1 TTTT-TAATA
30238 TTTTTATATA
1 TTTTTA-ATA
*
30248 TTTTTTATA
1 TTTTTAATA
30257 TTTTT-ATA
1 TTTTTAATA
30265 TTTTTTAATA
1 -TTTTTAATA
30275 TTTTTAA
1 TTTTTAA
30282 ACCGGCTCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
8 5 0.09
9 30 0.56
10 14 0.26
11 5 0.09
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTAATA
Found at i:30323 original size:31 final size:31
Alignment explanation
Indices: 30285--30346 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
30275 TTTTTAAACC
30285 GGCTCAAATAGATACTAAACGTTTCAAAATT
1 GGCTCAAATAGATACTAAACGTTTCAAAATT
*
30316 GGCTCAAATAGGTACTAAACGTTTCAAAATT
1 GGCTCAAATAGATACTAAACGTTTCAAAATT
30347 AGATCAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (31 bp):
GGCTCAAATAGATACTAAACGTTTCAAAATT
Found at i:30559 original size:39 final size:40
Alignment explanation
Indices: 30486--30565 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
30476 TTTTTAAGAC
* *
30486 AAATATGCTAAACTTGCATAATCTAAATATATCCTTGACA
1 AAATATGCTAAACTTGCATAATCTAAATAAATCCTTAACA
30526 AAATATGCTAAACTTGCATAAAT-TAAA-AAATCCTTAACA
1 AAATATGCTAAACTTGCAT-AATCTAAATAAATCCTTAACA
30565 A
1 A
30566 TAAAGCCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 11 0.30
40 23 0.62
41 3 0.08
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.30
Consensus pattern (40 bp):
AAATATGCTAAACTTGCATAATCTAAATAAATCCTTAACA
Found at i:33430 original size:17 final size:17
Alignment explanation
Indices: 33410--33455 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
33400 TATATCATAT
33410 TTTTCCACATATGATTG
1 TTTTCCACATATGATTG
33427 TTTTCCACATATGATTG
1 TTTTCCACATATGATTG
*
33444 CTTTCCACATAT
1 TTTTCCACATAT
33456 TATTATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.46
Consensus pattern (17 bp):
TTTTCCACATATGATTG
Found at i:34022 original size:27 final size:27
Alignment explanation
Indices: 33984--34038 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
33974 AAGGACTTCT
*
33984 CCTTCGACAATGCATCGATTAAGACAC
1 CCTTCAACAATGCATCGATTAAGACAC
34011 CCTTCAACAATGCATCGATTAAGACAC
1 CCTTCAACAATGCATCGATTAAGACAC
34038 C
1 C
34039 AATAAGGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.22
Consensus pattern (27 bp):
CCTTCAACAATGCATCGATTAAGACAC
Found at i:38141 original size:40 final size:38
Alignment explanation
Indices: 38089--39126 Score: 911
Period size: 39 Copynumber: 26.6 Consensus size: 38
38079 TTTACTAACT
* *
38089 CTTCCGGTGGGGAAGGGTAAACTGGGAATAAAACAACAA
1 CTTCCGGTGGGGAAGGGCAAAC-GGGAATAAAACAACAC
* * * *
38128 CTTCCGGTGGGGGATGGCAAAACGAGAATAAAACAATAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAATAAAACAACAC
* * ** *
38167 CTTCCGGTGAGGAAGGGTAAAATAGGAATAAAGCAACAC
1 CTTCCGGTGGGGAAGGG-CAAACGGGAATAAAACAACAC
* * *
38206 CTTTCGATGGGGAAGGGCAAAATGGGAATAAAACAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAATAAAACAACAC
** * * * *
38245 CTTCAAGTGGGGAAGGACAGACTGTGAATAAAACAATAC
1 CTTCCGGTGGGGAAGGGCAAAC-GGGAATAAAACAACAC
*
38284 CTTCCGGTGGGGAAGGGCAAAACGAGAAT-AAACAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAATAAAACAACAC
* * *
38322 CTTCCGGTGGGGAAGGGTAAAACGAGAAT-AAA-AACAT
1 CTTCCGGTGGGGAAGGG-CAAACGGGAATAAAACAACAC
* *
38359 CTTCCGGTGGGGAAAGGCAAAACAGGAATAAAAGCAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAATAAAA-CAACAC
* *
38399 CTTCCGGTGGGGAAGGGCAGACTGCGAATAAAACAACAC
1 CTTCCGGTGGGGAAGGGCAAAC-GGGAATAAAACAACAC
38438 CTTCCGGTGGGGAAGGGCAAAACGGGAATAAAAACAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAAT-AAAACAACAC
**
38478 CTTCTAGTGGGGAAGGGCAAAACGGGAATAAAAACAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAAT-AAAACAACAC
* *
38518 CTTCCAGTGGGGAAGGGCAAACTGGTAATAAAACAACAC
1 CTTCCGGTGGGGAAGGGCAAAC-GGGAATAAAACAACAC
* * *
38557 CTTCCGGTAGGGAAGGGTAAAAGGAGAAT-AAACAACAC
1 CTTCCGGTGGGGAAGGGCAAACGG-GAATAAAACAACAC
* ** * * *
38595 CTTTCGAAGGGAAAGAGCAAAACGGGAATAAAACAACAA
1 CTTCCGGTGGGGAAGGGC-AAACGGGAATAAAACAACAC
* * * * *
38634 CATCCGATGGGGAAGGGCAGCATGAGAATAAAACAACAC
1 CTTCCGGTGGGGAAGGGCA-AACGGGAATAAAACAACAC
* * * *
38673 CATCTGATGGGGAAGGGCAGAACGGGAATAAAACAATAC
1 CTTCCGGTGGGGAAGGGCA-AACGGGAATAAAACAACAC
* * * * *
38712 CTTCCGGCCGAGAAATGGCCAAACGTGAATAAAAACAACAC
1 CTTCCGG-TGGGGAA-GGGCAAACGGGAAT-AAAACAACAC
* * *
38753 TTTCCGGTGGGGAAGTGCAAAACGGGACTAAAAGCAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAATAAAA-CAACAC
* * ** *
38793 CTTCCGGTAGGGAAGGGCGGATTGGGAATAAAAAAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAATAAAACAACAC
* *
38832 CTTCCGGT-GGGAGAGGGCAATCTGGGAATAAGAACAAAAC
1 CTTCCGGTGGGGA-AGGGCAAAC-GGGAATAA-AACAACAC
* * * *
38872 CCTCTGGTAGGGAAGGGCAAAACGGGAATAAAAAAAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAAT-AAAACAACAC
* * * * *
38912 CTTCCGGTGGGGAATGACAAATTGGTAATAAAATAACAC
1 CTTCCGGTGGGGAAGGGCAAA-CGGGAATAAAACAACAC
* * **
38951 CTTCCGGTAGGAAATGGTAAAACGGGAAT-AAACAACAC
1 CTTCCGGTGGGGAA-GGGCAAACGGGAATAAAACAACAC
*
38989 CTTTCGGT-GGGAAGGGGCAAAACGGGAATAAAACAACAC
1 CTTCCGGTGGGGAA-GGGC-AAACGGGAATAAAACAACAC
* *
39028 CTTCTGGTGGGGAAGGGCAAAATGGGAATAAAACAACAC
1 CTTCCGGTGGGGAAGGGC-AAACGGGAATAAAACAACAC
* ** *
39067 CTTCCGGTGGGGAAGGGCAGACTAAGAATAAAACAACCC
1 CTTCCGGTGGGGAAGGGCAAAC-GGGAATAAAACAACAC
* * *
39106 CTTCCGATGGCGAAGAGCAAA
1 CTTCCGGTGGGGAAGGGCAAA
39127 ATACGGCTGG
Statistics
Matches: 814, Mismatches: 150, Indels: 70
0.79 0.15 0.07
Matches are distributed among these distances:
37 34 0.04
38 103 0.13
39 429 0.53
40 220 0.27
41 28 0.03
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (38 bp):
CTTCCGGTGGGGAAGGGCAAACGGGAATAAAACAACAC
Found at i:38862 original size:394 final size:388
Alignment explanation
Indices: 38095--39111 Score: 1221
Period size: 394 Copynumber: 2.6 Consensus size: 388
38085 AACTCTTCCG
* * *
38095 GTGGGGAAGGG-TAAACTGGGAAT-AAAACAACAACTTCCGGTGGGGGATGGCAAAAC-GAG-AA
1 GTGGGGAAGGGCAAAAC-GGGAATAAAAACAACACCTTCCGGTGGGGAATGGC-AAACTG-GTAA
* * *
38156 TAAAACAATACCTTCCGGT-GAGGAAGGGTAAAA-TAGGAATAAAGCAACACCTTTCGATGGGGA
63 TAAAACAACACCTTCCGGTAG-GGAAGGGTAAAAGGA-GAATAAA-CAACACCTTTCGATGGGAA
* * * * * * *
38219 AGGGCAAAATGGGAATAAAACAAC-ACCTTCAAGTGGGGAAGGACAGACTGTGAATAAAACAATA
125 AGGGCAAAACGGGAATAAAACAACAACATCCGA-TGGGGAAGGGCAGA-TGAGAATAAAACAACA
* * * * *
38283 CCTTCCGGTGGGGAAGGGCAAAACGAGAATAAACAACACCTTCCGGTGGGGAAGGGTAAAACGAG
188 CCTTCCGGTGGGGAAGGGCAGAACGAGAATAAACAACACCTTCCGGCGAGAAAGGGCAAAACGAG
* *
38348 AATAAAAACATCTTCCGGTGGGGAAAGGCAAAACAGGAATAAAAGCAACACCTTCCGGTGGGGAA
253 AATAAAAACAACTTCCGGTGGGGAAAGGCAAAACAGGAATAAAAGCAACACCTTCCGGTAGGGAA
* *
38413 GGGCAGACTGCGAATAAAACAACACCTTCCGGTGGGGAAGGGCAAAACGGGAATAAAAACAACAC
318 GGGCAGACTGCGAATAAAAAAACACCTTCCGGTGGGGAAGGGCAAAACGGGAATAAAAACAAAAC
*
38478 CTTCTA
383 CCTCTA
* *
38484 GTGGGGAAGGGCAAAACGGGAATAAAAACAACACCTTCCAGTGGGGAAGGGCAAACTGGTAATAA
1 GTGGGGAAGGGCAAAACGGGAATAAAAACAACACCTTCCGGTGGGGAATGGCAAACTGGTAATAA
* *
38549 AACAACACCTTCCGGTAGGGAAGGGTAAAAGGAGAATAAACAACACCTTTCGAAGGGAAAGAGCA
66 AACAACACCTTCCGGTAGGGAAGGGTAAAAGGAGAATAAACAACACCTTTCGATGGGAAAGGGCA
* *
38614 AAACGGGAATAAAACAACAACATCCGATGGGGAAGGGCAGCATGAGAATAAAACAACACCATCTG
131 AAACGGGAATAAAACAACAACATCCGATGGGGAAGGGCAG-ATGAGAATAAAACAACACCTTCCG
* * * * * *
38679 ATGGGGAAGGGCAGAACGGGAATAAAACAATACCTTCCGGCCGAGAAATGGCCAAACGTGAATAA
195 GTGGGGAAGGGCAGAACGAGAAT-AAACAACACCTTCCGG-CGAGAAAGGGCAAAACGAGAATAA
* *
38744 AAACAACACTTTCCGGTGGGG-AAGTGCAAAACGGGACTAAAAGCAACACCTTCCGGTAGGGAAG
258 AAAC-A-AC-TTCCGGTGGGGAAAG-GCAAAACAGGAATAAAAGCAACACCTTCCGGTAGGGAAG
* * * * *
38808 GGCGGATTGGGAATAAAAAAACACCTTCCGGT-GGGAGAGGGC-AATCTGGGAATAAGAACAAAA
319 GGCAGACTGCGAATAAAAAAACACCTTCCGGTGGGGA-AGGGCAAAAC-GGGAATAAAAACAAAA
*
38871 CCCTCTG
382 CCCTCTA
* * * *
38878 GTAGGGAAGGGCAAAACGGGAATAAAAAAAACACCTTCCGGTGGGGAATGACAAATTGGTAATAA
1 GTGGGGAAGGGCAAAACGGGAATAAAAACAACACCTTCCGGTGGGGAATGGCAAACTGGTAATAA
* * * * *
38943 AATAACACCTTCCGGTAGGAAATGGTAAAACGG-GAATAAACAACACCTTTCGGTGGGAAGGGGC
66 AACAACACCTTCCGGTAGGGAAGGGTAAAA-GGAGAATAAACAACACCTTTCGATGGGAAAGGGC
* * * * * *
39007 AAAACGGGAATAAAACAACACCTTCTGGTGGGGAAGGGCAAAATGGGAATAAAACAACACCTTCC
130 AAAACGGGAATAAAACAACAACATCCGATGGGGAAGGGC-AGATGAGAATAAAACAACACCTTCC
* *
39072 GGTGGGGAAGGGCAG-ACTAAGAATAAAACAACCCCTTCCG
194 GGTGGGGAAGGGCAGAAC-GAGAAT-AAACAACACCTTCCG
39112 ATGGCGAAGA
Statistics
Matches: 540, Mismatches: 69, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
389 112 0.21
390 89 0.16
391 23 0.04
392 1 0.00
393 13 0.02
394 299 0.55
395 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (388 bp):
GTGGGGAAGGGCAAAACGGGAATAAAAACAACACCTTCCGGTGGGGAATGGCAAACTGGTAATAA
AACAACACCTTCCGGTAGGGAAGGGTAAAAGGAGAATAAACAACACCTTTCGATGGGAAAGGGCA
AAACGGGAATAAAACAACAACATCCGATGGGGAAGGGCAGATGAGAATAAAACAACACCTTCCGG
TGGGGAAGGGCAGAACGAGAATAAACAACACCTTCCGGCGAGAAAGGGCAAAACGAGAATAAAAA
CAACTTCCGGTGGGGAAAGGCAAAACAGGAATAAAAGCAACACCTTCCGGTAGGGAAGGGCAGAC
TGCGAATAAAAAAACACCTTCCGGTGGGGAAGGGCAAAACGGGAATAAAAACAAAACCCTCTA
Found at i:39663 original size:50 final size:49
Alignment explanation
Indices: 39588--40427 Score: 690
Period size: 50 Copynumber: 16.9 Consensus size: 49
39578 AGAACCACAC
* *
39588 TTTTATTTCAAATTAATCAAAAGTTTGATCTTTTACTATAAAGATTTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTTACT-TAAAGATTTCAT
* * * * *
39638 TTTTATTACAAGTTAGTGAAAAGTTTAACCTTTAACTTTAAAGATTTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTTAC-TTAAAGATTTCAT
*
39688 TTTTA-T-C------A-C-AAA-TTTCATCTTTTAGCTTAAAGATTT-AGT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTTA-CTTAAAGATTTCA-T
* * * *
39727 CTTTATCACAAATTAATCAAAAATTTTATCTTTTAGCTTAAAGATTTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTTA-CTTAAAGATTTCAT
** *
39777 TTTTATTTACAAATTAATTGAAAGTTTCATCTTTTAACTTAAAGA-TTCTAT
1 TTTTA-TTACAAATTAATCAAAAGTTTAATCTTTT-ACTTAAAGATTTC-AT
* *
39828 TTTTATTTACAAATGAATTAAAAGTTTAATCTTTTAGCTTAAAGATTTCTAT
1 TTTTA-TTACAAATTAATCAAAAGTTTAATCTTTTA-CTTAAAGATTTC-AT
* * * * * *
39880 TTTTATTTTACAAATTAATTAAAAGTTCAATCTTTTAGTCCAGAGATCTCAT
1 TTTTA--TTACAAATTAATCAAAAGTTTAATCTTTTACT-TAAAGATTTCAT
* ** * *
39932 TTTTATTACAAATTAATCAAGAGTTCCATCATTTAATTCAAAGATTTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTTACTT-AAAGATTTCAT
* ** ** * *
39982 TTTTATTACAAATTAATCTAGTGTTCCATCATTTAGTTCAAAGATTTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTTACTT-AAAGATTTCAT
* * * * *
40032 TTTTATCA-AAAGTCAATCAAAATTTTCATCTTTTGGCTTAAAGATTTCATT
1 TTTTATTACAAA-TTAATCAAAAGTTTAATCTTTT-ACTTAAAGATTTCA-T
* ** * * * *
40083 TTTTATCATGAATCAATCAAAAATTTCATCTTGTAGCTTAAAGATTTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTTA-CTTAAAGATTTCAT
* * *
40133 TTTTATCATAAATTAATCAAAA-TTTAATCTTTTAACTTCAAAGATGTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTT-ACTT-AAAGATTTCAT
* *
40183 TTTTA-T-CATAATTCAATCAAAAATTTCATCTTTTAGCTTAAAGATTTCA-
1 TTTTATTACA-AATT-AATCAAAAGTTTAATCTTTTA-CTTAAAGATTTCAT
* * *
40232 TTTTATTACAAATTAATCAAAAATTCAAACTTTTTACTTAAAGATTTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATC-TTTTACTTAAAGATTTCAT
* * * * *
40282 CTTTATTACAAATTAATCAAAAATTCAAACTTTTTACTTAAACATTTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAATC-TTTTACTTAAAGATTTCAT
* * *
40332 TTTTATTACAAATTAATCAAAAATTTAATCCTTTTACTTTAAAGGTCTCAT
1 TTTTATTACAAATTAATCAAAAGTTTAAT-CTTTTAC-TTAAAGATTTCAT
* * *
40383 CTTTATTACAAATTAATCAAAAATTTAACCTTTTAGCTTAAAGAT
1 TTTTATTACAAATTAATCAAAAGTTTAATCTTTTA-CTTAAAGAT
40428 CACAAATTAA
Statistics
Matches: 671, Mismatches: 78, Indels: 82
0.81 0.09 0.10
Matches are distributed among these distances:
38 1 0.00
39 24 0.04
40 4 0.01
41 1 0.00
47 1 0.00
48 3 0.00
49 54 0.08
50 351 0.52
51 174 0.26
52 22 0.03
53 36 0.05
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.45
Consensus pattern (49 bp):
TTTTATTACAAATTAATCAAAAGTTTAATCTTTTACTTAAAGATTTCAT
Found at i:40130 original size:151 final size:149
Alignment explanation
Indices: 39728--40427 Score: 509
Period size: 151 Copynumber: 4.6 Consensus size: 149
39718 AGATTTAGTC
* * *
39728 TTTATCACAAA-TTAATCAAAAATTTTATCTTTTAGCTTAAAGATTTCATTTTTATTTACAAATT
1 TTTATCA-AAAGTCAATCAAAAATTTCATCTTTTAGCTTAAAGATTTCA-TTTTA-TTACAAATC
* ** * * *
39792 AATTGAAAGTTTC-ATCTTT-TAACTTAAAGA-TTCTATTTTTATTTACAAATGAATTAAAAGTT
63 AA-TCAAAAATTCAAACTTTGT-ACTTAAAGATTTC-ATTTTTA-TTACAAATTAATCAAAA-TT
* * *
39854 TAATCTTTTAGCTT-AAAGATTTCTATT
123 TAATCATTTAACTTCAAAGATGTC-ATT
* * * * * * *
39881 TTTATTTTACAAA-TTAAT-TAAAAGTTCAATCTTTTAG-TCCAGAGATCTCATTTTTATTACAA
1 TTTA--TCA-AAAGTCAATCAAAAATTTC-ATCTTTTAGCT-TAAAGATTTCA-TTTTATTACAA
* * * * * * * * *
39943 ATTAATCAAGAGTTCCATCATT-TAATTCAAAGATTTCATTTTTATTACAAATTAATC-TAGTGT
60 ATCAATCAAAAATTCAAACTTTGTACTT-AAAGATTTCATTTTTATTACAAATTAATCAAAAT-T
* * *
40006 TCCATCATTT-AGTTCAAAGATTTCATT
123 T-AATCATTTAACTTCAAAGATGTCATT
* *
40033 TTTATCAAAAGTCAATCAAAATTTTCATCTTTTGGCTTAAAGATTTCATTTT-TTATCATGAATC
1 TTTATCAAAAGTCAATCAAAAATTTCATCTTTTAGCTTAAAGATTTCATTTTATTA-CA--AATC
* * *
40097 AATCAAAAATTTC-ATC-TTGTAGCTTAAAGATTTCATTTTTATCATAAATTAATCAAAATTTAA
63 AATCAAAAA-TTCAAACTTTGTA-CTTAAAGATTTCATTTTTATTACAAATTAATCAAAATTTAA
*
40160 TCTTTTAACTTCAAAGATGTCATT
126 TCATTTAACTTCAAAGATGTCATT
* * *
40184 TTTATCATAATTCAATCAAAAATTTCATCTTTTAGCTTAAAGATTTCATTTTATTACAAATTAAT
1 TTTATCAAAAGTCAATCAAAAATTTCATCTTTTAGCTTAAAGATTTCATTTTATTACAAATCAAT
* * * * *
40249 CAAAAATTCAAACTTTTTACTTAAAGATTTCATCTTTATTACAAATTAATCAAAAATTCAAACTT
66 CAAAAATTCAAACTTTGTACTTAAAGATTTCATTTTTATTACAAATTAATC-AAAATTTAATCAT
* * *
40314 TTTACTT-AAACATTTCATT
130 TTAACTTCAAAGATGTCATT
* * * * *
40333 TTTATTACAAA-TTAATCAAAAATTTAATCCTTTTA-CTTTAAAGGTCTCATCTTTATTACAAAT
1 TTTATCA-AAAGTCAATCAAAAATTTCAT-CTTTTAGC-TTAAAGATTTCAT-TTTATTACAAAT
* * *
40396 TAATCAAAAATTTAACCTTT-TAGCTTAAAGAT
62 CAATCAAAAATTCAAACTTTGTA-CTTAAAGAT
40428 CACAAATTAA
Statistics
Matches: 452, Mismatches: 65, Indels: 62
0.78 0.11 0.11
Matches are distributed among these distances:
148 6 0.01
149 84 0.19
150 72 0.16
151 156 0.35
152 22 0.05
153 39 0.09
154 36 0.08
155 37 0.08
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.44
Consensus pattern (149 bp):
TTTATCAAAAGTCAATCAAAAATTTCATCTTTTAGCTTAAAGATTTCATTTTATTACAAATCAAT
CAAAAATTCAAACTTTGTACTTAAAGATTTCATTTTTATTACAAATTAATCAAAATTTAATCATT
TAACTTCAAAGATGTCATT
Found at i:40433 original size:39 final size:40
Alignment explanation
Indices: 40390--40466 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
40380 CATCTTTATT
* *
40390 ACAAATTAATCAAAAATTTAACCTTTTAGCTT-AAAGATC
1 ACAAATTAATCAAAAATTCAAACTTTTAGCTTCAAAGATC
40429 ACAAATTAATCAAAAATTCAAACTTTTAGCTTCAAAGA
1 ACAAATTAATCAAAAATTCAAACTTTTAGCTTCAAAGA
40467 CTTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 30 0.86
40 5 0.14
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (40 bp):
ACAAATTAATCAAAAATTCAAACTTTTAGCTTCAAAGATC
Found at i:46725 original size:19 final size:19
Alignment explanation
Indices: 46703--46754 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
46693 GGGCTGAAAT
46703 TAATTAATTATTAAATAAA
1 TAATTAATTATTAAATAAA
* * *
46722 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAAATAAA
46741 TAATT-ATTATTAAA
1 TAATTAATTATTAAA
46755 AATACCACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATTAATTATTAAATAAA
Found at i:50937 original size:33 final size:33
Alignment explanation
Indices: 50900--50974 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
50890 ACAAGCTGGA
*
50900 TCTTGACATGTTGCATCTAAATAATTATA-TGCC
1 TCTTGACAAGTTGCATCTAAATAATTATACT-CC
* *
50933 TCTTGACAAGTTGCCTCTAAATAATTTTACTCC
1 TCTTGACAAGTTGCATCTAAATAATTATACTCC
50966 TCTTGACAA
1 TCTTGACAA
50975 ATTCCCTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 37 0.97
34 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (33 bp):
TCTTGACAAGTTGCATCTAAATAATTATACTCC
Found at i:51843 original size:16 final size:16
Alignment explanation
Indices: 51822--51856 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
51812 AGAATTTAGA
*
51822 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCCCTG
51838 AAGCAGAAAAGCCCTG
1 AAGCAGAAAAGCCCTG
51854 AAG
1 AAG
51857 AATCAAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.26, T:0.09
Consensus pattern (16 bp):
AAGCAGAAAAGCCCTG
Found at i:56782 original size:67 final size:67
Alignment explanation
Indices: 56624--56993 Score: 276
Period size: 67 Copynumber: 5.5 Consensus size: 67
56614 GTATTTTCAA
* * * *
56624 ATTTCCA-AAATACCCTTTCGGTCGAAGGGTCA-T-TT-CCATCTTTTGCATTTAAGTGTAGTAT
1 ATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTC-T-TTTTGCATTCAAGTTTAGTAT
*
56685 TTTC
64 TTTG
* * * *
56689 ATTTTCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTACATTCAAATTTAGTATTT
1 ATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTAGTATTT
56754 TG
66 TG
* * * *
56756 ATTTCCAGAAATACCCTTTCGATCAAAGTGTCGGTCATGGTCTTTTTGCATTCAAGTTTAGTATT
1 ATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTC-TTGTCTTTTTGCATTCAAGTTTAGTATT
56821 TTCG
65 TT-G
* ** * * * * *
56825 -TTTCCAGAGATACCCTTTCGGTTGAAGGGTCAGT-TTCATCAGGTTGTTGCATTTAAATCTAGT
1 ATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTC---TTTTTGCATTCAAGTTTAGT
*
56888 -CTTT-
62 ATTTTG
* * * * ** *
56892 CTTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAAT-TCTGTCATTCTTGCATTTGAGTTTA--C
1 ATTTCCAGA-AATACCCTTTCGGTCAAAGGGTCAGTCT-TGTC-TTTTTGCATTCAAGTTTAGTA
56954 TTTTG
63 TTTTG
* * *
56959 ATTTCCAAAAATACCCTTTCGGTGAAGGGGTCAGT
1 ATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGT
56994 TTCATCATTT
Statistics
Matches: 245, Mismatches: 45, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
65 6 0.02
66 51 0.21
67 76 0.31
68 65 0.27
69 30 0.12
70 17 0.07
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (67 bp):
ATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTAGTATTT
TG
Found at i:56912 original size:69 final size:66
Alignment explanation
Indices: 56819--57002 Score: 178
Period size: 69 Copynumber: 2.7 Consensus size: 66
56809 AAGTTTAGTA
* *
56819 TTTTCGTTTCCAGAG-ATACCCTTTCGGTTGAAGGGTCAGTTTCATCAGGTTGTTGCATTTAAAT
1 TTTTC-TTTCCAAAGAATACCCTTTCGGTTGAAGGGTCAGTTTCATCA--TTCTTGCATTTAAAT
*
56883 CTAG
63 CTAC
** * * * * *
56887 TCTTTCTTTCCAAAGAATACCCTTTCGGTCAAAGGGTCA-ATTCTGTCATTCTTGCATTTGAGTT
1 T-TTTCTTTCCAAAGAATACCCTTTCGGTTGAAGGGTCAGTTTC-ATCATTCTTGCATTTAAATC
56951 TAC
64 TAC
*
56954 TTTTGATTTCCAAA-AATACCCTTTCGG-TGAAGGGGTCAGTTTCATCATT
1 TTTT-CTTTCCAAAGAATACCCTTTCGGTTGAA-GGGTCAGTTTCATCATT
57003 TCCGCATTTC
Statistics
Matches: 95, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
65 2 0.02
66 27 0.28
67 26 0.27
68 12 0.13
69 28 0.29
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (66 bp):
TTTTCTTTCCAAAGAATACCCTTTCGGTTGAAGGGTCAGTTTCATCATTCTTGCATTTAAATCTA
C
Found at i:57010 original size:66 final size:65
Alignment explanation
Indices: 56892--57053 Score: 177
Period size: 66 Copynumber: 2.5 Consensus size: 65
56882 TCTAGTCTTT
* * * *
56892 CTTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAATTCTGTCATTCTTGCATTTGAGTTTACTTT
1 CTTTCCAAA-AATACCCTTTCGGTCAAAGGGTCAATTCTATCATTCTCGCATTTCAGTTTA-TTC
56957 TGA
64 T-A
* * *
56960 -TTTCCAAAAATACCCTTTCGGTGAAGGGGTCAGTT-TCATCATT-TCCGCATTTCAGTTTATTC
1 CTTTCCAAAAATACCCTTTCGGTCAAAGGGTCAATTCT-ATCATTCT-CGCATTTCAGTTTATTC
57022 TA
64 TA
* *
57024 CTTTCCAAAAATGCCCTTTCGATCAAAGGG
1 CTTTCCAAAAATACCCTTTCGGTCAAAGGG
57054 CGAACTTTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
64 1 0.01
65 30 0.38
66 41 0.51
67 8 0.10
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (65 bp):
CTTTCCAAAAATACCCTTTCGGTCAAAGGGTCAATTCTATCATTCTCGCATTTCAGTTTATTCTA
Found at i:59127 original size:53 final size:53
Alignment explanation
Indices: 59062--59175 Score: 201
Period size: 53 Copynumber: 2.2 Consensus size: 53
59052 GAAATATCGA
* *
59062 GCATCCCATCACATGTGAACGGGGGAGTTTGTTGGAGTTCATATGTGAGTGTC
1 GCATCCCATCACATGTGAACGGGAGAGTTTGTTAGAGTTCATATGTGAGTGTC
*
59115 GCATCCCGTCACATGTGAACGGGAGAGTTTGTTAGAGTTCATATGTGAGTGTC
1 GCATCCCATCACATGTGAACGGGAGAGTTTGTTAGAGTTCATATGTGAGTGTC
59168 GCATCCCA
1 GCATCCCA
59176 CATCACAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (53 bp):
GCATCCCATCACATGTGAACGGGAGAGTTTGTTAGAGTTCATATGTGAGTGTC
Found at i:59726 original size:2 final size:2
Alignment explanation
Indices: 59721--59750 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
59711 TTTTTTTAAA
*
59721 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59751 TGTGCAACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:66266 original size:19 final size:18
Alignment explanation
Indices: 66233--66268 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
66223 TGGAAATAAT
66233 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
66251 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
66269 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.