Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007963.1 Hibiscus syriacus cultivar Beakdansim tig00110392_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: 1627826
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1136309 original size:66 final size:67
Alignment explanation
Indices: 1136159--1136319 Score: 227
Period size: 66 Copynumber: 2.4 Consensus size: 67
1136149 CAATTAACGG
* * *
1136159 TCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCAGTTGATTTGGTTCGATTAATAAT
1 TCAAATAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATCAATTGATTTGATTCGATTAATAAT
1136224 TT
66 TT
* * *
1136226 TCAAATAAATTTCGGTTCGATTAACGGTTAAAG-AAAAAAT-AATTTATTTTATTCGGTTAATAA
1 TCAAAT-AATTTCGGTTCGATTAACGGTTAAAGAAAAAAATCAATTGATTTGATTCGATTAATAA
1136289 TTT
65 TTT
*
1136292 TCAAATACATTTGGGTTCGATTAACGGT
1 TCAAATA-ATTTCGGTTCGATTAACGGT
1136320 CAAATAATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
65 1 0.01
66 46 0.54
67 13 0.15
68 25 0.29
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (67 bp):
TCAAATAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATCAATTGATTTGATTCGATTAATAAT
TT
Found at i:1136334 original size:26 final size:26
Alignment explanation
Indices: 1136292--1136505 Score: 130
Period size: 26 Copynumber: 8.0 Consensus size: 26
1136282 TTAATAATTT
* *
1136292 TCAAATACATTTGGGTTCGATTAACGG
1 TCAAATA-ATTTCGGTTCGATTAATGG
1136319 TCAAATAATTTCGGTTCGATTAATGG
1 TCAAATAATTTCGGTTCGATTAATGG
* * * * **
1136345 TTAAAGAAAAAAATTCGGTT--AATAATTT
1 -T---CAAATAATTTCGGTTCGATTAATGG
*
1136373 TCAAATAAATTTCGGTTCTATTAATGG
1 TCAAAT-AATTTCGGTTCGATTAATGG
* *
1136400 TCGAATAATTTCGATTCGATTAATGG
1 TCAAATAATTTCGGTTCGATTAATGG
* * * * **
1136426 TTAAAGAAAAAAATTCAGTTC-A-TAATTT
1 -T---CAAATAATTTCGGTTCGATTAATGG
* *
1136454 TCAAATAAATTTCGGTTTGATTAACGG
1 TCAAAT-AATTTCGGTTCGATTAATGG
1136481 TCAAATAATTTCGGTTCGATTAATG
1 TCAAATAATTTCGGTTCGATTAATG
1136506 TTAAAGAAAA
Statistics
Matches: 138, Mismatches: 35, Indels: 29
0.68 0.17 0.14
Matches are distributed among these distances:
24 6 0.04
25 17 0.12
26 53 0.38
27 30 0.22
28 9 0.07
29 1 0.01
30 22 0.16
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (26 bp):
TCAAATAATTTCGGTTCGATTAATGG
Found at i:1136335 original size:92 final size:81
Alignment explanation
Indices: 1136276--1136529 Score: 411
Period size: 81 Copynumber: 3.1 Consensus size: 81
1136266 AATTTATTTT
* *
1136276 ATTCGGTTAATAATTTTCAAATACATTTGGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTA
1136341 ATGGTTAAAGAAAAAA
66 ATGGTTAAAGAAAAAA
* * * *
1136357 ATTCGGTTAATAATTTTCAAATAAATTTCGGTTCTATTAATGGTCGAATAATTTCGATTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTA
1136422 ATGGTTAAAGAAAAAA
66 ATGGTTAAAGAAAAAA
* * *
1136438 ATTCAGTTCATAATTTTCAAATAAATTTCGGTTTGATTAACGGTCAAATAATTTCGGTTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTA
1136503 AT-GTTAAAGAAAAAAA
66 ATGGTTAAAG-AAAAAA
1136519 ATTCGGTTAAT
1 ATTCGGTTAAT
1136530 TTGGTTCGTT
Statistics
Matches: 157, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
80 7 0.04
81 150 0.96
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (81 bp):
ATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTA
ATGGTTAAAGAAAAAA
Found at i:1136569 original size:69 final size:69
Alignment explanation
Indices: 1136481--1136626 Score: 267
Period size: 69 Copynumber: 2.1 Consensus size: 69
1136471 TGATTAACGG
* *
1136481 TCAAAT-AATTTCGGTTCGATTAATGTTAAAGAAAAAAAATTCGGTTAATTTGGTTCGTTTAATA
1 TCAAATAAATTTCGGTTCGATTAATGTTAAAGAAAAAAAATTCAGTTAATTTGGTTCGGTTAATA
1136545 ATTT
66 ATTT
1136549 TCAAATAAATTTCGGTTCGATTAATGTTAAAGAAAAAAAATTCAGTTAATTTGGTTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAATGTTAAAGAAAAAAAATTCAGTTAATTTGGTTCGGTTAATA
1136614 ATTT
66 ATTT
1136618 TCAAATAAA
1 TCAAATAAA
1136627 ATATTTTTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 6 0.08
69 69 0.92
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (69 bp):
TCAAATAAATTTCGGTTCGATTAATGTTAAAGAAAAAAAATTCAGTTAATTTGGTTCGGTTAATA
ATTT
Found at i:1137630 original size:13 final size:13
Alignment explanation
Indices: 1137612--1137636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1137602 ATATTTCTTA
1137612 GAAAATAATTTTT
1 GAAAATAATTTTT
1137625 GAAAATAATTTT
1 GAAAATAATTTT
1137637 ACGTTGTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
GAAAATAATTTTT
Found at i:1140117 original size:19 final size:19
Alignment explanation
Indices: 1140071--1140118 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1140061 AATATTTTTT
1140071 TAAAATAATATTAAAATAA
1 TAAAATAATATTAAAATAA
* *
1140090 TATATTAATATT-AAATATA
1 TAAAATAATATTAAAATA-A
1140109 TAAAATAATA
1 TAAAATAATA
1140119 ATATTTAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATAATATTAAAATAA
Found at i:1146527 original size:322 final size:318
Alignment explanation
Indices: 1145941--1146574 Score: 919
Period size: 322 Copynumber: 2.0 Consensus size: 318
1145931 AATTCCAGCA
* *
1145941 AGCTGCTGTATTGTGTAGGTCAATTGGTCTAGCGGAGAAAATTCATGGTAAGGTTATTGCTTTCT
1 AGCTACTGTATTGTGTAGGTCAATTGGTCTAGCGGAGAAAATTCATAGTAAGGTTATTGCTTTCT
* * *
1146006 TAATTTGAATGCAATTCTTATCATGTGAATTCGGTTTATTTGATTTTGGGATTGAGTATTTTGCT
66 TAATTTGAATGCAATTCTTATCATGGGAATTCGGTTTATTTGATTTTGGGATTCAATATTTTGCT
* * * *
1146071 TGCTTTCCTATGTTTATGGGTGCAAATTTTGTTAACTTACTCGGTAGCAGTTTGTCTAGTCATGT
131 TGCTCTCATATGTTTATGGGTACAAATTTTGTTAACTTACTCGGTAACAGTTTGTCTAGTCATGT
* * *
1146136 ATGGTTGATTTAAATTATTTGTTGTCTGAAGGAGCTTTTAAGAATTGAAGTTTTAATATAGGTAT
196 ATGGTTGATTTAAATTATTTGGTGTCTGAAGGAGCTTTCAAGAATTGAAGTTTTAATATAGGGAT
* **
1146201 TGATATGTCATCATGTCTAGCTGTTTAAGGTATATGATTGGTGGTTGGTTAGGTGTCT
261 TGATATGTCATCATGTCTAGCTCTTTAAGGTATATGATTCATGGTTGGTTAGGTGTCT
* * * * *
1146259 AGCTACTGTATTGTGTAGGTCAATTGGTTTAGGGGAGAAAATTCATAGTAATGTT-TTGATTTTT
1 AGCTACTGTATTGTGTAGGTCAATTGGTCTAGCGGAGAAAATTCATAGTAAGGTTATTG-CTTTC
* * * * *
1146323 TTTATTTGAATGCAATTCTTATCATGGGAGTTTGGATTTGTTTGATTTTGGGATTCAATATTTTT
65 TTAATTTGAATGCAATTCTTATCATGGGAATTCGG-TTTATTTGATTTTGGGATTCAATATTTTG
* * * * *
1146388 CTTGCTCTCATATGTTTTATGGGTATATAAATTTTGTTAACTTACTCTGTAACTGTTTTTCTTGT
129 CTTGCTCTCATATG-TTTATGGG--TACAAATTTTGTTAACTTACTCGGTAACAGTTTGTCTAGT
*
1146453 CATGTATGGTTGATTTAGATTATTTGGTGTCTGAAGGAGCTTTCAAGAATTGAAGTTTTAATATA
191 CATGTATGGTTGATTTAAATTATTTGGTGTCTGAAGGAGCTTTCAAGAATTGAAGTTTTAATATA
* *
1146518 GGGATTGATATGTCATTATGTCTTGCTCTTTAAGGTATATGATTCATGGTTGGTTAG
256 GGGATTGATATGTCATCATGTCTAGCTCTTTAAGGTATATGATTCATGGTTGGTTAG
1146575 CGATGTCTTG
Statistics
Matches: 278, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
317 3 0.01
318 84 0.30
319 37 0.13
320 8 0.03
322 146 0.53
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (318 bp):
AGCTACTGTATTGTGTAGGTCAATTGGTCTAGCGGAGAAAATTCATAGTAAGGTTATTGCTTTCT
TAATTTGAATGCAATTCTTATCATGGGAATTCGGTTTATTTGATTTTGGGATTCAATATTTTGCT
TGCTCTCATATGTTTATGGGTACAAATTTTGTTAACTTACTCGGTAACAGTTTGTCTAGTCATGT
ATGGTTGATTTAAATTATTTGGTGTCTGAAGGAGCTTTCAAGAATTGAAGTTTTAATATAGGGAT
TGATATGTCATCATGTCTAGCTCTTTAAGGTATATGATTCATGGTTGGTTAGGTGTCT
Found at i:1149788 original size:38 final size:38
Alignment explanation
Indices: 1149737--1149814 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
1149727 ACCTGCACTA
1149737 TCACGAAGAATGACACCAATGGCTGAAGTAGCAGGTGG
1 TCACGAAGAATGACACCAATGGCTGAAGTAGCAGGTGG
1149775 TCACGAAGAATGACACCAATGGCTGAAGTAGCAGGTGG
1 TCACGAAGAATGACACCAATGGCTGAAGTAGCAGGTGG
1149813 TC
1 TC
1149815 GCGGGTAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (38 bp):
TCACGAAGAATGACACCAATGGCTGAAGTAGCAGGTGG
Found at i:1156686 original size:52 final size:54
Alignment explanation
Indices: 1156617--1156725 Score: 186
Period size: 52 Copynumber: 2.1 Consensus size: 54
1156607 TAAGGCACAT
*
1156617 CCTTGTGATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTA-TT-TATGTG
1 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTG
*
1156669 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATGTG
1 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTG
1156723 CCT
1 CCT
1156726 CATCTTGTGT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 42 0.79
53 2 0.04
54 9 0.17
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (54 bp):
CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTG
Found at i:1163128 original size:76 final size:77
Alignment explanation
Indices: 1162968--1163184 Score: 207
Period size: 76 Copynumber: 2.9 Consensus size: 77
1162958 CTTAGGTGAA
* * * *
1162968 ACCCATTTTTTTAATTAAAATGTT-GACATTCTATATCACAACGTATTTCTTAGTAAACCATGAC
1 ACCCATTTTATTAA-TAAAATATTAGACATTCTATATCACAACATATGTCTTAGTAAACCATGAC
*
1163032 ATTCTTGATCGCT
65 ATTCTTGAGCGCT
* * * * *
1163045 ACCCATTTTATTAATAAAAATATTAG-CATTCTA-GTCGCAACATATGTCTTAGTGAATCATTAC
1 ACCCATTTTATTAAT-AAAATATTAGACATTCTATATCACAACATATGTCTTAGTAAACCATGAC
1163108 ATTCTTGAGCGC-
65 ATTCTTGAGCGCT
* * * * *
1163120 ATCTCATTTTATTAATAAAATATT--A-ATTCTACATCACAATC-TATTTCTTTGTGAACCATGA
1 A-CCCATTTTATTAATAAAATATTAGACATTCTATATCACAA-CATATGTCTTAGTAAACCATGA
1163181 CATT
64 CATT
1163185 TTAGGCGCAA
Statistics
Matches: 117, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
73 6 0.05
74 25 0.21
75 10 0.09
76 48 0.41
77 27 0.23
78 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (77 bp):
ACCCATTTTATTAATAAAATATTAGACATTCTATATCACAACATATGTCTTAGTAAACCATGACA
TTCTTGAGCGCT
Found at i:1163427 original size:22 final size:22
Alignment explanation
Indices: 1163399--1163440 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1163389 ATTATTATAT
*
1163399 TTATAAC-TTTTCTAATTCCGTC
1 TTATAACATTTTAT-ATTCCGTC
1163421 TTATAACATTTTATATTCCG
1 TTATAACATTTTATATTCCG
1163441 CTTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (22 bp):
TTATAACATTTTATATTCCGTC
Found at i:1165629 original size:19 final size:20
Alignment explanation
Indices: 1165605--1165642 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1165595 CTGGTCTAAA
1165605 AATGACAAAACC-GAAAAAC
1 AATGACAAAACCAGAAAAAC
1165624 AATGACAAAACCAGAAAAA
1 AATGACAAAACCAGAAAAA
1165643 GTTACCGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.66, C:0.18, G:0.11, T:0.05
Consensus pattern (20 bp):
AATGACAAAACCAGAAAAAC
Found at i:1166314 original size:21 final size:21
Alignment explanation
Indices: 1166290--1166337 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1166280 AAAATTGTAT
*
1166290 CGATCACAAAAACATCGAAAC
1 CGATAACAAAAACATCGAAAC
*
1166311 CGATAATAAAAACATCGAAAC
1 CGATAACAAAAACATCGAAAC
1166332 CGATAA
1 CGATAA
1166338 TTATAATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.23, G:0.10, T:0.12
Consensus pattern (21 bp):
CGATAACAAAAACATCGAAAC
Found at i:1166338 original size:21 final size:21
Alignment explanation
Indices: 1166297--1166338 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1166287 TATCGATCAC
1166297 AAAAACATCGAAACCGATAAT
1 AAAAACATCGAAACCGATAAT
1166318 AAAAACATCGAAACCGATAAT
1 AAAAACATCGAAACCGATAAT
1166339 TATAATGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.19, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAAACATCGAAACCGATAAT
Found at i:1166693 original size:204 final size:193
Alignment explanation
Indices: 1166318--1166788 Score: 584
Period size: 204 Copynumber: 2.4 Consensus size: 193
1166308 AACCGATAAT
* * *
1166318 AAAAACATCGAAACCGATAATTATAATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATTTA
1 AAAAACATCGAAA-CGAAAATTATAATGTAATAGGT-AATTTACAATGT-ACCGGTATAAATATA
* * * * *
1166383 TCAGTTTTATGAGAAAATATGTCAGATAAGTATTGACACTTTGTAATTTGTGTCGATACATTTTG
63 TCGGTTTTATGAGAAAATAGGTCAAATAAGTATCGACACTTTATAATTTGTGTCGATACATTTTG
*
1166448 TCCATAATGAATGCCCAACGAGGTGCAAGAATAACGTGTCGATACATTTAAAATTGTATCGATCC
128 TCCATAATGAATGCCCAACGAGGTGCAAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCC
*
1166513 C
193 A
* * * *
1166514 AAAAACATCGAAACGAAAATTACAATGTTATAGGTAAGTTTACAATGTACCCAGTATAAATATAC
1 AAAAACATCGAAACGAAAATTATAATGTAATAGGTAA-TTTACAATGTA-CCGGTATAAATATAT
*
1166579 CGGTTTTATGAGAAAATAGGTCTAAATAATGTATCGACACCTTTATAGTTTGTGTCGATAC-TTT
64 CGGTTTTATGAGAAAATAGGTC-AAATAA-GTATCGACA-CTTTATAATTTGTGTCGATACATTT
* *
1166643 TTTCCAGAATGAATTAGGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATTG
126 TGTCC---AT-AA-T--GAATGCCCAACGAGGTGCAAGAATAAAGTGTCGATACATTTAAAATTG
1166708 TATCGATCCA
184 TATCGATCCA
* * * *
1166718 AAAAACAACGAAACTAATAATTATAATGCAATAGGTAAATTTGCAATGCTACCGGTATAAATATA
1 AAAAACATCGAAACGAA-AATTATAATGTAATAGGT-AATTTACAATG-TACCGGTATAAATATA
1166783 TCGGTT
63 TCGGTT
1166789 AAATGCCTAT
Statistics
Matches: 235, Mismatches: 25, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
194 3 0.01
195 60 0.26
196 18 0.08
197 15 0.06
198 19 0.08
200 2 0.01
201 2 0.01
202 1 0.00
204 70 0.30
205 41 0.17
206 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (193 bp):
AAAAACATCGAAACGAAAATTATAATGTAATAGGTAATTTACAATGTACCGGTATAAATATATCG
GTTTTATGAGAAAATAGGTCAAATAAGTATCGACACTTTATAATTTGTGTCGATACATTTTGTCC
ATAATGAATGCCCAACGAGGTGCAAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCA
Found at i:1166852 original size:23 final size:23
Alignment explanation
Indices: 1166802--1166846 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1166792 TGCCTATTTT
*
1166802 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1166825 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1166847 TGTTATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1167345 original size:13 final size:13
Alignment explanation
Indices: 1167313--1167348 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1167303 GAGCTGAGTC
*
1167313 GAGTTGAGCCACT
1 GAGTCGAGCCACT
*
1167326 GACTCGAGCCACT
1 GAGTCGAGCCACT
1167339 GAGTCGAGCC
1 GAGTCGAGCC
1167349 GCCAAGCCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (13 bp):
GAGTCGAGCCACT
Found at i:1172240 original size:6 final size:6
Alignment explanation
Indices: 1172229--1172266 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1172219 GACACGTATT
*
1172229 ACCACG ACCACG ACCACG ACCACG ACCCCG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1172267 CGAGACGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.29, C:0.55, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1172963 original size:21 final size:21
Alignment explanation
Indices: 1172924--1172964 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1172914 TTCAACTATC
* *
1172924 GCATTGCGATTGTCCAAGTTT
1 GCATTGCGATAGTACAAGTTT
*
1172945 GCATTGCGATAGTAGAAGTT
1 GCATTGCGATAGTACAAGTT
1172965 CGCAAATCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (21 bp):
GCATTGCGATAGTACAAGTTT
Found at i:1197776 original size:3 final size:3
Alignment explanation
Indices: 1197758--1197805 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
1197748 AGGGCTACAA
* *
1197758 AAT AAT -AT AA- ATT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1197804 AA
1 AA
1197806 CATAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 3 0.08
3 36 0.92
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1200501 original size:3 final size:3
Alignment explanation
Indices: 1200493--1200589 Score: 142
Period size: 3 Copynumber: 32.7 Consensus size: 3
1200483 TTAATATATT
* * * *
1200493 TAA TAA TAA TAG TAA AAA TAA TAA TAA TAA TAA TAA -AA AAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1200540 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1200588 TA
1 TA
1200590 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1202243 original size:113 final size:113
Alignment explanation
Indices: 1200882--1202240 Score: 2092
Period size: 113 Copynumber: 12.0 Consensus size: 113
1200872 AGATAATATC
* *
1200882 AAAC-AAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
1200946 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATT-ATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
* * **
1200995 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * *
1201060 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
* * **
1201108 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * *
1201173 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
* * **
1201221 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * *
1201286 TCATTATGAACCTTCTCTGGTAATGATGATCCACCAAATGATGGATTC
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
*** * *
1201334 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCCTCCTTCTTCAGATGACGAGTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTC
* * * *
1201399 TTCTCATTATGAACTTTCTCTGGCAATGATAATCCATTAAGTGATGAATTC
63 TTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
1201450 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
1201515 TCATTATGAACCTTCTTTGGCAATGATAATCCATCAAGTGATGAATTC
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
1201563 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
1201628 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAGATGATGGATTT
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
*
1201676 GAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
1201741 TCATTATGAACCTTCTCCGGCAATGATAATCCATCAAGTGATGAATTC
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
*
1201789 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTACAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
1201854 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTC
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
1201902 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
1201967 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAGATGATGGATTT
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
*
1202015 GAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1202080 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAGATGAT-AGATTT
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGA-ATTT
*
1202128 GAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * * * *
1202193 TCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTT
66 TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
1202241 GAATCTTTGC
Statistics
Matches: 1179, Mismatches: 61, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
113 1017 0.86
114 61 0.05
116 101 0.09
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
AAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACCTTCTCTGGCAATGATAATCCATCAAATGATGAATTT
Found at i:1203061 original size:83 final size:84
Alignment explanation
Indices: 1202966--1203173 Score: 355
Period size: 84 Copynumber: 2.5 Consensus size: 84
1202956 GTTCCTACTG
* * * *
1202966 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTTATGTTCCGAAT
1 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACAAATTCATCTTCCAAAT
*
1203030 TCAATGATTGGTTTTGCCA
66 TCAATGATTGGTTCTGCCA
*
1203049 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAAT
1 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACAAATTCATCTTCCAAAT
1203114 TCAATGATTGGTTCTGCCA
66 TCAATGATTGGTTCTGCCA
1203133 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1203174 TGATTCTGTT
Statistics
Matches: 118, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
83 42 0.36
84 76 0.64
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (84 bp):
AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACAAATTCATCTTCCAAAT
TCAATGATTGGTTCTGCCA
Found at i:1203293 original size:136 final size:136
Alignment explanation
Indices: 1203049--1203361 Score: 617
Period size: 136 Copynumber: 2.3 Consensus size: 136
1203039 GGTTTTGCCA
1203049 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAAT
1 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAAT
1203114 TCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATT
66 TCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATT
1203179 CTGTTC
131 CTGTTC
1203185 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAAT
1 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAAT
*
1203250 TCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAATATGCTTGATT
66 TCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATT
1203315 CTGTTC
131 CTGTTC
1203321 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1203362 TGATTCTGTC
Statistics
Matches: 176, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 176 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (136 bp):
AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAAT
TCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATT
CTGTTC
Found at i:1203325 original size:52 final size:52
Alignment explanation
Indices: 1203269--1203370 Score: 195
Period size: 52 Copynumber: 2.0 Consensus size: 52
1203259 GGTTCTGCCA
*
1203269 AATCAGATCAGATAACTCAAAGAACACTTCCAGAATATGCTTGATTCTGTTC
1 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTTC
1203321 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGT
1 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGT
1203371 CCAGAAGTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (52 bp):
AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTTC
Found at i:1211180 original size:30 final size:30
Alignment explanation
Indices: 1211144--1211203 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1211134 GATTTGTATA
* *
1211144 GGTGGAATACC-AGAGTGATAAATTGGTTCT
1 GGTGGAAAACCTAGAG-GATAAATGGGTTCT
*
1211174 GGTGGAAAACCTAGAGGATATATGGGTTCT
1 GGTGGAAAACCTAGAGGATAAATGGGTTCT
1211204 TGGTCAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (30 bp):
GGTGGAAAACCTAGAGGATAAATGGGTTCT
Found at i:1214883 original size:17 final size:17
Alignment explanation
Indices: 1214843--1214884 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1214833 ATACTTGCAA
*
1214843 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
1214861 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
1214878 ATAAAAA
1 ATAAAAA
1214885 ATTTGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:1217022 original size:3 final size:3
Alignment explanation
Indices: 1217014--1217108 Score: 163
Period size: 3 Copynumber: 31.7 Consensus size: 3
1217004 TTAATATATT
* *
1217014 TAA TAA TAA TAG TAA AAA 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
*
1217062 TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1217109 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1221852 original size:16 final size:16
Alignment explanation
Indices: 1221831--1221861 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1221821 TAATATTGAA
1221831 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
1221847 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
1221862 AAATTATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:1227412 original size:21 final size:21
Alignment explanation
Indices: 1227386--1227473 Score: 176
Period size: 21 Copynumber: 4.2 Consensus size: 21
1227376 ATAATGTCCA
1227386 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1227407 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1227428 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1227449 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1227470 TAAG
1 TAAG
1227474 AATCATATAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.28
Consensus pattern (21 bp):
TAAGGACCACATATCATTCCT
Found at i:1229009 original size:63 final size:63
Alignment explanation
Indices: 1228903--1229061 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 63
1228893 TAATGAAGGT
* * * *
1228903 ATGCATCGATGCACTACTGATGCATCGATGCACTGAGGGCATTCGATGTTCAT-TTTATTATAA
1 ATGCATCGATGCACTACTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AATAA
* * ** *
1228966 ATGCATCGATGCACTCCTTATGCATCGATGGACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTACTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAATAA
* *
1229029 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
1229062 CTTCAACAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 79 0.95
64 4 0.05
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAATAA
Found at i:1229053 original size:19 final size:20
Alignment explanation
Indices: 1229029--1229066 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1229019 ATTTAAATTA
1229029 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
1229048 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
1229067 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:1232743 original size:21 final size:21
Alignment explanation
Indices: 1232717--1232825 Score: 218
Period size: 21 Copynumber: 5.2 Consensus size: 21
1232707 ATAATGTCCA
1232717 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1232738 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1232759 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1232780 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1232801 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1232822 TAAG
1 TAAG
1232826 AATCATATAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 88 1.00
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (21 bp):
TAAGGACCACATATCATTCCT
Found at i:1234339 original size:19 final size:19
Alignment explanation
Indices: 1234315--1234367 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
1234305 TTTATTAGAA
1234315 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
1234334 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
1234353 ATGCATCGATGCACT
1 ATGCATCGATGCACT
1234368 GACGACATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:1234400 original size:82 final size:82
Alignment explanation
Indices: 1234251--1234429 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 82
1234241 TTAATAAAGG
* * *
1234251 TATGCATCGATGCACTACTGATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTATTAGAAA
1 TATGCATCGATGCACTACTGATGCATCGATGCACTGACGACATTCGATGTTCATTTTATAAGAAA
* *
1234316 TGCATCGATGCACTCCT
66 TGCAACGATGCACTCCA
* * ** **
1234333 TATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTA-AATTA
1 TATGCATCGATGCACTACTGATGCATCGATGCACTGACGACATTCGATGTTCAT-TTTATAAGAA
*
1234397 ATGCAACGATGCACTTCA
65 ATGCAACGATGCACTCCA
1234415 TATGCATCGATGCAC
1 TATGCATCGATGCAC
1234430 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
82 80 0.95
83 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (82 bp):
TATGCATCGATGCACTACTGATGCATCGATGCACTGACGACATTCGATGTTCATTTTATAAGAAA
TGCAACGATGCACTCCA
Found at i:1234425 original size:19 final size:20
Alignment explanation
Indices: 1234397--1234434 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1234387 ATTTAAATTA
1234397 ATGCAACGATGCA-CTTCAT
1 ATGCAACGATGCACCTTCAT
*
1234416 ATGCATCGATGCACCTTCA
1 ATGCAACGATGCACCTTCA
1234435 ACAAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (20 bp):
ATGCAACGATGCACCTTCAT
Found at i:1240036 original size:12 final size:12
Alignment explanation
Indices: 1240019--1240133 Score: 97
Period size: 12 Copynumber: 9.0 Consensus size: 12
1240009 TTTTCCATAT
1240019 TATTATTATTAA
1 TATTATTATTAA
*
1240031 TATTATTATTATCCT
1 TATTATTATTA---A
1240046 TATTATTATTAA
1 TATTATTATTAA
1240058 TATTATTATT-A
1 TATTATTATTAA
* *
1240069 TCATTGTTATTAT
1 T-ATTATTATTAA
*
1240082 TATTATTATTAT
1 TATTATTATTAA
*
1240094 TATTATTATTAT
1 TATTATTATTAA
*
1240106 TATTAAATATATATA
1 TATT-ATTAT-TA-A
1240121 TATATATTATTAA
1 TAT-TATTATTAA
1240134 AAAAAATTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 17
0.77 0.07 0.15
Matches are distributed among these distances:
11 2 0.02
12 55 0.64
13 6 0.07
14 4 0.05
15 18 0.21
16 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:1240145 original size:3 final size:3
Alignment explanation
Indices: 1240016--1240110 Score: 136
Period size: 3 Copynumber: 31.7 Consensus size: 3
1240006 TTTTTTTCCA
* ** *
1240016 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1240064 TAT TAT CAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1240111 AATATATATA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1240897 original size:13 final size:13
Alignment explanation
Indices: 1240879--1240903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1240869 ACCACCGTCA
1240879 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1240892 CGGTGGCCGGCG
1 CGGTGGCCGGCG
1240904 CGGAGTACGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.32, G:0.60, T:0.08
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:1241483 original size:19 final size:19
Alignment explanation
Indices: 1241445--1241480 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1241435 CAATTTAGTC
1241445 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
1241464 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
1241481 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:1241537 original size:22 final size:21
Alignment explanation
Indices: 1241508--1241551 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1241498 TAGAATTATC
**
1241508 TTTTATATATATTGTTAAATA
1 TTTTATATATATTCATAAATA
1241529 TTTTGATATATATTCATAAATA
1 TTTT-ATATATATTCATAAATA
1241551 T
1 T
1241552 ATATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTATATATATTCATAAATA
Found at i:1250036 original size:226 final size:227
Alignment explanation
Indices: 1249756--1250208 Score: 858
Period size: 226 Copynumber: 2.0 Consensus size: 227
1249746 ATGCCATTTG
1249756 GATTGAAAAATGCAGGGGCAACATATCAAAGCCATGGTAACTTTGTTTCATGACATGATGCACAA
1 GATTGAAAAATGCAGGGGCAACATATCAAAGCCATGGTAACTTTGTTTCATGACATGATGCACAA
*
1249821 AGAGATTGAAGTATATGTAGATGACATGATTGCCAAATCCAGAAC-GAAGAAGAACATATTCAAA
66 AGAGATTGAAGTATATGTAGATGACATGATTGCCAAATACAGAACGGAAGAAGAACATATTCAAA
1249885 ATCTGAGGAAGCTTTTCCAGAGATTGAGGAAGTATCAATT-AAGCTCAACCCCGCAAAATGCACT
131 ATCTGAGGAAGCTTTTCCAGAGATTGAGGAAGTATCAATTAAAGCTCAACCCCGCAAAATGCACT
1249949 TTTGGGGTAACTTCT-GGAAACTTTTGGGATT
196 TTTGGGGTAACTTCTGGGAAACTTTTGGGATT
1249980 GATTGAAAAATGCAGGGGCAACATATCAAAGAGCCATGGTAACTTTGTTTCATGACATGATGCAC
1 GATTGAAAAATGCAGGGGCAACATATC-AA-AGCCATGGTAACTTTGTTTCATGACATGATGCAC
1250045 AAAGAGATTGAAGTATATGTAGATGACATGATTGCCAAATACAGAACGGAAGAAGAACATATTCA
64 AAAGAGATTGAAGTATATGTAGATGACATGATTGCCAAATACAGAACGGAAGAAGAACATATTCA
1250110 AAATCTGAGGAAGCTTTTCCAGAGATTGAGGAAGTATCAATTAAAGCTCAACCCCGCAAAATGCA
129 AAATCTGAGGAAGCTTTTCCAGAGATTGAGGAAGTATCAATTAAAGCTCAACCCCGCAAAATGCA
1250175 CTTTTGGGGTAACTTCTGGGAAACTTTTGGGATT
194 CTTTTGGGGTAACTTCTGGGAAACTTTTGGGATT
1250209 TGTGGTCAGC
Statistics
Matches: 223, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
224 27 0.12
225 2 0.01
226 80 0.36
227 59 0.26
228 39 0.17
229 16 0.07
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (227 bp):
GATTGAAAAATGCAGGGGCAACATATCAAAGCCATGGTAACTTTGTTTCATGACATGATGCACAA
AGAGATTGAAGTATATGTAGATGACATGATTGCCAAATACAGAACGGAAGAAGAACATATTCAAA
ATCTGAGGAAGCTTTTCCAGAGATTGAGGAAGTATCAATTAAAGCTCAACCCCGCAAAATGCACT
TTTGGGGTAACTTCTGGGAAACTTTTGGGATT
Found at i:1252681 original size:20 final size:18
Alignment explanation
Indices: 1252656--1252722 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
1252646 AAAAAAAAAA
1252656 AAAAGAAAAAGAAGAGAAAG
1 AAAA-AAAAA-AAGAGAAAG
* *
1252676 AAAAGAAAAAAAAAAGAAGG
1 -AAA-AAAAAAAAGAGAAAG
*
1252696 AAAAAAGAAAAAGAAAAAG
1 AAAAAA-AAAAAGAGAAAG
1252715 AAAAAAAA
1 AAAAAAAA
1252723 GGGGTCAAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 5 0.13
19 18 0.46
20 7 0.18
21 8 0.21
22 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAGAAAG
Found at i:1252686 original size:22 final size:21
Alignment explanation
Indices: 1252643--1252720 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
1252633 ATTATGCTTG
* *
1252643 AAGAAAAAAAAAAAAAAGAAA
1 AAGAAAGAAAGAAAAAAGAAA
1252664 AAGAAGAGAAAGAAAAGAA-AAA
1 AAGAA-AGAAAGAAAA-AAGAAA
*
1252686 AA-AAAGAAGGAAAAAAGAAA
1 AAGAAAGAAAGAAAAAAGAAA
1252706 AAG-AA-AAAGAAAAAA
1 AAGAAAGAAAGAAAAAA
1252721 AAGGGGTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 11 0.22
20 16 0.33
21 7 0.14
22 13 0.27
23 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAAGAAAAAAGAAA
Found at i:1252690 original size:34 final size:34
Alignment explanation
Indices: 1252647--1252722 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 34
1252637 TGCTTGAAGA
*
1252647 AAAAAAAAAAAAAGAAAAAGAAGAGAAAG-AAAAG
1 AAAAAAAAAAAAAGAAAAA-AAGAAAAAGAAAAAG
* *
1252681 AAAAAAAAAAGAAGGAAAAAAGAAAAAGAAAAAG
1 AAAAAAAAAAAAAGAAAAAAAGAAAAAGAAAAAG
1252715 AAAAAAAA
1 AAAAAAAA
1252723 GGGGTCAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 8 0.21
34 30 0.79
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAAAAAGAAAAAAAGAAAAAGAAAAAG
Found at i:1252718 original size:11 final size:11
Alignment explanation
Indices: 1252643--1252719 Score: 72
Period size: 11 Copynumber: 7.2 Consensus size: 11
1252633 ATTATGCTTG
1252643 AAGAAAA-AAA
1 AAGAAAAGAAA
*
1252653 AAAAAAAGAAA
1 AAGAAAAGAAA
*
1252664 AAG--AAGAGA
1 AAGAAAAGAAA
1252673 AAGAAAAGAAA
1 AAGAAAAGAAA
* *
1252684 AAAAAAAGAAGG
1 AAGAAAAGAA-A
1252696 AA-AAAAGAAA
1 AAGAAAAGAAA
1252706 AAGAAAAAGAAA
1 AAG-AAAAGAAA
1252718 AA
1 AA
1252720 AAAGGGGTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
9 8 0.15
10 8 0.15
11 26 0.48
12 12 0.22
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:1253783 original size:51 final size:52
Alignment explanation
Indices: 1253660--1253864 Score: 344
Period size: 51 Copynumber: 4.0 Consensus size: 52
1253650 TATGTGCTCA
*
1253660 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
1253712 ATAGCATCTTCTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
1253763 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* *
1253813 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1253865 CAATCATTGA
Statistics
Matches: 143, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
50 46 0.32
51 51 0.36
52 46 0.32
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
Found at i:1253970 original size:50 final size:50
Alignment explanation
Indices: 1253895--1253996 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
1253885 TGAATTTGCC
1253895 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
* *
1253945 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1253995 AA
1 AA
1253997 CCAATCATTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:1254001 original size:133 final size:133
Alignment explanation
Indices: 1253763--1254131 Score: 659
Period size: 133 Copynumber: 2.8 Consensus size: 133
1253753 TTAGAAGAAC
1253763 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
*
1253828 AGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTG
66 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
1253893 CCA
131 CCA
1253896 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1253961 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
66 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
*
1254026 TCA
131 CCA
* *
1254029 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-ATAGCATCTTCTG
* *
1254094 GAAGTGTTCTTTGAGTAATCTGATCTGGTTAGA-AGAAC
64 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAAC
1254132 ATAGCATCTT
Statistics
Matches: 228, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
133 178 0.78
134 6 0.03
135 44 0.19
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (133 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
CCA
Found at i:1254138 original size:236 final size:235
Alignment explanation
Indices: 1253896--1254366 Score: 863
Period size: 236 Copynumber: 2.0 Consensus size: 235
1253886 GAATTTGCCA
1253896 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1253961 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
66 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
* * *
1254026 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTT
131 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-ATAGCATCTT
1254091 CTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGA-AGAAC
194 CTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGACAGAAC
1254132 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
*
1254197 AGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTG
66 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
1254262 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCT
131 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCT
* *
1254327 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAAC
196 GGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGACAGAAC
1254367 CAATCATGAA
Statistics
Matches: 228, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
234 44 0.19
235 6 0.03
236 178 0.78
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (235 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCT
GGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGACAGAAC
Found at i:1254152 original size:51 final size:52
Alignment explanation
Indices: 1254029--1254233 Score: 344
Period size: 51 Copynumber: 4.0 Consensus size: 52
1254019 GAATTTGTCA
*
1254029 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
1254081 ATAGCATCTTCTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
1254132 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* *
1254182 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1254234 CAATCATTGA
Statistics
Matches: 143, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
50 46 0.32
51 51 0.36
52 46 0.32
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
Found at i:1254336 original size:369 final size:368
Alignment explanation
Indices: 1253657--1254498 Score: 1607
Period size: 369 Copynumber: 2.3 Consensus size: 368
1253647 TTATATGTGC
1253657 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTT
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTT
1253722 CTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTT
66 CTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTT
1253787 TGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
131 TGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1253852 GGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTT
196 GGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTT
1253917 CTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
261 CTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
1253982 TCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
326 TCTGGTTTGACAGAACCAATCA-TGAATTTAGAAGATGAATTTG
1254026 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTT
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTT
1254091 CTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTT
66 CTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTT
1254156 TGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
131 TGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1254221 GGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTT
196 GGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTT
1254286 CTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
261 CTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
1254351 TCTGGTTTGACAGAACCAATCATGAATTTAGAAGATGAATTTG
326 TCTGGTTTGACAGAACCAATCATGAATTTAGAAGATGAATTTG
* * *
1254394 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-ATAGCATCTT
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTT
* *
1254457 CTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAAC
66 CTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGA-AGAAC
1254499 CAATCATTGA
Statistics
Matches: 467, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
366 44 0.09
367 6 0.01
368 70 0.15
369 347 0.74
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (368 bp):
TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTT
CTGGAAGTGTTCTTTGAGTAATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTT
TGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTT
CTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
TCTGGTTTGACAGAACCAATCATGAATTTAGAAGATGAATTTG
Found at i:1254339 original size:50 final size:50
Alignment explanation
Indices: 1254264--1254365 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
1254254 TGAATTTGCC
1254264 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
* *
1254314 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1254364 AA
1 AA
1254366 CCAATCATGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:1254370 original size:133 final size:133
Alignment explanation
Indices: 1254132--1254569 Score: 842
Period size: 133 Copynumber: 3.3 Consensus size: 133
1254122 TTAGAAGAAC
1254132 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
*
1254197 AGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTG
66 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
1254262 CCA
131 CCA
1254265 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1254330 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCA-TGAATTTAGAAGATGAATTTG
66 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
1254394 CCA
131 CCA
1254397 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
1254462 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
66 AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
**
1254527 TTA
131 CCA
1254530 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1254570 GTTTGGTAAG
Statistics
Matches: 301, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
132 132 0.44
133 169 0.56
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (133 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGA
AGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTTG
CCA
Found at i:1254455 original size:50 final size:50
Alignment explanation
Indices: 1254396--1254497 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
1254386 TGAATTTGCC
1254396 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
* *
1254446 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1254496 AA
1 AA
1254498 CCAATCATTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:1255403 original size:113 final size:112
Alignment explanation
Indices: 1255205--1255756 Score: 791
Period size: 113 Copynumber: 4.8 Consensus size: 112
1255195 TTAGCAAAGA
* *
1255205 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTTGATGGATCAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
1255270 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
* *
1255318 TGAATCCATCATTTGGTGGATCATTTTTCCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTTGATGGATCATTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
1255383 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
* * *
1255431 TAAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TGAATTCATCATTTGATGGATCA-T-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1255496 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
* * *
1255545 TGAATTCATCAAATTGATGGATAATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
1 TGAATTCATC-ATTTGATGGATCAT-TTTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCA
*
1255610 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
59 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
* ** * *
1255664 TGAATTCATCATTTGATAGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCGGA
1 TGAATTCATCATTTGATGGATC-ATTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGA
*
1255728 AGAAGGAAGAAAAAGTTCATAATGAGAAG
64 AGAAGGAAGAAGAAGTTCATAATGAGAAG
1255757 GACTCATCAA
Statistics
Matches: 405, Mismatches: 23, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
112 4 0.01
113 158 0.39
114 103 0.25
115 18 0.04
116 36 0.09
117 2 0.00
118 17 0.04
119 67 0.17
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (112 bp):
TGAATTCATCATTTGATGGATCATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
Found at i:1256013 original size:3 final size:3
Alignment explanation
Indices: 1256007--1256107 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
1255997 TTTTTTTCCA
* ** *
1256007 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1256055 TAT TAT CAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1256103 TAT TA
1 TAT TA
1256108 AAAATATATA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1256027 original size:12 final size:12
Alignment explanation
Indices: 1256010--1256131 Score: 111
Period size: 12 Copynumber: 9.7 Consensus size: 12
1256000 TTTTCCATAT
1256010 TATTATTATTAA
1 TATTATTATTAA
*
1256022 TATTATTATTATCCT
1 TATTATTATTA---A
1256037 TATTATTATTAA
1 TATTATTATTAA
1256049 TATTATTATT-A
1 TATTATTATTAA
* *
1256060 TCATTGTTATTAT
1 T-ATTATTATTAA
*
1256073 TATTATTATTAT
1 TATTATTATTAA
*
1256085 TATTATTATTAT
1 TATTATTATTAA
1256097 TATTATTATTAA
1 TATTATTATTAA
* *
1256109 AAATATATATATATA
1 TATTAT-TAT-TA-A
1256124 TATTATTA
1 TATTATTA
1256132 AAAAAATAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
11 2 0.02
12 66 0.72
13 4 0.04
14 4 0.04
15 16 0.17
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:1256897 original size:13 final size:13
Alignment explanation
Indices: 1256879--1256907 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1256869 ACCACCGTCA
1256879 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1256892 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1256905 CGG
1 CGG
1256908 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:1262560 original size:37 final size:37
Alignment explanation
Indices: 1262484--1262560 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1262474 TTTTTATATT
*
1262484 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
1262521 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
1262558 TTT
1 TTT
1262561 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:1262742 original size:20 final size:20
Alignment explanation
Indices: 1262706--1262743 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1262696 ATCCTATTCC
**
1262706 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1262726 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1262744 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1280362 original size:23 final size:23
Alignment explanation
Indices: 1280318--1280362 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1280308 AACTCAAAAT
*
1280318 ATGATATATGTCAACACATGATC
1 ATGATATATATCAACACATGATC
* *
1280341 ATGATATATATCATCACTTGAT
1 ATGATATATATCAACACATGAT
1280363 TTGATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (23 bp):
ATGATATATATCAACACATGATC
Found at i:1296731 original size:32 final size:32
Alignment explanation
Indices: 1296695--1296795 Score: 166
Period size: 32 Copynumber: 3.2 Consensus size: 32
1296685 CACAATAGCT
* * *
1296695 CAACACTTGAAACCGTTGGCTAATAATCAGTA
1 CAACACTCGAAGCTGTTGGCTAATAATCAGTA
1296727 CAACACTCGAAGCTGTTGGCTAATAATCAGTA
1 CAACACTCGAAGCTGTTGGCTAATAATCAGTA
*
1296759 CAACACTCGAAGCTGTTGGCTAATAATCAGTT
1 CAACACTCGAAGCTGTTGGCTAATAATCAGTA
1296791 CAACA
1 CAACA
1296796 AACTGTTAGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (32 bp):
CAACACTCGAAGCTGTTGGCTAATAATCAGTA
Found at i:1307969 original size:59 final size:58
Alignment explanation
Indices: 1307840--1307979 Score: 147
Period size: 58 Copynumber: 2.4 Consensus size: 58
1307830 GAAAGATTAG
* * *
1307840 GGATGAAATTAGAACATTTAAAAAATTGAAGACTAATTTAGAATGAGAGTTAATTTGA
1 GGATGAAATTAAAATATTTAAAAAATTGAAGACTAATTTAGAATGAGAGTTAATTTAA
* * * * * * * *
1307898 TGATGCAGTTAAAATATTTTAAAATTTGAAGA-TTATTTAGAGTGAGAATTATAATTTAA
1 GGATGAAATTAAAATATTTAAAAAATTGAAGACTAATTTAGAATGAG-AGT-TAATTTAA
*
1307957 GGATGAAATTAAAATATTCAAAA
1 GGATGAAATTAAAATATTTAAAA
1307980 GTTTAAGAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
57 12 0.19
58 27 0.42
59 25 0.39
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.34
Consensus pattern (58 bp):
GGATGAAATTAAAATATTTAAAAAATTGAAGACTAATTTAGAATGAGAGTTAATTTAA
Found at i:1311102 original size:2 final size:2
Alignment explanation
Indices: 1311095--1311136 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1311085 CTATTTCCCT
1311095 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1311137 ATAGCATCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1312629 original size:30 final size:31
Alignment explanation
Indices: 1312585--1312647 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
1312575 CATCGGAAGT
1312585 AGTAATATTTACCATGAAAACATTCAATTGA
1 AGTAATATTTACCATGAAAACATTCAATTGA
*
1312616 AGTAATA-TTACCATGAAAACATTCAGTTGA
1 AGTAATATTTACCATGAAAACATTCAATTGA
1312646 AG
1 AG
1312648 CTAAATATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (31 bp):
AGTAATATTTACCATGAAAACATTCAATTGA
Found at i:1313294 original size:11 final size:11
Alignment explanation
Indices: 1313278--1313302 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1313268 ACTTCTCCCA
1313278 CATTTTTGTTG
1 CATTTTTGTTG
1313289 CATTTTTGTTG
1 CATTTTTGTTG
1313300 CAT
1 CAT
1313303 GTTTCATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.60
Consensus pattern (11 bp):
CATTTTTGTTG
Found at i:1320550 original size:2 final size:2
Alignment explanation
Indices: 1320543--1320573 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1320533 GAAGGTAAGT
*
1320543 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1320574 GAAGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1323247 original size:2 final size:2
Alignment explanation
Indices: 1323240--1323266 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1323230 GAAGGTAAGT
1323240 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 T
1323267 GAAGAAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1323554 original size:13 final size:14
Alignment explanation
Indices: 1323523--1323551 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1323513 CTTCAAGCTC
1323523 TTAATCTTTTGCTT
1 TTAATCTTTTGCTT
1323537 TTAATCTTTTGCTT
1 TTAATCTTTTGCTT
1323551 T
1 T
1323552 AATTCATTTT
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:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTAATCTTTTGCTT
Found at i:1326164 original size:23 final size:23
Alignment explanation
Indices: 1326134--1326198 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
1326124 TTGGAACATA
*
1326134 TATGTGGTCTTTCGGGACAATTC
1 TATGTGGTCCTTCGGGACAATTC
*
1326157 TATGTGGTCCTTAGGGACAATTC
1 TATGTGGTCCTTCGGGACAATTC
1326180 TATGTGGTCCTTCGGGACA
1 TATGTGGTCCTTCGGGACA
1326199 TTTTATATGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.35
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAATTC
Found at i:1326496 original size:3 final size:3
Alignment explanation
Indices: 1326465--1326536 Score: 76
Period size: 3 Copynumber: 24.0 Consensus size: 3
1326455 TTGGGTTTTG
*
1326465 TAA TAT TAA TAA -ATA TAA TTAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1326510 TTA TTA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1326537 ATTTTAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 3 0.05
3 52 0.88
4 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1326911 original size:123 final size:122
Alignment explanation
Indices: 1326738--1326962 Score: 333
Period size: 123 Copynumber: 1.8 Consensus size: 122
1326728 GACCTATTTC
* * * * * * * *
1326738 CTTCTGTGATAGAGTCATTCAAAGGTTGAATAAGTTCTTCTTATTTTGAACTTCTTCTTTCTTTT
1 CTTCTGTGATAGAATCATGCAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCTT
* * *
1326803 CAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
66 CAAATAAGTTCTTCTTATTACGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
*
1326860 CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
1 CTTCTGTGATAGAATCATGC-AAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
1326925 TCAAATAAGTTCTTCTTATTACGAACTTTCTCTGGAAA
65 TCAAATAAGTTCTTCTTATTACGAACTTTCTCTGGAAA
1326963 TGTTGATCCA
Statistics
Matches: 90, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
122 17 0.19
123 73 0.81
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (122 bp):
CTTCTGTGATAGAATCATGCAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCTT
CAAATAAGTTCTTCTTATTACGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
Found at i:1327208 original size:116 final size:113
Alignment explanation
Indices: 1326879--1327210 Score: 427
Period size: 113 Copynumber: 2.9 Consensus size: 113
1326869 TAGAATTATG
* * * * *
1326879 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCTTCA-AATAAGTTCTTCTTA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGAATGAGTTCTTCTCA
* * *
1326943 TTACGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGAA
* *
1326991 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAG-ATGAATTCTTCT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTTCTTCTTCC-TCTTCAGAATGAGTTCTTCT
**** * * *
1327054 CATTATGAACTCGAACTGGAAAAACTGATCCATCAAGTGATGGATTTGAG
64 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGAA
* *
1327104 CATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCT-CTTC-AG-AATGAGTTCTTC
1327169 TCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGAT
63 TCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGAT
1327211 ATTAATTTAT
Statistics
Matches: 186, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
112 40 0.22
113 97 0.52
114 2 0.01
116 47 0.25
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGAATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGAA
Found at i:1328901 original size:3 final size:3
Alignment explanation
Indices: 1328893--1328944 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
1328883 TAAAATTATT
* * * * *
1328893 TAA TAA TAA TAA TAA -AA TAA TTA TAA TTA TAA TTA TTA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1328940 TAA TA
1 TAA TA
1328945 GAAACGAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1329707 original size:113 final size:113
Alignment explanation
Indices: 1329373--1330340 Score: 1450
Period size: 113 Copynumber: 8.6 Consensus size: 113
1329363 TCAAACAAAG
* * * * *
1329373 GTTGAACAAATTATTCTTATTATGAACTTCTTCTT-CATCTTCAGATAAG---TTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
** * * * * * * *
1329434 ACTTTCTCTGGAAAAGTTAATTCATC-AAGTGATGAATTCAGGC-AAAA
66 ACTCGCCCTGGCAATGCTGATCCATCGAA-TGATGAATTCAAGCGAAAA
* * *
1329481 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATG
1 -GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
** * * * * *
1329545 AACTTTCTCTGGAAATGTTGATCTATC-AAGTGATGAATT-AGAGCAAAAA
65 AACTCGCCCTGGCAATGCTGATCCATCGAA-TGATGAATTCA-AGCGAAAA
* * *
1329594 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
1329659 ACTCGCCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAA
66 ACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
*
1329707 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
1329772 ACTCGCTCTGGCAATGCTGGTCCATCGAATGATGAATTCAAGCGAAAA
66 ACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
* *
1329820 GTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTTATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
1329885 ACTCGCCCTGGCAATGCTGGTCCATAGAATGATGAATTCAAGCGAAAA
66 ACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
*
1329933 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
1329998 ACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
66 ACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
*
1330046 GTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
1330111 ACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
66 ACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
*
1330159 GTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
1330224 AATCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
66 ACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
1330272 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1330337 ACTC
66 ACTC
1330341 TTCTAGAAAT
Statistics
Matches: 809, Mismatches: 41, Indels: 14
0.94 0.05 0.02
Matches are distributed among these distances:
109 44 0.05
110 1 0.00
111 1 0.00
112 81 0.10
113 679 0.84
114 3 0.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
Found at i:1333701 original size:83 final size:83
Alignment explanation
Indices: 1333562--1333783 Score: 417
Period size: 83 Copynumber: 2.7 Consensus size: 83
1333552 CTGTGGTTCA
1333562 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
*
1333627 AAATTCAATGATTGATTT
66 AAATTCAATGATTGACTT
*
1333645 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1333710 AAATTCAATGATTGACTT
66 AAATTCAATGATTGACTT
*
1333728 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACAT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1333784 GGCATTTGTT
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 135 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
AAATTCAATGATTGACTT
Found at i:1334829 original size:16 final size:17
Alignment explanation
Indices: 1334776--1334830 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
1334766 TTCATAGAAG
*
1334776 AATAAATTGAATTTTCAAA
1 AATAAATTGAATCTT--AA
1334795 AATAAATTGAATCTT-A
1 AATAAATTGAATCTTAA
1334811 AATAAATTGAA-CTTAA
1 AATAAATTGAATCTTAA
1334827 AATA
1 AATA
1334831 GATAGAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 3 0.09
16 17 0.50
19 14 0.41
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
AATAAATTGAATCTTAA
Found at i:1335163 original size:9 final size:9
Alignment explanation
Indices: 1335149--1335204 Score: 71
Period size: 9 Copynumber: 6.2 Consensus size: 9
1335139 TCTTGACCCT
1335149 TTTTTTTTC
1 TTTTTTTTC
1335158 -TTTTTTTC
1 TTTTTTTTC
*
1335166 TTTTTCTTC
1 TTTTTTTTC
1335175 TTTTTTTTC
1 TTTTTTTTC
1335184 TTCTTTTTT-
1 TT-TTTTTTC
1335193 TTTCTTTTTC
1 TTT-TTTTTC
1335203 TT
1 TT
1335205 CTCTTCAAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 9 0.22
9 24 0.59
10 8 0.20
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1335178 original size:25 final size:25
Alignment explanation
Indices: 1335149--1335198 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
1335139 TCTTGACCCT
*
1335149 TTTTTTTTCTTTTTTTCTTTTTCTTC
1 TTTTTTTTCTTCTTTT-TTTTTCTTC
1335175 TTTTTTTTCTTCTTTTTTTTTCTT
1 TTTTTTTTCTTCTTTTTTTTTCTT
1335199 TTTCTTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (25 bp):
TTTTTTTTCTTCTTTTTTTTTCTTC
Found at i:1342541 original size:15 final size:15
Alignment explanation
Indices: 1342518--1342549 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1342508 TGAAATGAAT
1342518 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1342533 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1342548 AA
1 AA
1342550 ATGTATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1345888 original size:19 final size:21
Alignment explanation
Indices: 1345842--1345888 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
1345832 TGAAATATTA
*
1345842 ATAAGAAAATATATAAATACT
1 ATAAAAAAATATATAAATACT
*
1345863 AT-GAAAAATA-ATAAATA-T
1 ATAAAAAAATATATAAATACT
1345881 ATAAAAAA
1 ATAAAAAA
1345889 TTTGAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.14
19 11 0.50
20 6 0.27
21 2 0.09
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (21 bp):
ATAAAAAAATATATAAATACT
Found at i:1345889 original size:18 final size:20
Alignment explanation
Indices: 1345842--1345889 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
1345832 TGAAATATTA
1345842 ATAAGAAAATATATAAATACT
1 ATAA-AAAATATATAAATACT
*
1345863 ATGAAAAATA-ATAAATA-T
1 ATAAAAAATATATAAATACT
1345881 ATAAAAAAT
1 ATAAAAAAT
1345890 TTGAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 7 0.28
20 6 0.24
21 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
ATAAAAAATATATAAATACT
Found at i:1355046 original size:21 final size:18
Alignment explanation
Indices: 1355011--1355047 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1355001 GAGTTGTTGT
1355011 TGTTATATCACTTGCTGC
1 TGTTATATCACTTGCTGC
*
1355029 TGTTATATCACTTGTTGC
1 TGTTATATCACTTGCTGC
1355047 T
1 T
1355048 ATATCTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (18 bp):
TGTTATATCACTTGCTGC
Found at i:1355052 original size:15 final size:15
Alignment explanation
Indices: 1355007--1355052 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 15
1354997 GTCTGAGTTG
1355007 TTGTTGTTATATCAC
1 TTGTTGTTATATCAC
1355022 TTGCTGCTGTTATATCAC
1 TTG-T--TGTTATATCAC
*
1355040 TTGTTGCTATATC
1 TTGTTGTTATATC
1355053 TCAAATTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 11 0.41
16 1 0.04
17 1 0.04
18 14 0.52
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.50
Consensus pattern (15 bp):
TTGTTGTTATATCAC
Found at i:1368133 original size:18 final size:19
Alignment explanation
Indices: 1368098--1368134 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1368088 TCACGAATGT
1368098 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1368118 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1368135 TGATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1368731 original size:80 final size:80
Alignment explanation
Indices: 1368598--1368752 Score: 292
Period size: 80 Copynumber: 1.9 Consensus size: 80
1368588 ATATACCCCC
*
1368598 AAAAATCTACTATTTGTAATAAAACATTACCGGGAATGAGACTCCAGGCCAACCAAACATGAGAA
1 AAAAATCTACTATTGGTAATAAAACATTACCGGGAATGAGACTCCAGGCCAACCAAACATGAGAA
1368663 TGTGGGATTCCCACA
66 TGTGGGATTCCCACA
*
1368678 AAAAATCTACTATTGGTAATAAAACATTACCGGGAATGAGACTCCCGGCCAACCAAACATGAGAA
1 AAAAATCTACTATTGGTAATAAAACATTACCGGGAATGAGACTCCAGGCCAACCAAACATGAGAA
1368743 TGTGGGATTC
66 TGTGGGATTC
1368753 TCATCCCATG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (80 bp):
AAAAATCTACTATTGGTAATAAAACATTACCGGGAATGAGACTCCAGGCCAACCAAACATGAGAA
TGTGGGATTCCCACA
Found at i:1371724 original size:17 final size:18
Alignment explanation
Indices: 1371704--1371741 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1371694 TATAAATAAA
1371704 AAATAACGATAATC-AAT
1 AAATAACGATAATCAAAT
**
1371721 AAATAATTATAATCAAAT
1 AAATAACGATAATCAAAT
1371739 AAA
1 AAA
1371742 AAGTCAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (18 bp):
AAATAACGATAATCAAAT
Found at i:1371866 original size:7 final size:7
Alignment explanation
Indices: 1371854--1371878 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1371844 CCTGATTTTT
1371854 AAAATTA
1 AAAATTA
1371861 AAAATTA
1 AAAATTA
1371868 AAAATTA
1 AAAATTA
1371875 AAAA
1 AAAA
1371879 AAAAAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:1376663 original size:31 final size:31
Alignment explanation
Indices: 1376625--1376686 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1376615 CATGGCTCCA
1376625 TTTATTTTGACGTTTCATGCAAATCAAGAGC
1 TTTATTTTGACGTTTCATGCAAATCAAGAGC
1376656 TTTATTTTGACGTTTCATGCAAATCAAGAGC
1 TTTATTTTGACGTTTCATGCAAATCAAGAGC
1376687 GAGAACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTATTTTGACGTTTCATGCAAATCAAGAGC
Found at i:1380667 original size:24 final size:24
Alignment explanation
Indices: 1380640--1380686 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1380630 CTGTTCAACT
*
1380640 ATGTATT-TATTTATTTATTTATTC
1 ATGTATTGTATTT-TATATTTATTC
1380664 ATGTATTGTATTTTATATTTATT
1 ATGTATTGTATTTTATATTTATT
1380687 TTTAATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (24 bp):
ATGTATTGTATTTTATATTTATTC
Found at i:1382382 original size:17 final size:18
Alignment explanation
Indices: 1382343--1382384 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
1382333 AGGTAAAAAT
1382343 ATGATAAAACCGGTATCAA
1 ATGATAAAACCGGTA-CAA
1382362 ATGATAAAACCGGTA-AA
1 ATGATAAAACCGGTACAA
1382379 ATGATA
1 ATGATA
1382385 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (18 bp):
ATGATAAAACCGGTACAA
Found at i:1384580 original size:21 final size:21
Alignment explanation
Indices: 1384533--1384597 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1384523 AAGACAATCA
* *
1384533 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
1384555 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
1384575 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
1384596 AG
1 AG
1384598 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:1384692 original size:32 final size:33
Alignment explanation
Indices: 1384631--1384695 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1384621 AAATAGATGG
*
1384631 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
1384664 AGTGGTGAAAGAAGTTG-GGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1384696 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1386519 original size:18 final size:18
Alignment explanation
Indices: 1386472--1386508 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1386462 AAATGTAGGG
1386472 TTAATTTTGTATAAGATT
1 TTAATTTTGTATAAGATT
*
1386490 TTAATTTTGTATACGATT
1 TTAATTTTGTATAAGATT
1386508 T
1 T
1386509 ATATTTCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.57
Consensus pattern (18 bp):
TTAATTTTGTATAAGATT
Found at i:1387705 original size:192 final size:193
Alignment explanation
Indices: 1386635--1387699 Score: 1729
Period size: 193 Copynumber: 5.5 Consensus size: 193
1386625 GGCCAAAAGG
1386635 ATGTAATTTTTCAATCT-ACCGGTACAATTATACCGGTTTTATGTGAG-ATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* *
1386698 TGTCGACACTA-ATTAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACA--GTGCACCA
66 TGTCGACACTATA-TAGTTTGTGTCGATACTTATTT-CAGAATGAATGGAAAACAGGGTGCACC-
1386760 TAAAG-GTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
128 -AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
1386824 AT
192 AT
1386826 ATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAA--
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1386888 TGTCGACACTATATAGTTTGTGTCGATA-TTATTTCCAGAATGAATGGAAAACAGGGTGCACCCA
66 TGTCGACACTATATAGTTTGTGTCGATACTTATTT-CAGAATGAATGGAAAACAGGGTGCA-CC-
1386952 TAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
128 -AAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1387017 AAT
191 AAT
1387020 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTTATGTGAGAATATGTCTAAATAAT
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTTATGTGAGAATATGTCTAAATAAT
1387085 GTGTCGACACTAATATAGTTTGTGTCGATACTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
65 GTGTCGACACT-ATATAGTTTGTGTCGATACTTATTT-CAGAATGAATGGAAAACAGGGTGCACC
1387150 ATAAAGTG-CGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
128 --AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1387214 AAT
191 AAT
1387217 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* *
1387281 TGTCGACACTATATAGTTTGTGTCGATACTAATTT-ATATATGAATGGAAAACAGGGTGCACCAT
66 TGTCGACACTATATAGTTTGTGTCGATACTTATTTCAGA-ATGAATGGAAAACAGGGTGCACC--
1387345 AAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA-G-AA
128 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
1387407 T
193 T
1387408 ATGTAATTTTTCAATCTAACCGGTAC-ATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* * * *
1387472 TGTCGACACTAATATAGTTTGTGTCGATACTAATTT-AAATATAAATGGAAAACAGGATGCACC-
66 TGTCGACACT-ATATAGTTTGTGTCGATACTTATTTCAGA-ATGAATGGAAAACAGGGTGCACCA
1387535 AAGTGTCGATCCATATATATAAAAGTGTCGATCCCAAAATCA-CGAACCCAAAAGTATAATGTAA
129 AAGTGTCGATCCATATATA-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
1387599 T
193 T
1387600 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
1387665 TGTCGACACTATATAGTTTGTGTCGATACTGATTT
66 TGTCGACACTATATAGTTTGTGTCGATACTTATTT
1387700 AAATATCAAG
Statistics
Matches: 844, Mismatches: 7, Indels: 45
0.94 0.01 0.05
Matches are distributed among these distances:
189 42 0.05
190 63 0.07
191 131 0.16
192 127 0.15
193 133 0.16
194 89 0.11
195 67 0.08
196 26 0.03
197 84 0.10
198 22 0.03
199 28 0.03
200 32 0.04
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (193 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTATATAGTTTGTGTCGATACTTATTTCAGAATGAATGGAAAACAGGGTGCACCAAA
GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
Found at i:1389143 original size:18 final size:17
Alignment explanation
Indices: 1389122--1389197 Score: 75
Period size: 18 Copynumber: 4.5 Consensus size: 17
1389112 AGCGGTCGCA
1389122 GAAGATGAAGCTGACGAT
1 GAAGATGAAG-TGACGAT
* *
1389140 GAAGATGACGATGATGAT
1 GAAGATGAAG-TGACGAT
* *
1389158 GACGATGAAGTGGCGAT
1 GAAGATGAAGTGACGAT
1389175 GAAGATG-A-TGACGAT
1 GAAGATGAAGTGACGAT
*
1389190 GATGATGA
1 GAAGATGA
1389198 TGAAGATGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 12 0.26
16 1 0.02
17 11 0.23
18 23 0.49
ACGTcount: A:0.37, C:0.08, G:0.36, T:0.20
Consensus pattern (17 bp):
GAAGATGAAGTGACGAT
Found at i:1389146 original size:6 final size:6
Alignment explanation
Indices: 1389122--1389206 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
1389112 AGCGGTCGCA
* * * * *
1389122 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAG-T
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * *
1389169 GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
1389207 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
5 3 0.05
6 59 0.95
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:1389157 original size:3 final size:3
Alignment explanation
Indices: 1389137--1389210 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
1389127 TGAAGCTGAC
* * * * ** *
1389137 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA G-T GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1389184 GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1389211 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 17, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.36, C:0.05, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:1389210 original size:12 final size:12
Alignment explanation
Indices: 1389125--1389206 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
1389115 GGTCGCAGAA
*
1389125 GATGAAGCTGAC
1 GATGAAGATGAC
1389137 GATGAAGATGAC
1 GATGAAGATGAC
*
1389149 GATGATGATGAC
1 GATGAAGATGAC
*
1389161 GATGAAG-TGGC
1 GATGAAGATGAC
*
1389172 GATGAAGATGAT
1 GATGAAGATGAC
* * *
1389184 GACGATGATGAT
1 GATGAAGATGAC
1389196 GATGAAGATGA
1 GATGAAGATGA
1389207 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
11 10 0.17
12 49 0.83
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1391075 original size:176 final size:182
Alignment explanation
Indices: 1390520--1391314 Score: 1236
Period size: 178 Copynumber: 4.4 Consensus size: 182
1390510 CTTTCAACAT
* * * * *
1390520 ATTATAAT-AAATAGGTAA-TTTGCAATA-AACCGGTATAAATATACCGGTT-TATGCTCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTGTATGCACGAATA
*
1390581 GGTCTACAACCTATATCGACACTTTTT-ATATTGTGTCGGTACTTTATGTCTATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1390645 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AA-GTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
1390698 ATTATAATGTAATAGATAA-TTTGTAATATAA-CAGGTATAAATATACCGGTTGTATG-AGCGAA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCA-GTATAAATATACCGGTTGTATGCA-CGAA
1390760 TAGGTCTACAACC-ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGA
64 TAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGA
1390824 AAAA-TGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAA-CCATA
129 AAAAGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
1390876 ATTATAATGTAATAGATAATTTTGTAATATAA-CAGTATAAATATACCGGTTGTATG-ACGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTGTATGCACGAATA
1390939 GGTCTACAACCTATATCGACACTTTTTAATA-T-TGTCGGTACTTTATTGTCCATATTGGAAGAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTA-TGTCCATATTGGAAGAA
1391002 AAA-TGTCG-TACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAT-
130 AAAGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
1391052 ATTATAAATGT-ATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTTTTATGCGCGAAT
1 ATTAT-AATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTGTATGCACGAAT
1391115 AGGTCTACAAACCTATATCGACACTTTTTAATATTGTGTCGGTTACTTTATGTCCATATTGGAAG
65 AGGTCTAC-AACCTATATCGACACTTTTTAATATTGTGTCGG-TACTTTATGTCCATATTGGAAG
1391180 AAAAATGTGTCGATACGATTTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
128 AAAAA-GTGTCGATACGA-TTTAAAAAAGTGTCGACA-TTTACACATCGGAACCCATA
* * *
1391238 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATAT-CCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTGTATGCACGAATA
*
1391302 TGTCTACAACCTA
66 GGTCTACAACCTA
1391315 AAATGTGCGA
Statistics
Matches: 582, Mismatches: 10, Indels: 43
0.92 0.02 0.07
Matches are distributed among these distances:
176 92 0.16
177 70 0.12
178 98 0.17
179 75 0.13
180 60 0.10
181 66 0.11
182 5 0.01
183 5 0.01
184 18 0.03
185 30 0.05
186 58 0.10
187 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (182 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTGTATGCACGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AAGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:1393780 original size:23 final size:22
Alignment explanation
Indices: 1393754--1393805 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
1393744 AAACTACAAG
*
1393754 TATATAATGTAATAGGTATCGT
1 TATATAATGTAATAGGTAGCGT
1393776 T-TATAATGTAATAGGTAGCGCT
1 TATATAATGTAATAGGTAGCG-T
1393798 TATATAAT
1 TATATAAT
1393806 ATATTGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 18 0.67
22 3 0.11
23 6 0.22
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (22 bp):
TATATAATGTAATAGGTAGCGT
Found at i:1394258 original size:18 final size:17
Alignment explanation
Indices: 1394226--1394261 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1394216 GTAATTGGAG
1394226 TTTGAATTTAATTTCAA
1 TTTGAATTTAATTTCAA
*
1394243 TTTGAGTTTGAATTTCAA
1 TTTGAATTT-AATTTCAA
1394261 T
1 T
1394262 ATATATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (17 bp):
TTTGAATTTAATTTCAA
Found at i:1394559 original size:39 final size:39
Alignment explanation
Indices: 1394516--1394602 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1394506 TCCGATGCTC
*
1394516 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
1394555 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1394594 ATCAAAATC
1 ATCAAAATC
1394603 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:1394787 original size:38 final size:39
Alignment explanation
Indices: 1394728--1394813 Score: 138
Period size: 38 Copynumber: 2.2 Consensus size: 39
1394718 TCCGATGCTC
*
1394728 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
1394767 ATCAAAATTC-AATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1394805 ATCAAAATC
1 ATCAAAATC
1394814 TACAACTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 34 0.79
39 9 0.21
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.19
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:1394795 original size:211 final size:211
Alignment explanation
Indices: 1394431--1394854 Score: 832
Period size: 211 Copynumber: 2.0 Consensus size: 211
1394421 TATGATCTGG
1394431 GTGGTAAACAAATAGCAACTAAAATCTAAGTCTGAAATGCTTCTGAGTACCACCCAAATCATAAG
1 GTGGTAAACAAATAGCAACTAAAATCTAAGTCTGAAATGCTTCTGAGTACCACCCAAATCATAAG
1394496 TCTGAATACTTCCGATGCTCATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCAAA
66 TCTGAATACTTCCGATGCTCATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCAAA
1394561 ATTCAAATCTCATATGATGCCAAGCAAAAGGAAATCAAAATCTACAACTTGATTTTGAACATTGA
131 ATTCAAATCTCATATGATGCCAAGCAAAAGGAAATCAAAATCTACAACTTGATTTTGAACATTGA
1394626 TATGATATGTTCAGTT
196 TATGATATGTTCAGTT
1394642 GTGGTAAACAAATAGCAACTAAAATCTAAGTCTGAAATGCTTCTGAGTACCACCCAAATCATAAG
1 GTGGTAAACAAATAGCAACTAAAATCTAAGTCTGAAATGCTTCTGAGTACCACCCAAATCATAAG
1394707 TCTGAAATACTTCCGATGCTCATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCAA
66 TCTG-AATACTTCCGATGCTCATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCAA
1394772 AATTC-AATCTCATATGATGCCAAGCAAAAGGAAATCAAAATCTACAACTTGATTTTGAACATTG
130 AATTCAAATCTCATATGATGCCAAGCAAAAGGAAATCAAAATCTACAACTTGATTTTGAACATTG
1394836 ATATGATATGTTCAGTT
195 ATATGATATGTTCAGTT
1394853 GT
1 GT
1394855 TATCATGTTG
Statistics
Matches: 212, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
211 147 0.69
212 65 0.31
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (211 bp):
GTGGTAAACAAATAGCAACTAAAATCTAAGTCTGAAATGCTTCTGAGTACCACCCAAATCATAAG
TCTGAATACTTCCGATGCTCATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCAAA
ATTCAAATCTCATATGATGCCAAGCAAAAGGAAATCAAAATCTACAACTTGATTTTGAACATTGA
TATGATATGTTCAGTT
Found at i:1395263 original size:23 final size:23
Alignment explanation
Indices: 1395233--1395300 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1395223 TAAAATTATG
1395233 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1395256 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1395279 ATGTAATAGGTAGTGGTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1395301 TGTAAAGTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1395325 original size:46 final size:45
Alignment explanation
Indices: 1395228--1395325 Score: 101
Period size: 46 Copynumber: 2.1 Consensus size: 45
1395218 ATAGGTAAAA
* *
1395228 TTATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 TTATAATGTAATAGGTAGCGCTTATAT-ATGTAATAGGTATCCTTT
* * *
1395274 ATATAATGTAATAGGTAGTGGTTATAT-TGTAA-AGTGTCTATCCTTT
1 TTATAATGTAATAGGTAGCGCTTATATATGTAATAG-G--TATCCTTT
1395320 TTATAA
1 TTATAA
1395326 AAGTGTCTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
43 2 0.05
44 6 0.14
46 35 0.81
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (45 bp):
TTATAATGTAATAGGTAGCGCTTATATATGTAATAGGTATCCTTT
Found at i:1395328 original size:21 final size:21
Alignment explanation
Indices: 1395304--1395363 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
1395294 GTTATATTGT
1395304 AAAGTGTCTATCCTTTTTATA
1 AAAGTGTCTATCCTTTTTATA
1395325 AAAGTGTCTATCCTTTTTATA
1 AAAGTGTCTATCCTTTTTATA
* *
1395346 AAAGTGTCCATACTTTTT
1 AAAGTGTCTATCCTTTTT
1395364 TCACTGTGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
AAAGTGTCTATCCTTTTTATA
Found at i:1395712 original size:23 final size:23
Alignment explanation
Indices: 1395686--1395753 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1395676 AGGTAAAAAT
1395686 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1395709 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1395732 ATGTAATAGGTAGTGGTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1395754 TGTAAGTGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1396094 original size:424 final size:427
Alignment explanation
Indices: 1395326--1396100 Score: 1384
Period size: 424 Copynumber: 1.8 Consensus size: 427
1395316 CTTTTTATAA
1395326 AAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAAAATTAATTTAAGGT
1 AAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAAAATTAATTTAAGGT
1395391 TATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTA
66 TATC-TTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTA
*
1395456 CGTTACGATATATATTTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAATATCAAAA
130 CGTTACGATATATATTTAA-GTTATTAAATTAAAAATTCTAAATAATATTTTATAAATATC--AA
1395521 AAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
192 AAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
1395586 ACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTATAA
257 ACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTATAA
1395651 AAAGTATGGACACTTTCAATATAATAGGTAAAAATATGTAATAGGTAGCGCTTATATAATGTAAT
322 AAAGTATGGACACTTTCAATATAATAGGTAAAAATATGTAATAGGTAGCGCTTATATAATGTAAT
1395716 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGT
387 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGT
* *
1395757 AAGTGTCTATCCTTTTTTATAAAAGTGTCCATACTTTTTTCACTGTTGAAAACATTAATTTAAGG
1 AAGTGTCTATCC-TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAAAATTAATTTAAGG
1395822 TTATC-TTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTA
65 TTATCTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTA
1395885 CGTTACGATATATA-TT-A-TTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAA
130 CGTTACGATATATATTTAAGTTATTAAATTAAAAATTCTAAATAATATTTTAT-AAATATCAAAA
*
1395946 TAATCAAATAATTTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
194 AAATCAAATAA-TTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
1396011 CACTATT-CAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAA
258 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCC-TTTTATAA
1396075 AAAGTATGGACACTTTCAATATAATA
322 AAAGTATGGACACTTTCAATATAATA
1396101 TAATGTAATA
Statistics
Matches: 335, Mismatches: 5, Indels: 15
0.94 0.01 0.04
Matches are distributed among these distances:
423 60 0.18
424 94 0.28
425 32 0.10
426 7 0.02
427 1 0.00
428 2 0.01
429 20 0.06
430 52 0.16
431 12 0.04
432 55 0.16
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (427 bp):
AAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAAAATTAATTTAAGGT
TATCTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACGATATATATTTAAGTTATTAAATTAAAAATTCTAAATAATATTTTATAAATATCAAAAAA
ATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAC
TATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTATAAAAAG
TATGGACACTTTCAATATAATAGGTAAAAATATGTAATAGGTAGCGCTTATATAATGTAATAGGT
ATCGTTTATATAATGTAATAGGTAGTGGTTATATTGT
Found at i:1397762 original size:22 final size:22
Alignment explanation
Indices: 1397732--1397777 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1397722 TAATAAAATA
* *
1397732 TTATCTAAAATATTATTATTTT
1 TTATCTAAAATATCAATATTTT
*
1397754 TTATTTAAAATATCAATATTTT
1 TTATCTAAAATATCAATATTTT
1397776 TT
1 TT
1397778 TAATGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATCTAAAATATCAATATTTT
Found at i:1397829 original size:21 final size:21
Alignment explanation
Indices: 1397803--1397849 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1397793 AGTGTCGAAC
1397803 AATAACAAAATCAATAGAAAA
1 AATAACAAAATCAATAGAAAA
* *
1397824 AATAACAAAATCGATAGAAAT
1 AATAACAAAATCAATAGAAAA
1397845 AATAA
1 AATAA
1397850 TGTTTCCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.68, C:0.09, G:0.06, T:0.17
Consensus pattern (21 bp):
AATAACAAAATCAATAGAAAA
Found at i:1405129 original size:12 final size:12
Alignment explanation
Indices: 1405112--1405136 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1405102 ACTCTTTTCC
1405112 TCCTTCCGCTAA
1 TCCTTCCGCTAA
1405124 TCCTTCCGCTAA
1 TCCTTCCGCTAA
1405136 T
1 T
1405137 TAAGGAGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.40, G:0.08, T:0.36
Consensus pattern (12 bp):
TCCTTCCGCTAA
Found at i:1406634 original size:18 final size:17
Alignment explanation
Indices: 1406611--1406679 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
1406601 TATTTAAAAT
*
1406611 TTAAAATATAATAAATTA
1 TTAAAA-ATAAAAAATTA
**
1406629 TTAAAATATAAAAAACAA
1 TTAAAA-ATAAAAAATTA
* **
1406647 TTATTAAATAATGAATTA
1 TTA-AAAATAAAAAATTA
1406665 TTAAAAATAAAAAAT
1 TTAAAAATAAAAAAT
1406680 AAAATATTTA
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
17 9 0.23
18 28 0.72
19 2 0.05
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (17 bp):
TTAAAAATAAAAAATTA
Found at i:1417030 original size:22 final size:24
Alignment explanation
Indices: 1416981--1417035 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
1416971 AATGTTCATA
* * *
1416981 ATTTTATAAAATTAATTATCATTT
1 ATTTTATAAAAATAATTATAATTG
1417005 ATTTTA-AAAAATAATTA-AATTG
1 ATTTTATAAAAATAATTATAATTG
*
1417027 ATTTCATAA
1 ATTTTATAA
1417036 TCGAGTACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 8 0.31
23 12 0.46
24 6 0.23
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTTTATAAAAATAATTATAATTG
Found at i:1431096 original size:32 final size:30
Alignment explanation
Indices: 1431054--1431142 Score: 119
Period size: 32 Copynumber: 3.0 Consensus size: 30
1431044 GATTACTTGA
1431054 AATATCATCCTATCGGCAGCAGAGATATAT
1 AATATCATCCTATCGGCAGCAGAGATATAT
*
1431084 ATGATATCATCCTATCGGCAGCTGAG--ATAT
1 A--ATATCATCCTATCGGCAGCAGAGATATAT
* *
1431114 AATATCATCCTATCGGTAGCATAGATATA
1 AATATCATCCTATCGGCAGCAGAGATATA
1431143 CAAACATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
28 20 0.39
30 9 0.18
32 22 0.43
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (30 bp):
AATATCATCCTATCGGCAGCAGAGATATAT
Found at i:1431118 original size:28 final size:28
Alignment explanation
Indices: 1431054--1431142 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 28
1431044 GATTACTTGA
*
1431054 AATATCATCCTATCGGCAGCAGAGATATAT
1 AATATCATCCTATCGGCAGCTGAG--ATAT
1431084 ATGATATCATCCTATCGGCAGCTGAGATAT
1 A--ATATCATCCTATCGGCAGCTGAGATAT
*
1431114 AATATCATCCTATCGGTAGCAT-AGATAT
1 AATATCATCCTATCGGCAGC-TGAGATAT
1431142 A
1 A
1431143 CAAACATAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
28 25 0.46
29 1 0.02
30 6 0.11
32 22 0.41
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (28 bp):
AATATCATCCTATCGGCAGCTGAGATAT
Found at i:1436118 original size:23 final size:22
Alignment explanation
Indices: 1436092--1436140 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 22
1436082 TTATCACATC
1436092 AAATTTTTTAAAATTATTTAAAAAA
1 AAATTTTTTAAAA--A-TTAAAAAA
*
1436117 ATATTTTTTAAAAATTAAAAAA
1 AAATTTTTTAAAAATTAAAAAA
1436139 AA
1 AA
1436141 TAAAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
25 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTTTTTAAAAATTAAAAAA
Found at i:1436141 original size:23 final size:24
Alignment explanation
Indices: 1436094--1436142 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
1436084 ATCACATCAA
*
1436094 ATTTTTTAAAATTATTTAAAAAAAT
1 ATTTTTTAAAA-TATTAAAAAAAAT
1436119 ATTTTTTAAAA-ATTAAAAAAAAT
1 ATTTTTTAAAATATTAAAAAAAAT
1436142 A
1 A
1436143 AAATTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
25 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTTTTAAAATATTAAAAAAAAT
Done.