Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008840.1 Hibiscus syriacus cultivar Beakdansim tig00112044_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: 1122218
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:826113 original size:118 final size:121
Alignment explanation
Indices: 825892--826119 Score: 266
Period size: 118 Copynumber: 1.9 Consensus size: 121
825882 GTCATATAAA
* * *
825892 TATAATAAATAATAATTTATATTTTTTTACATAAATTATTTTAATATTTATTTTTCAATATCGAA
1 TATAAAAAATAATAATTTATATTTTTTTAAATAAATTATATTAATATTTA--TTTCAATATCGAA
* * * * * *
825957 GAAAAGGGCAGTCTTAATACAACTGGATGTCCTATTCTGGTATTTTAAAATTAAATAT
64 GAAAAGAGCAGTCTTAAGACAACTAGAAGTCATATTCTGATATTTTAAAATTAAATAT
* *
826015 TATAAAAAATTATAATTTA-ATTTTATTTAAAT-TATTATATTAATATTTA-TT-AATATCGAAG
1 TATAAAAAATAATAATTTATATTTT-TTTAAATAAATTATATTAATATTTATTTCAATATCGAAG
* * * *
826076 AAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTGATATTT
65 AAAAGAGCAGTCTTAAGACAACTAGAAGTCATATTCTGATATTT
826120 CTCAATAAAT
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
118 44 0.49
119 2 0.02
122 20 0.22
123 23 0.26
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.43
Consensus pattern (121 bp):
TATAAAAAATAATAATTTATATTTTTTTAAATAAATTATATTAATATTTATTTCAATATCGAAGA
AAAGAGCAGTCTTAAGACAACTAGAAGTCATATTCTGATATTTTAAAATTAAATAT
Found at i:827475 original size:24 final size:23
Alignment explanation
Indices: 827424--827501 Score: 79
Period size: 24 Copynumber: 3.4 Consensus size: 23
827414 ATATGTTTTT
* *
827424 CTTTCTTATTCT-TTTCTTTTTTG
1 CTTTCTT-TTCTCTATCTTCTTTG
827447 CTTTCTTTTCTCTATCTCTCTTTG
1 CTTTCTTTTCTCTATCT-TCTTTG
* * *
827471 GTTTCTTTCCTCTCTCTTCTTT-
1 CTTTCTTTTCTCTATCTTCTTTG
827493 CTTTCTTTT
1 CTTTCTTTT
827502 TTTATGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 11 0.24
23 16 0.35
24 19 0.41
ACGTcount: A:0.03, C:0.26, G:0.04, T:0.68
Consensus pattern (23 bp):
CTTTCTTTTCTCTATCTTCTTTG
Found at i:829343 original size:2 final size:2
Alignment explanation
Indices: 829338--829372 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
829328 TTAATCATTA
* *
829338 AT AT AT AC AT AT AC 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 AT A
829373 ATGATATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:832124 original size:115 final size:118
Alignment explanation
Indices: 831944--832241 Score: 383
Period size: 115 Copynumber: 2.5 Consensus size: 118
831934 TAGTATAATC
* *
831944 TTAAATTCTTAACTATAAAAATATATATTTTATTATTATTTTTAATTTATCGAATATATATATTT
1 TTAAATTCTTAACTATAAAAA-ATATATATT-TTATTATTTTTAATTTATAGAATATATATATTT
** *
832009 T-AGTTTAAAATAGGCCAAGTTTATTATTTGAGGTAAGAGTATATATTTAAAATAT
64 TGA-TTTAAAATAGGCCAAGTTTATTATTAAAGGTAAGAATATATATTTAAAATAT
* * *
832064 TTAAATTCTCAAATATAAAAAATATATATTTTATT-TTTTTAGTTTATAG-A-ATATATATTTTG
1 TTAAATTCTTAACTATAAAAAATATATATTTTATTATTTTTAATTTATAGAATATATATATTTTG
* *
832126 ATTTAAAGTAGGCCAAGTTTATTATTAAAGTTAAGAATATATATTTAAAATAT
66 ATTTAAAATAGGCCAAGTTTATTATTAAAGGTAAGAATATATATTTAAAATAT
* *
832179 TTACATTCTTAACTAT-AAAAATATATATTTTATTACTTTTCTTAATTTTTCA-AATATATATAT
1 TTAAATTCTTAACTATAAAAAATATATATTTTATTA--TTT-TTAATTTAT-AGAATATATATAT
832242 ATATATATAT
Statistics
Matches: 155, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
114 18 0.12
115 71 0.46
116 2 0.01
117 15 0.10
118 12 0.08
119 10 0.06
120 27 0.17
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (118 bp):
TTAAATTCTTAACTATAAAAAATATATATTTTATTATTTTTAATTTATAGAATATATATATTTTG
ATTTAAAATAGGCCAAGTTTATTATTAAAGGTAAGAATATATATTTAAAATAT
Found at i:832239 original size:2 final size:2
Alignment explanation
Indices: 832232--832265 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
832222 AATTTTTCAA
832232 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
832266 TTGTTTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:832274 original size:142 final size:143
Alignment explanation
Indices: 832114--832383 Score: 388
Period size: 142 Copynumber: 1.9 Consensus size: 143
832104 AGTTTATAGA
*
832114 ATATATATTTTGATTTAAAGTAGGCCAAGTTTATTATTAAAGTTAAGAATATATATTT-AAA-AT
1 ATATATATTTTGATTTAAAGTAGGCCAAATTTATTATTAAAGTTAAGAATATATATTTAAAATAT
* *
832177 A-TTTACATTCTTAACTATAAAAATATATATTTTATTACTTTTCTTAATTT-TTCAAATATATAT
66 AGTTTAAATTCTTAACTATAAAAATATATATTTTATT--TTTTATTAATTTATT-AAATATATAT
832240 ATATATATATATATAT
128 ATATATATATATATAT
* * *
832256 ATATATATATTTG-TTTAAAGTATGCCAAATTTATTATTTAAGTTAATAATATATATTTAAAATA
1 ATATATAT-TTTGATTTAAAGTAGGCCAAATTTATTATTAAAGTTAAGAATATATATTTAAAATA
* *
832320 TATGTTTAAATTCTTAACTATAAAAATATTTATTTTATTTTTTATTAATTTATTGAATATATAT
65 TA-GTTTAAATTCTTAACTATAAAAATATATATTTTATTTTTTATTAATTTATTAAATATATAT
832384 TTTAAAGTAT
Statistics
Matches: 114, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
142 49 0.43
143 7 0.06
144 23 0.20
145 2 0.02
146 33 0.29
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (143 bp):
ATATATATTTTGATTTAAAGTAGGCCAAATTTATTATTAAAGTTAAGAATATATATTTAAAATAT
AGTTTAAATTCTTAACTATAAAAATATATATTTTATTTTTTATTAATTTATTAAATATATATATA
TATATATATATAT
Found at i:833316 original size:64 final size:64
Alignment explanation
Indices: 833242--833442 Score: 230
Period size: 65 Copynumber: 3.1 Consensus size: 64
833232 TGCACTAAGA
* *
833242 GTGCACCGATGCATAAAATGCATTCGATGTTTCAAAATAACCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAACCTGAGTGCATCGATGCATGGATG
* *
833306 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCAT-GAT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAACCTGAGTGCATCGATGCATGGAT
*
833369 AT
64 -G
* * ** *
833371 GCGCATCGATGCATAAAATGCATTTGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-ACC-TGAGTGCATCGATGCATGGA-
833434 TG
63 TG
833436 GTGCATC
1 GTGCATC
833443 TGTGCATCAC
Statistics
Matches: 116, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 45 0.39
65 61 0.53
66 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAACCTGAGTGCATCGATGCATGGATG
Found at i:833391 original size:19 final size:19
Alignment explanation
Indices: 833354--833391 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
833344 AACCCTGAGT
* *
833354 GCATCGATGCATGATATGC
1 GCATCGATGCATAAAATGC
833373 GCATCGATGCATAAAATGC
1 GCATCGATGCATAAAATGC
833392 ATTTGATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (19 bp):
GCATCGATGCATAAAATGC
Found at i:836045 original size:44 final size:45
Alignment explanation
Indices: 835995--836079 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
835985 ATGCATGGCC
* *
835995 TTGTGTATCGATGCACATTC-AAGGCG-TGCATCGGTGCACTTTCA
1 TTGTGTATCGATACACATTCAAAGG-GATGCATCGATGCACTTTCA
836039 TTGTGTATCGATACACATTCAAAGGGATGCATCGATGCACT
1 TTGTGTATCGATACACATTCAAAGGGATGCATCGATGCACT
836080 GTTAAGTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 20 0.54
45 17 0.46
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (45 bp):
TTGTGTATCGATACACATTCAAAGGGATGCATCGATGCACTTTCA
Found at i:836089 original size:44 final size:44
Alignment explanation
Indices: 835997--836091 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
835987 GCATGGCCTT
* * *
835997 GTGTATCGATGCACATTCAAGGCGTGCATCGGTGCACTTTCATT
1 GTGTATCGATACACATTCAAGGCGTGCATCGATGCACTTTCATA
836041 GTGTATCGATACACATTCAAAGG-GATGCATCGATGCACTGTT-A-A
1 GTGTATCGATACACATTC-AAGGCG-TGCATCGATGCACT-TTCATA
836085 GTGTATC
1 GTGTATC
836092 TATGCATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 25 0.56
45 18 0.40
46 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (44 bp):
GTGTATCGATACACATTCAAGGCGTGCATCGATGCACTTTCATA
Found at i:839936 original size:17 final size:17
Alignment explanation
Indices: 839906--839972 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 17
839896 GTTGCAGCCA
** *
839906 GGGGGTATAAATACCCT
1 GGGGGTATCGATACCAT
839923 GGGGGTATCGATACCAT
1 GGGGGTATCGATACCAT
839940 --GGGTATCGATACCAT
1 GGGGGTATCGATACCAT
* *
839955 GAGGAGTATAGATACCAT
1 G-GGGGTATCGATACCAT
839973 CCGAGCAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
15 15 0.36
17 14 0.33
18 13 0.31
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (17 bp):
GGGGGTATCGATACCAT
Found at i:840862 original size:22 final size:21
Alignment explanation
Indices: 840820--840859 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
840810 GAGTTTATTT
*
840820 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
840841 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
840860 ATAACTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:842928 original size:65 final size:65
Alignment explanation
Indices: 842795--843002 Score: 248
Period size: 65 Copynumber: 3.2 Consensus size: 65
842785 TGCACTAAGA
* *
842795 GTGCATCGATGTATAAAATGCATTCGATG-TTTCAAAATAACCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTGAGTGCATCGATGCATGGATG
* *
842859 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCAT-GAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAACCTGAGTGCATCGATGCATGGAT
*
842922 AT
65 -G
** *
842924 GTGCATCGATGCATAAAATGCATTCGATG--TTCAATTTATTCCATG-GTGCATCGATGCATGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATA-ACC-TGAGTGCATCGATGCATGGA
842986 TTG
64 -TG
*
842989 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
843003 CACTTTGAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 45 0.36
65 70 0.56
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTGAGTGCATCGATGCATGGATG
Found at i:843841 original size:30 final size:31
Alignment explanation
Indices: 843770--843846 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
843760 CTTTAGATGG
* * *
843770 AATACTAATTTAATCTTTGAATTTTAGGTAA
1 AATATTAATTTAATCCTTAAATTTTAGGTAA
* *
843801 AATATCAATTTAATCCTTAAATTTTA-GTTA
1 AATATTAATTTAATCCTTAAATTTTAGGTAA
843831 AATATTAATTTAATCC
1 AATATTAATTTAATCC
843847 CTACATGTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 18 0.45
31 22 0.55
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (31 bp):
AATATTAATTTAATCCTTAAATTTTAGGTAA
Found at i:850130 original size:2 final size:2
Alignment explanation
Indices: 850118--850163 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
850108 TAACATAAAC
* *
850118 AT AT AT TT AT AT AC 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
850160 AT AT
1 AT AT
850164 TATTGTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:851318 original size:16 final size:16
Alignment explanation
Indices: 851297--851327 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
851287 CCATCGTATT
851297 TTATTATTTCATTTTC
1 TTATTATTTCATTTTC
*
851313 TTATTATTTTATTTT
1 TTATTATTTCATTTT
851328 AAATATTACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTATTTCATTTTC
Found at i:855723 original size:95 final size:95
Alignment explanation
Indices: 855559--855740 Score: 267
Period size: 95 Copynumber: 1.9 Consensus size: 95
855549 TAATATTTTA
* * *
855559 TATACAATAAAGCTTGATTTGTCCATCTAGAACAACTGGTTAAACGCCCCAGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGTTGTCCATCTAGAACAACTGGTTAAACGCCCCAGCTTTATGGAAAAG
*
855624 ATTCAGCTAGCCTGATAAAGGTGATTATAC
66 ATTCAGCTAACCTGATAAAGGTGATTATAC
* * * **
855654 TATACAATAAAGCTTGAGTTGTCCCTCTA-AAGCAATTGGTTAAATGCCCTGGCTTTATGGAAAA
1 TATACAATAAAGCTTGAGTTGTCCATCTAGAA-CAACTGGTTAAACGCCCCAGCTTTATGGAAAA
855718 GATTCAGCTAACCTGATAAAGGT
65 GATTCAGCTAACCTGATAAAGGT
855741 ATTTACATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 2 0.03
95 75 0.97
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGTTGTCCATCTAGAACAACTGGTTAAACGCCCCAGCTTTATGGAAAAG
ATTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:857068 original size:36 final size:36
Alignment explanation
Indices: 857028--857209 Score: 124
Period size: 36 Copynumber: 5.1 Consensus size: 36
857018 ATTTGTCTCA
857028 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
1 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
* * * * * * *
857064 CTTGAGATTGTCATT-CTT-ATAA-CAGACCTTGTCTCA
1 CTTGAGACTGT-TTTACTTGA-AAGAAGA-TTTATTTCC
*
857100 CTTGAGACTGTTTTACTTGAAAGATGATTTATTTCC
1 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
** * * * * * *
857136 CTCAAGATTGTCATT-CTT-AAA-ACAGACCTTGTCTCA
1 CTTGAGACTGT-TTTACTTGAAAGA-AGA-TTTATTTCC
857172 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
1 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
857208 CT
1 CT
857210 CAAGATTGTC
Statistics
Matches: 102, Mismatches: 32, Indels: 24
0.65 0.20 0.15
Matches are distributed among these distances:
34 1 0.01
35 13 0.13
36 74 0.73
37 13 0.13
38 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (36 bp):
CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
Found at i:857109 original size:72 final size:72
Alignment explanation
Indices: 857020--857231 Score: 379
Period size: 72 Copynumber: 2.9 Consensus size: 72
857010 TACAGATGAT
** *
857020 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTTGAGATTGTCATTCTTATA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
857085 ACAGACC
66 ACAGACC
*
857092 TTGTCTCACTTGAGACTGTTTTACTTGAAAGATGATTTATTTCCCTCAAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
857157 ACAGACC
66 ACAGACC
*
857164 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTTTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
857229 ACA
66 ACA
857232 AGATTTTATC
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 134 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (72 bp):
TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
ACAGACC
Found at i:857235 original size:36 final size:36
Alignment explanation
Indices: 857125--857237 Score: 88
Period size: 36 Copynumber: 3.1 Consensus size: 36
857115 CTTGAAAGAT
*
857125 GATTTATTTCCCTCAAGATTGTCATTCTTAAAAC-A
1 GATTTATTTCCCTCAAGATTGTCATTTTTAAAACAA
* * * * ** * * *
857160 GACCTTGTCTCACTTGAGACTGT--TTTACTTGAAAGAA
1 GA-TTTATTTCCCTCAAGATTGTCATTT--TTAAAACAA
857197 GATTTATTTCCCTCAAGATTGTCATTTTTAAAACAA
1 GATTTATTTCCCTCAAGATTGTCATTTTTAAAACAA
857233 GATTT
1 GATTT
857238 TATCTCGCTT
Statistics
Matches: 53, Mismatches: 19, Indels: 11
0.64 0.23 0.13
Matches are distributed among these distances:
34 2 0.04
35 2 0.04
36 43 0.81
37 3 0.06
38 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (36 bp):
GATTTATTTCCCTCAAGATTGTCATTTTTAAAACAA
Found at i:857382 original size:39 final size:39
Alignment explanation
Indices: 857337--857411 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
857327 CCTTGAAATG
* *
857337 AATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAGAA
* *
857376 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACA
857412 TAAACATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (39 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAGAA
Found at i:857414 original size:104 final size:103
Alignment explanation
Indices: 857234--857745 Score: 834
Period size: 104 Copynumber: 5.0 Consensus size: 103
857224 TTAAAACAAG
* * * * * *
857234 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAGAAAATTTTGTCTCCCTTGGGACAATTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAAATTTTGTCTCCCTTGAGACAGTTTCT
857299 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
65 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
857338 ATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAAATTTTGTCTCCCTTGAGACAGTTTCT
857403 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
65 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
857442 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAAAATTTTGTCTCCCTTGAGACAATTTAT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAAATTTTGTCTCCCTTGAGACAGTTTCT
*
857507 CTTAAAACATAAACATTGAAAACATTTCCCTTGAAATGA
65 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
857546 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC--AAATTTTGTCTCCCTTGAGACAGTTTCTC
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAATTTTGTCTCCCTTGAGACAGTTTCTC
857609 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
857647 ATTTTGTCACTCTTGAGATAGTTTCCCTTGAAAC--AAATTTTGTCTCCATTGAGACAGTTTCTC
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAATTTTGTCTCCCTTGAGACAGTTTCTC
* *
857710 TTGAAACATAAACTTTAAAAACAGTTTCCCTTGAAA
66 TTGAAACATAAACATTGAAAACA-TTTCCCTTGAAA
857746 CAAAACCTTT
Statistics
Matches: 390, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
101 146 0.37
102 12 0.03
104 232 0.59
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (103 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAATTTTGTCTCCCTTGAGACAGTTTCTC
TTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:857515 original size:39 final size:39
Alignment explanation
Indices: 857441--857519 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
857431 CCTTGAAATG
* * * * *
857441 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAA
1 AATTTTGTCTCCCTTGAGACAATTTACCTTAAAACATAA
*
857480 AATTTTGTCTCCCTTGAGACAATTTATCTTAAAACATAA
1 AATTTTGTCTCCCTTGAGACAATTTACCTTAAAACATAA
857519 A
1 A
857520 CATTGAAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (39 bp):
AATTTTGTCTCCCTTGAGACAATTTACCTTAAAACATAA
Found at i:857578 original size:36 final size:36
Alignment explanation
Indices: 857531--857616 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
857521 ATTGAAAACA
** * *
857531 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
857567 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
857603 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
857617 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:857679 original size:36 final size:36
Alignment explanation
Indices: 857632--857717 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
857622 ATTGAAAACA
** *
857632 TTTCCCTTGAAATGAATTTTGTCACTC-TTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCAC-CATTGAGACAG
*
857668 TTTCCCTTGAAACAAATTTTGTCTCCATTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCACCATTGAGACAG
*
857704 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
857718 TAAACTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 1 0.02
36 43 0.98
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCACCATTGAGACAG
Found at i:857846 original size:96 final size:96
Alignment explanation
Indices: 857558--857811 Score: 239
Period size: 101 Copynumber: 2.6 Consensus size: 96
857548 TTTGTCTCTC
* * * * *
857558 TTGAGATA-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGA-ATATGTTTCTCTTAAAACAAATTTTGCCTCCATGGAGACAGTTTCTCTTGAAACATAAAC
* * * ***
857622 ATTGAAAACA-TTTCCCTTGAAATGAATTTTGTCACT
65 TTTAAAAACAGTTTCCCTTGAAA-CAA---AAAC-CT
* * * *
857658 CTTGAGATA-GTTTCCCTTGAAACAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAA
1 -TTGA-ATATGTTTCTCTTAAAACAAATTTTGCCTCCATGGAGACAGTTTCTCTTGAAACATAAA
857722 CTTTAAAAACAGTTTCCCTTGAAAC-AAAACCT
64 CTTTAAAAACAGTTTCCCTTGAAACAAAAACCT
*
857754 TTGAATATGTTTCTCTTAAAACAAAATTTTGCCTCCCA-GGAGGCAGTTTCTCTTGAAA
1 TTGAATATGTTTCTCTTAAAAC-AAATTTTGCCT-CCATGGAGACAGTTTCTCTTGAAA
857812 AAACCTTTGA
Statistics
Matches: 137, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
94 3 0.02
95 16 0.12
96 30 0.22
97 4 0.03
100 1 0.01
101 71 0.52
102 12 0.09
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (96 bp):
TTGAATATGTTTCTCTTAAAACAAATTTTGCCTCCATGGAGACAGTTTCTCTTGAAACATAAACT
TTAAAAACAGTTTCCCTTGAAACAAAAACCT
Found at i:857866 original size:34 final size:34
Alignment explanation
Indices: 857809--857920 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
857799 GTTTCTCTTG
*
857809 AAAAAACCTTTGAAATCGTTTTCTCTTGAAACACA
1 AAAAAACCTTTGAAATCG-TTTCTCTTGAAACAAA
857844 AAAAAACCTTTGAAATCGTTTCTCTTGGAACACAAA
1 AAAAAACCTTTGAAATCGTTTCTCTT-GAA-ACAAA
* *
857880 AAGAAAACCTTGGAAATTGTTTCTCTTGAAACAAA
1 AA-AAAACCTTTGAAATCGTTTCTCTTGAAACAAA
857915 AAAAAA
1 AAAAAA
857921 AGAAAACCTT
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
34 12 0.17
35 28 0.39
36 9 0.13
37 22 0.31
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.28
Consensus pattern (34 bp):
AAAAAACCTTTGAAATCGTTTCTCTTGAAACAAA
Found at i:857941 original size:40 final size:37
Alignment explanation
Indices: 857811--857952 Score: 150
Period size: 40 Copynumber: 3.8 Consensus size: 37
857801 TTCTCTTGAA
*
857811 AAAACCTTTGAAATCGTTTTCTCTTGAAAC---ACAAA-
1 AAAACCTTTGAAAT-G-TTTCTCTTGAAACAAAAAAAAG
* *
857846 AAAACCTTTGAAATCGTTTCTCTTGGAAC-ACAAAAAG
1 AAAACCTTTGAAAT-GTTTCTCTTGAAACAAAAAAAAG
*
857883 AAAACCTTGGAAATTGTTTCTCTTGAAACAAAAAAAAAAG
1 AAAACCTTTGAAA-TGTTTCTCTTGAAAC--AAAAAAAAG
857923 AAAACCTTTGAACATGTTTCTCTTGAAACA
1 AAAACCTTTGAA-ATGTTTCTCTTGAAACA
857953 CCAAAGCTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
34 12 0.13
35 16 0.17
36 4 0.04
37 25 0.27
38 2 0.02
40 33 0.35
41 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (37 bp):
AAAACCTTTGAAATGTTTCTCTTGAAACAAAAAAAAG
Found at i:858285 original size:17 final size:17
Alignment explanation
Indices: 858252--858298 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
858242 TAACATAAAC
*
858252 ATATATTTATA-TACAT
1 ATATATATATATTACAT
858268 AT-TAATATATATTACAT
1 ATAT-ATATATATTACAT
858285 ATATATATATATTA
1 ATATATATATATTA
858299 TTGTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.04
16 8 0.30
17 17 0.63
18 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATATATTACAT
Found at i:859444 original size:16 final size:16
Alignment explanation
Indices: 859423--859453 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
859413 CCATCGTATT
859423 TTATTATTTCATTTTC
1 TTATTATTTCATTTTC
*
859439 TTATTATTTTATTTT
1 TTATTATTTCATTTT
859454 ATATATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTATTTCATTTTC
Found at i:859693 original size:40 final size:41
Alignment explanation
Indices: 859614--859709 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 41
859604 TTTGTTTTCC
*
859614 TTTATTTG--TTATTCTTCTATTTCATTTTGGTTATCTTA-
1 TTTATTTGATTTATTTTTCTATTTCATTTTGGTTATCTTAT
** * * *
859652 TTTATTTGATTTATTTTTCTATTTTGTTTTTGTTTTTTTAT
1 TTTATTTGATTTATTTTTCTATTTCATTTTGGTTATCTTAT
*
859693 TTTCATTTTATTTATTT
1 TTT-ATTTGATTTATTT
859710 CATTTACTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
38 8 0.17
40 24 0.51
41 3 0.06
42 12 0.26
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (41 bp):
TTTATTTGATTTATTTTTCTATTTCATTTTGGTTATCTTAT
Found at i:859708 original size:15 final size:13
Alignment explanation
Indices: 859684--859757 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 13
859674 TTTGTTTTTG
859684 TTTTTTTATTTTCA
1 TTTTTTTA-TTTCA
859698 TTTTATTTATTTCA
1 TTTT-TTTATTTCA
859712 TTTACTTTTTATCTTCA
1 -TT--TTTTTAT-TTCA
**
859729 TTTTGATATTTC-
1 TTTTTTTATTTCA
* *
859741 TTTTCTTCTTTCA
1 TTTTTTTATTTCA
859754 TTTT
1 TTTT
859758 ATCTTCTTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
12 9 0.18
13 7 0.14
14 14 0.29
15 6 0.12
16 7 0.14
17 6 0.12
ACGTcount: A:0.15, C:0.12, G:0.01, T:0.72
Consensus pattern (13 bp):
TTTTTTTATTTCA
Found at i:863145 original size:32 final size:31
Alignment explanation
Indices: 863108--863184 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
863098 TGGGGCCGTG
* *
863108 GGGCCTACCTAAGAACACATCTTAGGGCTGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
863140 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
863171 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
863185 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:865927 original size:378 final size:378
Alignment explanation
Indices: 865232--865992 Score: 1432
Period size: 378 Copynumber: 2.0 Consensus size: 378
865222 TTCCAGGGAC
865232 AATTCTTGTCATACTCAAACATAAGGGTATTTTCATAATTTCACCCTACCGGAGTATTCTCATAA
1 AATTCTTGTCATACTCAAACATAAGGGTATTTTCATAATTTCACCCTACCGGAGTATTCTCATAA
*
865297 TTTCCCATCCAAGTACCTTTAACATTTAACCTTTAAAATATAAGTTACAAATCCATGGTTGATTT
66 TTTCCCATCCAAGTACCTTTAACATTTAACCTTTAAAATATAAGTTACAAATCCATGGCTGATTT
865362 CTTTATCACAAATCACACAACTTGTAATTTAATTCTAACATTCCCTCACTCTCTTATATTAATCA
131 CTTTATCACAAATCACACAACTTGTAATTTAATTCTAACATTCCCTCACTCTCTTATATTAATCA
*
865427 TTCGATCCGAATTCAGTTATCGAATTTCTACCACATTCATATCGAGTGTATAAATTAATCAACTC
196 TTCGATCCGAATTCAGTTATCGAATTTATACCACATTCATATCGAGTGTATAAATTAATCAACTC
865492 CACAAAAGTGATCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGCATA
261 CACAAAAGTGATCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGCATA
* * *
865557 AAGAGGTAGTAAAATATTACCTTGATTTCCGTGCAATACTGATTGACTATAAA
326 AAGAGGTAGTAAAATATTACATCGATTTCCGTGCAATACTGATTGACCATAAA
*
865610 AATTCTTGTCATACTCAAACATAAGGGTATTTTCATAATTTTACCCTACCGGAGTATTCTCATAA
1 AATTCTTGTCATACTCAAACATAAGGGTATTTTCATAATTTCACCCTACCGGAGTATTCTCATAA
*
865675 TTTCTCATCCAAGTACCTTTAACATTTAACCTTTAAAATATAAGTTACAAATCCATGGCTGATTT
66 TTTCCCATCCAAGTACCTTTAACATTTAACCTTTAAAATATAAGTTACAAATCCATGGCTGATTT
865740 CTTTATCACAAATCACACAACTTGTAATTTAATTCTAACATTCCCTCACTCTCTTATATTAATCA
131 CTTTATCACAAATCACACAACTTGTAATTTAATTCTAACATTCCCTCACTCTCTTATATTAATCA
*
865805 TTCGATCCGAATTCAGTTGTCGAATTTATACCACATTCATATCGAGTGTATAAATTAATCAACTC
196 TTCGATCCGAATTCAGTTATCGAATTTATACCACATTCATATCGAGTGTATAAATTAATCAACTC
865870 CACAAAAGTGATCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGCATA
261 CACAAAAGTGATCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGCATA
* *
865935 AAGAGGTAGTAAAGTATTACATCGATTTTCGTGCAATACTGATTGACCATAAA
326 AAGAGGTAGTAAAATATTACATCGATTTCCGTGCAATACTGATTGACCATAAA
865988 AATTC
1 AATTC
865993 CATTCGAACG
Statistics
Matches: 373, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
378 373 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (378 bp):
AATTCTTGTCATACTCAAACATAAGGGTATTTTCATAATTTCACCCTACCGGAGTATTCTCATAA
TTTCCCATCCAAGTACCTTTAACATTTAACCTTTAAAATATAAGTTACAAATCCATGGCTGATTT
CTTTATCACAAATCACACAACTTGTAATTTAATTCTAACATTCCCTCACTCTCTTATATTAATCA
TTCGATCCGAATTCAGTTATCGAATTTATACCACATTCATATCGAGTGTATAAATTAATCAACTC
CACAAAAGTGATCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGCATA
AAGAGGTAGTAAAATATTACATCGATTTCCGTGCAATACTGATTGACCATAAA
Found at i:866407 original size:7 final size:7
Alignment explanation
Indices: 866395--866425 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
866385 TGGTCAACGC
866395 CGGTCAA
1 CGGTCAA
866402 CGGTCAA
1 CGGTCAA
*
866409 CAGTCAA
1 CGGTCAA
866416 CGGTCAA
1 CGGTCAA
866423 CGG
1 CGG
866426 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:866435 original size:13 final size:13
Alignment explanation
Indices: 866417--866464 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
866407 AACAGTCAAC
866417 GGTCAACGGGTCG
1 GGTCAACGGGTCG
866430 GGTCAACAGATCGGGTCG
1 GGT---CA-A-CGGGTCG
866448 GGTCAACGGGTCG
1 GGTCAACGGGTCG
866461 GGTC
1 GGTC
866465 GGGTTAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 14 0.47
14 1 0.03
15 2 0.07
16 2 0.07
17 1 0.03
18 10 0.33
ACGTcount: A:0.17, C:0.23, G:0.44, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:866487 original size:18 final size:18
Alignment explanation
Indices: 866423--866486 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
866413 CAACGGTCAA
* *
866423 CGGGTCGGGTCAACAGAT
1 CGGGTCGGGTCAACGGGT
866441 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
866459 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
866477 CGGGTCGGGT
1 CGGGTCGGGT
866487 TGTGACTGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.12, C:0.20, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:874032 original size:2 final size:2
Alignment explanation
Indices: 874025--874052 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
874015 GATTATTTTA
874025 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
874053 TTAAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:878055 original size:31 final size:32
Alignment explanation
Indices: 878005--878066 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
877995 TATAATTTTG
*
878005 AAAAATTAAAAGTTCAGATAC-TAAAACATAC
1 AAAAACTAAAAGTTCAGATACTTAAAACATAC
* * *
878036 AAAAACTAATAGTTTAGATACTTAACACATA
1 AAAAACTAAAAGTTCAGATACTTAAAACATA
878067 GTTTACCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (32 bp):
AAAAACTAAAAGTTCAGATACTTAAAACATAC
Found at i:880931 original size:19 final size:21
Alignment explanation
Indices: 880909--880948 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
880899 TACGATTTAG
*
880909 TTTCTATTT-TCA-TTATTTT
1 TTTCAATTTCTCATTTATTTT
880928 TTTCAATTTCTCATTTATTTT
1 TTTCAATTTCTCATTTATTTT
880949 AAGTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCAATTTCTCATTTATTTT
Found at i:881098 original size:151 final size:154
Alignment explanation
Indices: 880942--881292 Score: 383
Period size: 151 Copynumber: 2.3 Consensus size: 154
880932 AATTTCTCAT
* *
880942 TTATTTTAAGTTCATTTTTTACCAAATTTTAACCATATGCTCTTAAATCATCCCATAATACATAT
1 TTATTTTAAGTTCATTTTTTACCAAATTTTAACCATATGCTCTTAAACCATCCCAGAATACATAT
* * * * *
881007 GTGCTTTCAATTTCTCTTTTTTGAT-AATAATTT-TTTT-AATTTAATCTCTC-TTTTTTTATAA
66 GTACTTTCAATTCCTC-TTTGTGATAAATAATTTATTTTAAATTTAATCCCTCAATTTTTTATAA
*
881068 TTTTCTTATTTCTTCAATTCATTC-
130 TTTTCTTATTTCTTCAATTCATCCA
* * * * * **
881092 TCTATTTTAA-TTCATTTTTTTACCAAATTTGAACTACATGTTCTTAAACCTTCGTAGAATACAT
1 T-TATTTTAAGTTCA-TTTTTTACCAAATTTTAACCATATGCTCTTAAACCATCCCAGAATACAT
* * *
881156 TTGTACTTTCAATTCCTCTTTGTGATAACAATATTTTATTTTAAAATTTAGTCCCTCAATTTTTT
64 ATGTACTTTCAATTCCTCTTTGTGAT-A-AATAATTTATTTT-AAATTTAATCCCTCAATTTTTT
881221 ATAATTTTCTTATTTCTTCAATTCATCCA
126 ATAATTTTCTTATTTCTTCAATTCATCCA
* * * *
881250 TTATTTTAAGTCCGTTTTTTCACAAAACTTGT-ACCATATGCTC
1 TTATTTTAAGTTCATTTTTT-ACCAAA-TTTTAACCATATGCTC
881293 ATATACCACA
Statistics
Matches: 162, Mismatches: 26, Indels: 18
0.79 0.13 0.09
Matches are distributed among these distances:
150 12 0.07
151 63 0.39
153 7 0.04
154 4 0.02
156 11 0.07
157 47 0.29
158 16 0.10
159 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (154 bp):
TTATTTTAAGTTCATTTTTTACCAAATTTTAACCATATGCTCTTAAACCATCCCAGAATACATAT
GTACTTTCAATTCCTCTTTGTGATAAATAATTTATTTTAAATTTAATCCCTCAATTTTTTATAAT
TTTCTTATTTCTTCAATTCATCCA
Found at i:881727 original size:29 final size:29
Alignment explanation
Indices: 881674--881729 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
881664 ATTAGTATAG
**
881674 AAACTCGAATAACTCGAATCGAATTTCTT
1 AAACTCGAATAACTCGAATAAAATTTCTT
881703 AAACTCGAATCAACTCGAA-AAAATTTC
1 AAACTCGAAT-AACTCGAATAAAATTTC
881730 AAGTTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (29 bp):
AAACTCGAATAACTCGAATAAAATTTCTT
Found at i:885226 original size:25 final size:24
Alignment explanation
Indices: 885198--885244 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
885188 AATCTATGTG
*
885198 GTCCTTCAGGACATATTTCTACGCA
1 GTCCTTCAGGACA-AATTCTACGCA
*
885223 GTCCTTCGGGACAAATTCTACG
1 GTCCTTCAGGACAAATTCTACG
885245 TGGCACTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (24 bp):
GTCCTTCAGGACAAATTCTACGCA
Found at i:898145 original size:76 final size:77
Alignment explanation
Indices: 898065--898225 Score: 263
Period size: 77 Copynumber: 2.1 Consensus size: 77
898055 ATAACGTTTT
*
898065 GTGAAGTTTGAGTTTAAAAGA-TACATACAAATCATTCAATATTATGCTTAGATATGA-TATATA
1 GTGAAGTTTGAGTTTAAAAGATTACATACAAATCATACAATATTATGCTTAGATAT-ATTATATA
898128 AATACTGAAGAGA
65 AATACTGAAGAGA
* *
898141 GTGAAGTTTGAGTTTAAAATATTACATACAAATCGTACAATATTATGCTTAGATATATTATATAA
1 GTGAAGTTTGAGTTTAAAAGATTACATACAAATCATACAATATTATGCTTAGATATATTATATAA
*
898206 ATATTGAAGAGA
66 ATACTGAAGAGA
898218 GTGAAGTT
1 GTGAAGTT
898226 GGATGGGGTG
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
76 21 0.27
77 58 0.73
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (77 bp):
GTGAAGTTTGAGTTTAAAAGATTACATACAAATCATACAATATTATGCTTAGATATATTATATAA
ATACTGAAGAGA
Found at i:898880 original size:41 final size:42
Alignment explanation
Indices: 898829--898917 Score: 126
Period size: 41 Copynumber: 2.1 Consensus size: 42
898819 TGAAATCCAT
* * *
898829 TGTTTGTTTCACATAATTCGTTTTTTGAAAAATA-TTTTCTG
1 TGTTTGTTTCACATAATTCATTTTCTGAAAAATATTTTTCAG
* *
898870 TGTTTGTTTCACGTAATTTATTTTCTGAAAAATATTTTTCAG
1 TGTTTGTTTCACATAATTCATTTTCTGAAAAATATTTTTCAG
898912 TGTTTG
1 TGTTTG
898918 GTTGGAGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 30 0.71
42 12 0.29
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (42 bp):
TGTTTGTTTCACATAATTCATTTTCTGAAAAATATTTTTCAG
Found at i:899119 original size:33 final size:33
Alignment explanation
Indices: 899082--899147 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
899072 TTCATAGAAA
*
899082 ATATATTAAAT-TATTAATAATATAATATTATTT
1 ATATATTAAATATA-TAATAATATAATAATATTT
* *
899115 ATATATTTAATATATAATAATCTAATAATATTT
1 ATATATTAAATATATAATAATATAATAATATTT
899148 TAATAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (33 bp):
ATATATTAAATATATAATAATATAATAATATTT
Found at i:899157 original size:38 final size:34
Alignment explanation
Indices: 899079--899191 Score: 108
Period size: 38 Copynumber: 3.2 Consensus size: 34
899069 TAATTCATAG
*
899079 AAAATATA-TTAAATTATTAATAATATAATATTATTT
1 AAAATATATTTAAAATA-TAATAAT-TAATATT-TTT
*
899115 ---ATATATTTAATATATAATAATCTAATAATATTTT
1 AAAATATATTTAAAATATAATAAT-TAAT-AT-TTTT
*
899149 AATAATATATTTAAAATATACTAATTAATATTTTT
1 AA-AATATATTTAAAATATAATAATTAATATTTTT
899184 AAAATATA
1 AAAATATA
899192 ATAACACTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
33 16 0.25
34 17 0.26
35 7 0.11
36 2 0.03
37 4 0.06
38 19 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (34 bp):
AAAATATATTTAAAATATAATAATTAATATTTTT
Found at i:899160 original size:13 final size:12
Alignment explanation
Indices: 899095--899191 Score: 67
Period size: 11 Copynumber: 7.9 Consensus size: 12
899085 TATTAAATTA
899095 TTAATAATATAAT
1 TTAATAATAT-AT
* *
899108 ATTATTTATATAT
1 -TTAATAATATAT
899121 TTAATATATAATAAT
1 TTAATA-AT-AT-AT
*
899136 CTAATAATAT-T
1 TTAATAATATAT
899147 TTAATAATATAT
1 TTAATAATATAT
899159 TTAA-AATATA-
1 TTAATAATATAT
* *
899169 CTAATTAATATTT
1 TTAA-TAATATAT
899182 TTAA-AATATA
1 TTAATAATATA
899192 ATAACACTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
10 3 0.05
11 21 0.32
12 14 0.21
13 9 0.14
14 12 0.18
15 7 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
TTAATAATATAT
Found at i:899166 original size:22 final size:22
Alignment explanation
Indices: 899148--899191 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
899138 AATAATATTT
899148 TAATAATATATTTAAAATATAC
1 TAATAATATATTTAAAATATAC
*
899170 TAATTAATATTTTTAAAATATA
1 TAA-TAATATATTTAAAATATA
899192 ATAACACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATAATATATTTAAAATATAC
Found at i:899517 original size:14 final size:14
Alignment explanation
Indices: 899494--899536 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
899484 AATATAATTC
*
899494 ATTTTACGAAAAAT
1 ATTTTCCGAAAAAT
*
899508 ATTTTCCGAAAAAC
1 ATTTTCCGAAAAAT
899522 ATTTTCC-AAAAAT
1 ATTTTCCGAAAAAT
899535 AT
1 AT
899537 AATTCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 7 0.27
14 19 0.73
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (14 bp):
ATTTTCCGAAAAAT
Found at i:899569 original size:15 final size:14
Alignment explanation
Indices: 899537--899589 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
899527 CCAAAAATAT
* **
899537 AATTCATTTTTCGG
1 AATTCAATTTTCAA
899551 AATTCAATTTTCAA
1 AATTCAATTTTCAA
* *
899565 TAATTTATTTTTCAA
1 -AATTCAATTTTCAA
899580 AATTCAATTT
1 AATTCAATTT
899590 CCTAAAAGCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTCAATTTTCAA
Found at i:906941 original size:25 final size:25
Alignment explanation
Indices: 906913--906962 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
906903 GGTCTTATAT
906913 TCAAGTTCGGCTCCACCATCTATTA
1 TCAAGTTCGGCTCCACCATCTATTA
906938 TCAAGTTCGGCTCCACCATCTATTA
1 TCAAGTTCGGCTCCACCATCTATTA
906963 AGTATTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (25 bp):
TCAAGTTCGGCTCCACCATCTATTA
Found at i:914120 original size:45 final size:46
Alignment explanation
Indices: 914055--914160 Score: 162
Period size: 45 Copynumber: 2.3 Consensus size: 46
914045 GTGCACTAAA
* *
914055 AGTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATAGCTAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAAGCT-G
*
914100 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAATCTG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAAGCTG
914146 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
914161 AGTATGTGCA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
45 29 0.52
46 21 0.38
47 6 0.11
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (46 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAAGCTG
Found at i:916916 original size:23 final size:22
Alignment explanation
Indices: 916889--916966 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
916879 TGGCCTTGTA
916889 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACATTCAAGG-GTG
* * *
916912 CATCGGTGCACCTTC-ATGGTG
1 CATCGATGCACATTCAAGGGTG
* *
916933 TATCAATGCACATTCAAAGGGATG
1 CATCGATGCACATTC-AAGGG-TG
916957 CATCGATGCA
1 CATCGATGCA
916967 TGAAGCACAA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
21 14 0.33
22 2 0.05
23 16 0.38
24 10 0.24
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGGTG
Found at i:931426 original size:14 final size:14
Alignment explanation
Indices: 931407--931437 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
931397 ATCGAATGTT
931407 CATGCATCGATGCA
1 CATGCATCGATGCA
931421 CATGCATCGATGCA
1 CATGCATCGATGCA
931435 CAT
1 CAT
931438 ACTATGCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (14 bp):
CATGCATCGATGCA
Found at i:931492 original size:65 final size:63
Alignment explanation
Indices: 931422--931564 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 63
931412 ATCGATGCAC
* *
931422 ATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACA-ACCATGCATCAATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATT
931485 TG
62 TG
* *
931487 ATGCATCGATGCACCAGCCATGCATCAATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAACCATGCATCAATGCACTCAGGCTATTTTGAAACATCGAATGCATTTG
931551 ATGCATCGATGCAC
1 ATGCATCGATGCAC
931565 TCTTAGTGCA
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
63 1 0.01
64 31 0.44
65 34 0.48
66 5 0.07
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCAATGCACTCAGGCTATTTTGAAACATCGAATGCATTTG
Found at i:940645 original size:34 final size:34
Alignment explanation
Indices: 940581--940647 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
940571 AATATGAATT
* *
940581 ACAATTTCTCTTGATTTAACAAGGAGAAAACAATG
1 ACAATTTCTCTTGA-TTAAAAAGAAGAAAACAATG
940616 ACAATTATCTCTTG-TTAAAAAGAAGAAAACAA
1 ACAATT-TCTCTTGATTAAAAAGAAGAAAACAA
940648 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 16 0.55
35 6 0.21
36 7 0.24
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (34 bp):
ACAATTTCTCTTGATTAAAAAGAAGAAAACAATG
Found at i:944873 original size:57 final size:57
Alignment explanation
Indices: 944773--945061 Score: 463
Period size: 57 Copynumber: 5.0 Consensus size: 57
944763 TTGATTTCGT
* * * * * *
944773 TACTATGAGTATATGTGTTCTTTGTGAATAAATGATCATTTGAATAATGTTATGTGAAA
1 TACTATGAGTATA--TGTTCTATATGAGTAAATGATAAATTGAATAATGCTATGTGAAA
944832 TACTATGAGTATATGTTCTATATGAGTAAATGATAAATTGAATAATGCTATGTGAAA
1 TACTATGAGTATATGTTCTATATGAGTAAATGATAAATTGAATAATGCTATGTGAAA
*
944889 TACTATGAGTATATGTT-TAATATGAGTAAATGATAAATTGAATAGTGCTATGTGAAA
1 TACTATGAGTATATGTTCT-ATATGAGTAAATGATAAATTGAATAATGCTATGTGAAA
944946 TACTATGAGTATATGTTCTATATGAGTAAATGATAAATTGAATAATGCTATGTGAAA
1 TACTATGAGTATATGTTCTATATGAGTAAATGATAAATTGAATAATGCTATGTGAAA
**
945003 TACTATGAGTATATGTTCTATGCGAGTAAATGATAAATTGAATAATGCTATGTGAAA
1 TACTATGAGTATATGTTCTATATGAGTAAATGATAAATTGAATAATGCTATGTGAAA
945060 TA
1 TA
945062 TTTATATGGT
Statistics
Matches: 218, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
56 1 0.00
57 203 0.93
58 1 0.00
59 13 0.06
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (57 bp):
TACTATGAGTATATGTTCTATATGAGTAAATGATAAATTGAATAATGCTATGTGAAA
Found at i:945166 original size:23 final size:23
Alignment explanation
Indices: 945140--945210 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
945130 GGTTCTACGC
945140 GGTCTTTCGGGATAATTCTATGT
1 GGTCTTTCGGGATAATTCTATGT
* * *
945163 GGTCATTCGGGATAATTATACGT
1 GGTCTTTCGGGATAATTCTATGT
* * *
945186 GGCCCTTT-GGGACAAATCTATGT
1 GG-TCTTTCGGGATAATTCTATGT
945209 GG
1 GG
945211 CACTTCGGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 35 0.92
24 3 0.08
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (23 bp):
GGTCTTTCGGGATAATTCTATGT
Found at i:958106 original size:163 final size:162
Alignment explanation
Indices: 957828--958154 Score: 582
Period size: 163 Copynumber: 2.0 Consensus size: 162
957818 CTAAAACCCA
* *
957828 TGCAATTGAATACTGCTCCCTTCTGTTTAGTCTATTTAATGGCTAGGCTGAGCTATTTGTTTCTT
1 TGCAATTGAATACTACTCCCTTCTGTTTAGTCTATTAAATGGCTAGGCTGAGCTATTTGTTTCTT
957893 GCTTTTGTTCTTGTGATGTTCTTGTATGATTACAAATTTACAATGTGATGGATTTGTTGTTCAAA
66 GCTTTTGTTCTTGTGATGTTCTTGTATGATTACAAATTTACAATGTGATGGATTTGTTGTTCAAA
*
957958 TACTGAATATGAAAGTTGAAAAAGAGTTGATT
131 TACTGAATATGAAAGTTGAAAAAAAGTTGATT
957990 TGCAATTGAATACTACTCCCTTCTGTTTAGTCTATTAAATGGCTAGGCTGAGCTATTTGGTTTCT
1 TGCAATTGAATACTACTCCCTTCTGTTTAGTCTATTAAATGGCTAGGCTGAGCTATTT-GTTTCT
* **
958055 TGCTTTTGTTCTTGTGATGTTCTTGTATGATTGCAAATTTACAATGTGATGGATTTGTTGTTTGA
65 TGCTTTTGTTCTTGTGATGTTCTTGTATGATTACAAATTTACAATGTGATGGATTTGTTGTTCAA
*
958120 ATACTGAATATGAAGGTTGAAAAAAAGTTGATT
130 ATACTGAATATGAAAGTTGAAAAAAAGTTGATT
958153 TG
1 TG
958155 GTCCGTGAAA
Statistics
Matches: 157, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
162 56 0.36
163 101 0.64
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.43
Consensus pattern (162 bp):
TGCAATTGAATACTACTCCCTTCTGTTTAGTCTATTAAATGGCTAGGCTGAGCTATTTGTTTCTT
GCTTTTGTTCTTGTGATGTTCTTGTATGATTACAAATTTACAATGTGATGGATTTGTTGTTCAAA
TACTGAATATGAAAGTTGAAAAAAAGTTGATT
Found at i:961384 original size:83 final size:83
Alignment explanation
Indices: 961237--961669 Score: 600
Period size: 83 Copynumber: 5.2 Consensus size: 83
961227 TGTCATAGTG
* * * *
961237 TTTTCGATTATTATTTAGAGAACCTCTGCCATGTCATAGTGTTTCATCCCATCCAAAATGAAAGG
1 TTTTCCATTATTATTTAGAGAATCTATGCTATGTCATAGTGTTTCATCCCATCCAAAATGAAAGG
* * *
961302 TGCATTCCAGGGGAAGCG
66 CGCGTTCCAGGGGAAGCA
* * ** *
961320 TTTTCCATTATTATTCAGAGAATCTATGCTATGTCATAGTGTTCCATCCCATCTGAAATTAAAGG
1 TTTTCCATTATTATTTAGAGAATCTATGCTATGTCATAGTGTTTCATCCCATCCAAAATGAAAGG
961385 CGCGTTCCAGGGGAAGCA
66 CGCGTTCCAGGGGAAGCA
*
961403 TTTTCCATTATTATTAAGAGAATC-ACTGCTATGTCATAGTGTTTCATCCCATCCAAAATGAAAG
1 TTTTCCATTATTATTTAGAGAATCTA-TGCTATGTCATAGTGTTTCATCCCATCCAAAATGAAAG
* *
961467 GCACATTCCAGGGGAAGCA
65 GCGCGTTCCAGGGGAAGCA
* * * *
961486 TTTTCCATTATTATATAGAGAATCTTTTCTATGTCATAGTGTTTCATCCTATCCAAAATGAAAGG
1 TTTTCCATTATTATTTAGAGAATCTATGCTATGTCATAGTGTTTCATCCCATCCAAAATGAAAGG
*
961551 CGCGTTCAAGGGGAAG-A
66 CGCGTTCCAGGGGAAGCA
* * * *
961568 GTTTTCCATTATTATTTAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCTTCCAAAATGAAAG
1 -TTTTCCATTATTATTTAGAGAATCTATGCTATGTCATAGTGTTTCATCCCATCCAAAATGAAAG
*
961633 GCGCGTTCTAGGGGAAGCA
65 GCGCGTTCCAGGGGAAGCA
*
961652 TTTTCCATTGTTATTTAG
1 TTTTCCATTATTATTTAG
961670 CCCATTCGAA
Statistics
Matches: 310, Mismatches: 36, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
82 2 0.01
83 307 0.99
84 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (83 bp):
TTTTCCATTATTATTTAGAGAATCTATGCTATGTCATAGTGTTTCATCCCATCCAAAATGAAAGG
CGCGTTCCAGGGGAAGCA
Found at i:961809 original size:83 final size:83
Alignment explanation
Indices: 961682--961853 Score: 227
Period size: 83 Copynumber: 2.1 Consensus size: 83
961672 CATTCGAAAC
* * * * * * **
961682 GAAAGGTGCGTTCGATGGAAATCGTTTTCCATTATTGTTTAGAGAATCTATGTCATGTCATAGTG
1 GAAAGGTGCATTCGAGGGAAAGCATTTTCCATTATTATTCAGAGAATCTATACCATGTCATAGTG
961747 TCCCATCCCATCCAAAAT
66 TCCCATCCCATCCAAAAT
* *
961765 GAAAGGTGCATTCGAGGGGAAGCATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTG
1 GAAAGGTGCATTCGAGGGAAAGCATTTTCCATTATTATTCAGAGAATCTATACCATGTCATAGTG
* * *
961830 TTCCATCCCATTCGAAAT
66 TCCCATCCCATCCAAAAT
961848 GAAAGG
1 GAAAGG
961854 CGTGTGTTCC
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (83 bp):
GAAAGGTGCATTCGAGGGAAAGCATTTTCCATTATTATTCAGAGAATCTATACCATGTCATAGTG
TCCCATCCCATCCAAAAT
Found at i:970206 original size:92 final size:93
Alignment explanation
Indices: 970106--970293 Score: 353
Period size: 92 Copynumber: 2.0 Consensus size: 93
970096 TTTTAAGATC
970106 ATCAATTTTCTTTTGATGATCATCATTTAACCTTTGAAAGTAAATTTTGCAAATCC-AAATTTTC
1 ATCAATTTTCTTTTGATGATCATCATTT-ACCTTTGAAAGTAAATTTTGCAAATCCAAAATTTTC
970170 TTTTC-AACTCTTCTAGTTTGATTTACAA
65 TTTTCAAACTCTTCTAGTTTGATTTACAA
970198 ATCAATTTTCTTTTGATGATCATCATTTACCTTTGAAAGTAAATTTTGCAAATCCAAAATTTTCT
1 ATCAATTTTCTTTTGATGATCATCATTTACCTTTGAAAGTAAATTTTGCAAATCCAAAATTTTCT
970263 TTTCAAACTCTTCTAGTTTGATTTACAA
66 TTTCAAACTCTTCTAGTTTGATTTACAA
970291 ATC
1 ATC
970294 TTTGATTTTA
Statistics
Matches: 94, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 27 0.29
92 41 0.44
93 26 0.28
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.45
Consensus pattern (93 bp):
ATCAATTTTCTTTTGATGATCATCATTTACCTTTGAAAGTAAATTTTGCAAATCCAAAATTTTCT
TTTCAAACTCTTCTAGTTTGATTTACAA
Found at i:970383 original size:76 final size:76
Alignment explanation
Indices: 970298--970455 Score: 316
Period size: 76 Copynumber: 2.1 Consensus size: 76
970288 CAAATCTTTG
970298 ATTTTACTTTCAAGATCGTTGTTGTTTTGGGTATGAGTTTATTTTCATTTTTCAATTTTGAAACA
1 ATTTTACTTTCAAGATCGTTGTTGTTTTGGGTATGAGTTTATTTTCATTTTTCAATTTTGAAACA
970363 TCATTTTTTAT
66 TCATTTTTTAT
970374 ATTTTACTTTCAAGATCGTTGTTGTTTTGGGTATGAGTTTATTTTCATTTTTCAATTTTGAAACA
1 ATTTTACTTTCAAGATCGTTGTTGTTTTGGGTATGAGTTTATTTTCATTTTTCAATTTTGAAACA
970439 TCATTTTTTAT
66 TCATTTTTTAT
970450 ATTTTA
1 ATTTTA
970456 AAAACAATTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 82 1.00
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.56
Consensus pattern (76 bp):
ATTTTACTTTCAAGATCGTTGTTGTTTTGGGTATGAGTTTATTTTCATTTTTCAATTTTGAAACA
TCATTTTTTAT
Found at i:972437 original size:31 final size:30
Alignment explanation
Indices: 972390--972450 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 30
972380 AGTGCATCGG
972390 TGCAATAAGGTGCATCGATGCATAAAATGC
1 TGCAATAAGGTGCATCGATGCATAAAATGC
*
972420 TGCACTAAGAGTGCATCGATGCATAAAATGC
1 TGCAATAAG-GTGCATCGATGCATAAAATGC
972451 ATTCGATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (30 bp):
TGCAATAAGGTGCATCGATGCATAAAATGC
Found at i:973014 original size:21 final size:21
Alignment explanation
Indices: 972977--973016 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
972967 TATTGAGTTC
*
972977 ATATATAAATAATTTTTTTGA
1 ATATATAAATAAATTTTTTGA
972998 ATATAT-AATGAAATTTTTT
1 ATATATAAAT-AAATTTTTT
973017 ACACTGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
ATATATAAATAAATTTTTTGA
Found at i:984740 original size:13 final size:13
Alignment explanation
Indices: 984722--984774 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
984712 CCAGTTAATT
984722 AATTATTGTATTA
1 AATTATTGTATTA
*
984735 AATTATTAGT-TTT
1 AATTATT-GTATTA
*
984748 AA-TATTG-ACT-
1 AATTATTGTATTA
984758 AATTATTGTATTA
1 AATTATTGTATTA
984771 AATT
1 AATT
984775 GTTAGTCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
10 2 0.06
11 7 0.22
12 6 0.19
13 15 0.47
14 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (13 bp):
AATTATTGTATTA
Found at i:985707 original size:21 final size:21
Alignment explanation
Indices: 985681--985720 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
985671 AAAAATGTGT
*
985681 ATCGATGCACTGCTACAGTGC
1 ATCGATACACTGCTACAGTGC
985702 ATCGATACACTGCTACAGT
1 ATCGATACACTGCTACAGT
985721 AATTTCTGCA
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:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGATACACTGCTACAGTGC
Found at i:986196 original size:27 final size:27
Alignment explanation
Indices: 986158--986213 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
986148 TCATGTAATT
986158 TCCTTTTAATATTAGCGCTATCAGTGC
1 TCCTTTTAATATTAGCGCTATCAGTGC
986185 TCCTTTTAATATTAGCGCTATCAGTGC
1 TCCTTTTAATATTAGCGCTATCAGTGC
986212 TC
1 TC
986214 TATCTGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (27 bp):
TCCTTTTAATATTAGCGCTATCAGTGC
Found at i:986314 original size:59 final size:58
Alignment explanation
Indices: 986207--986564 Score: 266
Period size: 59 Copynumber: 6.1 Consensus size: 58
986197 TAGCGCTATC
* * * * *
986207 AGTGCTCTATCTGGAAAAT-CATACACTTAGTATGCTTCCCTTTTCATTTTAGAACACAA
1 AGTGCCCTAT-TGG-AAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
* * * *
986266 AGTGCCCTATTCGAAAATCCATATCA-TTAGTATGATTTCGTTACCATTTTAGCACATAA
1 AGTGCCCTATT-GGAAATCCATA-CACTTAGTATGATTTCCTTATCATTTTAGCACACAA
** * * * * **
986325 TA-TGCCCTATATGGAAATCCATA-TTTTCAATATGATTTCCTTATCA-TTTGGAACCCTT
1 -AGTGCCCTAT-TGGAAATCCATACACTT-AGTATGATTTCCTTATCATTTTAGCACACAA
** * * * * *
986383 AGTGCTTTATTGGAAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAA
1 AGTGCCCTATTGG-AAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
* * **
986442 TA-TGCCCTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCA-TTTAGCACACTC
1 -AGTGCCCTAT-TGGAAATCCATACACTT-AGTATGATTTCCTTATCATTTTAGCACACAA
* *
986500 AGTGCTCC-ATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTCTAGCACACAA
1 AGTGC-CCTAT-TGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
986559 AGTGCC
1 AGTGCC
986565 ATTCGGTAAT
Statistics
Matches: 228, Mismatches: 53, Indels: 37
0.72 0.17 0.12
Matches are distributed among these distances:
57 5 0.02
58 88 0.39
59 127 0.56
60 8 0.04
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (58 bp):
AGTGCCCTATTGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
Found at i:986405 original size:117 final size:117
Alignment explanation
Indices: 986273--986555 Score: 372
Period size: 117 Copynumber: 2.4 Consensus size: 117
986263 CAAAGTGCCC
* * * *
986273 TATTCGAAAATCCATATCA-TTAGTATGATTTCGTTACCATTTTAGCACATAATATGCCCTATAT
1 TATTCGAAAACCCATA-CACTCAGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATAT
*
986337 GGAAATCCATATTTTCAATATGATTTCCTTATCATTTGGAACCCTTAGTGCTT
65 GGAAATCCATAATTTCAATATGATTTCCTTATCATTTGGAACCCTTAGTGCTT
* *
986390 TATTGGAAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTG
1 TATTCGAAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATATG
* * * * *
986455 GAAATCCATAATTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTC
66 GAAATCCATAATTTCAATATGATTTCCTTATCATTTGGAACCCTTAGTGCTT
* * * * * *
986507 CATAT-GGAAATCCATACACTCAGTATGATTTCCTTATCATTCTAGCACA
1 TAT-TCGAAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACA
986556 CAAAGTGCCA
Statistics
Matches: 146, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
116 2 0.01
117 143 0.98
118 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (117 bp):
TATTCGAAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATATG
GAAATCCATAATTTCAATATGATTTCCTTATCATTTGGAACCCTTAGTGCTT
Found at i:986515 original size:58 final size:58
Alignment explanation
Indices: 986296--986563 Score: 215
Period size: 58 Copynumber: 4.6 Consensus size: 58
986286 ATATCATTAG
* * * ***
986296 TATGATTTCGTTACCATTTTAGCACA-TAATATGC-CCTATATGGAAATCCATATTTTCAA
1 TATGATTTCCTTATCA-TTTAGCACACTAA-GTGCTCC-ATATGGAAATCCATACACTCAA
* * * * ** * *
986355 TATGATTTCCTTATCATTTGGAACCCTTAGTGCTTTAT-TGGAAAACCCATACACTCAG
1 TATGATTTCCTTATCATTTAGCACACTAAGTGCTCCATATGG-AAATCCATACACTCAA
* * * * *
986413 TATGATTCCCTTACCATTTTAGCACA-TAATATGC-CCTATCTGGAAATCCATA-ATTTCAA
1 TATGATTTCCTTATCA-TTTAGCACACTAA-GTGCTCC-ATATGGAAATCCATACA-CTCAA
* *
986472 TATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAG
1 TATGATTTCCTTATCATTTAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAA
*
986530 TATGATTTCCTTATCATTCTAGCACACAAAGTGC
1 TATGATTTCCTTATCATT-TAGCACACTAAGTGC
986564 CATTCGGTAA
Statistics
Matches: 162, Mismatches: 35, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
57 3 0.02
58 86 0.53
59 70 0.43
60 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (58 bp):
TATGATTTCCTTATCATTTAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAA
Found at i:987049 original size:19 final size:19
Alignment explanation
Indices: 987025--987093 Score: 138
Period size: 19 Copynumber: 3.6 Consensus size: 19
987015 TATTTAGGTG
987025 TGCATCGATGCACTACTTA
1 TGCATCGATGCACTACTTA
987044 TGCATCGATGCACTACTTA
1 TGCATCGATGCACTACTTA
987063 TGCATCGATGCACTACTTA
1 TGCATCGATGCACTACTTA
987082 TGCATCGATGCA
1 TGCATCGATGCA
987094 TCTTGCCCAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTACTTA
Found at i:992837 original size:21 final size:21
Alignment explanation
Indices: 992811--992850 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
992801 AAAAATGTGT
*
992811 ATCGATGCACTGCTACAGTGC
1 ATCGATACACTGCTACAGTGC
992832 ATCGATACACTGCTACAGT
1 ATCGATACACTGCTACAGT
992851 AATTTCTGCA
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:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGATACACTGCTACAGTGC
Found at i:993461 original size:59 final size:58
Alignment explanation
Indices: 993398--993657 Score: 164
Period size: 58 Copynumber: 4.4 Consensus size: 58
993388 ATACCATTAG
** *
993398 TATGATTTTGTTACTATTTTAGCACATAATATGCCCTATATGGAAATCCATATTTTCAA
1 TATGATTTCCTTACTATTTTAGCACATAATATGCCCTAT-TGGAAATCCATAATTTCAA
* * * ** * * *
993457 TATGATTTCCTTA-TCA-TTTGGAACCCT--TAGTGCTTTATTGGAAAACCCATACA-CTCAG
1 TATGATTTCCTTACT-ATTTTAGCA-CATAATA-TGCCCTATTGG-AAATCCATA-ATTTCAA
* *
993515 TATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAA
1 TATGATTTCCTTACTATTTTAGCACATAATATGCCCTAT-TGGAAATCCATAATTTCAA
* * * *
993574 TATGATTTCCTTA-TCA-TTTAGCACACTCA-GTGCTCC-ATATGGAAATCCATACA-CTCAG
1 TATGATTTCCTTACT-ATTTTAGCACA-TAATATGC-CCTAT-TGGAAATCCATA-ATTTCAA
*
993632 TATGATTTCCTTA-TCATTCTAGCACA
1 TATGATTTCCTTACT-ATTTTAGCACA
993658 CAAAGTGTCA
Statistics
Matches: 156, Mismatches: 29, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
57 5 0.03
58 84 0.54
59 62 0.40
60 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (58 bp):
TATGATTTCCTTACTATTTTAGCACATAATATGCCCTATTGGAAATCCATAATTTCAA
Found at i:993517 original size:117 final size:117
Alignment explanation
Indices: 993396--993657 Score: 373
Period size: 117 Copynumber: 2.2 Consensus size: 117
993386 CCATACCATT
** * *
993396 AGTATGATTTTGTTACTATTTTAGCACATAATATGCCCTATATGGAAATCCATATTTTCAATATG
1 AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATATGGAAATCCATAATTTCAATATG
* * * **
993461 ATTTCCTTATCATTTGGAACCCTTAGTGCTTTAT-TGGAAAACCCATACACTC
66 ATTTCCTTATCATTTAGAACACTCAGTGCTCCATATGG-AAACCCATACACTC
* *
993513 AGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATG
1 AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATATGGAAATCCATAATTTCAATATG
* *
993578 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTC
66 ATTTCCTTATCATTTAGAACACTCAGTGCTCCATATGGAAACCCATACACTC
* *
993630 AGTATGATTTCCTTATCATTCTAGCACA
1 AGTATGATTTCCTTACCATTTTAGCACA
993658 CAAAGTGTCA
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
117 125 0.98
118 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (117 bp):
AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATATGGAAATCCATAATTTCAATATG
ATTTCCTTATCATTTAGAACACTCAGTGCTCCATATGGAAACCCATACACTC
Found at i:993519 original size:58 final size:57
Alignment explanation
Indices: 993433--993649 Score: 179
Period size: 58 Copynumber: 3.7 Consensus size: 57
993423 ATAATATGCC
*** *
993433 CTATATGGAAATCCATATTTTCAATATGATTTCCTTATCATTTGGAACCCTTAGTGCT
1 CTATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTT-GAACCCTTAGTGCT
* * * * * * * *
993491 TTAT-TGGAAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATA-TGCC
1 CTATATGG-AAATCCATACACTCAGTATGATTTCCTTATCATTTGAAC-CCT--TAGTGCT
* * * * * *
993550 CTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCT
1 CTATATGGAAATCCATACA-CTCAGTATGATTTCCTTATCATTT-GAACCCTTAGTGCT
*
993608 CCATATGGAAATCCATACACTCAGTATGATTTCCTTATCATT
1 CTATATGGAAATCCATACACTCAGTATGATTTCCTTATCATT
993650 CTAGCACACA
Statistics
Matches: 121, Mismatches: 29, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
57 6 0.05
58 73 0.60
59 36 0.30
60 6 0.05
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (57 bp):
CTATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTGAACCCTTAGTGCT
Found at i:995652 original size:21 final size:20
Alignment explanation
Indices: 995622--995660 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
995612 AAGTCCAATC
* *
995622 TAAAATCAAAGCAGCAAAAAA
1 TAAAACCAAAACAG-AAAAAA
995643 TAAAACCAAAACAGAAAA
1 TAAAACCAAAACAGAAAA
995661 CTCAGCTGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.69, C:0.15, G:0.08, T:0.08
Consensus pattern (20 bp):
TAAAACCAAAACAGAAAAAA
Found at i:998488 original size:23 final size:23
Alignment explanation
Indices: 998462--998548 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
998452 CAGCTCATAT
* *
998462 AAATACACCGAAGTGTCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
998485 AAATGCACC-ATAGTGCCACGTAG
1 AAATGCACCGA-AGTGCCACGTAG
* * *
998508 AATTGCACCGAAGTGCAATGTAG
1 AAATGCACCGAAGTGCCACGTAG
* *
998531 GAATGCACCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
998549 TATAATGTCC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
22 1 0.02
23 51 0.96
24 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.18
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1003014 original size:18 final size:18
Alignment explanation
Indices: 1002950--1003015 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 18
1002940 AACAAATCCC
*
1002950 TATA-ACACATATGCAATA
1 TATATACACATAAG-AATA
*
1002968 TATCATTACATATAAGAATA
1 TAT-A-TACACATAAGAATA
1002988 TATAT--ACATAAGAATA
1 TATATACACATAAGAATA
1003004 TATATACACATA
1 TATATACACATA
1003016 TACTCATCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 15 0.38
18 9 0.22
19 2 0.05
20 7 0.17
21 7 0.17
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.32
Consensus pattern (18 bp):
TATATACACATAAGAATA
Found at i:1003332 original size:23 final size:23
Alignment explanation
Indices: 1003305--1003381 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
1003295 CGGCTCGTAT
1003305 AAATGCACCGAAGTGCCGCATAG
1 AAATGCACCGAAGTGCCGCATAG
* *
1003328 AAATGCACCGTAGTGCCACATAG
1 AAATGCACCGAAGTGCCGCATAG
* * *
1003351 AATTGCACCGAAGTACCGCGTAG
1 AAATGCACCGAAGTGCCGCATAG
1003374 AAATGCAC
1 AAATGCAC
1003382 TATAGTGCCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCGCATAG
Found at i:1005259 original size:6 final size:7
Alignment explanation
Indices: 1005235--1005321 Score: 60
Period size: 8 Copynumber: 12.4 Consensus size: 7
1005225 AGTTAAGTTA
1005235 ATAATAT
1 ATAATAT
1005242 ATATATAT
1 ATA-ATAT
1005250 ATAATA-
1 ATAATAT
1005256 ATAATAT
1 ATAATAT
*
1005263 TTAAT-T
1 ATAATAT
1005269 A-AA-AT
1 ATAATAT
*
1005274 ACAATA-
1 ATAATAT
1005280 A-AAGTAT
1 ATAA-TAT
1005287 ATATATAT
1 ATA-ATAT
1005295 ATATATAT
1 ATA-ATAT
1005303 ATATATAT
1 ATA-ATAT
1005311 ATATATAT
1 ATA-ATAT
1005319 ATA
1 ATA
1005322 CAAAAACGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 17
0.78 0.02 0.19
Matches are distributed among these distances:
5 6 0.09
6 12 0.17
7 12 0.17
8 38 0.55
9 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:1005267 original size:13 final size:15
Alignment explanation
Indices: 1005235--1005321 Score: 78
Period size: 14 Copynumber: 6.1 Consensus size: 15
1005225 AGTTAAGTTA
1005235 ATAATATATATATAT
1 ATAATATATATATAT
1005250 ATAATA-ATA-ATAT
1 ATAATATATATATAT
* * *
1005263 TTAAT-TA-AAATACA
1 ATAATATATATATA-T
*
1005277 ATAAAAGTATATATAT
1 ATAATA-TATATATAT
1005293 AT-ATATATATATAT
1 ATAATATATATATAT
1005307 AT-ATATATATATAT
1 ATAATATATATATAT
1005321 A
1 A
1005322 CAAAAACGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
12 1 0.02
13 12 0.20
14 30 0.51
15 8 0.14
16 4 0.07
17 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
ATAATATATATATAT
Found at i:1005291 original size:2 final size:2
Alignment explanation
Indices: 1005284--1005321 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1005274 ACAATAAAAG
1005284 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1005322 CAAAAACGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1005463 original size:3 final size:3
Alignment explanation
Indices: 1005457--1005523 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
1005447 TAATAAAGAA
**
1005457 AAT AAT AAT AAT AAT AGG AA- AA- AAT AA- AAT GAA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
1005499 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1005524 CATCTATATA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
2 8 0.14
3 47 0.82
4 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1005565 original size:30 final size:29
Alignment explanation
Indices: 1005488--1005600 Score: 90
Period size: 30 Copynumber: 3.9 Consensus size: 29
1005478 AAATAAAATG
*
1005488 AAAATAATAATAATAATA-ATA-ATA-ATA
1 AAAATAATAATAAAAATATATATATATA-A
* ** *
1005515 ATAATAATACATCTATATATATATATATAA
1 AAAATAATA-ATAAAAATATATATATATAA
* * *
1005545 GAAATAATGATATAAAATATATATGTAATAA
1 AAAATAATAATA-AAAATATATATAT-ATAA
1005576 AAAATAATAATAAAAATATA-ATATA
1 AAAATAATAATAAAAATATATATATA
1005601 ACATAAATAA
Statistics
Matches: 65, Mismatches: 15, Indels: 11
0.71 0.16 0.12
Matches are distributed among these distances:
27 8 0.12
28 6 0.09
29 8 0.12
30 28 0.43
31 15 0.23
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATAATAATAAAAATATATATATATAA
Found at i:1005585 original size:26 final size:28
Alignment explanation
Indices: 1005533--1005601 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
1005523 ACATCTATAT
*
1005533 ATATATATATAAGAAATAATGATATAAA
1 ATATATATATAAGAAAAAATGATATAAA
* * *
1005561 ATATATATGTAATAAAAAATAATAATAAA
1 ATATATATATAAGAAAAAATGAT-ATAAA
1005590 A-ATATAATATAA
1 ATATAT-ATATAA
1005602 CATAAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (28 bp):
ATATATATATAAGAAAAAATGATATAAA
Found at i:1005601 original size:13 final size:13
Alignment explanation
Indices: 1005533--1005601 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 13
1005523 ACATCTATAT
1005533 ATATATATATAAGAA
1 ATATA-ATATAA-AA
*
1005548 ATAATGATATAAAA
1 AT-ATAATATAAAA
*
1005562 TATATATGTAATAAAA
1 -ATATA-AT-ATAAAA
1005578 A-ATAATAATAAAA
1 ATATAAT-ATAAAA
1005591 ATATAATATAA
1 ATATAATATAA
1005602 CATAAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
13 13 0.29
14 12 0.27
15 12 0.27
16 8 0.18
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATATAATATAAAA
Found at i:1005665 original size:31 final size:30
Alignment explanation
Indices: 1005587--1005668 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 30
1005577 AAATAATAAT
1005587 AAAAATATAATATAACATA-AATAAATAAATA
1 AAAAATATAAT-TAA-ATATAATAAATAAATA
*
1005618 ACCAAAAT-TAGA-TAAATATAGTAAATAAATA
1 A--AAAATATA-ATTAAATATAATAAATAAATA
1005649 GAAAAATATAATTAAATATA
1 -AAAAATATAATTAAATATA
1005669 TATATATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
30 9 0.21
31 25 0.58
32 3 0.07
33 6 0.14
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (30 bp):
AAAAATATAATTAAATATAATAAATAAATA
Found at i:1005671 original size:2 final size:2
Alignment explanation
Indices: 1005664--1005688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1005654 ATATAATTAA
1005664 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 A
1005689 ATAAGGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1009886 original size:20 final size:20
Alignment explanation
Indices: 1009857--1009905 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1009847 GCGATTATCT
* *
1009857 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
**
1009877 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCAAATTCG
*
1009897 TGTTGCGAT
1 CGTTGCGAT
1009906 TTTAAGTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:1011935 original size:20 final size:20
Alignment explanation
Indices: 1011910--1011956 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1011900 AGAAGAATAG
*
1011910 TCGCAACACGAAAATGATTA
1 TCGCAACACGAAAATGACTA
* **
1011930 TCGCAACGCGAATTTGACTA
1 TCGCAACACGAAAATGACTA
1011950 TCGCAAC
1 TCGCAAC
1011957 GGGATAATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1011986 original size:54 final size:54
Alignment explanation
Indices: 1011928--1012052 Score: 189
Period size: 54 Copynumber: 2.3 Consensus size: 54
1011918 CGAAAATGAT
1011928 TATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCAAAAACGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCAAAAACGAC
* * * *
1011982 TATCGCAACGCGGAA-ATGACTATCGCAACGGGATAATCGTAATGCGAAAATGAC
1 TATCGCAACGC-GAATTTGACTATCGCAACGGGATAATCGCAATGCAAAAACGAC
*
1012036 TATCGCAACACGAATTT
1 TATCGCAACGCGAATTT
1012053 AGTTTCGCGT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
53 3 0.05
54 57 0.90
55 3 0.05
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (54 bp):
TATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCAAAAACGAC
Found at i:1011988 original size:20 final size:20
Alignment explanation
Indices: 1011963--1012011 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1011953 CAACGGGATA
*
1011963 ATCGCAATGCAAAAACGACT
1 ATCGCAACGCAAAAACGACT
** *
1011983 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCAAAAACGACT
1012003 ATCGCAACG
1 ATCGCAACG
1012012 GGATAATCGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCAAAAACGACT
Found at i:1012076 original size:19 final size:19
Alignment explanation
Indices: 1012054--1012090 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1012044 CACGAATTTA
1012054 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
1012073 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
1012091 CTCGTTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.30, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:1012116 original size:33 final size:34
Alignment explanation
Indices: 1012074--1012154 Score: 119
Period size: 33 Copynumber: 2.4 Consensus size: 34
1012064 GCGATTTTGG
*
1012074 TTTCGCGTTGCGATTTTCTCGTTACGATAGTC-A
1 TTTCGCGTTGCGATTATCTCGTTACGATAGTCAA
*
1012107 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTATCTCGTTACGATAGTCAA
* *
1012141 ATTCACGTTGCGAT
1 TTTCGCGTTGCGAT
1012155 AGTCAAATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 30 0.70
34 13 0.30
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTATCTCGTTACGATAGTCAA
Found at i:1012151 original size:20 final size:20
Alignment explanation
Indices: 1012126--1012175 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1012116 GCGATTATCT
1012126 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
1012146 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
1012166 CGTTGCGATA
1 CGTTGCGATA
1012176 ATCATTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:1012781 original size:42 final size:42
Alignment explanation
Indices: 1012711--1012822 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 42
1012701 CTTTCATCGT
* * *
1012711 TCAAGAGGCCTCTCCTATCATTCGAGAGGCCCCTATCATCCC
1 TCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTATCATCCC
* * * **
1012753 TCAAGAGTCCCCTCCCATCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTATCATCCC
* * * *
1012795 TGAAGAGGTCCCTCCCAACATTCTAGAG
1 TCAAGAGGCCCCTCCCATCATTCAAGAG
1012823 CCTGATTCAC
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTATCATCCC
Found at i:1012793 original size:21 final size:20
Alignment explanation
Indices: 1012703--1012807 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 20
1012693 CGACTCACCT
*
1012703 TTCATCGTTCAAGAGGCCTC
1 TTCATCGTTCAAGAGGCCCC
* * *
1012723 TCCTATCATTCGAGAGGCCCC
1 TTC-ATCGTTCAAGAGGCCCC
** *
1012744 TATCATCCCTCAAGAGTCCCC
1 T-TCATCGTTCAAGAGGCCCC
*
1012765 TCCCATCGTTCAAGAGGCCCC
1 T-TCATCGTTCAAGAGGCCCC
* *
1012786 TGTCATCGTTGAAGAGGTCCC
1 T-TCATCGTTCAAGAGGCCCC
1012807 T
1 T
1012808 CCCAACATTC
Statistics
Matches: 65, Mismatches: 18, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
20 2 0.03
21 62 0.95
22 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.26
Consensus pattern (20 bp):
TTCATCGTTCAAGAGGCCCC
Found at i:1014217 original size:30 final size:30
Alignment explanation
Indices: 1014183--1014248 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
1014173 ATAAGAGTTG
*
1014183 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
*
1014213 ATTTGTTTCATTGATGTGTAAATAATTATT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
1014243 ATTTGT
1 ATTTGT
1014249 GCTTGTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTATT
Found at i:1014423 original size:20 final size:20
Alignment explanation
Indices: 1014398--1014615 Score: 168
Period size: 20 Copynumber: 11.8 Consensus size: 20
1014388 GCGATTTTCT
*
1014398 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
1014418 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
* *
1014437 CGTTGTGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
1014451 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1014471 CGTTGCGA-A-T---A-TCC
1 CGTTGCGATAGTCAAATTCG
*
1014485 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1014505 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
1014525 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* * *
1014539 CATTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
1014559 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
1014579 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
1014599 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
1014616 GAATGTGTAA
Statistics
Matches: 158, Mismatches: 22, Indels: 36
0.73 0.10 0.17
Matches are distributed among these distances:
14 30 0.19
15 2 0.01
16 3 0.02
17 1 0.01
18 2 0.01
19 16 0.10
20 104 0.66
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1014491 original size:34 final size:34
Alignment explanation
Indices: 1014415--1014512 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 34
1014405 ATAGTCAAAT
* * *
1014415 TCCCGTTGCGATAGTC-ATTTCGCGTTGTGATTA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGAATA
*
1014448 TCTCGTTGCGATAGTCAAATTCGCGTTGCGAATA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGAATA
*
1014482 TCCCATTGCGATAGTCAAATTCGCGTTGCGA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGA
1014513 TAGTCATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 15 0.26
34 43 0.74
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (34 bp):
TCCCGTTGCGATAGTCAAATTCGCGTTGCGAATA
Found at i:1014587 original size:54 final size:54
Alignment explanation
Indices: 1014451--1014587 Score: 220
Period size: 54 Copynumber: 2.5 Consensus size: 54
1014441 GTGATTATCT
* * *
1014451 CGTTGCGATAGTCAAATTCGCGTTGCGAATATCCCATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATATTCGCGTTGCGATTATCCCATTGCGATAGTCAAATTCA
* * *
1014505 CGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATATTCAAATTCA
1 CGTTGCGATAGTCATATTCGCGTTGCGATTATCCCATTGCGATAGTCAAATTCA
1014559 CGTTGCGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTCATATTCGCGTTGCGAT
1014588 AGTCATATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (54 bp):
CGTTGCGATAGTCATATTCGCGTTGCGATTATCCCATTGCGATAGTCAAATTCA
Found at i:1014813 original size:18 final size:18
Alignment explanation
Indices: 1014790--1014824 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1014780 AAGCCGGTTG
*
1014790 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1014808 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1014825 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1017101 original size:24 final size:24
Alignment explanation
Indices: 1017067--1017120 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1017057 CTGAAACATC
1017067 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1017091 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1017115 ATCAAA
1 ATCAAA
1017121 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1017969 original size:20 final size:20
Alignment explanation
Indices: 1017941--1018088 Score: 140
Period size: 20 Copynumber: 7.3 Consensus size: 20
1017931 AATTCAGTGA
*
1017941 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1017961 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
* *
1017981 TGCGATCA--CATATTATTGCGT
1 TGCGAT-AGTCAGA--ATCGCGT
*
1018002 TGCGATAGTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGT
*
1018022 TGCGATAATCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
** *
1018042 TGCGATCACGT-ATTATCACGT
1 TGCGAT-A-GTCAGAATCGCGT
*
1018063 TGCGATAGTCATAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
1018083 TACGAT
1 TGCGAT
1018089 CACGTGTTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
19 5 0.05
20 69 0.66
21 27 0.26
22 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:1018011 original size:61 final size:61
Alignment explanation
Indices: 1017941--1018088 Score: 224
Period size: 61 Copynumber: 2.4 Consensus size: 61
1017931 AATTCAGTGA
* * **
1017941 TGCGTTAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACATATTATTGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAATCAGAATCGCGTTGCGATCACATATTATCACGT
* *
1018002 TGCGATAGTCAGAATCTCGTTGCGATAATCAGAATCGCGTTGCGATCACGTATTATCACGT
1 TGCGATAGTCAGAATCGCGTTGCGATAATCAGAATCGCGTTGCGATCACATATTATCACGT
* *
1018063 TGCGATAGTCATAATCGCGTTACGAT
1 TGCGATAGTCAGAATCGCGTTGCGAT
1018089 CACGTGTTAT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 78 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (61 bp):
TGCGATAGTCAGAATCGCGTTGCGATAATCAGAATCGCGTTGCGATCACATATTATCACGT
Found at i:1018064 original size:41 final size:41
Alignment explanation
Indices: 1018019--1018109 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
1018009 GTCAGAATCT
*
1018019 CGTTGCGATAATCAGAATCGCGTTGCGATCACGTATTATCA
1 CGTTGCGATAATCAGAATCGCGTTACGATCACGTATTATCA
* * * *
1018060 CGTTGCGATAGTCATAATCGCGTTACGATCACGTGTTATCG
1 CGTTGCGATAATCAGAATCGCGTTACGATCACGTATTATCA
1018101 CGTTGCGAT
1 CGTTGCGAT
1018110 TTACATATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (41 bp):
CGTTGCGATAATCAGAATCGCGTTACGATCACGTATTATCA
Found at i:1018065 original size:21 final size:21
Alignment explanation
Indices: 1017974--1018109 Score: 97
Period size: 20 Copynumber: 6.6 Consensus size: 21
1017964 GATAGTCAGA
*
1017974 ATCGCGTTGCGATCACATATT
1 ATCGCGTTGCGATCACGTATT
* **
1017995 ATTGCGTTGCGAT-A-GTCAGA
1 ATCGCGTTGCGATCACGT-ATT
* *
1018015 ATCTCGTTGCGATAATCAG-A--
1 ATCGCGTTGCGATCA-C-GTATT
1018035 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCACGTATT
* *
1018056 ATCACGTTGCGAT-A-GTCATA
1 ATCGCGTTGCGATCACGT-ATT
* *
1018076 ATCGCGTTACGATCACGTGTT
1 ATCGCGTTGCGATCACGTATT
1018097 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
1018110 TTACATATTC
Statistics
Matches: 89, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.01
19 5 0.06
20 40 0.45
21 39 0.44
22 3 0.03
24 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (21 bp):
ATCGCGTTGCGATCACGTATT
Found at i:1018126 original size:20 final size:20
Alignment explanation
Indices: 1018098--1018150 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1018088 TCACGTGTTA
*
1018098 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1018118 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1018138 TCGCATTGCGATT
1 TCGCATTGCGATT
1018151 ATCTAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1025543 original size:10 final size:10
Alignment explanation
Indices: 1025530--1025563 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1025520 AAACGTGTCA
1025530 AAAACAAAAG
1 AAAACAAAAG
* *
1025540 AAAATAAAAA
1 AAAACAAAAG
1025550 AAAACAAAAG
1 AAAACAAAAG
1025560 AAAA
1 AAAA
1025564 TAGATGTACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (10 bp):
AAAACAAAAG
Found at i:1027459 original size:29 final size:29
Alignment explanation
Indices: 1027402--1027503 Score: 73
Period size: 29 Copynumber: 3.5 Consensus size: 29
1027392 AAAAAAATTG
**
1027402 AATACTTTAAGTACCTATTTTGATTAAAA
1 AATACTTTAAGTACCTATTTTGACCAAAA
* **
1027431 AATACTTTAGGTATTTATTTTGACCAAAA
1 AATACTTTAAGTACCTATTTTGACCAAAA
* * * * *
1027460 AGATAATTTTAGATGCTTATTTTGA-CTAAA
1 A-ATACTTTAAG-TACCTATTTTGACCAAAA
*
1027490 AATATTTTAA-TACC
1 AATACTTTAAGTACC
1027504 AAAATAAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
27 2 0.04
29 32 0.57
30 12 0.21
31 10 0.18
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (29 bp):
AATACTTTAAGTACCTATTTTGACCAAAA
Found at i:1028330 original size:32 final size:33
Alignment explanation
Indices: 1028261--1028337 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 33
1028251 ACTTTGTAGT
*
1028261 ATTTTTTATATTTAATGTATTGAATATCTTAATA
1 ATTTTTTATATTT-ATGTATTGAATATCTAAATA
**
1028295 ATTTTTTATATTT-TGTATTTTA-ATCTAAATA
1 ATTTTTTATATTTATGTATTGAATATCTAAATA
*
1028326 AATTTTTA-ATTT
1 ATTTTTTATATTT
1028338 TTAAATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 4 0.10
31 15 0.38
32 7 0.18
34 13 0.33
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.60
Consensus pattern (33 bp):
ATTTTTTATATTTATGTATTGAATATCTAAATA
Found at i:1030670 original size:10 final size:10
Alignment explanation
Indices: 1030655--1030680 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1030645 TAAATCATAC
1030655 TTGTATGGTG
1 TTGTATGGTG
1030665 TTGTATGGTG
1 TTGTATGGTG
1030675 TTGTAT
1 TTGTAT
1030681 AAATCATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.54
Consensus pattern (10 bp):
TTGTATGGTG
Found at i:1031700 original size:3 final size:3
Alignment explanation
Indices: 1031692--1031763 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
1031682 TCACTCACCA
1031692 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1031740 AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
1031764 TTGGGTTTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1032622 original size:36 final size:37
Alignment explanation
Indices: 1032548--1032622 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1032538 TACTATAATT
**
1032548 AATTTATATATATTTTTTTAAAAATTTTAAATTCATAA
1 AATTTATATATATTTTTTTAAAAA-TTTAAAAACATAA
*
1032586 AATTTATATA-ATTTTTTTACAAAA-TTAAAAAGATAA
1 AATTTATATATATTTTTTTA-AAAATTTAAAAACATAA
1032622 A
1 A
1032623 TAGGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 10 0.30
37 9 0.27
38 14 0.42
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
AATTTATATATATTTTTTTAAAAATTTAAAAACATAA
Found at i:1037085 original size:132 final size:132
Alignment explanation
Indices: 1036848--1037112 Score: 530
Period size: 132 Copynumber: 2.0 Consensus size: 132
1036838 ATAAGTTACT
1036848 TTCGTTTGTTTTAAAGATTGTGTTTTCAGCATAGCTTCTCTATTTTACACATATCATCGATTTTC
1 TTCGTTTGTTTTAAAGATTGTGTTTTCAGCATAGCTTCTCTATTTTACACATATCATCGATTTTC
1036913 TTGTCAATTGATACAAAACAATTCTTCATCTCGCTTATTTCTTCCCACAGTTCCCTAAACCCCTC
66 TTGTCAATTGATACAAAACAATTCTTCATCTCGCTTATTTCTTCCCACAGTTCCCTAAACCCCTC
1036978 AA
131 AA
1036980 TTCGTTTGTTTTAAAGATTGTGTTTTCAGCATAGCTTCTCTATTTTACACATATCATCGATTTTC
1 TTCGTTTGTTTTAAAGATTGTGTTTTCAGCATAGCTTCTCTATTTTACACATATCATCGATTTTC
1037045 TTGTCAATTGATACAAAACAATTCTTCATCTCGCTTATTTCTTCCCACAGTTCCCTAAACCCCTC
66 TTGTCAATTGATACAAAACAATTCTTCATCTCGCTTATTTCTTCCCACAGTTCCCTAAACCCCTC
1037110 AA
131 AA
1037112 T
1 T
1037113 ACATTTATTC
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (132 bp):
TTCGTTTGTTTTAAAGATTGTGTTTTCAGCATAGCTTCTCTATTTTACACATATCATCGATTTTC
TTGTCAATTGATACAAAACAATTCTTCATCTCGCTTATTTCTTCCCACAGTTCCCTAAACCCCTC
AA
Found at i:1039579 original size:31 final size:31
Alignment explanation
Indices: 1039543--1039601 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1039533 AACTTAAAAG
* *
1039543 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1039574 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1039602 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1039655 original size:22 final size:22
Alignment explanation
Indices: 1039624--1039669 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1039614 AATAATAAAT
1039624 TATTTAAAAATAAATCAATCCA
1 TATTTAAAAATAAATCAATCCA
*
1039646 TATTTTAAAATAAATCAATCCA
1 TATTTAAAAATAAATCAATCCA
1039668 TA
1 TA
1039670 CTAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (22 bp):
TATTTAAAAATAAATCAATCCA
Found at i:1039678 original size:22 final size:22
Alignment explanation
Indices: 1039630--1039677 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1039620 AAATTATTTA
**
1039630 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATAAT
1039652 AAAATAAATCAATCCATACTAAT
1 AAAATAAATCAATCCATA-TAAT
1039675 AAA
1 AAA
1039678 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAAATCAATCCATATAAT
Done.