Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013903.1 Kokia drynarioides strain JFW-HI SEQ_128932, 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: 131441
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:91 original size:3 final size:3
Alignment explanation
Indices: 85--124 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
75 ATATTTTTTT
* *
85 TAA TAA TAA TAA TAT TAA TAA TAT TAA TGAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
125 AAAACGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:364 original size:21 final size:23
Alignment explanation
Indices: 334--375 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
324 AAGGAAAACC
*
334 GTTTGGATCTAGGC-TAGATCTG
1 GTTTGGATCTAGACTTAGATCTG
356 GTTT-GATCTAGACTTAGATC
1 GTTTGGATCTAGACTTAGATC
376 CGTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (23 bp):
GTTTGGATCTAGACTTAGATCTG
Found at i:380 original size:21 final size:21
Alignment explanation
Indices: 332--380 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
322 AAAAGGAAAA
*
332 CCGTTTGGATCTAGGCTAGAT
1 CCGTTTGGATCTAGACTAGAT
*
353 CTGGTTT-GATCTAGACTTAGAT
1 C-CGTTTGGATCTAGAC-TAGAT
375 CCGTTT
1 CCGTTT
381 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (21 bp):
CCGTTTGGATCTAGACTAGAT
Found at i:1262 original size:59 final size:59
Alignment explanation
Indices: 1170--1536 Score: 465
Period size: 59 Copynumber: 6.3 Consensus size: 59
1160 TAAACTATCC
* * *
1170 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCTTCT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * * *
1229 AAAAATTACCATTTTTCCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTC-
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * * *
1287 AAAAATT-CCATTTTGCCCTCGAACTTCCAAAAAATCCCATTTTT-ATCCCCAAAACTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCC-AAAAATCCCATTTTTGA-CCCCGAACCTTCT
* *
1346 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCTTCT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* ** *
1405 AACAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCTTGAACCTTTT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * * *
1463 GAAAATTACGATTTTACCCTCGAACTTCAAAAAATCTCATTTTTTGACCCCGAACCTTC-
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTTGACCCCGAACCTTCT
* *
1522 CAAAACTACCATTTT
1 AAAAATTACCATTTT
1537 GCCCCCGTGC
Statistics
Matches: 273, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
57 20 0.07
58 85 0.31
59 132 0.48
60 36 0.13
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
Found at i:1375 original size:117 final size:116
Alignment explanation
Indices: 1169--1536 Score: 486
Period size: 117 Copynumber: 3.1 Consensus size: 116
1159 CTAAACTATC
* *
1169 CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCTTCTAAAAA
1 CAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTT-ACCTCGAACCTTCTAAAAA
* * * * *
1234 TTACCATTTTTCCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
65 TTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTT
* * * * *
1286 CAAAAATT-CCATTTTGCCCTCGAACTTCCAAAAAATCCCATTTTTATCCCCAAAACTTCCAAAA
1 CAAAAATTACCATTTTACCCTCGAACTTCC-AAAAATCCCATTTTTA-CCTCGAACCTTCTAAAA
*
1350 ATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCTT
64 ATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTT
* * * * *
1403 CTAACAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCTTGAACCTTTTGAAAA
1 C-AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTACCTCGAACCTTCTAAAAA
* *
1468 TTACGATTTTACCCTCGAACTTCAAAAAATCTCATTTTTTGACCCCGAACCTT
65 TTACCATTTTACCCTCGAACTTCCAAAAATCTCA-TTTTTGACCCCGAACCTT
* *
1521 CCAAAACTACCATTTT
1 CAAAAATTACCATTTT
1537 GCCCCCGTGC
Statistics
Matches: 217, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
116 20 0.09
117 138 0.64
118 39 0.18
119 20 0.09
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (116 bp):
CAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTACCTCGAACCTTCTAAAAAT
TACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTT
Found at i:1496 original size:176 final size:176
Alignment explanation
Indices: 1161--1543 Score: 540
Period size: 176 Copynumber: 2.2 Consensus size: 176
1151 GGAGGTCCCT
1161 AAACTATCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCT
1 AAACT-TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCT
*
1226 TCTAAAAATTACCATTTTTCCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCAAAA
65 TCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCAAAA
*
1291 ATTCCATTTTGCCCTCGAACTTCCAAAAAATCCCA-TTTTTATCCCCA
130 ATTCCATTTTACCCTCGAACTTCCAAAAAATCCCATTTTTTA-CCCCA
*
1338 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCTT
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCTT
* * *** * **
1403 CTAACAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCTTGAACCTTTTGAAA
66 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAAC-TTCAAAA
* * *
1467 ATTACGATTTTACCCTCGAACTT-CAAAAAATCTCATTTTTTGACCCCG
130 ATT-CCATTTTACCCTCGAACTTCCAAAAAATCCCATTTTTT-ACCCCA
* * *
1515 AACCTTCC-AAAACTACCATTTTGCCCCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCG
1544 TGCATCCGAA
Statistics
Matches: 184, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
175 11 0.06
176 134 0.73
177 38 0.21
178 1 0.01
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (176 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCTT
CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCAAAAA
TTCCATTTTACCCTCGAACTTCCAAAAAATCCCATTTTTTACCCCA
Found at i:4164 original size:24 final size:24
Alignment explanation
Indices: 4137--4211 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
4127 ACACGAACCT
*
4137 AGAATGATTAGCTCTTATGAGCCC
1 AGAATGGTTAGCTCTTATGAGCCC
*
4161 AGAATGGTTAGCTCTTATGAGCCT
1 AGAATGGTTAGCTCTTATGAGCCC
* *
4185 AGCATGGTTAGCTCTTACGAGCCC
1 AGAATGGTTAGCTCTTATGAGCCC
4209 AGA
1 AGA
4212 CTGAGTTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (24 bp):
AGAATGGTTAGCTCTTATGAGCCC
Found at i:18548 original size:55 final size:55
Alignment explanation
Indices: 18464--18572 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
18454 TTGAATTCCT
*
18464 TGTAATGATAATATCATCAACATAGACTAACACAACCATGCTAGTTTCATTAGTC
1 TGTAATGATAATATCATCAACATAGACTAACACAAACATGCTAGTTTCATTAGTC
18519 TGTAATGATAATATCATCAACATAGACTAACACAAACATGCTAGTTTCATTAGT
1 TGTAATGATAATATCATCAACATAGACTAACACAAACATGCTAGTTTCATTAGT
18573 GACTCGTACA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (55 bp):
TGTAATGATAATATCATCAACATAGACTAACACAAACATGCTAGTTTCATTAGTC
Found at i:20903 original size:27 final size:27
Alignment explanation
Indices: 20871--20968 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
20861 AATGGGTCAA
*
20871 GTCAACTTGGGTCAACGGGTTGGGTCG
1 GTCAACTTGGGTCAACGGGTCGGGTCG
* *
20898 GTCAACTTGGGTCAATGGGTCGGGTGG
1 GTCAACTTGGGTCAACGGGTCGGGTCG
* * ** *
20925 GTCAAATCGGGTCAACGGGTCATGTTG
1 GTCAACTTGGGTCAACGGGTCGGGTCG
* *
20952 GTCAACTCGAGTCAACG
1 GTCAACTTGGGTCAACG
20969 AGTATTGGGT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.24
Consensus pattern (27 bp):
GTCAACTTGGGTCAACGGGTCGGGTCG
Found at i:22927 original size:3 final size:3
Alignment explanation
Indices: 22919--22947 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
22909 CCTAAAAGTT
22919 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
22948 TTCACTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:25191 original size:19 final size:19
Alignment explanation
Indices: 25164--25222 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
25154 GTTGGTAAAA
*
25164 AAAGTTAACGGTCAAAGTC
1 AAAGTTAACGGTCAAGGTC
* *
25183 AAAGCTAACGATCAAGGTC
1 AAAGTTAACGGTCAAGGTC
25202 AAAGTTAACGGTCAAGGTC
1 AAAGTTAACGGTCAAGGTC
25221 AA
1 AA
25223 CGACTAACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (19 bp):
AAAGTTAACGGTCAAGGTC
Found at i:25215 original size:38 final size:39
Alignment explanation
Indices: 25164--25242 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 39
25154 GTTGGTAAAA
*
25164 AAAGTTAACGGTCAAAGTCAAAG-CTAACGATCAAGGTC
1 AAAGTTAACGGTCAAAGTCAAAGACTAACAATCAAGGTC
* *
25202 AAAGTTAACGGTCAAGGTCAACGACTAACAATCAAGGTC
1 AAAGTTAACGGTCAAAGTCAAAGACTAACAATCAAGGTC
25241 AA
1 AA
25243 TGGGTCAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 21 0.57
39 16 0.43
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (39 bp):
AAAGTTAACGGTCAAAGTCAAAGACTAACAATCAAGGTC
Found at i:25295 original size:27 final size:27
Alignment explanation
Indices: 25265--25333 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
25255 AATAGGTCGG
*
25265 GTCAACTC-AGTTCAATGGGTCGGGTCA
1 GTCAACTCGAG-TCAATAGGTCGGGTCA
* **
25292 GTCAACTCGAGTGAATAGGTCGGGTTG
1 GTCAACTCGAGTCAATAGGTCGGGTCA
*
25319 GTCAACTCGGGTCAA
1 GTCAACTCGAGTCAA
25334 CGAGTATTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (27 bp):
GTCAACTCGAGTCAATAGGTCGGGTCA
Found at i:29723 original size:16 final size:16
Alignment explanation
Indices: 29702--29736 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29692 AGTGAAAATG
* *
29702 AATTTTTTTTTCACTT
1 AATTTTCTTTTAACTT
29718 AATTTTCTTTTAACTT
1 AATTTTCTTTTAACTT
29734 AAT
1 AAT
29737 ATATATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTTCTTTTAACTT
Found at i:33782 original size:16 final size:16
Alignment explanation
Indices: 33761--33795 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33751 AGTGAAAATG
* *
33761 AATTTTTTTTTCACTT
1 AATTTTCTTTTAACTT
33777 AATTTTCTTTTAACTT
1 AATTTTCTTTTAACTT
33793 AAT
1 AAT
33796 ATATATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTTCTTTTAACTT
Found at i:36221 original size:20 final size:21
Alignment explanation
Indices: 36197--36251 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
36187 AACAATAGTA
36197 AAAACACATAAAATAAC-ATC
1 AAAACACATAAAATAACAATC
* *
36217 CAAACA-ACCAAAATAACAATC
1 AAAACACA-TAAAATAACAATC
36238 AAAACAGCATAAAA
1 AAAACA-CATAAAA
36252 AATAATAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 1 0.04
20 13 0.48
21 8 0.30
22 4 0.15
23 1 0.04
ACGTcount: A:0.65, C:0.22, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAACACATAAAATAACAATC
Found at i:36240 original size:12 final size:12
Alignment explanation
Indices: 36219--36438 Score: 59
Period size: 12 Copynumber: 19.1 Consensus size: 12
36209 ATAACATCCA
36219 AACAACCAAAAT
1 AACAACCAAAAT
* *
36231 AACAATCAAAAC
1 AACAACCAAAAT
* *
36243 AGCATA-AAAAAT
1 AACA-ACCAAAAT
* *
36255 AA-TAGCAAAAT
1 AACAACCAAAAT
* *
36266 AATAACAAAAAT
1 AACAACCAAAAT
* *
36278 AGCAACAAAAAT
1 AACAACCAAAAT
* *
36290 AACAGCAAAAAT
1 AACAACCAAAAT
* *
36302 AGCAACAAAAAT
1 AACAACCAAAAT
* *
36314 AAC-AGCATCAA-
1 AACAACCA-AAAT
** *
36325 AAC-AGTAAAAA
1 AACAACCAAAAT
36336 AAC-ACCAAAAT
1 AACAACCAAAAT
*
36347 AGCAACCAAAAT
1 AACAACCAAAAT
* ** *
36359 AGCAAAAAACAAA
1 AACAACCAA-AAT
* *
36372 AACAA-TAAAAA
1 AACAACCAAAAT
*
36383 AAC-ACCAAAAC
1 AACAACCAAAAT
36394 AACAA--AAAAT
1 AACAACCAAAAT
*
36404 AACAACCAAAAC
1 AACAACCAAAAT
*
36416 AATAA--AAAAT
1 AACAACCAAAAT
*
36426 AATAACCAAAAT
1 AACAACCAAAAT
36438 A
1 A
36439 GTAAAAAAAA
Statistics
Matches: 157, Mismatches: 38, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
10 22 0.14
11 38 0.24
12 90 0.57
13 7 0.04
ACGTcount: A:0.69, C:0.18, G:0.04, T:0.10
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:36318 original size:24 final size:24
Alignment explanation
Indices: 36261--36320 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
36251 AAATAATAGC
* *
36261 AAAATAATAACAAAAATAGCAACA
1 AAAATAACAGCAAAAATAGCAACA
36285 AAAATAACAGCAAAAATAGCAACA
1 AAAATAACAGCAAAAATAGCAACA
36309 AAAATAACAGCA
1 AAAATAACAGCA
36321 TCAAAACAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.68, C:0.15, G:0.07, T:0.10
Consensus pattern (24 bp):
AAAATAACAGCAAAAATAGCAACA
Found at i:36346 original size:45 final size:43
Alignment explanation
Indices: 36255--36424 Score: 134
Period size: 47 Copynumber: 3.8 Consensus size: 43
36245 CATAAAAAAT
* * * *
36255 AATAGCAA-AATAATAACAAA-AATAGCAACAAAAATAACAGCAAA
1 AATAGCAACAAAAATAACAAACAA-AACAATAAAAA-AACA-CCAA
* *
36299 AATAGCAACAAAAATAACAGCATCAAAACAGTAAAAAAACACCAA
1 AATAGCAACAAAAATAACA--AACAAAACAATAAAAAAACACCAA
* *
36344 AATAGCAACCAAAATAGCAAAAAACAAAAACAATAAAAAAACACC-A
1 AATAGCAA-CAAAA-A-TAACAAAC-AAAACAATAAAAAAACACCAA
*
36390 AA-A-CAACAAAAAATAACAACCAAAACAATAAAAAA
1 AATAGCAAC-AAAAATAACAAACAAAACAATAAAAAA
36425 TAATAACCAA
Statistics
Matches: 104, Mismatches: 13, Indels: 21
0.75 0.09 0.15
Matches are distributed among these distances:
41 14 0.13
42 5 0.05
43 2 0.02
44 15 0.14
45 21 0.20
46 14 0.13
47 28 0.27
48 5 0.05
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (43 bp):
AATAGCAACAAAAATAACAAACAAAACAATAAAAAAACACCAA
Found at i:36443 original size:22 final size:22
Alignment explanation
Indices: 36370--36464 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
36360 GCAAAAAACA
36370 AAAACAAT-AAAAA-AAC-ACC
1 AAAACAATAAAAAATAACAACC
*
36389 AAAACAACAAAAAATAACAACC
1 AAAACAATAAAAAATAACAACC
*
36411 AAAACAATAAAAAATAATAACC
1 AAAACAATAAAAAATAACAACC
* *
36433 AAAATAGTAAAAAA-AAGC-ACC
1 AAAACAATAAAAAATAA-CAACC
36454 AAAAACAATAA
1 -AAAACAATAA
36465 TATAATTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
19 7 0.11
20 5 0.08
21 8 0.13
22 43 0.68
ACGTcount: A:0.73, C:0.17, G:0.02, T:0.08
Consensus pattern (22 bp):
AAAACAATAAAAAATAACAACC
Found at i:36881 original size:17 final size:17
Alignment explanation
Indices: 36859--36894 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36849 TCAACAAAGG
*
36859 GCGATCATTCGTGAGGA
1 GCGATCATTCATGAGGA
*
36876 GCGATCGTTCATGAGGA
1 GCGATCATTCATGAGGA
36893 GC
1 GC
36895 CCGAGAAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (17 bp):
GCGATCATTCATGAGGA
Found at i:42677 original size:55 final size:56
Alignment explanation
Indices: 42592--42707 Score: 225
Period size: 55 Copynumber: 2.1 Consensus size: 56
42582 AAGCACCAAA
42592 GAATGTGTCAGAAATCCGTAGTTTCATTGGTTTAGCTGGTATTACCGTCGATTCGT
1 GAATGTGTCAGAAATCCGTAGTTTCATTGGTTTAGCTGGTATTACCGTCGATTCGT
42648 -AATGTGTCAGAAATCCGTAGTTTCATTGGTTTAGCTGGTATTACCGTCGATTCGT
1 GAATGTGTCAGAAATCCGTAGTTTCATTGGTTTAGCTGGTATTACCGTCGATTCGT
42703 GAATG
1 GAATG
42708 GATTTTCAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 55 0.93
56 4 0.07
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (56 bp):
GAATGTGTCAGAAATCCGTAGTTTCATTGGTTTAGCTGGTATTACCGTCGATTCGT
Found at i:49419 original size:19 final size:20
Alignment explanation
Indices: 49388--49444 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
49378 CATGATACCA
49388 ATTTTAAAATTTTTATAAA-T
1 ATTTT-AAATTTTTATAAATT
* *
49408 ATTTTGAA-TTTTAAAAATT
1 ATTTTAAATTTTTATAAATT
49427 ATTTTAAATTTTTTATAA
1 ATTTTAAA-TTTTTATAA
49445 TTTTTATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.27
19 10 0.33
20 5 0.17
21 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTAAATTTTTATAAATT
Found at i:49434 original size:28 final size:27
Alignment explanation
Indices: 49387--49440 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
49377 GCATGATACC
49387 AATTTTAAAATTTTTATAAATATTTTG
1 AATTTTAAAATTTTTATAAATATTTTG
*
49414 AATTTTAAAAATTATTT-TAAATTTTTT
1 AATTTT-AAAATT-TTTATAAATATTTT
49441 ATAATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 15 0.62
29 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
AATTTTAAAATTTTTATAAATATTTTG
Found at i:49446 original size:10 final size:9
Alignment explanation
Indices: 49389--49449 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
49379 ATGATACCAA
*
49389 TTTTAAAAT
1 TTTTTAAAT
49398 TTTTATAAAT
1 TTTT-TAAAT
* *
49408 ATTTTGAAT
1 TTTTTAAAT
**
49417 TTTAAAAAT
1 TTTTTAAAT
49426 TATTTTAAAT
1 T-TTTTAAAT
49436 TTTTTATAAT
1 TTTTTA-AAT
49446 TTTT
1 TTTT
49450 ATTGAAAAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
9 19 0.47
10 21 0.52
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:53961 original size:141 final size:142
Alignment explanation
Indices: 53652--53970 Score: 428
Period size: 141 Copynumber: 2.2 Consensus size: 142
53642 TTTATATTTT
* * *
53652 TTTTTATTTCA-ACTTGTTTTAAGCTTGTTTTTTTTTTTTAATGAATGTTTTTAATACGTTAGCT
1 TTTTTATTTCATA-TTGTTTTAAG-TT-TTTTATTTTTTTAATGAATGTTTTTAACACATTAGCT
* * * * *
53716 TCCTTAGTTAAATGGTTAAATAAAAATGATTTCATCATTGAGACTCAAGTTTAATTTCCCTTTCT
63 TCATTAGTTAAATGGCTAAATAAAAATGATTTCATCATTGAAACTCAAGTTCAATTCCCCTTTCT
*
53781 TAAAAACATTTATTA
128 TAAAAACATTTATAA
* * *
53796 TTTTTATTTCATGTTGTTTTAAGTTTTTTCTTTTTTTAATGAATGTTTTTAACATATTAGCTTCA
1 TTTTTATTTCATATTGTTTTAAGTTTTTTATTTTTTTAATGAATGTTTTTAACACATTAGCTTCA
* *
53861 TTAGTTAAATGGCTAAATAATAATGATTT-ATCATTGAAACTTAAGTTCAATTCCCCTTT-TCTA
66 TTAGTTAAATGGCTAAATAAAAATGATTTCATCATTGAAACTCAAGTTCAATTCCCCTTTCT-TA
* *
53924 AACACATTTGTAA
130 AAAACATTTATAA
*
53937 TTTTTATTTCATATTGTTTCAAGTTTTTTATTTT
1 TTTTTATTTCATATTGTTTTAAGTTTTTTATTTT
53971 AATTCATCTT
Statistics
Matches: 155, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
140 1 0.01
141 69 0.45
142 62 0.40
143 2 0.01
144 21 0.14
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (142 bp):
TTTTTATTTCATATTGTTTTAAGTTTTTTATTTTTTTAATGAATGTTTTTAACACATTAGCTTCA
TTAGTTAAATGGCTAAATAAAAATGATTTCATCATTGAAACTCAAGTTCAATTCCCCTTTCTTAA
AAACATTTATAA
Found at i:54261 original size:15 final size:15
Alignment explanation
Indices: 54237--54273 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
54227 TTTGACATAT
54237 AAATATTATAT-AAA
1 AAATATTATATCAAA
54251 AAATATATATATCAAA
1 AAATAT-TATATCAAA
54267 AAA-ATTA
1 AAATATTA
54274 GTTGATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.38
15 7 0.33
16 6 0.29
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATTATATCAAA
Found at i:57126 original size:29 final size:31
Alignment explanation
Indices: 57073--57132 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
57063 TGGAATTGAA
*
57073 AATAAAAAACTTAAAAAATTGAATC-AAATT
1 AATAAAAAACTTAAAAAAGTGAATCTAAATT
57103 AATAAAAAA-TTAAAAAAAGT-AATCTAAATT
1 AATAAAAAACTT-AAAAAAGTGAATCTAAATT
57133 TTTGTTCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (31 bp):
AATAAAAAACTTAAAAAAGTGAATCTAAATT
Found at i:57959 original size:7 final size:6
Alignment explanation
Indices: 57931--57969 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
57921 TCCATGTCAC
*
57931 TTTTAT TTTTAT TTTTAT TTTTAT GTTTTA- ATTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTT
57970 CCAGATGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.14
6 20 0.69
7 5 0.17
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:59204 original size:48 final size:48
Alignment explanation
Indices: 59133--59240 Score: 207
Period size: 48 Copynumber: 2.2 Consensus size: 48
59123 AAATGAAATA
59133 TTTACATCTTTTAAATGAAAAATAATAAAATTATTCGATTAACCATGG
1 TTTACATCTTTTAAATGAAAAATAATAAAATTATTCGATTAACCATGG
59181 TTTACATCTTTTAAATGAAAAATAATAAAATTATTCGATTAACCATGG
1 TTTACATCTTTTAAATGAAAAATAATAAAATTATTCGATTAACCATGG
*
59229 TTAACATCTTTT
1 TTTACATCTTTT
59241 TTTTTTTTTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (48 bp):
TTTACATCTTTTAAATGAAAAATAATAAAATTATTCGATTAACCATGG
Found at i:63570 original size:37 final size:37
Alignment explanation
Indices: 63514--63635 Score: 145
Period size: 37 Copynumber: 3.2 Consensus size: 37
63504 GTAATTTTAA
** *
63514 TCTAGAATTGCGCCCAAACATGTCGTTGCATGAGCACT
1 TCTAG-ATTGCGCCCAAACATGTCGCCGCATGAGAACT
*
63552 TTTAGATTGCGCCCAAACATGTCGCCGCATGAGAACT
1 TCTAGATTGCGCCCAAACATGTCGCCGCATGAGAACT
* * * *
63589 TCTAGATTGCGCCCAAAAACTGTTGCCACATGAGCACT
1 TCTAGATTGCGCCCAAACA-TGTCGCCGCATGAGAACT
*
63627 TCCAGATTG
1 TCTAGATTG
63636 AACCAAAATT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
37 46 0.63
38 27 0.37
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (37 bp):
TCTAGATTGCGCCCAAACATGTCGCCGCATGAGAACT
Found at i:63746 original size:26 final size:26
Alignment explanation
Indices: 63717--63770 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
63707 CACCTAGGAA
*
63717 TGTCGCTTCATGAACATGTACAGAAT
1 TGTCGCTGCATGAACATGTACAGAAT
* *
63743 TGTCGCTGCATGAACGTGTCCAGAAT
1 TGTCGCTGCATGAACATGTACAGAAT
63769 TG
1 TG
63771 CGCCCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTACAGAAT
Found at i:73075 original size:82 final size:81
Alignment explanation
Indices: 72974--73132 Score: 282
Period size: 82 Copynumber: 2.0 Consensus size: 81
72964 CGCTCGCACC
*
72974 AAGCTTCTTGGCACCTTGTCTGCCCCATCAATGACATACTTTTTCGGACATTTTCGTAACCTATG
1 AAGCTTCTTGGCACCTTGTCTGCCCCATCAATGACATACTTTTTCGGACATTTTCGCAACCTATG
73039 CGGCCCATGACACAAA
66 CGGCCCATGACACAAA
* *
73055 AAGCTTCTTGGGCACCTTGTCTGCCTCATCAATGACATACTTTTTCGGACATTTTCGCAACTTAT
1 AAGCTTCTT-GGCACCTTGTCTGCCCCATCAATGACATACTTTTTCGGACATTTTCGCAACCTAT
73120 GCGGCCCATGACA
65 GCGGCCCATGACA
73133 TAAGAAGCAC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 9 0.12
82 65 0.88
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (81 bp):
AAGCTTCTTGGCACCTTGTCTGCCCCATCAATGACATACTTTTTCGGACATTTTCGCAACCTATG
CGGCCCATGACACAAA
Found at i:76750 original size:52 final size:52
Alignment explanation
Indices: 76686--76790 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
76676 CTTTTCGAGG
*
76686 TACACATCCTATAAACTTGATAGCAAAGGAGTTCGAAATTTTCTAGTTTTCA
1 TACACATCCTATAAACTTGATAGCAAAGGAGTTCGAAATGTTCTAGTTTTCA
* * *
76738 TACACATCCTATAAGCTTGATTGCAAAGGAGTTTGAAATGTTCTAGTTTTCA
1 TACACATCCTATAAACTTGATAGCAAAGGAGTTCGAAATGTTCTAGTTTTCA
76790 T
1 T
76791 TTTGATGCCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (52 bp):
TACACATCCTATAAACTTGATAGCAAAGGAGTTCGAAATGTTCTAGTTTTCA
Found at i:79589 original size:46 final size:46
Alignment explanation
Indices: 79522--79613 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
79512 GCAAGATGGA
*
79522 TTACCCAATTTCACCGAAGGTCTTTGGTTGTGTTTGCTTCATTCAT
1 TTACCCAATTTCACAGAAGGTCTTTGGTTGTGTTTGCTTCATTCAT
*
79568 TTACCCAATTTCACAGAAGGTCTTTGGTTGTGTTTGCTTCGTTCAT
1 TTACCCAATTTCACAGAAGGTCTTTGGTTGTGTTTGCTTCATTCAT
79614 CTTTAACATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.43
Consensus pattern (46 bp):
TTACCCAATTTCACAGAAGGTCTTTGGTTGTGTTTGCTTCATTCAT
Found at i:83532 original size:192 final size:195
Alignment explanation
Indices: 83201--83562 Score: 606
Period size: 192 Copynumber: 1.9 Consensus size: 195
83191 GATGAACCCA
*
83201 GAAAAATTGAAACTATATTTGGTTCCAAGGAAAATTTGAAGAATAGCATTTTAACAATTCTTTAG
1 GAAAAATTGAAACTATATTTGGTTCCAAGGAAAATTT-AAGAATAGAATTTTAACAATTCTTTAG
* * *
83266 CATCTAAGAAAATTGTTTAAATTATAAATTATTTTATTTCAAATCTCTTTTCACTTTAAGACCTT
65 CATCAAAGAAAATTGTTTAAATTATAAAATATGTTATTTCAAATCTCTTTTCACTTTAAGACCTT
83331 CCTGAAAAATCTTCTTTCATTCTAATTTTACAATAAACAAAGCCTATAAAGAGCAAGTCTTGAAC
130 CCTGAAAAATCTTCTTTCATTCTAATTTTACAATAAACAAAGCCTATAAAGAGCAAGTCTTGAAC
83396 T
195 T
* * *
83397 GAAAAATTGAAACTATGA-TTGGTT-CATGG-AAATTT-TGAATAGAATTTTAACAATTCTTTGG
1 GAAAAATTGAAACTAT-ATTTGGTTCCAAGGAAAATTTAAGAATAGAATTTTAACAATTCTTTAG
83458 CATCAAAGAAAATTGTTTAAATTATAAAATATGTTATTTCAAATCTCTTTTCACTTTAAGACCTT
65 CATCAAAGAAAATTGTTTAAATTATAAAATATGTTATTTCAAATCTCTTTTCACTTTAAGACCTT
*
83523 TCTGAAAAATCTTCTTTCATTCTAATTTTACAATAAACAA
130 CCTGAAAAATCTTCTTTCATTCTAATTTTACAATAAACAA
83563 GAGCAAGTCT
Statistics
Matches: 157, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
192 124 0.79
194 6 0.04
195 4 0.03
196 22 0.14
197 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (195 bp):
GAAAAATTGAAACTATATTTGGTTCCAAGGAAAATTTAAGAATAGAATTTTAACAATTCTTTAGC
ATCAAAGAAAATTGTTTAAATTATAAAATATGTTATTTCAAATCTCTTTTCACTTTAAGACCTTC
CTGAAAAATCTTCTTTCATTCTAATTTTACAATAAACAAAGCCTATAAAGAGCAAGTCTTGAACT
Found at i:86461 original size:16 final size:16
Alignment explanation
Indices: 86434--86476 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
86424 TAGAGAGAAA
86434 GGAGA-GGG-GAGAGG
1 GGAGAGGGGAGAGAGG
86448 GGAGAGGGGAGAGAGG
1 GGAGAGGGGAGAGAGG
* *
86464 AGAGAGGAGAGAG
1 GGAGAGGGGAGAG
86477 GAAGAAGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.20
15 3 0.12
16 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (16 bp):
GGAGAGGGGAGAGAGG
Found at i:86475 original size:7 final size:7
Alignment explanation
Indices: 86428--86488 Score: 70
Period size: 7 Copynumber: 8.7 Consensus size: 7
86418 ACGTCATAGA
*
86428 GAGAAAG
1 GAGAGAG
*
86435 GAGAGGG
1 GAGAGAG
*
86442 GAGAGGG
1 GAGAGAG
*
86449 GAGAGGG
1 GAGAGAG
86456 GAGAGAG
1 GAGAGAG
86463 GAGAGAG
1 GAGAGAG
86470 GAGAGAG
1 GAGAGAG
86477 GA-AGAAG
1 GAGAG-AG
86484 GAGAG
1 GAGAG
86489 GAAATGGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
6 2 0.04
7 45 0.92
8 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (7 bp):
GAGAGAG
Found at i:94282 original size:15 final size:15
Alignment explanation
Indices: 94262--94292 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
94252 ATTAAACGAA
*
94262 AGTAGTAATAGTAAT
1 AGTAGTAATAATAAT
94277 AGTAGTAATAATAAT
1 AGTAGTAATAATAAT
94292 A
1 A
94293 ACCAATAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (15 bp):
AGTAGTAATAATAAT
Found at i:94993 original size:109 final size:110
Alignment explanation
Indices: 94802--95124 Score: 360
Period size: 109 Copynumber: 2.9 Consensus size: 110
94792 AGTTGTCGAT
* * * * *
94802 TGGTTAAGGATCCACAACCCCTCGCAAATAAAAGCTGTCAGAGAAAATCGTAGATACTCTGTTCA
1 TGGTTAAGGATCCACAATCCCTCGCAAATAAAAGCTGTCAGAGGAAATCGTGGATGCTCCGTTCA
* * ****
94867 TATAGTCACAGTTGGAATCTGTTAATCTATGAGTACATA-TTGGA
66 TATAGTCACAGTTGGAATCTGCTAATCTATGAGTACACAGCAAAA
* * * *
94911 TGGTTAAGGATCCACAATCCCTCGCACATAAAAGCTATTAGAGGAAATCATGGATGCTCCGTTCA
1 TGGTTAAGGATCCACAATCCCTCGCAAATAAAAGCTGTCAGAGGAAATCGTGGATGCTCCGTTCA
* **
94976 TATAGTCACAGTTGGAATTTGCTAATCTATGAAAACACAGCAAAA
66 TATAGTCACAGTTGGAATCTGCTAATCTATGAGTACACAGCAAAA
** * ** * * * *
95021 TGGTCGAGGATCCACAATCTCTCATAGATAAGAGTTGTCAGAGGAAATTGTGGATGCTCCGTTCA
1 TGGTTAAGGATCCACAATCCCTCGCAAATAAAAGCTGTCAGAGGAAATCGTGGATGCTCCGTTCA
* * * *
95086 TATTGTCGCAGTTGGAATCTACTAATCTGTGAGTACACA
66 TATAGTCACAGTTGGAATCTGCTAATCTATGAGTACACA
95125 TCGGACAAAC
Statistics
Matches: 176, Mismatches: 37, Indels: 1
0.82 0.17 0.00
Matches are distributed among these distances:
109 90 0.51
110 86 0.49
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (110 bp):
TGGTTAAGGATCCACAATCCCTCGCAAATAAAAGCTGTCAGAGGAAATCGTGGATGCTCCGTTCA
TATAGTCACAGTTGGAATCTGCTAATCTATGAGTACACAGCAAAA
Found at i:95624 original size:29 final size:29
Alignment explanation
Indices: 95592--95768 Score: 96
Period size: 29 Copynumber: 6.3 Consensus size: 29
95582 ATTTTTTAAG
* *
95592 AATATTGGCAAAATTGTAAAATTTGAAAA
1 AATAGTGGCAAAATTATAAAATTTGAAAA
* *
95621 AATAGT-G-ACAATTATAAAATCTGAAAA
1 AATAGTGGCAAAATTATAAAATTTGAAAA
** *
95648 ACCAGTGGCAAAACTATAAAATTTGAAAA
1 AATAGTGGCAAAATTATAAAATTTGAAAA
* * * * *
95677 CCA-A-TGACAAAACTGTAAAATATG-AAA
1 -AATAGTGGCAAAATTATAAAATTTGAAAA
* * * * *
95704 AACAGTGACAGAACTATAAAATTTGGAAA
1 AATAGTGGCAAAATTATAAAATTTGAAAA
** * * * *
95733 ACCAGTGACAAAACTGTAAAATCT-AAAA
1 AATAGTGGCAAAATTATAAAATTTGAAAA
95761 AATAGTGG
1 AATAGTGG
95769 AAGAGCTATA
Statistics
Matches: 116, Mismatches: 26, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.01
27 25 0.22
28 44 0.38
29 46 0.40
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.23
Consensus pattern (29 bp):
AATAGTGGCAAAATTATAAAATTTGAAAA
Found at i:95733 original size:57 final size:56
Alignment explanation
Indices: 95635--95781 Score: 197
Period size: 57 Copynumber: 2.6 Consensus size: 56
95625 GTGACAATTA
* *
95635 TAAAATCTGAAAAACCAGTGGCAAAACTATAAAATTTGAAAACCAATGACAAAACTG
1 TAAAATCTGAAAAA-CAGTGACAGAACTATAAAATTTGAAAACCAATGACAAAACTG
* *
95692 TAAAATATGAAAAACAGTGACAGAACTATAAAATTTGGAAAACCAGTGACAAAACTG
1 TAAAATCTGAAAAACAGTGACAGAACTATAAAATTT-GAAAACCAATGACAAAACTG
* * *
95749 TAAAATCTAAAAAATAGTGGA-AGAGCTATAAAA
1 TAAAATCTGAAAAACAGT-GACAGAACTATAAAA
95782 ATCTGTAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
56 20 0.25
57 58 0.73
58 2 0.03
ACGTcount: A:0.54, C:0.12, G:0.14, T:0.20
Consensus pattern (56 bp):
TAAAATCTGAAAAACAGTGACAGAACTATAAAATTTGAAAACCAATGACAAAACTG
Found at i:95761 original size:28 final size:29
Alignment explanation
Indices: 95608--95762 Score: 156
Period size: 28 Copynumber: 5.5 Consensus size: 29
95598 GGCAAAATTG
* ** *
95608 TAAAATTTGAAAAAATAGTGAC--AATTA
1 TAAAATCTGAAAAACCAGTGACAAAACTA
*
95635 TAAAATCTGAAAAACCAGTGGCAAAACTA
1 TAAAATCTGAAAAACCAGTGACAAAACTA
* * *
95664 TAAAATTTG-AAAACCAATGACAAAACTG
1 TAAAATCTGAAAAACCAGTGACAAAACTA
* *
95692 TAAAATATGAAAAA-CAGTGACAGAACTA
1 TAAAATCTGAAAAACCAGTGACAAAACTA
* * *
95720 TAAAATTTGGAAAACCAGTGACAAAACTG
1 TAAAATCTGAAAAACCAGTGACAAAACTA
*
95749 TAAAATCTAAAAAA
1 TAAAATCTGAAAAA
95763 TAGTGGAAGA
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 18 0.17
28 47 0.45
29 39 0.38
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (29 bp):
TAAAATCTGAAAAACCAGTGACAAAACTA
Found at i:96218 original size:33 final size:33
Alignment explanation
Indices: 96181--96244 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
96171 GATAAATTCT
*
96181 ATTAGGATTTGAAAAGGAATAATTTGAATTTTA
1 ATTAGGATTTGAAAAGGAATAATTTCAATTTTA
* * *
96214 ATTAGGATTTTAAAATGATTAATTTCAATTT
1 ATTAGGATTTGAAAAGGAATAATTTCAATTT
96245 CAAATTAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.44
Consensus pattern (33 bp):
ATTAGGATTTGAAAAGGAATAATTTCAATTTTA
Found at i:96661 original size:24 final size:25
Alignment explanation
Indices: 96606--96666 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
96596 TTACATGTGA
96606 AAATT-AATAAAATAAATAATACATT
1 AAATTAAAT-AAATAAATAATACATT
96631 AAATTAAATAAATAAATAACT-C-TT
1 AAATTAAATAAATAAATAA-TACATT
*
96655 AATTTAAATAAA
1 AAATTAAATAAA
96667 ATACATGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 13 0.39
25 16 0.48
26 4 0.12
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATTAAATAAATAAATAATACATT
Found at i:96737 original size:6 final size:6
Alignment explanation
Indices: 96726--96775 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
96716 CTGGACCTAA
96726 TAAATT TAAATT T--ATT TGAAATT TAAATT T--ATT ATAAATT TAAATT
1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT -TAAATT TAAATT
96772 TAAA
1 TAAA
96776 ATCTATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
4 7 0.18
5 1 0.03
6 23 0.61
7 7 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:96749 original size:17 final size:17
Alignment explanation
Indices: 96725--96773 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
96715 TCTGGACCTA
96725 ATAAATTTAAATTTATT
1 ATAAATTTAAATTTATT
96742 -TGAAATTTAAATTTATT
1 AT-AAATTTAAATTTATT
96759 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
96774 AAATCTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.03
17 28 0.93
18 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:96786 original size:23 final size:24
Alignment explanation
Indices: 96739--96787 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
96729 ATTTAAATTT
*
96739 ATTTGAAATTTAAATTTATTATAA
1 ATTTGAAATTTAAATCTATTATAA
96763 ATTT-AAATTTAAAATCTATT-TAA
1 ATTTGAAATTT-AAATCTATTATAA
96786 AT
1 AT
96788 AATGTCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTGAAATTTAAATCTATTATAA
Found at i:97536 original size:31 final size:30
Alignment explanation
Indices: 97478--97543 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
97468 TTAATGACCT
*
97478 TATTAATAATAAACAAGTTTTCCTTAATAA
1 TATTAATAATAAACAAGTTTTCATTAATAA
97508 TCATTAATAATAATA-AATGTTTT-ATTAATAA
1 T-ATTAATAATAA-ACAA-GTTTTCATTAATAA
97539 TATTA
1 TATTA
97544 TTATTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 5 0.16
31 21 0.66
32 6 0.19
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (30 bp):
TATTAATAATAAACAAGTTTTCATTAATAA
Found at i:98579 original size:30 final size:30
Alignment explanation
Indices: 98538--98749 Score: 168
Period size: 30 Copynumber: 7.1 Consensus size: 30
98528 TTCACCATCG
* *
98538 AACTTCTAAAAATCTCATTTTTGACCTCGA
1 AACTTCCAAAAATCCCATTTTTGACCTCGA
* * *
98568 AACTTCCAAAAATTCC-GTTTTCACCCTCG-
1 AACTTCCAAAAATCCCATTTTTGA-CCTCGA
* *
98597 AACTTCTAAAAATCCCATTTTTGACC-CAAA
1 AACTTCCAAAAATCCCATTTTTGACCTC-GA
*
98627 AACTTCCAAAAATCCCATTTTTGACC-CCA
1 AACTTCCAAAAATCCCATTTTTGACCTCGA
* * **
98656 AACTTCTAAAAATCCCATTTTTAACCTTTA
1 AACTTCCAAAAATCCCATTTTTGACCTCGA
* * *
98686 AACTTCCAAAAACTACCA-TTTTGCCCCCG-
1 AACTTCCAAAAA-TCCCATTTTTGACCTCGA
* * *
98715 AA-TGTCCAAAAAACTCCATTCTTGACCTTGA
1 AACT-TCCAAAAATC-CCATTTTTGACCTCGA
98746 AACT
1 AACT
98750 CTCAAAATTA
Statistics
Matches: 142, Mismatches: 29, Indels: 20
0.74 0.15 0.10
Matches are distributed among these distances:
28 2 0.01
29 59 0.42
30 74 0.52
31 6 0.04
32 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.31
Consensus pattern (30 bp):
AACTTCCAAAAATCCCATTTTTGACCTCGA
Found at i:98609 original size:59 final size:60
Alignment explanation
Indices: 98525--98697 Score: 226
Period size: 59 Copynumber: 2.9 Consensus size: 60
98515 TCAAAATTTT
* * * *
98525 GTTTTCACCATCGAACTTCTAAAAATCTCATTTTTGACCTCGAAACTTCCAAAAATTCC-
1 GTTTTCACCCTCGAACTTCTAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATCCCA
98584 GTTTTCACCCTCGAACTTCTAAAAATCCCATTTTTGACC-CAAAAACTTCCAAAAATCCCA
1 GTTTTCACCCTCGAACTTCTAAAAATCCCATTTTTGACCTC-AAAACTTCCAAAAATCCCA
* * * * **
98644 TTTTTGACCC-CAAACTTCTAAAAATCCCATTTTTAACCTTTAAACTTCCAAAAA
1 GTTTTCACCCTCGAACTTCTAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAA
98698 CTACCATTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
58 1 0.01
59 92 0.91
60 8 0.08
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (60 bp):
GTTTTCACCCTCGAACTTCTAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATCCCA
Found at i:98696 original size:29 final size:28
Alignment explanation
Indices: 98605--98696 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
98595 CGAACTTCTA
98605 AAAATCCCATTTTTGACCCAAAAACTTCC
1 AAAATCCCATTTTTGA-CCAAAAACTTCC
** *
98634 AAAAATCCCATTTTTGACCCCAAACTTCTA
1 -AAAATCCCATTTTTGACCAAAAACTTC-C
* **
98664 AAAATCCCATTTTTAACCTTTAAACTTCC
1 AAAATCCCATTTTTGACC-AAAAACTTCC
98693 AAAA
1 AAAA
98697 ACTACCATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
29 30 0.57
30 23 0.43
ACGTcount: A:0.39, C:0.28, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATCCCATTTTTGACCAAAAACTTCC
Found at i:98726 original size:59 final size:58
Alignment explanation
Indices: 98536--98766 Score: 225
Period size: 59 Copynumber: 3.9 Consensus size: 58
98526 TTTTCACCAT
* * * *
98536 CGAACTTCTAAAAATCTCATTTTTGACCTCGAAACTTCCAAAAATTCCGTTTT-CACCC
1 CGAACTTCTAAAAATCCCATTTTTGACCTTGAAACTTCCAAAAATACCATTTTGC-CCC
*** * *
98594 TCGAACTTCTAAAAATCCCATTTTTGACCCAAAAACTTCCAAAAATCCCATTTTTGACCC
1 -CGAACTTCTAAAAATCCCATTTTTGACCTTGAAACTTCCAAAAATACCA-TTTTGCCCC
* * *
98654 CAAACTTCTAAAAATCCCATTTTTAACCTTTAAACTTCCAAAAACTACCATTTTGCCCC
1 CGAACTTCTAAAAATCCCATTTTTGACCTTGAAACTTCCAAAAA-TACCATTTTGCCCC
* * * * *
98713 CGAA-TGTCCAAAAAACTCCATTCTTGACCTTGAAAC-TCTCAAAATTACCTTTTT
1 CGAACT-TCTAAAAATC-CCATTTTTGACCTTGAAACTTC-CAAAAATACCATTTT
98767 TTACCCCAAA
Statistics
Matches: 144, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 111 0.77
60 32 0.22
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (58 bp):
CGAACTTCTAAAAATCCCATTTTTGACCTTGAAACTTCCAAAAATACCATTTTGCCCC
Found at i:98841 original size:28 final size:28
Alignment explanation
Indices: 98810--98872 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
98800 CCGAATTTTC
98810 CCAAAATTACCATTTCACCCCCGAGAAT
1 CCAAAATTACCATTTCACCCCCGAGAAT
* *
98838 CCAAAATTACCATTTTACCCCCGAGTAT
1 CCAAAATTACCATTTCACCCCCGAGAAT
98866 CCGAAAA
1 CC-AAAA
98873 GACTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.22
Consensus pattern (28 bp):
CCAAAATTACCATTTCACCCCCGAGAAT
Found at i:98880 original size:29 final size:28
Alignment explanation
Indices: 98810--98882 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
98800 CCGAATTTTC
* *
98810 CCAAAATTACCATTTCACCCCCGAGAAT
1 CCAAAATGACCATTTTACCCCCGAGAAT
* *
98838 CCAAAATTACCATTTTACCCCCGAGTAT
1 CCAAAATGACCATTTTACCCCCGAGAAT
98866 CCGAAAA-GACTCATTTT
1 CC-AAAATGAC-CATTTT
98883 CAACTCCGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 30 0.75
29 10 0.25
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (28 bp):
CCAAAATGACCATTTTACCCCCGAGAAT
Found at i:100667 original size:18 final size:17
Alignment explanation
Indices: 100641--100675 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
100631 TCATGGTTGA
100641 TTGGAAAGAAAGATGAAG
1 TTGGAAAG-AAGATGAAG
*
100659 TTGGGAAGAAGATGAAG
1 TTGGAAAGAAGATGAAG
100676 GGGGAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (17 bp):
TTGGAAAGAAGATGAAG
Found at i:101020 original size:30 final size:30
Alignment explanation
Indices: 100986--101058 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
100976 AATTAAATCT
*
100986 TTTTATAAGAAAACAAATTTAC-ATTAATTA
1 TTTTATGAGAAAACAAATTT-CTATTAATTA
* **
101016 TTTTATGAGCAAACATGTTTCTATTAATTA
1 TTTTATGAGAAAACAAATTTCTATTAATTA
*
101046 TATTATGAGAAAA
1 TTTTATGAGAAAA
101059 ATATTTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (30 bp):
TTTTATGAGAAAACAAATTTCTATTAATTA
Found at i:101075 original size:31 final size:31
Alignment explanation
Indices: 101003--101087 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 31
100993 AGAAAACAAA
* * *
101003 TTTACATTAATTATTTTATGAG-CAAACATG
1 TTTATATTAATTATATTATGAGAAAAACATG
* * *
101033 TTTCTATTAATTATATTATGAGAAAAATATT
1 TTTATATTAATTATATTATGAGAAAAACATG
*
101064 TTTATATTAATTATAGTAT-AGAAA
1 TTTATATTAATTATATTATGAGAAA
101088 GTGCGTTGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 24 0.52
31 22 0.48
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (31 bp):
TTTATATTAATTATATTATGAGAAAAACATG
Found at i:102555 original size:2 final size:2
Alignment explanation
Indices: 102548--102578 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
102538 TTTTCTCCTT
102548 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
102579 GTCCTCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103109 original size:7 final size:7
Alignment explanation
Indices: 103097--103129 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
103087 AAAATACACA
103097 TAAACCT
1 TAAACCT
103104 TAAACCT
1 TAAACCT
*
103111 TAAACCA
1 TAAACCT
103118 T-AACCT
1 TAAACCT
103124 TAAACC
1 TAAACC
103130 CTAACCCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:103124 original size:13 final size:13
Alignment explanation
Indices: 103106--103135 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
103096 ATAAACCTTA
103106 AACCTTAAACCAT
1 AACCTTAAACCAT
*
103119 AACCTTAAACCCT
1 AACCTTAAACCAT
103132 AACC
1 AACC
103136 CTAACTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (13 bp):
AACCTTAAACCAT
Found at i:103254 original size:26 final size:26
Alignment explanation
Indices: 103157--103279 Score: 94
Period size: 26 Copynumber: 4.8 Consensus size: 26
103147 CCTTAACTTA
103157 ACCA-TAACCATT-AACCCT-AACACT
1 ACCATTAACC-TTAAACCCTAAACACT
*
103181 ATCCA-TAACCTTAAAACCT-AACACT
1 A-CCATTAACCTTAAACCCTAAACACT
* * * * * *
103206 AACCCTAAACCCTACATCTTAAACACT
1 -ACCATTAACCTTAAACCCTAAACACT
* * *
103233 ATCATTAACCTTAAACTCTAAACCCT
1 ACCATTAACCTTAAACCCTAAACACT
103259 ACCATTAACCTTAAACCCTAA
1 ACCATTAACCTTAAACCCTAA
103280 CATTAACCTT
Statistics
Matches: 76, Mismatches: 18, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
24 3 0.04
25 21 0.28
26 46 0.61
27 6 0.08
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.24
Consensus pattern (26 bp):
ACCATTAACCTTAAACCCTAAACACT
Found at i:103275 original size:19 final size:19
Alignment explanation
Indices: 103251--103292 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
103241 CCTTAAACTC
*
103251 TAAACCCTACCATTAACCT
1 TAAACCCTAACATTAACCT
103270 TAAACCCTAACATTAACCT
1 TAAACCCTAACATTAACCT
103289 TAAA
1 TAAA
103293 TATCAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAACCCTAACATTAACCT
Found at i:103303 original size:17 final size:14
Alignment explanation
Indices: 103272--103370 Score: 59
Period size: 12 Copynumber: 7.1 Consensus size: 14
103262 ATTAACCTTA
103272 AACCCT-AA-CATT
1 AACCCTAAATCATT
*
103284 AACCTTAAATATCAATT
1 AACCCT-AA-ATC-ATT
*
103301 AACCCT-AA-CATC
1 AACCCTAAATCATT
103313 AACCCTAAATCATT
1 AACCCTAAATCATT
*
103327 AACCTTAAATATCAATT
1 AACCCT-AA-ATC-ATT
*
103344 AACCCT-AA-CATC
1 AACCCTAAATCATT
103356 AACCCTAAATC-TT
1 AACCCTAAATCATT
103369 AA
1 AA
103371 ACATTAAACC
Statistics
Matches: 67, Mismatches: 8, Indels: 23
0.68 0.08 0.23
Matches are distributed among these distances:
12 21 0.31
13 9 0.13
14 12 0.18
15 5 0.07
16 4 0.06
17 16 0.24
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.27
Consensus pattern (14 bp):
AACCCTAAATCATT
Found at i:103356 original size:16 final size:16
Alignment explanation
Indices: 103294--103357 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 16
103284 AACCTTAAAT
103294 ATCAATTAACCCTAAC
1 ATCAATTAACCCTAAC
103310 ATC----AACCCTAA-
1 ATCAATTAACCCTAAC
* *
103321 ATC-ATTAACCTTAAAT
1 ATCAATTAACCCT-AAC
103337 ATCAATTAACCCTAAC
1 ATCAATTAACCCTAAC
103353 ATCAA
1 ATCAA
103358 CCCTAAATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
11 3 0.08
12 8 0.21
14 5 0.13
15 2 0.05
16 13 0.33
17 8 0.21
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (16 bp):
ATCAATTAACCCTAAC
Found at i:108401 original size:30 final size:29
Alignment explanation
Indices: 108358--108765 Score: 187
Period size: 30 Copynumber: 13.6 Consensus size: 29
108348 GAAGTTTTGG
*
108358 AGAATTTGGGGTTAAAATGTAATTTTGAA
1 AGAATTTGGGGTCAAAATGTAATTTTGAA
* * *
108387 AGAATTTAGGGGTTAAAAGGAAATTTT-ATGA
1 AGAATTT-GGGGTCAAAATGTAATTTTGA--A
*
108418 A-AATTTGGGGTCAAAATATAATTTT--A
1 AGAATTTGGGGTCAAAATGTAATTTTGAA
** *
108444 AGAAGGTTTATGGTCAAAATGTGATTTTGAGA
1 AGAA--TTTGGGGTCAAAATGTAATTTTGA-A
108476 A-AATTTGAGGGTCAAAATGTAATTTT-AA
1 AGAATTTG-GGGTCAAAATGTAATTTTGAA
*
108504 AGAAGTTTAGGGGTCAAAATGTGATTTTGGAA
1 AGAA-TTT-GGGGTCAAAATGTAATTTT-GAA
* * *
108536 A-AGTTTAAGAGTCAAAATGTAATTTTGGAA
1 AGAATTT-GGGGTCAAAATGTAATTTT-GAA
* * * * *
108566 A-AGTTTGGCAGTTAAAATGCAATTTTG-G
1 AGAATTTGG-GGTCAAAATGTAATTTTGAA
*
108594 AGAAGTGTGGGGGTTCAAAATGTAATTTTAGAGA
1 AGAA-T-TTGGGG-TCAAAATGTAATTTT-GA-A
* * * **
108628 AG-TTTTAGGGTTAAAATGTGTTTTTGCAA
1 AGAATTTGGGGTCAAAATGTAATTTTG-AA
* * **
108657 A-AGTTTGAGGGTGAAAATGGGATTTTGGAA
1 AGAATTTG-GGGTCAAAATGTAATTTT-GAA
* * *
108687 AG-GTTTGGAGGTTAAAATGTGATTTTGGAA
1 AGAATTTGG-GGTCAAAATGTAATTTT-GAA
**
108717 AG-ATTTGGGGGGTCAAAATGTGCTTTTGGAA
1 AGAATTT--GGGGTCAAAATGTAATTTT-GAA
108748 AG-ATTTGGGGGTCAAAAT
1 AGAATTT-GGGGTCAAAAT
108766 ATAGTTTTTA
Statistics
Matches: 304, Mismatches: 44, Indels: 61
0.74 0.11 0.15
Matches are distributed among these distances:
26 2 0.01
27 2 0.01
28 3 0.01
29 57 0.19
30 177 0.58
31 52 0.17
32 9 0.03
34 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
AGAATTTGGGGTCAAAATGTAATTTTGAA
Found at i:108532 original size:60 final size:60
Alignment explanation
Indices: 108352--108737 Score: 323
Period size: 60 Copynumber: 6.5 Consensus size: 60
108342 AAAAATGAAG
* * * **
108352 TTTTGGAGAATTTG-GGGTTAAAATGTAATTTTGAAAGAA-TTTAGGGGTTAAAAGGAAA
1 TTTTGGAAAATTTGAGGGTCAAAATGTAATTTTGAAAGAAGTTTAGGGGTTAAAATGTGA
* * * *
108410 TTTTATGAAAATTTG-GGGTCAAAATATAATTTT--AAGAAGGTTTA-TGGTCAAAATGTGA
1 TTTT-GGAAAATTTGAGGGTCAAAATGTAATTTTGAAAGAA-GTTTAGGGGTTAAAATGTGA
*
108468 TTTTGAGAAAATTTGAGGGTCAAAATGTAATTTT-AAAGAAGTTTAGGGGTCAAAATGTGA
1 TTTTG-GAAAATTTGAGGGTCAAAATGTAATTTTGAAAGAAGTTTAGGGGTTAAAATGTGA
* * * * **
108528 TTTTGGAAAAGTTTAAGAGTCAAAATGTAATTTTGGAA-AAGTTT-GGCAGTTAAAATGCAA
1 TTTTGGAAAA-TTTGAGGGTCAAAATGTAATTTTGAAAGAAGTTTAGG-GGTTAAAATGTGA
* * * * *
108588 TTTTGGAGAAGTGTGGGGGTTCAAAATGTAATTTT-AGAGAAGTTTTA-GGGTTAAAATGTGT
1 TTTTGGA-AAATTTGAGGG-TCAAAATGTAATTTTGAAAGAAG-TTTAGGGGTTAAAATGTGA
* * **
108649 TTTTGCAAAAGTTTGAGGGTGAAAATGGGATTTTGGAAAG--GTTT-GGAGGTTAAAATGTGA
1 TTTTGGAAAA-TTTGAGGGTCAAAATGTAATTTT-GAAAGAAGTTTAGG-GGTTAAAATGTGA
*
108709 TTTTGGAAAGATTTGGGGGGTCAAAATGT
1 TTTTGGAAA-ATTT-GAGGGTCAAAATGT
108738 GCTTTTGGAA
Statistics
Matches: 263, Mismatches: 43, Indels: 41
0.76 0.12 0.12
Matches are distributed among these distances:
57 5 0.02
58 26 0.10
59 61 0.23
60 109 0.41
61 55 0.21
62 7 0.03
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (60 bp):
TTTTGGAAAATTTGAGGGTCAAAATGTAATTTTGAAAGAAGTTTAGGGGTTAAAATGTGA
Found at i:108765 original size:121 final size:120
Alignment explanation
Indices: 108459--108774 Score: 338
Period size: 121 Copynumber: 2.6 Consensus size: 120
108449 GTTTATGGTC
*
108459 AAAATGTGATTTTGAGAAA-ATTT-GAGGGTCAAAATGTAATTTT-AAAGAAGTTTAGGGGTCAA
1 AAAATGTGATTTTG-GAAAGATTTGGGGGGTCAAAATGTAATTTTGAAAG-A-TTTAGGGGTCAA
* * *
108521 AATGTGATTTTGGAAAAGTTTAAGAGTCAAAATGTAATTTTGGAAAAGTTTGGCAGTT
63 AATGTGTTTTTGCAAAAGTTTAAGAGTCAAAATGGAATTTTGGAAAAGTTTGGCAGTT
** * * * *
108579 AAAATGCAATTTTGGAGAAG-TGTGGGGGTTCAAAATGTAATTTTAGAGAAGTTTTA-GGGTTAA
1 AAAATGTGATTTTGGA-AAGATTTGGGGGGTCAAAATGTAATTTT-GA-AAGATTTAGGGGTCAA
* * * * *
108642 AATGTGTTTTTGCAAAAGTTTGAGGGTGAAAATGGGATTTTGGAAAGGTTTGG-AGGTT
63 AATGTGTTTTTGCAAAAGTTTAAGAGTCAAAATGGAATTTTGGAAAAGTTTGGCA-GTT
** *
108700 AAAATGTGATTTTGGAAAGATTTGGGGGGTCAAAATGTGCTTTTGGAAAGATTTGGGGGTCAAAA
1 AAAATGTGATTTTGGAAAGATTTGGGGGGTCAAAATGTAATTTT-GAAAGATTTAGGGGTCAAAA
*
108765 TATAGTTTTT
65 TGT-GTTTTT
108775 AAATAAAATA
Statistics
Matches: 160, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
119 2 0.01
120 26 0.16
121 118 0.74
122 10 0.06
123 1 0.01
124 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (120 bp):
AAAATGTGATTTTGGAAAGATTTGGGGGGTCAAAATGTAATTTTGAAAGATTTAGGGGTCAAAAT
GTGTTTTTGCAAAAGTTTAAGAGTCAAAATGGAATTTTGGAAAAGTTTGGCAGTT
Found at i:111389 original size:49 final size:49
Alignment explanation
Indices: 111111--112047 Score: 681
Period size: 49 Copynumber: 19.1 Consensus size: 49
111101 GTTTTCTTAA
* * * * *
111111 GGTACTGGGTTCGCCGTTGCGGTCTTAACCTTTCCCTTCATATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
* ** * * * * *
111160 GGTGCCGAATTCGCCGTTGCAGACTTAATCC-TTCCCATCATATCTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-AT
* *** ** * * * *
111210 AGTATTAGGTTTACCATTACGACCTCAACCTTTCCCATTACA-CTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
* * * * * * *
111258 GGTGCCGGATTCGCCGTTGTGGTCTTAATCCTTT-CTATCACATCTTCAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCAT
** * * * * * * * * *
111307 GGTACTAGGTTTGTCGTTGCAGCCTTAAACTTTCCCTTTAAATCCTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
* * * * * *
111356 GGTATCGGGTTTGCCGTTGTGGCCTCAACCTTTCCTATCACATCTTTTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATC-TTCAT
* * *
111406 GGTATCGAGTTCGCCGTTGCAGCCTCAACCTTT--C--C-CATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
** * * * * *
111450 GGTACCGGGTTCATCGTTGCGGCCTCAACATTTTCCTTTAAATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
** * ** * *
111499 GGTACCGGGTTTACCGTTACGGCCTCAATATTTCCCTTCAAATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
** * *
111548 GGTATTGGGTTCGCCGTTGTGACCTCAACCTTTCCCATCACA-CTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
** * * * * * * * *
111596 GGTGTCGGATTCACCGTTGTGGCATTAATCTTT-CCATCACGTCATCTAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-AT
* * * *
111645 GGTACTGGGTTTC-CCGTTACGGCCTCAACCTTTCCCTTCAAATCTTCAT
1 GGTACCGGG-TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
* * * *
111694 GGTACCGCGTTCGTCGTTGCAGCCTCAACCTTTCCCATCACATCTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-AT
* * * * * *
111744 GGTACCGGGTTCGTCATTGCAGCCTTAACCTTTCCCTTCATATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
* * * * * *
111793 GGTATCGGGTTCGCAGTTGTGGACTCAACCTTTCCCATCACATTTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-AT
** * * * *
111843 GGTACTAGGTTCGCCGTTGTGGCCTCAACTTTTCCCATCACATTTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-AT
* *
111893 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATTTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-AT
* * * *
111943 GGTACCGGGTTCGTCGTTGCGGCCTCAACTTTTCCCATCACATTTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-AT
* * *
111993 GGTACCGGGTTCGCCGTTGCGTCCTCAACCTTTCCCTTCATATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
112042 GGTACC
1 GGTACC
112048 TTAGTTCATT
Statistics
Matches: 695, Mismatches: 174, Indels: 38
0.77 0.19 0.04
Matches are distributed among these distances:
44 30 0.04
45 4 0.01
46 2 0.00
47 7 0.01
48 62 0.09
49 299 0.43
50 291 0.42
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.35
Consensus pattern (49 bp):
GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
Found at i:111934 original size:100 final size:99
Alignment explanation
Indices: 111111--112047 Score: 639
Period size: 99 Copynumber: 9.6 Consensus size: 99
111101 GTTTTCTTAA
* * * * * * * **
111111 GGTACTGGGTTCGCCGTTGCGGTCTTAACCTTTCCCTTCATATCTTC-ATGGTGCCGAATTCGCC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
* * * * *
111175 GTTGCAGACTTAATCC-TTCCCATCATATCTTCTAA
66 GTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-AT
* *** ** * * * * * * *
111210 AGTATTAGGTTTACCATTACGACCTCAACCTTTCCCATTACA-CTTC-ATGGTGCCGGATTCGCC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
* * * * *
111273 GTTGTGGTCTTAATCCTTT-CTATCACATCTTCAA
66 GTTGCGGCCTCAA-CCTTTCCCATCACATCTTCAT
** * * * * * * * * * * * *
111307 GGTACTAGGTTTGTCGTTGCAGCCTTAAACTTTCCCTTTAAATCCTC-ATGGTATCGGGTTTGCC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
* * * *
111371 GTTGTGGCCTCAACCTTTCCTATCACATCTTTTAA
66 GTTGCGGCCTCAACCTTTCCCATCACATC-TTCAT
* * * * **
111406 GGTATCGAGTTCGCCGTTGCAGCCTCAACCTTT--C--C-CATCTTC-ATGGTACCGGGTTCATC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
* * * * *
111465 GTTGCGGCCTCAACATTTTCCTTTAAATCTTCAT
66 GTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
** * ** * * * **
111499 GGTACCGGGTTTACCGTTACGGCCTCAATATTTCCCTTCAAATCTTC-ATGGTATTGGGTTCGCC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
* *
111563 GTTGTGACCTCAACCTTTCCCATCACA-CTTCAT
66 GTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
** * * * * * * * * * *
111596 GGTGTCGGATTCACCGTTGTGGCATTAATCTTT-CCATCACGTCATCTATGGTACTGGGTTTC-C
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGG-TTCGC
* * *
111659 CGTTACGGCCTCAACCTTTCCCTTCAAATCTTCAT
65 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
* * * *
111694 GGTACCGCGTTCGTCGTTGCAGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGTC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
* * * * *
111759 ATTGCAGCCTTAACCTTTCCCTTCATATCTTCAT
66 GTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
* * * * * **
111793 GGTATCGGGTTCGCAGTTGTGGACTCAACCTTTCCCATCACATTTTCTAAGGTACTAGGTTCGCC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
* * * *
111858 GTTGTGGCCTCAACTTTTCCCATCACATTTTCTAA
66 GTTGCGGCCTCAACCTTTCCCATCACATCTTC-AT
* *
111893 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATTTTCTAAGGTACCGGGTTCGTC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
* * *
111958 GTTGCGGCCTCAACTTTTCCCATCACATTTTCTAA
66 GTTGCGGCCTCAACCTTTCCCATCACATCTTC-AT
* * * *
111993 GGTACCGGGTTCGCCGTTGCGTCCTCAACCTTTCCCTTCATATCTTC-ATGGTACC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACC
112048 TTAGTTCATT
Statistics
Matches: 667, Mismatches: 156, Indels: 30
0.78 0.18 0.04
Matches are distributed among these distances:
93 28 0.04
94 40 0.06
95 1 0.00
96 9 0.01
97 103 0.15
98 154 0.23
99 196 0.29
100 136 0.20
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.35
Consensus pattern (99 bp):
GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCC
GTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
Found at i:120644 original size:38 final size:38
Alignment explanation
Indices: 120591--120700 Score: 193
Period size: 38 Copynumber: 2.9 Consensus size: 38
120581 AGCATTCATG
* * *
120591 TAATTATATAATTTCAGAACGAATTCTGTCCAAAGAAA
1 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAAGAAA
120629 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAAGAAA
1 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAAGAAA
120667 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAA
1 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAA
120701 ATTTCTTTGG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 69 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (38 bp):
TAATTAAATAGTTTCAGAACAAATTCTGTCCAAAGAAA
Found at i:124810 original size:21 final size:21
Alignment explanation
Indices: 124775--124831 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
124765 CCCCTGCATT
124775 TTTATTTTGTTTTAATTTAAT-CC
1 TTTA-TTT-TTTTAATTT-ATGCC
124798 TTTATTTTTTTAATTTATGCC
1 TTTATTTTTTTAATTTATGCC
*
124819 TTTAATTTGTTTA
1 TTT-ATTTTTTTA
124832 CAATTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 2 0.06
21 14 0.45
22 11 0.35
23 4 0.13
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTATTTTTTTAATTTATGCC
Found at i:125059 original size:17 final size:15
Alignment explanation
Indices: 125033--125076 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
125023 AAATTATATC
125033 ATTT-TTATTTTCTT
1 ATTTATTATTTTCTT
*
125047 ATTTTAATTATTTTTTT
1 A-TTT-ATTATTTTCTT
125064 ATTTATTATTTTC
1 ATTTATTATTTTC
125077 AACTATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.44
16 3 0.12
17 10 0.40
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTATTATTTTCTT
Found at i:127854 original size:11 final size:11
Alignment explanation
Indices: 127840--127864 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
127830 AAAAATATTA
127840 TTTTAATTTTT
1 TTTTAATTTTT
127851 TTTTAATTTTT
1 TTTTAATTTTT
127862 TTT
1 TTT
127865 AGTTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTAATTTTT
Done.