Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 16 of 52
Found at i:2454917 original size:20 final size:20
Alignment explanation
Indices: 2454889--2454986 Score: 128
Period size: 20 Copynumber: 4.9 Consensus size: 20
2454879 GTAAAAAAAC
2454889 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTCA
* *
2454909 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTCA
2454929 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTCA
* *
2454949 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTCA
2454969 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
2454987 TGGGTACTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.03
20 63 0.94
21 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTCA
Found at i:2454934 original size:40 final size:40
Alignment explanation
Indices: 2454889--2454986 Score: 196
Period size: 40 Copynumber: 2.5 Consensus size: 40
2454879 GTAAAAAAAC
2454889 AGAATGTATCGATACATTCATACATGTATCGATACATTGA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGA
2454929 AGAATGTATCGATACATTCATACATGTATCGATACATTGA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGA
2454969 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
2454987 TGGGTACTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (40 bp):
AGAATGTATCGATACATTCATACATGTATCGATACATTGA
Found at i:2456395 original size:166 final size:164
Alignment explanation
Indices: 2456149--2456513 Score: 403
Period size: 166 Copynumber: 2.2 Consensus size: 164
2456139 CTTCAAAACT
* * ** *
2456149 AATTTAATAATAATATTAGATGAATTTTAAAAATTTTAAACCAAGAGAAATCACCTCGAAAACAT
1 AATTAAATAATAATATTTGAT-AATTTTAAAAATTAAAAACCAAGAAAAATCACCTCGAAAACAT
* * * * * ** *
2456214 TTACGGAGTAGAAAACTAGATTTTTTTGGAAATAGGGGGATTTCAAAG-AAAAATGA-AAGACTC
65 TTACGAAGCAGAAAACTACA-TTTTTCGGAAACAGGGAAATTTCAAAGAAAAAATGACAA-ACTA
* *
2456277 ATGAAAATAAATGAATTTTTTGAAACTGATTTAATATA
128 ATGAAAATAAATAAATTTTTT-AAACTGATTTAAAATA
* * ** *
2456315 AATTAAATAGTAATATTTGATAAATTTTAAAAATTAAAAACCATGAAAAATTTTCC-CGAAAATA
1 AATTAAATAATAATATTTGAT-AATTTTAAAAATTAAAAACCAAGAAAAA-TCACCTCGAAAACA
* * * *
2456379 TTTACGAAGCAGAAAACTCCATTTTTCGGAAGCATGGAAATTTCAAGGAAAAAATGACAAACTAA
64 TTTACGAAGCAGAAAACTACATTTTTCGGAAACAGGGAAATTTCAAAGAAAAAATGACAAACTAA
* *
2456444 TGAAAATGAATAAATTTTTTAAACTGATTTAAAATT
129 TGAAAATAAATAAATTTTTTAAACTGATTTAAAATA
* *
2456480 AATTAAATAATAATATTTTATTATTTTAAAAATT
1 AATTAAATAATAATATTTGATAATTTTAAAAATT
2456514 TTGTATCAAT
Statistics
Matches: 166, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
164 12 0.07
165 53 0.32
166 96 0.58
167 5 0.03
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (164 bp):
AATTAAATAATAATATTTGATAATTTTAAAAATTAAAAACCAAGAAAAATCACCTCGAAAACATT
TACGAAGCAGAAAACTACATTTTTCGGAAACAGGGAAATTTCAAAGAAAAAATGACAAACTAATG
AAAATAAATAAATTTTTTAAACTGATTTAAAATA
Found at i:2461990 original size:155 final size:154
Alignment explanation
Indices: 2461703--2462386 Score: 870
Period size: 155 Copynumber: 4.4 Consensus size: 154
2461693 CTTCGACGTG
* * *
2461703 AAAGGACTTAAAAAGGATAATGGATGAGA-AAATCCTATCCTAAATATCTACCTTTGGCATAAAA
1 AAAGGACTTAAAAAGGATAATAGATGAGATGAA-CCTATCCTAAATATCTACCTTCGGCATAAAA
* * ** * * * * * * * *
2461767 TCAGACCCGGTGATAACTTAAGACTCGAGTATGAAAAATTACGAAAATACTCTTAGGGGATACCT
65 GCGGACCTAGTAACAACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCTTA-GGGATACCT
* *
2461832 TTGACGTAAAAGTACCCGAGACCCTT
129 TTGACGTAAAAGTACCCGATACCCCT
* * * * * *
2461858 AAAGGACTTAAAATGGATCATGGATAAGATGAACTTATCCTAAACATCTACCTTCGGCATAAAAG
1 AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAG
* * * * * **
2461923 CGGACCTAGCAACAACCTAGGACTCAATTTTAAAAAAAATA-GAAAATGCCCTTAGAGGATATAT
66 CGGACCTAGTAACAACCTAGGACTCGATTCT-AAAAAATTACGAAAATACCCTTAG-GGATACCT
*
2461987 TTGACGTAAAAGTACCTGATACCCCT
129 TTGACGTAAAAGTACCCGATACCCCT
2462013 AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAG
1 AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAG
* *
2462078 CGGACCTAGTAACAACCTAGGACTCGATTCTCAAAAATTACGAAAATACCCCTAGGAGATACCTT
66 CGGACCTAGTAACAACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCTTAGG-GATACCTT
*
2462143 TGACGTAAAAGTACCCAATACCCCT
130 TGACGTAAAAGTACCCGATACCCCT
*
2462168 AAAGGACTT-AAAAGGATAATAGATGAGATAAACCTATCCTAAATATCTACCTTCGGCATAAAAG
1 AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAG
* ** * * *
2462232 CTGACCCGGTGACAACCTAGGACTCGATTCTGAAAAATTATGAAAATACCCTTAGGGGATACCTT
66 CGGACCTAGTAACAACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCTTA-GGGATACCTT
* * *
2462297 TGACTTAAAAGTACCTGATACCTCT
130 TGACGTAAAAGTACCCGATACCCCT
* * *
2462322 AAAGGACTTAAAAAGGATAATAGATGACATGAACCTATCCTAAATATCTATCTTTGGCATAAAAG
1 AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAG
2462387 TAGACTCGGT
Statistics
Matches: 461, Mismatches: 61, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
154 148 0.32
155 304 0.66
156 9 0.02
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (154 bp):
AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAG
CGGACCTAGTAACAACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCTTAGGGATACCTTT
GACGTAAAAGTACCCGATACCCCT
Found at i:2462356 original size:309 final size:310
Alignment explanation
Indices: 2461703--2462391 Score: 943
Period size: 309 Copynumber: 2.2 Consensus size: 310
2461693 CTTCGACGTG
* *
2461703 AAAGGACTTAAAAAGGATAATGGATGAGA-AAATCCTATCCTAAATATCTACCTTTGGCATAAAA
1 AAAGGACTTAAAAAGGATAATAGATGAGATGAA-CCTATCCTAAATATCTACCTTTGGCATAAAA
* * * * * * * * *
2461767 TCAGACCCGGTGATAACTTAAGACTCGAGTATGAAAAATTACGAAAATACTCTTAGGGGATACCT
65 GCAGACCCAGTAACAACCTAAGACTCGAGTATCAAAAATTACGAAAATACCCCTAGGAGATACCT
* * * * * *
2461832 TTGACGTAAAAGTACCCGAGACCCTTAAAGGACTTAAAATGGATCATGGATAAGATGAACTTATC
130 TTGACGTAAAAGTACCCAAGACCCCTAAAGGACTTAAAATGGATAATAGATAAGATAAACCTATC
* *
2461897 CTAAACATCTACCTTCGGCATAAAAGCGGACCTAGCAACAACCTAGGACTCAATTTTAAAAAAAA
195 CTAAACATCTACCTTCGGCATAAAAGCGGACCCAGCAACAACCTAGGACTCAATTTGAAAAAAAA
* *
2461962 TAGAAAATGCCCTTAGAGGATATATTTGACGTAAAAGTACCTGATACCCCT
260 TAGAAAATACCCTTAGAGGATACATTTGACGTAAAAGTACCTGATACCCCT
*
2462013 AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAG
1 AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTTGGCATAAAAG
* * * * *
2462078 CGGACCTAGTAACAACCTAGGACTCGATTCTCAAAAATTACGAAAATACCCCTAGGAGATACCTT
66 CAGACCCAGTAACAACCTAAGACTCGAGTATCAAAAATTACGAAAATACCCCTAGGAGATACCTT
* *
2462143 TGACGTAAAAGTACCCAATACCCCTAAAGGACTTAAAA-GGATAATAGATGAGATAAACCTATCC
131 TGACGTAAAAGTACCCAAGACCCCTAAAGGACTTAAAATGGATAATAGATAAGATAAACCTATCC
* * * ** * **
2462207 TAAATATCTACCTTCGGCATAAAAGCTGACCCGGTGACAACCTAGGACTCGATTCTGAAAAATTA
196 TAAACATCTACCTTCGGCATAAAAGCGGACCCAGCAACAACCTAGGACTCAATT-TGAAAAAAAA
* * * *
2462272 T-GAAAATACCCTTAGGGGATACCTTTGACTTAAAAGTACCTGATACCTCT
260 TAGAAAATACCCTTAGAGGATACATTTGACGTAAAAGTACCTGATACCCCT
* *
2462322 AAAGGACTTAAAAAGGATAATAGATGACATGAACCTATCCTAAATATCTATCTTTGGCATAAAAG
1 AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTTGGCATAAAAG
*
2462387 TAGAC
66 CAGAC
2462392 TCGGTAATCT
Statistics
Matches: 331, Mismatches: 46, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
309 176 0.53
310 153 0.46
311 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (310 bp):
AAAGGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTTGGCATAAAAG
CAGACCCAGTAACAACCTAAGACTCGAGTATCAAAAATTACGAAAATACCCCTAGGAGATACCTT
TGACGTAAAAGTACCCAAGACCCCTAAAGGACTTAAAATGGATAATAGATAAGATAAACCTATCC
TAAACATCTACCTTCGGCATAAAAGCGGACCCAGCAACAACCTAGGACTCAATTTGAAAAAAAAT
AGAAAATACCCTTAGAGGATACATTTGACGTAAAAGTACCTGATACCCCT
Found at i:2463067 original size:128 final size:125
Alignment explanation
Indices: 2462784--2463151 Score: 488
Period size: 128 Copynumber: 2.9 Consensus size: 125
2462774 TCAAAAAGTG
* * ** **
2462784 TCATTTCGTACCTTGATGGAAACCCGCCAAGATAC-AAAAAATTTGAAATCTTTTAATACCCCTA
1 TCATTTCGTACCTTAATGGATACCCGAAAAGATACGAAAATTTTTGAAATCTTTT-ATA-CCCTA
* * * *
2462848 CGGATACCCATAGGAATATAAAAGATTAAAAATAATTAATATTTATTTGTTTTTGAAAAAAA
64 CGGATACCCATAGGAATATAAAAAATTAAAAATGATTAATATTTATTTATGTTTGAAAAAAA
* * * **
2462910 TTATTTCGTACCTTAAAGTATACTTGAAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCTTA
1 TCATTTCGTACCTTAATGGATACCCGAAAAGATACGAAAA-TTTTTGAAATCTTTTATACCC-TA
*
2462975 CGGATACCTATAGGAATATAAAACAAATTAAAAATGATTAATATTTATTTATGTTTGAAAAAAA
64 CGGATACCCATAGGAATAT-AAA-AAATTAAAAATGATTAATATTTATTTATGTTTGAAAAAAA
2463039 -CATTTCGTACCTTAATGGATACCCGAAAAGATACGAAAACTTTTTGAAATCTTTTATATCCCTA
1 TCATTTCGTACCTTAATGGATACCCGAAAAGATACGAAAA-TTTTTGAAATCTTTTATA-CCCTA
* *
2463103 CGGATACCCATAGGAATATAAAAAATTAAAAACGATTAATATTTGTTTA
64 CGGATACCCATAGGAATATAAAAAATTAAAAATGATTAATATTTATTTA
2463152 AATTAACAGG
Statistics
Matches: 211, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
126 54 0.26
127 30 0.14
128 88 0.42
129 39 0.18
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (125 bp):
TCATTTCGTACCTTAATGGATACCCGAAAAGATACGAAAATTTTTGAAATCTTTTATACCCTACG
GATACCCATAGGAATATAAAAAATTAAAAATGATTAATATTTATTTATGTTTGAAAAAAA
Found at i:2465100 original size:20 final size:18
Alignment explanation
Indices: 2465062--2465100 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2465052 AAAATACCGT
*
2465062 ATTTCAAAAAAAAAGAAA
1 ATTTCAAAAAAAAACAAA
2465080 ATTTCAAGAAAAAAATCAAA
1 ATTTCAA-AAAAAAA-CAAA
2465100 A
1 A
2465101 GCTCATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.18
Consensus pattern (18 bp):
ATTTCAAAAAAAAACAAA
Found at i:2465203 original size:166 final size:165
Alignment explanation
Indices: 2464738--2465237 Score: 612
Period size: 166 Copynumber: 3.0 Consensus size: 165
2464728 GCTTTTCAAG
* * * *
2464738 AAAAGGAAAATTCCAACAAAAAAATTCCAAAACTCATGAAAATGAATTAATTTTTTAAAACTGAA
1 AAAAAGAAAATTTCAA-AAAAAAA-TCCAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAA
* * * * * * *
2464803 TTAATATG-AATCAAATGATGATGTTTTATGAATTCTAAAAATTGAAAACCGAGAAAAATCCCCT
64 TTAATATGAAAT-AAATAATGATATTTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCCTCT
* ** *
2464867 CGAAAAAATTTACAAAGTAGAAAATAACGTATTTAGAA
128 CAAAAAAATTTACGGAGTAGAAAATAACGTATTTAAAA
* * * *
2464905 AAAATGAGAGTTTCAAAGAAAAAATCCAAAACTCATAAAAATGAATGAATTTTTGAAAACTGAAT
1 AAAAAGAAAATTTCAAA-AAAAAATCCAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAAT
* *
2464970 TACTATGAAATAAATAATGATATTTGATGAATTTT-AAAATTAAAAACTGAGAAAAAACCTCTCA
65 TAATATGAAATAAATAATGATATTTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCCTCTCA
*
2465034 AAAAAATTTACGGAGTAGAAAATACCGTATTTCAAAA
130 AAAAAATTTACGGAGTAGAAAATAACGTATTT-AAAA
*
2465071 AAAAAGAAAATTTCAAGAAAAAAAT-CAAAAGCTCATGAAAATGAATGAATTTTTGAAAATTGAA
1 AAAAAGAAAATTTCAA-AAAAAAATCCAAAA-CTCATGAAAATGAATGAATTTTTGAAAACTGAA
** * * * *
2465135 TTAATATGAAATAAATAAAAATATTTGATGAATTTTAAAAATT-AAAATTAAGAGAAATCCTTTC
64 TTAATATGAAATAAATAATGATATTTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCCTCTC
* **
2465199 AAAAAAATTTACGGAGAAGAAAATCTCGTAATTTAAAA
129 AAAAAAATTTACGGAGTAGAAAATAACGT-ATTTAAAA
2465237 A
1 A
2465238 TACAATGAAT
Statistics
Matches: 289, Mismatches: 37, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
165 58 0.20
166 199 0.69
167 32 0.11
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (165 bp):
AAAAAGAAAATTTCAAAAAAAAATCCAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATT
AATATGAAATAAATAATGATATTTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCCTCTCAA
AAAAATTTACGGAGTAGAAAATAACGTATTTAAAA
Found at i:2471286 original size:157 final size:156
Alignment explanation
Indices: 2471088--2471402 Score: 343
Period size: 156 Copynumber: 2.0 Consensus size: 156
2471078 TTCCTTTTAT
* * * *
2471088 TTCATTAATTTTCCTTTTTTTCTTGAAATTCTTCTTATTTTC-GAAATACGAGGTTTT-TAACTC
1 TTCATTAATTTTCATTTTTTCCTTAAAATTCTTCTTATTTTCAAAAATACGA-GTTTTCT-ACTC
* ** * * ** * *
2471151 CGTAATTATTTTCAG-GAGGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTATTA
64 CATAAAGATTTTC-GCGAGGG-TTTTTCTCAATTTGAAATTTTTAAAATTCATCAAATATCATCA
2471215 TTTAATTCATATT-AATTCAATTTTCAAAAA
127 TTTAATTCATATTAAATT-AATTTTCAAAAA
* * ** *
2471245 TTCATTCATTTTTCATTTTTTCCTTAAAATTCTT-TTGTTTTCAAAAATTTGAGTTTTCTATTCC
1 TTCATT-AATTTTCATTTTTTCCTTAAAATTCTTCTTATTTTCAAAAATACGAGTTTTCTACTCC
* *
2471309 ATAAAGGTTTTCGCGAGGGTTTTTCTCAATTTGAAATTTTTAAAATTTATCAAATATCATCATTT
65 ATAAAGATTTTCGCGAGGGTTTTTCTCAATTTGAAATTTTTAAAATTCATCAAATATCATCATTT
* *
2471374 AATTCATATTAAATTATTTTTGAAAAA
130 AATTCATATTAAATTAATTTTCAAAAA
2471401 TT
1 TT
2471403 ATTTTATTTT
Statistics
Matches: 131, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
156 62 0.47
157 39 0.30
158 30 0.23
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (156 bp):
TTCATTAATTTTCATTTTTTCCTTAAAATTCTTCTTATTTTCAAAAATACGAGTTTTCTACTCCA
TAAAGATTTTCGCGAGGGTTTTTCTCAATTTGAAATTTTTAAAATTCATCAAATATCATCATTTA
ATTCATATTAAATTAATTTTCAAAAA
Found at i:2474374 original size:16 final size:17
Alignment explanation
Indices: 2474347--2474380 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2474337 TCCTACACGG
*
2474347 AATAATAAATTTATTTT
1 AATAATAAATTTAGTTT
2474364 AATAA-AAATTTAGTTT
1 AATAATAAATTTAGTTT
2474380 A
1 A
2474381 GACAATTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AATAATAAATTTAGTTT
Found at i:2475642 original size:19 final size:20
Alignment explanation
Indices: 2475618--2475677 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
2475608 TTTGAATTTC
2475618 AACAAT-TTGTATCGATACA
1 AACAATATTGTATCGATACA
2475637 AACAATAATTGTATCGATACA
1 AACAAT-ATTGTATCGATACA
* * *
2475658 TA-AGTGTTGTATCGATACA
1 AACAATATTGTATCGATACA
2475677 A
1 A
2475678 TGTATCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 19 0.54
20 2 0.06
21 14 0.40
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (20 bp):
AACAATATTGTATCGATACA
Found at i:2475683 original size:32 final size:32
Alignment explanation
Indices: 2475646--2475940 Score: 563
Period size: 32 Copynumber: 9.2 Consensus size: 32
2475636 AAACAATAAT
*
2475646 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
2475678 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
2475710 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
*
2475742 TGTATCGATGAATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
2475774 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
2475806 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
2475838 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
*
2475870 TGTATAGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
2475902 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
2475934 TGTATCG
1 TGTATCG
2475941 CTACGAAGCT
Statistics
Matches: 258, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 258 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (32 bp):
TGTATCGATGCATAAGTGTTGTATCGATACAA
Found at i:2476073 original size:20 final size:20
Alignment explanation
Indices: 2476048--2476085 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2476038 ATTTTACCCA
2476048 GATGTATCGATACATTATTC
1 GATGTATCGATACATTATTC
2476068 GATGTATCGATACATTAT
1 GATGTATCGATACATTAT
2476086 ACATGCAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (20 bp):
GATGTATCGATACATTATTC
Found at i:2487229 original size:20 final size:20
Alignment explanation
Indices: 2487204--2487241 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2487194 CTGTTGGACT
*
2487204 TAATGTATCGATACAATTCA
1 TAATGTATCAATACAATTCA
2487224 TAATGTATCAATACAATT
1 TAATGTATCAATACAATT
2487242 ATAGCCATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (20 bp):
TAATGTATCAATACAATTCA
Found at i:2487376 original size:13 final size:13
Alignment explanation
Indices: 2487358--2487382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2487348 TATAAAGAAC
2487358 ATGTATCGATACA
1 ATGTATCGATACA
2487371 ATGTATCGATAC
1 ATGTATCGATAC
2487383 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2488973 original size:36 final size:36
Alignment explanation
Indices: 2488926--2488999 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
2488916 TCCTTTGTTT
*
2488926 GGAAAGTTAAAAAGGTCGGCATTTTGGTGGGAATTA
1 GGAAAGTTAAAAAGGTCGGCATTATGGTGGGAATTA
*
2488962 GGAAAGTTAAAAAGGTCGGTATTATGGTGGGAATTA
1 GGAAAGTTAAAAAGGTCGGCATTATGGTGGGAATTA
2488998 GG
1 GG
2489000 GTCAACTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.27
Consensus pattern (36 bp):
GGAAAGTTAAAAAGGTCGGCATTATGGTGGGAATTA
Found at i:2489742 original size:33 final size:32
Alignment explanation
Indices: 2489701--2489779 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
2489691 GTTTTGGATG
* * * *
2489701 GATG-ATTTGATGAAAAAGAAAGTGTTTTCGTT
1 GATGAATTTGATGAAAAACAAAGAGATTT-GAT
*
2489733 GATGAATTTGACGAAAAACAAAGAGATTTGAT
1 GATGAATTTGATGAAAAACAAAGAGATTTGAT
2489765 GA-GAATTTGATGAAA
1 GATGAATTTGATGAAA
2489780 TTTGAAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 12 0.30
32 8 0.20
33 20 0.50
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.30
Consensus pattern (32 bp):
GATGAATTTGATGAAAAACAAAGAGATTTGAT
Found at i:2491017 original size:143 final size:143
Alignment explanation
Indices: 2490759--2491043 Score: 464
Period size: 143 Copynumber: 2.0 Consensus size: 143
2490749 CGAAAGTGCT
* * * *
2490759 CTTTCTATCAACTTTAGAACCACTAAAATCTGCATCCGAATAAGCATTTAAAGATAGAGAGGATT
1 CTTTCTATCAACTTTAGAACCACCAAAATCTGCATCCAAATAAGCATGTAAAAATAGAGAGGATT
*
2490824 CTTTTGGGTACCATAAACCTAAGTTAGGAGTATCTCGTAAGTATTAAAAAATTCTTTTTAC-AGC
66 CTTTTGGGTACCATAAACCTAAGTTAGGAGTATCTCATAAGTATTAAAAAATTCTTTTTACGA-C
2490888 AAGTAAGTGAGACA
130 AAGTAAGTGAGACA
*
2490902 CTTTCTATCAACTTTAGAACCACCAAAATCTGTATCCAAATAAGCATGTAAAAATAGAGAGGATT
1 CTTTCTATCAACTTTAGAACCACCAAAATCTGCATCCAAATAAGCATGTAAAAATAGAGAGGATT
* * * *
2490967 CTTTTGGGTACCATAAACCTAAGTTGGGAGTATCTCATAAGTATTTAAAAATTCTTTTTGCGATA
66 CTTTTGGGTACCATAAACCTAAGTTAGGAGTATCTCATAAGTATTAAAAAATTCTTTTTACGACA
2491032 AGTAAGTGAGAC
131 AGTAAGTGAGAC
2491044 TCTCTAGGTG
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
143 130 0.99
144 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (143 bp):
CTTTCTATCAACTTTAGAACCACCAAAATCTGCATCCAAATAAGCATGTAAAAATAGAGAGGATT
CTTTTGGGTACCATAAACCTAAGTTAGGAGTATCTCATAAGTATTAAAAAATTCTTTTTACGACA
AGTAAGTGAGACA
Found at i:2494514 original size:3 final size:3
Alignment explanation
Indices: 2494506--2494539 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2494496 CGAGTCAACC
* *
2494506 TCA TCA TCA TCA TCA TCA TCT TCA TCT TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
2494540 TATTAATGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:2497121 original size:13 final size:13
Alignment explanation
Indices: 2497103--2497127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2497093 ATATTACTTA
2497103 GTATCGATACATT
1 GTATCGATACATT
2497116 GTATCGATACAT
1 GTATCGATACAT
2497128 GTTCTGTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2497124 original size:33 final size:32
Alignment explanation
Indices: 2497082--2497145 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
2497072 CACACCCAAA
2497082 TGTATCGATACATATTACT-TAGTATCGATACAT
1 TGTATCGATACATATT-CTGT-GTATCGATACAT
*
2497115 TGTATCGATACATGTTCTGTGTATCGATACA
1 TGTATCGATACATATTCTGTGTATCGATACA
2497146 CCATAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATATTCTGTGTATCGATACAT
Found at i:2497255 original size:32 final size:32
Alignment explanation
Indices: 2497214--2497275 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2497204 TACATGGTAA
*
2497214 ATTGTATCGATACATTAAGCCCAATGGCTATT
1 ATTGTATCGATACATTAAGCCCAACGGCTATT
*
2497246 ATTGTATCGATACATTGAGCCCAACGGCTA
1 ATTGTATCGATACATTAAGCCCAACGGCTA
2497276 GAATTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (32 bp):
ATTGTATCGATACATTAAGCCCAACGGCTATT
Found at i:2497750 original size:36 final size:35
Alignment explanation
Indices: 2497703--2497805 Score: 118
Period size: 34 Copynumber: 2.9 Consensus size: 35
2497693 AGTGATTGAG
2497703 AGGTTCTATCTTAACCTTTGAAAAAGATAGGGAGAA
1 AGGTTCTATCTTAACCTTTG-AAAAGATAGGGAGAA
* * ** * *
2497739 AGGTTCTATCTTTACATGGGAAAAGATAGTGA-AG
1 AGGTTCTATCTTAACCTTTGAAAAGATAGGGAGAA
* *
2497773 AGGTTCTATCTTAGCCTGTGAAAAGATAGGGAG
1 AGGTTCTATCTTAACCTTTGAAAAGATAGGGAG
2497806 GTTCTATCTT
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
34 28 0.51
35 11 0.20
36 16 0.29
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (35 bp):
AGGTTCTATCTTAACCTTTGAAAAGATAGGGAGAA
Found at i:2497782 original size:34 final size:34
Alignment explanation
Indices: 2497701--2497815 Score: 105
Period size: 34 Copynumber: 3.4 Consensus size: 34
2497691 AAAGTGATTG
* * * *
2497701 AGAGGTTCTATCTTAACCTTTGAAAAAGATAGGGA
1 AGAGGTTCTATCTTTACCATGGGAAAAGATA-GGA
*
2497736 GAAAGGTTCTATCTTTA-CATGGGAAAAGATAGTGA
1 -AGAGGTTCTATCTTTACCATGGGAAAAGATAG-GA
*
2497771 AGAGGTTCTATC-TTAGCC-TGTGAAAAGATAGG-
1 AGAGGTTCTATCTTTA-CCATGGGAAAAGATAGGA
2497803 -GAGGTTCTATCTT
1 AGAGGTTCTATCTT
2497816 AGCCTTCAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
31 11 0.16
32 1 0.01
33 4 0.06
34 24 0.35
35 14 0.21
36 14 0.21
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (34 bp):
AGAGGTTCTATCTTTACCATGGGAAAAGATAGGA
Found at i:2497829 original size:30 final size:31
Alignment explanation
Indices: 2497772--2497831 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2497762 AGATAGTGAA
*
2497772 GAGGTTCTATCTTAGCCTGTGAAAAGATAGG
1 GAGGTTCTATCTTAGCCTGTCAAAAGATAGG
2497803 GAGGTTCTATCTTAGCCT-TCAAAAGATAG
1 GAGGTTCTATCTTAGCCTGTCAAAAGATAG
2497832 TGTTGTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (31 bp):
GAGGTTCTATCTTAGCCTGTCAAAAGATAGG
Found at i:2499444 original size:21 final size:22
Alignment explanation
Indices: 2499420--2499477 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
2499410 GAACTAGAGG
*
2499420 AGAAAATGAATGAGTTGGAA-A
1 AGAAAATGAATGAGTTGCAAGA
2499441 AGAAAA-GAAATGAGTTGCAAGA
1 AGAAAATG-AATGAGTTGCAAGA
*
2499463 TGAAAAT-AATGAGTT
1 AGAAAATGAATGAGTT
2499478 AACTAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 25 0.78
22 6 0.19
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.21
Consensus pattern (22 bp):
AGAAAATGAATGAGTTGCAAGA
Found at i:2503178 original size:13 final size:13
Alignment explanation
Indices: 2503160--2503184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2503150 ATATTGCTTA
2503160 GTATCGATACATT
1 GTATCGATACATT
2503173 GTATCGATACAT
1 GTATCGATACAT
2503185 ATTCTTTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2503886 original size:31 final size:31
Alignment explanation
Indices: 2503776--2503907 Score: 122
Period size: 34 Copynumber: 4.0 Consensus size: 31
2503766 CGAAGTGATT
* *
2503776 GAGAGGTTCTAGCTTAACCTTTGAAAAAGATAGG
1 GAGAGGTTCTATCTTAGCC-TTG-AAAAGATA-G
** *
2503810 GAGAAAGGTTCTATCTTTTCCTGTGAAAAGACAG
1 GAG--AGGTTCTATCTTAGCCT-TGAAAAGATAG
2503844 TGAAGAGGTTCTATCTTAGCCTATGAAAAGATAG
1 -G-AGAGGTTCTATCTTAGCCT-TGAAAAGATAG
*
2503878 G-GAGGTTCTATCTTAGCCTTCAAAAGATAG
1 GAGAGGTTCTATCTTAGCCTTGAAAAGATAG
2503908 TATTGTAAGG
Statistics
Matches: 84, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
30 10 0.12
31 18 0.21
33 1 0.01
34 29 0.35
35 9 0.11
36 17 0.20
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (31 bp):
GAGAGGTTCTATCTTAGCCTTGAAAAGATAG
Found at i:2503905 original size:30 final size:31
Alignment explanation
Indices: 2503848--2503907 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2503838 AGACAGTGAA
*
2503848 GAGGTTCTATCTTAGCCTATGAAAAGATAGG
1 GAGGTTCTATCTTAGCCTATCAAAAGATAGG
2503879 GAGGTTCTATCTTAGCCT-TCAAAAGATAG
1 GAGGTTCTATCTTAGCCTATCAAAAGATAG
2503908 TATTGTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (31 bp):
GAGGTTCTATCTTAGCCTATCAAAAGATAGG
Found at i:2504293 original size:21 final size:21
Alignment explanation
Indices: 2504269--2504324 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
2504259 AACATGGTCT
2504269 TGTATCGATACATTTCAAACA
1 TGTATCGATACATTTCAAACA
***
2504290 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCAAACA
2504310 TGTATCGATACATTT
1 TGTATCGATACATTT
2504325 ACTCGTTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCAAACA
Found at i:2504336 original size:21 final size:20
Alignment explanation
Indices: 2504266--2504342 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
2504256 GTCAACATGG
*
2504266 TCTTGTATCGATACATTTCAA
1 TCTTGTATCGATACATTT-AC
* * *
2504287 ACATGTATCGATACATTCAC
1 TCTTGTATCGATACATTTAC
2504307 T-TATGTATCGATACATTTAC
1 TCT-TGTATCGATACATTTAC
*
2504327 TCGTTGTATCAATACA
1 TC-TTGTATCGATACA
2504343 AATTGTAGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 18 0.40
21 26 0.58
22 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (20 bp):
TCTTGTATCGATACATTTAC
Found at i:2508284 original size:15 final size:15
Alignment explanation
Indices: 2508266--2508338 Score: 67
Period size: 15 Copynumber: 4.8 Consensus size: 15
2508256 TTGAAATATA
*
2508266 AAATAACTTAAATTT
1 AAATAATTTAAATTT
*
2508281 AAATGATTTTAAA-TT
1 AAAT-AATTTAAATTT
* * *
2508296 AAATTATTTGATTTT
1 AAATAATTTAAATTT
*
2508311 AAAATAACTTAAATTT
1 -AAATAATTTAAATTT
2508327 AAATAATTTAAA
1 AAATAATTTAAA
2508339 AGTTAAATCC
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
14 4 0.09
15 23 0.52
16 17 0.39
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
AAATAATTTAAATTT
Found at i:2508630 original size:20 final size:20
Alignment explanation
Indices: 2508601--2508639 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2508591 TCAACAAAAT
*
2508601 TTTTTTAATTTATTTTTAAA
1 TTTTTAAATTTATTTTTAAA
2508621 TTTTTAAATTTATTTTTAA
1 TTTTTAAATTTATTTTTAA
2508640 CATAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTAAATTTATTTTTAAA
Found at i:2508661 original size:26 final size:27
Alignment explanation
Indices: 2508631--2508690 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 27
2508621 TTTTTAAATT
*
2508631 TATTTTTAACATAAATAT--ATTTTAA
1 TATTTTTAACATAAATATAAATTTAAA
* *
2508656 TA-ATTTAATATAAATATAAATTTAAA
1 TATTTTTAACATAAATATAAATTTAAA
2508682 TATTTTTAA
1 TATTTTTAA
2508691 TTATTATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 13 0.46
25 2 0.07
26 8 0.29
27 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTTTTAACATAAATATAAATTTAAA
Found at i:2508739 original size:34 final size:36
Alignment explanation
Indices: 2508645--2508773 Score: 133
Period size: 35 Copynumber: 3.6 Consensus size: 36
2508635 TTTAACATAA
* * *
2508645 ATATATTTTAATAATTTAATATAAATATAAATTTAA
1 ATATATTTTAATTATTTAATATAAATATAATTTTAT
* *
2508681 ATAT-TTTTAATTA-TTATTTGATATAATATGATTTTAT
1 ATATATTTTAATTATTTA-AT-ATA-AATATAATTTTAT
2508718 ATATATTTT-ATTATTTAATATAAATATAATTTTA-
1 ATATATTTTAATTATTTAATATAAATATAATTTTAT
* *
2508752 ATA-ATTTTAAATATTTATTATA
1 ATATATTTTAATTATTTAATATA
2508774 TATGTTTATA
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
33 5 0.06
34 17 0.22
35 20 0.26
36 10 0.13
37 19 0.24
38 7 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (36 bp):
ATATATTTTAATTATTTAATATAAATATAATTTTAT
Found at i:2511990 original size:2 final size:2
Alignment explanation
Indices: 2511985--2512029 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
2511975 TATATATATT
* *
2511985 TG TG TG CG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2512027 TG T
1 TG T
2512030 ACACATGCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.04, G:0.49, T:0.47
Consensus pattern (2 bp):
TG
Found at i:2513449 original size:2 final size:2
Alignment explanation
Indices: 2513442--2513550 Score: 101
Period size: 2 Copynumber: 54.0 Consensus size: 2
2513432 GGTGGTGTGA
* * ** *
2513442 AT AT AT AT AT AT AT AT TT AT AT AT AT GT AT AT GC AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * **
2513484 AT AT CT AT AT AT GT AGT AT TT GT GC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2513527 AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
2513551 GCATATAGAT
Statistics
Matches: 85, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
2 83 0.98
3 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2517611 original size:3 final size:3
Alignment explanation
Indices: 2517603--2517652 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2517593 ATTTATTTAT
2517603 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2517651 TT
1 TT
2517653 CTAAAATGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2525104 original size:32 final size:32
Alignment explanation
Indices: 2525068--2525140 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
2525058 TTCAGTGTAC
*
2525068 CGATACATTATGGGTTTTTGACCCAAATATAT
1 CGATACATTATAGGTTTTTGACCCAAATATAT
* * *
2525100 CGATACATTATAGGTTTTTGACCTAAGTGTAT
1 CGATACATTATAGGTTTTTGACCCAAATATAT
2525132 CGATACATT
1 CGATACATT
2525141 CTTCAATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (32 bp):
CGATACATTATAGGTTTTTGACCCAAATATAT
Found at i:2526286 original size:32 final size:32
Alignment explanation
Indices: 2526239--2526309 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
2526229 TTCAACAATT
2526239 TGTATCGATAAATAAGTGTTATATCGATACAA
1 TGTATCGATAAATAAGTGTTATATCGATACAA
* * * *
2526271 TGTATTGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATAAATAAGTGTTATATCGATACAA
2526303 TGTATCG
1 TGTATCG
2526310 CTACGAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATAAATAAGTGTTATATCGATACAA
Found at i:2526372 original size:13 final size:13
Alignment explanation
Indices: 2526354--2526378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2526344 ATTACTCAAA
2526354 TGTATCGATACAT
1 TGTATCGATACAT
2526367 TGTATCGATACA
1 TGTATCGATACA
2526379 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2526431 original size:51 final size:52
Alignment explanation
Indices: 2526387--2526514 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2526377 CACTGATCTT
* *
2526387 TGTATCGATACATGCAGGCAAATTTGCGC-GATGTATCAATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
2526438 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
2526490 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2526515 TTATATTTCG
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 27 0.38
52 45 0.62
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:2538524 original size:1 final size:1
Alignment explanation
Indices: 2538518--2538638 Score: 62
Period size: 1 Copynumber: 121.0 Consensus size: 1
2538508 CGTCCTCCAC
** * * * * * * ** * *
2538518 AAAAAAAAACCAAATAAACAAAAAAAAAGAAGAAGAAAAAAAAACAAAACGAAAAAAAAACAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * * * *
2538583 AAAAAAAAAAACAAAACGAAAAAAAAACAAACAAATAAAAAAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2538639 TAACAACAAC
Statistics
Matches: 84, Mismatches: 36, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:2538556 original size:16 final size:16
Alignment explanation
Indices: 2538533--2538644 Score: 126
Period size: 16 Copynumber: 7.1 Consensus size: 16
2538523 AAAACCAAAT
*
2538533 AAAC-AAAAAAAAAGA
1 AAACGAAAAAAAAACA
2538548 AGAA-GAAAAAAAAACA
1 A-AACGAAAAAAAAACA
2538564 AAACGAAAAAAAAAC-
1 AAACGAAAAAAAAACA
*
2538579 AAACAAAAAAAAAAACA
1 AAAC-GAAAAAAAAACA
2538596 AAACGAAAAAAAAAC-
1 AAACGAAAAAAAAACA
*
2538611 AAACAAATAAAAAAACA
1 AAACGAA-AAAAAAACA
2538628 AAAC-AAAAAAATAACA
1 AAACGAAAAAAA-AACA
2538644 A
1 A
2538645 CAACAACAAC
Statistics
Matches: 85, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
15 18 0.21
16 59 0.69
17 8 0.09
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.02
Consensus pattern (16 bp):
AAACGAAAAAAAAACA
Found at i:2538573 original size:32 final size:30
Alignment explanation
Indices: 2538533--2538644 Score: 145
Period size: 32 Copynumber: 3.5 Consensus size: 30
2538523 AAAACCAAAT
*
2538533 AAACAAAAAAAAAGAAGA-AGAAAAAAAAACA
1 AAACAAAAAAAAACAA-ACA-AAAAAAAAACA
2538564 AAACGAAAAAAAAACAAACAAAAAAAAAAACA
1 AAAC-AAAAAAAAACAAAC-AAAAAAAAAACA
2538596 AAACGAAAAAAAAACAAACAAATAAAAAAACA
1 AAAC-AAAAAAAAACAAACAAA-AAAAAAACA
2538628 AAACAAAAAAATAACAA
1 AAACAAAAAAA-AACAA
2538645 CAACAACAAC
Statistics
Matches: 75, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
31 15 0.20
32 59 0.79
33 1 0.01
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.02
Consensus pattern (30 bp):
AAACAAAAAAAAACAAACAAAAAAAAAACA
Found at i:2538623 original size:48 final size:48
Alignment explanation
Indices: 2538516--2538647 Score: 153
Period size: 48 Copynumber: 2.7 Consensus size: 48
2538506 GGCGTCCTCC
* *
2538516 ACAAAAAAAAACCAAATA-AACAAAAAAAAAGAAGAAGAAAAAAAAACAAA
1 ACAAAAAAAAAACAAA-ACAA-AAAAAAAAACAA-AAGAAAAAAAAACAAA
*
2538566 ACGAAAAAAAAAC-AAACAAAAAAAAAAACAAAACGAAAAAAAAAC-AA
1 ACAAAAAAAAAACAAAACAAAAAAAAAAACAAAA-GAAAAAAAAACAAA
2538613 ACAAATAAAAAAACAAAACAAAAAAATAACAACAA
1 ACAAA-AAAAAAACAAAACAAAAAAA-AA-AACAA
2538648 CAACAACAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
47 8 0.11
48 31 0.43
49 15 0.21
50 13 0.18
51 5 0.07
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (48 bp):
ACAAAAAAAAAACAAAACAAAAAAAAAAACAAAAGAAAAAAAAACAAA
Found at i:2540144 original size:28 final size:29
Alignment explanation
Indices: 2540087--2540148 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
2540077 CACCTTTTCC
* * * *
2540087 AAAGCCCACAAGTCCGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCAACTCTTCA
2540116 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCAACTCTTCA
2540144 AAAGC
1 AAAGC
2540149 ACATAAGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCAACTCTTCA
Found at i:2540191 original size:31 final size:28
Alignment explanation
Indices: 2540112--2540192 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 28
2540102 GTGGTATCTT
**
2540112 TTCAAAAGCC-CACAAGTCAGTGGCAACC
1 TTCAAAAGCCACACAAGTTGGT-GCAACC
*
2540140 TTCAAAAG-CACATAAGTTGGTGCAACC
1 TTCAAAAGCCACACAAGTTGGTGCAACC
2540167 TTATCAAAAGTCCACACAAGTTGGTG
1 -T-TCAAAAG-CCACACAAGTTGGTG
2540193 GCATCTTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 7 0.16
28 17 0.39
29 7 0.16
31 13 0.30
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (28 bp):
TTCAAAAGCCACACAAGTTGGTGCAACC
Found at i:2540402 original size:101 final size:101
Alignment explanation
Indices: 2540199--2541403 Score: 1362
Period size: 101 Copynumber: 11.9 Consensus size: 101
2540189 GGTGGCATCT
* *
2540199 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTT-T-GCCTTTAAGACCA
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCA
* * * *
2540261 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
65 ATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
* * * *
2540298 TCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCACCTTTAGGTCTAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
2540363 TATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
66 TATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
* * * *
2540399 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
2540461 TATCGCTGGCCTTGAATCAGCATATTGGCATCTTTGTCA
66 TATCGCTGGCCTTGAATCAGCATATTGGCA-CTTT-T-A
* * *
2540500 CCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
* * *
2540565 TATCTCTGGCCTTGAATCAGCATATTTGCACTTTTG
66 TATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
* * * * *
2540601 CCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
* *
2540663 TATCGCTGGCCTTAAATCAACATATTGGCACCTTTGTCA
66 TATCGCTGGCCTTGAATCAGCATATTGGCA-CTTT-T-A
* * * *
2540702 CCTTTAAGT-CAATATCGCTGACTTTGAATCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
* * * *
2540766 TATCGCTAGCCTTGAGTTAGCATATTGGCACTTTTG
66 TATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
* * * * * *
2540802 TTTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAAC--T-TCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
* * *
2540864 TATTGCTGGCCTTGAATCAGCATATTTGCGTCTTTGTCA
66 TATCGCTGGCCTTGAATCAGCATATTGGC-ACTTT-T-A
* * *
2540903 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTGT---CTTTAAGACCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
* * * *
2540965 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
66 TATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
*
2541001 TCTTTAAGTCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
* * * *
2541066 TATCGCTGGCTTTGAATCAGCACATTGGCACCTTCA
66 TATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
* *
2541102 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
* * *
2541167 TGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
66 TATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
* * * * * **
2541203 TCTTTAAGTCCAGTATTGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTT-AAGTCCA
* * * * *
2541268 ATGTTGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCA
65 ATATCGCTGGCCTTGAATCAGCATATTGGCA--CTT-TTA
* * ** * * * * * **
2541308 TCTTTAAGTCTAATGTCGCTAACCGTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAACC
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CC--TTTGTCACCTTTAAGTC
* * *
2541373 CAATATCGTTGGCCGTGAATCAGCGTATTGG
63 CAATATCGCTGGCCTTGAATCAGCATATTGG
2541404 TCCCTTTATC
Statistics
Matches: 952, Mismatches: 122, Indels: 56
0.84 0.11 0.05
Matches are distributed among these distances:
98 208 0.22
99 23 0.02
100 43 0.05
101 468 0.49
102 39 0.04
103 46 0.05
104 46 0.05
105 36 0.04
106 2 0.00
107 31 0.03
108 10 0.01
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (101 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAA
TATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
Found at i:2540423 original size:150 final size:150
Alignment explanation
Indices: 2540199--2541347 Score: 1309
Period size: 150 Copynumber: 7.6 Consensus size: 150
2540189 GGTGGCATCT
** * *
2540199 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTGCCTTTAAGACCAATG
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATA
* * *
2540264 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCTTTGAATC
65 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
*
2540329 AGCATATTGGCGCCTTTGTCA
130 AGCATATTGGCACCTTTGTCA
* * * * *
2540350 CCTTTAGGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGACCAATGT
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATAT
* *
2540415 CGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
66 CGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCA
*
2540480 GCATATTGGCATCTTTGTCA
131 GCATATTGGCACCTTTGTCA
* * * *
2540500 CCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-ACTTT-T-ATCTTTAAGTCCAA
* * * ** * *
2540565 TATCTCTGGCCTTGAATCAGCATATTTGCACTTTTGCCTTTAAGACCAATGTCGCTGGCCTTGAA
63 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAA
*
2540630 TCAGCACATTGGCACC--T-TCA
128 TCAGCATATTGGCACCTTTGTCA
* * *
2540650 TCTTTAAGTCCAATATCGCTGGCCTTAAATCAACATATTGGCACCTTTGTCACCTTTAAGT-CAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTT-T-ATCTTTAAGTCCAA
* * * *
2540714 TATCGCTGACTTTGAATCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAATATCGCTAGCCTT
63 TATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCACCTTTAAGTCCAATATCGCTGGCCTT
* * *
2540779 GAGTTAGCATATTGGCACTTTTGT--
125 GAATCAGCATATTGGCACCTTTGTCA
* * * *
2540803 T-TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAAC-TTCATCTTTAAGTCCAATA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-ACTTTTATCTTTAAGTCCAATA
* * * *
2540866 TTGCTGGCCTTGAATCAGCATATTTGCGTCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGA
65 TCGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCACCTTTAAGTCCAATATCGCTGGCCTTGA
*
2540931 ATCAGCATATTGGCA-CTTT-T-G
127 ATCAGCATATTGGCACCTTTGTCA
* * * * *
2540952 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATAT
* *
2541017 CGCTGGTCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAATATCGCTGGCTTTGAA
66 CGCTGGCCTTGAATCAGCATATTGGCACC--T-TCACCTTTAAGTCCAATATCGCTGGCCTTGAA
*
2541082 TCAGCACATTGGCACC--T-TCA
128 TCAGCATATTGGCACCTTTGTCA
*
2541102 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-ACTTT-T-ATCTTTAAGTCCAA
* * * *
2541167 TGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAGTATTGCTGGCCTTGAA
63 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAA
* *
2541232 TCAGCATATTGGCGCCTTCGTCA
128 TCAGCATATTGGCACCTTTGTCA
** * * * * * *
2541255 TCTTTAAAACCCAATGTTGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCTTTAAGTCTA
1 TCTTT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--CTT-TTATCTTTAAGTCCA
* ** * *
2541320 ATGTCGCTAACCGTGAATCAGCACATTG
62 ATATCGCTGGCCTTGAATCAGCATATTG
2541348 ACATCCTTTT
Statistics
Matches: 868, Mismatches: 99, Indels: 59
0.85 0.10 0.06
Matches are distributed among these distances:
148 1 0.00
149 47 0.05
150 519 0.60
151 17 0.02
152 76 0.09
153 135 0.16
154 68 0.08
155 4 0.00
156 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (150 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATAT
CGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCA
GCATATTGGCACCTTTGTCA
Found at i:2541250 original size:49 final size:49
Alignment explanation
Indices: 2540199--2541403 Score: 1269
Period size: 49 Copynumber: 23.8 Consensus size: 49
2540189 GGTGGCATCT
* **
2540199 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTG
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * *
2540249 CCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* *
2540298 TCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
* * * * *
2540350 CCTTTAGGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
2540399 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
2540448 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-C-CT-TCA
* * *
2540500 CCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
* * * * **
2540552 CCTTTAAGTCCAATATCTCTGGCCTTGAATCAGCATATTTGCACTTTTG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * *
2540601 CCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* *
2540650 TCTTTAAGTCCAATATCGCTGGCCTTAAATCAACATATTGGCACCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
* * * *
2540702 CCTTTAAGT-CAATATCGCTGACTTTGAATCAGCATATTGGCGCCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
* * * * * **
2540753 CCTTTAAGTCCAATATCGCTAGCCTTGAGTTAGCATATTGGCACTTTTG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * * *
2540802 TTTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAACTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * *
2540851 TCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTTGCGTCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCA
* * **
2540903 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
2540952 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
2541001 TCTTTAAGTCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
* * *
2541053 CCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
2541102 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
*
2541154 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
2541203 TCTTTAAGTCCAGTATTGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-T--TCA
** * * * * *
2541255 TCTTTAAAACCCAATGTTGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCA
1 TCTTT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--CCT-TCA
* * ** * * *
2541308 TCTTTAAGTCTAATGTCGCTAACCGTGAATCAGCACATTGACATCCTTTTTCTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CC----T-TCA
** * * *
2541363 TCTTTAAACCCAATATCGTTGGCCGTGAATCAGCGTATTGG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
2541404 TCCCTTTATC
Statistics
Matches: 971, Mismatches: 153, Indels: 57
0.82 0.13 0.05
Matches are distributed among these distances:
49 488 0.50
50 12 0.01
51 56 0.06
52 338 0.35
53 39 0.04
54 1 0.00
55 37 0.04
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
Found at i:2548714 original size:13 final size:13
Alignment explanation
Indices: 2548696--2548722 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2548686 ACATTATGCT
2548696 TTGTATCGATACA
1 TTGTATCGATACA
2548709 TTGTATCGATACA
1 TTGTATCGATACA
2548722 T
1 T
2548723 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2548719 original size:33 final size:32
Alignment explanation
Indices: 2548677--2548741 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
2548667 CATATCCAGA
* * *
2548677 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGAT-CATTGTATCAATACAT
2548710 TGTATCGATACATGATCATTGTATCAATACAT
1 TGTATCGATACATGATCATTGTATCAATACAT
2548742 GCACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCAATACAT
Found at i:2548752 original size:20 final size:19
Alignment explanation
Indices: 2548707--2548763 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
2548697 TGTATCGATA
2548707 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
*
2548726 CATTGTATCAATACATGCA-
1 CATTGTATCGATACATG-AT
2548745 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
2548764 AACTGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:2548816 original size:20 final size:18
Alignment explanation
Indices: 2548791--2548857 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 18
2548781 TTACCATTGT
2548791 TTGTATCGATACATGGCATA
1 TTGTATCGATACAT-GCA-A
2548811 TTGTATCGAT--A--CAA
1 TTGTATCGATACATGCAA
2548825 -TGTATCGATACATGACAAA
1 TTGTATCGATACATG-C-AA
2548844 TTGTATCGATACAT
1 TTGTATCGATACAT
2548858 TGTCCCCAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
15 3 0.08
18 2 0.05
19 2 0.05
20 23 0.57
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACATGCAA
Found at i:2548829 original size:33 final size:33
Alignment explanation
Indices: 2548792--2548856 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2548782 TACCATTGTT
* *
2548792 TGTATCGATACATGGCATATTGTATCGATACAA
1 TGTATCGATACATGACAAATTGTATCGATACAA
2548825 TGTATCGATACATGACAAATTGTATCGATACA
1 TGTATCGATACATGACAAATTGTATCGATACA
2548857 TTGTCCCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGACAAATTGTATCGATACAA
Found at i:2548830 original size:13 final size:13
Alignment explanation
Indices: 2548812--2548836 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2548802 CATGGCATAT
2548812 TGTATCGATACAA
1 TGTATCGATACAA
2548825 TGTATCGATACA
1 TGTATCGATACA
2548837 TGACAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2550460 original size:15 final size:14
Alignment explanation
Indices: 2550436--2550468 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2550426 GTCAACCATC
2550436 AAAT-ATGATGAAG
1 AAATGATGATGAAG
2550449 ATAATGATGATGAAG
1 A-AATGATGATGAAG
2550464 AAATG
1 AAATG
2550469 GCTATGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 7 0.39
15 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (14 bp):
AAATGATGATGAAG
Found at i:2551626 original size:28 final size:28
Alignment explanation
Indices: 2551545--2551626 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2551535 TTTTGGAGAT
*
2551545 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
2551573 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
2551601 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
2551627 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:2551769 original size:51 final size:51
Alignment explanation
Indices: 2551609--2551943 Score: 205
Period size: 51 Copynumber: 6.4 Consensus size: 51
2551599 GAAATAACGA
* * *
2551609 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
2551661 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
2551714 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * * ** *
2551765 GGTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGGAGTATCCTCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT-G-GTAT-TTTGAAAATAAAATCGG
* * * *
2551820 GGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATT-G-GTATTTTGAAAATAAAATCGG
* ** * *
2551874 AGTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTGGTATTTTGAAAATAAAATCGG
* * *
2551925 AGTTGGAATATCCTCGATT
1 GGTTGGAGTATCCCCGATT
2551944 GTGGAGAATT
Statistics
Matches: 215, Mismatches: 50, Indels: 37
0.71 0.17 0.12
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
51 73 0.34
52 20 0.09
53 47 0.22
54 33 0.15
55 18 0.08
56 4 0.02
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:2551796 original size:28 final size:28
Alignment explanation
Indices: 2551762--2551834 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
2551752 AAAATAAAGT
2551762 CGGGGTTGGAGTATCCCCTC-AGAAATAA
1 CGGGGTTGGAGTATCCCCTCGAG-AATAA
*
2551790 CGGGGTTGGAGTAT--CCTCGATGATTAA
1 CGGGGTTGGAGTATCCCCTCGA-GAATAA
*
2551817 CGGGGTTGGAGTGTCCCC
1 CGGGGTTGGAGTATCCCC
2551835 GATTGTGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 4 0.10
27 18 0.46
28 15 0.38
29 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAGAATAA
Found at i:2554318 original size:13 final size:13
Alignment explanation
Indices: 2554300--2554325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2554290 ACAAAGATCC
2554300 ATGTATCGATACA
1 ATGTATCGATACA
2554313 ATGTATCGATACA
1 ATGTATCGATACA
2554326 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2554321 original size:33 final size:33
Alignment explanation
Indices: 2554279--2554345 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2554269 AAAATTTCCA
***
2554279 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2554312 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2554345 A
1 A
2554346 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2554389 original size:19 final size:18
Alignment explanation
Indices: 2554365--2554432 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2554355 CAGTAGCTAA
2554365 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2554384 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2554399 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2554416 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2554433 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2554405 original size:13 final size:13
Alignment explanation
Indices: 2554387--2554411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2554377 ACAATACTTA
2554387 TGTATCGATACAT
1 TGTATCGATACAT
2554400 TGTATCGATACA
1 TGTATCGATACA
2554412 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2554409 original size:32 final size:32
Alignment explanation
Indices: 2554368--2554430 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2554358 TAGCTAATTA
*
2554368 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2554400 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2554431 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2554512 original size:21 final size:21
Alignment explanation
Indices: 2554488--2554607 Score: 240
Period size: 21 Copynumber: 5.7 Consensus size: 21
2554478 CATTTGTAGG
2554488 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2554509 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2554530 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2554551 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2554572 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2554593 ATGTATCGATACATT
1 ATGTATCGATACATT
2554608 TGGAATTTTT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 99 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2554542 original size:63 final size:64
Alignment explanation
Indices: 2554468--2554609 Score: 234
Period size: 63 Copynumber: 2.2 Consensus size: 64
2554458 GTTGGGACCC
* **
2554468 TGTATCGATACATTTGTA-GGATGTATCGATACATTCCACAAATGTATCGATACATTCCACAAA
1 TGTATCGATACATTTGCACAAATGTATCGATACATTCCACAAATGTATCGATACATTCCACAAA
*
2554531 TGTATCGATACA-TTCCACAAATGTATCGATACATTCCACAAATGTATCGATACATTCCACAAA
1 TGTATCGATACATTTGCACAAATGTATCGATACATTCCACAAATGTATCGATACATTCCACAAA
2554594 TGTATCGATACATTTG
1 TGTATCGATACATTTG
2554610 GAATTTTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
62 3 0.04
63 67 0.93
64 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (64 bp):
TGTATCGATACATTTGCACAAATGTATCGATACATTCCACAAATGTATCGATACATTCCACAAA
Found at i:2554630 original size:14 final size:14
Alignment explanation
Indices: 2554611--2554638 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2554601 ATACATTTGG
2554611 AATTTTTTTTTTTT
1 AATTTTTTTTTTTT
2554625 AATTTTTTTTTTTT
1 AATTTTTTTTTTTT
2554639 TTCAAACACT
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:0.00, T:0.86
Consensus pattern (14 bp):
AATTTTTTTTTTTT
Found at i:2555319 original size:55 final size:53
Alignment explanation
Indices: 2555235--2556407 Score: 1691
Period size: 55 Copynumber: 21.3 Consensus size: 53
2555225 ATAAATTGTA
* * * * *
2555235 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
2555290 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
2555345 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2555400 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* * *
2555455 TCCTGTTCTTTGAGGACAGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGAC-TGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2555510 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2555565 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
* *
2555620 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
2555675 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2555730 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2555785 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2555840 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2555895 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2555950 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
* *
2556005 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2556060 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
* *
2556115 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
2556170 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
2556225 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
2556280 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2556335 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2556390 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
2556408 AAAAAGCGGA
Statistics
Matches: 1050, Mismatches: 45, Indels: 46
0.92 0.04 0.04
Matches are distributed among these distances:
53 2 0.00
54 30 0.03
55 991 0.94
56 25 0.02
57 2 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (53 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
Found at i:2555530 original size:26 final size:26
Alignment explanation
Indices: 2555501--2555590 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
2555491 GTGTGGGCTT
2555501 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
2555527 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
2555554 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
2555582 TGAAAGGTG
1 TGAAAGGTG
2555591 CCACCAACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:2555809 original size:26 final size:26
Alignment explanation
Indices: 2555723--2555810 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
2555713 GTGGGCTTTA
*
2555723 AAAGGTGTCCTGCTCTTTGAGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** * *
2555749 AAAGGTG-CCACCAACTTGTGTGGG-CTTT
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
2555777 AAGAGGTGTCCTGCTCTTTGGGGACTG
1 AA-AGGTGTCCTGCTCTTTGGGGACTG
2555804 AAAGGTG
1 AAAGGTG
2555811 CCACCAACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
25 3 0.07
26 15 0.33
27 9 0.20
28 8 0.17
29 8 0.17
30 3 0.07
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.28
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:2555974 original size:26 final size:26
Alignment explanation
Indices: 2555890--2555975 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
2555880 GGGCTTTGAG
*
2555890 AGGTGTCCTGCTCTTTGAGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
2555916 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
2555944 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
2555971 AGGTG
1 AGGTG
2555976 CCACCAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 9 0.20
28 8 0.18
29 8 0.18
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:2556275 original size:27 final size:27
Alignment explanation
Indices: 2556190--2556275 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
2556180 TGAGGACTGG
2556190 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
** * * * **
2556217 AAAAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AAAA--TG-CCACCAACTTGTGTGGGCTTT
2556245 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
2556272 AAAA
1 AAAA
2556276 GGTGTCCTGC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (27 bp):
AAAATGCCACCAACTTGTGTGGGCTTT
Found at i:2557387 original size:16 final size:15
Alignment explanation
Indices: 2557368--2557414 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2557358 CTTTTCTCTC
2557368 TTTTTCTTTGTTTTGT
1 TTTTTCTTTGTTTT-T
*
2557384 TTTTTTTTTGTTTTT
1 TTTTTCTTTGTTTTT
*
2557399 TTTTTGTTT-TTTTT
1 TTTTTCTTTGTTTTT
2557413 TT
1 TT
2557415 GAAGAGAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 7 0.24
15 9 0.31
16 13 0.45
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTGTTTTT
Found at i:2557394 original size:11 final size:11
Alignment explanation
Indices: 2557378--2557415 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
2557368 TTTTTCTTTG
2557378 TTTTGTTTTTT
1 TTTTGTTTTTT
2557389 TTTTGTTTTTT
1 TTTTGTTTTTT
2557400 TTTTGTTTTTT
1 TTTTGTTTTTT
2557411 TTTTG
1 TTTTG
2557416 AAGAGAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:2569362 original size:28 final size:28
Alignment explanation
Indices: 2569281--2569362 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2569271 TTTTGGAGAT
*
2569281 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
2569309 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
2569337 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
2569363 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:2569505 original size:51 final size:51
Alignment explanation
Indices: 2569345--2569515 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2569335 GAAATAACGA
* * *
2569345 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
2569397 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
2569450 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
2569501 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2569516 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:2569561 original size:27 final size:28
Alignment explanation
Indices: 2569498--2569573 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2569488 AAAATAAAGT
*
2569498 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
2569526 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2569553 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2569574 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2572054 original size:13 final size:13
Alignment explanation
Indices: 2572036--2572061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2572026 ACAAAGATCC
2572036 ATGTATCGATACA
1 ATGTATCGATACA
2572049 ATGTATCGATACA
1 ATGTATCGATACA
2572062 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2572057 original size:33 final size:33
Alignment explanation
Indices: 2572015--2572081 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2572005 AAAATTTCCA
***
2572015 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2572048 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2572081 A
1 A
2572082 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2572125 original size:19 final size:18
Alignment explanation
Indices: 2572101--2572168 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
2572091 CAGTAGCTAA
2572101 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2572120 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2572135 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
2572152 TTATGTATTGATACAAA
1 TTATGTATCGATACAAA
2572169 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2572141 original size:13 final size:13
Alignment explanation
Indices: 2572123--2572147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2572113 ACAATACTTA
2572123 TGTATCGATACAT
1 TGTATCGATACAT
2572136 TGTATCGATACA
1 TGTATCGATACA
2572148 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2572145 original size:32 final size:32
Alignment explanation
Indices: 2572104--2572166 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2572094 TAGCTAATTA
*
2572104 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
2572136 TGTATCGATACAAAACTTATGTATTGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2572167 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2572248 original size:21 final size:21
Alignment explanation
Indices: 2572224--2572280 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
2572214 CATTTGTAGG
2572224 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2572245 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2572266 ATGTATCGATACATT
1 ATGTATCGATACATT
2572281 TGGAATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2572319 original size:11 final size:11
Alignment explanation
Indices: 2572288--2572319 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2572278 ATTTGGAATT
2572288 TTTTTTTTTTA
1 TTTTTTTTTTA
*
2572299 TTTTTATTTTA
1 TTTTTTTTTTA
2572310 TTTTTTTTTT
1 TTTTTTTTTT
2572320 CAAACACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:2578644 original size:24 final size:24
Alignment explanation
Indices: 2578599--2578645 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2578589 GATTTCATGT
*
2578599 TTATTATATGCATTATTCTCTTTCA
1 TTATTATATGCA-TATTATCTTTCA
2578624 TTATTATATTGC-TATTATCTTT
1 TTATTATA-TGCATATTATCTTT
2578646 ATGAATGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 8 0.40
26 3 0.15
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATTATATGCATATTATCTTTCA
Found at i:2579418 original size:19 final size:20
Alignment explanation
Indices: 2579355--2579446 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 20
2579345 AACCCTTGTA
* *
2579355 TGTATCGATACAT-ATCCAGA
1 TGTATCGATACATGATGCA-T
* *
2579375 TGTATCGATACATTATGCTT
1 TGTATCGATACATGATGCAT
*
2579395 TGTATCGATAGATGAT-CAT
1 TGTATCGATACATGATGCAT
*
2579414 TGTATCG--ACATGCAT-AAT
1 TGTATCGATACATG-ATGCAT
*
2579432 TGTATCAATACATGA
1 TGTATCGATACATGA
2579447 AACTGGCAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
17 4 0.07
18 10 0.17
19 10 0.17
20 32 0.54
21 3 0.05
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGATGCAT
Found at i:2579493 original size:13 final size:13
Alignment explanation
Indices: 2579475--2579499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2579465 TACCACTGTT
2579475 TGTATCGATACAA
1 TGTATCGATACAA
2579488 TGTATCGATACA
1 TGTATCGATACA
2579500 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2579969 original size:32 final size:33
Alignment explanation
Indices: 2579906--2579970 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
2579896 TTTCAATGAT
*
2579906 TTGTATCGATACATAAAGTGTTGTATTGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
*
2579939 TTGTATCGATACAT-AAGTTTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
2579971 ATTTAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (33 bp):
TTGTATCGATACATAAAGTGTTGTATCGATACA
Found at i:2580069 original size:52 final size:52
Alignment explanation
Indices: 2580013--2580141 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2580003 CACTGATCTT
* *
2580013 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2580065 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2580117 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2580142 TTAAATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2585094 original size:21 final size:21
Alignment explanation
Indices: 2585068--2585124 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2585058 GAATTTTATA
2585068 TGAATGCATTGATACCCTAGG
1 TGAATGCATTGATACCCTAGG
*
2585089 TGAATGCTTTGATACCCTAGG
1 TGAATGCATTGATACCCTAGG
*
2585110 TGAATACATTGATAC
1 TGAATGCATTGATAC
2585125 AATATTTGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (21 bp):
TGAATGCATTGATACCCTAGG
Found at i:2588694 original size:82 final size:82
Alignment explanation
Indices: 2588541--2588707 Score: 219
Period size: 81 Copynumber: 2.0 Consensus size: 82
2588531 TCCCAAAGGT
* * * ** *
2588541 AAAATTTCACAAAGTAAATTTCAATTTTTGTTAGAACAAGGTTGGGTATCCTTTCAGAATAGTAG
1 AAAATTCCACAAAGTAAATTTCAAATTTTGTTAGAACAAGATTGGGTATCCGCTCAGAATAATAG
*
2588606 GGATGGAG-TTTCCTAA
66 GGATGGAGTTTTCCCAA
* * * *
2588622 AAAATTCCACGAAGTAAATTTGAAATTTTGTTAGAACGAGATTGGAGTATCCGCTCAGAATAATG
1 AAAATTCCACAAAGTAAATTTCAAATTTTGTTAGAACAAGATTGG-GTATCCGCTCAGAATAATA
2588687 GGGATGGAGTTTTCCCAA
65 GGGATGGAGTTTTCCCAA
2588705 AAA
1 AAA
2588708 TTATATAAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 39 0.53
82 24 0.33
83 10 0.14
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (82 bp):
AAAATTCCACAAAGTAAATTTCAAATTTTGTTAGAACAAGATTGGGTATCCGCTCAGAATAATAG
GGATGGAGTTTTCCCAA
Found at i:2589336 original size:24 final size:24
Alignment explanation
Indices: 2589283--2589330 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
2589273 CTCGAAAGGG
*
2589283 AAATTTGTAAAATTTTTGAGAAAA
1 AAATTTGTAAAATCTTTGAGAAAA
2589307 AAATTT-TAAAATCTTTGA-AAAA
1 AAATTTGTAAAATCTTTGAGAAAA
2589329 AA
1 AA
2589331 TCATTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.26
23 11 0.48
24 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
AAATTTGTAAAATCTTTGAGAAAA
Found at i:2594992 original size:13 final size:13
Alignment explanation
Indices: 2594970--2595027 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
2594960 AGCAGTAGCT
*
2594970 TTGTAGCGATACA
1 TTGTATCGATACA
2594983 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
2594999 CTTATGTATCGATACA
1 --T-TGTATCGATACA
2595015 TTGTATCGATACA
1 TTGTATCGATACA
2595028 AATTGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2600124 original size:36 final size:35
Alignment explanation
Indices: 2600001--2600136 Score: 181
Period size: 35 Copynumber: 3.9 Consensus size: 35
2599991 AAGACAGAAC
* * *
2600001 CTCCCTATCTTTT-GAAGGTTAAGATAGCACC--T
1 CTCCCTATCTTTTCAAAGGCTAAGATAGAACCTTT
2600033 CTCCCTATCTTTTCACAA-GCTAAGATAGAACCTTT
1 CTCCCTATCTTTTCA-AAGGCTAAGATAGAACCTTT
* *
2600068 CTCCCTATCTTTTCACAGGCTAAGATAAAACCTTT
1 CTCCCTATCTTTTCAAAGGCTAAGATAGAACCTTT
2600103 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCT
1 CTCCCTATC-TTTTCAAAGGCTAAGATAGAACCT
2600137 CTCAATCACT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
32 13 0.14
33 12 0.13
34 3 0.03
35 41 0.45
36 22 0.24
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (35 bp):
CTCCCTATCTTTTCAAAGGCTAAGATAGAACCTTT
Found at i:2600129 original size:71 final size:67
Alignment explanation
Indices: 2600001--2600136 Score: 184
Period size: 71 Copynumber: 2.0 Consensus size: 67
2599991 AAGACAGAAC
* * **
2600001 CTCCCTATCTTTTGAAGGTTAAGATAGCACCTCTCCCTATCTTTTCACAAGCTAAGATAGAACCT
1 CTCCCTATCTTTTCAAGGCTAAGATAAAACCTCTCCCTATCTTTTCACAAGCTAAGATAGAACCT
2600066 TT
66 TT
2600068 CTCCCTATCTTTTCACAGGCTAAGATAAAACCTTTCTCCCTATCTTTTTCA-AAGGCTAAGATAG
1 CTCCCTATCTTTTCA-AGGCTAAGATAAAACC--TCTCCCTATC-TTTTCACAA-GCTAAGATAG
2600132 AACCT
61 AACCT
2600137 CTCAATCACT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
67 14 0.23
68 13 0.22
70 12 0.20
71 21 0.35
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (67 bp):
CTCCCTATCTTTTCAAGGCTAAGATAAAACCTCTCCCTATCTTTTCACAAGCTAAGATAGAACCT
TT
Found at i:2600717 original size:13 final size:13
Alignment explanation
Indices: 2600699--2600723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2600689 ACAAAGAACA
2600699 TGTATCGATACAG
1 TGTATCGATACAG
2600712 TGTATCGATACA
1 TGTATCGATACA
2600724 TTCAAGGGTT
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2604236 original size:19 final size:20
Alignment explanation
Indices: 2604212--2604265 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
2604202 ACATTATGCT
**
2604212 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGCACAA
2604231 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCACAA
2604251 TTGTATCGATACATG
1 TTGTATCGATACATG
2604266 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:2607920 original size:21 final size:20
Alignment explanation
Indices: 2607874--2607926 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
2607864 ATAGCCAAAC
**
2607874 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
2607894 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACAC-AAAAAA
2607914 TTGTATCGATACA
1 TTGTATCGATACA
2607927 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:2611990 original size:15 final size:15
Alignment explanation
Indices: 2611970--2612008 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2611960 TAAAAATGTC
*
2611970 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2611985 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
2612000 CCAAATGAA
1 CAAAATGAA
2612009 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2614096 original size:13 final size:13
Alignment explanation
Indices: 2614078--2614115 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2614068 CATTTTTCTT
2614078 TGTATCGATACAA
1 TGTATCGATACAA
*
2614091 TGTATCGATACAC
1 TGTATCGATACAA
*
2614104 TATATCGATACA
1 TGTATCGATACA
2614116 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2614599 original size:21 final size:20
Alignment explanation
Indices: 2614557--2614599 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2614547 GGCAGCACCA
* *
2614557 CCAGGTCGCGACCGGCACTC
1 CCAGGTCACAACCGGCACTC
*
2614577 CCAGGTCACAACCAGGCAGTC
1 CCAGGTCACAACC-GGCACTC
2614598 CC
1 CC
2614600 CATACTAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.21, C:0.44, G:0.26, T:0.09
Consensus pattern (20 bp):
CCAGGTCACAACCGGCACTC
Found at i:2615778 original size:23 final size:21
Alignment explanation
Indices: 2615736--2615778 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
2615726 GTTTAATGTT
**
2615736 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
2615757 TTTGCATTGTACTTTGAATTTT
1 TTTGC-TTG-ACTTTGAATTTT
2615779 TAATCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.60
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:2616672 original size:13 final size:13
Alignment explanation
Indices: 2616654--2616679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2616644 TACACAAAGT
2616654 ATGTATCGATACA
1 ATGTATCGATACA
2616667 ATGTATCGATACA
1 ATGTATCGATACA
2616680 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2616698 original size:34 final size:32
Alignment explanation
Indices: 2616636--2616700 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2616626 TAGCCAAACT
**
2616636 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
2616668 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
2616701 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:2620325 original size:13 final size:13
Alignment explanation
Indices: 2620307--2620333 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2620297 GCAATATTCT
2620307 TTGTATCGATACA
1 TTGTATCGATACA
2620320 TTGTATCGATACA
1 TTGTATCGATACA
2620333 T
1 T
2620334 GAGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2622231 original size:22 final size:21
Alignment explanation
Indices: 2622206--2622249 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
2622196 TTTTAAATGA
2622206 TTATCAAGGGAGAGAAAATTTT
1 TTATCAAGGGAGAG-AAATTTT
*
2622228 TTATCAAGGGGGAGAAATTTT
1 TTATCAAGGGAGAGAAATTTT
2622249 T
1 T
2622250 AAACGAGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (21 bp):
TTATCAAGGGAGAGAAATTTT
Found at i:2623188 original size:20 final size:20
Alignment explanation
Indices: 2623162--2623217 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2623152 CCCTACCACT
2623162 ATTTGTATCGATACATGACT-
1 ATTTGTATCGATACATGA-TA
*
2623182 GTTTGTATCGATACATGATA
1 ATTTGTATCGATACATGATA
*
2623202 AATTGTATCGATACAT
1 ATTTGTATCGATACAT
2623218 TACTTCAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (20 bp):
ATTTGTATCGATACATGATA
Found at i:2626149 original size:65 final size:63
Alignment explanation
Indices: 2626051--2626208 Score: 212
Period size: 65 Copynumber: 2.4 Consensus size: 63
2626041 ACCTACAACA
* *
2626051 CTATCTTTTGAAGGCTAAGGTAGAACTTTCCTATCTTTTCACAAGCTAAGATAGAACC-T-CC
1 CTATCTTTTCAAGGCTAAGATAGAACTTTCCTATCTTTTCACAAGCTAAGATAGAACCTTCCC
2626112 CTATCTTTTCACAGGCTAAGATAGAACTTCTTCCCTATCTTTTCACAAGCTAAGATAGAACCTTT
1 CTATCTTTTCA-AGGCTAAGATAGAAC-T-TT-CCTATCTTTTCACAAGCTAAGATAGAACC-TT
2626177 CCCC
61 -CCC
2626181 CTATCTTTTTCAAAGGCTAAGATAGAAC
1 CTATC-TTTTC-AAGGCTAAGATAGAAC
2626209 CTCTCAATCA
Statistics
Matches: 85, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
61 10 0.12
62 14 0.16
63 1 0.01
64 2 0.02
65 29 0.34
67 1 0.01
69 7 0.08
70 20 0.24
71 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (63 bp):
CTATCTTTTCAAGGCTAAGATAGAACTTTCCTATCTTTTCACAAGCTAAGATAGAACCTTCCC
Found at i:2626152 original size:34 final size:32
Alignment explanation
Indices: 2626051--2626208 Score: 187
Period size: 31 Copynumber: 4.8 Consensus size: 32
2626041 ACCTACAACA
* *
2626051 CTATCTTTTGA-AGGCTAAGGTAGAACTTT-C
1 CTATCTTTTCACAGGCTAAGATAGAACTTTCC
* *
2626081 CTATCTTTTCACAAGCTAAGATAGAAC-CTCC
1 CTATCTTTTCACAGGCTAAGATAGAACTTTCC
2626112 CTATCTTTTCACAGGCTAAGATAGAACTTCTTCC
1 CTATCTTTTCACAGGCTAAGATAGAAC-T-TTCC
*
2626146 CTATCTTTTCACAAGCTAAGATAGAACCTTTCCCC
1 CTATCTTTTCACAGGCTAAGATAGAA-CTTT--CC
*
2626181 CTATCTTTTTCAAAGGCTAAGATAGAAC
1 CTATC-TTTTCACAGGCTAAGATAGAAC
2626209 CTCTCAATCA
Statistics
Matches: 110, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.10
31 40 0.36
33 2 0.02
34 29 0.26
35 9 0.08
36 19 0.17
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (32 bp):
CTATCTTTTCACAGGCTAAGATAGAACTTTCC
Found at i:2626764 original size:20 final size:19
Alignment explanation
Indices: 2626739--2626789 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
2626729 CAGTTTTATC
* *
2626739 TATCGATACATTTTATAGTG
1 TATCGATACATGTAATA-TG
*
2626759 TATCGATACTAAGTAATATG
1 TATCGATAC-ATGTAATATG
2626779 TATCGATACAT
1 TATCGATACAT
2626790 CTGGGTGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (19 bp):
TATCGATACATGTAATATG
Found at i:2632640 original size:29 final size:30
Alignment explanation
Indices: 2632589--2632649 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
2632579 GATAAAAGTT
* * * *
2632589 TTAGAGATAATATTTGT-TTTTAATGTAAA
1 TTAGAGATAACATTTGTCCTTAAAAGTAAA
*
2632618 TTAGAGATAGCATTTGTCCTTAAAAGTAAA
1 TTAGAGATAACATTTGTCCTTAAAAGTAAA
2632648 TT
1 TT
2632650 TAATGTTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.43
Consensus pattern (30 bp):
TTAGAGATAACATTTGTCCTTAAAAGTAAA
Found at i:2633060 original size:27 final size:27
Alignment explanation
Indices: 2633022--2633075 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2633012 CTTCTCTTAT
2633022 ATAGGGACACACAAGATTATAATAAAG
1 ATAGGGACACACAAGATTATAATAAAG
2633049 ATAGGGACACACAAGATTATAATAAAG
1 ATAGGGACACACAAGATTATAATAAAG
2633076 TAGTTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.11, G:0.19, T:0.19
Consensus pattern (27 bp):
ATAGGGACACACAAGATTATAATAAAG
Found at i:2633809 original size:34 final size:33
Alignment explanation
Indices: 2633777--2633842 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
2633767 TGTTAATTTC
*
2633777 TTTTATATTTTATATAATTTATTATAATAATTTAA
1 TTTTA-ATTTTAAATAATTTATT-TAATAATTTAA
* *
2633812 TTTTAATTTTAAATTATTTATTTAAAAATTT
1 TTTTAATTTTAAATAATTTATTTAATAATTT
2633843 GATCGTTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 8 0.29
34 15 0.54
35 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TTTTAATTTTAAATAATTTATTTAATAATTTAA
Found at i:2636425 original size:13 final size:13
Alignment explanation
Indices: 2636407--2636453 Score: 69
Period size: 12 Copynumber: 3.5 Consensus size: 13
2636397 AAATATCATC
2636407 TTTAAAATTATTT
1 TTTAAAATTATTT
2636420 TTTAAAATTA-TT
1 TTTAAAATTATTT
2636432 TTTAAAATTAATTTT
1 TTTAAAATT-A-TTT
2636447 TTTAAAA
1 TTTAAAA
2636454 ATTTAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.35
13 11 0.35
15 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTAAAATTATTT
Found at i:2636435 original size:12 final size:12
Alignment explanation
Indices: 2636407--2636447 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 12
2636397 AAATATCATC
2636407 TTTAAAATTATTT
1 TTTAAAATTA-TT
2636420 TTTAAAATTATT
1 TTTAAAATTATT
2636432 TTTAAAATTAATT
1 TTTAAAATT-ATT
2636445 TTT
1 TTT
2636448 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTAAAATTATT
Found at i:2636457 original size:25 final size:24
Alignment explanation
Indices: 2636407--2636457 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
2636397 AAATATCATC
2636407 TTTAAAATTATTTTTTAAAATTATT
1 TTTAAAATTATTTTTTAAAA-TATT
2636432 TTTAAAATTAATTTTTTTAAAA-ATT
1 TTTAAAATT-A-TTTTTTAAAATATT
2636457 T
1 T
2636458 AAAAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 13 0.54
26 1 0.04
27 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTAAAATTATTTTTTAAAATATT
Found at i:2636497 original size:32 final size:33
Alignment explanation
Indices: 2636456--2636530 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
2636446 TTTTAAAAAT
* *
2636456 TTAAAAATAATATTTATC-TTAATATTATTAAA
1 TTAAAAATAATATTTATCACTAATATAATTAAA
*
2636488 TTAAAAATAATATTTGTCACTAATATAATTAAA
1 TTAAAAATAATATTTATCACTAATATAATTAAA
* *
2636521 ATCAAAATAA
1 TTAAAAATAA
2636531 AAAAAATGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 17 0.46
33 20 0.54
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (33 bp):
TTAAAAATAATATTTATCACTAATATAATTAAA
Found at i:2641295 original size:22 final size:22
Alignment explanation
Indices: 2641270--2641312 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2641260 TTATTTAATA
*
2641270 AAAATTTATTTTTAAA-AAATTT
1 AAAATTT-TATTTAAATAAATTT
2641292 AAAATTTTATTTAAATAAATT
1 AAAATTTTATTTAAATAAATT
2641313 CGATTAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATTTTATTTAAATAAATTT
Done.