Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009448.1 Hibiscus syriacus cultivar Beakdansim tig00113548_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: 757038
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:239471 original size:28 final size:28
Alignment explanation
Indices: 239418--239485 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
239408 ACGCCATCAC
*
239418 TTTTTTATTTTGTCAATGAATATATTCT-
1 TTTTTTATTTTATCAATGAATATATT-TA
**
239446 TTTTTTATTTTATTTAT-AATATTATTTA
1 TTTTTTATTTTATCAATGAATA-TATTTA
239474 TTTATTTATTTT
1 TTT-TTTATTTT
239486 TTATATTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 5 0.15
28 21 0.62
29 8 0.24
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTTATTTTATCAATGAATATATTTA
Found at i:239482 original size:12 final size:13
Alignment explanation
Indices: 239438--239499 Score: 58
Period size: 12 Copynumber: 5.0 Consensus size: 13
239428 TGTCAATGAA
* *
239438 TATATTCTTTTTT
1 TATATTATTTATT
*
239451 TATTTTATTTA-T
1 TATATTATTTATT
*
239463 AATATTATTTATT
1 TATATTATTTATT
239476 TAT-TTATTT-TT
1 TATATTATTTATT
*
239487 TATATTATATATT
1 TATATTATTTATT
239500 AGATAAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
11 5 0.13
12 21 0.54
13 13 0.33
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TATATTATTTATT
Found at i:239491 original size:24 final size:25
Alignment explanation
Indices: 239438--239499 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
239428 TGTCAATGAA
* *
239438 TATATTCTTTTTTTATTTTATTTAT
1 TATATTATTTATTTATTTTATTTAT
* *
239463 AATATTATTTATTTA-TTTATTTTT
1 TATATTATTTATTTATTTTATTTAT
*
239487 TATATTATATATT
1 TATATTATTTATT
239500 AGATAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (25 bp):
TATATTATTTATTTATTTTATTTAT
Found at i:239694 original size:16 final size:16
Alignment explanation
Indices: 239673--239714 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
239663 TGAGAAAAAT
239673 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
*
239689 TTAATTTAATTTTAAA
1 TTAATTTAAATTTAAA
*
239705 ATAATATTAA
1 TTAAT-TTAA
239715 TAAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:240779 original size:48 final size:48
Alignment explanation
Indices: 240720--240848 Score: 195
Period size: 48 Copynumber: 2.7 Consensus size: 48
240710 AACTGGTGCC
* * * *
240720 ACTCGGGCTAGTCAAGCTACTCAGTCAGAGGGACCGGAGAACGATTCG
1 ACTCCGGCTAGTCAATCTACTCAGTCAGAAGGACCGAAGAACGATTCG
* *
240768 ACTCCGGCTAGTCTATCTACTCTGTCAGAAGGACCGAAGAACGATTCG
1 ACTCCGGCTAGTCAATCTACTCAGTCAGAAGGACCGAAGAACGATTCG
*
240816 ACTCTGGCTAGTCAATCTACTCAGTCAGAAGGA
1 ACTCCGGCTAGTCAATCTACTCAGTCAGAAGGA
240849 TTAACTTTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (48 bp):
ACTCCGGCTAGTCAATCTACTCAGTCAGAAGGACCGAAGAACGATTCG
Found at i:241729 original size:14 final size:13
Alignment explanation
Indices: 241710--241749 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
241700 ACATATTAAA
241710 TAATAAATATAAT
1 TAATAAATATAAT
*
241723 TATATAACTATAAT
1 TA-ATAAATATAAT
241737 TAATAAATA-AAT
1 TAATAAATATAAT
241749 T
1 T
241750 TTAGGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 12 0.50
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAAATATAAT
Found at i:245922 original size:24 final size:24
Alignment explanation
Indices: 245895--245966 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
245885 TTATTTTATA
*
245895 TGATTTACGACTTGAATTCTGTTC
1 TGATTTACGACCTGAATTCTGTTC
** *
245919 TGATACATGACCTGAATTCTGTTC
1 TGATTTACGACCTGAATTCTGTTC
* *
245943 TGATTT-CTGATCTGGATTCTGTTC
1 TGATTTAC-GACCTGAATTCTGTTC
245967 AGATATCTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATTTACGACCTGAATTCTGTTC
Found at i:245945 original size:12 final size:12
Alignment explanation
Indices: 245907--245999 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
245897 ATTTACGACT
245907 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
245919 TG-ATACATGACC
1 TGAATTC-TGTTC
245931 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
245943 TGATTTCTGATC
1 TGAATTCTGTTC
*
245955 TGGATTCTGTTC
1 TGAATTCTGTTC
*
245967 AG-ATATCTGTTC
1 TGAAT-TCTGTTC
*
245979 TGAATTCTGTTT
1 TGAATTCTGTTC
*
245991 TGATTTCTG
1 TGAATTCTG
246000 ATATCTCCGT
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
11 5 0.08
12 52 0.84
13 5 0.08
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:245962 original size:48 final size:48
Alignment explanation
Indices: 245910--246001 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
245900 TACGACTTGA
*
245910 ATTCTGTTCTGATA-CATGACCTGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCAGATATC-TGACCTGAATTCTGTTCTGATTTCTGATCTGG
** *
245958 ATTCTGTTCAGATATCTGTTCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCAGATATCTGACCTGAATTCTGTTCTGATTTCTGAT
246002 ATCTCCGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.48
Consensus pattern (48 bp):
ATTCTGTTCAGATATCTGACCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:245975 original size:24 final size:24
Alignment explanation
Indices: 245907--246001 Score: 111
Period size: 24 Copynumber: 4.0 Consensus size: 24
245897 ATTTACGACT
*
245907 TGAATTCTGTTCTGATA-CATGACC
1 TGAATTCTGTTCTGATATC-TGATC
*
245931 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* * *
245955 TGGATTCTGTTCAGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
245979 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
246002 ATCTCCGTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 58 0.98
25 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:256033 original size:45 final size:46
Alignment explanation
Indices: 255982--256079 Score: 135
Period size: 45 Copynumber: 2.1 Consensus size: 46
255972 TATTTTTTGA
*
255982 TCAAAATAAGTATCTAACTTTATACGACGTGTCAACATCTTA-TGG
1 TCAAAATAAGTATCTAACTTTATACGACGTGTCAACATCCTATTGG
* * * *
256027 TCAAAATAAGTATCTCATTTTATATGATGTGTCAACATCCTATTGG
1 TCAAAATAAGTATCTAACTTTATACGACGTGTCAACATCCTATTGG
256073 TCCAAAA
1 T-CAAAA
256080 ATATTTTCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 37 0.80
46 4 0.09
47 5 0.11
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (46 bp):
TCAAAATAAGTATCTAACTTTATACGACGTGTCAACATCCTATTGG
Found at i:258706 original size:24 final size:27
Alignment explanation
Indices: 258656--258708 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
258646 TCTGTTGTAA
*
258656 TAAAATATTTAATTCACTTTTTTATTT
1 TAAAATATTTAATTCACATTTTTATTT
258683 TAAAATATTTAA-T-A-ATTTTTATTT
1 TAAAATATTTAATTCACATTTTTATTT
258707 TA
1 TA
258709 CAGTATAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
26 1 0.04
27 12 0.48
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (27 bp):
TAAAATATTTAATTCACATTTTTATTT
Found at i:259170 original size:11 final size:10
Alignment explanation
Indices: 259145--259190 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
259135 CTTGTTTTTT
*
259145 TTTCTATTTG
1 TTTCTGTTTG
259155 TTTCTGTTTGG
1 TTTCTGTTT-G
259166 TTTCTGGTTCTG
1 TTTCT-GTT-TG
259178 TTTCTGTTTG
1 TTTCTGTTTG
259188 TTT
1 TTT
259191 GTCTGTGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 13 0.41
11 9 0.28
12 9 0.28
13 1 0.03
ACGTcount: A:0.02, C:0.11, G:0.20, T:0.67
Consensus pattern (10 bp):
TTTCTGTTTG
Found at i:259202 original size:23 final size:23
Alignment explanation
Indices: 259153--259202 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
259143 TTTTTCTATT
**
259153 TGTTTCTGTTTGGTTTCTGGTTC
1 TGTTTCTGTTTGGTTTCTGGTGA
*
259176 TGTTTCTGTTTGTTTGTCT-GTGA
1 TGTTTCTGTTTGGTT-TCTGGTGA
259199 TGTT
1 TGTT
259203 GGAATCCACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.02, C:0.10, G:0.26, T:0.62
Consensus pattern (23 bp):
TGTTTCTGTTTGGTTTCTGGTGA
Found at i:281223 original size:18 final size:17
Alignment explanation
Indices: 281191--281225 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
281181 ATGAGTGTAT
*
281191 AATTTTTATTAATAATA
1 AATTTTGATTAATAATA
281208 AATTTTGATATAATAATA
1 AATTTTGAT-TAATAATA
281226 TATACAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTTGATTAATAATA
Found at i:281638 original size:76 final size:74
Alignment explanation
Indices: 281471--281640 Score: 250
Period size: 74 Copynumber: 2.3 Consensus size: 74
281461 TACGAAACCC
* * * * *
281471 ATCAACAAACCCTTGAATTATGTTTCATTATAATATTTCTTATATATTTTAAGAATACAAGTGCA
1 ATCAACAAACCCTTGAATTACGTTTCATTATAATATTTATTAAATATTTTAAGAAAACAAATGCA
281536 TGGTCACCA
66 TGGTCACCA
* *
281545 ATCAACAAACCCTTGAATTACGTTTCCTTATAATATTTTATTAAATATTTTAAGAAAACAAATGT
1 ATCAACAAACCCTTGAATTACGTTTCATTATAATA-TTTATTAAATATTTTAAGAAAACAAATGC
281610 ATGGTCATCCA
65 ATGGTCA-CCA
*
281621 ATTAACAAACCCTTGAATTA
1 ATCAACAAACCCTTGAATTA
281641 GCAGTAAATA
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 33 0.38
75 31 0.36
76 22 0.26
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (74 bp):
ATCAACAAACCCTTGAATTACGTTTCATTATAATATTTATTAAATATTTTAAGAAAACAAATGCA
TGGTCACCA
Found at i:282983 original size:2 final size:2
Alignment explanation
Indices: 282976--283010 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
282966 GGATTGTTCA
282976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
283011 TGGCAGTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:283812 original size:53 final size:53
Alignment explanation
Indices: 283750--283857 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
283740 TCATATGTTC
*
283750 CAAATTTATCTTTTTTAGGTGAAAATTTAATGGTCTTATGAGTTGGACATTAA
1 CAAATTTATCTTTTTTAGGTGAAAATTTAATGGTCTTATGAGTTAGACATTAA
*
283803 CAAATTTATCTTTTTTAGTTGAAAATTTAATGGTCTTATGAGTTAGACATTAA
1 CAAATTTATCTTTTTTAGGTGAAAATTTAATGGTCTTATGAGTTAGACATTAA
283856 CA
1 CA
283858 TGTTGACTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (53 bp):
CAAATTTATCTTTTTTAGGTGAAAATTTAATGGTCTTATGAGTTAGACATTAA
Found at i:291615 original size:2 final size:2
Alignment explanation
Indices: 291610--291657 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
291600 TACGTGTGTC
291610 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
291649 TA TA TA TA T
1 TA TA TA TA T
291658 GGTTATATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:297142 original size:62 final size:63
Alignment explanation
Indices: 297069--297187 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
297059 ATTGTTCAAG
** * * *
297069 GTGTATCGATGCATGAG-GTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCGATGCACAAGAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATTA
* *
297131 GTGTATCGATGCACAAGTAGTGCATTGATGCACCCCCTTAAAATACAAACATCGAAT
1 GTGTATCGATGCACAAG-AGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAT
297188 ATGATTTATG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 15 0.31
64 33 0.69
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATTA
Found at i:297172 original size:64 final size:64
Alignment explanation
Indices: 297093--297229 Score: 170
Period size: 64 Copynumber: 2.1 Consensus size: 64
297083 GAGGTGTATC
* * * *
297093 GATGCACTCCTTTAAAATAAAAACATCGAATGTCA-TTAGTGTATCGATGCACA-AGTAGTGCAT
1 GATGCACCCCCTTAAAATAAAAACATCGAATATCATTTA-TGTACCGATGCACAGAGTA-TGCAT
297156 T
64 T
* * * *
297157 GATGCACCCCCTTAAAATACAAACATCGAATATGATTTATGTACCGATGCATAGATTATGCATT
1 GATGCACCCCCTTAAAATAAAAACATCGAATATCATTTATGTACCGATGCACAGAGTATGCATT
297221 GATGCACCC
1 GATGCACCC
297230 GTCAAGGGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 57 0.90
65 6 0.10
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (64 bp):
GATGCACCCCCTTAAAATAAAAACATCGAATATCATTTATGTACCGATGCACAGAGTATGCATT
Found at i:298075 original size:2 final size:2
Alignment explanation
Indices: 298068--298162 Score: 190
Period size: 2 Copynumber: 47.5 Consensus size: 2
298058 AAAGCATTGT
298068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298110 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298152 TA TA TA TA TA T
1 TA TA TA TA TA T
298163 GCCTCACTAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:301058 original size:23 final size:23
Alignment explanation
Indices: 301014--301058 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
301004 ATTATTATAT
*
301014 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
301037 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
301059 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:305898 original size:21 final size:21
Alignment explanation
Indices: 305856--305898 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
305846 TTTCTGGGCT
* *
305856 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
305877 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
305898 A
1 A
305899 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:306636 original size:23 final size:23
Alignment explanation
Indices: 306592--306636 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
306582 ATTATTATAT
*
306592 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
306615 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
306637 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:307417 original size:6 final size:6
Alignment explanation
Indices: 307402--307442 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
307392 GGCTACCCAG
* *
307402 AGAGGA AGAGGT AGAGCT AGAGGT AGAGGT AGAGGT AGAGG
1 AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT AGAGG
307443 AAGAAGTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.02, G:0.49, T:0.12
Consensus pattern (6 bp):
AGAGGT
Found at i:307429 original size:18 final size:18
Alignment explanation
Indices: 307402--307446 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
307392 GGCTACCCAG
307402 AGAGGAAGAGGTAGAGCT
1 AGAGGAAGAGGTAGAGCT
* *
307420 AGAGGTAGAGGTAGAGGT
1 AGAGGAAGAGGTAGAGCT
307438 AGAGGAAGA
1 AGAGGAAGA
307447 AGTTAGTCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.47, T:0.11
Consensus pattern (18 bp):
AGAGGAAGAGGTAGAGCT
Found at i:308582 original size:13 final size:13
Alignment explanation
Indices: 308553--308593 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
308543 ATTTGGATCG
*
308553 ATTCATT-ATGGT
1 ATTCATTGATGAT
308565 ATTCATTGATGAT
1 ATTCATTGATGAT
308578 ATTCATTGATGAT
1 ATTCATTGATGAT
308591 ATT
1 ATT
308594 TTAGTGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (13 bp):
ATTCATTGATGAT
Found at i:311874 original size:18 final size:18
Alignment explanation
Indices: 311851--311921 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
311841 AGGGATTATC
311851 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
311869 AGTGGTTCTTCAGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
311888 CAGTTGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
311907 AGTTGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
311922 TAAATATTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 28 0.64
19 4 0.09
20 12 0.27
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:319060 original size:2 final size:2
Alignment explanation
Indices: 319053--319077 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
319043 AATCAATGTG
319053 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 T
319078 TCTAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:327165 original size:10 final size:10
Alignment explanation
Indices: 327152--327201 Score: 55
Period size: 10 Copynumber: 4.6 Consensus size: 10
327142 TCATATTTTT
327152 AATAAATTAA
1 AATAAATTAA
327162 AATAAATTTAA
1 AATAAA-TTAA
327173 TATATTAAATTAA
1 -A-A-TAAATTAA
*
327186 AATAAATTCA
1 AATAAATTAA
327196 AATAAA
1 AATAAA
327202 GTTAGTCTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 19 0.54
11 5 0.14
12 2 0.06
13 5 0.14
14 4 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AATAAATTAA
Found at i:327173 original size:19 final size:19
Alignment explanation
Indices: 327149--327186 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
327139 TAGTCATATT
327149 TTTAATAAATTAAAATAAA
1 TTTAATAAATTAAAATAAA
* *
327168 TTTAATATATTAAATTAAA
1 TTTAATAAATTAAAATAAA
327187 ATAAATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATAAATTAAAATAAA
Found at i:335932 original size:31 final size:31
Alignment explanation
Indices: 335897--335958 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
335887 TTAATCTTAT
335897 TTTGATAATTCATCGTAAAAATATTAATGAC
1 TTTGATAATTCATCGTAAAAATATTAATGAC
335928 TTTGATAATTCATCGTAAAAATATTAATGAC
1 TTTGATAATTCATCGTAAAAATATTAATGAC
335959 GAAGTTGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (31 bp):
TTTGATAATTCATCGTAAAAATATTAATGAC
Found at i:349970 original size:14 final size:14
Alignment explanation
Indices: 349951--349983 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
349941 CTTTGGGCAT
349951 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
349965 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
349979 CCGAG
1 CCGAG
349984 CTATGCGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.39, G:0.33, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:350044 original size:21 final size:21
Alignment explanation
Indices: 350019--350058 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
350009 GGAATCACGC
350019 GAGGAGCAGGAGGGAGTGCGA
1 GAGGAGCAGGAGGGAGTGCGA
*
350040 GAGGAGTAGGAGGGAGTGC
1 GAGGAGCAGGAGGGAGTGC
350059 ATGGCGACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.57, T:0.07
Consensus pattern (21 bp):
GAGGAGCAGGAGGGAGTGCGA
Found at i:357788 original size:12 final size:12
Alignment explanation
Indices: 357771--357804 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
357761 AGACATCACA
357771 CCTCATCAGAAT
1 CCTCATCAGAAT
*
357783 CCTCATCTGAAT
1 CCTCATCAGAAT
*
357795 CCTCCTCAGA
1 CCTCATCAGA
357805 GCTGCTATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.38, G:0.09, T:0.26
Consensus pattern (12 bp):
CCTCATCAGAAT
Found at i:372632 original size:16 final size:17
Alignment explanation
Indices: 372608--372640 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
372598 TTTTTAAAAG
372608 TTTGATTTTAG-TTAAT
1 TTTGATTTTAGATTAAT
*
372624 TTTGTTTTTAGATTAAT
1 TTTGATTTTAGATTAAT
372641 GAAGTGATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (17 bp):
TTTGATTTTAGATTAAT
Found at i:379385 original size:21 final size:21
Alignment explanation
Indices: 379359--379417 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
379349 GCGCTGTATT
379359 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
379380 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
379400 TCGCGTTGCGATAGTTGA
1 TCGCGTTGCGATAGTTGA
379418 TTGCGATAGT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:379427 original size:54 final size:54
Alignment explanation
Indices: 379364--379468 Score: 160
Period size: 54 Copynumber: 1.9 Consensus size: 54
379354 GTATTTCGCG
379364 TTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGA
1 TTGCGATAGTCT-AAAAT-GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGA
* *
379418 TTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 TTGCGATAGTCTAAAATGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
379469 GTACAGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
53 1 0.02
54 45 0.96
55 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (54 bp):
TTGCGATAGTCTAAAATGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGA
Found at i:379444 original size:21 final size:21
Alignment explanation
Indices: 379418--379486 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
379408 CGATAGTTGA
379418 TTGCGATAGTCTACAGTGTCG
1 TTGCGATAGTCTACAGTGTCG
* * *
379439 TTGCGAT--TTTCCA-TTTCGCG
1 TTGCGATAGTCTACAGTGT--CG
*
379459 TTGCGATAGTGTACAGTGTCG
1 TTGCGATAGTCTACAGTGTCG
379480 TTGCGAT
1 TTGCGAT
379487 TTTCTTTTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.05
19 4 0.11
20 9 0.24
21 16 0.43
22 4 0.11
23 2 0.05
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.38
Consensus pattern (21 bp):
TTGCGATAGTCTACAGTGTCG
Found at i:379475 original size:41 final size:40
Alignment explanation
Indices: 379418--379509 Score: 148
Period size: 41 Copynumber: 2.3 Consensus size: 40
379408 CGATAGTTGA
*
379418 TTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCG
1 TTGCGATAGTCTACAGTGTCGTTGCGATTTT-CATTTCCCG
* *
379459 TTGCGATAGTGTACAGTGTCGTTGCGATTTTCTTTTCCCG
1 TTGCGATAGTCTACAGTGTCGTTGCGATTTTCATTTCCCG
379499 TTGCGATAGTC
1 TTGCGATAGTC
379510 GTTGCGATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 17 0.36
41 30 0.64
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Consensus pattern (40 bp):
TTGCGATAGTCTACAGTGTCGTTGCGATTTTCATTTCCCG
Found at i:379514 original size:31 final size:32
Alignment explanation
Indices: 379476--379541 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
379466 AGTGTACAGT
* *
379476 GTCGTTGCGATTTT-CTTTTCCCGTTGCGATA
1 GTCGTTGCGATTTTCCATTTCCAGTTGCGATA
*
379507 GTCGTTGCGATTTTCCATTTCGAGTTGCGATA
1 GTCGTTGCGATTTTCCATTTCCAGTTGCGATA
379539 GTC
1 GTC
379542 TACAGTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.42
Consensus pattern (32 bp):
GTCGTTGCGATTTTCCATTTCCAGTTGCGATA
Found at i:379683 original size:15 final size:15
Alignment explanation
Indices: 379663--379695 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
379653 TTTCCATTTC
*
379663 GCGTTGCGATTTGTT
1 GCGTTGCGATGTGTT
379678 GCGTTGCGATGTGTT
1 GCGTTGCGATGTGTT
379693 GCG
1 GCG
379696 ATCATTGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.39, T:0.39
Consensus pattern (15 bp):
GCGTTGCGATGTGTT
Found at i:379760 original size:31 final size:32
Alignment explanation
Indices: 379722--379787 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
379712 AGTGTACAGT
* *
379722 GTCGTTGCGATTTT-CTTTTCCCGTTGCGATA
1 GTCGTTGCGATTTTCCATTTCCAGTTGCGATA
*
379753 GTCGTTGCGATTTTCCATTTCGAGTTGCGATA
1 GTCGTTGCGATTTTCCATTTCCAGTTGCGATA
379785 GTC
1 GTC
379788 TACAGTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.42
Consensus pattern (32 bp):
GTCGTTGCGATTTTCCATTTCCAGTTGCGATA
Found at i:380963 original size:21 final size:21
Alignment explanation
Indices: 380939--381036 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
380929 GACACTGTAG
380939 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
** *
380960 ACTATCGCAACGCGA-AATGA
1 ACTATCGCAACGCGATTTTCA
** * *
380980 AAAATCGCAACGAC-ACTGT-A
1 ACTATCGCAACG-CGATTTTCA
381000 TACTATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGATTTTCA
*
381022 AATATCGCAACGCGA
1 ACTATCGCAACGCGA
381037 AATGTAACGC
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 15 0.25
21 44 0.73
22 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:380996 original size:62 final size:62
Alignment explanation
Indices: 380899--381040 Score: 257
Period size: 62 Copynumber: 2.3 Consensus size: 62
380889 TCCAGTATCG
*
380899 CTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCAA
1 CTATCGCAACGCGAAATGAAAAATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCAA
*
380961 CTATCGCAACGCGAAATGAAAAATCGCAACGACACTGTATACTATCGCAACGCGATTTTCAA
1 CTATCGCAACGCGAAATGAAAAATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCAA
*
381023 ATATCGCAACGCGAAATG
1 CTATCGCAACGCGAAATG
381041 TAACGCGAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 77 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (62 bp):
CTATCGCAACGCGAAATGAAAAATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCAA
Found at i:381248 original size:31 final size:33
Alignment explanation
Indices: 381182--381250 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 33
381172 CGATTTTCTC
* *
381182 TTAAAATAAAATGAAATTTAAAAAATTTAAATA
1 TTAAAATAAAATCAAAATTAAAAAATTTAAATA
* *
381215 TTAAAAT-AAATCAAAATT-AATAATTTAATTA
1 TTAAAATAAAATCAAAATTAAAAAATTTAAATA
381246 TTAAA
1 TTAAA
381251 TGCATAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 16 0.50
32 9 0.28
33 7 0.22
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (33 bp):
TTAAAATAAAATCAAAATTAAAAAATTTAAATA
Found at i:386701 original size:33 final size:30
Alignment explanation
Indices: 386609--386711 Score: 102
Period size: 29 Copynumber: 3.4 Consensus size: 30
386599 GAAAAAGATT
**
386609 AAATATTTTATGTACTTATTTTGACC-AAA
1 AAATATTTTAAATACTTATTTTGACCAAAA
* * **
386638 AAATATTTTAGATACCTATTTTGATTAAAA
1 AAATATTTTAAATACTTATTTTGACCAAAA
386668 AAATATAACTTTAAATACTTATTTTGACC-AAA
1 AAATAT---TTTAAATACTTATTTTGACCAAAA
386700 AAATAATTTTAA
1 AAAT-ATTTTAA
386712 GTAATTTAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
29 21 0.35
30 14 0.23
32 7 0.12
33 18 0.30
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.42
Consensus pattern (30 bp):
AAATATTTTAAATACTTATTTTGACCAAAA
Found at i:404612 original size:21 final size:21
Alignment explanation
Indices: 404583--404866 Score: 278
Period size: 21 Copynumber: 13.4 Consensus size: 21
404573 ATTTTGGACT
404583 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
404604 ATCGTAACGCGAATTTGGAATAA
1 ATCGCAA--CGAATTTGGAATAA
404627 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
404648 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
404669 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
404690 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
404711 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
404732 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
404753 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
404774 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
404795 ATCGTAACGTGAACTTGGACT--
1 ATCGCAAC--GAATTTGGAATAA
404816 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
404837 ATCGTAACGAATTTAGAATAA
1 ATCGCAACGAATTTGGAATAA
404858 ATCGCAACG
1 ATCGCAACG
404867 CGAACTTCGA
Statistics
Matches: 222, Mismatches: 23, Indels: 36
0.79 0.08 0.13
Matches are distributed among these distances:
19 39 0.18
21 124 0.56
23 59 0.27
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:404686 original size:63 final size:61
Alignment explanation
Indices: 404576--404906 Score: 253
Period size: 63 Copynumber: 5.2 Consensus size: 61
404566 CGTTGCGATT
* * * * *
404576 TTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCGAATTTGGAATAAATCGCAA-CGAAT
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAA--CGAACTTGGAATAAATCGCAACCGAAC
* *
404639 TTGGAATAAATCGCAACGCGAACTTCGACT-ATCGCAACGAACTTGGAATAAATCGCAACGCGAA
1 TTGGAAT--ATCGCAA--CGAACTTGGAATAATCGCAACGAACTTGGAATAAATCGCAAC-CGAA
404703 C
61 C
* * *
404704 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGAACTTGGAATAAATCGCAAC-CGAAC
* * * * *
404767 TTCGACTATCGCAACGAACTTGGAATAAATCGTAACGTGAACTTGGACT--ATCGCAA-CGAAT
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAAC--GAACTTGGAATAAATCGCAACCGAAC
* * * * *
404828 TTGGAATAAATCGTAACGAATTTAGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACACGA
1 TTGGAAT--ATCGCAACGAACTTGGAAT-AATCGCAA--CGAACTTGGAATAAATCGCAAC-CGA
404891 AC
60 AC
*
404893 TTGGACTATCGCAA
1 TTGGAATATCGCAA
404907 TGCGAATATG
Statistics
Matches: 224, Mismatches: 28, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
61 18 0.08
63 154 0.69
65 43 0.19
67 9 0.04
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (61 bp):
TTGGAATATCGCAACGAACTTGGAATAATCGCAACGAACTTGGAATAAATCGCAACCGAAC
Found at i:404758 original size:105 final size:105
Alignment explanation
Indices: 404613--404897 Score: 516
Period size: 105 Copynumber: 2.7 Consensus size: 105
404603 AATCGTAACG
404613 CGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
1 CGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
404678 AACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
66 AACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
404718 CGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
1 CGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
* *
404783 AACTTGGAATAAATCGTAACGTGAACTTGGACTATCGCAA
66 AACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
* *
404823 CGAATTTGGAATAAATCGTAACGAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACA
1 CGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGC-A-A
404888 CGAACTTGGA
64 CGAACTTGGA
404898 CTATCGCAAT
Statistics
Matches: 174, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
105 162 0.93
106 1 0.01
107 11 0.06
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (105 bp):
CGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
AACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
Found at i:404882 original size:21 final size:21
Alignment explanation
Indices: 404858--404912 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
404848 TTTAGAATAA
404858 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
404879 ATCGCAACACGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
404900 ATCGCAATGCGAA
1 ATCGCAACGCGAA
404913 TATGTAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:404904 original size:42 final size:42
Alignment explanation
Indices: 404583--404912 Score: 204
Period size: 42 Copynumber: 7.8 Consensus size: 42
404573 ATTTTGGACT
* * *
404583 ATCGC-AACGAATTTGGAATAAATCGTAACGCGAATTTGGAATAA
1 ATCGCAAACGAACTTGGAAT-AATCGCAA-GCGAACTTGGAAT-A
* * *
404627 ATCGC-AACGAATTTGGAATAAATCGCAACGCGAACTTCGACT-
1 ATCGCAAACGAACTTGGAAT-AATCGCAA-GCGAACTTGGAATA
*
404669 ATCGC-AACGAACTTGGAATAAATCGCAACGCGAACTTGGACT-
1 ATCGCAAACGAACTTGGAAT-AATCGCAA-GCGAACTTGGAATA
* *
404711 ATCGC-AACGAATTTGGAATAAATCGCAA-CGAATTTGGAATAA
1 ATCGCAAACGAACTTGGAAT-AATCGCAAGCGAACTTGGAAT-A
* * *
404753 ATCGCAACGCGAACTTCGACT-ATCGCAA-CGAACTTGGAATAA
1 ATCGCAA-ACGAACTTGGAATAATCGCAAGCGAACTTGGAAT-A
* * *
404795 ATCG-TAACGTGAACTTGGACT-ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAAC--GAACTTGGAATAATCGCAAGCGAACTTGGAAT-A
* * * * *
404837 ATCG-TAACGAATTTAGAATAAATCGCAACGCGAACTTCGACT-
1 ATCGCAAACGAACTTGGAAT-AATCGCAA-GCGAACTTGGAATA
*
404879 ATCGCAACACGAACTTGGACT-ATCGCAATGCGAA
1 ATCGCAA-ACGAACTTGGAATAATCGCAA-GCGAA
404913 TATGTAAATC
Statistics
Matches: 245, Mismatches: 29, Indels: 26
0.82 0.10 0.09
Matches are distributed among these distances:
40 19 0.08
41 1 0.00
42 157 0.64
43 2 0.01
44 66 0.27
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (42 bp):
ATCGCAAACGAACTTGGAATAATCGCAAGCGAACTTGGAATA
Found at i:405609 original size:17 final size:17
Alignment explanation
Indices: 405584--405628 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
405574 CACATCTAAA
*
405584 ATTTAAAATTATCATAT
1 ATTTTAAATTATCATAT
* *
405601 ATTTTAAATTTTTATAT
1 ATTTTAAATTATCATAT
*
405618 ATTTTTAATTA
1 ATTTTAAATTA
405629 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTATCATAT
Found at i:411437 original size:23 final size:22
Alignment explanation
Indices: 411384--411444 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
411374 AGTTCATCTC
411384 ATAATTATACAAATAAAATAAA
1 ATAATTATACAAATAAAATAAA
* *
411406 ATTATTTATA-AAATACTAATCAAA
1 A-TAATTATACAAATA-AAAT-AAA
*
411430 ATAATTATTCAAATA
1 ATAATTATACAAATA
411445 TAATTCAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 6 0.19
23 16 0.52
24 9 0.29
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAATTATACAAATAAAATAAA
Found at i:411448 original size:23 final size:22
Alignment explanation
Indices: 411384--411457 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
411374 AGTTCATCTC
* *
411384 ATAATTATACAAATAAAATAAA
1 ATAATTATTCAAATATAATAAA
* *
411406 ATTATT-TATAAAATACTAATCAAA
1 ATAATTAT-TCAAATA-TAAT-AAA
**
411430 ATAATTATTCAAATATAATTCA
1 ATAATTATTCAAATATAATAAA
411452 ATAATT
1 ATAATT
411458 TTGGGATACT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
21 1 0.03
22 17 0.43
23 7 0.17
24 14 0.35
25 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATTATTCAAATATAATAAA
Found at i:413746 original size:2 final size:2
Alignment explanation
Indices: 413739--413769 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
413729 ATGCAGATTC
413739 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
413770 GGTACATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:416431 original size:25 final size:26
Alignment explanation
Indices: 416376--416435 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
416366 TTATAAAATT
* *
416376 AGATCAAATCAAAACCTGTCGAGTTC
1 AGATCAAATCAAAACCTGCCAAGTTC
*
416402 AGATCAAATC-AAATCTGCCAAGTTC
1 AGATCAAATCAAAACCTGCCAAGTTC
416427 AGATCAAAT
1 AGATCAAAT
416436 GACCAACTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (26 bp):
AGATCAAATCAAAACCTGCCAAGTTC
Found at i:422678 original size:201 final size:201
Alignment explanation
Indices: 422333--422741 Score: 782
Period size: 201 Copynumber: 2.0 Consensus size: 201
422323 AATATTTAAA
422333 TTAAATTGTCTTTAAATTATTGGTTCAAGTAATTGTATATATAGAAAATCTCCATTGTGAGACTC
1 TTAAATTGTCTTTAAATTATTGGTTCAAGTAATTGTATATATAGAAAATCTCCATTGTGAGACTC
*
422398 ATCTATCAAAGTCACATGAGTAACGTAGATCTGTCCGGATTAATCAGAGTAAAACCTAGAATCGA
66 ATCTATCAAAGTCACATGAGTAACGTAGATCTGTCCGAATTAATCAGAGTAAAACCTAGAATCGA
422463 GAGAGAAAAAACTTAAACTATGCTATTTTTTGCTTTAGATACCTAAATTATTTTCTGGTCAAACT
131 GAGAGAAAAAACTTAAACTATGCTATTTTTTGCTTTAGATACCTAAATTATTTTCTGGTCAAACT
422528 ATATAT
196 ATATAT
422534 TTAAATTGTCTTTAAATTATTGGTTCAAGTAATTGTATATATAGAAAATCTCCATTGTGAGACTC
1 TTAAATTGTCTTTAAATTATTGGTTCAAGTAATTGTATATATAGAAAATCTCCATTGTGAGACTC
* *
422599 ATCTATCAAAGTCACATGAGTAACGTAGATCTGTCCGAATTAGTCAGAGTAAAACCTAGAATCGG
66 ATCTATCAAAGTCACATGAGTAACGTAGATCTGTCCGAATTAATCAGAGTAAAACCTAGAATCGA
422664 GAGAGAAAAAACTTAAACTATGCTATTTTTTGCTTTAGATACCTAAATTATTTTCTGGTCAAACT
131 GAGAGAAAAAACTTAAACTATGCTATTTTTTGCTTTAGATACCTAAATTATTTTCTGGTCAAACT
*
422729 ATTTAT
196 ATATAT
422735 TTAAATT
1 TTAAATT
422742 ATTATATGTA
Statistics
Matches: 204, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 204 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (201 bp):
TTAAATTGTCTTTAAATTATTGGTTCAAGTAATTGTATATATAGAAAATCTCCATTGTGAGACTC
ATCTATCAAAGTCACATGAGTAACGTAGATCTGTCCGAATTAATCAGAGTAAAACCTAGAATCGA
GAGAGAAAAAACTTAAACTATGCTATTTTTTGCTTTAGATACCTAAATTATTTTCTGGTCAAACT
ATATAT
Found at i:422896 original size:20 final size:21
Alignment explanation
Indices: 422851--422897 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
422841 AATAAGTACT
422851 TAATTTTATATGACATGTAAA
1 TAATTTTATATGACATGTAAA
*
422872 -CATTTTAT-TGACCATG-AAA
1 TAATTTTATATGA-CATGTAAA
422891 TAATTTT
1 TAATTTT
422898 CTAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (21 bp):
TAATTTTATATGACATGTAAA
Found at i:423864 original size:7 final size:7
Alignment explanation
Indices: 423854--423879 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
423844 AAAAGTTGAA
423854 TTTTTAT
1 TTTTTAT
423861 TTTTTAT
1 TTTTTAT
423868 TTTTTAT
1 TTTTTAT
423875 TTTTT
1 TTTTT
423880 GACGGAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:428202 original size:9 final size:10
Alignment explanation
Indices: 428183--428245 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
428173 ATACTAATTG
*
428183 TTTTGTAATT
1 TTTTGTGATT
428193 TTTTGT-ATT
1 TTTTGTGATT
*
428202 TTTTTTGTATT
1 TTTTGTG-ATT
*
428213 TTTTCTGATT
1 TTTTGTGATT
*
428223 TTTTAT-ATT
1 TTTTGTGATT
*
428232 TTTTATGATT
1 TTTTGTGATT
428242 TTTT
1 TTTT
428246 TTAAATTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
9 17 0.36
10 21 0.45
11 9 0.19
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTGTGATT
Found at i:428205 original size:11 final size:11
Alignment explanation
Indices: 428191--428247 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
428181 TGTTTTGTAA
428191 TTTTTTGTATT
1 TTTTTTGTATT
428202 TTTTTTGTATT
1 TTTTTTGTATT
*
428213 TTTTCTG-A--
1 TTTTTTGTATT
*
428221 TTTTTTATATT
1 TTTTTTGTATT
*
428232 TTTTATG-ATT
1 TTTTTTGTATT
428242 TTTTTT
1 TTTTTT
428248 AAATTCAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
8 5 0.14
9 1 0.03
10 9 0.24
11 22 0.59
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTGTATT
Found at i:428207 original size:21 final size:21
Alignment explanation
Indices: 428183--428247 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
428173 ATACTAATTG
*
428183 TTTTGTAATTTTT-TGTATTTT
1 TTTTGTATTTTTTCTG-ATTTT
428204 TTTTGTATTTTTTCTGA--TT
1 TTTTGTATTTTTTCTGATTTT
* *
428223 TTTTATATTTTTTATGATTTT
1 TTTTGTATTTTTTCTGATTTT
428244 TTTT
1 TTTT
428248 AAATTCAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 17 0.45
21 19 0.50
22 2 0.05
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.77
Consensus pattern (21 bp):
TTTTGTATTTTTTCTGATTTT
Found at i:428224 original size:19 final size:19
Alignment explanation
Indices: 428202--428245 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
428192 TTTTTGTATT
* *
428202 TTTTTTGTATTTTTTCTGA
1 TTTTTTATATTTTTTATGA
428221 TTTTTTATATTTTTTATGA
1 TTTTTTATATTTTTTATGA
428240 TTTTTT
1 TTTTTT
428246 TTAAATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTTTATATTTTTTATGA
Found at i:428665 original size:32 final size:29
Alignment explanation
Indices: 428623--428682 Score: 75
Period size: 32 Copynumber: 2.0 Consensus size: 29
428613 ATGTTTTATT
*
428623 TATATTTTTTATCTTGATATTTATTAGAAATA
1 TATATGTTTTAT-TTGATATTT-TTA-AAATA
*
428655 TATATGTTTTATTTTATATTTTTAAAAT
1 TATATGTTTTATTTGATATTTTTAAAAT
428683 TAATATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 3 0.12
31 8 0.31
32 11 0.42
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (29 bp):
TATATGTTTTATTTGATATTTTTAAAATA
Found at i:428802 original size:16 final size:17
Alignment explanation
Indices: 428770--428808 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
428760 GTTTCATCTC
*
428770 TACAGTAGAGATAGAGA
1 TACATTAGAGATAGAGA
428787 TACATTAGAG-TAGAGA
1 TACATTAGAGATAGAGA
*
428803 TGCATT
1 TACATT
428809 GAACATGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.26
Consensus pattern (17 bp):
TACATTAGAGATAGAGA
Found at i:431779 original size:30 final size:31
Alignment explanation
Indices: 431745--431822 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
431735 ATTTAATAAA
431745 ATAACATTTTGATCATTTACTTAATC-ATTT
1 ATAACATTTTGATCATTTACTTAATCAATTT
* *
431775 ATAAC-TTTTTAGTCATTTACTTTATCAATTT
1 ATAACATTTTGA-TCATTTACTTAATCAATTT
* *
431806 ATAATATTATGATCATT
1 ATAACATTTTGATCATT
431823 GAGACATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 5 0.12
30 18 0.45
31 13 0.32
32 4 0.10
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (31 bp):
ATAACATTTTGATCATTTACTTAATCAATTT
Found at i:431822 original size:31 final size:29
Alignment explanation
Indices: 431752--431822 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 29
431742 AAAATAACAT
431752 TTTGATCATTTACTTAATCATTTATAACT-
1 TTTGATCATTTACTTAATCATTTATAA-TA
* *
431781 TTTTAGTCATTTACTTTATCAATTTATAATA
1 TTTGA-TCATTTACTTAATC-ATTTATAATA
431812 TTATGATCATT
1 TT-TGATCATT
431823 GAGACATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 4 0.11
30 14 0.40
31 15 0.43
32 2 0.06
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTGATCATTTACTTAATCATTTATAATA
Found at i:433159 original size:27 final size:27
Alignment explanation
Indices: 433128--433180 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
433118 AATAAATTTA
*
433128 ATTTAACTAAAAAATATATATTTATAT
1 ATTTAACTAAAAAATATATATATATAT
* * *
433155 ATTTAATTTAAATATATATATATATA
1 ATTTAACTAAAAAATATATATATATA
433181 CCCGACCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTAACTAAAAAATATATATATATAT
Found at i:433205 original size:24 final size:24
Alignment explanation
Indices: 433178--433232 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
433168 ATATATATAT
* * *
433178 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
433202 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
433226 ATACCCG
1 ATACCCG
433233 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:433215 original size:12 final size:12
Alignment explanation
Indices: 433178--433232 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
433168 ATATATATAT
*
433178 ATACCCGACCCG
1 ATACCCGACCCA
* * *
433190 ATTCTCGGCCCA
1 ATACCCGACCCA
433202 ATACCCGACCCA
1 ATACCCGACCCA
*
433214 ATACCCGGCCCA
1 ATACCCGACCCA
433226 ATACCCG
1 ATACCCG
433233 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:435531 original size:37 final size:36
Alignment explanation
Indices: 435480--435553 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
435470 CATTAAATCT
*
435480 TTTTATATTTTAAATTTTGTAAAAAAAATATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAAAATATATAAA
* *
435516 TTTTATGAATTTAAATTTTTTAAATAAAATATATAAA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAATATATAAA
435553 T
1 T
435554 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 6 0.18
37 28 0.82
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTTATAATTTAAATTTTGTAAAAAAAATATATAAA
Found at i:439478 original size:60 final size:60
Alignment explanation
Indices: 439398--439523 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
439388 AAATAATCCC
* * * * *
439398 GACTATAGGATATTACTTTATTAAGTAC-ATTGATTATTAAAAGTTATAAAATAATCTTCT
1 GACTATAGAATATTACTTTATTAAGT-CGATTAACTATTAAAAGTTACAAAATAATCATCT
* * * *
439458 GACTATATAATATTATTTTATTAAGTCGTTTAACTATTAAAAGTTACAAAATAGTCATCT
1 GACTATAGAATATTACTTTATTAAGTCGATTAACTATTAAAAGTTACAAAATAATCATCT
439518 GACTAT
1 GACTAT
439524 TCATTATGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (60 bp):
GACTATAGAATATTACTTTATTAAGTCGATTAACTATTAAAAGTTACAAAATAATCATCT
Found at i:442327 original size:36 final size:36
Alignment explanation
Indices: 442246--442334 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
442236 TTAAAATTGT
* *
442246 GCTCGACTCGTGCTCATTAAAAAAAATTGATGCTCA
1 GCTCGACTCGTACTCGTTAAAAAAAATTGATGCTCA
* *
442282 GCTCAACTCGTACTCGTTAAAAAAAATTGATGTTC-
1 GCTCGACTCGTACTCGTTAAAAAAAATTGATGCTCA
442317 GACTCGACTCG-ACTCGTT
1 G-CTCGACTCGTACTCGTT
442335 GTTTATTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
35 8 0.17
36 39 0.83
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (36 bp):
GCTCGACTCGTACTCGTTAAAAAAAATTGATGCTCA
Found at i:442364 original size:21 final size:21
Alignment explanation
Indices: 442323--442368 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
442313 GTTCGACTCG
* *
442323 ACTCGACTCGTTGTTTATTAA
1 ACTCGACTCGTTGCTCATTAA
*
442344 ACTCGACTCGTTGCTCGTTAA
1 ACTCGACTCGTTGCTCATTAA
442365 ACTC
1 ACTC
442369 ACTAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (21 bp):
ACTCGACTCGTTGCTCATTAA
Found at i:442585 original size:22 final size:22
Alignment explanation
Indices: 442555--442599 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
442545 CTAATGTAAC
* *
442555 AATCTACAAATTCACCAAACTA
1 AATCCACAAAGTCACCAAACTA
442577 AATCCACAAAGTCACCAAACTA
1 AATCCACAAAGTCACCAAACTA
442599 A
1 A
442600 CATATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.29, G:0.02, T:0.18
Consensus pattern (22 bp):
AATCCACAAAGTCACCAAACTA
Found at i:442601 original size:65 final size:65
Alignment explanation
Indices: 442512--442642 Score: 187
Period size: 65 Copynumber: 2.0 Consensus size: 65
442502 TTAAATTAAC
* *
442512 AATCCACAAATACACTAAACTAACATATTAGAA-CTA-ATGTAACAATCTACAAATTCACCAAAC
1 AATCCACAAATACACCAAACTAACATATTA-AATCTACAT-TAACAATCTACAAATACACCAAAC
442575 TA
64 TA
*
442577 AATCCACAAAGT-CACCAAACTAACATATTAAATCTACATTAACAATCTACAAATACATCAAACT
1 AATCCACAAA-TACACCAAACTAACATATTAAATCTACATTAACAATCTACAAATACACCAAACT
442641 A
65 A
442642 A
1 A
442643 CATATTAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
64 2 0.03
65 55 0.92
66 3 0.05
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.23
Consensus pattern (65 bp):
AATCCACAAATACACCAAACTAACATATTAAATCTACATTAACAATCTACAAATACACCAAACTA
Found at i:455997 original size:60 final size:60
Alignment explanation
Indices: 455890--456006 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
455880 AAATAGTCGA
* * *
455890 ATGACCATTTAATAATTTTTAATAATCAATGAACTCAACAAACCAATA-CTCTATAATTGG
1 ATGACCATTTAATAACTTTTAATAATCAAGGAACTCAACAAAACAATATCT-TATAATTGG
* * * * *
455950 ATGATCATTTTATAACTTTTAATAATCAAGGGACTTAATAAAACAATATCTTATAAT
1 ATGACCATTTAATAACTTTTAATAATCAAGGAACTCAACAAAACAATATCTTATAAT
456007 CGTGGACATG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (60 bp):
ATGACCATTTAATAACTTTTAATAATCAAGGAACTCAACAAAACAATATCTTATAATTGG
Found at i:464941 original size:71 final size:65
Alignment explanation
Indices: 464850--465048 Score: 251
Period size: 66 Copynumber: 3.0 Consensus size: 65
464840 TTATTTAGTT
* * *
464850 AAATAAATTTCAGTTTGATTAATGGTTACAGAAAAAAAAATTCGGTTAATTTGATTCGGTTAATA
1 AAATAAATTTCGGTTCGATTAACGGTTA-AGAAAAAAAAA-T---TT-ATTTGATTCGGTTAATA
464915 ATTTTC
60 ATTTTC
* *
464921 AAATAAATTTCGGTTCGATTAACGGTTAAGGAAAAAATAATTTATTTTATTCGGTTAATAATTTT
1 AAATAAATTTCGGTTCGATTAACGGTTAA-GAAAAAAAAATTTATTTGATTCGGTTAATAATTTT
464986 C
65 C
*
464987 AAATAAATTTCGGTTCGATTAACGGTTAA-AGAAAAAAAA--TATTTTATTCGGTTAATAATTTT
1 AAATAAATTTCGGTTCGATTAACGGTTAAGA-AAAAAAAATTTATTTGATTCGGTTAATAATTTT
465049 GGGTGTGATT
Statistics
Matches: 120, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
63 23 0.19
64 1 0.01
65 7 0.06
66 51 0.43
67 2 0.02
70 2 0.02
71 34 0.28
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (65 bp):
AAATAAATTTCGGTTCGATTAACGGTTAAGAAAAAAAAATTTATTTGATTCGGTTAATAATTTTC
Found at i:464949 original size:37 final size:37
Alignment explanation
Indices: 464906--465015 Score: 103
Period size: 37 Copynumber: 3.2 Consensus size: 37
464896 TAATTTGATT
464906 CGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
1 CGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
* * * **
464943 CGGTTAAGGAA----AAAAT-AATTT--ATTTTATT--
1 CGGTTAA-TAATTTTCAAATAAATTTCGGTTCGATTAA
464972 CGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
1 CGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
465009 CGGTTAA
1 CGGTTAA
465016 AGAAAAAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
28 2 0.04
29 7 0.13
31 5 0.09
32 4 0.08
33 10 0.19
34 4 0.08
35 5 0.09
37 14 0.26
38 2 0.04
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (37 bp):
CGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
Found at i:464997 original size:66 final size:63
Alignment explanation
Indices: 464898--465048 Score: 257
Period size: 66 Copynumber: 2.3 Consensus size: 63
464888 AATTCGGTTA
* *
464898 ATTTGATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAGGAAAAAATAATT
1 ATTTTATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAA-AA--
464963 T
63 T
464964 ATTTTATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAAAT
1 ATTTTATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAAAT
465027 ATTTTATTCGGTTAATAATTTT
1 ATTTTATTCGGTTAATAATTTT
465049 GGGTGTGATT
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
63 23 0.28
65 2 0.02
66 58 0.70
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (63 bp):
ATTTTATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAAAT
Found at i:465074 original size:78 final size:78
Alignment explanation
Indices: 464985--465261 Score: 314
Period size: 79 Copynumber: 3.5 Consensus size: 78
464975 TTAATAATTT
* *
464985 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAAAT-ATT-TTATTCGGTT-AATAATT
1 TCAAAT-AATTTCGGTTCGATTAA-GGTTAAAGAAAAAAAATCATTATAATT--GTTAAATAAAT
*
465047 TTGGGTGT-GATTAACAG
62 TTCGGT-TCGATTAACAG
* *
465064 TCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAAATCGGTTAATAATTTTTAAATAAATT
1 TCAAATAATTTCGGTTCGATTAA-GGTTAAAGAAAAAAAATC-ATT-ATAATTGTTAAATAAATT
*
465129 TCGGTTCGATTAACGG
63 TCGGTTCGATTAACAG
* *
465145 TCAAATAATTTCGGTTCGATTAATGTTAAAG-AAAAAAATCGGTTACTAATT-TTCAAATAAATT
1 TCAAATAATTTCGGTTCGATTAAGGTTAAAGAAAAAAAATC-ATTA-TAATTGTT-AAATAAATT
* *
465208 TCGGTTCAATTAACGG
63 TCGGTTCGATTAACAG
*
465224 TCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAA
1 TCAAATAATTTCGGTTCGATTAAGGTTAAAGAAAAAAA
465262 TTTGTTAATA
Statistics
Matches: 180, Mismatches: 9, Indels: 17
0.87 0.04 0.08
Matches are distributed among these distances:
78 37 0.21
79 79 0.44
80 18 0.10
81 42 0.23
82 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (78 bp):
TCAAATAATTTCGGTTCGATTAAGGTTAAAGAAAAAAAATCATTATAATTGTTAAATAAATTTCG
GTTCGATTAACAG
Found at i:465156 original size:26 final size:26
Alignment explanation
Indices: 465120--465246 Score: 105
Period size: 26 Copynumber: 4.8 Consensus size: 26
465110 AATAATTTTT
465120 AAATAAATTTCGGTTCGATTAACGGTC
1 AAAT-AATTTCGGTTCGATTAACGGTC
* * *
465147 AAATAATTTCGGTTCGATTAATGTTAA
1 AAATAATTTCGGTTCGATTAACGGT-C
* ** * ***
465174 AGAAAAAAATCGGTT--ACTAATTTTC
1 A-AATAATTTCGGTTCGATTAACGGTC
*
465199 AAATAAATTTCGGTTCAATTAACGGTC
1 AAAT-AATTTCGGTTCGATTAACGGTC
465226 AAATAATTTCGGTTCGATTAA
1 AAATAATTTCGGTTCGATTAA
465247 TGTTAAAGAA
Statistics
Matches: 78, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
24 2 0.03
25 9 0.12
26 42 0.54
27 15 0.19
28 10 0.13
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (26 bp):
AAATAATTTCGGTTCGATTAACGGTC
Found at i:465300 original size:79 final size:79
Alignment explanation
Indices: 465056--465286 Score: 372
Period size: 79 Copynumber: 2.9 Consensus size: 79
465046 TTTGGGTGTG
* *
465056 ATTAACAGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAAATCGGTTAATAATTTTTA
1 ATTAACGGTCAAATAATTTCGGTTCGATTAAT-GTTAAAG-AAAAAAATCGGTTAATAATTTTCA
*
465121 AATAAATTTCGGTTCG
64 AATAAATTTCGGTTCA
*
465137 ATTAACGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAATCGGTTACTAATTTTCAAA
1 ATTAACGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAATCGGTTAATAATTTTCAAA
465202 TAAATTTCGGTTCA
66 TAAATTTCGGTTCA
** *
465216 ATTAACGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAATTTGTTAATAATTTTGAAA
1 ATTAACGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAATCGGTTAATAATTTTCAAA
*
465281 TTAATT
66 TAAATT
465287 ATTTTTTCCT
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
79 103 0.73
80 7 0.05
81 31 0.22
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.37
Consensus pattern (79 bp):
ATTAACGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAATCGGTTAATAATTTTCAAA
TAAATTTCGGTTCA
Found at i:465833 original size:30 final size:30
Alignment explanation
Indices: 465799--465869 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
465789 TTAATTAAAA
465799 AGTTTGGTGGTAAGATCGCTTAATGACCAT
1 AGTTTGGTGGTAAGATCGCTTAATGACCAT
465829 AGTTTGGTGGTAAGATCGCTTAATGACCAT
1 AGTTTGGTGGTAAGATCGCTTAATGACCAT
465859 AGTTTGGTGGT
1 AGTTTGGTGGT
465870 CTCCCGCGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35
Consensus pattern (30 bp):
AGTTTGGTGGTAAGATCGCTTAATGACCAT
Found at i:466937 original size:138 final size:137
Alignment explanation
Indices: 466815--467067 Score: 354
Period size: 137 Copynumber: 1.8 Consensus size: 137
466805 AATATATTTA
466815 AATAAAACAAATGAATAAAA-AT-AA-ATATACAGATAAT-AATAAAAGGAAAAAAAATATATGT
1 AATAAAA-AAAT-AA-AAAATATAAAGATATACAGATAATAAATAAAA-G--AAAAAA-ATATGT
* * *
466876 TTATATACGCTATCAGTAATACTTAAAAT-ATAAAATTAACGATGGTTATGTATAGAGATAAATA
59 TTATATACGCTATCAATAATACTTAAAATAATAAAAATAACGATGATTATGTATAGAGATAAATA
466940 AAAATAAATACTTAC
124 AAAAT-AATACTTAC
* *
466955 AGTAAAAAAATAAAAAATATAAAGATATACATATAATAAATAAAAGAAAAAAATATGTTTATATA
1 AATAAAAAAATAAAAAATATAAAGATATACAGATAATAAATAAAAGAAAAAAATATGTTTATATA
467020 CGCTATCAATAATACTTAAAATAATAAAAATAACGATGATTATGTATA
66 CGCTATCAATAATACTTAAAATAATAAAAATAACGATGATTATGTATA
467068 CATATATATA
Statistics
Matches: 103, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
137 38 0.37
138 33 0.32
139 6 0.06
140 19 0.18
141 7 0.07
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (137 bp):
AATAAAAAAATAAAAAATATAAAGATATACAGATAATAAATAAAAGAAAAAAATATGTTTATATA
CGCTATCAATAATACTTAAAATAATAAAAATAACGATGATTATGTATAGAGATAAATAAAAATAA
TACTTAC
Found at i:467120 original size:137 final size:137
Alignment explanation
Indices: 466814--467147 Score: 360
Period size: 138 Copynumber: 2.4 Consensus size: 137
466804 AAATATATTT
*
466814 AAATAAAACAAATGAATAAAAATAAATATACAGATAAT-AATAAAAGGAAAAAAAATATATGTTT
1 AAATAAAA-AAAT-AATAAAAATAAATATACATATAATAAATAAAAGG-AAAAAAATATATGTTT
* * * *
466878 ATATACGCTATCAGTAATACTTAAAATATAAAATTAACGATGGTTATGTATAGAGATAAATAAAA
63 ATATACGCTATCAATAATACTTAAAATATAAAAATAACGATGATTATGTATACAGATAAATAAAA
466943 ATAAATACTTA
128 ATAAATAC-TA
* *
466954 CAGTAAAAAAATAA-AAAATATAAAGATATACATATAATAAATAAAA-G-AAAAAA-ATATGTTT
1 AAATAAAAAAATAATAAAA-AT-AA-ATATACATATAATAAATAAAAGGAAAAAAATATATGTTT
* *
467015 ATATACGCTATCAATAATACTTAAAATAATAAAAATAACGATGATTATGTATACATATATATAAG
63 ATATACGCTATCAATAATACTTAAAAT-ATAAAAATAACGATGATTATGTATACAGATAAATAA-
467080 TATAATAAA-A-TA
126 -A-AATAAATACTA
** * *
467092 AAATAAAATTATACATAAAAATATATATATATATATATATAAAT-AAAGGAATAAAA
1 AAATAAAAAAATA-ATAAAAATA-A-ATATACATATA-ATAAATAAAAGGAAAAAAA
467148 CGTAATAATA
Statistics
Matches: 164, Mismatches: 16, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
137 38 0.23
138 53 0.32
139 23 0.14
140 32 0.20
141 18 0.11
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (137 bp):
AAATAAAAAAATAATAAAAATAAATATACATATAATAAATAAAAGGAAAAAAATATATGTTTATA
TACGCTATCAATAATACTTAAAATATAAAAATAACGATGATTATGTATACAGATAAATAAAAATA
AATACTA
Found at i:468937 original size:105 final size:105
Alignment explanation
Indices: 468553--469499 Score: 1546
Period size: 106 Copynumber: 9.0 Consensus size: 105
468543 GTTGTGAAGT
* * *
468553 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
468618 CTGGAGTCAAATATCCTTCGTTGTGACGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
468659 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
468724 CTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
468765 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
468830 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
468871 TGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
468936 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
468976 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
469041 CTGGAGTCCAATATCCTTCGTTGTGAAGTTTG-AATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTC
* * *
469082 TGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
469147 TGGAGTCCAATATCCTTCGTTGTGAAGTTTGAAAAT---TC
66 TGGAGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTC
* * *
469185 TGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
469250 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
469290 TGACATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG-TGAACTTG-GTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
469353 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * *
469393 TGATATTGGGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
469458 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
469498 TG
1 TG
469500 GAAAACCTGC
Statistics
Matches: 799, Mismatches: 33, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
102 7 0.01
103 187 0.23
104 15 0.02
105 279 0.35
106 308 0.39
107 3 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:468984 original size:211 final size:210
Alignment explanation
Indices: 468553--469499 Score: 1548
Period size: 211 Copynumber: 4.5 Consensus size: 210
468543 GTTGTGAAGT
* * *
468553 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAG-AATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * * *
468618 CTGGAGTCAAATATCCTTCGTTGTGACGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGA
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTAATTGAGAA-ATGTTTGTTGA
* * *
468683 CAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGATGT
129 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
468748 GAAGTTGAAATTGGCTC
194 GAAGTTGAAATTGGCTC
468765 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
468830 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTATTTGAGAAATGTTTGTTGAC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTAATTGAGAAATGTTTGTTGAC
468895 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
468960 AAGTTGAAATTGGCTC
195 AAGTTGAAATTGGCTC
* *
468976 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 TGAAATTGAGAA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
469041 CTGGAGTCCAATATCCTTCGTTGTGAAGTTTG-AATTGGCTCTGTATTTGAGAAATGTTTGTTGA
65 CTGGAGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTCTGTAATTGAGAAATGTTTGTTGA
*
469105 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGT
129 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
*
469170 GAAGTTTGAAAAT---TC
194 GAAG-TTGAAATTGGCTC
* * * *
469185 TGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
469250 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-ACATTGAGAAATATTTGTTGAC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTA-ATTGAGAAATGTTTGTTGAC
469314 AACCAGCGGTCCCTTCGTCGTGAAG-TGAACTTG-GTTGTCTGGAGTCCAATATCCTTCGTTGTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
469377 AAGTTGAAATTGGCTC
195 AAGTTGAAATTGGCTC
* * * * *
469393 TGATATTGGGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTC
1 TGAAATTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
469458 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
469500 GAAAACCTGC
Statistics
Matches: 697, Mismatches: 30, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
205 7 0.01
206 33 0.05
207 11 0.02
208 234 0.34
209 12 0.02
211 282 0.40
212 118 0.17
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (210 bp):
TGAAATTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTAATTGAGAAATGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
AGTTGAAATTGGCTC
Found at i:470116 original size:52 final size:52
Alignment explanation
Indices: 470060--470159 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
470050 TTCTTTTTTC
* *
470060 TTTTTCCTTTTTTT-AATTTTAGGGCGCCCT-TCCGGGTTTTCACCCTAAACGT
1 TTTTTCCTTTTTTTCAA-CTTAGGACGCCCTCT-CGGGTTTTCACCCTAAACGT
** *
470112 TTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTCCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
470160 GCGAAAGTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 38 0.93
53 3 0.07
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (52 bp):
TTTTTCCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGT
Found at i:471381 original size:59 final size:58
Alignment explanation
Indices: 471281--471398 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 58
471271 TCTCTGTCAA
471281 GGACATATCAGCTGCCAACCTTCTAAGGGTTCTCTTATCGGTTTCAGTGGCTTTTTCTG
1 GGACATATCAGCTGCCAACCTTCTAAGGGTTCTCTTATCGGTTTCAGTGGC-TTTTCTG
471340 GGACATATCCAGCTGCCAACCTTCTAAGGGTT-TCTTATCGGTTTCAGTGGCTTTTCTG
1 GGACATAT-CAGCTGCCAACCTTCTAAGGGTTCTCTTATCGGTTTCAGTGGCTTTTCTG
471398 G
1 G
471399 ATAACTCCGA
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
58 8 0.14
59 27 0.47
60 23 0.40
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (58 bp):
GGACATATCAGCTGCCAACCTTCTAAGGGTTCTCTTATCGGTTTCAGTGGCTTTTCTG
Found at i:480441 original size:27 final size:26
Alignment explanation
Indices: 480402--480487 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
480392 AATATAGAAT
*
480402 ATAAAAAGAATATATATGATGGTAATA
1 ATAAAAAG-ATATATATAATGGTAATA
* * * *
480429 ATAATAAAGATATAAACAATGGGAAAA
1 ATAA-AAAGATATATATAATGGTAATA
* *
480456 ATAAGAAGATATATATAATAGTAATAA
1 ATAAAAAGATATATATAATGGTAAT-A
480483 ATAAA
1 ATAAA
480488 TAAAAAACTA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
26 15 0.33
27 26 0.58
28 4 0.09
ACGTcount: A:0.60, C:0.01, G:0.13, T:0.26
Consensus pattern (26 bp):
ATAAAAAGATATATATAATGGTAATA
Found at i:480969 original size:2 final size:2
Alignment explanation
Indices: 480962--480986 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
480952 ATACATAAAA
480962 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
480987 AATAAAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:487774 original size:24 final size:26
Alignment explanation
Indices: 487729--487778 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
487719 CGTTCGTGAA
*
487729 AGTTCGATTATATGTTCGTTTATGTT
1 AGTTCGATTATATGTTCATTTATGTT
487755 AGTTC-ATT-TATGTTCATTTATGTT
1 AGTTCGATTATATGTTCATTTATGTT
487779 CGAACAGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.65
25 3 0.13
26 5 0.22
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (26 bp):
AGTTCGATTATATGTTCATTTATGTT
Found at i:492886 original size:39 final size:39
Alignment explanation
Indices: 492817--492992 Score: 255
Period size: 39 Copynumber: 4.5 Consensus size: 39
492807 AACCAAAGCA
* * * *
492817 GGACTTGCCA-CTCTTGACGCAGCAGAATGCTCATTATCC
1 GGACTTG-CAGCTCTCGATGCAGCAGGATGCTCATCATCC
* *
492856 GGACTTGCAACTCTCGATGCAACAGGATGCTCATCATCC
1 GGACTTGCAGCTCTCGATGCAGCAGGATGCTCATCATCC
*
492895 GAACTTGCAGCTCTCGATGCAGCAGGATGCTCATCATCC
1 GGACTTGCAGCTCTCGATGCAGCAGGATGCTCATCATCC
*
492934 GAACTTGCAGCTCTCGATGCAGCAGGATGCTCATCATCC
1 GGACTTGCAGCTCTCGATGCAGCAGGATGCTCATCATCC
*
492973 GGGCTTGCAGCTCTCGATGC
1 GGACTTGCAGCTCTCGATGC
492993 TCCATCATGT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
38 2 0.02
39 124 0.98
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
GGACTTGCAGCTCTCGATGCAGCAGGATGCTCATCATCC
Found at i:501007 original size:50 final size:50
Alignment explanation
Indices: 500944--501045 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
500934 TTTATCCTAT
*
500944 TTTAGTATGTATTTATTTTAAAATTAATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTAATTATTGGGATATCTTGTGTTGTA
*
500994 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTGTTGTA
1 TTTAGTATGTATTTATTTTAAAATTAATTATTGGGATATCTTGTGTTGTA
501044 TT
1 TT
501046 CAATAATTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTAATTATTGGGATATCTTGTGTTGTA
Found at i:501647 original size:30 final size:30
Alignment explanation
Indices: 501613--501676 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
501603 CCGCATGAAG
501613 CATTGGTCGCCCAGACCACCCGACGACCTT
1 CATTGGTCGCCCAGACCACCCGACGACCTT
*
501643 CATTGGTCGCCCAGATCACCCGACGACCTT
1 CATTGGTCGCCCAGACCACCCGACGACCTT
501673 CATT
1 CATT
501677 CGAACTGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.41, G:0.19, T:0.20
Consensus pattern (30 bp):
CATTGGTCGCCCAGACCACCCGACGACCTT
Found at i:507026 original size:21 final size:21
Alignment explanation
Indices: 507000--507045 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
506990 CAAGTTCAAG
507000 ACACTTGAAGAATATTACAAA
1 ACACTTGAAGAATATTACAAA
507021 ACACTTGAAGAATATTACAAA
1 ACACTTGAAGAATATTACAAA
507042 ACAC
1 ACAC
507046 CTATCCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (21 bp):
ACACTTGAAGAATATTACAAA
Found at i:516819 original size:17 final size:18
Alignment explanation
Indices: 516776--516816 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
516766 AATTTATATT
516776 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
516793 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
516811 ATTAAA
1 AGTAAA
516817 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:517118 original size:51 final size:50
Alignment explanation
Indices: 517010--517134 Score: 128
Period size: 50 Copynumber: 2.5 Consensus size: 50
517000 GATAAATAGG
* * * * * * * *
517010 TATAGCGCGGAACAGGGGGCGCGTTATAGCCACGTGTAACCCAGTCAGCG
1 TATAGCGCGGTACAGGGGGCGCGCTATACCCACGTGGAACCAAATCAACA
**
517060 TATAGCGCGGTACAGGGGGCGCGCTATACCCCACGTGGCTCCAAATCAACA
1 TATAGCGCGGTACAGGGGGCGCGCTATA-CCCACGTGGAACCAAATCAACA
517111 TATAGCGCGGGT-CA-GGGGCGCGCT
1 TATAGCGC-GGTACAGGGGGCGCGCT
517135 TTACTGCTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
50 36 0.57
51 24 0.38
52 3 0.05
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.16
Consensus pattern (50 bp):
TATAGCGCGGTACAGGGGGCGCGCTATACCCACGTGGAACCAAATCAACA
Found at i:527585 original size:2 final size:2
Alignment explanation
Indices: 527578--527633 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
527568 TCCTGCAAGA
527578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
527620 A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
527634 ATACTAACTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:528472 original size:2 final size:2
Alignment explanation
Indices: 528465--528503 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
528455 TTGAATTGAA
528465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
528504 AAGAACACCC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:529857 original size:20 final size:20
Alignment explanation
Indices: 529829--529868 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
529819 TACGATGGTT
*
529829 ATTTTATAATAATTTGATAA
1 ATTTAATAATAATTTGATAA
* *
529849 ATTTAATAATTATTTTATAA
1 ATTTAATAATAATTTGATAA
529869 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTAATAATAATTTGATAA
Found at i:531826 original size:16 final size:17
Alignment explanation
Indices: 531805--531847 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
531795 ATTTGGGAAT
531805 ACATTACT-GGAATGTA
1 ACATTACTGGGAATGTA
531821 ACATTACTATGGGAATGTA
1 ACATTAC--TGGGAATGTA
*
531840 GCATTACT
1 ACATTACT
531848 ATGAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.30
17 1 0.04
18 1 0.04
19 14 0.61
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (17 bp):
ACATTACTGGGAATGTA
Found at i:531837 original size:19 final size:19
Alignment explanation
Indices: 531813--531850 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
531803 ATACATTACT
531813 GGAATGTAACATTACTATG
1 GGAATGTAACATTACTATG
*
531832 GGAATGTAGCATTACTATG
1 GGAATGTAACATTACTATG
531851 AAAATGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
GGAATGTAACATTACTATG
Found at i:531864 original size:19 final size:19
Alignment explanation
Indices: 531815--531857 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
531805 ACATTACTGG
* **
531815 AATGTAACATTACTATGGG
1 AATGTAGCATTACTATGAA
531834 AATGTAGCATTACTATGAA
1 AATGTAGCATTACTATGAA
531853 AATGT
1 AATGT
531858 TGTATTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (19 bp):
AATGTAGCATTACTATGAA
Found at i:533923 original size:16 final size:16
Alignment explanation
Indices: 533904--533937 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
533894 CAATATACGA
533904 ATAAACATATATTTAT
1 ATAAACATATATTTAT
**
533920 ATAAATGTATATTTAT
1 ATAAACATATATTTAT
533936 AT
1 AT
533938 TTATATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAACATATATTTAT
Found at i:534011 original size:16 final size:18
Alignment explanation
Indices: 533979--534012 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
533969 TATTAATGTA
533979 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
533997 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
534013 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:534674 original size:130 final size:130
Alignment explanation
Indices: 534470--534717 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
534460 AATTTTCTTC
* *
534470 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGCGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGCGCTAACACATGTCAGAT
** *
534535 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
534600 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGCGCTAACACATGTCAGAT
534665 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
534718 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGCGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:535165 original size:35 final size:35
Alignment explanation
Indices: 535115--535190 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
535105 AATTGAATTT
* *
535115 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
535150 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
535185 AATTGA
1 AATTGA
535191 TGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:535591 original size:3 final size:3
Alignment explanation
Indices: 535567--535613 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
535557 GTCTTTTTTA
*
535567 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT TAT TAT
535612 TA
1 TA
535614 AATTATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 3 0.08
3 29 0.76
4 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:535592 original size:10 final size:10
Alignment explanation
Indices: 535567--535625 Score: 77
Period size: 10 Copynumber: 5.8 Consensus size: 10
535557 GTCTTTTTTA
535567 TATTATTTAAT
1 TATTA-TTAAT
535578 T-TTATTAAT
1 TATTATTAAT
535587 TATTATTAAT
1 TATTATTAAT
535597 TATTATT-AT
1 TATTATTAAT
535606 TATTATTAAAT
1 TATTATT-AAT
535617 TATATATTA
1 TAT-TATTA
535626 CAAATTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
9 15 0.34
10 18 0.41
11 7 0.16
12 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTATTAAT
Found at i:535772 original size:25 final size:25
Alignment explanation
Indices: 535743--535840 Score: 164
Period size: 25 Copynumber: 4.0 Consensus size: 25
535733 AACCAACCCC
535743 TCAGATTAGGGTTTCAAACCCTAAA
1 TCAGATTAGGGTTTCAAACCCTAAA
535768 TCAGATTAGGGTTTCAAACCCTAAA
1 TCAGATTAGGGTTTCAAACCCTAAA
535793 TCAGATTAGGGTTTCAAACCCTAAA
1 TCAGATTAGGGTTTCAAACCCTAAA
*
535818 ACA-ATTTAGGGTTTC-AACCCTAA
1 TCAGA-TTAGGGTTTCAAACCCTAA
535841 TCCCCTAATT
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
24 9 0.13
25 62 0.87
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (25 bp):
TCAGATTAGGGTTTCAAACCCTAAA
Found at i:550657 original size:130 final size:130
Alignment explanation
Indices: 550342--550650 Score: 415
Period size: 130 Copynumber: 2.3 Consensus size: 130
550332 TCAACATCAA
*
550342 CTGACCAGA-CTTCCTCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATAA
1 CTGACCAGATC-TCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAACCAGCCGTCCTCATAA
* * * * *
550406 CGTAGGAACCGAGTTATCACCCTTCCTAAAGGTGGCCAGAGTTTTTCATCATGTATGAACCGTGT
64 CGTAGGAACCGAGTTATCA--C--CCTAAAGATGGCCAGAATTCTTCATCATGTAGGAACAGTGT
550471 CATCCC
125 CATCCC
* * * * *
550477 CAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACG
1 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTCCTCATAACG
* *
550542 TAGGAACCGTGTTATCA-CCTAAAGATGGCCAAGAATTCTTCATCATGTAGGAGCAGTGTCATCC
66 TAGGAACCGAGTTATCACCCTAAAGATGGCC-AGAATTCTTCATCATGTAGGAACAGTGTCATCC
550606 C
130 C
*
550607 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGA
1 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGA
550651 CGACCAGACC
Statistics
Matches: 154, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
129 12 0.08
130 68 0.44
134 38 0.25
135 35 0.23
136 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (130 bp):
CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTCCTCATAACG
TAGGAACCGAGTTATCACCCTAAAGATGGCCAGAATTCTTCATCATGTAGGAACAGTGTCATCCC
Found at i:550858 original size:9 final size:10
Alignment explanation
Indices: 550840--550901 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 10
550830 GTCTTTTTTA
550840 TATTATTTAAT
1 TATTA-TTAAT
550851 T-TTATTAAT
1 TATTATTAAT
550860 TATTTATT-AT
1 TA-TTATTAAT
550870 TATTATTATTAT
1 TATTATTA--AT
550882 TATTATTAAAT
1 TATTATT-AAT
550893 TATATATTA
1 TAT-TATTA
550902 CAAATTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
9 11 0.25
10 7 0.16
11 12 0.27
12 13 0.30
13 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATTATTAAT
Found at i:550861 original size:17 final size:16
Alignment explanation
Indices: 550840--550889 Score: 68
Period size: 15 Copynumber: 3.1 Consensus size: 16
550830 GTCTTTTTTA
550840 TATTATTTAATT-TTAT
1 TATTATTT-ATTATTAT
550856 TAATTATTTATTATTAT
1 T-ATTATTTATTATTAT
550873 TATTA-TTATTATTAT
1 TATTATTTATTATTAT
550888 TA
1 TA
550890 AATTATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 12 0.38
16 8 0.25
17 12 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTATTTATTATTAT
Found at i:550871 original size:3 final size:3
Alignment explanation
Indices: 550840--550889 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
550830 GTCTTTTTTA
*
550840 TAT TAT T-T AAT T-T TAT TAAT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TA-T TAT TAT TAT TAT TAT TAT TAT
550885 TAT TA
1 TAT TA
550890 AATTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 3 0.07
3 32 0.78
4 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:551048 original size:25 final size:25
Alignment explanation
Indices: 551019--551116 Score: 164
Period size: 25 Copynumber: 4.0 Consensus size: 25
551009 AACCAACCCC
551019 TCAGATTAGGGTTTCAAACCCTAAA
1 TCAGATTAGGGTTTCAAACCCTAAA
551044 TCAGATTAGGGTTTCAAACCCTAAA
1 TCAGATTAGGGTTTCAAACCCTAAA
551069 TCAGATTAGGGTTTCAAACCCTAAA
1 TCAGATTAGGGTTTCAAACCCTAAA
*
551094 ACA-ATTTAGGGTTTC-AACCCTAA
1 TCAGA-TTAGGGTTTCAAACCCTAA
551117 TCCCCTAACT
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
24 9 0.13
25 62 0.87
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (25 bp):
TCAGATTAGGGTTTCAAACCCTAAA
Found at i:553838 original size:31 final size:31
Alignment explanation
Indices: 553765--553841 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
553755 GTTAACGCGT
553765 GGTGACCACATCTTAAATAAATAAAAACAAA
1 GGTGACCACATCTTAAATAAATAAAAACAAA
* ** * * *
553796 AGTGAGAACATCTTAATTAAATAAGAACGAA
1 GGTGACCACATCTTAAATAAATAAAAACAAA
*
553827 GGTGATCACATCTTA
1 GGTGACCACATCTTA
553842 TGTATTTTGA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (31 bp):
GGTGACCACATCTTAAATAAATAAAAACAAA
Done.