Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007936.1 Hibiscus syriacus cultivar Beakdansim tig00110346_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2869312
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:2006304 original size:22 final size:22
Alignment explanation
Indices: 2006257--2006304 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2006247 ATTAAGTCGT
* * *
2006257 TGGGCCTAATTGGGATAAAATT
1 TGGGCCCAATTGGCATAAAATA
2006279 TGGGCCCAATTGGACATAAAA-A
1 TGGGCCCAATTGG-CATAAAATA
2006301 TGGG
1 TGGG
2006305 ATTTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (22 bp):
TGGGCCCAATTGGCATAAAATA
Found at i:2009293 original size:3 final size:3
Alignment explanation
Indices: 2009280--2009315 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2009270 GTTATTGTTG
*
2009280 TTA TTA GTA TTA TTA TTA TTA TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2009316 ACAAAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2010572 original size:19 final size:20
Alignment explanation
Indices: 2010528--2010593 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
2010518 ATCGATAAGA
*
2010528 GTATCGATACTCTACCCTTG
1 GTATCGACACTCTACCCTTG
2010548 GTATCGACACTCTACCCTT-
1 GTATCGACACTCTACCCTTG
*
2010567 GTATCGACAATCTACCCTTG
1 GTATCGACACTCTACCCTTG
2010587 GTATCGA
1 GTATCGA
2010594 TACTTCCATG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 18 0.42
20 25 0.58
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (20 bp):
GTATCGACACTCTACCCTTG
Found at i:2018009 original size:17 final size:17
Alignment explanation
Indices: 2017983--2018015 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
2017973 CCACCAATAG
2017983 AAAAAGTTCCCTTTTTAT
1 AAAAAGTT-CCTTTTTAT
2018001 AAAAA-TTCCTTTTTA
1 AAAAAGTTCCTTTTTA
2018016 AATTCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 2 0.13
18 5 0.33
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AAAAAGTTCCTTTTTAT
Found at i:2022048 original size:22 final size:22
Alignment explanation
Indices: 2022023--2022066 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2022013 TAGTTATTAC
*
2022023 ATATATGATTTTTATCATGAAT
1 ATATATGATGTTTATCATGAAT
*
2022045 ATATATGATGTTTATTATGAAT
1 ATATATGATGTTTATCATGAAT
2022067 GTTACTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
ATATATGATGTTTATCATGAAT
Found at i:2022367 original size:61 final size:61
Alignment explanation
Indices: 2022216--2022354 Score: 170
Period size: 61 Copynumber: 2.2 Consensus size: 61
2022206 GCAGGTTTAT
* *
2022216 ATTAGCACTAGTGTGTAAGGACACTAAATGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
1 ATTAGCACTAGAGTGTAA--AC-CT-AGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
* * ** **
2022281 ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTGTCATATCTGG
1 ATTAGCACTAGAGTGTAAACCTAGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
2022342 ATTAGCACTAGAG
1 ATTAGCACTAGAG
2022355 CTTAAGTTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
61 45 0.68
62 2 0.03
63 2 0.03
65 17 0.26
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (61 bp):
ATTAGCACTAGAGTGTAAACCTAGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
Found at i:2038672 original size:22 final size:22
Alignment explanation
Indices: 2038627--2038672 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2038617 AATAGTTATT
* * *
2038627 ATATATGTGATTTTTATCATGA
1 ATATATATGATGTTTATCAAGA
*
2038649 ATATATATGATGTTTATTAAGA
1 ATATATATGATGTTTATCAAGA
2038671 AT
1 AT
2038673 GTTACTTCGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (22 bp):
ATATATATGATGTTTATCAAGA
Found at i:2038966 original size:61 final size:60
Alignment explanation
Indices: 2038864--2038978 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 60
2038854 ATTGGAGGGC
*
2038864 ACAACCTTATGTGTCATATCCATATTAGTACTAGGGCGTAAGCCTAGTGTAGGTGGTGGGT
1 ACAACCTTATGTGTCATAT-CATATTAGTACTAGAGCGTAAGCCTAGTGTAGGTGGTGGGT
* *
2038925 ACAACCTTATGTGTCATAT-ATGGATTA-TCACTAGAGTGTAAGCTTAGTGTAGGT
1 ACAACCTTATGTGTCATATCAT--ATTAGT-ACTAGAGCGTAAGCCTAGTGTAGGT
2038979 TTAGCACTAC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
59 2 0.04
60 1 0.02
61 45 0.94
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (60 bp):
ACAACCTTATGTGTCATATCATATTAGTACTAGAGCGTAAGCCTAGTGTAGGTGGTGGGT
Found at i:2042076 original size:25 final size:24
Alignment explanation
Indices: 2042048--2042099 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 24
2042038 TCCTTTGTAT
2042048 ATCTTTATTTGCAACCAATGTGGGA
1 ATCTTT-TTTGCAACCAATGTGGGA
*
2042073 ATC---TTTGCACCCAATGTGGGA
1 ATCTTTTTTGCAACCAATGTGGGA
2042094 ATCTTT
1 ATCTTT
2042100 GCATTATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
21 20 0.87
25 3 0.13
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (24 bp):
ATCTTTTTTGCAACCAATGTGGGA
Found at i:2042081 original size:21 final size:21
Alignment explanation
Indices: 2042055--2042102 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2042045 TATATCTTTA
2042055 TTTGCAACCAATGTGGGAATC
1 TTTGCAACCAATGTGGGAATC
*
2042076 TTTGCACCCAATGTGGGAATC
1 TTTGCAACCAATGTGGGAATC
2042097 TTTGCA
1 TTTGCA
2042103 TTATACACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (21 bp):
TTTGCAACCAATGTGGGAATC
Found at i:2046320 original size:2 final size:2
Alignment explanation
Indices: 2046313--2046374 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
2046303 GATTCATACG
2046313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2046355 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
2046375 CATAAAATCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2046828 original size:39 final size:40
Alignment explanation
Indices: 2046725--2046843 Score: 102
Period size: 39 Copynumber: 3.0 Consensus size: 40
2046715 ACCATACACC
* * *
2046725 CAGTAAGGGCTTACCCTGTGCACAAATTAA-AGGAGAC-TA
1 CAGTAAGGACTTACCCTGAGCACAAA-GAAGAGGAGACTTA
* * * *
2046764 CTGTAAGGTCTTATCCT-ATGTACAAAGAAGAGGAG-CTTA
1 CAGTAAGGACTTACCCTGA-GCACAAAGAAGAGGAGACTTA
** *
2046803 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTTA
1 CAGTAAGGACTTACCCTGAGCACAAAGAAGAGGAGACTTA
2046843 C
1 C
2046844 CAGAACCTGG
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
38 3 0.05
39 54 0.86
40 6 0.10
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.21
Consensus pattern (40 bp):
CAGTAAGGACTTACCCTGAGCACAAAGAAGAGGAGACTTA
Found at i:2058718 original size:28 final size:28
Alignment explanation
Indices: 2058674--2058742 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
2058664 ATGTAGTGAT
2058674 TGTAAAAATATAGGTTGTTATTGTAATA
1 TGTAAAAATATAGGTTGTTATTGTAATA
* *
2058702 TGTAAACATAT-GAGTTGTTATTGTAATT
1 TGTAAAAATATAG-GTTGTTATTGTAATA
2058730 TGTAAAAAGTATA
1 TGTAAAAA-TATA
2058743 TTTCATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.03
28 31 0.89
29 3 0.09
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.42
Consensus pattern (28 bp):
TGTAAAAATATAGGTTGTTATTGTAATA
Found at i:2058775 original size:29 final size:29
Alignment explanation
Indices: 2058719--2058878 Score: 139
Period size: 29 Copynumber: 5.5 Consensus size: 29
2058709 ATATGAGTTG
* *
2058719 TTATTGTAATTTGTAAAAAG-TATATTTCA
1 TTATTGTAATTTATAAAAAGAT-TTTTTCA
*
2058748 TTATTGCAATTTATAAAAAGATTTTTTC-
1 TTATTGTAATTTATAAAAAGATTTTTTCA
* * * * *
2058776 TCTATTCTAAATTATAAAAAGATTTGTCCT
1 T-TATTGTAATTTATAAAAAGATTTTTTCA
* *
2058806 TTATTGTAGTTTATAAGAAGATTTATCTTC-
1 TTATTGTAATTTATAAAAAGATTT-T-TTCA
* * *
2058836 -TATTATAATTTATAAAAAGATTTGTCCA
1 TTATTGTAATTTATAAAAAGATTTTTTCA
2058864 TTATTGTAATTTATA
1 TTATTGTAATTTATA
2058879 CAAATCTTTA
Statistics
Matches: 104, Mismatches: 20, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
27 2 0.02
28 1 0.01
29 97 0.93
30 2 0.02
31 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (29 bp):
TTATTGTAATTTATAAAAAGATTTTTTCA
Found at i:2058827 original size:58 final size:58
Alignment explanation
Indices: 2058746--2058878 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 58
2058736 AAGTATATTT
* * *
2058746 CATTATTGCAATTTATAAAAAGATTT-TTTCTCTATTCTAAATTATAAAAAGATTTGTC
1 CATTATTGTAATTTATAAAAAGATTTATCT-TCTATTATAAATTATAAAAAGATTTGTC
* * * *
2058804 CTTTATTGTAGTTTATAAGAAGATTTATCTTCTATTATAATTTATAAAAAGATTTGTC
1 CATTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTGTC
2058862 CATTATTGTAATTTATA
1 CATTATTGTAATTTATA
2058879 CAAATCTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
58 63 0.97
59 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (58 bp):
CATTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTGTC
Found at i:2058903 original size:58 final size:58
Alignment explanation
Indices: 2058725--2058911 Score: 159
Period size: 58 Copynumber: 3.2 Consensus size: 58
2058715 GTTGTTATTG
* * * * * * *
2058725 TAATTTGTAAAAAGTATATT-T-CATTATTGCAATTTATAAAAAGATTT-TTTCTCTATTC
1 TAATTTATAAAAAG-AT-TTGTCCATTATTGTAATTTATAAGAAGATTTATCT-TCAAATA
* * * * *
2058783 TAAATTATAAAAAGATTTGTCCTTTATTGTAGTTTATAAGAAGATTTATCTTCTATTA
1 TAATTTATAAAAAGATTTGTCCATTATTGTAATTTATAAGAAGATTTATCTTCAAATA
** *
2058841 TAATTTATAAAAAGATTTGTCCATTATTGTAATTTATACA-AATCTTTATCCTT-AAATG
1 TAATTTATAAAAAGATTTGTCCATTATTGTAATTTATA-AGAAGATTTAT-CTTCAAATA
2058899 TAATTTATAAAAA
1 TAATTTATAAAAA
2058912 AATATTTAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
56 2 0.02
57 3 0.03
58 97 0.90
59 6 0.06
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (58 bp):
TAATTTATAAAAAGATTTGTCCATTATTGTAATTTATAAGAAGATTTATCTTCAAATA
Found at i:2060243 original size:32 final size:32
Alignment explanation
Indices: 2060165--2060284 Score: 125
Period size: 32 Copynumber: 3.8 Consensus size: 32
2060155 AAGGGGATTT
* *
2060165 CTTGGGGCCTTAGAGCCTAACCAA-TGAATAC
1 CTTGGGGCCTAAGAGCCTACCCAAGTGAATAC
* * * *
2060196 CTTAGGCCCTCAGAGCCTACCCAAGTGAGTAC
1 CTTGGGGCCTAAGAGCCTACCCAAGTGAATAC
* * * *
2060228 CTTGGGGCCTAAGAGCATACCCAAGGGAACAT
1 CTTGGGGCCTAAGAGCCTACCCAAGTGAATAC
* *
2060260 CTCGGGGCCTAATAGCCTACCCAAG
1 CTTGGGGCCTAAGAGCCTACCCAAG
2060285 AGTCACCTTA
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
31 20 0.28
32 52 0.72
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (32 bp):
CTTGGGGCCTAAGAGCCTACCCAAGTGAATAC
Found at i:2065341 original size:31 final size:32
Alignment explanation
Indices: 2065306--2065390 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
2065296 TAATAGGATG
* * * *
2065306 CCTTGGGGCCTTAGAGCCTACCCATG-GAATA
1 CCTTGGGACCTAAAAGCCTACCCAAGAGAATA
* * *
2065337 CCTTGGGACCTCAAAGCCTACACAAGAGAGTA
1 CCTTGGGACCTAAAAGCCTACCCAAGAGAATA
2065369 CCTTGGGACCTAAAAGCCTACC
1 CCTTGGGACCTAAAAGCCTACC
2065391 TAAGGGAACA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (32 bp):
CCTTGGGACCTAAAAGCCTACCCAAGAGAATA
Found at i:2068999 original size:59 final size:60
Alignment explanation
Indices: 2068910--2069092 Score: 203
Period size: 60 Copynumber: 3.1 Consensus size: 60
2068900 CTTTAGGGTT
* *
2068910 GCTCTTTTGCTTTGTGC-TTAGGGTAAGTCCTTATGGACCTAGGGGCACT-CCATCAAGTG
1 GCTCTTTTGCTTTGCGCATTA-GGTAAGTCCTTATGGACCTAGGGGCACTCCCCTCAAGTG
* * * * *
2068969 GCT-TATTTGCTTTGCGCATTTGGTATGTCCTTATGGACAT-GGGGCCACTCCCCTTAGGTG
1 GCTCT-TTTGCTTTGCGCATTAGGTAAGTCCTTATGGACCTAGGGG-CACTCCCCTCAAGTG
* * * * *
2069029 GCTCTTTTGCTTTGTGCATTAGGTAAGTTCTTGTAGACCTAGAGGCACTCCCCTCAAGTG
1 GCTCTTTTGCTTTGCGCATTAGGTAAGTCCTTATGGACCTAGGGGCACTCCCCTCAAGTG
2069089 GCTC
1 GCTC
2069093 CTACGCTTCG
Statistics
Matches: 101, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
58 5 0.05
59 35 0.35
60 57 0.56
61 4 0.04
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (60 bp):
GCTCTTTTGCTTTGCGCATTAGGTAAGTCCTTATGGACCTAGGGGCACTCCCCTCAAGTG
Found at i:2070191 original size:21 final size:21
Alignment explanation
Indices: 2070161--2070204 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2070151 TCATTTATAA
2070161 GATGCCAATAATTATCAACAT
1 GATGCCAATAATTATCAACAT
*
2070182 GATGCTAATAATTATCAACAT
1 GATGCCAATAATTATCAACAT
2070203 GA
1 GA
2070205 ATATGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (21 bp):
GATGCCAATAATTATCAACAT
Found at i:2073165 original size:19 final size:19
Alignment explanation
Indices: 2073137--2073181 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2073127 AACAGTAAGT
*
2073137 ATTCAACCAGAACCGATAA
1 ATTCATCCAGAACCGATAA
2073156 ATTCATCCAGAACCGATAA
1 ATTCATCCAGAACCGATAA
2073175 ATTCATC
1 ATTCATC
2073182 AAGTCTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.22
Consensus pattern (19 bp):
ATTCATCCAGAACCGATAA
Found at i:2080706 original size:2 final size:2
Alignment explanation
Indices: 2080701--2080744 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
2080691 AATTAAGATT
* *
2080701 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TG TA TA TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
2080744 T
1 T
2080745 TTATGCATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2084327 original size:2 final size:2
Alignment explanation
Indices: 2084316--2084347 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2084306 CAAAACAAGA
2084316 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2084348 CACGTTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2086034 original size:14 final size:14
Alignment explanation
Indices: 2086015--2086078 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
2086005 ACACGTATAT
*
2086015 ATAATAACTGAAAA
1 ATAATAACAGAAAA
2086029 ATAATAACAGAAAA
1 ATAATAACAGAAAA
* * *
2086043 ATAATAACACATAT
1 ATAATAACAGAAAA
*
2086057 ATATATAACTGAAAA
1 ATA-ATAACAGAAAA
2086072 ATAATAA
1 ATAATAA
2086079 GTATTATGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 31 0.76
15 10 0.24
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (14 bp):
ATAATAACAGAAAA
Found at i:2100493 original size:18 final size:18
Alignment explanation
Indices: 2100470--2100576 Score: 83
Period size: 18 Copynumber: 5.6 Consensus size: 18
2100460 GATGCAATTA
2100470 GTATCGATACTGAAGTCG
1 GTATCGATACTGAAGTCG
* *
2100488 GTATCGATATTGATG-CAATG
1 GTATCGATACTGAAGTC---G
2100508 AGTATCGATACTGAAGTCG
1 -GTATCGATACTGAAGTCG
* *
2100527 GTATCGATATTGATG-CAATG
1 GTATCGATACTGAAGTC---G
*
2100547 AGTATCGATACAGAAGTCG
1 -GTATCGATACTGAAGTCG
2100566 GTATCGATACT
1 GTATCGATACT
2100577 AAGAGAAAGG
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
17 2 0.03
18 36 0.52
19 2 0.03
20 2 0.03
21 25 0.36
22 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (18 bp):
GTATCGATACTGAAGTCG
Found at i:2100495 original size:39 final size:39
Alignment explanation
Indices: 2100451--2100576 Score: 207
Period size: 39 Copynumber: 3.2 Consensus size: 39
2100441 GAAGAACAAC
* *
2100451 ATCGATACCGATGCAATTAGTATCGATACTGAAGTCGGT
1 ATCGATACTGATGCAATGAGTATCGATACTGAAGTCGGT
*
2100490 ATCGATATTGATGCAATGAGTATCGATACTGAAGTCGGT
1 ATCGATACTGATGCAATGAGTATCGATACTGAAGTCGGT
* *
2100529 ATCGATATTGATGCAATGAGTATCGATACAGAAGTCGGT
1 ATCGATACTGATGCAATGAGTATCGATACTGAAGTCGGT
2100568 ATCGATACT
1 ATCGATACT
2100577 AAGAGAAAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (39 bp):
ATCGATACTGATGCAATGAGTATCGATACTGAAGTCGGT
Found at i:2100514 original size:21 final size:21
Alignment explanation
Indices: 2100488--2100556 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
2100478 ACTGAAGTCG
2100488 GTATCGATATTGATGCAATGA
1 GTATCGATATTGATGCAATGA
* *
2100509 GTATCGATACTGA---AGTCG-
1 GTATCGATATTGATGCAAT-GA
2100527 GTATCGATATTGATGCAATGA
1 GTATCGATATTGATGCAATGA
2100548 GTATCGATA
1 GTATCGATA
2100557 CAGAAGTCGG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 14 0.36
19 1 0.03
20 1 0.03
21 23 0.59
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (21 bp):
GTATCGATATTGATGCAATGA
Found at i:2101107 original size:54 final size:54
Alignment explanation
Indices: 2101010--2101614 Score: 887
Period size: 54 Copynumber: 11.3 Consensus size: 54
2101000 TTACCAAATG
* * *
2101010 GGCACTATGTGTGCAACTTAAGAAATTTATAATAAGTTAATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* ** * *
2101064 GGCGCTACATGTGCAACTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
2101118 GGCACTATATGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCATATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
2101172 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
2101226 GGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
2101280 GGCACTATGTGTGCAACTTAAG--A---ATAATAAGGTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
2101329 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*** *
2101383 TTAACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* **
2101437 GGCACTATGTGTGCAACTTAAGAAATTCGTAATAAGTTTATGAATTTTTATATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * *
2101491 GGCATTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * *
2101545 GGCACTTTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTCCTTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
2101599 GGCACTACGGGTGCAA
1 GGCACTATGTGTGCAA
2101615 ACCATAAAAT
Statistics
Matches: 501, Mismatches: 45, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
49 45 0.09
51 1 0.00
52 1 0.00
54 454 0.91
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.38
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
Found at i:2101511 original size:265 final size:265
Alignment explanation
Indices: 2101010--2101606 Score: 881
Period size: 265 Copynumber: 2.2 Consensus size: 265
2101000 TTACCAAATG
*
2101010 GGCACTATGTGTGCAACTTAAGAAATTTATAATAAGTTAATGAATTTCCGTATTGGCGCTACATG
1 GGCACTATGTGTGCAACTTAAG--A---ATAATAAGTTAATGAATTTCCGTATTGGCACTACATG
*
2101075 TGCAACTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATTGGCACTATATGTGCAACTTAAG
61 TGCAACTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATTGGAACTATATGTGCAACTTAAG
2101140 AAATTCATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAAATTCATAAT
126 AAATTCATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAAATTCATAAT
*
2101205 AAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATGAA
191 AAGTTTATGAATTTTTATATTGGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATGAA
*
2101270 TTTCCGTATT
256 TTTCCATATT
* ***
2101280 GGCACTATGTGTGCAACTTAAGAATAATAAGGTT-ATGAATTTTCGTATTGGCACTGTGTGTGCA
1 GGCACTATGTGTGCAACTTAAGAATAATAA-GTTAATGAATTTCCGTATTGGCACTACATGTGCA
* * ** * *
2101344 ACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTTTAACTGTGTGTGCAACTTAAGAAAT
65 ACTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATTGGAACTATATGTGCAACTTAAGAAAT
* *
2101409 TCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACTTAAGAAATTCGTAATAAGT
130 TCATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGT
* * *
2101474 TTATGAATTTTTATATTGGCATTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTC
195 TTATGAATTTTTATATTGGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATGAATTTC
2101539 CATATT
260 CATATT
* * * *
2101545 GGCACTTTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTCCTTATTGGCACTAC
1 GGCACTATGTGTGCAACTTAAG--A---ATAATAAGTTAATGAATTTCCGTATTGGCACTAC
2101607 GGGTGCAAAC
Statistics
Matches: 295, Mismatches: 25, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
265 240 0.81
266 3 0.01
267 1 0.00
268 1 0.00
269 3 0.01
270 47 0.16
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (265 bp):
GGCACTATGTGTGCAACTTAAGAATAATAAGTTAATGAATTTCCGTATTGGCACTACATGTGCAA
CTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATTGGAACTATATGTGCAACTTAAGAAATT
CATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTT
TATGAATTTTTATATTGGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATGAATTTCC
ATATT
Found at i:2101601 original size:319 final size:319
Alignment explanation
Indices: 2101010--2101614 Score: 967
Period size: 319 Copynumber: 1.9 Consensus size: 319
2101000 TTACCAAATG
* **
2101010 GGCACTATGTGTGCAACTTAAGAAATTTATAATAAGTTAATGAATTTCCGTATTGGCGCTACATG
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTAATGAATTTCCGTATTGGAACTACATG
2101075 TGCAACTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATTGGCACTATATGTGCAACTTAAG
66 TGCAACTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATTGGCACTATATGTGCAACTTAAG
2101140 AAATTCATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAAATTCATAAT
131 AAATTCATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAAATTCATAAT
*** *
2101205 AAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATGAA
196 AAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATAAA
* *
2101270 TTTCCGTATTGGCACTATGTGTGCAACTTAAGAATAATAAGGTTATGAATTTTCGTATT
261 TTTCCGTATTGGCACTACGGGTGCAACTTAAGAATAATAAGGTTATGAATTTTCGTATT
* * * ** ***
2101329 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTTTAACTGTGTG
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTAATGAATTTCCGTATTGGAACTACATG
* * *
2101394 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACTTAAG
66 TGCAACTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATTGGCACTATATGTGCAACTTAAG
* * * *
2101459 AAATTCGTAATAAGTTTATGAATTTTTATATTGGCATTGTGTGTGCAACTTAAGAAATTCATAAT
131 AAATTCATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAAATTCATAAT
* *
2101524 AAGTTTATGAATTTCCATATTGGCACTTTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAA
196 AAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATAAA
*
2101589 TTTCCTTATTGGCACTACGGGTGCAA
261 TTTCCGTATTGGCACTACGGGTGCAA
2101615 ACCATAAAAT
Statistics
Matches: 259, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
319 259 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.38
Consensus pattern (319 bp):
GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTAATGAATTTCCGTATTGGAACTACATG
TGCAACTTAAGAAATTCATAATAAGCTTATGAATTTTCCTATTGGCACTATATGTGCAACTTAAG
AAATTCATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAAATTCATAAT
AAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACTTAAAAAATTCATAATAAGTTTATAAA
TTTCCGTATTGGCACTACGGGTGCAACTTAAGAATAATAAGGTTATGAATTTTCGTATT
Found at i:2108238 original size:54 final size:54
Alignment explanation
Indices: 2108151--2108855 Score: 1024
Period size: 54 Copynumber: 13.1 Consensus size: 54
2108141 TTACCAAATA
* **
2108151 GGCACTATGTATGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
2108205 GGCATTATGTCTGCAACTTAAGAAAATCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
2108259 GGCACTATGTCTGTAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
2108313 GGAACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
2108367 GGCACTTTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * *
2108421 TGCACTGTGTGTGCAACTTAAGAAATTAATAATAAGTTTCTGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
2108475 GGCACTGTGTGTACAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * **
2108529 GGCACTGTGTGTGCAACTTAAG-AATTCATAATAAGTTTATTAATTTCTATATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
2108582 GGCACTATGTGTGCTACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
2108636 GGCACTGTGTGTGCAACTTAAGAAATTC---ATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * * * * **
2108687 GACATTGTATGTGCAACTTAAGAAACTCATGATAAGTTTATGAATTTTTGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* **
2108741 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTATATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
2108795 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGATTATGAAATTT-TGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATG-AATTTCCGTATT
2108849 GGCACTA
1 GGCACTA
2108856 CGAATGCAAA
Statistics
Matches: 596, Mismatches: 50, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
51 46 0.08
53 49 0.08
54 496 0.83
55 5 0.01
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:2112029 original size:46 final size:46
Alignment explanation
Indices: 2111994--2112387 Score: 608
Period size: 46 Copynumber: 8.5 Consensus size: 46
2111984 ATTTATACAT
2111994 TTAATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
1 TTAA-TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
2112041 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
1 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
* * * * *
2112087 TTAATTATGGCATCCTTTCATTCCTTAATACATCCTTTTATTCATT
1 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
* *
2112133 TTAATTATGGCATCCTTTCATACCTTAATGCAACCTTTCATGCATC
1 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
2112179 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
1 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
* * * * * *
2112225 TTAATTATGGCATCCTTTGATGCCTTATTACATCATTTCATGGATT
1 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
* ** *
2112271 TTAATTATGGAATATTTTCATGCCTTAATGCATCCTTTCATGCATT
1 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
*
2112317 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTC
1 TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
*
2112363 TTAAGTATGGCATCCTTTCATGCCT
1 TTAATTATGGCATCCTTTCATGCCT
2112388 CTTAAGTATG
Statistics
Matches: 314, Mismatches: 33, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
46 310 0.99
47 4 0.01
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.43
Consensus pattern (46 bp):
TTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATC
Found at i:2112039 original size:12 final size:12
Alignment explanation
Indices: 2112022--2112086 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
2112012 TCATGCCTTA
2112022 ATGCATCCTTTC
1 ATGCATCCTTTC
*
2112034 ATGCAT-CTTAATT
1 ATGCATCCTT--TC
2112047 ATGGCATCCTTTC
1 AT-GCATCCTTTC
*
2112060 ATG---CC-TTA
1 ATGCATCCTTTC
2112068 ATGCATCCTTTC
1 ATGCATCCTTTC
2112080 ATGCATC
1 ATGCATC
2112087 TTAATTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
11 5 0.12
12 16 0.39
13 6 0.15
14 4 0.10
15 3 0.07
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.40
Consensus pattern (12 bp):
ATGCATCCTTTC
Found at i:2112425 original size:46 final size:46
Alignment explanation
Indices: 2112372--2112489 Score: 173
Period size: 46 Copynumber: 2.6 Consensus size: 46
2112362 CTTAAGTATG
* * * *
2112372 GCATCCTTTCATGCCTCTTAAGTATGGCATCCTTTCATGTCTTAAT
1 GCATCCTTTCATGCATCTTAATTATGACATCCTTTCATGCCTTAAT
* * *
2112418 GCCTCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTATT
1 GCATCCTTTCATGCATCTTAATTATGACATCCTTTCATGCCTTAAT
2112464 GCATCCTTTCATGCATCTTAATTATG
1 GCATCCTTTCATGCATCTTAATTATG
2112490 CATTTTTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.43
Consensus pattern (46 bp):
GCATCCTTTCATGCATCTTAATTATGACATCCTTTCATGCCTTAAT
Found at i:2112807 original size:81 final size:81
Alignment explanation
Indices: 2112648--2112811 Score: 229
Period size: 81 Copynumber: 2.0 Consensus size: 81
2112638 CAGAGCTAAT
* * * * *
2112648 CCATTATTCTTTTACTCAACAGGGTTTAACCGTTCATCTAACTGGCATAATTGATACCTTTCTAT
1 CCATTATTCTTCTACTCAACAGGATTTAACCGTTCATCTAACTAGCATAAATGACACCTTTCTAT
*
2112713 CAATTGCATAGTTAGG
66 CAATTGCACAGTTAGG
* * *
2112729 CCATTATTCTTCTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAAATGACACTTTTCTGT
1 CCATTATTCTTCTACTCAACAGGATTTAACCGTTCATCTAACTAGCATAAATGACACCTTTCTAT
* *
2112794 CATTTGTACAGTTAGG
66 CAATTGCACAGTTAGG
2112810 CC
1 CC
2112812 TCAAAGGAAC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (81 bp):
CCATTATTCTTCTACTCAACAGGATTTAACCGTTCATCTAACTAGCATAAATGACACCTTTCTAT
CAATTGCACAGTTAGG
Found at i:2112852 original size:68 final size:68
Alignment explanation
Indices: 2112761--2113148 Score: 623
Period size: 68 Copynumber: 5.7 Consensus size: 68
2112751 TATTTAACCG
* * *
2112761 TTCATCTAACTAGCATAAATGACACTTTTCTGTCATTTGTACAGTTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
2112826 CCT
66 CCT
* *
2112829 TTCATCTAACTAGCATAAATGACACCTTTCTTTCATTTGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
2112894 CCT
66 CCT
* * * * *
2112897 TTTATCTAACTGGAATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAAGAACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
2112962 CCT
66 CCT
* *
2112965 TTCATCTAACTGGAATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
2113030 CCT
66 CCT
* *
2113033 TTCATCTAACTAGCTTAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
2113098 CCT
66 CCT
* * *
2113101 TTCATCTAACTGGCATAAATGACACATTTATGTCATTTGCACAGTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCATTTGCACAGTTAG
2113149 ACCTATAATC
Statistics
Matches: 297, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 297 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTAGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:2113487 original size:53 final size:54
Alignment explanation
Indices: 2113363--2113503 Score: 194
Period size: 53 Copynumber: 2.6 Consensus size: 54
2113353 ATCTATTTCT
* * * *
2113363 CATACAGAAATTCATACGCTTAGTATGAATTTCTCAGTTCGCACCCATAGTGCC
1 CATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTCGCACACAAAGTGCA
* * ***
2113417 CATACTGAAATTCATACACTTAGTATGAATTTTTTTTTTC-CACACAAAGTGCA
1 CATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTCGCACACAAAGTGCA
2113470 CATACAGAAATTCATACACTTAGTATGAATTTCT
1 CATACAGAAATTCATACACTTAGTATGAATTTCT
2113504 TAAATTTTTG
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
53 42 0.55
54 34 0.45
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (54 bp):
CATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTCGCACACAAAGTGCA
Found at i:2114044 original size:95 final size:95
Alignment explanation
Indices: 2113848--2114070 Score: 311
Period size: 95 Copynumber: 2.3 Consensus size: 95
2113838 TCTGACTCTA
* * * *
2113848 TAGTATCGATACCCCTACCATGGTATCCATACTACTATATTATTGTACCGATACCCCCTTCCGGT
1 TAGTATCGATACCCTTACCATGGTATCGATACTACTATATTATGGTACCGATACCCCATTCCGGT
** **
2113913 ATCGATACCAATTTTTTATTCGATGTTTCC
66 ATCGATACCAATTTTAGATTCGATGTGACC
*
2113943 TAGTATCGATACCCTTACCATGGTATCGATACTACTATGTTATGGTACCGATACCCCATTCCGGT
1 TAGTATCGATACCCTTACCATGGTATCGATACTACTATATTATGGTACCGATACCCCATTCCGGT
*
2114008 ATCGATACCCATTTTAGATTCGATGTGACC
66 ATCGATACCAATTTTAGATTCGATGTGACC
* * * * *
2114038 TGGTATCAAAAACCTTTCCATGGTATCGATACT
1 TAGTATCGATACCCTTACCATGGTATCGATACT
2114071 CCCTAATTGG
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 113 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (95 bp):
TAGTATCGATACCCTTACCATGGTATCGATACTACTATATTATGGTACCGATACCCCATTCCGGT
ATCGATACCAATTTTAGATTCGATGTGACC
Found at i:2118573 original size:3 final size:3
Alignment explanation
Indices: 2118560--2118601 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
2118550 CTAACAACAG
*
2118560 TAT TAT AAT TAT TAGCT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT TAT T
2118602 TAAAACATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 32 0.91
5 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2131369 original size:12 final size:12
Alignment explanation
Indices: 2131352--2131392 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
2131342 TTGCACCGAT
2131352 ACGGATACGGGG
1 ACGGATACGGGG
2131364 ACGGATACGGGG
1 ACGGATACGGGG
**
2131376 ACGGGGACGGGG
1 ACGGATACGGGG
2131388 ACGGA
1 ACGGA
2131393 AAACGGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.54, T:0.05
Consensus pattern (12 bp):
ACGGATACGGGG
Found at i:2131372 original size:18 final size:18
Alignment explanation
Indices: 2131349--2131385 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2131339 ATGTTGCACC
*
2131349 GATACGGATACGGGGACG
1 GATACGGAGACGGGGACG
*
2131367 GATACGGGGACGGGGACG
1 GATACGGAGACGGGGACG
2131385 G
1 G
2131386 GGACGGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.51, T:0.08
Consensus pattern (18 bp):
GATACGGAGACGGGGACG
Found at i:2131379 original size:6 final size:6
Alignment explanation
Indices: 2131358--2131391 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2131348 CGATACGGAT
**
2131358 ACGGGG ACGGAT ACGGGG ACGGGG ACGGGG ACGG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGG
2131392 AAAACGGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.21, C:0.18, G:0.59, T:0.03
Consensus pattern (6 bp):
ACGGGG
Found at i:2134123 original size:43 final size:43
Alignment explanation
Indices: 2134016--2134209 Score: 230
Period size: 43 Copynumber: 4.5 Consensus size: 43
2134006 CCTATAAAGT
* * * *
2134016 TAGCGGCGTTTTTGGAACAAACGCCACAATAGGTTGATATTTA
1 TAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCGATATCTA
** * *
2134059 TAGC-GCCGTTTTGGAACAAACGCAACAAAAGGTCGAGATCTA
1 TAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCGATATCTA
* *
2134101 TAGCGGCATTTTTGGAACAAACGGCGCAAAAGGTCGATATCTA
1 TAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCGATATCTA
* * * * *
2134144 TAGCAGCGTTTTTGGAACAAACACCGCAAAAGGTC-ATATATA
1 TAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCGATATCTA
2134186 TAGCGGCATTTTTGGATACAAACG
1 TAGCGGCATTTTTGGA-ACAAACG
2134210 TAGCTAATTA
Statistics
Matches: 128, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
42 55 0.43
43 73 0.57
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (43 bp):
TAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCGATATCTA
Found at i:2134188 original size:85 final size:85
Alignment explanation
Indices: 2134016--2134209 Score: 248
Period size: 85 Copynumber: 2.3 Consensus size: 85
2134006 CCTATAAAGT
* * * * *
2134016 TAGCGGCGTTTTTGGAACAAACGCCACAATAGGTTGATATTTATAGCGCCGTTTTGGAACAAACG
1 TAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCGATATCTATAGCGCCGTTTTGGAACAAACA
*
2134081 CAACAAAAGGTCGAGATCTA
66 CAACAAAAGGTCGAGATATA
* *
2134101 TAGCGGCATTTTTGGAACAAACGGCGCAAAAGGTCGATATCTATAGCAG-CGTTTTTGGAACAAA
1 TAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCGATATCTATAGC-GCCG-TTTTGGAACAAA
** *
2134165 CACCGCAAAAGGTC-ATATATA
64 CACAACAAAAGGTCGAGATATA
2134186 TAGCGGCATTTTTGGATACAAACG
1 TAGCGGCATTTTTGGA-ACAAACG
2134210 TAGCTAATTA
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
85 64 0.67
86 31 0.33
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (85 bp):
TAGCGGCATTTTTGGAACAAACGCCACAAAAGGTCGATATCTATAGCGCCGTTTTGGAACAAACA
CAACAAAAGGTCGAGATATA
Found at i:2138549 original size:23 final size:23
Alignment explanation
Indices: 2138489--2138549 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
2138479 TAGCTCATAT
*
2138489 AAATGCACCAAAGTGCCACGTAG
1 AAATGCACCAGAGTGCCACGTAG
* *
2138512 AATTGCACC-GTAGTGCCGCGTAG
1 AAATGCACCAG-AGTGCCACGTAG
2138535 AAATGCACCAGAGTG
1 AAATGCACCAGAGTG
2138550 TCATGTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (23 bp):
AAATGCACCAGAGTGCCACGTAG
Found at i:2145276 original size:23 final size:23
Alignment explanation
Indices: 2145250--2145300 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
2145240 GATGAGATGG
2145250 TAGCTGAG-TAGCTGGAGTGTCA-C
1 TAGCT-AGCTAGCTGGAGTGT-AGC
*
2145273 TAGCTAGCTAGCTTGAGTGTAGC
1 TAGCTAGCTAGCTGGAGTGTAGC
2145296 TAGCT
1 TAGCT
2145301 CAAACTCACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (23 bp):
TAGCTAGCTAGCTGGAGTGTAGC
Found at i:2147635 original size:19 final size:19
Alignment explanation
Indices: 2147611--2147648 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2147601 AAACAAGGAT
2147611 AAAAAT-TAAAATAAGAAGA
1 AAAAATATAAAATAA-AAGA
*
2147630 AAAAATATATAATAAAAGA
1 AAAAATATAAAATAAAAGA
2147649 GAACAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (19 bp):
AAAAATATAAAATAAAAGA
Found at i:2156461 original size:3 final size:3
Alignment explanation
Indices: 2156455--2156492 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2156445 ATAATAGGTA
* *
2156455 TCT TCT TCT TCT TCT TCT TCC TCT TCT TCC TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2156493 CATGCAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:2161681 original size:81 final size:81
Alignment explanation
Indices: 2161546--2161710 Score: 276
Period size: 81 Copynumber: 2.0 Consensus size: 81
2161536 TTCTTTTGTG
*
2161546 GTGTCAAGCGATCTAGGTAGGAAAAATATTTGTGGAAAGAACCTGGGAGCGAGGATCCAAGTGGC
1 GTGTCAAGCGATCTAGGTAGGAAAAATATTTGTGGAAAGAACCTGGGAGCGAGGATCCAAGTGAC
*
2161611 TTGTTGGTGGACCTTA
66 TAGTTGGTGGACCTTA
* * *
2161627 GTGTCAAGTGATCTAGGTAGGAAAAATATTTGTGTAGAGAACCTGGGAGCGAGGATCCAAGTGAC
1 GTGTCAAGCGATCTAGGTAGGAAAAATATTTGTGGAAAGAACCTGGGAGCGAGGATCCAAGTGAC
*
2161692 TAGTTGGTGGATCTTA
66 TAGTTGGTGGACCTTA
2161708 GTG
1 GTG
2161711 GATTATACCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.26
Consensus pattern (81 bp):
GTGTCAAGCGATCTAGGTAGGAAAAATATTTGTGGAAAGAACCTGGGAGCGAGGATCCAAGTGAC
TAGTTGGTGGACCTTA
Found at i:2168681 original size:20 final size:19
Alignment explanation
Indices: 2168653--2168702 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2168643 AATAGGTGGA
*
2168653 TATCTATACCAAAGGTTTAG
1 TATCGATACCAAAGG-TTAG
*
2168673 TATCGATACTAAAAGGTTAG
1 TATCGATAC-CAAAGGTTAG
*
2168693 TATCGGTACC
1 TATCGATACC
2168703 CATAAATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (19 bp):
TATCGATACCAAAGGTTAG
Found at i:2171281 original size:17 final size:17
Alignment explanation
Indices: 2171259--2171318 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 17
2171249 AAATTGGAGT
2171259 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
2171276 ACAAAAAG-AAG-AAA-
1 ACAAAAAGAAAGAAAAG
*
2171290 A-AAATAGAAA-AAAAG
1 ACAAAAAGAAAGAAAAG
* *
2171305 AAAAAAAAAAAGAA
1 ACAAAAAGAAAGAA
2171319 GAATTTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
13 5 0.14
14 6 0.17
15 4 0.11
16 10 0.29
17 10 0.29
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:2171304 original size:21 final size:20
Alignment explanation
Indices: 2171264--2171318 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
2171254 GGAGTACAAA
* *
2171264 AAGAAAGAAAAGACAAAAAG
1 AAGAAAAAAAAGAAAAAAAG
2171284 AAGAAAAAAATAGAAAAAAAG
1 AAGAAAAAAA-AGAAAAAAAG
*
2171305 AAAAAAAAAAAGAA
1 AAGAAAAAAAAGAA
2171319 GAATTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (20 bp):
AAGAAAAAAAAGAAAAAAAG
Found at i:2172625 original size:24 final size:25
Alignment explanation
Indices: 2172598--2172651 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
2172588 AAATCATGGT
2172598 TTTTGGAA-AACCAAAAGAT-ATGAC
1 TTTTGGAAGAACCAAAAG-TCATGAC
*
2172622 TTTT-GAAGAACCAATAGTCATGAC
1 TTTTGGAAGAACCAAAAGTCATGAC
2172646 TTTTGG
1 TTTTGG
2172652 TGATTCACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 4 0.15
24 21 0.81
25 1 0.04
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (25 bp):
TTTTGGAAGAACCAAAAGTCATGAC
Found at i:2175032 original size:22 final size:21
Alignment explanation
Indices: 2174996--2175036 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2174986 CATCTCCATT
2174996 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
2175017 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
2175037 TTCCACAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:2175524 original size:21 final size:21
Alignment explanation
Indices: 2175499--2175555 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
2175489 CGTGAACAGT
*
2175499 GGGGAATTGGTTCCCTGCTGG
1 GGGGAATCGGTTCCCTGCTGG
*
2175520 GGGGAATCGGTTCCCTGTTGG
1 GGGGAATCGGTTCCCTGCTGG
*
2175541 GGGGAATCGATTCCC
1 GGGGAATCGGTTCCC
2175556 CTTTTACATT
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:0.12, C:0.21, G:0.40, T:0.26
Consensus pattern (21 bp):
GGGGAATCGGTTCCCTGCTGG
Found at i:2176203 original size:40 final size:40
Alignment explanation
Indices: 2176157--2176277 Score: 215
Period size: 40 Copynumber: 3.0 Consensus size: 40
2176147 CCGTAGTGCC
2176157 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
* *
2176197 ACACATAAGGTCGTGCCCACCATATACACTGAACTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
*
2176237 ACACATAAGGTCGTGCCCACCATATACACCAAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
2176277 A
1 A
2176278 TAAACCTGCA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
Found at i:2183688 original size:40 final size:40
Alignment explanation
Indices: 2183499--2183699 Score: 321
Period size: 40 Copynumber: 5.0 Consensus size: 40
2183489 TCGAAGTGCC
*
2183499 ACACATAAGGTCGTGCCCACCATATACACAGAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
* * *
2183539 ACATATAAGGTTGTGCCCACCATATACACCAAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
*
2183579 ACATATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
2183619 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
* * * *
2183659 ACACATAAGGTCCTGCTCACCATATACACCAAACTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
2183699 A
1 A
2183700 TAAACCTGCA
Statistics
Matches: 150, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 150 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (40 bp):
ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
Found at i:2190523 original size:90 final size:90
Alignment explanation
Indices: 2190370--2190547 Score: 279
Period size: 90 Copynumber: 2.0 Consensus size: 90
2190360 CCTAACAAAC
* *
2190370 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGTTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAAGTATTTTATTATTTCAAATTAATTAAATCTAT
* *
2190435 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
2190460 CCTTTTATATCCAAGTTAACCC-AATCATATTAAAG-ATTTTATTATTTCAAATTAATTAAATCT
1 CCTTTTATAGCCAAGTT-ACCCTAATCATATT-AAGTATTTTATTATTTCAAATTAATTAAATCT
2190523 ATATTTAATTAATTGAAATTAAATA
64 ATATTTAATTAATTGAAATTAAATA
2190548 TTCGGGATTA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
90 75 0.93
91 6 0.07
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAAGTATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:2191244 original size:28 final size:28
Alignment explanation
Indices: 2191204--2191271 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
2191194 GTCACATAAT
2191204 AATCCAAGACATACGCTCATAGTGGGTC
1 AATCCAAGACATACGCTCATAGTGGGTC
2191232 AATCCAAGACATACGCTCATAGTGGGTC
1 AATCCAAGACATACGCTCATAGTGGGTC
*
2191260 AATCCAATACAT
1 AATCCAAGACAT
2191272 TGTTCTCTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (28 bp):
AATCCAAGACATACGCTCATAGTGGGTC
Found at i:2194528 original size:17 final size:17
Alignment explanation
Indices: 2194506--2194538 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2194496 CCGACCGACT
*
2194506 CGACCCGATCGTTGACC
1 CGACCCGACCGTTGACC
2194523 CGACCCGACCGTTGAC
1 CGACCCGACCGTTGAC
2194539 TGTTGACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.15
Consensus pattern (17 bp):
CGACCCGACCGTTGACC
Found at i:2212997 original size:90 final size:90
Alignment explanation
Indices: 2212844--2213010 Score: 273
Period size: 90 Copynumber: 1.9 Consensus size: 90
2212834 CCTAACACAC
* * *
2212844 CCTTTTATAGCCAAGTTATCATAATCATATTAGGGTTTATATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCAAAGTTACCATAATCATATTAGGATTTATATTATTTCAAATTAATTAAATCTAT
2212909 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGGAATTTAATAAT
* *
2212934 CCTTTTATATCAAAGTTACCCTAATCATATTAAGGATTT-TATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCAAAGTTACCATAATCATATT-AGGATTTATATTATTTCAAATTAATTAAATCTA
2212998 TATTTAATTAATT
65 TATTTAATTAATT
2213011 AAAATTAAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
90 65 0.92
91 6 0.08
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCAAAGTTACCATAATCATATTAGGATTTATATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGGAATTTAATAAT
Found at i:2214011 original size:16 final size:15
Alignment explanation
Indices: 2213990--2214027 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
2213980 ACTCTAACAA
2213990 ATAAAATATTATAAAT
1 ATAAAATATTA-AAAT
2214006 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
2214021 A-AAAATA
1 ATAAAATA
2214028 AAATAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 6 0.27
15 5 0.23
16 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:2214028 original size:19 final size:16
Alignment explanation
Indices: 2213988--2214032 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 16
2213978 ATACTCTAAC
2213988 AAATAAAATATTATAA
1 AAATAAAATATTATAA
*
2214004 ATATAAAATATTAAAATAA
1 AAATAAAATATT---ATAA
2214023 AAATAAAATA
1 AAATAAAATA
2214033 AAATAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.46
19 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAAAATATTATAA
Found at i:2214082 original size:21 final size:21
Alignment explanation
Indices: 2214056--2214095 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2214046 CAAAACTCAT
*
2214056 GTATAATAAAATTCAAATCAC
1 GTATAACAAAATTCAAATCAC
2214077 GTATAACAAAATTCAAATC
1 GTATAACAAAATTCAAATC
2214096 TAATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.28
Consensus pattern (21 bp):
GTATAACAAAATTCAAATCAC
Found at i:2216219 original size:3 final size:3
Alignment explanation
Indices: 2216211--2216237 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2216201 AAGTTAAATC
2216211 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2216238 ATTTGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2219785 original size:2 final size:2
Alignment explanation
Indices: 2219778--2220033 Score: 129
Period size: 2 Copynumber: 137.5 Consensus size: 2
2219768 ATATTATACC
* *
2219778 AT AT AT AT AT AC ACT AT AT A- AT A- AA AT ACT AT A- AT AT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
2219818 AT AT CAT AT TT GAT AT AT A- AT A- AA AT A- AT AT AA AT AT -T AT
1 AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2219858 A- AT AT AT AT AT AT -T AT A- AT AT A- AT AC AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
2219897 A- AT AT AT A- AT AT A- AT AT TT TT ACT AT AT AT A- AT ACC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT
2219937 A- AT AT A- AT AT A- AT AT A- AT AT A- AT AT A- AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2219971 AT AT AT AT ACT AT A- AT AC AT ACT AT AT AT A- AT AT AT ACT AT
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT
2220012 AT AT AT A- AT AT -T AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2220034 AAAAAATCCC
Statistics
Matches: 199, Mismatches: 16, Indels: 78
0.68 0.05 0.27
Matches are distributed among these distances:
1 29 0.15
2 153 0.77
3 17 0.09
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2219847 original size:8 final size:9
Alignment explanation
Indices: 2219834--2219971 Score: 63
Period size: 9 Copynumber: 15.0 Consensus size: 9
2219824 TATTTGATAT
2219834 ATAATA-AA
1 ATAATATAA
2219842 ATAATATAA
1 ATAATATAA
*
2219851 ATATTATAA
1 ATAATATAA
*
2219860 TATATATATATT
1 -ATA-ATATA-A
2219872 ATAATAT-A
1 ATAATATAA
2219880 ATACATAT-A
1 ATA-ATATAA
*
2219889 CT-ATATATA
1 ATAATATA-A
2219898 AT-ATATAA
1 ATAATATAA
**
2219906 TATAATATTT
1 -ATAATATAA
* * *
2219916 TTACTATAT
1 ATAATATAA
* *
2219925 ATAATACCAT
1 ATAATA-TAA
2219935 ATAATATAA
1 ATAATATAA
2219944 TATAATATAA
1 -ATAATATAA
2219954 TATAATAT-A
1 -ATAATATAA
2219963 ATAATATAA
1 ATAATATAA
2219972 TATATATACT
Statistics
Matches: 102, Mismatches: 16, Indels: 23
0.72 0.11 0.16
Matches are distributed among these distances:
7 4 0.04
8 17 0.17
9 38 0.37
10 36 0.35
11 7 0.07
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (9 bp):
ATAATATAA
Found at i:2219848 original size:22 final size:20
Alignment explanation
Indices: 2219792--2220021 Score: 79
Period size: 21 Copynumber: 11.4 Consensus size: 20
2219782 ATATATACAC
* *
2219792 TATATAATAAAATACTATAA
1 TATATAATAAAATAATATTA
**
2219812 TATATAATATCAT-AT-TTGA
1 TATATAATAAAATAATATT-A
*
2219831 TATATAATAAAATAATATAAA
1 TATATAATAAAATAATAT-TA
*
2219852 TATTATAAT-ATATATATATTA
1 TA-TATAATAAAATA-ATATTA
* *
2219873 TAATATAATACATATACTA-TA
1 T-ATATAATA-AAATAATATTA
*
2219894 TATAATATATAATATAATATT-
1 TAT-ATA-ATAAAATAATATTA
* * **
2219915 T-T-TACTATATATAATACCA
1 TATATAATA-AAATAATATTA
*
2219934 TATA-ATATAATATAATA-TA
1 TATATA-ATAAAATAATATTA
*
2219953 -ATATAATATAATAATATAATA
1 TATATAATAAAATAATAT--TA
* * *
2219974 TATATACTATAATACATACTA
1 TATATAATAAAATA-ATATTA
* *
2219995 TATATAAT-ATATACTA-TA
1 TATATAATAAAATAATATTA
2220013 TATATAATA
1 TATATAATA
2220022 TTATAATATA
Statistics
Matches: 162, Mismatches: 24, Indels: 49
0.69 0.10 0.21
Matches are distributed among these distances:
17 2 0.01
18 33 0.20
19 18 0.11
20 29 0.18
21 43 0.27
22 29 0.18
23 8 0.05
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATAATAAAATAATATTA
Found at i:2219863 original size:5 final size:5
Alignment explanation
Indices: 2219832--2220031 Score: 138
Period size: 5 Copynumber: 41.0 Consensus size: 5
2219822 CATATTTGAT
* *
2219832 ATATA ATA-A A-ATA ATATA A-ATA TTATA ATATA TATATA TTATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATATA
* * * * *
2219880 ATA-C ATATA CTAT- ATATAA TATATA ATATA ATAT- TTTTA CTAT- ATATA
1 ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA ATATA
**
2219928 ATACC ATATA ATATA ATATA ATATA ATATA ATAT- A-ATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* *
2219975 ATATA CTATA ATA-C ATACTA TATATA ATATA TACTATA TATATA ATAT-
1 ATATA ATATA ATATA ATA-TA -ATATA ATATA -A-TATA -ATATA ATATA
2220023 -TATA ATATA
1 ATATA ATATA
2220032 TAAAAAAATC
Statistics
Matches: 154, Mismatches: 21, Indels: 40
0.72 0.10 0.19
Matches are distributed among these distances:
3 6 0.04
4 27 0.18
5 95 0.62
6 13 0.08
7 13 0.08
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:2220017 original size:91 final size:96
Alignment explanation
Indices: 2219807--2220036 Score: 193
Period size: 103 Copynumber: 2.4 Consensus size: 96
2219797 AATAAAATAC
* * *
2219807 TATAATATATAATATCATATT-T---GATAT-ATA-ATAAAATAATATAAATATTAT-A-ATAT-
1 TATAATATATAATATAATATTATACATATATAATACATAAAATAATATAAATAATATAATATATA
2219863 AT-ATATATTATAATATAATACATATACTATA
66 ATAATATATTATAATATAATACA-ATACTATA
*
2219894 TATAATATATAATATAATATTTTTACTATATATAATACCATATAATATAATATAATATAATATAA
1 TATAATATATAATATAATA-TTATAC-ATATATAATA-CATA-AA-ATAATATAA-ATAATATAA
*
2219959 TATAATAAT-ATAATATATATACTATAATAC-ATACTATA
60 TAT-ATAATAAT-ATAT-TATAATATAATACAATACTATA
* *
2219997 TATAATATATACTAT-ATA-TATA-ATATTATAATATATAAAA
1 TATAATATATAATATAATATTATACATA-TATAATACATAAAA
2220037 AAATCCCAGA
Statistics
Matches: 117, Mismatches: 7, Indels: 29
0.76 0.05 0.19
Matches are distributed among these distances:
87 18 0.15
88 2 0.02
89 1 0.01
93 4 0.03
94 3 0.03
96 4 0.03
97 4 0.03
98 15 0.13
99 13 0.11
100 4 0.03
101 2 0.02
102 5 0.04
103 26 0.22
104 4 0.03
105 12 0.10
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (96 bp):
TATAATATATAATATAATATTATACATATATAATACATAAAATAATATAAATAATATAATATATA
ATAATATATTATAATATAATACAATACTATA
Found at i:2222465 original size:13 final size:13
Alignment explanation
Indices: 2222449--2222477 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2222439 AAGGAGTTTA
2222449 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
2222462 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
2222475 AAA
1 AAA
2222478 GCCAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:2225553 original size:23 final size:24
Alignment explanation
Indices: 2225522--2225568 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2225512 AATAGGTATA
*
2225522 TGGTTCTTAAGGA-AATTTATATG
1 TGGTCCTTAAGGACAATTTATATG
* *
2225545 TGGTCCTTATGGACATTTTATATG
1 TGGTCCTTAAGGACAATTTATATG
2225569 GCACTTTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.45
Consensus pattern (24 bp):
TGGTCCTTAAGGACAATTTATATG
Found at i:2225597 original size:23 final size:23
Alignment explanation
Indices: 2225570--2225630 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2225560 TTTTATATGG
*
2225570 CACTTTGGTGCATTTCTACGCGA
1 CACTTCGGTGCATTTCTACGCGA
* * *
2225593 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGA
2225616 CACTTCGGTGCATTT
1 CACTTCGGTGCATTT
2225631 ATATGAGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.34
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGA
Found at i:2232461 original size:21 final size:21
Alignment explanation
Indices: 2232413--2232485 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
2232403 GGGTCTACGC
* *
2232413 GGTCCTTCGGGACATATAT-G
1 GGTCCTTTGGAACATATATGG
** *
2232433 TATCCTTTGGAACATTTATGG
1 GGTCCTTTGGAACATATATGG
*
2232454 GGTCCTTT-GAGACATATATGT
1 GGTCCTTTGGA-ACATATATGG
2232475 GGTCC-TTGGAA
1 GGTCCTTTGGAA
2232486 TAGGTATATG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 19 0.46
21 22 0.54
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (21 bp):
GGTCCTTTGGAACATATATGG
Found at i:2232525 original size:23 final size:24
Alignment explanation
Indices: 2232494--2232540 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2232484 AATAGGTATA
* *
2232494 TGGTTCTTAAGGAGA-TTTATATG
1 TGGTCCTTAAGGACATTTTATATG
*
2232517 TGGTCCTTATGGACATTTTATATG
1 TGGTCCTTAAGGACATTTTATATG
2232541 GAACTTCGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (24 bp):
TGGTCCTTAAGGACATTTTATATG
Found at i:2252201 original size:16 final size:17
Alignment explanation
Indices: 2252182--2252218 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2252172 TAAAATATTA
2252182 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
2252198 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
2252215 TTTT
1 TTTT
2252219 TTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:2253453 original size:15 final size:15
Alignment explanation
Indices: 2253441--2253471 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2253431 GATATTCGAG
2253441 TATGTGTTCTTCGGA
1 TATGTGTTCTTCGGA
2253456 TATGTGTTCTTCGGA
1 TATGTGTTCTTCGGA
2253471 T
1 T
2253472 TAGATTGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (15 bp):
TATGTGTTCTTCGGA
Found at i:2259364 original size:2 final size:2
Alignment explanation
Indices: 2259357--2259388 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2259347 ATTTATTTTC
2259357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2259389 TAATAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2260431 original size:15 final size:15
Alignment explanation
Indices: 2260411--2260440 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2260401 TTTAAAATAT
*
2260411 TTATAATTTTTAAAA
1 TTATAATTTATAAAA
2260426 TTATAATTTATAAAA
1 TTATAATTTATAAAA
2260441 AACAATGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATAATTTATAAAA
Found at i:2261474 original size:25 final size:25
Alignment explanation
Indices: 2261399--2261479 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
2261389 TTCCCTTGTT
* * *
2261399 TCCGTCCCCGAAATGAATCTCCGTC
1 TCCGTCCCCAAAATAAATCTTCGTC
* * *
2261424 ACCATCTCCAAAATAAATC-TCTGTC
1 TCCGTCCCCAAAATAAATCTTC-GTC
2261449 TCCGTCCCCAAAATAAATCTTCGTC
1 TCCGTCCCCAAAATAAATCTTCGTC
2261474 TCCGTC
1 TCCGTC
2261480 GGGTTTTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
24 1 0.02
25 42 0.93
26 2 0.04
ACGTcount: A:0.26, C:0.37, G:0.10, T:0.27
Consensus pattern (25 bp):
TCCGTCCCCAAAATAAATCTTCGTC
Found at i:2261937 original size:33 final size:34
Alignment explanation
Indices: 2261895--2261967 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
2261885 GAGTTTGTAT
*
2261895 TATATAATTAATATAAAAAATAT-AACTATTATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
2261928 TATATAATTAATATAAAAAATATAAAATATTATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
2261962 TATATA
1 TATATA
2261968 TATAATCGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 23 0.61
34 15 0.39
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (34 bp):
TATATAATTAATATAAAAAATATAAAATATTATA
Found at i:2262410 original size:83 final size:84
Alignment explanation
Indices: 2262315--2262471 Score: 210
Period size: 85 Copynumber: 1.9 Consensus size: 84
2262305 CAGCTTTGTT
* * *
2262315 TACAAATGCCGCAATAATGTTAATCTATAGTGG-TGTTTTTTCGAA-AAACATCGCAACAAAGTA
1 TACAAATGCCGCAATAAGGTTAACCTATAATGGATGTTTTTTC-AATAAACATCGCAACAAAGTA
2262378 GTAATTTAGCGGCATTTTTA
65 GTAATTTAGCGGCATTTTTA
* * * *
2262398 TACAAATGCCGCAATAGGGTTAACCTATAATGGTATTTTTTTTCAATAAACATCGCAACAGATTA
1 TACAAATGCCGCAATAAGGTTAACCTATAATGG-ATGTTTTTTCAATAAACATCGCAACAAAGTA
*
2262463 GTACTTTAG
65 GTAATTTAG
2262472 TGGTTTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 29 0.46
84 2 0.03
85 32 0.51
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (84 bp):
TACAAATGCCGCAATAAGGTTAACCTATAATGGATGTTTTTTCAATAAACATCGCAACAAAGTAG
TAATTTAGCGGCATTTTTA
Found at i:2262479 original size:83 final size:81
Alignment explanation
Indices: 2262295--2262500 Score: 209
Period size: 83 Copynumber: 2.5 Consensus size: 81
2262285 CCACCAAATG
* * ** * *
2262295 GTAACTTTAGCAGCTTTGTTTACAAATGCCGCAATAATGTTAATCTATAGTGGTGTTTTTTCGAA
1 GTAA-TTTAGCGGATTT-TTTACAAATGCCGCAATAGGGTTAACCTATAATGGTGTTTTTTCGAA
2262360 AAACATCGCAACAAAGTA
64 AAACATCGCAACAAAGTA
*
2262378 GTAATTTAGCGGCATTTTTATACAAATGCCGCAATAGGGTTAACCTATAATGGTATTTTTTTTC-
1 GTAATTTAGCGG-ATTTTT-TACAAATGCCGCAATAGGGTTAACCTATAATGG--TGTTTTTTCG
* *
2262442 AATAAACATCGCAACAGATTA
62 AA-AAACATCGCAACAAAGTA
* * * * *
2262463 GTACTTTAGTGG-TTTTTTACAAAAGTCGTAATAGGGTT
1 GTAATTTAGCGGATTTTTTACAAATGCCGCAATAGGGTT
2262501 CAGCTTTAGT
Statistics
Matches: 104, Mismatches: 14, Indels: 11
0.81 0.11 0.09
Matches are distributed among these distances:
82 27 0.26
83 41 0.39
84 2 0.02
85 34 0.33
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (81 bp):
GTAATTTAGCGGATTTTTTACAAATGCCGCAATAGGGTTAACCTATAATGGTGTTTTTTCGAAAA
ACATCGCAACAAAGTA
Found at i:2264985 original size:18 final size:18
Alignment explanation
Indices: 2264962--2265024 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
2264952 TATTTTTCTT
*
2264962 GAAGGACCACTATATCCC
1 GAAGGACCACTATGTCCC
*
2264980 GAAGGACCACTATGTCTC
1 GAAGGACCACTATGTCCC
*
2264998 GAAGGACTACTATGTCCC
1 GAAGGACCACTATGTCCC
2265016 GAAGGACCA
1 GAAGGACCA
2265025 TTGTAATCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (18 bp):
GAAGGACCACTATGTCCC
Found at i:2267114 original size:4 final size:4
Alignment explanation
Indices: 2267105--2267132 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2267095 AACTCCAGAG
2267105 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
2267133 TCTTCCTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:2270508 original size:22 final size:23
Alignment explanation
Indices: 2270477--2270519 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2270467 GAATATATAT
**
2270477 ATATATTACTCGTATTGTTGTCG
1 ATATATTACTAATATTGTTGTCG
2270500 ATAT-TTACTAATATTGTTGT
1 ATATATTACTAATATTGTTGT
2270520 TTGTTTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (23 bp):
ATATATTACTAATATTGTTGTCG
Found at i:2272106 original size:21 final size:21
Alignment explanation
Indices: 2272072--2272134 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
2272062 CTGACGCAAG
* * *
2272072 AGAGAACCATAGAGAGTAGCG
1 AGAGAAGCAGAGAGAGTAGCA
* *
2272093 AGAGAAGTAGAGAGAGTAGTA
1 AGAGAAGCAGAGAGAGTAGCA
* *
2272114 ATAGAAGCAGAGAGAGAAGCA
1 AGAGAAGCAGAGAGAGTAGCA
2272135 GCATTTCCGA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.35, T:0.10
Consensus pattern (21 bp):
AGAGAAGCAGAGAGAGTAGCA
Found at i:2274522 original size:16 final size:16
Alignment explanation
Indices: 2274501--2274532 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2274491 ACTATTCACA
*
2274501 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
2274517 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
2274533 ATCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:2281807 original size:84 final size:85
Alignment explanation
Indices: 2281687--2281854 Score: 275
Period size: 84 Copynumber: 2.0 Consensus size: 85
2281677 TGGTAATATC
* * * *
2281687 ATTATGGTAAGATTTGGCGCATAAAAGTACACGTAAGCATTAATC-ATTATATTATTGCTATGGT
1 ATTATGGTAAGATTTGGCACATAAAAGCACACGTAAGCATTAACCAATGATATTATTGCTATGGT
2281751 ATTATTACCATATAACTTTT
66 ATTATTACCATATAACTTTT
* *
2281771 ATTATGGTAAGATTTGGCACATAAAAGCGCATGTAAGCATTAACCAATGATATTATTGCTATGGT
1 ATTATGGTAAGATTTGGCACATAAAAGCACACGTAAGCATTAACCAATGATATTATTGCTATGGT
2281836 ATTATTACCATATAACTTT
66 ATTATTACCATATAACTTT
2281855 GGTCTTTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 40 0.52
85 37 0.48
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (85 bp):
ATTATGGTAAGATTTGGCACATAAAAGCACACGTAAGCATTAACCAATGATATTATTGCTATGGT
ATTATTACCATATAACTTTT
Found at i:2282322 original size:14 final size:14
Alignment explanation
Indices: 2282303--2282331 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2282293 TTGATTTTGA
2282303 TATAATTATATTAT
1 TATAATTATATTAT
2282317 TATAATTATATTAT
1 TATAATTATATTAT
2282331 T
1 T
2282332 CTTGTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATAATTATATTAT
Found at i:2283759 original size:25 final size:26
Alignment explanation
Indices: 2283707--2283756 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2283697 GGACTAGTGA
2283707 TATTTATATTAAATATTATTTAGTAAT
1 TATTTATATT-AATATTATTTAGTAAT
*
2283734 TATTTATATT-ATGTTATTT-GTAA
1 TATTTATATTAATATTATTTAGTAA
2283757 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 8 0.36
27 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (26 bp):
TATTTATATTAATATTATTTAGTAAT
Found at i:2295068 original size:18 final size:17
Alignment explanation
Indices: 2295019--2295070 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
2295009 ATAAATATTT
2295019 TATATTTTA-ATAATTAA
1 TATATTTTATAT-ATTAA
2295036 T-TATTTCTATAATATTAA
1 TATATTT-TAT-ATATTAA
2295054 TATACTTTTATATATTA
1 TATA-TTTTATATATTA
2295071 GGATAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.17
17 3 0.10
18 12 0.40
19 7 0.23
20 3 0.10
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTTATATATTAA
Found at i:2295632 original size:58 final size:58
Alignment explanation
Indices: 2295541--2296054 Score: 459
Period size: 58 Copynumber: 8.9 Consensus size: 58
2295531 CGTCTCGACA
* *
2295541 CTAACTTTGTAAGGAAAATAAATTATTGAATTTATTTTCTTGAGAATCTTAAATGATT
1 CTAACTTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATT
* * * *** * *
2295599 GTAACTCTAG-AAGGAAAATAAATAT-TTTAATTTATCCCCTTAAGAATCTTAAATTATT
1 CTAACT-TTGTAAGGAAAATAAAT-TGTTAAATTTATTTTCTTGAGAATCTTAAATGATT
* * * * * *
2295657 TTAACTTTGCAAGGAAAATAAATAGTTAAATTTATTTCCTTGAGAATTTTAAATGAAT
1 CTAACTTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATT
* * * * * *
2295715 CTAACTTTGTAA-AAGAAATAAATTGTTAATTTTATTCTCTTGAGAAACATGAATGATT
1 CTAACTTTGTAAGGA-AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATT
* * *
2295773 TTAACTTTGTAAGGAAAATAAATTG-TAGAATTTATTTTCTTGAGAATCGTAGATGATT
1 CTAACTTTGTAAGGAAAATAAATTGTTA-AATTTATTTTCTTGAGAATCTTAAATGATT
* ** *
2295831 CTATCATTTAAAAGG-AAATAAATTGTTAAATTTATTTTCTTGAGAATTTTAAATGATT
1 CTAAC-TTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATT
* * * * ** * *
2295889 AT-ATTTTGCACAAGTTAATAAACTGTTAAATTTATTTTCTTGAGAATTTTAAATGATT
1 CTAACTTTGTA-AGGAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATT
* * * * ** * *
2295947 AT-ATTTTGCACAAGTTAATAAACTGTTAAATTTATTTTCTTGAGAATCTTAAATTATT
1 CTAACTTTGTA-AGGAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATT
* * * *
2296005 CT-ATTTTGTTAAAGTAAATAAATTGTTAAATTTATTTTCTTGTGAATCTT
1 CTAACTTTG-TAAGGAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTT
2296055 GAATAAAAAA
Statistics
Matches: 384, Mismatches: 60, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
56 4 0.01
57 7 0.02
58 359 0.93
59 14 0.04
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.43
Consensus pattern (58 bp):
CTAACTTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATT
Found at i:2295884 original size:31 final size:31
Alignment explanation
Indices: 2295849--2295942 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 31
2295839 TAAAAGGAAA
2295849 TAAATTGTTAAATTTATTTTCTTGAGAATTT
1 TAAATTGTTAAATTTATTTTCTTGAGAATTT
* * *
2295880 TAAA-TG----A-TTATATT-TTGCACAAGTTAA
1 TAAATTGTTAAATTTATTTTCTTG-AGAA-TT-T
*
2295907 TAAACTGTTAAATTTATTTTCTTGAGAATTT
1 TAAATTGTTAAATTTATTTTCTTGAGAATTT
2295938 TAAAT
1 TAAAT
2295943 GATTATATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 20
0.63 0.10 0.27
Matches are distributed among these distances:
24 3 0.07
25 9 0.20
26 3 0.07
27 4 0.09
28 2 0.04
30 2 0.04
31 8 0.17
32 3 0.07
33 9 0.20
34 3 0.07
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (31 bp):
TAAATTGTTAAATTTATTTTCTTGAGAATTT
Found at i:2295910 original size:27 final size:27
Alignment explanation
Indices: 2295880--2295968 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 27
2295870 TTGAGAATTT
2295880 TAAATGATTATATTTTGCACAAGTTAA
1 TAAATGATTATATTTTGCACAAGTTAA
* * *
2295907 TAAACTGTTAAATTTATTTTCTTG-AGAA-TT-T
1 TAAA-TG----A-TTATATT-TTGCACAAGTTAA
2295938 TAAATGATTATATTTTGCACAAGTTAA
1 TAAATGATTATATTTTGCACAAGTTAA
2295965 TAAA
1 TAAA
2295969 CTGTTAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 20
0.64 0.08 0.28
Matches are distributed among these distances:
24 3 0.07
25 9 0.20
26 3 0.07
27 8 0.17
28 2 0.04
30 2 0.04
31 4 0.09
32 3 0.07
33 9 0.20
34 3 0.07
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (27 bp):
TAAATGATTATATTTTGCACAAGTTAA
Found at i:2296307 original size:97 final size:98
Alignment explanation
Indices: 2296084--2296373 Score: 327
Period size: 97 Copynumber: 2.9 Consensus size: 98
2296074 GAAATTATTT
* * ** *
2296084 TCTTATATGATTCT-TTATCTTTTAAAAGAAAATAGCTCATAAAATTTATTTTCTTGTTTTGTAA
1 TCTTATATGATTCTGATATC---TAAAAGGAAATAAATCATAAAATTTATTTTCTAGTTTTGTAA
* * **
2296148 AAGGAAATAAAATTATTGAATTTATTTT-CTTGTGAA
63 AAGGAAAT-AAATTGTTAAATTTATTTTCCTAATGAA
* * * * *
2296184 TCTTATGTGATTCTGGTTTCTAAAAGGAAATTAATCATATAATTTATTTTCTAGTTTTGTAAAAG
1 TCTTATATGATTCTGATATCTAAAAGGAAATAAATCATAAAATTTATTTTCTAGTTTTGTAAAAG
2296249 GAAATAAATTGTTAAATTTATTTTCCTAAT-AA
66 GAAATAAATTGTTAAATTTATTTTCCTAATGAA
* ** *
2296281 TCTTATATGATTCTGATATGTAAAAGGAAATAAATTGTAGAATTTATTTTCCTA-TTTTGTAAAA
1 TCTTATATGATTCTGATATCTAAAAGGAAATAAATCATAAAATTTATTTT-CTAGTTTTGTAAAA
* *
2296345 GGAAATAAATCGTTAGATTTATTTTCCTA
65 GGAAATAAATTGTTAAATTTATTTTCCTA
2296374 TTATGTAAAA
Statistics
Matches: 164, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
97 98 0.60
98 50 0.30
100 13 0.08
101 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (98 bp):
TCTTATATGATTCTGATATCTAAAAGGAAATAAATCATAAAATTTATTTTCTAGTTTTGTAAAAG
GAAATAAATTGTTAAATTTATTTTCCTAATGAA
Found at i:2296353 original size:39 final size:38
Alignment explanation
Indices: 2296299--2296415 Score: 173
Period size: 39 Copynumber: 3.0 Consensus size: 38
2296289 GATTCTGATA
2296299 TGTAAAAGGAAATAAATTGTAGAATTTATTTTCCTATTT
1 TGTAAAAGGAAATAAATTGTAG-ATTTATTTTCCTATTT
* *
2296338 TGTAAAAGGAAATAAATCGTTAGATTTATTTTCCTATTA
1 TGTAAAAGGAAATAAATTG-TAGATTTATTTTCCTATTT
*
2296377 TGTAAAAGGAAATAAATTGTTGGATTTATTTT-CTATTT
1 TGTAAAAGGAAATAAATTG-TAGATTTATTTTCCTATTT
2296415 T
1 T
2296416 AGGAAATAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
38 6 0.08
39 63 0.88
40 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (38 bp):
TGTAAAAGGAAATAAATTGTAGATTTATTTTCCTATTT
Found at i:2296525 original size:24 final size:23
Alignment explanation
Indices: 2296479--2296526 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
2296469 ATATGATTCT
*
2296479 TGTAAAAGGAAAAAATAGTTGGA
1 TGTAAAAGAAAAAAATAGTTGGA
2296502 TGTAAAAGAAAATAAATCAG-TGGA
1 TGTAAAAGAAAA-AAAT-AGTTGGA
2296526 T
1 T
2296527 TGAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 9 0.41
25 2 0.09
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (23 bp):
TGTAAAAGAAAAAAATAGTTGGA
Found at i:2300900 original size:31 final size:31
Alignment explanation
Indices: 2300865--2300976 Score: 172
Period size: 31 Copynumber: 3.6 Consensus size: 31
2300855 TACGTTGATT
2300865 TTGAGAATATGATGTTTAAATGTAGCAAAAA
1 TTGAGAATATGATGTTTAAATGTAGCAAAAA
*
2300896 TTGAGAATATGATGTTTACATGTAGCAAAAA
1 TTGAGAATATGATGTTTAAATGTAGCAAAAA
2300927 TTGAGAATATGATGTTTAAATGTAG-AAAAA
1 TTGAGAATATGATGTTTAAATGTAGCAAAAA
* *
2300957 TTTTAAAATATGCATGTTTA
1 -TTGAGAATATG-ATGTTTA
2300977 GGATCTTTAG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
30 5 0.07
31 63 0.84
32 7 0.09
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.36
Consensus pattern (31 bp):
TTGAGAATATGATGTTTAAATGTAGCAAAAA
Found at i:2302974 original size:5 final size:5
Alignment explanation
Indices: 2302957--2303026 Score: 68
Period size: 5 Copynumber: 14.0 Consensus size: 5
2302947 ACCATCTTAG
* * * * * *
2302957 ATCAT ATCTT ATCAT ATCAT ATCAT GTCAT GTCAT GTCAT GTCAT GTCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
* *
2303007 GTCAT ATCTT ATCAT ATCAT
1 ATCAT ATCAT ATCAT ATCAT
2303027 TTCTATCACA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 59 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (5 bp):
ATCAT
Found at i:2303510 original size:11 final size:11
Alignment explanation
Indices: 2303494--2303518 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2303484 GACTTAATTG
2303494 AATTTATCAAA
1 AATTTATCAAA
2303505 AATTTATCAAA
1 AATTTATCAAA
2303516 AAT
1 AAT
2303519 AATTCAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTTATCAAA
Found at i:2307891 original size:20 final size:20
Alignment explanation
Indices: 2307862--2307899 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2307852 TTTCAAAGGG
2307862 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
2307882 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
2307900 GAATAAATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:2307958 original size:19 final size:19
Alignment explanation
Indices: 2307927--2307980 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
2307917 AATGTAGTTT
*
2307927 ATGCATTGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
*
2307946 AT-CTATCGATGCACTCTTC
1 ATGC-ATCGATGCACTCTCC
2307965 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
2307981 AGGTTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 29 0.94
20 1 0.03
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.31
Consensus pattern (19 bp):
ATGCATCGATGCACTCTCC
Found at i:2308083 original size:64 final size:65
Alignment explanation
Indices: 2307950--2308084 Score: 173
Period size: 64 Copynumber: 2.1 Consensus size: 65
2307940 CTCTCCATCT
* ** * * * *
2307950 ATCGATGCACTCTTCATGCATCGATGCACTCAGGTTTTAATGAAAATATCGAATGCATTTTATGC
1 ATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATAC
* * *
2308015 ATCGATGCACACACCATGCATCGATGTACTTAGG-CTTATTCAAAACATCGAATGCATTTTATAC
1 ATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATAC
2308079 ATCGAT
1 ATCGAT
2308085 ACAAACTTAG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 31 0.52
65 29 0.48
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (65 bp):
ATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATAC
Found at i:2313346 original size:12 final size:12
Alignment explanation
Indices: 2313329--2313354 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2313319 TTGTCAATAC
2313329 CACAAGGCCATG
1 CACAAGGCCATG
2313341 CACAAGGCCATG
1 CACAAGGCCATG
2313353 CA
1 CA
2313355 TTGATGCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.23, T:0.08
Consensus pattern (12 bp):
CACAAGGCCATG
Found at i:2315970 original size:20 final size:20
Alignment explanation
Indices: 2315941--2315978 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2315931 TTTCAAAGGG
2315941 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
2315961 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
2315979 GAATAAATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:2316149 original size:64 final size:65
Alignment explanation
Indices: 2315989--2316150 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
2315979 GAATAAATTG
* * * * *
2315989 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTGTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
* * *
2316054 AACATCGAATGCATTTTATGCATCGATGCACACACCATGTATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
**
2316118 AATGTCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
2316151 TTAGTGCACC
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
64 37 0.43
65 50 0.57
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:2316164 original size:64 final size:64
Alignment explanation
Indices: 2315989--2316168 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 64
2315979 GAATAAATTG
* * * *
2315989 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTGTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACT-CATGCATCGATGCACTCAGGTCTTAATCAA
* * * *
2316054 AACATCGAATGCATTTTATGCATCGATGCACACACCATGTATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACAC-TCATGCATCGATGCACTCAGGTCTTAATCAA
** * *
2316118 AATGTCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACACTCA-TGCATCGATGCACT
2316169 AAGTGTTCCA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 49 0.49
65 49 0.49
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:2325440 original size:40 final size:40
Alignment explanation
Indices: 2325382--2325461 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
2325372 ACGGTGTATA
*
2325382 AGGTGGGCAAGGCCCGACCTCAGCACTACAGTGCATTATT
1 AGGTGAGCAAGGCCCGACCTCAGCACTACAGTGCATTATT
* * **
2325422 AGGTGAGCATGGCTCGACCTCAGCACTATTGTGCATTATT
1 AGGTGAGCAAGGCCCGACCTCAGCACTACAGTGCATTATT
2325462 TGACTCCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (40 bp):
AGGTGAGCAAGGCCCGACCTCAGCACTACAGTGCATTATT
Found at i:2326085 original size:29 final size:29
Alignment explanation
Indices: 2326050--2326107 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2326040 TTTTGAATTG
2326050 GTAACCAAAAATATTATATTACAATTTTT
1 GTAACCAAAAATATTATATTACAATTTTT
2326079 GTAACCAAAAATATTATATTACAATTTTT
1 GTAACCAAAAATATTATATTACAATTTTT
2326108 CTCTGAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (29 bp):
GTAACCAAAAATATTATATTACAATTTTT
Found at i:2326960 original size:2 final size:2
Alignment explanation
Indices: 2326953--2327006 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2326943 CTCATACTTA
2326953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2326995 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2327007 TCCTAATCTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2327299 original size:21 final size:21
Alignment explanation
Indices: 2327275--2327327 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2327265 AAACAATAGA
2327275 CTTGATTGCATGATGAATAAT
1 CTTGATTGCATGATGAATAAT
* *
2327296 CTTGATTGCAAGATGAATAGT
1 CTTGATTGCATGATGAATAAT
2327317 CTTGATTGCAT
1 CTTGATTGCAT
2327328 AAACTCACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (21 bp):
CTTGATTGCATGATGAATAAT
Found at i:2329440 original size:8 final size:8
Alignment explanation
Indices: 2329427--2329468 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 8
2329417 TTATAAGAAA
2329427 TTTTATAT
1 TTTTATAT
2329435 TTTTATATT
1 TTTTATA-T
2329444 TTTTATATT
1 TTTTATA-T
2329453 TTTTATAT
1 TTTTATAT
*
2329461 TTCTATAT
1 TTTTATAT
2329469 ATATTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 15 0.47
9 17 0.53
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTATAT
Found at i:2329448 original size:9 final size:9
Alignment explanation
Indices: 2329427--2329462 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2329417 TTATAAGAAA
2329427 TTTTATA-T
1 TTTTATATT
2329435 TTTTATATT
1 TTTTATATT
2329444 TTTTATATT
1 TTTTATATT
2329453 TTTTATATT
1 TTTTATATT
2329462 T
1 T
2329463 CTATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATATT
Found at i:2329602 original size:29 final size:30
Alignment explanation
Indices: 2329529--2329602 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
2329519 ATTTTATCAT
*
2329529 TTTTAAAATAATTATGCTATATTTTAAAAA
1 TTTTAAAATAATTAAGCTATATTTTAAAAA
* *
2329559 TTTTGAAAA-ATTTAAGC-ATCTTTT-AAAA
1 TTTT-AAAATAATTAAGCTATATTTTAAAAA
2329587 TTTTAATAATAATTAA
1 TTTTAA-AATAATTAA
2329603 TATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.05
28 10 0.27
29 11 0.30
30 10 0.27
31 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (30 bp):
TTTTAAAATAATTAAGCTATATTTTAAAAA
Found at i:2329788 original size:10 final size:10
Alignment explanation
Indices: 2329773--2329800 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2329763 AAAATTAATA
2329773 TTTAAATATT
1 TTTAAATATT
2329783 TTTAAATATT
1 TTTAAATATT
2329793 TTTAAATA
1 TTTAAATA
2329801 ATAAACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTAAATATT
Found at i:2331665 original size:66 final size:66
Alignment explanation
Indices: 2331528--2331675 Score: 215
Period size: 66 Copynumber: 2.2 Consensus size: 66
2331518 TGGGGTATTA
* * * *
2331528 CACTCCACCTCATGCACCACAAAGGTAAATGAGTCTCATCAAGTGATCAATACAGTGTTTAGTTA
1 CACTCCACCTCATGCACCACAAAGGTAAACGAGTCTCATCAAGTGATCAATACAGTATTCAGTAA
2331593 T
66 T
* *
2331594 CACTCCACCTCATGCACCACAAAGGTACACGAGTCTCATCGAGTGATCAATACAGTATTCAGTAA
1 CACTCCACCTCATGCACCACAAAGGTAAACGAGTCTCATCAAGTGATCAATACAGTATTCAGTAA
2331659 T
66 T
* * *
2331660 TACTCCATCTCGTGCA
1 CACTCCACCTCATGCA
2331676 TCACCGATTC
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 73 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (66 bp):
CACTCCACCTCATGCACCACAAAGGTAAACGAGTCTCATCAAGTGATCAATACAGTATTCAGTAA
T
Found at i:2334812 original size:21 final size:22
Alignment explanation
Indices: 2334788--2334832 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
2334778 ACCTTAACCA
2334788 AATTCATCTTTAAACATT-TCC
1 AATTCATCTTTAAACATTATCC
* * *
2334809 AATTGATTTTTAATCATTATCC
1 AATTCATCTTTAAACATTATCC
2334831 AA
1 AA
2334833 GCCTAGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTCATCTTTAAACATTATCC
Found at i:2335399 original size:20 final size:20
Alignment explanation
Indices: 2335370--2335568 Score: 119
Period size: 20 Copynumber: 9.7 Consensus size: 20
2335360 ATAGTCCAAA
*
2335370 TTCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
*** *
2335390 TTCGCGTTGCGAAAGTCCAAA
1 TTCGCGTTGCGATTTTCC-AT
* *
2335411 ATCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* ** * *
2335431 TTCACGTTTGCGATAGTCTAAA
1 TTCGCG-TTGCGATTTTC-CAT
* * ** * *
2335453 ATCGCATTTGCGATAGTCAAAA
1 TTCGC-GTTGCGATTTTC-CAT
2335475 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* * ** *
2335495 TTCTCATTGCGATAGTCCAAA
1 TTCGCGTTGCGATTTTCC-AT
*
2335516 TTCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
2335536 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
*
2335556 TTCGGGTTGCGAT
1 TTCGCGTTGCGAT
2335569 AGTCTAAAAT
Statistics
Matches: 135, Mismatches: 39, Indels: 10
0.73 0.21 0.05
Matches are distributed among these distances:
20 65 0.48
21 48 0.36
22 22 0.16
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:2335416 original size:41 final size:41
Alignment explanation
Indices: 2335356--2335590 Score: 195
Period size: 41 Copynumber: 5.7 Consensus size: 41
2335346 CAGTTTCCAA
*
2335356 TGCGATAGTCCAAATTCGCATTGCGATTTTCCATTTCGCGT
1 TGCGATAGTCCAAAATCGCATTGCGATTTTCCATTTCGCGT
* *
2335397 TGCGAAAGTCCAAAATCGCATTGCGATTTTCCATTTCACGTT
1 TGCGATAGTCCAAAATCGCATTGCGATTTTCCATTTCGCG-T
* ** * *
2335439 TGCGATAGTCTAAAATCGCATTTGCGATAGTCAAAATTCGCGT
1 TGCGATAGTCCAAAATCGCA-TTGCGATTTTC-CATTTCGCGT
** ** * ** * *
2335482 TGCGATTTTCC-ATTTCTCATTGCGATAGTCCAAATTCGCAT
1 TGCGATAGTCCAAAATCGCATTGCGATTTTCC-ATTTCGCGT
** ** * *
2335523 TGCGATTTTCC-ATTTCGCGTTGCGATTTTCCATTTCGGGT
1 TGCGATAGTCCAAAATCGCATTGCGATTTTCCATTTCGCGT
*
2335563 TGCGATAGTCTAAAATCGCATTTGCGAT
1 TGCGATAGTCCAAAATCGCA-TTGCGAT
2335591 AGTCGAAATT
Statistics
Matches: 157, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
40 14 0.09
41 88 0.56
42 31 0.20
43 18 0.11
44 6 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (41 bp):
TGCGATAGTCCAAAATCGCATTGCGATTTTCCATTTCGCGT
Done.