Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004123.1 Hibiscus syriacus cultivar Beakdansim tig00009023_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: 1596068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1246921 original size:42 final size:42
Alignment explanation
Indices: 1246875--1246956 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1246865 TTATATTATA
* * *
1246875 TTATTAAAAGTATTAATAAATA-TATTTTAATAATAAATATTT
1 TTATTAAAA-TAATAATAAATAGCATATTAATAATAAATATTT
* *
1246917 TTATTAAAATAATATTAAATAGCATATTAATATTAAATAT
1 TTATTAAAATAATAATAAATAGCATATTAATAATAAATAT
1246957 ATAAAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 10 0.29
42 24 0.71
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (42 bp):
TTATTAAAATAATAATAAATAGCATATTAATAATAAATATTT
Found at i:1250224 original size:5 final size:5
Alignment explanation
Indices: 1250206--1250247 Score: 75
Period size: 5 Copynumber: 8.2 Consensus size: 5
1250196 TTCAGTATGC
1250206 TATAA TATATA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATA-A TATAA TATAA TATAA TATAA TATAA TATAA T
1250248 GTTTTGATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:1251085 original size:2 final size:2
Alignment explanation
Indices: 1251078--1251116 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1251068 ATTAGGGATT
1251078 TA TA TA TA TA TA TA TA TA TA -A TA -A TA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1251116 T
1 T
1251117 TTAATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1252688 original size:16 final size:17
Alignment explanation
Indices: 1252650--1252695 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
1252640 TGTTTACGAG
1252650 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
1252668 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
*
1252684 GGAATTGAAATC
1 GGAATTGGAATC
1252696 AAATTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.44
18 15 0.56
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:1253306 original size:37 final size:38
Alignment explanation
Indices: 1253220--1253313 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
1253210 TTTTCACCTT
*
1253220 AAACCCGAACTCGAC-CTGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACTC-GACCCGAATATCACACTTAAAA
1253259 AAACCCGACCCGACTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
1253296 AAACCCGACCCGACTCGA
1 AAACCCGACCCGACTCGA
1253314 ATATATGAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
37 21 0.40
38 24 0.45
39 8 0.15
ACGTcount: A:0.38, C:0.37, G:0.12, T:0.13
Consensus pattern (38 bp):
AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
Found at i:1253501 original size:230 final size:223
Alignment explanation
Indices: 1253179--1253797 Score: 826
Period size: 230 Copynumber: 2.7 Consensus size: 223
1253169 TATAAGGTAA
* * * * * *
1253179 AATTATATAT-TTTTTTGGGGTCGGTCCGGTTTTTTCACCTTAAACCCGAACTCGACCTGACCCG
1 AATTATATATATATTTTCGGGTCGGTCCAGTTTTTTCACCCTAAACCCGAACCCGACCAGACCCG
1253243 AATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCG
66 AATATCACACTT-AAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCG
* * * *
1253308 ACTCGAATATATGAATTAGAAATTTGACCCGACCCGACCCGAAATAATAAAAAAAATATTTTTAT
130 AC-CGAA-ACA--AAATA-AAATTTCACCAGACCCGACCCGAAATAAT-AAAAAAATATTTTTAT
*
1253373 TTAATAAAAACATTAACTTAATCCGACCCAACCCG
189 TTAATAAAAACAGTAACTTAATCCGACCCAACCCG
* *
1253408 AATTATATATATATTTTCGAGTCGGTCCAGTTTTTTCACCCTAAACCCGAACCCGACCAGACACG
1 AATTATATATATATTTTCGGGTCGGTCCAGTTTTTTCACCCTAAACCCGAACCCGACCAGACCCG
1253473 AATATCACACTTAAAAAACCCAGACCCGACT-----CGAATATCACACTTAAAAAACCCGACCCG
66 AATATCACACTTAAAAAACCC-GACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCG
* * * *
1253533 ACCTAAACAAAATAAAGTTTCATCAGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATA
130 ACCGAAACAAAATAAAATTTCACCAGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATA
* *
1253598 AAAACAGTGACTTAATCCGACCCGACCCG
195 AAAACAGTAACTTAATCCGACCCAACCCG
1253627 AA-T-TATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGAACCCGACCTGACCC
1 AATTATATATATATTTTCGGGTCGGTCCAG-TTTTTTCACCCTAAACCCGAACCCGACC--A---
* *
1253690 GACCCGAATATCACACTTAAAAAAACCGATCCGACTCGACCCGAATATCACACTTAAAAAACCCG
60 GACCCGAATATCACACTTAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCG
*
1253755 ACCCGACCCG-AACAAAATAAAGTTTCATCC-GACCCGACCCGAA
125 ACCCGA-CCGAAACAAAATAAAATTTCA-CCAGACCCGACCCGAA
1253798 TATATGAATT
Statistics
Matches: 350, Mismatches: 25, Indels: 32
0.86 0.06 0.08
Matches are distributed among these distances:
217 24 0.07
218 29 0.08
219 49 0.14
220 26 0.07
221 4 0.01
222 8 0.02
223 27 0.08
224 3 0.01
225 31 0.09
227 60 0.17
228 3 0.01
229 19 0.05
230 67 0.19
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (223 bp):
AATTATATATATATTTTCGGGTCGGTCCAGTTTTTTCACCCTAAACCCGAACCCGACCAGACCCG
AATATCACACTTAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGA
CCGAAACAAAATAAAATTTCACCAGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAA
AAACAGTAACTTAATCCGACCCAACCCG
Found at i:1253522 original size:32 final size:32
Alignment explanation
Indices: 1253457--1253534 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 32
1253447 CCTAAACCCG
*
1253457 AACCCGACCAGACACGAATATCACACTTAAAA
1 AACCCGACCCGACACGAATATCACACTTAAAA
*
1253489 AACCCAGACCCGACTCGAATATCACACTTAAAA
1 AACCC-GACCCGACACGAATATCACACTTAAAA
1253522 AACCCGACCCGAC
1 AACCCGACCCGAC
1253535 CTAAACAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 13 0.30
33 30 0.70
ACGTcount: A:0.42, C:0.36, G:0.10, T:0.12
Consensus pattern (32 bp):
AACCCGACCCGACACGAATATCACACTTAAAA
Found at i:1253739 original size:37 final size:37
Alignment explanation
Indices: 1253678--1253761 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 37
1253668 AAACCCGAAC
* *
1253678 CCGACCTGACCCGACCCGAATATCACACTTAAAAAAA
1 CCGACCCGACTCGACCCGAATATCACACTTAAAAAAA
* *
1253715 CCGATCCGACTCGACCCGAATATCACACTTAAAAAAC
1 CCGACCCGACTCGACCCGAATATCACACTTAAAAAAA
1253752 CCGACCCGAC
1 CCGACCCGAC
1253762 CCGAACAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.37, C:0.38, G:0.12, T:0.13
Consensus pattern (37 bp):
CCGACCCGACTCGACCCGAATATCACACTTAAAAAAA
Found at i:1257362 original size:2 final size:2
Alignment explanation
Indices: 1257355--1257405 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1257345 CGTTATAACT
1257355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1257397 TA TA TA TA T
1 TA TA TA TA T
1257406 TCTTGTTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1262579 original size:21 final size:23
Alignment explanation
Indices: 1262553--1262604 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1262543 AGGGAATCGA
1262553 TCCCCCCATG-A-GGGAACCAAT
1 TCCCCCCATGAAGGGGAACCAAT
** *
1262574 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCAAT
1262597 TCCCCCCA
1 TCCCCCCA
1262605 CAGGGGAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.23, C:0.40, G:0.19, T:0.17
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCAAT
Found at i:1270016 original size:14 final size:14
Alignment explanation
Indices: 1269997--1270030 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1269987 TAAGGTTGGG
1269997 TCATGGAAGTGCAT
1 TCATGGAAGTGCAT
1270011 TCATGGAAGTGCAT
1 TCATGGAAGTGCAT
1270025 TCATGG
1 TCATGG
1270031 TAGATTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (14 bp):
TCATGGAAGTGCAT
Found at i:1270548 original size:20 final size:20
Alignment explanation
Indices: 1270518--1270575 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1270508 TACTGGTATC
* *
1270518 AAGGGTGGGTATTGATACTA
1 AAGGGTAGGTATCGATACTA
*
1270538 TAGGGTAGGTATCGATACTA
1 AAGGGTAGGTATCGATACTA
1270558 AAGGGGTTA-GTATCGATA
1 AA-GGG-TAGGTATCGATA
1270576 TCATCATACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 18 0.56
21 12 0.38
22 2 0.06
ACGTcount: A:0.31, C:0.07, G:0.33, T:0.29
Consensus pattern (20 bp):
AAGGGTAGGTATCGATACTA
Found at i:1271821 original size:24 final size:25
Alignment explanation
Indices: 1271783--1271829 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1271773 TAATGAAATT
1271783 AATATAATAATAAAATTATATTTTA
1 AATATAATAATAAAATTATATTTTA
*
1271808 AATATTATAA-AAAATTATATTT
1 AATATAATAATAAAATTATATTT
1271830 AGAATTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AATATAATAATAAAATTATATTTTA
Found at i:1271830 original size:23 final size:26
Alignment explanation
Indices: 1271783--1271838 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
1271773 TAATGAAATT
*
1271783 AATATAATAATAAAATTATATTTTA-
1 AATATTATAATAAAATTATATTTTAG
1271808 AATATTATAA-AAAATTATA-TTTAG
1 AATATTATAATAAAATTATATTTTAG
1271832 AAT-TTAT
1 AATATTAT
1271839 CCTCGTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.28
24 12 0.41
25 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AATATTATAATAAAATTATATTTTAG
Found at i:1274776 original size:24 final size:22
Alignment explanation
Indices: 1274748--1274808 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
1274738 ATCCAGTCGA
1274748 ATTTATATTTAATAACAAATATTT
1 ATTTATATTTAA-AACAAAT-TTT
* *
1274772 ATTTATTTTTTTAAAAGAAATTTT
1 ATTTA--TATTTAAAACAAATTTT
*
1274796 ATTTAAATTTAAA
1 ATTTATATTTAAA
1274809 TGTTAAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 6 0.19
24 13 0.42
25 6 0.19
26 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTATATTTAAAACAAATTTT
Found at i:1274931 original size:3 final size:3
Alignment explanation
Indices: 1274923--1274949 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1274913 TTTAAATTGA
1274923 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1274950 TGTTCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1276286 original size:19 final size:16
Alignment explanation
Indices: 1276247--1276282 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1276237 CGAAATACAA
1276247 AATAT-AATAATTCAT
1 AATATAAATAATTCAT
1276262 AATATAAATAATTCAT
1 AATATAAATAATTCAT
*
1276278 TATAT
1 AATAT
1276283 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAAATAATTCAT
Found at i:1276970 original size:60 final size:60
Alignment explanation
Indices: 1276877--1277012 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 60
1276867 TCAAATTATA
* * *
1276877 ACTCTCATTTTAAATTTATCTTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATG
1 ACTCTCATTTTAAATTTATCCTTAAACTTTTAAATATTCTAATTTCATACCTAAACTATG
* * *
1276937 ACTCTCATTTTGAA-TTAGTCCTTACACTTTTAAATATTCTAATTTCATACCTGAACTATG
1 ACTCTCATTTTAAATTTA-TCCTTAAACTTTTAAATATTCTAATTTCATACCTAAACTATG
*
1276997 ACTTTC-TTTCTAAATT
1 ACTCTCATTT-TAAATT
1277013 GGTCACCAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
59 6 0.09
60 58 0.89
61 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (60 bp):
ACTCTCATTTTAAATTTATCCTTAAACTTTTAAATATTCTAATTTCATACCTAAACTATG
Found at i:1277267 original size:29 final size:27
Alignment explanation
Indices: 1277178--1277268 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 27
1277168 ATATACGTAT
*
1277178 AGTTTGGGATAAAATTGGAATGTTCAAAA
1 AGTTTGGGAT-AAATTGAAATGTTC-AAA
* * * * *
1277207 AGTTTGGGATCAATTTAGAATG-GCCAT
1 AGTTTGGGATAAATTGA-AATGTTCAAA
1277234 AGTTTGGGGATGAAATTGAAATGTTCAAA
1 AGTTT-GGGAT-AAATTGAAATGTTCAAA
1277263 AGTTTG
1 AGTTTG
1277269 AGAATTAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
27 6 0.13
28 15 0.32
29 26 0.55
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.33
Consensus pattern (27 bp):
AGTTTGGGATAAATTGAAATGTTCAAA
Found at i:1277279 original size:57 final size:56
Alignment explanation
Indices: 1277176--1277285 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 56
1277166 GTATATACGT
* *
1277176 ATAGTTTGGGATAAAATTGGAATGTTCAAAAAGTTTGGGATCAATTTAGAATGGCC
1 ATAGTTTGGGATAAAATTGAAATGTTCAAAAAGTTTGGAATCAATTTAGAATGGCC
* * *
1277232 ATAGTTTGGGGATGAAATTGAAATGTTC-AAAAGTTTGAGAATTAATTTATAATG
1 ATAGTTT-GGGATAAAATTGAAATGTTCAAAAAGTTTG-GAATCAATTTAGAATG
1277286 ATAGTAATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
56 16 0.34
57 31 0.66
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.35
Consensus pattern (56 bp):
ATAGTTTGGGATAAAATTGAAATGTTCAAAAAGTTTGGAATCAATTTAGAATGGCC
Found at i:1280986 original size:2 final size:2
Alignment explanation
Indices: 1280979--1281007 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1280969 ATAGATGGGG
1280979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1281008 TAAATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1287508 original size:26 final size:23
Alignment explanation
Indices: 1287478--1287525 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 23
1287468 TATATGTTTA
1287478 GTACCTAAACTATTACTTTTGTTTTG
1 GTACCTAAACT-TTA-TTTT-TTTTG
1287504 GTACCTAAACTTTATTTTTTTT
1 GTACCTAAACTTTATTTTTTTT
1287526 AAATCATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 4 0.18
25 3 0.14
26 11 0.50
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (23 bp):
GTACCTAAACTTTATTTTTTTTG
Found at i:1290770 original size:22 final size:21
Alignment explanation
Indices: 1290730--1290771 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1290720 GAAAGTTACT
*
1290730 GTAGCAGGGTATCGATTCCCA
1 GTAGCAGGGAATCGATTCCCA
*
1290751 GTAGCAGGGGAATCGGTTCCC
1 GTAGCA-GGGAATCGATTCCC
1290772 CTTTTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.21
Consensus pattern (21 bp):
GTAGCAGGGAATCGATTCCCA
Found at i:1294038 original size:31 final size:31
Alignment explanation
Indices: 1294000--1294077 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
1293990 AGGGTCGAGG
*
1294000 GTTTACCTATGTTCTTTGGGACATATGGATT
1 GTTTACCTATGTTCTTTGGGACATATGGACT
*
1294031 GTTTACCTATGTTCTTTGGGACATATGGGCT
1 GTTTACCTATGTTCTTTGGGACATATGGACT
* *
1294062 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
1294078 CGGAATCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (31 bp):
GTTTACCTATGTTCTTTGGGACATATGGACT
Found at i:1294757 original size:12 final size:12
Alignment explanation
Indices: 1294739--1294772 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1294729 CGAAATTTTT
1294739 CACTGTTCATGG
1 CACTGTTCATGG
* *
1294751 TACTGTTCACGG
1 CACTGTTCATGG
1294763 CACTGTTCAT
1 CACTGTTCAT
1294773 ACAGTATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (12 bp):
CACTGTTCATGG
Found at i:1299267 original size:23 final size:23
Alignment explanation
Indices: 1299202--1299267 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
1299192 AAGGACTCGG
* *
1299202 GAACATGTTCATTTAATGTGCAC
1 GAACATGTTCATTTAACGTTCAC
*
1299225 GAACATGTTCATTTAGCGTTCAC
1 GAACATGTTCATTTAACGTTCAC
1299248 GAACATGTTCATTTAACGTT
1 GAACATGTTCATTTAACGTT
1299268 TATTTATCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (23 bp):
GAACATGTTCATTTAACGTTCAC
Found at i:1314467 original size:18 final size:18
Alignment explanation
Indices: 1314429--1314467 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1314419 AACAAGCTCA
*
1314429 TCATAAACTCTTTTCTCC
1 TCATAAACTCTTCTCTCC
* *
1314447 TCATCAACTCTTCTCTGC
1 TCATAAACTCTTCTCTCC
1314465 TCA
1 TCA
1314468 ACATGAGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.03, T:0.41
Consensus pattern (18 bp):
TCATAAACTCTTCTCTCC
Found at i:1324221 original size:16 final size:16
Alignment explanation
Indices: 1324185--1324245 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
1324175 TAATAAATAA
*
1324185 ACGAACATAAACGAAG
1 ACGAACATAAACGAAC
* *
1324201 TCGAAAATAAACGAAC
1 ACGAACATAAACGAAC
*
1324217 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1324233 ACGAACATAAACG
1 ACGAACATAAACG
1324246 TTGGAGACCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1325821 original size:14 final size:14
Alignment explanation
Indices: 1325804--1325834 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1325794 AGCGCACATA
*
1325804 AACGAACATAATCG
1 AACGAACATAAACG
1325818 AACGAACATAAACG
1 AACGAACATAAACG
1325832 AAC
1 AAC
1325835 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1325826 original size:24 final size:24
Alignment explanation
Indices: 1325799--1325845 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1325789 AAATGAGCGC
*
1325799 ACATAAACGAACATAATCGAACGA
1 ACATAAACGAACATAACCGAACGA
1325823 ACATAAACGAACATAACCGAACG
1 ACATAAACGAACATAACCGAACG
1325846 TTCACGAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.23, G:0.13, T:0.11
Consensus pattern (24 bp):
ACATAAACGAACATAACCGAACGA
Found at i:1330685 original size:2 final size:2
Alignment explanation
Indices: 1330680--1330719 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1330670 TTTAAAAAAT
1330680 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1330720 TTTCAAAGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1330864 original size:37 final size:37
Alignment explanation
Indices: 1330702--1331008 Score: 346
Period size: 37 Copynumber: 8.4 Consensus size: 37
1330692 TATATATATA
* **
1330702 TATATATATATATTATATTTTCAAAGACCGTTTT-ATAAAC
1 TATATAT-TATA-TATGTTTTCAAA-AATGTTTTCA-AAAC
* * *
1330742 TATATA--ATATATGCTTTCAAAGATGTTTTTTTAAAA-
1 TATATATTATATATGTTTTCAAAAATG--TTTTCAAAAC
* *
1330778 -ACTATATTATATATGTTTTCAAAAAT-ATTTAAAAAC
1 TA-TATATTATATATGTTTTCAAAAATGTTTTCAAAAC
* *
1330814 TATATA-T-TATATGTTTTCAACAACGTTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
1330849 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
* *
1330886 TATATATTATATACGTTTTCAAAAATGTTTTCAAAAT
1 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
* *
1330923 TATATATAATATATGTTTTCAAAAATATTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
*
1330960 TATATATTATATACG-TTT-AAAAATGTTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
1330995 TATATATTATATAT
1 TATATATTATATAT
1331009 TATATTTTCA
Statistics
Matches: 231, Mismatches: 25, Indels: 27
0.82 0.09 0.10
Matches are distributed among these distances:
34 15 0.06
35 53 0.23
36 22 0.10
37 118 0.51
38 17 0.07
40 6 0.03
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (37 bp):
TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
Found at i:1330878 original size:12 final size:12
Alignment explanation
Indices: 1330861--1330958 Score: 56
Period size: 12 Copynumber: 8.0 Consensus size: 12
1330851 TATATTATAT
1330861 ATGTTTTCAAAA
1 ATGTTTTCAAAA
1330873 ATGTTTTCAAAA
1 ATGTTTTCAAAA
* * * *
1330885 CTATATATT-ATAT
1 --ATGTTTTCAAAA
*
1330898 ACGTTTTCAAAA
1 ATGTTTTCAAAA
1330910 ATGTTTTCAAAA
1 ATGTTTTCAAAA
* * * *
1330922 TTATATAT-AATAT
1 ATGT-TTTCAA-AA
1330935 ATGTTTTCAAAA
1 ATGTTTTCAAAA
*
1330947 ATATTTTCAAAA
1 ATGTTTTCAAAA
1330959 CTATATATTA
Statistics
Matches: 61, Mismatches: 19, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
11 4 0.07
12 43 0.70
13 9 0.15
14 5 0.08
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:1331780 original size:201 final size:200
Alignment explanation
Indices: 1331409--1331989 Score: 682
Period size: 201 Copynumber: 2.9 Consensus size: 200
1331399 TGGCTTCTTG
* * * * * * *
1331409 TTGCCAAATCGTAGTCAACCTTGGTTTTCTTCTAGGCTTAAGGACTTCGGTTTAAAATTCAACCA
1 TTGCTAAATCGCAGCCAACCTAGGTATTCTTCTAGGCTTAAAGACTTCGGTTTAAAATTCAACCG
* * *** * *
1331474 AAAAGTAGTTCCTTGTTGCTACCATATGGTTGATACACCCTCGAGCTGAATAGAATCGAACTCGA
66 GAAAGTAGTTCCTTGCTGCTACCATGCAGTTGATACGCCCTCGAGCTGAATGGAATCGAACTCGA
* * * * * *
1331539 AAGTTTTTGTTGACAGATAACCCTTATCGCA-TTGAGCTATGCTGTAAATTAGGCTAGGAGATAT
131 AAATTTTTGTTGACATATAA--CTTTTCTCACTTGAGCTATGCTGTAAATTAGGCTAGGAAATAG
1331603 TTCCTCA
194 TTCCTCA
* * *
1331610 TTGTTAAATCGCAGCCAACCTAGGTCTTCTTCTAGGCTTAAAGTA-TTTGGTTTAAAATTCAACC
1 TTGCTAAATCGCAGCCAACCTAGGTATTCTTCTAGGCTTAAAG-ACTTCGGTTTAAAATTCAACC
*
1331674 GGAAAGTAGTTCCTTGCTGCTACCATGCAGTTGATACGCCCTCGAGCTGAATGGAATCAAACTCG
65 GGAAAGTAGTTCCTTGCTGCTACCATGCAGTTGATACGCCCTCGAGCTGAATGGAATCGAACTCG
** * * * * * *
1331739 AAAATTTTCATTGACATACAACTTTTCTCAACTTAAGCTATGTTGTAAATTTGGTTGGGAAATAG
130 AAAATTTTTGTTGACATATAACTTTTCTC-ACTTGAGCTATGCTGTAAATTAGGCTAGGAAATAG
**
1331804 TTCCTTG
194 TTCCTCA
* * * * *
1331811 TTGCTAAATCACAGCTAACCTAGGTATTTTTCTAGGCTTAAAGACATCAGTTTAAAATTCAACCG
1 TTGCTAAATCGCAGCCAACCTAGGTATTCTTCTAGGCTTAAAGACTTCGGTTTAAAATTCAACCG
* * *
1331876 GAAAGTAGTTCCTTGCTGTTACCATGCAGTTGATATGCCCTCGAGCTGAATGGAATCGAACT-AA
66 GAAAGTAGTTCCTTGCTGCTACCATGCAGTTGATACGCCCTCGAGCTGAATGGAATCGAACTCGA
** *
1331940 AAAGTTTTTGTTGACATATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT
131 AAA-TTTTTGTTGACATATAACTTTTCTC-ACTTGAGCTATGCTGTAAAT
1331990 GGTTTCTCTA
Statistics
Matches: 321, Mismatches: 54, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
199 6 0.02
200 6 0.02
201 308 0.96
202 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (200 bp):
TTGCTAAATCGCAGCCAACCTAGGTATTCTTCTAGGCTTAAAGACTTCGGTTTAAAATTCAACCG
GAAAGTAGTTCCTTGCTGCTACCATGCAGTTGATACGCCCTCGAGCTGAATGGAATCGAACTCGA
AAATTTTTGTTGACATATAACTTTTCTCACTTGAGCTATGCTGTAAATTAGGCTAGGAAATAGTT
CCTCA
Found at i:1349695 original size:20 final size:21
Alignment explanation
Indices: 1349646--1349696 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1349636 TTATTTTGAG
1349646 TATATGTATTT-AATATACATA
1 TATATGT-TTTGAATATACATA
1349667 TATATGTTTTGAATAT-CATA
1 TATATGTTTTGAATATACATA
1349687 TGATA-GTTTT
1 T-ATATGTTTT
1349697 ACTTGAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (21 bp):
TATATGTTTTGAATATACATA
Found at i:1351808 original size:2 final size:2
Alignment explanation
Indices: 1351801--1351832 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1351791 TTTGAAAAAT
1351801 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1351833 TTTCAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1351859 original size:32 final size:32
Alignment explanation
Indices: 1351821--1352005 Score: 97
Period size: 35 Copynumber: 5.3 Consensus size: 32
1351811 TATATATATA
1351821 TATATATTATATTTTCAAAAACCGTTTTATAAAC
1 TATATA-TATATTTTCAAAAA-CGTTTTATAAAC
* * *
1351855 TATATAATATATGCTTTCAAAGATGTTTTTTAAAC
1 TATAT-ATATAT--TTTCAAAAACGTTTTATAAAC
* * *
1351890 TATATATATGTTTTCAAAAA--TATTTAAAAAT
1 TATATATATATTTTCAAAAACGT-TTTATAAAC
* * * *
1351921 TATATATTATACGTTTTTAACAACATTTTCAAAAAC
1 TATATA-TATA--TTTTCAAAAACGTTTT-ATAAAC
*
1351957 TATATATTATATATGATTTCAAAAATGTTTTCA-AAAC
1 --TATA-TATATAT--TTTCAAAAACGTTTT-ATAAAC
1351994 TATATATTATAT
1 TATATA-TATAT
1352006 ACGTTTTTAA
Statistics
Matches: 119, Mismatches: 16, Indels: 31
0.72 0.10 0.19
Matches are distributed among these distances:
30 1 0.01
31 12 0.10
32 11 0.09
34 25 0.21
35 28 0.24
36 15 0.13
37 4 0.03
38 21 0.18
39 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (32 bp):
TATATATATATTTTCAAAAACGTTTTATAAAC
Found at i:1351873 original size:36 final size:33
Alignment explanation
Indices: 1351821--1352005 Score: 108
Period size: 34 Copynumber: 5.4 Consensus size: 33
1351811 TATATATATA
*
1351821 TATATATTATATTTTCAAAAACCGTTTTATAAAC
1 TATATAATATATTTTCAAAAA-CGTTTTATAAAC
* * *
1351855 TATATAATATATGCTTTCAAAGATGTTTTTTAAAC
1 TATATAATATAT--TTTCAAAAACGTTTTATAAAC
* * *
1351890 TATAT-ATATGTTTTCAAAAA--TATTTAAAAAT
1 TATATAATATATTTTCAAAAACGT-TTTATAAAC
* * * * *
1351921 TATATATTATACGTTTTTAACAACATTTTCAAAAAC
1 TATATAATATA--TTTTCAAAAACGTTTT-ATAAAC
*
1351957 TATATATTATATATGATTTCAAAAATGTTTTCA-AAAC
1 TATATA--ATATAT--TTTCAAAAACGTTTT-ATAAAC
*
1351994 TATATATTATAT
1 TATATAATATAT
1352006 ACGTTTTTAA
Statistics
Matches: 118, Mismatches: 20, Indels: 25
0.72 0.12 0.15
Matches are distributed among these distances:
30 1 0.01
31 11 0.09
32 11 0.09
34 24 0.20
35 23 0.19
36 21 0.18
37 10 0.08
38 17 0.14
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (33 bp):
TATATAATATATTTTCAAAAACGTTTTATAAAC
Found at i:1352001 original size:37 final size:37
Alignment explanation
Indices: 1351832--1352080 Score: 232
Period size: 37 Copynumber: 6.9 Consensus size: 37
1351822 ATATATTATA
* *
1351832 TTTTCAAAAACCGTTTT-ATAAACTATATA--ATATATG
1 TTTTCAAAAA-TGTTTTCA-AAACTATATATTATATACG
* * **
1351868 CTTTCAAAGATGTTTTTTAAAC--TATA-TATAT--G
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
* * *
1351900 TTTTCAAAAAT-ATTTAAAAATTATATA-T-TATACG
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
* * ** *
1351934 TTTTTAACAACATTTTCAAAAACTATATATTATATATG
1 TTTTCAAAAATGTTTTC-AAAACTATATATTATATACG
*
1351972 ATTTCAAAAATGTTTTCAAAACTATATATTATATACG
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
* *
1352009 TTTTTAAAAATGTTTTCAAAATTATATATTATATACG
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
*
1352046 TTTTCAAAAATATTTTCAAAACTATATATTATATA
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATA
1352081 TTATATTATC
Statistics
Matches: 174, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
31 6 0.03
32 13 0.07
33 9 0.05
34 13 0.07
35 12 0.07
36 18 0.10
37 86 0.49
38 17 0.10
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
Found at i:1352062 original size:74 final size:75
Alignment explanation
Indices: 1351892--1352080 Score: 269
Period size: 74 Copynumber: 2.6 Consensus size: 75
1351882 TTTTAAACTA
* * *
1351892 TATATATGTTTTCAAAAATA-TTTAAAAATTATATA-T-TATACGTTTTTAACAACATTTTCAAA
1 TATATATGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTTAAAAACATTTTCAAA
1351954 AACTATATAT
66 AACTATATAT
* * **
1351964 TATATATGATTTCAAAAATGTTTTCAAAACTATATATTATATACGTTTTTAAAAATGTTTTC-AA
1 TATATATGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTTAAAAACATTTTCAAA
*
1352028 AATTATATAT
66 AACTATATAT
*
1352038 TATATACGTTTTCAAAAATATTTTCAAAACTATATATTATATA
1 TATATATGTTTTCAAAAATATTTTCAAAACTATATATTATATA
1352081 TTATATTATC
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
72 18 0.17
73 13 0.13
74 52 0.50
75 20 0.19
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (75 bp):
TATATATGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTTAAAAACATTTTCAAA
AACTATATAT
Found at i:1358437 original size:2 final size:2
Alignment explanation
Indices: 1358430--1358516 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
1358420 TGCACTTTAT
1358430 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
1358472 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
1358514 TC T
1 TC T
1358517 TCCCCAAAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1359141 original size:30 final size:29
Alignment explanation
Indices: 1359073--1359154 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
1359063 TTAAGAGTAT
* *
1359073 ACTCATAATAATAAATATTAAAAAAATGG
1 ACTCATAATAATAAATAATAAAAAAATAG
*
1359102 ACTTC-TAATAA-AAAGTACATAAAAAATTAG
1 AC-TCATAATAATAAA-TA-ATAAAAAAATAG
1359132 ACTCATAATAATAACA-AATAAAA
1 ACTCATAATAATAA-ATAATAAAA
1359155 TTTAGAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
28 3 0.07
29 18 0.41
30 20 0.45
31 2 0.05
32 1 0.02
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.26
Consensus pattern (29 bp):
ACTCATAATAATAAATAATAAAAAAATAG
Found at i:1363693 original size:23 final size:21
Alignment explanation
Indices: 1363666--1363713 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1363656 ATTTTAATTA
1363666 AATTACATTTTTAACTAATTTAT
1 AATTACA-TTTTAA-TAATTTAT
* *
1363689 AATTATATTTTAATACTTTAT
1 AATTACATTTTAATAATTTAT
1363710 AATT
1 AATT
1363714 TAACGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 6 0.26
23 6 0.26
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTACATTTTAATAATTTAT
Found at i:1364229 original size:10 final size:10
Alignment explanation
Indices: 1364214--1364240 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1364204 TTGACTTTAG
1364214 ATTAATATAA
1 ATTAATATAA
1364224 ATTAATATAA
1 ATTAATATAA
1364234 ATTAATA
1 ATTAATA
1364241 CTTCAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTAATATAA
Found at i:1368092 original size:28 final size:30
Alignment explanation
Indices: 1368059--1368122 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
1368049 ATGTTTTGTT
*
1368059 TATTAAATTT-TTAAA-AGTTATAAAATAG
1 TATTAAATTTATTAAATAATTATAAAATAG
1368087 TATTAAATTTATTAAATAATTATAAAATAG
1 TATTAAATTTATTAAATAATTATAAAATAG
1368117 TCATTA
1 T-ATTA
1368123 TAATAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 10 0.31
29 5 0.16
30 13 0.41
31 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (30 bp):
TATTAAATTTATTAAATAATTATAAAATAG
Found at i:1368146 original size:11 final size:11
Alignment explanation
Indices: 1368130--1368178 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
1368120 TTATAATAAA
1368130 TTATAAAATTT
1 TTATAAAATTT
1368141 TTATAAAA--T
1 TTATAAAATTT
1368150 TTA-AAAATTAT
1 TTATAAAATT-T
*
1368161 TTATAACATTT
1 TTATAAAATTT
1368172 TTATAAA
1 TTATAAA
1368179 TTAATGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
8 4 0.12
9 4 0.12
11 19 0.59
12 5 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
TTATAAAATTT
Found at i:1368156 original size:19 final size:21
Alignment explanation
Indices: 1368120--1368181 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
1368110 AAAATAGTCA
*
1368120 TTATAATAAATTATAAAATT-T
1 TTATAA-AATTTATAAAATTAT
1368141 TTATAAAATTTA-AAAATTAT
1 TTATAAAATTTATAAAATTAT
* *
1368161 TTATAACATTTTTATAAATTA
1 TTATAAAATTTATA-AAATTA
1368182 ATGGTCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 6 0.17
20 16 0.46
21 7 0.20
22 6 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATAAAATTTATAAAATTAT
Found at i:1368808 original size:23 final size:23
Alignment explanation
Indices: 1368743--1368827 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
1368733 TGAACTTATT
*
1368743 TATTTTCTAAAAATAAA-AAAAAA
1 TATTTT-TAAAAATAAATATAAAA
*
1368766 TATTTTTAAAATTTAAATATAAAA
1 TATTTTTAAAA-ATAAATATAAAA
*
1368790 TA-TTTTAATAAATAAATATTAAA
1 TATTTTTAA-AAATAAATATAAAA
* *
1368813 -ATTATTAAAATTAAA
1 TATTTTTAAAAATAAA
1368828 AAATAAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
22 12 0.23
23 31 0.60
24 9 0.17
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
TATTTTTAAAAATAAATATAAAA
Found at i:1372114 original size:27 final size:27
Alignment explanation
Indices: 1372084--1372137 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1372074 AATGAATTTT
*
1372084 TTTTTCATTTTAATAATTTTAAGAAAA
1 TTTTCCATTTTAATAATTTTAAGAAAA
**
1372111 TTTTCCATTTTAATTTTTTTAAGAAAA
1 TTTTCCATTTTAATAATTTTAAGAAAA
1372138 CTTCAAGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTTCCATTTTAATAATTTTAAGAAAA
Found at i:1378493 original size:3 final size:3
Alignment explanation
Indices: 1378487--1378511 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1378477 TCAAAATCAT
1378487 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
1378512 AACCCTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1384562 original size:19 final size:19
Alignment explanation
Indices: 1384513--1384562 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
1384503 TTTTAATCCC
*
1384513 TTATTATTCTATATATTTAA
1 TTATTATT-TTTATATTTAA
1384533 TTA-TATCTTTTATCATTT-A
1 TTATTAT-TTTTAT-ATTTAA
1384552 TTATTATTTTT
1 TTATTATTTTT
1384563 CTTTATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTATTTTTATATTTAA
Found at i:1384638 original size:2 final size:2
Alignment explanation
Indices: 1384628--1384663 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1384618 CATTATTTTT
1384628 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1384664 TTAACTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1384696 original size:8 final size:8
Alignment explanation
Indices: 1384685--1384724 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1384675 TTCCTATTTG
1384685 TTTTCTAT
1 TTTTCTAT
1384693 TTTTCTAT
1 TTTTCTAT
1384701 TTTTCTAT
1 TTTTCTAT
*
1384709 TTTT-GAT
1 TTTTCTAT
1384716 TTTT-TAT
1 TTTTCTAT
1384723 TT
1 TT
1384725 ATTACTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 10 0.33
8 20 0.67
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (8 bp):
TTTTCTAT
Found at i:1384896 original size:31 final size:31
Alignment explanation
Indices: 1384827--1384896 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
1384817 CACATTTTAT
1384827 TTTA-TTTTTTATTTTCTCTTCTTTATTGTA
1 TTTATTTTTTTATTTTCTCTTCTTTATTGTA
*
1384857 TTTGTTTTTTTATTTTACT-TTCTTTATT-TCA
1 TTTATTTTTTTATTTT-CTCTTCTTTATTGT-A
1384888 TTTATTTTT
1 TTTATTTTT
1384897 GCTACTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 4 0.11
31 29 0.83
32 2 0.06
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.76
Consensus pattern (31 bp):
TTTATTTTTTTATTTTCTCTTCTTTATTGTA
Found at i:1388936 original size:99 final size:99
Alignment explanation
Indices: 1388765--1388969 Score: 295
Period size: 99 Copynumber: 2.1 Consensus size: 99
1388755 CGTATACCCA
* *
1388765 GATTATTATATATACACAATAAAGCTTGAACTGTCCCTCTAGAACAATTGGTTAAATGCCCCGTC
1 GATTATAATATATACACAATAAAGCTTGAACTGTCCCTCTAGAACAATTGGTTAAATGCCCCGAC
* *
1388830 TTTATGGATAAGATTCAGTTAGCCTGATAAAGGT
66 TTTATGGATAAGATTCAGCTAACCTGATAAAGGT
* * * * *
1388864 GATTATAATATCTATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAATGCCTCGA
1 GATTATAATATATACACAATAAAGCTTGAACTGTCCCTCTAGA-ACAATTGGTTAAATGCCCCGA
*
1388928 CTTTATGGATAAGATTCAGCTAACCTGATAAAGTT
65 CTTTATGGATAAGATTCAGCTAACCTGATAAAGGT
*
1388963 GTTTATA
1 GATTATA
1388970 TATTGAGTTG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 1 0.01
99 93 0.99
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (99 bp):
GATTATAATATATACACAATAAAGCTTGAACTGTCCCTCTAGAACAATTGGTTAAATGCCCCGAC
TTTATGGATAAGATTCAGCTAACCTGATAAAGGT
Found at i:1390005 original size:64 final size:64
Alignment explanation
Indices: 1389904--1390391 Score: 751
Period size: 64 Copynumber: 7.6 Consensus size: 64
1389894 TGTAGCTTTT
* ** *
1389904 AGAGTCAATTTTAACTTCACAACGAAGGATATTGGACTCAACAAATGACTTTCCAGTTTTATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
** *
1389968 AGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAACAATTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * * * *
1390032 AGAGTCAATTTCAACTTCACAGCTAAGGATATTAGACTTAACAAACGACTTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAAC-TTTCCAGTTTCATTC
* * * * *
1390097 AGAGTCAATTTGAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAATTTCATTT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
*
1390161 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTCCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
1390225 AGAGTCGATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
*
1390289 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTTATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
1390353 AGAGTCAATTTCAACTTCACAGCGAAGGATATTTGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
1390392 GAAACAATGC
Statistics
Matches: 388, Mismatches: 35, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
64 330 0.85
65 58 0.15
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:1390557 original size:121 final size:121
Alignment explanation
Indices: 1390415--1391725 Score: 1938
Period size: 121 Copynumber: 10.8 Consensus size: 121
1390405 TTACACAATA
* * *
1390415 TTGGATTTCAACTTCATGACGAAGGATATCCAATTTAAAGCTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* * * ** * **
1390480 CCACGATTTCAACTTCACAATGAAGGATATCGTGCCCACAAGAAGCAACACATCTA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* * * * * *
1390536 TTGGATTTCAACTTCACGACGAATGATATCAAATTCAAAGCTTAAATTCATAACGAAAGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* *
1390601 CCACGATTTCAACTTCACGATGAAGGATATCATGCCCACAAGCAGCAATGCAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* * ** *
1390657 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAAGCTCAATTTCACAACGAATAAGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* * *
1390722 CCACGATTTCAACTTCATGACGAAGGATATCGTGGCCACAAGCAGAAATGCAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
*
1390778 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* *
1390843 CCACGATTTCAACTTCATGACGAAGGATATCGTGCCCACAAGCAACAATGCAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* * * **
1390899 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAAGCTCAACTTCACAATGAATGAGCTGT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* * *
1390964 CCACGATTTCAACTTCATGACGAAGGATATCGTGTCCACAAGCAGCAATACAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* * *
1391020 TTGGATTTCAACTTCACGAAGAACGATATCTAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* * ** *
1391085 CCACGATTTCAACTTCACGACGAAGGATATCATGCCCACAAGTAATAATACAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* *
1391141 TTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* * *
1391206 CCACGATTTCAAATTCACGACGAAGGATATCGTGCCCACAAGGAGCGATGCAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* * * *
1391262 TTGTATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCATAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* * * *
1391327 CCACGATTTCAATTTCACGATGAAGGATATCGTGTCCACAAGCAGTAATGCAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* *
1391383 TTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* * *
1391448 CCATGATTTCAAATTCACGACGAAGGATATCGTGCCCACAAGCAGCGATGCAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* * *
1391504 TTGGATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCATAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* * *
1391569 CCACGATTTCAACTTCACGATGAAGGATATCGTGTCCACAAGCAGTAATGCAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
* * * * *
1391625 TTAGATTTCAACTTCACGACGAAGGATATCCAATTCAAAACTCAACTTTACAACGAATGAGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
*
1391690 CTACGATTTCAACTTCACGACGAAGGATATCGTGCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCC
1391726 TAACGGAACA
Statistics
Matches: 1071, Mismatches: 119, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 1071 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (121 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
Found at i:1390792 original size:55 final size:55
Alignment explanation
Indices: 1390726--1390928 Score: 151
Period size: 55 Copynumber: 3.5 Consensus size: 55
1390716 AGTCATCCAC
1390726 GATTTCAACTTCATGACGAAGGATATCGTGGCCACAAGCAGAAATGCAACCCTTG
1 GATTTCAACTTCATGACGAAGGATATCGTGGCCACAAGCAGAAATGCAACCCTTG
* * * * * ** * *
1390781 GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCA-CAACGAAGGAGCCATCC
1 GATTTCAACTTCATGACGAAGGATAT-C--GT---GGC-C-AC--AAGC-A-GAA-ATGCAACCC
**
1390845 -AC
53 TTG
*
1390847 GATTTCAACTTCATGACGAAGGATATCGTGCCCACAAGCA-ACAATGCAACCCTTG
1 GATTTCAACTTCATGACGAAGGATATCGTGGCCACAAGCAGA-AATGCAACCCTTG
1390902 GATTTCAACTTCATGACGAAGGATATC
1 GATTTCAACTTCATGACGAAGGATATC
1390929 CAATTCAAAG
Statistics
Matches: 109, Mismatches: 23, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
54 6 0.06
55 52 0.48
56 3 0.03
57 1 0.01
58 3 0.03
59 1 0.01
60 1 0.01
61 2 0.02
62 1 0.01
63 3 0.03
64 1 0.01
65 3 0.03
66 27 0.25
67 5 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (55 bp):
GATTTCAACTTCATGACGAAGGATATCGTGGCCACAAGCAGAAATGCAACCCTTG
Found at i:1391344 original size:66 final size:66
Alignment explanation
Indices: 1391266--1391598 Score: 212
Period size: 66 Copynumber: 5.4 Consensus size: 66
1391256 CAACCCTTGT
1391266 ATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCATAACGAAGGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCATAACGAAGGAGCCATCCAC
1391331 G
66 G
* * * ** * * *
1391332 ATTTCAATTTCACGATGAAGGATA-TC--GT----G-TCCACAAGCAGTAATGCA--A-CC--CT
1 ATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCAC-TTCA-TAACGAAGGAGCCATCC
**
1391384 TGG
64 ACG
* * * * * *
1391387 ATTTCAACTTCATGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCAT
1 ATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCATAACGAAGGAGCCATCCAC
1391452 G
66 G
* * * * * * * * **
1391453 ATTTCAAATTCACGACGAAGGATA-TC--GT----GC-CCAC--AAGCAGCGATGCAACC--CTT
1 ATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCA-TAACGAAGGAGCCATCCA
*
1391506 GG
65 CG
1391508 ATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCATAACGAAGGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCATAACGAAGGAGCCATCCAC
1391573 G
66 G
*
1391574 ATTTCAACTTCACGATGAAGGATAT
1 ATTTCAACTTCACGACGAAGGATAT
1391599 CGTGTCCACA
Statistics
Matches: 190, Mismatches: 49, Indels: 56
0.64 0.17 0.19
Matches are distributed among these distances:
55 49 0.26
56 4 0.02
57 11 0.06
58 11 0.06
59 5 0.03
60 5 0.03
61 4 0.02
62 5 0.03
63 11 0.06
64 10 0.05
65 4 0.02
66 71 0.37
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (66 bp):
ATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCCACTTCATAACGAAGGAGCCATCCAC
G
Found at i:1392536 original size:11 final size:11
Alignment explanation
Indices: 1392520--1392544 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1392510 AAAGCATGTG
1392520 TATATATATTA
1 TATATATATTA
1392531 TATATATATTA
1 TATATATATTA
1392542 TAT
1 TAT
1392545 GTATTATTGT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATATTA
Found at i:1393321 original size:30 final size:30
Alignment explanation
Indices: 1393286--1393352 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1393276 CGGCCGACGA
* *
1393286 GGCGGCGAGTGGCTGTGTTTTGGAAAACAC
1 GGCGGCGAGTGGCCGTGTTCTGGAAAACAC
1393316 GGCGGCGAGTGGCCGTGTTCTGGAAAACAC
1 GGCGGCGAGTGGCCGTGTTCTGGAAAACAC
*
1393346 GACGGCG
1 GGCGGCG
1393353 TGTTCATCCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.42, T:0.18
Consensus pattern (30 bp):
GGCGGCGAGTGGCCGTGTTCTGGAAAACAC
Found at i:1393916 original size:28 final size:27
Alignment explanation
Indices: 1393873--1393929 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1393863 TTCTTTTGTC
*
1393873 TTTATTATTATTATTATTATATTTATT
1 TTTATTATTATTATTATTATAATTATT
*
1393900 TTTATTTATT-TTAATTATTTTAATTATT
1 TTTA-TTATTATT-ATTATTATAATTATT
1393928 TT
1 TT
1393930 AAGTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTATTATTATTATTATTATAATTATT
Found at i:1393938 original size:9 final size:9
Alignment explanation
Indices: 1393876--1393931 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
1393866 TTTTGTCTTT
1393876 ATTATTATT-
1 ATTATT-TTA
*
1393885 ATTATTATA
1 ATTATTTTA
*
1393894 TTTATTTTTA
1 ATTA-TTTTA
*
1393904 TTTATTTTA
1 ATTATTTTA
1393913 ATTATTTTA
1 ATTATTTTA
1393922 ATTATTTTA
1 ATTATTTTA
1393931 A
1 A
1393932 GTTTTTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 1 0.02
9 32 0.78
10 8 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTATTTTA
Found at i:1393939 original size:19 final size:18
Alignment explanation
Indices: 1393898--1393939 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1393888 ATTATATTTA
*
1393898 TTTTTATTTATTTTAATT
1 TTTTTAATTATTTTAATT
*
1393916 ATTTTAATTATTTTAAGTT
1 TTTTTAATTATTTTAA-TT
1393935 TTTTT
1 TTTTT
1393940 CTTTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTAATTATTTTAATT
Found at i:1393939 original size:28 final size:28
Alignment explanation
Indices: 1393877--1393939 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
1393867 TTTGTCTTTA
* *
1393877 TTATTATT-ATTATTATATTTATTTTTAT
1 TTATT-TTAATTATTATAATTATTTTAAT
*
1393905 TTATTTTAATTATTTTAATTATTTTAAGT
1 TTATTTTAATTATTATAATTATTTTAA-T
1393934 TT-TTTT
1 TTATTTT
1393940 CTTTTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.07
28 25 0.83
29 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (28 bp):
TTATTTTAATTATTATAATTATTTTAAT
Found at i:1393990 original size:31 final size:31
Alignment explanation
Indices: 1393941--1394006 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1393931 AGTTTTTTTC
* *
1393941 TTTTTTCTTTTCTCTTCTTTATTGCATTTGT
1 TTTTTTATTTTCTCTTCTTTATTGCATTTAT
*
1393972 TTTTTTATTTTACT-TTCTTTATTTCATTTAT
1 TTTTTTATTTT-CTCTTCTTTATTGCATTTAT
1394003 TTTT
1 TTTT
1394007 GCTACTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.11, C:0.12, G:0.03, T:0.74
Consensus pattern (31 bp):
TTTTTTATTTTCTCTTCTTTATTGCATTTAT
Found at i:1394863 original size:30 final size:27
Alignment explanation
Indices: 1394809--1394863 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
1394799 AAAATAATTT
**
1394809 TATTTTATATATTTTATATTAATATAA
1 TATTTTATATATTTTATAAAAATATAA
1394836 TATTTTAGTATCATTTTAATAAAAATAT
1 TATTTTA-TAT-ATTTT-ATAAAAATAT
1394864 TAATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 3 0.13
29 5 0.22
30 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTTTATATATTTTATAAAAATATAA
Found at i:1394895 original size:22 final size:22
Alignment explanation
Indices: 1394858--1394910 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1394848 ATTTTAATAA
1394858 AAATATTAATTATTAACATAATT
1 AAATA-TAATTATTAACATAATT
* * *
1394881 AAATATATTTATTAATATTATT
1 AAATATAATTATTAACATAATT
1394903 ATAATATA
1 A-AATATA
1394911 CTCATTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATATAATTATTAACATAATT
Found at i:1394920 original size:22 final size:23
Alignment explanation
Indices: 1394869--1394932 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
1394859 AATATTAATT
* * * *
1394869 ATTAACATAATTA-AATATATTT
1 ATTAATATTATTATAATATACTC
1394891 ATTAATATTATTATAATATACTC
1 ATTAATATTATTATAATATACTC
*
1394914 ATT-ATATTATAATAATATA
1 ATTAATATTATTATAATATA
1394933 TGATACTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 26 0.72
23 10 0.28
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTAATATTATTATAATATACTC
Found at i:1395057 original size:27 final size:29
Alignment explanation
Indices: 1395009--1395073 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
1394999 AATTTCTTAA
1395009 AAAATAATATTATTGAATTA-TTAATAGT
1 AAAATAATATTATTGAATTATTTAATAGT
* *
1395037 AAAA-AATATTATT-TATATATTTAATATT
1 AAAATAATATTATTGAAT-TATTTAATAGT
*
1395065 AATATAATA
1 AAAATAATA
1395074 ATCAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.06
27 11 0.35
28 14 0.45
29 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
AAAATAATATTATTGAATTATTTAATAGT
Found at i:1395278 original size:14 final size:14
Alignment explanation
Indices: 1395234--1395280 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1395224 AAAATACTAG
*
1395234 AAATAATATTTTAAT
1 AAATAATA-TTAAAT
*
1395249 -AATAATATTAGTAT
1 AAATAATATTA-AAT
1395263 AAATAATATTAAAT
1 AAATAATATTAAAT
1395277 AAAT
1 AAAT
1395281 TATTCTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 2 0.07
14 15 0.56
15 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:1396331 original size:3 final size:3
Alignment explanation
Indices: 1396323--1396356 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1396313 AAGTTATAAT
1396323 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1396357 ATTTCTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1397294 original size:14 final size:14
Alignment explanation
Indices: 1397275--1397302 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1397265 CTTATGTGAT
1397275 TTGTACAATAATTA
1 TTGTACAATAATTA
1397289 TTGTACAATAATTA
1 TTGTACAATAATTA
1397303 GCATATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTGTACAATAATTA
Found at i:1403232 original size:22 final size:22
Alignment explanation
Indices: 1403204--1403369 Score: 287
Period size: 22 Copynumber: 7.5 Consensus size: 22
1403194 TTCAGTATTT
1403204 GTCCCGAAGGACCATTGGATAC
1 GTCCCGAAGGACCATTGGATAC
1403226 GTCCCGAAGGACCATTGGATAC
1 GTCCCGAAGGACCATTGGATAC
*
1403248 GTCCTGAAGGACCATTGGATAC
1 GTCCCGAAGGACCATTGGATAC
1403270 GTCCCGAAGGACCATTGGATAC
1 GTCCCGAAGGACCATTGGATAC
*
1403292 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCATTGGATAC
* *
1403314 GTCCCGAAGGATCACTGGATAC
1 GTCCCGAAGGACCATTGGATAC
*
1403336 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCATTGGATAC
1403358 GTCCCGAAGGAC
1 GTCCCGAAGGAC
1403370 TCATATACCC
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 139 1.00
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (22 bp):
GTCCCGAAGGACCATTGGATAC
Found at i:1409162 original size:22 final size:22
Alignment explanation
Indices: 1409130--1409229 Score: 173
Period size: 22 Copynumber: 4.5 Consensus size: 22
1409120 TTCAGTATTT
1409130 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
1409152 GTCTCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
1409174 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
**
1409196 GTCCCGTTGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
1409218 GTCCCGAAGGAC
1 GTCCCGAAGGAC
1409230 TAATATACCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:1421140 original size:2 final size:2
Alignment explanation
Indices: 1421133--1421161 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1421123 TATGGTAAGG
1421133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1421162 CGTAGGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1422040 original size:44 final size:43
Alignment explanation
Indices: 1421947--1422040 Score: 107
Period size: 44 Copynumber: 2.2 Consensus size: 43
1421937 TACCATTATA
* * * * *
1421947 AAGGAAGTATCGGTACTGTACTTGGGTACCGATACTATTAAAT
1 AAGGAAATATCGATACTGTACATGGGTACAGACACTATTAAAT
* * *
1421990 AGGGAAATATCGATACTGTACCATGGGTAGAGACACTATTTAAT
1 AAGGAAATATCGATACTGTA-CATGGGTACAGACACTATTAAAT
1422034 AAGGAAA
1 AAGGAAA
1422041 ATGTGAATTA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
43 17 0.41
44 24 0.59
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (43 bp):
AAGGAAATATCGATACTGTACATGGGTACAGACACTATTAAAT
Found at i:1422663 original size:23 final size:22
Alignment explanation
Indices: 1422626--1422703 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 22
1422616 TTCTTATGGA
**
1422626 CATTTTATATGGCACTTCGGTG
1 CATTTTATGCGGCACTTCGGTG
*
1422648 CATTTCTATGCGGCACTTCGGTA
1 CATTT-TATGCGGCACTTCGGTG
* *
1422671 CAATTTTACGTGGCACTTCGGTG
1 C-ATTTTATGCGGCACTTCGGTG
1422694 CATTTATATG
1 CATTT-TATG
1422704 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.20
23 33 0.72
24 4 0.09
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (22 bp):
CATTTTATGCGGCACTTCGGTG
Found at i:1428177 original size:2 final size:2
Alignment explanation
Indices: 1428170--1428200 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1428160 TATGGTAAGG
1428170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1428201 CACGTGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1429059 original size:44 final size:44
Alignment explanation
Indices: 1428988--1429082 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 44
1428978 TACCATTATA
* * *
1428988 AAGGAAGTATCGGTACTGTACCTTGGGTACCGATACTATTAAAT
1 AAGGAAATATCGATACTGTACCCTGGGTACCGATACTATTAAAT
* *
1429032 AGGGAAATATCGATACTGTACCCTGGGTACCGATACTATTTAAT
1 AAGGAAATATCGATACTGTACCCTGGGTACCGATACTATTAAAT
1429076 AAGGAAA
1 AAGGAAA
1429083 ATATGAATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (44 bp):
AAGGAAATATCGATACTGTACCCTGGGTACCGATACTATTAAAT
Found at i:1429591 original size:21 final size:19
Alignment explanation
Indices: 1429567--1429618 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 19
1429557 ATATATGTAA
1429567 TCCTTTGGAACATATATACGG
1 TCCTTTGGAACATAT-T-CGG
*
1429588 TCCTTTGAGACACATATTTGG
1 TCCTTTG-GA-ACATATTCGG
1429609 TCCTTTGGAA
1 TCCTTTGGAA
1429619 TATGTATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 16 0.57
22 3 0.11
23 6 0.21
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (19 bp):
TCCTTTGGAACATATTCGG
Found at i:1429630 original size:21 final size:20
Alignment explanation
Indices: 1429567--1429630 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
1429557 ATATATGTAA
*
1429567 TCCTTTGGAACATATATACGG
1 TCCTTTGGAACAT-TATATGG
*
1429588 TCCTTTGAGACACA-TATTTGG
1 TCCTTTG-GA-ACATTATATGG
*
1429609 TCCTTTGGAATATGTATATGG
1 TCCTTTGGAACAT-TATATGG
1429630 T
1 T
1429631 TCTTAAGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 26 0.74
22 2 0.06
23 3 0.09
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (20 bp):
TCCTTTGGAACATTATATGG
Found at i:1429658 original size:23 final size:21
Alignment explanation
Indices: 1429625--1429667 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
1429615 GGAATATGTA
*
1429625 TATGGTTCTTAAGGAGATTTC
1 TATGGTTCTTAAGGACATTTC
*
1429646 TATGTGTTCCTTATGGACATTT
1 TATG-GTT-CTTAAGGACATTT
1429668 TATATGACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (21 bp):
TATGGTTCTTAAGGACATTTC
Found at i:1429702 original size:23 final size:23
Alignment explanation
Indices: 1429675--1429740 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
1429665 TTTTATATGA
1429675 CACTTCGGTGCATTTCTACGCGG
1 CACTTCGGTGCATTTCTACGCGG
* *
1429698 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
* *
1429721 CACTTCAGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
1429741 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:1432696 original size:40 final size:39
Alignment explanation
Indices: 1432615--1432706 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
1432605 TTTTCTTCAG
* *
1432615 TTTTTACATTTCATTTCGAAATAACAATCCATTTAATTT
1 TTTTTATATTTCATTTCGAAATAACAATACATTTAATTT
* * *
1432654 TTTTTATAGTTTCATTTCGAAATAATAATAATATTTGATTT
1 TTTTTATA-TTTCATTTCGAAATAACAAT-ACATTTAATTT
1432695 TTTTTA-ATTTCA
1 TTTTTATATTTCA
1432707 GAATAATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 12 0.26
40 20 0.43
41 14 0.30
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (39 bp):
TTTTTATATTTCATTTCGAAATAACAATACATTTAATTT
Found at i:1433348 original size:28 final size:28
Alignment explanation
Indices: 1433302--1433362 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1433292 ACTGCACCTT
* *
1433302 TTATTTTTATTTATTTTTGTTTTGGTAC
1 TTATTTTTATTTATTTTTGATTTAGTAC
*
1433330 TTATTTTTATTT-TATTTTGATTTAGTCC
1 TTATTTTTATTTAT-TTTTGATTTAGTAC
1433358 TTATT
1 TTATT
1433363 AGTCTTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.70
Consensus pattern (28 bp):
TTATTTTTATTTATTTTTGATTTAGTAC
Found at i:1433481 original size:16 final size:16
Alignment explanation
Indices: 1433460--1433506 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1433450 AATTTAGTCC
1433460 TTATATTTAAATTTTA
1 TTATATTTAAATTTTA
*
1433476 TTATATTTAGATTCTTA
1 TTATATTTAAATT-TTA
*
1433493 -TATATTTTAATTTT
1 TTATATTTAAATTTT
1433507 CTTTATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 22 0.81
17 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATATTTAAATTTTA
Found at i:1446156 original size:2 final size:2
Alignment explanation
Indices: 1446149--1446226 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
1446139 CATTTATCCT
1446149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1446191 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1446227 CCATTGTTGT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1446535 original size:7 final size:7
Alignment explanation
Indices: 1446519--1446573 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 7
1446509 CATCCATCAG
1446519 AAAA-AA
1 AAAAGAA
1446525 AAAAGAAA
1 AAAAG-AA
1446533 AAAAGAGA
1 AAAAGA-A
1446541 AAAGAGAA
1 AAA-AGAA
*
1446549 AAGAGAA
1 AAAAGAA
1446556 AAAA-AA
1 AAAAGAA
1446562 AAAGAGAA
1 AAA-AGAA
1446570 AAAA
1 AAAA
1446574 AAGAAATTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
6 9 0.22
7 10 0.24
8 19 0.46
9 3 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1446550 original size:14 final size:14
Alignment explanation
Indices: 1446525--1446575 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
1446515 TCAGAAAAAA
1446525 AAAAGAAAAAAAGAG
1 AAAA-AAAAAAAGAG
* *
1446540 AAAAGAGAAAAGAG
1 AAAAAAAAAAAGAG
1446554 AAAAAAAAAAAGAG
1 AAAAAAAAAAAGAG
1446568 AAAAAAAA
1 AAAAAAAA
1446576 GAAATTGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 28 0.88
15 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:1446561 original size:28 final size:28
Alignment explanation
Indices: 1446517--1446571 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1446507 CTCATCCATC
1446517 AGAAAAAAAAAAGAAAAAAAGAGAAAAG
1 AGAAAAAAAAAAGAAAAAAAGAGAAAAG
*
1446545 AGAAAAGAGAAAA-AAAAAAAGAGAAAA
1 AGAAAA-AAAAAAGAAAAAAAGAGAAAA
1446572 AAAAGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (28 bp):
AGAAAAAAAAAAGAAAAAAAGAGAAAAG
Found at i:1448001 original size:33 final size:33
Alignment explanation
Indices: 1447918--1448525 Score: 777
Period size: 33 Copynumber: 18.2 Consensus size: 33
1447908 GTAGATCAAA
* * * *
1447918 ATCGACATTCAAAACCATCCCATAAGGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1447951 ATCGACATTTCAAATCCATCACAGAAAGAGATGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* **
1447985 ATCGACATTCAAATCCATCACA-AAAAATATGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1448017 ATCGACATTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * * *
1448051 ATCGACATTTCAAATCCATCGCATAAGGAGATGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
*
1448085 ATCGACATTCAAATCCATCATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1448118 ATCGACATTCAAATCCATCACAGAAGGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1448151 ATCGACATTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
*
1448185 ATCGGCATTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* **
1448219 ATCGATATTTCAAATCCATCACAGAAAGAGGTAA
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
1448253 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * *
1448286 ATCGACATTCTAATCCATTATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1448319 ATCGACGTTGAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1448352 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *** *
1448385 ATCGATATTTTGATCCATCACAGAAAGAGGTGA
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * **
1448418 ATCAACATTCAAATCAATCACAAAAAGAGGCAG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * *
1448451 ATCGGCATTTTAAATCCATCACAGAAAGAGGCGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * * * *
1448485 ATTGACTTTCAAATTCATCATAGAAAGAGATGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1448518 ATCGACAT
1 ATCGACAT
1448526 CTTAATCTAT
Statistics
Matches: 499, Mismatches: 71, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
32 15 0.03
33 292 0.59
34 192 0.38
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (33 bp):
ATCGACATTCAAATCCATCACAGAAAGAGGTGG
Found at i:1448539 original size:100 final size:100
Alignment explanation
Indices: 1447918--1448525 Score: 799
Period size: 100 Copynumber: 6.1 Consensus size: 100
1447908 GTAGATCAAA
* * * * *
1447918 ATCGACATTCAAAACCATCCCATAAGGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGAT
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
* **
1447983 GGATCGACATTCAAATCCATCACA-AAAAATATGG
66 GGATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
1448017 ATCGACATTTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCGCATAAGGAGA
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGG
*
1448082 TGGATCGACATTCAAATCCATCATAGAAAGAGGTGG
65 TGGATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1448118 ATCGACATTCAAATCCATCACAGAAGGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
*
1448183 GGATCGGCATTTCAAATCCATCACAGAAAGAGGTGG
66 GGATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* **
1448219 ATCGATATTTCAAATCCATCACAGAAAGAGGTAAATCGACA-TTCAAATCCATCACAGAAAGAGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGG
* * *
1448283 TGGATCGACATTCTAATCCATTATAGAAAGAGGTGG
65 TGGATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1448319 ATCGACGTTGAAATCCATCACAGAAAGAGGTGGATCGACA-TTCAAATCCATCACAGAAAGAGGT
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
* *** *
1448383 GGATCGATATTTTGATCCATCACAGAAAGAGGTGA
66 GGATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * ** * * *
1448418 ATCAACATTCAAATCAATCACAAAAAGAGGCAGATCGGCATTTTAAATCCATCACAGAAAGAGGC
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
* * * * *
1448483 GGATTGACTTTCAAATTCATCATAGAAAGAGATGG
66 GGATCGACATTCAAATCCATCACAGAAAGAGGTGG
1448518 ATCGACAT
1 ATCGACAT
1448526 CTTAATCTAT
Statistics
Matches: 446, Mismatches: 58, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
99 122 0.27
100 217 0.49
101 77 0.17
102 30 0.07
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (100 bp):
ATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
GGATCGACATTCAAATCCATCACAGAAAGAGGTGG
Found at i:1449120 original size:39 final size:40
Alignment explanation
Indices: 1449058--1449133 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
1449048 GGTAGTTTTT
*
1449058 TCCAATTAATATTTTTTAGAGTTTTATTTCAAAATAACAA
1 TCCAATTAATATTTTTTAGAGTTTCATTTCAAAATAACAA
* * *
1449098 TCCAGTTAAT-TTTTTTATAGTTTCATTTCGAAATAA
1 TCCAATTAATATTTTTTAGAGTTTCATTTCAAAATAA
1449134 TAATAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 23 0.72
40 9 0.28
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (40 bp):
TCCAATTAATATTTTTTAGAGTTTCATTTCAAAATAACAA
Found at i:1449931 original size:16 final size:16
Alignment explanation
Indices: 1449910--1449949 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1449900 TTCCTAGTCC
1449910 TTATATTTAAATT-TT
1 TTATATTTAAATTCTT
*
1449925 ATTATATTTAGATTCTT
1 -TTATATTTAAATTCTT
1449942 TTATATTT
1 TTATATTT
1449950 TATATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATATTTAAATTCTT
Found at i:1449959 original size:16 final size:16
Alignment explanation
Indices: 1449910--1449986 Score: 59
Period size: 18 Copynumber: 4.6 Consensus size: 16
1449900 TTCCTAGTCC
*
1449910 TTATA-TTTAAATTTT
1 TTATATTTTATATTTT
*
1449925 ATTATA-TTTAGATTCTT
1 -TTATATTTTATATT-TT
1449942 TTATATTTTATATTTTT
1 TTATATTTTATA-TTTT
*
1449959 TTATTATTTGTATTTTTT
1 TTA-TATTT-TATATTTT
1449977 TTATTATTTT
1 TTA-TATTTT
1449987 GTTTAATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
16 17 0.32
17 13 0.25
18 20 0.38
19 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (16 bp):
TTATATTTTATATTTT
Found at i:1449975 original size:18 final size:18
Alignment explanation
Indices: 1449921--1449986 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
1449911 TATATTTAAA
* *
1449921 TTTTATTATATTTAGATTC
1 TTTTATTAT-TTTATATTT
1449940 TTTTA-TATTTTATATTT
1 TTTTATTATTTTATATTT
1449957 TTTTATTATTTGTAT-TTT
1 TTTTATTATTT-TATATTT
1449975 TTTTATTATTTT
1 TTTTATTATTTT
1449987 GTTTAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 13 0.30
18 22 0.51
19 8 0.19
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATTATTTTATATTT
Found at i:1449986 original size:9 final size:9
Alignment explanation
Indices: 1449940--1450012 Score: 55
Period size: 9 Copynumber: 8.3 Consensus size: 9
1449930 ATTTAGATTC
1449940 TTTTA-TAT
1 TTTTATTAT
1449948 TTTATATT-T
1 TTT-TATTAT
1449957 TTTTATTAT
1 TTTTATTAT
* *
1449966 TTGTATTTT
1 TTTTATTAT
1449975 TTTTATTAT
1 TTTTATTAT
*
1449984 TTTGT-TTAA
1 TTT-TATTAT
*
1449993 TTTTAGTAT
1 TTTTATTAT
*
1450002 TTAT-TTAT
1 TTTTATTAT
1450010 TTT
1 TTT
1450013 ATTTTAAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
8 13 0.26
9 35 0.70
10 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTATTAT
Found at i:1450015 original size:9 final size:9
Alignment explanation
Indices: 1449945--1450016 Score: 53
Period size: 10 Copynumber: 8.1 Consensus size: 9
1449935 GATTCTTTTA
1449945 TATTTTATAT
1 TATTTTAT-T
*
1449955 TTTTTTA-T
1 TATTTTATT
1449963 TATTTGTATT
1 TATTT-TATT
*
1449973 TTTTTTA-T
1 TATTTTATT
*
1449981 TATTTTGTT
1 TATTTTATT
*
1449990 TAATTTTA-G
1 T-ATTTTATT
1449999 TA-TTTATT
1 TATTTTATT
1450007 TATTTTATT
1 TATTTTATT
1450016 T
1 T
1450017 TAAAATTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
7 4 0.08
8 14 0.29
9 14 0.29
10 16 0.33
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (9 bp):
TATTTTATT
Found at i:1455037 original size:29 final size:29
Alignment explanation
Indices: 1454994--1455097 Score: 192
Period size: 29 Copynumber: 3.6 Consensus size: 29
1454984 TTTCATATGT
1454994 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
1455022 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1455051 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1455080 TCATGTAGCTCATGTCAT
1 TCATGTAGCTCATGTCAT
1455098 GTTTTCATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 7 0.10
29 66 0.90
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1455113 original size:29 final size:29
Alignment explanation
Indices: 1454994--1455114 Score: 120
Period size: 29 Copynumber: 4.2 Consensus size: 29
1454984 TTTCATATGT
* * *
1454994 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCATATCA
* * * *
1455022 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCATATCA
* * *
1455051 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCATATCA
*
1455080 TCATGTAGCTCATGTCATGTTTTCATATCA
1 TCATGTAGCTCATGTCAT-TTCTCATATCA
1455110 -CATGT
1 TCATGT
1455115 GTATTTGAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
28 7 0.08
29 71 0.84
30 7 0.08
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCATATCA
Found at i:1455114 original size:58 final size:57
Alignment explanation
Indices: 1454994--1455114 Score: 172
Period size: 58 Copynumber: 2.1 Consensus size: 57
1454984 TTTCATATGT
* * * *
1454994 TCATGTACTCATGTCATTTCTCTTGTGATCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTACTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCATTTCTCATATCA
*
1455051 TCATGTAGCTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCATGTTTTCATATCA
1 TCATGTA-CTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCAT-TTCTCATATCA
1455110 -CATGT
1 TCATGT
1455115 GTATTTGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
57 7 0.12
58 43 0.75
59 7 0.12
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (57 bp):
TCATGTACTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCATTTCTCATATCA
Found at i:1457126 original size:18 final size:18
Alignment explanation
Indices: 1457103--1457145 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1457093 AAGGGTCGAT
1457103 TGAGGCAATAAGAGTCGG
1 TGAGGCAATAAGAGTCGG
1457121 TGAGGCAATAAGAGTCGG
1 TGAGGCAATAAGAGTCGG
1457139 TGAGGCA
1 TGAGGCA
1457146 TCCCGTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.40, T:0.16
Consensus pattern (18 bp):
TGAGGCAATAAGAGTCGG
Found at i:1458826 original size:2 final size:2
Alignment explanation
Indices: 1458814--1458846 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1458804 TTTATCCTTT
1458814 TA TA T- TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1458847 TGTTGTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1458828 original size:9 final size:9
Alignment explanation
Indices: 1458814--1458847 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
1458804 TTTATCCTTT
1458814 TATATTATA
1 TATATTATA
1458823 TATATTATA
1 TATATTATA
1458832 TATATATATA
1 TATAT-TATA
1458842 TATATT
1 TATATT
1458848 GTTGTACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATATTATA
Found at i:1461241 original size:33 final size:33
Alignment explanation
Indices: 1461158--1461930 Score: 1010
Period size: 33 Copynumber: 23.2 Consensus size: 33
1461148 GTAGATCAGA
* * *
1461158 ATCGACATTCAAATCTATCCCAGAAGGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1461191 ATCGACATTTCAAATCCATCACAGAAAGAGATGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * * *
1461225 ATCAACATTCAAATCCATCACAAAAAAAGATGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
1461258 ATCGATATTTCAAATCTATCAGAGAAAGAGGTAG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
*
1461292 ATCGACATTTCAAATCCATCACAGAAGGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
*
1461326 ATCGACATTTAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1461359 ATCGACATTCAAATCCATCATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1461392 ATCGACGTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1461425 ATCGATATTCAAATCCATCACAGAAGGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1461458 ATCGACATTTCAAATCCATCACAGAAAAAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* *
1461492 ATCAACATTTAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1461525 ATCTACATTTCAAATCCATCACA-AAAGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * *
1461558 ATCGACATTTCAAATCCATCATAGAAGGAGGTGA
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
*
1461592 ATCGACATTCAAATCCATCACAAAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1461625 ATCGACATTCAAATCCATCATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1461658 ATCGACGTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1461691 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
***
1461724 ATCGACATTTTGATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*** * *
1461757 ATCGACATTTTGATCCATCACAGAAAAAGGTGA
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
1461790 ATCAACATTCAAATCAATCACAAAAAGAGGTAG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1461823 ATCGACATTTCAAATCCATCACAAAAAGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * * *
1461857 ATTGACATTCAAATTCATCACATAAAGAGATGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
1461890 ATCGACA-TCTTAATCTATCACAGAAGGAGCTGG
1 ATCGACATTC-AAATCCATCACAGAAAGAGGTGG
*
1461923 ATCAACAT
1 ATCGACAT
1461931 CAACTTTTTG
Statistics
Matches: 653, Mismatches: 79, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
32 2 0.00
33 478 0.73
34 173 0.26
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (33 bp):
ATCGACATTCAAATCCATCACAGAAAGAGGTGG
Found at i:1461502 original size:166 final size:165
Alignment explanation
Indices: 1461158--1461930 Score: 994
Period size: 166 Copynumber: 4.6 Consensus size: 165
1461148 GTAGATCAGA
* * * * *
1461158 ATCGACATTCAAATCTATCCCAGAAGGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAGAT
1 ATCGACATTTAAATCCATCACAGAAAGAGGTGGATCGACA-TTCAAATCCATCACAGAAAGAGGT
* * * * * * *
1461223 GGATCAACATTCAAATCCATCACAAAAAAAGATGGATCGATATTTCAAATCTATCAGAGAAAGAG
65 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACA-TTCAAATCCATCACAGAAAGAG
* **
1461288 GTAGATCGACATTTCAAATCCATCACAGAAGGAGGTGG
129 GTGGATCGACA-TTCAAATCCATCACAGAAAAAGGTGG
*
1461326 ATCGACATTTAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCATAGAAAGAGGTG
1 ATCGACATTTAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTG
* * *
1461391 GATCGACGTTCAAATCCATCACAGAAAGAGGTGGATCGATATTCAAATCCATCACAGAAGGAGGT
66 GATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGT
1461456 GGATCGACATTTCAAATCCATCACAGAAAAAGGTGG
131 GGATCGACA-TTCAAATCCATCACAGAAAAAGGTGG
* *
1461492 ATCAACATTTAAATCCATCACAGAAAGAGGTGGATCTACATTTCAAATCCATCACA-AAAGAGGT
1 ATCGACATTTAAATCCATCACAGAAAGAGGTGGATCGACA-TTCAAATCCATCACAGAAAGAGGT
* * * *
1461556 GGATCGACATTTCAAATCCATCATAGAAGGAGGTGAATCGACATTCAAATCCATCACAAAAAGAG
65 GGATCGACA-TTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAG
* *
1461621 GTGGATCGACATTCAAATCCATCATAGAAAGAGGTGG
129 GTGGATCGACATTCAAATCCATCACAGAAAAAGGTGG
* *
1461658 ATCGACGTTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTG
1 ATCGACATTTAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTG
*** *** *
1461723 GATCGACATTTTGATCCATCACAGAAAGAGGTGGATCGACATTTTGATCCATCACAGAAAAAGGT
66 GATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGT
* * * *
1461788 GAATCAACATTCAAATCAATCACA-AAAAGAGGTAG
131 GGATCGACATTCAAATCCATCACAGAAAA-AGGTGG
* * * * *
1461823 ATCGACATTTCAAATCCATCACAAAAAGAGGTGGATTGACATTCAAATTCATCACATAAAGAGAT
1 ATCGACATTT-AAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGT
* * * * *
1461888 GGATCGACA-TCTTAATCTATCACAGAAGGAGCTGGATCAACAT
65 GGATCGACATTC-AAATCCATCACAGAAAGAGGTGGATCGACAT
1461931 CAACTTTTTG
Statistics
Matches: 536, Mismatches: 63, Indels: 14
0.87 0.10 0.02
Matches are distributed among these distances:
164 3 0.01
165 95 0.18
166 269 0.50
167 133 0.25
168 36 0.07
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (165 bp):
ATCGACATTTAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTG
GATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGT
GGATCGACATTCAAATCCATCACAGAAAAAGGTGG
Found at i:1463393 original size:26 final size:27
Alignment explanation
Indices: 1463335--1463391 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
1463325 TTTCTTTATT
1463335 ATTT-GTATTTTTTATTATTTTGTTTA
1 ATTTAGTATTTTTTATTATTTTGTTTA
1463361 ATTTTAGTATTTATTTATT-TTATT-TTTA
1 A-TTTAGTATTT-TTTATTATT-TTGTTTA
1463389 ATT
1 ATT
1463392 AGGATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
26 1 0.04
27 5 0.19
28 13 0.48
29 8 0.30
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (27 bp):
ATTTAGTATTTTTTATTATTTTGTTTA
Found at i:1473062 original size:13 final size:13
Alignment explanation
Indices: 1473044--1473068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1473034 GGGTTGTGTG
1473044 TTCAGGCCTGTAT
1 TTCAGGCCTGTAT
1473057 TTCAGGCCTGTA
1 TTCAGGCCTGTA
1473069 ACCTGAAAAA
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:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (13 bp):
TTCAGGCCTGTAT
Found at i:1473964 original size:20 final size:21
Alignment explanation
Indices: 1473939--1473990 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1473929 TTTTCCCAAT
*
1473939 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1473959 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1473980 TCGCAATGCGA
1 TCGCAATGCGA
1473991 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1474004 original size:20 final size:20
Alignment explanation
Indices: 1473979--1474032 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1473969 AATTGGGAAA
1473979 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTTACT
1473999 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTTACT
1474019 ATCGCAATGCGATA
1 ATCGCAATGCGATA
1474033 ATACAAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATACTTACT
Found at i:1474023 original size:61 final size:61
Alignment explanation
Indices: 1473976--1474092 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1473966 GCGAATTGGG
* * * * * *
1473976 AAAATCGCAATGCGATACTTACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1474037 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
1474093 TCTGACTTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1474031 original size:40 final size:40
Alignment explanation
Indices: 1473979--1474112 Score: 126
Period size: 40 Copynumber: 3.3 Consensus size: 40
1473969 AATTGGGAAA
* * *
1473979 ATCGCAATGCGATACTTACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACTATCGCAACGCGATACTGACT
* * * *
1474019 ATCGCAATGCGATA-ATACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTTAC--TATCGCAACGCGATACTGACT
* * * * *
1474060 TTCGCAACGCGATTCTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTTACTATCGCAACGCGATACTGACT
*
1474100 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1474113 TTACATAGCG
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 44 0.57
41 28 0.36
42 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (40 bp):
ATCGCAACGCGATACTTACTATCGCAACGCGATACTGACT
Found at i:1474066 original size:20 final size:20
Alignment explanation
Indices: 1474041--1474113 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
1474031 TAATACAAAA
* *
1474041 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1474061 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1474081 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1474101 TCGCAACGCGATT
1 TCGCAACGCGATT
1474114 TACATAGCGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1474664 original size:18 final size:18
Alignment explanation
Indices: 1474619--1474683 Score: 85
Period size: 19 Copynumber: 3.5 Consensus size: 18
1474609 TTCGAGAATG
*
1474619 AAAATCGCAACGCGGAAT
1 AAAATCGCAACGCGAAAT
*
1474637 AACTATCGCAACGCGAAAT
1 AA-AATCGCAACGCGAAAT
*
1474656 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-T
1474675 AAAATCGCA
1 AAAATCGCA
1474684 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
18 16 0.39
19 25 0.61
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:1474701 original size:19 final size:19
Alignment explanation
Indices: 1474679--1474863 Score: 158
Period size: 19 Copynumber: 10.1 Consensus size: 19
1474669 GAAACCAAAA
*
1474679 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1474698 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1474717 TCGCGTTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
1474735 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1474755 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* * **
1474771 T-G-GTCGCAATAGTCATT
1 TCGCGTTGCGATTTTCATT
1474788 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1474802 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
1474822 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1474842 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1474862 TC
1 TC
1474864 ACCAAAAGAC
Statistics
Matches: 136, Mismatches: 15, Indels: 30
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 8 0.06
19 62 0.46
20 26 0.19
21 14 0.10
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1474792 original size:33 final size:33
Alignment explanation
Indices: 1474750--1474838 Score: 124
Period size: 33 Copynumber: 2.6 Consensus size: 33
1474740 GTTGCGATTT
* *
1474750 TCATTTCGCGTTGCGATTGTCTGGTCGCAATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCAATAG
* *
1474783 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCAATAG
1474816 TCATTTTCCGCGTTGCGATTCTC
1 TCA-TTT-CGCGTTGCGATTCTC
1474839 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 32 0.64
34 3 0.06
35 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCAATAG
Found at i:1474851 original size:20 final size:20
Alignment explanation
Indices: 1474802--1474861 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1474792 GTTGCGATTC
** *
1474802 TCTCGTTGCGATAGTCATTT
1 TCTCGTTGCGATTCTCATTA
*
1474822 TCCGCGTTGCGATTCTCATTA
1 T-CTCGTTGCGATTCTCATTA
*
1474843 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
1474862 TCACCAAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:1475174 original size:159 final size:159
Alignment explanation
Indices: 1474969--1475287 Score: 622
Period size: 159 Copynumber: 2.0 Consensus size: 159
1474959 TTTGGTATAT
1474969 CTAACTTGGTATGTTTATTGTTTTTTTGTAGAAATTTTTTTCGGCTTCATTGACATTAAGGAATA
1 CTAACTTGGTATGTTTATTGTTTTTTTGTAGAAATTTTTTTCGGCTTCATTGACATTAAGGAATA
1475034 AAGTTAGCCTAGCCACTACAATTGCTTCGAAGCTTTCACCTGCACAAAGAAAATTGTTTGAAGAA
66 AAGTTAGCCTAGCCACTACAATTGCTTCGAAGCTTTCACCTGCACAAAG-AAATTGTTTGAAGAA
1475099 ACCTGCTTCGGGCCATGGCTGAGAGTACAG
130 ACCTGCTTCGGGCCATGGCTGAGAGTACAG
1475129 CTAACTTGGTATGTTTATTG-TTTTTTGTAGAAATTTTTTTCGGCTTCATTGACATTAAGGAATA
1 CTAACTTGGTATGTTTATTGTTTTTTTGTAGAAATTTTTTTCGGCTTCATTGACATTAAGGAATA
1475193 AAGTTAGCCTAGCCACTACAATTGCTTCGAAGCTTTCACCTGCACAAAGAAATTGTTTGAAGAAA
66 AAGTTAGCCTAGCCACTACAATTGCTTCGAAGCTTTCACCTGCACAAAGAAATTGTTTGAAGAAA
1475258 CCTGCTTCGGGCCATGGCTGAGAGTACAG
131 CCTGCTTCGGGCCATGGCTGAGAGTACAG
1475287 C
1 C
1475288 ATCCGGGTGG
Statistics
Matches: 159, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
158 46 0.29
159 93 0.58
160 20 0.13
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (159 bp):
CTAACTTGGTATGTTTATTGTTTTTTTGTAGAAATTTTTTTCGGCTTCATTGACATTAAGGAATA
AAGTTAGCCTAGCCACTACAATTGCTTCGAAGCTTTCACCTGCACAAAGAAATTGTTTGAAGAAA
CCTGCTTCGGGCCATGGCTGAGAGTACAG
Found at i:1477002 original size:42 final size:42
Alignment explanation
Indices: 1476942--1477034 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1476932 GCCCGACTCG
* * *
1476942 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCATCGTTCAAAAGGCC
* * *
1476984 CCTATCATTCCTCGAGAGTCCCCTCCCATCGTTCAAAAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCATCGTTCAAAAGGCC
* *
1477026 ACTGTCATC
1 CCTATCATC
1477035 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.25
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCATCGTTCAAAAGGCC
Done.