Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 35
Found at i:949040 original size:29 final size:30
Alignment explanation
Indices: 948989--949050 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
948979 AAATTTTGTC
* * **
948989 TAGTGACTAAATTGTAAGTTTTG-AAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
949018 TAGTGACTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
949048 TAG
1 TAG
949051 GGAACAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (30 bp):
TAGTGACTAAAGTATAAACTTTGAAAAGTT
Found at i:949075 original size:30 final size:29
Alignment explanation
Indices: 948997--949077 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 29
948987 TCTAGTGACT
* * * * *
948997 AAATTGTAAGTTTTGAAAGTTTAGTGACT
1 AAATTATAACTTTTAAAAGTTTAGGGACA
* *
949026 AAAGTATAAACTTTGAAAAGTTTAGGGAACA
1 AAATTAT-AACTTTTAAAAGTTTAGGG-ACA
*
949057 AAATTATAATTTTTAAAAGTT
1 AAATTATAACTTTTAAAAGTT
949078 ATATATTTGA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 5 0.12
30 27 0.68
31 8 0.20
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (29 bp):
AAATTATAACTTTTAAAAGTTTAGGGACA
Found at i:950324 original size:20 final size:20
Alignment explanation
Indices: 950281--950325 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
950271 TGGAAGGTTG
*
950281 TTTGGGAACCAAATTGCAAG
1 TTTGGGAACCAAATTGCAAA
*
950301 TTTGGGAACCAAATTGTAAA
1 TTTGGGAACCAAATTGCAAA
950321 TTTGG
1 TTTGG
950326 TAAATTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (20 bp):
TTTGGGAACCAAATTGCAAA
Found at i:952592 original size:20 final size:20
Alignment explanation
Indices: 952569--952622 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
952559 TTCCATATTC
*
952569 TTCCATACTCTTCCATAAGG-
1 TTCCACACTCTTCCA-AAGGA
952589 TTCCACACATC-TCCAAAGGA
1 TTCCACAC-TCTTCCAAAGGA
952609 TTCCACACTCTTCC
1 TTCCACACTCTTCC
952623 GCAAGCTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.20
20 22 0.73
21 2 0.07
ACGTcount: A:0.26, C:0.37, G:0.07, T:0.30
Consensus pattern (20 bp):
TTCCACACTCTTCCAAAGGA
Found at i:957265 original size:40 final size:40
Alignment explanation
Indices: 957181--957268 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
957171 TTCCACAAGC
* * *** * *
957181 TTCTAGAGAGTTCTACACTTCTCTAGAGTTCTTTGGAATA
1 TTCTAGAAAATTCTACACTTCTCTAGAAAGCTTAGAAATA
957221 TTCTAGAAAATTCTACACTTCTCTAGAAAGCTATAGAAAT-
1 TTCTAGAAAATTCTACACTTCTCTAGAAAGCT-TAGAAATA
957261 TTCTAGAA
1 TTCTAGAA
957269 CCTCTCCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 35 0.88
41 5 0.12
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (40 bp):
TTCTAGAAAATTCTACACTTCTCTAGAAAGCTTAGAAATA
Found at i:958003 original size:60 final size:60
Alignment explanation
Indices: 957899--958020 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
957889 TAAAGAATAG
* * *
957899 TCAGGTGACCATTTTGTTACTTTTAATAGTTAAGGGACTCAATAATA-CAACTCTC-TATAA
1 TCAGGGGACCATTTTGTAACTTTTAATAGTTAAGAGACTCAATAA-AGCAACTC-CATATAA
* * *
957959 TCAGGGGACCATTTTGTAACTTTTAATAGTTGATAGACTTAATAAAGCAACTCCATATAA
1 TCAGGGGACCATTTTGTAACTTTTAATAGTTAAGAGACTCAATAAAGCAACTCCATATAA
958019 TC
1 TC
958021 GAGAGGTACT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
59 2 0.04
60 52 0.96
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (60 bp):
TCAGGGGACCATTTTGTAACTTTTAATAGTTAAGAGACTCAATAAAGCAACTCCATATAA
Found at i:961301 original size:7 final size:7
Alignment explanation
Indices: 961289--961437 Score: 95
Period size: 7 Copynumber: 21.4 Consensus size: 7
961279 AATCGAAATA
961289 AGGGTTT
1 AGGGTTT
961296 AGGGTTT
1 AGGGTTT
* *
961303 ATGATTT
1 AGGGTTT
961310 AGGGTTT
1 AGGGTTT
* **
961317 ATGACTT
1 AGGGTTT
* *
961324 AAGGATT
1 AGGGTTT
961331 AGGGTTT
1 AGGGTTT
*
961338 AGGATTT
1 AGGGTTT
*
961345 A-TGTCTT
1 AGGGT-TT
*
961352 AGGGATT
1 AGGGTTT
** *
961359 AATGCTT
1 AGGGTTT
* *
961366 AAGGCTT
1 AGGGTTT
961373 AGGGTTT
1 AGGGTTT
961380 AGGGTTT
1 AGGGTTT
*
961387 AGGATTT
1 AGGGTTT
961394 AGGGTTT
1 AGGGTTT
*
961401 AGAGTTT
1 AGGGTTT
*
961408 AAGGTTT
1 AGGGTTT
* *
961415 AGGATGT
1 AGGGTTT
961422 A-GGTTT
1 AGGGTTT
961428 AGGGTTT
1 AGGGTTT
961435 AGG
1 AGG
961438 TTGGAATATA
Statistics
Matches: 106, Mismatches: 33, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
6 5 0.05
7 100 0.94
8 1 0.01
ACGTcount: A:0.23, C:0.03, G:0.34, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:961354 original size:42 final size:41
Alignment explanation
Indices: 961289--961401 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 41
961279 AATCGAAATA
961289 AGGGTTTAGGGTTTATGATTTAGGGTTTATGACTTAAGGATT
1 AGGGTTTAGGGTTTATGATTTAGGGTTTATG-CTTAAGGATT
* * *
961331 AGGGTTTAGGATTTATG-TCTTAGGGATTAATGCTTAAGGCTT
1 AGGGTTTAGGGTTTATGAT-TTAGGG-TTTATGCTTAAGGATT
*
961373 AGGGTTTAGGGTTTAGGATTTAGGGTTTA
1 AGGGTTTAGGGTTTATGATTTAGGGTTTA
961402 GAGTTTAAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
41 4 0.06
42 52 0.84
43 6 0.10
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.42
Consensus pattern (41 bp):
AGGGTTTAGGGTTTATGATTTAGGGTTTATGCTTAAGGATT
Found at i:961410 original size:42 final size:42
Alignment explanation
Indices: 961289--961437 Score: 153
Period size: 42 Copynumber: 3.6 Consensus size: 42
961279 AATCGAAATA
*
961289 AGGGTTTAGGGTTTATGATTTAGGGTTTATGA-CTTAAGGATT
1 AGGGTTTAGGGTTTAGGATTTAGGGTTTA-GAGCTTAAGGATT
* * * *
961331 AGGGTTTAGGATTTATG-TCTTAGGGATTA-ATGCTTAAGGCTT
1 AGGGTTTAGGGTTTAGGAT-TTAGGGTTTAGA-GCTTAAGGATT
* *
961373 AGGGTTTAGGGTTTAGGATTTAGGGTTTAGAGTTTAAGGTTT
1 AGGGTTTAGGGTTTAGGATTTAGGGTTTAGAGCTTAAGGATT
* * *
961415 AGGATGTA-GGTTTAGGGTTTAGG
1 AGGGTTTAGGGTTTAGGATTTAGG
961438 TTGGAATATA
Statistics
Matches: 91, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
40 1 0.01
41 15 0.16
42 73 0.80
43 2 0.02
ACGTcount: A:0.23, C:0.03, G:0.34, T:0.41
Consensus pattern (42 bp):
AGGGTTTAGGGTTTAGGATTTAGGGTTTAGAGCTTAAGGATT
Found at i:963849 original size:29 final size:28
Alignment explanation
Indices: 963799--963853 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
963789 GTAAACATAA
* *
963799 ATAATATTTTTAATATTTATATTTTTAT
1 ATAATATTTTTAAGATGTATATTTTTAT
*
963827 ATAATGTTTTTATAGATGTATATTTTT
1 ATAATATTTTTA-AGATGTATATTTTT
963854 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (28 bp):
ATAATATTTTTAAGATGTATATTTTTAT
Found at i:968363 original size:40 final size:40
Alignment explanation
Indices: 968249--968366 Score: 209
Period size: 40 Copynumber: 3.0 Consensus size: 40
968239 CTCAATAATA
* * *
968249 AACAGCAAAGGATCTGTGTATAAATGAGTGAAGGAAAATG
1 AACAGCAAAGAATCTGTGTGTAAATGAGTGAAGGCAAATG
968289 AACAGCAAAGAATCTGTGTGTAAATGAGTGAAGGCAAATG
1 AACAGCAAAGAATCTGTGTGTAAATGAGTGAAGGCAAATG
968329 AACAGCAAAGAATCTGTGTGTAAATGAGTGAAGGCAAA
1 AACAGCAAAGAATCTGTGTGTAAATGAGTGAAGGCAAA
968367 GCAATGTTGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.44, C:0.09, G:0.27, T:0.19
Consensus pattern (40 bp):
AACAGCAAAGAATCTGTGTGTAAATGAGTGAAGGCAAATG
Found at i:969396 original size:36 final size:37
Alignment explanation
Indices: 969287--969399 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 37
969277 AAAAAACATA
969287 AATTCAAATATGTTTAAGTGTACATTTCATTTAAATG
1 AATTCAAATATGTTTAAGTGTACATTTCATTTAAATG
* * * * * *
969324 -ATTGAGATTTG-TTAAATCTTCAGACATATCATTTAAA-G
1 AATTCAAATATGTTTAAGT-GT---ACATTTCATTTAAATG
969362 AATTCAAATATGTTTAAGTGTACATTTCATTTAAATG
1 AATTCAAATATGTTTAAGTGTACATTTCATTTAAATG
969399 A
1 A
969400 TTTAGATTTG
Statistics
Matches: 57, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
35 5 0.09
36 22 0.39
37 2 0.04
38 1 0.02
39 22 0.39
40 5 0.09
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (37 bp):
AATTCAAATATGTTTAAGTGTACATTTCATTTAAATG
Found at i:969410 original size:75 final size:75
Alignment explanation
Indices: 969287--969437 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
969277 AAAAAACATA
969287 AATTCAAATATGTTTAAGTGTACATTTCATTTAAATGATTGAGATTTGTTAAATCTTCAGACATA
1 AATTCAAATATGTTTAAGTGTACATTTCATTTAAATGATTGAGATTTGTTAAATCTTCAGACATA
*
969352 TCATTTAAAG
66 TAATTTAAAG
*
969362 AATTCAAATATGTTTAAGTGTACATTTCATTTAAATGATTTAGATTTGTTAAATCTTCAGACATA
1 AATTCAAATATGTTTAAGTGTACATTTCATTTAAATGATTGAGATTTGTTAAATCTTCAGACATA
969427 TAATTTAAAG
66 TAATTTAAAG
969437 A
1 A
969438 TATTTTTCTA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (75 bp):
AATTCAAATATGTTTAAGTGTACATTTCATTTAAATGATTGAGATTTGTTAAATCTTCAGACATA
TAATTTAAAG
Found at i:970807 original size:23 final size:23
Alignment explanation
Indices: 970781--970859 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
970771 GGGAATGTTA
970781 GAAACATCATTCAATTCTGAATT
1 GAAACATCATTCAATTCTGAATT
* ** *
970804 GAAAAATCAGGCTT-AATAAGTG--TA
1 GAAACATCA---TTCAAT-TCTGAATT
970828 GAAACATCATTCAATTCTGAATT
1 GAAACATCATTCAATTCTGAATT
970851 GAAACATCA
1 GAAACATCA
970860 GGCTTAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
21 4 0.10
22 3 0.07
23 18 0.44
24 9 0.22
25 3 0.07
26 4 0.10
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (23 bp):
GAAACATCATTCAATTCTGAATT
Found at i:970833 original size:47 final size:47
Alignment explanation
Indices: 970779--970869 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
970769 CAGGGAATGT
970779 TAGAAACATCATTCAATTCTGAATTGAAAAATCAGGCTTAATAAGTG
1 TAGAAACATCATTCAATTCTGAATTGAAAAATCAGGCTTAATAAGTG
*
970826 TAGAAACATCATTCAATTCTGAATTGAAACATCAGGCTTAATAA
1 TAGAAACATCATTCAATTCTGAATTGAAAAATCAGGCTTAATAA
970870 CTGTCGCTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (47 bp):
TAGAAACATCATTCAATTCTGAATTGAAAAATCAGGCTTAATAAGTG
Found at i:973221 original size:12 final size:12
Alignment explanation
Indices: 973197--973230 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
973187 GATGCATTAA
973197 TTAATTGATAATT
1 TTAATT-ATAATT
973210 TTAATTATAATT
1 TTAATTATAATT
*
973222 TCAATTATA
1 TTAATTATA
973231 TTATAATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (12 bp):
TTAATTATAATT
Found at i:973727 original size:22 final size:22
Alignment explanation
Indices: 973691--973732 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
973681 GTTTAGTCTC
* * *
973691 CTTAATGAGATATTTTGGATGG
1 CTTAATGAAACATTTCGGATGG
973713 CTTAATGAAACATTTCGGAT
1 CTTAATGAAACATTTCGGAT
973733 AACTTATCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (22 bp):
CTTAATGAAACATTTCGGATGG
Found at i:983252 original size:98 final size:98
Alignment explanation
Indices: 983083--983310 Score: 359
Period size: 98 Copynumber: 2.3 Consensus size: 98
983073 ACACTAGGAA
*
983083 GCTAACTCATTTACTATAAATTTATGACATATTCGTTTATACAAGTCAATGACTACAAACCTCTT
1 GCTAACTCATTTACTATAAATTTATGACATATTCGTTTATACAACTCAATGACTACAAACCTCTT
* * *
983148 CATCTAACCATCTAGATACGATGTAAATCTATG
66 CATCTAACCAGCTACATACGATGTAAATATATG
* * *
983181 GCTAACTAATTTACTATAAATTTATGACATATTTGTTTATACAACTCAATGATTACAAACCTCTT
1 GCTAACTCATTTACTATAAATTTATGACATATTCGTTTATACAACTCAATGACTACAAACCTCTT
983246 CATCTAACCAGCTACATACGATGTAAATATATG
66 CATCTAACCAGCTACATACGATGTAAATATATG
* *
983279 GCTAACTCATTTGCGT-TAGATTTATGACATAT
1 GCTAACTCATTTAC-TATAAATTTATGACATAT
983311 CAATTGAATA
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
98 118 0.99
99 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (98 bp):
GCTAACTCATTTACTATAAATTTATGACATATTCGTTTATACAACTCAATGACTACAAACCTCTT
CATCTAACCAGCTACATACGATGTAAATATATG
Found at i:985406 original size:20 final size:22
Alignment explanation
Indices: 985383--985428 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
985373 TATTATAAGT
*
985383 ATATTTAT-GAATAT-ATAAAA
1 ATATTTATACAATATAATAAAA
985403 ATATTTATACAATATAATAAAA
1 ATATTTATACAATATAATAAAA
985425 ATAT
1 ATAT
985429 CACTAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 5 0.22
22 10 0.43
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATTTATACAATATAATAAAA
Found at i:986695 original size:3 final size:3
Alignment explanation
Indices: 986687--986775 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
986677 TTAATATATT
*
986687 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
986735 TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
986776 TTAGTATCTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:987514 original size:114 final size:114
Alignment explanation
Indices: 987082--987495 Score: 731
Period size: 114 Copynumber: 3.6 Consensus size: 114
987072 AGAATTATGC
* *
987082 AAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
987147 TATGAACTTTCTCTGGAAAAGCTGATCCATCAA-ATGATGGATTCAAGT
66 TATGAACTTTCTCTGGAAAAGTTAATCCATCAATTTGATGAATTCAGGT
987195 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
987260 TATGAACTTTCTCTGGAAAAGTTAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGTTAATCCATCAATTTGATGAATTCAGGT
*
987309 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAG
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
987374 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGTTAATCCATCAATTTGATGAATTCAGGT
987423 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
987488 TATGAACT
66 TATGAACT
987496 CTACCTGGCA
Statistics
Matches: 288, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
113 94 0.33
114 194 0.67
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (114 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGTTAATCCATCAATTTGATGAATTCAGGT
Found at i:989231 original size:83 final size:83
Alignment explanation
Indices: 988175--989216 Score: 1834
Period size: 83 Copynumber: 12.6 Consensus size: 83
988165 GTAGTTCTTA
* * * * * * *
988175 CCAAAACAGATTAGATAACTCAAAGGACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
988240 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
988258 CTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGA-ACATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA-ACACATTCATCTTCTA
988322 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* *
988341 CTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
988406 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
988424 CCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
988489 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
988507 TCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
*
988572 ATTCAATGATTTGTTCTG
66 ATTCAATGATTGGTTCTG
*
988590 CCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
988655 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
988673 CCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
*
988738 ATTCAATGATTTGTTCTG
66 ATTCAATGATTGGTTCTG
*
988756 CCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
988821 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
988839 TCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
*
988904 ATTCAATTATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
988922 CCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
*
988987 ATTCAATGATTTGTTCTG
66 ATTCAATGATTGGTTCTG
*
989005 CCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
989070 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
989088 TCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
*
989153 ATTCAATGATTTGTTCTG
66 ATTCAATGATTGGTTCTG
989171 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
989217 TGGCAAATTC
Statistics
Matches: 925, Mismatches: 32, Indels: 4
0.96 0.03 0.00
Matches are distributed among these distances:
82 1 0.00
83 924 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
ATTCAATGATTGGTTCTG
Found at i:990381 original size:8 final size:8
Alignment explanation
Indices: 990368--990437 Score: 86
Period size: 8 Copynumber: 8.4 Consensus size: 8
990358 CTTGACCCCC
990368 TTTCTTTT
1 TTTCTTTT
*
990376 TTTCTTCT
1 TTTCTTTT
*
990384 TTTCTTCT
1 TTTCTTTT
990392 TTTCTTTT
1 TTTCTTTT
990400 TTTCTTTT
1 TTTCTTTT
*
990408 CTCCTTTTTTT
1 -T--TTCTTTT
990419 TTTCTTTT
1 TTTCTTTT
990427 TTTCTTTT
1 TTTCTTTT
990435 TTT
1 TTT
990438 TTTCTTCAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
8 47 0.85
9 1 0.02
10 1 0.02
11 6 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTCTTTT
Found at i:990393 original size:19 final size:19
Alignment explanation
Indices: 990369--990443 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
990359 TTGACCCCCT
*
990369 TTCTTTTTTTCTTCTTTTC
1 TTCTTTTTTTTTTCTTTTC
990388 TTCTTTTCTTTTTTTCTTTTC
1 TTC-TTT-TTTTTTTCTTTTC
* *
990409 TCCTTTTTTTTTTCTTTTT
1 TTCTTTTTTTTTTCTTTTC
990428 TTCTTTTTTTTTTCTT
1 TTCTTTTTTTTTTCTT
990444 CAAGCATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 30 0.60
20 6 0.12
21 14 0.28
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTCTTTTTTTTTTCTTTTC
Found at i:990404 original size:21 final size:20
Alignment explanation
Indices: 990367--990444 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 20
990357 CCTTGACCCC
*
990367 CTTTCTTTTTTTCTTCTTTT
1 CTTTTTTTTTTTCTTCTTTT
990387 CTTCTTTTCTTTTT-TTCTTTT
1 CTT-TTTT-TTTTTCTTCTTTT
*
990408 CTCCTTTTTTTTTTCTTTTTTT
1 CT--TTTTTTTTTTCTTCTTTT
990430 C-TTTTTTTTTTCTTC
1 CTTTTTTTTTTTCTTC
990445 AAGCATAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 13 0.26
20 3 0.06
21 17 0.34
22 16 0.32
23 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
CTTTTTTTTTTTCTTCTTTT
Found at i:1001136 original size:19 final size:19
Alignment explanation
Indices: 1001112--1001153 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1001102 TTTTATAAGT
*
1001112 ATATTTAT-GAATATATAAA
1 ATATTTATACAATATA-AAA
1001131 ATATTTATACAATATAAAA
1 ATATTTATACAATATAAAA
1001150 ATAT
1 ATAT
1001154 CACTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATTTATACAATATAAAA
Found at i:1002214 original size:3 final size:3
Alignment explanation
Indices: 1002206--1002300 Score: 154
Period size: 3 Copynumber: 31.7 Consensus size: 3
1002196 TTAATATATT
1002206 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1002254 CAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1002301 TTAGTATCTT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1005276 original size:30 final size:31
Alignment explanation
Indices: 1005205--1005284 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
1005195 TTAGAGATTC
* **
1005205 AATTGATATTTTATATAAAGTTTAAGGGTTG
1 AATTAATATTTTATATAAAGTTTAAGGGTCA
* * *
1005236 AATTAGTATTTTGTGTAAAGTTTAA-GGTCA
1 AATTAATATTTTATATAAAGTTTAAGGGTCA
*
1005266 AATTAATATTTTATTTAAA
1 AATTAATATTTTATATAAA
1005285 ATTCAAGACT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (31 bp):
AATTAATATTTTATATAAAGTTTAAGGGTCA
Found at i:1011759 original size:15 final size:14
Alignment explanation
Indices: 1011739--1011777 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
1011729 ATTTCCTTAT
1011739 TTTTTAAATAAAATA
1 TTTTTAAA-AAAATA
*
1011754 TTTTT-AAAAATTA
1 TTTTTAAAAAAATA
1011767 TTTTTAAAAAA
1 TTTTTAAAAAA
1011778 TTTGAACGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 10 0.45
14 7 0.32
15 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTTTAAAAAAATA
Found at i:1013592 original size:18 final size:19
Alignment explanation
Indices: 1013564--1013599 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1013554 AAGTTTTCAT
1013564 TTTATTTAATTTAAATTAG
1 TTTATTTAATTTAAATTAG
1013583 TTTA-TTAATTTAAATTA
1 TTTATTTAATTTAAATTA
1013600 TTAGTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTATTTAATTTAAATTAG
Found at i:1013632 original size:17 final size:17
Alignment explanation
Indices: 1013607--1013642 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1013597 TTATTAGTTT
1013607 GTTAATTTAGGGTTAGG
1 GTTAATTTAGGGTTAGG
*
1013624 GTTAGTTTAGGGTTAGG
1 GTTAATTTAGGGTTAGG
1013641 GT
1 GT
1013643 AAAAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.39, T:0.42
Consensus pattern (17 bp):
GTTAATTTAGGGTTAGG
Found at i:1013836 original size:30 final size:30
Alignment explanation
Indices: 1013802--1013883 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
1013792 TTAAATTCTA
* * * *
1013802 ATTAAAAAATTGTTTATTAGTTTAGGCTAT
1 ATTAAAGAATAGTTTATTAGTTAAAGCTAT
*
1013832 ATTAAAGAATAGTTTATTAGTTAAAGTTAT
1 ATTAAAGAATAGTTTATTAGTTAAAGCTAT
1013862 ATTAAAGAATAGTTTATTAGTT
1 ATTAAAGAATAGTTTATTAGTT
1013884 GTTTAAGGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.45
Consensus pattern (30 bp):
ATTAAAGAATAGTTTATTAGTTAAAGCTAT
Found at i:1013849 original size:15 final size:15
Alignment explanation
Indices: 1013831--1013880 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1013821 GTTTAGGCTA
1013831 TATTAAAGAATAGTT
1 TATTAAAGAATAGTT
***
1013846 TATTAGTTAA-AGTT
1 TATTAAAGAATAGTT
1013860 ATATTAAAGAATAGTT
1 -TATTAAAGAATAGTT
1013876 TATTA
1 TATTA
1013881 GTTGTTTAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (15 bp):
TATTAAAGAATAGTT
Found at i:1013966 original size:15 final size:16
Alignment explanation
Indices: 1013938--1013971 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1013928 GTTTGTTACT
1013938 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
1013954 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
1013969 TTA
1 TTA
1013972 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:1016220 original size:17 final size:17
Alignment explanation
Indices: 1016200--1016241 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1016190 ACTAGTATCA
1016200 AATAATTAAATATTAAT
1 AATAATTAAATATTAAT
* * *
1016217 AATAAATCATTATTAAT
1 AATAATTAAATATTAAT
1016234 AATAATTA
1 AATAATTA
1016242 GTAAATCATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATTAAATATTAAT
Found at i:1016390 original size:14 final size:14
Alignment explanation
Indices: 1016369--1016676 Score: 173
Period size: 14 Copynumber: 22.3 Consensus size: 14
1016359 ATTAGTAATA
1016369 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1016383 AGTATTAAATCATT
1 ATTATTAAATCATT
*
1016397 ATTA-TAAA--ATC
1 ATTATTAAATCATT
*
1016408 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1016422 ACTATTAAATCATT
1 ATTATTAAATCATT
1016436 ATTATTAAAT-ATT
1 ATTATTAAATCATT
*
1016449 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1016461 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1016475 ATTA-T-AATGATT
1 ATTATTAAATCATT
* *
1016487 ATTACTAAATCACT
1 ATTATTAAATCATT
*
1016501 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1016513 ATTATCAAATCATT
1 ATTATTAAATCATT
* *
1016527 ACGAAATAATCAAATCATT
1 -----ATTATTAAATCATT
* *
1016546 AAATATT-AA-CATC
1 -ATTATTAAATCATT
1016559 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
1016573 ACTA-T-AATGATT
1 ATTATTAAATCATT
*
1016585 ATTATCAAATCATT
1 ATTATTAAATCATT
*
1016599 ATTAAATCATCAAATCAATA
1 ATT--AT--T-AAATC-ATT
*
1016619 AATATTAAATCATT
1 ATTATTAAATCATT
* *
1016633 ACTA-T-AATGATT
1 ATTATTAAATCATT
1016645 ATTATTAAATCA-T
1 ATTATTAAATCATT
*
1016658 AATATTAAAATCATT
1 ATTATT-AAATCATT
1016673 ATTA
1 ATTA
1016677 AATCATCAAA
Statistics
Matches: 228, Mismatches: 37, Indels: 57
0.71 0.11 0.18
Matches are distributed among these distances:
11 9 0.04
12 54 0.24
13 29 0.13
14 96 0.42
15 13 0.06
16 3 0.01
18 2 0.01
19 18 0.08
20 4 0.02
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1016584 original size:72 final size:71
Alignment explanation
Indices: 1016487--1016717 Score: 304
Period size: 72 Copynumber: 3.2 Consensus size: 71
1016477 TATAATGATT
* ** *
1016487 ATTACTAAATCACTATTATAATGATTATTATCAAATCATTACGAAATAATCAAATCATTAAATAT
1 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTATTAAATCATCAAATCATTAAATAT
1016552 TAACATC
66 TAA-ATC
* * *
1016559 ATTATTAAATCATTACTATAATGATTATTATCAAATCATTATTAAATCATCAAATCAATAAATAT
1 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTATTAAATCATCAAATCATTAAATAT
1016624 TAAATC
66 TAAATC
* *
1016630 ATTACTATAATGATTATTATTAAATCATAATATTA--AAATCATTATTAAATCATCAAATCATTA
1 ATTACTA-AATCATTATTA-T-AATGAT--TATTATCAAATCATTATTAAATCATCAAATCATTA
1016693 AATATTAAAATC
61 AATATT-AAATC
1016705 ATTACTAAATCAT
1 ATTACTAAATCAT
1016718 CAAATCATTA
Statistics
Matches: 140, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
71 9 0.06
72 70 0.50
73 1 0.01
74 43 0.31
75 12 0.09
76 5 0.04
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.39
Consensus pattern (71 bp):
ATTACTAAATCATTATTATAATGATTATTATCAAATCATTATTAAATCATCAAATCATTAAATAT
TAAATC
Found at i:1016633 original size:8 final size:8
Alignment explanation
Indices: 1016599--1016730 Score: 58
Period size: 8 Copynumber: 15.9 Consensus size: 8
1016589 TCAAATCATT
1016599 ATTAAATC
1 ATTAAATC
*
1016607 ATCAAATC
1 ATTAAATC
*
1016615 AATAAAT-
1 ATTAAATC
1016622 ATTAAATC
1 ATTAAATC
* *
1016630 ATTACTATA
1 ATTA-AATC
* * *
1016639 ATGATTATT
1 ATTA-AATC
1016648 ATTAAATC
1 ATTAAATC
1016656 A-T-AAT-
1 ATTAAATC
1016661 ATTAAAATC
1 ATT-AAATC
1016670 ATTATTAAATC
1 ---ATTAAATC
*
1016681 ATCAAATC
1 ATTAAATC
1016689 ATTAAAT-
1 ATTAAATC
1016696 ATTAAAATC
1 ATT-AAATC
1016705 ATTACTAAATC
1 A-T--TAAATC
*
1016716 ATCAAATC
1 ATTAAATC
1016724 ATTAAAT
1 ATTAAAT
1016731 TTTAAAAACT
Statistics
Matches: 94, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
5 1 0.01
6 4 0.04
7 10 0.11
8 50 0.53
9 12 0.13
10 2 0.02
11 11 0.12
12 4 0.04
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (8 bp):
ATTAAATC
Found at i:1016684 original size:14 final size:14
Alignment explanation
Indices: 1016645--1016684 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
1016635 TATAATGATT
1016645 ATTATTAAATCAT-
1 ATTATTAAATCATC
*
1016658 AATATTAAA--ATC
1 ATTATTAAATCATC
1016670 ATTATTAAATCATC
1 ATTATTAAATCATC
1016684 A
1 A
1016685 AATCATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
11 2 0.09
12 8 0.36
13 8 0.36
14 4 0.18
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTATTAAATCATC
Found at i:1016699 original size:35 final size:35
Alignment explanation
Indices: 1016651--1016737 Score: 142
Period size: 35 Copynumber: 2.5 Consensus size: 35
1016641 GATTATTATT
*
1016651 AAATCA-T-AATATTAAAATCATTATTAAATCATC
1 AAATCATTAAATATTAAAATCATTACTAAATCATC
1016684 AAATCATTAAATATTAAAATCATTACTAAATCATC
1 AAATCATTAAATATTAAAATCATTACTAAATCATC
*
1016719 AAATCATTAAATTTTAAAA
1 AAATCATTAAATATTAAAA
1016738 ACTCTTCTCG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 6 0.12
34 1 0.02
35 43 0.86
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (35 bp):
AAATCATTAAATATTAAAATCATTACTAAATCATC
Found at i:1016802 original size:14 final size:14
Alignment explanation
Indices: 1016783--1016871 Score: 76
Period size: 14 Copynumber: 6.4 Consensus size: 14
1016773 AAATTCAACT
*
1016783 TCATTATTACTAAA
1 TCATTATTATTAAA
* *
1016797 TCATTACTATCAAA
1 TCATTATTATTAAA
*
1016811 TCATTAAATATTAAA
1 TCATT-ATTATTAAA
*
1016826 TCATTACTA-T-AA
1 TCATTATTATTAAA
*
1016838 TGATTATTATTAAA
1 TCATTATTATTAAA
*
1016852 TCA-TAATATTAAAA
1 TCATTATTATT-AAA
1016866 TCATTA
1 TCATTA
1016872 CTAAATCATC
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
12 9 0.15
13 8 0.13
14 29 0.48
15 14 0.23
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (14 bp):
TCATTATTATTAAA
Found at i:1016825 original size:29 final size:26
Alignment explanation
Indices: 1016783--1016855 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 26
1016773 AAATTCAACT
* *
1016783 TCATTATTACTAAATCATTACTATCAAA
1 TCATTAATATTAAATCATTACTAT--AA
1016811 TCATTAAATATTAAATCATTACTATAA
1 TCATT-AATATTAAATCATTACTATAA
* *
1016838 TGATTATTATTAAATCAT
1 TCATTAATATTAAATCAT
1016856 AATATTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 12 0.30
27 6 0.15
28 5 0.12
29 17 0.43
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.42
Consensus pattern (26 bp):
TCATTAATATTAAATCATTACTATAA
Found at i:1016831 original size:8 final size:8
Alignment explanation
Indices: 1016808--1016934 Score: 50
Period size: 8 Copynumber: 15.4 Consensus size: 8
1016798 CATTACTATC
1016808 AAATCATT
1 AAATCATT
1016816 AAAT-ATT
1 AAATCATT
1016823 AAATCATT
1 AAATCATT
* * *
1016831 ACTATAATG
1 A-AATCATT
* *
1016840 ATTATTATT
1 A-AATCATT
1016849 AAATCA-T
1 AAATCATT
1016856 -AAT-ATT
1 AAATCATT
1016862 AAAATCATTACT
1 -AAATCA-T--T
*
1016874 AAATCATC
1 AAATCATT
1016882 AAATCATT
1 AAATCATT
1016890 AAAT-ATT
1 AAATCATT
1016897 AAAATCATTACT
1 -AAATCA-T--T
*
1016909 AAATCATC
1 AAATCATT
*
1016917 ATATCATT
1 AAATCATT
1016925 AAAT-ATT
1 AAATCATT
1016932 AAA
1 AAA
1016935 AACTCTTATC
Statistics
Matches: 91, Mismatches: 14, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
5 1 0.01
6 4 0.04
7 17 0.19
8 38 0.42
9 13 0.14
10 4 0.04
11 12 0.13
12 2 0.02
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (8 bp):
AAATCATT
Found at i:1016867 original size:40 final size:40
Alignment explanation
Indices: 1016788--1016915 Score: 146
Period size: 35 Copynumber: 3.3 Consensus size: 40
1016778 CAACTTCATT
1016788 ATTACTAAATCATTACTATCAAATCATTAAATATTAAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAAATC
* * *
1016828 ATTACTATAATGATTATTATTAAATCA-T-AATATTAAAATC
1 ATTACTA-AATCATTACTATCAAATCATTAAATATT-AAATC
1016868 ATTACT-AA--A-T-C-ATCAAATCATTAAATATTAAAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATT-AAATC
1016903 ATTACTAAATCAT
1 ATTACTAAATCAT
1016916 CATATCATTA
Statistics
Matches: 75, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
33 8 0.11
34 1 0.01
35 19 0.25
36 3 0.04
38 3 0.04
39 6 0.08
40 19 0.25
41 16 0.21
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.38
Consensus pattern (40 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAAATC
Found at i:1016887 original size:19 final size:19
Alignment explanation
Indices: 1016863--1016925 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
1016853 CATAATATTA
1016863 AAATCATTACTAAATCATC
1 AAATCATTACTAAATCATC
*
1016882 AAATCA-T--TAAAT-ATTA
1 AAATCATTACTAAATCA-TC
1016898 AAATCATTACTAAATCATC
1 AAATCATTACTAAATCATC
*
1016917 ATATCATTA
1 AAATCATTA
1016926 AATATTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 1 0.03
16 12 0.33
17 1 0.03
18 1 0.03
19 20 0.56
20 1 0.03
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATCATTACTAAATCATC
Found at i:1016899 original size:35 final size:35
Alignment explanation
Indices: 1016849--1016935 Score: 151
Period size: 35 Copynumber: 2.5 Consensus size: 35
1016839 GATTATTATT
1016849 AAATCA-T-AATATTAAAATCATTACTAAATCATC
1 AAATCATTAAATATTAAAATCATTACTAAATCATC
1016882 AAATCATTAAATATTAAAATCATTACTAAATCATC
1 AAATCATTAAATATTAAAATCATTACTAAATCATC
*
1016917 ATATCATTAAATATTAAAA
1 AAATCATTAAATATTAAAA
1016936 ACTCTTATCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 6 0.12
34 1 0.02
35 44 0.86
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (35 bp):
AAATCATTAAATATTAAAATCATTACTAAATCATC
Found at i:1016988 original size:14 final size:14
Alignment explanation
Indices: 1016969--1017002 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1016959 AAATTCAACT
* *
1016969 TCATTATTACTAAA
1 TCATTACTACCAAA
1016983 TCATTACTACCAAA
1 TCATTACTACCAAA
1016997 TCATTA
1 TCATTA
1017003 AATATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (14 bp):
TCATTACTACCAAA
Found at i:1017046 original size:49 final size:49
Alignment explanation
Indices: 1016968--1017090 Score: 219
Period size: 49 Copynumber: 2.5 Consensus size: 49
1016958 TAAATTCAAC
*
1016968 TTCATTATTACTAAATCATTACTACCAAATCATTAAATATTAATAATAAT
1 TTCATTATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAT
1017018 TTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAT
*
1017067 TTCATTATTATTAATCATTACTAT
1 TTCATTATTACTAATCATTACTAT
1017091 AAGAGAAAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
49 59 0.83
50 12 0.17
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.44
Consensus pattern (49 bp):
TTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAT
Found at i:1017198 original size:19 final size:19
Alignment explanation
Indices: 1017174--1017210 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1017164 ATGACCAATA
*
1017174 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1017193 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1017211 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1017259 original size:20 final size:20
Alignment explanation
Indices: 1017245--1017304 Score: 93
Period size: 21 Copynumber: 3.0 Consensus size: 20
1017235 TTCGCAACGT
1017245 GATTTTGACTATCGCAATGC
1 GATTTTGACTATCGCAATGC
**
1017265 GATTTTAGAAAATCGCAATGC
1 GATTTT-GACTATCGCAATGC
1017286 GATTTTGACTATCGCAATG
1 GATTTTGACTATCGCAATG
1017305 TGATAATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (20 bp):
GATTTTGACTATCGCAATGC
Found at i:1017281 original size:21 final size:21
Alignment explanation
Indices: 1017255--1017357 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
1017245 GATTTTGACT
*
1017255 ATCGCAATGCGATTTTAGAAA
1 ATCGCAATGCGATTTTACAAA
*
1017276 ATCGCAATGCGATTTTGAC--T
1 ATCGCAATGCGATTTT-ACAAA
* ** *
1017296 ATCGCAATGTGATAATACATA
1 ATCGCAATGCGATTTTACAAA
* **
1017317 ATCGCAACGCGATAATACAAA
1 ATCGCAATGCGATTTTACAAA
*
1017338 ATTGCAATGCGATTTT-CAAA
1 ATCGCAATGCGATTTTACAAA
1017358 GCGCTATTAG
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.03
20 17 0.26
21 46 0.70
22 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAATGCGATTTTACAAA
Found at i:1017320 original size:41 final size:41
Alignment explanation
Indices: 1017236--1017329 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
1017226 GTTTCCAGAT
* ** *
1017236 TCGCAACGTGATTTTGACTATCGCAATGCGATTTTAGAAAA
1 TCGCAACGCGATTTTGACTATCGCAATGCGATAATACAAAA
* * *
1017277 TCGCAATGCGATTTTGACTATCGCAATGTGATAATACATAA
1 TCGCAACGCGATTTTGACTATCGCAATGCGATAATACAAAA
1017318 TCGCAACGCGAT
1 TCGCAACGCGAT
1017330 AATACAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
TCGCAACGCGATTTTGACTATCGCAATGCGATAATACAAAA
Found at i:1017973 original size:20 final size:20
Alignment explanation
Indices: 1017924--1017993 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
1017914 GCAATTTTAG
* * *
1017924 TTTCGCGTTGCGATAGTCAA
1 TTTCGTGTTGCGATATTCAT
* *
1017944 ATTCGCGTTGCGATATTCAT
1 TTTCGTGTTGCGATATTCAT
* *
1017964 TTTCTTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATATTCAT
1017984 TTTCGTGTTG
1 TTTCGTGTTG
1017994 TGATTTTAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.47
Consensus pattern (20 bp):
TTTCGTGTTGCGATATTCAT
Found at i:1017998 original size:20 final size:20
Alignment explanation
Indices: 1017945--1018000 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1017935 GATAGTCAAA
* *
1017945 TTCGCGTTGCGATATTCATT
1 TTCGTGTTGCGATTTTCATT
*
1017965 TTCTTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
1017985 TTCGTGTTGTGATTTT
1 TTCGTGTTGCGATTTT
1018001 AAGTTTCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1018007 original size:20 final size:20
Alignment explanation
Indices: 1017945--1018007 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
1017935 GATAGTCAAA
* * * *
1017945 TTCGCGTTGCGATATTCATT
1 TTCGTGTTGCGATTTTAAGT
* * *
1017965 TTCTTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTAAGT
*
1017985 TTCGTGTTGTGATTTTAAGT
1 TTCGTGTTGCGATTTTAAGT
1018005 TTC
1 TTC
1018008 AGAAACTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.13, C:0.14, G:0.19, T:0.54
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTAAGT
Found at i:1019188 original size:16 final size:16
Alignment explanation
Indices: 1019167--1019199 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1019157 CCATATATAA
1019167 ACAAGTTATTACTAGT
1 ACAAGTTATTACTAGT
1019183 ACAAGTTATTACTAGT
1 ACAAGTTATTACTAGT
1019199 A
1 A
1019200 AGTGTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
ACAAGTTATTACTAGT
Found at i:1019850 original size:20 final size:20
Alignment explanation
Indices: 1019827--1019895 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
1019817 GAAACTTAAA
1019827 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1019847 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1019867 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1019887 ATCGCAACG
1 ATCGCAACG
1019896 GGATAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1019960 original size:18 final size:19
Alignment explanation
Indices: 1019929--1019971 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1019919 AAATCGCAAC
* *
1019929 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCATT
1019948 GCGATTTTA-TTTCGCATT
1 GCGATTTTAGTTTCGCATT
1019966 GCGATT
1 GCGATT
1019972 ATCCCGTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:1020001 original size:20 final size:20
Alignment explanation
Indices: 1019976--1020064 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
1019966 GCGATTATCC
*
1019976 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
1019996 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* *
1020016 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
* *
1020036 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
*
1020056 TGTTGCGAT
1 CGTTGCGAT
1020065 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:1020036 original size:40 final size:40
Alignment explanation
Indices: 1019977--1020064 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
1019967 CGATTATCCC
*
1019977 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTCCGT
** *
1020017 GTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTCCGT
1020057 GTTGCGAT
1 GTTGCGAT
1020065 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (40 bp):
GTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTCCGT
Found at i:1020610 original size:21 final size:21
Alignment explanation
Indices: 1020515--1020616 Score: 80
Period size: 21 Copynumber: 4.9 Consensus size: 21
1020505 GCCCGACTCA
1020515 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1020536 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** * *
1020557 CCTATCATCCCTCAAAAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
1020578 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1020599 TCTGTCATCGTTGAAGAG
1 CCTGTCATCGTTCAAGAG
1020617 TTCCCTCCCA
Statistics
Matches: 59, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
20 1 0.02
21 57 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1020623 original size:42 final size:42
Alignment explanation
Indices: 1020515--1020637 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
1020505 GCCCGACTCA
* * * *
1020515 CCTGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
* ** *
1020557 CCTATCATCCCTCAAAAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
1020599 TCTGTCATCGTTGAAGAGTTCCCTCCCACCATTCTAGAG
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAG
1020638 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:1022209 original size:20 final size:20
Alignment explanation
Indices: 1022184--1022501 Score: 226
Period size: 20 Copynumber: 16.9 Consensus size: 20
1022174 GCGATTTTCT
*
1022184 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
1022204 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
1022224 CGTTGCGATAGTCAAAATCG
1 CGTTGCGATAGTCAAATTCG
** * * *
1022244 CAATGCGAAAGCCAAAATCG
1 CGTTGCGATAGTCAAATTCG
*** *
1022264 CCACGCGAAAGTC-AATTCG
1 CGTTGCGATAGTCAAATTCG
* * * *
1022283 TGTTGCGATGGTCTAATACG
1 CGTTGCGATAGTCAAATTCG
* *
1022303 CTTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* *
1022317 CGTCGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
1022337 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
1022357 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* * *
1022371 CGTTGCAATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
1022391 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1022411 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1022431 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
1022445 CGTTGCGATAGTC-AATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1022464 CATTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
1022484 CGTTGCGATAGTCAAATT
1 CGTTGCGATAGTCAAATT
1022502 TACATTGCGA
Statistics
Matches: 238, Mismatches: 41, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
14 32 0.13
16 3 0.01
18 3 0.01
19 27 0.11
20 173 0.73
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1022345 original size:54 final size:54
Alignment explanation
Indices: 1022267--1022419 Score: 182
Period size: 54 Copynumber: 2.9 Consensus size: 54
1022257 AAAATCGCCA
* ** * * * *
1022267 CGCGAAAGTC-AATTCGTGTTGCGATGGTCTAATACGCTTTGCGATTTTCTCGT
1 CGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGT
* * *
1022320 CGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATTTTCTCGT
1 CGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGT
* * *
1022374 TGCAATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGAT
1022420 AGTCAAATTC
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
53 9 0.11
54 75 0.89
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (54 bp):
CGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGT
Found at i:1022375 original size:34 final size:34
Alignment explanation
Indices: 1022337--1022472 Score: 132
Period size: 34 Copynumber: 3.9 Consensus size: 34
1022327 GTCAAATTCC
1022337 CGTTGCGATAATCAAATTCACGTTGCGATTTTCT
1 CGTTGCGATAATCAAATTCACGTTGCGATTTTCT
* *
1022371 CGTTGCAATAATCAAATTCACGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCACGTTGCGAT--T----TTCT
* *
1022411 CGTTGCGATAGTCAAATTCGCGTTGCGATTTT-T
1 CGTTGCGATAATCAAATTCACGTTGCGATTTTCT
* * *
1022444 GCGTTGCGATAGTC-AATTCGCATTGCGAT
1 -CGTTGCGATAATCAAATTCACGTTGCGAT
1022473 AGTCAAATTC
Statistics
Matches: 88, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
33 14 0.16
34 43 0.49
36 1 0.01
38 1 0.01
40 29 0.33
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAATCAAATTCACGTTGCGATTTTCT
Found at i:1022407 original size:74 final size:73
Alignment explanation
Indices: 1022321--1022512 Score: 269
Period size: 74 Copynumber: 2.6 Consensus size: 73
1022311 TTTTCTCGTC
*
1022321 GCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATTTTCT-CGTTGCAATAATCA
1 GCGATAGTCAAATTCCCGTTGCGATAGTCAAATTCACGTTGCGATTTT-TGCGTTGCAATAATC-
*
1022385 AATTCACGTT
64 AATTCACATT
* * * *
1022395 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAGTCAA
1 GCGATAGTCAAATTCCCGTTGCGATAGTCAAATTCACGTTGCGATTTTTGCGTTGCAATAATCAA
*
1022460 TTCGCATT
66 TTCACATT
* * *
1022468 GCGATAGTCAAATTCTCGTTGCGATAGTCAAATTTACATTGCGAT
1 GCGATAGTCAAATTCCCGTTGCGATAGTCAAATTCACGTTGCGAT
1022513 ATTTAAATGA
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
73 50 0.47
74 56 0.53
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (73 bp):
GCGATAGTCAAATTCCCGTTGCGATAGTCAAATTCACGTTGCGATTTTTGCGTTGCAATAATCAA
TTCACATT
Found at i:1022473 original size:53 final size:54
Alignment explanation
Indices: 1022391--1022492 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 54
1022381 ATCAAATTCA
*
1022391 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTTG
*
1022445 CGTTGCGATAGTC-AATTCGCATTGCGATAGTCAAATTCTCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGAT
1022493 AGTCAAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 33 0.72
54 13 0.28
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:1022509 original size:20 final size:19
Alignment explanation
Indices: 1022447--1022513 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
1022437 GATTTTTGCG
*
1022447 TTGCGATAGTC-AATTCGCA
1 TTGCGATAGTCAAATT-TCA
*
1022466 TTGCGATAGTCAAATTCTCG
1 TTGCGATAGTCAAATT-TCA
1022486 TTGCGATAGTCAAATTTACA
1 TTGCGATAGTCAAATTT-CA
1022506 TTGCGATA
1 TTGCGATA
1022514 TTTAAATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.28
20 31 0.72
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (19 bp):
TTGCGATAGTCAAATTTCA
Found at i:1022743 original size:140 final size:140
Alignment explanation
Indices: 1022491--1022773 Score: 494
Period size: 140 Copynumber: 2.0 Consensus size: 140
1022481 TCTCGTTGCG
* * *
1022491 ATAGTCAAATTTACATTGCGATATTTAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTGAACAAATCA
* *
1022556 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1022621 AATACACATA
131 AATACACATA
* * *
1022631 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTGAACAAATCA
1022696 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1022761 AATACACATA
131 AATACACATA
1022771 ATA
1 ATA
1022774 AAACGTTTGC
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTGAACAAATCA
TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1024915 original size:3 final size:3
Alignment explanation
Indices: 1024907--1024957 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1024897 CTTCGGGGAT
* * *
1024907 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TGC TTC TTA TTC TTA TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1024955 TTC
1 TTC
1024958 AGGGTTATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.04, C:0.29, G:0.02, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:1025199 original size:24 final size:24
Alignment explanation
Indices: 1025148--1025199 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1025138 ATCTGAGTAT
** *
1025148 TGACCAAGATCAAATTCCGGGTAT
1 TGACCAAGATCAAATTCCGAATAC
*
1025172 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAATTCCGAATAC
1025196 TGAC
1 TGAC
1025200 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAATTCCGAATAC
Found at i:1026031 original size:20 final size:20
Alignment explanation
Indices: 1026006--1026145 Score: 158
Period size: 20 Copynumber: 6.9 Consensus size: 20
1025996 GAAATTCAAT
*
1026006 GTTGCGAAAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1026026 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1026046 GTTACGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
1026066 GTTGCGATTACGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
1026087 GTTGCGATAGTCAGAATAGC
1 GTTGCGATAGTCAGAATCGC
**
1026107 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
1026128 ATTGCGATAGTCAGAATC
1 GTTGCGATAGTCAGAATC
1026146 ACAATGCGAT
Statistics
Matches: 100, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
19 4 0.04
20 64 0.64
21 28 0.28
22 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1026098 original size:41 final size:41
Alignment explanation
Indices: 1026006--1026196 Score: 201
Period size: 41 Copynumber: 4.7 Consensus size: 41
1025996 GAAATTCAAT
* **
1026006 GTTGCGAAAGTCAGAATCGCGTTGCGA-TA-GTCAGAATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTACGT-ATTATCGC
*
1026046 GTTACGATAGTCAGAATCGCGTTGCGATTACGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTACGTATTATCGC
* *
1026087 GTTGCGATAGTCAGAATAGCGTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTACGTATTATCGC
* * ** *
1026128 ATTGCGATAGTCAGAATCACAATGCGATTTACATA-T-TCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGA-TTACGTATTATCGC
* * * *
1026168 ATTGCGATAGTAAAAATCGCCTTGCGATT
1 GTTGCGATAGTCAGAATCGCGTTGCGATT
1026197 CTGGAAACTG
Statistics
Matches: 129, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.02
40 51 0.40
41 69 0.53
42 7 0.05
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (41 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTACGTATTATCGC
Found at i:1026232 original size:20 final size:19
Alignment explanation
Indices: 1026209--1026254 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1026199 GGAAACTGGT
* *
1026209 TTGCGATAATGGAGATCGCG
1 TTGCGAT-ATAGAGATCGCA
*
1026229 TTGCGATTTAGAGATCGCA
1 TTGCGATATAGAGATCGCA
1026248 TTGCGAT
1 TTGCGAT
1026255 TTTATTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATATAGAGATCGCA
Found at i:1026244 original size:19 final size:19
Alignment explanation
Indices: 1026220--1026256 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1026210 TGCGATAATG
*
1026220 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1026239 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1026257 TATTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1026392 original size:14 final size:14
Alignment explanation
Indices: 1026373--1026406 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1026363 AATAATAATT
*
1026373 TCATTATTATTAAA
1 TCATTACTATTAAA
1026387 TCATTACTATTAAA
1 TCATTACTATTAAA
1026401 TCATTA
1 TCATTA
1026407 AATATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
TCATTACTATTAAA
Found at i:1026457 original size:49 final size:49
Alignment explanation
Indices: 1026340--1026591 Score: 450
Period size: 49 Copynumber: 5.1 Consensus size: 49
1026330 TTATTTTCTC
* *
1026340 TTACTATAAAATCATTAAATATTAATAATAATTTCATTATTATTAAATCA
1 TTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT-AATCA
*
1026390 TTACTATTAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 TTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* *
1026439 TTACTATCAAATCATTAAATATTAATAATAATTTAAATATTACTAATCA
1 TTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1026488 TTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 TTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1026537 TTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 TTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1026586 TTACTA
1 TTACTA
1026592 AATAATTATT
Statistics
Matches: 195, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
49 153 0.78
50 42 0.22
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (49 bp):
TTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
Found at i:1026524 original size:22 final size:22
Alignment explanation
Indices: 1026499--1026575 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
1026489 TACTATCAAA
1026499 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
* *
1026521 TCATTATTACTAATCATTACT-ATCAA-A
1 TC---ATTA--AAT-ATTAATAAT-AATT
1026548 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
1026570 TCATTA
1 TCATTA
1026576 TTACTAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
21 7 0.17
22 13 0.31
24 4 0.10
25 4 0.10
27 7 0.17
28 7 0.17
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.44
Consensus pattern (22 bp):
TCATTAAATATTAATAATAATT
Found at i:1030167 original size:19 final size:19
Alignment explanation
Indices: 1030126--1030196 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
1030116 AAAAAAATGG
* *
1030126 AAAATAACAAAACACGTAA-
1 AAAATAATAAAA-AAGTAAT
1030145 AAAATAATAAAAAAGTAAT
1 AAAATAATAAAAAAGTAAT
*
1030164 -AAA-AATAAATAAAATGAAT
1 AAAATAATAAA-AAAGT-AAT
*
1030183 AAAATGATAAAAAA
1 AAAATAATAAAAAA
1030197 AACAAAGACA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 6 0.14
18 12 0.28
19 14 0.33
20 6 0.14
21 5 0.12
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAATAATAAAAAAGTAAT
Found at i:1030398 original size:14 final size:15
Alignment explanation
Indices: 1030379--1030424 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
1030369 CATGATATTA
1030379 AGAAAAAAA-ATAAT
1 AGAAAAAAATATAAT
1030393 AGAAAAAAATATAAT
1 AGAAAAAAATATAAT
1030408 A-AAGTAAAAATATAAT
1 AGAA--AAAAATATAAT
1030424 A
1 A
1030425 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.38
15 6 0.21
16 12 0.41
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (15 bp):
AGAAAAAAATATAAT
Found at i:1030460 original size:43 final size:43
Alignment explanation
Indices: 1030399--1030661 Score: 127
Period size: 43 Copynumber: 6.0 Consensus size: 43
1030389 TAATAGAAAA
* *
1030399 AAATATAAT-AAAGTAAAAATATAATATATATATATATATATAT
1 AAATA-AATAAAAATAAAAATATAATATATAAATATATATATAT
*
1030442 AAATAAATAAAAATAAAAATAAAATAT-TAAGA-A-A-ATATAT
1 AAATAAATAAAAATAAAAATATAATATATAA-ATATATATATAT
* * *
1030482 ATATATATAAAAACGTATAAAATATAATAT-TAAGAAAATATATATAT
1 AAATAAATAAAAA--TA-AAAATATAATATAT-A-AATATATATATAT
* * * * * *
1030529 ACAT-AGTAAATGGAGAAAAAT-TAATACATATATATATATAATAAT
1 AAATAAATAAA--AATAAAAATATAATATATAAATATATAT-AT-AT
* * * * *
1030574 ATATATAATAAAAATAATATAATATAAAATAAAAAAAGGA-ATATAAT
1 AAATA-AATAAAAATAA-A-AATATAATATATAAATA-TATATAT-AT
*
1030621 AAATAAAT--AAATAAAATATATAAT-TAAAAATATATATATAT
1 AAATAAATAAAAATAAAA-ATATAATATATAAATATATATATAT
1030662 GGGACAAAAT
Statistics
Matches: 169, Mismatches: 28, Indels: 48
0.69 0.11 0.20
Matches are distributed among these distances:
40 17 0.10
41 4 0.02
42 20 0.12
43 48 0.28
44 16 0.09
45 16 0.09
46 10 0.06
47 26 0.15
48 11 0.07
49 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (43 bp):
AAATAAATAAAAATAAAAATATAATATATAAATATATATATAT
Found at i:1030577 original size:12 final size:12
Alignment explanation
Indices: 1030560--1030584 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1030550 TAATACATAT
1030560 ATATATATAATA
1 ATATATATAATA
1030572 ATATATATAATA
1 ATATATATAATA
1030584 A
1 A
1030585 AAATAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATAATA
Found at i:1030577 original size:14 final size:13
Alignment explanation
Indices: 1030558--1030660 Score: 51
Period size: 14 Copynumber: 7.8 Consensus size: 13
1030548 ATTAATACAT
1030558 ATATATATATAATA
1 ATATATATATAA-A
1030572 ATATATATAATAAAA
1 ATATATAT-AT-AAA
1030587 ATAATATAATATAAA
1 AT-ATAT-ATATAAA
1030602 ATA-A-A-A-AAA
1 ATATATATATAAA
1030611 GGA-ATATA-AT-AA
1 --ATATATATATAAA
* *
1030623 ATAAATAAATAAA
1 ATATATATATAAA
1030636 ATATATA-ATTAAAA
1 ATATATATA-T-AAA
1030650 ATATATATATA
1 ATATATATATA
1030661 TGGGACAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 31
0.69 0.02 0.30
Matches are distributed among these distances:
9 3 0.04
10 3 0.04
11 7 0.10
12 7 0.10
13 11 0.15
14 20 0.28
15 11 0.15
16 8 0.11
17 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
ATATATATATAAA
Found at i:1030592 original size:21 final size:21
Alignment explanation
Indices: 1030566--1030661 Score: 78
Period size: 21 Copynumber: 4.7 Consensus size: 21
1030556 ATATATATAT
1030566 ATAATAATATATATAATAAAA
1 ATAATAATATATATAATAAAA
*
1030587 ATAAT-ATAATATAAAATAAAA
1 ATAATAAT-ATATATAATAAAA
* *
1030608 A-AAGGAATATA-ATAA-ATAA
1 ATAA-TAATATATATAATAAAA
*
1030627 ATAAATAAAATATATAATTAAAA
1 AT-AATAATATATATAA-TAAAA
1030650 AT-AT-ATATATAT
1 ATAATAATATATAT
1030662 GGGACAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
19 4 0.07
20 19 0.32
21 29 0.49
22 2 0.03
23 5 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAATAATATATATAATAAAA
Found at i:1030653 original size:12 final size:11
Alignment explanation
Indices: 1030564--1030654 Score: 51
Period size: 12 Copynumber: 7.5 Consensus size: 11
1030554 ACATATATAT
*
1030564 ATATAATAATAT
1 ATATAATAA-AA
1030576 ATATAATAAAAATA
1 ATATAAT--AAA-A
1030590 ATATAATATAAA
1 ATATAATA-AAA
*
1030602 ATA-AAAAAAGGA
1 ATATAATAAA--A
1030614 ATATAATAAATA
1 ATATAATAAA-A
1030626 A-ATAAATAAAA
1 ATAT-AATAAAA
1030637 TATATAATTAAAA
1 -ATATAA-TAAAA
1030650 ATATA
1 ATATA
1030655 TATATATGGG
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
10 2 0.03
11 6 0.09
12 32 0.50
13 15 0.23
14 9 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
ATATAATAAAA
Found at i:1032289 original size:109 final size:105
Alignment explanation
Indices: 1032064--1032319 Score: 307
Period size: 109 Copynumber: 2.4 Consensus size: 105
1032054 AGTATTGTTC
* * *
1032064 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGT-GTGAAGTTGAAATTGGCTCTGGAAATGGAAAATTGTTTGTTGACA
* *
1032129 ACCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
65 ACCAGCCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCT
* * * *
1032170 CGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAATTGAAAAGTTGTTTGTT
1 CGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCT---GGAAATGGAAAA-TTGTTTGTT
* * * *
1032235 GACAA-TAGTCGCCCCTTCATTATGAATTTGAGCTTGTGTTGTCT
61 GACAACCAGCCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCT
* *
1032279 TGAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGGCTCTG
1 CGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTG
1032320 AAACTGATAA
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
106 35 0.28
107 1 0.01
109 76 0.60
110 14 0.11
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGGAAATGGAAAATTGTTTGTTGACAA
CCAGCCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCT
Found at i:1033147 original size:67 final size:65
Alignment explanation
Indices: 1033061--1033220 Score: 194
Period size: 65 Copynumber: 2.4 Consensus size: 65
1033051 ACGGTGACAC
* ** *
1033061 GGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTCTTTCAAGAGAAATTGTCT
1 GGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGATTTTG--TTTCAAGAGAAACTGTCT
1033126 CAA
63 CAA
* *
1033129 GGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAA
1 GGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAA
** * * *
1033194 GAAAGACGAAATTTGTTTCAAGAGAAA
1 GGGAGACAAAATTTGTTTTAAGGGAAA
1033221 CTGTCTCAAG
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
65 40 0.50
67 30 0.38
68 10 0.12
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (65 bp):
GGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAA
Found at i:1033209 original size:36 final size:36
Alignment explanation
Indices: 1033169--1033475 Score: 200
Period size: 36 Copynumber: 8.9 Consensus size: 36
1033159 ATTCAAAGAT
* *
1033169 TTTGTTTCAAGGGAAACTGTCTCAAGAAAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
1033205 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
1033241 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * *
1033278 TTTATTTCAA-ATAAAACATAT-TC---A-A-A--TAA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACGAAA
* *
1033307 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* *
1033343 TTTATTTCAAGAGAAACTGTCTCAAGAGAGATGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
1033379 TTTATTTCAAGGGAAA-TGTTTTC-----A-ATG--T
1 TTTGTTTCAAGAGAAACTG-TCTCAAGAGAGACGAAA
* *
1033407 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * *
1033444 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1033476 TAAAATCTTT
Statistics
Matches: 210, Mismatches: 37, Indels: 47
0.71 0.13 0.16
Matches are distributed among these distances:
28 4 0.02
29 32 0.15
30 5 0.02
31 2 0.01
32 2 0.01
33 1 0.00
34 2 0.01
35 4 0.02
36 98 0.47
37 58 0.28
38 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:1033266 original size:37 final size:36
Alignment explanation
Indices: 1033181--1033272 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
1033171 TGTTTCAAGG
* * * * *
1033181 GAAACTGTCTCAAGAAAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
1033217 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
*
1033254 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
1033273 TGAAATTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 22 0.45
37 27 0.55
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:1033279 original size:138 final size:138
Alignment explanation
Indices: 1033115--1033373 Score: 374
Period size: 138 Copynumber: 1.9 Consensus size: 138
1033105 GTCTTTCAAG
* * * ** * * *
1033115 AGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
1033180 GGAAACTGTCTCAAGAAAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
66 GGAAACTGTCTCAAGAAAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
1033245 GTTCCAAA
131 GTTCCAAA
** * * *
1033253 AGAAACTGTCTCAAGGGAGATGAAATTTATTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
*
1033318 GGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGA
66 GGAAACTGTCTCAAGAAAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGA
1033374 TGAAATTTAT
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 105 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAAAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:1033327 original size:102 final size:101
Alignment explanation
Indices: 1033203--1033481 Score: 362
Period size: 101 Copynumber: 2.8 Consensus size: 101
1033193 AGAAAGACGA
* * *
1033203 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTTCAAGAGAAACTGTCTCAAG
* *
1033268 GGAGATGAAATTTATTTCAAATAAAACATATTCAAAT
66 AGAGATGAAATTTATTTCAAAGAAAACATATTC-AAT
*
1033305 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGAGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTTCAAGAGAAACTGTCTCAAG
* * ** *
1033369 AGAGATGAAATTTATTTCAAGGGAAATGTTTTCAAT
66 AGAGATGAAATTTATTTCAAAGAAAACATATTCAAT
** * * * *
1033405 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTTCAAGAGAAACTGTCTCAA
* *
1033470 GCGAGATAAAAT
65 GAGAGATGAAAT
1033482 CTTTTTTTTT
Statistics
Matches: 155, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
100 5 0.03
101 81 0.52
102 69 0.45
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (101 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTTCAAGAGAAACTGTCTCAAG
AGAGATGAAATTTATTTCAAAGAAAACATATTCAAT
Found at i:1033461 original size:37 final size:37
Alignment explanation
Indices: 1033410--1033481 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
1033400 TCAATGTTTA
* *
1033410 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
* *
1033447 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
1033482 CTTTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
Found at i:1034086 original size:10 final size:11
Alignment explanation
Indices: 1034061--1034086 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1034051 ATATCAATTA
1034061 AAAAAGTTTTG
1 AAAAAGTTTTG
1034072 AAAAAGTTTTG
1 AAAAAGTTTTG
1034083 AAAA
1 AAAA
1034087 TATTGCCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (11 bp):
AAAAAGTTTTG
Found at i:1034928 original size:69 final size:69
Alignment explanation
Indices: 1034813--1034950 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
1034803 TGTCTCTCTC
* * *
1034813 TTGATGCTCTATAATCTTTGAGTGGAGTGATTTAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATAATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1034878 TCAT
66 TCAT
* *
1034882 TTGATGCTCTATAATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATAATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1034947 TCAT
66 TCAT
1034951 AGTTTGAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.39
Consensus pattern (69 bp):
TTGATGCTCTATAATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:1035051 original size:13 final size:14
Alignment explanation
Indices: 1035022--1035071 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
1035012 TTTTTCTTCA
1035022 ATTTTC-CTTTGTT
1 ATTTTCTCTTTGTT
1035035 -TTTTCTCTTT-TT
1 ATTTTCTCTTTGTT
1035047 ATTTTCTCTTTGATT
1 ATTTTCTCTTTG-TT
*
1035062 TTTTTC-CTTT
1 ATTTTCTCTTT
1035072 TTTCTCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 7 0.22
13 14 0.44
14 4 0.12
15 7 0.22
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTTTCTCTTTGTT
Found at i:1035064 original size:26 final size:26
Alignment explanation
Indices: 1035022--1035073 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1035012 TTTTTCTTCA
*
1035022 ATTTTCCTTTGTTTTTTCT-CTTTTT
1 ATTTTCCTTTGATTTTTCTCCTTTTT
*
1035047 ATTTTCTCTTTGATTTTTTTCCTTTTT
1 ATTTTC-CTTTGATTTTTCTCCTTTTT
1035074 TCTCTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 11 0.48
27 6 0.26
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (26 bp):
ATTTTCCTTTGATTTTTCTCCTTTTT
Found at i:1038274 original size:45 final size:43
Alignment explanation
Indices: 1038225--1038359 Score: 109
Period size: 45 Copynumber: 3.0 Consensus size: 43
1038215 TTAAGAAAAA
*
1038225 AAATAGAAAAAAATAAAATAAAGTAAAAATATAATATATATAAAT
1 AAATA-AAAAAAATAAAATTAAG-AAAAATATAATATATATAAAT
1038270 AAATAAAAACAAAAATAGAATATTAAG-AAAA-A-AATATATATAAA-
1 AAAT--AAA-AAAAATA-AA-ATTAAGAAAAATATAATATATATAAAT
* * *
1038314 AACATATAAAATATAATATTAAGAAAAA-ATATATATATAGTAAAT
1 AA-ATAAAAAAAATAAAATTAAGAAAAATATA-ATATATA-TAAAT
1038359 A
1 A
1038360 GAGAAAAATT
Statistics
Matches: 75, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
40 6 0.08
41 6 0.08
42 7 0.09
43 9 0.12
44 6 0.08
45 19 0.25
46 3 0.04
47 12 0.16
48 2 0.03
49 5 0.07
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (43 bp):
AAATAAAAAAAATAAAATTAAGAAAAATATAATATATATAAAT
Found at i:1038346 original size:37 final size:35
Alignment explanation
Indices: 1038266--1038350 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 35
1038256 TAATATATAT
*
1038266 AAATAAATAAAAACAAAAATAGAATATTAAGAAAAA
1 AAATATATAAAAACAAAAATAGAATATTAAG-AAAA
*
1038302 AATATATATAAAAACATATAAAATATAATATTAAGAAAA
1 AA-ATATATAAAAAC--A-AAAATAGAATATTAAGAAAA
1038341 AATATATATA
1 AA-ATATATA
1038351 TAGTAAATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 2 0.05
37 11 0.26
39 15 0.35
40 15 0.35
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (35 bp):
AAATATATAAAAACAAAAATAGAATATTAAGAAAA
Found at i:1038437 original size:25 final size:27
Alignment explanation
Indices: 1038387--1038437 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1038377 CTATACATAT
*
1038387 ATATATATATATATATAATGACATAAG
1 ATATATATATATATATAATAACATAAG
*
1038414 ATATATATA-ATATA-AATAATATAA
1 ATATATATATATATATAATAACATAA
1038438 TATAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 5 0.23
27 9 0.41
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATATAATAACATAAG
Found at i:1039385 original size:14 final size:14
Alignment explanation
Indices: 1039366--1039392 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1039356 CACATATACA
1039366 ACAACAAAAAATAG
1 ACAACAAAAAATAG
1039380 ACAACAAAAAATA
1 ACAACAAAAAATA
1039393 ATAAATTACC
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:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:1039385 original size:17 final size:17
Alignment explanation
Indices: 1039363--1039395 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1039353 TTACACATAT
1039363 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
1039380 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
1039396 AATTACCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:1039813 original size:28 final size:30
Alignment explanation
Indices: 1039773--1039835 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
1039763 ATTTTTTATA
*
1039773 TAATATAATATATAACTTAAATTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1039803 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1039831 TAATA
1 TAATA
1039836 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1039842 original size:28 final size:28
Alignment explanation
Indices: 1039777--1039842 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
1039767 TTTATATAAT
*
1039777 ATAATATATAACTTAAATTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
1039805 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
1039833 ATAATTTATA
1 ATAATATATA
1039843 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:1039845 original size:21 final size:21
Alignment explanation
Indices: 1039812--1039860 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1039802 CTAATATAAT
1039812 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1039833 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1039854 ATTAACT
1 A-TAACT
1039861 AAATTTTAGT
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:1040256 original size:44 final size:44
Alignment explanation
Indices: 1040206--1040298 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 44
1040196 CGCTGCAATA
*
1040206 ATGCAGCTATAGATGTAGGAATCTCCCAGCTATGGATGCAACGC
1 ATGCAGCTACAGATGTAGGAATCTCCCAGCTATGGATGCAACGC
* *
1040250 ATGCAGCTACGGATGTAGGAATCTCCTAGCTATGGATGCAACGC
1 ATGCAGCTACAGATGTAGGAATCTCCCAGCTATGGATGCAACGC
1040294 ATGCA
1 ATGCA
1040299 TGAGAGAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (44 bp):
ATGCAGCTACAGATGTAGGAATCTCCCAGCTATGGATGCAACGC
Found at i:1041175 original size:33 final size:33
Alignment explanation
Indices: 1041132--1041205 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
1041122 GATGGGGAGT
*
1041132 TTGGAGGCAGATGGTTTAAAGGGTTGGGATGAG
1 TTGGAAGCAGATGGTTTAAAGGGTTGGGATGAG
1041165 TTGGAAGCAGATGGTTTAAAGGGTTGGGATGAG
1 TTGGAAGCAGATGGTTTAAAGGGTTGGGATGAG
1041198 TTGGAAGC
1 TTGGAAGC
1041206 CATGGCTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.26, C:0.04, G:0.43, T:0.27
Consensus pattern (33 bp):
TTGGAAGCAGATGGTTTAAAGGGTTGGGATGAG
Found at i:1046164 original size:16 final size:15
Alignment explanation
Indices: 1046120--1046165 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
1046110 TAGGCGGTAT
1046120 ATATAAATATATAAA
1 ATATAAATATATAAA
* *
1046135 AGA-AAGTATATAAA
1 ATATAAATATATAAA
1046149 ATATAAATATATTAAA
1 ATATAAATATA-TAAA
1046165 A
1 A
1046166 ATTTATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 12 0.48
15 8 0.32
16 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (15 bp):
ATATAAATATATAAA
Found at i:1048334 original size:18 final size:18
Alignment explanation
Indices: 1048311--1048380 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
1048301 ACGTAGAATT
*
1048311 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
1048329 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1048347 TGTTCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1048365 TGTCCCGAAGAACCAC
1 TGTCCCGAAGGACCAC
1048381 GTAGACCCTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1049258 original size:24 final size:20
Alignment explanation
Indices: 1049201--1049238 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1049191 TTCCCCTTGA
1049201 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1049221 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1049239 TTAATATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1052800 original size:18 final size:18
Alignment explanation
Indices: 1052777--1052882 Score: 142
Period size: 18 Copynumber: 5.9 Consensus size: 18
1052767 ACGTAGAATT
1052777 TGTCCCGTAA-GACCACTA
1 TGTCCCG-AAGGACCACTA
*
1052795 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
* *
1052813 TATCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
1052831 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
1052849 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1052867 TGTCCCAAAGAACCAC
1 TGTCCCGAAGGACCAC
1052883 GTATACCCTC
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
17 2 0.03
18 77 0.97
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1053211 original size:15 final size:16
Alignment explanation
Indices: 1053160--1053220 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 16
1053150 AATTAATCAT
*
1053160 TTATATTCATATATCACC
1 TTATATTCATATA--AAC
* *
1053178 TTCATA-TCACATAATC
1 TT-ATATTCATATAAAC
1053194 TTAT-TTCATATAAAC
1 TTATATTCATATAAAC
1053209 TTATATTCATAT
1 TTATATTCATAT
1053221 CTATTATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 14 0.39
16 11 0.31
18 8 0.22
19 3 0.08
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (16 bp):
TTATATTCATATAAAC
Found at i:1053757 original size:24 final size:20
Alignment explanation
Indices: 1053703--1053740 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1053693 TTCCCCTTGA
1053703 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1053723 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1053741 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1065220 original size:16 final size:16
Alignment explanation
Indices: 1065201--1065252 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1065191 TATTGTATTA
1065201 TATAATAAATACATAT
1 TATAATAAATACATAT
* *
1065217 TATATTACATACTATAT
1 TATAATAAATAC-ATAT
1065234 T-TAA-ATAATACATAT
1 TATAATA-AATACATAT
1065249 TATA
1 TATA
1065253 TTGGGTATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 6 0.21
16 18 0.62
17 5 0.17
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAATAAATACATAT
Found at i:1071231 original size:58 final size:57
Alignment explanation
Indices: 1071154--1071262 Score: 184
Period size: 58 Copynumber: 1.9 Consensus size: 57
1071144 ACGCGAATTT
*
1071154 TAGTACTGTTTACCTATATCGGTAATTAGCGTTAG-GAAATTTGAAAATCGCATTGCGA
1 TAGTACTGTTTACCGATATCGGTAATTAGCGTT-GCG-AATTTGAAAATCGCATTGCGA
1071212 TAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCA
1 TAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCA
1071263 ATGTAAACAA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
57 16 0.33
58 33 0.67
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (57 bp):
TAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGA
Found at i:1071351 original size:20 final size:20
Alignment explanation
Indices: 1071322--1071402 Score: 135
Period size: 20 Copynumber: 4.0 Consensus size: 20
1071312 ACCGATATAG
1071322 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
1071342 GTAAATAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
1071362 GTAAATAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
1071382 GTAAACAGTATTATCGCAAT
1 GTAAACAGTACTATCGCAAT
1071402 G
1 G
1071403 CAATTTTCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:1071701 original size:2 final size:2
Alignment explanation
Indices: 1071694--1071722 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1071684 GTGGATCTTA
1071694 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 A
1071723 AGGTTATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1071929 original size:2 final size:2
Alignment explanation
Indices: 1071922--1071975 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1071912 ATTTTATCCT
1071922 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
1071964 TA -A TA TA TA TA T
1 TA TA TA TA TA TA T
1071976 TAATTTTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1072293 original size:3 final size:3
Alignment explanation
Indices: 1072278--1072339 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
1072268 TTATCCCGTT
* * * *
1072278 TTA TTA TTT TTA TTA TTA TAA TAA TAA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
1072327 TTA ATA TTA TTA T
1 TTA TTA TTA TTA T
1072340 ATTTACATGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1073959 original size:2 final size:2
Alignment explanation
Indices: 1073952--1074010 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1073942 GAAAAACAAT
1073952 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
1073994 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1074011 TCAATATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1074122 original size:26 final size:27
Alignment explanation
Indices: 1074070--1074140 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
1074060 ATATTTTTAA
** *
1074070 ATAAATAAATATTTTATTTTTATTTTT
1 ATAAATATTTATTTTATTTTAATTTTT
1074097 ATAAAT-TTTATTTT-TTTTAATGTTTT
1 ATAAATATTTATTTTATTTTAAT-TTTT
*
1074123 ATTAATATTTA-TTTATTT
1 ATAAATATTTATTTTATTT
1074141 ATTTTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 6 0.16
26 18 0.49
27 13 0.35
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (27 bp):
ATAAATATTTATTTTATTTTAATTTTT
Done.