Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008072.1 Hibiscus syriacus cultivar Beakdansim tig00110570_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: 1263316
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 4 of 5
Found at i:995660 original size:40 final size:40
Alignment explanation
Indices: 995573--995679 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
995563 GAATTTCTTT
**
995573 TTCGCAACACAAGTTTCCTTTTCGCAACAAGATTTTCTAAA
1 TTCGCAACACAA-TTTTATTTTCGCAACAAGATTTTCTAAA
* ** *
995614 TT-GCAACACGAATTTTGTTTTCGCAACTCGATTTTC-GAA
1 TTCGCAACAC-AATTTTATTTTCGCAACAAGATTTTCTAAA
*
995653 TTCGCAACA-ACTTTTATTTTCGCAACA
1 TTCGCAACACAATTTTATTTTCGCAACA
995680 CAAATGTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
38 15 0.27
39 4 0.07
40 33 0.59
41 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.36
Consensus pattern (40 bp):
TTCGCAACACAATTTTATTTTCGCAACAAGATTTTCTAAA
Found at i:996628 original size:24 final size:24
Alignment explanation
Indices: 996592--996645 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
996582 GTATTCGAAA
*
996592 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTAGGTCAATACTCGGAC
* *
996616 TTTGATCTAGGTCAGTACTCGGAT
1 TTTGATCTAGGTCAATACTCGGAC
996640 TTTGAT
1 TTTGAT
996646 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (24 bp):
TTTGATCTAGGTCAATACTCGGAC
Found at i:999245 original size:20 final size:20
Alignment explanation
Indices: 999202--999264 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
999192 CGATTGTTGT
* *
999202 GAAAGTCAAATTCGCAACGT
1 GAAAATCAAATTCGCAACGC
999222 GAAAATCAAATTCGTC-ACGC
1 GAAAATCAAATTCG-CAACGC
* *
999242 GAAAATAAAAATCGCAACGC
1 GAAAATCAAATTCGCAACGC
999262 GAA
1 GAA
999265 TTTGACTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACGC
Found at i:1000824 original size:21 final size:21
Alignment explanation
Indices: 1000798--1000873 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1000788 GTGAATCGGG
*
1000798 CTCTTGAACGATGAGAGAGGT
1 CTCTTGAACGATGAGAGAGGC
* *
1000819 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGAGAGAGGC
1000840 CTCTTGAACGATG-G-GAGGC
1 CTCTTGAACGATGAGAGAGGC
1000859 CATCTTGAACGATGA
1 C-TCTTGAACGATGA
1000874 CAGGTGAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.10
20 13 0.27
21 31 0.63
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGAGGC
Found at i:1001038 original size:4 final size:4
Alignment explanation
Indices: 1001017--1001058 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1001007 GGGCCGCTAA
* * *
1001017 AAAT AAAT TAAT ACAT AAAT AAGT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1001059 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1001290 original size:21 final size:21
Alignment explanation
Indices: 1001260--1001306 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1001250 ACCGTTTTCG
*
1001260 TCACGTAAAGTAAC-GACCTCA
1 TCACGCAAAG-AACTGACCTCA
*
1001281 TCACGCAAAGCACTGACCTCA
1 TCACGCAAAGAACTGACCTCA
1001302 TCACG
1 TCACG
1001307 TAACTCCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.17
Consensus pattern (21 bp):
TCACGCAAAGAACTGACCTCA
Found at i:1002267 original size:20 final size:20
Alignment explanation
Indices: 1002237--1002315 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
1002227 CACTGAATAT
1002237 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* * *
1002257 TTATTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
1002276 -TGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
1002295 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
1002315 T
1 T
1002316 AATCCCTCGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 14 0.29
19 1 0.02
20 34 0.69
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:1002289 original size:38 final size:38
Alignment explanation
Indices: 1002238--1002312 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
1002228 ACTGAATATT
*
1002238 TGTCCCGAAGGACCACTGATTATTCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTGATTATCCCGAAGAACCACTA
* * *
1002276 TGTCCCGAAGGACCACTGTTTGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACTGATTATCCCGAAGAACCACT
1002313 GATAATCCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (38 bp):
TGTCCCGAAGGACCACTGATTATCCCGAAGAACCACTA
Found at i:1003152 original size:364 final size:364
Alignment explanation
Indices: 1002483--1003210 Score: 1456
Period size: 364 Copynumber: 2.0 Consensus size: 364
1002473 GGTCATGTTC
1002483 CATATTCATATCTCATAGCATATCACATAGCTTCTATTCTTTCTCACGTAGTCACATAGATCCAT
1 CATATTCATATCTCATAGCATATCACATAGCTTCTATTCTTTCTCACGTAGTCACATAGATCCAT
1002548 GGCATATAACATAATCCAAATTGCATATAATCACGTAGATCATTTCTTAGATGTTCATGTAAACC
66 GGCATATAACATAATCCAAATTGCATATAATCACGTAGATCATTTCTTAGATGTTCATGTAAACC
1002613 TAAATATTATATCTTGTTCACATACAATCATATACACTTCATATAGTACATAGAAACACCTAGAA
131 TAAATATTATATCTTGTTCACATACAATCATATACACTTCATATAGTACATAGAAACACCTAGAA
1002678 CATTTCCACATAGCTTATATAAATTTTCAGAGTCCTTTCATATTACTTGATAACATATATCATAT
196 CATTTCCACATAGCTTATATAAATTTTCAGAGTCCTTTCATATTACTTGATAACATATATCATAT
1002743 ATGTATATAATAACTTATGTCATATCATCTACTTTATGCTTCATTTCTTTGTATCCCCTTAGATT
261 ATGTATATAATAACTTATGTCATATCATCTACTTTATGCTTCATTTCTTTGTATCCCCTTAGATT
1002808 ACATAAACTATGTAGTATTTCTAAACATATATTGTTTAA
326 ACATAAACTATGTAGTATTTCTAAACATATATTGTTTAA
1002847 CATATTCATATCTCATAGCATATCACATAGCTTCTATTCTTTCTCACGTAGTCACATAGATCCAT
1 CATATTCATATCTCATAGCATATCACATAGCTTCTATTCTTTCTCACGTAGTCACATAGATCCAT
1002912 GGCATATAACATAATCCAAATTGCATATAATCACGTAGATCATTTCTTAGATGTTCATGTAAACC
66 GGCATATAACATAATCCAAATTGCATATAATCACGTAGATCATTTCTTAGATGTTCATGTAAACC
1002977 TAAATATTATATCTTGTTCACATACAATCATATACACTTCATATAGTACATAGAAACACCTAGAA
131 TAAATATTATATCTTGTTCACATACAATCATATACACTTCATATAGTACATAGAAACACCTAGAA
1003042 CATTTCCACATAGCTTATATAAATTTTCAGAGTCCTTTCATATTACTTGATAACATATATCATAT
196 CATTTCCACATAGCTTATATAAATTTTCAGAGTCCTTTCATATTACTTGATAACATATATCATAT
1003107 ATGTATATAATAACTTATGTCATATCATCTACTTTATGCTTCATTTCTTTGTATCCCCTTAGATT
261 ATGTATATAATAACTTATGTCATATCATCTACTTTATGCTTCATTTCTTTGTATCCCCTTAGATT
1003172 ACATAAACTATGTAGTATTTCTAAACATATATTGTTTAA
326 ACATAAACTATGTAGTATTTCTAAACATATATTGTTTAA
1003211 TAGTATTTTA
Statistics
Matches: 364, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
364 364 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (364 bp):
CATATTCATATCTCATAGCATATCACATAGCTTCTATTCTTTCTCACGTAGTCACATAGATCCAT
GGCATATAACATAATCCAAATTGCATATAATCACGTAGATCATTTCTTAGATGTTCATGTAAACC
TAAATATTATATCTTGTTCACATACAATCATATACACTTCATATAGTACATAGAAACACCTAGAA
CATTTCCACATAGCTTATATAAATTTTCAGAGTCCTTTCATATTACTTGATAACATATATCATAT
ATGTATATAATAACTTATGTCATATCATCTACTTTATGCTTCATTTCTTTGTATCCCCTTAGATT
ACATAAACTATGTAGTATTTCTAAACATATATTGTTTAA
Found at i:1007975 original size:31 final size:31
Alignment explanation
Indices: 1007887--1008137 Score: 228
Period size: 31 Copynumber: 8.1 Consensus size: 31
1007877 AGAGTCGAGG
1007887 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
1007918 GAATTACCTATCTT-T--TGAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
*
1007948 TTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
1007979 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
1008011 GTATACCTATGTTCTACGGAATATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
1008042 GAATTACCTATGTGT-TTC-GAGACATATAGACA
1 GTA-TACCTATGT-TCTACGGA-ACATATGGACA
* *
1008074 ATATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * * *
1008105 GTTTACCTAGGTTCTTCGGAACCTATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
1008136 GT
1 GT
1008138 TACTGAGGAT
Statistics
Matches: 176, Mismatches: 29, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
29 11 0.06
30 14 0.08
31 89 0.51
32 61 0.35
33 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:1008004 original size:32 final size:31
Alignment explanation
Indices: 1007890--1008086 Score: 176
Period size: 32 Copynumber: 6.3 Consensus size: 31
1007880 GTCGAGGGTA
*
1007890 TACCTATGTTCTACG-GAACATATGGACAGAAT
1 TACCTATGTT-TTCGAG-ACATATGGACAGAAT
* **
1007922 TACCTATCTTTT-GAGACATATGGACATTA-
1 TACCTATGTTTTCGAGACATATGGACAGAAT
*
1007951 TACCTATGTTCTACG-GAACATATGGACAGAAT
1 TACCTATGTT-TTCGAG-ACATATGGACAGAAT
*
1007983 TACCTATGTCTTTCGAGACATATGGACAGTA-
1 TACCTATGT-TTTCGAGACATATGGACAGAAT
* *
1008014 TACCTATGTTCTACG-GAATATATGGACAGAAT
1 TACCTATGTT-TTCGAG-ACATATGGACAGAAT
*
1008046 TACCTATGTGTTTCGAGACATATAGAC--AAT
1 TACCTATGT-TTTCGAGACATATGGACAGAAT
1008076 ATACCTATGTT
1 -TACCTATGTT
1008087 CTAAGGAACA
Statistics
Matches: 136, Mismatches: 16, Indels: 28
0.76 0.09 0.16
Matches are distributed among these distances:
29 9 0.07
30 21 0.15
31 48 0.35
32 54 0.40
33 4 0.03
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (31 bp):
TACCTATGTTTTCGAGACATATGGACAGAAT
Found at i:1008027 original size:63 final size:63
Alignment explanation
Indices: 1007887--1008113 Score: 361
Period size: 63 Copynumber: 3.7 Consensus size: 63
1007877 AGAGTCGAGG
*
1007887 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA--TCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
*
1007948 TTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* * *
1008011 GTATACCTATGTTCTACGGAATATATGGACAGAATTACCTATGTGTTTCGAGACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* * *
1008074 ATATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
1008114 GGTTCTTCGG
Statistics
Matches: 154, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
61 40 0.26
62 7 0.05
63 107 0.69
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:1012347 original size:32 final size:32
Alignment explanation
Indices: 1012311--1012491 Score: 216
Period size: 32 Copynumber: 5.8 Consensus size: 32
1012301 GTTCTACGGA
1012311 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
*
1012343 ACATATGGAC--AATATACCTATGT-TCTACG-G
1 ACATATGGACAGAAT-TACCTATGTCT-TTCGAG
1012373 AACATATGGACAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAATTACCTATGTCTTTCGAG
* *
1012406 ACATATGGACAGTA-TACCTATGT-TCTAC-AG
1 ACATATGGACAGAATTACCTATGTCT-TTCGAG
1012436 AACATATGGACAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAATTACCTATGTCTTTCGAG
* *
1012469 ACATATAGACAGTA-TACCTATGT
1 ACATATGGACAGAATTACCTATGT
1012492 TCTAAGGAAC
Statistics
Matches: 129, Mismatches: 8, Indels: 25
0.80 0.05 0.15
Matches are distributed among these distances:
30 8 0.06
31 55 0.43
32 58 0.45
33 8 0.06
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAG
Found at i:1012370 original size:63 final size:63
Alignment explanation
Indices: 1012291--1012508 Score: 400
Period size: 63 Copynumber: 3.5 Consensus size: 63
1012281 AGAGTCGAGG
1012291 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
*
1012354 ATATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
1012417 GTATACCTATGTTCTACAGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
*
1012480 GTATACCTATGTTCTAAGGAACATATGGA
1 GTATACCTATGTTCTACGGAACATATGGA
1012509 TAGTTTACCT
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 149 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:1012504 original size:31 final size:31
Alignment explanation
Indices: 1012291--1012547 Score: 240
Period size: 31 Copynumber: 8.2 Consensus size: 31
1012281 AGAGTCGAGG
1012291 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
1012322 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
1012354 ATATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
1012385 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
1012417 GTATACCTATGTTCTACAGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
1012448 GAATTACCTATG-TCTTTC-GAGACATATAGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
1012480 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * * *
1012511 GTTTACCTAGGTTCTTCGGAACCTATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
1012542 GT-TACC
1 GTATACC
1012548 GAGGATCTTT
Statistics
Matches: 186, Mismatches: 25, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
30 4 0.02
31 103 0.55
32 79 0.42
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:1014904 original size:18 final size:18
Alignment explanation
Indices: 1014881--1014973 Score: 105
Period size: 18 Copynumber: 4.9 Consensus size: 18
1014871 ACTGAATATT
1014881 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1014899 TGTCCCGAATGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1014918 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
* *
1014937 TGTCCCAAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
1014957 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1014974 GATAATCCCT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
18 30 0.48
19 2 0.03
20 30 0.48
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1014928 original size:38 final size:38
Alignment explanation
Indices: 1014880--1014973 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 38
1014870 CACTGAATAT
* *
1014880 TTGTCCCGAAGGACCACTATGTCCCGAATGACCACTGA
1 TTGTCCCGAAGGACCACTATGTCCCAAAGGACCACTGA
* * *
1014918 TTGTTCCGAAGAACCACTATGTCCCAAAGGACCACTGT
1 TTGTCCCGAAGGACCACTATGTCCCAAAGGACCACTGA
1014956 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
1014974 GATAATCCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGGACCACTATGTCCCAAAGGACCACTGA
Found at i:1014933 original size:20 final size:20
Alignment explanation
Indices: 1014880--1014976 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
1014870 CACTGAATAT
1014880 TTGTCCCGAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
1014899 -TGTCCCGAATGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
1014918 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
* *
1014937 -TGTCCCAAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
1014956 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
1014976 T
1 T
1014977 AATCCCTCGA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 30 0.47
19 2 0.03
20 32 0.50
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:1017106 original size:13 final size:13
Alignment explanation
Indices: 1017088--1017112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1017078 ACGGGAGGAG
1017088 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
1017101 AGGAAGAAGAAG
1 AGGAAGAAGAAG
1017113 TTCTGGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAGA
Found at i:1017452 original size:42 final size:42
Alignment explanation
Indices: 1017405--1017503 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
1017395 TGTGATGGAA
* *
1017405 TAGGTGATGGCTCTCAGTGTGAAGATGTATAATCGGCTCGAT
1 TAGGTGATGGCTCTCAGTGTCAAGATGTAGAATCGGCTCGAT
* *
1017447 TAGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGGCTCGAT
1 TAGGTGATGGCTCTCAGTGTCAAGATGTAGAATCGGCTCGAT
* *
1017489 CAGATGATGGCTCTC
1 TAGGTGATGGCTCTC
1017504 GAAGTGGGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.29
Consensus pattern (42 bp):
TAGGTGATGGCTCTCAGTGTCAAGATGTAGAATCGGCTCGAT
Found at i:1019023 original size:20 final size:20
Alignment explanation
Indices: 1019000--1019083 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
1018990 TTTGAAACTT
**
1019000 AAATTCGCAACATGAAAATA
1 AAATTCGCAACGCGAAAATA
1019020 AAATTCGCAACGCGAAAATCA
1 AAATTCGCAACGCGAAAAT-A
*
1019041 AAA-TCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATA
* *
1019060 AAATTCGCAACGTGAAACTA
1 AAATTCGCAACGCGAAAATA
1019080 AAAT
1 AAAT
1019084 CGCTTTGCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.05
20 49 0.88
21 4 0.07
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:1019642 original size:19 final size:20
Alignment explanation
Indices: 1019607--1019649 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1019597 GTTTTGAATT
*
1019607 CGAAAATAAAACTCGCGTTG
1 CGAAAATAAAACGCGCGTTG
1019627 CGAAAAT-AAACGCGCGTTG
1 CGAAAATAAAACGCGCGTTG
1019646 CGAA
1 CGAA
1019650 TTTGGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
CGAAAATAAAACGCGCGTTG
Found at i:1024727 original size:29 final size:29
Alignment explanation
Indices: 1024649--1024730 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
1024639 CAGTGGTCGT
* ** *
1024649 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAACG
* *
1024678 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAACG
*
1024707 AGGTCGCCATGCACTCGCGGCGAC
1 AGGTCGCCATGCACTCCCGGCGAC
1024731 ATCCCCTGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.18, C:0.40, G:0.29, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAACG
Found at i:1025011 original size:29 final size:29
Alignment explanation
Indices: 1024950--1025033 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
1024940 ATGAATCCTT
** * **
1024950 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
1024979 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
1025008 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
1025034 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:1026323 original size:23 final size:23
Alignment explanation
Indices: 1026297--1026356 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1026287 CGTGAATTCA
*
1026297 GCTGTATTATTGCAACACTTATT
1 GCTGCATTATTGCAACACTTATT
* * *
1026320 GCTGCATTATTACAGCCCTTATT
1 GCTGCATTATTGCAACACTTATT
1026343 GCTGCATTATTGCA
1 GCTGCATTATTGCA
1026357 CTCCTTCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (23 bp):
GCTGCATTATTGCAACACTTATT
Found at i:1026814 original size:27 final size:29
Alignment explanation
Indices: 1026750--1026814 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
1026740 TATATTAAAA
1026750 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
** *
1026779 -AATTTTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1026805 AAATAGTTAA
1 AAATAATTAA
1026815 GTTATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.03
27 15 0.50
28 14 0.47
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1026999 original size:22 final size:23
Alignment explanation
Indices: 1026964--1027015 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
1026954 ACAAAAAATT
1026964 AGTTA-ATTAGTTTGGTAGTTTA
1 AGTTATATTAGTTTGGTAGTTTA
*
1026986 AGTTATATTA-TTTGTTAGTTTA
1 AGTTATATTAGTTTGGTAGTTTA
1027008 AGTTATAT
1 AGTTATAT
1027016 CATATAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (23 bp):
AGTTATATTAGTTTGGTAGTTTA
Found at i:1027239 original size:29 final size:29
Alignment explanation
Indices: 1027202--1027279 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
1027192 TAGTAATAAA
1027202 TTATAATTAAAAATCA-TTTATTAGTTTAA-G
1 TTAT-ATTAAAAAT-AGTTTATTAG-TTAACG
1027232 TTATATTAAAAAATAGTTTATTAGTTAACG
1 TTATATT-AAAAATAGTTTATTAGTTAACG
1027262 TTATATTAAAGAATAGTT
1 TTATATTAAA-AATAGTT
1027280 AAAGTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (29 bp):
TTATATTAAAAATAGTTTATTAGTTAACG
Found at i:1027248 original size:22 final size:22
Alignment explanation
Indices: 1027223--1027303 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
1027213 AATCATTTAT
*
1027223 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAGAA
1027245 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAGTTTA--AG-T----T-ATATTAAAGAA
*
1027275 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
1027297 TAGTTTA
1 TAGTTTA
1027304 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 24 0.50
23 1 0.02
24 2 0.04
25 1 0.02
27 1 0.02
28 2 0.04
29 1 0.02
30 16 0.33
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:1029758 original size:59 final size:59
Alignment explanation
Indices: 1029623--1029758 Score: 147
Period size: 59 Copynumber: 2.3 Consensus size: 59
1029613 AATATTTAGT
* * *
1029623 AATTCGACTATTTTAAATCATTAGTATCAAATAATTAAATATTAATAATAAATCATTATT
1 AATTTGACTATTATAAATCATTAGTATCAAATAATTAAATATT-ATAATAAATCATTATA
* *
1029683 AA--T-AATAATTAGTAAATCATTAGTATCAAATCATTAAATATT-TAA-AAATCATTAATA
1 AATTTGACT-ATTA-TAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATT-ATA
1029740 AATTTGACTATGTATAAAT
1 AATTTGACTAT-TATAAAT
1029759 TTAAACTCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
56 8 0.13
57 9 0.14
58 3 0.05
59 37 0.59
60 6 0.10
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (59 bp):
AATTTGACTATTATAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATTATA
Found at i:1029900 original size:3 final size:3
Alignment explanation
Indices: 1029885--1029979 Score: 70
Period size: 3 Copynumber: 32.7 Consensus size: 3
1029875 CTATTAAATC
* * * *
1029885 ATT ATT ATC ATT ATT ATT ATT A-A ATT ATT ATT ATC ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
1029932 A-A ATC ATT ATT ATC ATT ATT ATT A-A ATC ATT ATT ATA ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1029978 AT
1 AT
1029980 CAAATCATTA
Statistics
Matches: 72, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
2 3 0.04
3 69 0.96
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:1029900 original size:26 final size:26
Alignment explanation
Indices: 1029821--1030087 Score: 225
Period size: 26 Copynumber: 10.6 Consensus size: 26
1029811 ATTAGTAATA
*
1029821 ATTATTAAATCATTAATATTAAATTATT
1 ATTATTAAATCATTATTA-T-AATTATT
* * *
1029849 ATTATAAAATCATTACTA-AATAATT
1 ATTATTAAATCATTATTATAATTATT
* *
1029874 ACTATTAAATCATTATTATCATTATT
1 ATTATTAAATCATTATTATAATTATT
* * *
1029900 ATTATTAAATTATTATTATCATCATT
1 ATTATTAAATCATTATTATAATTATT
*
1029926 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTATTATAATTATT
*
1029949 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATTATT
* * * *
1029975 ATTATCAAATCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATTAT--T
* *
1030002 ATCATT-AA--A-TATT-TAA--ATC
1 ATTATTAAATCATTATTATAATTATT
*
1030021 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATTATT
* *
1030047 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATTATT
*
1030073 ATTATCAAATCATTA
1 ATTATTAAATCATTA
1030088 CTAAATCATC
Statistics
Matches: 199, Mismatches: 26, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.03
20 2 0.01
21 2 0.01
22 1 0.01
23 30 0.15
24 6 0.03
25 28 0.14
26 105 0.53
27 4 0.02
28 16 0.08
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.46
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATTATT
Found at i:1029902 original size:23 final size:23
Alignment explanation
Indices: 1029846--1029978 Score: 131
Period size: 23 Copynumber: 5.4 Consensus size: 23
1029836 ATATTAAATT
* * *
1029846 ATTATTATAAAATCATTACTAAATA
1 ATTATTATTAAATCATTA-T-TATC
*
1029871 ATTACTATTAAATCATTATTATC
1 ATTATTATTAAATCATTATTATC
*
1029894 ATTATTATTATTAAATTATTATTATCATC
1 ---ATTATTATTAAATCATTA-T-T-ATC
1029923 ATTATTATTAAATCATTATTATC
1 ATTATTATTAAATCATTATTATC
*
1029946 ATTATTATTAAATCATTATTATA
1 ATTATTATTAAATCATTATTATC
*
1029969 ATGATTATTA
1 ATTATTATTA
1029979 TCAAATCATT
Statistics
Matches: 93, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
23 36 0.39
24 2 0.02
25 17 0.18
26 33 0.35
27 1 0.01
28 1 0.01
29 3 0.03
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTATTATTAAATCATTATTATC
Found at i:1029989 original size:23 final size:23
Alignment explanation
Indices: 1029838--1030172 Score: 134
Period size: 26 Copynumber: 13.7 Consensus size: 23
1029828 AATCATTAAT
* *
1029838 ATTA-AATTATTATTATAAAATC
1 ATTATAATCATTATTATTAAATC
* *
1029860 ATTACTAAATAATTACTATTAAATC
1 ATTA-T-AATCATTATTATTAAATC
* *
1029885 ATTATTATCATTATTATTATTAAATT
1 ATTA-TA--ATCATTATTATTAAATC
1029911 ATTATTATCATCATTATTATTAAATC
1 ATTA-TA--ATCATTATTATTAAATC
*
1029937 ATTATTATCATTATTATTAAATC
1 ATTATAATCATTATTATTAAATC
* *
1029960 ATTATTATAATGATTATTATCAAATC
1 ---ATTATAATCATTATTATTAAATC
* *
1029986 ATTACTAAATCATCAAATCATTAAAT-
1 ATTA-T-AATCAT--TATTATTAAATC
*
1030012 ATT-TAAATCATTATTA--AATCATT
1 ATTAT-AATCATTATTATTAA--ATC
* *
1030035 ATTATAATGATTATTACTAAATC
1 ATTATAATCATTATTATTAAATC
* *
1030058 ATTATTATAATGATTATTATCAAATC
1 ---ATTATAATCATTATTATTAAATC
* *
1030084 ATTACTAAATCATCAAATAATTAAAT-
1 ATTA-T-AATCAT--TATTATTAAATC
*
1030110 ATTA-AAT--TTATTATTAAATTT
1 ATTATAATCATTATTATTAAA-TC
*
1030131 ATTATTAAATCATTA-T-TTAAATT
1 ATTA-T-AATCATTATTATTAAATC
*
1030154 ATTATTAAATCATTTTTAT
1 ATTA-T-AATCATTATTAT
1030173 GGTTAATTGA
Statistics
Matches: 249, Mismatches: 30, Indels: 65
0.72 0.09 0.19
Matches are distributed among these distances:
19 8 0.03
20 3 0.01
21 5 0.02
22 9 0.04
23 59 0.24
24 21 0.08
25 35 0.14
26 93 0.37
27 16 0.06
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (23 bp):
ATTATAATCATTATTATTAAATC
Found at i:1030026 original size:98 final size:97
Alignment explanation
Indices: 1029924--1030160 Score: 342
Period size: 98 Copynumber: 2.5 Consensus size: 97
1029914 ATTATCATCA
1029924 TTATTATTAAATCATTATT-ATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCAT
1 TTATTATTAAATCATTATTAATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCAT
*
1029988 TACTAAATCATCAAATCATTAAATATTTAAATC
66 TACTAAATCATCAAATAATTAAATA-TTAAATC
* *
1030021 --ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATC
1 TTATTATTAAATCATTA-T-TAATCATTATTATTAAATCATTATTATAATGATTATTATCAAATC
1030084 ATTACTAAATCATCAAATAATTAAATATTAAAT-
64 ATTACTAAATCATCAAATAATTAAATATTAAATC
* *
1030117 TTATTATTAAATTTATTATTAAATCATTA-T-TTAAATTATTATTA
1 TTATTATTAAA-TCATTATT-AATCATTATTATTAAATCATTATTA
1030161 AATCATTTTT
Statistics
Matches: 126, Mismatches: 7, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
95 15 0.12
96 13 0.10
97 9 0.07
98 84 0.67
99 5 0.04
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (97 bp):
TTATTATTAAATCATTATTAATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATAATTAAATATTAAATC
Found at i:1030124 original size:12 final size:12
Alignment explanation
Indices: 1030109--1030163 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
1030099 AATAATTAAA
1030109 TATTAAATTTAT
1 TATTAAATTTAT
1030121 TATTAAATTTAT
1 TATTAAATTTAT
*
1030133 TATTAAA-TCAT
1 TATTAAATTTAT
1030144 TATTTAAA-TTAT
1 TA-TTAAATTTAT
1030156 TATTAAAT
1 TATTAAAT
1030164 CATTTTTATG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTAAATTTAT
Found at i:1030362 original size:17 final size:18
Alignment explanation
Indices: 1030342--1030376 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1030332 TATTAGTAAA
1030342 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
1030359 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
1030377 ACTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:1030451 original size:49 final size:49
Alignment explanation
Indices: 1030374--1030610 Score: 438
Period size: 49 Copynumber: 4.8 Consensus size: 49
1030364 ATTATTAATA
*
1030374 ATTACTAATCATTACTATCAAATAATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1030423 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
1030472 ATTACTAATCATTACTATCAAATCTTTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
1030521 ATTAATAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1030570 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1030611 GATGGGTGCC
Statistics
Matches: 182, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 182 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:1034039 original size:22 final size:21
Alignment explanation
Indices: 1034005--1034045 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1033995 CGTATTTATG
1034005 CCTTCTTCATTTCCTTTCTTTT
1 CCTTCTTCATTT-CTTTCTTTT
**
1034027 CCTTCTTTGTTTCTTTCTT
1 CCTTCTTCATTTCTTTCTT
1034046 CGAATCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.66
Consensus pattern (21 bp):
CCTTCTTCATTTCTTTCTTTT
Found at i:1034421 original size:28 final size:28
Alignment explanation
Indices: 1034383--1034436 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1034373 TAAATATAAT
1034383 ATATAACTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
1034411 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
1034437 ATTTATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:1034443 original size:28 final size:28
Alignment explanation
Indices: 1034378--1034443 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
1034368 TTATATAAAT
1034378 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
1034406 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
1034434 ATAATTTATA
1 ATAATATATA
1034444 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:1034446 original size:21 final size:21
Alignment explanation
Indices: 1034413--1034461 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1034403 CTAATATAAT
1034413 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1034434 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1034455 ATTAACT
1 A-TAACT
1034462 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1035056 original size:29 final size:29
Alignment explanation
Indices: 1035014--1035069 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1035004 CGAGAACGTT
1035014 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
1035043 GGACGCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
1035070 GCTGGTTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.39, T:0.14
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTATAA
Found at i:1043861 original size:15 final size:13
Alignment explanation
Indices: 1043841--1043878 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
1043831 CTTTCTTAGC
1043841 ATTATCATATATATT
1 ATTATCAT-TAT-TT
1043856 ATTATCATTATTT
1 ATTATCATTATTT
1043869 A-TATCATTAT
1 ATTATCATTAT
1043879 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 3 0.13
15 8 0.35
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATCATTATTT
Found at i:1044023 original size:2 final size:2
Alignment explanation
Indices: 1044016--1044041 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1044006 CATATCCATC
1044016 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
1044042 TGTATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1044177 original size:23 final size:23
Alignment explanation
Indices: 1044151--1044232 Score: 128
Period size: 23 Copynumber: 3.6 Consensus size: 23
1044141 CGTATACATG
* *
1044151 CACCGAAGTGCCGCGTAGAATTA
1 CACCGTAGTGCCACGTAGAATTA
* *
1044174 CACCGTAGTGCTACGTAGAATTG
1 CACCGTAGTGCCACGTAGAATTA
1044197 CACCGTAGTGCCACGTAGAATTA
1 CACCGTAGTGCCACGTAGAATTA
1044220 CACCGTAGTGCCA
1 CACCGTAGTGCCA
1044233 TATAATAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (23 bp):
CACCGTAGTGCCACGTAGAATTA
Found at i:1049143 original size:18 final size:18
Alignment explanation
Indices: 1049119--1049163 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1049109 ACTTTCTTAG
1049119 CATTATCATATATATTAT-T
1 CATTATCAT-TAT-TTATAT
1049138 -ATTATCATTATTTATAT
1 CATTATCATTATTTATAT
1049155 CATTATCAT
1 CATTATCAT
1049164 CAAATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 16 0.67
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (18 bp):
CATTATCATTATTTATAT
Found at i:1049147 original size:12 final size:13
Alignment explanation
Indices: 1049119--1049160 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
1049109 ACTTTCTTAG
*
1049119 CATTATCATATAT
1 CATTATTATATAT
1049132 -ATTATTAT-TAT
1 CATTATTATATAT
1049143 CATTATT-TATAT
1 CATTATTATATAT
1049155 CATTAT
1 CATTAT
1049161 CATCAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (13 bp):
CATTATTATATAT
Found at i:1049159 original size:21 final size:22
Alignment explanation
Indices: 1049129--1049175 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1049119 CATTATCATA
* *
1049129 TATATTATTATTATC-ATTATT
1 TATATCATTATCATCAATTATT
1049150 TATATCATTATCATCAAATTATT
1 TATATCATTATCATC-AATTATT
1049173 TAT
1 TAT
1049176 CACATGATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
23 9 0.41
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATCATTATCATCAATTATT
Found at i:1049437 original size:23 final size:23
Alignment explanation
Indices: 1049419--1049479 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1049409 CTCGTATACA
*
1049419 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1049442 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1049465 TGTACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1049480 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1053629 original size:21 final size:20
Alignment explanation
Indices: 1053590--1053629 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1053580 GGAATTATGG
*
1053590 TATTTCTGATTTAATAAAAT
1 TATTTCTGATTTAAGAAAAT
*
1053610 TATTTCTTGATTTTAGAAAA
1 TATTTC-TGATTTAAGAAAA
1053630 AAATAGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TATTTCTGATTTAAGAAAAT
Found at i:1053795 original size:21 final size:22
Alignment explanation
Indices: 1053762--1053802 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1053752 GGTTAAAATA
1053762 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
1053784 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
1053803 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:1054487 original size:19 final size:19
Alignment explanation
Indices: 1054431--1054493 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1054421 CTATTTAAAC
**
1054431 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1054451 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1054471 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1054490 TAAA
1 TAAA
1054494 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1054521 original size:64 final size:68
Alignment explanation
Indices: 1054396--1054593 Score: 199
Period size: 64 Copynumber: 2.8 Consensus size: 68
1054386 TAAAACATCT
* * ** *
1054396 TAAATTCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC--CTA-AAAAAT-AATATAAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAAT
*
1054456 ATTC
65 ATCC
1054460 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC------AAAGATAAAA-ATAAA
1054525 AATAATATCC
59 AATAATATCC
* *
1054535 TAAAACTTAATTAAAATACTAAAAGCCTATTTAAACTAAAATACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAA-CCTATTTAAACTAAAATACAAAGATAAAA-ATAA
1054594 TGTTTAAAAT
Statistics
Matches: 113, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
63 5 0.04
64 35 0.31
70 15 0.13
72 1 0.01
73 4 0.04
74 2 0.02
75 32 0.28
76 19 0.17
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.29
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAATA
TCC
Found at i:1056355 original size:21 final size:21
Alignment explanation
Indices: 1056331--1056387 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
1056321 AAAGTTCGCT
**
1056331 AAAAAATAAAAAAATAAAATG
1 AAAAAATAAAAAAATAAAAAC
*
1056352 AAAATA-AAAAAAATAAAAAC
1 AAAAAATAAAAAAATAAAAAC
*
1056372 AAAAATATAACAAAAT
1 AAAAA-ATAAAAAAAT
1056388 GGGTTGCCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 16 0.55
21 6 0.21
22 7 0.24
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.14
Consensus pattern (21 bp):
AAAAAATAAAAAAATAAAAAC
Found at i:1060289 original size:15 final size:15
Alignment explanation
Indices: 1060269--1060299 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1060259 TTCCTCTTGT
1060269 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
1060284 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
1060299 T
1 T
1060300 GTTTTTCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.42
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:1061979 original size:15 final size:17
Alignment explanation
Indices: 1061959--1062006 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 17
1061949 AAAATAAAAT
1061959 AAATAA-ATAA-AAGAA
1 AAATAATATAATAAGAA
1061974 AAATAATATAATAAGAA
1 AAATAATATAATAAGAA
*
1061991 ATATTAATAGTAATAA
1 A-AATAATA-TAATAA
1062007 ATATAAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.21
16 4 0.14
17 6 0.21
18 6 0.21
19 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (17 bp):
AAATAATATAATAAGAA
Found at i:1062757 original size:68 final size:73
Alignment explanation
Indices: 1062671--1062876 Score: 264
Period size: 68 Copynumber: 2.8 Consensus size: 73
1062661 AAACTAAAAC
* **
1062671 ATCTTAAATCCTAATTAAAACACTCAAAA-CTATTTAAACTAAAATACCTA-A-AAATAATAAAA
1 ATCTTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAT-ATAAAA
1062733 TAT-AAT-AT
64 TATAAATAAT
1062741 -TC-TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAATATAAAATA
1 ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAATATAAAATA
1062804 TAAAAATAAT
66 T--AAATAAT
* *
1062814 ATCTTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAA
1 ATCTTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGAT-AAATATAA
1062877 TGTTTAAAAT
Statistics
Matches: 120, Mismatches: 5, Indels: 15
0.86 0.04 0.11
Matches are distributed among these distances:
67 4 0.03
68 38 0.32
69 12 0.10
70 4 0.03
72 3 0.03
73 2 0.02
74 2 0.02
75 18 0.15
76 29 0.24
77 8 0.07
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (73 bp):
ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAATATAAAATA
TAAATAAT
Found at i:1062835 original size:75 final size:79
Alignment explanation
Indices: 1062721--1062876 Score: 250
Period size: 76 Copynumber: 2.0 Consensus size: 79
1062711 AAAATACCTA
*
1062721 AAAATAATAAAATATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATA
1 AAAATAATAAAATATAATATTCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATA
1062785 CAAAGAT-AAATAT
66 CAAAGATAAAATAT
*
1062798 AAAAT-ATAAAA-ATAATA-TCTTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAAT
1 AAAATAATAAAATATAATATTC-TAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAAT
1062860 ACAAAGATAAAATAT
65 ACAAAGATAAAATAT
1062875 AA
1 AA
1062877 TGTTTAAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
74 2 0.03
75 24 0.32
76 35 0.47
77 13 0.18
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.29
Consensus pattern (79 bp):
AAAATAATAAAATATAATATTCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATA
CAAAGATAAAATAT
Found at i:1065118 original size:56 final size:56
Alignment explanation
Indices: 1065051--1065162 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
1065041 GCATGTGTGT
1065051 TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
1 TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
1065107 TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
1 TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
1065163 AAGATGGTAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (56 bp):
TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
Found at i:1066324 original size:47 final size:49
Alignment explanation
Indices: 1066270--1066482 Score: 218
Period size: 51 Copynumber: 4.3 Consensus size: 49
1066260 AAATTATAAT
*
1066270 TTAACACATACTTACACCGGTGT-AGTGAATAAAATAAAAATGTAACAA
1 TTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAATGTAACAA
* ** * * *
1066318 TT-ACACATAATTACACTAGTG-CAGTAAATAAAAGAAAAATGTAGAACAC
1 TTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAATGT--AACAA
* * *
1066367 TTAACACATACTTACATCGGTATAAGTAAATAAAATAAAAAAGTATA-ATA
1 TTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAATGTA-ACA-A
* * *
1066417 CTTAAGACATACTTACACTGGTGTAAGTAAATAAAATAACAAATTGTAACAC
1 -TTAACACATACTTACACCGGTGTAAGTAAATAAAATAA-AAA-TGTAACAA
1066469 TTAACACATACTTA
1 TTAACACATACTTA
1066483 TATTGGTATA
Statistics
Matches: 132, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
47 34 0.26
48 2 0.02
49 8 0.06
50 15 0.11
51 65 0.49
52 4 0.03
53 4 0.03
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.26
Consensus pattern (49 bp):
TTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAATGTAACAA
Found at i:1066468 original size:102 final size:97
Alignment explanation
Indices: 1066270--1066492 Score: 254
Period size: 102 Copynumber: 2.2 Consensus size: 97
1066260 AAATTATAAT
* * * *
1066270 TTAACACATACTTACACCGGTGT-AGTGAATAAAATAAAAATGTAACAATTACACATAATTACAC
1 TTAACACATACTTACATCGGTATAAGTAAATAAAATAAAAAAGTAACAATTACACATAATTACAC
*
1066334 TAGTGCAGTAAATAAAAGAAAAATGTAGAACAC
66 TAGTGAAGTAAATAAAAGAAAAATGTA-AACAC
* *
1066367 TTAACACATACTTACATCGGTATAAGTAAATAAAATAAAAAAGTATA-ATACTTAAGACATACTT
1 TTAACACATACTTACATCGGTATAAGTAAATAAAATAAAAAAGTA-ACA-A-TT-ACACATAATT
* *
1066431 ACACTGGTGTAAGTAAATAAAATAACAAATTGT-AACAC
62 ACACTAGTG-AAGTAAATAAAAGAA-AAA-TGTAAACAC
* *
1066469 TTAACACATACTTATATTGGTATA
1 TTAACACATACTTACATCGGTATA
1066493 GTACGTGCAT
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
97 21 0.20
98 20 0.19
99 2 0.02
100 2 0.02
101 16 0.15
102 40 0.37
103 3 0.03
104 3 0.03
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.27
Consensus pattern (97 bp):
TTAACACATACTTACATCGGTATAAGTAAATAAAATAAAAAAGTAACAATTACACATAATTACAC
TAGTGAAGTAAATAAAAGAAAAATGTAAACAC
Found at i:1066847 original size:16 final size:18
Alignment explanation
Indices: 1066826--1066862 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1066816 ATCATTTAGT
*
1066826 ATTAAC-TATTTAAT-TA
1 ATTAACTTATTAAATGTA
1066842 ATTAACTTATTAAATGTA
1 ATTAACTTATTAAATGTA
1066860 ATT
1 ATT
1066863 GTTAAAACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTAACTTATTAAATGTA
Found at i:1071419 original size:30 final size:31
Alignment explanation
Indices: 1071362--1071420 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1071352 TTAATGGCAG
*
1071362 AGTGAGCAAAATGATTAAATCTGAAAGTTTC
1 AGTGAGCAAAATGATCAAATCTGAAAGTTTC
*
1071393 AGTGAGCAAATTGATCAAAT-TGAAAGTT
1 AGTGAGCAAAATGATCAAATCTGAAAGTT
1071421 GAGTGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.29
Consensus pattern (31 bp):
AGTGAGCAAAATGATCAAATCTGAAAGTTTC
Found at i:1072340 original size:165 final size:157
Alignment explanation
Indices: 1072068--1072389 Score: 556
Period size: 165 Copynumber: 2.0 Consensus size: 157
1072058 TTTCCAAAAC
1072068 GGGTCTGTTCGAGAAGAAAGGGCACGTGGCTTTTGTTCATTAGCATCCGTGGCCGTCATGTTCGT
1 GGGTCTGTTCGAGAAGAAAGGGCACGTGGCTTTTGTTCATTAGCATCCGTGGCCGTCATGTTCGT
1072133 CGTTGTTCTTTACGGTGTTTTGAGATGCGAAAGCGTCTGGGTTCATCTGGGTTCGACTATGGTAT
66 CGTTGTTCTTTACGGTGTTTTGAGATGCGAAAGCGTCTGGGTTCATCTGGGTTCGACTATGG--T
1072198 TGGGCATGCTCTGGATGCAAAATACGTACGTCGGT
129 TGGG---G--CTGGATGC-AAATACGTACGTCGGT
1072233 GGGTCTGTTCGAGAAGAAAGGGCACGTGGCCTTTTGTTCATTAGCATCCGTGGCCGTCATGTTCG
1 GGGTCTGTTCGAGAAGAAAGGGCACGTGG-CTTTTGTTCATTAGCATCCGTGGCCGTCATGTTCG
1072298 TCG-TGTTCTTTACGGTGTTTTGAGATGCGAAAGCGTCTGGGTTCATCTGGGTTCGACTATGGTT
65 TCGTTGTTCTTTACGGTGTTTTGAGATGCGAAAGCGTCTGGGTTCATCTGGGTTCGACTATGGTT
1072362 GGGGCTGGATGCAAATACGTACGTCGGT
130 GGGGCTGGATGCAAATACGTACGTCGGT
1072390 CATGATTCTG
Statistics
Matches: 156, Mismatches: 0, Indels: 10
0.94 0.00 0.06
Matches are distributed among these distances:
157 16 0.10
158 8 0.05
160 1 0.01
163 5 0.03
165 88 0.56
166 38 0.24
ACGTcount: A:0.17, C:0.18, G:0.32, T:0.32
Consensus pattern (157 bp):
GGGTCTGTTCGAGAAGAAAGGGCACGTGGCTTTTGTTCATTAGCATCCGTGGCCGTCATGTTCGT
CGTTGTTCTTTACGGTGTTTTGAGATGCGAAAGCGTCTGGGTTCATCTGGGTTCGACTATGGTTG
GGGCTGGATGCAAATACGTACGTCGGT
Found at i:1080036 original size:20 final size:21
Alignment explanation
Indices: 1079998--1080036 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1079988 ATACTTTAGA
*
1079998 GAAATACTAAAACATAATATG
1 GAAATACTAAAACAAAATATG
*
1080019 GAAATA-TAAAATAAAATA
1 GAAATACTAAAACAAAATA
1080037 CTTATAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (21 bp):
GAAATACTAAAACAAAATATG
Found at i:1080480 original size:27 final size:26
Alignment explanation
Indices: 1080444--1080502 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1080434 TAAGTAATTT
* *
1080444 ATTTTCTTTTTCTATAAAATTTTTTAA
1 ATTTTATTTTT-TATAAAATTTTATAA
* *
1080471 GTTTTATTTTTTCTAAAATTTTATAA
1 ATTTTATTTTTTATAAAATTTTATAA
1080497 ATTTTA
1 ATTTTA
1080503 AATTAAGCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTTATTTTTTATAAAATTTTATAA
Found at i:1094344 original size:18 final size:18
Alignment explanation
Indices: 1094323--1094358 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1094313 AGACAGATAG
1094323 ACAAAAGAAGAAAACAAA
1 ACAAAAGAAGAAAACAAA
1094341 ACAAAAGAAGAAAACAAA
1 ACAAAAGAAGAAAACAAA
1094359 GGGCCGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (18 bp):
ACAAAAGAAGAAAACAAA
Found at i:1098049 original size:25 final size:28
Alignment explanation
Indices: 1097994--1098048 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1097984 CATTTAAGCC
*
1097994 TTATTATTATTAGTTAAATAAAAAACTT
1 TTATTATTATTAGGTAAATAAAAAACTT
*
1098022 TTATTATTATT-GGTAAA-AAATAACTT
1 TTATTATTATTAGGTAAATAAAAAACTT
1098048 T
1 T
1098049 AGCTTTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.36
27 5 0.20
28 11 0.44
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (28 bp):
TTATTATTATTAGGTAAATAAAAAACTT
Found at i:1101035 original size:10 final size:10
Alignment explanation
Indices: 1101020--1101048 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1101010 GGTTTATTTG
1101020 TTCATTTTAA
1 TTCATTTTAA
1101030 TTCATTTTAA
1 TTCATTTTAA
1101040 TTCATTTTA
1 TTCATTTTA
1101049 TGTATAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCATTTTAA
Found at i:1101221 original size:19 final size:19
Alignment explanation
Indices: 1101194--1101232 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1101184 TATCTTTGTA
*
1101194 ATTAGTTTAAATAGGTTTT
1 ATTAGTTTAAATAAGTTTT
* *
1101213 ATTATTTTAATTAAGTTTT
1 ATTAGTTTAAATAAGTTTT
1101232 A
1 A
1101233 CGATATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (19 bp):
ATTAGTTTAAATAAGTTTT
Found at i:1101391 original size:64 final size:64
Alignment explanation
Indices: 1101251--1101399 Score: 171
Period size: 63 Copynumber: 2.3 Consensus size: 64
1101241 TTTTTATATT
* *
1101251 TTATCTTTG-TTTTAGGTATTTTAGTTTAAATAAGTTTTAGTATTTTAATTAGAATTTAGAATA
1 TTATATTTGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGAATA
* * *
1101314 TTATATTAT-TTTTTAGGTATTTTGGTTTAAAT-AGTTTAAGTGTTTTAATTAGGATTTA-AGAT
1 TTATATT-TGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGA-AT
*
1101376 G
64 A
* *
1101377 TTTTAGTTTGTTTTTAGGAATTT
1 TTATA-TTTGTTTTTAGGTATTT
1101400 GAAGGCTATA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 36 0.49
64 36 0.49
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (64 bp):
TTATATTTGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGAATA
Found at i:1101710 original size:161 final size:161
Alignment explanation
Indices: 1101538--1101860 Score: 574
Period size: 161 Copynumber: 2.0 Consensus size: 161
1101528 TTGGTTATGC
* *
1101538 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAGCGAAGACTCAATTCTAAACGTGAGAATTGTAA
1 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGACTCAATTCTAAACGTGAAAATTGTAA
*
1101603 GGTACTTAAATCGCTTCAGATTTTTCTCTCTGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
66 GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
*
1101668 TTGACATTGATCCGGATATTGTTATGGTTAA
131 TTGACATTGATCCGGATATTGTTACGGTTAA
* *
1101699 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGGCTCAATTTTAAACGTGAAAATTGTAA
1 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGACTCAATTCTAAACGTGAAAATTGTAA
*
1101764 GGTACTTAAATCGCTTCGGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
66 GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
*
1101829 TTGACATTGGTCCGGATATTGTTACGGTTAA
131 TTGACATTGATCCGGATATTGTTACGGTTAA
1101860 T
1 T
1101861 GTTTGAAGAA
Statistics
Matches: 154, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
161 154 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (161 bp):
TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGACTCAATTCTAAACGTGAAAATTGTAA
GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
TTGACATTGATCCGGATATTGTTACGGTTAA
Found at i:1102161 original size:17 final size:17
Alignment explanation
Indices: 1102120--1102162 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1102110 AATCTCTTTA
1102120 ATTTGTTTTTTAATTATT
1 ATTT-TTTTTTAATTATT
*
1102138 -TTCTTTTTTTAATTCTT
1 ATT-TTTTTTTAATTATT
1102155 ATTTTTTT
1 ATTTTTTT
1102163 ACTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTTTTTTTAATTATT
Found at i:1102680 original size:25 final size:25
Alignment explanation
Indices: 1102642--1102691 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1102632 TTGTTCTTCT
1102642 TTTGGCTCTACTGAGCTAAAGAGAA
1 TTTGGCTCTACTGAGCTAAAGAGAA
*
1102667 TTTGGCTCTGCTGAGCTAAAGAGAA
1 TTTGGCTCTACTGAGCTAAAGAGAA
1102692 ATGTACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (25 bp):
TTTGGCTCTACTGAGCTAAAGAGAA
Found at i:1103685 original size:127 final size:127
Alignment explanation
Indices: 1103457--1103685 Score: 307
Period size: 127 Copynumber: 1.8 Consensus size: 127
1103447 TCATGGCTGC
* * *
1103457 TTCATCACATCTTCATCACGGCTATTGCTCTTCGATTTGGATTTCGATTCTGGTGAGGTTGTTCC
1 TTCATCACATCTTCATCACGGCTATTGCTCTTCGATTTGGACTTCGATTCTAGTGAGATTGTTCC
* * ** * *
1103522 AGTATTGTTCTCGATTACATTGGTTTCCTACTTTTTGATCTGGATATTCGATTCCTGATTGT
66 AGTATTGTTCTCGATTAAACTGGCGTACTACATTTTGATCTGGATATTCGATTCCTGATTGT
* *
1103584 TTCATCACATCTTTATCACTG-TAGTTGCTCTTCGATTTGGACTTCGATTCTAGTGAGATTGTTC
1 TTCATCACATCTTCATCACGGCTA-TTGCTCTTCGATTTGGACTTCGATTCTAGTGAGATTGTTC
* * * *
1103648 TAGTTTTGTTCTCGATTAAACTGGCGTATTGCATTTTG
65 CAGTATTGTTCTCGATTAAACTGGCGTACTACATTTTG
1103686 TGCCTTTTTC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
126 2 0.02
127 84 0.98
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (127 bp):
TTCATCACATCTTCATCACGGCTATTGCTCTTCGATTTGGACTTCGATTCTAGTGAGATTGTTCC
AGTATTGTTCTCGATTAAACTGGCGTACTACATTTTGATCTGGATATTCGATTCCTGATTGT
Found at i:1111929 original size:25 final size:25
Alignment explanation
Indices: 1111880--1111929 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1111870 TTGTCGTTGC
*
1111880 TTTCAAGCATTGGATCGATGACATA
1 TTTCAAGCATTGGATCGACGACATA
* *
1111905 TTTCAAGCATTGGCTCGACGGCATA
1 TTTCAAGCATTGGATCGACGACATA
1111930 ACGTAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (25 bp):
TTTCAAGCATTGGATCGACGACATA
Found at i:1114201 original size:37 final size:38
Alignment explanation
Indices: 1114146--1114229 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
1114136 TGGTAACCAA
1114146 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
1114183 CTTTGAAAAATA-GTTTTTCAAAGTTTGTTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
1114220 -GTTGAAAAAT
1 CTTTGAAAAAT
1114230 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1118461 original size:31 final size:31
Alignment explanation
Indices: 1118423--1118517 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
1118413 GAACCTCGGC
* *
1118423 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
1118454 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
1118485 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
1118516 AA
1 AA
1118518 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:1118683 original size:17 final size:19
Alignment explanation
Indices: 1118651--1118686 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1118641 CATATATCTC
1118651 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
1118670 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
1118687 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:1119282 original size:64 final size:65
Alignment explanation
Indices: 1119174--1119297 Score: 180
Period size: 64 Copynumber: 1.9 Consensus size: 65
1119164 CAATGAAGGT
* * * *
1119174 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGT-TTTTATTTAATGGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCCATTCGATGTGTTCTATTTAATGGGG
*
1119238 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTGTTCTATTTAA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCC-ATTCGATGTGTTCTATTTAA
1119298 ATTCATACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 5 0.09
64 39 0.74
65 9 0.17
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCCATTCGATGTGTTCTATTTAATGGGG
Found at i:1119309 original size:64 final size:63
Alignment explanation
Indices: 1119177--1119333 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 63
1119167 TGAAGGTATG
* * * * *
1119177 CATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTAATGGGGATG
1 CATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTCTATTTAAT-GGCATA
* * *
1119241 CATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTGTTCTATTTAAAT-TCAT
1 CATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGT-TTCTATTT-AATGGCAT
1119304 A
63 A
* *
1119305 CATCGATGCACTGCATGTGCATCGATGCA
1 CATCGATGCACTACTTGTGCATCGATGCA
1119334 CCTTAAACAA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
63 5 0.06
64 64 0.81
65 7 0.09
66 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (63 bp):
CATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTCTATTTAATGGCATA
Found at i:1122614 original size:18 final size:19
Alignment explanation
Indices: 1122576--1122614 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1122566 ATCAGAAAAG
* *
1122576 AAGCCCTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
1122595 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
1122613 AA
1 AA
1122615 AAGAAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.56, C:0.18, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:1126574 original size:21 final size:20
Alignment explanation
Indices: 1126550--1126613 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1126540 AACTTTGAAA
1126550 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1126571 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
1126585 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1126606 AAATGTTT
1 AAATGTTT
1126614 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1126588 original size:35 final size:36
Alignment explanation
Indices: 1126542--1126663 Score: 158
Period size: 35 Copynumber: 3.4 Consensus size: 36
1126532 TGGTAACCAA
1126542 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
1126579 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* * *
1126614 CTTTGAAAAATAATTTTTCAAAGTTTAGTAGATGTTT
1 CTTTGAAAAATGA-TTTTCAAAGTTTGGTAAATGTTT
* *
1126651 -GTTAAAAAATGAT
1 CTTTGAAAAATGAT
1126664 AATGAGATAA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 35 0.47
36 14 0.19
37 26 0.35
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1133616 original size:29 final size:30
Alignment explanation
Indices: 1133576--1133646 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
1133566 AAAAGAATAT
*
1133576 AAAATATATTTTATTCTTATTTTAA-ATTA
1 AAAATATATTTTATTCTTATCTTAACATTA
* *
1133605 AAAATATATTTTATTGTTATCTTAACTTTTA
1 AAAATATATTTTATTCTTATCTTAAC-ATTA
1133636 AAAATATATTT
1 AAAATATATTT
1133647 AAACATCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 23 0.62
31 14 0.38
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (30 bp):
AAAATATATTTTATTCTTATCTTAACATTA
Found at i:1133762 original size:29 final size:28
Alignment explanation
Indices: 1133729--1133831 Score: 124
Period size: 29 Copynumber: 3.7 Consensus size: 28
1133719 TTTATAAAAG
1133729 TTAAAATAAGAATAAAATATACTTTTAAT
1 TTAAAATAAGAATAAAATATA-TTTTAAT
1133758 TTAAAATAAGAATAAAATATATTTTTAAT
1 TTAAAATAAGAATAAAATATA-TTTTAAT
*
1133787 TTAAAATAA-AAT---ATATATTTTTAT
1 TTAAAATAAGAATAAAATATATTTTAAT
**
1133811 ATTAAAATAATTATAAAATAT
1 -TTAAAATAAGAATAAAATAT
1133832 TTTAAGCTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
24 6 0.09
25 14 0.21
26 2 0.03
28 3 0.05
29 41 0.62
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (28 bp):
TTAAAATAAGAATAAAATATATTTTAAT
Found at i:1133888 original size:2 final size:2
Alignment explanation
Indices: 1133881--1133919 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1133871 TGATAAAGAT
1133881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1133920 TTGTACATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1134002 original size:28 final size:30
Alignment explanation
Indices: 1133942--1134004 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1133932 ATAAAAAATG
*
1133942 TATTTAATAAGTTAAGACAAAATTAAAATA
1 TATTTAATAAGTTAAGACAAAATTAAAAGA
*
1133972 TATTTAATAAGTTTA-A-AAAA-TAAAAGGA
1 TATTTAATAAGTTAAGACAAAATTAAAA-GA
1134000 TATTT
1 TATTT
1134005 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 10 0.33
29 1 0.03
30 14 0.47
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (30 bp):
TATTTAATAAGTTAAGACAAAATTAAAAGA
Found at i:1134008 original size:30 final size:29
Alignment explanation
Indices: 1133929--1133996 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
1133919 TTTGTACATT
* *
1133929 AAAATAAAAAATGTATTTAATAAGTTAAGAC
1 AAAAT-AAAAATATATTTAATAAGTTTA-AC
*
1133960 AAAATTAAAATATATTTAATAAGTTTAA-
1 AAAATAAAAATATATTTAATAAGTTTAAC
1133988 AAAATAAAA
1 AAAATAAAA
1133997 GGATATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 8 0.24
29 1 0.03
30 19 0.58
31 5 0.15
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAATAAAAATATATTTAATAAGTTTAAC
Found at i:1141710 original size:2 final size:2
Alignment explanation
Indices: 1141703--1141729 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1141693 TTCAAAAGGT
1141703 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1141730 CAGGGGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1146438 original size:10 final size:10
Alignment explanation
Indices: 1146423--1146467 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
1146413 TTTTTTTTTA
1146423 ATTAAAATAT
1 ATTAAAATAT
1146433 ATT-AAAT-T
1 ATTAAAATAT
*
1146441 A-TAAAATAG
1 ATTAAAATAT
*
1146450 ATAAAAATAT
1 ATTAAAATAT
1146460 ATTAAAAT
1 ATTAAAAT
1146468 TAGATAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
7 1 0.04
8 6 0.21
9 5 0.18
10 16 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:1146473 original size:21 final size:22
Alignment explanation
Indices: 1146442--1146487 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
1146432 TATTAAATTA
1146442 TAAAATAGATAAA-AAT-ATAT
1 TAAAATAGATAAATAATCATAT
1146462 TAAAATTAGATAAATAATCATAT
1 TAAAA-TAGATAAATAATCATAT
1146485 TAA
1 TAA
1146488 TTTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 8 0.35
22 3 0.13
23 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
TAAAATAGATAAATAATCATAT
Found at i:1146521 original size:26 final size:26
Alignment explanation
Indices: 1146492--1146552 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1146482 TATTAATTTT
1146492 TTTTTGTAATTTTTCGGGTTTTTATA
1 TTTTTGTAATTTTTCGGGTTTTTATA
* * * * *
1146518 TTTTTATATTTTTTCTGTTTTTTTTA
1 TTTTTGTAATTTTTCGGGTTTTTATA
*
1146544 TATTTGTAA
1 TTTTTGTAA
1146553 AATTAATATT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.16, C:0.03, G:0.10, T:0.70
Consensus pattern (26 bp):
TTTTTGTAATTTTTCGGGTTTTTATA
Found at i:1168340 original size:30 final size:30
Alignment explanation
Indices: 1168306--1168377 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
1168296 CATGGGGTCG
***
1168306 CCGAACCAGCTCATAATGTTACGCATGGGA
1 CCGAACCAGCTCATAACAATACGCATGGGA
*
1168336 CCGAACCAGCTCATTACAATACGCATGGGA
1 CCGAACCAGCTCATAACAATACGCATGGGA
1168366 CCGAACCAGCTC
1 CCGAACCAGCTC
1168378 GTGATCATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.31, C:0.32, G:0.21, T:0.17
Consensus pattern (30 bp):
CCGAACCAGCTCATAACAATACGCATGGGA
Found at i:1180701 original size:22 final size:23
Alignment explanation
Indices: 1180658--1180708 Score: 86
Period size: 22 Copynumber: 2.2 Consensus size: 23
1180648 TGCTCTTCAC
1180658 TCAAACTAACTTGATATATATAGT
1 TCAAACTAACTTGA-ATATATAGT
1180682 TCAAACTAACTTG-ATATATAGT
1 TCAAACTAACTTGAATATATAGT
1180704 TCAAA
1 TCAAA
1180709 GATATAACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 14 0.52
24 13 0.48
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (23 bp):
TCAAACTAACTTGAATATATAGT
Found at i:1184675 original size:4 final size:4
Alignment explanation
Indices: 1184666--1184692 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1184656 CAATGCATGT
1184666 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1184693 CAAAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1184833 original size:13 final size:13
Alignment explanation
Indices: 1184815--1184840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1184805 TTAGATTAAC
1184815 AAATATATGAATT
1 AAATATATGAATT
1184828 AAATATATGAATT
1 AAATATATGAATT
1184841 GATAAGATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AAATATATGAATT
Found at i:1186602 original size:25 final size:24
Alignment explanation
Indices: 1186567--1186613 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1186557 ATTCATTGGA
* *
1186567 TAAATTTAAAATATTGATTTTATT
1 TAAATTTAAAAAATTAATTTTATT
1186591 TAAATTTTAAAAAATTAATTTTA
1 TAAA-TTTAAAAAATTAATTTTA
1186614 AAAAAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAAATTTAAAAAATTAATTTTATT
Found at i:1187685 original size:21 final size:21
Alignment explanation
Indices: 1187659--1187703 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1187649 AAAAATAGTA
1187659 AAAAAACATTAATAGTTTAGAT
1 AAAAAA-ATTAATAGTTTAGAT
* *
1187681 AAAAAAATTAATATTTTATAT
1 AAAAAAATTAATAGTTTAGAT
1187702 AA
1 AA
1187704 TTTTTTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAAAAATTAATAGTTTAGAT
Found at i:1193223 original size:2 final size:2
Alignment explanation
Indices: 1193212--1193373 Score: 58
Period size: 2 Copynumber: 82.0 Consensus size: 2
1193202 TTAAAACAAT
* *
1193212 TA TA -A TA TA TA TA TA TA TA TA -A CTA TA TA GTT TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * * * *
1193254 -A T- TT TA TA TA T- TG TA TA TA AA TA TG TA GTG TA TA TA TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T-A TA
* * *
1193294 CTA TA TA AA T- TA TA T- TA TA TA CTA TA TA AA CTA TA TGA TT TA
1 -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA T-A TA TA
* *
1193336 T- TA -A TA TA AA CTA TA TA TA TA AA T- 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 TA
1193374 GTTATATTAA
Statistics
Matches: 118, Mismatches: 22, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
1 11 0.09
2 96 0.81
3 11 0.09
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1193355 original size:13 final size:13
Alignment explanation
Indices: 1193339--1193369 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1193329 TGATTTATTA
1193339 ATATAAACTATAT
1 ATATAAACTATAT
*
1193352 ATATAAATTATAT
1 ATATAAACTATAT
1193365 ATATA
1 ATATA
1193370 TATAGTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:1193386 original size:29 final size:29
Alignment explanation
Indices: 1193354--1193409 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1193344 AACTATATAT
* *
1193354 ATAAATTATATATATATATAG-TTATATTA
1 ATAAACTACATAT-TATATAGTTTATATTA
*
1193383 ATAAACTACATATTTTATAGTTTATAT
1 ATAAACTACATATTATATAGTTTATAT
1193410 ACTTTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (29 bp):
ATAAACTACATATTATATAGTTTATATTA
Found at i:1193461 original size:24 final size:21
Alignment explanation
Indices: 1193295--1193490 Score: 104
Period size: 21 Copynumber: 9.0 Consensus size: 21
1193285 ATATATGAAC
*
1193295 TATATAAA-T-TATATTATATAC
1 TATATAAACTATATATTA-AT-T
*
1193316 TATATAAACTATATGATTTATT
1 TATATAAACTATAT-ATTAATT
* *
1193338 AATATAAACTATATATATAAAT
1 TATATAAACTATATAT-TAATT
*
1193360 TATATATA-TATATAGTT-ATAT
1 TATATAAACTATATA-TTAAT-T
*
1193381 TA-ATAAACTACATATTTTATAGTT
1 TATATAAACT--ATATATTA-A-TT
*
1193405 TATAT--ACTTTATA-TAA-T
1 TATATAAACTATATATTAATT
*
1193422 TATATTAAAACTATATAGTTCATT
1 TATA-T-AAACTATATA-TTAATT
1193446 AGTATATAAACTATATATTAATT
1 --TATATAAACTATATATTAATT
*
1193469 TATATAAATATATATATTAATT
1 TATATAAA-CTATATATTAATT
1193491 GAAAGAATTG
Statistics
Matches: 136, Mismatches: 16, Indels: 45
0.69 0.08 0.23
Matches are distributed among these distances:
17 5 0.04
18 1 0.01
19 1 0.01
20 7 0.05
21 39 0.29
22 38 0.28
23 19 0.14
24 18 0.13
25 4 0.03
26 4 0.03
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (21 bp):
TATATAAACTATATATTAATT
Found at i:1194694 original size:27 final size:24
Alignment explanation
Indices: 1194638--1194700 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
1194628 GCAGAAATGT
1194638 TGGTTGTTGTTGCCTGCTACTTAC
1 TGGTTGTTGTTGCCTGCTACTTAC
1194662 TGGTTGTTGTTGCCTGCTACTTAC
1 TGGTTGTTGTTGCCTGCTACTTAC
1194686 TGGTTGTTGTTGCCT
1 TGGTTGTTGTTGCCT
1194701 TATAATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.06, C:0.19, G:0.27, T:0.48
Consensus pattern (24 bp):
TGGTTGTTGTTGCCTGCTACTTAC
Found at i:1195274 original size:14 final size:14
Alignment explanation
Indices: 1195257--1195283 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1195247 ATTTATAACC
1195257 TAAGAATCATAATA
1 TAAGAATCATAATA
1195271 TAAGAATCATAAT
1 TAAGAATCATAAT
1195284 TAATATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (14 bp):
TAAGAATCATAATA
Found at i:1195289 original size:18 final size:18
Alignment explanation
Indices: 1195266--1195328 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
1195256 CTAAGAATCA
*
1195266 TAATATAAGAATCATAAT
1 TAATATAAAAATCATAAT
*
1195284 TAATATAATAAATCTATTTAT
1 TAATATAA-AAATC-A-TAAT
* **
1195305 TAATTTAATTATCATAAT
1 TAATATAAAAATCATAAT
1195323 TAATAT
1 TAATAT
1195329 TTATTATAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 16 0.46
19 5 0.14
20 4 0.11
21 10 0.29
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATATAAAAATCATAAT
Found at i:1205049 original size:31 final size:30
Alignment explanation
Indices: 1204957--1205050 Score: 75
Period size: 31 Copynumber: 3.1 Consensus size: 30
1204947 TTAAAAGTTT
* *
1204957 AAAA-AATCATTAAATGTATCAAATTTTTAT
1 AAAATAATCATTAAATTTATC-AATTTTTAC
** * **
1204987 AAAAT-GGCAATTAAATTTGTCAGATAATTAC
1 AAAATAATC-ATTAAATTTATCA-ATTTTTAC
1205018 AAAATAATCATTAAATTTATCAATTTTTTAC
1 AAAATAATCATTAAATTTATCAA-TTTTTAC
1205049 AA
1 AA
1205051 TTATTATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
30 7 0.15
31 39 0.83
32 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (30 bp):
AAAATAATCATTAAATTTATCAATTTTTAC
Found at i:1205813 original size:30 final size:30
Alignment explanation
Indices: 1205779--1205835 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1205769 ACATAAATAT
*
1205779 TAATATTATTAATATTTTAT-TTTTTAAAAA
1 TAATA-TATTAATATATTATATTTTTAAAAA
*
1205809 TAATATCTTAATATATTATATTTTTAA
1 TAATATATTAATATATTATATTTTTAA
1205836 GCTGTTCACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATATATTAATATATTATATTTTTAAAAA
Found at i:1210869 original size:15 final size:15
Alignment explanation
Indices: 1210837--1210884 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1210827 TTAATTTTAA
*
1210837 ATTTAAAATATAAAAT
1 ATTTAAAAAAT-AAAT
1210853 ATTTAAAAAATAAAT
1 ATTTAAAAAATAAAT
* *
1210868 ATTCAAAAATTAAAT
1 ATTTAAAAAATAAAT
1210883 AT
1 AT
1210885 ATCATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 19 0.66
16 10 0.34
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTTAAAAAATAAAT
Found at i:1211274 original size:3 final size:3
Alignment explanation
Indices: 1211266--1211342 Score: 95
Period size: 3 Copynumber: 25.0 Consensus size: 3
1211256 CGGGTCTTTT
1211266 TTA TTA TTA TT- TATA TATA TATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
1211313 TTA TTA TTTA TTA TTA -TA TTA TTA ATA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
1211343 CATTTTACAT
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
2 3 0.04
3 53 0.78
4 12 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1215079 original size:31 final size:32
Alignment explanation
Indices: 1215043--1215104 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1215033 ATTTTACATG
1215043 TACTAACTTATTT-TTCTCTTTTGCTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGCTTGTGTA
*
1215074 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGCTTGTGT
1215105 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.15, C:0.16, G:0.10, T:0.60
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGCTTGTGTA
Found at i:1216541 original size:26 final size:25
Alignment explanation
Indices: 1216512--1216589 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
1216502 AATTTTTGAC
1216512 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
1216538 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
1216558 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
1216584 ATTCTT
1 ATTCTT
1216590 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:1216550 original size:20 final size:20
Alignment explanation
Indices: 1216527--1216601 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
1216517 ATCTCTTTGA
1216527 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
1216547 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
1216573 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
1216592 CACCTTGAAA
1 GACCTTGAAA
1216602 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:1218404 original size:14 final size:14
Alignment explanation
Indices: 1218385--1218412 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1218375 CAGATTGAGA
1218385 ACACATACATACAT
1 ACACATACATACAT
1218399 ACACATACATACAT
1 ACACATACATACAT
1218413 GATACATAAA
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:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
ACACATACATACAT
Found at i:1219007 original size:36 final size:36
Alignment explanation
Indices: 1218957--1219074 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 36
1218947 TGAGAATTTT
* * *
1218957 AAAACAATTTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAA-ATTTTGTCTCGATTGAGACAATTTCTTTA
* *
1218994 AAAGCAAATTTTGTCTCGATTGAGACAGCTTTC--TA
1 AAAACAAATTTTGTCTCGATTGAGACA-ATTTCTTTA
* *
1219029 AAAACAAATTTTGTCTCGTTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
1219065 AAAACAAATT
1 AAAACAAATT
1219075 CCGCCTCACT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
34 4 0.06
35 26 0.38
36 29 0.42
37 10 0.14
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
Found at i:1219090 original size:71 final size:72
Alignment explanation
Indices: 1218957--1219091 Score: 166
Period size: 71 Copynumber: 1.9 Consensus size: 72
1218947 TGAGAATTTT
* ** * ** * *
1218957 AAAACAATTTTTTGTCTCGCTTGAGACAATTTCTTTCAAAGCAAATTTTGTCTCGATTGAGACAG
1 AAAACAATATTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
1219022 CTTTCTA
66 CTTTCTA
*
1219029 AAAACAA-ATTTTGTCTCGTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTC-ACTGGAGACA
1 AAAACAATATTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGA-TGGAGACA
1219092 TTTTTCGTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
70 1 0.02
71 45 0.85
72 7 0.13
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (72 bp):
AAAACAATATTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
CTTTCTA
Found at i:1219258 original size:36 final size:36
Alignment explanation
Indices: 1219177--1219258 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
1219167 ATTTTGTTTT
* * *
1219177 GCTTGAGACAATTTCTTTAAAAACAAAGTTTGTATC
1 GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
* * *
1219213 ACTTAAGACAAATTCTCTT-AAAACAAACTTCGTCTC
1 GCTTGAGACAAATTCT-TTAAAAACAAACTTCGTATC
1219249 GCTTGAGACA
1 GCTTGAGACA
1219259 TTTTTCCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 35 0.95
37 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (36 bp):
GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
Found at i:1219358 original size:105 final size:102
Alignment explanation
Indices: 1219232--1219470 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 102
1219222 AAATTCTCTT
* * *
1219232 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
*
1219296 TAAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
1219337 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
1219402 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
1219439 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
1219471 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 7 0.06
104 4 0.03
105 78 0.66
106 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:1219461 original size:36 final size:36
Alignment explanation
Indices: 1219416--1219535 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 36
1219406 ACAAAGTTGA
**
1219416 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
1219452 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * *
1219488 TCTCA-TTCGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTT-GAGACAATTTCTCTAAAAACAAACTTT-G
*
1219522 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
1219536 TCATTTTCTC
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
33 3 0.04
34 17 0.24
35 12 0.17
36 38 0.54
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Done.