Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006071.1 Hibiscus syriacus cultivar Beakdansim tig00014370_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: 851632
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 4 of 4
Found at i:758656 original size:13 final size:15
Alignment explanation
Indices: 758626--758654 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
758616 TATGAGCTAG
758626 TATATAAATAATTTT
1 TATATAAATAATTTT
758641 TATATAAAT-ATTTT
1 TATATAAATAATTTT
758655 ATTGTTGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATAAATAATTTT
Found at i:768308 original size:19 final size:20
Alignment explanation
Indices: 768286--768324 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
768276 TAGTGTGAAA
768286 TTTAAAT-TTATT-ATTAAAT
1 TTTAAATATT-TTAATTAAAT
768305 TTTAAATATTTTAATTAAAT
1 TTTAAATATTTTAATTAAAT
768325 CTGTAAAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAAATATTTTAATTAAAT
Found at i:768781 original size:20 final size:19
Alignment explanation
Indices: 768744--768782 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
768734 ATAAAATTGG
768744 ATATGATTTAAAATTATAT
1 ATATGATTTAAAATTATAT
768763 ATAT-ATTTATAATATTATAT
1 ATATGATTTA-AA-ATTATAT
768783 TTTAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
ATATGATTTAAAATTATAT
Found at i:771224 original size:23 final size:23
Alignment explanation
Indices: 771194--771252 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
771184 ATGCTATAGT
771194 GTTTGAAAGGTTGTGCATGACAA
1 GTTTGAAAGGTTGTGCATGACAA
771217 GTTTGAAAGGTTGTGCATGACAA
1 GTTTGAAAGGTTGTGCATGACAA
771240 GTTTGAAA-GTTGT
1 GTTTGAAAGGTTGT
771253 TAATGCCCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.34
Consensus pattern (23 bp):
GTTTGAAAGGTTGTGCATGACAA
Found at i:775353 original size:12 final size:12
Alignment explanation
Indices: 775336--775360 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
775326 ATCTATAATT
775336 TCTTGTAATTTC
1 TCTTGTAATTTC
775348 TCTTGTAATTTC
1 TCTTGTAATTTC
775360 T
1 T
775361 TATTTCTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTTGTAATTTC
Found at i:779184 original size:16 final size:15
Alignment explanation
Indices: 779163--779192 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
779153 TAAAAAGATC
779163 ATAAATAAAGTAAAAA
1 ATAAATAAA-TAAAAA
779179 ATAAATAAATAAAA
1 ATAAATAAATAAAA
779193 CAAACAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
ATAAATAAATAAAAA
Found at i:780971 original size:84 final size:84
Alignment explanation
Indices: 780851--781090 Score: 275
Period size: 84 Copynumber: 2.8 Consensus size: 84
780841 ATAATTTTAT
* * * * * *
780851 TGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGTGCGTAGTC
1 TGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAATC
* * *
780916 GAACTCGAGGGTC-TTTGG
66 GAACTCAAAGATCTTTTGG
* * * * * *
780934 TTGGCATATATCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAAT
1 -TGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAAT
780999 CGAACTCAAAGATCTTTTGG
65 CGAACTCAAAGATCTTTTGG
* * * **
781019 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTAAAGGTGAGTTTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTG-CCTTAGAGCTGAGCATAAT
781084 CGAACTC
65 CGAACTC
781091 GAGGGTTTGG
Statistics
Matches: 130, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
84 103 0.79
85 27 0.21
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (84 bp):
TGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAATC
GAACTCAAAGATCTTTTGG
Found at i:781224 original size:37 final size:36
Alignment explanation
Indices: 781166--781439 Score: 112
Period size: 36 Copynumber: 7.9 Consensus size: 36
781156 AAAGATTGAA
* * *
781166 GTTTCAAGGGGAAACTGTCTCAAGAGAGATAAAATTTT
1 GTTTCAA-GGGAAACTATCTCAAGAGAGACAAAA-TTC
*
781204 GTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* * * * * ***
781240 ATTTCAAGGGAAA-TTTTTCCA-A-TG--TTTA-T-
1 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* * *
781269 ATTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
1 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTC
* ** * * * * *
781306 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTT
1 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* * *
781342 GTTTCAAGGGAAA-TAGAT-TC-----A-A-ATATTTT
1 GTTTCAAGGGAAACT--ATCTCAAGAGAGACAAAATTC
* *
781371 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* * *
781407 GTTTCAAGGAAAACTGTCTAAAGAGAGACAAAA
1 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
781440 CTTGGAAAAT
Statistics
Matches: 176, Mismatches: 41, Indels: 40
0.68 0.16 0.16
Matches are distributed among these distances:
28 1 0.01
29 31 0.18
30 8 0.05
31 3 0.02
32 1 0.01
33 1 0.01
34 3 0.02
35 7 0.04
36 64 0.36
37 50 0.28
38 7 0.04
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
Found at i:781293 original size:102 final size:101
Alignment explanation
Indices: 781167--781439 Score: 314
Period size: 102 Copynumber: 2.7 Consensus size: 101
781157 AAGATTGAAG
* * *
781167 TTTCAAGGGGAAACTGTCTCAAGAGAGATAAAATTTTGTTTCAAGGGAACCTATCTCAAGAGAGA
1 TTTCAA-GGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
** * *
781232 CAAAATTCATTTCAAGGGAAAT-TTTTCCAATGTTTATA
64 CAAAATTCATTTCAAGGGAAATAGATTCAAATATTT-TA
* * * * ** * *
781270 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAGAC
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* ** *
781335 GAAATTTGTTTCAAGGGAAATAGATTCAAATATTTTG
65 AAAATTCATTTCAAGGGAAATAGATTCAAATATTTTA
* *
781372 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACTGTCTAAAGAGAGACA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
781437 AAA
66 AAA
781440 CTTGGAAAAT
Statistics
Matches: 138, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
101 27 0.20
102 96 0.70
103 15 0.11
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (101 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
AAATTCATTTCAAGGGAAATAGATTCAAATATTTTA
Found at i:781415 original size:36 final size:36
Alignment explanation
Indices: 781368--781439 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
781358 ATTCAAATAT
* *
781368 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGAAAACTGTCTAAAGAGAGACAAAA
781404 TTTGTTTCAAGGAAAACTGTCTAAAGAGAGACAAAA
1 TTTGTTTCAAGGAAAACTGTCTAAAGAGAGACAAAA
781440 CTTGGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (36 bp):
TTTGTTTCAAGGAAAACTGTCTAAAGAGAGACAAAA
Found at i:782690 original size:33 final size:32
Alignment explanation
Indices: 782652--782740 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 32
782642 ATTCCCAAAG
* *
782652 ATGCCCCAATATTCGATGTTGAATCTCAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTC-AAAAA
*
782685 ATGCCCCAACATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
*
782717 ATGCCCCAGCATTTGATGTTGAAT
1 ATGCCCCAACATTTGATGTTGAAT
782741 TTTTAAAGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 27 0.53
33 24 0.47
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAA
Found at i:783796 original size:69 final size:69
Alignment explanation
Indices: 783680--783817 Score: 233
Period size: 69 Copynumber: 2.0 Consensus size: 69
783670 TCTCTCTCTC
*
783680 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
783745 TCAT
66 TCAT
**
783749 TTGATGCTCTATGATCTTCGAGTGAAGT-AGTTCAGTGATTCGGAAATGATTGTGCTTGATCAAT
1 TTGATGCTCTATGATCTTCGAGTGAAGTGA-TTCAGTGATTCAAAAATGATTGTGCTTGATCAAT
783813 CTCAT
65 CTCAT
783818 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:786949 original size:21 final size:20
Alignment explanation
Indices: 786916--786954 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
786906 AATTATCCTA
*
786916 AAAAAAATCATAAATAAAGT
1 AAAAAAATAATAAATAAAGT
786936 AAAAAAATAAATAAATAAA
1 AAAAAAAT-AATAAATAAA
786955 ACAAACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAAAAATAATAAATAAAGT
Found at i:796075 original size:19 final size:19
Alignment explanation
Indices: 796032--796129 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
796022 CTGCTGGAAA
* * *
796032 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
796052 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
796071 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
796091 CCGGTTTGACCGG-TCTGT
1 CCGGTTTGACCGGTTCTGA
796109 CTCGGTTTGACCGG-TCTGA
1 C-CGGTTTGACCGGTTCTGA
796128 CC
1 CC
796130 CGACCCGACC
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
18 5 0.08
19 38 0.58
20 15 0.23
21 8 0.12
ACGTcount: A:0.13, C:0.29, G:0.28, T:0.31
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:796093 original size:29 final size:30
Alignment explanation
Indices: 796030--796104 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
796020 GGCTGCTGGA
*
796030 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
796061 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
796089 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
796105 CTGTCTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:796123 original size:9 final size:9
Alignment explanation
Indices: 796031--796129 Score: 81
Period size: 10 Copynumber: 10.3 Consensus size: 9
796021 GCTGCTGGAA
*
796031 ACCGGTTTA
1 ACCGGTTTG
*
796040 ACCGGTTTTCA
1 ACCGG-TTT-G
796051 ACCGGTTCTG
1 ACCGGTT-TG
796061 ACCGGTTTG
1 ACCGGTTTG
*
796070 ACCGGTTTCA
1 ACCGGTTT-G
*
796080 ACCGGTTCG
1 ACCGGTTTG
796089 AACCGGTTTG
1 -ACCGGTTTG
*
796099 ACCGGTCTG
1 ACCGGTTTG
*
796108 TCTCGGTTTG
1 AC-CGGTTTG
*
796118 ACCGGTCTG
1 ACCGGTTTG
796127 ACC
1 ACC
796130 CGACCCGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.46
11 7 0.09
ACGTcount: A:0.14, C:0.28, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:796152 original size:22 final size:22
Alignment explanation
Indices: 796126--796168 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
796116 TGACCGGTCT
796126 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
796148 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
796169 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:797119 original size:63 final size:63
Alignment explanation
Indices: 797051--797174 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
797041 CTAATGTGAC
* ** * *
797051 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
797114 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
797175 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:809250 original size:20 final size:20
Alignment explanation
Indices: 809227--809278 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
809217 AACGCGATCC
809227 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
809247 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
809267 CCAAAATCGCAA
1 CCAGAATCGCAA
809279 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:809295 original size:21 final size:20
Alignment explanation
Indices: 809268--809366 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
809258 AATCAGTTTC
809268 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
809289 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
809310 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
809330 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
809351 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
809367 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:809395 original size:20 final size:20
Alignment explanation
Indices: 809333--809526 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
809323 CGATTTTCCA
* ** *
809333 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
809353 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
809373 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
809393 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
809413 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
809433 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
809453 ATATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
809473 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
809493 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
809514 AAATCGCAACGCG
1 AAATCGCAACGCG
809527 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:809417 original size:60 final size:60
Alignment explanation
Indices: 809333--809526 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
809323 CGATTTTCCA
* ** * *
809333 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
809393 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
809453 ATATCGCAATGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
809514 AAATCGCAACGCG
1 AAATCGCAACGCG
809527 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 80 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:809947 original size:33 final size:33
Alignment explanation
Indices: 809908--809978 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
809898 TTCACTTAGA
*
809908 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
809941 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
809974 TTTCA
1 TTTCA
809979 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:810118 original size:14 final size:14
Alignment explanation
Indices: 810099--810153 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
810089 AGAATGACTG
810099 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
810113 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
810132 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
810146 TCGCAACG
1 TCGCAACG
810154 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:810166 original size:33 final size:33
Alignment explanation
Indices: 810099--810169 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
810089 AGAATGACTG
***
810099 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
810132 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
810165 TCGCA
1 TCGCA
810170 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:810187 original size:19 final size:19
Alignment explanation
Indices: 810165--810262 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
810155 GAAACCAAAA
*
810165 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
810184 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
810198 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
810217 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
810231 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
810250 TCGCGTTGCGATT
1 TCGCGTTGCGATT
810263 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:810206 original size:14 final size:14
Alignment explanation
Indices: 810187--810276 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
810177 TTTCATTTCG
810187 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
810201 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
810220 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
810234 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
810251 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
810267 CGTTGCGATT
1 CGTTGCGATT
810277 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:810212 original size:33 final size:33
Alignment explanation
Indices: 810170--810284 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
810160 CAAAATCGCA
810170 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
810203 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
810236 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
810269 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
810285 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:812499 original size:14 final size:14
Alignment explanation
Indices: 812480--812515 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
812470 ATTGTTTAAT
812480 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
812494 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
812508 TGATTTGT
1 TGATTTGT
812516 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:812637 original size:19 final size:19
Alignment explanation
Indices: 812621--812722 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
812611 AAAAATGACT
812621 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
812640 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
812659 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
812673 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
812692 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
812712 ATCGCAATGCG
1 ATCGCAATGCG
812723 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:812771 original size:33 final size:33
Alignment explanation
Indices: 812729--813056 Score: 217
Period size: 33 Copynumber: 9.5 Consensus size: 33
812719 TGCGTTTATA
812729 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
812762 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
812798 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
812833 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
812871 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
812904 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
812944 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
812975 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* * *
813008 ATTTCGCGTTGCGATTTTCAT-GTTGGGATTTTC
1 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
*
813041 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
813057 GTATTTTCCG
Statistics
Matches: 251, Mismatches: 20, Indels: 48
0.79 0.06 0.15
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 126 0.50
34 3 0.01
35 19 0.08
36 20 0.08
37 4 0.02
38 53 0.21
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:812775 original size:19 final size:19
Alignment explanation
Indices: 812751--813056 Score: 356
Period size: 19 Copynumber: 17.4 Consensus size: 19
812741 GATTATCTCG
812751 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
812770 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
812789 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
812803 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
812822 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
812841 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
812860 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
812879 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
812894 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
812912 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
812931 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
812945 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
812964 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
812983 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
812997 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
813016 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
813030 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
813049 TTGCGATT
1 TTGCGATT
813057 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 13, Indels: 50
0.80 0.04 0.16
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.12
17 31 0.12
18 2 0.01
19 151 0.61
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:812826 original size:71 final size:71
Alignment explanation
Indices: 812751--812990 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
812741 GATTATCTCG
812751 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
812816 TTCGCA
66 TTCGCA
* *
812822 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
812885 TT-ATGTCG-G
61 TTCATTTCGCA
*
812894 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
812958 TTCGCA
66 TTCGCA
812964 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
812991 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 107 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:813056 original size:52 final size:52
Alignment explanation
Indices: 812751--813028 Score: 327
Period size: 52 Copynumber: 5.2 Consensus size: 52
812741 GATTATCTCG
*
812751 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCGCGTTGCGATTTTCATTTCGCA
* *
812803 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCGCGTTGCGATTTTCATTTCGCA
* *
812860 TTGCGATTTTAATTTCGCATTGCGATTAT-GTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCG-C-GTTGCGATTTTCATTTCGCA
*
812912 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
* *
812964 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
813016 TTGCGATTTTCAT
1 TTGCGATTTTCAT
813029 GTTGGGATTT
Statistics
Matches: 209, Mismatches: 8, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
51 4 0.02
52 169 0.81
53 2 0.01
54 3 0.01
55 7 0.03
57 24 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
Found at i:815590 original size:24 final size:24
Alignment explanation
Indices: 815556--815602 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
815546 CTGAAACATC
815556 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
815580 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
815603 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:816301 original size:20 final size:20
Alignment explanation
Indices: 816273--816641 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
816263 AAATTTCAGT
* * * *
816273 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
816293 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
816313 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
816333 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
816353 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
816373 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
816393 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
816413 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
816433 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
816453 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
816473 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
816493 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
816513 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
816533 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
816553 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
816573 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
816593 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
816613 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
816633 GTTGCGATT
1 GTTGCGATT
816642 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:817843 original size:3 final size:3
Alignment explanation
Indices: 817835--817860 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
817825 GGAGTTGAGT
817835 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
817861 TTGATTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:819359 original size:24 final size:25
Alignment explanation
Indices: 819318--819364 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
819308 ACTCAAAAAA
819318 AAAATTAGAAGCTCGATTGAAGTCT
1 AAAATTAGAAGCTCGATTGAAGTCT
* *
819343 AAAATTCG-AGCTTGATTGAAGT
1 AAAATTAGAAGCTCGATTGAAGT
819365 GAAATAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGTCT
Found at i:819390 original size:14 final size:14
Alignment explanation
Indices: 819371--819398 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
819361 AAGTGAAATA
819371 ATAGTTATATAATT
1 ATAGTTATATAATT
819385 ATAGTTATATAATT
1 ATAGTTATATAATT
819399 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:821707 original size:13 final size:13
Alignment explanation
Indices: 821689--821715 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
821679 AATTTAAAAT
821689 CAGTCTTTTCTTG
1 CAGTCTTTTCTTG
821702 CAGTCTTTTCTTG
1 CAGTCTTTTCTTG
821715 C
1 C
821716 CTGACCCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.26, G:0.15, T:0.52
Consensus pattern (13 bp):
CAGTCTTTTCTTG
Found at i:826969 original size:12 final size:12
Alignment explanation
Indices: 826952--826977 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
826942 CCTCGAAGAC
826952 CTCTCTTACCAT
1 CTCTCTTACCAT
826964 CTCTCTTACCAT
1 CTCTCTTACCAT
826976 CT
1 CT
826978 AATCCCCAAC
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:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCTCTTACCAT
Found at i:830208 original size:31 final size:31
Alignment explanation
Indices: 830173--830233 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
830163 CATTTATTGG
830173 ACTTTGATTTTAATCCTCAATGCAGTTTTAT
1 ACTTTGATTTTAATCCTCAATGCAGTTTTAT
830204 ACTTTGATTTTAATCCTCAATGCAGTTTTA
1 ACTTTGATTTTAATCCTCAATGCAGTTTTA
830234 CACATTCCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (31 bp):
ACTTTGATTTTAATCCTCAATGCAGTTTTAT
Found at i:843161 original size:34 final size:34
Alignment explanation
Indices: 843118--843182 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
843108 TGAAAAGAAG
843118 AATGAAATATTTAATAAACCAGCACAATAATGCA
1 AATGAAATATTTAATAAACCAGCACAATAATGCA
843152 AATGAAATATTTAATAAACCAGCACAATAAT
1 AATGAAATATTTAATAAACCAGCACAATAAT
843183 CCCCATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.25
Consensus pattern (34 bp):
AATGAAATATTTAATAAACCAGCACAATAATGCA
Found at i:845277 original size:43 final size:43
Alignment explanation
Indices: 845210--845334 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 43
845200 ATATAAGATT
* * *
845210 CAAATGATTCAGCTCAGTTATAAAGTTCACACTATTAACCTAA
1 CAAAGGATTCAGCTCAATTCTAAAGTTCACACTATTAACCTAA
* * * *
845253 CAAAGGATTCGGCTCACTTCTAAAGTTCACACTATTAAGCTAG
1 CAAAGGATTCAGCTCAATTCTAAAGTTCACACTATTAACCTAA
* * * * *
845296 CAATGAATTCATCTCAATACTAAAGTTCACATTATTAAC
1 CAAAGGATTCAGCTCAATTCTAAAGTTCACACTATTAAC
845335 AAAATAGAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (43 bp):
CAAAGGATTCAGCTCAATTCTAAAGTTCACACTATTAACCTAA
Found at i:851423 original size:21 final size:19
Alignment explanation
Indices: 851394--851432 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
851384 TAATATACTG
*
851394 ATTATATATAATGTATTAATT
1 ATTAAATATAA-GT-TTAATT
851415 ATTAAATATAAGTTTAAT
1 ATTAAATATAAGTTTAAT
851433 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTAAATATAAGTTTAATT
Done.