Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008192.1 Hibiscus syriacus cultivar Beakdansim tig00110809_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: 1702141
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1279889 original size:21 final size:21
Alignment explanation
Indices: 1279849--1279892 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1279839 TATTTTGAAT
**
1279849 AAAAAATATATAATTTTTTTA
1 AAAAAATATATAATAATTTTA
*
1279870 AAAAAATATATGATAATTTTA
1 AAAAAATATATAATAATTTTA
1279891 AA
1 AA
1279893 TTTTAGGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAAATATATAATAATTTTA
Found at i:1279966 original size:6 final size:6
Alignment explanation
Indices: 1279948--1279978 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1279938 TATCTCCCTC
*
1279948 CGCCCA CGACCA CGCCCA CGCCCA CGCCCA C
1 CGCCCA CGCCCA CGCCCA CGCCCA CGCCCA C
1279979 TACACTCCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.65, G:0.16, T:0.00
Consensus pattern (6 bp):
CGCCCA
Found at i:1285551 original size:45 final size:45
Alignment explanation
Indices: 1285501--1285609 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
1285491 GATAAAAATT
* * **
1285501 TACCTAAAACGTTATTTTTCTAACTGAAATATTAATATTGGGTGC
1 TACCTAAAATGTTATTTTTCTAACAGAAATATTAATATTGGACGC
* * *
1285546 TACCTAAAATATTATTTTTCTACCAGAAATGTTAATATTGGACGC
1 TACCTAAAATGTTATTTTTCTAACAGAAATATTAATATTGGACGC
*
1285591 TACCTAACATGTTATTTTT
1 TACCTAAAATGTTATTTTT
1285610 TCTACCGATT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (45 bp):
TACCTAAAATGTTATTTTTCTAACAGAAATATTAATATTGGACGC
Found at i:1285944 original size:2 final size:2
Alignment explanation
Indices: 1285937--1285967 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1285927 ATGCCTCTGC
1285937 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 A
1285968 GTTAGAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1286911 original size:189 final size:189
Alignment explanation
Indices: 1286568--1286969 Score: 578
Period size: 189 Copynumber: 2.1 Consensus size: 189
1286558 ACAATATCTT
* * * * *
1286568 TTAATTTGAAATATTCAAAAGATAAAACT-TCTTTTATCTTTCAAACTAAAATATGTATTATTTT
1 TTAATTTGCAATAGTCAAAAGGT-AAACTAT-TTTTATCTTTCAAACTAAAACATATATTATTTT
* *
1286632 AATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAGTTAAAAAGATAACAAATATC
64 AATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATACC
*
1286697 TTTTTAAATTGACATATTCAAAGAGTAATTATCCTACTAATATTCAAATTAAATAA-TA-TA
129 TTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAA-AAGTACTA
* * *
1286757 TTAATTTGCAATGGTTAAAAGGTAAACTATTTTTA-CTATTCAAACTTAAACATATATTATTTTA
1 TTAATTTGCAATAGTCAAAAGGTAAACTATTTTTATCT-TTCAAACTAAAACATATATTATTTTA
*
1286821 ATTTGAAATATACAAAAGTATGTAATTATCTTTCAATATTCAAAATTAAAAAGATAACAAATACC
65 ATTTGAAATATACAAAAGTATATAATTATCTTT-AATATTCAAAATTAAAAAGATAACAAATACC
* * * *
1286886 TTTTTAAGTTGACTTATTAAAAGAGTAATTGTCCTACTAATATTCAAATTAAAAAGTATCTT
129 TTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAAAGTA-CTA
1286948 TTAATTTGCAATAGTCAAAAGG
1 TTAATTTGCAATAGTCAAAAGG
1286970 ACTATGAATT
Statistics
Matches: 189, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
187 2 0.01
188 67 0.35
189 99 0.52
191 21 0.11
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (189 bp):
TTAATTTGCAATAGTCAAAAGGTAAACTATTTTTATCTTTCAAACTAAAACATATATTATTTTAA
TTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATACCTT
TTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAAAGTACTA
Found at i:1287416 original size:37 final size:36
Alignment explanation
Indices: 1287318--1287418 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
1287308 TTTTGTCCTA
1287318 CTAGGATTCAAACT-CTCAAAAATAGGATAGAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATAGGATAGAATTCTG
* *
1287355 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
** *
1287391 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAAAATAGGAT
1287419 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
36 26 0.46
37 30 0.54
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
Found at i:1287885 original size:11 final size:11
Alignment explanation
Indices: 1287865--1287946 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
1287855 TTAATTATTT
*
1287865 TTATTCTAATA
1 TTATTTTAATA
*
1287876 TTATTTTAATG
1 TTATTTTAATA
1287887 TT-TTTTAA-A
1 TTATTTTAATA
*
1287896 GTTATTAT-ATA
1 -TTATTTTAATA
1287907 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
1287921 TTATATTTATTA
1 TTAT-TTTAATA
*
1287933 TTATTTTACTA
1 TTATTTTAATA
1287944 TTA
1 TTA
1287947 ACGTATATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
10 10 0.18
11 28 0.50
12 7 0.12
13 6 0.11
14 5 0.09
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:1288150 original size:21 final size:22
Alignment explanation
Indices: 1288126--1288176 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1288116 TATATACATT
*
1288126 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
1288147 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
1288169 TTTATTAT
1 ATTATTAT
1288177 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:1291555 original size:20 final size:20
Alignment explanation
Indices: 1291503--1291567 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
1291493 AAAGGCAAAT
1291503 AAAAA-AAAGAA-AAGAAGCA
1 AAAAAGAAAGAACAAGAA-CA
1291522 AAAAAGGAAA-AACAAGAACA
1 AAAAA-GAAAGAACAAGAACA
* *
1291542 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAGAACAAGAACA
1291562 AAAAAG
1 AAAAAG
1291568 GGAACAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.22
20 23 0.57
21 8 0.20
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAGAACAAGAACA
Found at i:1293151 original size:36 final size:36
Alignment explanation
Indices: 1293054--1293312 Score: 248
Period size: 36 Copynumber: 7.3 Consensus size: 36
1293044 ATTGAAAACA
* *
1293054 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
* *
1293090 TTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACAG
1293127 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
* * * *
1293163 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA-G
* * * *
1293192 TTTTCTTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
** * *
1293228 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGACAG
* * *
1293265 TTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAG
1293301 TTTCCCTTGAAA
1 TTTCCCTTGAAA
1293313 CAAAATCTTT
Statistics
Matches: 183, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 19 0.10
30 2 0.01
35 6 0.03
36 89 0.49
37 65 0.36
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
Found at i:1293173 original size:73 final size:73
Alignment explanation
Indices: 1293054--1293323 Score: 290
Period size: 73 Copynumber: 3.8 Consensus size: 73
1293044 ATTGAAAACA
* * *
1293054 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTTTGTCTCTCT
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
1293119 TGAGACAG
66 TGAGACAG
*
1293127 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-------TAT-T
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
*
1293184 TGA-ATATG
66 TGAGACA-G
* * * * ** * * *
1293192 TTTTCTTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
1293257 TGAGACAG
66 TGAGACAG
* * *
1293265 TTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTG
1 TTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT-TTTG
1293324 AATTTATTTC
Statistics
Matches: 158, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
64 2 0.01
65 49 0.31
66 2 0.01
72 8 0.05
73 91 0.58
74 6 0.04
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (73 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
TGAGACAG
Found at i:1293175 original size:138 final size:136
Alignment explanation
Indices: 1293002--1293379 Score: 495
Period size: 138 Copynumber: 2.7 Consensus size: 136
1292992 TTTTTAAAAC
* * * * *
1293002 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAACATTGAATATATTTCCCTTGAAAC
* * *
1293067 AAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCC
65 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCC
1293132 CTTGAAA
130 CTTGAAA
* * * *
1293139 TAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAA
1 -AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACA-TTGAATATATTTCCCTTGAAA
* * * *
1293204 CAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTC
64 CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTC
*
1293269 TCTTGAAA
129 CCTTGAAA
* * * * * *
1293277 CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAAA
1 AAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-CATTGAATATATTTCCCTTGAAA
*
1293342 CAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
64 CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1293380 CAAAATCTTC
Statistics
Matches: 206, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
137 10 0.05
138 196 0.95
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (136 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACATTGAATATATTTCCCTTGAAACA
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCC
TTGAAA
Found at i:1293202 original size:102 final size:103
Alignment explanation
Indices: 1293090--1293279 Score: 303
Period size: 102 Copynumber: 1.9 Consensus size: 103
1293080 CTTGAGATAG
*
1293090 TTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTC
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTC
1293154 TTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
65 TTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
** * *
1293193 TTTCT-TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
*
1293257 TGAGACAGTTTCTCTTGAAACAA
66 TGAGACAGTTTCCCTTGAAACAA
1293280 TTTTCGTCTA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
101 28 0.35
102 47 0.59
103 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (103 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
TGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:1293313 original size:36 final size:36
Alignment explanation
Indices: 1293193--1293316 Score: 162
Period size: 37 Copynumber: 3.4 Consensus size: 36
1293183 TTGAATATGT
*
1293193 TTTCT-TTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
1293228 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
1293265 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAAATTTT-GTCTCTCTTGAGACAG
*
1293301 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
1293317 ATCTTTGAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
35 10 0.13
36 33 0.43
37 34 0.44
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1293378 original size:65 final size:65
Alignment explanation
Indices: 1293274--1293448 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 65
1293264 GTTTCTCTTG
** * **
1293274 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCT
1293338 A
65 A
* *
1293339 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
1293404 TA
64 TA
* * *
1293406 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1293449 CAGATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 25 0.26
66 12 0.13
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:1293408 original size:67 final size:67
Alignment explanation
Indices: 1293265--1293447 Score: 219
Period size: 68 Copynumber: 2.7 Consensus size: 67
1293255 CTTGAGACAG
* * ** * **
1293265 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
1293327 TTA
65 TTA
* *
1293330 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1293395 TA
66 TA
* * *
1293397 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1293448 ACAGATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 31 0.31
66 8 0.08
67 29 0.29
68 32 0.32
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:1294212 original size:106 final size:107
Alignment explanation
Indices: 1294052--1294349 Score: 420
Period size: 106 Copynumber: 2.8 Consensus size: 107
1294042 GCCATCCGCG
* * *
1294052 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGAA
*
1294117 GGGACGGCTGGTTGTCAACAAACAACTTCTC-AATTTCAGAGCCA
63 GGGACGGCTGATTGTCAACAAACAACTTCTCAAATTTCAGAGCCA
* * * *
1294161 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAATGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
1294226 ACCGCTGCTTGTCAAC-AACAATTTTTCAAATTTCAGAGCCA
66 ACGGCTGATTGTCAACAAACAACTTCTCAAATTTCAGAGCCA
* * *
1294267 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1294332 ACGGCTGATTGTCAACAA
66 ACGGCTGATTGTCAACAA
1294350 GATTTTGTTC
Statistics
Matches: 167, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
105 9 0.05
106 132 0.79
107 4 0.02
109 22 0.13
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (107 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGATTGTCAACAAACAACTTCTCAAATTTCAGAGCCA
Found at i:1295021 original size:37 final size:36
Alignment explanation
Indices: 1294923--1295023 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 36
1294913 TTTTGTCCTA
1294923 CTAGGATTCAAACT-CTCAAAAATAGGATAGAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATAGGATAGAATTCTG
*
1294960 CTAGGATTCAACTCCTAAAAATAGGATAGAATT-TCG
1 CTAGGATTAAACTCCTAAAAATAGGATAGAATTCT-G
** *
1294996 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAAAATAGGAT
1295024 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
35 1 0.02
36 25 0.45
37 30 0.54
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
Found at i:1295768 original size:21 final size:22
Alignment explanation
Indices: 1295735--1295794 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
1295725 ATTTATATTA
*
1295735 TATTATATTATTATTATTTTACTT
1 TATTATA--ATTATTATTTTACGT
* *
1295759 TATTA-AATTATTTTTTTTCGT
1 TATTATAATTATTATTTTACGT
*
1295780 TATTATATTTATTAT
1 TATTATAATTATTAT
1295795 ATATATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 17 0.57
22 7 0.23
23 1 0.03
24 5 0.17
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATAATTATTATTTTACGT
Found at i:1300105 original size:83 final size:83
Alignment explanation
Indices: 1299958--1300116 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 83
1299948 GTTTTTGTAC
* * * * *
1299958 AAACGCCACGATAATGTTATTTATAGTGGCGTTTGTTCAAAAAATGACGGTATAAATTAGTAATT
1 AAACGCCACAATAATATTATTTATAGTGGCGTTTGTGCAAAAAATGACGGTATAAAGTAATAATT
1300023 TAGCT-GCGTTTATTAAAT
66 TAG-TGGCGTTTATTAAAT
* * * *
1300041 AAACGCCGCAATAATATTGTTTATAGTGGCGTTTGTGCAAAAAATGTC-GTAATAGAGTAATAAT
1 AAACGCCACAATAATATTATTTATAGTGGCGTTTGTGCAAAAAATGACGGT-ATAAAGTAATAAT
1300105 TTAGTGGCGTTT
65 TTAGTGGCGTTT
1300117 TACAAGAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
82 3 0.05
83 62 0.95
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (83 bp):
AAACGCCACAATAATATTATTTATAGTGGCGTTTGTGCAAAAAATGACGGTATAAAGTAATAATT
TAGTGGCGTTTATTAAAT
Found at i:1301131 original size:14 final size:14
Alignment explanation
Indices: 1301112--1301138 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1301102 TTTATTATTT
1301112 CTAGATATATTATA
1 CTAGATATATTATA
1301126 CTAGATATATTAT
1 CTAGATATATTAT
1301139 GCCATTTCCT
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:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
CTAGATATATTATA
Found at i:1308630 original size:43 final size:43
Alignment explanation
Indices: 1308583--1308667 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
1308573 ATATATTTAG
*
1308583 CGGCGTTTGT-GATAAAAACGCCGCGAAATCTCAAGACATATTA
1 CGGCGTTT-TCGACAAAAACGCCGCGAAATCTCAAGACATATTA
* * *
1308626 CGGCGTTTTCGACGAAAATGCCGCTAAATCTCAAGACATATT
1 CGGCGTTTTCGACAAAAACGCCGCGAAATCTCAAGACATATT
1308668 CTGCGGCGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (43 bp):
CGGCGTTTTCGACAAAAACGCCGCGAAATCTCAAGACATATTA
Found at i:1308765 original size:44 final size:43
Alignment explanation
Indices: 1308668--1308784 Score: 146
Period size: 44 Copynumber: 2.7 Consensus size: 43
1308658 AAGACATATT
* * * * *
1308668 CTGCGGCGTTTGTAGGAAAACGTCGCT-AAATATCAACATCTT
1 CTGCGGCGTTTGTAAGAAAACGCCGCTAAAAAATAAACATCTA
*
1308710 CTGCGGCGTTTGTAAGAAAAACGCCGGTAAAAAATAAACATCTA
1 CTGCGGCGTTTGTAAG-AAAACGCCGCTAAAAAATAAACATCTA
*
1308754 CTGCGACGTTTGTGAAGAAAACGCCGCTAAA
1 CTGCGGCGTTTGT-AAGAAAACGCCGCTAAA
1308785 CATCAACGCC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 15 0.23
43 9 0.14
44 37 0.58
45 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (43 bp):
CTGCGGCGTTTGTAAGAAAACGCCGCTAAAAAATAAACATCTA
Found at i:1308833 original size:43 final size:43
Alignment explanation
Indices: 1308779--1308895 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
1308769 AGAAAACGCC
* * *
1308779 GCTAAACATCAACGCCTATTGCGGCGTTTGTCTGCCAAATACA
1 GCTAAATATCAACACCTATTGCGGCGTTTGTCTGCCAAACACA
* * * *
1308822 GTTAAATATCAACACCTATTGCGGCGTTTTTCTGCCAAACGCC
1 GCTAAATATCAACACCTATTGCGGCGTTTGTCTGCCAAACACA
* *
1308865 GCTAAATATCAATACCTTTTGCGGCGTTTGT
1 GCTAAATATCAACACCTATTGCGGCGTTTGT
1308896 TGAACAACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
GCTAAATATCAACACCTATTGCGGCGTTTGTCTGCCAAACACA
Found at i:1310490 original size:19 final size:19
Alignment explanation
Indices: 1310466--1310505 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1310456 ATATAATATG
*
1310466 TAGTAAATTAAAAGAGGAT
1 TAGTAAATTAAAAGAAGAT
1310485 TAGTAAATTAAAAGAAGAT
1 TAGTAAATTAAAAGAAGAT
1310504 TA
1 TA
1310506 TGAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (19 bp):
TAGTAAATTAAAAGAAGAT
Found at i:1311155 original size:24 final size:24
Alignment explanation
Indices: 1311116--1311191 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 24
1311106 TATAATTTCA
*
1311116 AAAATATATAATATATATAGGTTTTG
1 AAAATATAT-A-ATATATAGTTTTTG
*
1311142 AAGATATAT-A-ATATAGTTTTTG
1 AAAATATATAATATATAGTTTTTG
*
1311164 AAAACATATAATATATAGTTTTT-
1 AAAATATATAATATATAGTTTTTG
1311187 AAAAT
1 AAAAT
1311192 GGTTTTTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 18 0.42
23 6 0.14
24 11 0.26
26 8 0.19
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.42
Consensus pattern (24 bp):
AAAATATATAATATATAGTTTTTG
Found at i:1311238 original size:14 final size:14
Alignment explanation
Indices: 1311219--1311247 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1311209 TATAATATAG
1311219 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1311233 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1311247 T
1 T
1311248 AATATATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACATA
Found at i:1311246 original size:38 final size:37
Alignment explanation
Indices: 1311158--1311309 Score: 193
Period size: 38 Copynumber: 4.0 Consensus size: 37
1311148 TATAATATAG
**
1311158 TTTTTGAAAACATATAATATATAGTTTTTAAAATGGT-
1 TTTTTGAAAACATATAATATATAGTTTTTAAAA-CATA
1311195 TTTTTGAAAACATAT-ATAATATAGTTTTTGAAAACATA
1 TTTTTGAAAACATATAAT-ATATAGTTTTT-AAAACATA
*
1311233 TTTTTGAAAACATATAATATATAGTTTTTAAAACACGA
1 TTTTTGAAAACATATAATATATAGTTTTTAAAACA-TA
*
1311271 TTTTTCAAAACATAT-ATAATATAGTTTTTGAAAACATA
1 TTTTTGAAAACATATAAT-ATATAGTTTTT-AAAACATA
1311309 T
1 T
1311310 ACTATATTTT
Statistics
Matches: 103, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
36 2 0.02
37 35 0.34
38 58 0.56
39 8 0.08
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (37 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAACATA
Found at i:1311304 original size:76 final size:75
Alignment explanation
Indices: 1311158--1311309 Score: 259
Period size: 76 Copynumber: 2.0 Consensus size: 75
1311148 TATAATATAG
** * *
1311158 TTTTTGAAAACATATAATATATAGTTTTTAAAATGGTTTTTTGAAAACATATATAATATAGTTTT
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAACGATTTTTCAAAACATATATAATATAGTTTT
1311223 TGAAAACATA
66 TGAAAACATA
1311233 TTTTTGAAAACATATAATATATAGTTTTTAAAACACGATTTTTCAAAACATATATAATATAGTTT
1 TTTTTGAAAACATATAATATATAGTTTTTAAAA-ACGATTTTTCAAAACATATATAATATAGTTT
1311298 TTGAAAACATA
65 TTGAAAACATA
1311309 T
1 T
1311310 ACTATATTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
75 33 0.46
76 39 0.54
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (75 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAAACGATTTTTCAAAACATATATAATATAGTTTT
TGAAAACATA
Found at i:1311315 original size:22 final size:20
Alignment explanation
Indices: 1311270--1311324 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 20
1311260 TTAAAACACG
1311270 ATTTTTCAAAACATATATAATAT
1 ATTTTT-AAAAC--ATATAATAT
*
1311293 AGTTTTTGAAAACATATACTAT
1 A-TTTTT-AAAACATATAATAT
1311315 ATTTTTAAAA
1 ATTTTTAAAA
1311325 TGGTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 5 0.17
22 9 0.31
23 1 0.03
24 10 0.34
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTTTTAAAACATATAATAT
Found at i:1311353 original size:18 final size:18
Alignment explanation
Indices: 1311330--1311460 Score: 86
Period size: 19 Copynumber: 7.5 Consensus size: 18
1311320 TAAAATGGTT
1311330 TTTTTG-AAACATATATA
1 TTTTTGAAAACATATATA
1311347 GTTTTTGAAAACATAT-TA
1 -TTTTTGAAAACATATATA
1311365 -TTTTGAAAACATATATA
1 TTTTTGAAAACATATATA
* * *
1311382 TATATAT-ATATATATATATA
1 T-T-TTTGA-AAACATATATA
1311402 GTTTTT-AAAAC----A-A
1 -TTTTTGAAAACATATATA
1311415 TTTTTGAAAACATATATAA
1 TTTTTGAAAACATATAT-A
*
1311434 TATTTGAAAACATAT-TA
1 TTTTTGAAAACATATATA
1311451 TATTTTGAAA
1 T-TTTTGAAA
1311461 TATAATATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 30
0.70 0.06 0.23
Matches are distributed among these distances:
12 5 0.06
13 6 0.07
14 1 0.01
16 14 0.16
17 5 0.06
18 18 0.20
19 28 0.31
20 12 0.13
21 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTTTGAAAACATATATA
Found at i:1311382 original size:2 final size:2
Alignment explanation
Indices: 1311375--1311401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1311365 TTTTGAAAAC
1311375 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 A
1311402 GTTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1311720 original size:43 final size:43
Alignment explanation
Indices: 1311655--1311750 Score: 149
Period size: 43 Copynumber: 2.2 Consensus size: 43
1311645 TCTACTTGAA
* * *
1311655 CCAGCAGGCCAAGACTGGGAAGCTAGGAGTAAAGCACGAATAC
1 CCAGCAGGCCAAGACTGAGAAGCAAAGAGTAAAGCACGAATAC
1311698 CCAGCAGGCCAAGA-TCGAGAAGCAAAGAGTAAAGCACGAATAC
1 CCAGCAGGCCAAGACT-GAGAAGCAAAGAGTAAAGCACGAATAC
1311741 CCAGCAGGCC
1 CCAGCAGGCC
1311751 TGATCCAGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 1 0.02
43 48 0.98
ACGTcount: A:0.39, C:0.26, G:0.28, T:0.07
Consensus pattern (43 bp):
CCAGCAGGCCAAGACTGAGAAGCAAAGAGTAAAGCACGAATAC
Found at i:1317471 original size:10 final size:10
Alignment explanation
Indices: 1317456--1317506 Score: 66
Period size: 10 Copynumber: 5.1 Consensus size: 10
1317446 CATTTAAATG
1317456 ATAAACGAAC
1 ATAAACGAAC
1317466 ATAAACGAAC
1 ATAAACGAAC
* *
1317476 GTAAATGAAC
1 ATAAACGAAC
*
1317486 ATAAACGGAC
1 ATAAACGAAC
*
1317496 ATAAATGAAC
1 ATAAACGAAC
1317506 A
1 A
1317507 ACACAAACAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1317485 original size:20 final size:20
Alignment explanation
Indices: 1317456--1317506 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1317446 CATTTAAATG
*
1317456 ATAAACGAACATAAACGAAC
1 ATAAATGAACATAAACGAAC
* *
1317476 GTAAATGAACATAAACGGAC
1 ATAAATGAACATAAACGAAC
1317496 ATAAATGAACA
1 ATAAATGAACA
1317507 ACACAAACAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (20 bp):
ATAAATGAACATAAACGAAC
Found at i:1318554 original size:23 final size:23
Alignment explanation
Indices: 1318485--1318542 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1318475 CTCGTATAAA
*
1318485 TACACCGAAGTGCCACATAGAAT
1 TACACCAAAGTGCCACATAGAAT
* *
1318508 TGCACCAAAGTGCCACGTAGAAT
1 TACACCAAAGTGCCACATAGAAT
1318531 TACACCAAAGTG
1 TACACCAAAGTG
1318543 TCATATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (23 bp):
TACACCAAAGTGCCACATAGAAT
Found at i:1320149 original size:24 final size:20
Alignment explanation
Indices: 1320096--1320153 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1320086 TTCCCCTTGA
*
1320096 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
1320116 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1320139 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1320154 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1320250 original size:64 final size:63
Alignment explanation
Indices: 1320141--1320278 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 63
1320131 TCTTTAACAT
*
1320141 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTC-TTTTTAA-GG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCA-CTTCGATGTTTCCATTTTTAATGG
* * *
1320203 AAGTGCATCGATGCACT-CCTTATGCATCGATGCACTAACTGCA-TTCGATGTTTCCATTTTTAA
1 --GTGCATCGATGCACTACC-CATGCATCGATACAC-AAAT-CACTTCGATGTTTCCATTTTTAA
1320266 TGG
61 TGG
1320269 GTGCATCGAT
1 GTGCATCGAT
1320279 ACACACTGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
63 2 0.03
64 49 0.75
65 10 0.15
66 4 0.06
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACTTCGATGTTTCCATTTTTAATGG
Found at i:1323588 original size:23 final size:23
Alignment explanation
Indices: 1323558--1323607 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1323548 CTCATATAAA
1323558 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1323581 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1323604 TGCA
1 TGCA
1323608 TTGAAATGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1323617 original size:23 final size:23
Alignment explanation
Indices: 1323558--1323618 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1323548 CTCATATAAA
*
1323558 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAATGCCACGTAGAAT
* *
1323581 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAATGCCACGTAGAAT
**
1323604 TGCATTGAAATGCCA
1 TGCACCGAAATGCCA
1323619 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAATGCCACGTAGAAT
Found at i:1325184 original size:20 final size:20
Alignment explanation
Indices: 1325159--1325196 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1325149 TTCCCCTTGA
1325159 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
1325179 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
1325197 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:1325296 original size:64 final size:64
Alignment explanation
Indices: 1325208--1325365 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 64
1325198 TAACATGTGT
* * *
1325208 ATCGATGCACTACCCATGCATCGATACACA-AATCACCTTCGATGTTT-TTATTTTAAGGGAGTG
1 ATCGATGCACTTCCTATGCATCGATACACATAATCACATTCGATGTTTCTT-TTTTAAGGG-GTG
1325271 C
64 C
* * * *
1325272 ATCGATGTAC-TCCTTATGCATCGATGCA-ATAATTACATTCGATGTTTCCTTTTTTAATGGGTG
1 ATCGATGCACTTCC-TATGCATCGATACACATAATCACATTCGATGTTT-CTTTTTTAAGGGGTG
1325335 C
64 C
*
1325336 ATCGATGCACTTCCTGTGCATCGATACACA
1 ATCGATGCACTTCCTATGCATCGATACACA
1325366 CTGAACAATT
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
63 3 0.04
64 61 0.78
65 12 0.15
66 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (64 bp):
ATCGATGCACTTCCTATGCATCGATACACATAATCACATTCGATGTTTCTTTTTTAAGGGGTGC
Found at i:1326227 original size:14 final size:13
Alignment explanation
Indices: 1326208--1326258 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
1326198 CTGTTCAAAC
1326208 ATAAATGAACGAA
1 ATAAATGAACGAA
1326221 TATAAATGAAC---
1 -ATAAATGAACGAA
*
1326232 ATAAATGAACAAA
1 ATAAATGAACGAA
1326245 CATAAATGAACGAA
1 -ATAAATGAACGAA
1326259 CGAGCTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
10 10 0.31
14 22 0.69
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.18
Consensus pattern (13 bp):
ATAAATGAACGAA
Found at i:1326234 original size:24 final size:24
Alignment explanation
Indices: 1326205--1326255 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1326195 CCTCTGTTCA
* *
1326205 AACATAAATGAACGAATATAAATG
1 AACATAAATGAACAAACATAAATG
1326229 AACATAAATGAACAAACATAAATG
1 AACATAAATGAACAAACATAAATG
1326253 AAC
1 AAC
1326256 GAACGAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.18
Consensus pattern (24 bp):
AACATAAATGAACAAACATAAATG
Found at i:1327300 original size:21 final size:22
Alignment explanation
Indices: 1327276--1327320 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1327266 TGAAGTGCCA
*
1327276 CATAT-AAATGTCTCGAAGGAC
1 CATATAAAATGTCCCGAAGGAC
*
1327297 CATATAGAAATGTCCCGAATGAC
1 CATATA-AAATGTCCCGAAGGAC
1327320 C
1 C
1327321 GCGTAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
23 15 0.75
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (22 bp):
CATATAAAATGTCCCGAAGGAC
Found at i:1327327 original size:23 final size:23
Alignment explanation
Indices: 1327301--1327374 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1327291 AAGGACCATA
1327301 TAGAAATGTCCCGAATGACCGCG
1 TAGAAATGTCCCGAATGACCGCG
* * * *
1327324 TAGAAATATCCCAAATCACCACG
1 TAGAAATGTCCCGAATGACCGCG
* * *
1327347 TAGAATTGTCCCGAAGGACCGTG
1 TAGAAATGTCCCGAATGACCGCG
1327370 TAGAA
1 TAGAA
1327375 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (23 bp):
TAGAAATGTCCCGAATGACCGCG
Found at i:1327512 original size:14 final size:14
Alignment explanation
Indices: 1327451--1327559 Score: 60
Period size: 14 Copynumber: 7.4 Consensus size: 14
1327441 TTATACTATT
* *
1327451 TCACATAACTTATA
1 TCACATAGCATATA
*
1327465 TCACATAGACAAATAA
1 TCACATAG-CATAT-A
* *
1327481 TTACATAG-ATCATG
1 TCACATAGCAT-ATA
1327495 TCACATAGCATATA
1 TCACATAGCATATA
*
1327509 TCACATTTGCATATAA
1 TCACA-TAGCATAT-A
*
1327525 TCAAATAGTTCA-ATA
1 TCACATAG--CATATA
* *
1327540 TCACATAACTTATA
1 TCACATAGCATATA
1327554 TCACAT
1 TCACAT
1327560 TTTCATATAA
Statistics
Matches: 72, Mismatches: 14, Indels: 18
0.69 0.13 0.17
Matches are distributed among these distances:
13 1 0.01
14 31 0.43
15 23 0.32
16 15 0.21
17 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (14 bp):
TCACATAGCATATA
Found at i:1327557 original size:45 final size:44
Alignment explanation
Indices: 1327451--1327588 Score: 161
Period size: 45 Copynumber: 3.1 Consensus size: 44
1327441 TTATACTATT
* * * * *
1327451 TCACATAACTTATATCACA-TAGACAAATAATTACATAGATCATG
1 TCACATAACTTATATCACATTTG-CATATAATCAAATAGATCATA
* * *
1327495 TCACATAGCATATATCACATTTGCATATAATCAAATAGTTCAATA
1 TCACATAACTTATATCACATTTGCATATAATCAAATAGATC-ATA
* *
1327540 TCACATAACTTATATCACATTTTCATATAATCAAATAGATCATG
1 TCACATAACTTATATCACATTTGCATATAATCAAATAGATCATA
1327584 TCACA
1 TCACA
1327589 GAGCATGAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
44 38 0.48
45 41 0.52
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.33
Consensus pattern (44 bp):
TCACATAACTTATATCACATTTGCATATAATCAAATAGATCATA
Found at i:1328115 original size:15 final size:15
Alignment explanation
Indices: 1328095--1328123 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1328085 TACTTATCCA
1328095 TTAGTATCGATACAC
1 TTAGTATCGATACAC
1328110 TTAGTATCGATACA
1 TTAGTATCGATACA
1328124 ACTCTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TTAGTATCGATACAC
Found at i:1329385 original size:27 final size:26
Alignment explanation
Indices: 1329341--1329402 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
1329331 TTTTAATTCC
**
1329341 AATAAAAGAGCTGTTAAATATCTTTT
1 AATAAAAGAGCTAATAAATATCTTTT
* *
1329367 AAATAAAAGAGGTAATAAATCTCTTTT
1 -AATAAAAGAGCTAATAAATATCTTTT
1329394 AATAAAAGA
1 AATAAAAGA
1329403 AATAAATCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.32
Consensus pattern (26 bp):
AATAAAAGAGCTAATAAATATCTTTT
Found at i:1329410 original size:23 final size:24
Alignment explanation
Indices: 1329355--1329417 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
1329345 AAAGAGCTGT
*
1329355 TAAATATCTTTTAAATAAAAGAGGTAA
1 TAAATCTCTTTT-AATAAAAGA-G-AA
1329382 TAAATCTCTTTTAATAAAAGA-AA
1 TAAATCTCTTTTAATAAAAGAGAA
*
1329405 TAAATCTATTTTA
1 TAAATCTCTTTTA
1329418 TTTTTATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 14 0.41
26 9 0.26
27 11 0.32
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
TAAATCTCTTTTAATAAAAGAGAA
Found at i:1330541 original size:16 final size:16
Alignment explanation
Indices: 1330520--1330551 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1330510 TTTATTTGTC
1330520 TAAATGTCATGAAAAG
1 TAAATGTCATGAAAAG
*
1330536 TAAATGTCATGGAAAG
1 TAAATGTCATGAAAAG
1330552 CTTGATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
TAAATGTCATGAAAAG
Found at i:1332479 original size:31 final size:31
Alignment explanation
Indices: 1332444--1332507 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
1332434 TTCAAAATCA
*
1332444 TACCTAATGTTTACTTTTTGTTTCATTTTAG
1 TACCTAACGTTTACTTTTTGTTTCATTTTAG
*
1332475 TACCTGACGTTTACTTTTTGTTTCATTTTAG
1 TACCTAACGTTTACTTTTTGTTTCATTTTAG
1332506 TA
1 TA
1332508 TACCATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (31 bp):
TACCTAACGTTTACTTTTTGTTTCATTTTAG
Found at i:1346719 original size:30 final size:30
Alignment explanation
Indices: 1346683--1346786 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 30
1346673 ATAATTTATT
* * *
1346683 TAAAATAAATTACCTAAAAATTATTTTACG
1 TAAAATAAATTACATGAAAATTATTTTACA
* *
1346713 TAAAATAAATTACATGAAAACTATTTTTCA
1 TAAAATAAATTACATGAAAATTATTTTACA
* ** * *
1346743 TAAAATGAATTATTTGAAATTTGTTTTACA
1 TAAAATAAATTACATGAAAATTATTTTACA
1346773 TAAAATAAATTACA
1 TAAAATAAATTACA
1346787 CTTTCTAAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (30 bp):
TAAAATAAATTACATGAAAATTATTTTACA
Found at i:1347379 original size:17 final size:17
Alignment explanation
Indices: 1347345--1347378 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1347335 AAGTTGGGTA
1347345 TCGGGTCGGGTCAATTT
1 TCGGGTCGGGTCAATTT
1347362 TCGGGT-GGGTCAATTT
1 TCGGGTCGGGTCAATTT
1347378 T
1 T
1347379 TAGGTCGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.12, C:0.15, G:0.35, T:0.38
Consensus pattern (17 bp):
TCGGGTCGGGTCAATTT
Found at i:1347598 original size:2 final size:2
Alignment explanation
Indices: 1347591--1347623 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1347581 CTAATCAAGC
1347591 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 A
1347624 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1348673 original size:13 final size:13
Alignment explanation
Indices: 1348650--1348741 Score: 63
Period size: 14 Copynumber: 7.5 Consensus size: 13
1348640 TTAAATTAAA
1348650 AATATAATATTAT
1 AATATAATATTAT
* *
1348663 CATATATTATTAT
1 AATATAATATTAT
* *
1348676 AATAT-A-ACT-G
1 AATATAATATTAT
1348686 AATAT-ATA-T-T
1 AATATAATATTAT
*
1348696 AATATAATATTGAA
1 AATATAATATT-AT
1348710 AATATAATATTATT
1 AATATAATATTA-T
*
1348724 AATATTATATTAT
1 AATATAATATTAT
1348737 -ATATA
1 AATATA
1348742 TTAAATATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
10 12 0.19
11 6 0.10
12 5 0.08
13 17 0.27
14 22 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (13 bp):
AATATAATATTAT
Found at i:1348720 original size:60 final size:58
Alignment explanation
Indices: 1348631--1348765 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 58
1348621 TGGTCGTGCT
*
1348631 TATATATT-ATTAA-ATTAAAAATATAATATTATCATATATTATTATAATATA-ACTGAA
1 TATATATTAATTAATATTAAAAATATAATATTATCA-ATATTA-TATAATATATACTAAA
* * * *
1348688 TATATATTAATATAATATTGAAAATATAATATTATTAATATTATATTATATATATTAAA
1 TATATATTAAT-TAATATTAAAAATATAATATTATCAATATTATATAATATATACTAAA
*
1348747 TATTTTATTAATTAATATT
1 TA-TATATTAATTAATATT
1348766 TTTATTAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
57 8 0.12
58 10 0.15
59 22 0.33
60 27 0.40
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (58 bp):
TATATATTAATTAATATTAAAAATATAATATTATCAATATTATATAATATATACTAAA
Found at i:1348742 original size:28 final size:28
Alignment explanation
Indices: 1348651--1348742 Score: 80
Period size: 28 Copynumber: 3.1 Consensus size: 28
1348641 TAAATTAAAA
* *
1348651 ATATAATATTATCATATATTATTATAATAT
1 ATATAATATTATTA-ATATTA-TATTATAT
* *
1348681 A-ACTGAATATATATTAATATAATATTGA-AA
1 ATA-T-AATAT-TATTAATATTATATT-ATAT
1348711 ATATAATATTATTAATATTATATTATAT
1 ATATAATATTATTAATATTATATTATAT
1348739 ATAT
1 ATAT
1348743 TAAATATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
27 1 0.02
28 19 0.38
29 6 0.12
30 8 0.16
31 12 0.24
32 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
ATATAATATTATTAATATTATATTATAT
Found at i:1348755 original size:21 final size:19
Alignment explanation
Indices: 1348711--1348760 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
1348701 AATATTGAAA
*
1348711 ATATAATATTATTAATATT
1 ATATTATATTATTAATATT
1348730 ATATTATATATATTAAATATT
1 ATATTATAT-TATT-AATATT
*
1348751 TTATTA-ATTA
1 ATATTATATTA
1348761 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.37
20 6 0.22
21 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTATATTATTAATATT
Found at i:1348760 original size:16 final size:16
Alignment explanation
Indices: 1348717--1348773 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
1348707 GAAAATATAA
1348717 TATT-ATTAATATTATAT
1 TATTAATTAATATT-T-T
1348734 TATATATATTAA-ATATTT
1 TAT-TA-ATTAATAT-TTT
1348752 TATTAATTAATATTTT
1 TATTAATTAATATTTT
1348768 TATTAA
1 TATTAA
1348774 AATTATGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 14 0.40
17 7 0.20
18 5 0.14
19 3 0.09
20 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAATTAATATTTT
Found at i:1348840 original size:88 final size:88
Alignment explanation
Indices: 1348736--1348913 Score: 356
Period size: 88 Copynumber: 2.0 Consensus size: 88
1348726 TATTATATTA
1348736 TATATATTAAATATTTTATTAATTAATATTTTTATTAAAATTATGCTATTATATTATATTAATAT
1 TATATATTAAATATTTTATTAATTAATATTTTTATTAAAATTATGCTATTATATTATATTAATAT
1348801 ATTTACAAAGTTAGTTCAAGTAG
66 ATTTACAAAGTTAGTTCAAGTAG
1348824 TATATATTAAATATTTTATTAATTAATATTTTTATTAAAATTATGCTATTATATTATATTAATAT
1 TATATATTAAATATTTTATTAATTAATATTTTTATTAAAATTATGCTATTATATTATATTAATAT
1348889 ATTTACAAAGTTAGTTCAAGTAG
66 ATTTACAAAGTTAGTTCAAGTAG
1348912 TA
1 TA
1348914 AGCATCTTAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (88 bp):
TATATATTAAATATTTTATTAATTAATATTTTTATTAAAATTATGCTATTATATTATATTAATAT
ATTTACAAAGTTAGTTCAAGTAG
Found at i:1349165 original size:13 final size:13
Alignment explanation
Indices: 1349129--1349174 Score: 74
Period size: 13 Copynumber: 3.4 Consensus size: 13
1349119 AGGGACAACC
1349129 AACATGTAATGAT
1 AACATGTAATGAT
1349142 AACATAAGTAATGAT
1 AACAT--GTAATGAT
1349157 AACATGTAATGAT
1 AACATGTAATGAT
1349170 AACAT
1 AACAT
1349175 ATGTCCTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 18 0.58
15 13 0.42
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (13 bp):
AACATGTAATGAT
Found at i:1349178 original size:15 final size:15
Alignment explanation
Indices: 1349132--1349178 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1349122 GACAACCAAC
1349132 ATGTAATGATAACAT
1 ATGTAATGATAACAT
*
1349147 AAGTAATGATAAC--
1 ATGTAATGATAACAT
1349160 ATGTAATGATAACAT
1 ATGTAATGATAACAT
1349175 ATGT
1 ATGT
1349179 CCTAGAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 12 0.43
15 16 0.57
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (15 bp):
ATGTAATGATAACAT
Found at i:1350672 original size:9 final size:10
Alignment explanation
Indices: 1350655--1350685 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1350645 ATAACCTGGT
1350655 AATTTAAAAA
1 AATTTAAAAA
1350665 AA-TTAAAAA
1 AATTTAAAAA
1350674 AATTTAAAAA
1 AATTTAAAAA
1350684 AA
1 AA
1350686 ACAAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AATTTAAAAA
Found at i:1350691 original size:19 final size:19
Alignment explanation
Indices: 1350655--1350691 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1350645 ATAACCTGGT
**
1350655 AATTTAAAAAAATTAAAAA
1 AATTTAAAAAAAACAAAAA
1350674 AATTTAAAAAAAACAAAA
1 AATTTAAAAAAAACAAAA
1350692 TTATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (19 bp):
AATTTAAAAAAAACAAAAA
Found at i:1351778 original size:16 final size:16
Alignment explanation
Indices: 1351742--1351792 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1351732 AAAAAATTAA
*
1351742 AAATAAAGATA-AAAT
1 AAATAAATATATAAAT
* *
1351757 ATAATACATGTATAAAT
1 A-AATAAATATATAAAT
*
1351774 AAATAAATATATAATT
1 AAATAAATATATAAAT
1351790 AAA
1 AAA
1351793 CAATCTTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 1 0.04
16 22 0.79
17 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
AAATAAATATATAAAT
Found at i:1355951 original size:19 final size:20
Alignment explanation
Indices: 1355902--1355951 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1355892 CTATTGAAAA
1355902 AATT-TAATATTATAATATC
1 AATTATAATATTATAATATC
*
1355921 AATTA-AAAATTATAAT-TC
1 AATTATAATATTATAATATC
1355939 -ATTCATAATATTA
1 AATT-ATAATATTA
1355952 ATTCCAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 20 0.77
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTATAATATTATAATATC
Found at i:1360542 original size:17 final size:18
Alignment explanation
Indices: 1360522--1360555 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1360512 TAGATCATTC
1360522 AAATTA-TAATAAAAATA
1 AAATTATTAATAAAAATA
*
1360539 AAATTATTAATTAAAAT
1 AAATTATTAATAAAAAT
1360556 TTAAATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTATTAATAAAAATA
Found at i:1362064 original size:2 final size:2
Alignment explanation
Indices: 1362057--1362127 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1362047 TTCTCTAATT
1362057 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
1362099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1362128 TCAATAACAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1362517 original size:9 final size:9
Alignment explanation
Indices: 1362503--1362532 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1362493 TTAGAACCAC
1362503 AATAAAAAA
1 AATAAAAAA
1362512 AAT-AAAAA
1 AATAAAAAA
1362520 AATAAAAAA
1 AATAAAAAA
1362529 AATA
1 AATA
1362533 TATATATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AATAAAAAA
Found at i:1364961 original size:30 final size:29
Alignment explanation
Indices: 1364923--1364980 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
1364913 AGAATTTACA
* *
1364923 TGAACTACGTGATTAAATGTATATGTGAC
1 TGAACTACGAGATTAAATGAATATGTGAC
* *
1364952 TGAAGCTACGAGTTTATATGAATATGTGA
1 TGAA-CTACGAGATTAAATGAATATGTGA
1364981 TATGTCTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (29 bp):
TGAACTACGAGATTAAATGAATATGTGAC
Found at i:1365244 original size:23 final size:23
Alignment explanation
Indices: 1365211--1365273 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1365201 TATCTTATAT
1365211 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * *
1365234 GGCACTTCGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
*
1365257 GGCACTCCGGTGCATTT
1 GGCACTACGGTGCATTT
1365274 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:1365594 original size:2 final size:2
Alignment explanation
Indices: 1365587--1365627 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1365577 AATATGTATG
1365587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1365628 TTATGTTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1366189 original size:27 final size:27
Alignment explanation
Indices: 1366154--1366236 Score: 139
Period size: 27 Copynumber: 3.1 Consensus size: 27
1366144 CCGCCATCAC
1366154 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCATAGCAT
1366181 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCATAGCAT
* * *
1366208 CACTTTGAACTTTAAAGTCCACAGCAT
1 CACTTTGAACTTGAAACTCCATAGCAT
1366235 CA
1 CA
1366237 AGATCTTCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.29
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCATAGCAT
Found at i:1373022 original size:21 final size:21
Alignment explanation
Indices: 1372996--1373044 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1372986 TTCGTCGTAT
1372996 ACTGTCACAACAACATTGTGA
1 ACTGTCACAACAACATTGTGA
*
1373017 ACTGTCACATCAACATTGTGA
1 ACTGTCACAACAACATTGTGA
*
1373038 ATTGTCA
1 ACTGTCA
1373045 TGTAATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (21 bp):
ACTGTCACAACAACATTGTGA
Found at i:1373893 original size:5 final size:6
Alignment explanation
Indices: 1373877--1373902 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1373867 ATAATCTTTT
1373877 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
1373903 GATAATTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:1374071 original size:29 final size:30
Alignment explanation
Indices: 1374039--1374110 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
1374029 ATCTTCAAAG
*
1374039 AAATTTTTTATTCAAATAT-AT-CTCATTAA
1 AAATTATTT-TTCAAATATAATACTCATTAA
*
1374068 AAATTATTTCTC-AATATAATACTCATTAA
1 AAATTATTTTTCAAATATAATACTCATTAA
*
1374097 CAATTATTTTTCAA
1 AAATTATTTTTCAA
1374111 TCTATCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.14
28 4 0.11
29 26 0.72
30 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (30 bp):
AAATTATTTTTCAAATATAATACTCATTAA
Found at i:1374717 original size:3 final size:3
Alignment explanation
Indices: 1374711--1374766 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
1374701 ATCTTTTTTT
1374711 TTA TTA -TA TTA TTA TTA TTA TT- TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
1374755 TTTA TTA TTA TT
1 -TTA TTA TTA TT
1374767 TTGTTTACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 3 0.06
3 42 0.86
4 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1375708 original size:2 final size:2
Alignment explanation
Indices: 1375701--1375726 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1375691 CTTAGATTAC
1375701 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
1375727 TAAGTGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1376953 original size:16 final size:16
Alignment explanation
Indices: 1376915--1376945 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1376905 ATTTGTGTAT
1376915 ATATATTATTATATAG
1 ATATATTATTATATAG
*
1376931 ATGTATTATTATATA
1 ATATATTATTATATA
1376946 TTTATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATATTATTATATAG
Found at i:1376968 original size:22 final size:21
Alignment explanation
Indices: 1376943--1376984 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1376933 GTATTATTAT
1376943 ATATTTATATTTT-TTTCATTTC
1 ATATTTAT-TTTTATTT-ATTTC
1376965 ATATTTATTTTTATTTATTT
1 ATATTTATTTTTATTTATTT
1376985 ATTGTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (21 bp):
ATATTTATTTTTATTTATTTC
Found at i:1376985 original size:14 final size:15
Alignment explanation
Indices: 1376966--1376995 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1376956 TTTCATTTCA
1376966 TATTTATT-TTTATT
1 TATTTATTGTTTATT
1376980 TATTTATTGTTTATT
1 TATTTATTGTTTATT
1376995 T
1 T
1376996 TATTCTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TATTTATTGTTTATT
Found at i:1386574 original size:21 final size:21
Alignment explanation
Indices: 1386550--1386592 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1386540 TTCATATTCG
* *
1386550 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1386571 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1386592 T
1 T
1386593 AGTCCATAAA
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:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1392657 original size:23 final size:23
Alignment explanation
Indices: 1392631--1392675 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1392621 CACCACAGCT
*
1392631 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
1392654 CGTAGAATTGCATCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1392676 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1393330 original size:19 final size:20
Alignment explanation
Indices: 1393293--1393330 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1393283 TTTTTTTATA
*
1393293 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1393313 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1393331 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1393381 original size:21 final size:21
Alignment explanation
Indices: 1393357--1393399 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1393347 TTCATATTCG
* *
1393357 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1393378 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1393399 T
1 T
1393400 AGTCCATAAA
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:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1396259 original size:60 final size:60
Alignment explanation
Indices: 1396151--1396265 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
1396141 CGGGTGATCA
* * ** *
1396151 TTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAGTAACGTCCTATAATTGATGGGTCG
1 TTTTATAACTGTTAATAGTCAAGGGACTCAACAAAACAACGTCCTATAATAGATGGGTCG
* * *
1396211 TTTTATAACTGTTAATAGTCGAGGGACTCAACAAAACAATGTCTTATAATAGATG
1 TTTTATAACTGTTAATAGTCAAGGGACTCAACAAAACAACGTCCTATAATAGATG
1396266 TGTCATTTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (60 bp):
TTTTATAACTGTTAATAGTCAAGGGACTCAACAAAACAACGTCCTATAATAGATGGGTCG
Found at i:1401247 original size:13 final size:13
Alignment explanation
Indices: 1401226--1401285 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
1401216 ATTTTGTTAG
1401226 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
1401239 TATTGTA-TTATT
1 TATTTTATTTAAT
1401251 TGA-TTT-TTTAAT
1 T-ATTTTATTTAAT
*
1401263 TATTTTATTTAAA
1 TATTTTATTTAAT
1401276 TATTTTATTT
1 TATTTTATTT
1401286 TTTTTGCAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
11 1 0.03
12 15 0.39
13 22 0.58
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:1401890 original size:318 final size:317
Alignment explanation
Indices: 1401311--1401945 Score: 1173
Period size: 318 Copynumber: 2.0 Consensus size: 317
1401301 AATGGAAAGC
*
1401311 GGTCTGCTTCGTTTGGATGGAAATCTGTATAAGTTAACGGAAACAATGATGTTGGATATCTGTAC
1 GGTCTGCTTCGTTTGGATGGAAATCTGTATAAGTTAACAGAAACAATGATGTTGGATATCTGTAC
1401376 TGAAGCGACGACATTCTCCTAGTTGAGAGGATTGCTGTGAATGTTTACCGGTTGAGAGCATATTT
66 TGAAGCGACGACATTCTCCTAGTTGAGAGGATTGCTGTGAATGTTTACCGGTTGAGAGCATATTT
*
1401441 ATAGCCGAGATAAAAGTTTAAAAGTCGAGAAATACGAATATAATTATTCAAGGCACGACCCATGC
131 ATAGCCGAGAGAAAAGTTTAAAAGTCGAGAAATACGAATATAATTATTCAAGGCACGACCCATGC
* *
1401506 ACCGTAAACATCATTGTTTCCGTTAACTTATACAAATTTCCATCCAAACGAAGCAGACCGCTTTC
196 ACCGTAAACATCATTGTTTCCGTTAACTTATACAAATTTCCATCCAAACGAAACAGACCACTTTC
1401571 CATTTTATAACTGCAAAAAAAAATAAAATATTTAAATAAAATAATT-AAAAAATCAAAT
261 CATTTTATAACTGC--AAAAAAATAAAATATTTAAATAAAATAATTAAAAAAATCAAAT
1401629 GGTCTGCTTCGTTTGGATGGAAATCTGTATAAGTTAACAGAAACAATGATGTTGGATATCTGTAC
1 GGTCTGCTTCGTTTGGATGGAAATCTGTATAAGTTAACAGAAACAATGATGTTGGATATCTGTAC
*
1401694 TGAAGCGACGACATTCTCCTAGTTGAGAGGATTGCTGTGAATGTTTACGGGTTGAGAGCATATTT
66 TGAAGCGACGACATTCTCCTAGTTGAGAGGATTGCTGTGAATGTTTACCGGTTGAGAGCATATTT
* *
1401759 ATAGCCGAGAGAAAAGTTTAAAAGTCGAGAAATACGAATATAATTATTCAAGGCGCGACTCATGC
131 ATAGCCGAGAGAAAAGTTTAAAAGTCGAGAAATACGAATATAATTATTCAAGGCACGACCCATGC
*
1401824 ATCGTAAACATCATTGTTTCCGTTAACTTATACAAATTTCCATCCAAACGAAACAGACCACTTTC
196 ACCGTAAACATCATTGTTTCCGTTAACTTATACAAATTTCCATCCAAACGAAACAGACCACTTTC
1401889 CATTTTATAACTGCAAAAAAATAAAATATTTAAATAAAATAATTAAAAAAATCAAAT
261 CATTTTATAACTGCAAAAAAATAAAATATTTAAATAAAATAATTAAAAAAATCAAAT
1401946 AATACAATAA
Statistics
Matches: 308, Mismatches: 8, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
316 30 0.10
317 12 0.04
318 266 0.86
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (317 bp):
GGTCTGCTTCGTTTGGATGGAAATCTGTATAAGTTAACAGAAACAATGATGTTGGATATCTGTAC
TGAAGCGACGACATTCTCCTAGTTGAGAGGATTGCTGTGAATGTTTACCGGTTGAGAGCATATTT
ATAGCCGAGAGAAAAGTTTAAAAGTCGAGAAATACGAATATAATTATTCAAGGCACGACCCATGC
ACCGTAAACATCATTGTTTCCGTTAACTTATACAAATTTCCATCCAAACGAAACAGACCACTTTC
CATTTTATAACTGCAAAAAAATAAAATATTTAAATAAAATAATTAAAAAAATCAAAT
Found at i:1401925 original size:13 final size:13
Alignment explanation
Indices: 1401907--1401940 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1401897 AACTGCAAAA
*
1401907 AAATAAAATATTT
1 AAATAAAATAATT
1401920 AAATAAAATAATT
1 AAATAAAATAATT
1401933 AAA-AAAAT
1 AAATAAAAT
1401941 CAAATAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:1405682 original size:124 final size:122
Alignment explanation
Indices: 1405460--1405708 Score: 407
Period size: 124 Copynumber: 2.0 Consensus size: 122
1405450 GGAGAACCAA
1405460 ATATGTATTTATGGGAATATTAAGGTAATTTATGGAAGATCTTTTGGGTCTGATTACTCTAATAT
1 ATATGTATTTATGGGAATATTAAGGTAATTTATGGAAGATCTTTTGGGTCTGATTACTCTAATAT
1405525 TGATGATTTGGATTCAAACTCGTCTTCAAATAAAGAGTAGGTGAAATAATAAATAAAGATG
66 T-ATGATTTGGATTCAAACTCGTCTTCAAATAAAGAGTAGGTG--A-AATAAATAAAGATG
1405586 ATATGTATTTATGGGAAAATATTTAAGGTAA-TTATGGAAGATC-TTTGGGTCTGATTACTCTAA
1 ATATGTATTTATGGG--AATA-TTAAGGTAATTTATGGAAGATCTTTTGGGTCTGATTACTCTAA
1405649 TA-T-TGATTTGGATTCAAACTCGTCTTCAAATAAAGAGTAGGTGAAATAAATAAAGATG
63 TATTATGATTTGGATTCAAACTCGTCTTCAAATAAAGAGTAGGTGAAATAAATAAAGATG
1405707 AT
1 AT
1405709 TATTGATCAA
Statistics
Matches: 120, Mismatches: 0, Indels: 11
0.92 0.00 0.08
Matches are distributed among these distances:
121 16 0.13
122 1 0.01
124 40 0.33
126 16 0.13
127 22 0.18
128 16 0.13
129 9 0.08
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (122 bp):
ATATGTATTTATGGGAATATTAAGGTAATTTATGGAAGATCTTTTGGGTCTGATTACTCTAATAT
TATGATTTGGATTCAAACTCGTCTTCAAATAAAGAGTAGGTGAAATAAATAAAGATG
Found at i:1424797 original size:46 final size:45
Alignment explanation
Indices: 1424684--1424844 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 45
1424674 GCATGCAAAT
* ** *
1424684 TAGCTTACGAGCTTAT--GAAT-AATGACAAGTATATTGGTAAAA
1 TAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTAAAA
*
1424726 TAGCTTACGAGCTTATGGAATTAAATGGTAAGTATTTTGGTAAAA
1 TAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTAAAA
* * *
1424771 TATGCCTAAGAGCTTATGGGATTAAAT-GTAAG--GTTTGGT-AAA
1 TA-GCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTAAAA
* *
1424813 TAAACTTACGAGCTTATGAGA-TAAATGGTAAG
1 T-AGCTTACGAGCTTATGGGATTAAATGGTAAG
1424845 AGATTTTATC
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
41 5 0.05
42 39 0.39
43 7 0.07
44 2 0.02
45 26 0.26
46 21 0.21
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.32
Consensus pattern (45 bp):
TAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTAAAA
Found at i:1428363 original size:32 final size:32
Alignment explanation
Indices: 1428312--1428377 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1428302 TAATAAACAA
* *
1428312 AATTAAACCAAATACATTAAGAA-AAATCCAAC
1 AATTAAACAAAATAAATTAA-AATAAATCCAAC
*
1428344 AATTTAACAAAATAAATTAAAATAAATCCAAC
1 AATTAAACAAAATAAATTAAAATAAATCCAAC
1428376 AA
1 AA
1428378 AATAATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.62, C:0.15, G:0.02, T:0.21
Consensus pattern (32 bp):
AATTAAACAAAATAAATTAAAATAAATCCAAC
Found at i:1428389 original size:32 final size:32
Alignment explanation
Indices: 1428307--1428396 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
1428297 AATGGTAATA
* *
1428307 AACAAAATTAAACCAAATACATTAAGAAAAATCC
1 AACAAAA-T-AACAAAATAAATTAAGAAAAATCC
**
1428341 AACAATTTAACAAAATAAATTAA-AATAAATCC
1 AACAAAATAACAAAATAAATTAAGAA-AAATCC
** *
1428373 AACAAAATAATGAAATAAAGTAAG
1 AACAAAATAACAAAATAAATTAAG
1428397 TATTAAATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
31 2 0.04
32 37 0.82
33 1 0.02
34 5 0.11
ACGTcount: A:0.63, C:0.12, G:0.04, T:0.20
Consensus pattern (32 bp):
AACAAAATAACAAAATAAATTAAGAAAAATCC
Found at i:1428922 original size:30 final size:30
Alignment explanation
Indices: 1428866--1428925 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1428856 CTCTAGGAGT
* *
1428866 GGTCATAAAACTCTGTGATGGCGGCGGCGG
1 GGTCATAAAACTCGGTGACGGCGGCGGCGG
*
1428896 GGTCATAAAAC-CAGGTGACGGTGGCGGCGG
1 GGTCATAAAACTC-GGTGACGGCGGCGGCGG
1428926 CATCATCGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.22, C:0.20, G:0.42, T:0.17
Consensus pattern (30 bp):
GGTCATAAAACTCGGTGACGGCGGCGGCGG
Found at i:1432138 original size:19 final size:20
Alignment explanation
Indices: 1432114--1432152 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1432104 GTATTATTGA
1432114 ACAAAA-AAAAATTAAACAT
1 ACAAAATAAAAATTAAACAT
*
1432133 ACAAAATAAATATTAAACAT
1 ACAAAATAAAAATTAAACAT
1432153 TATTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (20 bp):
ACAAAATAAAAATTAAACAT
Found at i:1432349 original size:159 final size:151
Alignment explanation
Indices: 1432075--1432385 Score: 477
Period size: 159 Copynumber: 2.0 Consensus size: 151
1432065 AATATAAAAT
1432075 ATAAAAGGTAATTTATATTCTCATATAATGTATTATTGAACAAAAAAAAATTAAACATACAAAAT
1 ATAAAAGGTAATTTATATTCTCATATAATGTATTATTGAAC-AAAAAAAATTAAACATACAAAAT
1432140 AAATATTAAACATTATTTATAAATTGTAGACGTTTATTGTTTATCTCGAT-AACATTTAATTTAT
65 AAATATTAAACATTATTTATAAATTGTAGACGTTTATTGTTTATCTCGATAAACATTTAATTTAT
1432204 TAAA-TATAT-AAAGAGGCCAG
130 TAAATTATATAAAAGAGGCCAG
1432224 ATAAAAGGTAATTTTATATATTCTCATATATAATGTTATTATTGAAC-AAAAAAATTAAACATAC
1 ATAAAAGGTAA--TT-TATATTCTC--ATATAATG-TATTATTGAACAAAAAAAATTAAACATAC
1432288 AAAATAAATTATTAAACATTTATTTTATAAAATATTGTAGACGTTTATTGTTTATCTCGATAAAC
60 AAAATAAA-TATTAAACA-TTA-TTTAT--AA-ATTGTAGACGTTTATTGTTTATCTCGATAAAC
1432353 ATTTAATTTATTAAATTATATAAAAGAGGCCAG
119 ATTTAATTTATTAAATTATATAAAAGAGGCCAG
1432386 TCTTGCCATC
Statistics
Matches: 147, Mismatches: 0, Indels: 17
0.90 0.00 0.10
Matches are distributed among these distances:
149 11 0.07
151 2 0.01
152 9 0.06
153 25 0.17
154 17 0.12
155 14 0.10
156 5 0.03
158 2 0.01
159 28 0.19
160 18 0.12
161 5 0.03
162 11 0.07
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (151 bp):
ATAAAAGGTAATTTATATTCTCATATAATGTATTATTGAACAAAAAAAATTAAACATACAAAATA
AATATTAAACATTATTTATAAATTGTAGACGTTTATTGTTTATCTCGATAAACATTTAATTTATT
AAATTATATAAAAGAGGCCAG
Found at i:1433420 original size:2 final size:2
Alignment explanation
Indices: 1433413--1433479 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
1433403 GCTATGAATG
1433413 AT AT AT AT AT A- 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
1433454 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
1433480 CTTACATTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1439499 original size:20 final size:20
Alignment explanation
Indices: 1439474--1439514 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1439464 AAAAAAAAAA
1439474 CTCTCTTCTATTCTTTAATC
1 CTCTCTTCTATTCTTTAATC
1439494 CTCTCTTCTATTCTTTAATC
1 CTCTCTTCTATTCTTTAATC
1439514 C
1 C
1439515 AGATCTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.54
Consensus pattern (20 bp):
CTCTCTTCTATTCTTTAATC
Found at i:1440765 original size:2 final size:2
Alignment explanation
Indices: 1440748--1440785 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1440738 ACAAAAGTTT
*
1440748 TA TA T- TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1440786 CTACCTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1446243 original size:76 final size:76
Alignment explanation
Indices: 1446117--1446269 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
1446107 AAGTTATCAT
1446117 TGGGTACTGCTAAATATACCAAATCATATCAACTTTTGACAACCTTTACTAAACTTACCAATCAA
1 TGGGTACTGCTAAATATACCAAATCATATCAACTTTTGACAACCTTTACTAAACTTACCAATCAA
1446182 GCCATTATTTA
66 GCCATTATTTA
1446193 TGGGTACTGCTAAATATACCAAATCATATCAACTTTTGACAACCTTTACTAAACTTACCAATCAA
1 TGGGTACTGCTAAATATACCAAATCATATCAACTTTTGACAACCTTTACTAAACTTACCAATCAA
1446258 GCCATTATTTA
66 GCCATTATTTA
1446269 T
1 T
1446270 AGTTGCCGGC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (76 bp):
TGGGTACTGCTAAATATACCAAATCATATCAACTTTTGACAACCTTTACTAAACTTACCAATCAA
GCCATTATTTA
Found at i:1446252 original size:39 final size:39
Alignment explanation
Indices: 1446133--1446253 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 39
1446123 CTGCTAAATA
1446133 TACCAAATCATATCAACTTTTGACAACCTTTACTAAACT
1 TACCAAATCATATCAACTTTTGACAACCTTTACTAAACT
* *** *
1446172 TACC-AATCA-AGCCATTA-TTTATGGGTA-C--TGCTAAA-T
1 TACCAAATCATA-TCA--ACTTT-TGACAACCTTTACTAAACT
1446208 ATACCAAATCATATCAACTTTTGACAACCTTTACTAAACT
1 -TACCAAATCATATCAACTTTTGACAACCTTTACTAAACT
1446248 TACCAA
1 TACCAA
1446254 TCAAGCCATT
Statistics
Matches: 60, Mismatches: 10, Indels: 24
0.64 0.11 0.26
Matches are distributed among these distances:
36 5 0.08
37 15 0.25
38 14 0.23
39 21 0.35
40 5 0.08
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (39 bp):
TACCAAATCATATCAACTTTTGACAACCTTTACTAAACT
Found at i:1446379 original size:36 final size:36
Alignment explanation
Indices: 1446332--1446418 Score: 174
Period size: 36 Copynumber: 2.4 Consensus size: 36
1446322 TCACATTGAA
1446332 ACTCATGTCTCCCACCAAAATAAGGAATTATTTGGC
1 ACTCATGTCTCCCACCAAAATAAGGAATTATTTGGC
1446368 ACTCATGTCTCCCACCAAAATAAGGAATTATTTGGC
1 ACTCATGTCTCCCACCAAAATAAGGAATTATTTGGC
1446404 ACTCATGTCTCCCAC
1 ACTCATGTCTCCCAC
1446419 GCCGTACTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (36 bp):
ACTCATGTCTCCCACCAAAATAAGGAATTATTTGGC
Found at i:1449929 original size:19 final size:19
Alignment explanation
Indices: 1449905--1449951 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1449895 TGAGCTGTAA
1449905 CCACTCACCAC-GTCATGCT
1 CCACTCACC-CTGTCATGCT
*
1449924 CCACTCACCCTTTCATGCT
1 CCACTCACCCTGTCATGCT
*
1449943 TCACTCACC
1 CCACTCACC
1449952 TTTTTATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.19, C:0.49, G:0.06, T:0.26
Consensus pattern (19 bp):
CCACTCACCCTGTCATGCT
Found at i:1460610 original size:22 final size:19
Alignment explanation
Indices: 1460563--1460610 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
1460553 GTAAAAATAC
1460563 AAAAAATTTAAATTAGATT
1 AAAAAATTTAAATTAGATT
1460582 ACTAAAAATTTAAATATATGTATT
1 A--AAAAATTTAAAT-TA-G-ATT
1460606 AAAAA
1 AAAAA
1460611 TACTAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
21 12 0.50
22 6 0.25
23 1 0.04
24 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAAAATTTAAATTAGATT
Found at i:1461098 original size:25 final size:25
Alignment explanation
Indices: 1461069--1461117 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1461059 ATAAATTTTG
*
1461069 ACTAATCCAAAATTTGTAAGTCTCT
1 ACTAATCCAAAATTTGTAAATCTCT
** *
1461094 ACTAATTTAAATTTTGTAAATCTC
1 ACTAATCCAAAATTTGTAAATCTC
1461118 GATTAATTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (25 bp):
ACTAATCCAAAATTTGTAAATCTCT
Found at i:1466955 original size:2 final size:2
Alignment explanation
Indices: 1466948--1466981 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1466938 TTTAAAATTA
1466948 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
1466982 TAGCCTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1468760 original size:17 final size:18
Alignment explanation
Indices: 1468718--1468763 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1468708 ACTATTGAAT
*
1468718 TTTAAGATTTTATATTCGA
1 TTTAA-ATTATATATTCGA
1468737 TTTAAATTATATATTCGA
1 TTTAAATTATATATTCGA
1468755 -TTAAATTAT
1 TTTAAATTAT
1468764 TCGAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
19 5 0.19
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (18 bp):
TTTAAATTATATATTCGA
Found at i:1470515 original size:117 final size:117
Alignment explanation
Indices: 1470367--1470590 Score: 292
Period size: 117 Copynumber: 1.9 Consensus size: 117
1470357 TAAAAATTAT
* * *
1470367 CTTCTTTTGAAATCTAAAATAGAATTGGAAAATCAAAATGAAATGTTG-AGAAAGGAGTTAGAGC
1 CTTCTTTAGAAATCTAAAATAGAATTGGAAAATCAAAATGAAATATTGAAG-AAGGAGTTAGAAC
* *
1470431 TTTCAAAAACGAAATCTGAAAACT-TTGAAAAATAAATTTTCGAATTAAACAAA
65 TTTCAAAAACGAAATCTG-AAACTATTGAAAAAGAAAATTTCGAATTAAACAAA
* * * *
1470484 CTTCTTCTAGAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAAGAAGGATTTAGAAC
1 CTTCTT-TAGAAATCTAAAATAGAATTGGAAAATCAAAATGAAATATTGAAGAAGGAGTTAGAAC
* * *
1470548 TTTCAAAAATGAAATTTGAAAGTATTGAAAAAGAAAATTTCGA
65 TTTCAAAAACGAAATCTGAAACTATTGAAAAAGAAAATTTCGA
1470591 TTTGAAAGTT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
116 4 0.04
117 81 0.88
118 7 0.08
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (117 bp):
CTTCTTTAGAAATCTAAAATAGAATTGGAAAATCAAAATGAAATATTGAAGAAGGAGTTAGAACT
TTCAAAAACGAAATCTGAAACTATTGAAAAAGAAAATTTCGAATTAAACAAA
Found at i:1471006 original size:20 final size:21
Alignment explanation
Indices: 1470974--1471019 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
1470964 ATACATGAGT
1470974 TTTTAATCTTAAATAATTATG
1 TTTTAATCTTAAATAATTATG
1470995 TTTTAA-CTTAAATAATTATG
1 TTTTAATCTTAAATAATTATG
1471015 TTTTA
1 TTTTA
1471020 TCTCATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTTAATCTTAAATAATTATG
Found at i:1476954 original size:17 final size:18
Alignment explanation
Indices: 1476912--1476957 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1476902 ACTATTGAAT
*
1476912 TTTAAGATTTTATATTCAA
1 TTTAA-ATTATATATTCAA
*
1476931 TTTAAATTATATATTCGA
1 TTTAAATTATATATTCAA
1476949 -TTAAATTAT
1 TTTAAATTAT
1476958 TTGAATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (18 bp):
TTTAAATTATATATTCAA
Found at i:1479358 original size:16 final size:16
Alignment explanation
Indices: 1479325--1479359 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1479315 AAGTATAATT
1479325 TAAAAAAATTAAATAC
1 TAAAAAAATTAAATAC
1479341 TAAAACAAATTAAA-AC
1 TAAAA-AAATTAAATAC
1479357 TAA
1 TAA
1479360 TAATAGAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAAAATTAAATAC
Found at i:1480690 original size:25 final size:27
Alignment explanation
Indices: 1480646--1480705 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
1480636 TCAGGTCGAG
1480646 TCGGGTCGATTTTTTAAAAG-TGGTGT
1 TCGGGTCGATTTTTTAAAAGATGGTGT
*
1480672 TCGGGTCGATTTTTT-AAAGATTGTGT
1 TCGGGTCGATTTTTTAAAAGATGGTGT
*
1480698 TCGAGTCG
1 TCGGGTCG
1480706 GGTTGGATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.18, C:0.10, G:0.30, T:0.42
Consensus pattern (27 bp):
TCGGGTCGATTTTTTAAAAGATGGTGT
Found at i:1500563 original size:29 final size:28
Alignment explanation
Indices: 1500478--1500567 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 28
1500468 TATTTGTATT
* *
1500478 TTTTTA-TCAAAATAAATACTTAACTTTATA
1 TTTTTAGTCAAAATAGATACTTAA---AATA
*
1500508 TTTTTAGTCAAAATAGATACTTGAAATA
1 TTTTTAGTCAAAATAGATACTTAAAATA
* *
1500536 TTTTTTGATCAAAATAGGTA-TCTAAAATA
1 TTTTTAG-TCAAAATAGATACT-TAAAATA
1500565 TTT
1 TTT
1500568 AATTTTTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
28 10 0.20
29 20 0.39
30 6 0.12
31 15 0.29
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTTTAGTCAAAATAGATACTTAAAATA
Found at i:1508023 original size:20 final size:21
Alignment explanation
Indices: 1507998--1508043 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1507988 TAAGCTACCC
1507998 AAAGGCAAA-AAACATGTCAT
1 AAAGGCAAAGAAACATGTCAT
* *
1508018 AAAGGCAAAGATACGTGTCAT
1 AAAGGCAAAGAAACATGTCAT
1508039 AAAGG
1 AAAGG
1508044 AAGAGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.50, C:0.13, G:0.22, T:0.15
Consensus pattern (21 bp):
AAAGGCAAAGAAACATGTCAT
Found at i:1508191 original size:17 final size:19
Alignment explanation
Indices: 1508155--1508191 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1508145 AATTAGATTG
1508155 ATAAATAAATTGAAAAAGA
1 ATAAATAAATTGAAAAAGA
*
1508174 ATAAA-AAA-TGAAAGAGA
1 ATAAATAAATTGAAAAAGA
1508191 A
1 A
1508192 AGAAGTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (19 bp):
ATAAATAAATTGAAAAAGA
Found at i:1508507 original size:17 final size:18
Alignment explanation
Indices: 1508487--1508523 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
1508477 AATAAATATG
1508487 AACTCAACTCAAACT-GA
1 AACTCAACTCAAACTCGA
1508504 AACTCAACTCAAACTCGA
1 AACTCAACTCAAACTCGA
1508522 AA
1 AA
1508524 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.49, C:0.30, G:0.05, T:0.16
Consensus pattern (18 bp):
AACTCAACTCAAACTCGA
Found at i:1515549 original size:14 final size:14
Alignment explanation
Indices: 1515530--1515585 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1515520 CGTTCGTGAA
1515530 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
1515544 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
1515557 --TT-GTTTATGTT
1 CGTTCGATTATGTT
1515568 CGTTCGATTATGTT
1 CGTTCGATTATGTT
1515582 CGTT
1 CGTT
1515586 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:1515564 original size:24 final size:24
Alignment explanation
Indices: 1515537--1515606 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
1515527 GAACGTTCGA
*
1515537 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1515561 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1515585 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
1515607 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Done.